commit 90854ff447f414578ea982e0d745a8a3ffebcfcc Merge: 13b863f13 8d258d627 Author: Marc Day Date: Wed Mar 4 17:30:16 2020 -0800 Merge pull request #733 from AMReX-Codes/fix_EB_setCoveredFace Fix EB_set_covered_face: now use the input value. Also duplicate commit 8d258d627009d72b1abd7a965d3f508cf1ecec2e Author: Lucas Esclapez Date: Wed Mar 4 16:39:14 2020 -0800 Fix EB_set_covered_face: now use the input value. Also duplicate function to set a range of the MF component. Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp commit 13b863f13087c37059da213ad529004922dfc9ac Merge: 140cb7755 ab61246c9 Author: Andrew Myers Date: Wed Mar 4 15:57:33 2020 -0800 Merge pull request #732 from AMReX-Codes/jmsexton/particle_bounds Fix for single-precision RedistributeCPU PeriodicShift particle loss commit 140cb77557cb1317a4b9d3d6300e121ab508ea48 Merge: 95b6bd026 c4e43f977 Author: Andrew Myers Date: Wed Mar 4 15:53:44 2020 -0800 Merge pull request #724 from Alpine-DAV/task/2020_03_bp_fix_particle_type Conduit Blueprint: fix case needed for single prec particles commit ab61246c94253360286720e495784bc56c204582 Author: Jean M. Sexton Date: Wed Mar 4 15:06:16 2020 -0800 Update fix for case where ProbLo is not 0 Src/Particle/AMReX_ParticleContainerI.H commit 5f597a48da3d16e4f0b5d0309cf51944fbbe6d44 Author: Jean M. Sexton Date: Wed Feb 12 15:03:39 2020 -0800 Fix for single precision mis-match by testing using particle typename Src/Particle/AMReX_ParticleContainerI.H commit 95b6bd02601533e8344b1cf9adfe92ebefe987a6 Author: Weiqun Zhang Date: Wed Mar 4 12:56:41 2020 -0800 In computing RHS, we always double at Neumann boundary as before. Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit b4fb49694b774fbb9f0c225f4502eca4c28d189a Merge: c12a5bb1d f0520630b Author: WeiqunZhang Date: Wed Mar 4 10:36:23 2020 -0800 Merge pull request #729 from cselab/fabian/pullreq Fix minor typo Tools/libamrex/configure.py commit c12a5bb1d570c36601a65636172f2e5ef3472acd Merge: b1dd0837b 24edcb625 Author: Weiqun Zhang Date: Wed Mar 4 10:34:49 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b1dd0837bf3dc3178ad678b94a52f8c7aab822b0 Merge: 8b34c06a9 10bc01fcd Author: Weiqun Zhang Date: Wed Mar 4 10:31:07 2020 -0800 Merge branch 'development' into FlashFluxRegister commit 24edcb6259e1f24043f5cd37ecdb4d22d1257bb2 Merge: 10bc01fcd 4e6459dba Author: Andrew Myers Date: Wed Mar 4 10:31:06 2020 -0800 Merge pull request #726 from lucafedeli88/fix_doc_random Make amrex::Random() return numbers in the same interval for both CPU and GPU: [0:1) commit 10bc01fcdf4d99227a9b1e7a26746e5ecb064251 Author: Weiqun Zhang Date: Wed Mar 4 10:30:28 2020 -0800 fix typo Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 8b34c06a92e0acdbbf6a1df803d17db55ca70bf9 Merge: 181bb4da8 78738d2a7 Author: WeiqunZhang Date: Wed Mar 4 10:29:50 2020 -0800 Merge pull request #728 from kweide/FlashFluxRegister Additional variant of FlashFluxRegister load method (untested) commit f0520630bac450dd8e6b893870a455054530bcdc Author: Fabian Wermelinger Date: Wed Mar 4 10:16:00 2020 -0800 Fix minor typo Tools/libamrex/configure.py Tools/libamrex/configure.py commit d824c19abbdeb878bac71ed17bb4b71f388589d4 Author: Weiqun Zhang Date: Wed Mar 4 09:31:59 2020 -0800 fix Neumann for divu too Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 78738d2a72b94e64d75d5e103a1392c79c0ac38c Author: Klaus Weide Date: Wed Mar 4 11:52:22 2020 -0600 fix for amrex_flash_fluxregister_load_FOO procedure names Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90 commit ff1c7b75bc2eaf265fa4196b3514802621be3f11 Author: Klaus Weide Date: Wed Mar 4 09:36:55 2020 -0600 Additional variant of FlashFluxRegister load method (untested) 1. Add another variant of load method, amrex_flash_fluxregister_load_1_area, Since we will frequently use this for FLASH. This is for when we have area factors, but do not use an additional (cflux) input as in amrex_flash_fluxregister_load_2_area. It turns out we never need a separate scalar scaling factor in this case, so I also removed that. 2. Rename previous amrex_flash_fluxregister_load_area -> amrex_flash_fluxregister_load_2_area and amrex_fi_flash_fluxregister_load_area -> amrex_fi_flash_fluxregister_load_2_area 3. Fix: Replace sf_f -> my_sf_f, sf_c -> my_sf_c in a couple amrex_fi_flash_fluxregister_load_foo calls, as apparently intended. Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.H Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90 commit 4e6459dba8f31aea57f64b67e45ca97ec13ebfe7 Author: Luca Fedeli Date: Wed Mar 4 16:06:02 2020 +0100 now random() returns numbers in [0.0,1.0) for both CPU and GPU Src/Base/AMReX_Random.cpp commit 6334f7bf4f575ebaca623a8ee7cfcd0bb6b788d4 Author: Luca Fedeli Date: Wed Mar 4 16:05:20 2020 +0100 fixed comment Src/Base/AMReX_Random.H commit 8145c74df5ecfe5323d5bd2faccd8135dfe3bd3c Merge: 83a524253 1576d43ae Author: Weiqun Zhang Date: Tue Mar 3 19:25:16 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 83a524253000630c1a66b4aea1400b854b20b08f Author: Weiqun Zhang Date: Tue Mar 3 19:25:09 2020 -0800 should not multiple by 2 at Neumann BC when using RAP Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 1576d43ae80b89b1b0dcf77ce8cc566d780ecf46 Author: Andrew Myers Date: Tue Mar 3 15:43:15 2020 -0800 decrease max buffer size Src/Particle/AMReX_ParticleUtil.H commit c26dc922e9206876f46895ffdccf633f7caee136 Author: Andrew Myers Date: Tue Mar 3 15:42:35 2020 -0800 can exit early from the no particle case Src/Particle/AMReX_ParticleUtil.H commit 5649c6852924ef80c024f225224e407cc35168ef Author: Andrew Myers Date: Tue Mar 3 15:42:11 2020 -0800 make sure to handle the invalid particle case here Src/Particle/AMReX_ParticleContainerI.H commit c4e43f9770c3848ff949ea6e1316ff35362a361b Author: Cyrus Harrison Date: Tue Mar 3 12:44:43 2020 -0800 fix particle case where ParticleReal is needed Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H commit 629caac3a465e3b6737fa3000d541f59e36b6db1 Author: Andrew Myers Date: Tue Mar 3 11:54:20 2020 -0800 prevent overflow error Src/Particle/AMReX_ParticleUtil.H commit 4833a5afd190e94c1aa6a59e64eeed9e97c95a61 Merge: 7253600f3 0de7a5d5c Author: Andrew Myers Date: Mon Mar 2 15:52:08 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7253600f3c5b862192062ccc1cdd29b67000198c Author: Andrew Myers Date: Mon Mar 2 15:51:57 2020 -0800 another tweak to particle_compare Tools/Postprocessing/C_Src/particle_compare.cpp commit 0de7a5d5c7fcd5e2a98a4e9bba32667e577e3adf Merge: c8edfea76 09f0b527c Author: Weiqun Zhang Date: Mon Mar 2 14:25:12 2020 -0800 Merge branch 'development' into dpcpp commit c8edfea76bea1f36f42486f795d4a92c8616d412 Author: Weiqun Zhang Date: Mon Mar 2 14:22:18 2020 -0800 add cl::intel_reqd_sub_group_size and get rid of compiler warnings Src/Base/AMReX_FBI.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuLaunchMacrosG.H Src/Base/AMReX_GpuQualifiers.H Src/Base/AMReX_Machine.cpp Src/Base/AMReX_Reduce.H commit 09f0b527c1445acaf3e658f394bb082f8e916d96 Author: Weiqun Zhang Date: Mon Mar 2 14:11:53 2020 -0800 update DPC++ notes Docs/Notes/Readme.dpcpp commit 8e8ec1193d63f0be359384fb270de0753f8e8504 Merge: 384886805 95b50cdd4 Author: Weiqun Zhang Date: Mon Mar 2 14:05:41 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 95b50cdd4ac4537602f19c63abc6037afd464d57 Author: Andrew Myers Date: Mon Mar 2 13:38:36 2020 -0800 need to do this at run time instead of compile time Tools/Postprocessing/C_Src/particle_compare.cpp commit af204601007dc1234fc04656dd6dba2d54d45d3c Author: Andrew Myers Date: Mon Mar 2 13:16:43 2020 -0800 make particle_compare respect single precision Tools/Postprocessing/C_Src/particle_compare.cpp commit 384886805e1aa8b698e2f7773ebc81026474fe90 Merge: 1838cd852 e95f2e39c Author: Weiqun Zhang Date: Mon Mar 2 10:23:32 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e95f2e39ced27bd0156f7f6f4af8261af3d8fe88 Merge: 15c6c1f8a 2bc004ba1 Author: Andrew Myers Date: Mon Mar 2 10:19:49 2020 -0800 Merge branch 'atmyers/memopt' into development commit 1838cd8525e01550861ca753d41a577b497286bc Author: Weiqun Zhang Date: Mon Mar 2 09:12:22 2020 -0800 update CHANGES CHANGES commit 2bc004ba13af329afa089a7eca7a9fc6c7050763 Author: Andrew Myers Date: Sat Feb 29 16:22:43 2020 -0800 ability to do a 'chunked' partition Src/Particle/AMReX_ParticleUtil.H commit fae5b61121d4d458e4eec4758a5fb965f85468af Author: Andrew Myers Date: Sat Feb 29 16:22:28 2020 -0800 swap particle routine Src/Particle/AMReX_ParticleTransformation.H commit 15c6c1f8a9fa10630bac0089a994bf8602aa9f03 Author: Michele Rosso Date: Fri Feb 28 17:38:55 2020 -0800 CMake: set versioning variables before project() CMakeLists.txt Tools/CMake/AMReXInstallHelpers.cmake commit 38a05d82937c83dbd6f836627a46e9c2c579e0dc Merge: c931c7d9f 1dcd4211a Author: mic84 Date: Fri Feb 28 14:44:40 2020 -0800 Merge pull request #721 from ax3l/topic-ciTutorials CI: Make Tutorials commit 1dcd4211a29e1090234cba142598bebd97bec885 Author: Axel Huebl Date: Fri Feb 28 14:33:07 2020 -0800 CI: Make Tutorials Remove demonstrator `CMakeLists.txt` files from tutorials as they confuse the tutorial superbuild. Build tutorials with and without CUDA. .github/workflows/cmake.yml .github/workflows/cmake/dependencies_nvcc.sh Tutorials/Basic/HelloWorld_C/CMakeLists.txt Tutorials/Particles/CellSortedParticles/CMakeLists.txt commit c931c7d9fea196bfdbd323d11e568c3417e58aea Author: Michele Rosso Date: Fri Feb 28 12:49:13 2020 -0800 CMake: add defines for Clang version Tools/CMake/AMReX_Config.cmake commit 7bbbefa6a6e90d2b16e30e937c6ec9a8e2e9ff1b Author: Michele Rosso Date: Fri Feb 28 12:47:15 2020 -0800 CMake: allow building with Cray compiler Partially fixes issue #719 Tools/CMake/AMReX_Config.cmake commit 1de49bb0e6dad2c4ad956bed2b3aab5b76221a0d Author: Michele Rosso Date: Fri Feb 28 12:45:49 2020 -0800 CMake: update flags target + add Clang flags Tools/CMake/AMReXFlagsTargets.cmake commit ed10b2cc2e2d2b402244e651b1b9bedca691c3f9 Author: Andrew Myers Date: Fri Feb 28 12:31:53 2020 -0800 ifdef out function if no GPU Src/Particle/AMReX_ParticleUtil.H commit 9d83139348d2165eee02632d78017e2de9cbdf0e Author: Andrew Myers Date: Fri Feb 28 15:20:08 2020 -0500 add missing header Src/Particle/AMReX_ParticleUtil.H commit d0a4223dbfb411edc53113c654d747756673f687 Author: Andrew Myers Date: Fri Feb 28 15:13:17 2020 -0500 move partition step into its own function Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_ParticleUtil.H commit df3f3221dd00984f7f5a8d416f781125da6d7e7c Author: Andrew Myers Date: Fri Feb 28 14:10:59 2020 -0500 move lev, grid calculations to be on-the-fly Src/Particle/AMReX_ParticleContainerI.H commit b63b147984b2d7b8229a35965e7e1cbfb7bcd917 Author: Weiqun Zhang Date: Fri Feb 28 09:40:23 2020 -0800 fix gpu race conditions in YAFluxRegister::FineAdd Src/Boundary/AMReX_YAFluxRegister_1D_K.H Src/Boundary/AMReX_YAFluxRegister_2D_K.H Src/Boundary/AMReX_YAFluxRegister_3D_K.H commit c8ad86b8c2323f487d307e020118c0d97627494e Merge: b5790393e 73f2191c8 Author: Andrew Myers Date: Thu Feb 27 21:41:41 2020 -0800 Merge pull request #718 from AMReX-Codes/empic-offset Initialize the particles in the first cell of each tile for EM PIC tutorial commit b5790393e51d9460e581494c6d50e8309d418945 Merge: b14219bd0 886c4288b Author: Michele Rosso Date: Thu Feb 27 21:29:36 2020 -0500 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b14219bd0ce6c72638bcd97840cee2bd2179108b Author: Michele Rosso Date: Thu Feb 27 21:26:12 2020 -0500 CMake: do not enable CUDA via AMReX_SetupCUDA. From now on, application codes will need to enable CUDA directly instead of relying on AMReX_SetupCUDA. However, AMReX_SetupCUDA must still be included by application codes to setup the CUDA build environment for linking to AMReX. CMakeLists.txt Tools/CMake/AMReX_SetupCUDA.cmake commit 73f2191c8e46e06db5e3413761c34e5491b938b2 Author: Donald E. Willcox Date: Thu Feb 27 17:41:50 2020 -0800 Subtract the number of particles in the first cell of each tile to get the offset index for the first particle in each cell. Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainerInit.cpp commit 886c4288b43e11594f5ca5c16a17f2f30047914b Merge: a79c4c5b8 fae0cd9f6 Author: Axel Huebl Date: Thu Feb 27 13:42:29 2020 -0800 Merge pull request #705 from ax3l/fix-warnExpansionToDefined Fix Warning in AMREX_DEVICE_COMPILE commit fae0cd9f6a031f2d22b6b2fa7d32f9c986a70e7a Author: Axel Huebl Date: Wed Feb 26 14:12:31 2020 -0800 Remove defines in AMREX_DEVICE_COMPILE Adding `defined()` in a macro is raising warnings of undefined behavior (clang) or non-portable behavior (gcc). This patch seems to work on for CUDA, DPC++ and non-gpu. (HIP untested.) Co-authored-by: Weiqun Zhang Src/Base/AMReX_GpuQualifiers.H commit e21a4097653a3660e89e160823a0a6a6084dc96a Author: Axel Huebl Date: Tue Feb 25 23:36:36 2020 -0800 Fix Warning in AMREX_DEVICE_COMPILE Calling the macro `AMREX_DEVICE_COMPILE` with `()` in pre-processor calls seams to be an alternative, non-portable way of checking `defined()`. Modern versions of GCC issue a `-Wexpansion-to-defined` warning on this. Remove the `()` from `AMREX_DEVICE_COMPILE()` calls since they should not be needed. Src/Base/AMReX.H Src/Base/AMReX_Array4.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_GpuAtomic.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuRange.H Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_IF_Polynomial.H commit a79c4c5b86ecb01be1cd385609a89f44ea4bf8fc Merge: f8ac70cf3 7bb0c471b Author: mic84 Date: Thu Feb 27 12:38:21 2020 -0800 Merge pull request #716 from ax3l/fix-enableFortranCmake CMake: CXX Downstream Transitive Fortran commit 7bb0c471badb0d6a2eec4a4ac2bdb1834b5ff846 Author: Axel Huebl Date: Thu Feb 27 10:45:11 2020 -0800 CMake: Fix Transtive Fortran Libs CMake currently has the bug that some transitive, implicit language dependencies as not commuted downstream if the downstream project does not `enable_language` the same lang. as upstream. This is mostly visible in missing `-lgfortran` links. This adds a useful work-around by just exposing these implicit Fortran "standard" libraries as explicit link dependencies. Src/CMakeLists.txt commit f8ac70cf34875c53aff2c6d783d460853e6c7ce1 Merge: bb7415391 500203f05 Author: Andrew Myers Date: Thu Feb 27 10:39:04 2020 -0800 Merge pull request #713 from ax3l/topic-ciBadges Readme: Add CI Badges commit 221eff35c33a3fad22ec1fa96a2abe3fe8276640 Author: Axel Huebl Date: Thu Feb 27 10:37:39 2020 -0800 CMake: CXX Downstream Transtive Fortran CMake currently has the bug that some transitive, implicit language dependencies as not commuted downstream if the downstream project does not `enable_language` the same lang. as upstream. This is mostly visible in missing `-lgfortran` links. This triggers this bug. Tutorials/Basic/HelloWorld_C/CMakeLists.txt commit bb741539180de4bbe676dea9ecefd7cf08017258 Merge: ac4bb39d3 eff1a67a0 Author: mic84 Date: Thu Feb 27 10:29:14 2020 -0800 Merge pull request #714 from ax3l/fix-offWarningClangGfortran CMake Tools: Fix CXX Host Compiler Check commit eff1a67a07d40540d1190578c9e388ea0b777c78 Author: Axel Huebl Date: Wed Feb 26 23:38:10 2020 -0800 CMake Tools: Fix CXX Host Compiler Check False Warning with Clang+Gfortran builds. Tools/CMake/AMReX_Config.cmake commit 500203f05af9219c2d55b3c897b2be20d57b0b86 Author: Axel Huebl Date: Wed Feb 26 22:28:58 2020 -0800 Readme: Add CI Badges Add Travis-CI and GitHub Action status badges for the `development` branch. README.md commit ac4bb39d31ed49e2e05e0bd949f28f585a784374 Merge: 5597d97a9 0a8ae6265 Author: Andrew Myers Date: Wed Feb 26 19:33:33 2020 -0800 Merge pull request #712 from ax3l/topic-ghActionCMake CI: Add GitHub Workflow for CMake commit 0a8ae626518e97a24068dd13346db529ca024d55 Author: Axel Huebl Date: Wed Feb 26 16:12:40 2020 -0800 CI: Add GitHub Workflow for CMake Add a CI job via GitHub actions to ensure CMake builds are not breaking. .github/workflows/cmake.yml .github/workflows/cmake/dependencies.sh Tutorials/Basic/HelloWorld_C/CMakeLists.txt Tutorials/Particles/CellSortedParticles/CMakeLists.txt commit 5597d97a9bc44433190a3c5204da0fcbb40f040a Merge: 04d71698b 51419a97f Author: mic84 Date: Wed Feb 26 17:27:48 2020 -0800 Merge pull request #711 from ax3l/fix-newFortranInterfaceFile CMake: New Fortran Interface File commit 04d71698b5ae9623fda36ab65121f4fe8f9f3ac9 Merge: af1a7bc59 17bfd54f3 Author: mic84 Date: Wed Feb 26 17:24:29 2020 -0800 Merge pull request #710 from ax3l/topic-cmakeAlias CMake: AMReX::amrex Alias commit 51419a97f8da1ea082b2b1945e9a135dbb729996 Author: Axel Huebl Date: Wed Feb 26 16:06:02 2020 -0800 CMake: New Fortran Interface File Add a new Fortran file to the F_Interface sources. Fixes a compile issue. Src/F_Interfaces/CMakeLists.txt commit 17bfd54f33361262788011f4694b7bc338656a20 Author: Axel Huebl Date: Wed Feb 26 14:44:47 2020 -0800 CMake Targets: More Namespace Aliases Add installed namespace alias to all public AMReX targets. Tools/CMake/AMReXFlagsTargets.cmake commit c2387c7c1aa38ad5c24295ef689dff11405b1f1c Author: Axel Huebl Date: Wed Feb 26 14:41:10 2020 -0800 CMake: AMReX::amrex Alias Adding a project alias on `CMakeLists.txt` level that is identical to the installed CMake namespace. This is a community-convention in CMake and makes sure that both `add_subdirectory(AMReX_DIR)` as well as `find_package(AMReX)` targets can just be accessed as `AMReX::amrex` in all cases in user code. Src/CMakeLists.txt commit af1a7bc59f37107817b1f2dd4cb9ea275a12c18b Merge: 091fd194f 4c018bf1d Author: WeiqunZhang Date: Wed Feb 26 12:14:13 2020 -0800 Merge pull request #709 from AMReX-Codes/load_balance_api Load balance api commit 091fd194fcb6c4398eb8dc197b922aaa84a454b4 Author: Weiqun Zhang Date: Wed Feb 26 12:04:39 2020 -0800 make Tools/GNUMake/comps/gnu.mak commit 4c018bf1d89a407cc956707ed8bb7249ff7481ca Author: Andrew Myers Date: Wed Feb 26 12:01:23 2020 -0800 Add rcost version of makeSFC Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit ecb2178db580c2d95b993600d4a2d918b9f07b65 Author: Andrew Myers Date: Wed Feb 26 11:46:55 2020 -0800 add nmax argument to rcost version of makeKnapSack Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit e7d931ce8668d7b770af4adf3be6b2b179df3e1b Author: Weiqun Zhang Date: Wed Feb 26 09:12:14 2020 -0800 fix USE_CUDA=TRUE BL_NO_FORT=TRUE Tools/GNUMake/sites/Make.unknown commit 4846da2898492af24b33de1bb2fb0964b6df47f0 Merge: b0b60ea86 b77866483 Author: Michael Zingale Date: Tue Feb 25 21:13:40 2020 -0500 Merge branch 'development' of ssh://github.com/AMReX-Codes/AMReX into development commit b0b60ea8662dc5281a2c21c459840a92a3f6dd40 Author: Michael Zingale Date: Tue Feb 25 21:13:27 2020 -0500 strings should not be gpu managed Tools/F_scripts/write_probin.py commit b77866483aeb205a04c9c606d5711a233b6b8931 Author: Weiqun Zhang Date: Tue Feb 25 11:39:03 2020 -0800 make some Macs even more happier with make Tools/GNUMake/sites/Make.unknown commit d7bf794daf52ee3eaf88c5f0448910948c5c9c4f Author: Weiqun Zhang Date: Tue Feb 25 11:13:14 2020 -0800 make some Macs happy with make Tools/GNUMake/sites/Make.unknown commit abf769dda75e4ad216be0aea117637d8cc7fd1af Author: Weiqun Zhang Date: Tue Feb 25 08:53:19 2020 -0800 fix for hip Tools/GNUMake/Make.defs Tools/GNUMake/comps/gnu.mak commit c9112ae993d204b4166cf6adb44777e91831a5f8 Merge: 26c4c2de0 623565219 Author: Andrew Myers Date: Tue Feb 25 01:47:08 2020 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 26c4c2de02edda271fe68dc26e03102de337616a Author: Andrew Myers Date: Tue Feb 25 01:46:49 2020 -0500 use Send instead of Asend in particle communication Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit 62356521921644da26b05f31c24d10410cd9a61f Author: Weiqun Zhang Date: Mon Feb 24 16:08:06 2020 -0800 If one compiles with NVCC_CCBIN=gcc-x, it will be used as the nvcc host compiler Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/nvcc.mak commit d874356991b1ebff40b147d38cb857b25d48d6e4 Merge: 3a981afe3 9f448be77 Author: Andrew Myers Date: Mon Feb 24 16:37:22 2020 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3a981afe3e466145ff452e762212bed57f353a8f Author: Andrew Myers Date: Mon Feb 24 16:23:39 2020 -0500 make these temporary instead of member data Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit d74cbd5dcfd1f913806ccb532dc7195110b814db Author: Andrew Myers Date: Mon Feb 24 16:23:04 2020 -0500 shrink to fit and capacity methods for ParticleTile Src/Particle/AMReX_ParticleTile.H commit 9f448be777d36fa4982ceb1b8f7b2d3b30c163f6 Merge: ef81e58b1 b5e3065b9 Author: Weiqun Zhang Date: Mon Feb 24 12:36:45 2020 -0800 Merge branch 'dpcpp' into development commit ef81e58b102ffa50fe823eb5f943bfe6b0048403 Author: Weiqun Zhang Date: Mon Feb 24 11:26:16 2020 -0800 add CArena::heap_space_actually_used Src/Base/AMReX_Arena.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp commit 1df1dc956966b8668733a3a5de389fadb1ff5653 Merge: 64108935e 2a04939eb Author: WeiqunZhang Date: Mon Feb 24 10:24:51 2020 -0800 Merge pull request #701 from AMReX-Codes/cgilet_dev Cgilet dev commit 64108935ea2bd45c6884b99e67022bdea5461256 Author: Weiqun Zhang Date: Mon Feb 24 10:17:25 2020 -0800 add CArena::sizeOf to return the size of momory held by a pointer Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp commit b5e3065b94787e8f3309b70eb9a8fbf32c0781ae Author: Weiqun Zhang Date: Mon Feb 24 09:45:37 2020 -0800 cannot use sycl::abs directly because it returns unsigned int given int. Src/Base/AMReX_Math.H commit b62ed62d0e5653b13d967a804ae6f661dfed328f Author: Weiqun Zhang Date: Mon Feb 24 09:37:14 2020 -0800 FBI: we can assume thread safety if not using OpenMP. Src/Base/AMReX_FabArrayBase.cpp commit 2a04939ebc21d6eb1406a77cfc06b389e3a32e6d Author: cgilet Date: Mon Feb 24 08:16:57 2020 -0500 Allow EBFabFactories with Basic EB support to use boxArray() and DistributionMap() Src/EB/AMReX_EBFabFactory.cpp commit e778f2555e692210f6fed9faeefb340007accf7c Merge: 0a9ae7feb 433143b8c Author: cgilet Date: Mon Feb 24 08:13:25 2020 -0500 Merge remote-tracking branch 'origin/development' into cgilet_dev commit 659af89ed75ce61856d665e56e20e7c8f79ec858 Author: Weiqun Zhang Date: Sun Feb 23 13:29:49 2020 -0800 make the heat equation problem bigger and there is no need to create plotmf Tutorials/GPU/HeatEquation_EX1_C/Exec/default/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit 433143b8cfa6006d06b8cfd9f1533119d8fd6010 Merge: c88ed39da 0e9ba3c2f Author: Michael Zingale Date: Sun Feb 23 16:06:59 2020 -0500 Merge branch 'development' of ssh://github.com/AMReX-Codes/AMReX into development commit c88ed39da8b63e2b2c0d0a85dec3e1e919b3d0e8 Author: Michael Zingale Date: Sun Feb 23 16:04:19 2020 -0500 add character support Tools/F_scripts/write_probin.py commit 93afab8e774a7b45aef246003bfac32b65374e1f Author: Weiqun Zhang Date: Sun Feb 23 09:35:57 2020 -0800 set USE_CUDA=FALSE when USE_HIP=TRUE Tools/GNUMake/Make.defs commit da3ec35909db2b4c2d2a86b5ca61675306366283 Author: Weiqun Zhang Date: Sun Feb 23 09:33:43 2020 -0800 Heat equation tutorial: merge CUDA and HIP Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/Make.package Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/mykernel.H Tutorials/GPU/HeatEquation_EX1_C/Exec/default/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/default/Make.package Tutorials/GPU/HeatEquation_EX1_C/Exec/default/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Exec/default/inputs_3d_hip Tutorials/GPU/HeatEquation_EX1_C/Exec/default/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Exec/default/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/default/mykernel.H Tutorials/GPU/HeatEquation_EX1_C/Exec/default/run.ascent Tutorials/GPU/HeatEquation_EX1_C/Exec/default/run.nocuda.script Tutorials/GPU/HeatEquation_EX1_C/Exec/default/run.summit Tutorials/GPU/HeatEquation_EX1_C/Exec/default/run.summitdev commit 8a055daa5ecac0a58ea15fd7a8e694f819262b83 Author: Weiqun Zhang Date: Sun Feb 23 09:12:30 2020 -0800 remove enable_if for non-DPC++ Src/Base/AMReX_Reduce.H commit 927562bbc33a7ca43cec54bcec90864554fed504 Merge: 123aeb60b 0e9ba3c2f Author: Weiqun Zhang Date: Sun Feb 23 09:08:02 2020 -0800 Merge branch 'development' into dpcpp commit 0e9ba3c2f38554925f6c534c04b0b3f14c55dcd5 Author: Weiqun Zhang Date: Sat Feb 22 22:38:38 2020 -0800 one more int -> long Src/Base/AMReX_FabArrayBase.H commit 123aeb60bd4ce934acdb16ba689e138e9e2486a7 Author: Weiqun Zhang Date: Sat Feb 22 21:28:20 2020 -0800 update DPC++ notes Docs/Notes/Readme.dpcpp commit f0c2dd5482be91b5f8f5d0f4904394ce6bf3810a Author: Weiqun Zhang Date: Sat Feb 22 20:59:11 2020 -0800 get around DPC++ bug? Src/Base/AMReX_Reduce.H commit 359400ec0c4aa9c072f2a0f65cd2ac12018c85a4 Author: Weiqun Zhang Date: Sat Feb 22 19:52:53 2020 -0800 make GpuTuple's default ctor host device function Src/Base/AMReX_Tuple.H commit 82aef1ea3366a84ff614b3c69edcd7dcda97029d Author: Weiqun Zhang Date: Sat Feb 22 18:13:39 2020 -0800 update ParallelReduce tutorial Tutorials/GPU/ParallelReduce/main.cpp commit 4eb8a033683e4ed555e16f063730ee472534bffe Author: Weiqun Zhang Date: Sat Feb 22 18:13:12 2020 -0800 fix a typo Src/Base/AMReX_GpuLaunchFunctsG.H commit bd63083377478893b4594c767b6eae152de78136 Author: Weiqun Zhang Date: Sat Feb 22 18:12:12 2020 -0800 avoid capture GpuTuple by value in reduction because dpc++ does like it's not standard layout Src/Base/AMReX_Reduce.H commit 62c841af63e18ea97c2fa86c63a24afdc527ce76 Merge: 51565fcf4 27a8f2e6f Author: Weiqun Zhang Date: Sat Feb 22 17:30:23 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 51565fcf416bcfc348c2522d4bc9965983310e11 Author: Weiqun Zhang Date: Sat Feb 22 17:30:03 2020 -0800 int -> long to avoid overflow Src/Base/AMReX_FabArrayBase.H commit 27a8f2e6f91e09de6d3a40898de8d83872d770d2 Author: Andrew Myers Date: Sat Feb 22 19:17:02 2020 -0500 ManagedVector -> DeviceVector throughout ParticleContainer Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_NeighborList.H Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_StructOfArrays.H commit b0eed55e72ff5c394851d3949e5ebaf48eb1bdb9 Merge: d05f6fae7 2fc188e83 Author: Weiqun Zhang Date: Fri Feb 21 21:32:35 2020 -0800 Merge branch 'dpcpp' into development commit 2fc188e836ec2246172f3cfe36d34c2fa9a6870b Author: Weiqun Zhang Date: Fri Feb 21 21:32:11 2020 -0800 note to GpuTuple and DPC++ Docs/Notes/Readme.dpcpp commit d05f6fae7aa048f2ec1ab035fed38f5e37244a82 Author: Max Katz Date: Fri Feb 21 20:40:33 2020 -0800 Deal with the case where extern is in a subdirectory Tools/F_scripts/write_probin.py commit be4c7a6651cb58634fe0b496aa9bd2c6b1a4c3fe Author: Weiqun Zhang Date: Fri Feb 21 16:04:51 2020 -0800 fix DPCPP launch macros Src/Base/AMReX_GpuLaunchMacrosG.H Tutorials/GPU/Launch/Make.package commit a022fd12431b2667efaf7aeaa6d4c263a2803b90 Author: Weiqun Zhang Date: Fri Feb 21 14:59:03 2020 -0800 DPCPP: abort in amrex::launch if shared memory is asked Src/Base/AMReX_GpuLaunchFunctsG.H commit da22993303c459a4d6a50abb6dc1dbed3a0addc8 Merge: f493fe490 c692bb822 Author: WeiqunZhang Date: Fri Feb 21 14:12:46 2020 -0800 Merge pull request #700 from ax3l/fix-FBIConstr FAB: Fix Constructor Calls commit c692bb822ab632527433a3b0fd297b3ce02aa81a Author: Axel Huebl Date: Fri Feb 21 13:38:53 2020 -0800 FAB: Fix Constructor Calls This fixes a bug in `Array4CopyTag` construction while pushing back to a vector. The current call does not what one expects to do, as hinted by the nvcc warning: ``` Src/Base/AMReX_FBI.H(920): warning: variable "zero" was set but never used detected during: instantiation of "void amrex::FabArray::FBEP_nowait(int, int, const amrex::IntVect &, const amrex::Periodicity &, __nv_bool, __nv_bool) [with FAB=amrex::FArrayBox, F=amrex::FArrayBox, =void]" Src/Base/AMReX_FabArray.H(1993): here instantiation of "void amrex::FabArray::FillBoundary_nowait(int, int, const amrex::IntVect &, const amrex::Periodicity &, __nv_bool) [with FAB=amrex::FArrayBox]" Src/Base/AMReX_FabArray.H(1870): here instantiation of "void amrex::FabArray::FillBoundary(const amrex::Periodicity &, __nv_bool) [with FAB=amrex::FArrayBox]" Src/Base/AMReX_FBI.H(955): warning: variable "zero" was set but never used detected during: instantiation of "void amrex::FabArray::FillBoundary_finish() [with FAB=amrex::FArrayBox, F=amrex::FArrayBox, =void]" Src/Base/AMReX_FabArray.H(1871): here instantiation of "void amrex::FabArray::FillBoundary(const amrex::Periodicity &, __nv_bool) [with FAB=amrex::FArrayBox]" ``` Basically the last arguments were not passed to object construction of `amrex::Array4CopyTag`. Further fixes: - add missing includes - move created r-values in (`emplace_back`) Src/Base/AMReX_FBI.H commit f493fe4904bb853ff4f0c4da7c36b29c833330d6 Merge: 35320890a ca0c4678f Author: Weiqun Zhang Date: Fri Feb 21 13:21:57 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit ca0c4678f584f8eb430bbc9b267597aa09487b5c Merge: 0518a258e 8a6dd0dac Author: Weiqun Zhang Date: Fri Feb 21 13:21:44 2020 -0800 Merge branch 'dpcpp' into development commit 8a6dd0dac3b20beb183c7ba7ab6169489b08b852 Author: Weiqun Zhang Date: Fri Feb 21 13:21:19 2020 -0800 notes on DPC++ Docs/Notes/Readme.dpcpp commit 35320890a198571bb59aaf0516de98577efe6365 Merge: 0518a258e 6b2090414 Author: Weiqun Zhang Date: Fri Feb 21 13:19:45 2020 -0800 Merge branch 'dpcpp' into development commit 6b209041463b0a23373f6fcf40f75df689ed5b27 Author: Weiqun Zhang Date: Fri Feb 21 13:08:49 2020 -0800 wait and throw Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuReduce.H commit ce56eebe6b78548eb503f5d4b84810b4368e3774 Author: Weiqun Zhang Date: Fri Feb 21 12:52:32 2020 -0800 update comments Src/Base/AMReX_GpuDevice.cpp commit 0518a258e5451ae4f76b02e209629b0e1487f1f4 Author: Michele Rosso Date: Fri Feb 21 15:29:20 2020 -0500 CMake+CUDA: no need to specify libcuda manually Tools/CMake/AMReX_Config.cmake commit 9d1c4cd8f4efacd91b86617d2438d6c11895399c Author: Michele Rosso Date: Fri Feb 21 15:13:07 2020 -0500 CMake:add missing sources from Extern/ProfParser Src/Extern/ProfParser/CMakeLists.txt commit 757546f183155d5334cdea0d35dbf0d7005e2ca9 Author: Weiqun Zhang Date: Fri Feb 21 09:48:44 2020 -0800 do not define dim3 for non-dpcpp Src/Base/AMReX_GpuTypes.H commit cbebdc6bd95889bfd1e9deeaaa3ec9c03ae52bfb Author: Weiqun Zhang Date: Fri Feb 21 09:40:41 2020 -0800 remove shared_mem_bytes option from FabReduce and VecReduce Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_Reduce.H commit 67baf386e645aa56f747c76b02733581b8e94dc7 Merge: 11f7ef7e5 f97cf7053 Author: Weiqun Zhang Date: Fri Feb 21 09:18:18 2020 -0800 Merge branch 'development' into dpcpp commit 11f7ef7e54dbd1397f65e7de0c1cfef159397280 Author: Weiqun Zhang Date: Thu Feb 20 21:55:33 2020 -0800 DPC++: implement AnyOf Src/Base/AMReX_Reduce.H commit 014d2307b64cbb18b99a6c2ada63b4954eb5a275 Author: Weiqun Zhang Date: Thu Feb 20 21:42:19 2020 -0800 DPC++: implement some functions used by FillBoundary Src/Base/AMReX_FBI.H commit a4b6de85308a5ad6afeea79c460f305eb35f77b1 Author: Weiqun Zhang Date: Thu Feb 20 21:11:47 2020 -0800 fix a number of cmath functions with hack Src/Base/AMReX_IntVect.H Src/Base/AMReX_RealVect.H Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H Src/EB/AMReX_algoim_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/Particle/AMReX_Particle_mod_K.H Src/Particle/AMReX_TracerParticle_mod_K.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.H Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_tagging.H Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H commit fce045dab6801bbfbcd00f9ec0cf77ce20efb224 Author: Weiqun Zhang Date: Thu Feb 20 18:50:57 2020 -0800 update dpcpp todo comments Src/Base/AMReX_BaseFab.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuMemory.H Src/Base/AMReX_GpuUtility.H commit b48ec2d5f603dde6bd700943e2c756265b27df4e Merge: 9bd350730 ce6646faa Author: Weiqun Zhang Date: Thu Feb 20 18:39:59 2020 -0800 Merge branch 'development' into dpcpp commit 9bd350730e25c33e5f8cfb7b96be91e1eede735f Merge: 5ccc26233 77ae1ad61 Author: Weiqun Zhang Date: Thu Feb 20 18:39:51 2020 -0800 Merge branch 'dpcpp2' into dpcpp commit f97cf7053ad11b92b32a08320942a66e640d67b6 Merge: 44260fdad ce6646faa Author: Michele Rosso Date: Thu Feb 20 18:28:22 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 44260fdad6531678db85c69e29a13012df4b2818 Author: Michele Rosso Date: Thu Feb 20 18:28:08 2020 -0800 CMake: fix how ProfParser is built Src/CMakeLists.txt Src/Extern/ProfParser/CMakeLists.txt commit 77ae1ad61d6624eadc2897f304e1ee08a89d3e8f Author: Weiqun Zhang Date: Thu Feb 20 17:35:03 2020 -0800 link to libsycl-cmath Src/Base/AMReX_COORDSYS_2D_C.H Src/Base/AMReX_GpuComplex.H Src/Base/AMReX_Math.H Src/Base/AMReX_MultiFabUtil_nd_C.H Tools/GNUMake/Make.defs Tools/GNUMake/comps/dpcpp.mak commit adbc4974a58bc9a942b21a2705b7c6567d27ebd7 Author: Weiqun Zhang Date: Thu Feb 20 16:47:23 2020 -0800 link to libsycl-glibc Tools/GNUMake/Make.defs Tools/GNUMake/comps/dpcpp.mak commit ce6646faa941595691a1d74852a46344807addfb Merge: dfe5737dc 181bb4da8 Author: Weiqun Zhang Date: Thu Feb 20 15:43:36 2020 -0800 Merge branch 'FlashFluxRegister' into development commit dfe5737dc86c8ef73be3f5410f24e012bc79251b Author: Michele Rosso Date: Thu Feb 20 15:15:03 2020 -0800 CMake+CUDA: link to nvToolsExt when ENABLE_BASE_PROFILE is on Tools/CMake/AMReX_Config.cmake commit 181bb4da8a7ba1b2e253d5146e233116e750ef70 Author: Weiqun Zhang Date: Thu Feb 20 09:12:41 2020 -0800 Optimization thanks to Klaus's suggestion Src/AmrCore/AMReX_AmrCore.cpp commit 216b40c7758df3f28b6ba64a51e541f08d3ca8d2 Author: Weiqun Zhang Date: Wed Feb 19 15:52:44 2020 -0800 NodalOverset test: use sigma strategy Tests/LinearSolvers/NodalOverset/MyTest.cpp commit 9f068dd90f382a7f10b90a31756bfba8b90b8fcd Author: Weiqun Zhang Date: Wed Feb 19 15:22:38 2020 -0800 AmrCore::regrid: if coarse level changes, we need to remake fine level so that flux register can be updated Src/AmrCore/AMReX_AmrCore.cpp commit 256f9dce8f1171d12fa1e4c24df5caa749238cf1 Merge: ebcf8b6be 1b321b42c Author: Weiqun Zhang Date: Wed Feb 19 14:17:26 2020 -0800 Merge branch 'weiqun/dev' into development commit 1b321b42c57219a30d35245fa81722963a1594f1 Author: Weiqun Zhang Date: Wed Feb 19 13:34:10 2020 -0800 missing Make.package Tests/LinearSolvers/NodalOverset/Make.package commit 0b213e763f5d676bad76aeeafc7eb5d987fd15ea Author: Weiqun Zhang Date: Wed Feb 19 13:32:24 2020 -0800 let user set nodal solver Dirichlet mask Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit f426d488a7aea710759c9c6e9d2c213458f591a1 Author: Weiqun Zhang Date: Wed Feb 19 13:30:44 2020 -0800 template average_down_nodes Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H commit c7171be9a0a4e20bf3664f4efdaf8af06b01e0b1 Author: Weiqun Zhang Date: Wed Feb 19 13:28:43 2020 -0800 move is_nodal and is_cell_centered from MultiFab to FabArrayBase Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 4f6bf3ffcc68edc12fa678155308f1efd65e59df Author: Weiqun Zhang Date: Wed Feb 19 13:27:21 2020 -0800 add new test NodalOverset Tests/LinearSolvers/NodalOverset/GNUmakefile Tests/LinearSolvers/NodalOverset/MyTest.H Tests/LinearSolvers/NodalOverset/MyTest.cpp Tests/LinearSolvers/NodalOverset/main.cpp commit ebcf8b6be148db34531f94acb6e10d9b8f1c678e Merge: 6e6ca81fc 260ed2ea5 Author: Andrew Myers Date: Wed Feb 19 10:19:25 2020 -0800 Merge branch 'development' into sort_particles_bin commit bda04ad279e4cd180724f3e40a4662c9aea840f9 Author: Weiqun Zhang Date: Wed Feb 19 09:15:43 2020 -0800 FlashFluxRegister: isFluxDensity Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.H Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90 commit 2d89d62be53564531ec5367b7161828763a99117 Merge: 2d4ad21e3 260ed2ea5 Author: Weiqun Zhang Date: Tue Feb 18 14:00:20 2020 -0800 Merge branch 'development' into FlashFluxRegister commit 260ed2ea541dba448a498f7f55aa546dd9e552ea Author: Andrew Myers Date: Tue Feb 18 09:46:03 2020 -0800 fix index error in mac tracer advection Src/Particle/AMReX_TracerParticle_mod_K.H commit 0e586a4f723076db26ba1cd5f4ad6b2631c89155 Merge: 3eefcb61b 30af3ac1f Author: Andrew Myers Date: Tue Feb 18 09:31:34 2020 -0800 Merge branch 'particle_io_filter' into development commit 6e6ca81fc27984470e6c63c8ec2bd679fbf6b9c8 Author: atmyers Date: Mon Feb 17 14:44:28 2020 -0800 bugfix Src/Particle/AMReX_ParticleContainerI.H commit 191c506198a54a9595cdf9a106665251e7796518 Author: atmyers Date: Mon Feb 17 14:26:51 2020 -0800 Add SortParticlesByBin Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 30af3ac1f2791fb1bb9277d9cc736e247d0ae3c1 Author: atmyers Date: Mon Feb 17 13:38:47 2020 -0800 fix the io filter Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_Particles.H commit 2f215787be278d17b3d8c4d7584e0c7a6740e268 Author: Weiqun Zhang Date: Sun Feb 16 18:59:09 2020 -0800 more detail in abort message Src/Base/AMReX_FBI.H Src/Base/AMReX_MultiFabUtil_nd_C.H Src/Base/AMReX_Reduce.H commit 5ccc26233ee28f31c597536e5ce8b7b1fe2ae0ff Author: Weiqun Zhang Date: Sun Feb 16 13:20:31 2020 -0800 remove abort in DPC++ reduce Src/Base/AMReX_GpuReduce.H commit 3050822eb81a18c4abeff7914c32621982c84e7b Author: Weiqun Zhang Date: Sun Feb 16 13:20:31 2020 -0800 remove abort in DPC++ reduce Src/Base/AMReX_GpuReduce.H commit 3f3363040f599457e3c57205f513059c6a833c7b Author: Weiqun Zhang Date: Sun Feb 16 11:35:19 2020 -0800 clean up Tools/GNUMake/comps/dpcpp.mak commit 98feeae1fea0b189369f65586ac86917c52f4b42 Author: Weiqun Zhang Date: Sun Feb 16 10:03:36 2020 -0800 amrex::Math Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_COORDSYS_1D_C.H Src/Base/AMReX_COORDSYS_2D_C.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_GpuComplex.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_Math.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_RealVect.H Src/Base/CMakeLists.txt Src/Base/Make.package Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H commit df360db74ac22f344bfb7e87ddb5537034d1bdb5 Author: Weiqun Zhang Date: Sun Feb 16 08:43:48 2020 -0800 Revert "use scyl::abs and sycl::copysign. This commit should be reverted once they are in std:: in future version of DPC++" This reverts commit d729af65b53d644a20c656db342c55d02f797093. Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/Base/AMReX_BaseFab.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H commit dd2dcbb50225c8667fec5901b2da39934a9ee9a4 Author: Weiqun Zhang Date: Sun Feb 16 08:43:19 2020 -0800 Revert "missing using sycl::abs. This should be reverted too eventually." This reverts commit e12071d6ae63e82d5677a816847bbc8172f041fd. Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H commit ac94eb008f92c29d63dd120e28fb51b953ab480b Author: Weiqun Zhang Date: Sun Feb 16 08:42:04 2020 -0800 always add -DNDEBUG to get around compiler bug Tools/GNUMake/Make.defs commit 72bc471a9880f6a88adcd7636ba5eef4019e7657 Author: Weiqun Zhang Date: Sat Feb 15 21:29:54 2020 -0800 avoid NDEBUG Src/Base/AMReX_Machine.cpp commit 3de96d0f3f9e838906ce8d372f6c6004488e2182 Author: Weiqun Zhang Date: Sat Feb 15 21:21:42 2020 -0800 use amrex::Abort and ASSERT Src/Base/AMReX.H Src/Base/AMReX_Machine.cpp commit 30d97c53aae0fdc8d869e2fd0a82e762a5e1ed86 Author: Weiqun Zhang Date: Sat Feb 15 20:41:56 2020 -0800 more detail in abort message Src/Base/AMReX_GpuAssert.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuLaunchMacrosG.H commit 3eefcb61b16075d8430b42b4bd489a3c449aa088 Merge: acc3983bf 4a0750ceb Author: WeiqunZhang Date: Sat Feb 15 15:30:34 2020 -0800 Merge pull request #696 from AMReX-Codes/stream Add stream benchmark commit 1682082c205279c90761bf9ceca18331ebecae4f Author: Weiqun Zhang Date: Sat Feb 15 15:13:15 2020 -0800 wait and throw Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp commit 4a0750ceb5797b40d1908ccefd29034cb5f074fc Author: Max Katz Date: Sat Feb 15 13:32:38 2020 -0800 Add stream benchmark Tests/Stream/GNUmakefile Tests/Stream/Make.package Tests/Stream/inputs Tests/Stream/main.cpp commit 782c85bdad46b63a5556644f461b79549da8b1a9 Author: atmyers Date: Fri Feb 14 23:31:39 2020 -0800 particle type -> superparticletype Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleIO.H commit de222755c62c52465e91cb8be8cb18fac8563e97 Author: Weiqun Zhang Date: Fri Feb 14 19:56:29 2020 -0800 add placeholders for deviceReduce Src/Base/AMReX_GpuReduce.H commit 309497d6e418932b2a735a8927cf762f2e11417e Author: Weiqun Zhang Date: Fri Feb 14 19:19:15 2020 -0800 use abort() instead of assert(0) Src/Base/AMReX_GpuAssert.H commit f739f4f29fd76c8015e7547e81072e447ec4efb5 Author: Weiqun Zhang Date: Fri Feb 14 16:38:08 2020 -0800 no need for __SYCL_DEVICE_ONLY__ Src/Base/AMReX_BaseFab.H commit 24a8439691715dcbc2c920044864a781ba7f7c55 Author: Weiqun Zhang Date: Thu Feb 13 21:54:34 2020 -0800 remove shared memory from paralle for because it may be unsafe Src/Base/AMReX_GpuLaunchFunctsG.H commit a0f62de2dfbea094016373431bebae4f1a224b97 Author: Weiqun Zhang Date: Thu Feb 13 19:42:08 2020 -0800 DPC++: start reduction Src/Base/AMReX_BlockMutex.cpp Src/Base/AMReX_FBI.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_Reduce.H commit e12071d6ae63e82d5677a816847bbc8172f041fd Author: Weiqun Zhang Date: Thu Feb 13 19:41:06 2020 -0800 missing using sycl::abs. This should be reverted too eventually. Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H commit d729af65b53d644a20c656db342c55d02f797093 Author: Weiqun Zhang Date: Thu Feb 13 15:13:50 2020 -0800 use scyl::abs and sycl::copysign. This commit should be reverted once they are in std:: in future version of DPC++ Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/Base/AMReX_BaseFab.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H commit bbbcd9aa6878f382396e0bb58a1931db7367e90a Merge: 21ac50f88 acc3983bf Author: atmyers Date: Thu Feb 13 15:10:25 2020 -0800 Merge branch 'development' into particle_io_filter commit 65607c3afde96b44da3aa7e7374165d3476b4f1c Author: Weiqun Zhang Date: Thu Feb 13 15:09:20 2020 -0800 fix some issue in launch macros Src/Base/AMReX_GpuLaunchMacrosG.H commit 4abf4fd3b9f66ae666a062419d16d60b9f53867d Author: Weiqun Zhang Date: Thu Feb 13 15:09:02 2020 -0800 add override Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H commit 21ac50f8851b0ab2f449dc0af12ffb2aad91da87 Author: atmyers Date: Thu Feb 13 14:56:26 2020 -0800 add a filter to control which particles get written out Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_Particles.H commit acc3983bf509b9d52398a3f3275681bce4787bd7 Merge: 513ce3e58 189d422b1 Author: WeiqunZhang Date: Thu Feb 13 14:29:55 2020 -0800 Merge pull request #695 from maikel/feature/VirtualMakeBaseGrids Feature/virtual make base grids commit c1239d87db8c645ad1f96b258c70db2adaa6fd06 Author: Weiqun Zhang Date: Thu Feb 13 14:04:31 2020 -0800 fix launch macros Src/Base/AMReX_GpuLaunchMacrosG.H commit 189d422b17b4d86902cf14a29cbc9a47cbbc64c2 Author: Maikel Nadolski Date: Thu Feb 13 22:24:59 2020 +0100 Add const qualifier to PostProcessBaseGrids Src/AmrCore/AMReX_AmrMesh.H commit f2b611455bb06f0002232a156472b7c8faeaaf21 Author: Weiqun Zhang Date: Thu Feb 13 13:19:16 2020 -0800 DPC++: for now streamSynchronize in Elixir and AsyncArray clear() Src/Base/AMReX_GpuAsyncArray.H Src/Base/AMReX_GpuElixir.cpp commit fdc9b78e9fe73d26ccb070a407359b768c2c0c4b Author: Maikel Nadolski Date: Thu Feb 13 22:16:10 2020 +0100 Add a virtual member function to AmrMesh This commit adds a PostProcessBaseGrids member function. This makes it possible to alter the box array for the coarsest level before it is being used. Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit 8b06937d743d85fcbfe25d3fc5997d1cdd252636 Author: Weiqun Zhang Date: Thu Feb 13 12:38:19 2020 -0800 Gpu::Atomic: add missing features and cleanup Src/Base/AMReX_GpuAtomic.H commit c342cf23d52d4c726fb0d6c325314809333f29e1 Author: Weiqun Zhang Date: Thu Feb 13 05:18:31 2020 -0800 put Gpu::Atomic in a new file Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuAtomic.H Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_GpuUtility.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 466ce93dc4fb442c9970bf8ae8f8e0b29ee487a4 Author: Weiqun Zhang Date: Wed Feb 12 20:02:47 2020 -0800 DPC++: Gpu::Atomic::Add Src/Base/AMReX_GpuUtility.H commit b672e58f15704095c3152ec39403a0686f441cac Author: Weiqun Zhang Date: Wed Feb 12 16:31:09 2020 -0800 DPC++ add async error handler Src/Base/AMReX_GpuDevice.cpp commit ff8f6919bfbec13f1d91536977aded0fd3041e44 Author: Weiqun Zhang Date: Wed Feb 12 16:11:50 2020 -0800 some minor changes Src/Base/AMReX_BaseFab.H Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_IF_Polynomial.H commit 96152c8131c824d3fcd639c7a5ff354937097377 Author: Weiqun Zhang Date: Wed Feb 12 15:01:04 2020 -0800 DPC++: always wait after memcpy Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuLaunchFunctsG.H commit c48951d6dc4467e5191619a3fe7cbc9deac14999 Author: Weiqun Zhang Date: Wed Feb 12 14:28:11 2020 -0800 redefined AMREX_DEVICE_COMPILE as a macro Src/Base/AMReX.H Src/Base/AMReX_Array4.H Src/Base/AMReX_GpuAssert.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuPrint.H Src/Base/AMReX_GpuQualifiers.H Src/Base/AMReX_GpuRange.H commit 19d107b7d2a9b11bf57e2fbf25b4a70dbe94f05e Author: Weiqun Zhang Date: Wed Feb 12 13:40:58 2020 -0800 DPC++: assert Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Array4.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuAssert.H Src/Base/AMReX_GpuPrint.H Src/Base/AMReX_MultiFabUtil_nd_C.H Src/Base/AMReX_TypeTraits.H Src/Base/CMakeLists.txt Src/Base/Make.package commit a2672f9914133ca5076586b18296f1ded2d9cfdd Author: Weiqun Zhang Date: Wed Feb 12 12:33:26 2020 -0800 DPC++: printf Src/Base/AMReX_Array4.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuPrint.H Src/Base/CMakeLists.txt Src/Base/Make.package commit d5cc5b6092aafe5fbdb22324aca3a5f00be425f6 Merge: dba00ad0a f8b373097 Author: Weiqun Zhang Date: Wed Feb 12 12:03:43 2020 -0800 Merge branch 'dpcpp' of https://github.com/AMReX-Codes/amrex into dpcpp commit f8b3730978638e9bdafaf758930ff99147decbed Author: Weiqun Zhang Date: Wed Feb 12 12:03:15 2020 -0800 have to use sycl::floor Src/Base/AMReX_MultiFabUtil_nd_C.H commit dba00ad0aadda62859ef45e47bd892c2ededa767 Merge: 815e84ce9 06d7acd55 Author: Weiqun Zhang Date: Wed Feb 12 11:47:05 2020 -0800 Merge branch 'dpcpp' of https://github.com/AMReX-Codes/amrex into dpcpp commit 06d7acd5520eabb96fef579f080c825cbe024e8d Author: Weiqun Zhang Date: Wed Feb 12 11:46:40 2020 -0800 make sure sycl doesn't see virtual funcitons Src/Base/AMReX.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_GpuRange.H Src/Base/AMReX_ParmParse.H commit faa519bec35fbb8127bbea3cf2175c5de436f651 Author: Weiqun Zhang Date: Wed Feb 12 05:59:18 2020 -0800 launch macros in DPC++ Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuLaunchMacrosC.H Src/Base/AMReX_GpuLaunchMacrosG.H Src/Base/AMReX_GpuRange.H Src/Base/AMReX_PODVector.H Src/Base/AMReX_Random.cpp commit 1659c4916e8d4786f321ad085d54f93dc98cb351 Author: Weiqun Zhang Date: Tue Feb 11 13:04:28 2020 -0800 launch functions in DPC++ Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuRange.H commit cf560e4377daa877c206adf67e0c5d4e115c7c62 Merge: cd1a86b64 513ce3e58 Author: Weiqun Zhang Date: Tue Feb 11 10:31:39 2020 -0800 Merge branch 'development' into dpcpp commit 513ce3e58d7b430396950dd4d2de1b09d9b90da6 Author: Weiqun Zhang Date: Tue Feb 11 10:31:08 2020 -0800 add Gpu::synchronize Src/EB/AMReX_EBMultiFabUtil.cpp commit 815e84ce99cfd280be2304b808c973455705cb11 Author: Weiqun Zhang Date: Tue Feb 11 10:29:05 2020 -0800 IsDeviceLambda always return true for DPC++ Src/Base/AMReX_FabArray.H Src/Base/AMReX_TypeTraits.H commit cd1a86b6439bfbec3dda1a13da5a5935ca747e42 Merge: 00280b7c5 9b4230d74 Author: Weiqun Zhang Date: Tue Feb 11 08:54:35 2020 -0800 Merge branch 'dpcpp' of https://github.com/AMReX-Codes/amrex into dpcpp commit 00280b7c501f7b38616e866c687b10e7c7fe0ecd Author: Weiqun Zhang Date: Tue Feb 11 08:54:28 2020 -0800 more place holders Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Random.H commit 9b4230d74b8765b10eac1bbe856668dbd263830e Merge: 2481c8c17 f3404a76b Author: Weiqun Zhang Date: Tue Feb 11 08:53:06 2020 -0800 Merge branch 'development' into dpcpp commit f3404a76b7b23b85ebbc1ed4cc8071ce40e5b577 Author: Weiqun Zhang Date: Tue Feb 11 08:50:08 2020 -0800 use __CUDA_ARCH__ and __HIP_DEVICE_COMPILE__ directly in preparation for DPC++ Src/Base/AMReX.cpp Src/Base/AMReX_Array4.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuRange.H Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_Random.cpp Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_IF_Polynomial.H commit 792a4dc053c8407d528d2c1ae213f491cce5a580 Author: Andrew Myers Date: Mon Feb 10 22:36:55 2020 -0800 need to skip the size-0 entries in this loop, if we are going to do this in the one-box case Src/Particle/AMReX_ParticleCommunication.H commit 89f4d2bae16d90fcdc5da498cffbf3cefa94217b Author: Andrew Myers Date: Mon Feb 10 18:49:54 2020 -0800 remove these early exits from the particle communication code Src/Particle/AMReX_ParticleCommunication.H commit 1d2baa79613784fa81d9713b2c910b60428e9af3 Author: Weiqun Zhang Date: Mon Feb 10 10:43:32 2020 -0800 add variadic version of std::is_same Src/Base/AMReX_TypeTraits.H commit 98a6acf6a9b15a4c161bed8dceac355e3d80d8d4 Author: Weiqun Zhang Date: Sun Feb 9 07:12:08 2020 -0800 implicit conversion for 1d Src/Base/AMReX_Box.H commit f5524d5d23de01ccdf1f3e9bb0410be1845c2771 Author: Weiqun Zhang Date: Sat Feb 8 20:13:16 2020 -0800 move some RealVect functions from cpp to H file Src/Base/AMReX_IntVect.H Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp commit b7c8d430c287cf45548d15e25f5d035c2d9b6c29 Merge: 2435aeb92 c5e27f5e8 Author: WeiqunZhang Date: Sat Feb 8 20:14:33 2020 -0800 Merge pull request #690 from AMReX-Codes/write_probin simplify write_probin + add C++ parameter support commit c5e27f5e8dde3f49f5fa48ec62a42e25a61a197f Author: Max Katz Date: Sat Feb 8 19:54:27 2020 -0800 Add __managed__ attribute to extern parameters Tools/F_scripts/write_probin.py commit 3a83174cbf007db38efe31e0d61378af945578fe Merge: 68235784f 2435aeb92 Author: Max Katz Date: Sat Feb 8 19:19:07 2020 -0800 Merge branch 'development' into write_probin commit 2481c8c179306c2cbd4500b3cbf4a04b78fad8aa Author: Weiqun Zhang Date: Sat Feb 8 16:36:29 2020 -0800 make sure all queues use the same context with an empty async handler Src/Base/AMReX_GpuDevice.cpp commit 2435aeb92b66ded0a5089023d845da88a400583c Author: Max Katz Date: Sat Feb 8 10:30:11 2020 -0800 Add AMREX_GPU_CONSTANT and AMREX_GPU_MANAGED Src/Base/AMReX_GpuQualifiers.H commit 364b5020383331c5971694faa1b463f090362055 Author: Weiqun Zhang Date: Sat Feb 8 06:56:01 2020 -0800 placeholder in Array4 assert Src/Base/AMReX_Array4.H Src/Base/AMReX_GpuUtility.H commit 5427daa5f1824f6b19d5f9c2e71e478d18d95f17 Author: Weiqun Zhang Date: Fri Feb 7 16:30:44 2020 -0800 store subgroup size Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuLaunchFunctsG.H commit 808fb3299e6c9d51fde497b4e7bb92f458613364 Author: Weiqun Zhang Date: Fri Feb 7 15:00:41 2020 -0800 fix some ifdefs Src/Base/AMReX_GpuDevice.H commit eb5a9f3c9a5a3cd2413438e81038461972793943 Author: Weiqun Zhang Date: Fri Feb 7 14:54:38 2020 -0800 minor change to make Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/comps/dpcpp.mak commit 3e40cdd11606c4c8ee8753400d215ee3042ee919 Author: Weiqun Zhang Date: Fri Feb 7 13:33:47 2020 -0800 ParalleFor inside MFIter works Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuTypes.H Tools/GNUMake/Make.defs commit 857a24719b8024da82dc6e814efb496380ca5665 Author: Weiqun Zhang Date: Fri Feb 7 12:59:32 2020 -0800 ParallelFor works for a simple example Src/Base/AMReX_Array4.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuLaunchFunctsG.H Tools/GNUMake/Make.rules Tools/GNUMake/comps/dpcpp.mak commit de7637126376c8c5b3fe8c7a02bfba4a08405954 Author: Weiqun Zhang Date: Fri Feb 7 10:24:31 2020 -0800 update Arena Src/Base/AMReX_Arena.cpp Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp commit 6557d83295441800bb22a68b6750591c6b357519 Author: Weiqun Zhang Date: Thu Feb 6 21:38:49 2020 -0800 place holders and device properties Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BlockMutex.H Src/Base/AMReX_BlockMutex.cpp Src/Base/AMReX_FBI.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuAsyncArray.H Src/Base/AMReX_GpuAsyncArray.cpp Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuElixir.cpp Src/Base/AMReX_GpuError.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuLaunchMacrosG.H Src/Base/AMReX_GpuMemory.H Src/Base/AMReX_GpuQualifiers.H Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_Random.cpp Src/Base/AMReX_Reduce.H Src/Base/AMReX_Scan.H Src/Base/CMakeLists.txt Src/Base/Make.package Tools/GNUMake/Make.defs commit 6756c3efd8a51e651baada30ff74c217cda0ca98 Author: Weiqun Zhang Date: Thu Feb 6 16:24:35 2020 -0800 compile with dpcpp Src/Base/AMReX_GpuTypes.H commit 3698f3bea94250191548536a105a845223115a63 Merge: c53903aa8 e239da0d8 Author: Weiqun Zhang Date: Thu Feb 6 11:52:41 2020 -0800 Merge branch 'development' into dpcpp commit 2d4ad21e36918559cfb1fe66454c8d9ae51a5ce3 Author: Weiqun Zhang Date: Thu Feb 6 11:24:20 2020 -0800 FlashFluxRegister: add addition load/store with area argument Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.H Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90 commit 56398465f0bcd4ebec74fca580126a9fead27391 Author: Weiqun Zhang Date: Thu Feb 6 10:55:36 2020 -0800 FlashFluxRegister: add addition load Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.H Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90 commit e239da0d890edf86ec671a9946fdda2967e4a947 Merge: 619210646 e094f3bf5 Author: WeiqunZhang Date: Thu Feb 6 09:20:01 2020 -0800 Merge pull request #684 from lucafedeli88/add_poisson_random_distribution Add Poisson random distribution commit 619210646d22d309f25d6fd96ee656c6c27d5b4c Merge: 8fb159073 cda488174 Author: WeiqunZhang Date: Thu Feb 6 08:53:25 2020 -0800 Merge pull request #687 from Alpine-DAV/task/2020_02_blueprint_multi_topo Conduit Blueprint Update to support Multiple Topologies commit 8fb159073f78a80b825a2f709db25785cbc19bd6 Author: Weiqun Zhang Date: Wed Feb 5 14:31:04 2020 -0800 fix bug in nodal solver bc Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H commit cda48817449e9a4caac6dc91b426cf82f3b0b17d Author: Cyrus Harrison Date: Wed Feb 5 15:23:59 2020 -0600 blueprint: dont reset output node when wrapping data Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H commit 7d41281ca474d2baaa3536d20d113fca1b0ac1a4 Merge: 158aeb0e4 eb79e19bd Author: Andrew Myers Date: Wed Feb 5 10:08:39 2020 -0800 Merge pull request #686 from AMReX-Codes/jmsexton/hdf5 Fix for USE_CUDA=TRUE case commit eb79e19bdb2ce90ab9d51e6185f356b74f37e94f Author: Jean M. Sexton Date: Wed Feb 5 12:58:03 2020 -0500 Fix for USE_CUDA=TRUE case Tests/HDF5Benchmark/GNUmakefile commit e094f3bf5af9f036197d7115db995c6255b3f875 Author: Luca Fedeli Date: Wed Feb 5 02:10:41 2020 +0100 add Poisson random distribution Src/Base/AMReX_Random.H Src/Base/AMReX_Random.cpp commit 158aeb0e46b670e31995a6337af60b41793b672e Author: Andrew Myers Date: Wed Feb 5 03:09:02 2020 -0500 remove some timers I don't need anymore Src/Particle/AMReX_ParticleCommunication.cpp commit b00b4bd6fb8d7ec3cbce19ed75b0e4cca24798a7 Author: Andrew Myers Date: Wed Feb 5 02:54:10 2020 -0500 an optmization for ParticleCopyPlan::buildMPI start in the local case Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit 1cdd45be688446625c608153789c760dec5a6ee5 Merge: 5ba81cc43 254d55756 Author: WeiqunZhang Date: Tue Feb 4 16:16:28 2020 -0800 Merge pull request #656 from AMReX-Codes/kngott/hip [WIP] First draft of Changes for HIP commit 254d557566ddb4a5803c8dad09a9f86a01e34ad9 Author: Weiqun Zhang Date: Tue Feb 4 16:15:49 2020 -0800 fix typo Tests/GPU/RandomNumberGeneration/GNUmakefile commit 5c7ef0a2db57dc45661dd8c94e19bf275121f5ce Author: Weiqun Zhang Date: Tue Feb 4 15:32:28 2020 -0800 change DEBUG Tutorials/GPU/ParallelReduce/GNUmakefile commit e876dca2122e1e962e48c6bf09dded05379b8202 Author: Weiqun Zhang Date: Tue Feb 4 15:24:49 2020 -0800 restore USE_CUDA=TRUE Tests/GPU/RandomNumberGeneration/GNUmakefile commit 3977578cfc04ab95e16ec870880e0d6ffad3d5b9 Author: Weiqun Zhang Date: Tue Feb 4 14:58:07 2020 -0800 add amrex:: because macros doesn't know namespace Src/Base/AMReX_GpuLaunch.H commit 93573d6d4a6a40113ece1d507ca16a00e5cac07c Author: Weiqun Zhang Date: Tue Feb 4 14:44:18 2020 -0800 fix for USE_MPI and CUDA >= 10 Src/Base/AMReX_GpuDevice.cpp commit 66f8b5b63b1f3941fa1b4eb456138cf5e75e501c Author: Weiqun Zhang Date: Tue Feb 4 13:32:35 2020 -0800 use gcc in HelloWorld Tutorials/Basic/HelloWorld_C/GNUmakefile commit b70bcb5280685a122f21ddea2f24038821dfb705 Author: Weiqun Zhang Date: Tue Feb 4 13:31:27 2020 -0800 disable USE_HIP in tutorials by default Tutorials/Basic/HelloWorld_C/GNUmakefile Tutorials/GPU/Launch/GNUmakefile Tutorials/GPU/ParallelReduce/GNUmakefile commit dd661613e4fd6969f98dd8beb3018533207e24c3 Merge: 6a11a2b76 5ba81cc43 Author: Weiqun Zhang Date: Tue Feb 4 13:27:06 2020 -0800 Merge branch 'development' into kngott/hip commit 5ba81cc43f885bc5ef12e3d48e2c7f2866203a2e Author: Weiqun Zhang Date: Tue Feb 4 13:08:08 2020 -0800 fix setBndry for 1d and 2d. update setDomainBndry Src/Base/AMReX_FabArray.H commit 25bf9a8defc09581a7b9b854e47804a1c6da8cf1 Merge: 6688dbb2d 4f4bd460d Author: WeiqunZhang Date: Tue Feb 4 12:54:31 2020 -0800 Merge pull request #673 from AMReX-Codes/kngott/newBndry New version of setBndry for GPUs. commit 6688dbb2d3f98848acf6d44b8bd550b0192d7fe3 Merge: d2ccbb9fb 4d31715c4 Author: WeiqunZhang Date: Tue Feb 4 12:27:56 2020 -0800 Merge pull request #653 from AMReX-Codes/ebtensor_flux Ebtensor flux commit d2ccbb9fbd08d32ba89a51f2a6fd5f91f207ee1c Author: Weiqun Zhang Date: Tue Feb 4 11:55:50 2020 -0800 Tutorials/Amr: remove duplicated code Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_octree_F/Source/Src_2d/advect_2d_mod.F90 commit 7e60b7df5de1dff7ce5a5634662a4716246042f6 Merge: bad9864a7 d0dbb0d81 Author: Weiqun Zhang Date: Tue Feb 4 11:54:44 2020 -0800 Merge branch 'FlashFluxRegister' into development commit bad9864a77f7e591bffc125f29a0bf9e2633e3cc Author: Weiqun Zhang Date: Tue Feb 4 11:50:14 2020 -0800 FillPatch: no need to do interpolation of the time is exact Src/AmrCore/AMReX_FillPatchUtil.cpp commit 63f767d14b42e2cbffc4e85595ad159db59f3d96 Author: Weiqun Zhang Date: Tue Feb 4 11:49:36 2020 -0800 if Cluster::new_chop fails, switch to Cluster::chop Src/AmrCore/AMReX_Cluster.cpp commit b18cff108cb7201db9a0735abb7b8f2a24afb7b5 Author: Weiqun Zhang Date: Mon Feb 3 15:18:44 2020 -0800 Option to specify number of ghost cells in fill coarse patch Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp commit b6da11ba5e441994d79efd2700b418fd35f29ab5 Author: Andy Nonaka Date: Mon Feb 3 18:44:21 2020 -0800 update caption of advection tutorial figs Docs/sphinx_documentation/source/AmrCore.rst commit 0207561e2a17f54d2aa0575c0c2bd316323853dc Author: Andrew Myers Date: Mon Feb 3 15:49:40 2020 -0800 fix docstrings Src/Particle/AMReX_ParticleTransformation.H commit 07128cae84e8791b865d6a4b7e885477afc92cbf Merge: 46383fbcd 777485c10 Author: WeiqunZhang Date: Mon Feb 3 09:30:07 2020 -0800 Merge pull request #657 from kcdodd/development Change cell bilinear to work with odd refinement ratio commit 46383fbcd40886255d6bfb3fa31f54301ad80969 Merge: 83196e6ca ae712c807 Author: WeiqunZhang Date: Mon Feb 3 09:27:51 2020 -0800 Merge pull request #674 from ax3l/fix-shadowVisMF VisMF: Remove Shadow Warning commit 83196e6caaaa8565b0a4813f71374bc3310fdab6 Author: Weiqun Zhang Date: Mon Feb 3 09:20:40 2020 -0800 update CHANGES CHANGES commit c944434d17ef4a73f6054556577959d9ef53a768 Merge: da62e6e96 cb928f7f8 Author: Weiqun Zhang Date: Mon Feb 3 09:17:33 2020 -0800 Merge branch 'weiqun/AmrInfo' into development commit da62e6e96091ca6cb281687042a74ab1f80a4de4 Merge: e41605ce8 d7a0a1ce7 Author: Weiqun Zhang Date: Mon Feb 3 09:17:05 2020 -0800 Merge branch 'weiqun/bl_no_fort' into development commit e41605ce80832a2ce6e20987ab8a00ace77640b1 Merge: 8aeaa8d29 f51c71492 Author: Weiqun Zhang Date: Mon Feb 3 09:16:16 2020 -0800 Merge branch 'weiqun/mfiter' into development commit 8aeaa8d299e7e149bb3e6194e9f6ac1757dbb25d Merge: 579d412fb 95995073f Author: Weiqun Zhang Date: Mon Feb 3 09:13:53 2020 -0800 Merge branch 'master' into development commit 95995073ff23e4051330c9f96fd2d195d77b9468 Author: Weiqun Zhang Date: Mon Feb 3 09:12:48 2020 -0800 update CHANGES CHANGES commit 579d412fbda9ab503e6ff70ded1a7b7c3feca3ad Merge: 1c150e13c 35561853f Author: WeiqunZhang Date: Sat Feb 1 21:57:05 2020 -0800 Merge pull request #683 from ax3l/fix-floatBuild Fix Build With Single Precision commit 68235784f4befdf8bfb403548b7a71d5c8ba8795 Author: Michael Zingale Date: Sat Feb 1 20:55:18 2020 -0500 add to the C++ header Tools/F_scripts/write_probin.py commit 2d469809a74c0dbf8c264a6f9762aebaaa6d2d20 Author: Michael Zingale Date: Sat Feb 1 20:13:32 2020 -0500 fix python Tools/F_scripts/write_probin.py commit 4ed278c1f2580126c5549934cf611f460fca0325 Author: Michael Zingale Date: Sat Feb 1 20:08:45 2020 -0500 revert parameter name: Tools/F_scripts/write_probin.py commit b5e28cb34a876bf106d3aa01f0521644eb98e423 Author: Michael Zingale Date: Sat Feb 1 19:50:41 2020 -0500 fix comment Tools/F_scripts/write_probin.py commit fb021a9fd776f21bc1a5120b343befa965a0f135 Merge: 9cd8f7d83 1d948eb5f Author: Michael Zingale Date: Sat Feb 1 19:47:35 2020 -0500 Merge branch 'write_probin' of ssh://github.com/AMReX-Codes/AMReX into write_probin commit 9cd8f7d832e622fbac5da5487caa88fb1d96a79e Author: Michael Zingale Date: Sat Feb 1 19:47:20 2020 -0500 get rid of the option of 2 different parameter lists Tools/F_scripts/write_probin.py commit 1d948eb5f68bf4840b8d876d7f9ac1e54d827753 Author: Michael Zingale Date: Sat Feb 1 19:46:49 2020 -0500 add the C++ code Tools/F_scripts/write_probin.py commit 930b240be66811a96b589036c73aa28c0e3b8016 Author: Michael Zingale Date: Sat Feb 1 19:09:26 2020 -0500 add the Fortran -> C++ headers Tools/F_scripts/write_probin.py commit ae1d0234318751a72e96be7c14cc4fa0477a37fc Author: Michael Zingale Date: Sat Feb 1 18:43:29 2020 -0500 automagically write the functions that will send F90 to C++ Tools/F_scripts/write_probin.py commit 10026f541588accc967ed0810721995f3a2bb373 Author: Michael Zingale Date: Sat Feb 1 18:07:52 2020 -0500 some cleaning / linting Tools/F_scripts/write_probin.py commit 35561853f9ce4c119bab66f667ccf7a90130e0fc Author: Axel Huebl Date: Sat Feb 1 14:03:15 2020 -0800 Fix Build With Single Precision With float builds (mismatched types in `max()`). Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit c53903aa81985bd28e61917d09bf64fe58e5e8af Author: Weiqun Zhang Date: Fri Jan 31 12:35:26 2020 -0800 add dpcpp.mak Tools/GNUMake/Make.defs Tools/GNUMake/comps/dpcpp.mak commit 48336e63e1ce25d5914608b5576087366f9e0175 Merge: 1c150e13c d7a0a1ce7 Author: Weiqun Zhang Date: Fri Jan 31 11:07:20 2020 -0800 Merge branch 'weiqun/bl_no_fort' into dpcpp commit d0dbb0d81c454a9631101e2affc29e5380a9a45c Author: Weiqun Zhang Date: Fri Jan 31 10:20:53 2020 -0800 BoxArray: this is probably better than the previous fix because it is more backward compatible Src/Base/AMReX_BoxArray.cpp commit 1c150e13cc228a494cfa5407ab13c4eafdaf3a0d Author: Weiqun Zhang Date: Fri Jan 31 09:22:52 2020 -0800 create a local device copy of BCRec vector before using it on GPU Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit 65d7768c697735c9cea4753c0d1f337ef281b046 Author: Weiqun Zhang Date: Thu Jan 30 21:33:33 2020 -0800 FlashFluxRegister tutorial: communicate only for fine levels Tutorials/Amr/Advection_octree_F2/Source/evolve_mod.F90 commit 4a39c1e39a10002510bec1488ca6affb36dc298f Author: Weiqun Zhang Date: Thu Jan 30 21:23:29 2020 -0800 fix a corner case in building BoxArray hash map Src/Base/AMReX_BoxArray.cpp commit e3ef3bdad1132e4b66a11c1b3b9a2dd6ef3a087b Author: Weiqun Zhang Date: Thu Jan 30 21:22:10 2020 -0800 FlashFluxRegister: bugs fixed Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90 Tutorials/Amr/Advection_octree_F/Source/evolve_mod.F90 Tutorials/Amr/Advection_octree_F2/Source/evolve_mod.F90 commit f9f9bf99825196b9852b14356005bba86bd5083f Author: Weiqun Zhang Date: Thu Jan 30 15:07:52 2020 -0800 Tutorial using FlashFluxRegister Tutorials/Amr/Advection_octree_F2/Exec/Make.Adv Tutorials/Amr/Advection_octree_F2/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_octree_F2/Exec/SingleVortex/Make.package Tutorials/Amr/Advection_octree_F2/Exec/SingleVortex/Prob.f90 Tutorials/Amr/Advection_octree_F2/Exec/SingleVortex/face_velocity_2d.F90 Tutorials/Amr/Advection_octree_F2/Exec/SingleVortex/inputs Tutorials/Amr/Advection_octree_F2/README Tutorials/Amr/Advection_octree_F2/Source/Make.package Tutorials/Amr/Advection_octree_F2/Source/Src_2d/Make.package Tutorials/Amr/Advection_octree_F2/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_octree_F2/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/Advection_octree_F2/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_octree_F2/Source/amr_data_mod.F90 Tutorials/Amr/Advection_octree_F2/Source/averagedown_mod.F90 Tutorials/Amr/Advection_octree_F2/Source/bc_mod.F90 Tutorials/Amr/Advection_octree_F2/Source/compute_dt_mod.F90 Tutorials/Amr/Advection_octree_F2/Source/evolve_mod.F90 Tutorials/Amr/Advection_octree_F2/Source/fillpatch_mod.F90 Tutorials/Amr/Advection_octree_F2/Source/fmain.F90 Tutorials/Amr/Advection_octree_F2/Source/initdata.F90 Tutorials/Amr/Advection_octree_F2/Source/my_amr_mod.F90 Tutorials/Amr/Advection_octree_F2/Source/plotfile_mod.F90 Tutorials/Amr/Advection_octree_F2/Source/tagging_mod.F90 commit 45d4129ee9d11b909facae43b2b18ade93a3bff0 Merge: 42f309685 132644d12 Author: Andrew Myers Date: Thu Jan 30 14:51:56 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 42f309685957060b64d1890f71c67390fd8b79dd Author: Andrew Myers Date: Thu Jan 30 14:51:45 2020 -0800 fix circular dependency Src/Particle/AMReX_ParticleLocator.H commit b83eb41c531812c77680a06995a930ec8a5e3308 Author: Weiqun Zhang Date: Thu Jan 30 14:23:56 2020 -0800 FlashFluxRegister: fix BoxList index type Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp commit 1ad3bc59c8824d064e31a0a0a774bb7f375cc588 Author: Weiqun Zhang Date: Thu Jan 30 14:18:40 2020 -0800 octree iterator for a given level Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Src/F_Interfaces/Octree/AMReX_octree_mod.F90 commit 05eee0753e044cd006f36dc18d288ce975107ad1 Author: Weiqun Zhang Date: Thu Jan 30 13:43:23 2020 -0800 pass boxarray and distributionmap when building amrex_flash_fluxregister Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.H Src/F_Interfaces/AmrCore/AMReX_FlashFluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90 Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_flash_fluxregister_mod.F90 Src/F_Interfaces/AmrCore/Make.package Src/F_Interfaces/Octree/AMReX_octree_mod.F90 Src/F_Interfaces/Octree/Make.package commit 4526bad3e16650ff977fbfbaf3139676a37620fb Author: Weiqun Zhang Date: Thu Jan 30 13:18:05 2020 -0800 amrex_flash_fluxregister Src/F_Interfaces/Octree/AMReX_FlashFluxRegister.H Src/F_Interfaces/Octree/AMReX_FlashFluxRegister.cpp Src/F_Interfaces/Octree/AMReX_flash_fluxregister_fi.cpp Src/F_Interfaces/Octree/AMReX_flash_fluxregister_mod.F90 Src/F_Interfaces/Octree/AMReX_octree_mod.F90 Src/F_Interfaces/Octree/Make.package commit 4d31715c453450081eed133b33f5e01d0e1710ea Author: cgilet Date: Thu Jan 30 12:28:14 2020 -0800 Remove unused variable Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 5b85c37424a1eea50e6453e706e1e285dc070e3e Merge: 84ad87832 132644d12 Author: cgilet Date: Thu Jan 30 12:20:43 2020 -0800 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 84ad878322897eeb4e31467d27a13b4fd18dbe62 Author: cgilet Date: Thu Jan 30 12:20:37 2020 -0800 Clean up. Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 30200aac0fc6655155808df488d430b33b5fc21b Author: Weiqun Zhang Date: Thu Jan 30 11:25:37 2020 -0800 FlashFluxRegister Src/F_Interfaces/Octree/AMReX_FlashFluxRegister.H Src/F_Interfaces/Octree/AMReX_FlashFluxRegister.cpp Src/F_Interfaces/Octree/Make.package commit cb928f7f8a293368ca5ef01bf301a2ba4799283e Merge: 1be9d8e4a 837fd0006 Author: WeiqunZhang Date: Thu Jan 30 09:45:11 2020 -0800 Merge pull request #680 from maikel/weiqun/AmrInfo Make AmrMesh destructor default commit 837fd000663561f243cf87a7be53d77b680abd56 Author: Maikel Nadolski Date: Thu Jan 30 18:32:56 2020 +0100 Make AmrMesh destructor default Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit 1be9d8e4a4eedf28c402577e504b6c68da6cd197 Author: Weiqun Zhang Date: Thu Jan 30 09:01:20 2020 -0800 remove Initialize and Finalize from AmrCore and AmrMesh Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit d1b4cdf59eaac24425dac4207a3dc25ed87e7cfb Author: Weiqun Zhang Date: Thu Jan 30 08:58:59 2020 -0800 AmrMesh: protect AmrInfo and friend operator<< Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit 132644d1284725a871363524432850ec2309eee7 Author: Weiqun Zhang Date: Wed Jan 29 21:28:09 2020 -0800 fix periodic bug in tensor solver Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 904d1e467d812b52a723aeababae26778602cde6 Merge: bb99a132a 6e6c61988 Author: Andrew Myers Date: Wed Jan 29 20:01:21 2020 -0800 Merge pull request #679 from houjun/development Add support to restart from HDF5 particle checkpoint file commit 6df5eb895866b9bff4fd1ab9f8b41f8412e7a4da Author: cgilet Date: Wed Jan 29 18:50:48 2020 -0800 WIP debugging corner fill issue Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 501797081a8342e2909b7fb26c86d94bd3b5b2e6 Merge: b6333220f bb99a132a Author: cgilet Date: Wed Jan 29 14:59:05 2020 -0800 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 6e6c619885139703392767ce47e080fabab6794e Merge: 9e9ee041a bb99a132a Author: Houjun Tang Date: Wed Jan 29 13:04:38 2020 -0800 Merge remote-tracking branch 'upstream/development' into development commit 9e9ee041a0fd769e4c281866c7a1fd8774e586d4 Author: Houjun Tang Date: Wed Jan 29 13:02:20 2020 -0800 Add support to restart from checkpointed HDF5 particle file Src/Base/AMReX_PlotFileUtil.cpp Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_Particles.H Tests/HDF5Benchmark/main.cpp commit 6e2e393a3f2f77f0d8d48377af7ab17f1211b68d Merge: 320d84950 bb99a132a Author: Weiqun Zhang Date: Wed Jan 29 09:29:29 2020 -0800 Merge branch 'development' into weiqun/AmrInfo commit 320d84950ef63a1877df84b8e1a632749cef33e0 Author: Weiqun Zhang Date: Wed Jan 29 09:28:55 2020 -0800 New constructor for AmrMesh and AmrCore that does not use ParmParse Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit bb99a132ab7748b9e0731d05222ef519cb704c15 Author: cgilet Date: Wed Jan 29 11:12:44 2020 -0500 Some clean up. Src/EB/AMReX_EB_utils.cpp commit 0a9ae7feb3c3724f2545cc32a9151683c58b4b44 Author: cgilet Date: Wed Jan 29 10:55:00 2020 -0500 Some clean up. Src/EB/AMReX_EB_utils.cpp commit fa4e6c7affdae58b2cad8dc15d64357875642a25 Merge: 7db3feafc b354cd246 Author: WeiqunZhang Date: Wed Jan 29 07:46:15 2020 -0800 Merge pull request #678 from AMReX-Codes/cgilet_dev Fix apply_eb_redistrubution() to work in 3D. commit b354cd24697893d639768b6fdea570dbf7175eb1 Author: cgilet Date: Wed Jan 29 09:56:01 2020 -0500 Fix apply_eb_redistrubution() to work in 3D. Src/EB/AMReX_EB_utils.cpp commit 7db3feafc0e69da95269aad228de24a64a5bdd29 Author: Emmanuel Motheau Date: Tue Jan 28 16:05:58 2020 -0800 Some changes in eb_redistribution to avoid evaluating the redistribution near physical boundaries with data outside of the domain Src/EB/AMReX_EB_utils.cpp commit 1151ed097aaa86dd75f1a0fef763018fbad266f6 Author: Jean M. Sexton Date: Tue Jan 28 18:45:40 2020 -0500 Update summit MPS command -- is now a bsub command Tutorials/GPU/run.summit commit d7a0a1ce7a0f4f180481d622a53869b206e67e3d Merge: 006fb72dd 63db443ec Author: Weiqun Zhang Date: Tue Jan 28 15:30:48 2020 -0800 Merge branch 'development' into weiqun/bl_no_fort commit 63db443ecc827316dfbb1d427e26737a15fc8abf Merge: 5a46f0876 6c6b1cce0 Author: Weiqun Zhang Date: Tue Jan 28 13:25:47 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 006fb72ddc6285f189d9a333258090fce168c174 Author: Weiqun Zhang Date: Tue Jan 28 12:59:27 2020 -0800 no need to link to libgfortran Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/llvm.mak commit 6c6b1cce00b9a661162519b238edf1b62b167bc4 Merge: da8cc8f77 2eaec9ca3 Author: Andrew Myers Date: Tue Jan 28 12:52:52 2020 -0800 Merge pull request #676 from AMReX-Codes/jmsexton/particle Added check for RedistributeCPU edge case commit 5a46f0876cb1e68f630f693c7b29136c9db98679 Merge: 8074518b9 da8cc8f77 Author: Weiqun Zhang Date: Tue Jan 28 11:55:07 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1194f53ab371217b4505781d1cec980ad52c9c5c Author: Weiqun Zhang Date: Tue Jan 28 11:45:33 2020 -0800 update configure for BL_NO_FORT Tools/libamrex/configure.py commit 7c7a4535b844fcde494af35bb50ee1c9916c3a11 Author: Weiqun Zhang Date: Tue Jan 28 11:22:10 2020 -0800 BL_NO_FORT: EB Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EB_utils.H Src/EB/AMReX_EB_utils.cpp Src/EB/Make.package commit 160f96943fbd2b252556bcc02cc5da43bc7af475 Author: Weiqun Zhang Date: Tue Jan 28 10:40:52 2020 -0800 BL_NO_FORT in Amr Src/Amr/Make.package Tutorials/GPU/Advection_AmrCore/Exec/Make.Adv Tutorials/GPU/CNS/Exec/Make.CNS commit 41a4d7babbf5a7917bb409b14c1954ccca7e81d8 Author: Weiqun Zhang Date: Tue Jan 28 10:21:51 2020 -0800 BL_NO_FORT in AmrCore Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/Make.package Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/GNUmakefile commit 671d8c7f6be7d728b684f83f7620bd6208e80cce Author: Weiqun Zhang Date: Tue Jan 28 09:49:39 2020 -0800 BL_NO_FORT in Particle Src/Particle/Make.package commit bc4c6aac2fa32530f6e927d3fc071e5d4511f0d0 Author: Weiqun Zhang Date: Tue Jan 28 09:41:35 2020 -0800 BL_NO_FORT in MLMG Src/Boundary/Make.package Src/Boundary/OpenSource.txt Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/Make.package Tests/NoFort/GNUmakefile Tools/GNUMake/Make.defs Tutorials/LinearSolvers/ABecLaplacian_C/GNUmakefile commit 05b2962978cc1b777aff73d8872243dd61f022c1 Author: Weiqun Zhang Date: Mon Jan 27 20:25:18 2020 -0800 port fab_filcc to C++ Src/Base/AMReX_Box.H Src/Base/AMReX_FilCC_C.H Src/Base/AMReX_FilCC_C.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 7209a80fe15c90b305df885d1f82f28c09b0f4a9 Author: Weiqun Zhang Date: Mon Jan 27 20:01:15 2020 -0800 add more fortran free files to BL_NO_FORT build Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_MFCopyDescriptor.cpp Src/Base/Make.package commit f51c71492fb20af3a42a573b00f93244ae0e6bbe Author: Weiqun Zhang Date: Mon Jan 27 09:10:39 2020 -0800 make MFIter(BoxArray const&, DistributionMapping,...) omp safe Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit b6333220f7b4b7839f7c2f7c7c437dcf1b9e0d12 Merge: ab776fafd da8cc8f77 Author: cgilet Date: Mon Jan 27 07:31:05 2020 -0800 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit ae712c80786141943d971847fce185c36e2ad871 Author: Axel Huebl Date: Fri Jan 24 17:19:01 2020 -0800 VisMF: Remove Shadow Warning Change a private static interface to use the only-usage, same-class static control variable it passes to avoid variable name shadowing. Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp commit da8cc8f77873a0a4d2f78c9e72cc1be0485befad Merge: 7f8851058 b8ef5d998 Author: Andrew Myers Date: Fri Jan 24 16:41:18 2020 -0800 Merge pull request #672 from ax3l/fix-shadowTilingPC ParticleContainer: Fix Warnings commit 7f8851058a71b6f2dc5a51f9c5c56b9936eeb426 Merge: 566f7f301 9ffb30302 Author: Andrew Myers Date: Fri Jan 24 16:42:21 2020 -0800 Merge branch 'development' into atmyers/sparse_bins commit 9ffb3030240eefc7386c9fe74f1955da5035403a Author: Andrew Myers Date: Fri Jan 24 16:26:21 2020 -0800 add missing include Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 4f4bd460de9e70e98c6142b46cd6526b672ffd63 Author: Kevin Gott Date: Fri Jan 24 19:25:18 2020 -0500 New version of setBndry. Src/Base/AMReX_FabArray.H commit b8ef5d9987ac2aa321cc6fbcc66211adc828c6d8 Author: Axel Huebl Date: Fri Jan 24 15:38:06 2020 -0800 ParticleContainer: Fix Warnings Remove shadowed variable and unused local variable warnings. Src/Particle/AMReX_ParticleContainerI.H commit 566f7f3011082eac0c6da3b6c0094c0bdb2ce268 Author: Andrew Myers Date: Fri Jan 24 15:19:55 2020 -0800 reset default to the 'dense' binning strategy for now Src/Particle/AMReX_Particles.H commit f4f4e58a812165e2bbb1b3e6b29853d14b12c5d3 Merge: f3fea82c4 894d62fb9 Author: Andrew Myers Date: Fri Jan 24 15:19:07 2020 -0800 Merge branch 'development' into atmyers/sparse_bins commit 504ecec3a32977ffaa434d0844289a565d5ac83a Author: Michele Rosso Date: Fri Jan 24 15:02:56 2020 -0800 NodalProjector: some minor cleaning/tweaks Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 7d08b1050aceb4f2a0e5967bc9cb6a4f7829896a Author: Michele Rosso Date: Fri Jan 24 15:00:48 2020 -0800 NodalProjector: print norm0(RHS) after projection Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 1937e03b37e544600f1a664a7b256adcfbbe4b09 Author: Michele Rosso Date: Fri Jan 24 14:57:55 2020 -0800 NodalProjector: add code to handle fine->coarse averaging of velocity and fluxes Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit f3fea82c4d9ed6cc9f3b0cbcbf0dca78410a567b Author: Andrew Myers Date: Fri Jan 24 12:03:41 2020 -0800 typo Src/Particle/AMReX_SparseBins.H commit 8a2fd6187b9e90f58e6994465058ff5697e94072 Author: Andrew Myers Date: Fri Jan 24 12:01:58 2020 -0800 getIndex needs to handle the corner case where there is only 1 bin Src/Particle/AMReX_SparseBins.H commit 8074518b9837ea08d723dce71461176b6c3c876e Author: Weiqun Zhang Date: Fri Jan 24 08:49:42 2020 -0800 simply using amrex_long = int64_t Src/Base/AMReX_INT.H commit 894d62fb9435079e68935283d0276eac4b6ccd98 Author: Weiqun Zhang Date: Fri Jan 24 08:42:28 2020 -0800 long -> unsigned int Src/AmrCore/AMReX_AmrMesh.H commit 0db3c698c1ebae58cf1c38512d097b33edcf27cd Author: Weiqun Zhang Date: Fri Jan 24 08:22:55 2020 -0800 fix compilation Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 17eff2c9519c89eaff474405ed5d2ce422feaac0 Author: Weiqun Zhang Date: Fri Jan 24 05:59:05 2020 -0800 LinOp: use m_factory because a_factory might be empty Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit cc51f217b2c2d4fb0c0e1e01565a4484040ba0c5 Author: Weiqun Zhang Date: Thu Jan 23 18:59:21 2020 -0800 more robust way of detecting if SetDistributionMapping has been called Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit c26aa8d8d1804edf0f569e7c88b44b359af55eb7 Author: Weiqun Zhang Date: Thu Jan 23 18:37:23 2020 -0800 fix my recent mistake Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.cpp commit 42487a9727a897d5ed9132d7927a0cf7403d9db0 Author: Weiqun Zhang Date: Thu Jan 23 16:47:36 2020 -0800 Nodal sovler sigma: use EB_average_down Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 0d34582e63e20023ae869e799699441ef3de3f1e Author: Andrew Myers Date: Thu Jan 23 15:05:13 2020 -0800 forgot to set m_items Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_SparseBins.H commit 244eae34b42c4b80211d3441747d013f1f7603fb Author: Andrew Myers Date: Thu Jan 23 14:48:29 2020 -0800 fix potential overflow Src/Particle/AMReX_BinIterator.H commit f46cb25f27b04d44a2fc7cf5036c653bc6944577 Author: Andrew Myers Date: Thu Jan 23 14:46:27 2020 -0800 fix CPU compile Src/Particle/AMReX_BinIterator.H Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_SparseBins.H commit 862991fb628b1424977642f3fe1bd285f3ae7968 Author: Andrew Myers Date: Thu Jan 23 14:24:06 2020 -0800 attempting to use SparseBins in the particle locator Src/Particle/AMReX_BinIterator.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_SparseBins.H commit 76997aff394d16fe6651208253dfc8377d01aaae Author: Andrew Myers Date: Thu Jan 23 14:10:19 2020 -0800 a convenient typedef Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_SparseBins.H commit b765e68bdb9e596bb212736e89bce199690d536e Author: Andrew Myers Date: Thu Jan 23 14:06:36 2020 -0800 implement sparse bins search Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_SparseBins.H commit 77af59996f27dce021f308e1ac503d08a82e3023 Author: Andrew Myers Date: Thu Jan 23 13:07:43 2020 -0800 Within a bin, DenseBins and SparseBins can use the same iterator type Src/Particle/AMReX_BinIterator.H Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_SparseBins.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 989e07bb1fa4c6be29ca81946ed0ee00b555d8af Author: Andrew Myers Date: Thu Jan 23 13:00:27 2020 -0800 adding SparseBinIteratorFactory Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_SparseBins.H commit 775e28a5dc48183ad743abe2365879d8b5bf0508 Author: Andrew Myers Date: Thu Jan 23 12:52:18 2020 -0800 forgot to check in SparseBins Src/Particle/AMReX_SparseBins.H commit 5b092dbf36a27a4202ec2c38a36bafc9c8b2db14 Author: Andrew Myers Date: Thu Jan 23 12:52:00 2020 -0800 some useful typedefs Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_Particles.H commit c01fd4cc6c12d2e8bdd2b289b8d8d4c5206559f6 Author: Weiqun Zhang Date: Thu Jan 23 11:16:30 2020 -0800 AmrCore: allow MakeNewLevelFromScratch to ignore DistribitionMapping provided Src/AmrCore/AMReX_AmrMesh.cpp commit ebdf408d57cf97f6725c060e20f40ddf90ed0f6b Author: Weiqun Zhang Date: Thu Jan 23 10:13:22 2020 -0800 AmrCore: allow users to ignore the DistributionMapping provided Src/AmrCore/AMReX_AmrCore.cpp commit 524089d5595e0b15a66fd3f2c9b95fd299a183d5 Author: Weiqun Zhang Date: Wed Jan 22 20:10:44 2020 -0800 FillPatchTwoLevels: option to specify number of ghost cells Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp commit 1afe9f6016668ce38f0618062ed3334262ddee09 Author: Andrew Myers Date: Wed Jan 22 16:15:44 2020 -0800 refactor dense bins to make it easier to incorporate sparse Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_Particles.H Tests/Particles/SparseBins/main.cpp commit 65d3931dc38b2943c4de338176a05e6b56580608 Author: Andrew Myers Date: Wed Jan 22 14:21:11 2020 -0800 code to compute a sparse binning structure Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/CMakeLists.txt Src/Particle/Make.package Tests/Particles/SparseBins/GNUmakefile Tests/Particles/SparseBins/Make.package Tests/Particles/SparseBins/inputs Tests/Particles/SparseBins/main.cpp commit 14a3ddf18378bd222af5a16e2783ccc838778453 Author: Weiqun Zhang Date: Wed Jan 22 09:54:37 2020 -0800 no need to use D_TERM Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit c7fc3839d028bc3462c7de3bdc8554986a7d7634 Author: Weiqun Zhang Date: Wed Jan 22 09:49:59 2020 -0800 D_DECL -> AMREX_D_DECL Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp commit 595d8ab664fc925dab140813a1948c8926c97623 Author: Weiqun Zhang Date: Wed Jan 22 09:10:02 2020 -0800 fix warning Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 606e77ee1c52ded983d6ffa3e7f06ba00e0d129f Author: Emmanuel Motheau Date: Wed Jan 22 09:02:50 2020 -0800 minor cosmetic cleaning Src/EB/AMReX_EBMultiFabUtil.cpp commit 2935b7c5b8f9798066642b9a5cf5a5038ecac30e Merge: b64d2da3c 62cf78e7c Author: emotheau Date: Wed Jan 22 09:01:15 2020 -0800 Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines commit 62cf78e7cb92ff36c34a4ce438de240620d4d4d5 Author: Weiqun Zhang Date: Tue Jan 21 20:43:39 2020 -0800 MacProjector: no ghost cells needed if mac velocity is already on centroid Src/LinearSolvers/Projections/AMReX_MacProjector.cpp commit b64d2da3c84cb35c5224c82c6bf7f4c0ad0b2d33 Author: emotheau Date: Tue Jan 21 12:47:47 2020 -0800 Revert "fix to fill the ghost cells" This reverts commit c4049b0b9df0e156c40a61bd45eb6ec91c6f9a04. Src/EB/AMReX_EBMultiFabUtil.cpp commit 93e1db54733f48abdf8673b3bce46e9d6e83c8b3 Merge: c4049b0b9 d2fa9bade Author: emotheau Date: Tue Jan 21 12:47:26 2020 -0800 Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines commit d2fa9bade3efad29d78c280aeed643e33c326d62 Author: Jean M. Sexton Date: Tue Jan 21 12:39:33 2020 -0800 Fix run script comment to use absolute path Tutorials/GPU/run.corigpu commit 6f3858aa732f30e83a64acb4cab45116f4f4bfe1 Merge: ba9f8b69e af6f14ba1 Author: Andrew Myers Date: Tue Jan 21 12:23:19 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ba9f8b69e854378037d3772513af766ed99c1313 Author: Andrew Myers Date: Tue Jan 21 12:23:10 2020 -0800 make USE_CUDA=FALSE on this test by default Tests/GPU/Vector/GNUmakefile commit af6f14ba15160bc7550e5949838c9edbd958595e Merge: d118fde5d 8e2fd193c Author: Andrew Myers Date: Tue Jan 21 14:24:21 2020 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d118fde5d9dcdfe1fff0ca3dff15a52d43adfc49 Author: Andrew Myers Date: Tue Jan 21 14:23:46 2020 -0500 this IO proc check is redundant and also wrong Tests/Particles/Redistribute/main.cpp commit 8e2fd193ce03a69b1dfaaf40a8dc17dfe1be2397 Author: Andrew Myers Date: Tue Jan 21 11:08:52 2020 -0800 tweak test Tests/GPU/Vector/main.cpp commit 5139018e829be1cd19935e612f676c04b63af010 Merge: cb13a92a7 96067acc0 Author: Andrew Myers Date: Tue Jan 21 11:06:50 2020 -0800 Merge branch 'device_vector_refactor' into development commit 96067acc0556cb78dffa2325dd22792e8e4ac596 Author: Andrew Myers Date: Tue Jan 21 10:58:19 2020 -0800 adding tests of the various host / device vectors Tests/GPU/Vector/GNUmakefile Tests/GPU/Vector/Make.package Tests/GPU/Vector/inputs Tests/GPU/Vector/main.cpp commit afe303a531644b985babb7b91cbc6d2910f056fc Author: Andrew Myers Date: Tue Jan 21 10:48:54 2020 -0800 add missing const_cast Src/Base/AMReX_PODVector.H commit 0f69edc4ea938f3bcf1474dd0186a581eb1111cc Author: Andrew Myers Date: Fri Jan 17 20:01:06 2020 -0800 these function signatures need to be consistent Src/Base/AMReX_PODVector.H commit 1cc226c0d88e442b872974de9495f91688bff5a7 Author: Andrew Myers Date: Fri Jan 17 17:18:51 2020 -0800 do memmove Src/Base/AMReX_PODVector.H commit 31bc6d60f5114c8914830fecaf748ef6e5b0b024 Author: Andrew Myers Date: Fri Jan 17 16:32:32 2020 -0800 add missing streamSync here Src/Base/AMReX_PODVector.H commit ebecf9179b5e978a70a270085bfd1d546af19dba Author: Andrew Myers Date: Fri Jan 17 16:13:07 2020 -0800 fixing a couple of bugs Src/Base/AMReX_PODVector.H commit 272037d3f4d7e8ab3c442c42712fd72d02844de0 Author: Andrew Myers Date: Fri Jan 17 15:17:20 2020 -0800 handling initializer list Src/Base/AMReX_PODVector.H Tests/Particles/Redistribute/main.cpp commit 2e19bfdc3572870602ffd13741c78bd517b52655 Author: Andrew Myers Date: Fri Jan 17 14:57:55 2020 -0800 also do memcpy Src/Base/AMReX_PODVector.H commit cb13a92a7dea859eb6aefe4eaf0e2d355394484d Author: Weiqun Zhang Date: Fri Jan 17 14:52:51 2020 -0800 ParmParse: private -> protected Src/Base/AMReX_ParmParse.H commit 4acb943b783387e71b85d177b2fde12a92b8c06e Author: Andrew Myers Date: Fri Jan 17 13:54:22 2020 -0800 adding uninitializedFillNImpl Src/Base/AMReX_GpuAllocators.H Src/Base/AMReX_PODVector.H commit 7a1a2eff68ffd25074afe7bc7c9f16429e6ae2e9 Author: Weiqun Zhang Date: Fri Jan 17 12:29:27 2020 -0800 fix typo Src/Base/AMReX_GpuLaunchFunctsG.H commit 4acf2a63d524bb441b9b525d8e530c9edf52e0d5 Author: Andrew Myers Date: Fri Jan 17 12:14:16 2020 -0800 some indentation fixes Src/Base/AMReX_PODVector.H commit 325c64198c0d5d8628f45f28fd8bbe534d8451cc Merge: 602e7b5c6 4cbc0b076 Author: Weiqun Zhang Date: Thu Jan 16 18:25:51 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 602e7b5c6879d52e308cdb911c1dbfb1cf5911ee Author: Weiqun Zhang Date: Thu Jan 16 18:25:42 2020 -0800 fix constexpr Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp commit 4cbc0b076a70a299fd4d8b0c51c6c3d6aa34f2ce Author: Jean M. Sexton Date: Thu Jan 16 15:38:56 2020 -0800 Updating job scripts Tutorials/GPU/run.corigpu Tutorials/GPU/run.summit commit 6a11a2b76ba9e313cdb36154891f708ef5ea1ad5 Author: Kevin Gott Date: Thu Jan 16 12:33:27 2020 -0800 Forgot about those pesky non-GPU cases. Src/Base/AMReX_Random.cpp commit f287145a31628c72d82321150360068549014bf1 Merge: 13c8bcc20 d630f805c Author: Andrew Myers Date: Thu Jan 16 12:30:39 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 13c8bcc2063d7be4c3b97a5c82a13817a28f2415 Author: Andrew Myers Date: Thu Jan 16 12:30:29 2020 -0800 docstrings for amrex::Partition and amrex::StablePartition Src/Base/AMReX_Partition.H commit 77e303911cdd46196196ac81dee4c46b1f8f0ba3 Author: Andrew Myers Date: Thu Jan 16 12:16:00 2020 -0800 remove call to deprecated function Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainerInit.cpp commit 78e9520f837e1e264a60a30aded03dcb08093735 Author: Andrew Myers Date: Thu Jan 16 12:15:50 2020 -0800 change default compiler for Cuda version to gcc Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/GNUmakefile commit 344a8c6b63bce34d54236d0a393c50a50310cd4a Author: Andrew Myers Date: Thu Jan 16 12:15:22 2020 -0800 docstrings for GpuComplex Src/Base/AMReX_GpuComplex.H commit d630f805c813b42c792fa702c02a170f204c247e Merge: a9e916ee5 b2980f606 Author: Weiqun Zhang Date: Thu Jan 16 09:48:19 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a9e916ee5e08a9261e0d88c1ca3eefbf8947a880 Author: Weiqun Zhang Date: Thu Jan 16 09:48:13 2020 -0800 fix launch region test Tests/GPU/CudaGraphs/GraphBoundary/Prob.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H commit b2980f606550a06b53b1f1447444446a12655318 Merge: dabc2f815 b0db4dcc9 Author: Andrew Myers Date: Thu Jan 16 09:47:42 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b0db4dcc9127dff2a131e29701165ca52b6591c5 Merge: bea550b91 a38660845 Author: WeiqunZhang Date: Thu Jan 16 08:46:19 2020 -0800 Merge pull request #661 from rporcu/development Added 'TheZeroVector', 'TheUnitVector' and 'floor' functions to class RealVect commit bea550b9152bbf2437c5806f00c11694e4af3331 Author: Weiqun Zhang Date: Wed Jan 15 21:20:53 2020 -0800 add explicit Src/Base/AMReX_Box.H commit ab776fafdbeec1eaffdd57bf4ea84fbc71cb93f3 Author: cgilet Date: Wed Jan 15 18:43:10 2020 -0800 Fix const qualifier so compiles with CUDA Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 040c84dc265997e1200e3a83a5bb723d5090fdfc Author: cgilet Date: Wed Jan 15 18:42:03 2020 -0800 Remove unused variable Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit c4049b0b9df0e156c40a61bd45eb6ec91c6f9a04 Author: Emmanuel Motheau Date: Wed Jan 15 17:53:34 2020 -0800 fix to fill the ghost cells Src/EB/AMReX_EBMultiFabUtil.cpp commit 5739ef3224892249e24b8f6c92b504d59275db51 Author: cgilet Date: Wed Jan 15 17:53:44 2020 -0500 In MLTensorOp::compFlux(), surroundingnodes -> nodaltilebox Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 565787cbb6bfff2defb0db99acbe6d6a311d635b Author: cgilet Date: Wed Jan 15 17:52:02 2020 -0500 Create MLEBTensorOp::compCrossTerms() for use in apply() and compFlux(). This fixes a bug in compFlux. Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit b8cfd00a3afc36964ff6060789ec9700668596fc Author: kngott Date: Wed Jan 15 12:32:07 2020 -0800 Fix the portable Random. Src/Base/AMReX_BlockMutex.cpp Src/Base/AMReX_Random.cpp commit a386608453ce9e6388312ee5027a6a5edca7f107 Author: Roberto Porcu Date: Wed Jan 15 11:51:06 2020 -0800 Add constructor from Real pointer for class RealVect Src/Base/AMReX_RealVect.H commit 18ecc20415d1f5c79baf33c2039028de29239a3a Merge: ac3545b95 947d9e343 Author: cgilet Date: Wed Jan 15 09:28:57 2020 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit b08ab5622e8787a529c010b332a241208a9a47ba Author: Roberto Porcu Date: Tue Jan 14 18:12:56 2020 -0800 Added functions 'ceil' and 'round' to class RealVect Src/Base/AMReX_RealVect.H commit 8925b2fdca8ee7d3f5993c9c09eddfd026bf6e0a Merge: cd5c7ac26 947d9e343 Author: Roberto Porcu Date: Tue Jan 14 17:59:53 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit dc0923f9e8152980e45154f28cf8cea5949fc3a6 Merge: aa828e74d 947d9e343 Author: emotheau Date: Tue Jan 14 10:33:48 2020 -0800 Merge remote-tracking branch 'origin/mr/projections' into Emmanuel/new_EB_interpolation_routines commit dabc2f815b460322a20a868fdb468ce3a0d18ff5 Merge: 9b1bfb419 947d9e343 Author: Andrew Myers Date: Mon Jan 13 17:06:54 2020 -0800 Merge branch 'development' into atmyers/no_thrust commit 9b1bfb419470070a161ba97a35807907a7a8d0ce Author: Andrew Myers Date: Mon Jan 13 16:55:29 2020 -0800 fix typo Src/Base/AMReX_Partition.H commit 947d9e3436b094f6e589142adc26b8014472762a Author: Michele Rosso Date: Mon Jan 13 15:41:25 2020 -0800 CMake: add all tutorials in Tutorials/LinearSolvers Tutorials/LinearSolvers/ABecLaplacian_F/CMakeLists.txt Tutorials/LinearSolvers/MAC_Projection_EB/CMakeLists.txt Tutorials/LinearSolvers/MultiComponent/CMakeLists.txt Tutorials/LinearSolvers/NodalPoisson/CMakeLists.txt Tutorials/LinearSolvers/Nodal_Projection_EB/CMakeLists.txt Tutorials/LinearSolvers/NodeTensorLap/CMakeLists.txt commit cd5c7ac267da7d447163248d1500dbd8184e4779 Author: Roberto Porcu Date: Mon Jan 13 14:32:39 2020 -0800 Fix a bug in 'floor' function of class RealVect Src/Base/AMReX_RealVect.H commit 2fdc11e2ae7ec90a903e437f53c6de2f2a6c1261 Author: Roberto Porcu Date: Mon Jan 13 14:05:37 2020 -0800 Added 'TheZeroVector', 'TheUnitVector' and 'floor' functions to class RealVect Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp commit 72d45e3f7eaadd0c3fe08e4598c1db0ba95c8552 Merge: 08cd45f51 02f2f7ab5 Author: Michele Rosso Date: Mon Jan 13 13:57:31 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mr/projections commit 02f2f7ab5f0a1a842bfce8501f8d98c915cbff2e Merge: 7df8b8c41 9efcce292 Author: WeiqunZhang Date: Mon Jan 13 11:18:37 2020 -0800 Merge pull request #660 from rporcu/development Fix a bug which can give errors when compiling commit 9efcce2927ce02b7076d1adec0019a3ff4e62e6e Author: Roberto Porcu Date: Mon Jan 13 10:56:29 2020 -0800 Fix a bug which can give errors when compiling Src/Particle/AMReX_Particle.H commit 6d3cfa2245def205035cf98a1daa1fdd5d5a4211 Merge: fb963c2ab 7df8b8c41 Author: Andrew Myers Date: Mon Jan 13 10:14:46 2020 -0800 Merge branch 'development' into atmyers/no_thrust commit aa828e74dd1afd4f57de7a5c74aedb08b194a1cc Merge: 0b2a9061f 7df8b8c41 Author: emotheau Date: Sun Jan 12 09:46:16 2020 -0800 Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines commit 08cd45f514e77632cfd6299914efb4ec7f55f13e Author: Michele Rosso Date: Sat Jan 11 16:54:22 2020 -0800 NodalProjector: some bug fixes and some improvements Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 157ea50d8b10c9fdde260ebc33a48c7a97887d8b Merge: c329146ba 7df8b8c41 Author: Michele Rosso Date: Sat Jan 11 16:04:19 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mr/projections commit 7df8b8c41acb95ec37f99c0f9f05485214b47e39 Author: Ann Almgren Date: Sat Jan 11 14:11:33 2020 -0800 Rename amrex_compute ... rather than just compute... Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H commit d88da679371ddde9616694cd03cab24a7fda6a5d Author: Ann Almgren Date: Sat Jan 11 14:10:28 2020 -0800 Add routines to take convective differences -- analogous to the amrex_compute_divergence routine but doing convective not conservative differencing Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H commit c329146ba73867c093ac65108fff221209e6a5f2 Merge: 4059601c2 e3ee5ec4e Author: Michele Rosso Date: Fri Jan 10 14:37:28 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mr/projections commit 2b51b4ad41c03e1e510cca66c8586aa1933cd495 Author: kngott Date: Fri Jan 10 14:13:33 2020 -0800 Small changes for compatibility when running CUDA. Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_Random.cpp commit 37e298b954bc1d58d64a78d78a026fe8f1109fd4 Author: Kevin Gott Date: Fri Jan 10 14:04:48 2020 -0800 Avoid std::uninitialized_fill for hip. Tests/GPU/Locking/main.cpp commit e3ee5ec4e9d9fa3fa8721637be94959528618678 Merge: 1b8a5df28 10047f0fd Author: WeiqunZhang Date: Fri Jan 10 13:07:23 2020 -0800 Merge pull request #659 from rporcu/development Prevent rvalue component assignment for RealVect class commit fb963c2ab125e215f4f55922cd0a13bb2da567d3 Author: Andrew Myers Date: Fri Jan 10 13:06:00 2020 -0800 fix 'divide real by complex' operator Src/Base/AMReX_GpuComplex.H commit ff7a6c05c7f91516b59cf0b18acf61cfb3a320f2 Author: Andrew Myers Date: Fri Jan 10 12:55:58 2020 -0800 implement << operator for GpuComplex Src/Base/AMReX_GpuComplex.H commit b1a15e11911ceaa61cb268d7566e87a2db5961d2 Merge: 8feb9190e 1b8a5df28 Author: Andrew Myers Date: Fri Jan 10 12:28:51 2020 -0800 Merge branch 'development' into atmyers/no_thrust commit 0126fe7ba0b933942e48ad49778c512d6f622db9 Author: Kevin Gott Date: Thu Jan 9 21:13:16 2020 -0800 Add mutex to manual MemcpyToSymbol. Src/Base/AMReX_Random.cpp commit 10047f0fd9c3d069e6cb4802267d3e9516f913e8 Author: Roberto Porcu Date: Thu Jan 9 16:09:30 2020 -0800 Prevent rvalue component assignment for RealVect class Src/Base/AMReX_RealVect.H commit 4059601c22c24e94239e9d9654a15533c1349b2e Author: Michele Rosso Date: Thu Jan 9 15:44:57 2020 -0800 NodalProjector: re-write code and add support for multilevel projection Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 1b8a5df28a28ea6e772ef484d2656d356ccf76c0 Merge: 8025684f1 76ae5a48d Author: Andrew Myers Date: Thu Jan 9 15:08:29 2020 -0800 Merge pull request #658 from rporcu/development Fix compilation bug for latest functions added in AMReX_Particle.H commit 76ae5a48d933e88dd914fa90526eaa1dc2c37ca9 Author: Roberto Porcu Date: Thu Jan 9 14:56:57 2020 -0800 Fixed compilation bug for latest functions added i AMReX_Particle.H when AMREX_SPACEDIM == 1 Src/Particle/AMReX_Particle.H commit 4dd8768421c6dbef6b81b935311610919b82d0e9 Merge: 97c20cbc2 8025684f1 Author: Roberto Porcu Date: Thu Jan 9 14:55:38 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 8feb9190e1c2c594071c482510f31b5c71d71734 Merge: 8df86cbe5 e05597aa9 Author: Andrew Myers Date: Thu Jan 9 13:48:03 2020 -0800 Merge branch 'development' into atmyers/no_thrust commit 8025684f102a436363545a05cff78f79f8989d19 Merge: 3242cf6b5 e05597aa9 Author: Weiqun Zhang Date: Thu Jan 9 13:31:11 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3242cf6b56e25d7d159215fb142840cff63eeafd Author: Weiqun Zhang Date: Thu Jan 9 13:31:07 2020 -0800 MLMG: functions to set constant coefficients Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 8d53e7d09f94314bb08258ad34ce3e21e548453d Merge: 4c0f641b4 e05597aa9 Author: Michele Rosso Date: Thu Jan 9 10:35:19 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mr/projections commit e05597aa9c286e40190cf5f6dd6954a77fbbed9a Author: Ann Almgren Date: Thu Jan 9 06:53:24 2020 -0800 fix some spelling typos Docs/sphinx_documentation/source/LinearSolvers.rst commit 6a23789bf103ffc3270a779d1ed1db3c79f38972 Author: Ann Almgren Date: Thu Jan 9 06:34:03 2020 -0800 More spelling corrections (thanks ispell!) Docs/sphinx_documentation/source/GPU.rst commit 19801cd67d7ffae99686a9c35adc9ace91405e6c Author: Ann Almgren Date: Thu Jan 9 06:30:00 2020 -0800 Fix typo Docs/sphinx_documentation/source/GPU.rst commit 97c20cbc214403b48456e0b5849a2acbacdc8b53 Merge: a06d5eae7 bdf13a08d Author: Roberto Porcu Date: Wed Jan 8 16:29:59 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit a06d5eae7bd082891bfd154fdb0b7a3b4e564a4a Author: Roberto Porcu Date: Wed Jan 8 15:18:51 2020 -0800 Revert "Add functions norm and norm_sqr to class RealVect" This reverts commit 569147cb0c57a5287616c089889ff2a3974cf920. Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp commit 422bf36d4b69510d8af756c5f714373271428336 Author: Kevin Gott Date: Wed Jan 8 15:00:52 2020 -0800 Add a Fix comment. Src/Base/AMReX_RealVect.H commit 777485c10e70de501fd764e798a699cd8bdf2f3f Author: Carter Dodd Date: Wed Jan 8 17:00:07 2020 -0600 Change cell bilinear to work with odd refinement ratio Src/AmrCore/AMReX_INTERP_3D.F90 commit 4a072355862da0831247965050b6eedfd88144a9 Author: Kevin Gott Date: Wed Jan 8 14:27:23 2020 -0800 Adjusting for HIP. Currently blows up at PODVector.H, line 82 due to std::uninitialized_fill_n. Tests/GPU/Locking/main.cpp commit 569147cb0c57a5287616c089889ff2a3974cf920 Author: Roberto Porcu Date: Wed Jan 8 14:09:12 2020 -0800 Add functions norm and norm_sqr to class RealVect Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp commit bdf13a08d09914da5031151926dc0e2f33cda9bc Merge: a40267939 ce5ccf96c Author: Andrew Myers Date: Wed Jan 8 13:38:42 2020 -0800 Merge pull request #654 from rporcu/development Added functionality of extract a RealVect from Particle class commit 3a8e9339cc3f1d0ff2be4804fe590b08cbfa51fb Author: Kevin Gott Date: Wed Jan 8 13:31:35 2020 -0800 Make sure HIP-nvcc is off for now. Tools/GNUMake/Make.defs commit ce5ccf96c83f28cbd374cf40213221da5a41e2d3 Author: Roberto Porcu Date: Wed Jan 8 13:24:37 2020 -0800 Added functionality of extract a RealVect from Particle class Src/Particle/AMReX_Particle.H commit 33b0ea5704b093944aaac4a219783e1b37391a9d Author: Kevin Gott Date: Wed Jan 8 13:23:05 2020 -0800 std::sqrt and HIP don't mix. Src/Base/AMReX_RealVect.H commit 694519eec65c409b1432af411f3f89f30402754b Author: Kevin Gott Date: Wed Jan 8 13:22:47 2020 -0800 Adjust for state of HIP Random. Tutorials/GPU/ParallelReduce/main.cpp commit 10d3b3bf377e826860df22035653c304aa3143ee Merge: 535171fe6 a40267939 Author: Kevin Gott Date: Wed Jan 8 12:50:59 2020 -0800 Merge branch 'development' into kngott/hip commit ac3545b95243a4ece30fc9ea3e3451dec55fef00 Merge: 3af08a34f a40267939 Author: cgilet Date: Wed Jan 8 11:23:40 2020 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit a40267939e69cf290e341b59ed305ba7b90b0b31 Author: Weiqun Zhang Date: Tue Jan 7 20:22:36 2020 -0800 assert -> AMREX_ASSERT, std::min -> amrex::min and std::max -> amrex::max Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp commit 29e2a4c208548c946dff143f2a2225b812a7b9f9 Merge: 3adb1cf98 c8b4613af Author: Andrew Myers Date: Tue Jan 7 17:25:41 2020 -0800 Merge pull request #652 from rporcu/development Adding AMREX_GPU_HOST_DEVICE to functions and members of class RealVect commit c8b4613afdfbff86a20ce829e4f0c8f76e444047 Merge: 12e86adee 3adb1cf98 Author: Roberto Porcu Date: Tue Jan 7 17:11:10 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 12e86adee8a3a795d3f096a616b35cabb330b421 Author: Roberto Porcu Date: Tue Jan 7 17:02:15 2020 -0800 Added function crossProduct to class RealVect Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp commit 054c82f64983386cd6556d35ebc7c2772d1c1f68 Author: Roberto Porcu Date: Tue Jan 7 16:50:28 2020 -0800 Adding AMREX_GPU_HOST_DEVICE attribute to functions and members of class RealVect Src/Base/AMReX_IntVect.H Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp commit 3adb1cf98b4342d452cd15f3f4ff8f1ffe228905 Author: Andrew Myers Date: Tue Jan 7 15:39:24 2020 -0800 add correctness testing for checkpoint / restart in HDF5Benchmark test Tests/HDF5Benchmark/inputs Tests/HDF5Benchmark/main.cpp commit 99fbe5124cb2fecf0aefa38a46a0cb8b79427d92 Author: Andrew Myers Date: Tue Jan 7 10:46:19 2020 -0800 fix spaces Src/Particle/AMReX_ParticleTransformation.H commit b169255bb1be38437d463fb8c07daded609bdd21 Merge: f349c9281 8afb5a0cc Author: WeiqunZhang Date: Tue Jan 7 08:25:54 2020 -0800 Merge pull request #650 from eschnett/patch-2 Convert comment to English commit 8afb5a0cc4595cb775797b3e0729577af5d682af Author: Erik Schnetter Date: Tue Jan 7 10:10:39 2020 -0500 Convert comment to English Tools/CMake/AMReX_Defines.cmake commit f349c9281fc44483ece891d0b53880da84fbe005 Author: Andrew Myers Date: Mon Jan 6 16:48:47 2020 -0800 ignore unused return value Src/Particle/AMReX_ParticleIO.H commit 0b2a9061f9c06ac195df6ffaec8a1e3e8a4e479b Author: Emmanuel Motheau Date: Mon Jan 6 15:52:04 2020 -0800 bug fix missing copy for regular cells Src/EB/AMReX_EBMultiFabUtil.cpp commit 8a68df8be50c19b2865efea2abde49e47d105e56 Merge: 321ffaa01 fee20d598 Author: Emmanuel Motheau Date: Mon Jan 6 14:18:21 2020 -0800 Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines commit fee20d598e0a6aa81f203bc3ebff3f3eaf890689 Author: Andrew Myers Date: Mon Jan 6 12:34:32 2020 -0800 docstrings for the particle reduction functions Src/Particle/AMReX_ParticleReduce.H commit f43565c1819a289ef33815f82b085bd62d6926b6 Merge: 951e96e92 f9a7ede20 Author: Andrew Myers Date: Mon Jan 6 10:40:27 2020 -0800 Merge pull request #646 from houjun/development Add support to write particle data in HDF5 format commit 951e96e9228b944a32f3e60d192dd6180a0e0e98 Merge: a85d41ab4 d916a6eff Author: Weiqun Zhang Date: Mon Jan 6 09:45:30 2020 -0800 Merge branch 'development' into weiqun/dev commit d916a6eff191b243e728d6f5ac0fc6f89ba2f630 Merge: 431a095e2 bd75e0212 Author: WeiqunZhang Date: Mon Jan 6 09:26:17 2020 -0800 Merge pull request #649 from sudormroot/master The defition of single_level() should be 'void' rather 'int', otherwise compilers will report errors. commit 431a095e248a29ef6b7ccf6f75305991cc0abb3c Author: Weiqun Zhang Date: Mon Jan 6 09:17:53 2020 -0800 fix the pull-request just merged Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/Base/AMReX_MultiFabUtil.cpp Src/EB/AMReX_EB2_Level.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit c176aa1075d38b4f1ef2d418b5ac745cb39eea84 Merge: 00820c2fe 710b4425e Author: WeiqunZhang Date: Mon Jan 6 08:57:53 2020 -0800 Merge pull request #639 from rporcu/development Added begin and end methods to IntVect and RealVect classes commit bd75e0212eb8a682a298bc136a8308aceab77efe Author: sudormroot Date: Sun Jan 5 11:34:47 2020 +0800 The defition of single_level() should be 'void' rather 'int', otherwise, in some cases, the comiplers will report errors. OldTutorials/PIC_C/single_level.cpp commit 00820c2fe01cdf3db3e28060decd58774c566263 Author: Weiqun Zhang Date: Sat Jan 4 19:23:02 2020 -0800 constexpr void -> void so that it works with C++11 Src/Base/AMReX_Utility.H commit f9a7ede20ad1bd1c35c1a8dd8e64fa7b9e29d78a Author: Houjun Tang Date: Fri Jan 3 13:20:34 2020 -0800 Remove particle write in ascii format Tests/HDF5Benchmark/main.cpp commit e1a8379ba3ed30ac80a54949fb21a07b2363dba9 Author: Houjun Tang Date: Fri Jan 3 13:12:58 2020 -0800 Add environmental var option to set Lustre stripe parameters Src/Particle/AMReX_ParticleIO.H commit 7a2533e7a6e0c31671d20c5c9f48b8a108b0c6a5 Author: Houjun Tang Date: Fri Jan 3 10:47:10 2020 -0800 Fix an attribute write error with multiple levels Src/Particle/AMReX_ParticleIO.H commit 6059c02cd52b5be9b3ad4069bd6cb9c2cdec4254 Merge: ac2b3fedf 6d686a4ef Author: Houjun Tang Date: Fri Jan 3 10:20:33 2020 -0800 Solve conflicts with merge commit ac2b3fedfc532d4db51b4d05dd0db38470b2f92c Author: Houjun Tang Date: Fri Jan 3 10:04:47 2020 -0800 Add particle data write in HDF5 format Src/Base/AMReX_PlotFileUtil.cpp Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_Particles.H Tests/HDF5Benchmark/main.cpp commit 710b4425e729738ccd76b83993c0e80dab14061c Author: Roberto Porcu Date: Thu Jan 2 10:49:29 2020 -0800 Removed comment for variable that is needed in 1D or 2D simulations Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp commit a85d41ab4d3b289918d8eaa57f2d0bb9fd47be39 Author: Weiqun Zhang Date: Wed Jan 1 21:12:33 2020 -0800 need to inline TopIndexSpace Src/EB/AMReX_EB2.H commit 4aa0d32b1776fff9c5dfe5c4353e833275da1148 Merge: e27d8e57d 6d686a4ef Author: Weiqun Zhang Date: Wed Jan 1 21:07:53 2020 -0800 Merge branch 'development' into weiqun/dev commit 6d686a4ef19a8d9f91243c31972faaa724af4301 Merge: e00bc7c72 d7371e67c Author: Weiqun Zhang Date: Wed Jan 1 08:57:36 2020 -0800 Merge branch 'weiqun/comm' into development commit e00bc7c72a9d14ff4d206a087bff29417ee1e3a4 Merge: 05236f33a 0bcf0a4dc Author: Weiqun Zhang Date: Wed Jan 1 08:57:19 2020 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0bcf0a4dc4e548b1f949469546126aae708f9b6b Author: Weiqun Zhang Date: Wed Jan 1 08:46:57 2020 -0800 update CHANGES CHANGES commit d7371e67c896df7bdc73e3fd17550cf0d0f8da3b Author: Weiqun Zhang Date: Wed Jan 1 08:13:53 2020 -0800 ignore_unuesd: variadic and gpu host device Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_Utility.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H commit e26f14e4ff9d53122429d59642c397f0701edbb8 Author: Weiqun Zhang Date: Tue Dec 31 23:11:54 2019 -0800 clean up and avoid potential OMP issues Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit 12f9121277569977b009a818fb41888ae9ff93ae Author: Weiqun Zhang Date: Tue Dec 31 22:56:07 2019 -0800 fix assertion Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H commit f3b4d00add8e4fe90ba86323766f429145243f70 Author: Weiqun Zhang Date: Tue Dec 31 22:30:54 2019 -0800 support up to 128 GB of communication data for FabArray Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ccse-mpi.H commit 2fb740e3b1ef7ef1680c012ccd6be7c2cf3585ad Author: Weiqun Zhang Date: Tue Dec 31 21:30:36 2019 -0800 two new FabArray functions are for USE_MPI only Src/Base/AMReX_FabArrayCommI.H commit 05236f33a2de6db21ff35c94ece3c8df29f4cacd Author: Weiqun Zhang Date: Tue Dec 31 21:18:14 2019 -0800 support up to 16 GB of communication data for FabArray Src/Base/AMReX_Arena.cpp Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 61bd7bccc79ff30d3444322158e9b4c4025c2e00 Author: Weiqun Zhang Date: Tue Dec 31 16:48:48 2019 -0800 add amrex::aligned_size Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp commit d8a5a7804d17d10886e30c979c2c68123a389661 Merge: 229a5733d 92ea08fb1 Author: WeiqunZhang Date: Tue Dec 31 11:39:45 2019 -0800 Merge pull request #643 from eschnett/patch-1 Always check MPI buffer size for overflow commit e27d8e57dc38085092b58e4cbf4b95cac853de5a Author: Weiqun Zhang Date: Tue Dec 31 11:28:18 2019 -0800 minor Src/EB/AMReX_EB2.H commit 92ea08fb134a5ca975f65c87ecd72fa7e017a802 Author: Erik Schnetter Date: Tue Dec 31 11:45:00 2019 -0500 Always check MPI buffer size for overflow Always check MPI buffer size for overflow. This check is very fast compared to the overall communication time. Src/Base/AMReX_FabArrayCommI.H commit 229a5733d205a4e041501e55f3ede4e200c72f29 Merge: 93474ce25 5a69909eb Author: WeiqunZhang Date: Mon Dec 30 20:01:51 2019 -0800 Merge pull request #640 from AMReX-Codes/block_reduce_fix Handle an edge case where the block size is less than a warp commit 5a69909ebf92c3dae8d9b7d9ea4efd4b0e82a7eb Author: Weiqun Zhang Date: Mon Dec 30 11:58:08 2019 -0800 avoid std::max because in C++11 it doesn't work on GPU and because blockDim.x and warpSize are not the same integer type (one is unsinged whereas the other is signed) Src/Base/AMReX_GpuReduce.H commit 93474ce2568f495eea27878932c81afe4e663157 Author: Max Katz Date: Sat Dec 28 03:45:09 2019 -0800 Use a 1D block/thread layout for most loops Src/Base/AMReX_GpuDevice.cpp Tools/F_scripts/write_cuda_headers.py commit c222d054906086ff344359aa75764c61c930ea86 Author: Max Katz Date: Sat Dec 28 00:57:53 2019 -0800 Select a better block layout for 1D and 2D Src/Base/AMReX_GpuDevice.cpp commit b9f7ef5c966e8ed163786accae66ff2aeab57000 Author: Max Katz Date: Fri Dec 27 00:17:34 2019 -0800 Add GPU pragma option for a device sync Tools/F_scripts/write_cuda_headers.py commit 8ccc3cd5a1851c81ad0eab9b3ba3bd3b96845bee Author: Max Katz Date: Wed Dec 25 01:27:00 2019 -0800 Handle an edge case where the block size is less than a warp Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_fort_mod.F90 commit 321ffaa01288e58bf598b0c74717203d164a21a2 Author: Marc Day Date: Mon Dec 23 13:14:35 2019 -0800 Only setVal result components that will be filled. Src/EB/AMReX_EBMultiFabUtil.cpp commit b81e25fe39a3df6b3bffd483f45f36ece4a4b89f Author: Roberto Porcu Date: Mon Dec 23 11:42:01 2019 -0800 Fix some warning messages Src/AmrCore/AMReX_Interp_3D_C.H Src/Base/AMReX_MultiFabUtil.cpp Src/EB/AMReX_EB2_Level.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 5116f0fff4c9dcc6749307da2148a0ecae064199 Author: Roberto Porcu Date: Sun Dec 22 15:23:47 2019 -0800 Added begin and end methods to IntVect and RealVect classes Src/Base/AMReX_IntVect.H Src/Base/AMReX_RealVect.H commit e3a74e3bbc35c8397784529d2f6f798dc312c56b Author: Marc Day Date: Fri Dec 20 21:06:27 2019 -0800 Use consistent stencil to move cell-centered data to cell and face centroids. Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit 8df86cbe57b468b2f1b26c4d545d1c9ac015a5bf Author: Andrew Myers Date: Fri Dec 20 11:26:51 2019 -0800 that is not how complex numbers work Src/Base/AMReX_GpuComplex.H commit 81cdd2fabc8c1f5df563918055a1cb57c3a58151 Author: Emmanuel Motheau Date: Thu Dec 19 15:43:38 2019 -0800 Revert "WIP fixing interplation" This reverts commit a1a9aa36c224a746b8aa6f37fa6e4423c4a191c9. Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H commit 8864e584c97a5f5b12abfa0b6d30940481f61152 Author: Weiqun Zhang Date: Thu Dec 19 15:40:48 2019 -0800 MacProjector: no need for FillBoundary if already on centroid Src/LinearSolvers/Projections/AMReX_MacProjector.cpp commit e3cafd516ab77609311c46516ac513a23ea9eb39 Merge: afa7b2f1b 6b3e01d08 Author: Andrew Myers Date: Thu Dec 19 15:23:59 2019 -0800 Merge branch 'development' into atmyers/no_thrust commit afa7b2f1b47036186defd394deaecd2399fe086b Author: Andrew Myers Date: Thu Dec 19 14:55:31 2019 -0800 fix typo Src/Base/AMReX_Partition.H commit a1a9aa36c224a746b8aa6f37fa6e4423c4a191c9 Author: Emmanuel Motheau Date: Thu Dec 19 14:30:10 2019 -0800 WIP fixing interplation Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H commit 635f494ba6259351633e4fbf8ff28ead00e9b493 Author: Weiqun Zhang Date: Thu Dec 19 13:52:34 2019 -0800 add GetVecOfArrOfConstPtrs Src/Base/AMReX_Vector.H commit 39815517fb5ced5b7ff02ffcbad5d05480182d72 Author: Weiqun Zhang Date: Thu Dec 19 13:52:20 2019 -0800 skip ccmask if already on centroids Src/EB/AMReX_EBMultiFabUtil.cpp commit 6b3e01d08ce6faea3172b1216a197364535e6c87 Merge: a86c6214b cb6a1b680 Author: Andrew Myers Date: Thu Dec 19 13:33:18 2019 -0800 Merge pull request #638 from AMReX-Codes/dw/pmesh In ParticleToMesh, apply SumBoundary & finalize MultiFab for both GPU and CPU commit ec3565dad59eff36e73f1b92f5b4d99286356e9b Author: Weiqun Zhang Date: Thu Dec 19 13:23:23 2019 -0800 NodalProjector: simga may not have ghost cells. No need to call FillBoundary. Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 62c73dc62c51b4be51b5612486da02992a77a4b8 Author: Weiqun Zhang Date: Thu Dec 19 13:21:38 2019 -0800 EBCellFlag::setCovered: simply assign covered value Src/EB/AMReX_EBCellFlag.H commit cb6a1b6807cb7d9d35592479a97181af94e47e0c Author: Donald E. Willcox Date: Thu Dec 19 13:08:09 2019 -0800 Move SumBoundary and MultiFab copy & cleanup outside the not-in-launch-region scope. Src/Particle/AMReX_ParticleMesh.H commit a86c6214bccaaf9301e0e46a4a53f6749d82aae5 Author: Oscar Antepara Date: Thu Dec 19 13:06:46 2019 -0800 [Docs] Adding addtional comments on Paraview section Docs/sphinx_documentation/source/Visualization.rst commit 5d18ef5881e898a7a3c5d2c0e867dae4e3de3efe Merge: 7cb7eec99 000d63c22 Author: Andrew Myers Date: Thu Dec 19 12:50:02 2019 -0800 merging development into atmyers/no_thrust commit 000d63c2232e7154a6ca1b0e45f16c07d93bce09 Merge: 7224b4874 30fc8a486 Author: Andrew Myers Date: Thu Dec 19 12:48:35 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7224b4874199e3e294dbd04996ab6885bbff7f76 Author: Andrew Myers Date: Thu Dec 19 12:48:20 2019 -0800 a host / device version of swap Src/Base/AMReX_Algorithm.H Src/Base/AMReX_PODVector.H Src/Base/AMReX_Partition.H commit b243addba8a1185db6c85d49ef066b8e2e093264 Author: Marc Day Date: Wed Dec 18 18:31:52 2019 -0800 Fix cc2cent interp stencil in 2D Src/EB/AMReX_EBMultiFabUtil_2D_C.H commit 7cb7eec99be61f3bff2260dbf3981f8dc527f057 Author: Andrew Myers Date: Wed Dec 18 15:54:02 2019 -0800 more code reuse in amrex::Partition and amrex::StablePartition Src/Base/AMReX_Partition.H commit e7a9c07ab1704989ae724864e21ee6a693cf37fe Author: Andrew Myers Date: Wed Dec 18 15:07:57 2019 -0800 fix spaces Src/Particle/AMReX_ParticleTransformation.H commit 9daa261059a6018ee9aeb24715c5b2019d35e5d2 Author: Andrew Myers Date: Wed Dec 18 15:07:46 2019 -0800 reorder these functions Src/Base/AMReX_Partition.H commit b7ac1482d3d083bdd521ed15431645c182e187dd Merge: 996448eeb 30fc8a486 Author: Weiqun Zhang Date: Wed Dec 18 14:17:08 2019 -0800 Merge branch 'development' into weiqun/dev commit 30fc8a4866fbf413a1326cdbbaff9a7bf9f68a35 Merge: 9e07891b6 641d8dcde Author: Weiqun Zhang Date: Wed Dec 18 14:14:32 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 996448eebc22acb000c79c298733d4a4db25dd01 Author: Weiqun Zhang Date: Wed Dec 18 13:05:17 2019 -0800 Make FillPatchSingleLevel safe when the destination is the same as source. Change the interface of virtual PhysBCFunctBase::FillBoundary that unfortunately breaks backward compatibility. Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_PhysBCFunct.H Src/F_Interfaces/Base/AMReX_FPhysBC.H Src/F_Interfaces/Base/AMReX_FPhysBC.cpp commit 3af08a34fa3f42fbf452fccd27106b5fa8e0fde6 Author: cgilet Date: Wed Dec 18 17:00:36 2019 -0500 Fix testing for regular cells in compFluxes and compGrad. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 27d6d6af9743bc8fde5d0ad713468ca0a87c7845 Author: Andrew Myers Date: Wed Dec 18 13:35:37 2019 -0800 ensure that the Partition and ParallelScan Tests still work Tests/GPU/Partition/main.cpp Tutorials/GPU/ParallelScan/main.cpp commit 85c7b4ae8f2774f7e62cf076aa68d4d04185b0d3 Author: Andrew Myers Date: Wed Dec 18 13:35:11 2019 -0800 move implementation of inclusive_scan and exclusive_scan to get around circular dependency issue Src/Base/AMReX_GpuContainers.H Src/Base/AMReX_Scan.H commit cbd5449e87756323bb777857e6eba14d26ff3a53 Author: Andrew Myers Date: Wed Dec 18 13:34:23 2019 -0800 add alternate versions of Parition and StablePartition Src/Base/AMReX_Partition.H commit ec2a638557acfea6a19bbcb5b3e93b149ae1a189 Author: cgilet Date: Wed Dec 18 16:27:28 2019 -0500 Add MLEBTensorOp::compFlux at face centroids Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 9e07891b61e1dd2a7b9c91355e61b4d52c538754 Author: Weiqun Zhang Date: Wed Dec 18 09:49:56 2019 -0800 OrientationIter: ok -> isValid for consistence with MFIter Src/Base/AMReX_Orientation.H commit 9ac7cae1d4078d9f861e152c13c67a2e96cdb40a Merge: 7b910274e 641d8dcde Author: cgilet Date: Wed Dec 18 09:38:10 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 535171fe692aff50d59cc4a77e8572f61ec2c7eb Merge: 7e5d552ac 641d8dcde Author: Kevin Gott Date: Wed Dec 18 04:08:03 2019 -0800 Merge branch 'development' into kngott/hip commit a419a251db0c6a366b629d41a9a69d7ce6ebda6e Merge: ef5b4e0c7 641d8dcde Author: Andrew Myers Date: Tue Dec 17 17:21:31 2019 -0800 Merge branch 'development' into atmyers/no_thrust commit ef5b4e0c7ac350fcc927abf5c77ebafa72311521 Merge: acf8069c0 c41153d02 Author: Andrew Myers Date: Tue Dec 17 17:18:41 2019 -0800 Merge branch 'development' into atmyers/no_thrust commit acf8069c0696a3936770f1585d85bd5e75016048 Author: Andrew Myers Date: Tue Dec 17 17:18:14 2019 -0800 less confusing implementation of complex int pow Src/Base/AMReX_GpuComplex.H commit 641d8dcdeb714bc8732367656e04f8cf16a64852 Merge: c41153d02 65fa25ad2 Author: Andrew Myers Date: Tue Dec 17 17:17:58 2019 -0800 Merge pull request #637 from eschnett/development Avoid compiler warnings commit 0ed011ea98e30954124332a3306e4063ab354b18 Author: Marc Day Date: Tue Dec 17 15:26:49 2019 -0800 Add destComp to EB_interp_CC_to_Centroid Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit c41153d028e8ecd6bd554b7b2a4124d60b99431e Author: Michele Rosso Date: Tue Dec 17 15:10:21 2019 -0800 CMake: fix problems with PETSc support Src/CMakeLists.txt Src/Extern/HYPRE/CMakeLists.txt Src/Extern/PETSc/CMakeLists.txt Tools/CMake/AMReX_Options.cmake commit 3057948b866038918e11a05df8bec501c36cd3c0 Merge: 14ef2853d 7b899fb11 Author: mic84 Date: Tue Dec 17 15:00:09 2019 -0800 Merge pull request #636 from petsc/add-petsc Add support for CMake to handle PETSc commit 689d4f0a5622f115c6b7b6adaed739638c06b971 Author: Andrew Myers Date: Tue Dec 17 14:42:54 2019 -0800 COMPLEX -> GPUCOMPLEX Src/Base/AMReX_GpuComplex.H commit 27b383f419ce63fdc957515aef91f891281a649a Author: Andrew Myers Date: Tue Dec 17 14:21:05 2019 -0800 add amrex::GpuComplex Src/Base/AMReX_GpuComplex.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 65fa25ad21e2db05312c80ccac697c906b4b71e4 Author: Erik Schnetter Date: Tue Dec 17 15:57:52 2019 -0500 Avoid compiler warnings Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_StructOfArrays.H commit 4df4e7de6a416b649c69a4efba6ac6a7996637c3 Merge: 8a620ff52 14ef2853d Author: Andrew Myers Date: Tue Dec 17 10:58:59 2019 -0800 Merge branch 'development' into atmyers/no_thrust commit 14ef2853dd8fdb203a3929a2c3524e7b1d0c4b8e Author: Max Katz Date: Mon Dec 16 22:49:23 2019 -0800 Move some NVCC options to be included for C source files Tools/GNUMake/comps/nvcc.mak commit 11f1e8cd6bda49ad247cc43675c30173049fbaf2 Author: Max Katz Date: Mon Dec 16 22:48:54 2019 -0800 Include C sources in the CUDA preprocessing Tools/GNUMake/Make.rules commit 064096631b08ddd897b20d380f00ac09fa2e8314 Merge: 1d4e5e54a b3ad48e97 Author: Emmanuel Motheau Date: Mon Dec 16 16:39:57 2019 -0800 Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines commit 1d4e5e54ada199391b535d8948a358f607f03ede Author: Emmanuel Motheau Date: Mon Dec 16 16:39:41 2019 -0800 CC2Face and CC2FaceCentroid in 3D now Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit 7b910274ea8749ce8db9e30c6d1ccc04adb2f9e9 Merge: 4426b6f51 b3ad48e97 Author: cgilet Date: Mon Dec 16 19:13:13 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit b3ad48e9769a1c56277cb9f748a0016bc20a03da Author: Weiqun Zhang Date: Mon Dec 16 10:32:16 2019 -0800 add std:: Src/Base/AMReX_PODVector.H commit 168546f5a82370e96698a8e67ed4f16b92b46c78 Author: Weiqun Zhang Date: Mon Dec 16 10:32:05 2019 -0800 fix typo CHANGES commit 4426b6f51fe2ce5c7fbb5a31a6767c0b9c814b1f Merge: 5f13c077b 1f49dd4d7 Author: cgilet Date: Mon Dec 16 10:25:59 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 7b899fb1129968fdfd8b9d1aae03844666ac2bda Author: Barry Smith Date: Sun Dec 15 21:10:58 2019 -0600 Add support for CMake to handle PETSc Add missing include files to Src/EB/CMakeLists.txt Src/CMakeLists.txt Src/EB/CMakeLists.txt Src/Extern/PETSc/CMakeLists.txt Tools/CMake/FindPETSc.cmake commit 1f49dd4d7ada38ad55a664f20efbe12ee797bd2d Author: Weiqun Zhang Date: Sat Dec 14 18:27:15 2019 -0800 FabArray ReduceMin and ReduceMax that can take three FabArrays Src/Base/AMReX_FabArrayUtility.H commit 8ac6dd1cfe8208a8c917e37af477299ea7da581c Author: Weiqun Zhang Date: Sat Dec 14 18:25:28 2019 -0800 add FabArray::isAllRegular Src/Base/AMReX_FabArray.H commit f6e52621d832a540bdc275be9193f801d5f6a8ad Author: Weiqun Zhang Date: Sat Dec 14 10:05:10 2019 -0800 only need to fill one ghost cell Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit acb2cdf017e108a76720603e074cebafdc05ed4e Author: Weiqun Zhang Date: Sat Dec 14 10:04:03 2019 -0800 new Orientation constructor Src/Base/AMReX_Orientation.H commit 718059572908cb9b60bc410714912d7c43d9a559 Author: Weiqun Zhang Date: Sat Dec 14 10:03:24 2019 -0800 make it safe to construct zero-component Fab Src/Base/AMReX_BaseFab.H commit 877a0a6942453382d2a90c43cd293c303e4c11ef Author: Weiqun Zhang Date: Sat Dec 14 10:02:29 2019 -0800 add new funcitons to AmrMesh to return vector of Geometry, BoxArray and DistributionMapping on a range of levels Src/AmrCore/AMReX_AmrMesh.H commit ba4ad021ce2382c6e16133014e11a3c3eb21de9c Author: Marc Day Date: Fri Dec 13 19:23:12 2019 -0800 Add scomp/dcomp to functions for face centroid Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H commit 34dc19797f9ab3258b2e408df3b2f7626c0256ce Author: Marc Day Date: Fri Dec 13 18:51:52 2019 -0800 Remove grow op on interp function..remnant of where orig code was stolen from Src/EB/AMReX_EBMultiFabUtil_2D_C.H commit 7c3355f3b780328308dfd3bc6096099c0fcf361d Merge: f4414814b 4a61da636 Author: Emmanuel Motheau Date: Fri Dec 13 16:04:00 2019 -0800 Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines commit f4414814b4f756e2fc34e7785f549c86572d542b Author: Emmanuel Motheau Date: Fri Dec 13 16:03:40 2019 -0800 some cleaning note that CC2FaceCentroid is missing in 3D Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit ffdb6d4784fa92db7ed8719ecef57b8c5f3f7863 Author: Emmanuel Motheau Date: Fri Dec 13 15:58:23 2019 -0800 new design of CC2Centroid to get the correct cells without using a normal new routine to interpolate cc to face centroid Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit 2eaec9ca348163b8f01ef0945d32313540f6ed08 Author: Jean M. Sexton Date: Fri Dec 13 11:56:02 2019 -0800 Added check for RedistributeCPU edge case where particle gets reset to lo boundary, but is not contained in the Box it came from Src/Particle/AMReX_ParticleContainerI.H commit 3cfe2892ae04304c784e3fc51547cba561947fd4 Author: Emmanuel Motheau Date: Fri Dec 13 11:09:49 2019 -0800 3Putting 3D version Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit 5f13c077b51fe6e52e3e8faf79ffc85631ec9c89 Merge: b57339f9d 4a61da636 Author: cgilet Date: Fri Dec 13 10:19:05 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 1333126c7d3424e647b29c476cf4046c10d57645 Author: Emmanuel Motheau Date: Thu Dec 12 15:18:56 2019 -0800 Some cleaning Src/EB/AMReX_EBMultiFabUtil.cpp commit 8a620ff52ca7961b1913b2694ae234074033f019 Merge: cc6c2eee9 4a61da636 Author: Andrew Myers Date: Thu Dec 12 17:37:32 2019 -0500 Merge branch 'development' into atmyers/no_thrust commit 4a61da6361aab928844b287fc4ce1f7c1aec1fc3 Author: Andrew Myers Date: Thu Dec 12 17:37:02 2019 -0500 fix global parameter shadowing Src/Particle/AMReX_ParticleBufferMap.cpp commit 4c0f641b416f75a265b182d11499b84129601609 Merge: 87dcbf4ca 76eacd2d4 Author: Michele Rosso Date: Thu Dec 12 14:30:44 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mr/projections commit cc6c2eee90621faea08a2cbdaeba28a9f90a0fa1 Author: Andrew Myers Date: Thu Dec 12 16:52:11 2019 -0500 remove old file from make system, restore some missing , Src/Base/AMReX_GpuContainers.H Src/Base/AMReX_PODVector.H Src/Base/Make.package commit 1edf7b511ae935462d1d5aceee740beccd5973d4 Author: Andrew Myers Date: Thu Dec 12 16:40:10 2019 -0500 removing all thrust calls from amrex Docs/sphinx_documentation/source/GPU.rst Src/Base/AMReX_GpuAllocators.H Src/Base/AMReX_GpuAllocators.cpp Src/Base/AMReX_GpuContainers.H Src/Base/AMReX_PODVector.H Src/Base/CMakeLists.txt commit d845b99c21a22f3be0b8fb27546c9e5d19412b7e Author: Andrew Myers Date: Thu Dec 12 16:31:08 2019 -0500 fix cpu versions of exclusive and inclusive scan Src/Base/AMReX_GpuContainers.H commit 31b160939dd23752accbaaf81c3eaf3b6440b944 Merge: b908085c5 76eacd2d4 Author: Andrew Myers Date: Thu Dec 12 15:40:35 2019 -0500 Merge branch 'development' into atmyers/scan_compare commit a301fb0b155b72c1b1f2f92a12b126d300d17ad2 Author: Emmanuel Motheau Date: Wed Dec 11 21:05:34 2019 -0800 cleaning of the 2D routine Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H commit d1c0a59fedebea2a10168485be5b518b2b2101a3 Merge: ffac3b20d 76eacd2d4 Author: emotheau Date: Wed Dec 11 20:44:40 2019 -0800 Merge remote-tracking branch 'origin/development' into Emmanuel/new_EB_interpolation_routines commit ffac3b20d949c0f15704d3fabe30c537edc2fa7f Author: Emmanuel Motheau Date: Wed Dec 11 20:42:31 2019 -0800 WIP : create a new routine to interpolate Cell Center values to Centroid Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H commit 76eacd2d4e93690ca58bb2cb5631fb3c5ec1fc97 Merge: 1f68dcd79 c47be85ea Author: Ann Almgren Date: Wed Dec 11 15:34:30 2019 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 1f68dcd79aa147cfe9729f72b3706f050a26ddaa Author: Ann Almgren Date: Wed Dec 11 15:33:47 2019 -0800 Update MAC_Projection_EB tutorial so that when regtest = 1 we don't plot zvel (used for regression testing with GPUs) Tutorials/LinearSolvers/MAC_Projection_EB/inputs_3d Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp commit 7e5d552acb0782200eca68e24924ca92ade3f65b Author: Kevin Gott Date: Wed Dec 11 14:07:51 2019 -0800 Clean up hip make system. Tools/GNUMake/Make.defs Tools/GNUMake/comps/hip.mak commit c47be85ea2bdd75e1b32aa957faf5b014dfe247f Author: Weiqun Zhang Date: Wed Dec 11 13:45:06 2019 -0800 Need to set coverd cells in rhs_cc Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 132da2fc1b34808ff5c5fbb3d98cfe4e86655e25 Author: Ann Almgren Date: Wed Dec 11 13:27:02 2019 -0800 Set default maxorder to 3 not 2 Src/LinearSolvers/Projections/AMReX_MacProjector.cpp commit 37b16b8726b7e50299ba58c045b777ec07b415f7 Merge: af94aba9f a0ace5d7d Author: Kevin Gott Date: Wed Dec 11 12:55:13 2019 -0800 Merge branch 'development' into kngott/hip commit a0ace5d7dda9f988a7b347c07625213115a7043e Author: Kevin Gott Date: Wed Dec 11 15:51:54 2019 -0500 __CUDA_ARCH__ inside functions instead of defining separate functions (hip-clang error) Src/Base/AMReX_Random.H Src/Base/AMReX_Random.cpp commit af94aba9fbc125b2badec14bef1898fc14af472e Author: Kevin Gott Date: Wed Dec 11 12:29:46 2019 -0800 More function marking for hip-clang. Src/Base/AMReX_BaseFab.H commit b57339f9d0eef48704c6d78910e337d6c65c5bd0 Merge: 52e89cb5e fb77faa77 Author: cgilet Date: Wed Dec 11 14:43:32 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 87dcbf4cad113d03452214113f64e2184384eb26 Author: Michele Rosso Date: Wed Dec 11 11:14:50 2019 -0800 NodalProjector: rename m_solver m_mlmg Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit cfae24fc18d70042e3d3876439d46a45f099245d Author: Michele Rosso Date: Wed Dec 11 11:09:40 2019 -0800 NodalProjector: rename m_matrix m_linop Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit fb77faa7788e451086e5a154b87ca28f3840850b Author: Weiqun Zhang Date: Wed Dec 11 09:59:43 2019 -0800 fix communicator bug when there is only one multigrid level and the solvability needs to be fixed Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 52e89cb5e2aed8d996024a37d51204d48a9f8d22 Merge: b7c3b9663 83d260789 Author: cgilet Date: Wed Dec 11 12:22:43 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 83d2607895f0bd55f3c60357f4d28c6ed72d1604 Author: Michele Rosso Date: Tue Dec 10 17:37:14 2019 -0800 MacProjector: remove debug statement Src/LinearSolvers/Projections/AMReX_MacProjector.cpp commit 1316ffea99dd68c9f7cd507a87c194dcfd6d3d08 Author: Michele Rosso Date: Tue Dec 10 17:36:13 2019 -0800 Update MAC_Projection_EB test Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp commit 602458ef2db85ced14767df9d58b3438e703c97c Merge: e955b762f 26566bddf Author: Michele Rosso Date: Tue Dec 10 17:30:23 2019 -0800 Merge branch 'mr/projections' into development commit b908085c5ff3a2b07a98283278b453b17060d9b3 Author: Andrew Myers Date: Tue Dec 10 20:08:59 2019 -0500 use amrex scan instead of thrust Src/Base/AMReX_GpuContainers.H commit 26566bddf3ce711a18875fc9172bb2ab6019b478 Author: Michele Rosso Date: Tue Dec 10 16:54:41 2019 -0800 MacProjector: give user access to linear operator and MLMG. Remove setters which now are superfluous. Create MLMG and set options from input file in constructor. Src/LinearSolvers/Projections/AMReX_MacProjector.H Src/LinearSolvers/Projections/AMReX_MacProjector.cpp commit e955b762fa8730e72e29d1cd8add67771541842d Author: Andrew Myers Date: Tue Dec 10 14:59:28 2019 -0800 fix incorrect table description in documentation Docs/sphinx_documentation/source/InputsPlotFiles.rst commit 48389658e669987dfb04e9becb471ac3ff2e4201 Author: Weiqun Zhang Date: Tue Dec 10 11:38:01 2019 -0800 fix a warning Src/EB/AMReX_EB2_GeometryShop.H commit 2b61c191228903a2428679b4629ab6f2ca992359 Author: Oscar Antepara Date: Tue Dec 10 10:22:46 2019 -0800 Fixing MAC solver options Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp commit db1af7f7e79e9161350ef3a1bb6eef81dfa9dd5a Merge: 5bc079c07 50ef8caf4 Author: Michele Rosso Date: Mon Dec 9 14:39:52 2019 -0800 Merge branch 'mr/projections' into development commit 50ef8caf46b5f860fb7613397e5d61697c7043e9 Merge: 414c612db b90b8e6bf Author: Michele Rosso Date: Mon Dec 9 14:39:32 2019 -0800 Merge branch 'development' into mr/projections commit 5bc079c077ce2951e5ee7eb3b6781f7f91ac232f Author: Andrew Myers Date: Mon Dec 9 12:20:44 2019 -0800 more BL_ -> AMREX_ Src/Base/AMReX_REAL.H Src/Base/AMReX_fort_mod.F90 Src/Particle/AMReX_Particles.H commit a142bcd9645f4870a7188896aa8fe4b07600041b Author: Andrew Myers Date: Mon Dec 9 12:16:39 2019 -0800 more BL_ -> AMREX_ Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_TracerParticles.H commit ad0d8d932d9e5e43b933523758a780ac3a0da804 Author: Andrew Myers Date: Mon Dec 9 12:14:04 2019 -0800 more BL_ -> AMREX_ Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_ParticleInit.H commit b4d9ba2a2e8bc1304db77dafaca61b6bd15aeffc Author: Andrew Myers Date: Mon Dec 9 12:12:45 2019 -0800 BL_LAZY -> AMREX_LAZY Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit cf0eb5abdb8ab2b3471c6af224434c298d891471 Author: Andrew Myers Date: Mon Dec 9 12:09:15 2019 -0800 BL_USE_MPI -> AMREX_USE_MPI Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleMPIUtil.H Src/Particle/AMReX_ParticleMPIUtil.cpp commit e9774330cdad03f32a032c7cf96e228b728c05db Author: Andrew Myers Date: Mon Dec 9 11:56:57 2019 -0800 rename AMReX_ParIterI.H -> AMReX_ParIter.H Src/Particle/AMReX_ParIter.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 2eea940dfb33bd4618baebbadf8e92e5a0914c41 Author: Andrew Myers Date: Mon Dec 9 11:55:45 2019 -0800 move implementation of ParIter Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit b7c3b9663a83280ab7e3754839f0b5431026a8b9 Merge: 967e4714d 92796866a Author: cgilet Date: Mon Dec 9 14:22:06 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 92796866a1e29cd7bee09a1ec1e7bd861f674019 Author: Weiqun Zhang Date: Mon Dec 9 09:41:10 2019 -0800 add MLMG::getEBFluxes Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 967e4714dca2e4f85e7e22906b63b7264c31ce53 Merge: c38f0ad0c 176ddfb42 Author: cgilet Date: Mon Dec 9 11:29:52 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 176ddfb42a8fad26546c97ae375668f86e6ea511 Author: Weiqun Zhang Date: Mon Dec 9 08:15:11 2019 -0800 fix 2d EB computeDivergence and computeGradient Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_2D_C.H commit c38f0ad0c50446c6137da38ba8e306802f7786ab Merge: 1e8b113eb 6da97bf2e Author: cgilet Date: Sat Dec 7 19:23:14 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 6da97bf2e88339dfcacc06b39f155d59a737db9d Author: Max Katz Date: Sat Dec 7 10:13:22 2019 -0800 Specify in suffix if using OpenMP offload Tools/GNUMake/Make.defs commit 0dd98b29476de7912daf398ab25cd367c9448ef5 Author: Kevin Gott Date: Fri Dec 6 18:34:43 2019 -0800 Nearly fixed. Likely managed isn't appropriately covered. Src/Base/AMReX_BlockMutex.cpp Src/Base/AMReX_Random.cpp commit 6fe39a9a3b1526eb7c4f5621aecd0729ef2d17f9 Merge: 09d141246 7f6fda150 Author: Kevin Gott Date: Fri Dec 6 18:31:06 2019 -0800 Merge branch 'development' into kngott/hip commit 8077bb161ccc35e1614e5e9d042cdb1a38de15f5 Merge: a3b980c0f a11fd3129 Author: Andrew Myers Date: Fri Dec 6 17:23:29 2019 -0800 Merge pull request #632 from AMReX-Codes/twoway_transform Two-way particle transforms commit a3b980c0fa20a7443e846f53bbc049ba4d607cc7 Author: Andrew Myers Date: Fri Dec 6 17:14:39 2019 -0800 further tweaks to locking test Tests/GPU/Locking/inputs Tests/GPU/Locking/main.cpp commit f31bd4db90f244afcf410b556dda1eb6dc0bdad3 Author: Andrew Myers Date: Fri Dec 6 17:05:11 2019 -0800 tweak output of Locking test Tests/GPU/Locking/main.cpp commit a11fd312932613318fb36140debf02d6a1bea552 Merge: 649a93609 7ab190632 Author: Andrew Myers Date: Fri Dec 6 16:59:06 2019 -0800 Merge branch 'development' into twoway_transform commit 649a9360903787bb2871a77387e15de7b1b87887 Author: Andrew Myers Date: Fri Dec 6 16:53:31 2019 -0800 implement and test two-way filter and transform Src/Particle/AMReX_ParticleTransformation.H Tests/Particles/ParticleTransformations/main.cpp commit b90b8e6bfc31ea11814f9d8429aada1742c1ce26 Merge: 5fb00e4fb 894073467 Author: Michele Rosso Date: Fri Dec 6 16:27:09 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 5fb00e4fb7478a718d0be095d1784a449436d9b4 Author: Michele Rosso Date: Fri Dec 6 16:26:59 2019 -0800 computeGradient(): add support for RZ geometry Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_2D_C.H commit 7ab190632778e02209bb81166977ccbc8ac7ad76 Merge: 312cefcb4 95a9fadc7 Author: Weiqun Zhang Date: Fri Dec 6 16:26:54 2019 -0800 Merge branch 'development' into weiqun/dev commit 95a9fadc711b7b2cf67341968add29ac304918be Author: Weiqun Zhang Date: Fri Dec 6 16:24:00 2019 -0800 fix CXXSTD for nvcc with gcc > 5 Tools/GNUMake/comps/nvcc.mak commit 04921b7ca747b52d1ae09ebb58dd7d761b632a4e Author: Michele Rosso Date: Fri Dec 6 16:21:25 2019 -0800 computeDivergence(): add support for RZ geometry Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_2D_C.H commit 8940734673b0a3c78d0a45d702af309ab5cf77b7 Author: Weiqun Zhang Date: Fri Dec 6 16:06:29 2019 -0800 for nvcc we have to make sure CXXSTD is defined Tools/GNUMake/comps/nvcc.mak commit 06d572123f35b4549ae454c70378c670b4d064b9 Author: Andrew Myers Date: Fri Dec 6 15:59:46 2019 -0800 remove extraneous word from comment Src/Particle/AMReX_ParticleTransformation.H commit 4f3baa1f511de6ea4f95a38444510afd00e372a7 Author: Andrew Myers Date: Fri Dec 6 15:58:01 2019 -0800 allow the Src and Dst particle tile types to be different for the transform functions Src/Particle/AMReX_ParticleTransformation.H commit aeedcfb8fa889c75d29089114f4b5c05a7301556 Author: Andrew Myers Date: Fri Dec 6 15:41:45 2019 -0800 implement and test two-way transforms Src/Particle/AMReX_ParticleTransformation.H Src/Particle/AMReX_Particles.H Tests/Particles/ParticleTransformations/main.cpp commit 7f6fda150746b5ea28d7a03a665de778b0422b77 Merge: 37e9837a5 61ac2c10e Author: WeiqunZhang Date: Fri Dec 6 15:18:53 2019 -0800 Merge pull request #631 from AMReX-Codes/lock_reimplement Lock reimplement commit 37e9837a5155d0e84ddb7b10a79858dbd1ca3f90 Merge: 73887393b b89efa4f9 Author: WeiqunZhang Date: Fri Dec 6 15:14:36 2019 -0800 Merge pull request #630 from ax3l/topic-cxxStdControl CXXSTD: Project Control of C++ Std commit 61ac2c10eb319f82359d7bf0459cf72818694783 Author: Andrew Myers Date: Fri Dec 6 15:09:50 2019 -0800 fix order of namespace and #ifdef Src/Base/AMReX_BlockMutex.cpp commit b89efa4f91c57d2aca2d3c3ef2dc9e380b6549e7 Author: Axel Huebl Date: Thu Dec 5 11:16:06 2019 -0800 CXXSTD: Project Control of C++ Std Add a new option, defaulting to C++11, to give projects control over the required C++ standard of a project. This improves the current logic, which does not cleanly fail if a compiler does not support e.g. C++14 but instead gave hard-to-read error messages such as "hm, dunno what std::make_unique is" :) Now the compiler will fail with messages such as: "gcc: error: unrecognized command line option ‘-std=c++14’" which is better and safes us from re-implementing a ton of logic that CMake provides out-of-the-box. Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/GNUMake/comps/cray.mak Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/hip.mak Tools/GNUMake/comps/ibm.mak Tools/GNUMake/comps/intel.mak Tools/GNUMake/comps/llvm-flang.mak Tools/GNUMake/comps/llvm.mak Tools/GNUMake/comps/nag.mak Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak commit 3ccbe87a08a088b8b8f7489f329a0ef658fddec9 Author: Andrew Myers Date: Fri Dec 6 15:04:40 2019 -0800 put these implementations in namespace amrex Src/Base/AMReX_BlockMutex.cpp commit 01460ac3ca15d9f4fd6c6bf8c4ffe604ffa9a6bf Author: Andrew Myers Date: Fri Dec 6 15:04:21 2019 -0800 add __threadfence() Tests/GPU/Locking/main.cpp commit 69a147983dde0aafc7fb3e6a5d33ee4cc1ba2ddf Author: Michele Rosso Date: Fri Dec 6 14:28:00 2019 -0800 computeDivergence(): fix assertions to work with any AMREX_SPACEDIM Src/Base/AMReX_MultiFabUtil.cpp commit c8e1e80fc6786025c50f40d1feb4b0ed67a23018 Author: Andrew Myers Date: Fri Dec 6 14:00:15 2019 -0800 actually add file Src/Base/AMReX_BlockMutex.cpp commit 53eeb3bdb0127d5df00ac0302a024c25cc0e9d54 Author: Andrew Myers Date: Fri Dec 6 13:58:35 2019 -0800 split up the declaration and definition for BlockMutex Src/Base/AMReX_BlockMutex.H Src/Base/CMakeLists.txt Src/Base/Make.package commit aaca60b4412beabe8bcfd6c72443e53200a335dd Author: Andrew Myers Date: Fri Dec 6 13:42:31 2019 -0800 no need to duplicate this static_assert Src/Base/AMReX_Random.cpp commit f9ff6d55770f19f6a35fb15307c2251790c12229 Author: Andrew Myers Date: Fri Dec 6 13:39:43 2019 -0800 add block counting to the locking test Tests/GPU/Locking/main.cpp commit 09d141246f5604b55473ef5d63373bb8928d4eb9 Merge: 0dddab8b9 ef32bae9b Author: Kevin Gott Date: Fri Dec 6 13:36:21 2019 -0800 Merge branch 'development' into kngott/hip commit 719bc1dac122e4ec493564e3b23c562c7a47c33b Author: Andrew Myers Date: Fri Dec 6 13:29:58 2019 -0800 forgot to add new file Src/Base/AMReX_BlockMutex.H commit 4ea1f817aebdfee17e40eefe48000652d6957d7b Author: Andrew Myers Date: Fri Dec 6 13:20:31 2019 -0800 impose a naming convention on the global random state and lock variables Src/Base/AMReX_Random.cpp commit 644a57ab38967e467d7a09423cc8154e3812125a Author: Andrew Myers Date: Fri Dec 6 13:15:28 2019 -0800 package the locking together in a BlockMutex class. Src/Base/AMReX_Random.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Tests/GPU/Locking/main.cpp commit 312cefcb47ae3128a3ac32e9f69ce1a28dbfa6a6 Author: Weiqun Zhang Date: Fri Dec 6 09:42:27 2019 -0800 nodal solver on gpu: need to call nodal sync if there are more than one Jacobi sweeps Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 1a9236fe85793ab0159ba211dce6bbb0cb489a55 Author: Weiqun Zhang Date: Fri Dec 6 09:36:47 2019 -0800 tweak nodal solver smoother for gpu Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 73887393b3ecf5b74bd5d6d6c9501ace1b82f400 Author: Andrew Myers Date: Thu Dec 5 16:49:41 2019 -0800 update the section of the documentation about Particles on GPUs Docs/sphinx_documentation/source/GPU.rst commit a1b6ca7e99ab4b449669691b0ed32dd86c7a4ef0 Author: Kevin Gott Date: Thu Dec 5 16:31:40 2019 -0800 Add documentation performance comment about thrust execution policies. Docs/sphinx_documentation/source/GPU.rst commit fbc7120148cf929a96a195496f64390d752e7d24 Author: Andrew Myers Date: Thu Dec 5 16:12:13 2019 -0800 modify this test to execute 100 times in a loop Tests/GPU/Locking/main.cpp commit 37333baa385f2331809314ce6662a993894fccda Author: Andrew Myers Date: Thu Dec 5 11:11:17 2019 -0800 move print statement Tests/GPU/RandomNumberGeneration/main.cpp commit bc1d03ca3bbf58d4aa80ba228b35375897c9b099 Author: Andrew Myers Date: Thu Dec 5 11:06:06 2019 -0800 clean up random number test a little bit Tests/GPU/RandomNumberGeneration/main.cpp commit 52b41848a0b56293f73377742a2da6a9981a5404 Author: Andrew Myers Date: Thu Dec 5 10:50:33 2019 -0800 reimplement lock using 64-bit CAS to simultaneously update the block and the counts. Src/Base/AMReX_Random.cpp Tests/GPU/Locking/main.cpp commit 414c612dbf534495be2f4e4487b3f2ef025e6725 Author: Michele Rosso Date: Wed Dec 4 15:13:26 2019 -0800 MacProjector: streamline handling of solver options Src/LinearSolvers/Projections/AMReX_MacProjector.H Src/LinearSolvers/Projections/AMReX_MacProjector.cpp Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 241958426f906c736bcdb0d82d421aec5b9b233c Author: Michele Rosso Date: Wed Dec 4 14:41:05 2019 -0800 NodalProjector: streamline handling of solver options Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 87659c492175758c3852e5a54b527f68063247eb Merge: bf2a384ae cade61bab Author: Weiqun Zhang Date: Wed Dec 4 13:09:53 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit cade61bab73ab0c2a54fed5ead5e5998a7a50d22 Merge: 95e4d5d0f 743d6528e Author: Andrew Myers Date: Wed Dec 4 12:07:25 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 95e4d5d0f1ee64e4cf5bdbcaf2567688a6398d18 Author: Andrew Myers Date: Wed Dec 4 12:07:07 2019 -0800 change the way this buffer is unpacked to work around potential alignment issues Src/Particle/AMReX_ParticleContainerI.H commit bf2a384ae585bcf60412d5db818206228e97b668 Author: Weiqun Zhang Date: Wed Dec 4 11:47:01 2019 -0800 fix template parameter for std::uninitialized_fill Src/Base/AMReX_PODVector.H commit 743d6528e7ec70ba9eba0147a811b08459a57639 Author: Weiqun Zhang Date: Wed Dec 4 09:51:51 2019 -0800 missed return type Src/LinearSolvers/MLMG/AMReX_MLLinOp.H commit d446b898e5f2b06d6128150e8c0f9dd967cac469 Author: Weiqun Zhang Date: Wed Dec 4 09:47:52 2019 -0800 linear solver on gpu: change the default grid size for agglomeration and consolidation Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tests/LinearSolvers/CellEB2/MyTest.H Tests/LinearSolvers/NodeEB/MyTest.H commit 1e8b113eb085e57b10b110a0abfde1ed8c5f2896 Merge: 53dc15c5d dec4a355a Author: cgilet Date: Wed Dec 4 09:39:32 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit dec4a355a219649e600082488c0f56695b927097 Author: Weiqun Zhang Date: Tue Dec 3 17:04:15 2019 -0800 NodeEB test: agglomeration and consolidation parameters Tests/LinearSolvers/NodeEB/MyTest.cpp commit 0942c988fff2a4afba393a0624a9b8f4325f66bc Author: Weiqun Zhang Date: Tue Dec 3 16:54:46 2019 -0800 mod NodeEB test for scaling test Tests/LinearSolvers/NodeEB/MyTest.H Tests/LinearSolvers/NodeEB/MyTest.cpp Tests/LinearSolvers/NodeEB/main.cpp commit a9cc81390af9dbc3edb9b91fc16119ab5c93817d Author: Andrew Myers Date: Tue Dec 3 16:30:18 2019 -0800 this method needs to return an iterator Src/Base/AMReX_PODVector.H commit 6449a981f699ecdfe77e04b109fec24f99072fd1 Author: Andrew Myers Date: Tue Dec 3 16:17:32 2019 -0800 fix indentation Src/Base/AMReX_PODVector.H commit 3653f7a0e03a685a4f6418a39425b30c05a47c47 Merge: 01ffd98a0 b260d6c18 Author: Andrew Myers Date: Tue Dec 3 16:13:28 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 01ffd98a03e9886fad94e19352fa5b50f8e72f6e Author: Andrew Myers Date: Tue Dec 3 16:13:18 2019 -0800 handle some shadowing and unused variable warnings Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleTransformation.H Src/Particle/AMReX_ParticleUtil.H commit 0eb208e85b08210ac9210a09a13358b766fc1f90 Author: Andrew Myers Date: Tue Dec 3 16:12:42 2019 -0800 handle some edge cases involving inserting into empty PODVectors Src/Base/AMReX_PODVector.H commit b260d6c18959315e6dfa34129a5c8bb6018c23c0 Author: Weiqun Zhang Date: Tue Dec 3 18:16:38 2019 -0500 CellEB2 test: parameters for agglomeration and consolidation Tests/LinearSolvers/CellEB2/MyTest.H Tests/LinearSolvers/CellEB2/MyTest.cpp commit 62a3fddd70ad5c2fe1609b082fbf52f1843b5abb Author: Andrew Myers Date: Tue Dec 3 15:15:58 2019 -0800 remove unused variable Src/Particle/AMReX_DenseBins.H commit d22796ba00d244f52aff0cef8709076cc1d3a86c Author: Kevin Gott Date: Tue Dec 3 14:42:42 2019 -0800 Remove the CPU version of AMREX_GPU_LAUNCH_HOST_DEVICE_LAMBDA_ASYNC. GPU version was previously removed. Src/Base/AMReX_GpuLaunchMacrosC.H commit 3a302579f324d82feb230bf2d94e71b98c84cb51 Author: Weiqun Zhang Date: Tue Dec 3 13:43:52 2019 -0800 fix pragma omp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 0dddab8b93745bd98fe0cdd1a2c30615c89a6364 Author: Kevin Gott Date: Tue Dec 3 13:44:05 2019 -0800 Adjust inputs to allow HeatEquation to run without managed memory. Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/inputs_3d commit ef32bae9b31cb84832585951dbad68f2ced173af Author: Weiqun Zhang Date: Tue Dec 3 13:43:52 2019 -0800 fix pragma omp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 2432d57283d89c8119563ab1b766eca74c0a4f64 Author: Weiqun Zhang Date: Tue Dec 3 13:10:54 2019 -0800 missed amrex:: Tests/LinearSolvers/CellEB2/main.cpp commit 4983655bb9d2bf5447a4b6fb5d39e172e08489ba Author: Weiqun Zhang Date: Tue Dec 3 13:08:41 2019 -0800 CellEB2: don't write plotfile if doing scaling test Tests/LinearSolvers/CellEB2/main.cpp commit 23301bc0e8dadc314fbd5428cec86fb35c9fa452 Author: Weiqun Zhang Date: Tue Dec 3 11:25:27 2019 -0800 add some functions to MLMG for querying residuals, number of iterations, etc. after solve() is called. Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 20d46361f4f97904d367b0c32a07467b56634308 Author: Weiqun Zhang Date: Tue Dec 3 08:00:32 2019 -0800 FArrayBox::initVal: do it on gpu for non-NaN too Src/Base/AMReX_FArrayBox.cpp commit ada03e9e12b68ac1d387954f8e036ea80f311607 Author: Weiqun Zhang Date: Mon Dec 2 21:23:40 2019 -0800 FArrayBox: use = to initialize snan on gpu Src/Base/AMReX_FArrayBox.cpp commit 4d1241931fb9ada9fcfb917efcccbe1b2c304f72 Author: Weiqun Zhang Date: Mon Dec 2 21:22:30 2019 -0800 add init_snan support for float Src/Base/AMReX_MemPool.cpp commit f56afb3f73707efbf11cac196e2278801c8f829d Author: Weiqun Zhang Date: Mon Dec 2 21:21:19 2019 -0800 fix for single precision Src/Base/AMReX_MultiFab.cpp commit 3a9d8424bf023bf3db1e03a7e1255b569ade59f8 Merge: e6c89b702 794fa55d8 Author: Weiqun Zhang Date: Mon Dec 2 16:03:30 2019 -0800 Merge branch 'weiqun/dev' into development commit e6c89b7022900bd632370e09b6cadbbc19fb4259 Author: Max Katz Date: Mon Dec 2 13:38:02 2019 -0800 Move OMP offload flags into ibm.mak Tools/GNUMake/comps/ibm.mak Tools/GNUMake/sites/Make.olcf commit 794fa55d826160dedb9d77398ccc9e4fc8f3262b Merge: 2f66352f9 6eff05406 Author: Weiqun Zhang Date: Mon Dec 2 12:30:46 2019 -0800 Merge branch 'development' into weiqun/dev commit 53dc15c5dbf844f5d96fffe1d2c0347779057641 Merge: 999ffc0ac 9a76d9296 Author: cgilet Date: Mon Dec 2 15:12:32 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 6eff05406bfa79b29393b66e6bc1a1cc3e916a45 Merge: 855b6f06d 9a76d9296 Author: Weiqun Zhang Date: Mon Dec 2 12:08:22 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2f66352f995b419d613591638ad7bdfd9313f943 Author: Weiqun Zhang Date: Mon Dec 2 11:52:10 2019 -0800 CellEB2 test on gpu Tests/LinearSolvers/CellEB2/Make.package Tests/LinearSolvers/CellEB2/MyTest.H Tests/LinearSolvers/CellEB2/MyTest.cpp Tests/LinearSolvers/CellEB2/MyTest_F.H Tests/LinearSolvers/CellEB2/MyTest_K.H Tests/LinearSolvers/CellEB2/mytest_f.F90 commit 9a76d9296e2edff37564c7b9e5775dc8c7dee100 Author: cgilet Date: Mon Dec 2 14:50:53 2019 -0500 Minor changes in single_level_weighted_redistribute(): add assert, be consistent about not filling ghost cells for div_out Src/EB/AMReX_EB_utils.cpp commit d1ae9b09d22b7767fef2b423ca1af3b111e39101 Merge: f859e5d5a 855b6f06d Author: Weiqun Zhang Date: Mon Dec 2 11:21:54 2019 -0800 Merge branch 'development' into weiqun/dev commit 855b6f06d26da7f372e2a700ab30b3ffcc52e578 Author: Weiqun Zhang Date: Mon Dec 2 10:03:21 2019 -0800 move some functions used by EBLSCore into its own file Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtilI.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 999ffc0ac546dcc9c154ba67ebfe074262bac23a Author: cgilet Date: Mon Dec 2 11:45:09 2019 -0500 Update single_level_weighted_redistribute() Src/EB/AMReX_EB_utils.cpp commit 996b17a6f32f6bfc73db03c1bbc6612b77b84fd2 Merge: 35faf597a 6df31e81f Author: Weiqun Zhang Date: Mon Dec 2 08:41:55 2019 -0800 Merge branch 'master' into development commit 6df31e81f592bf418eed2e27b92ed80704ec6edb Author: Weiqun Zhang Date: Mon Dec 2 08:41:05 2019 -0800 update CHANGES CHANGES commit 66b99cc6be1e6a3dd509adc08ef2824f081d9553 Merge: e0793daf5 35faf597a Author: cgilet Date: Mon Dec 2 08:37:05 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 35faf597a624b6db4aa2b5bcb529112c00677b11 Author: Johannes Blaschke Date: Sat Nov 30 17:37:08 2019 +0100 remove amrex submodule, wrong repo .gitmodules amrex commit 546501bd7fc7826f4a43f33fd7305ad970ce7ab4 Author: Johannes Blaschke Date: Sat Nov 30 17:22:53 2019 +0100 add amrex .gitmodules amrex commit 87871e0737dad93bc6099fe70c5ed38b4d886ad9 Author: Kevin Gott Date: Fri Nov 29 13:31:29 2019 -0800 ParallelScan working, but extremely slow. Src/Base/AMReX_Scan.H Tutorials/GPU/ParallelScan/main.cpp commit fc3284cf655b87a67d0aed3f810b0754956998de Merge: ffeefa3cd e4bf359f9 Author: Weiqun Zhang Date: Wed Nov 27 21:05:32 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ffeefa3cd6780bfd1a7ce275bce76b93e8328ff4 Author: Weiqun Zhang Date: Wed Nov 27 21:04:47 2019 -0800 BndryFunc: make RunOnGpu() and hasFabVersion() virtual Src/Amr/AMReX_StateDescriptor.H commit e0793daf52574e5a7a6c041970dffacb4ce07553 Merge: 7a4c86803 e4bf359f9 Author: cgilet Date: Wed Nov 27 21:54:33 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit e4bf359f9785980e4f97d5297802372e4351a66c Author: atmyers Date: Wed Nov 27 14:29:02 2019 -0800 add missing header Src/Base/AMReX_PODVector.H commit 29154d6799af1ab84291f46451d8742e796c98e8 Merge: e3c7060ec 5a9eb93e2 Author: atmyers Date: Wed Nov 27 12:06:57 2019 -0800 Merge branch 'development' into amrex_mutex commit 7a4c86803705abbf914d2b946e05525b2bd7497f Merge: def134f31 5a9eb93e2 Author: cgilet Date: Wed Nov 27 05:28:07 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit e3c7060ec66b61e1b92201d79a172feb4cd1aea7 Author: Andrew Myers Date: Tue Nov 26 14:48:25 2019 -0800 move the position of the __threadfence() to after the random states are updated Src/Base/AMReX_Random.cpp commit a771933089eba7d3a2afb5c115358cbbe7657567 Author: Andrew Myers Date: Tue Nov 26 14:09:24 2019 -0800 change the way that get_state and free_state are implemented Src/Base/AMReX_Random.cpp commit 69da24c8e53c98d39cb8a12b9101afbce1515e78 Author: Andrew Myers Date: Tue Nov 26 14:09:07 2019 -0800 make the Test for random number generation harder to pass Tests/GPU/RandomNumberGeneration/main.cpp commit f859e5d5a817243c48cca6aa3a3cf96a4bb043ef Author: Weiqun Zhang Date: Tue Nov 26 13:45:05 2019 -0800 use BuildMask function Src/EB/AMReX_EBMultiFabUtil.cpp commit b7e7169b04fadb8cec843ae3cae241974f3dc430 Author: Andrew Myers Date: Tue Nov 26 13:38:01 2019 -0800 fix spaces Src/Base/AMReX_Random.cpp commit 5a9eb93e2e9e8b2654f26e41773c2629b8f11794 Author: Weiqun Zhang Date: Tue Nov 26 13:26:21 2019 -0800 to not break MCNodalLinOP Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 02308fdb9697cee6ff1c33fbb354a5da5b782bda Author: Weiqun Zhang Date: Tue Nov 26 10:16:41 2019 -0800 remove duplicated codes Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 7d942b770ae2dae69601cf732f78595d4557f240 Author: Weiqun Zhang Date: Tue Nov 26 09:48:50 2019 -0800 rework on nodal dirichlet mask Src/Base/AMReX_FabArray.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 62200685e1a2f5189adccc2019e91fe50c463016 Author: Weiqun Zhang Date: Tue Nov 26 09:25:42 2019 -0800 YAFluxRegister: use the new RecvLayoutMask Src/Boundary/AMReX_YAFluxRegister.cpp commit 7b82f477de8c2eec2f930a2b2db5cf1c11a63786 Merge: f5685afcb 79a1ad326 Author: Weiqun Zhang Date: Tue Nov 26 08:48:27 2019 -0800 Merge branch 'development' into weiqun/dev commit 79a1ad3263b4ff2b28c2b546059dcb3d7fa43b41 Merge: 0483c6452 a09447c59 Author: WeiqunZhang Date: Tue Nov 26 08:46:55 2019 -0800 Merge pull request #628 from AMReX-Codes/statedata_arena Explicitly specify which Arena StateData uses commit 0483c645204ab47d605faa6b53e5b8e5058b4551 Merge: 00fd9d5b5 9f745227c Author: WeiqunZhang Date: Tue Nov 26 08:45:52 2019 -0800 Merge pull request #627 from AMReX-Codes/multifab_swap Add a MultiFab operation that explicitly swaps dst/src data commit 9f745227cd1b81eaf488e04c0b84876410156781 Author: Max Katz Date: Tue Nov 26 00:04:39 2019 -0800 Fix the ghost cell check Src/Base/AMReX_MultiFab.cpp commit 48bea0d564aad983b7dc7cae3f1acc089cc3cd98 Merge: fc70ed662 00fd9d5b5 Author: Max Katz Date: Mon Nov 25 23:52:25 2019 -0800 Merge branch 'development' into multifab_swap commit fc70ed662497bb0a8ad0269f196e214dc904db87 Author: Max Katz Date: Mon Nov 25 23:44:51 2019 -0800 Take a shortcut in MultiFab::Swap() when we can Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_MultiFab.cpp commit a5637789fe754c0f375478001d4835451f987e5d Merge: 4005d1ee6 12495f58e Author: Kevin Gott Date: Mon Nov 25 17:55:19 2019 -0800 Merge branch 'kngott/hip' of https://github.com/AMReX-Codes/amrex into kngott/hip commit 4005d1ee6806b805872f96888cdf46283c4005d5 Author: Kevin Gott Date: Mon Nov 25 17:54:58 2019 -0800 Add the complex MPI support to HIP in Device::Initialize and cleanup Device::Finalize. Src/Base/AMReX_GpuDevice.cpp commit f5685afcba5724cbf18642b51605e6399f34d3ed Author: Weiqun Zhang Date: Mon Nov 25 16:30:03 2019 -0800 nodal solver: reimplement cc mask Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 00fd9d5b5119152557f6817808b597c218e7c55d Author: Andrew Myers Date: Mon Nov 25 16:02:12 2019 -0800 BL_ASSERT -> AMREX_ASSERT Src/Particle/AMReX_LoadBalanceKD.cpp Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParGDB.H Src/Particle/AMReX_Particle.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_ParticleMPIUtil.cpp Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 4a69bfc94177548a65fb8f7759b804fcd5c1ff4a Merge: 9701edadc 444f52ad3 Author: Andrew Myers Date: Mon Nov 25 13:06:55 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9701edadcee9175a2c2ed74da496e4bd842e87da Author: Andrew Myers Date: Mon Nov 25 13:06:46 2019 -0800 an All-To-All communication pattern for comparison Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit 2a3a292bf15685beecfcf1f86a0aaf7fcd24a619 Author: Weiqun Zhang Date: Mon Nov 25 12:20:31 2019 -0800 MLEBABecLap: build mask using existing function in FabArray Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 444f52ad3ae50b9fc293418926791809891cd25d Merge: de0c7e23c 170a35f79 Author: Andrew Myers Date: Mon Nov 25 14:56:41 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit de0c7e23c4225a8babde92a7b7271d447786b23d Author: Andrew Myers Date: Mon Nov 25 14:56:25 2019 -0500 pp.get -> pp.query Tests/Particles/Redistribute/main.cpp commit 617c3207e4727530a017fed6c9a861d2c701e537 Author: Weiqun Zhang Date: Mon Nov 25 10:48:29 2019 -0800 return Arena* instead of const Arena* so that it can be used Src/Base/AMReX_FabArray.H commit 170a35f799eed2458aea27fc6f46fba31c644bfe Merge: 24025381d 2fcac05af Author: Weiqun Zhang Date: Mon Nov 25 10:43:24 2019 -0800 Merge branch 'weiqun/dev' into development commit 24025381de60d6079b37f538fa0b8d1c54044821 Merge: ae9e49076 5c68e71cb Author: Weiqun Zhang Date: Mon Nov 25 10:43:19 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2fcac05af9ad81c99210ed9a1b2085f25805dcd4 Author: Weiqun Zhang Date: Mon Nov 25 10:20:20 2019 -0800 remove an incorrect assertion Src/Base/AMReX_FBI.H commit def134f319146ba444c9fb3f50189f3fe7bfb734 Merge: eaec842fb 5c68e71cb Author: cgilet Date: Mon Nov 25 13:16:31 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 5c68e71cb2a298c49655a126208fff63e28ace83 Author: cgilet Date: Mon Nov 25 13:12:11 2019 -0500 MLNodeLaplacian::compSyncResidualCoarse() - crse_cc_mask only needs 1 ghost cell; fix tests on the mask. Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit eaec842fb2406628bb20cedb41eff7c0faf7bec9 Merge: f1b5dd463 3d6ca8339 Author: cgilet Date: Mon Nov 25 09:33:03 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 3d6ca8339341d614c5a92583deb5bdb077b8877a Author: cgilet Date: Mon Nov 25 09:30:27 2019 -0500 MLNodeLaplacian::compSyncResidualCoarse() - crse_cc_mask needs 2 ghost cells. Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit f1b5dd4632a581f414819abe7b43a949a41fd442 Merge: 40fdece92 80e93bc6f Author: cgilet Date: Mon Nov 25 09:08:25 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit a09447c59f68ad18d47d655f1703f0065334a114 Author: Max Katz Date: Sun Nov 24 14:18:03 2019 -0500 Explicitly specify which Arena StateData uses Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp commit 1fc57045c8684648c25cb9a25a7e31a00c8eeeee Author: Max Katz Date: Sun Nov 24 14:14:59 2019 -0500 Add a MultiFab operation that explicitly swaps dst/src data Also add this as an option for StateData Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit ae9e490765c067b9e7e59f0b67c16d48804339a5 Author: Weiqun Zhang Date: Sat Nov 23 07:41:02 2019 -0800 fix new bug in 835565 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 4e1fa187606e1c56faf95cce4af72a9074b59af5 Author: Weiqun Zhang Date: Sat Nov 23 07:25:36 2019 -0800 remove unused variable Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit d83caae0220fdd73d5165f36024a514ae47cb6bb Author: Weiqun Zhang Date: Fri Nov 22 19:18:01 2019 -0800 around gcc bug Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 80e93bc6f2a84a8446a75af9a4d54a399dc55d7b Author: Andrew Myers Date: Fri Nov 22 17:20:35 2019 -0800 include lower offset Src/Particle/AMReX_ParticleLocator.H commit 835565c0d2f33774c25a5e236d1b9c349009c047 Author: Weiqun Zhang Date: Fri Nov 22 16:11:28 2019 -0800 redo some box intersection stuff in MLMG Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 0e8f1090d42e90fe748be624f8b7a397d14a1cbd Author: Weiqun Zhang Date: Fri Nov 22 15:45:58 2019 -0800 fix gpu compilation Src/Boundary/AMReX_YAFluxRegister.cpp commit 18e82a7f86614202999bf16377e8f0d82622d408 Author: Weiqun Zhang Date: Fri Nov 22 15:36:09 2019 -0800 reimplement YAFluxRegister part 2 Src/Base/AMReX_MultiFabUtil.cpp Src/Boundary/AMReX_YAFluxRegister.cpp commit 5415d7693a5ec2854adfb10871cf18b90fd9b478 Author: Weiqun Zhang Date: Fri Nov 22 15:20:39 2019 -0800 use Reduce::AnyOf in nodal solver Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 91bf436699f80f5fdf1c8c1e477c72e43b157b0e Author: Weiqun Zhang Date: Fri Nov 22 15:14:14 2019 -0800 reimplement YAFluxRegister part 1 Src/Boundary/AMReX_YAFluxRegister.cpp commit 391efbe4551c21c5275893794087e21751462a51 Author: Weiqun Zhang Date: Fri Nov 22 15:13:38 2019 -0800 add Reduce::AnyOf Src/Base/AMReX_Reduce.H commit b83a5fec7b9c3a325f1b1d5d3366d0aea3b43c2f Merge: ed145fd73 493ac1bdd Author: Andrew Myers Date: Fri Nov 22 14:52:40 2019 -0800 Merge branch 'development' into dense_bins_locator commit 493ac1bdd15734df3318c27d96c402008b5da3c0 Author: Andrew Myers Date: Fri Nov 22 14:05:46 2019 -0800 change the function to return a bool instead of Aborting Src/Base/AMReX_ParmParse.H Src/Base/AMReX_ParmParse.cpp commit 0ae97890972ae3526e2e8bff7306e5c815c4082b Author: Andrew Myers Date: Fri Nov 22 13:36:45 2019 -0800 add a function to abort if there are unused ParmParse entries Src/Base/AMReX_ParmParse.H Src/Base/AMReX_ParmParse.cpp commit ed145fd731c9823cf3bcfe65431c08e14ff35edf Author: Andrew Myers Date: Fri Nov 22 11:52:20 2019 -0800 resuse DenseBins in the ParticleLocator Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_ParticleLocator.H commit b2a6e0047aaaff4d80f59f7cca730aa8eece9d60 Author: Weiqun Zhang Date: Fri Nov 22 11:07:15 2019 -0800 around gcc bug Src/Base/AMReX_iMultiFab.cpp commit f497645a89e794933b7b4efb8718aff93d358c2a Author: Weiqun Zhang Date: Fri Nov 22 10:25:15 2019 -0800 reimplement MultiMask define Src/Boundary/AMReX_MultiMask.cpp commit 5a780b13a37d999bf429d22d73f140c4e7fee35f Author: Weiqun Zhang Date: Fri Nov 22 10:24:51 2019 -0800 minor change in Vector to use size_type Src/Base/AMReX_Vector.H commit 4e6d1072c4244f1824819b442991721313295858 Author: Andrew Myers Date: Fri Nov 22 09:41:26 2019 -0800 don't use amrex:: namespace explicitly here for conciseness. Src/Particle/AMReX_ParticleMesh.H Src/Particle/AMReX_ParticleUtil.H commit 2719314d4886a37d061cd28533f28ae7c5c886bb Author: Weiqun Zhang Date: Fri Nov 22 09:37:36 2019 -0800 reimplement owner mask Src/Base/AMReX_iMultiFab.cpp commit 40fdece922beded6bacf31841f8b48c16d40b365 Merge: c039fa4b8 9290bd95f Author: cgilet Date: Fri Nov 22 10:23:57 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 9290bd95f8e9d5253b067dd8f642d62f2846cfb6 Author: Weiqun Zhang Date: Thu Nov 21 16:06:56 2019 -0800 fix a new typo in launch macro Src/Base/AMReX_GpuLaunchMacrosG.H commit 8659e105ba31e44c66e083dc165f5e41d0951c5d Author: Weiqun Zhang Date: Thu Nov 21 10:21:14 2019 -0800 nodal solver: sync residual for RAP Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 35ee52b5afe946538c9dfd3d4ea285f0a7d77e19 Author: Weiqun Zhang Date: Thu Nov 21 09:51:16 2019 -0800 nodal solver: build grid stencil in case we need it for sync solve. Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit e6d54dd925c18305550350f05c766f229937856a Author: Andrew Myers Date: Thu Nov 21 14:37:02 2019 -0800 enable these functions only for PC Src/Base/AMReX_TypeTraits.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleMesh.H Src/Particle/AMReX_ParticleReduce.H Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_Particles.H commit 46c5d862af5b23d975cb7631d6d118b3f8482d70 Author: Andrew Myers Date: Thu Nov 21 13:01:51 2019 -0800 automatically set USE_PARTICLES=TRUE in Src/Particles/Make.package Src/Particle/Make.package commit 3c46b3bc097b464a034fa52965d7c8fab317503f Author: Andrew Myers Date: Thu Nov 21 13:01:27 2019 -0800 add is_particle_iterator and is_particle_container type traits Src/Base/AMReX_TypeTraits.H commit 3f6d0aea35ef00824df3e63c39cd06e85c18eb0e Author: Andrew Myers Date: Thu Nov 21 13:01:02 2019 -0800 a version of numParticlesOutOfRange that operates only a single tile Src/Particle/AMReX_ParticleUtil.H commit 27b95072b3219769fad0236b2e1502335aad88ee Author: Andrew Myers Date: Thu Nov 21 13:00:39 2019 -0800 fix spaces Src/Particle/AMReX_ParticleContainerI.H commit 086cd4ff88d3f0707d7c631c20a85e702a6869a0 Author: Andrew Myers Date: Thu Nov 21 13:00:21 2019 -0800 move getTileIndex to .H file for inline Src/Particle/AMReX_ParticleUtil.cpp commit 44ed49e18a36d615de72551461c37d2ddded2c45 Author: Andrew Myers Date: Thu Nov 21 12:59:55 2019 -0800 add a method allowing users to get a Geom from a ParIter Src/Particle/AMReX_Particles.H commit fe4deba955bc400f281e14823df444f07af8d6be Author: Andrew Myers Date: Thu Nov 21 12:59:23 2019 -0800 have the particle iterator store a reference to the parent particle container Src/Particle/AMReX_ParIterI.H commit 35857d1b94d43b763544b967212155115b37706f Author: Andrew Myers Date: Wed Nov 20 17:03:03 2019 -0800 been doing my briefs wrong for Doxygen... Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H Src/Particle/AMReX_ParticleTransformation.H Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_Particles.H commit 5dd897a42921ca269a50ee6eb57181965f2b2b72 Merge: a55752dad 9caed27b2 Author: Andrew Myers Date: Wed Nov 20 16:53:15 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a55752dad4c5f275018585b4aed218cb59baeb31 Author: Andrew Myers Date: Wed Nov 20 16:53:06 2019 -0800 docstrings for numOutOfRange Src/Particle/AMReX_ParticleUtil.H commit 9caed27b27b7ddfe845bca438aba04cabb1ebb03 Author: Michele Rosso Date: Wed Nov 20 16:48:15 2019 -0800 EB redistribution: enable 2D support Src/EB/AMReX_EB_utils.cpp commit c039fa4b8c896a0bbb2159db21ea31da85069a2d Author: Michele Rosso Date: Wed Nov 20 16:48:15 2019 -0800 EB redistribution: enable 2D support Src/EB/AMReX_EB_utils.cpp commit 197fc9cfdbc32b5ab1844a08776ee36ff41dff84 Author: Ann Almgren Date: Wed Nov 20 16:35:44 2019 -0800 Add CITATION file for AMReX CITATION commit ac13b081be818f1be21e5674563281e108399d29 Merge: 314bac3b0 27d5b67b8 Author: Weiqun Zhang Date: Wed Nov 20 16:25:55 2019 -0800 Merge branch 'weiqun/dev' into development commit 27d5b67b8c2e2c70a2f39dc42b59574c71934222 Author: Weiqun Zhang Date: Wed Nov 20 16:25:40 2019 -0800 nodal solver sync residual: WIP for RAP Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 314bac3b0c4a6d0b71f626bd3dd56a808662e29e Author: Andrew Myers Date: Wed Nov 20 15:55:44 2019 -0800 remove faulty assertion Src/Particle/AMReX_DenseBins.H commit 12495f58e5a593c8f9813da12d5d507cfbf504de Author: Kevin Gott Date: Wed Nov 20 16:03:34 2019 -0700 Fix HIP FIX comments Src/Base/AMReX_Extension.H Src/Base/AMReX_FBI.H commit 02b2a78a15dae7995376a2feefde95324f519cba Author: Weiqun Zhang Date: Wed Nov 20 14:45:54 2019 -0800 SumBoundary: avoid self copy Src/Base/AMReX_MultiFab.cpp commit 2878975eea836ed1faf31333203f8620b9f8aadf Merge: 287628d16 b2b25ecde Author: Weiqun Zhang Date: Wed Nov 20 12:52:53 2019 -0800 Merge branch 'weiqun/dev' into development commit b2b25ecde00661c5c43d7abf631e4c8beb96549a Author: Weiqun Zhang Date: Wed Nov 20 12:52:21 2019 -0800 FArrayBox::initVal is back on gpu now Src/Base/AMReX_FArrayBox.cpp commit cb641be78db3bedfdb2b912a643188f34892e535 Author: Weiqun Zhang Date: Wed Nov 20 12:46:56 2019 -0800 make launch macros more robust Src/Base/AMReX_GpuLaunchMacrosG.H commit 287628d1670a35eb43faa7aab57bd3f6fb4b39d3 Author: Andrew Myers Date: Wed Nov 20 10:58:29 2019 -0800 make aborting if not all found an option Tools/Plotfile/fcompare.cpp commit af7f581acf30a8511e6587929fcddbbd944f03e6 Author: Andrew Myers Date: Wed Nov 20 10:32:55 2019 -0800 have fcompare and particle_compare fail if the same variables are not present in the two plotfiles Tools/Plotfile/fcompare.cpp Tools/Postprocessing/C_Src/particle_compare.cpp commit 3d1a926ae223c1f211c41a7e9421dc7d45e3e9a4 Author: Andrew Myers Date: Wed Nov 20 10:24:45 2019 -0800 go back to using lower-case phi for the advection tutorials Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/Amr/Advection_F/Source/plotfile_mod.F90 commit a98084048d6a33c8b4a7f9d49c1689dfd1c33393 Author: Weiqun Zhang Date: Wed Nov 20 09:55:09 2019 -0800 fix function name that has changed Src/Base/AMReX_FabArray.H commit 2ad4eeef14b73037f53e384697c9de031f932433 Merge: 7a85162b1 2ebb04e3b Author: Weiqun Zhang Date: Wed Nov 20 09:47:36 2019 -0800 Merge branch 'development' into weiqun/dev commit 7a85162b1a943b39eefd8d4b1437172852a51f98 Author: Weiqun Zhang Date: Wed Nov 20 09:47:03 2019 -0800 new makeFineMask that reuses parallel copy meta data Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 2ebb04e3bba1dde5a0867c34b2af427074aefa1e Merge: 8ccb49243 2428e4b72 Author: WeiqunZhang Date: Wed Nov 20 08:53:09 2019 -0800 Merge pull request #584 from shashankNREL/SY/FixSplineIF Fixes to the spline IF routines commit 2428e4b72e94a38e2a4cad013db657cfaf855a70 Author: ShashankNREL Date: Wed Nov 20 08:28:11 2019 -0700 Made changes to solve thomas based on Weiqun suggestions on PR Src/EB/AMReX_distFcnElement.H Src/EB/AMReX_distFcnElement.cpp commit 8ccb4924350932f0966b360de0ebf4f202f91dfd Author: Weiqun Zhang Date: Tue Nov 19 16:33:56 2019 -0800 comment out buggy code Src/Base/AMReX_FArrayBox.cpp commit 8cebd7adddb62d54cb33e2be70387478a5d5446f Author: Weiqun Zhang Date: Tue Nov 19 16:33:56 2019 -0800 comment out buggy code Src/Base/AMReX_FArrayBox.cpp commit 5043e3da5516c46f48be96edcf8b9ffbf9063682 Merge: 3d4af42b4 67b75e6ae Author: Andrew Myers Date: Tue Nov 19 14:16:09 2019 -0800 Merge pull request #624 from ax3l/doc-exposeParticleTemplates Particles: Expose Template Arguments commit 67b75e6ae5e0b7f714555613730395996f8b272c Author: Axel Huebl Date: Tue Nov 19 14:45:34 2019 -0700 Particles: Expose Template Arguments In order to code more generically downstream in WarpX, let's expose the template arguments that make up a particle and particle container as public constexpr. Src/Particle/AMReX_Particle.H Src/Particle/AMReX_Particles.H commit 12399e56f2e3387a6bf6dac3ea6e736b9a81d001 Merge: fe9d140a9 6d37dc0ed Author: Weiqun Zhang Date: Tue Nov 19 12:45:10 2019 -0800 Merge branch 'development' into weiqun/dev commit 3d4af42b4e34b1d6e90bbd3d49ac8f5c908dd96d Merge: df8048126 287b51a44 Author: Andrew Myers Date: Tue Nov 19 12:15:42 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit df8048126ebde947f4a13d7a63dcffa7deb014af Author: Andrew Myers Date: Tue Nov 19 12:15:31 2019 -0800 implement add / copy for particle container in a GPU friendly way Src/Particle/AMReX_ParticleContainerI.H commit e71ac9acf2f88fd6e69c8dbb7ab74639e60f4eb5 Author: Andrew Myers Date: Tue Nov 19 12:15:10 2019 -0800 add copyParticles form of transformation Src/Particle/AMReX_ParticleTransformation.H commit 287b51a44c2773cd52b45760d20a14f0e77e740a Author: Brandon Runnels Date: Tue Nov 19 13:10:26 2019 -0700 added option in libamrex configure script to specify cuda-arch (#623) * added option in libamrex configure script to specify cuda-arch * fixed strip() incompatibility Tools/libamrex/configure.py commit 2bd8e58c343a7341c028144fe8b73daac94d5c1d Author: Andrew Myers Date: Tue Nov 19 11:43:01 2019 -0800 fix some more spaces Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_DenseBins.H commit 6d37dc0ed95c333fde769b6eaf11216be55ca83f Merge: a14330338 2bd8e58c3 Author: Weiqun Zhang Date: Tue Nov 19 11:41:44 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4b8b172e9f36158d8c3ed22d16a4cfa895aae358 Author: Andrew Myers Date: Tue Nov 19 11:41:41 2019 -0800 fix some spaces Src/Particle/AMReX_ParticleBufferMap.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit a14330338d3bfd5ef641cd6a19adaad19a39840b Author: Weiqun Zhang Date: Tue Nov 19 11:41:34 2019 -0800 update assertion Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit c15288de79954e4e461d1909277b2cbfcd0b2555 Author: Andrew Myers Date: Tue Nov 19 11:41:08 2019 -0800 use rvalue references in MeshToParticle, ParticleToMesh Src/Particle/AMReX_ParticleMesh.H commit 3ced2a0f9def9f421661a64fd1bc8ea2a5a16999 Author: Andrew Myers Date: Tue Nov 19 11:36:51 2019 -0800 also change the non-Gpu version of these typedefs Src/Base/AMReX_GpuContainers.H commit 9363da4120aa31ca5bd0b0b43e0a2778390ff51a Author: Andrew Myers Date: Tue Nov 19 11:32:27 2019 -0800 remove CUDA ifdef Src/Particle/AMReX_ParticleContainerI.H commit 035cda7f62bc87b42cbc1f01fdbaa54105ace0e2 Author: Andrew Myers Date: Tue Nov 19 11:32:07 2019 -0800 EnforcePeriodicGPU -> EnforcePeriodic Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 82b858c0b9a349b469f4bcd6496f55a9aa78a2ba Merge: f3d15c7c9 62c21eb50 Author: Andrew Myers Date: Tue Nov 19 11:23:23 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f3d15c7c98c9d7599734aad145d7cad9847fee11 Author: Andrew Myers Date: Tue Nov 19 11:23:12 2019 -0800 update the docs re: thrust vectors Docs/sphinx_documentation/source/GPU.rst commit fe9d140a9cb8ba39de45e906862509267a28a3d0 Author: Weiqun Zhang Date: Tue Nov 19 11:17:10 2019 -0800 reimplement gpu version of overlap mask Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp commit f7bae241940435183bf69107f753912edd3fc6ce Author: Andrew Myers Date: Tue Nov 19 11:05:17 2019 -0800 add some docstrings to the GpuContainers Src/Base/AMReX_GpuContainers.H commit 4ec687126594fbcc6ac88e74f971898fae2480f6 Author: Andrew Myers Date: Tue Nov 19 10:58:22 2019 -0800 ManagedDeviceVector -> ManagedVector Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_NeighborList.H Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_StructOfArrays.H Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainerInit.cpp commit 710f1005c197f11d11e117ed346f0d026e769d7a Author: Andrew Myers Date: Tue Nov 19 10:54:59 2019 -0800 PinnedDeviceVector -> PinnedVector, same for Polymorphic Src/Base/AMReX_GpuContainers.H Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_Particles.H commit 62c21eb5042386c2df313711a35884abc893edbb Merge: 96678ef9f d74880c24 Author: Weiqun Zhang Date: Tue Nov 19 10:48:58 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 96678ef9f0ef2f9f4ff65a47a4492cb24fca6404 Author: Weiqun Zhang Date: Tue Nov 19 10:35:02 2019 -0800 init signaling nan on gpu in FArrayBox::initVal Src/Base/AMReX_FArrayBox.cpp commit aa35927a5560663d3a85f128ab06215a35388a24 Author: Andrew Myers Date: Tue Nov 19 10:32:39 2019 -0800 remove old thrust test Tests/Particles/StructOfArrays/CudaManagedAllocator.H Tests/Particles/StructOfArrays/GNUmakefile Tests/Particles/StructOfArrays/Make.package Tests/Particles/StructOfArrays/StructOfArrays.H Tests/Particles/StructOfArrays/main.cpp commit d74880c24661e52efd72721b737f469142e1b29b Author: Weiqun Zhang Date: Tue Nov 19 10:29:06 2019 -0800 fix typo Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 10e87c8c885886eaa7a7807e3b01421eb0630053 Author: Andrew Myers Date: Tue Nov 19 10:24:09 2019 -0800 remove unneeded thrust includes Src/Base/AMReX_Vector.H Src/Particle/AMReX_NeighborList.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_StructOfArrays.H commit 9ccd911bc3c7dc4669cb6632658500c32d484915 Author: Weiqun Zhang Date: Tue Nov 19 10:24:01 2019 -0800 fix typo Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit c11fa7e2b52aba3b73dbc15d46ad08c606bfdb12 Author: Andrew Myers Date: Tue Nov 19 10:16:54 2019 -0800 remove unused file / function Src/Particle/AMReX_Functors.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 61b6572c7cc78b63e48b97b16fc0c0aa92f19230 Merge: 9cb35a8f8 cdcbb30fa Author: Andrew Myers Date: Tue Nov 19 10:13:42 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9cb35a8f8d975eacbdd7d666bd25c25d703adadf Author: Andrew Myers Date: Tue Nov 19 10:13:35 2019 -0800 reuse copyParticle function in Redistribute Src/Particle/AMReX_ParticleContainerI.H commit cdcbb30fafd4d663cbf7d0081ffbbba2324d01af Author: Weiqun Zhang Date: Tue Nov 19 09:44:48 2019 -0800 rename myArena to arena Src/Base/AMReX_FabArray.H commit 9db1dcfd1241ad2414f354350dceb94192ba24af Author: Weiqun Zhang Date: Tue Nov 19 09:22:05 2019 -0800 fix a couple issues with tiling and gpu Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.H Src/EB/AMReX_MultiCutFab.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 45c4f105e0ba922f342e71602ce4d7ae24a888fa Merge: 39f32c04e c32c4ef90 Author: Andrew Myers Date: Mon Nov 18 16:42:27 2019 -0800 Merge branch 'development' into particle_transformation commit 39f32c04e8458c1309cd18db8cb36cbcbc2b26aa Author: Andrew Myers Date: Mon Nov 18 16:41:58 2019 -0800 add some enable_if and decltype for maximum obfuscation Src/Particle/AMReX_ParticleTransformation.H commit c32c4ef907455b468133dcc1dc308c1e3b2ff7e8 Merge: 7211f49c6 1c4c3b41a Author: Weiqun Zhang Date: Mon Nov 18 15:58:39 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7211f49c66f2ada9428b5f1fb0d77a15cf905b7a Author: Weiqun Zhang Date: Mon Nov 18 15:58:29 2019 -0800 fix corner case for EB tensor solver Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 746138fe50177ca3fe8dd5271bfb96180fd502e9 Merge: 11a5b29c6 1c4c3b41a Author: Andrew Myers Date: Mon Nov 18 15:35:51 2019 -0800 Merge branch 'development' into particle_transformation commit 1c4c3b41a2afdfe5d1ef709405d1273e5b2a420c Author: Andrew Myers Date: Mon Nov 18 15:35:25 2019 -0800 use forwarding references in AMReX_ParticleReduce.H Src/Particle/AMReX_ParticleReduce.H commit e0c1b584b16c91feacc454d561c1810ca9dbf214 Author: Weiqun Zhang Date: Mon Nov 18 13:14:25 2019 -0800 add some LaunchSafeGuards Src/AmrCore/AMReX_TagBox.cpp commit 11a5b29c6195531df84ecf44e455c126b9bd30f7 Author: Andrew Myers Date: Mon Nov 18 15:25:36 2019 -0800 use std::forward Src/Particle/AMReX_ParticleTransformation.H Tests/Particles/ParticleTransformations/main.cpp commit bebfeef519bd08542bc9411342d0e7c1346f96fa Author: Andrew Myers Date: Mon Nov 18 14:50:15 2019 -0800 move all the transformation stuff to a separate file Src/Particle/AMReX_ParticleTransformation.H Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit c2684bf83346d1294aa657e7fdea3fb00a4b01a4 Author: Andrew Myers Date: Mon Nov 18 10:40:31 2019 -0800 fix spaces Src/Particle/AMReX_Particles.H commit 9aceafeac86c47f33ab107b147f17b5feb3fe4e9 Author: Andrew Myers Date: Mon Nov 18 13:47:10 2019 -0800 fix and test filterAndTransform Src/Particle/AMReX_ParticleUtil.H Tests/Particles/ParticleTransformations/main.cpp commit ff65d907946f9682f580264d5cbcef12644d4863 Merge: 21b546b50 ad4b5e44b Author: Andrew Myers Date: Mon Nov 18 13:25:53 2019 -0800 Merge branch 'development' into particle_transformation commit 21b546b50ad4b2a7adb3b29c213e83369ce822de Author: Andrew Myers Date: Mon Nov 18 13:25:27 2019 -0800 make filter tests more strict Tests/Particles/ParticleTransformations/main.cpp commit eab2c41f7975f0eb894e5c324b2be2e8a5585c01 Author: Andrew Myers Date: Mon Nov 18 13:15:49 2019 -0800 add assertion Tests/Particles/ParticleTransformations/main.cpp commit 7c37936bd8e19d24028f28f88a6b147d7b3f8de0 Author: Andrew Myers Date: Mon Nov 18 13:13:24 2019 -0800 fix name Tests/Particles/ParticleTransformations/main.cpp commit 1700c05a6e8e059e79da3b393e90b184681f0f71 Author: Andrew Myers Date: Mon Nov 18 13:11:52 2019 -0800 fixes for filter Src/Particle/AMReX_ParticleUtil.H Tests/Particles/ParticleTransformations/main.cpp commit 392e8e657f5f19e949c84e394c7203d89d23987c Author: Andrew Myers Date: Mon Nov 18 12:52:42 2019 -0800 some fixes for filter Src/Particle/AMReX_ParticleUtil.H Tests/Particles/ParticleTransformations/main.cpp commit ad4b5e44b689dd646a2a84e0b7c280f97a620d5f Author: Weiqun Zhang Date: Mon Nov 18 12:08:32 2019 -0800 add single precision compile test Tests/SinglePrecision/GNUmakefile Tests/SinglePrecision/Make.package Tests/SinglePrecision/main.cpp Tools/CompileTesting/compiletesting.py commit 8d5ea2ba1f229ec56d9b2c149dd77502db27a102 Author: Weiqun Zhang Date: Mon Nov 18 11:10:38 2019 -0800 remove BaseFab RunOn because it doesn't work and there is no nice ways to fix it Src/Base/AMReX_BaseFab.H commit be8f3ee2dd8a5ff45f1d0f80955583a77bbb85a4 Author: Andrew Myers Date: Mon Nov 18 11:07:01 2019 -0800 some refactoring of the transform test Tests/Particles/ParticleTransformations/main.cpp commit a83e60cc605840315324bbc27ad8aa64ed5489ed Author: Weiqun Zhang Date: Mon Nov 18 10:59:07 2019 -0800 rm BaseFab::ForEach Src/Base/AMReX_BaseFab.H Tests/ThirdPartyLib/foo.cpp commit fa0019fa87bcc9d96a462f9e0bd703b6f0a0e9ea Merge: 56d7a4811 1fb685098 Author: cgilet Date: Mon Nov 18 13:50:20 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit c417dcb88228506db3f9cfef078d4e63539af9d3 Author: Andrew Myers Date: Mon Nov 18 10:41:06 2019 -0800 Stronger test of transformations Tests/Particles/ParticleTransformations/main.cpp commit 1cadd8d58a100b71e2837ff846162430cb00bf72 Author: Andrew Myers Date: Mon Nov 18 10:40:31 2019 -0800 fix spaces Src/Particle/AMReX_Particles.H commit 8ee7189c178699e4043c61fe126602012d79d9d8 Merge: b09e55a78 1fb685098 Author: Andrew Myers Date: Mon Nov 18 10:09:26 2019 -0800 Merge branch 'development' into particle_transformation commit 1fb6850985edc7fcd4e27ec77a4bd489cbe20aa2 Merge: 68fde2d01 9ac2e098e Author: WeiqunZhang Date: Mon Nov 18 08:32:48 2019 -0800 Merge pull request #621 from ax3l/fix-warningFinal PhysBCFunct: Final Warning commit 9ac2e098eecc16fc145a60fd0abfa1e6a9bf3f47 Author: Axel Huebl Date: Mon Nov 18 00:34:27 2019 -0700 PhysBCFunct: Final Warning Warning with Clang: ``` ../amrex/Src/Base/AMReX_PhysBCFunct.H:112:42: warning: class with destructor marked 'final' cannot be inherited from [-Wfinal-dtor-non-final-class] virtual ~PhysBCFunctNoOp () override final {} ^ ../amrex/Src/Base/AMReX_PhysBCFunct.H:106:7: note: mark 'amrex::PhysBCFunctNoOp' as 'final' to silence this warning class PhysBCFunctNoOp ``` Src/Base/AMReX_PhysBCFunct.H commit 68fde2d01e72be3508515b7ab025f84f40443aa4 Author: Weiqun Zhang Date: Sun Nov 17 18:37:36 2019 -0800 rm deprecated Fortran files Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.H commit cbd7a1cf20f95d625376b1277f5dcbc4d027aa29 Merge: 9030b5014 90934d9ee Author: Weiqun Zhang Date: Sun Nov 17 17:06:40 2019 -0800 Merge branch 'development' into weiqun/dev commit 9030b50141e8fd8bc3f9ad7f5b5ce91f6cea89f0 Author: Weiqun Zhang Date: Sun Nov 17 17:04:28 2019 -0800 nodal solver on gpu: reflux Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/Make.package commit c160447d76d9ebf6b804d965c3eae741c6cca6dc Merge: 48d516e59 90934d9ee Author: Kevin Gott Date: Fri Nov 15 16:27:29 2019 -0800 Merge branch 'development' into kngott/hip commit 90934d9ee7ad23bdc09cfaee5af0d3f1fc6f09e6 Author: Kevin Gott Date: Fri Nov 15 16:26:13 2019 -0800 Add access to the Arena used to build a FabArray through a BaseFab::DataAllocator. Src/Base/AMReX_FabArray.H commit 4be4a0708b2aad836a7724c495a0df6fa459c621 Author: Weiqun Zhang Date: Fri Nov 15 16:20:15 2019 -0800 fix warning Src/Base/AMReX_GpuContainers.H commit c13ebb340521fa9a5c956200b355bc26fd79c25a Author: Weiqun Zhang Date: Fri Nov 15 16:20:15 2019 -0800 fix warning Src/Base/AMReX_GpuContainers.H commit cdc50cd79c4930cc40afbe4d2839a018cc16c9e5 Author: Weiqun Zhang Date: Fri Nov 15 15:25:57 2019 -0800 nodal solver on gpu: coarse sync residual Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 44c13b6e74de796e44cb27e117a80e0f9500827c Author: Weiqun Zhang Date: Fri Nov 15 15:24:11 2019 -0800 some very important spaces to me Src/Base/AMReX_Random.H Src/Base/AMReX_Random.cpp commit 4c8f92e9a433b0fe31ec1f2ab97405f0ddc87f6f Author: Kevin Gott Date: Fri Nov 15 14:06:19 2019 -0800 Use Pinned Arena for plotting. Avoids unneeded memory movement. Src/Base/AMReX_PlotFileUtil.cpp commit 68df422245f0afab24e0850e360ad21a58d8cb55 Author: Andrew Myers Date: Fri Nov 15 13:48:49 2019 -0800 need to include Base in makefile Tools/Postprocessing/C_Src/GNUmakefile commit 6ed5e9e0b00cb38283e552c66bd2b40e0a14b5a2 Author: Andrew Myers Date: Fri Nov 15 13:46:33 2019 -0800 remove debug print Tools/Postprocessing/C_Src/particle_compare.cpp commit c3d63ebc88fb0c24b404f82aae3316b10f879204 Author: Andrew Myers Date: Fri Nov 15 13:45:05 2019 -0800 fix some typos in fcompare.cpp Tools/Plotfile/fcompare.cpp commit 4d2a108aa3c741a07634c1d7085089be5507652e Author: Andrew Myers Date: Fri Nov 15 13:44:41 2019 -0800 make particle_compare respect a relative tolerance Tools/Postprocessing/C_Src/particle_compare.cpp commit 1ea08d1f9fd8284dd57b3404c210dd3e14a48140 Author: Andrew Myers Date: Fri Nov 15 13:14:06 2019 -0800 sort particle data by id and cpu before comparing Tools/Postprocessing/C_Src/particle_compare.cpp commit 7ea50f93a52a6a4762bddb4fa210eac5d1fc33e5 Author: Weiqun Zhang Date: Fri Nov 15 09:33:42 2019 -0800 fix the number of components Tutorials/LinearSolvers/NodalPoisson/MyTestPlotfile.cpp commit 027f49dcd3f2a03fadd99d69ab6e0e2ce7b0ef71 Author: Weiqun Zhang Date: Fri Nov 15 09:24:55 2019 -0800 fix variable names Tutorials/LinearSolvers/NodalPoisson/MyTestPlotfile.cpp commit fd2562ca51b9323457c5a7bfd6bc6a7d182792f1 Author: Weiqun Zhang Date: Fri Nov 15 08:52:01 2019 -0800 remove some variables from plotfile for gpu regression test Tests/LinearSolvers/NodeEB/MyTest.H Tests/LinearSolvers/NodeEB/MyTest.cpp Tutorials/LinearSolvers/NodalPoisson/MyTest.H Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp Tutorials/LinearSolvers/NodalPoisson/MyTestPlotfile.cpp commit 48d516e5910bcea5b1953233490c211600e19066 Author: Kevin Gott Date: Thu Nov 14 16:53:36 2019 -0800 First draft for Pinned copy I/O HeatEquation. Need to store Arena and use same one throughout before it will work. Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit b09e55a7825ef17cdb47f18dfe5e8a9288afa257 Author: Andrew Myers Date: Thu Nov 14 16:38:16 2019 -0800 AMREX_FOR_1D -> AMREX_HOST_DEVICE_FOR_1D, to respect launch region flag Src/Particle/AMReX_ParticleUtil.H commit 33d3f3ee2cad0fd1a1e53228b038c90e144cbc3f Merge: 48f234ad7 36e367a76 Author: Weiqun Zhang Date: Thu Nov 14 16:31:11 2019 -0800 Merge branch 'weiqun/dev' into development commit 0f1dd267c4a6a3a524197a9e2d050cd92b1943b9 Author: Andrew Myers Date: Thu Nov 14 16:31:09 2019 -0800 make the test abort on error Tests/Particles/ParticleTransformations/main.cpp commit 48f234ad74dbd9ae172c5f58e98bff20ca93b509 Merge: 70e179712 5b6cfcee7 Author: Weiqun Zhang Date: Thu Nov 14 16:31:04 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 56bdc2d60177c0254243bd6a58d6f8917487cedb Author: Andrew Myers Date: Thu Nov 14 16:29:33 2019 -0800 use forwarding references for function objects Src/Particle/AMReX_ParticleUtil.H commit 2009324530ee06b949610dade3e8c0df49aee11f Author: Andrew Myers Date: Thu Nov 14 16:22:37 2019 -0800 fix comment Src/Particle/AMReX_ParticleUtil.H commit 36e367a76b5566bd9eca8c0bccfc74635ce09035 Author: Weiqun Zhang Date: Thu Nov 14 15:54:07 2019 -0800 fix index type Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 75bd9dea7cac13d9b2df89b78ca8015d9d6d88dd Merge: e3e8dec7e 5b6cfcee7 Author: Andrew Myers Date: Thu Nov 14 15:22:47 2019 -0800 Merge branch 'development' into particle_transformation commit 5b6cfcee77eabcd700d08ac249dba9ae77cc969e Author: Andrew Myers Date: Thu Nov 14 15:20:04 2019 -0800 add an additional debug assert Src/Particle/AMReX_DenseBins.H commit 2cd6d22522bc55eac3241ec566a7af6779506810 Author: Andrew Myers Date: Thu Nov 14 15:19:28 2019 -0800 use Gpu::copy instead of dtod_memcpy, which is a no-op on the CPU Src/Particle/AMReX_DenseBins.H commit 565ef89cd550063e6e76c9541562671638c7730f Author: Weiqun Zhang Date: Thu Nov 14 15:17:28 2019 -0800 fix a warning on calling host function from host device function Src/Base/AMReX_MultiFabUtil.cpp commit b17e30315ac37e6ab29f1b0b3503d6ef444fba9e Author: Weiqun Zhang Date: Thu Nov 14 15:17:05 2019 -0800 make Array4::operator bool host and device Src/Base/AMReX_Array4.H commit 70e1797123b56b9ee205bd16bf131f7aef077f2b Merge: 4d943c1ba 5a50b5606 Author: Weiqun Zhang Date: Thu Nov 14 15:10:04 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4d943c1ba67abb3acf0ebb6ca3c4b8069a388d52 Author: Weiqun Zhang Date: Thu Nov 14 15:09:37 2019 -0800 nodal solver on gpu: coarse residual Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 8bb5472aaae9073de55615cb5ca5e42138724c03 Author: Weiqun Zhang Date: Thu Nov 14 14:11:42 2019 -0800 refactor makeFineMask for gpu Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit e3e8dec7e6f15ce110477619f77f69488ebf016b Merge: 720fac67f 5a50b5606 Author: Andrew Myers Date: Thu Nov 14 13:54:49 2019 -0800 Merge branch 'development' into particle_transformation commit 5a50b5606119803a8d51ea6d6079aa0cfa9ad715 Merge: c0a7fe42c 6528cb8ff Author: Andrew Myers Date: Thu Nov 14 13:51:09 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c0a7fe42c8d830abdf1a8a0bdd76fb9466fabf5d Author: Andrew Myers Date: Thu Nov 14 13:51:01 2019 -0800 need to handle the cpu-only case in these functions Src/Base/AMReX_GpuContainers.H commit 720fac67f6fc774f71a6dab262257611cb8c1290 Author: Andrew Myers Date: Thu Nov 14 13:45:47 2019 -0800 initial test for particle transformations Src/Particle/AMReX_Particles.H Tests/Particles/ParticleTransformations/GNUmakefile Tests/Particles/ParticleTransformations/Make.package Tests/Particles/ParticleTransformations/inputs Tests/Particles/ParticleTransformations/main.cpp commit b240248e0211d6c26c12d8c81d04d86d63ec14f5 Author: Andrew Myers Date: Thu Nov 14 11:33:00 2019 -0800 start adding some general particle transformation and filtering routines Src/Particle/AMReX_ParticleUtil.H commit 6528cb8ff3a3262c44d057e41278f203aed24059 Merge: f5447afff c5a905f9c Author: Weiqun Zhang Date: Thu Nov 14 11:06:00 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f5447affff5227c193223eff27d66236f3a1de45 Author: Weiqun Zhang Date: Thu Nov 14 11:05:20 2019 -0800 nodal solver on gpu: coarse contribution to divu Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit a73aff5ca5531445ff9de86ca8248bd99195e377 Author: Weiqun Zhang Date: Thu Nov 14 11:04:23 2019 -0800 add operator bool to Array4 Src/Base/AMReX_Array4.H commit c5a905f9c86f6cd01db22e9908b12fba4a3bfee9 Merge: 7e48eebdc 1ba041d5e Author: Andrew Myers Date: Thu Nov 14 10:34:25 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7e48eebdc9b66a9654d15d499cb7e1a03c42a68d Author: Andrew Myers Date: Thu Nov 14 10:34:16 2019 -0800 remove over-zealous assertion Src/Particle/AMReX_StructOfArrays.H commit 1ba041d5e01119843c8f7dc28af08f79e1eb8d73 Merge: 10d28a9d7 6993f575d Author: WeiqunZhang Date: Thu Nov 14 10:22:26 2019 -0800 Merge pull request #619 from AMReX-Codes/amrex_copy Amrex copy commit 6993f575d1fc066c9c2b34a3d82b0cb6fd5d4a02 Author: Andrew Myers Date: Thu Nov 14 10:13:48 2019 -0800 add static_assert for trivial copyability Src/Base/AMReX_GpuContainers.H commit 68ab26a5a12a0e5303d117ffae2f05a2020ee1e8 Author: Andrew Myers Date: Thu Nov 14 10:03:17 2019 -0800 fix copy/paste error in docstring Src/Base/AMReX_GpuContainers.H commit ecb9cc684742df3aedf9cbdaecf6d7ed12015d64 Merge: d0bd9c5f0 10d28a9d7 Author: Andrew Myers Date: Thu Nov 14 10:01:44 2019 -0800 Merge branch 'development' into amrex_copy commit 10d28a9d71915a3414d39c415a637eb6421a5d50 Author: Andrew Myers Date: Thu Nov 14 09:59:45 2019 -0800 the number of bins is actually m_offsets.size()-1 Src/Particle/AMReX_DenseBins.H commit 48eb5dd04b527b1c07fdbce13092c20689eb8e8d Author: Weiqun Zhang Date: Thu Nov 14 09:24:47 2019 -0800 nodal solver on gpu: fine contribution to rhs Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 9a23c7183dbd8a5ea6c090158339f4e3e241cfc0 Author: Kevin Gott Date: Wed Nov 13 16:10:57 2019 -0800 qFix AMREX_HIP_OR_CUDA in MemPool init. Src/Base/AMReX_MemPool.cpp commit d5a3155a69d725d9d27fb93bb7fdfe1f5d019f77 Author: Kevin Gott Date: Tue Nov 12 23:38:41 2019 -0800 First MPI HIP adjustments (MPI is WIP -- Pretty much just turned on at this point). Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArray.H Tools/GNUMake/Make.defs commit 1b4e3be21ce46a50bb0b1fded08143b00ef186e8 Author: Weiqun Zhang Date: Wed Nov 13 15:11:41 2019 -0800 fix xsdk Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_distFcnElement.cpp commit 7f8ed54a37c63595ebeb833f97d6f2f185cd9e7c Author: Andrew Myers Date: Wed Nov 13 14:36:45 2019 -0800 same for the DenseBins structure Src/Particle/AMReX_Particles.H commit eb07ef0ad439ed8102cb9933a989bc9f826325d6 Author: Andrew Myers Date: Wed Nov 13 14:35:42 2019 -0800 need m_ptile_r whether compiling for GPU or not Src/Particle/AMReX_Particles.H commit 7889aafb0f94ff8779053fe1d1ed17bcc8bc8caf Merge: d2873df72 1f2bf04a9 Author: Andrew Myers Date: Wed Nov 13 14:27:05 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d2873df725a94211fa34fd294a6dd1e28e5a14b1 Author: Andrew Myers Date: Wed Nov 13 14:26:56 2019 -0800 don't need this AMREX_USE_CUDA guard Src/Particle/AMReX_ParticleContainerI.H commit 1db352a80fee8f8449f66bc4b7f36e8e82bb4907 Author: Andrew Myers Date: Wed Nov 13 14:26:25 2019 -0800 add inputs for test that bins particles by cell Tests/Particles/Redistribute/inputs.rt.cuda.sort commit 56d7a4811789427693b5fc713b4ad2ef59910aca Merge: 59eeb0763 009035716 Author: Michele Rosso Date: Wed Nov 13 14:25:16 2019 -0800 Merge branch 'ebtensor_flux' of https://github.com/AMReX-Codes/amrex into ebtensor_flux commit 59eeb076366317d552bb87c852432ec96703a0b7 Author: Michele Rosso Date: Wed Nov 13 14:24:18 2019 -0800 Fix comp index when calling EB_set_covered in redistribution Src/EB/AMReX_EB_utils.cpp commit 1f2bf04a9679583ed584521beac076c67178ab4f Author: Michele Rosso Date: Wed Nov 13 14:24:18 2019 -0800 Fix comp index when calling EB_set_covered in redistribution Src/EB/AMReX_EB_utils.cpp commit 3aafafce0b92bad887f61e38f7a8f39c80815701 Author: Andrew Myers Date: Wed Nov 13 14:07:09 2019 -0800 replace runtime_real with runtime_int here Src/Particle/AMReX_ParticleUtil.H commit 64b73396e30d5f63d298212324165c0785a7d985 Author: Andrew Myers Date: Wed Nov 13 14:01:09 2019 -0800 add some docstrings for copyParticle, gather, and scatter Src/Particle/AMReX_ParticleUtil.H commit d0bd9c5f0e7a1447fdc3eb25c8959ab21ae18f30 Author: Andrew Myers Date: Wed Nov 13 13:50:46 2019 -0800 docstrings Src/Base/AMReX_GpuContainers.H commit 261021614bf01e723ef19b8887a77846e32c525c Merge: c64c79dac 36510da21 Author: Andrew Myers Date: Wed Nov 13 13:31:07 2019 -0800 Merge branch 'development' into amrex_copy commit c64c79dac467117b060173d06235f69d78f10a86 Author: Andrew Myers Date: Wed Nov 13 13:29:40 2019 -0800 fix silly mistake uncovered by this PR Tests/Particles/Redistribute/main.cpp commit 36510da21a1b72b60a84fa8e91c7bc62c5b8d417 Author: Andrew Myers Date: Wed Nov 13 16:27:57 2019 -0500 use new swap method of ParticleTile Src/Particle/AMReX_ParticleContainerI.H commit 0090357160cd10e979e93a5cce08f5a5a920cc3f Author: cgilet Date: Wed Nov 13 16:06:07 2019 -0500 MLEBTensorOp::compFlux abort if Location!=FaceCenter. Clean up. Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit b6417984f53637b46a9da91ce20035e59a4d8d52 Author: Andrew Myers Date: Wed Nov 13 12:50:13 2019 -0800 add async versions Src/Base/AMReX_GpuContainers.H commit 54e8ee080c80877dd681c85003bf1cb88e9ed93f Author: Andrew Myers Date: Wed Nov 13 12:48:53 2019 -0800 replace thrust_copy with amrex_copy Docs/sphinx_documentation/source/GPU.rst Src/Base/AMReX_GpuContainers.H Src/Particle/AMReX_NeighborList.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_ParticleBufferMap.cpp Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_ParticleLocator.H Tests/Particles/Intersection/main.cpp Tests/Particles/NeighborParticles/MDParticleContainer.cpp Tests/Particles/ParticleReduce/main.cpp Tests/Particles/Redistribute/main.cpp Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit 332449fd89e397868960ebb284d5a7d1fd948b05 Author: Andrew Myers Date: Wed Nov 13 10:22:26 2019 -0800 thrust_copy is in the Gpu:: namespace Tests/Particles/NeighborParticles/MDParticleContainer.cpp commit 34645a00e1c87610685b1ae252971acb7916cda7 Author: Weiqun Zhang Date: Wed Nov 13 10:12:17 2019 -0800 for eb nodal on gpu, do a Jacobi sweep before Gauss Seidel Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 5b40efd92ba57adc0d0d2c9ead76a4c2fde4f453 Merge: b2f84c682 0f06ef173 Author: Andrew Myers Date: Tue Nov 12 17:24:07 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b2f84c68254fa47e195ed78f5335656a5d9c70c1 Author: Andrew Myers Date: Tue Nov 12 17:23:18 2019 -0800 clean up building this neighbor copy op and add a missing stream sync Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 2560ba3f6d5611bf0e8db737d87a8a350cce5dbe Author: Andrew Myers Date: Tue Nov 12 17:22:38 2019 -0800 adjust size of counts so we don't have a weird +1 Src/Particle/AMReX_ParticleCommunication.H commit 42ea577c013f9a549da3561f0ff508cd8d6c4442 Author: Andrew Myers Date: Tue Nov 12 17:21:31 2019 -0800 use 'size' here so these assertions will work when neighbor particles are in play Src/Particle/AMReX_ParticleTile.H commit 9adff268a8503036b43117dc0d6217641589a578 Author: Kevin Gott Date: Tue Nov 12 16:56:20 2019 -0800 More no-GPU fixes. Src/Base/AMReX_IntVect.H Src/Base/AMReX_Random.cpp commit 0f06ef173c73b02b6fce5c42e47b5c5319d8b152 Author: Andrew Myers Date: Tue Nov 12 19:10:08 2019 -0500 fix typo Src/Particle/AMReX_ParticleUtil.H commit d68a42f82fae0ba80d5e539f03ba1021007ea14a Author: Kevin Gott Date: Tue Nov 12 15:15:50 2019 -0800 Adjustments for no GPU builds. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MultiFabUtil_nd_C.H Src/Base/AMReX_Random.cpp commit 2b0fc101c66c19afd005e250b980f87d1a0fe115 Merge: 48da3810f 2ae351001 Author: Andrew Myers Date: Tue Nov 12 18:09:43 2019 -0500 fix merge conflict commit 48da3810f15396881ce258575caf657a388f36f4 Author: Andrew Myers Date: Tue Nov 12 18:06:58 2019 -0500 update test Tests/Particles/Redistribute/main.cpp commit b7eada1ddb27a812ae9400861b137e67bcd91a19 Author: Andrew Myers Date: Tue Nov 12 18:06:36 2019 -0500 go ahead and implement scatter too, why not Src/Particle/AMReX_ParticleUtil.H commit b2e1acd0121876838a696ee1e6ca280d3b88f9dc Author: Andrew Myers Date: Tue Nov 12 18:02:07 2019 -0500 implement gather in terms of a general copyParticle host / device function Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_ParticleUtil.H commit b89f9410cb1254dcc4a260941301289e0afe5b1f Author: Andrew Myers Date: Tue Nov 12 17:02:26 2019 -0500 a few missing helper routines for ParticleTile Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_StructOfArrays.H commit 396d683a6c67b4706f03a3434971d52a862d2b58 Author: Andrew Myers Date: Tue Nov 12 16:49:19 2019 -0500 implement our own gather particles routine, remove calls to the thrust one Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_ParticleUtil.H commit 2ae35100185894fc60f2ed462b04d778dd2f60c6 Author: Weiqun Zhang Date: Tue Nov 12 12:54:53 2019 -0800 add IntVect n_filled to FabArray to help users to keep track of how many ghost cells have been updated by FillBoundary ParallelCopy Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H commit 579e4acb0d11c0153cc37d8e4e87eaf58f96982c Author: Andrew Myers Date: Tue Nov 12 15:54:43 2019 -0500 remove unused variables Src/Particle/AMReX_ParticleContainerI.H commit f7022bc0cd8dbabc7d27084d7a8eb8317e8cf1ee Author: Andrew Myers Date: Tue Nov 12 15:48:57 2019 -0500 reuse m_ptile_r for temp storage Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 221a83733409f1571a1bcc825b5eac68bb9a5004 Author: Weiqun Zhang Date: Tue Nov 12 12:26:52 2019 -0800 nodal solver: smooth on gpu and do it twice Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit df8077f1ebcfef69554ce4153e62d656b4458076 Author: Weiqun Zhang Date: Tue Nov 12 10:17:00 2019 -0800 nodal solver: build stencil on gpu Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit df08f2a96b39447969546da112bd044b47de0d56 Author: Weiqun Zhang Date: Tue Nov 12 09:38:54 2019 -0800 removed more LaunchSafeGuards from nodal solver Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 7e004ac7afc300a2b39f4e26f240987f763ee418 Author: Kevin Gott Date: Tue Nov 12 11:06:42 2019 -0800 Revert to using long through __shfl_down overload. Src/Base/AMReX_iMultiFab.cpp commit 8565ca92b6cbc0792b760e0c47c08869c975337e Author: Kevin Gott Date: Tue Nov 12 11:06:16 2019 -0800 Hipify thrust::cuda::par function. Src/Base/AMReX_GpuAllocators.H commit 30b0f4802fca19fc5be696243dc65240ae87d921 Author: Kevin Gott Date: Tue Nov 12 11:05:51 2019 -0800 Turn <<<>>> into GPU safe macro. Src/Base/AMReX_FBI.H commit f8696499d0c7ea5748ae1143402b0f4b1ac6e971 Merge: ac4fcaec6 59f36ddb9 Author: Andrew Myers Date: Tue Nov 12 10:01:07 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ac4fcaec64e9da2b5ad4687d52b70d276b27ecba Author: Andrew Myers Date: Tue Nov 12 10:00:53 2019 -0800 call should be to the free function, not to a member here Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit e20874a14e511544500e5cd254238e7f05e54e18 Merge: 0555fdb08 59f36ddb9 Author: Kevin Gott Date: Mon Nov 11 21:10:52 2019 -0800 Merge branch 'development' into kngott/hip commit 59f36ddb9dd17ee6117f88f2b8048e935200a763 Author: Weiqun Zhang Date: Mon Nov 11 20:44:20 2019 -0800 fix using namespace Cuda Src/Base/AMReX_Gpu.H commit 5ae01cdf653f3befb1560adab43a6539e56b57fe Author: Weiqun Zhang Date: Mon Nov 11 20:38:59 2019 -0800 add array and const_array functions taking starting component to FabArray and BaseFab Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H commit 0555fdb08168719f44e0c2a5a991987fe4f3e379 Merge: 7bf2daf44 90b92d7af Author: Kevin Gott Date: Mon Nov 11 17:57:46 2019 -0800 Merge branch 'development' into kngott/hip commit 90b92d7af6f7a4072a109d1f9d16a4bb06b9a089 Author: Kevin Gott Date: Mon Nov 11 20:56:22 2019 -0500 Change Cuda->Gpu in filenames and thrust/container/allocator calls throughout. Docs/sphinx_documentation/source/GPU.rst Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuAllocators.H Src/Base/AMReX_GpuAllocators.cpp Src/Base/AMReX_GpuContainers.H Src/Base/CMakeLists.txt Src/Base/Make.package Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_NeighborList.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_ParticleBufferMap.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_StructOfArrays.H Tests/GPU/Locking/main.cpp Tests/GPU/Partition/main.cpp Tests/GPU/RandomNumberGeneration/main.cpp Tests/Particles/NeighborParticles/MDParticleContainer.cpp Tests/Particles/ParticleReduce/main.cpp Tests/Particles/Redistribute/main.cpp Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit 70888ba18aad792d86c9c0118df9e1dbd623f4fe Author: Kevin Gott Date: Mon Nov 11 20:24:08 2019 -0500 Convert CudaContainers and CudaAllocators to Gpu. Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaAllocators.cpp Src/Base/AMReX_CudaContainers.H Src/Particle/AMReX_ParticleContainerI.H Tests/GPU/Partition/main.cpp Tutorials/GPU/ParallelScan/main.cpp commit 7bf2daf44f083abdcfafc8706a75c12da61b0bef Merge: 3f4e6c459 eb1893293 Author: Kevin Gott Date: Mon Nov 11 17:19:20 2019 -0800 Merge branch 'development' into kngott/hip commit e7a2105a0c742a75014c3436d95b765cc41c68c7 Author: Andrew Myers Date: Mon Nov 11 19:43:49 2019 -0500 optionally make this test do an extra particle sort step Tests/Particles/Redistribute/inputs Tests/Particles/Redistribute/main.cpp commit eb1893293b51ab41a956b55c5e3e7d033743bee4 Author: Andrew Myers Date: Mon Nov 11 16:37:34 2019 -0800 add an additional out-of-range check to neighbor list construction Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit b4ce8259c671e82686a97b2cd9e2f8262d1fd7ce Author: Weiqun Zhang Date: Mon Nov 11 16:27:48 2019 -0800 removed some LaunchSafeGuards in MLNodeLaplacian Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 2c05760c7024bd7e481b8fe61d30f58d564e0c3f Author: Andrew Myers Date: Mon Nov 11 19:23:18 2019 -0500 implement Sort in terms of DeviceBins Src/Particle/AMReX_ParticleContainerI.H commit 16cb1736c6fac7c16fa8f158f34dc5a7d839456d Author: Andrew Myers Date: Mon Nov 11 19:22:48 2019 -0500 remove some unused temporaries Src/Particle/AMReX_Particles.H commit ddc0eb0ffd555adf37af5916186e86dad4c37f66 Author: Andrew Myers Date: Mon Nov 11 19:22:25 2019 -0500 thrust_copy -> dtod_memcpy Src/Particle/AMReX_DenseBins.H commit 2391378e1c500ded00ee79605222ce378e773993 Author: Andrew Myers Date: Mon Nov 11 19:21:34 2019 -0500 have this resize run on the device when compiling with GPUs Src/Base/AMReX_PODVector.H commit 3f4e6c459079ea9c7e153772cf52aebed6974c9f Author: Kevin Gott Date: Mon Nov 11 16:02:38 2019 -0800 Couple small HIP things. Src/Base/AMReX_Random.cpp Src/Base/AMReX_Scan.H commit cbaac3ca18d05263280a9b046bd16fb9569fbbec Author: Kevin Gott Date: Mon Nov 11 16:02:05 2019 -0800 Add long wrapper for shfl_down and label old HIP FIX problems. Src/Base/AMReX_GpuUtility.H commit ebcabb5fac9dc15d057b92f273ade6df91e3d27f Author: Kevin Gott Date: Mon Nov 11 16:01:27 2019 -0800 Turn on all reductions and adjust for noexcept. Tutorials/GPU/ParallelReduce/main.cpp commit 9a8eb64d40b6a57e028d2eb00a0cedfdaac73e77 Author: Weiqun Zhang Date: Mon Nov 11 15:45:00 2019 -0800 forgot ifdef AMREX_USE_GPU Src/Base/AMReX_FBI.H commit b5888ec7ec70fff8dcb122ae4af9fe6ad7524025 Author: Weiqun Zhang Date: Mon Nov 11 15:09:37 2019 -0800 FabArray::BuildMask on gpu Src/Amr/AMReX_Extrapolater.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp commit 38806b84b77c56a6b402b616887ab8b7c880865f Author: Max Katz Date: Mon Nov 11 16:39:42 2019 -0500 Allow code to compile for either old or no-host builds Src/Base/AMReX_filcc_mod.F90 commit 87866225d0c2fcc2b0aa2f02b06ef0f9bceb0425 Author: Andrew Myers Date: Mon Nov 11 15:33:20 2019 -0500 begin refactor of SortParticlesByCell Src/Particle/AMReX_ParticleContainerI.H commit 0b42353eb502a4932cb033ac4ba2bc970055aa0d Author: Andrew Myers Date: Mon Nov 11 15:11:09 2019 -0500 remove unnecessary thrust::reduce call in NeighborList::build Src/Particle/AMReX_NeighborList.H commit 601e50e193299dedf4235be659eb15690614bcb9 Merge: ef3d74d8f 79feacd34 Author: Andrew Myers Date: Mon Nov 11 14:25:58 2019 -0500 Merge branch 'runtime_soa' into development commit ef3d74d8f5f658c056f7769c574b3a57fb568c02 Author: Weiqun Zhang Date: Mon Nov 11 09:12:51 2019 -0800 Fortran: add a new parallel copy routine that takes array for the number of ghost cells Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit f8b6e68f3c0926818f3dc19d744fd0d942167f23 Merge: 3b043e2f0 33c2f5ba7 Author: WeiqunZhang Date: Mon Nov 11 08:37:45 2019 -0800 Merge pull request #617 from AMReX-Codes/update_default_cuda_arch Update the default CUDA architecture to cc70 (Volta V100) commit 3b043e2f046ae7a14c65609e713e4388864c34dd Author: Max Katz Date: Sun Nov 10 21:36:03 2019 -0800 ifdef out CPU boundary fill functions for device-only pragma build Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Src/Base/AMReX_filcc_mod.F90 Src/Base/Make.package commit 000dc4a4fc9923f1630382978432ffe0da8fe007 Author: Max Katz Date: Sun Nov 10 21:28:41 2019 -0800 Define a default value for a new make variable Tools/GNUMake/Make.defs commit dec363e8debd435d0433ff0e3310a0e79185ba23 Author: Max Katz Date: Sun Nov 10 21:03:15 2019 -0800 Add a define if we're using the no-host version Tools/GNUMake/Make.defs commit e69b83ec82e7d39f217235b2b801b17f98386fe6 Author: Max Katz Date: Sun Nov 10 20:27:02 2019 -0800 Add option for GPU pragmas to generate only a device version Tools/F_scripts/gpu_fortran.py Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit d5a165a5caf09133042e2a374597a7a0caa34586 Author: Max Katz Date: Sun Nov 10 19:13:33 2019 -0800 Implement amrex_fab_filcc without amrex_get_loop_bounds Src/Base/AMReX_filcc_mod.F90 commit 6c12c4635898d0c0c1bd7b9854e0030dda13b580 Author: Weiqun Zhang Date: Sat Nov 9 16:50:32 2019 -0800 add IntVect ghost cells version of some MultiFab functions including Saxpy Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit eee7c23bd787baeb9a1e694b2bca0e56b75cefec Author: Weiqun Zhang Date: Sat Nov 9 07:25:00 2019 -0800 Node solver: remove some LaunchSafeGuards Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 33c2f5ba71986f98560ea1fd303082bad021b0d5 Author: Max Katz Date: Sat Nov 9 10:03:10 2019 -0500 Update the default CUDA architecture to cc70 (Volta V100) Tools/GNUMake/Make.defs commit a3d1d251280e6af9166ab69275582ca416637e1a Merge: 588acf6c3 24a241195 Author: Weiqun Zhang Date: Fri Nov 8 18:41:57 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 588acf6c30cbf2493733855bcc2d7fd1cab188b0 Author: Weiqun Zhang Date: Fri Nov 8 18:41:45 2019 -0800 fix unused variables Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit c2e6bb8fa46933e4d41493bddeaf8cf26353f04b Author: Weiqun Zhang Date: Fri Nov 8 16:21:40 2019 -0800 nodal eb on gpu: 2d intergral Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 79feacd34e1cee491707ca0c23db89549ff59230 Merge: b2a130904 24a241195 Author: Andrew Myers Date: Fri Nov 8 19:17:06 2019 -0500 Merge branch 'development' into runtime_soa commit 24a24119549449df8ccc2006a22fc313d5964585 Author: Andrew Myers Date: Fri Nov 8 19:16:44 2019 -0500 remove this execution policy for now Src/Base/AMReX_CudaContainers.H commit b2a130904ff346d5f9b8a457d2671a76cace019d Merge: 5b4f12ec5 e046b8380 Author: Andrew Myers Date: Fri Nov 8 19:05:35 2019 -0500 Merge branch 'development' into runtime_soa commit 5b4f12ec5ccf9d56883bb72f66abf793d4dc180b Author: Andrew Myers Date: Fri Nov 8 19:05:00 2019 -0500 add some AMREX_RESTRICT Src/Particle/AMReX_ParticleTile.H commit 60453081737ecb90e2802a531291eb169c900383 Author: Andrew Myers Date: Fri Nov 8 18:51:44 2019 -0500 need to include these changes to ParticleTile as well Src/Particle/AMReX_ParticleTile.H commit 8b7b612b2650c9fd4607b15ce135e82b94108f9a Author: Andrew Myers Date: Fri Nov 8 18:50:48 2019 -0500 account for optional components in RedistributeGPU Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_Particles.H commit 91edde8c1f6c9d754bb1a477be0226fe75379f4a Author: Weiqun Zhang Date: Fri Nov 8 15:32:38 2019 -0800 eb nodal on gpu: rhcc Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 8f981aa1bd11babb736e2d4d875cb194ed52c919 Author: Weiqun Zhang Date: Fri Nov 8 15:02:31 2019 -0800 fix new bug in eb nodal Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H commit 12e9b802da07d511642273dbb8053384973f8681 Author: cgilet Date: Fri Nov 8 18:09:12 2019 -0500 For MLEBTensorOp::compFlux, fix cut cell flux bogus value for 2D Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H commit 77e91467656bfd887275aec4b7e199a8560d2cfb Author: cgilet Date: Fri Nov 8 18:05:47 2019 -0500 Fix MLEBTensorOp::compFlux Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit a1517373fe8e763fcb09624f19c23e624d378d0a Author: Weiqun Zhang Date: Fri Nov 8 14:57:33 2019 -0800 eb nodal on gpu: mknewu Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 57204eceac9daf994fc9bf26a6d8658828c35260 Author: Weiqun Zhang Date: Fri Nov 8 13:49:02 2019 -0800 eb nodal on gpu: divu Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit f5abe8f92709931bebe2be94b7dc8427176dd351 Author: Kevin Gott Date: Fri Nov 8 13:37:59 2019 -0800 Additional cleanup. Src/Base/AMReX_GpuLaunchMacrosG.H Src/Base/AMReX_Random.cpp Src/Base/AMReX_iMultiFab.cpp commit 47a21c7119422f9b68857bf405aeb8a40f12b36a Author: Kevin Gott Date: Fri Nov 8 13:37:19 2019 -0800 Clean up tests. Tests/GPU/RandomNumberGeneration/GNUmakefile Tests/GPU/RandomNumberGeneration/main.cpp Tutorials/GPU/ParallelReduce/main.cpp commit 59e3e09d668846f74b42a582577e0928b8a2e333 Author: Kevin Gott Date: Fri Nov 8 13:12:45 2019 -0800 Remove unneeded ifdef. Src/Base/AMReX_CudaAllocators.H commit 8585b7355f94155ec5a55a0d11bc7e258b6502fb Merge: c2cd069f6 e046b8380 Author: Kevin Gott Date: Fri Nov 8 13:08:42 2019 -0800 Merge branch 'development' into kngott/hip commit e046b8380fb224d2c1907a298631268d34d24220 Author: Andrew Myers Date: Fri Nov 8 13:08:54 2019 -0800 remove unused CudaManagedAllocator Src/Base/AMReX_CudaAllocators.H commit 831c5eb261e5854d1b1aef6a7dc88e0d861ba788 Author: Weiqun Zhang Date: Fri Nov 8 13:08:19 2019 -0800 eb nodal on gpu: set stencil Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit c2cd069f62760f2a21ebe6e56785692c17801079 Author: Kevin Gott Date: Fri Nov 8 12:59:36 2019 -0800 Turn ThrustAllocator on for HIP. Src/Base/AMReX_CudaAllocators.H commit c1d779f6b35dc37e028e7130b206957479cf8a3c Merge: 65d2e75df 0724655c7 Author: Andrew Myers Date: Fri Nov 8 12:51:23 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 65d2e75df238d70d3c5bdcddc17c71df2b216c03 Author: Andrew Myers Date: Fri Nov 8 12:51:09 2019 -0800 remove unused functors Src/Particle/AMReX_Functors.H commit a53d13e27d64b661537337acb9cb282db5cf9cf4 Author: Andrew Myers Date: Fri Nov 8 12:47:14 2019 -0800 be explicit about thrust::device execution policy Src/Base/AMReX_CudaContainers.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Tutorials/GPU/ParallelReduce/main.cpp commit 5095c1d31d413c362a6aac8af94d36389caca1a5 Author: Weiqun Zhang Date: Fri Nov 8 11:35:52 2019 -0800 eb nodal on gpu: set_connection Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit d9700f8f34345589319a0e4f0e8dcb2f53e7bb8b Merge: 36db7483c 0724655c7 Author: Kevin Gott Date: Fri Nov 8 11:33:25 2019 -0800 Merge branch 'development' into kngott/hip commit eecd2e9249a25f51545220abfa801caa09c5c4a9 Merge: f8a77ae6b d16ea0b40 Author: cgilet Date: Fri Nov 8 13:40:08 2019 -0500 Merge branch 'ebtensor_flux' of https://github.com/AMReX-Codes/amrex into ebtensor_flux commit f8a77ae6b78187947ae1181d4f5345de8ffc1032 Merge: 080e7e5bb 0724655c7 Author: cgilet Date: Fri Nov 8 13:34:27 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 0724655c79ad654d9854b6c1b08d464fe8e2c454 Author: Weiqun Zhang Date: Fri Nov 8 09:55:34 2019 -0800 remove deprecated Fortran functions Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H commit 36d7010244cd11cba58de6f5ae56cc387d368a59 Merge: e84230eee a1028667d Author: Weiqun Zhang Date: Fri Nov 8 09:50:00 2019 -0800 Merge branch 'development' into weiqun/dev commit e84230eeef9db0984f2746998868b918f8948942 Author: Weiqun Zhang Date: Thu Nov 7 13:48:27 2019 -0800 mlndlap_stencil_rap on gpu Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit ff77ff5c018d9705d0fb7da1737819a067a49147 Author: Weiqun Zhang Date: Thu Nov 7 13:48:09 2019 -0800 add Array1D, Array2D and Array3D Src/Base/AMReX_Array.H commit a1028667d2717709365c9d4e26d3510a8e83195d Author: Max Katz Date: Thu Nov 7 16:35:17 2019 -0500 Report numerical CUDA error Src/Base/AMReX_GpuError.H commit 37dfb6a61677b5b23c3e89ac0b44eb3ecfd3ecc9 Merge: 63afc1a8c 84bfe1c88 Author: Andrew Myers Date: Thu Nov 7 11:56:02 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 63afc1a8c5d7c1c1ed7d27aa93397d4535440ee7 Author: Andrew Myers Date: Thu Nov 7 11:55:53 2019 -0800 const versions of offsetsPtr and permutationPtr Src/Particle/AMReX_DenseBins.H commit d16ea0b402a908f7ab001338d2b0e1b8e0573e08 Author: Michele Rosso Date: Thu Nov 7 11:35:15 2019 -0800 MacProjector: allow to set BCs on a per-level basis Src/LinearSolvers/Projections/AMReX_MacProjector.H Src/LinearSolvers/Projections/AMReX_MacProjector.cpp commit f33f9fb2212ce1dc199af852f03fae680cf45595 Author: Michele Rosso Date: Wed Nov 6 15:51:17 2019 -0800 NodalProjector: fix bug in definition of nodal grids Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 84bfe1c882cde213b36edbd5e6a1562bb29b6d61 Merge: 0f4e414c2 22e72d8d2 Author: Michele Rosso Date: Thu Nov 7 11:35:21 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 0f4e414c2acf523956e623163b7cf76b9d02e969 Author: Michele Rosso Date: Thu Nov 7 11:35:15 2019 -0800 MacProjector: allow to set BCs on a per-level basis Src/LinearSolvers/Projections/AMReX_MacProjector.H Src/LinearSolvers/Projections/AMReX_MacProjector.cpp commit 22e72d8d23022abacbcf5606afcd6ae3d505588c Merge: c0f04cd80 56f12b305 Author: Andrew Myers Date: Wed Nov 6 16:46:26 2019 -0800 Merge pull request #614 from AMReX-Codes/dense_bins Expose "dense bins" data structure so that WarpX can use it to implement binary collisions commit 56f12b30596a039854e08551f2a84380542aec42 Author: Andrew Myers Date: Wed Nov 6 16:40:33 2019 -0800 add an extra entry to counts to avoid having +1/-1 below Src/Particle/AMReX_DenseBins.H commit 79af7510b2c1baa000de1005fa82304528eb72ba Author: Andrew Myers Date: Wed Nov 6 15:58:42 2019 -0800 streamSynchronize at the end of DenseBins Src/Particle/AMReX_DenseBins.H commit f0025a27571e08bcafa5bd6901f341f80043988f Author: Andrew Myers Date: Wed Nov 6 15:57:16 2019 -0800 use AMREX_D_DECL for 2D Src/Particle/AMReX_NeighborList.H commit 97bbac3f56abc4a4443e8b6d1a6ea08084015e46 Author: Andrew Myers Date: Wed Nov 6 15:56:12 2019 -0800 add AMReX_BLProfiler.H Src/Particle/AMReX_DenseBins.H commit fe0fc251bddd419edfa8448263eda3e9d7dee94c Author: Andrew Myers Date: Wed Nov 6 15:55:12 2019 -0800 make these types public Src/Particle/AMReX_DenseBins.H commit 6ade6cba596dca28cdc9d796cf3ed1559bee378d Author: Andrew Myers Date: Wed Nov 6 15:54:44 2019 -0800 fix comment Src/Particle/AMReX_DenseBins.H commit 2e21fc9c661ca35d0e7522df033b415dbdf820ff Merge: 61dcbaa80 c0f04cd80 Author: Andrew Myers Date: Wed Nov 6 15:54:03 2019 -0800 Merge branch 'development' into dense_bins commit c0f04cd8026cb9a8b8005dad538603c01dbf445c Author: Michele Rosso Date: Wed Nov 6 15:51:17 2019 -0800 NodalProjector: fix bug in definition of nodal grids Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit b3f61ed7e39fc4804797f368aa6375bfa067ec7f Merge: 2f3c50d35 c0f04cd80 Author: Andrew Myers Date: Wed Nov 6 18:49:53 2019 -0500 Merge branch 'development' into runtime_soa commit 8711a19dd19900d3dd995f8135540745bc1d31ef Merge: 6ef9a077f 35f5533c9 Author: Weiqun Zhang Date: Wed Nov 6 15:40:08 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6ef9a077f1e8d9ef9b5900552a30ec1a943f42d1 Author: Weiqun Zhang Date: Wed Nov 6 15:00:00 2019 -0800 MLNodeTensorLap tutorial: use cg and increase bottom max iters Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp Tutorials/LinearSolvers/NodeTensorLap/MyTest.cpp commit 36db7483c79126aade748ace7d1dc80f0a0742dc Merge: 325280b0f 35f5533c9 Author: Kevin Gott Date: Wed Nov 6 14:30:12 2019 -0800 Merge branch 'development' into kngott/hip commit 325280b0f8f6e29ee9bfa21f6b00ea2a2be2a886 Author: Kevin Gott Date: Wed Nov 6 14:29:49 2019 -0800 Add rocprim and rocthrust header-only libraries. Tools/GNUMake/comps/hip.mak commit e2170b2631f83b17325fa3e10800c37de840d7a3 Merge: 01aa57f00 af86a6307 Author: Kevin Gott Date: Wed Nov 6 14:29:01 2019 -0800 Merge branch 'development' into kngott/hip commit 35f5533c99716234b7dfd7dcb1e173f8ab4556ff Merge: a2591763e d59b7720c Author: Andrew Myers Date: Wed Nov 6 16:16:00 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a2591763e7737e451fb5baa84fc17ca52250c5f6 Author: Andrew Myers Date: Wed Nov 6 16:15:35 2019 -0500 add missing device synchronize after packing buffer but before copying to pinned memory. Src/Particle/AMReX_ParticleContainerI.H commit d59b7720c0bebf4e387ddfe84cc70f7a3050a56e Merge: 85c29e209 9b91f4656 Author: Weiqun Zhang Date: Wed Nov 6 10:58:35 2019 -0800 Merge branch 'nodal_tensor_poisson' into development commit 9b91f4656962489d0fc12bf4755bd101d182a76a Author: Weiqun Zhang Date: Tue Nov 5 16:14:42 2019 -0800 MLNodeTensorLaplacian: hypre Src/Extern/HYPRE/AMReX_HypreNodeLap.H Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp Tutorials/LinearSolvers/NodeTensorLap/GNUmakefile Tutorials/LinearSolvers/NodeTensorLap/MyTest.H Tutorials/LinearSolvers/NodeTensorLap/MyTest.cpp commit 080e7e5bb934dadada13965eb1ec9ab289de4676 Merge: 64a0e43ec 85c29e209 Author: cgilet Date: Wed Nov 6 12:03:05 2019 -0500 Merge remote-tracking branch 'origin/development' into ebtensor_flux commit 85c29e20975c15d2aa8deeb7a054f7cee24b7a84 Author: Ann Almgren Date: Tue Nov 5 15:40:45 2019 -0800 fix oops Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 801eae4f835a61dbe7619d65eb23e6073f746082 Author: Ann Almgren Date: Tue Nov 5 15:33:44 2019 -0800 Need to call normalize on the tilebox not the full box.Z Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 61dcbaa8079e9d67320835979be9f4a3567a824f Author: Andrew Myers Date: Tue Nov 5 15:30:57 2019 -0800 Revert "start to implement particle locator in terms of DenseBins" This reverts commit 88667acc9ef08bb94b8aa9a041dc67e0cabd475d. Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_ParticleLocator.H commit 1a8f0c42c6ba355efcf9c30b4a9b5337c650985a Author: Andrew Myers Date: Tue Nov 5 14:59:39 2019 -0800 make sure we re-calculate the comm_size when enableInverse is toggled Src/Particle/AMReX_NeighborParticles.H commit 88667acc9ef08bb94b8aa9a041dc67e0cabd475d Author: Andrew Myers Date: Tue Nov 5 14:26:11 2019 -0800 start to implement particle locator in terms of DenseBins Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_ParticleLocator.H commit 5879144b515a9d92f091b95fbfc40993d84471a8 Author: Andrew Myers Date: Tue Nov 5 13:49:19 2019 -0800 expose dense bins data structure so it can be used to implement binary collisions in WarpX Src/Particle/AMReX_DenseBins.H Src/Particle/AMReX_NeighborList.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit a5de669544c962d54ed0804965e2823885b21f2c Author: Weiqun Zhang Date: Tue Nov 5 13:35:56 2019 -0800 tutorial for Nodal Tenosr Laplacian solver Tutorials/LinearSolvers/NodeTensorLap/GNUmakefile Tutorials/LinearSolvers/NodeTensorLap/Make.package Tutorials/LinearSolvers/NodeTensorLap/MyTest.H Tutorials/LinearSolvers/NodeTensorLap/MyTest.cpp Tutorials/LinearSolvers/NodeTensorLap/MyTestPlotfile.cpp Tutorials/LinearSolvers/NodeTensorLap/main.cpp commit b684d4d6f8a70ccb7f558ea70c9cc27103dd3958 Author: Weiqun Zhang Date: Tue Nov 5 13:02:49 2019 -0800 MLNodeTensorLaplacian: 3d Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H commit 2f3c50d35e68a49dd0506ecfa304a644b7249800 Author: Andrew Myers Date: Tue Nov 5 14:20:28 2019 -0500 add some runtime components to the redistribute tests Tests/Particles/Redistribute/inputs.rt.cuda Tests/Particles/Redistribute/inputs.rt.cuda.mr Tests/Particles/Redistribute/inputs.rt.cuda.nonperiodic commit 589cc7d2d0837c20d9cb5db21647b810b57548a8 Author: Andrew Myers Date: Tue Nov 5 14:13:56 2019 -0500 also update the type of the snd/rcv buffers in neighbor particles Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit c2205e7fd5804a0665de4c9edfe4b902fe376ccb Author: Andrew Myers Date: Tue Nov 5 14:03:30 2019 -0500 restore get/set superparticle, which is used in the reductions Src/Particle/AMReX_ParticleTile.H commit 9936f1a678620837a409e0263082f056faf9a2e5 Merge: 61abca22f b15c2e110 Author: WeiqunZhang Date: Tue Nov 5 10:52:19 2019 -0800 Merge pull request #613 from dpgrote/fix_xlinker Mini PR: Fix XLinker option to allow spaces in directory names commit ab8b5f9cefa31bccba06b10940787f3220ac7ea7 Author: Andrew Myers Date: Tue Nov 5 13:40:45 2019 -0500 add runtime components setting in the inputs files Tests/Particles/Redistribute/inputs.rt Tests/Particles/Redistribute/inputs.rt.cuda Tests/Particles/Redistribute/inputs.rt.cuda.mr Tests/Particles/Redistribute/inputs.rt.cuda.nonperiodic commit 832c843e0b7d2f1bb0318b0ade08c3c499d18703 Author: Houjun Tang Date: Mon Nov 4 15:55:04 2019 -0800 Change the HDF5 benchmark to use the new HDF5 write plot file implementation, fix a memory access issue for 1 level data. Src/Base/AMReX_PlotFileUtil.cpp Tests/HDF5Benchmark/GNUmakefile Tests/HDF5Benchmark/Make.package Tests/HDF5Benchmark/WritePlotfileHDF5.H Tests/HDF5Benchmark/WritePlotfileHDF5.cpp Tests/HDF5Benchmark/main.cpp commit 3998472ef2fa64ae60e69fd1e7cd9c347eff54d0 Author: Andrew Myers Date: Mon Nov 4 16:18:29 2019 -0500 make the runtime comps 0 by default Tests/Particles/Redistribute/inputs commit 475bea54f00df2059cd9f78bc58d3ccd1513fb1b Author: Andrew Myers Date: Mon Nov 4 16:17:40 2019 -0500 parmparse the runtime components Tests/Particles/Redistribute/inputs Tests/Particles/Redistribute/main.cpp commit 27d7bf753b59351528f4d1177c663a04d29fc984 Author: Andrew Myers Date: Mon Nov 4 16:09:34 2019 -0500 setup redistribute test to use runtime components Tests/Particles/Redistribute/main.cpp commit 49b528d030aad0b12ab6e97bdea089d5a27cb410 Author: Andrew Myers Date: Mon Nov 4 16:07:54 2019 -0500 set up particle tile data with runtime information on the fly Src/Particle/AMReX_ParticleTile.H commit a102297082382fc3ac892c8e6be1f8cb1c026b5f Author: Andrew Myers Date: Mon Nov 4 16:07:28 2019 -0500 use ptile for temp storage in partition Src/Particle/AMReX_ParticleContainerI.H commit 6f809949092e5ba95c7a5f19e32a08765cc69c0b Author: Andrew Myers Date: Mon Nov 4 16:05:57 2019 -0500 also define and return in the local unpack Src/Particle/AMReX_ParticleCommunication.H commit e86a3873a52c0251264bb2e3696524bce67fcdda Author: Andrew Myers Date: Mon Nov 4 16:04:31 2019 -0500 make sure we set up the runtime components in the non-local unpack Src/Particle/AMReX_ParticleCommunication.H commit 61abca22fe057a2f5110fd79368557d61becbfa5 Author: Ann Almgren Date: Mon Nov 4 12:52:22 2019 -0800 If we leave in the Gpuable line, the garuda compiler complains (error) when DEBUG=TRUE Src/EB/AMReX_EB2_IF_Polynomial.H commit d0ac3e47072ca46ea1764fd45c15a2e2ac6d2ada Author: Andrew Myers Date: Mon Nov 4 15:41:00 2019 -0500 formatting fix Src/Particle/AMReX_StructOfArrays.H commit f0737616f8d4540e720224458ea8ac9b33ef5c8c Author: Weiqun Zhang Date: Mon Nov 4 11:00:55 2019 -0800 MLNodeTensorLaplacian: set sigma Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp commit a689647040c434b23700ff2d64807d64a7ca1231 Author: Weiqun Zhang Date: Mon Nov 4 10:48:56 2019 -0800 MLNodeTensorLaplacian: 2d normalize Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp commit 80ed13a70033116361b7ce5a66b6e9bd3fd17364 Author: Weiqun Zhang Date: Mon Nov 4 10:41:08 2019 -0800 MLNodeTensorLaplacian: 2d Gauss Seidel Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp commit 30ddb556ac47bb9080ac78f3d64c85c21a96228f Author: Weiqun Zhang Date: Mon Nov 4 10:31:13 2019 -0800 MLNodeTensorLaplacian: 2d A dot x Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp commit b15c2e110d7aa2d41368ee58bdc972c9f58dc88b Author: Dave Grote Date: Mon Nov 4 10:13:48 2019 -0800 Fix XLinker option to allow spaces in direector names Tools/GNUMake/Make.defs commit 3716dd293e01f7b0ff8d25f81693f2092efdb4ff Author: Weiqun Zhang Date: Mon Nov 4 08:52:55 2019 -0800 MLNodeTensorLaplacian: move applyBC to MLNodeLinOp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 45f4644bbdb0eb9c91debe78ea51035a7bd071e7 Author: Weiqun Zhang Date: Fri Nov 1 16:00:42 2019 -0700 MLNodeTensorLaplacian: WIP Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp Src/LinearSolvers/MLMG/Make.package commit 64a0e43ec76cd796b65bfe856fe5d032ec13126d Merge: ed865e19a de6ca75a4 Author: cgilet Date: Mon Nov 4 10:39:17 2019 -0500 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit de6ca75a4115f428006aba7e62b99fc42c6ee882 Merge: 93fb085d2 b562730d1 Author: WeiqunZhang Date: Fri Nov 1 14:08:57 2019 -0700 Merge pull request #612 from AMReX-Codes/prefixsum-tutorial In PrefixSum tutorial, update exclusive sum using sorted grid IDs. commit b562730d1e0a1b9cfa8a289a6e0e9e1a3d525dad Author: Donald E. Willcox Date: Fri Nov 1 14:00:10 2019 -0700 In PrefixSum tutorial, update exclusive sum using the previous sorted grid ID. Test with different values in each cell. Tutorials/Basic/PrefixSum_MultiFab/Parallel-Prefix-Sum.ipynb Tutorials/Basic/PrefixSum_MultiFab/main.cpp commit 92e4eba0b8873340bb925781d4c1558554ad0677 Author: Weiqun Zhang Date: Mon Oct 21 16:15:42 2019 -0700 skeleton of MLNodeTensorLaplacian Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeTensorLaplacian.cpp Src/LinearSolvers/MLMG/Make.package commit da2352d3efd432bb9bd0e5638eaf8d884eee89ee Author: Andrew Myers Date: Fri Nov 1 14:20:51 2019 -0400 make this member protected Src/Particle/AMReX_Particles.H commit 2a1ceb0f8cf51cf876d2978e1330e1d1512881e6 Author: Andrew Myers Date: Fri Nov 1 13:38:57 2019 -0400 remove setStream call included by mistake Src/Particle/AMReX_ParticleCommunication.H commit 0eace2c37669e8a532b0ab1255cf597ce456afe7 Author: Andrew Myers Date: Fri Nov 1 13:37:42 2019 -0400 include the runtime components in the initial partition Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 93fb085d28349cab33892726dfa3107a85a7719e Author: Weiqun Zhang Date: Fri Nov 1 07:54:09 2019 -0700 update CHANGES CHANGES commit 23f943f3b542771626be01815e85264ef11a7562 Author: Weiqun Zhang Date: Thu Oct 31 20:30:15 2019 -0700 AmrCore::regrid: return if the base level is already the max level. Src/AmrCore/AMReX_AmrCore.cpp commit 0a548e2d55b37a2975e9978af37a35c157a518f2 Author: Andrew Myers Date: Thu Oct 31 19:51:06 2019 -0400 fix cpu compilation Src/Particle/AMReX_ParticleTile.H commit 8a16ff0bdf3580f5c2d143097b332d36c3787b91 Author: Andrew Myers Date: Thu Oct 31 19:43:04 2019 -0400 make the snd / rcv buffers char Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_Particles.H commit 1bed794443769d2e9671cefc8185e1c9f8f0c195 Author: Michele Rosso Date: Thu Oct 31 15:37:30 2019 -0700 NodalProjector: remove unused member variable Src/LinearSolvers/Projections/AMReX_NodalProjector.H commit 01aa57f00e248731e81499f64209de60337201c5 Author: Kevin Gott Date: Thu Oct 31 15:19:23 2019 -0700 Add libraries. cuRand and hipRand working! Src/Base/AMReX_Random.cpp commit 8eb40c72a12e2c9b34cca1e074adbf1080f1c48d Author: Kevin Gott Date: Thu Oct 31 15:17:03 2019 -0700 More noexcepts. Src/Base/AMReX_BaseFabUtility.H commit 131013be420e421eff7368e22366bb4fad1b69c2 Author: Kevin Gott Date: Thu Oct 31 15:16:42 2019 -0700 Another failed initialization list. Good reproducer option? Src/Base/AMReX_BaseFab.H commit 6b0e5635ae0bf426e86a2940d9d34a7360541aeb Author: Kevin Gott Date: Thu Oct 31 17:55:45 2019 -0400 Generalize HIP path names. Tools/GNUMake/comps/hip.mak commit 0eb3b9fe7379d374a9d395a94689587591ea8c7e Author: Kevin Gott Date: Thu Oct 31 17:49:33 2019 -0400 Features needed for HIPrand run on CUDA. Need to test on dogora. Src/Base/AMReX.cpp Src/Base/AMReX_Random.cpp Tests/GPU/RandomNumberGeneration/main.cpp commit af86a630721e70e7c6fc15261625ded9e718cc74 Author: Michele Rosso Date: Thu Oct 31 14:14:05 2019 -0700 NodalProjector: add option to pass LPInfo to constructor Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit f8d866799704b727ceaf0c11d1ba2b568bc0b330 Merge: dcebc687d f4a35c104 Author: Kevin Gott Date: Thu Oct 31 14:55:47 2019 -0400 Merge branch 'development' into kngott/hip Conflicts: Src/Base/AMReX_BaseFab.H commit f4a35c104a845d7899cd415faf8b63b0c8e01f5f Author: Michele Rosso Date: Wed Oct 30 12:46:51 2019 -0700 NodalProjector: fix bug introduced with 2D support Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 2a68633c0bd443add5f161c923f68eb97b810598 Merge: 98ceb9fe8 a8be3e547 Author: WeiqunZhang Date: Wed Oct 30 10:48:02 2019 -0700 Merge pull request #607 from AMReX-Codes/mf-prefix-sum Add MultiFab parallel prefix sum tutorial example. commit 98ceb9fe82fb48ea2984bdaf977d83dd448d068f Author: MaxThevenet Date: Wed Oct 30 10:34:39 2019 -0700 Add one version of FillBoundary (#609) * FabArray::FillBoundary takes argument nghost, with default loop on comps * typo Src/Base/AMReX_FabArray.H commit 1a72e71f424d6048c018c03153ad5cb983b3b177 Author: Weiqun Zhang Date: Wed Oct 30 09:27:35 2019 -0700 add EBFArrayBoxFactory::isAllRegular Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp commit ed865e19a7fd916a967ace1e1b3bc6c5ecf9f720 Merge: cda80bddd 460f09ded Author: cgilet Date: Wed Oct 30 10:32:23 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit 460f09ded8f092991391f695e28029f7f69f103f Author: Max Katz Date: Wed Oct 30 02:23:12 2019 -0400 Set OpenACC stream to be the same as the CUDA stream Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_acc_mod.F90 commit e29f50788131ddedd1902a55aa7b7f86205e68bb Author: Max Katz Date: Wed Oct 30 02:22:46 2019 -0400 For OpenACC where CCOMP is not pgc++, still include openacc.h Tools/GNUMake/comps/pgi.mak commit f85e6b74ceb81b3aab645a5cdfe6cda6ec632e8a Author: Weiqun Zhang Date: Tue Oct 29 20:17:49 2019 -0700 fix a typo Src/Base/AMReX_FabArrayUtility.H commit c2de4f065e7b9f7800d7be42df43d2202fe1c0df Merge: e28acba15 1f3a7218e Author: WeiqunZhang Date: Tue Oct 29 15:22:18 2019 -0700 Merge pull request #610 from michaeljbrazell/mjb/reducesum_bug small bug fix for a three MultiFab ReduceSum commit e28acba15a29bb53d24bd51d0a22fb209c741f7c Author: Weiqun Zhang Date: Tue Oct 29 15:15:23 2019 -0700 remove stray #define thanks to Christoph Behrens Src/Base/AMReX_REAL.H commit 1f3a7218ead8eaf20d976d6f865b4b55b0e0cf62 Author: michael brazell Date: Tue Oct 29 15:11:52 2019 -0700 small bug fix for a three MultiFab ReduceSum Src/Base/AMReX_FabArrayUtility.H commit 8d41fd1464bdad85e5906515f2819d0a488dff76 Author: Max Katz Date: Tue Oct 29 17:23:19 2019 -0400 Add peak at OLCF Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.olcf commit 2aa98d63215411f8c79a1c02658c9a40c3e9781f Author: Michele Rosso Date: Mon Oct 28 18:06:00 2019 -0700 NodalProjector: print diagnostics only if verbosity is enabled Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit e5a6a30a20bc0ec8767b2083875b2331fb7f65e6 Author: Michele Rosso Date: Mon Oct 28 18:02:41 2019 -0700 NodalProjector: replace unique_ptr with standard pointers Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 8667a8b6afff5bf7004bb3ab8ead4609c3eeb6b9 Author: cgilet Date: Mon Oct 28 13:24:00 2019 -0400 Make NodalProjector::define 2D compatable. Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 11a827828ff1cc67b61f507483c2349a7cb73d8a Author: Max Katz Date: Mon Oct 28 09:49:21 2019 -0700 Remove debugging print Src/AmrCore/AMReX_AmrMesh.cpp commit cda80bdddd5324e87d5930f38992ed9870aa1353 Merge: fcd43fc98 78f137017 Author: cgilet Date: Mon Oct 28 09:44:42 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit 78f137017a853031a2fbbb836fe551d42aafad55 Author: Max Katz Date: Sun Oct 27 19:13:21 2019 -0700 Only include PTX output from PGI if verbose Tools/GNUMake/comps/pgi.mak commit 25038cff1c6eb479e64b2915b780ddd9578ffd63 Author: Max Katz Date: Sun Oct 27 01:12:13 2019 -0700 Revert "Only define __device__, etc. if using CUDA or HIP" This reverts commit a359ba48869801b27e93d059ce6a32b5a2432674. Src/Base/AMReX_GpuQualifiers.H commit a359ba48869801b27e93d059ce6a32b5a2432674 Author: Max Katz Date: Sun Oct 27 00:34:55 2019 -0700 Only define __device__, etc. if using CUDA or HIP Src/Base/AMReX_GpuQualifiers.H commit e5beed1deb1cef6219517165a2b1ea59ce697c61 Author: Weiqun Zhang Date: Sat Oct 26 07:08:34 2019 -0700 put NodalProjector into namespace amrex Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 13eb92adddabb2e8c8b47d4e27a02ddce0826d05 Author: Weiqun Zhang Date: Fri Oct 25 21:22:55 2019 -0700 In error message, tell people how to get around blocking_factor not power of 2 error. Src/AmrCore/AMReX_AmrMesh.cpp commit fcd43fc985a4cd33e3f7ec9b267348a0ae468fb8 Merge: b63e500c5 40b6d10b9 Author: cgilet Date: Fri Oct 25 22:10:28 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit 40b6d10b9a66b90372b34bd2722fa698ffa0d861 Author: Ann Almgren Date: Fri Oct 25 18:45:47 2019 -0700 Add documentation about: 1) blocking_factor must be power of 2 2) using n_error_buf to make larger grids. Docs/sphinx_documentation/source/GridCreation.rst Docs/sphinx_documentation/source/InputsLoadBalancing.rst commit 91041eaecd42dc53248bd32b8c8d28d1a5f72d64 Merge: 24f3d9a0f 4bfb4a49e Author: Ann Almgren Date: Fri Oct 25 18:22:19 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 24f3d9a0fe9e71e561657e5b5620965ef0a600b8 Author: Ann Almgren Date: Fri Oct 25 18:20:09 2019 -0700 Enforce in AmrCore (as in Amr) that blocking_factor must be a multiple of 2. Src/AmrCore/AMReX_AmrMesh.cpp commit dcebc687dcaa659d0b51acfdcf2f93447aa965bf Author: Kevin Gott Date: Fri Oct 25 16:56:13 2019 -0700 Go back to managed Vector. Src/Base/AMReX_CudaContainers.H commit 6ac62729324b2d29cf4eb47c34363f7eca405f84 Author: Kevin Gott Date: Fri Oct 25 16:15:38 2019 -0700 More Random Number Generator Updates Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaContainers.H Src/Base/AMReX_Random.cpp Tests/GPU/RandomNumberGeneration/main.cpp commit a8be3e547940658a05047b265f4220830c553d8c Author: Donald E. Willcox Date: Fri Oct 25 16:09:04 2019 -0700 Add MultiFab parallel prefix sum tutorial example. Tutorials/Basic/PrefixSum_MultiFab/GNUmakefile Tutorials/Basic/PrefixSum_MultiFab/Make.package Tutorials/Basic/PrefixSum_MultiFab/Parallel-Prefix-Sum.ipynb Tutorials/Basic/PrefixSum_MultiFab/README.md Tutorials/Basic/PrefixSum_MultiFab/inputs Tutorials/Basic/PrefixSum_MultiFab/main.cpp commit 4bfb4a49e450be7496868b4bffb1c9fe57aebafc Author: Michele Rosso Date: Fri Oct 25 15:35:39 2019 -0700 NodalProjector: check grid type of arguments of computeRHS Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 4962b5b0b090c6eccdd31de442aa8d6cbeff5549 Author: Kevin Gott Date: Fri Oct 25 14:31:09 2019 -0700 1st attempt: Random without MemcpyToSymbol Src/Base/AMReX_Random.cpp commit 8099e621779c9877025a3d8e74e51eb7e491c99f Merge: 3698ac187 383f172eb Author: Michele Rosso Date: Fri Oct 25 13:06:13 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 3698ac1878968a4b65c036fabccf515cc6ae5d47 Author: Michele Rosso Date: Fri Oct 25 13:06:06 2019 -0700 NodalProjector: pass arguments to compRHS in correct order Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit 383f172eb61aa68f6968b6047db1b2ea3a06163f Author: Weiqun Zhang Date: Fri Oct 25 12:40:52 2019 -0700 add AmrMesh function to return level number given domain box Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit a013cf1a8d1da9802ce835b654bb2408b1d0a34f Merge: 154108bcc b5ab12940 Author: Michele Rosso Date: Fri Oct 25 12:36:11 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 154108bcc5059909f7c8210879afce0c5b5d80b3 Author: Michele Rosso Date: Fri Oct 25 12:36:04 2019 -0700 NodalProjector: add non-EB version Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp commit b5ab1294044e8e59d757a58867ca6ada12ce01ea Merge: b18fedf93 c7eed7b74 Author: Andrew Myers Date: Fri Oct 25 12:29:56 2019 -0700 Merge pull request #606 from houjun/development Add support to write plotfile in HDF5 format commit b63e500c5f0bc5b412c07684e3b4698442c69ad9 Author: cgilet Date: Fri Oct 25 14:57:45 2019 -0400 WIP - add EBTensorOp::compFlux() with restriction that cut cell fluxes are not set to a bogus value Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit df99040e2d231b7d1363795d00907d81e04e455f Merge: 3dd9b1fbf f14e222b2 Author: cgilet Date: Fri Oct 25 14:45:36 2019 -0400 Merge branch 'TensorFluxes' of https://github.com/cgilet/amrex into TensorFluxes commit f14e222b2285759d6d54ecb1d19ce64a42a1f333 Merge: b8a007896 b18fedf93 Author: cgilet Date: Fri Oct 25 14:42:00 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit c7eed7b7422069fef81eea75e848569e5da885a0 Author: Houjun Tang Date: Fri Oct 25 09:40:29 2019 -0700 Add support to write plotfile in HDF5 format Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_PlotFileUtil.cpp commit b18fedf9394ac56b0761500a1613db78456fcba2 Author: Ann Almgren Date: Thu Oct 24 22:30:00 2019 -0700 Add NodalProjector class to amrex/Src/LinearSolvers/Projections Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/Projections/AMReX_NodalProjector.H Src/LinearSolvers/Projections/AMReX_NodalProjector.cpp Src/LinearSolvers/Projections/Make.package commit c2d00af5274b001ad7044328d7e795e7b69dadcc Author: Kevin Gott Date: Thu Oct 24 17:18:19 2019 -0700 Simplify the abort fix. Src/Base/AMReX_Machine.cpp commit a81ba79a9dff4010e2499e32ef2df9ea6ae95877 Author: Weiqun Zhang Date: Thu Oct 24 12:24:53 2019 -0700 Reduce* for FabArray can now take lambda working on Array4. bug fix and optimization in the new EB functions added to MulitFab. tidy. Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_REAL.H commit 450005e2c30acf9b8f5124a98055a2b31642eeb5 Author: Weiqun Zhang Date: Thu Oct 24 11:00:45 2019 -0700 add AMREX_REAL_MIN, AMREX_REAL_MAX and AMREX_REAL_LOWEST for convenice. Src/Base/AMReX_REAL.H commit dccb597defdbad7b6631b3807318fbbba01969b5 Author: Weiqun Zhang Date: Wed Oct 23 15:54:19 2019 -0700 rm AMREX_PRAGMA_SIMD for reduce loops Src/Base/AMReX_Reduce.H commit 3b4d3eb62cbe9385d6cb7fb1511a85e0c6eec1bf Author: Weiqun Zhang Date: Wed Oct 23 15:53:02 2019 -0700 make launch functions macros safe with empty boxes Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuLaunchMacrosG.H Src/Base/AMReX_GpuRange.H commit 6dc2bb812dd7551cb8505174bb10ee0b97599e0d Author: atmyers Date: Thu Oct 24 04:44:39 2019 -0700 make sure dummy_mf gets updated Src/Particle/AMReX_ParticleContainerI.H commit 1a23a5bebf84221093ee98f3afc5133bece8e115 Author: Kevin Gott Date: Wed Oct 23 16:45:47 2019 -0700 Fix make system and get rpath working. Tools/GNUMake/Make.defs Tools/GNUMake/comps/hip.mak commit 1200d2d30ee4888241401f6024b45adf3a03b6ae Author: Kevin Gott Date: Wed Oct 23 16:45:02 2019 -0700 More NOEXCEPTs Src/Base/AMReX_GpuLaunch.H commit 97c16aa7082dad9f7462e9641a93f17587050be5 Author: Kevin Gott Date: Wed Oct 23 16:44:50 2019 -0700 Get rid of memcpy_to_symbol. Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_Random.cpp commit 16e40e20a0cc68090864d9df8f834fce73a3367f Author: Kevin Gott Date: Wed Oct 23 16:44:26 2019 -0700 AMREX_NOEXCEPT and additional initialization lists. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Extension.H commit 8b41978d4d374453f8f82f3ce73e05bc1496e193 Author: Andrew Myers Date: Wed Oct 23 19:19:23 2019 -0400 nghsot -> nghost Src/Base/AMReX_FabArray.H commit 48448d3f22e47320ea3ffaea9bc47ac9152cf499 Merge: 0e35ea04f 58dbb83dd Author: Andrew Myers Date: Wed Oct 23 18:17:17 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0e35ea04f1c3ad0c53613095ee15cb5651c5f37f Author: Andrew Myers Date: Wed Oct 23 18:16:42 2019 -0400 add missing Gpu::Device::synchronize() to InitFromBinaryFile Src/Particle/AMReX_ParticleInit.H commit 58dbb83dde3819c47889fcc87c66e3586b65f675 Author: Weiqun Zhang Date: Wed Oct 23 14:47:09 2019 -0700 remove FabView from BaseFab Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFabUtility.H Src/Boundary/AMReX_Mask.H Src/EB/AMReX_EB2_GeometryShop.H Tests/Vectorization/kc.H Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H commit 435945dbe9a47a9747de5ec04e4d9da25c2a3ebe Merge: 059da7f8e 7a3dd93a2 Author: Andrew Myers Date: Wed Oct 23 16:13:44 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 059da7f8ec7a20366de320f032cfbca4f1ee81d0 Author: Andrew Myers Date: Wed Oct 23 16:13:23 2019 -0400 when deciding if a particle stays or not, we must also consider the case that particles have been added to the correct grids, not NOT on the correct procs Src/Particle/AMReX_ParticleBufferMap.H Src/Particle/AMReX_ParticleBufferMap.cpp Src/Particle/AMReX_ParticleContainerI.H commit 7a3dd93a268240613c281317a4ecf5528e432dc2 Author: Weiqun Zhang Date: Wed Oct 23 12:24:30 2019 -0700 fix some warnings Src/Base/AMReX_GpuLaunch.H Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tests/LinearSolvers/EBTensor/MyTest.cpp Tests/LinearSolvers/EBTensor/MyTest_K.H commit facd92610307f9941b69702f827bb7e0c78c6f3b Author: Weiqun Zhang Date: Wed Oct 23 11:19:46 2019 -0700 rm unused file Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H Src/LinearSolvers/MLMG/Make.package commit e1d732ef4e73fda2008dec5e10b2a7e870aed319 Merge: 655ecdeee 15680a2b6 Author: WeiqunZhang Date: Wed Oct 23 12:09:09 2019 -0700 Merge pull request #604 from kcdodd/development Change MPI_Frotran to MPI_Fortran commit 15680a2b648497cd2234cef58039c85425f8d8e6 Author: Carter Dodd Date: Wed Oct 23 13:44:03 2019 -0500 Change MPI_Frotran to MPI_Fortran Src/F_Interfaces/CMakeLists.txt commit 063bd4a8b252e8ef88131af425deccd6a5da806f Merge: 2496d739e 655ecdeee Author: Kevin Gott Date: Wed Oct 23 11:43:35 2019 -0700 Merge branch 'development' into kngott/hip commit 655ecdeee7aad5562b814f60883700aa289eca3b Author: Weiqun Zhang Date: Wed Oct 23 11:01:26 2019 -0700 Replace AMREX_IS_D_LAMBDA with armex::IsDeviceLambda. This will fix a template parameter deduction issue. Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_TypeTraits.H commit 065880a558609b35cf49b58eba965f3016eaad59 Author: Weiqun Zhang Date: Wed Oct 23 10:23:23 2019 -0700 missed a return Src/Base/AMReX_FabArrayUtility.H commit b14a4101f4be01aee5aecf928098afc4310a8464 Author: Max Katz Date: Wed Oct 23 07:18:56 2019 -0700 Avoid race conditions in reduction code called multiple times cuda-memcheck --tool racecheck reported race conditions in this code if we called the block reduction multiple times in a kernel, since some warps in the first reduction could be reading from shared memory at the same time as other warps in the second reduction were writing to it. By inserting a syncthreads prior to the first write to shared memory, we avoid this (at some performance cost for the cases where we only call the reduction once in a kernel). Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_fort_mod.F90 commit 3dd9b1fbf3a1382c192195989eef05bc24c0a091 Merge: b82e52a9e 569b3a879 Author: cgilet Date: Wed Oct 23 09:48:50 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit 2496d739ef8797475e9b7f7eb3bd729647e9c0c9 Author: Kevin Gott Date: Tue Oct 22 15:31:42 2019 -0700 Label std::abort() HIP FIX. Src/Base/AMReX_Machine.cpp commit 821aed502eeb91f549b526673bf1140562caac15 Author: Kevin Gott Date: Tue Oct 22 15:30:37 2019 -0700 Saving before noexcept attempt. Src/Base/AMReX_GpuQualifiers.H Tools/GNUMake/Make.defs Tools/GNUMake/comps/hip.mak commit 569b3a87942e8694988340c2aa5a9f51d511ca06 Author: Max Katz Date: Tue Oct 22 12:32:31 2019 -0400 Reorder to work around XL compiler bug Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 7b59157d0300b1a21d6e1dc50de7e1d937be0ffe Merge: 82e099981 97e1c30d2 Author: Kevin Gott Date: Tue Oct 22 09:17:45 2019 -0700 Merge branch 'development' into kngott/hip commit 97e1c30d26bc65462397cd191fb43e58ba8847f8 Author: Kevin Gott Date: Tue Oct 22 12:14:43 2019 -0400 Temporary fix for std::abort in HIP. This allows AMReX to compile with HIP on Summit. Src/Base/AMReX_Machine.cpp commit 8108b109e0bff06160f8aee072ca141a5de8d963 Author: Kevin Gott Date: Tue Oct 22 12:14:06 2019 -0400 Fix HIP error messages in cudaGraphs. Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuError.H Src/Base/AMReX_GpuQualifiers.H Tools/GNUMake/Make.defs commit 04667ad3ac2d2d965323ad53ac186cbd6e298959 Author: Kevin Gott Date: Tue Oct 22 12:10:59 2019 -0400 Update HIP calls. Src/Base/AMReX_Arena.cpp commit 01191b3556720a64908b0a4531c842270f4d00b9 Author: Ann Almgren Date: Mon Oct 21 18:14:31 2019 -0700 Fix redistribute so it doesn't assume we start at component 0. Src/EB/AMReX_EB_utils.cpp commit 70189babbc3e668b2ca09b5f8f20b7d06eacec0a Author: Ann Almgren Date: Mon Oct 21 17:29:40 2019 -0700 Fix compilation of AMReX_EB_utils.cpp in 2D. Src/EB/AMReX_EB_utils.H Src/EB/AMReX_EB_utils.cpp commit 780b8e79fec0d66be89e8a16238177324fc7264a Merge: 2a2d76985 efc6cb73a Author: Ann Almgren Date: Mon Oct 21 16:18:29 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 2a2d76985979869be641189a1ca629b1fe1b0914 Author: Ann Almgren Date: Mon Oct 21 16:18:16 2019 -0700 Oops -- accidentally committed the un-weighted version. Src/EB/AMReX_EB_utils.cpp commit efc6cb73a87c8298380ef856a6c21b694fb50b48 Author: Weiqun Zhang Date: Mon Oct 21 16:17:06 2019 -0700 BaseFab::linComb missed default template parameter Src/Base/AMReX_BaseFab.H commit 3cf553a4111390195ed0cf779adb8f79eda4a01b Merge: bb3879709 a4c8bb310 Author: Ann Almgren Date: Mon Oct 21 15:43:20 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit bb38797090ef04648b84f3edb8a61edecec5c311 Author: Ann Almgren Date: Mon Oct 21 15:43:02 2019 -0700 Move single-level redistribution code from incflo to amrex/Src/EB. Src/EB/AMReX_EB_utils.H Src/EB/AMReX_EB_utils.cpp commit 82e09998140a6bd263b967e3ae1763f92d8d88e9 Merge: 8d37d1371 a4c8bb310 Author: Kevin Gott Date: Mon Oct 21 12:09:25 2019 -0700 qMerge branch 'development' into kngott/hip commit 8d37d13719cfc269a864923a7df08dd87cb4196e Merge: 047bdcadf e70f2ce38 Author: Kevin Gott Date: Mon Oct 21 12:08:50 2019 -0700 Merge branch 'development' into kngott/hip commit a4c8bb3105e27cbafc157444f1053a8ac7d9ec2a Author: Weiqun Zhang Date: Mon Oct 21 10:01:55 2019 -0700 InterpBndryData: make sure index is within bound for 2d refratio=4 case Src/Boundary/AMReX_InterpBndryData_2D_K.H commit b82e52a9e96aa909e564f95928c1980422dfc9ad Merge: e847d1bcb f30313027 Author: cgilet Date: Mon Oct 21 10:59:48 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit e847d1bcb024841711328ef7f2ad0621e854f985 Merge: 216d9d177 e1cc614cb Author: cgilet Date: Mon Oct 21 10:56:53 2019 -0400 Merge branch 'development' into TensorFluxes commit f3031302726fbdfcd9134023fc8edfe6837a4d3a Author: Weiqun Zhang Date: Sun Oct 20 18:31:08 2019 -0700 add std:: Src/AmrCore/AMReX_Cluster.cpp Src/Base/AMReX_RealBox.H Tools/C_util/Statistics/ComputeAmrDataStat.cpp commit 358ef0a8db2f804eb047e9e0899c45a40d1034a0 Merge: 479026e2f 9eb0bbb36 Author: Weiqun Zhang Date: Sun Oct 20 17:17:23 2019 -0700 Merge branch 'fix_tensor_corner' into development commit 9eb0bbb367b356f3b597396d469304c556265405 Author: Weiqun Zhang Date: Sun Oct 20 15:38:11 2019 -0700 Merge branch 'development' into fix_tensor_corner Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_Derive.H Src/Amr/AMReX_Derive.cpp Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_ParmParse.cpp Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_EB2_3D_C.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_Particles.H Tutorials/Basic/HelloWorld_C/main.cpp commit 479026e2fefc8a83e4141b0dd318b13167e1abd0 Author: Weiqun Zhang Date: Sun Oct 20 15:24:55 2019 -0700 make set_eb_data gpu host device function Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_C.H commit 81e232b808e9377351a2a8262012966cbc453304 Author: Weiqun Zhang Date: Sun Oct 20 15:13:47 2019 -0700 MLMG tensor: cleanup Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 9cf94b2ee2e6636415a64a3ff2216c901e2ac667 Author: Weiqun Zhang Date: Sun Oct 20 14:19:49 2019 -0700 MLMG: fill corners for 3d tensor Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit a3b9fd304b18982f3cf79c0ad16b6fdddb41e775 Author: Weiqun Zhang Date: Sun Oct 20 12:09:56 2019 -0700 MLMG: fill edges for 3d tensor Src/Boundary/AMReX_InterpBndryData_1D_K.H Src/Boundary/AMReX_InterpBndryData_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit bf54daf1e8ad240b080794343e06691db7a83f90 Author: Ann Almgren Date: Sat Oct 19 19:49:30 2019 -0700 We had "abs" rather than "std::abs" in two lines in one of the RAP interpolation routines -- turns out that plain abs turns 5.1 into 5 and 0.51 into 0 ... not what was intended! Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H commit 71f1046c4eb9024d92f28aa8609d0a8f5937d75f Author: Ann Almgren Date: Sat Oct 19 15:18:14 2019 -0700 When we set cells to covered because vfrac < small_volfrac, we must also make sure that any originally Regular cells touching them get relabeled to SingleValued and their EB-related data must be set correctly. Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_C.H commit 34d5fe1690acb406a2264fa3effb49d7416d481d Merge: b1257ac69 aaa370f67 Author: Emmanuel Motheau Date: Fri Oct 18 15:24:31 2019 -0700 Merge pull request #600 from AMReX-Codes/feature_nd_Pele Feature nd pele/IAMR commit be9f7c769b2d8cfa2d5f301395c1efd50e534bdb Author: Weiqun Zhang Date: Fri Oct 18 14:37:29 2019 -0700 WIP: MLMGBndry/InterpBndry in 2d fills corners too Src/Amr/AMReX_AmrLevel.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_InterpBndryData_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H commit b1257ac698f1ebfa1c66e0bbd5eea1ccb36717b2 Merge: e70f2ce38 eb5dc2c38 Author: WeiqunZhang Date: Fri Oct 18 10:11:46 2019 -0700 Merge pull request #601 from AMReX-Codes/abort_on_unused_inputs Abort on unused inputs commit eb5dc2c38f757bc9bfd4c03dace14ab971681408 Author: Andrew Myers Date: Fri Oct 18 09:51:12 2019 -0700 Add option to abort at the end of the run if unused variables are in the ParmParse table, instead of exiting cleanly. Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_ParmParse.cpp commit aaa370f67d62f39fd29ed2cf28a1f3200aa29eed Merge: d6ef59517 e70f2ce38 Author: Lucas Esclapez Date: Thu Oct 17 18:49:04 2019 -0700 Merge branch 'development' into feature_nd_Pele commit d6ef59517321e9e20fd58a9422524fcfe98fb9f9 Author: Lucas Esclapez Date: Thu Oct 17 18:47:46 2019 -0700 [Feature_nd_Pele] Missing change for 3D bc function in some amr level derive call. Src/Amr/AMReX_AmrLevel.cpp commit e70f2ce3815ddf0cabc2e90699fae4e70014c315 Merge: e06822805 b698cf1c8 Author: Weiqun Zhang Date: Thu Oct 17 16:24:59 2019 -0700 Merge branch 'weiqun/dev' into development commit e06822805d87b3f1e0282b845fb0e10064b70e41 Author: Andrew Myers Date: Thu Oct 17 15:38:29 2019 -0700 fix typo Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 3000392f00ec9e0c33e3a0d7b3094d5442f7c728 Author: Weiqun Zhang Date: Thu Oct 17 15:33:51 2019 -0700 tensor 2d: test for true corner Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H commit 773b62fea2db2d51fb94d0f4fcea45c11a3c885d Author: Weiqun Zhang Date: Thu Oct 17 14:16:39 2019 -0700 use amrex::coarsen for int coarsening Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H commit fbae03c4d4682018d5449c547450a0ccdb0e24d0 Author: Weiqun Zhang Date: Thu Oct 17 14:03:42 2019 -0700 replace hardwired numbers with enum Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H commit 9f472e7a6a2d971fcd3dc216cd6c2fc9d23576d7 Author: Weiqun Zhang Date: Thu Oct 17 13:52:44 2019 -0700 add new file to gnu make and cmake systems Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/Make.package commit 6549b5c5d7efa4ae8eafaf361c67045afb7063dd Merge: 3547f94d8 1c8a5eae0 Author: Andrew Myers Date: Thu Oct 17 12:36:57 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3547f94d8faf12fe2daca7b78f6f3e53cc4452f2 Author: Andrew Myers Date: Thu Oct 17 12:36:34 2019 -0700 fix typo Src/Particle/AMReX_Particles.H commit 5a50c3cc1e8f31c74d35d8399a61e9d7aa959292 Author: Andrew Myers Date: Thu Oct 17 12:35:02 2019 -0700 ba -> BoxArray Src/Particle/AMReX_Particles.H commit 4b5883f1c175a9e6c91dcd3098d005e8d7c0bac4 Author: Andrew Myers Date: Thu Oct 17 12:34:29 2019 -0700 fix typo Src/Particle/AMReX_Particles.H commit c7b47f7b96cb77eb8cef9599a586da4492c49e99 Merge: ff0962f62 e0fe94e2b Author: Weiqun Zhang Date: Thu Oct 17 12:20:27 2019 -0700 Merge branch 'development' into pr-598 commit 1c8a5eae0be02992bb115744aa3a21027e0f76bd Merge: e0fe94e2b 995d59713 Author: WeiqunZhang Date: Thu Oct 17 12:16:44 2019 -0700 Merge pull request #599 from lucafedeli88/enable_range_based_loops_for_GpuArray added begin() and end() to GpuArray commit b698cf1c8a17274e9f7b0ad2172b09910ec2ae49 Merge: 26b1da4b9 e0fe94e2b Author: Weiqun Zhang Date: Thu Oct 17 12:15:51 2019 -0700 Merge branch 'development' into weiqun/dev commit e0fe94e2b596efe0e50e2374cb6443ecc63ebb65 Author: Weiqun Zhang Date: Thu Oct 17 12:15:30 2019 -0700 fix some makefiles for the MacProjector change GNUmakefile.in Tutorials/EB/MacProj/GNUmakefile Tutorials/LinearSolvers/MAC_Projection_EB/GNUmakefile commit 26b1da4b98b7c40ae9233a3178c411119fbb70ea Merge: 59123d3ba 649d337df Author: Weiqun Zhang Date: Thu Oct 17 11:25:08 2019 -0700 Merge branch 'development' into weiqun/dev commit 59123d3babadd22b04670e40de6424ce51b32ac5 Author: Weiqun Zhang Date: Wed Oct 16 14:47:25 2019 -0700 add RunOn to more BaseFab functions Src/Base/AMReX_BaseFab.H commit 649d337dfbe4e1198d59212603228b55976f5124 Author: Ann Almgren Date: Thu Oct 17 10:06:57 2019 -0700 Move MacProjector* out of LinearSolvers/MLMG into LinearSolvers/Projections. Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/Make.package Src/LinearSolvers/Projections/AMReX_MacProjector.H Src/LinearSolvers/Projections/AMReX_MacProjector.cpp Src/LinearSolvers/Projections/Make.package commit 995d59713f82758fd0acc9adb38b5a0c10ab384b Author: Luca Fedeli Date: Thu Oct 17 10:06:06 2019 +0200 added begin() and end() to GpuArray Src/Base/AMReX_Array.H commit ff0962f62031e28a9b3b58d779a5efafcf6167b1 Author: cgilet Date: Thu Oct 17 00:27:59 2019 -0400 Add updated mltensor_fill_corners(). Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 123b205f423d230bfedab3378b0c5a942efeb3ca Merge: 748de5548 77ec7f824 Author: Andrew Myers Date: Wed Oct 16 16:23:32 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 748de554883a052b3e1e80a1669a7ddcc9bd0660 Author: Andrew Myers Date: Wed Oct 16 16:23:23 2019 -0700 fix compilation of electrostatic pic tutorial Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H commit 77ec7f82482abd9713a3ce58b1da3d77d4e43ec5 Merge: 56b13a4cd 400e8979e Author: Andrew Myers Date: Wed Oct 16 14:18:24 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 56b13a4cdd03a7a8bd466653e5f509dc13c19280 Author: Andrew Myers Date: Wed Oct 16 14:18:03 2019 -0400 fix intersection test Tests/Particles/Intersection/main.cpp commit 216d9d177f5ee879a9b345707afc58d68264c6f2 Merge: b8a007896 8dec29757 Author: cgilet Date: Wed Oct 16 13:29:25 2019 -0400 Merge remote-tracking branch 'origin/mltensor_corner_fill_fix' into TensorFluxes commit 8dec29757e5202f2cf9b6fb6f38f19cd4b33e239 Author: cgilet Date: Wed Oct 16 13:11:10 2019 -0400 More clean up. Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H commit 0dca0a3cd53e5ff81b18c3d9d186acf42b896d0b Author: cgilet Date: Wed Oct 16 12:58:37 2019 -0400 Clean up. Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H commit 1d15f830ac53d68b0567d831d6dd5a0524865346 Author: cgilet Date: Wed Oct 16 11:37:29 2019 -0400 Add missing colon. Remove debugging Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit e0b8fd1998bd4ea3da90abdf0b1dc672acabd183 Merge: df0bca92b 400e8979e Author: cgilet Date: Wed Oct 16 10:28:55 2019 -0400 Merge remote-tracking branch 'upstream/development' into mltensor_corner_fill_fix commit 400e8979e998bf2fa527cf0a37ebf40000c81bb0 Merge: 98bad7d9e 5ea0b820c Author: WeiqunZhang Date: Tue Oct 15 16:07:41 2019 -0700 Merge pull request #595 from AMReX-Codes/doc_Paraview [Docs] Update Paraview section with new implementations of Paraview 5.7. commit 98bad7d9ed9d5ef85535f7b0bc37e755e288b72f Merge: a341eb2a1 e35d1b441 Author: Andrew Myers Date: Tue Oct 15 14:41:44 2019 -0700 Merge pull request #594 from AMReX-Codes/jmsexton/particle host_device enforcePeriodic matching cpu version, fab setVal -> multifab setVal commit a341eb2a14d03c99223efe9ffaf7ac26a4cc866e Author: Max Katz Date: Tue Oct 15 14:18:43 2019 -0700 Fix grammar Src/Base/AMReX_GpuDevice.cpp commit 5ea0b820ce1b3bf03a160df918c3ac4734aa4f84 Author: Lucas Esclapez Date: Tue Oct 15 12:33:07 2019 -0700 [Docs] Update Paraview section with new implementations of Paraview 5.7. Docs/sphinx_documentation/source/Visualization.rst commit b0059a75cf1577f8ee7a8b26adba9f3e017bac1c Author: Weiqun Zhang Date: Tue Oct 15 09:41:59 2019 -0700 use abspath for rpath Tools/GNUMake/Make.defs commit 1ae35f4ae3e972021e4bab862a2fb2731483bac5 Author: Weiqun Zhang Date: Tue Oct 15 09:30:33 2019 -0700 add -L when USE_RPATH Tools/GNUMake/Make.defs commit 85ed44b64d9639a56fb7a787fd11fcf5f0b5c47c Merge: 712bf0366 80b81ef67 Author: Lucas Esclapez Date: Mon Oct 14 17:52:40 2019 -0700 Merge branch 'development' into feature_nd_Pele commit 80b81ef67ccde3329b1750013bd3b6b23efc4f13 Merge: 166054781 0f91d4099 Author: WeiqunZhang Date: Mon Oct 14 16:03:59 2019 -0700 Merge pull request #592 from DUGKS/dugks-dev add mathematical boundary types : HOEXTRAPLI commit 16605478186e2afddbd1d1f8d95a636304e7044f Merge: fe5a776cc 3b09a1ae2 Author: WeiqunZhang Date: Mon Oct 14 15:39:58 2019 -0700 Merge pull request #593 from AMReX-Codes/convergence_tool Convergence tool commit fe5a776cccf5fa17928447d1099923b5d2ac299a Merge: 359987a52 f20376b52 Author: WeiqunZhang Date: Mon Oct 14 15:33:11 2019 -0700 Merge pull request #590 from ax3l/topic-rpathSupport Linker: Use RPath commit f20376b52d09eff0bb43f23c1bfcad037abdcf80 Author: Axel Huebl Date: Thu Oct 10 11:13:55 2019 -0400 USE_RPATH: Do not yet enable by default Let's test this for a period of time on volunteering downstream projects (WarpX, Castro, ...?). Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/GNUMake/Make.defs commit 359987a5250a1efe5942e0dc7870f9a842b925ee Author: Weiqun Zhang Date: Mon Oct 14 14:53:16 2019 -0700 More Reduce functions can now take a device lambda. Src/Base/AMReX_FabArrayUtility.H Tutorials/GPU/EBCNS/Source/CNS.cpp commit 047bdcadf28393b504a72804c2622d62483bdd0f Merge: 0ca88a9fc 73df36dd4 Author: Kevin N Gott Date: Mon Oct 14 11:54:07 2019 -0700 Merge branch 'development' into kngott/hip commit 73df36dd43d7470546002ec7e1de11efa200b41f Author: Weiqun Zhang Date: Mon Oct 14 11:26:08 2019 -0700 ReduceMin can now take a device lambda. However if the lambda is a device lambda and the launch region is off, a runtime error will occur. Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_TypeTraits.H Tutorials/GPU/CNS/Source/CNS.cpp commit c5d26fa455f918f1f42a032d5a5e713d3b7805b4 Author: Weiqun Zhang Date: Mon Oct 14 09:26:28 2019 -0700 print out the total number of gpus used only if nvcc >= 10 Src/Base/AMReX_GpuDevice.cpp commit 11c2e22468c8618a5bd9e6a6c267ac914816a3ed Author: Andrew Myers Date: Mon Oct 14 10:52:47 2019 -0700 docstrings for the Particle IO routines Src/Particle/AMReX_Particles.H commit 4d142407aa449f0216a922c5b2f39590c3f66a85 Author: Andrew Myers Date: Mon Oct 14 10:27:52 2019 -0700 docstring formatting changes Src/Particle/AMReX_Particles.H commit b01480ff2d2fc77d4f88e4a545222f72a2e58411 Author: Andrew Myers Date: Mon Oct 14 10:09:43 2019 -0700 more docstrings for ParticleContainer Src/Particle/AMReX_Particles.H commit 84cd795ae6f26e0edeef423aebdcc91ba9db4c3c Author: Andrew Myers Date: Mon Oct 14 09:52:42 2019 -0700 remove unused function Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit c2d9a42ff7ae517d8043968288a064cd04a19e1e Author: Andrew Myers Date: Mon Oct 14 09:51:59 2019 -0700 add some docstrings to the ParticleContainer constructors / define methods Src/Particle/AMReX_Particles.H commit 27de2eb3548a7f6b4653593c753cbcfdd10c8813 Author: Weiqun Zhang Date: Sat Oct 12 16:20:11 2019 -0700 add RunOn to BaseFab functions Src/Base/AMReX_BaseFab.H Src/Base/AMReX_MultiFabUtil.cpp Tutorials/Basic/HelloWorld_C/main.cpp commit 3b09a1ae20af430862cbae4a7911e8df43984e62 Author: Michael Zingale Date: Sat Oct 12 13:13:39 2019 -0400 make the output more readable, disable latex by default Tools/C_util/Convergence/RichardsonConvergenceTest.cpp commit a82a0b7b7b9fdea32ee274aff81c2c99c91265e8 Merge: 12ab2a8c8 9795a115a Author: Michael Zingale Date: Sat Oct 12 12:27:27 2019 -0400 Merge branch 'development' into convergence_tool commit 0f91d40997422fc3f0e6ff8fcc7ecdb1c87ef7d2 Author: DUGKS Date: Sat Oct 12 21:17:39 2019 +0800 add HOEXTRAPCC boundary type Src/Base/AMReX_BC_TYPES.H Src/Base/AMReX_FilCC_1D_C.H Src/Base/AMReX_FilCC_2D_C.H Src/Base/AMReX_FilCC_3D_C.H Src/Base/AMReX_bc_types.fi Src/Base/AMReX_bc_types_mod.F90 Src/Base/AMReX_filcc_mod.F90 commit 48813578815b0ae945aa253b3ecfea6634c46cf5 Author: Michele Rosso Date: Fri Oct 11 16:09:01 2019 -0700 Fix args order in call to MultiFab constructor when computing EB-norm0 Src/Base/AMReX_MultiFab.cpp commit c9fd84471ec06f25c5f51606657931801c4dff93 Author: atmyers Date: Fri Oct 11 13:15:00 2019 -0700 expand the particle reduction tests Tests/Particles/ParticleReduce/main.cpp commit a1e36e8a7e401c0225aa9158c3753bbf355981e7 Author: atmyers Date: Fri Oct 11 13:14:43 2019 -0700 update the particle reduction functions to work with SoA data Src/Particle/AMReX_ParticleReduce.H commit 4ce592981a97d903b8c9fd762c595c623881f901 Author: atmyers Date: Fri Oct 11 13:14:19 2019 -0700 do some bounds checking for the particle components if DEBUG=TRUE Src/Particle/AMReX_Particle.H commit ae7e94ce585c9c79ccd9c584a0382e56e253cd16 Author: atmyers Date: Fri Oct 11 13:14:01 2019 -0700 fix some order of initialization issues Src/Particle/AMReX_ParticleLocator.H commit e35d1b441460523e6bbd28096d2508ccf65219a9 Author: Jean M. Sexton Date: Fri Oct 11 13:33:22 2019 -0400 Make one setVal a multifab setVal, make enforcePeriodic match cpu version to fix losing particles in single precision Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleUtil.H commit df0bca92bf0bba3de4507efe9e920f450f333f05 Author: cgilet Date: Fri Oct 11 13:23:28 2019 -0400 give accurate error message Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 2104413e402443609ed2a78bae2624f5092eeabf Author: cgilet Date: Fri Oct 11 12:11:16 2019 -0400 Fix applyBCTensor: Must take StateMode into account. Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 7b59e30417b3ed14ebaf7d496746d843b5f5d9d7 Merge: 5c79b3fcb f52bc498c Author: WeiqunZhang Date: Fri Oct 11 08:51:00 2019 -0700 Merge pull request #589 from eschnett/development Avoid compiler warnings commit 961c432f42154f1667ec5b21973200d086004b09 Merge: f22974629 5c79b3fcb Author: cgilet Date: Fri Oct 11 10:23:23 2019 -0400 Merge remote-tracking branch 'upstream/development' into mltensor_corner_fill_fix commit 5c79b3fcb047c88cd7e66a0316e636144ac8e9ea Author: Kevin Gott Date: Fri Oct 11 07:07:09 2019 -0400 Clean up CudaGraphs and Tests. Only preferred method remains. Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp Tests/GPU/CudaGraphs/CrazyGraphs/GNUmakefile Tests/GPU/CudaGraphs/CrazyGraphs/main.cpp Tests/GPU/CudaGraphs/GraphBoundary/inputs_3d Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp Tests/GPU/CudaGraphs/GraphWithMemcpy/main.cpp Tests/GPU/CudaGraphs/Readme.txt commit c442aa016c01d4ad433babc1193a3984131609af Author: DUGKS Date: Fri Oct 11 16:23:59 2019 +0800 add mathematical boundary types : HOEXTRAPLI Src/Base/AMReX_BC_TYPES.H Src/Base/AMReX_FilCC_1D_C.H Src/Base/AMReX_FilCC_2D_C.H Src/Base/AMReX_FilCC_3D_C.H Src/Base/AMReX_bc_types_mod.F90 Src/Base/AMReX_filcc_mod.F90 commit fa9fa75ed24b5b92635a7281eec8ff7e5a23e33a Merge: 89665c06b 3bdad942e Author: Andrew Myers Date: Fri Oct 11 00:31:27 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 89665c06b9751cffd5bdc2d7df8f0a164e304afe Author: Andrew Myers Date: Fri Oct 11 00:24:38 2019 -0400 calculate the early exit properly for local=false Src/Particle/AMReX_ParticleCommunication.cpp commit e189badc59e0f58ec82f97e6d25898f3751a73d2 Author: Andrew Myers Date: Fri Oct 11 00:23:40 2019 -0400 make sure the local option gets passed through correctly Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleContainerI.H commit 0ca88a9fc9ecf33145ca2ca73d4b342d4199e254 Author: Kevin Gott Date: Thu Oct 10 13:24:34 2019 -0400 Turn Random back on in ParallelReduce tests. Tutorials/GPU/ParallelReduce/main.cpp commit 4eb3509fa381ebb01e871f6814901bf4abed615d Author: Kevin Gott Date: Thu Oct 10 13:22:48 2019 -0400 Mark {{ Initialization lists for now. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_PlotFileDataImpl.H commit 403c106c6adb32d170da36d8c6cf147218e30fdd Author: Kevin Gott Date: Thu Oct 10 11:33:35 2019 -0400 Fix and use the memcpy_to_symbol wrapper. Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_Random.cpp commit 1ce6e08f9d19822004476a11c7ba1b869cb186f3 Author: Kevin Gott Date: Thu Oct 10 10:44:35 2019 -0400 Strip managed variable out of Random for HIP compatibility. Src/Base/AMReX_Random.cpp commit ec9f6eab8faa711a1a78bc910135057829236fc1 Author: Axel Huebl Date: Thu Oct 10 10:03:43 2019 -0400 Linker: Use RPath Although AMReX does not come with much dependencies besides runtimes, the build system allows to add various libraries for downstream application dependencies. In the case of WarpX, we link auxiliary libraries for I/O among others. When linking against shared libraries, these dependent libraries (think: `.so`|`.dylib`|`.dll` files) must be present and accessible at runtime again. Usually, one sets their paths in `export LD_LIBRARY_PATH` hints which is both cumbersome for users as well as bad for file-systems which will be heavily loaded with meta-data operations while searching for the corresponding dependencies, especially at scale. Luckily, all modern Unix systems support RPath hints, which embed the location of a dependent shared library at link time into the generated binary. https://en.wikipedia.org/wiki/Rpath We now enable this feature by default. The linker flag is implemented in a generic way that works with the most common compilers: - clang :heavy_check_mark: - gcc :heavy_check_mark: - nvcc :heavy_check_mark: - icc :heavy_check_mark: - pgcc :heavy_check_mark: - xlC :heavy_check_mark: - crayc++ "classic" :heavy_multiplication_x: - crayc++ 9.0+ "LLVM": :heavy_check_mark: In case there are any regressions or the intentional wish to not use RPaths, users can just set `USE_RPATH=FALSE` as `make` option. Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/GNUMake/Make.defs commit 3bdad942ec16517eb6a54b18f20caaca1c8dcc0f Merge: 549059051 0eacdb29a Author: Andy Nonaka Date: Wed Oct 9 14:47:25 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 5490590517022cf77e381c1dcad2b4b31907ec9d Author: Andy Nonaka Date: Wed Oct 9 14:46:02 2019 -0700 get the NeighborList particle tutorial running again. instead of crashing right away, it now crashes after 15 time steps for unknown reason Tutorials/Particles/NeighborList/GNUmakefile Tutorials/Particles/NeighborList/inputs Tutorials/Particles/NeighborList/inputs.mr Tutorials/Particles/NeighborList/main.cpp commit 0eacdb29ae47d886b5f1c76bda72eb4f4bd02054 Author: cgilet Date: Wed Oct 9 16:51:02 2019 -0400 Minor fix in EB_computeDivergence: Only assert on 3rd dimension if AMREX_SPACEDIM==3 Src/EB/AMReX_EBMultiFabUtil.cpp commit f22974629f98c615d355d6e992b395d727078b84 Author: cgilet Date: Wed Oct 9 16:17:49 2019 -0400 Update MLEBTensor::applyBCTensor Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 80772118a56485df060c2fd9ad20e55549a442e4 Author: cgilet Date: Wed Oct 9 16:15:32 2019 -0400 Force inline Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H commit f37b0b042166f60a6546674c5bb3b85a0cc7e516 Merge: 4769a2ac3 885244605 Author: Kevin Gott Date: Wed Oct 9 14:26:58 2019 -0400 Merge branch 'development' into kngott/hip commit 4769a2ac3ea92f47903588fa69e94cbdf7347af9 Author: Kevin Gott Date: Wed Oct 9 10:38:15 2019 -0700 Wrap libraries and includes for HIP. Tests/GPU/RandomNumberGeneration/GNUmakefile commit 13eca6aa43316985f4905b76bc9572d5ac4d330d Author: Kevin Gott Date: Wed Oct 9 10:35:08 2019 -0700 First draft of HIP for random. Need to fix memcpytoSymbol wrapper and make gpu_nstates non-managed. Src/Base/AMReX_Random.H Src/Base/AMReX_Random.cpp commit 8ab2387559309fbcc5a90b96dcc9fa74c89e1300 Author: Kevin Gott Date: Wed Oct 9 10:33:49 2019 -0700 memcpytoSymbol wrapper. [WIP] Doesn't seem to be working in Random.cpp Src/Base/AMReX_GpuDevice.H commit 50e0c80b6d61a5e29e99cbaa96d8d10c964d3d6f Author: Kevin Gott Date: Wed Oct 9 10:32:59 2019 -0700 Initialize Random after Arenas to allow Arena use in Random Initiatlize. Src/Base/AMReX.cpp commit d5d63f4acbdae21647103115183ae176f3603c89 Author: Kevin Gott Date: Wed Oct 9 10:31:52 2019 -0700 Add HIPrand librarys and includes to the GNUmakefile for RandomNumberGenerator. Tests/GPU/RandomNumberGeneration/GNUmakefile commit 64cacd87f25a2f470e7d0375db5642237a99216d Author: Kevin Gott Date: Wed Oct 9 10:27:57 2019 -0700 Is this library needed? Src/Base/AMReX_GpuUtility.H commit 0853e8894715f8676bbdf2d152fc595941abd13c Author: cgilet Date: Wed Oct 9 12:28:44 2019 -0400 Bug fix for case BCMode::Homogeneous Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit ec0661f4e7be5be728d018c0414e0ef80394a47b Merge: b37f31d11 885244605 Author: cgilet Date: Wed Oct 9 11:31:43 2019 -0400 Merge remote-tracking branch 'upstream/development' into mltensor_corner_fill_fix commit b37f31d11856ce4c51be7d4759c8d22ba2279ad7 Author: cgilet Date: Wed Oct 9 11:31:23 2019 -0400 WIP - MLMG not converging. Corner/edge cells fill appears reasonable Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 8852446050243fd25b7cd19ca9f42acbd59d2b18 Merge: 1d95b09a4 3c8f0a0e0 Author: Andrew Myers Date: Wed Oct 9 06:48:13 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1d95b09a4a53e337e90a122fdda06d8021054048 Author: Andrew Myers Date: Wed Oct 9 06:47:49 2019 -0700 allow thrust::complex in PODVector, even though it doesn't strictly meet the requirements of std::is_trivially_copyable Src/Base/AMReX_PODVector.H commit 933e038fa72300f75c67b9808a7d2932d0728d4a Merge: 91ba5bd81 3c8f0a0e0 Author: Kevin Gott Date: Tue Oct 8 17:38:03 2019 -0700 Merge branch 'development' into kngott/hip commit 3c8f0a0e09ef546f6d84d0c6076f72dec6e09412 Author: Michele Rosso Date: Tue Oct 8 15:58:05 2019 -0700 CMake: add AMReX_Random.H and AMReX_Random.cpp to CMakeLists Src/Base/CMakeLists.txt commit 576c2ec3eadcffb7dd31701f803b0b3ba13febf6 Merge: bc6bf1bc6 65ac979f8 Author: Kevin Gott Date: Tue Oct 8 16:40:50 2019 -0400 Merge branch 'kngott/random' into development commit 65ac979f83576d39ecb72aac0b616f04fae32a51 Author: Kevin Gott Date: Tue Oct 8 16:40:01 2019 -0400 Fixing Random libraries. Src/Base/AMReX_Random.H Src/Base/AMReX_Utility.H commit 10fbcbd5b03ff2fb155ce1743420e2b3af7941d0 Author: Kevin Gott Date: Tue Oct 8 12:35:28 2019 -0700 Move Random functionality to separate file. Src/Base/AMReX.cpp Src/Base/AMReX_Random.H Src/Base/AMReX_Random.cpp Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Base/Make.package commit 91ba5bd817de294fe209ff4dbd80689727d1b57c Author: Kevin Gott Date: Tue Oct 8 12:05:54 2019 -0700 1st version of HIP HeatEquation. No output. Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/Make.package Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/HIP/mykernel.H commit 8febe5df20d537ae0f48b31b8a44f73ebd3c9e73 Author: Kevin Gott Date: Tue Oct 8 12:04:47 2019 -0700 Setup testing of ParallelReduce tutorial. Tutorials/GPU/ParallelReduce/GNUmakefile Tutorials/GPU/ParallelReduce/main.cpp commit b9a968838f183abf6dd8f4c004a40441282ad7ac Author: Kevin Gott Date: Tue Oct 8 12:03:39 2019 -0700 Updated makefiles for testing. Tutorials/Basic/HelloWorld_C/GNUmakefile Tutorials/GPU/Launch/GNUmakefile commit 4acb9d206017acbf939160184a447af0d91d02d5 Author: Kevin Gott Date: Tue Oct 8 11:59:47 2019 -0700 HelloWorld Work around for HIP shuffle intrinsics. Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_iMultiFab.cpp commit bc6bf1bc6fc1344800ab2e5a4b2f176ae3903176 Merge: e438852e8 8d6e7aa70 Author: Andrew Myers Date: Tue Oct 8 10:28:12 2019 -0700 Merge branch 'development' into atmyers/vector_memory_usage commit 8d6e7aa70534daa0806e8b079cd92e38dbb85732 Merge: 6538bf277 f710a2ece Author: Andrew Myers Date: Tue Oct 8 10:27:41 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6538bf27750cff7cd1b1451c35c9fdb474017c68 Author: Andrew Myers Date: Tue Oct 8 10:27:24 2019 -0700 fix ParticleMesh test Tests/Particles/ParticleMesh/main.cpp commit e438852e895334993305d17183fddd170c8815b3 Author: Andrew Myers Date: Tue Oct 8 12:57:00 2019 -0400 offload 'assign' in PODVector Src/Base/AMReX_PODVector.H commit a66f667c68c2acfc48bca5d9214363c309fc6a9b Author: Andrew Myers Date: Tue Oct 8 12:31:01 2019 -0400 templated implementation of == and != for the Allocators Src/Base/AMReX_CudaAllocators.H commit 03309d39e529972ca0b078f3d8dea1ab9dc7ff8a Author: Andrew Myers Date: Tue Oct 8 08:39:53 2019 -0700 fix cpu compilation Src/Base/AMReX_CudaContainers.H commit f52bc498ce64c5f80179da44e9fd7344aacb3147 Author: Erik Schnetter Date: Tue Oct 8 11:31:58 2019 -0400 Avoid compiler warnings Avoid warnings about signed/unsigned comparisons and about unused variables. Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArrayCommI.H commit e748a8abe124d4701ab51b84f5cec95647c640ad Author: Andrew Myers Date: Tue Oct 8 08:26:12 2019 -0700 some refactoring and simplication of the gpu allocators Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaContainers.H commit f710a2ece1801eaa1957793bd9947e22b0cbf6d9 Merge: f5d8542dd 4a5eb3854 Author: WeiqunZhang Date: Tue Oct 8 08:08:01 2019 -0700 Merge pull request #588 from ax3l/fix-printfWarnings GCC 7.4.0 Warnings in Prints commit f5d8542dd8f3296fb8e3542910f1a63001749134 Merge: 09161d1ae 73be13728 Author: WeiqunZhang Date: Tue Oct 8 08:07:10 2019 -0700 Merge pull request #586 from AMReX-Codes/bugfix-install add a missing D in the Make.package file for MLNodeLap commit f4a49b6b58fea95dd4caa5d9d87aace5b32bd13b Merge: 8d1e5dcd9 09161d1ae Author: Andrew Myers Date: Tue Oct 8 07:00:04 2019 -0700 merging development into amrex/vector_memory_usage commit 09161d1aea878bf6124fddca1fe4d6ddf65a51e0 Merge: 7c5cc638a f5d599be8 Author: Andrew Myers Date: Tue Oct 8 06:40:31 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7c5cc638a29b8dadbdc379f64b946ec8ee31725b Author: Andrew Myers Date: Tue Oct 8 06:40:08 2019 -0700 iterate over map directly when early exiting from RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H commit 4a5eb3854f95f89fd22dcc2998592fe847062b25 Author: Axel Huebl Date: Tue Oct 8 09:24:01 2019 -0400 GCC 7.4.0 Warnings in Prints Fix warnings of the type ``` In file included from /usr/include/stdio.h:862, from /usr/include/c++/8/cstdio:42, from ../amrex/Src/Base/AMReX_ParallelDescriptor.cpp:2: /usr/include/x86_64-linux-gnu/bits/stdio2.h:64:35: note: ‘__builtin___snprintf_chk’ output between 105 and 617 bytes into a destination of size 512 return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __bos (__s), __fmt, __va_arg_pack ()); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ../amrex/Src/Base/AMReX_ParallelDescriptor.cpp: In function ‘void amrex::ParallelDescriptor::Barrier(const string&)’: ../amrex/Src/Base/AMReX_ParallelDescriptor.cpp:198:23: warning: ‘%s’ directive output may be truncated writing up to 512 bytes into a region of size 383 [-Wformat-truncation=] snprintf(buf, N, "AMReX MPI Error: File %s, line %d, %s: %s", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ``` when compiling with WarpX. Src/Base/AMReX_ParallelDescriptor.cpp commit 73be13728b7cd7d2afef3c4c41cda338069eed8a Author: Brandon Runnels Date: Mon Oct 7 15:30:05 2019 -0600 add a missing D in the Make.package file Src/LinearSolvers/MLMG/Make.package commit f5d599be8681700ca43bc1b45cecae6388ee5563 Author: Ann Almgren Date: Sat Oct 5 15:07:36 2019 -0700 The point of passing in "loc" is to use it! Replace "MLMG::Location::FaceCenter" by loc in call to get Fluxes. Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit 49dd1dc17aea9d3aa52fda94e7a0303d5fc940c6 Merge: e65c42630 e016a3c17 Author: WeiqunZhang Date: Sat Oct 5 14:56:42 2019 -0700 Merge pull request #585 from AMReX-Codes/max_gpu_streams Reduce number of CUDA streams to 4 commit e016a3c17119fc6c951d25d8555e2c85bb735c29 Author: Max Katz Date: Sat Oct 5 16:27:47 2019 -0400 Reduce number of CUDA streams to 4 Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_MFIter.cpp commit e65c426305574d5f4d8eaf4bc74806e96b7c54c1 Author: Weiqun Zhang Date: Fri Oct 4 20:23:31 2019 -0700 for gpu regression tests, avoid saving errors in plotfiles Tests/LinearSolvers/CellEB2/MyTest.cpp Tests/LinearSolvers/EBTensor/MyTestPlotfile.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTestPlotfile.cpp commit 97e2ca380b40238a0c2cf017f3c6c0a6063bd90f Author: Weiqun Zhang Date: Fri Oct 4 17:58:22 2019 -0700 add inputs for Nodal Poisson regression test Tutorials/Basic/HelloWorld_C/main.cpp Tutorials/LinearSolvers/NodalPoisson/inputs-rt commit bd740871493c8b752e9146ab202f7a1f1d76599c Author: cgilet Date: Fri Oct 4 16:50:28 2019 -0400 WIP - bug fix in mltensor_fill_edges(). some clean-up Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H commit f33765db0ca580c217d3aceddd27a5564e89ed00 Author: Emmanuel Motheau Date: Fri Oct 4 13:26:43 2019 -0700 update EB/MacProj tutorial to match last version of AMReX Tutorials/EB/MacProj/main.cpp commit b022c48758eb4cccb7088abb096447130b2092c3 Author: Weiqun Zhang Date: Fri Oct 4 13:17:17 2019 -0700 add a new function for removing duplicates using hash Src/Base/AMReX_Vector.H commit c1ddf16cf1081f6610fd98ecf05ed223cff1733c Author: Kevin Gott Date: Fri Oct 4 12:54:14 2019 -0700 Add fortran to hip builds. Straight copy from llvm using gfortran. Tools/GNUMake/Make.defs Tools/GNUMake/comps/hip.mak commit 65864eedb5e23383e7efbb7504a0df3ae4548b05 Author: Kevin Gott Date: Fri Oct 4 12:53:47 2019 -0700 shfl note. Src/Base/AMReX_GpuReduce.H commit e1cc614cbbbd8c239f753f6cb5bab8dc3d954480 Merge: 729e587b1 b4b746c20 Author: cgilet Date: Fri Oct 4 15:05:06 2019 -0400 Merge remote-tracking branch 'upstream/development' into development commit d4765a4d9167699522b454cb8fc2463f08322870 Author: Kevin Gott Date: Thu Oct 3 13:21:35 2019 -0700 Cleanup. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Geometry.H commit b4b746c209c84b07089637970b5a75583d614a9f Merge: 10f100fbf 57b4cb44c Author: Andrew Myers Date: Thu Oct 3 12:19:02 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 10f100fbf9b3cf44cc830c704b63db7914ca2cf4 Author: Andrew Myers Date: Thu Oct 3 12:18:54 2019 -0700 fix corner case bug in ParticleCopyPlan::build Src/Particle/AMReX_ParticleCommunication.H commit 402fcb84d0a267d15ec00ab3f35844506ac12c84 Author: Kevin Gott Date: Thu Oct 3 11:50:28 2019 -0700 Callback on HIP. Src/Base/AMReX_GpuAsyncArray.H Src/Base/AMReX_GpuAsyncArray.cpp Src/Base/AMReX_GpuElixir.cpp commit da243b9d6e6e53ed01ece017e94f5a0f57f7d796 Author: Kevin Gott Date: Wed Oct 2 17:45:02 2019 -0700 Covert to AMREX_HIP_TO_CUDA. Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_MultiFabUtil_nd_C.H commit 3771c387622a8eff24bc21464064b52c6f5012c7 Merge: d74ffb5f7 57b4cb44c Author: Kevin Gott Date: Wed Oct 2 16:36:07 2019 -0700 Merge branch 'development' into kngott/hip commit d74ffb5f76ac5af81f59cd9dde4284b1379787aa Author: Kevin Gott Date: Wed Oct 2 16:34:59 2019 -0700 Add label to update Random to HIP. Src/Base/AMReX_Utility.cpp commit baf59775d65699732e79b504a045b47b5f49851e Author: Kevin Gott Date: Wed Oct 2 15:56:32 2019 -0700 Label FabView HIP changes. Src/Base/AMReX_BaseFab.H commit c0383712a6a9ac4edb7906797351fc385c7b6d8a Author: Kevin Gott Date: Wed Oct 2 15:55:05 2019 -0700 Add labels to HIP FIX comments. Src/Base/AMReX.cpp Src/Base/AMReX_Array4.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_GpuAsyncArray.H Src/Base/AMReX_GpuElixir.cpp Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_Utility.cpp commit cbe9b036475d8b389f550d69b1e0d5945d1ade51 Author: Kevin Gott Date: Wed Oct 2 15:54:19 2019 -0700 std function wrappings for HIP. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MultiFabUtil_nd_C.H commit 45dea4ee63900cf0279ce43cf4666554c0cf1b8a Author: Kevin Gott Date: Wed Oct 2 15:52:18 2019 -0700 Add iMultiFab destructor for HIP. Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit e109c09555caa6d68b467ae4c9e0df527498017b Author: Kevin Gott Date: Wed Oct 2 15:51:10 2019 -0700 __all_sync and __any_sync for HIP Src/Base/AMReX_FBI.H commit 70bf3f6c8c3382ef7c90f96c0623b1228b0e2608 Author: Kevin Gott Date: Wed Oct 2 15:22:25 2019 -0700 Add a CPU CArena option for HIP. Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_MemPool.cpp commit 57b4cb44ce139837ca6781753f1bdc742577d806 Author: Weiqun Zhang Date: Wed Oct 2 14:00:13 2019 -0700 readBoxArray: make the special flag optional Src/Base/AMReX_BoxArray.H commit 888627a51a70e41c08936f15bc5d2f4124f81a23 Author: Andrew Myers Date: Wed Oct 2 16:51:59 2019 -0400 add another specialization for placementNew that explicitly does nothing for arithmetic types Src/Base/AMReX_BaseFab.H commit f7a9aca15339c62c0de7e957e8478d5d6ae60f09 Author: Weiqun Zhang Date: Wed Oct 2 13:11:10 2019 -0700 make gnu make NVCC_HOST_COMP more robust Tools/GNUMake/Make.defs commit 712bf03660bcc6e217a8f311b75d4247619be9a0 Author: Lucas Esclapez Date: Wed Oct 2 11:59:01 2019 -0700 [feature_nd_Pele] Add a 3D version of bc in Derive for dim. agnostic codes. Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_Derive.H Src/Amr/AMReX_Derive.cpp commit e264d988bc2cbce6e935311ddd72cc24ccf2084d Author: shashankNREL Date: Fri Sep 6 10:18:07 2019 -0600 Fixes to the spline IF routines Src/EB/AMReX_distFcnElement.H Src/EB/AMReX_distFcnElement.cpp Tutorials/EB/GeometryGeneration/main.cpp commit 426d53f3fddec8929510fd72016dc5d7f8a34796 Merge: 2d74db3e4 21cd5e9d5 Author: Ann Almgren Date: Wed Oct 2 07:17:54 2019 -0700 Merge branch 'development' into mr/multicomp-div commit 0a943d6494e39b68ed6c2e023415c2a058f5ce75 Author: Kevin Gott Date: Tue Oct 1 17:07:48 2019 -0700 manual memset. alloc doesn't seem to be working. Src/Base/AMReX_MemPool.cpp commit cddc61edb8087ae4db6865e720a6d192d45f1c4f Author: Kevin Gott Date: Tue Oct 1 17:07:22 2019 -0700 FabView Constructor wrappers for DEBUG and USE_HIP=FALSE. Src/Base/AMReX_BaseFab.H commit 7a28de7090c95721b9f9758c61dfe8ab4f366f2a Author: Kevin Gott Date: Tue Oct 1 16:30:15 2019 -0700 HIP doesn't like memset? HelloWorld is running with HIP. Src/Base/AMReX_MemPool.cpp commit c54ddb9b51d082c64f718eaca475891fb5e0d79e Author: Kevin Gott Date: Tue Oct 1 16:20:50 2019 -0700 Remove the C++14 flag. Tools/GNUMake/comps/hip.mak commit 23158e6e1c67debe5e35d8c169073a1729846624 Author: Kevin Gott Date: Tue Oct 1 15:40:51 2019 -0700 Comment out virtual destructor. Conflict with LLVM 'key function'? Src/Base/AMReX_iMultiFab.H commit ec6cf9ead1656008e9f06a95ea18d50b024980de Author: Kevin Gott Date: Tue Oct 1 15:40:12 2019 -0700 Comment out std distribution functions. Src/Base/AMReX_Utility.cpp commit 69abba26249a39ddb960ffca0db3541930fa7f7d Author: Kevin Gott Date: Tue Oct 1 15:39:46 2019 -0700 More launch macros. Src/Base/AMReX_Reduce.H commit 669563202eb32642b0d06aa8c9ff45360ea68931 Author: Kevin Gott Date: Tue Oct 1 15:39:34 2019 -0700 std::floor to floor. Src/Base/AMReX_MultiFabUtil_nd_C.H commit 7637c320df7f9229087d0cd2117a0ca7312e4730 Author: Kevin Gott Date: Tue Oct 1 15:39:23 2019 -0700 std::abs to abs. Src/Base/AMReX_IntVect.H commit a9739d023216cc9cba1ad48ef82018aefa2d4c2a Author: Kevin Gott Date: Tue Oct 1 15:39:07 2019 -0700 Comment out _shfl_down_sync. Src/Base/AMReX_GpuReduce.H commit 702380d2b2c64189284b6cc9d4873b958b69f29b Author: Kevin Gott Date: Tue Oct 1 15:38:39 2019 -0700 Comment out callback functions. Src/Base/AMReX_GpuAsyncArray.H Src/Base/AMReX_GpuAsyncArray.cpp Src/Base/AMReX_GpuElixir.cpp commit 3d8823103209544936c3b29d98efc5e5a35197b0 Author: Kevin Gott Date: Tue Oct 1 15:38:14 2019 -0700 Comment out _any_sync and _all_sync. Src/Base/AMReX_FBI.H commit 1dbade18dce93b21f6f6be34b3f3ee835948ef22 Author: Kevin Gott Date: Tue Oct 1 15:37:53 2019 -0700 Getting around failing initalization lists. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_Geometry.H commit 9c7af0b42aec50f4718f9e7ccb1e26103ef9121e Author: Kevin Gott Date: Tue Oct 1 15:37:12 2019 -0700 Comment out printf on device. Src/Base/AMReX.cpp Src/Base/AMReX_Array4.H commit 44dda57c810fc0910b80fc190b7624768d7e9dc0 Author: Kevin Gott Date: Tue Oct 1 15:36:48 2019 -0700 Launch Macro. Switch between (<<< >>>) and hipLaunchKernelGGL. Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuLaunchMacrosG.H commit ff9d110a8df5ae76f889b604459d8365a5566f04 Author: Kevin Gott Date: Tue Oct 1 15:34:54 2019 -0700 hipHostAlloc -> hipHostMalloc & hipFreeHost -> hipHostFree Src/Base/AMReX_Arena.cpp commit 016c8c69080e92e0fa03ce9767361af2aa97ec13 Author: Kevin Gott Date: Tue Oct 1 15:22:47 2019 -0700 DEBUG=FALSE and NO_FORT build. Tutorials/Basic/HelloWorld_C/GNUmakefile commit 963157d641d5b54545424b5a7d67373b06e0243e Author: Kevin Gott Date: Tue Oct 1 15:22:15 2019 -0700 lineinfo unknown and start tracking down -std=c++11 flags. Tools/GNUMake/comps/hip.mak commit 21cd5e9d514cd03ab0484437fedb23d60f79e3bb Author: Andrew Myers Date: Tue Oct 1 15:18:05 2019 -0700 update success string Tests/Particles/ParticleReduce/main.cpp commit a702d61e5f641b865ef8cdd277b992df7b2ddf53 Merge: 3f7f5bd7a 7677542c1 Author: Andrew Myers Date: Tue Oct 1 15:14:03 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3f7f5bd7a976ff8c016588c2f83923edba67425d Author: Andrew Myers Date: Tue Oct 1 15:13:54 2019 -0700 rewrite particle reductions in the new style Src/Particle/AMReX_ParticleReduce.H commit c3c988d571b2fad3371b8a5e6aa2b3f62e1ee4f9 Author: Andrew Myers Date: Tue Oct 1 15:13:31 2019 -0700 update ParticleReduce test Tests/Particles/ParticleReduce/main.cpp commit 7677542c118b1405fee20269e3255e3e90e3ae75 Merge: 9b5661c26 e855117de Author: Andrew Myers Date: Tue Oct 1 14:45:07 2019 -0700 Merge pull request #583 from AMReX-Codes/single_precision_random Single precision random commit e855117de60f15d53cc1c4c846503ff1b04041b7 Merge: 560fd6028 9b5661c26 Author: Andrew Myers Date: Tue Oct 1 14:24:08 2019 -0700 Merge branch 'development' into single_precision_random commit 560fd602803a2b101800db991fe985afee522ba1 Author: Andrew Myers Date: Tue Oct 1 14:19:32 2019 -0700 Real -> amrex::Real Src/Base/AMReX_Utility.cpp commit bb9e6d05f711ed3b542c2d7687aa65cdf00c7df2 Author: Andrew Myers Date: Tue Oct 1 14:15:41 2019 -0700 Random and RandomNormal for single and double precision Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 9b5661c2688bf1830d28f9946539a64898a17a00 Merge: d8ca1afea 8325434e7 Author: Andrew Myers Date: Tue Oct 1 13:57:48 2019 -0700 Merge pull request #581 from ax3l/fix-tracerNarrowingFloat Tracer Particles: Fix Narrow Warnings commit 8325434e78eb1c0c6d7c0209ba7884e2e38b88b2 Author: Axel Huebl Date: Tue Oct 1 13:48:04 2019 -0700 Tracer Particles: Narrow Warnings Mitigate some narrowing warnings in tracer particles when compiling in single precision: ``` Src/Particle/AMReX_TracerParticle_mod_K.H:86:27: warning: narrowing conversion of ‘(1.0e+0 - ((double)xint))’ from ‘double’ to ‘amrex::Real {aka float}’ inside { } [-Wnarrowing] ``` Src/Particle/AMReX_TracerParticle_mod_K.H commit 2d74db3e46cbef70e4cecc058df5b32e23893c5d Author: Michele Rosso Date: Tue Oct 1 12:25:14 2019 -0700 Make EB_computeDivergence components-aware Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit ee212d24264b1d422df130b65ea6289787b909a9 Merge: 4c82eaf6a d8ca1afea Author: Michele Rosso Date: Tue Oct 1 10:43:19 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mr/mf-eb-methods commit d8ca1afea2951d5a688ef1033141810e0c44cece Merge: 52844b32b 4fe85db20 Author: Weiqun Zhang Date: Tue Oct 1 06:48:43 2019 -0700 Merge branch 'weiqun/dev' into development commit 52844b32b7da11e9733b9a7f4a782e51de7f5e1e Author: Weiqun Zhang Date: Tue Oct 1 06:47:12 2019 -0700 update CHANGES CHANGES commit 1bf4ddac8b38d2d977e48edecd10217a004cee41 Merge: 5ae0c56b2 340101075 Author: Weiqun Zhang Date: Tue Oct 1 06:31:17 2019 -0700 Merge branch 'development' commit 4fe85db203e054e29614d4d6c65f17bb90b63ecd Author: Weiqun Zhang Date: Mon Sep 30 19:58:28 2019 -0700 gpu nodal rap: restriction Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 34010107597c0dbded205cd31863f7c8245b36ee Author: Weiqun Zhang Date: Mon Sep 30 20:07:45 2019 -0700 fix dangling pointer Src/Base/AMReX.cpp commit 22920e65ced01ddabcfdc52aabe763db7cee0ef8 Author: Max Katz Date: Mon Sep 30 18:06:37 2019 -0700 Add flag for enabling ptxas verbosity Tools/GNUMake/Make.defs Tools/GNUMake/comps/nvcc.mak commit cf2d049e030c233191062ade79a11c7cc76b9420 Author: Max Katz Date: Mon Sep 30 18:06:09 2019 -0700 Do not use device_prop.uuid for CUDA < 10 Src/Base/AMReX_GpuDevice.cpp commit 252075f0e3bb8d386bd5184069d827ef89b30201 Author: Max Katz Date: Mon Sep 30 16:39:46 2019 -0700 Add Device method for returning GPU model name Src/Base/AMReX_GpuDevice.H commit eaf52bfab001ea21e160686edc9c5027b196174d Author: Weiqun Zhang Date: Mon Sep 30 12:51:34 2019 -0700 gpu nodal rap: interpadd Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 60efe17127489c72aa65395783f67021530ef2d4 Author: Andrew Myers Date: Mon Sep 30 12:32:43 2019 -0700 tweak these prints as well Tests/Particles/NeighborParticles/MDParticleContainer.cpp commit d1fe3d525f8b95bb1440ee57124ff925cee931c3 Author: Andrew Myers Date: Mon Sep 30 12:29:54 2019 -0700 tweak this test to diff a plain txt file Tests/Particles/NeighborParticles/MDParticleContainer.cpp Tests/Particles/NeighborParticles/main.cpp commit df2a588594569f6566c469ce7e7df9a82e0b4286 Merge: f5abd965c 08ca414aa Author: cgilet Date: Mon Sep 30 14:15:46 2019 -0400 Merge remote-tracking branch 'upstream/development' into mltensor_corner_fill_fix Conflicts: Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 05e26be781a0007f9ab42fa0cd8302cdf94bbed8 Author: Andrew Myers Date: Mon Sep 30 11:05:37 2019 -0700 add more inputs scripts to the redistribute test for regression testing Tests/Particles/Redistribute/inputs.rt.cuda Tests/Particles/Redistribute/inputs.rt.cuda.mr Tests/Particles/Redistribute/inputs.rt.cuda.nonperiodic commit f5abd965cbc6cbfc72e06e9999b661ee901213a5 Author: cgilet Date: Mon Sep 30 12:04:34 2019 -0400 Updates for 3D. Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 513285140f2439c58eacbdb72ba779300e372a25 Author: Weiqun Zhang Date: Sun Sep 29 21:37:49 2019 -0700 gpu nodal: jacobi stencil version Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 188a86b7e164559cdb9870556092b2809eca5c18 Author: Weiqun Zhang Date: Sun Sep 29 21:27:38 2019 -0700 gpu nodal: gauss seidel stencil version Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 9e394158e360edf6724da39318ff841a09ce3688 Author: Weiqun Zhang Date: Sun Sep 29 21:07:21 2019 -0700 gpu nodal: normalize stencil version Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 8036a9af14aeda487d22f1eec0b4997123a4c330 Author: Weiqun Zhang Date: Sun Sep 29 20:47:05 2019 -0700 gpu nodal: A dot x stencil version Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 9c621b87a6e7a5948305e1e96c8b2c8fcd12fbf8 Author: Weiqun Zhang Date: Sun Sep 29 20:29:01 2019 -0700 nodal gpu: set stencil Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 37ee49354acb3c0061354c3f71d74ba21c7e6744 Author: Weiqun Zhang Date: Sun Sep 29 17:02:20 2019 -0700 gpu nodal: fill bc for nodal phi Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp commit a410e97e96ba67a296daf329d4b8d1f56fcd69f7 Author: Weiqun Zhang Date: Sun Sep 29 15:56:33 2019 -0700 gpu nodal: fix bug Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit b9ebae323021e87930a440de9884a9f7274cc4ab Author: Weiqun Zhang Date: Sun Sep 29 15:24:39 2019 -0700 2d compiles Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H commit 789f7cf8ee888dd5ce2f6b8fb1b6fef9a9daab0c Author: Weiqun Zhang Date: Sun Sep 29 15:04:37 2019 -0700 gpu nodal: fill bc for sigma Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp commit 9bd7b2478bf9445e806bb8b677f3e2b5ca8e34fe Merge: cbf2b6ed6 d06bb0163 Author: Weiqun Zhang Date: Sun Sep 29 07:24:20 2019 -0700 Merge branch 'development' into weiqun/dev commit 08ca414aae319cc16bd17e5a3e1f8d7f321843b3 Author: Ann Almgren Date: Sat Sep 28 17:26:10 2019 -0700 Update MAC projector documentation to reflect that, when USE_EB=TRUE, we must now specify whether the incoming (and outgoing) face velocities are defined on face centers or centroids Docs/sphinx_documentation/source/LinearSolvers.rst commit 3db27393026313980c9aad7598701c04009e9f4c Author: Ann Almgren Date: Sat Sep 28 17:21:13 2019 -0700 Create interface in the absence of EB that does not require the specification of FaceCenter vs FaceCentroid. Src/LinearSolvers/MLMG/AMReX_MacProjector.H commit 11a75a4f85d1ea97ab1b9167c56112a2fcde3326 Merge: 5eb1284f5 a77df29d1 Author: Ann Almgren Date: Sat Sep 28 17:12:03 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 5eb1284f5f728d4c02252802062fcf59745ad4eb Author: Ann Almgren Date: Sat Sep 28 17:11:11 2019 -0700 We must now specify whether the MAC projection is being given normal velocities at face centers or at face centroids. Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MacProjector.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp commit a77df29d1ac3a3065a66f07439b575770f280259 Author: Weiqun Zhang Date: Sat Sep 28 12:58:30 2019 -0700 fix the inputs for gpu regression test Tutorials/GPU/CNS/Exec/RT/inputs-rt commit e89aa2e81aa5295d975315346f304c2ecfaea32a Author: Weiqun Zhang Date: Sat Sep 28 12:45:23 2019 -0700 add inputs for gpu regression tests Tutorials/GPU/CNS/Exec/RT/inputs-rt Tutorials/GPU/CNS/Exec/Sod/inputs-rt commit d015bc199db2be057818f0f2b74cafd0a3df33df Author: Weiqun Zhang Date: Fri Sep 27 22:51:18 2019 -0700 add garuda Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.ccse commit 0c66e507bff803685156a885bf40151c28ba8fbe Author: Kevin Gott Date: Fri Sep 27 17:01:08 2019 -0700 BaseFab host device. Src/Base/AMReX_BaseFab.H commit dbbdc9147b545e5f8888c61a38f28ccc53884c52 Author: Kevin Gott Date: Fri Sep 27 16:40:18 2019 -0700 __host__ __device__ on declarations and functions test. Src/Base/AMReX_IntVect.H commit 549441a02e361f50cac1766b75c40f00721c1217 Author: Kevin Gott Date: Fri Sep 27 16:36:06 2019 -0700 Corresponding HIP makefile for the build system. Tutorials/Basic/HelloWorld_C/GNUmakefile commit 04c807e00fe2000cf5729a1c621d3c27f5d1aec7 Author: Kevin Gott Date: Fri Sep 27 16:35:35 2019 -0700 Add hip library. Why is this needed? It's in AMReX_Gpu.H Src/Base/AMReX_GpuQualifiers.H commit ccaa8ac08229ba7967ebd4b8a75fa13c5f633968 Author: Kevin Gott Date: Fri Sep 27 16:35:06 2019 -0700 Quick first hack-y build system update for HIP. Tools/GNUMake/Make.defs Tools/GNUMake/comps/hip.mak commit d06bb0163dccaf90727384a9fa1fadde83c89885 Author: Michele Rosso Date: Fri Sep 27 12:32:23 2019 -0700 CMake: fix typo Src/Extern/Conduit/CMakeLists.txt commit 1eb71314a37ce3f2ed4ba89100332dc27a2bffd0 Author: Max Katz Date: Fri Sep 27 09:44:22 2019 -0700 Count number of GPUs used in total Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp commit fb8979ed4241e61f2224fd6a2920fdfced349ab5 Merge: 601a9b9a1 f9faeb44e Author: WeiqunZhang Date: Thu Sep 26 17:11:36 2019 -0700 Merge pull request #578 from ax3l/topic-userLiteralForParticleReal C++ User Literal for amrex::ParticleReal (_prt) commit f9faeb44eca7f77e372630e71c39ee7996ca0042 Author: Axel Huebl Date: Thu Sep 26 17:05:40 2019 -0700 Typo & Doxygen Src/Base/AMReX_REAL.H commit 847031eeed14ba317c8f430eb7ebf3cfca011cb9 Author: Axel Huebl Date: Thu Sep 26 16:33:08 2019 -0700 C++ User Literal for amrex::ParticleReal (_prt) Same as the literal for `amrex::Real`. Src/Base/AMReX_REAL.H commit 601a9b9a14f5c611453c940a447de52825b8a342 Merge: 0e72ccbae 6bd523064 Author: WeiqunZhang Date: Thu Sep 26 16:17:04 2019 -0700 Merge pull request #577 from ax3l/topic-userLiteralForReal C++ User Literal for amrex::Real (_rt) commit 6bd523064f73b5b34287953a7019cee8e62ce15b Author: Axel Huebl Date: Thu Sep 26 15:30:57 2019 -0700 Use new Real literal in code base Src/Amr/AMReX_Amr.cpp Src/AmrCore/AMReX_AmrCore.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/Base/AMReX_FArrayBox.cpp Src/Particle/AMReX_Particle.H Src/Particle/AMReX_ParticleContainerI.H commit 2740beba2747512312aeddb7e64508cffa74e199 Author: Axel Huebl Date: Thu Sep 26 15:32:16 2019 -0700 C++ User Literal for amrex::Real (_rt) This adds a user literal for `amrex::Real`. This is a C++11 feature and allows to type constants properly instead of relying on implicit conversation. A typical fallacy is the following user code: ```C++ auto const mypi = 3.14; Real const sphere_volume = 4/3 * mypi * pow(r,3); ``` The first term `4/3` makes the whole expression an `int` until the result is casted to `amrex::Real`. Urgh! We can do better, with `amrex::Real(4)/::amrex:Real(3)` but who wants to write such verbose code, right? So C++11 user literals to the rescue! ```C++ auto const mypi = 3.14_rt; // that's a real, too! Real const sphere_volume 4_rt / 3_rt * mypi * pow(r,3); ``` Src/Base/AMReX_REAL.H commit 0e72ccbaea4726a50b384e7dfd82bf16d63ba317 Merge: 269c594d2 32ebb6ef0 Author: Andrew Myers Date: Thu Sep 26 17:55:41 2019 -0400 Merge branch 'development' into multilevel_gpu_redistribute commit 32ebb6ef0e6d9b9bd26742cfe9fb91888d246579 Author: Weiqun Zhang Date: Thu Sep 26 14:51:14 2019 -0700 add int8_t support in typecheck Tools/typechecker/typechecker.py commit 379f3a32d425e0e0f7ce795ecf841bac64cfd86c Author: Weiqun Zhang Date: Thu Sep 26 14:49:29 2019 -0700 add amrex::Long Src/Base/AMReX_BLFort.H Src/Base/AMReX_INT.H Src/Base/AMReX_IntVect.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 269c594d219431df59461773806fc8057c302c83 Author: Andrew Myers Date: Thu Sep 26 17:46:34 2019 -0400 handle case that people have added particles on grids that aren't owned by the proc in question Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H commit 9795a115a655d76d8640808ec6685f5540c83718 Merge: b4878b2d9 dd454d645 Author: Andrew Myers Date: Thu Sep 26 13:37:50 2019 -0700 Merge pull request #576 from AMReX-Codes/single_precision various fixes for single precision and particle real commit dd454d6453482280bc50558dc8cf66d9c451cccb Author: Weiqun Zhang Date: Thu Sep 26 13:30:13 2019 -0700 various fixes for single precision and particle real Src/Base/AMReX_REAL.H Src/Base/AMReX_VectorIO.H Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H Src/Particle/AMReX_Particle.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_Particle_mod_K.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_StructOfArrays.H Src/Particle/AMReX_TracerParticle_mod_K.H commit f01ab73cce078d94d8690685a958a97b9bc51bc2 Author: Andrew Myers Date: Thu Sep 26 15:37:05 2019 -0400 remove m_need_handshake, which isn't used any more Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 2b38cbc144d8ff520f8c8ca877eb85558d82b2bf Author: Andrew Myers Date: Thu Sep 26 15:36:50 2019 -0400 update neighbor_copy_op with level information Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 04dcdcd1c6fb033a77e86466f9089aa425874cd7 Author: Andrew Myers Date: Thu Sep 26 15:11:26 2019 -0400 also remove the redistribute mask from enforce periodic Src/Particle/AMReX_ParticleContainerI.H commit 7326602dcde8baac331da913092a9413aa29bd5e Author: Andrew Myers Date: Thu Sep 26 14:38:01 2019 -0400 don't need mask in RedistributeGPU any more Src/Particle/AMReX_ParticleContainerI.H commit cbf2b6ed6657905929424408242b418a5d99e87d Author: Weiqun Zhang Date: Wed Sep 25 21:23:37 2019 -0700 gpu nodal: interpadd Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 8b8596a2b0cd72496b19260c3b43c5aed3a3791a Merge: 4995f4850 b4878b2d9 Author: Andrew Myers Date: Wed Sep 25 17:50:57 2019 -0700 Merge branch 'development' into multilevel_gpu_redistribute commit 4995f4850fcca7a976ce14fffc340c6907dbd356 Author: Andrew Myers Date: Wed Sep 25 17:29:02 2019 -0700 skip invalid particles in numOutOfRange Src/Particle/AMReX_ParticleUtil.H commit b4878b2d9fb49459613fd75481faba994026261e Author: Ann Almgren Date: Wed Sep 25 17:25:52 2019 -0700 fix formatting? Docs/sphinx_documentation/source/BuildingAMReX.rst commit 8d19d87cebcd5c541a511c8309c007a0d0cd710c Author: Ann Almgren Date: Wed Sep 25 16:54:15 2019 -0700 Add comments about AMReX on Windows (per Weiqun) Docs/sphinx_documentation/source/BuildingAMReX.rst commit 865d0cc869a28bbeb652e25e587fde0d65858e90 Author: Andrew Myers Date: Wed Sep 25 15:00:19 2019 -0700 update test for 1 and 2D Tests/Particles/Redistribute/main.cpp commit d1ac695c7065cf2d2c3404abb71436404ca59b5b Author: Andrew Myers Date: Wed Sep 25 14:35:20 2019 -0700 add methods for changing the geometry object of particle locator Src/Particle/AMReX_ParticleLocator.H commit e87b9fb0d9c6fe408ffa6bdbea1f7addf80fe546 Author: Andrew Myers Date: Wed Sep 25 14:34:25 2019 -0700 need to set lev_max here Src/Particle/AMReX_ParticleContainerI.H commit 4323f4a92fc6e7047f2f14e72d4f451616d07281 Author: Andrew Myers Date: Wed Sep 25 13:21:47 2019 -0700 need to clamp these quantities in 2D Src/Particle/AMReX_ParticleLocator.H commit a048ccd734f6111a8d92192d9adaa175ff49d5b6 Merge: f14ddd316 7887bec4e Author: Weiqun Zhang Date: Wed Sep 25 12:37:01 2019 -0700 Merge branch 'development' into weiqun/dev commit 7887bec4e42d0159a8363ea3412bf38302a95af9 Merge: 262253405 6b6541b82 Author: WeiqunZhang Date: Wed Sep 25 09:14:57 2019 -0700 Merge pull request #574 from awehrfritz/UNSW Tools/GNUMake - Add Australian machines commit 262253405762f0fe6157811b03a5359fb01039b7 Merge: cbaf25271 e8b2897fb Author: Andy Nonaka Date: Wed Sep 25 08:07:28 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit cbaf25271fec4e4af2f3f6d9bfe0f8d22c550a84 Author: Andy Nonaka Date: Wed Sep 25 08:07:09 2019 -0700 note about subset -> levels in VisIt Docs/sphinx_documentation/source/Visualization.rst commit e8b2897fbad5000bfed9217593c4f9e95f467412 Author: Ann Almgren Date: Tue Sep 24 18:02:57 2019 -0700 slight clean-up of tensor solve section Docs/sphinx_documentation/source/LinearSolvers.rst commit f14ddd3165a1f4f40f7ffad32e1e823d31b27d09 Author: Weiqun Zhang Date: Tue Sep 24 16:57:12 2019 -0700 gpu nodal: restriction Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 1a5ac037f25e1e67ddb94fe4401791611770731c Author: Ann Almgren Date: Tue Sep 24 16:38:19 2019 -0700 Add code snippet for calling the tensor solve explicitly Docs/sphinx_documentation/source/LinearSolvers.rst commit be66cdd8799bd3ca0407e5ff4ac6be6726201273 Author: Ann Almgren Date: Tue Sep 24 16:26:29 2019 -0700 update tensor stencil Docs/sphinx_documentation/source/LinearSolvers.rst commit 1092555104d6defbb56382fc116f951bf373be4b Author: Andrew Myers Date: Tue Sep 24 19:22:29 2019 -0400 fix new bug in ParticleBufferMap Src/Particle/AMReX_ParticleBufferMap.cpp commit e147f7ce2cfe86964988b699fcf930dcec353b43 Merge: e8f0f7e67 9c9a0a06a Author: Ann Almgren Date: Tue Sep 24 15:37:19 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit e8f0f7e676a47ebcd1077c9558b03eb97c95b789 Author: Ann Almgren Date: Tue Sep 24 15:35:48 2019 -0700 Update formulat in tensor solve documentation Docs/sphinx_documentation/source/LinearSolvers.rst commit b6573e052f209edaaf8cd00b80c8889b4a5da9e0 Author: Andrew Myers Date: Tue Sep 24 18:23:35 2019 -0400 fix assertion Src/Particle/AMReX_ParticleCommunication.H commit 71b522d2a69a6928389997056b6fad6d7ad1a7db Merge: 708e9c168 9c9a0a06a Author: Andrew Myers Date: Tue Sep 24 14:51:04 2019 -0700 Merge branch 'development' into multilevel_gpu_redistribute commit 9c9a0a06a8feebbb2c074523d1c66e560f590e47 Merge: 8d954539d 6b43d94ac Author: Andrew Myers Date: Tue Sep 24 14:50:22 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8d954539dd519c40b47210292236651adc4bd46c Author: Andrew Myers Date: Tue Sep 24 14:50:02 2019 -0700 make the return type of this function template match the function body Src/Base/AMReX_Tuple.H commit 708e9c1684eae233cb488fceb541b132a337121e Author: Andrew Myers Date: Tue Sep 24 14:49:26 2019 -0700 don't need to use std::forward here any more Src/Particle/AMReX_ParticleLocator.H commit 58d9ed56a23a468881abfcb134f7548257dca149 Author: Andrew Myers Date: Tue Sep 24 14:44:52 2019 -0700 need temporaries for the lev Src/Particle/AMReX_Particles.H commit 1b03d8222181d7090bbeea3ea0d072d1b1436123 Author: Andrew Myers Date: Tue Sep 24 14:39:01 2019 -0700 missed a factor of the level offset in building the buffer map Src/Particle/AMReX_ParticleBufferMap.cpp commit 6035739c4ddb08449c629a80e3c1ccc00d0aafd6 Author: Andrew Myers Date: Tue Sep 24 12:28:47 2019 -0700 use tuple in the grid assignor Src/Particle/AMReX_ParticleLocator.H commit c2965543d182d701ec902b739fcf876f81f28541 Author: Andrew Myers Date: Tue Sep 24 12:28:22 2019 -0700 computing dst lev Src/Particle/AMReX_ParticleContainerI.H commit c94faf1d98f21f8301b686e3a9f2b24dbb6a6d0e Author: Andrew Myers Date: Tue Sep 24 12:27:56 2019 -0700 lev -> dst_lev Src/Particle/AMReX_ParticleCommunication.H commit dd725ce778f21ec881665b3c4de28387ba27946b Author: Andrew Myers Date: Tue Sep 24 10:39:32 2019 -0700 more flexible construction for AmrParticleLocator Src/Particle/AMReX_ParticleLocator.H commit 65cfaf4e51378e64b0520edd756fe95c72adacfe Author: Andrew Myers Date: Tue Sep 24 10:27:26 2019 -0700 another form of () for the particle locator Src/Particle/AMReX_ParticleLocator.H commit cc7a096d9f353dd02eefa5f1dc54004b5da05c76 Author: Andrew Myers Date: Tue Sep 24 10:26:49 2019 -0700 move this call to outside the loop over levels Src/Particle/AMReX_ParticleContainerI.H commit 6b43d94acf9d6b6ff8fe02e75f24b4f3a9def543 Author: Weiqun Zhang Date: Tue Sep 24 09:49:31 2019 -0700 EB Tensor solver: enforce periodic boundary Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 4c9753effcb26ae91fed7c0ac59b58901aa0d982 Author: Weiqun Zhang Date: Mon Sep 23 21:28:00 2019 -0700 Tensor solver: enforce periodic boundary Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit d6621ef23e56b12c4d507b7ee30347098d6b9119 Author: Andrew Myers Date: Mon Sep 23 20:32:53 2019 -0400 move the loop over levels to inside the particle locator Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleLocator.H commit f6f9c07671099e8491ea4b16f04ffb723794f04a Author: Ann Almgren Date: Mon Sep 23 16:58:24 2019 -0700 update tensor stuff Docs/sphinx_documentation/source/LinearSolvers.rst commit 4c82eaf6a205a5f28a4a3c2acb52d9f4d0d8ade9 Author: Michele Rosso Date: Mon Sep 23 16:56:53 2019 -0700 MultiFab: add EB-aware implementation of norm0, max and min Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 1ab0ae0e695a6b17c7066073f7a6724642374062 Author: Andrew Myers Date: Mon Sep 23 19:56:48 2019 -0400 fix some (new) bugs in the particle locator Src/Particle/AMReX_ParticleLocator.H commit 009c0464c60d82abe0a1833dbdf2e4e644305d0e Author: Ann Almgren Date: Mon Sep 23 16:50:51 2019 -0700 Fix math Docs/sphinx_documentation/source/LinearSolvers.rst commit dd54261f0fea76edaee50c9717745ef7b6b0af8a Merge: 3a190dba3 bb5102a3d Author: Ann Almgren Date: Mon Sep 23 16:27:37 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 3a190dba32b0234a8d7162d530cde614ca0c0c10 Author: Ann Almgren Date: Mon Sep 23 16:27:05 2019 -0700 intro to tensor solve Docs/sphinx_documentation/source/LinearSolvers.rst commit bb5102a3d089c3970013d9fe8b5b682b9767a93a Author: Weiqun Zhang Date: Mon Sep 23 16:20:29 2019 -0700 fix tensor solver's domain bc corners Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit b8a0078969fbf6f8863f85134d11945f84aa9b03 Author: cgilet Date: Mon Sep 23 12:23:35 2019 -0400 A little clean-up Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit e551b6529b8e2d3a90421c1d3e47f0c29d24e31e Author: Ann Almgren Date: Mon Sep 23 08:44:02 2019 -0700 Fix 1 --> ncomp in AssignDensity; we were a bit mix-n-match before. Src/AmrCore/AMReX_AmrParticles.H commit c8de07def83a3d8cfc7cea04897886365e24c5d2 Merge: 604bfe578 7fba3e3dc Author: cgilet Date: Mon Sep 23 09:41:18 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit 7fba3e3dc355adfb80598f0a36cb781f952b2f9e Author: Weiqun Zhang Date: Sun Sep 22 18:09:40 2019 -0700 avoid gcc bug Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H commit f05a9a9bdfa46fdd63ae76b270cef3a4dce60515 Author: Weiqun Zhang Date: Sun Sep 22 17:36:38 2019 -0700 gpu nodal: gauss seidel Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit ee07f5946d9efb4d3761a59552aacd4c158cf2a7 Author: Weiqun Zhang Date: Sun Sep 22 17:00:01 2019 -0700 gpu nodal: jacobi Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit e06eaeb899c7b88cb2096832e09138450b03a35a Author: Weiqun Zhang Date: Sun Sep 22 16:25:04 2019 -0700 gpu nodal: normalize Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 6c269fc00fd944bcf38d273c73182e9146884ddf Author: Weiqun Zhang Date: Sun Sep 22 13:45:44 2019 -0700 fix 1d Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H commit 855a7cc83f01aede716128a21b3db67e3e32397e Merge: 025826679 8ff86c866 Author: Weiqun Zhang Date: Sun Sep 22 12:56:14 2019 -0700 Merge branch 'development' into weiqun/dev commit 0258266798dfcbcd5418c30f441ae200994b77e6 Author: Weiqun Zhang Date: Sun Sep 22 12:55:06 2019 -0700 gpu nodal: adotx aa version Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 4495a342a378e951987316dbb1ff672a0800d6ce Author: Weiqun Zhang Date: Sun Sep 22 12:34:23 2019 -0700 gpu nodal: adotx ha version Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 22806d9aec73f85cc926f495d704eab26c977a79 Author: Weiqun Zhang Date: Sun Sep 22 10:26:58 2019 -0700 nodal gpu: average down sigma Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 8ff86c866a91b050d76d6fb5b5adff827abf73ae Author: Weiqun Zhang Date: Sat Sep 21 21:08:57 2019 -0700 fix nodal mc test Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp commit fee4280d75b0ff547b3d2e181fbd2d0e43a4327d Author: Weiqun Zhang Date: Sat Sep 21 19:56:51 2019 -0700 gpu nodal: dot mask Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 30a1c7fcd01217fb51985225c27e9473dd9850f6 Author: Weiqun Zhang Date: Sat Sep 21 19:12:08 2019 -0700 gpu nodal: res mask Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit a87e9a69a253d4d8ce491f5d8102426344d997c3 Author: Weiqun Zhang Date: Sat Sep 21 19:05:32 2019 -0700 gpu nodal: dirichlet mask Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 63895bebe24b1f1bac1ad75d2ae040363db063d6 Author: Weiqun Zhang Date: Sat Sep 21 17:55:50 2019 -0700 gpu nodal: nodal mask Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 382ff1e37337101e8f4be2b1c97a5f4a25749b3d Author: Weiqun Zhang Date: Sat Sep 21 16:58:45 2019 -0700 gpu nodal: fix sign Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H commit 668c771c2ad2c3769336b7b05b540428a96ae67d Author: Weiqun Zhang Date: Sat Sep 21 09:19:32 2019 -0700 gpu nodal: pass the correct mask to divu Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 1730b80935297f0d67b4f979e4d697e38cbf7324 Author: Weiqun Zhang Date: Sat Sep 21 09:19:32 2019 -0700 gpu nodal: fix bug in the new Neumann BC Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H commit f0cd4972f5672fd8301eead35e63bb8fa648647d Author: Weiqun Zhang Date: Sat Sep 21 08:13:20 2019 -0700 gpu nodal: mknewu Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit a0c5e5bc49a5666b62046a9d7eb54af687a65dd8 Author: Weiqun Zhang Date: Sat Sep 21 07:43:24 2019 -0700 gpu nodal: rhcc Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit aecfaac0c9bb25f3efc37acb460476efa9419921 Author: Weiqun Zhang Date: Fri Sep 20 22:22:57 2019 -0700 gpu nodal: divu Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit f4e5f794a904b4f7c3fbf6f234a91a77c617ded8 Author: Weiqun Zhang Date: Fri Sep 20 21:36:54 2019 -0700 gpu nodal: impose neumann bc Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit c09df42b9c48d741b5d85240cb4153dd2544e51e Author: Weiqun Zhang Date: Fri Sep 20 18:50:00 2019 -0700 add AMREX_HOST_DEVICE_PARALLEL_FOR_?D Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchMacrosC.H Src/Base/AMReX_GpuLaunchMacrosG.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_iMultiFab.cpp Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_FabSet.cpp Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_MultiMask.cpp Src/Boundary/AMReX_YAFluxRegister.cpp Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBMultiFabUtil.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit f14e67fe31362271ffc662c7df6d4f3ed82771b6 Author: Weiqun Zhang Date: Fri Sep 20 16:55:38 2019 -0700 gpu nodal: ported some anyd functions Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_ND_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/Make.package commit 365e6fe25d53f73009711df529b22b77c928c186 Author: Andrew Myers Date: Fri Sep 20 19:52:02 2019 -0400 update Redistribute test for multiple levels Tests/Particles/Redistribute/inputs Tests/Particles/Redistribute/inputs.rt Tests/Particles/Redistribute/main.cpp commit eb5a3b0ece251ab929adab9fb446a8a88de96399 Author: Andrew Myers Date: Fri Sep 20 19:51:36 2019 -0400 fix error in level offset calculation in ParticleBufferMap Src/Particle/AMReX_ParticleBufferMap.cpp commit 0ec6b98c4a1a7f7c879693cb41ca299e2deda7ba Author: Weiqun Zhang Date: Fri Sep 20 16:24:20 2019 -0700 add some empty files in preparation for rewriting nodal solver kernels Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_ND_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/Make.package commit c5741c3453f02ee519e535d8505c7fd3a4c49972 Author: Andrew Myers Date: Fri Sep 20 19:14:47 2019 -0400 particle locator seems to be accounting for multiple levels correctly Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleLocator.H Src/Particle/AMReX_Particles.H commit e18c745c841f9fe7fe667ecfb0c60b6c6d662c39 Author: Weiqun Zhang Date: Fri Sep 20 16:12:55 2019 -0700 add a missing if(Gpu::notInLaunchRegion()) Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit 9a31237d3d33b03e033adca6bac12e1a8c502ee3 Author: Weiqun Zhang Date: Fri Sep 20 15:52:34 2019 -0700 MLMG: nodal interp on gpu Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_F.H Src/LinearSolvers/MLMG/AMReX_MLMG_K.H Src/LinearSolvers/MLMG/Make.package commit 47452a7f260a5bb593d879ec9d2110b96a0b3e3c Author: Andrew Myers Date: Fri Sep 20 18:35:01 2019 -0400 Amr version of ParticleLocator Src/Particle/AMReX_ParticleLocator.H commit 3704fab038f39f3ce235247649198754149b6de1 Author: Weiqun Zhang Date: Fri Sep 20 14:37:55 2019 -0700 MLMG: eb_cc_interp on gpu Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_3D_K.H commit 6dd2e53e55feb0a41d03375e9978852da5f07003 Author: Andrew Myers Date: Fri Sep 20 16:52:08 2019 -0400 do loop over levels throughout particle communication code Src/Particle/AMReX_ParticleCommunication.H commit ff6c0905821ed3f0f4556e119f223733dd9b9bd1 Author: Andrew Myers Date: Fri Sep 20 16:30:31 2019 -0400 add loop over levels to pack and build Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_Particles.H commit d201a99febec9afda90863fc7b621164a68d1e85 Author: Andrew Myers Date: Fri Sep 20 16:30:05 2019 -0400 methods for computing the neighbor procs on the fly, without as mask Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_ParticleUtil.cpp commit 29c931195fb62c97eb049c1f3acf1344ab93447f Author: Andrew Myers Date: Fri Sep 20 16:29:17 2019 -0400 a few more methods for particle buffer map Src/Particle/AMReX_ParticleBufferMap.H commit 0495381007db8b4f34e702c3ee6882b5940b5307 Author: Weiqun Zhang Date: Fri Sep 20 12:53:31 2019 -0700 add regression test inputs for EBTensor Tests/LinearSolvers/EBTensor/inputs.rt.3d commit 604bfe57864dea0d494c3d9110ca315ff51a38c1 Merge: 53d92ea59 9e3e53a18 Author: cgilet Date: Fri Sep 20 15:35:37 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit 729e587b1d8ec48e36015bae5ab85dbe696a0bab Merge: 98e7a291b 9e3e53a18 Author: cgilet Date: Fri Sep 20 15:34:50 2019 -0400 Merge remote-tracking branch 'upstream/development' into development commit 98e7a291b39232aaada90c239af5ad6a1d7ee688 Merge: 9761856f0 8bea79bc1 Author: cgilet Date: Fri Sep 20 15:27:58 2019 -0400 Merge remote-tracking branch 'upstream/development' into development commit 53d92ea59c9ff8f50cac7dfff77f0b7a3a093a3b Merge: b5b4458cd 8bea79bc1 Author: cgilet Date: Fri Sep 20 15:26:03 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit b5b4458cd482bc117305e876789a0f5ff4af4ccc Merge: 206b699ad 152654438 Author: cgilet Date: Fri Sep 20 15:10:09 2019 -0400 Merge branch 'TensorFluxes' of https://github.com/cgilet/amrex into TensorFluxes Conflicts: Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 206b699adc2f6ae8395ae29bb1c949311c34bff4 Author: cgilet Date: Fri Sep 20 14:10:31 2019 -0400 WIP - 2D now compiles 2D not tested further. Cut cell fluxes not yet defined correctly. Set to bogus val to know if they're being used. 3D not done yet. Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H commit 9e3e53a185ccd8b9319978017f4eaac2b5e9d7f6 Author: Weiqun Zhang Date: Fri Sep 20 09:47:02 2019 -0700 rm Gpu::LaunchSafeGuard from MLEBTensorOp::apply Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 0a32afc17c3e9111d802fee054dd9032295794e1 Author: Weiqun Zhang Date: Thu Sep 19 17:16:17 2019 -0700 fix habec Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit 7409a2954fc262744fd58564fecb53e3c4e2c881 Author: Weiqun Zhang Date: Thu Sep 19 15:48:10 2019 -0700 MLEBABecLap::interpolation on gpu and rm deprecated files Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H Src/LinearSolvers/MLMG/AMReX_MG_K.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H Src/LinearSolvers/MLMG/Make.package commit 0ca550a1cba9470c0c15adaab4a7e728bfa0c568 Author: Andrew Myers Date: Thu Sep 19 18:54:06 2019 -0400 generalize the ParticleCopyOp for multi-level Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H commit 5ae0c56b22f684f3c3c75fba553ea76e56910613 Merge: 8b333c594 5bcbf0158 Author: Weiqun Zhang Date: Thu Sep 19 13:35:40 2019 -0700 Merge branch 'master' of github.com:AMReX-Codes/amrex commit ee5afb44cae36bab87a248c5d760965621727f17 Author: Weiqun Zhang Date: Thu Sep 19 13:27:09 2019 -0700 MLEBABecLap::normalize on gpu Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H commit 4d2800ed9c71c329ca99de66971a1171dfbbdbda Author: Andrew Myers Date: Thu Sep 19 14:55:24 2019 -0400 extending the particle buffer map to work with multiple levels Src/Particle/AMReX_ParticleBufferMap.H Src/Particle/AMReX_ParticleBufferMap.cpp Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H commit d8a6f643d26f843d7840b33ef4d024b1aa8ff4b3 Author: Weiqun Zhang Date: Thu Sep 19 09:48:13 2019 -0700 clean up Src/Base/AMReX.cpp Src/Base/AMReX_FabArray.H commit 6b6541b82888047dbedf49b271d16a34d3de7017 Author: Armin Wehrfritz Date: Thu Sep 19 03:47:11 2019 +1000 Tools/GNUMake - Add Australian machines Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.nci Tools/GNUMake/sites/Make.pawsey commit cc850f3c226bf3601a5cdf64882ebcf9fcc5a488 Merge: 76b13c404 80b8217f7 Author: Weiqun Zhang Date: Wed Sep 18 18:31:16 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 76b13c404350209767b1f3bed8d9719ce93bfc84 Author: Weiqun Zhang Date: Wed Sep 18 18:28:37 2019 -0700 cleanup Src/Base/AMReX_GpuLaunchFunctsG.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H commit 80b8217f7b5935ab252bda506ef62a9036233926 Author: Stefan Vater Date: Thu Sep 19 03:28:14 2019 +0200 some modifications for the Nodal poisson tutorial program (#563) * - fixed exact solution for 2d - added plotting routine * added averaging from nodal to cell values for plotting Tutorials/LinearSolvers/NodalPoisson/Make.package Tutorials/LinearSolvers/NodalPoisson/MyTest.H Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp Tutorials/LinearSolvers/NodalPoisson/MyTestPlotfile.cpp Tutorials/LinearSolvers/NodalPoisson/main.cpp commit 8711847fabd23b791102cee40f0b5a41cfd7eeaa Author: Weiqun Zhang Date: Wed Sep 18 15:32:02 2019 -0700 MLEBABecLap::compGrad on gpu Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H commit 6ac8d216cd6be9bc5bd78a76738e25ad11902f94 Author: Weiqun Zhang Date: Wed Sep 18 12:51:56 2019 -0700 MLEBABecLap::FFlux on gpu Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit f5982cba3cb6cc2419cc854b031a4ee75dfb33a9 Author: Weiqun Zhang Date: Tue Sep 17 17:24:58 2019 -0700 cleanup Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H commit fe0d367630173204a66693ea0e8df82c649c0e74 Merge: 8e766a0a9 ad1556b95 Author: Andrew Myers Date: Tue Sep 17 15:28:56 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8e766a0a9198787221df0f33fd01e662b6e406ae Author: Andrew Myers Date: Tue Sep 17 15:28:39 2019 -0700 remove incorrect assertion(s) Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit ad1556b95893ef63847a905b1d1b1dc3278ea5a4 Author: Weiqun Zhang Date: Tue Sep 17 15:26:38 2019 -0700 manually write out the loops so that gcc 8 does not crash Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H commit 4bd9128689f404636566b990ef9587cf9b589b40 Author: Weiqun Zhang Date: Tue Sep 17 15:06:24 2019 -0700 fix new bug: have to rebuild array4 because fab has been shifted Src/Boundary/AMReX_MultiMask.cpp commit 7fb3f3137741b8e5d7e3c79ba8d84ad3eae7c69c Author: Weiqun Zhang Date: Tue Sep 17 14:55:00 2019 -0700 fix typo Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H commit a8c42f72a22e6e959eae9889f23701dbbaeb6c2d Author: Weiqun Zhang Date: Tue Sep 17 13:42:11 2019 -0700 fix a new bug I merged into development this morning. The original beta has only one component. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit a3cbbc33ed11558c8d60099ad8a4402e80ce5989 Author: Ann Almgren Date: Tue Sep 17 12:27:02 2019 -0700 Update nodal projection code snippet Docs/sphinx_documentation/source/LinearSolvers.rst commit 2810d4ee465736b74546f8f793b70091bed72b03 Author: Ann Almgren Date: Tue Sep 17 11:46:16 2019 -0700 Update formatting slightly and README. Tutorials/LinearSolvers/MAC_Projection_EB/README Tutorials/LinearSolvers/Nodal_Projection_EB/README Tutorials/LinearSolvers/Nodal_Projection_EB/main.cpp commit 547a35bcdbd71df03aec74e0f35088279c799b67 Merge: ad44f42a8 be6099872 Author: Weiqun Zhang Date: Tue Sep 17 11:40:11 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ad44f42a8e7eab503f4450a09fdf5b6e489107ee Author: Weiqun Zhang Date: Tue Sep 17 11:39:53 2019 -0700 fix Nodal_Project_EB tutorial Tutorials/LinearSolvers/Nodal_Projection_EB/main.cpp commit be6099872c053ceb170abfe36a75a40565a551a2 Merge: 0163f2c31 f05738efb Author: asalmgren Date: Tue Sep 17 11:11:49 2019 -0700 Merge pull request #569 from AMReX-Codes/fi_lincomb_fix Fix indexing in fortran interface for MultiFab::LinComb commit f05738efbdfe999eb6ff87616c7247d200fb5504 Author: Donald E. Willcox Date: Tue Sep 17 11:06:04 2019 -0700 Decrement source component for multifab 2 in amrex_multifab_lincomb for the Fortran interface. Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 1cf917f16228e44787f53674317e9bb303d8bcb7 Merge: 0163f2c31 c06a87761 Author: Weiqun Zhang Date: Tue Sep 17 11:02:28 2019 -0700 Merge branch 'weiqun/dev' into development commit 0163f2c3166aea51671d89f313a5577db1506fec Author: Ann Almgren Date: Tue Sep 17 10:37:40 2019 -0700 Update documentation about tutorials. Docs/sphinx_documentation/source/LinearSolvers.rst Docs/sphinx_tutorials/source/LinearSolvers_Tutorial.rst commit bfab45347f260d3932e72e08b48d6103feb97666 Author: Ann Almgren Date: Tue Sep 17 10:08:12 2019 -0700 Add example of nodal projection with EB analogous to the example in MAC_Projection_EB. Current commit does not compile. Tutorials/LinearSolvers/Nodal_Projection_EB/GNUmakefile Tutorials/LinearSolvers/Nodal_Projection_EB/Make.package Tutorials/LinearSolvers/Nodal_Projection_EB/README Tutorials/LinearSolvers/Nodal_Projection_EB/inputs_3d Tutorials/LinearSolvers/Nodal_Projection_EB/main.cpp commit 77464a2dc1aea64850e03df06d46727ac31d024d Author: Ann Almgren Date: Tue Sep 17 08:11:32 2019 -0700 Simplify the EB MAC projection tutorial so it just sets nine obstacles rather than reading in the IDs from the inputs Tutorials/LinearSolvers/MAC_Projection_EB/README Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp commit bc4cb2a66373ee1e6fdbb34cbcc2d73cf8da0631 Author: Andrew Myers Date: Mon Sep 16 19:22:40 2019 -0400 slight optimization(s) Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H commit 1eb8c0bb73235dcdff40b691939e8cf7d8ab7471 Merge: 7aeb51867 813d80eff Author: Michele Rosso Date: Mon Sep 16 14:32:35 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 7aeb51867b6bf0e5cfd557a2c14e06aa502c5464 Author: Michele Rosso Date: Mon Sep 16 14:32:22 2019 -0700 Update doc on nodal projection Docs/sphinx_documentation/source/LinearSolvers.rst commit 8f3cd7e2cd1cf100ae77acf8a071fbd7c2270295 Author: cgilet Date: Mon Sep 16 16:37:59 2019 -0400 WIP - make sure coarse-fine boundary corner cells get filled for AllPeriodic case. fix const qualifier in relation to m_bndry_sol in applyBCTensor. 2D seems to work 3D not finished yet Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 813d80eff45ef11551f40841de250c4e4939cc39 Author: Andy Nonaka Date: Mon Sep 16 12:21:40 2019 -0700 small update to docs Docs/sphinx_documentation/source/AmrLevel_Chapter.rst commit a51369da052cf58647dccc648ef9835deb78f67d Author: cgilet Date: Mon Sep 16 15:10:58 2019 -0400 WIP - Add MLEBTensorOp::compFluxes(). Needs testing. Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit c06a8776144148ad95ef6bfd64f3d99fcf97f86a Author: Weiqun Zhang Date: Sun Sep 15 13:09:22 2019 -0700 WIP: MLEBABecLap: gsrb on gpu Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H commit 7d51de29b245dc14ee2184f472d3048f573e1771 Author: Weiqun Zhang Date: Sun Sep 15 15:26:35 2019 -0700 EB nodal solver: average cell-centered rhs to node Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 0d84e6624b9cd3e4b22be3393990c96728fc4b6b Author: Ann Almgren Date: Sun Sep 15 07:03:34 2019 -0700 update documentation re bc's for linear solvers Src/LinearSolvers/MLMG/AMReX_MLLinOp.H commit 885d754073edc9bf56d400c5fb246e9455116a93 Author: Ann Almgren Date: Sun Sep 15 07:03:18 2019 -0700 Add more detail re bc's for linear solvers Docs/sphinx_documentation/source/LinearSolvers.rst commit 2b5a4aea43255fd1a0d91418c16e282c5c08c4f7 Author: Ann Almgren Date: Sat Sep 14 19:15:30 2019 -0700 Update to section on Linear Solvers: Boundary Conditions Docs/sphinx_documentation/source/LinearSolvers.rst commit 56d630a1c6eaf2dc1d72d0dd47a62e3bf9c71a0a Author: Weiqun Zhang Date: Sat Sep 14 16:47:22 2019 -0700 MLEBABecLap: adotx on gpu Src/Base/AMReX_Array4.H Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H Src/LinearSolvers/MLMG/Make.package commit 26b39e1409f04c60a69a57bc7dc44922e4a3ddef Merge: 9a5b0bb87 6f9899a7d Author: Michele Rosso Date: Sat Sep 14 16:53:01 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 9a5b0bb871040ea79efe76ee58987bb4a129e3ed Author: Michele Rosso Date: Sat Sep 14 16:52:48 2019 -0700 CMake: add missing include statement Tools/CMake/AMReXTargetHelpers.cmake commit 6f9899a7daf4285562ae55e67dfd2c1f2b305332 Author: Ann Almgren Date: Sat Sep 14 16:43:12 2019 -0700 Update the solver bc stuff and the MacProjection section. Docs/sphinx_documentation/source/LinearSolvers.rst commit e96d7d3313e04d207e2299e02a89e67b27fc5a8c Author: Ann Almgren Date: Sat Sep 14 15:31:18 2019 -0700 Update section about boundary conditions for linear solvers Docs/sphinx_documentation/source/LinearSolvers.rst commit 82d6740a2a3c242a8bc3cf34125fc3a356e15ec2 Author: Ann Almgren Date: Fri Sep 13 20:15:49 2019 -0700 fix typos Docs/sphinx_documentation/source/LinearSolvers.rst commit b245cf834a35886ecc699d3207bcca38cc6541ec Author: Weiqun Zhang Date: Fri Sep 13 18:30:41 2019 -0700 more gpu support in MLEBABecLap Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 0f85e86799fc2f2b98ac1c19ad2edc0dcc94a0ab Author: Weiqun Zhang Date: Fri Sep 13 17:44:37 2019 -0700 update FlowerIF Tests/LinearSolvers/CellEB/MyEB.H Tests/LinearSolvers/CellEB2/MyEB.H Tests/LinearSolvers/EBConvergenceTest/MyEB.H Tests/LinearSolvers/EBflux_grad/MyEB.H commit 8bea79bc1b791cc03fb84c0c33f6785e55b7225b Merge: c74a301f3 710a6e27c Author: Michele Rosso Date: Fri Sep 13 17:40:12 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit c74a301f37824f9ce07eb7ed1b3ee8dc6b89acfe Author: Michele Rosso Date: Fri Sep 13 17:39:58 2019 -0700 Doc: add snippet for nodal projection Docs/sphinx_documentation/source/LinearSolvers.rst commit 46945f64c1f86ba53cac0e9c8527ac3ea73ce3f9 Merge: e5f38ef0b 710a6e27c Author: Weiqun Zhang Date: Fri Sep 13 11:58:59 2019 -0700 Merge branch 'development' into weiqun/dev commit 710a6e27cd66ceae50be12d7f3ea8a531467487e Merge: a14fc38b5 4b8c74ab0 Author: WeiqunZhang Date: Fri Sep 13 11:16:23 2019 -0700 Merge pull request #560 from bcfriesen/bcf/cce9 Tools: update compiler flags for Cray compiler v9 commit 4c2f0c3777aed2b5431b84e81efbbfd8f6a91afb Merge: fd1f8a178 a14fc38b5 Author: cgilet Date: Fri Sep 13 10:41:01 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit 9dc876f06e0105796fb99c66f3fac76359410c92 Author: cgilet Date: Fri Sep 13 10:28:02 2019 -0400 WIP - 2D appears to work for MLTensorOp not fully tested yet Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_nd_K.H commit a14fc38b5cd72cea29d3266786a3d9c6a1af6380 Merge: e862c7cad 874ff1463 Author: Michele Rosso Date: Thu Sep 12 16:41:29 2019 -0700 Merge branch 'mr/cmake' into development commit 874ff1463ec98d52a20be9a48bd01e5586539c9a Author: Michele Rosso Date: Thu Sep 12 16:07:02 2019 -0700 Revert "CMake: improve handling of arguments passed to makebuildinfo.py" This reverts commit d5b3fc454829f592002b11978becbbcf9fc5262e. Tools/CMake/AMReXBuildInfo.cmake commit d5b3fc454829f592002b11978becbbcf9fc5262e Author: Michele Rosso Date: Thu Sep 12 14:42:51 2019 -0700 CMake: improve handling of arguments passed to makebuildinfo.py Tools/CMake/AMReXBuildInfo.cmake commit f4541be06e99d6bef4322a98dfc3f1f7a6c82af5 Author: Michele Rosso Date: Thu Sep 12 13:34:27 2019 -0700 CMake: add quotes to arguments when invoking build info script Tools/CMake/AMReXBuildInfo.cmake commit e862c7cad8cde6df6f042d18a9643050a36748cf Author: Ann Almgren Date: Thu Sep 12 12:50:52 2019 -0700 Add first text about nodal approximate projection. Docs/sphinx_documentation/source/LinearSolvers.rst commit a470582609c7c15f37564a8959d9d1f01c695951 Author: Ann Almgren Date: Thu Sep 12 11:34:31 2019 -0700 Update to reflect we can't do level solves with this functionality yet. Docs/sphinx_documentation/source/LinearSolvers.rst commit e7a7197ef6e5346ad428c17acb52e89111561e0c Author: Michele Rosso Date: Thu Sep 12 10:55:07 2019 -0700 CMake: use verbatim mode to issue command to makebuildinfo python script Tools/CMake/AMReXBuildInfo.cmake commit 46e31853f16b646e7623f80c200092f0cc7d354e Author: Ann Almgren Date: Thu Sep 12 02:57:18 2019 -0700 add inhomog Neumann as boundary type Docs/sphinx_documentation/source/LinearSolvers.rst commit e5f38ef0b7cfdbbe81159f06b233b143cfe7e658 Author: Weiqun Zhang Date: Wed Sep 11 16:54:28 2019 -0700 prepare some linear solver tests for gpu Tests/LinearSolvers/CellEB/MyTest.H Tests/LinearSolvers/CellEB/MyTest.cpp Tests/LinearSolvers/EBflux_grad/MyTest.H Tests/LinearSolvers/EBflux_grad/MyTest.cpp Tests/LinearSolvers/NodeEB/MyTest.H Tests/LinearSolvers/NodeEB/MyTest.cpp commit ccc31d3a7ed23107b78b25bff70d28fa821219e3 Author: Weiqun Zhang Date: Wed Sep 11 15:34:28 2019 -0700 gpu for Mask Src/Boundary/AMReX_MultiMask.cpp commit b4456bdcddd44b7c230bd180164fc4b843183da4 Author: Weiqun Zhang Date: Wed Sep 11 15:12:50 2019 -0700 add inhomogNeumann to opeartor<< and minor clean up Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_LO_BCTYPES.cpp commit dd44de3b579d5a97d73b05e4d84cdc7c9fde77c1 Author: Weiqun Zhang Date: Wed Sep 11 15:12:24 2019 -0700 minor changes to get NodalPoisson test compile with cuda Tutorials/LinearSolvers/NodalPoisson/MyTest.H Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp commit 2e630fa1f65f0aa41a87e7ac111129e1fd60d5e2 Merge: ff0562b0e 849b156cd Author: Andrew Myers Date: Wed Sep 11 17:57:47 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ff0562b0e85da1998c3b99a081eb7baa0a2a74b0 Author: Andrew Myers Date: Wed Sep 11 17:48:30 2019 -0400 always get the list of neighbor ranks from the redistribute mask Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_Particles.H commit 5a27509322f39b7b2f1b0ced4db0e87dcfd083fe Author: Andrew Myers Date: Wed Sep 11 17:47:53 2019 -0400 these memcopies need to be synchronous Src/Particle/AMReX_ParticleContainerI.H commit 849b156cdf2630ca3bc96c079372238bd2cd330c Merge: 7e4107cfc 87ae6d956 Author: WeiqunZhang Date: Wed Sep 11 14:32:53 2019 -0700 Merge pull request #561 from ax3l/topic-constCorrectness FabConv: Little Const-Correctness Params commit 7e4107cfcf8f972fc2ecf9ef791414c42d7280af Merge: 4de8483e8 14374b294 Author: WeiqunZhang Date: Wed Sep 11 14:31:14 2019 -0700 Merge pull request #562 from ax3l/doc-mpiCUDA Docs: Intro (+MPI/CUDA) commit 14374b2942e625ec8e079749f068b34aec7c0523 Author: Axel Huebl Date: Wed Sep 11 14:21:23 2019 -0700 Docs: Intro (+MPI/CUDA) Update the introduction in the docs: AMReX also supports MPI/CUDA these days :) Docs/sphinx_documentation/source/Introduction.rst commit 87ae6d956ff7971480427769610da28b5e20e5a6 Author: Axel Huebl Date: Wed Sep 11 14:15:13 2019 -0700 Little Const-Correctness Params Just two little places found when compiling WarpX with clang tidy and: https://clang.llvm.org/extra/clang-tidy/checks/readability-non-const-parameter.html Src/Base/AMReX_FabConv.cpp commit 4b8c74ab082d3cbc938c6a02359529602d0e3998 Author: Brian Friesen Date: Wed Sep 11 10:48:47 2019 -0700 Tools: update compiler flags for Cray compiler v9 In CCE 9, Cray overhauled their C/C++ compilers and moved to clang/LLVM, so the flags for C/C++ compilers are totally different than in previous versions of CCE. Confusingly, the Fortran compiler was *not* changed significantly in CCE 9, so its flags are the same as before. As a result, we need some more complex logic to get the right flags for the right version of CCE. Tools/GNUMake/comps/cray.mak commit 4de8483e8eb94521da3e093950094ba8c19934ed Author: cgilet Date: Wed Sep 11 13:43:10 2019 -0400 Fix typo, n-> icomp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 2913f6fc86f120da2b924a49f07c5ae417fc7cad Author: Weiqun Zhang Date: Wed Sep 11 10:22:16 2019 -0700 need to update the multi-component version of setDomainBC Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit f0c20884844f91826387825fcd08c0a09d3a4516 Author: Candace Gilet Date: Wed Sep 11 12:18:41 2019 -0400 Make sure Vector bounds check catches negative indices. (#559) * Make sure Vector bounds check catches negative indices. * Cleaner way to check Vector bounds Src/Base/AMReX_Vector.H commit 9761856f05a53e2f326e2edbd0b31c4192c6064a Merge: 3f3a112eb 1c4ccf63a Author: cgilet Date: Wed Sep 11 12:15:19 2019 -0400 Merge remote-tracking branch 'upstream/development' into development commit 3f3a112eb7883b452067ea6ab96f8148e0c41da8 Author: cgilet Date: Wed Sep 11 12:14:36 2019 -0400 Cleaner way to check Vector bounds Src/Base/AMReX_Vector.H commit 1c4ccf63a9fd2d8dde427acbb03b752aadc421a1 Author: Weiqun Zhang Date: Tue Sep 10 21:04:39 2019 -0700 inhomogeneous Neummann in curvilinear coordinates Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 813d84af454a5e63a2ce206bfd082c92db176cfc Author: cgilet Date: Tue Sep 10 20:55:03 2019 -0400 Make sure Vector bounds check catches negative indices. Src/Base/AMReX_Vector.H commit 2024e1eb9f1cd97478b2e2cad4512a46b3cb488c Merge: 8f0a3e2f7 c2973daf6 Author: Andrew Myers Date: Tue Sep 10 16:31:18 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8f0a3e2f79041b7dc36b9aa5e8cc72eab4ffb159 Author: Andrew Myers Date: Tue Sep 10 16:30:37 2019 -0400 need to add a Barrier at the start of communicateParticles Src/Particle/AMReX_ParticleCommunication.H commit c2973daf6d7e173ae7f98e38cd13e07092ac2ca7 Author: Weiqun Zhang Date: Tue Sep 10 10:33:12 2019 -0700 minor optimization Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H commit 28a188f8f1d2c15fbaa494338d1d117face3c676 Author: Weiqun Zhang Date: Tue Sep 10 09:56:54 2019 -0700 fix test problem boundary Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H commit 150be7eff61820b3977468169da7d70339f61117 Author: Weiqun Zhang Date: Mon Sep 9 22:15:45 2019 -0700 MLMG: inhomogeneous Neumann Src/Boundary/AMReX_LO_BCTYPES.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTestPlotfile.cpp Tutorials/LinearSolvers/ABecLaplacian_C/initProb.cpp Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H Tutorials/LinearSolvers/ABecLaplacian_C/inputs-inhomNeumann commit d6274065aae59a857d78b447e297039db57d7e15 Author: Weiqun Zhang Date: Sun Sep 8 16:12:05 2019 -0700 fix order of initialization Src/Particle/AMReX_ParticleLocator.H commit 3b71cec65230059ed855d85906a8d3e1787992da Author: Weiqun Zhang Date: Sun Sep 8 14:38:27 2019 -0700 fix some bugs in BaseFab Src/Base/AMReX_BaseFab.H commit b2def6857e169b4550e6cfc20af2adb4d3b513ab Merge: 681e26fcc e68fea90b Author: Weiqun Zhang Date: Sat Sep 7 18:28:41 2019 -0700 Merge branch 'weiqun/dev' into development commit e68fea90b25d62e5db25042253416c3b7eb6342e Author: Weiqun Zhang Date: Sat Sep 7 21:25:13 2019 -0400 fix type Src/Base/AMReX_GpuReduce.H commit 23fe1fdcaebf7de50f5a56c16a6fe05c68f965ed Author: Weiqun Zhang Date: Sat Sep 7 18:14:32 2019 -0700 fix new bug Src/Base/AMReX_GpuReduce.H commit e38ce09cbec46f7957a017816adbb75d125edf91 Author: Weiqun Zhang Date: Sat Sep 7 18:03:18 2019 -0700 minor Src/Base/AMReX_Reduce.H commit 7f2a0638b5dd6019eaac37402a698215d4eb3ef4 Author: Weiqun Zhang Date: Sat Sep 7 16:14:42 2019 -0700 optimization of iMultiFab::sum Src/Base/AMReX_iMultiFab.cpp commit 89c67d7719ef8b5f89a79de6fdaa5155e114acc4 Author: Weiqun Zhang Date: Sat Sep 7 15:56:16 2019 -0700 reimplement FabArray Reduce Src/Base/AMReX_FabArrayUtility.H commit 8379b5e693c5b18eb12695bed8231c8ca298477e Author: Weiqun Zhang Date: Sat Sep 7 15:55:34 2019 -0700 add ReduceOpLogicalAnd and Or Src/Base/AMReX_Reduce.H commit 5fb0534a1eaeb4881a8c024a67c2798932c4a509 Author: Weiqun Zhang Date: Sat Sep 7 14:53:00 2019 -0700 add deviceReduceLogicalAnd and Or Src/Base/AMReX_Functional.H Src/Base/AMReX_GpuReduce.H commit 681e26fcc5f278831fc872763cde7f6e8a442c48 Merge: be011ea23 9123506a9 Author: asalmgren Date: Sat Sep 7 13:08:12 2019 -0700 Merge pull request #558 from cgilet/development Development commit be011ea23dbf8191a16be6fa6c5bc0fe9302f582 Author: Weiqun Zhang Date: Sat Sep 7 12:22:36 2019 -0700 ReduceOps now takes lambda on Box Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_Reduce.H Src/Base/AMReX_Utility.H Tutorials/GPU/ParallelReduce/main.cpp commit 84d03ef59721e5d99eefa24ea901ee4cb8e02d8e Merge: b757ac5da 186ee7d0b Author: Michele Rosso Date: Fri Sep 6 16:44:55 2019 -0700 Merge branch 'mr/cmake' into development commit 186ee7d0b3fbf4b79efa01ef00cd4d6fe33e3326 Author: Michele Rosso Date: Fri Sep 6 16:41:45 2019 -0700 CMake: improve build summary printout Src/CMakeLists.txt Tools/CMake/AMReX_Config.cmake commit f409f198cda15d4078d159b1788e4e8163216555 Author: Michele Rosso Date: Fri Sep 6 15:19:24 2019 -0700 CMake: add comments to document new modules Tools/CMake/AMReXBuildInfo.cmake Tools/CMake/AMReXTargetHelpers.cmake commit 631c34c1bc72ef4f1ba7de9df7c94712e386bfc0 Author: Michele Rosso Date: Fri Sep 6 14:39:21 2019 -0700 CMake: add GIT info in BuildInfo Tools/CMake/AMReXBuildInfo.cmake commit b757ac5da35c89933fc9cf70a612337f53d02b8e Author: Weiqun Zhang Date: Fri Sep 6 12:41:41 2019 -0700 move -> forward because we have recently changed the parameters from r-value to forwarding reference Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H commit bc86cdaaaaf5270cfd5e5fbcb92855dcdba30b3a Author: Michele Rosso Date: Fri Sep 6 11:30:05 2019 -0700 CMake: make OpenMP imported targets GLOBAL Tools/CMake/AMReX_Config.cmake commit 66dfdf26951223b89eca9142d5346a5b92d70a43 Author: Michele Rosso Date: Fri Sep 6 11:20:17 2019 -0700 CMake: make imported targets GLOBAL Src/Base/CMakeLists.txt Src/Extern/Conduit/CMakeLists.txt Src/F_Interfaces/CMakeLists.txt Tools/CMake/FindHYPRE.cmake Tools/CMake/FindSUNDIALS.cmake commit 82ebfcda63d0474c73e5cdbbad1167054affceb5 Author: Weiqun Zhang Date: Fri Sep 6 09:47:27 2019 -0700 added PETSc to linear solver doc Docs/sphinx_documentation/source/LinearSolvers.rst commit 9123506a9042a78bb725ad25a4cf32297d9de3f2 Author: cgilet Date: Fri Sep 6 11:21:53 2019 -0400 update MACProjector documentation and tutorial Docs/sphinx_documentation/source/LinearSolvers.rst Docs/sphinx_tutorials/source/LinearSolvers_Tutorial.rst commit 4882573be3a2518baeb5c51ec0d8bd5063467085 Author: cgilet Date: Fri Sep 6 11:09:26 2019 -0400 Update so commented examples will work if uncommented. Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp commit 2acf77029659f692e25d6f0ad7f2ac205fc8504a Author: cgilet Date: Fri Sep 6 11:02:44 2019 -0400 Update comments to reflect what code actually does Tutorials/LinearSolvers/MAC_Projection_EB/inputs_3d commit 81d8d53b7e8a8b8e6d10ea4f536ab547bf3eddb4 Author: Ann Almgren Date: Fri Sep 6 02:08:38 2019 -0700 Add comment that Dirichlet bc's are assumed to be homogeneous Docs/sphinx_documentation/source/LinearSolvers.rst commit 271841af891579e698d64f71902f20ce3d02338e Author: Ann Almgren Date: Fri Sep 6 02:04:44 2019 -0700 Merge the description of non-zero S with the rest of the text. Docs/sphinx_documentation/source/LinearSolvers.rst commit f93bd948c63cd8c12091f642e0ff499faae648df Author: Michele Rosso Date: Thu Sep 5 18:32:11 2019 -0700 CMake: handle amrex path when generating build info Tools/CMake/AMReXBuildInfo.cmake commit e8550a2e76d64e63d10dcddc7e5d80f898dfca9e Author: Michele Rosso Date: Thu Sep 5 18:27:39 2019 -0700 CMake: make get_target_prop_recursive() more robust Tools/CMake/AMReXTargetHelpers.cmake commit 48d8d23b180e6726fdbfb70644633e241ab4bb1b Author: Michele Rosso Date: Thu Sep 5 16:08:56 2019 -0700 CMake: fix typo Tools/CMake/AMReXBuildInfo.cmake commit 6cf7f07b240f543dba2a89da31eb8edc203ce3fd Author: Michele Rosso Date: Thu Sep 5 16:07:46 2019 -0700 CMake: make BuildInfo module more robust Tools/CMake/AMReXBuildInfo.cmake commit 9429f9c7032095961fc946accfdfc2c7362b8e36 Author: Andy Nonaka Date: Thu Sep 5 15:49:12 2019 -0700 note on how to specific non-zero divergence for MAC projection tutorial Docs/sphinx_documentation/source/LinearSolvers.rst commit b854bf32d1b425de187f303d08aef33a48dca20e Merge: 3b1a54c35 208896999 Author: Ann Almgren Date: Thu Sep 5 15:26:46 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 3b1a54c355efba2b3ae636009ceb7eaa73ec9e49 Author: Ann Almgren Date: Thu Sep 5 15:10:48 2019 -0700 Fix typo Docs/sphinx_documentation/source/LinearSolvers_Chapter.rst commit 2088969992827da49f8b84b54131329ea5bccb73 Author: Weiqun Zhang Date: Thu Sep 5 15:03:23 2019 -0700 latest AMReX regression test script Tools/RegressionTesting/AMReX-tests.ini commit 7491ccac6760e0475449f0d1abd0bfe197ede6cd Author: Ann Almgren Date: Thu Sep 5 14:52:38 2019 -0700 hypre --> External Solvers (still needs petsc info) Docs/sphinx_documentation/source/LinearSolvers.rst commit d0639ac8b738508466d4399aee6227c5ba999e5a Author: Ann Almgren Date: Thu Sep 5 14:49:55 2019 -0700 Swap B <--> beta in linear solver notation Docs/sphinx_documentation/source/LinearSolvers.rst Docs/sphinx_documentation/source/LinearSolvers_Chapter.rst commit 7429a3d238cac9e13dfbc58959ebe48010e66674 Author: Weiqun Zhang Date: Thu Sep 5 14:35:56 2019 -0700 minor change and make it work for C++11 Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp commit d3430c9c50a2e9f68d434041e19b91d8705f65b2 Author: Andy Nonaka Date: Thu Sep 5 13:37:44 2019 -0700 updated mac projection tutorial documentation + comments Docs/sphinx_documentation/source/LinearSolvers.rst Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp commit c074e359fffbb7988c4b50eda7bdf55be485133b Author: Michele Rosso Date: Thu Sep 5 10:36:20 2019 -0700 CMake: update some modules to reflect new changes Tools/CMake/AMReXTypecheck.cmake Tools/CMake/AMReX_Config.cmake commit 5bcbf0158cfff4ddc110df23f32555b007246658 Author: Ann Almgren Date: Thu Sep 5 06:39:21 2019 -0700 Update docs Docs/sphinx_documentation/source/LinearSolvers.rst commit 0b68bdd8736bcca68bfc3a493af111b865866e8d Author: Ann Almgren Date: Thu Sep 5 06:32:42 2019 -0700 Update MACProjector documentation and tutorial. Docs/sphinx_documentation/source/LinearSolvers.rst Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp commit 2697b419c50cbbdc32408775981dae35e58fdf16 Author: Ann Almgren Date: Thu Sep 5 04:10:00 2019 -0700 Fix formatting Docs/sphinx_documentation/source/LinearSolvers.rst commit 551411e4bd4f01e6e9f525bedeeb050fbef58ce9 Author: Ann Almgren Date: Thu Sep 5 04:10:00 2019 -0700 Fix formatting Docs/sphinx_documentation/source/LinearSolvers.rst commit fda4eb56c39c1efac759b8dccd791119a1159438 Author: Ann Almgren Date: Thu Sep 5 03:55:26 2019 -0700 Update with code snippet for MAC Projection. Docs/sphinx_documentation/source/LinearSolvers.rst commit ef086550f1b653ae9bdd13ac2cf886b227b3c44a Author: Ann Almgren Date: Thu Sep 5 03:55:26 2019 -0700 Update with code snippet for MAC Projection. Docs/sphinx_documentation/source/LinearSolvers.rst commit 2b64aa5cd64230a58f0990b5c6d74ed5d5e1ee89 Author: Ann Almgren Date: Thu Sep 5 03:23:30 2019 -0700 change default Tutorials/LinearSolvers/MAC_Projection_EB/Backtrace.0 Tutorials/LinearSolvers/MAC_Projection_EB/GNUmakefile commit c91decace3fb56f6cfb6f6c3c8ca6192e34c31a1 Author: Ann Almgren Date: Thu Sep 5 03:22:27 2019 -0700 Oops -- didn't want to commit the plotfile Tutorials/LinearSolvers/MAC_Projection_EB/plt00000/Header Tutorials/LinearSolvers/MAC_Projection_EB/plt00000/Level_0/Cell_D_00000 Tutorials/LinearSolvers/MAC_Projection_EB/plt00000/Level_0/Cell_H commit 6c9d7d051420199e21cc47fcd1615a19eb167fdc Author: Ann Almgren Date: Thu Sep 5 03:21:37 2019 -0700 Add new tutorial demonstrating MACProjection with EB obstacles. Tutorials/LinearSolvers/MAC_Projection_EB/Backtrace.0 Tutorials/LinearSolvers/MAC_Projection_EB/GNUmakefile Tutorials/LinearSolvers/MAC_Projection_EB/Make.package Tutorials/LinearSolvers/MAC_Projection_EB/README Tutorials/LinearSolvers/MAC_Projection_EB/inputs_3d Tutorials/LinearSolvers/MAC_Projection_EB/main.cpp Tutorials/LinearSolvers/MAC_Projection_EB/plt00000/Header Tutorials/LinearSolvers/MAC_Projection_EB/plt00000/Level_0/Cell_D_00000 Tutorials/LinearSolvers/MAC_Projection_EB/plt00000/Level_0/Cell_H commit 93b861602d2ea8401e9ceaf42b0cd5633747ffde Author: Ann Almgren Date: Thu Sep 5 02:13:40 2019 -0700 Update linear solver section of documentation Docs/sphinx_documentation/source/LinearSolvers.rst Docs/sphinx_documentation/source/LinearSolvers_Chapter.rst commit 8541794c52763b74903504250f1d193eccc14fb8 Author: Ann Almgren Date: Thu Sep 5 02:13:40 2019 -0700 Update linear solver section of documentation Docs/sphinx_documentation/source/LinearSolvers.rst Docs/sphinx_documentation/source/LinearSolvers_Chapter.rst commit 57ede8fcef54c1bf35ae7ead5abc9c9df8bf10d5 Author: Michele Rosso Date: Wed Sep 4 17:51:18 2019 -0700 CMake: change paradigm to include build info into app code. * Create a dedicated CMake module * Let application code to drive the inclusion of build info into consuming target. Src/CMakeLists.txt Tools/CMake/AMReXBuildInfo.cmake commit 2e1e06ab30f6376a5ace67ba5e2c9569839aff22 Author: Michele Rosso Date: Wed Sep 4 17:49:53 2019 -0700 CMake: add a module to collect helpers to handle targets Tools/CMake/AMReXTargetHelpers.cmake commit 67f7ddd6b9ce6587b1bfab02aee2559bca12da01 Author: Michele Rosso Date: Wed Sep 4 17:38:24 2019 -0700 CMake: improve GENEX handling. * Group genex-related macros/functions in a dedicated module file * evaluate_genex: add support for NOT operation * evaluate_genex: improve handling of COMPILE_LANGUAGE genex Tools/CMake/AMReXGenexHelpers.cmake Tools/CMake/AMReX_Utils.cmake commit 98e8d75a970a1ddf16a131ce5eb1ea13f34e805e Merge: 46f5048b6 c07f773ad Author: Andrew Myers Date: Wed Sep 4 19:02:55 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 46f5048b6953bb1a2f46fd98fb0325c21bb3d00b Author: Andrew Myers Date: Wed Sep 4 19:02:33 2019 -0400 optimization - reduce number of messages sent in communicateParticles Src/Particle/AMReX_ParticleCommunication.cpp commit fd1f8a178c616d4f905f3d78205246e1f80bb4d0 Merge: 6ce99e1cb c07f773ad Author: cgilet Date: Wed Sep 4 16:49:24 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit c07f773adb75dab6b6b379c5fa7a3ee92af134a9 Author: Andrew Myers Date: Wed Sep 4 13:03:56 2019 -0700 a fix for the local + CPU + single precision particles Src/Particle/AMReX_ParticleContainerI.H commit 9953023e3cc262f03ee48ddc2af95072ae3a2d6a Merge: bf5c79af2 6ee558d71 Author: Andrew Myers Date: Wed Sep 4 10:59:22 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit bf5c79af27a7f7c80b37f794ef8d0271ddb291a3 Author: Andrew Myers Date: Wed Sep 4 10:59:11 2019 -0700 convert image to png (docs) (travis) Docs/sphinx_documentation/source/LinearSolvers.rst Docs/sphinx_documentation/source/LinearSolvers/refluxfreecoarsefine.png commit bbf04bac080cce251e873672a501fc99c80f5015 Author: Andrew Myers Date: Wed Sep 4 10:51:19 2019 -0700 (travis) remove this package .travis.yml commit 6ee558d71105f77dfc86dff43ea4b331fd58ce47 Author: Weiqun Zhang Date: Wed Sep 4 10:21:14 2019 -0700 fcompare: option to set a relative tolerance Tools/Plotfile/fcompare.cpp commit 5e5853e466048b4024fcd4e9d56e474466d22137 Author: Andrew Myers Date: Tue Sep 3 17:01:32 2019 -0700 add svg package to travis build .travis.yml commit 7cde9939486aaef6696829b17704d800c5ce1fb3 Merge: f5809b3ea e41d0a7bd Author: Andrew Myers Date: Tue Sep 3 16:50:24 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f5809b3ea41f40d48f357a0f5176c16438042a71 Author: Andrew Myers Date: Tue Sep 3 16:50:09 2019 -0700 seems that we need travis_wait again .travis.yml commit e41d0a7bdf0aad2e69779a8394fea5d81a82d557 Author: Weiqun Zhang Date: Tue Sep 3 16:25:53 2019 -0700 remove noexcept so that Intel 18 is happy Src/EB/AMReX_EBCellFlag.H commit 8b333c59482de5faab116deba5035459f3d3e3b5 Author: Weiqun Zhang Date: Tue Sep 3 16:25:53 2019 -0700 remove noexcept so that Intel 18 is happy Src/EB/AMReX_EBCellFlag.H commit aa5580ec0d39be4b30eebef04460f81ee60276ee Author: Andrew Myers Date: Tue Sep 3 16:24:30 2019 -0700 move assignment and constructor for ParticleContainer Src/Particle/AMReX_Particles.H commit a12a745e1d2a8d765b93ad34a4e46655d71143ee Merge: 153cb29a8 3ccbfac2e Author: Andrew Myers Date: Tue Sep 3 18:39:25 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 153cb29a899656617391c3bc8e7985d059331e66 Author: Andrew Myers Date: Tue Sep 3 18:38:50 2019 -0400 need to reset the m_need_handshake flag when calling fillNeighbors Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit defa9ec6e9035d2922f46ee8d22c916bc4db8d67 Author: Michele Rosso Date: Tue Sep 3 15:29:06 2019 -0700 Add missing include guards. CMake: do no process installed headers with name ending in "*I.H" since they are meant to always be included by host headers which are properly processed after installation. Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_ParticleInit.H Tools/CMake/modify_installed_headers.cmake commit 3ccbfac2ef76b050b0e103e2165b7ddab08f0c59 Author: Weiqun Zhang Date: Tue Sep 3 13:12:22 2019 -0700 MultiComponent tutorial: call Finalize() Tutorials/LinearSolvers/MultiComponent/main.cpp commit e6e43b2f8f7ee3b4b0f532fff4387e64b9b91cbe Merge: d22f48e76 7dae967e6 Author: WeiqunZhang Date: Tue Sep 3 12:09:45 2019 -0700 Merge pull request #556 from AMReX-Codes/mcmlmg-test Mcmlmg test commit 7dae967e6acf37f6e6289f978d6c6ad622c57bae Author: Brandon Runnels Date: Tue Sep 3 12:21:53 2019 -0600 added sphinx documentation Docs/sphinx_documentation/source/LinearSolvers.rst Docs/sphinx_documentation/source/LinearSolvers/refluxfreecoarsefine.pdf Docs/sphinx_documentation/source/LinearSolvers/refluxfreecoarsefine.svg Docs/sphinx_tutorials/source/LinearSolvers_Tutorial.rst commit d22f48e7698c1a4b70a7c59c070a509e8886c141 Author: Andrew Myers Date: Tue Sep 3 10:26:32 2019 -0700 add missing parameter to inputs.rt Tests/Particles/Redistribute/inputs.rt commit 92b3b82b9c7f6e9e136c21bc2cf42561f1305c1f Author: Andrew Myers Date: Tue Sep 3 10:25:00 2019 -0700 change test name Tests/Particles/Intersection/main.cpp commit 5e3b459330802b70ac9723f1afba603727039c25 Merge: e5907d750 6e3ebfdbf Author: Andrew Myers Date: Tue Sep 3 10:24:17 2019 -0700 Merge branch 'global_redistribute_gpu' into development commit e2fbf908df7841675a8de5f0c0277d266fd25766 Author: Brandon Runnels Date: Tue Sep 3 11:17:16 2019 -0600 added documentation to tutorial Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.H Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp Tutorials/LinearSolvers/MultiComponent/inputs Tutorials/LinearSolvers/MultiComponent/main.cpp commit e5907d75066ebce083cd3d896cc59c79503cefe7 Author: Weiqun Zhang Date: Tue Sep 3 09:07:09 2019 -0700 update CHANGES CHANGES commit ddc9047dba951e1664698ee21749c6bdec54c309 Merge: 14f1d357d de7689ee7 Author: Brandon Runnels Date: Tue Sep 3 09:47:15 2019 -0600 Merge branch 'development' into mcmlmg-test commit 14f1d357da91a5f90a93d1ecd06448917a52e24e Author: Brandon Runnels Date: Tue Sep 3 09:46:40 2019 -0600 moved to tutorials Tutorials/LinearSolvers/MultiComponent/GNUmakefile Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.H Tutorials/LinearSolvers/MultiComponent/MCNodalLinOp.cpp Tutorials/LinearSolvers/MultiComponent/Make.package Tutorials/LinearSolvers/MultiComponent/inputs Tutorials/LinearSolvers/MultiComponent/main.cpp commit de7689ee70de360b7ab9302bb45c2ae6393ae635 Author: Jean Sexton Date: Sat Aug 31 14:22:15 2019 -0400 Fix typo Src/Particle/AMReX_NeighborParticlesI.H commit b547bcf44848fa1b6a2c5835bd6c354e3eb5fe80 Merge: 154fdebd1 43c4ba856 Author: Weiqun Zhang Date: Fri Aug 30 16:56:31 2019 -0700 Merge branch 'weiqun/dev' into development commit 43c4ba856a5b7208b46ad3c2fbc41b409f8ac613 Author: Weiqun Zhang Date: Fri Aug 30 16:43:36 2019 -0700 add explicit host dtors so that host device versions are not generated Src/EB/AMReX_EB2_IF_Complement.H Src/EB/AMReX_EB2_IF_Difference.H Src/EB/AMReX_EB2_IF_Extrusion.H Src/EB/AMReX_EB2_IF_Intersection.H Src/EB/AMReX_EB2_IF_Lathe.H Src/EB/AMReX_EB2_IF_Rotation.H Src/EB/AMReX_EB2_IF_Translation.H Src/EB/AMReX_EB2_IF_Union.H commit 9126bc4d43e40bd6aad871819fad9cfe12622543 Author: Weiqun Zhang Date: Fri Aug 30 13:29:48 2019 -0700 PolynomialIF on GPU Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuMemory.H Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_IF_Intersection.H Src/EB/AMReX_EB2_IF_Polynomial.H Src/EB/AMReX_EB2_IF_Translation.H Src/EB/AMReX_EB2_IF_Union.H commit 6e3ebfdbfd6d82ac0aed3be9dc13fb6a075df93f Merge: 8b1401341 cf21d0ac2 Author: Andrew Myers Date: Fri Aug 30 13:47:22 2019 -0700 Merge branch 'global_redistribute_gpu' of github.com:AMReX-Codes/amrex into global_redistribute_gpu commit 8b1401341cbc549533349772816dc70f570c0c58 Merge: 3423031e2 154fdebd1 Author: Andrew Myers Date: Fri Aug 30 13:47:03 2019 -0700 Merge branch 'development' into global_redistribute_gpu commit 154fdebd10aebfef974096c85a12b175934c81f7 Author: Andrew Myers Date: Fri Aug 30 13:45:37 2019 -0700 fix typos Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleContainerI.H commit 5838c6f66d0feafaea914912f1a2cbf1a0bc29f4 Author: Andrew Myers Date: Fri Aug 30 13:44:22 2019 -0700 call base fab setVal instead of fab array one in threaded region (avoids race condition) Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleContainerI.H commit cf21d0ac28b4081f8ec64826f9c9a94b70d22e89 Author: Andrew Myers Date: Fri Aug 30 15:20:32 2019 -0400 fix typo in test Tests/Particles/Redistribute/main.cpp commit 53aae1628d1b3355c4a0a252b7b0e3a8ad398dd5 Merge: 125e9c6a4 d823b8dca Author: Andrew Myers Date: Fri Aug 30 15:08:56 2019 -0400 Merge branch 'development' into global_redistribute_gpu commit d823b8dcaefea0c0d3e8c56d230a8d3f7d0c5fbb Author: Andrew Myers Date: Fri Aug 30 11:27:14 2019 -0700 use an ifdef for MPI in these particle comm routines Src/Particle/AMReX_ParticleCommunication.cpp commit 8c7764950110aea23d6563dabdb7d622e9895110 Author: Andrew Myers Date: Fri Aug 30 11:08:55 2019 -0700 workaround for gcc 8.2 bug Src/Particle/AMReX_ParticleLocator.H commit 125e9c6a45ed350c0a6ac9bda15e6aa1d56a5ebc Author: Andrew Myers Date: Thu Aug 29 21:17:19 2019 -0400 some more error checking Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleLocator.H commit 4751677f62a330a523768933c893498bd82e2270 Author: Andrew Myers Date: Thu Aug 29 21:15:02 2019 -0400 set this size so it can be used in error checking Src/Particle/AMReX_ParticleTile.H commit cfdc3c1772df31276c06413f5eaefc4d188e1577 Author: Weiqun Zhang Date: Thu Aug 29 17:51:46 2019 -0700 rm deprecated functions Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H commit 3423031e2ec2f8250ff4e5c806a6e78331ab3715 Author: Andrew Myers Date: Thu Aug 29 17:35:51 2019 -0700 make sure we rebuild the particle locator even if not local Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleLocator.H commit 5317b6b1905f58245b92bc611abe0928d81151a7 Merge: b9d2cb3d1 0e94a6e65 Author: Weiqun Zhang Date: Thu Aug 29 17:34:16 2019 -0700 Merge branch 'development' into weiqun/dev commit 0e94a6e655efc88f7482aff9c05e273843541ea9 Author: Andrew Myers Date: Thu Aug 29 19:47:35 2019 -0400 fix particle locator for 2D Src/Particle/AMReX_ParticleLocator.H commit d200a7b82328c79c1e066dc3a087b1fd829b08ef Author: Andrew Myers Date: Thu Aug 29 19:48:55 2019 -0400 fix dmap in test Tests/Particles/Redistribute/main.cpp commit 90370334f44c6140872524ebfa25007141e0808c Author: Andrew Myers Date: Thu Aug 29 19:48:31 2019 -0400 update Intersection test for multiple levels Tests/Particles/Intersection/inputs Tests/Particles/Intersection/main.cpp commit 66197a8082e5e1ca4ca3109909bb2004067466e2 Author: Andrew Myers Date: Thu Aug 29 19:47:35 2019 -0400 fix particle locator for 2D Src/Particle/AMReX_ParticleLocator.H commit 9416dd3abf8e0ca9fa021598c65979b660fd6b39 Author: Andrew Myers Date: Thu Aug 29 19:47:11 2019 -0400 add timer Src/Particle/AMReX_ParticleBufferMap.cpp commit b9d2cb3d1b6d6149ac60754714aa6d087b76cf2e Author: Weiqun Zhang Date: Thu Aug 29 16:25:29 2019 -0700 should not include old header Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit a63aa3f5ca0110425807056255971cd857ac0a1e Author: Weiqun Zhang Date: Thu Aug 29 16:17:28 2019 -0700 rm deprecated Fortran files Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H Src/EB/CMakeLists.txt Src/EB/Make.package commit 60762be7d9b6f76280b619a55d3de0c586d74e40 Author: Weiqun Zhang Date: Thu Aug 29 16:03:48 2019 -0700 EBMultiFabUtil on GPU Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit 9db5d048cefc04e47bb20a62c94d653b21be74d5 Author: Andrew Myers Date: Thu Aug 29 15:54:12 2019 -0400 add test for global gpu redistribute Tests/Particles/Redistribute/inputs Tests/Particles/Redistribute/main.cpp commit a0c6ec463e94333730b25d57fd01bac226aac0b0 Author: Andrew Myers Date: Thu Aug 29 15:53:46 2019 -0400 allow non-local redistribute to be dispatched to the GPU Src/Particle/AMReX_ParticleContainerI.H commit 79cdb9cce4ddb5ec099e5ce934379ce458051781 Author: Andrew Myers Date: Thu Aug 29 15:26:41 2019 -0400 implement non-local mpi communication pattern for gpu redistribute Src/Particle/AMReX_ParticleCommunication.cpp commit 714527a2bda6f9b06bd30c5a02ba2f3fbe520041 Merge: 8977f24c1 a99e3f930 Author: Andrew Myers Date: Thu Aug 29 14:39:33 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a99e3f930ad900f3695d1ea0dafef56b3c649a61 Merge: 3dea69a42 e239f9700 Author: Weiqun Zhang Date: Thu Aug 29 10:33:16 2019 -0700 Merge branch 'weiqun/dev' into development commit 3dea69a421499ff0a2c03f63368b59362238763c Author: Weiqun Zhang Date: Thu Aug 29 10:33:10 2019 -0700 add an assertion Src/Base/AMReX_FabArray.H commit e239f97000a7f9134f552f3267a1ddc08020d872 Merge: be74f37dd c81c15d0c Author: Weiqun Zhang Date: Thu Aug 29 10:07:23 2019 -0700 Merge branch 'development' into weiqun/dev commit be74f37ddb38bf5e5f5b8eff23396f14593d9164 Author: Weiqun Zhang Date: Thu Aug 29 10:06:59 2019 -0700 tidy Src/AmrCore/AMReX_Interpolater.cpp Src/Base/AMReX_GpuLaunch.H Src/Boundary/AMReX_YAFluxRegister.cpp Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EBInterpolater.cpp commit c81c15d0ca39cec7a059154ac5588fc2142c841e Author: Weiqun Zhang Date: Thu Aug 29 09:09:15 2019 -0700 fix knapsack when nmax is very small Src/Base/AMReX_DistributionMapping.cpp commit 0e34fd80798ea1ba239c22e6bce0f77e03ebd799 Author: Weiqun Zhang Date: Thu Aug 29 04:42:45 2019 -0700 EBFluxRegister: rm Fortran Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_1d.F90 Src/EB/AMReX_EBFluxRegister_2D_C.H Src/EB/AMReX_EBFluxRegister_2d.F90 Src/EB/AMReX_EBFluxRegister_3D_C.H Src/EB/AMReX_EBFluxRegister_3d.F90 Src/EB/AMReX_EBFluxRegister_F.H Src/EB/CMakeLists.txt Src/EB/Make.package commit 78780152efe0818c3fa7b69132187dac0a3a1043 Author: Weiqun Zhang Date: Wed Aug 28 22:09:38 2019 -0700 avoid name conflicts Src/Base/AMReX_GpuLaunchMacrosG.H commit 59a7a3cae1e0e472014b3588530b8123120dc557 Author: Weiqun Zhang Date: Wed Aug 28 21:58:06 2019 -0700 EBFluxRegister: rereflux Src/Base/AMReX_GpuLaunchMacrosG.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_2D_C.H Src/EB/AMReX_EBFluxRegister_3D_C.H commit 922b00cb9a808dcc0ad3e20b1c39cbbde287be10 Author: Weiqun Zhang Date: Wed Aug 28 18:05:17 2019 -0700 EBFluxRegister: fine add dm Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_2D_C.H Src/EB/AMReX_EBFluxRegister_3D_C.H Src/EB/AMReX_EBFluxRegister_nd.F90 commit bf2c3185530185dc49d95de673bcac498cedc869 Author: Weiqun Zhang Date: Wed Aug 28 17:05:00 2019 -0700 EBFluxRegister fine_add: rm a temporary array Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_2D_C.H Src/EB/AMReX_EBFluxRegister_3D_C.H commit 8977f24c1c8df116b26a90de2fee297302f613e9 Author: Andrew Myers Date: Wed Aug 28 19:53:22 2019 -0400 some more code reuse Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleUtil.H commit a69e529b8b1dc35f56db3aa44756de2af6e3b71a Author: Andrew Myers Date: Wed Aug 28 19:47:00 2019 -0400 some code reuse Src/Particle/AMReX_ParticleUtil.H commit 00e59e29adcfc0dba2d86519a4c12b6736e7d94f Author: Andrew Myers Date: Wed Aug 28 19:37:12 2019 -0400 fix cpu compile Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleLocator.H commit f5f0b9fa342073b3cf465e75831003737fc9d5af Author: Andrew Myers Date: Wed Aug 28 19:18:24 2019 -0400 use the new non-local distributor in the gpu redistribute Src/Particle/AMReX_ParticleContainerI.H commit 7e20d6b5afff0c2a3b4639d8e4e985fd5306e969 Author: Weiqun Zhang Date: Wed Aug 28 16:15:52 2019 -0700 EBFluxRegister: fineadd Src/Base/AMReX_Array4.H Src/Base/AMReX_GpuLaunch.H Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_2D_C.H Src/EB/AMReX_EBFluxRegister_3D_C.H commit e342f0fe5fcf0113b8cb78b8ca51413eb25af57a Author: Andrew Myers Date: Wed Aug 28 18:06:56 2019 -0400 a particle locator to the ParticleContainer class Src/Particle/AMReX_Particles.H commit 9ccf6aa9f5152ff4d2dec456b0eeae53da9bb4a8 Author: Andrew Myers Date: Wed Aug 28 18:06:28 2019 -0400 a get particle cell function Src/Particle/AMReX_ParticleUtil.H commit 1a20e5a85c0b000370e2ad3db64564b22e14218b Author: Andrew Myers Date: Wed Aug 28 17:29:47 2019 -0400 test for the GPU boxarray intersection class Tests/Particles/Intersection/GNUmakefile Tests/Particles/Intersection/Make.package Tests/Particles/Intersection/inputs Tests/Particles/Intersection/main.cpp Tests/Particles/Intersection/script.sh commit aa01a3fe137ea6c3bcfad2fccac73353d768833b Author: Andrew Myers Date: Wed Aug 28 17:28:00 2019 -0400 add class for locating particles on the gpu with no assumption of locality Src/Particle/AMReX_ParticleLocator.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit fba37449f111e5aedd615cf1100b414f91b48735 Author: Andrew Myers Date: Wed Aug 28 17:27:23 2019 -0400 add early exit for size 0 messages Src/Particle/AMReX_ParticleCommunication.cpp commit aea2a610cfeeccca2ca90c7ce4d005bc1b81b68a Author: Weiqun Zhang Date: Wed Aug 28 08:31:34 2019 -0700 EBFluxRegister: crseadd Src/Boundary/AMReX_YAFluxRegister.cpp Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_2D_C.H Src/EB/AMReX_EBFluxRegister_3D_C.H Src/EB/AMReX_EBFluxRegister_C.H Src/EB/CMakeLists.txt Src/EB/Make.package commit dcfcc8913e79a711f32d570c05af3237b7e19f7e Merge: 65725efc2 894c8fce2 Author: Weiqun Zhang Date: Tue Aug 27 21:04:49 2019 -0700 Merge branch 'weiqun/dev' into development commit 894c8fce2b7e56db1d09ed6bca1cc410848a0b3b Author: Weiqun Zhang Date: Tue Aug 27 20:26:27 2019 -0700 prefer const_array() to implicit conversion of the result of array() Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/GPU.rst Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interpolater.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_YAFluxRegister.cpp Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB2_MultiGFab.cpp Src/EB/AMReX_EBAmrUtil.cpp Src/EB/AMReX_EBMultiFabUtil.cpp Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 3c37722eff101496a9c58865f2d4b1218073f507 Author: Weiqun Zhang Date: Tue Aug 27 17:26:29 2019 -0700 make sure no race condition in LaunchSafeGuard even in omp parallel region Docs/sphinx_documentation/source/Basics.rst Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interpolater.cpp Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EBInterpolater.cpp commit a9afc431fac41c43c03ab475912250a3e30eaf43 Author: Weiqun Zhang Date: Tue Aug 27 15:49:19 2019 -0700 GPU: EBInterpolater Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBInterp_F.H Src/EB/AMReX_EBInterpolater.cpp Src/EB/AMReX_ebinterp_1d.F90 Src/EB/AMReX_ebinterp_2d.F90 Src/EB/AMReX_ebinterp_3d.F90 Src/EB/CMakeLists.txt Src/EB/Make.package commit fc1692745a6fa32d6b0d56ee8be28ea76a451985 Author: Weiqun Zhang Date: Tue Aug 27 15:07:50 2019 -0700 EBCellFlag: rm region Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBCellFlag.cpp Src/EB/AMReX_EBFArrayBox.cpp commit 64c8f7675ea0cd987b0863e631cbf3bf1f1b31ac Author: Weiqun Zhang Date: Tue Aug 27 14:10:23 2019 -0700 add MultiCutFab::const_array Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit cba670315e49f91fe3053be2088daa5b1314ae66 Author: Weiqun Zhang Date: Tue Aug 27 13:39:02 2019 -0700 EB2_Level: more gpu Src/EB/AMReX_EB2_Level.cpp commit 65725efc2bf7751cebf6f1c386ba3ad6a86f12df Author: Andrew Myers Date: Tue Aug 27 13:28:46 2019 -0700 rewrite the buffer_size calculation to be more idiomatic Src/Particle/AMReX_ParticleContainerI.H commit 3928fed015f34f9965a8f6c634e5304e0b438832 Merge: 8da669c4f ebc39d618 Author: Andrew Myers Date: Tue Aug 27 13:15:23 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8da669c4f061ee49cd62ad867944b55766221c34 Author: Andrew Myers Date: Tue Aug 27 13:15:14 2019 -0700 tweak particle mesh test Tests/Particles/ParticleMesh/main.cpp commit ef3902eeb99d772c57154791c32473360768be06 Author: Weiqun Zhang Date: Tue Aug 27 13:13:18 2019 -0700 minor Src/EB/AMReX_EB2_Level.cpp commit 402637d2711fc374d3943b5322dc6264309aa9a5 Author: Weiqun Zhang Date: Tue Aug 27 12:52:56 2019 -0700 fix a bug Src/EB/AMReX_EB2_IF_Box.H commit 761d8a9552f224223c4d4586aa755645b936e0b3 Author: Weiqun Zhang Date: Tue Aug 27 12:42:23 2019 -0700 EB: rm deprecated parameter Src/EB/AMReX_EB2.H Src/EB/AMReX_EB2.cpp commit 0586b839c0c274f6b5fc11700d9539ca4e031074 Author: Weiqun Zhang Date: Tue Aug 27 12:32:38 2019 -0700 GeometryShop: getBoxType on gpu Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB2_Level.cpp commit ebc39d6187e19116b6e362e3c1e461863edc7015 Merge: 340e3abf3 380553753 Author: Andrew Myers Date: Tue Aug 27 15:29:58 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 340e3abf3376d0ac9884fdce21ec440e855e71c8 Author: Andrew Myers Date: Tue Aug 27 15:29:42 2019 -0400 don't use int for total number of particles in this test Tests/Particles/Redistribute/main.cpp commit 38055375316c69ac4a771d631d379caf9044991f Author: Andrew Myers Date: Tue Aug 27 12:28:36 2019 -0700 tweak test Tests/Particles/ParticleMesh/main.cpp Tools/RegressionTesting/AMReX-tests.ini commit f0f3191df1d3cb80f3c01e060a86bdfbcc1d731d Author: Andrew Myers Date: Tue Aug 27 12:19:54 2019 -0700 add an automated test for particle-mesh operations Tools/RegressionTesting/AMReX-tests.ini commit f908ec50eb029557dc66842a001a607d52ac138e Merge: 2b3deeb29 52d69dfe4 Author: Andrew Myers Date: Tue Aug 27 11:36:10 2019 -0700 Merge branch 'mpi_datatype' into development commit 2b3deeb29e5323da48d8099bcafa24eeecea2205 Merge: 12ca00ade ae311bc3d Author: Andrew Myers Date: Tue Aug 27 13:53:58 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 12ca00ade9868ba7418558230617b831170cd484 Author: Andrew Myers Date: Tue Aug 27 13:53:37 2019 -0400 early exit from these MPI routines when we only have 1 process Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit ae311bc3de7238e370eef30cf9b043c275e12dbe Author: Weiqun Zhang Date: Tue Aug 27 10:42:30 2019 -0700 Option to use default stream in MFIter Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit d4b4e218bf70c771314872b8a2c368c4b19a2421 Merge: 854fff57a a1be34f59 Author: Weiqun Zhang Date: Mon Aug 26 20:55:52 2019 -0700 Merge branch 'weiqun/dev' into development commit a1be34f591c78b2c270316511f82bf9818a9d5fb Author: Weiqun Zhang Date: Mon Aug 26 20:55:26 2019 -0700 fix new bug in eb_set_covered_nodes Src/EB/AMReX_EBMultiFabUtil_3D_C.H commit 52d69dfe4dd4441379bbcd830d2523a872701941 Author: Andrew Myers Date: Mon Aug 26 18:10:47 2019 -0700 use an mpi data type other than char to up the limit on the number of particles that can be communicated (cpu-only) Src/Particle/AMReX_ParticleContainerI.H commit 729605a3f2da3ffa1230b84f421a25f2b2d6c26b Author: Weiqun Zhang Date: Mon Aug 26 16:11:18 2019 -0700 EBCellFlag: fix new OMP issue Src/EB/AMReX_EBCellFlag.cpp commit 5bdbffe1c587bf14d3f73d7cb2bd51f79ea9e402 Author: Andrew Myers Date: Mon Aug 26 15:33:42 2019 -0700 add a MPI data type for unsigned long long Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ccse-mpi.H commit 93cc9c329a226ef1c67aff56edf9cd562925ec35 Author: Weiqun Zhang Date: Mon Aug 26 13:44:14 2019 -0700 EB: fix a new 2d bug Src/EB/AMReX_EB2_2D_C.H Src/EB/AMReX_EB2_Level.cpp commit 3f05fde3684fa0160a412ca814aa46390079ea59 Author: Weiqun Zhang Date: Mon Aug 26 13:24:32 2019 -0700 EBCellFlagFab: getType on GPU Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuControl.cpp Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBCellFlag.cpp Src/EB/AMReX_EBCellFlag_F.H Src/EB/AMReX_distFcnElement.cpp Src/EB/AMReX_ebcellflag_mod.F90 Src/EB/CMakeLists.txt Src/EB/Make.package commit 5e9025dedc8586d47eeab2b9c6ca93e8835d6b19 Author: Weiqun Zhang Date: Sun Aug 25 21:23:23 2019 -0700 wip Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBFArrayBox.cpp commit 854fff57a43d461ad3bf63f7938b2382c22e8145 Author: Weiqun Zhang Date: Sun Aug 25 20:41:52 2019 -0700 distFcnElement: pass x by reference Src/EB/AMReX_distFcnElement.H Src/EB/AMReX_distFcnElement.cpp commit bdd6c5f92f4bea9ca9e3fb082dc483604a427be7 Author: Weiqun Zhang Date: Sun Aug 25 20:38:25 2019 -0700 GPU: compute integrals Src/EB/AMReX_algoim.cpp commit 25207dd0e38125177def659f333d82a708c630cc Author: Weiqun Zhang Date: Sun Aug 25 19:13:18 2019 -0700 GPU: eb_set_covered Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3D_C.H Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H commit 3f787566c3a2c4b8dabfd349bbbe3a78602540a0 Merge: 270f82850 ac6e5b2e6 Author: Weiqun Zhang Date: Sun Aug 25 15:40:12 2019 -0700 Merge branch 'weiqun/dev' into development commit ac6e5b2e606ce0cad4b5838ce9a25a57f775e9f9 Author: Weiqun Zhang Date: Sun Aug 25 15:35:53 2019 -0700 EB 3d: For uncovered cell, set self-connection Src/EB/AMReX_EB2_3D_C.H commit d6e08d10f8343a5c94feda240795d530682aa208 Author: Weiqun Zhang Date: Sun Aug 25 08:52:24 2019 -0700 EB GPU: fix bugs in the new coarsen_from_fine function Src/EB/AMReX_EB2_3D_C.H commit 2577dbc2746afa9371ed6a5a1b088114378403cc Author: Weiqun Zhang Date: Sat Aug 24 22:11:36 2019 -0700 GPU: build_cellflags_from_ap Src/EB/AMReX_EB2_2D_C.H Src/EB/AMReX_EB2_3D_C.H Src/EB/AMReX_EB2_F.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_eb2_2d.F90 Src/EB/AMReX_eb2_3d.F90 Src/EB/CMakeLists.txt Src/EB/Make.package commit c5369be591962d7e59083d7d5aa591a6e762622b Author: Weiqun Zhang Date: Sat Aug 24 18:07:53 2019 -0700 switch to use C++ coarsen_from_fine Src/EB/AMReX_EB2_F.H Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_eb2_2d.F90 Src/EB/AMReX_eb2_3d.F90 commit 4d6092040f16fb56ad8f736df63fa01d54722bfe Author: Weiqun Zhang Date: Sat Aug 24 17:06:15 2019 -0700 GPU: coarsen from fine Src/EB/AMReX_EB2_2D_C.H Src/EB/AMReX_EB2_3D_C.H Src/EB/AMReX_EB2_Level.cpp commit 270f82850c6226e8fb3d3f3eba1896c177b5aef6 Author: Andrew Myers Date: Fri Aug 23 17:49:36 2019 -0700 tweak test Tests/Particles/Redistribute/inputs.rt Tests/Particles/Redistribute/main.cpp Tools/RegressionTesting/AMReX-tests.ini commit 35bd3f3c925182db59466ab5461028a48d74c5b9 Author: Andrew Myers Date: Fri Aug 23 17:30:51 2019 -0700 turn off CUDA by default Tests/Particles/Redistribute/GNUmakefile commit c0c065f763f5fef80e258fff1f9ba6f028264819 Author: Andrew Myers Date: Fri Aug 23 17:30:25 2019 -0700 config entry for redistribute test Tools/RegressionTesting/AMReX-tests.ini commit 91643e5ddff8b7056565577a5767c16ea6afe9a0 Author: Andrew Myers Date: Fri Aug 23 17:29:59 2019 -0700 configure this as a self-test Tests/Particles/Redistribute/main.cpp commit 26bf0451e9eb6a33307fd246c41002dceda223d8 Author: Andrew Myers Date: Fri Aug 23 17:29:46 2019 -0700 regtest inputs for Redistribute Tests/Particles/Redistribute/inputs.rt commit 37d0af91228b8c088bb7c9dc4f497b057a768f72 Author: Andrew Myers Date: Fri Aug 23 17:04:52 2019 -0700 enable omp in numParticlesOutOfRange Src/Particle/AMReX_ParticleUtil.H commit ceade23fdff9f8488cd27a609704b2d48b603174 Author: Andrew Myers Date: Fri Aug 23 17:04:29 2019 -0700 combine two forms of OK() Src/Particle/AMReX_ParticleContainerI.H commit 8d8be572f26fc9554639a1100d2000dc14471a22 Author: Andrew Myers Date: Fri Aug 23 19:50:19 2019 -0400 tweak RedistributeTest inputs and script Tests/Particles/Redistribute/inputs Tests/Particles/Redistribute/script.sh commit 3d9c9d137bdb79fd965a22c2debc6c37cf8b178c Author: Andrew Myers Date: Fri Aug 23 19:45:40 2019 -0400 reimplement OKGPU in terms of numParticlesOutOfRange Src/Particle/AMReX_ParticleContainerI.H commit 9482ce4d328a3fb3bdab4b2ad67c5f2b22c305eb Author: Andrew Myers Date: Fri Aug 23 19:45:12 2019 -0400 add overload for numParticlesOutOfRange that lets you set the levels Src/Particle/AMReX_ParticleUtil.H commit 2dea0722fdfbdb7e14bb83a6e67002b62895e20e Author: Andrew Myers Date: Fri Aug 23 17:24:08 2019 -0400 small world bug (gpu, newish) - need to apply periodic boundary conditions to particles that cross a periodic domain BUT stay on the same grid Src/Particle/AMReX_ParticleContainerI.H commit 58f3c02c1bbb81a8b4a85fdd1f3e2a34a26c104a Author: Andrew Myers Date: Fri Aug 23 13:53:03 2019 -0400 function to validate that the particles are in range of the local redistribute function Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleUtil.H commit 6ce99e1cbbe7ceebbd49ac38159e20b9635adc6e Merge: 3a7b72ae0 5f03f8885 Author: cgilet Date: Fri Aug 23 10:55:24 2019 -0400 Merge remote-tracking branch 'upstream/development' into TensorFluxes commit 3cbd931af1040d8c3149e9e2661c3599f082f67a Author: Weiqun Zhang Date: Thu Aug 22 11:58:14 2019 -0700 switch to use C++ check_mvmc Src/EB/AMReX_EB2_2D_C.H Src/EB/AMReX_EB2_3D_C.H Src/EB/AMReX_EB2_F.H Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_eb2_2d.F90 Src/EB/AMReX_eb2_3d.F90 commit 5f03f888551dda59d93aedfc969d521daf359364 Merge: baf9440a4 31e09e1a8 Author: Weiqun Zhang Date: Thu Aug 22 09:33:52 2019 -0700 Merge branch 'weiqun/dev' into development commit 31e09e1a8e8010a9fccb5e5b906c41a7948f5d9f Author: Weiqun Zhang Date: Thu Aug 22 09:32:12 2019 -0700 add Gpu::synchronize after fabs are allocated in case kernesl are launched to do placement new Src/Base/AMReX_FabArray.H commit 9c9a011a3beecaf1a3ac62edd0da01555cb83864 Author: Weiqun Zhang Date: Wed Aug 21 15:31:23 2019 -0700 wip Src/Base/AMReX_FabArray.H Src/EB/AMReX_EB2_2D_C.H Src/EB/AMReX_EB2_3D_C.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_EBMultiFabUtil.cpp commit baf9440a400343559ccc6f2900672847a9d07dc1 Author: kngott Date: Wed Aug 21 14:19:54 2019 -0700 Add number of streams to MFIter Info options. Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit e194c9fd60f287a0db16241f0a89a22756bfc803 Author: kngott Date: Wed Aug 21 14:15:36 2019 -0700 Make numGpuStreams available when USE_GPU=FALSE. Src/Base/AMReX_GpuDevice.H commit 5f4bf301b4f7341c079a9a192b95080afc31326f Merge: 79368fd17 6548be8eb Author: Andrew Myers Date: Wed Aug 21 12:48:17 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 79368fd17794aced1663b969fc01c67ba4bf376d Author: Andrew Myers Date: Wed Aug 21 12:48:06 2019 -0700 add a couple of convenience functions to ParIter Src/Particle/AMReX_Particles.H commit 6548be8eb97fe37b11367af1b3e0ea6a344b0195 Author: kngott Date: Wed Aug 21 12:30:19 2019 -0700 Update CoriGPU example run script. Tutorials/GPU/run.corigpu commit 4e505b013040e4d06d588aed451a111887063b8d Merge: 5b4897633 515161d9d Author: Weiqun Zhang Date: Wed Aug 21 06:15:44 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 515161d9dd98a4546c253e917908c884bcae8a13 Author: kngott Date: Tue Aug 20 18:35:39 2019 -0700 Thread multiple test and results on linear solver. Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/inputs.test Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-1.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-16.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-2.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-32.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-4.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-64.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-mpi-8.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-1.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-16.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-2.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-32.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-4.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-64.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/knl-omp-8.sh Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/main.diff Tutorials/LinearSolvers/ABecLaplacian_C/threadmultiple_test/results.org commit 9d024f5e7aee7a3bf2363208e5c675a1023fc119 Author: Andrew Myers Date: Tue Aug 20 17:30:19 2019 -0700 always do handshake in fillNeighbors Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 5b4897633468e84d0308b43af539b36bb5531670 Author: Weiqun Zhang Date: Tue Aug 20 15:39:27 2019 -0700 ParallelFor taking multiple Boxes and lambdas Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H Tools/CompileTesting/compiletesting.py commit c2242813fae3dd93955dd9f84cd420a534b18a0f Author: Weiqun Zhang Date: Tue Aug 20 14:02:53 2019 -0700 EB integral: add integral of x*y*z Src/EB/AMReX_algoim.H Src/EB/AMReX_algoim.cpp Src/EB/AMReX_algoim_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 70dd9e297e147eba22b5c68f26ce97ebd1cfe2cf Merge: ceb65e828 de06cb406 Author: Andrew Myers Date: Tue Aug 20 13:21:42 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ceb65e82821acabba6423f3b919f555a2217c2d7 Author: Andrew Myers Date: Tue Aug 20 13:21:15 2019 -0400 only need to call doHandShake after regrid, not every Redistribute Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit de06cb406b1512219e29cd176ceb11b67db7cbf2 Author: Weiqun Zhang Date: Mon Aug 19 17:06:25 2019 -0700 comments on pinned arena. simplify an Array4 ctor. Src/Base/AMReX_Arena.cpp Src/Base/AMReX_Array4.H commit 9042c7a6da942d20811e309f0f643c51c68cca37 Author: Andrew Myers Date: Mon Aug 19 17:05:42 2019 -0700 2D bugfix Src/Particle/AMReX_ParticleContainerI.H commit 57af3b517cc7007227b9a293a6ac3baa25c42752 Author: Andrew Myers Date: Mon Aug 19 16:37:24 2019 -0700 move all the particle IO routines into a separate file Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleIO.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 80d0f14a5c40ec03f0b586f0371369c71972946c Author: Weiqun Zhang Date: Mon Aug 19 13:04:45 2019 -0700 HostDevice::Atomic::Add that does OMP atomic for host code Src/Base/AMReX_GpuUtility.H commit 7d7ad4971b60dffed8b7cad6a0856a1d62d3e8c4 Merge: d9b59d9d3 53d31af55 Author: WeiqunZhang Date: Sun Aug 18 18:12:02 2019 -0700 Merge pull request #550 from AMReX-Codes/convergence_cleanup Convergence cleanup commit 53d31af55c5de0e9ffda2fe50a82ae5aca638764 Author: Michael Zingale Date: Sun Aug 18 19:51:51 2019 -0400 remove unused files + fix 1-d compilation Src/Extern/ProfParser/AMReX_AVGDOWN_1D.F Tools/C_util/Convergence/AVGDOWN_1D.F Tools/C_util/Convergence/AVGDOWN_2D.F Tools/C_util/Convergence/AVGDOWN_3D.F Tools/C_util/Convergence/AVGDOWN_F.H Tools/C_util/Convergence/Add.cpp Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameDomainRefinedFD.cpp Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/GNUmakefile.temp Tools/C_util/Convergence/Make.package.SAVE Tools/C_util/Convergence/Make.package.temp commit 12ab2a8c80c35815a18477bb53e95a6c2070c754 Author: Michael Zingale Date: Sun Aug 18 19:41:14 2019 -0400 some work on making a no-Latex version Tools/C_util/Convergence/AVGDOWN_1D.F Tools/C_util/Convergence/AVGDOWN_2D.F Tools/C_util/Convergence/AVGDOWN_3D.F Tools/C_util/Convergence/RichardsonConvergenceTest.cpp commit d9b59d9d35ba9e13a1c99ea71c7c8dc08fb66338 Merge: 0f872f167 32b9136cd Author: Andrew Myers Date: Fri Aug 16 11:44:28 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0f872f1678125c4c8c2eebeb0bcb70e014a07ccc Author: Andrew Myers Date: Fri Aug 16 11:44:17 2019 -0700 a test for the multilevel redistribute mask Tests/Particles/AssignMultiLevelDensity/main.cpp Tests/Particles/ParticleReduce/main.cpp commit 32b9136cdafbb8d65581bd35d40a4150840b0eac Author: Weiqun Zhang Date: Fri Aug 16 11:32:11 2019 -0700 option to add extra flags from command line Tools/GNUMake/Make.defs Tools/GNUMake/comps/nvcc.mak commit d727d3cf67ab3f39130ddcf07bf105f51f8145d7 Author: Kevin Gott Date: Fri Aug 16 13:42:17 2019 -0400 Thread Multiple time Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/results.org commit 070b57330f2caff61b944f7e531e392d47ccc2a7 Merge: 609eec49e ec6cd0ac4 Author: Weiqun Zhang Date: Fri Aug 16 09:59:05 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 609eec49e3905dde9381699c686b8084a4a90f97 Author: Weiqun Zhang Date: Fri Aug 16 09:58:49 2019 -0700 add new constructors for alias Fab to avoid implicit conversion Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp commit ec6cd0ac42ef7691dbe5397ffefdda39dc594f18 Author: Kevin Gott Date: Thu Aug 15 20:08:31 2019 -0400 Make all scaling tests gcc. Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-16.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-32.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-8.sh commit 171cca87ea1edc170d4bbe02200d15d6c1ea494a Author: Andrew Myers Date: Thu Aug 15 11:43:06 2019 -0700 add test for particle reduce Src/Particle/AMReX_ParticleReduce.H Tests/Particles/ParticleReduce/GNUmakefile Tests/Particles/ParticleReduce/Make.package Tests/Particles/ParticleReduce/inputs Tests/Particles/ParticleReduce/main.cpp Tests/Particles/Redistribute/main.cpp commit eef3ad762f19bd876aec45edff6d14173b940c9e Author: Andrew Myers Date: Thu Aug 15 11:04:19 2019 -0700 also use the ParIter in AMReX_ParticleReduce.H Src/Particle/AMReX_ParticleReduce.H commit 728376e95a096d832a98ce6c3e39f1c567da4bdb Author: Andrew Myers Date: Thu Aug 15 10:50:22 2019 -0700 make code shorter using ParIter Src/Particle/AMReX_ParticleMesh.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit c7386d42adb81b9e1651616f2e671c4ae47a140a Author: Andrew Myers Date: Thu Aug 15 10:34:14 2019 -0700 fix some things in MeshToParticle Src/Particle/AMReX_ParticleMesh.H Tests/Particles/ParticleMesh/main.cpp commit 3d9d027151e9fbc5d3275ec82cf68a6de082fefd Author: Andrew Myers Date: Thu Aug 15 09:59:07 2019 -0700 implement lambda MeshToParticle Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleMesh.H Tests/Particles/ParticleMesh/main.cpp commit 0a4f15d22cb164c2000e69e05fcdf0d687a5dbad Author: Weiqun Zhang Date: Thu Aug 15 07:07:25 2019 -0700 fix compFlux for 1d Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 1ec334618e3a7b26cb7709311ef3e7ebb49e7bc3 Author: Weiqun Zhang Date: Wed Aug 14 19:11:22 2019 -0700 periodicShift MultiFab Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit b1985b5367656c5268c833a59d7d0722ff01303a Author: Andrew Myers Date: Wed Aug 14 16:41:33 2019 -0700 fix off-by-one error Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit cb60df2e7c90acf1199e13be0de382fa06221a96 Author: Andrew Myers Date: Wed Aug 14 16:36:54 2019 -0700 add timer Src/Particle/AMReX_ParticleMesh.H commit 885b8bd79d8e48916cda2bd1c518f1bb29e0845a Author: Andrew Myers Date: Wed Aug 14 16:30:30 2019 -0700 this pointer should not be unique Src/Particle/AMReX_ParticleMesh.H commit bc10e7c9cb5d9b1d4e20a94087d5c4480d533f93 Author: Andrew Myers Date: Wed Aug 14 16:30:12 2019 -0700 tweak inputs Tests/Particles/ParticleMesh/inputs commit 7e8356407c99c6df5510c34590689b05bc9bb723 Author: Andrew Myers Date: Wed Aug 14 16:18:35 2019 -0700 add particle mesh lambda test Tests/Particles/ParticleMesh/GNUmakefile Tests/Particles/ParticleMesh/Make.package Tests/Particles/ParticleMesh/inputs Tests/Particles/ParticleMesh/main.cpp commit 1bdd2088d7ee36007460607b0799930f3c70d408 Author: Andrew Myers Date: Wed Aug 14 13:58:56 2019 -0700 implementing a general particle-to-mesh function with lambdas Src/Particle/AMReX_ParticleMesh.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 192b9b4e5a7346e13909862c616c7be8f6c82a17 Author: Andrew Myers Date: Wed Aug 14 13:55:05 2019 -0700 And, Or -> LogicalAnd, LogicalOr Src/Particle/AMReX_ParticleReduce.H commit c42512f8a222cd9b3adf7537ce1247be36913242 Merge: e9442d7d4 ada9bc92b Author: Andrew Myers Date: Wed Aug 14 13:46:20 2019 -0700 Fixing merge conflict commit ada9bc92be7419e1551f21b2fd131d34590a1c63 Author: Andrew Myers Date: Wed Aug 14 13:41:34 2019 -0700 need to reset m_nrcvs when doing early exit Src/Particle/AMReX_ParticleCommunication.cpp commit 31d205c6461f58e334bae83aeae88f65f6d9aad4 Author: Weiqun Zhang Date: Wed Aug 14 13:26:59 2019 -0700 forgot a new file Src/Boundary/AMReX_LO_BCTYPES.cpp commit df5f53dac55ba2702ed12c76a782acbebf24ed97 Author: Weiqun Zhang Date: Wed Aug 14 13:05:09 2019 -0700 operator<< for LinOpBCType Src/Boundary/AMReX_LO_BCTYPES.H Src/Boundary/CMakeLists.txt Src/Boundary/Make.package commit 68ada3995fc17a065cf2c91d29aed23ab604479c Author: Weiqun Zhang Date: Wed Aug 14 12:52:29 2019 -0700 MLMG: coarsen geometry correctly without using any system defaults in case special geometry is passed in Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 88f7656aba0db352443cf835ca295a994e466e63 Merge: 7f4860a0b aacc44432 Author: Weiqun Zhang Date: Wed Aug 14 12:06:50 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7f4860a0b045cfc434ff454d86ca0bf11358d52f Author: Weiqun Zhang Date: Wed Aug 14 12:06:25 2019 -0700 Atomic::And -> Atomic::LogicalAnd, Atomic::Or -> Atomic::LogicalOr Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_GpuUtility.H Src/Particle/AMReX_ParticleUtil.H commit e9442d7d4b3db07e053e4b25c7882d75d57295c4 Author: Andrew Myers Date: Wed Aug 14 10:58:44 2019 -0700 move the particle reduction functions into their own file. Src/Particle/AMReX_ParticleReduce.H Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit aacc44432e0b4451ef379d2a83cbe34b0573c808 Merge: 6c385dcd4 771bba473 Author: Andrew Myers Date: Wed Aug 14 10:37:47 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6c385dcd4cdda596b3fdf7edc7be855e6bbe597f Author: Andrew Myers Date: Wed Aug 14 10:37:25 2019 -0700 add additional overloads for particle reduction operations Src/Particle/AMReX_ParticleUtil.H commit 771bba473538bd14b047069c10f5f8f68a19c163 Author: Ann Almgren Date: Wed Aug 14 10:35:32 2019 -0700 Move DataServicesTest0 from OldTutorials into Tests Tests/DataServicesTest0/DataServicesTest0.cpp Tests/DataServicesTest0/GNUmakefile commit de12cf02b83f75009d20dc338181fdfcb1162195 Merge: 5e50341ba e6dc5e5d5 Author: Andrew Myers Date: Wed Aug 14 10:23:37 2019 -0700 Merge branch 'development' into redistribute_opt commit e6dc5e5d555148a680a7d0607d1cd427437ecce8 Merge: 53718455c bae57531c Author: Weiqun Zhang Date: Wed Aug 14 09:55:27 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 53718455c526a2d703fbbf8061d8bbb847a07d34 Author: Weiqun Zhang Date: Wed Aug 14 09:54:30 2019 -0700 makeFineMask: add optional arguments specifying coarse and fine flag values Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit bae57531c6de026e9e5d7387631f968e99169d7c Author: Michele Rosso Date: Wed Aug 14 09:49:55 2019 -0700 CMake: remove C_CellMG Src/LinearSolvers/CMakeLists.txt commit 6e9d1efd575b7ff0bbb08379b24d750827db5c31 Author: Weiqun Zhang Date: Wed Aug 14 09:04:33 2019 -0700 rename for consistence Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_Reduce.H commit f4dfb3abc804faba09ad6251b018cbe63f313b8c Merge: 7db30d349 a716b5636 Author: WeiqunZhang Date: Wed Aug 14 08:46:34 2019 -0700 Merge pull request #547 from cgilet/development Development commit a716b563644e45576bae83093559419be6be4a40 Author: cgilet Date: Wed Aug 14 10:38:00 2019 -0400 Clean up MLTensorOp::compFluxes(). Remove unnecessary variable. Fix comments. Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 7db30d34928e838b76222b8953dbe7dcb8701fee Author: Weiqun Zhang Date: Wed Aug 14 07:23:21 2019 -0700 rm C_CellMG from many makefile because MLMG no longer uses files in C_CellMG GNUmakefile.in Tests/LinearSolvers/CellEB/GNUmakefile Tests/LinearSolvers/CellEB2/GNUmakefile Tests/LinearSolvers/ComparisonTest/COEF_1D.F Tests/LinearSolvers/ComparisonTest/COEF_3D.F Tests/LinearSolvers/ComparisonTest/COEF_F.H Tests/LinearSolvers/ComparisonTest/COMP_NORM_1d.f90 Tests/LinearSolvers/ComparisonTest/COMP_NORM_3d.f90 Tests/LinearSolvers/ComparisonTest/COMP_NORM_F.H Tests/LinearSolvers/ComparisonTest/GNUmakefile Tests/LinearSolvers/ComparisonTest/Make.package Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir-ord2 Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir-ord3 Tests/LinearSolvers/ComparisonTest/inputs-rt-Neu Tests/LinearSolvers/ComparisonTest/inputs.3d Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.H Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp Tests/LinearSolvers/EBConvergenceTest/GNUmakefile Tests/LinearSolvers/EBTensor/GNUmakefile Tests/LinearSolvers/EBflux_grad/GNUmakefile Tests/LinearSolvers/MLMG/GNUmakefile Tests/LinearSolvers/NodeEB/GNUmakefile Tools/CompileTesting/compiletesting.py Tutorials/Basic/HeatEquation_EX3_C/Exec/GNUmakefile Tutorials/EB/MacProj/GNUmakefile Tutorials/EB/Poisson/GNUmakefile Tutorials/ForkJoin/MLMG/GNUmakefile Tutorials/LinearSolvers/ABecLaplacian_C/GNUmakefile Tutorials/LinearSolvers/ABecLaplacian_F/GNUmakefile Tutorials/LinearSolvers/NodalPoisson/GNUmakefile Tutorials/SDC/MISDC_ADR_2d/Exec/GNUmakefile commit f9dfbed3bd7efcc918f42e6c48dd347bfca85ad5 Author: Weiqun Zhang Date: Wed Aug 14 06:38:11 2019 -0700 remove old regression tests Tools/RegressionTesting/AMReX-tests.ini commit ade441e1b4fcfa1aed74e687e6aa13f375e8e601 Author: Weiqun Zhang Date: Wed Aug 14 06:32:23 2019 -0700 fix 2d EB Src/EB/AMReX_EBFluxRegister_2d.F90 commit 670a39ffb9d143d08b437cf522ffd32a17871e71 Merge: c23bf865d d05dbfeff Author: Tan Nguyen Date: Wed Aug 14 01:47:27 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c23bf865d9bfc8286b69b9f2861d2267602d2c69 Author: Tan Nguyen Date: Wed Aug 14 01:47:14 2019 -0700 update the make system of AmrTask tutorials Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.mpi Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.mpi.omp Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.mpi.pthreads Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.upcxx Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/SingleVortex/GNUmakefile Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/Make.Adv.mpi Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/Make.Adv.upcxx Tutorials/AmrTask/MiniApps/Adv_phaseAsync/Exec/SingleVortex/GNUmakefile Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.mpi Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.upcxx Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/Backtrace.0 Tutorials/AmrTask/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/GNUmakefile Tutorials/AmrTask/MiniApps/Advection_AmrLevel/CMakeLists.txt Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/Make.Adv Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/Make.package Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/Prob.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/inputs Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/inputs.tracers Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/SingleVortex/probin Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/Make.package Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_2d.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_3d.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/inputs Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/inputs.regt Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/probdata.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/probin Tutorials/AmrTask/MiniApps/Advection_AmrLevel/README Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Adv_F.H Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.H Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/LevelBldAdv.cpp Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Make.package Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_2d/Make.package Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_2d/compute_flux_2d.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_2d/slope_2d.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_3d/Make.package Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_3d/compute_flux_3d.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_3d/slope_3d.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_nd/Adv_nd.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_nd/Make.package Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_nd/Tagging_nd.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/Src_nd/tagging_params.f90 Tutorials/AmrTask/MiniApps/Advection_AmrLevel/Source/main.cpp Tutorials/AmrTask/MiniApps/HeatEquation/GNUmakefile Tutorials/AmrTask/MiniApps/HeatEquation/Make.package Tutorials/AmrTask/MiniApps/HeatEquation/advance.cpp Tutorials/AmrTask/MiniApps/HeatEquation/advance_2d.f90 Tutorials/AmrTask/MiniApps/HeatEquation/advance_3d.f90 Tutorials/AmrTask/MiniApps/HeatEquation/init_phi_2d.f90 Tutorials/AmrTask/MiniApps/HeatEquation/init_phi_3d.f90 Tutorials/AmrTask/MiniApps/HeatEquation/inputs_2d Tutorials/AmrTask/MiniApps/HeatEquation/inputs_3d Tutorials/AmrTask/MiniApps/HeatEquation/main.cpp Tutorials/AmrTask/MiniApps/HeatEquation/myfunc.H Tutorials/AmrTask/MiniApps/HeatEquation/myfunc_F.H Tutorials/AmrTask/MiniApps/HeatEquation/physbc.cpp Tutorials/AmrTask/MiniApps/SMC_fixed_dt/GNUmakefile Tutorials/AmrTask/MiniApps/SMC_fixed_dt/LiDryer.c Tutorials/AmrTask/MiniApps/SMC_fixed_dt/Make.package Tutorials/AmrTask/MiniApps/SMC_fixed_dt/SMC.H Tutorials/AmrTask/MiniApps/SMC_fixed_dt/SMC.cpp Tutorials/AmrTask/MiniApps/SMC_fixed_dt/SMC_F.H Tutorials/AmrTask/MiniApps/SMC_fixed_dt/SMC_advance.cpp Tutorials/AmrTask/MiniApps/SMC_fixed_dt/SMC_init.cpp Tutorials/AmrTask/MiniApps/SMC_fixed_dt/SMC_io.cpp Tutorials/AmrTask/MiniApps/SMC_fixed_dt/chemistry_module.f90 Tutorials/AmrTask/MiniApps/SMC_fixed_dt/derivative_stencil.f90 Tutorials/AmrTask/MiniApps/SMC_fixed_dt/init_data.f90 Tutorials/AmrTask/MiniApps/SMC_fixed_dt/inputs_SMC Tutorials/AmrTask/MiniApps/SMC_fixed_dt/kernels.f90 Tutorials/AmrTask/MiniApps/SMC_fixed_dt/main.cpp Tutorials/AmrTask/MiniApps/SMC_fixed_dt/make_plot.f90 Tutorials/AmrTask/MiniApps/SMC_fixed_dt/transport_properties.f90 Tutorials/AmrTask/MiniApps/SMC_fixed_dt/variables.f90 Tutorials/AmrTask/UnitTests/001_TokenRing.C Tutorials/AmrTask/UnitTests/002_Jacobi_StaticGraph.C Tutorials/AmrTask/UnitTests/003_Jacobi_DynamicGraph.C Tutorials/AmrTask/UnitTests/Makefile commit d05dbfeffe10781c32a38fb52628afc2053966b4 Author: Weiqun Zhang Date: Tue Aug 13 21:31:24 2019 -0700 make some changes for xSDK Src/EB/AMReX_WriteEBSurface.H Src/EB/AMReX_WriteEBSurface.cpp Src/EB/AMReX_WriteEB_F.H Src/EB/AMReX_eb_to_pvd.F90 commit ecac33b3aeb641a41b322035f5356e4fc8cf9c6a Merge: 16d860b57 118aa768a Author: Weiqun Zhang Date: Tue Aug 13 21:15:07 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 118aa768af28d9a2275aafc9e8e52efa967174af Author: Ann Almgren Date: Tue Aug 13 17:18:42 2019 -0700 Remove old multigrid tutorial OldTutorials/MultiGrid_C/CMakeLists.txt OldTutorials/MultiGrid_C/COEF_2D.F90 OldTutorials/MultiGrid_C/COEF_3D.F90 OldTutorials/MultiGrid_C/COEF_F.H OldTutorials/MultiGrid_C/GNUmakefile OldTutorials/MultiGrid_C/Make.package OldTutorials/MultiGrid_C/README OldTutorials/MultiGrid_C/RHS_2D.F90 OldTutorials/MultiGrid_C/RHS_3D.F90 OldTutorials/MultiGrid_C/RHS_F.H OldTutorials/MultiGrid_C/inputs OldTutorials/MultiGrid_C/inputs-rt-c-neu OldTutorials/MultiGrid_C/inputs-rt-c-ord2 OldTutorials/MultiGrid_C/inputs-rt-c-ord3 OldTutorials/MultiGrid_C/main.cpp OldTutorials/MultiGrid_C/writePlotFile.H OldTutorials/MultiGrid_C/writePlotFile.cpp OldTutorials/README_C commit 08ae566b43256f52e3661e9bad6170b0a057fdcb Author: Ann Almgren Date: Tue Aug 13 17:17:03 2019 -0700 Add new tutorial OldTutorials/libamrex_C/MyAmr.H OldTutorials/libamrex_C/MyAmr.cpp OldTutorials/libamrex_C/main.cpp OldTutorials/libamrex_C/myf.f90 Tutorials/Basic/Build_with_libamrex/GNUmakefile Tutorials/Basic/Build_with_libamrex/MyParams.H Tutorials/Basic/Build_with_libamrex/main.cpp Tutorials/Basic/Build_with_libamrex/my_func.f90 Tutorials/Basic/Build_with_libamrex/test_parameters.cpp commit 4d4cd41815f93bf32fb4c5479ce0e961d063c387 Author: Ann Almgren Date: Tue Aug 13 17:16:49 2019 -0700 Add new tutorial Docs/sphinx_tutorials/source/Basic_Tutorial.rst commit 5e50341ba0aef1298ca6fb9db5bb774112a8a891 Merge: edcc70809 308dd11e3 Author: Andrew Myers Date: Tue Aug 13 16:48:26 2019 -0700 Merge branch 'development' into redistribute_opt commit edcc7080948b5cbf9d9c427ff63f17aaed9ae271 Author: Andrew Myers Date: Tue Aug 13 16:47:30 2019 -0700 handle non-gpu aware mpi in a better in the particle communication routines Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 5a69ff8d5aadc76e628cb49731685f74fe59e359 Author: Andrew Myers Date: Tue Aug 13 16:05:35 2019 -0700 restore use_gpu_aware_mpi flag to false by default Tests/Particles/Redistribute/inputs commit b56633051f7c28e4a86a92df139b195731228824 Author: Andrew Myers Date: Tue Aug 13 15:39:07 2019 -0700 fix indentation Src/Particle/AMReX_TracerParticle_mod_K.H commit 308dd11e319ce0679b4eca02bdea1fbc51321fbb Author: Ann Almgren Date: Tue Aug 13 13:47:19 2019 -0700 Move the EB writing files into Src/EB instead of Tutorials and/or mfix code. Src/EB/AMReX_WriteEBSurface.H Src/EB/AMReX_WriteEBSurface.cpp Src/EB/AMReX_WriteEB_F.H Src/EB/AMReX_eb_to_pvd.F90 Src/EB/CMakeLists.txt Src/EB/Make.package Src/Extern/ProfParser/AMReX_AVGDOWN_1D.F Tutorials/EB/Donut/Src/EB_F.H Tutorials/EB/Donut/Src/Make.package Tutorials/EB/Donut/Src/main.cpp commit 586db39e8fbc6c58ced9ecfe07f33c069d514143 Author: Ann Almgren Date: Tue Aug 13 13:22:50 2019 -0700 Fix comments only in interpolation routines Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/AmrCore/AMReX_Interpolater.cpp Src/EB/AMReX_WriteEBSurface.cpp Src/EB/CMakeLists.txt Src/EB/Make.package commit 0a1f2eaafe7902e03c461c8a3b1f0036ec7e3e2b Author: Ann Almgren Date: Tue Aug 13 12:39:17 2019 -0700 1) remove Racetrack -- that was committed by accident 2) move Src/AmrTask/tutorials to Tutorials/AmrTask Src/EB/AMReX_EB2_IF_Racetrack.H Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.mpi.omp Tutorials/AmrTask/MiniApps/Adv_Async_OnDemand/Exec/Make.Adv.mpi.pthreads 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Tutorials/AmrTask/MiniApps/SMC_fixed_dt/kernels.f90 Tutorials/AmrTask/MiniApps/SMC_fixed_dt/main.cpp Tutorials/AmrTask/MiniApps/SMC_fixed_dt/make_plot.f90 Tutorials/AmrTask/MiniApps/SMC_fixed_dt/transport_properties.f90 Tutorials/AmrTask/MiniApps/SMC_fixed_dt/variables.f90 Tutorials/AmrTask/UnitTests/001_TokenRing.C Tutorials/AmrTask/UnitTests/002_Jacobi_StaticGraph.C Tutorials/AmrTask/UnitTests/003_Jacobi_DynamicGraph.C Tutorials/AmrTask/UnitTests/Makefile commit 16d860b57dd4abf85038dda325a867b749440a42 Merge: b847a8e0e eaa906d14 Author: Weiqun Zhang Date: Tue Aug 13 12:32:00 2019 -0700 Merge branch 'newcomm' into development commit b847a8e0e002f8aab1599c81f321425d020d3c2a Merge: 52e1d1a74 517ab1749 Author: Weiqun Zhang Date: Tue Aug 13 12:31:49 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5e16c94e05d83187c42840d39c3f8e1d4191de7f Author: Ann Almgren Date: Tue Aug 13 12:30:05 2019 -0700 1) get rid of "dble" in Src code 2) get rid of hard-wired single- or double-precision constants (use,e.g one/half/zero instead) Src/AmrCore/AMReX_INTERP_1D.F90 Src/EB/AMReX_EB2_IF_Racetrack.H Src/EB/AMReX_EBFluxRegister_2d.F90 Src/EB/AMReX_EBFluxRegister_3d.F90 Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EB_Tagging.F90 Src/EB/AMReX_EB_geometry.F90 Src/EB/AMReX_EB_levelset_F.F90 Src/EB/AMReX_compute_normals.F90 commit eaa906d141dab348348201fa479a771563162fb2 Author: Weiqun Zhang Date: Tue Aug 13 11:10:01 2019 -0700 revert accidental changes Tutorials/LinearSolvers/ABecLaplacian_C/main.cpp commit 517ab17494ef1573381b0945cc23cdcaa869e674 Merge: 9f6e25387 263696141 Author: WeiqunZhang Date: Tue Aug 13 10:48:10 2019 -0700 Merge pull request #548 from rhouim/development Development commit 1e81d89f07a052626d8e9c66989aab52d6387ad0 Author: Weiqun Zhang Date: Tue Aug 13 10:26:12 2019 -0700 clean up the vector version of FillBoundary Src/Base/AMReX_FabArrayCommI.H commit b5bb22c2afda8de6d734f287f701155029349f9c Author: Weiqun Zhang Date: Tue Aug 13 12:26:54 2019 -0400 add the latest linear solver scaling test result Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/results.org commit 9be40eb052b9a4f11b42d775da475f6e908f8421 Merge: c74e4815d 52e1d1a74 Author: Weiqun Zhang Date: Tue Aug 13 00:12:53 2019 -0400 Merge branch 'newcomm' of github.com:AMReX-Codes/amrex into newcomm commit c74e4815d1830fda8d73667f0b39ae613a9f1d4c Author: Weiqun Zhang Date: Tue Aug 13 00:12:27 2019 -0400 add linear solver scaling test stuff Tutorials/LinearSolvers/ABecLaplacian_C/main.cpp Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/inputs.test Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/main.diff Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/results.org Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-1.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-1024.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-128.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-16.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-2.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-2048.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-256.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-32.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-4.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-512.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-64.sh Tutorials/LinearSolvers/ABecLaplacian_C/scalingtest/run-8.sh commit f408471870b1181b03f3d95e5e6fcee5e1fc2e60 Merge: 33fe3c0b1 9f6e25387 Author: Andrew Myers Date: Mon Aug 12 20:25:42 2019 -0400 Merge branch 'development' into redistribute_opt commit 33fe3c0b133f654e1b80ea8fd08cd3f33cfb4ab3 Author: Andrew Myers Date: Mon Aug 12 20:25:32 2019 -0400 powers of 6 for summit Tests/Particles/Redistribute/inputs Tests/Particles/Redistribute/script.sh commit f0e432ea42076beaf9cdb94ead9590179e5648d2 Author: Andrew Myers Date: Mon Aug 12 20:24:56 2019 -0400 remove commented out code Src/Particle/AMReX_ParticleContainerI.H commit 1e1daf5ce88f500239a425d607bfbc5a5cf5ea11 Author: Andrew Myers Date: Mon Aug 12 20:00:52 2019 -0400 fix Redistribute test to be more sensitive to soa errors Tests/Particles/Redistribute/main.cpp commit fd78b6dc7184560c87294a2aaf39228d2c5edbbd Author: Andrew Myers Date: Mon Aug 12 20:00:20 2019 -0400 fix new bug Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 9f6e253870f79786887976360bd48f0148b59c51 Author: Andrew Myers Date: Mon Aug 12 19:46:35 2019 -0400 remove un-needed synchronization points Src/Base/AMReX_Utility.cpp commit 65eb36d682fbdedbbafa6bfba20e58432d567a63 Author: Andrew Myers Date: Mon Aug 12 19:45:56 2019 -0400 use volatile in this test Tests/GPU/Locking/main.cpp commit 52e1d1a742323d8c2fb910e7f05dfeb95a0f2ff9 Merge: 37a0164ee 791287c50 Author: Weiqun Zhang Date: Mon Aug 12 16:09:06 2019 -0700 Merge branch 'development' into newcomm commit 2636961416ed82cb4fd83a07c4f76024d9a6f2fa Author: Ryan Houim Date: Mon Aug 12 17:41:04 2019 -0400 Fixed some bugs with the interpolation routines. Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 commit 37a0164ee9f3062936442bb9cdd211a9ae8094fd Author: Weiqun Zhang Date: Mon Aug 12 12:58:59 2019 -0700 fuse kernels in ParallelCopy Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_PCI.H commit ab4a72d15242cd2a03accc7b532d1b297c3f82f5 Author: Ryan Houim Date: Mon Aug 12 15:52:36 2019 -0400 This commit fixes a strange issue with AMReX cell bilinear interp. We setup a 1D simulation (planar flame) on a 2D grid. After some time steps there would be significant transverse velocities (which should be zero) that affected the flame. This only occured with the Intel compiler with DEBUG=False and with the cell_bilinear interpolation. Compiling with GNU orIntel with DEBUG=True did not produce this behavior. Rearranging the interpolation procedure to the method typically done by students when interpolating tables by hand seems to work fine where the data is first interpolated long x-lines, then the x-line interpolated data is interpolated in the y-direction, and finally the y-interpolated data is interpolated in the z-direction to give the final value. Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 commit a38f680682f4c7a739d024c046657cbc184d022d Author: Weiqun Zhang Date: Mon Aug 12 11:01:58 2019 -0700 reorganize ParallelCopy's local copy Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_PCI.H commit 8d69ffa438d9e3bed5200a8f3edf3fc0c90723f4 Author: Weiqun Zhang Date: Mon Aug 12 10:34:05 2019 -0700 fix new bugs Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArrayCommI.H commit 761d8c1947becf7eedd448e8a64051af6bc10ac7 Author: cgilet Date: Mon Aug 12 12:48:21 2019 -0400 Add MLTensorOp::compFluxes() Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 621050ca4e4a6461addba6e0700faf05e64b0c1c Author: cgilet Date: Mon Aug 12 12:45:39 2019 -0400 Fix typo in error message Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H commit 3a7b72ae06aca33255729cb90ed348f28c1e981d Author: cgilet Date: Mon Aug 12 11:18:47 2019 -0400 In MLCellLinOp::compFlux(), make sure temporary flux is sized to hold all components. Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit e6487a12c2a4997e05d80ae22293d13a1481db40 Author: cgilet Date: Fri Aug 9 16:14:58 2019 -0400 WIP Add MLTensorOp::getFluxes(). Compiles, but no further testing. Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit e4473691da57b779ff4c01de6692e2449c8db7c7 Author: cgilet Date: Fri Aug 9 16:13:14 2019 -0400 Fix typo in error message Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H commit e74869b9f92f4189cba71b486c0b5aad9aeeb485 Author: Weiqun Zhang Date: Sun Aug 11 22:04:15 2019 -0700 fix index for maskfabs Src/Base/AMReX_FBI.H commit d26b4339c906736a1b2ee4d231ce108fd6e41ec0 Author: Weiqun Zhang Date: Sun Aug 11 21:11:13 2019 -0700 tidy Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArrayCommI.H commit ddc4ff11883c25a11a0d412477fbf31292b1b7d0 Author: Weiqun Zhang Date: Sun Aug 11 23:26:38 2019 -0400 minor Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArray.H commit 18ccd1e3d1058f36d42762d10bc29f60391dd1c9 Author: Weiqun Zhang Date: Sun Aug 11 18:59:47 2019 -0700 fuse gpu kernels in fillboundary and reorganization Src/Base/AMReX_FBI.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_PCI.H Src/Base/CMakeLists.txt Src/Base/Make.package commit c91769c61d3989c21be9764ddcaa975449d65550 Author: Weiqun Zhang Date: Sat Aug 10 20:15:15 2019 -0700 remove deprecated PreAllocatable and isCopyOMPSafe Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 55687df178235310f6320991550ce9b164acdcb7 Author: Weiqun Zhang Date: Sat Aug 10 18:10:35 2019 -0700 fix omp for StreamIter Src/Base/AMReX_GpuUtility.cpp commit f87eef80b992308489e249e16a0d5bb40640f06c Author: Weiqun Zhang Date: Sat Aug 10 17:56:12 2019 -0700 fuse local copy part of parallel copy Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_TypeTraits.H Src/EB/AMReX_EBCellFlag.H commit d791526436fa97981c9c056e7bb58507d951f07c Author: Weiqun Zhang Date: Sat Aug 10 11:29:15 2019 -0700 generalize fab_to_fab function and operator interfaces Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_TypeTraits.H Src/EB/AMReX_EBCellFlag.H commit 791287c504a9432ffec2d39025c205d38912935d Author: Ann Almgren Date: Sat Aug 10 06:53:44 2019 -0700 Replace 1.e-14 by "small" and 1.e-15 by "tiny" to be consistent with 2d Src/EB/AMReX_EB2_3D_C.cpp commit 2800e250048d4a8f82a5f04aa5a7975704110bf4 Author: Weiqun Zhang Date: Fri Aug 9 22:01:52 2019 -0700 amrex::HasAtomicAdd Src/Base/AMReX_TypeTraits.H commit 82293086d35f68f9fb93784639d2c3594296c6d8 Author: Weiqun Zhang Date: Fri Aug 9 21:51:46 2019 -0700 amrex::IsCopyAtomicSafe Src/Base/AMReX_TypeTraits.H Src/EB/AMReX_EBCellFlag.H commit 9473356e537b9e8f8115956be3b1b418444ebea0 Author: Weiqun Zhang Date: Fri Aug 9 21:08:28 2019 -0700 fix compilation for cuda < 10 Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_GpuDevice.cpp commit c71b7f750963b6069b1a43c6df401690da5be1c5 Author: Weiqun Zhang Date: Fri Aug 9 19:23:03 2019 -0700 add eb2.small_volfrac Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_C.H Src/EB/AMReX_EB2_Level.H commit 242a4681e96daab4f694b984ed7da57c20236f94 Merge: 7747ed8b2 82ec36483 Author: Weiqun Zhang Date: Fri Aug 9 17:14:52 2019 -0700 Merge branch 'kngott/cudaGraphs' into weiqun/fuse commit 7747ed8b2ac01c71d61a18828346d2967c9ca5c0 Author: Weiqun Zhang Date: Fri Aug 9 17:05:32 2019 -0700 fused local copy Src/Base/AMReX_FabArrayCommI.H commit a13411582284a4d153bc8a98b619f9106f8b7ae0 Merge: 95a5c05f6 739c6e2b8 Author: Andrew Myers Date: Fri Aug 9 13:44:47 2019 -0700 Merge pull request #544 from ChrisDeGrendele/rng2 RNGs are now assigned a block instead of a thread + a test problem to test locking commit 2c0b7895d6b0d310d277546abe81b513b8049d19 Author: Andrew Myers Date: Fri Aug 9 16:43:15 2019 -0400 fix debug build error Src/Particle/AMReX_ParticleCommunication.cpp commit 739c6e2b8bb4cd57f77491de95fecceb6e77766a Author: Chris DeGrendele Date: Fri Aug 9 13:31:30 2019 -0700 Added threadfence to ensure global memory write is complete Src/Base/AMReX_Utility.cpp Tests/GPU/Locking/main.cpp commit 1526544389fe6d61a211933a528a61a7d1392159 Author: cgilet Date: Fri Aug 9 16:14:58 2019 -0400 WIP Add MLTensorOp::getFluxes(). Compiles, but no further testing. Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 45799e5e57b7fc25fbcd08326d813536ea72e080 Author: cgilet Date: Fri Aug 9 16:13:14 2019 -0400 Fix typo in error message Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H commit fcc8d67cd202cbf5d16b4f209b7f414dcb7eff20 Merge: f82d01b77 95a5c05f6 Author: Andrew Myers Date: Fri Aug 9 14:45:28 2019 -0400 Merge branch 'development' into redistribute_opt commit f82d01b776441dd5ff97322e2f8bee3f39a55565 Author: Andrew Myers Date: Fri Aug 9 14:35:59 2019 -0400 replace redistribute with the new version Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleUtil.H Tests/Particles/Redistribute/main.cpp commit 4a23270e6176509e89b11a2b323a52316a1af75e Author: Andrew Myers Date: Fri Aug 9 14:08:12 2019 -0400 some AMREX_RESTRICT Src/Particle/AMReX_ParticleTile.H commit 11a7a35ffd157b3fa6b0b14f70795a73f06e06b7 Author: Andrew Myers Date: Fri Aug 9 14:05:22 2019 -0400 remove print Src/Particle/AMReX_ParticleContainerI.H commit dfd64e543a0fc24f41789f23207d2719ea011942 Author: Andrew Myers Date: Fri Aug 9 14:04:06 2019 -0400 assert that the soa / aos data is correct Tests/Particles/Redistribute/main.cpp commit 05806423d774d515877bb3cedc7e975d3ef47832 Author: Andrew Myers Date: Fri Aug 9 13:35:27 2019 -0400 update inputs Tests/Particles/Redistribute/inputs commit 1299f207063c949f75e9c385d99370880eaf7bd9 Author: Andrew Myers Date: Fri Aug 9 13:35:02 2019 -0400 add some soa data to the test Tests/Particles/Redistribute/main.cpp commit 8dc79bff811c46e83a232d645a35cbba4d062921 Author: Andrew Myers Date: Fri Aug 9 13:34:39 2019 -0400 handling soa data Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_Particles.H commit 95a5c05f64a4ab616c378f52a3dcbca9f6920a2c Author: Ann Almgren Date: Fri Aug 9 06:27:39 2019 -0700 update to VisIt caveat Docs/sphinx_documentation/source/Visualization.rst commit fbe9bf92f5dc2195d65e95dcc0fac5d83c866d91 Author: Weiqun Zhang Date: Thu Aug 8 20:08:19 2019 -0700 fix bug in fixing small EB cell faces Src/EB/AMReX_EB2_3D_C.cpp commit 82ec364831468afbbc607f9863ce450d5a596244 Merge: 70983ebe2 86f307d6d Author: Kevin Gott Date: Thu Aug 8 19:18:29 2019 -0400 Merge branch 'development' into kngott/cudaGraphs Conflicts: Src/Base/AMReX_GpuDevice.cpp commit 86f307d6dce4b7522a33f0d0dc45f39db81e5c2d Author: Ann Almgren Date: Thu Aug 8 11:09:14 2019 -0700 Add comments about how VisIt reads "Cycle" from plotfile names Docs/sphinx_documentation/source/Visualization.rst commit 023cd207660536bd1ca25949f1cbe3db3dc93c0c Author: Chris DeGrendele Date: Thu Aug 8 10:43:49 2019 -0700 Modify test problem to actually test Tests/GPU/Locking/main.cpp commit f5d1874f04b4608b170a72bde11596e8c05725b1 Merge: cfc5cccf8 2434d7e32 Author: Andrew Myers Date: Thu Aug 8 13:09:59 2019 -0400 Merge branch 'development' into redistribute_opt commit 70983ebe25c5282d7caecd8bbe9a8d4c56a608a0 Author: Kevin Gott Date: Wed Aug 7 20:35:59 2019 -0400 Move graph building inside (N_recv > 0) check. Src/Base/AMReX_FabArrayCommI.H commit 2434d7e3259b0197150c838a28af1aea0740d93d Author: Weiqun Zhang Date: Wed Aug 7 17:11:12 2019 -0700 change GpuTuple::operator= to match std Src/Base/AMReX_Tuple.H commit bdc6df80e0a0a6d2f9a90dd662b8ff01a5badf3e Author: Weiqun Zhang Date: Wed Aug 7 16:56:54 2019 -0700 ForwardAsTuple Src/Base/AMReX_Tuple.H commit cfc5cccf888e6483edc48e6cf944da9146872a2a Merge: 2e26e5034 9689fd410 Author: Andrew Myers Date: Wed Aug 7 19:49:50 2019 -0400 Merge branch 'development' into redistribute_opt commit 9689fd410b0559ca53558c853ed1152bf49bd56b Author: Weiqun Zhang Date: Wed Aug 7 16:48:56 2019 -0700 missed a move Src/Base/AMReX_Tuple.H commit 2e26e5034f2ac5c69f6790db7903f5ba07434a8e Merge: 1c2dff71e 6824cf393 Author: Andrew Myers Date: Wed Aug 7 19:44:34 2019 -0400 Merge branch 'development' into redistribute_opt commit 1c2dff71ee2eb34d9688f05abc212e3bf36fa9cc Author: Andrew Myers Date: Wed Aug 7 19:44:03 2019 -0400 use gpu-aware mpi in this test Tests/Particles/Redistribute/inputs commit 4edc3425d73024c4c74fe5f42ed129524a6fe205 Author: Andrew Myers Date: Wed Aug 7 19:43:39 2019 -0400 use the ParticleTileData in pack/unpack Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H commit 6824cf3938252b3300819f16cc52ec97e23a9b63 Author: Weiqun Zhang Date: Wed Aug 7 16:43:02 2019 -0700 GpuTuple: Tie and operator= Src/Base/AMReX_Tuple.H commit b254a88d5be753460ca3ad64393d44c9291cb862 Author: Chris DeGrendele Date: Tue Aug 6 12:31:24 2019 -0700 RNGs are now assigned a block instead of a thread Other random function as well Safer locking mechanism by thread block for older GPUs Now test problem actually uses locking Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Tests/GPU/Locking/GNUmakefile Tests/GPU/Locking/Make.package Tests/GPU/Locking/main.cpp commit d93a7fcf21a09f94aedcbba9da98bd758a68df66 Author: Andrew Myers Date: Wed Aug 7 15:51:23 2019 -0400 method for accessing all particle data on the GPU (whether AoS or SoA) Src/Particle/AMReX_ParticleTile.H commit af18445d0554fb3618a2d5d5cf5aaa1de0deeb7b Author: Andrew Myers Date: Wed Aug 7 15:50:37 2019 -0400 respect the use_gpu_aware_mpi flag Src/Particle/AMReX_Particles.H commit c3d8e1364e89a7a3953940b6e1ef48945e7f587f Author: Weiqun Zhang Date: Wed Aug 7 12:39:51 2019 -0700 GpuTuple: allow conversion Src/Base/AMReX_Tuple.H commit 0f560f16e7fd1ee51fea5dcee5b2c426b7ce8e96 Author: Kevin Gott Date: Wed Aug 7 13:49:41 2019 -0400 Fix GraphInit test. Tests/GPU/CudaGraphs/GraphInitTest/main.cpp commit 87d8763c1447704aca79a07f29145dc9789d6f5c Author: Weiqun Zhang Date: Wed Aug 7 09:46:35 2019 -0700 Apply Src/Base/AMReX_Tuple.H commit 0d22440333fd2a69c6e679a06c4bd22fc3652049 Author: Kevin Gott Date: Wed Aug 7 12:27:44 2019 -0400 Add working InitGraph. Src/Base/AMReX_GpuDevice.cpp commit 886043ce824bb64b00f953eabb894d33157ff3a2 Merge: 423815920 77d237072 Author: Andrew Myers Date: Tue Aug 6 23:58:04 2019 -0400 Merge branch 'development' into redistribute_opt commit 42381592002288dd8befdaeb837bcbb909a7cd5b Author: Andrew Myers Date: Tue Aug 6 23:51:01 2019 -0400 allow overlapping communication / computation when building the mpi copy plan Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H commit 77d237072a38fd22cee606c43cd7e2b01f258e14 Author: Weiqun Zhang Date: Tue Aug 6 19:51:19 2019 -0700 TupleCat Src/Base/AMReX_Tuple.H commit 54dc2dad25282be528bf3f8b747acbea835052a8 Author: Kevin Gott Date: Tue Aug 6 20:13:06 2019 -0400 Simplified init function. Tests/GPU/CudaGraphs/GraphInitTest/main.cpp commit a600f8938d1a330c97a08091621b8acbaeea18b9 Author: Kevin Gott Date: Tue Aug 6 19:16:57 2019 -0400 Minimized graph init. Tests/GPU/CudaGraphs/GraphInitTest/main.cpp commit 594d923f02c70367c44a6a470441fc4f60b39a69 Author: Kevin Gott Date: Tue Aug 6 17:38:32 2019 -0400 Working version of graph init: events. Tests/GPU/CudaGraphs/GraphInitTest/main.cpp commit b6663b603a62055d1552d924697aadb30b51bf33 Author: Brandon Runnels Date: Tue Aug 6 15:13:48 2019 -0600 fixed the problem! it was that the boundary conditions were not getting set properly Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Tests/LinearSolvers/MultiComponent/MCNodalLinOp.cpp Tests/LinearSolvers/MultiComponent/main.cpp commit 3677bc10b2017b646e7236090531150d1ef38849 Author: Tan Nguyen Date: Tue Aug 6 14:00:33 2019 -0700 review lock-free sync points in the MPI backend Src/AmrTask/rts_impls/mpi/Perilla.cpp commit a4bf299130ffd2724bc182f0c3de4d20bb4f3f9d Author: Brandon Runnels Date: Tue Aug 6 13:06:58 2019 -0600 added makefile Tests/LinearSolvers/MultiComponent/GNUmakefile commit f7052bb41c982a058ecff422f5bcc56be31adcf6 Author: Brandon Runnels Date: Tue Aug 6 09:51:52 2019 -0600 updated BC update Tests/LinearSolvers/MultiComponent/main.cpp commit 6eb09db23168b4545dc157fab6a930c751044a74 Merge: 2700d4d59 ff55c9428 Author: Brandon Runnels Date: Tue Aug 6 09:42:45 2019 -0600 Merge branch 'development' into mcmlmg-test commit 2700d4d597b1a138d7e8f54de48402cd459b4ae0 Author: Brandon Runnels Date: Tue Aug 6 09:42:11 2019 -0600 Generally working but bottom solver still failing Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Tests/LinearSolvers/MultiComponent/MCNodalLinOp.cpp Tests/LinearSolvers/MultiComponent/inputs Tests/LinearSolvers/MultiComponent/main.cpp commit 2aaba3d3885201eecac3701b7a1c5000f5ddc0f8 Merge: ff66e5289 ff55c9428 Author: Andrew Myers Date: Mon Aug 5 23:31:46 2019 -0400 Merge branch 'development' into redistribute_opt commit ff66e5289d5a5e842a9a36970c08b97a146f29e6 Author: Andrew Myers Date: Mon Aug 5 23:30:51 2019 -0400 use amrex::Scan instead of thrust::partition in the particle redistribute Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit ff55c942886292597964419d1295f8814320096f Merge: 65dcf8497 94babdd07 Author: WeiqunZhang Date: Mon Aug 5 11:49:14 2019 -0700 Merge pull request #539 from rporcu/rporcu Roberto Porcu commit 94babdd078c89685a6c0b48a37cb76f040c4a0fa Author: Roberto Porcu Date: Mon Aug 5 11:14:31 2019 -0700 Remove Warnings for getFluxes method which is only partially overwritten in MLCellABecLap and MLNodeLaplacian classes Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H commit 088742ca77293903ee1afc15cf2c6945f28801ca Author: Roberto Porcu Date: Mon Aug 5 11:01:27 2019 -0700 Add missing header files Src/Particle/AMReX_Particle.H commit 65e1b425c7493634a9cd33f50f1c710ab088f3d5 Author: Roberto Porcu Date: Mon Aug 5 11:00:52 2019 -0700 Add getter of Gpu shared memory size in Device properties Src/Base/AMReX_GpuDevice.H commit 2737d0882329c50f472de4d7392da1284a896573 Author: Roberto Porcu Date: Mon Aug 5 10:59:29 2019 -0700 Add dataPtr() and size() methods to struct Array4 Src/Base/AMReX_Array4.H commit 65dcf849756de2964c6591efd1e9774d036afaf9 Author: Weiqun Zhang Date: Sat Aug 3 20:25:53 2019 -0700 ignore command line argument after -- Docs/sphinx_documentation/source/Basics.rst Src/Base/AMReX.cpp commit 0781f234a2c3d6d8085b44df7924f33bd470bb81 Author: Weiqun Zhang Date: Sat Aug 3 18:46:24 2019 -0700 put omp pragma inside ifdef Src/Base/AMReX_GpuReduce.H commit f475ebbe5652f0fea3da5f5fa9bcc9f7bce3745d Author: Ann Almgren Date: Sat Aug 3 16:08:28 2019 -0700 re-try formatting Docs/sphinx_documentation/source/Basics.rst commit 419c206a209bf3341dbdc4584e313e4404245f8e Author: Ann Almgren Date: Sat Aug 3 15:52:44 2019 -0700 Fix formatting Docs/sphinx_documentation/source/Basics.rst commit fa4e94e73826d07e66be2f642ecd17c862a39085 Merge: 1fc0d65af 5e331663d Author: Ann Almgren Date: Sat Aug 3 15:38:00 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 1fc0d65af9747bed9763af6cfe671eb7709a5a56 Author: Ann Almgren Date: Sat Aug 3 15:18:46 2019 -0700 Add section about setting argc=2 so amrex doesn't try to read past the inputs file name on the command line Docs/sphinx_documentation/source/Basics.rst commit 170612e5c6fbe5876054cc8e1a840e9a1a4e4c2b Merge: 3342f8a69 5e331663d Author: Andrew Myers Date: Sat Aug 3 17:21:44 2019 -0400 Merge branch 'development' into redistribute_opt commit 5e331663dbe7660a0a6c53ed0e962f7526d786c8 Merge: 2ef6a2654 46603bd56 Author: Andrew Myers Date: Sat Aug 3 17:20:19 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2ef6a2654d27db0f6b684412b9e8c1990697ffff Author: Andrew Myers Date: Sat Aug 3 17:20:08 2019 -0400 GPU version of Random_int Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 46603bd560b5320b1632cb81044c9558e9f4b16c Author: Weiqun Zhang Date: Sat Aug 3 10:23:16 2019 -0700 amrex::StablePartition Src/Base/AMReX_Partition.H Tests/GPU/Partition/main.cpp commit 447467a2ca9070e762c4e2f899344995b7437207 Author: Weiqun Zhang Date: Sat Aug 3 09:27:49 2019 -0700 partition: return number of trues Src/Base/AMReX_Partition.H Src/Base/AMReX_Scan.H Tests/GPU/Partition/main.cpp commit 7b1218a95d91008a0f64e636aaf866acf73f5d76 Author: Weiqun Zhang Date: Fri Aug 2 21:22:32 2019 -0700 update Partition test Tests/GPU/Partition/main.cpp commit 72fa78191009c5aa59cf3c080d6f53d592517b9a Author: Weiqun Zhang Date: Fri Aug 2 21:19:36 2019 -0700 amrex::Partition Src/Base/AMReX_Partition.H Src/Base/AMReX_Scan.H commit f7cd6b1e861475cff4079a9e83ddd811f0a15e10 Author: Weiqun Zhang Date: Fri Aug 2 19:18:08 2019 -0700 generailize scan to take functions Src/Base/AMReX_Partition.H Src/Base/AMReX_Scan.H commit 5e0364ede713a5498a133deb924f120ae2ed90dd Author: Weiqun Zhang Date: Fri Aug 2 18:57:33 2019 -0700 fix some typos Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_Partition.H commit e24375a168eec82f140f61140c1798a996f3c8af Author: Weiqun Zhang Date: Fri Aug 2 18:50:03 2019 -0700 #ifdef put gpu scan code Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_Partition.H Src/Base/AMReX_Scan.H Src/Base/CMakeLists.txt Src/Base/Make.package commit acaa4accdd6b45cbf0ed5ddad33434480f2da376 Author: Kevin Gott Date: Fri Aug 2 20:15:04 2019 -0400 Current Graph Init test. Tests/GPU/CudaGraphs/GraphInitTest/inputs_3d Tests/GPU/CudaGraphs/GraphInitTest/main.cpp commit e9ca8a659ab875953a303e4640b0b97c2e372999 Merge: ed78373ca 77a3f1443 Author: Weiqun Zhang Date: Fri Aug 2 16:17:54 2019 -0700 Merge branch 'weiqun/reduce' into development commit ed78373caf181de9c8296029d57adc70feb57978 Author: Andrew Myers Date: Fri Aug 2 18:52:07 2019 -0400 an indepedent test of the particle partition Tests/GPU/Partition/GNUmakefile Tests/GPU/Partition/Make.package Tests/GPU/Partition/inputs Tests/GPU/Partition/main.cpp commit 77a3f144355fbee91e0cd0b01cc78ee01c83a78c Author: Weiqun Zhang Date: Fri Aug 2 13:59:40 2019 -0700 scan: use volatile Src/Base/AMReX_Scan.H commit 3342f8a69a33919e372f8ecccde7b7da6e34074b Author: Andrew Myers Date: Fri Aug 2 16:55:45 2019 -0400 thrust::device_vector -> Gpu::DeviceVector Src/Particle/AMReX_ParticleContainerI.H commit b3d94513b4d7667285e1fb36b267446b1fe402a8 Merge: 82f5ac98f ca5a52aaa Author: Andrew Myers Date: Fri Aug 2 16:31:42 2019 -0400 Merge branch 'development' into redistribute_opt commit 82f5ac98fa6ad129c06557f4e307639409ba0eba Author: Andrew Myers Date: Fri Aug 2 16:30:50 2019 -0400 use point-to-point communication to determine the number of bytes to rcv when the communication pattern is local Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 7e741729b398b1d57dcc981f69c27f5d932c654c Author: Weiqun Zhang Date: Fri Aug 2 10:20:23 2019 -0700 scan: use __threadfence for reliability Src/Base/AMReX_Scan.H commit 2644fbd97511396fb98c24fb40fc2595f1383f68 Author: Weiqun Zhang Date: Thu Aug 1 22:52:49 2019 -0400 scan: avoid asyncarray and devicescalar Src/Base/AMReX_Scan.H commit ca5a52aaa23326c721e2a018babc0e124c559759 Author: Ann Almgren Date: Thu Aug 1 18:18:09 2019 -0700 "gird" --> "grid" Tutorials/EB/Donut/Src/eb_to_pvf.F90 commit f932e70b1782b7d6f28ab99d76e53be30056b087 Author: Weiqun Zhang Date: Thu Aug 1 20:49:57 2019 -0400 scan test: add synchronize just in case Tutorials/GPU/ParallelScan/main.cpp commit 638350d3dce8ca0578ad90e47ee19e764b45463d Author: Weiqun Zhang Date: Thu Aug 1 18:09:32 2019 -0400 scan: optimization Src/Base/AMReX_Scan.H commit 34db41214c8c5735b9e92292ecb61de7bcc447a7 Author: Weiqun Zhang Date: Thu Aug 1 14:35:43 2019 -0400 scan: tweak # of chunks Src/Base/AMReX_Scan.H commit eadcd7d920b6d400be4cc7aeef5071c5f272a665 Author: Andrew Myers Date: Thu Aug 1 14:21:08 2019 -0400 use non-blocking sends in the communicateParticles and ParticleCopyPlan::buildMPI routines Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit ef49aede8faf56cce0830b03207f41f0b0dee173 Author: Weiqun Zhang Date: Thu Aug 1 11:04:46 2019 -0700 scan: parallel lookback Src/Base/AMReX_Scan.H commit bdd1146139e8727a513d451075f900c172eb81fd Author: Weiqun Zhang Date: Thu Aug 1 08:59:24 2019 -0700 update CHANGES CHANGES commit 61f1e13fa792c43c74b8c6ad6f6c09f943c4fbde Author: Weiqun Zhang Date: Wed Jul 31 21:37:43 2019 -0700 scan: memory fence optimization Src/Base/AMReX_Scan.H Tutorials/GPU/ParallelScan/main.cpp commit 0612e24c3b08634bc9aa3eb7069dca92bd4f2e09 Merge: 195c33ea4 9d2e2f9eb Author: Andrew Myers Date: Wed Jul 31 20:55:44 2019 -0400 Merge branch 'development' into redistribute_opt commit 9eae7666a72f9dfcc0b5ece5299cbee04e06e481 Author: Weiqun Zhang Date: Wed Jul 31 20:52:19 2019 -0400 scan: tweak the number of chunks Src/Base/AMReX_Scan.H Tutorials/GPU/ParallelScan/main.cpp commit 195c33ea4ed9dfb30772cb21795a59c15d7ad859 Author: Andrew Myers Date: Wed Jul 31 20:13:03 2019 -0400 fix typo affecting debug mode Src/Particle/AMReX_ParticleCommunication.H commit 9d2e2f9eb7965452094969f0e110e5f9c21b32c2 Author: Andrew Myers Date: Wed Jul 31 17:06:17 2019 -0700 fix omp in tracer particles Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit 635c8ef1fe80a6faf932f2ab89f6004067e419bc Author: Weiqun Zhang Date: Wed Jul 31 17:04:26 2019 -0700 add ParallelScan test Tutorials/GPU/ParallelScan/GNUmakefile Tutorials/GPU/ParallelScan/Make.package Tutorials/GPU/ParallelScan/main.cpp commit e227e1f6cf55483d0470a0426a13aad1b9d9cad9 Author: Weiqun Zhang Date: Wed Jul 31 16:38:01 2019 -0700 first version of scan Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Scan.H Src/Base/CMakeLists.txt Src/Base/Make.package commit e7e5b278f52622ddfe4b9b14480545823d98abcb Author: Andrew Myers Date: Wed Jul 31 16:53:22 2019 -0700 continue should be return here Src/Particle/AMReX_TracerParticles.cpp commit 4a44d161435fbc8851fb703cf6cf5c9726d1e6d5 Author: Andrew Myers Date: Wed Jul 31 16:38:40 2019 -0700 a little bit of reorganization Src/Particle/AMReX_TracerParticles.cpp commit 6a6450baae2af9580b5d3da45979d8a1dd7ca335 Author: Andrew Myers Date: Wed Jul 31 14:44:21 2019 -0700 fix mac advection for tracer particles Src/Particle/AMReX_TracerParticle_mod_K.H commit 642c426f9569205a6971983b103fded626289ddf Author: Andrew Myers Date: Wed Jul 31 17:26:40 2019 -0400 overlap communication with computation in Redistribute Src/Particle/AMReX_ParticleContainerI.H commit 0fafac148a195e22957368dd27e2d6918c2c71d3 Author: Andrew Myers Date: Wed Jul 31 16:14:34 2019 -0400 split up start and finish in the MPI communicateParticles so it can be overlapped Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleBufferMap.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit a462ca2d58940080ac3de6dbfa6b710e27c582a6 Merge: aeb258bb9 d2e6d3bef Author: Ann Almgren Date: Wed Jul 31 13:07:02 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit aeb258bb9d0053e98bc09d7e5e796a08bdba9af7 Author: Ann Almgren Date: Wed Jul 31 13:02:31 2019 -0700 Fix bug in mac_interpolate used in advection of tracer particles. Src/Particle/AMReX_TracerParticle_mod_K.H commit dcb93bb13c63828ba66688a0ccc581fdf8ce3d47 Author: Andrew Myers Date: Wed Jul 31 15:17:48 2019 -0400 fix resize error Src/Particle/AMReX_ParticleCommunication.cpp commit 0c6f20b985bbb9bd8b464ad14f15eafde19dd94f Author: Andrew Myers Date: Wed Jul 31 15:06:53 2019 -0400 remove commented out code Src/Particle/AMReX_ParticleCommunication.H commit 6857533cb1b75d7378fe23358e20ad099472b308 Author: Andrew Myers Date: Wed Jul 31 15:05:26 2019 -0400 remove redundant all-to-all in communicateParticles Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit 85a771b89d83ebd2d97a37393f781fdc1aaa4820 Merge: 3ff256be3 d2e6d3bef Author: Weiqun Zhang Date: Wed Jul 31 11:39:57 2019 -0700 Merge branch 'development' into weiqun/reduce commit d2e6d3bef73a2c3d71fc858274234e52cb861ae2 Author: Donald E. Willcox Date: Tue Jul 30 21:04:45 2019 -0700 Fix case-sensitive bug in gpu_fortran.py preprocessor script. (#522) Tools/F_scripts/gpu_fortran.py commit 85496a17b45b36b455eff1fee60a7b6fcf922f6c Merge: 8f1d48066 4c12aefee Author: Marc Day Date: Tue Jul 30 17:10:43 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8f1d48066464203ff95f5668162b57fa32479365 Author: Marc Day Date: Tue Jul 30 17:10:38 2019 -0700 Add tool to generate turbulence files from plotfiles Tools/Postprocessing/C_Src/GNUmakefile Tools/Postprocessing/C_Src/PlotfileToTurb.cpp Tools/Postprocessing/C_Src/PlotfileToTurb_nd.f90 commit ce9c92570e2024563f1aa433dd0731d3747d0abc Author: Andrew Myers Date: Tue Jul 30 20:09:27 2019 -0400 missed a couple Src/Particle/AMReX_ParticleCommunication.cpp commit 34fb2138d17a2af7039ea836b20c3bdc1104daf8 Author: Kevin Gott Date: Tue Jul 30 20:09:15 2019 -0400 Basic init test running. Need to add graphs to it. Tests/GPU/CudaGraphs/GraphInitTest/main.cpp commit 999d47bf898f6ab0a21a86ebe5d7f8a63a5f35be Author: Andrew Myers Date: Tue Jul 30 20:00:26 2019 -0400 fix CPU compilation Src/Particle/AMReX_ParticleCommunication.H commit 44b032ae6bf16a52b1ad8c724bcd9058c747eb8b Author: Andrew Myers Date: Tue Jul 30 19:55:18 2019 -0400 add timer around the partition Src/Particle/AMReX_ParticleContainerI.H commit f6dd0745745c80373c5b7864c128cfab59a70d5f Merge: 9e5c978e4 4c12aefee Author: Andrew Myers Date: Tue Jul 30 19:25:20 2019 -0400 Merge branch 'development' into redistribute_opt commit 9e5c978e4541dd5450dee08941b2d556ff101483 Author: Andrew Myers Date: Tue Jul 30 19:24:37 2019 -0400 perform an initial partition to keep the size of the redistribute copy operation down Src/Particle/AMReX_ParticleContainerI.H commit 2d00b3528f2651c03df7a35d28e505784075c83d Merge: e97c11f52 4c12aefee Author: Kevin Gott Date: Tue Jul 30 18:58:21 2019 -0400 Merge branch 'development' into kngott/cudaGraphs commit 4c12aefeecff2237b5dcfe9ae0ef011152480ec5 Author: Kevin Gott Date: Tue Jul 30 18:56:28 2019 -0400 Set initial stream after device setup to the default stream. Src/Base/AMReX_GpuDevice.cpp commit 7c3406b581e48c164c9c375f3e82933c6ec131c9 Author: Tan Nguyen Date: Tue Jul 30 12:28:09 2019 -0700 fix a small error in the AMFIter Src/AmrTask/rts_impls/runtime_common/RGIter.cpp Src/AmrTask/rts_impls/runtime_common/WorkerThread.H Src/AmrTask/rts_impls/runtime_common/WorkerThread.cpp Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Adv.cpp Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Adv_advance.cpp commit 3ff256be3db2a99a1dafde6a11ef8767503f3ec0 Author: Weiqun Zhang Date: Tue Jul 30 11:57:51 2019 -0700 reduce tutorial: use long for sum of iMultiFab for consistence with iMultiFab::sum function Tutorials/GPU/ParallelReduce/main.cpp commit e175bd32d2654e4688ec5415730c82326d17b33c Author: Weiqun Zhang Date: Tue Jul 30 11:50:25 2019 -0700 fix type in reduce Src/Base/AMReX_GpuReduce.H commit e97c11f52301e782bf46d26f418431aeb8f78ef6 Author: Kevin Gott Date: Tue Jul 30 14:50:17 2019 -0400 Start of GraphInitTest. Tests/GPU/CudaGraphs/GraphInitTest/GNUmakefile Tests/GPU/CudaGraphs/GraphInitTest/Make.package Tests/GPU/CudaGraphs/GraphInitTest/inputs_3d Tests/GPU/CudaGraphs/GraphInitTest/main.cpp commit 8c71a33e996b37bb85b9cf0428e604566779d122 Author: Weiqun Zhang Date: Tue Jul 30 11:18:11 2019 -0700 finish simplification of reduce interface Src/Base/AMReX_Reduce.H Src/Base/AMReX_Tuple.H Tutorials/GPU/ParallelReduce/main.cpp commit d40d1b51f662ee6ad75afd76ae8b635950d3d96c Merge: 404093011 c435f1725 Author: Kevin Gott Date: Tue Jul 30 13:51:18 2019 -0400 Merge branch 'development' into kngott/cudaGraphs commit c435f17256bdde59ba2d97dc8b22efef36294f27 Author: Andrew Myers Date: Tue Jul 30 10:18:19 2019 -0700 id_rsa_travis -> deploy_key build_and_deploy.sh commit ae7d17e3385605929b91cafae69d13d13fd401ce Author: Andrew Myers Date: Tue Jul 30 13:17:55 2019 -0400 don't actually need to clear the copy op and plan here Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleContainerI.H commit b35b11d3603cebd57e17e5f12ab76db510851f24 Author: Andrew Myers Date: Tue Jul 30 13:14:40 2019 -0400 parmparse nsteps in redistribute test Tests/Particles/Redistribute/inputs Tests/Particles/Redistribute/main.cpp commit 5e23f67abee723d30800728b6af10243a33a03a8 Author: Andrew Myers Date: Tue Jul 30 10:07:10 2019 -0700 update deploy key used by Travis CI build_and_deploy.sh deploy_key.enc id_rsa_travis.enc commit c36da1b9ce6e0d617eb40c750a11c138beadc431 Author: Weiqun Zhang Date: Tue Jul 30 07:20:28 2019 -0700 simplify the interface for reduce Src/Base/AMReX_BaseFab.H Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_Reduce.H Src/Base/CMakeLists.txt Src/Base/Make.package Tutorials/GPU/ParallelReduce/main.cpp commit 0a7d7ede15c5f16d5a6895eaf94ecedd5e10d008 Author: Andrew Myers Date: Mon Jul 29 17:09:21 2019 -0700 more 1D compilation errors Src/Particle/AMReX_TracerParticle_mod_K.H commit a64098fc599f2226038d6ebf66b6719e5cf6686d Merge: fa305a66a 6bfbf7a85 Author: Andrew Myers Date: Mon Jul 29 17:07:06 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit fa305a66a796d5539cd7ea4fab3ff40a5135b0f4 Author: Andrew Myers Date: Mon Jul 29 17:06:53 2019 -0700 fix 1D tracer particles Src/Particle/AMReX_TracerParticle_mod_K.H commit 19dc33d67858ce5af57e10871661dd007a18cfd4 Author: Andrew Myers Date: Mon Jul 29 15:59:34 2019 -0400 keep around the redistribute copy plan and op so it doesn't need to do any reallocation Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 5ac27793979bb717c748afaa33df77ea20c65cc0 Author: Andrew Myers Date: Mon Jul 29 15:53:14 2019 -0400 avoid pushing back onto device vector in particle communication Src/Particle/AMReX_ParticleCommunication.cpp commit 6bfbf7a855612bbb9feb57ed2cc06886d79b1184 Author: Ann Almgren Date: Mon Jul 29 12:44:15 2019 -0700 two *.H files were missing from Make.package Src/Particle/Make.package commit b2d7b6e6c6b28ef2b079198b158794bd953e6a5e Author: Andrew Myers Date: Mon Jul 29 15:25:18 2019 -0400 fix routine name in profile region Src/Particle/AMReX_ParticleCommunication.H commit a109045b9b348939f7fc2b888d56233b3336c54e Author: Andrew Myers Date: Mon Jul 29 15:04:01 2019 -0400 move early exit Src/Particle/AMReX_ParticleContainerI.H commit b8e65ba9b84960377194203bba12005b511bae47 Author: Andrew Myers Date: Mon Jul 29 15:03:21 2019 -0400 actually used the parmparsed values of move_dir and do_random Tests/Particles/Redistribute/inputs Tests/Particles/Redistribute/main.cpp commit d83cdf20f41397855568dd05a7976e4c5dff6979 Author: Andrew Myers Date: Mon Jul 29 14:27:16 2019 -0400 change repo in submission script Tests/Particles/NeighborParticles/script.sh Tests/Particles/Redistribute/script.sh commit c1241a30fa489b472937542beb2819cd7f51e76e Author: Andrew Myers Date: Mon Jul 29 14:26:59 2019 -0400 add random move option for redistribute test Tests/Particles/Redistribute/main.cpp commit 8462a16a6f3fc2f0d00473110644b3823e770a4e Author: Andrew Myers Date: Mon Jul 29 14:06:52 2019 -0400 update script Tests/Particles/NeighborParticles/script.sh commit bde2410220cbc1ef9347b1c8e6845a526dfed445 Author: Andrew Myers Date: Mon Jul 29 14:06:13 2019 -0400 properly handle particles that leave the domain in non-periodic directions. Src/Particle/AMReX_ParticleCommunication.H commit 084c65b1dc0747e6d40c55510968c333827623ca Author: Andrew Myers Date: Mon Jul 29 13:58:54 2019 -0400 fix typo in script Tests/Particles/Redistribute/script.sh commit 73419cdc516e385d2cb5256fc62a9dac54dbfbc7 Merge: 8ece044e4 1fb39f31f Author: Andrew Myers Date: Mon Jul 29 13:38:14 2019 -0400 Merge branch 'development' into redistribute_opt commit 4c9d24f50f6cf91621c46ee296ffce13ac9302fd Author: Weiqun Zhang Date: Sun Jul 28 19:28:19 2019 -0400 Reduce::Min, Reduce::Max and Reduce::MinMax Src/Base/AMReX_Functional.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H Tutorials/GPU/ParallelReduce/main.cpp commit afc2e95bfa741d417f3144fcc21e5acc3e95f3bd Author: Weiqun Zhang Date: Sun Jul 28 15:12:22 2019 -0400 ParallelForReduce -> FabReduce and VecReduce. add Reduce::Sum Src/Base/AMReX_Functional.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuReduce.H Src/Base/CMakeLists.txt Src/Base/Make.package Tutorials/GPU/ParallelReduce/main.cpp commit 1fb39f31fb562f2e4a9be65460fa934bce095307 Author: Ann Almgren Date: Sun Jul 28 10:27:33 2019 -0700 Remove setMaxCoarseningLevel since it wasn't working anyway Src/LinearSolvers/MLMG/AMReX_MacProjector.H commit b71f8ba00072968e011a03c2e5411e344bcb4eef Author: Ann Almgren Date: Sun Jul 28 10:14:13 2019 -0700 Add a new MacProjector constructor that takes an lp_info so that we can pass m_max_coarsening_level in Src/LinearSolvers/MLMG/AMReX_MacProjector.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit 97f9d33b27b47077172a7827d442e9df47888ce8 Author: Weiqun Zhang Date: Sat Jul 27 12:39:44 2019 -0400 ParallelForReduce: more overloads Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuMemory.H Src/Base/AMReX_GpuReduce.H Tutorials/GPU/ParallelReduce/main.cpp commit 7fba84decfa028f11897823ba26534b11f3b8743 Author: Weiqun Zhang Date: Sat Jul 27 11:03:58 2019 -0400 ParallelForReduce Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuReduce.H Tests/GPU/ParallelReduce/main.cpp Tutorials/GPU/ParallelReduce/GNUmakefile Tutorials/GPU/ParallelReduce/Make.package Tutorials/GPU/ParallelReduce/main.cpp commit ed0526c0a5a3ddea62d3724c3452f0fe1de8ea37 Merge: ab56cec54 aeea6f860 Author: Weiqun Zhang Date: Sat Jul 27 00:03:17 2019 -0400 Merge branch 'development' into weiqun/reduce commit 8ece044e46899d04b44182ee3f80dda23748cc83 Author: Andrew Myers Date: Fri Jul 26 17:57:56 2019 -0400 checking particle redistribute test Tests/Particles/Redistribute/GNUmakefile Tests/Particles/Redistribute/Make.package Tests/Particles/Redistribute/inputs Tests/Particles/Redistribute/main.cpp Tests/Particles/Redistribute/script.sh commit 575f8c22b93a25a493d01b85b4e3a0b541376a93 Author: Andrew Myers Date: Fri Jul 26 17:38:41 2019 -0400 forgot to put * Src/Particle/AMReX_ParticleContainerI.H commit 6435213c3005ccb03b75c321e54cd6878759663b Author: Andrew Myers Date: Fri Jul 26 17:32:34 2019 -0400 implement unpack policies so that the same communication routines can handle both redistribute and neighbor unpacking patterns Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleContainerI.H commit a240a70b5dc478574e92a43320f875745072797f Author: Andrew Myers Date: Fri Jul 26 16:11:40 2019 -0400 do the same for communicateParticles Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H commit ab56cec54fae7a57e9ec4d40dba8af583e9faf77 Author: Weiqun Zhang Date: Fri Jul 26 12:35:42 2019 -0700 reducesum using __shfl_down_sync Src/Base/AMReX_GpuReduce.H Tests/GPU/ParallelReduce/GNUmakefile Tests/GPU/ParallelReduce/Make.package Tests/GPU/ParallelReduce/main.cpp commit c2d4a1812653c9c44aa47ac05da5c6aa2ff8af41 Author: Andrew Myers Date: Fri Jul 26 15:28:16 2019 -0400 move pack and unpack buffers out of neighbor particle container so they can be reused. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit ec30df1753adbe599f768a6a6bb853605fddb35f Author: Brandon Runnels Date: Fri Jul 26 13:06:32 2019 -0600 works with multilevel and multigrid, but bottom solve is still failing Tests/LinearSolvers/MultiComponent/inputs commit 056ddd101d28cdcd855526c7622cc7a14f631762 Author: Brandon Runnels Date: Fri Jul 26 13:03:37 2019 -0600 variable inputs working, but bottom solver is still failing for mglev>0 Tests/LinearSolvers/MultiComponent/MCNodalLinOp.H Tests/LinearSolvers/MultiComponent/MCNodalLinOp.cpp Tests/LinearSolvers/MultiComponent/inputs Tests/LinearSolvers/MultiComponent/main.cpp commit a1eb330698aa851537d99b337e151dc407fe7eba Author: Andrew Myers Date: Fri Jul 26 14:48:44 2019 -0400 remove extra clearNeighbors calls Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 9f8f517abe87c52c26cb36ffc9bacd5ee48f5927 Author: Andrew Myers Date: Fri Jul 26 14:42:42 2019 -0400 also build the parallel portion of the copy plan Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit 5e80a7b3fc479fa86d468c736361a535f9328042 Author: Andrew Myers Date: Fri Jul 26 14:29:28 2019 -0400 build method for ParticleCopyPlan Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp Src/Particle/AMReX_Particles.H commit d1e9bbeb0a0c4166951f4316a4d44cc848514bdd Author: Andrew Myers Date: Fri Jul 26 14:01:52 2019 -0400 seperate the op and the plan Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit aeea6f860ff09a41b8f5d5a007de9bb4fe5ab125 Author: Kevin Gott Date: Fri Jul 26 13:49:46 2019 -0400 if (Gpu::notInLaunchRegion()) Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.cpp commit a79e4b36f1cbfe9514b2f594afd7b59bb7e40fd3 Author: Kevin Gott Date: Fri Jul 26 12:41:03 2019 -0400 OwnerMask -> GPU. Src/Base/AMReX_iMultiFab.cpp commit e115aed9d82952bf5006279454a56e300f3eaeb0 Author: Andrew Myers Date: Fri Jul 26 13:45:55 2019 -0400 create structs for particle copy ops and plans Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleCommunication.H Src/Particle/AMReX_ParticleCommunication.cpp commit e9d52a432e43132157077a7ef2ca54f6a456f9c1 Merge: ffd9f083f 3aacadf61 Author: Andrew Myers Date: Fri Jul 26 13:09:37 2019 -0400 Merge branch 'development' into redistribute_opt commit 3aacadf6156a3d41890e4399541deb002f360e32 Author: Andrew Myers Date: Fri Jul 26 13:09:09 2019 -0400 add an explanatory comment about the default number of cuda random states. Src/Base/AMReX_Utility.cpp commit 90d7228cc72b1130ad2ffe0643934e50d4d822b4 Author: Andrew Myers Date: Fri Jul 26 13:07:42 2019 -0400 make it so that users no longer need to call InitRandomSeedOnDevice explicitly Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Tests/GPU/RandomNumberGeneration/main.cpp commit ffd9f083f7e471389dfc78a17f404c90d684ccf4 Merge: 5984fbfff f616b7f6d Author: Andrew Myers Date: Fri Jul 26 12:54:30 2019 -0400 Merge branch 'development' into redistribute_opt commit f616b7f6de7e67d0b099ac25bc1993c05f7387bb Author: Andrew Myers Date: Fri Jul 26 12:52:49 2019 -0400 use std namespace for floor, don't use line continuation symbols Src/Particle/AMReX_TracerParticle_mod_K.H commit 5984fbfffe0ea5afe9b28f77ddadfae4a13ab901 Merge: 3d244b6ae 657f6ed95 Author: Andrew Myers Date: Fri Jul 26 12:47:25 2019 -0400 Merge branch 'development' into redistribute_opt commit 657f6ed95361a21fc99821d8ad77652976804789 Merge: 42c7deea2 4973fbde3 Author: Andrew Myers Date: Fri Jul 26 09:42:25 2019 -0700 Merge pull request #534 from ChrisDeGrendele/tracerparticles_2 This adds gpu support to tracer particles commit 42c7deea23cf9a485ded3cce8e8aebb8b9d380c8 Author: Weiqun Zhang Date: Fri Jul 26 12:21:47 2019 -0400 value_type -> Real Src/Base/AMReX_VisMF.cpp commit 4973fbde31fc456afeb5bff2904f7b0c4ff5768f Author: Chris DeGrendele Date: Fri Jul 26 02:01:44 2019 -0400 Fixed segfault error Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit c0b443ad262cfd1d89cfecd7cabb2f2f27bc7769 Author: Chris DeGrendele Date: Thu Jul 25 22:34:21 2019 -0700 commit the changes Src/Particle/AMReX_TracerParticles.cpp Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 6237d8b1d161b53126ae64e4e4144532fbd0b9aa Merge: fcccc468b 6b8490488 Author: Chris DeGrendele Date: Thu Jul 25 22:24:47 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into tracerparticles_2 commit fcccc468b8bf80818c8917b7d6c535d3f7a3510b Author: Chris DeGrendele Date: Thu Jul 25 22:10:38 2019 -0700 fixed off by 1 index error again Src/Particle/AMReX_TracerParticle_mod_K.H commit 2c7061b99816f3769c2314ffc769a321a8642552 Author: Chris DeGrendele Date: Thu Jul 25 22:07:35 2019 -0700 tracer Src/Particle/AMReX_TracerParticle_mod_K.H commit 3d244b6ae50e32ef002efd7383c91376958f3d58 Author: Andrew Myers Date: Fri Jul 26 00:01:23 2019 -0400 more work on refactoring the particle communication code Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit beff4528531b4bb06c29b5eb427a5d5c6ffa07ff Author: Andrew Myers Date: Thu Jul 25 22:46:09 2019 -0400 remove some unused variables Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 9ecec84fd4666ed5553f98e1c9ce23f033efdaa6 Merge: d59a0dddf 6b8490488 Author: Andrew Myers Date: Thu Jul 25 22:36:14 2019 -0400 Merge branch 'development' into redistribute_opt commit 6b84904884bdfb590e9514466dc049d281779906 Author: Andrew Myers Date: Thu Jul 25 22:31:45 2019 -0400 make sure these variables are initialized Src/Base/AMReX_Utility.cpp commit 41d2d8e1caedd7ce4b9a0dafb4354c1433803a50 Author: Andrew Myers Date: Thu Jul 25 20:50:18 2019 -0400 remove sync I just added Src/Base/AMReX_Utility.cpp commit 03bee98c21341217406f99c9a12f9e98274685e8 Merge: 871274838 aa5859f10 Author: Andrew Myers Date: Thu Jul 25 20:41:04 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 871274838d8a3a3daf941a4c36dc3703042d16da Author: Andrew Myers Date: Thu Jul 25 20:40:40 2019 -0400 turn on TINY_PROFILE by default Tests/GPU/RandomNumberGeneration/GNUmakefile commit aa5859f1008f15a0bb098a16ed6634465b1bf0ab Merge: 97c5af13e ef65a0833 Author: Weiqun Zhang Date: Thu Jul 25 17:31:40 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 97c5af13ea19ac57e6837e44238ec51550533445 Author: Weiqun Zhang Date: Thu Jul 25 17:31:01 2019 -0700 when there are callbacks in MFIter, use two streams only Src/Base/AMReX_GpuAsyncArray.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuElixir.cpp Src/Base/AMReX_MFIter.cpp commit ef65a0833ad7c52ca3541d3cd3abcbfd78acb106 Author: kngott Date: Thu Jul 25 17:19:35 2019 -0700 OverlapMask on the GPU. Src/Base/AMReX_MultiFab.cpp commit ba6548e2298c0888cba7619972c81897865ce87e Author: Andrew Myers Date: Thu Jul 25 20:15:09 2019 -0400 Should call device synchronize after initializing the random seeds Src/Base/AMReX_Utility.cpp commit feb5cb73d6ae1c2d7e71265266ba40b9a58038ce Author: Andrew Myers Date: Thu Jul 25 20:03:59 2019 -0400 parmparse nstates and ndraw in the random number generation test Tests/GPU/RandomNumberGeneration/main.cpp commit 5bda6320eea1f39397de700ab1af7cf341f29cda Author: Brandon Runnels Date: Thu Jul 25 17:25:51 2019 -0600 wip - currently works but bottom solve is failing Tests/LinearSolvers/MultiComponent/MCNodalLinOp.H Tests/LinearSolvers/MultiComponent/MCNodalLinOp.cpp Tests/LinearSolvers/MultiComponent/inputs Tests/LinearSolvers/MultiComponent/main.cpp commit a48715892fb2f47278622d57009699760f43a2e7 Author: Andrew Myers Date: Thu Jul 25 18:51:48 2019 -0400 don't need separate variables for host and device size of the state array Src/Base/AMReX_Utility.cpp commit 071ac6db464052ce7da4133c3ae4be0ced3a782c Author: Andrew Myers Date: Thu Jul 25 18:46:07 2019 -0400 remove unused function Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 1e8c2b97ef1685a2aabb707a07f63e1fff197982 Author: Andrew Myers Date: Thu Jul 25 18:45:39 2019 -0400 some renaming Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit a77461897ec4e834952d46229ef612b132ee9838 Author: Andrew Myers Date: Thu Jul 25 17:58:36 2019 -0400 some reorganization Src/Base/AMReX_Utility.cpp commit c410dac72416b5b04b99cb675917db35e5b71c89 Author: Andrew Myers Date: Thu Jul 25 17:51:36 2019 -0400 also use the locks in amrex::RandomNormal Src/Base/AMReX_Utility.cpp commit b149905cc452537012eec660aee92533bfafcca3 Author: Andrew Myers Date: Thu Jul 25 17:50:31 2019 -0400 update random number gpu test Tests/GPU/RandomNumberGeneration/main.cpp commit 1eaefe8613a6b5dd249689d139af5e8a51fdeb46 Author: Andrew Myers Date: Thu Jul 25 17:50:10 2019 -0400 also add a free_state function to release the lock Src/Base/AMReX_Utility.cpp commit 52df4fa163429337471dd59e9399a579fdaf82fc Author: Andrew Myers Date: Thu Jul 25 17:40:21 2019 -0400 use same nstates variable to keep track of both the random states and the lock array Src/Base/AMReX_Utility.cpp commit f67d30532356bf13e657048f29204114d0fe6cf7 Author: Andrew Myers Date: Thu Jul 25 17:39:20 2019 -0400 fix index bug in amrex::Random Src/Base/AMReX_Utility.cpp commit a2bac25ea0cdc2660cc4e67aba16af21ac79907b Merge: afae43581 00c04983b Author: Andrew Myers Date: Thu Jul 25 14:37:57 2019 -0700 Merge pull request #532 from ChrisDeGrendele/gpu_rng Random number generation on gpus commit 4476e6467e1e06a759dfc810ca7e3295f54e421d Author: Brandon Runnels Date: Thu Jul 25 15:33:37 2019 -0600 re-committed with spurious files removed Tests/LinearSolvers/MultiComponent/MCNodalLinOp.H Tests/LinearSolvers/MultiComponent/MCNodalLinOp.cpp Tests/LinearSolvers/MultiComponent/Make.package Tests/LinearSolvers/MultiComponent/inputs Tests/LinearSolvers/MultiComponent/main.cpp commit afae4358107e9ef2038bf0cef57cd17e1d909d66 Author: kngott Date: Wed Jul 24 14:19:09 2019 -0700 Remove hanging variable. Src/Base/AMReX_Utility.cpp commit dbd34ef7d8df87ae857ebb74de2ee26163fd9152 Author: atmyers Date: Thu Jul 25 10:04:16 2019 -0700 change add command in build_and_deploy.sh build_and_deploy.sh commit c1ed0624107e5d59aa2844a758f248841dae4409 Author: Weiqun Zhang Date: Thu Jul 25 09:18:52 2019 -0700 fix c++ std flag when pgi is used as nvcc host compiler Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak commit 48f7b776539eec3dd2e67e4b382d1f23da40ce99 Author: Weiqun Zhang Date: Wed Jul 24 18:23:03 2019 -0700 fix id_rsa_travis path build_and_deploy.sh commit 00c04983b85170f22f935f328fc2ce92854d75da Author: Chris DeGrendele Date: Wed Jul 24 17:26:56 2019 -0700 get_state should only be declared if we're using gpus Src/Base/AMReX_Utility.cpp commit 8ef4e522230db189dafbc35ef195b440ab0c743c Author: Weiqun Zhang Date: Wed Jul 24 17:09:37 2019 -0700 move doc to AMReX-Codes.github.io build_and_deploy.sh commit 6fc8c4fe0c86011f87b9d94e8f5e929d998be266 Author: Chris DeGrendele Date: Wed Jul 24 17:01:04 2019 -0700 fixed whitespaces Src/Base/AMReX_Utility.cpp commit 1aa2e1cb9536e59b597c4efd0978c93eb692d06a Author: Chris DeGrendele Date: Wed Jul 24 16:58:28 2019 -0700 fixed Src/Base/AMReX_GpuUtility.cpp commit c9a5dedc5c9d9ed3c425d1e490b3c1065bbaa99e Author: Chris DeGrendele Date: Wed Jul 24 16:48:41 2019 -0700 Forgot }; Src/Base/AMReX_Utility.cpp Tests/GPU/RandomNumberGeneration/main.cpp commit 835955b5db26a9cae9af59bf2d40688b796e6fcc Author: Chris DeGrendele Date: Wed Jul 24 16:42:15 2019 -0700 Tracer Particle GPU support Src/Base/AMReX_Utility.cpp Src/Particle/AMReX_Particle.H Src/Particle/AMReX_Particle_mod_K.H Tests/GPU/RandomNumberGeneration/GNUmakefile Tests/GPU/RandomNumberGeneration/launc_gpu.sh Tests/GPU/RandomNumberGeneration/main.cpp Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile commit 9d188b68941752929bc773c148c142eec1091a34 Author: Chris DeGrendele Date: Wed Jul 24 16:28:59 2019 -0700 Random Number Generation on GPUs Src/Base/AMReX_GpuUtility.cpp Src/Particle/AMReX_Particle.H Src/Particle/AMReX_Particle_mod_K.H Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp Tests/GPU/RandomNumberGeneration/GNUmakefile Tests/GPU/RandomNumberGeneration/launc_gpu.sh Tests/GPU/RandomNumberGeneration/main.cpp Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 1f1d33b3501a4ff196fff33ed0eab2bf14be0d31 Author: Chris DeGrendele Date: Wed Jul 24 15:55:20 2019 -0700 one last thing Src/Base/AMReX_GpuUtility.H commit 515f806204da038a0bba837fa99292967d2fd887 Author: Chris DeGrendele Date: Wed Jul 24 15:51:41 2019 -0700 removed more files Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/Backtrace.0 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/Backtrace.0 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/viz.py commit 11f3083ce180730a320f08c4b97ef4e7520f9e6e Author: Weiqun Zhang Date: Wed Jul 24 15:47:46 2019 -0700 trigger travis LICENSE commit 7d24bde614ef990809cfb4cc5d573e25a033e863 Author: Chris DeGrendele Date: Wed Jul 24 15:47:25 2019 -0700 Removed old func decleration Src/Base/AMReX_Utility.H commit 02e7008130c996e58f8b3075162a302740a34151 Author: Chris DeGrendele Date: Wed Jul 24 15:44:22 2019 -0700 removed more unnecessary commits Src/Particle/#AMReX_TracerParticles.cpp# Src/Particle/out.txt Tests/GPU/Particles/Redistribute/Backtrace.0 Tests/GPU/RandomNumberGeneration/out.txt Tutorials/GPU/NeighborList/#MDParticleContainer.cpp# commit 480d23b4aae7e2609550cada11de7345312de80a Author: Chris DeGrendele Date: Wed Jul 24 15:40:17 2019 -0700 Deleted accidental pushes Src/Base/#AMReX_FArrayBox.H# Src/Base/#AMReX_FArrayBox.cpp# Src/Base/#AMReX_GpuUtility.cpp# Src/Particle/#AMReX_TracerParticles.cpp# Src/Particle/AMReX_TracerParticles.cpp Src/Particle/out.txt Tests/GPU/Particles/Redistribute/Backtrace.0 Tests/GPU/RandomNumberGeneration/GNUmakefile Tests/GPU/RandomNumberGeneration/launc_gpu.sh Tests/GPU/RandomNumberGeneration/main.cpp Tests/GPU/RandomNumberGeneration/out.txt Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00000/Header Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00000/Level_0/Cell_D_00000 Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00000/Level_0/Cell_H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00100/Header Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00100/Level_0/Cell_D_00000 Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00100/Level_0/Cell_H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00183/Header Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00183/Level_0/Cell_D_00000 Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00183/Level_0/Cell_H Tutorials/GPU/NeighborList/#MDParticleContainer.cpp# Tutorials/Particles/NeighborList/Backtrace.0.0 commit 025cf6896dd8ae6a8308de5acfe82fc6e9cb29d3 Author: Chris DeGrendele Date: Wed Jul 24 15:33:02 2019 -0700 Merged back into Random() funct Src/Base/AMReX_Utility.cpp commit 38d5f319d694d41d52863d4efdd0b7ec2fc537a9 Merge: d9f39e91e 652be8caf Author: Chris DeGrendele Date: Wed Jul 24 15:22:36 2019 -0700 synced with no devicevector version commit d59a0dddff1701858f2c7fc1d0ddce53af554863 Author: Andrew Myers Date: Wed Jul 24 17:54:15 2019 -0400 just do construction of the map on the CPU Src/Particle/AMReX_ParticleBufferMap.H Src/Particle/AMReX_ParticleBufferMap.cpp commit 1da7a0c3fec4672961440ba3a7e23bc29bbc480e Merge: 59135b59f 652be8caf Author: Weiqun Zhang Date: Wed Jul 24 14:46:27 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d9f39e91e2f46fb9ae95d38c35a7e3227e81588f Author: Chris DeGrendele Date: Wed Jul 24 14:36:25 2019 -0700 GPU random number generation Src/Base/AMReX_Utility.cpp commit 652be8caf8e5646dfcbdfeeb7724015fee58ac77 Author: jmsexton03 Date: Wed Jul 24 14:13:37 2019 -0700 Update run.summit w/1 resource set per GPU comment Tutorials/GPU/run.summit commit f032d1a24e7e1863bd31f4ed32c583c05468b9b6 Author: Andrew Myers Date: Wed Jul 24 16:49:50 2019 -0400 forgot to add these files Src/Particle/AMReX_ParticleBufferMap.H Src/Particle/AMReX_ParticleBufferMap.cpp commit aab85761734361a5dc480511c4ba464340f9e956 Author: Andrew Myers Date: Wed Jul 24 16:49:18 2019 -0400 some tweaks to the ParticleBufferMap class Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Tests/Particles/NeighborParticles/script.sh commit d025a77bcd414b6ba5f12087e3352ae32183943c Author: Andrew Myers Date: Wed Jul 24 15:22:24 2019 -0400 reorganize some of the recent changes to the neighbor particle code Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 0f07833e9840cd999b436d693cc14befc44b4c4f Author: Andrew Myers Date: Wed Jul 24 13:57:21 2019 -0400 remove commented code Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit a081f685e8c1a30d1f87b7e9146edba4196ff8c0 Author: Andrew Myers Date: Wed Jul 24 13:56:53 2019 -0400 some cleanup in BuildRedistributeMask Src/Particle/AMReX_ParticleContainerI.H commit cd92465e44b5bd0cba21640d5e4511a6e90a37a2 Author: Brandon Runnels Date: Wed Jul 24 11:16:20 2019 -0600 implementing nodal multicomponent mlmg test Tests/LinearSolvers/MultiComponent/Make.package Tests/LinearSolvers/MultiComponent/inputs Tests/LinearSolvers/MultiComponent/main.cpp commit b4c450ffd9a860235b1bf23144a20e59630afbfa Author: kngott Date: Tue Jul 23 16:57:39 2019 -0700 MultiFab functions test. Tests/GPU/ScratchPad/GNUmakefile Tests/GPU/ScratchPad/inputs_3d Tests/GPU/ScratchPad/main.cpp commit a44c170d2133489df4fbef879ed17ae810f39654 Author: kngott Date: Tue Jul 23 16:57:06 2019 -0700 Self-dot and updated MultiFab::norm2 function. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit b18ef7e4a9f09279334468519bab8eef012cc328 Author: Andrew Myers Date: Tue Jul 23 19:41:37 2019 -0400 remove this unit test, as it has been rolled into the other one Tutorials/GPU/NeighborParticlesUnitTest/CMakeLists.txt Tutorials/GPU/NeighborParticlesUnitTest/CheckPair.H Tutorials/GPU/NeighborParticlesUnitTest/Constants.H Tutorials/GPU/NeighborParticlesUnitTest/GNUmakefile Tutorials/GPU/NeighborParticlesUnitTest/MDParticleContainer.H Tutorials/GPU/NeighborParticlesUnitTest/MDParticleContainer.cpp Tutorials/GPU/NeighborParticlesUnitTest/Make.package Tutorials/GPU/NeighborParticlesUnitTest/README.md Tutorials/GPU/NeighborParticlesUnitTest/inputs Tutorials/GPU/NeighborParticlesUnitTest/main.cpp Tutorials/GPU/NeighborParticlesUnitTest/script.sh commit e8dcd23abb85c937f51d135f9bde28e66ccb849f Merge: 801ae877f 176c08c88 Author: Andrew Myers Date: Tue Jul 23 19:37:37 2019 -0400 Merge branch 'development' into mfix_hackathon commit 176c08c88e6ed1ae296f5c4ed978aa2d4fed08c1 Merge: 1b7e1ba08 8428b2e4c Author: Andrew Myers Date: Tue Jul 23 19:36:54 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1b7e1ba08c0769dd6ece79fafc0f3a394aed8a4b Author: Andrew Myers Date: Tue Jul 23 19:36:42 2019 -0400 remove use of thrust vector as global variable Src/Base/AMReX_Utility.cpp commit 801ae877fe57cebf77dd81db0f6bae62fc8360ac Author: Andrew Myers Date: Tue Jul 23 18:43:39 2019 -0400 move test to Tests Tests/Particles/NeighborParticles/CMakeLists.txt Tests/Particles/NeighborParticles/CheckPair.H Tests/Particles/NeighborParticles/Constants.H Tests/Particles/NeighborParticles/GNUmakefile Tests/Particles/NeighborParticles/MDParticleContainer.H Tests/Particles/NeighborParticles/MDParticleContainer.cpp Tests/Particles/NeighborParticles/Make.package Tests/Particles/NeighborParticles/README.md Tests/Particles/NeighborParticles/inputs Tests/Particles/NeighborParticles/main.cpp Tests/Particles/NeighborParticles/script.sh commit 6132139f20861230a13665afa4e1509b25f77e9f Author: Andrew Myers Date: Tue Jul 23 18:41:02 2019 -0400 consolidate and reorganize test Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.H Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp Tutorials/GPU/NeighborListUnitTest/inputs Tutorials/GPU/NeighborListUnitTest/main.cpp Tutorials/GPU/NeighborListUnitTest/script.sh commit 879675e28623dd2cc97ba0b0ab76670713963033 Author: Andrew Myers Date: Tue Jul 23 18:14:08 2019 -0400 use the wrapped version of exclusive_scan Src/Base/AMReX_CudaContainers.H Src/Particle/AMReX_NeighborList.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Tutorials/GPU/NeighborParticlesUnitTest/script.sh commit 042c0843617427175d03ce3a96da38a22bda370c Author: Andrew Myers Date: Tue Jul 23 18:11:15 2019 -0400 modify print statements in test Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp Tutorials/GPU/NeighborListUnitTest/main.cpp commit 28ddeecbab0a6ef3853006ae0f109686f7f96469 Author: Andrew Myers Date: Tue Jul 23 17:35:07 2019 -0400 compute num_copies in a cleaner way Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 0f164619c31e1e62c23eaef70726455548e30d03 Author: Andrew Myers Date: Tue Jul 23 17:14:54 2019 -0400 std::cout -> amrex::Print() Tutorials/GPU/NeighborListUnitTest/main.cpp commit 5c0d705b1663046f6c432582e7aa188cccde55b2 Author: Andrew Myers Date: Tue Jul 23 17:14:18 2019 -0400 fix rcv buffer offset calculation Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 632334d0b853c9b4a6e6902481a43ed04ef56e6f Author: Andrew Myers Date: Tue Jul 23 16:32:12 2019 -0400 remove some now unused functions Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit ba6b0e878bb62ea4bcf8155af911b95a4b1ee64b Author: Andrew Myers Date: Tue Jul 23 16:15:55 2019 -0400 fix timer name Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 4c5334f042bc803608a8fb85c70eb45c36793af2 Author: Andrew Myers Date: Tue Jul 23 16:15:34 2019 -0400 this doesn't need to be a member Src/Particle/AMReX_NeighborParticles.H commit fa60bc9a68c26b722deaed63f2240028556c127b Author: Andrew Myers Date: Tue Jul 23 16:07:09 2019 -0400 put this operator in the amrex namespace so amrex::Print() can find it Tutorials/GPU/NeighborListUnitTest/main.cpp commit dc6af275df929b7a83708b2938766d7103427464 Author: Andrew Myers Date: Tue Jul 23 15:38:46 2019 -0400 fix mpi neighbor particle test Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 2907fdba33a12862f5bcc1720b5affb15b3b3a1b Author: Andrew Myers Date: Tue Jul 23 13:50:29 2019 -0400 modify some prints Tutorials/GPU/NeighborListUnitTest/main.cpp commit 67d1f2263dc8cefd8eac9d7c0acdd3bb6950643b Author: Andrew Myers Date: Tue Jul 23 13:49:52 2019 -0400 some work towards fixing the MPI portion of updateNeighbors... almost right now. Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 6973fc099634be086fb3504f39f6fa99b4f9ce03 Author: Andrew Myers Date: Tue Jul 23 13:23:18 2019 -0400 templated overload of << for pair Tutorials/GPU/NeighborListUnitTest/main.cpp commit e8061cb4c5c452e70c8f78ffe63802729136f132 Author: Andrew Myers Date: Tue Jul 23 13:22:58 2019 -0400 modify test to compare both min and max of the inter-particle spacing Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.H Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp commit 7e0ba56d38b84289540a582076933e09e2f61efa Author: Andrew Myers Date: Mon Jul 22 20:20:08 2019 -0400 some work on debugging parallel Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 59135b59f3546dd7fb17924dd997197a4b603e71 Author: Weiqun Zhang Date: Mon Jul 22 15:23:53 2019 -0700 fix the fix that tried to remove hardwired warp size Src/Base/AMReX_FabArrayUtility.H commit 8428b2e4c25c8118926de172169db43db2b5cd8d Merge: 25ff00a05 7ba86ce80 Author: Weiqun Zhang Date: Mon Jul 22 11:20:13 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 25ff00a05f1d6b01d4887630243959b64dad4baa Author: Weiqun Zhang Date: Mon Jul 22 11:19:55 2019 -0700 add compiler generated move for AmrMesh and AmrCore Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrMesh.H commit 7ba86ce807a69e3f4419ce4f368f2c5b40e66b3f Merge: 782aaa6f0 6c95169d3 Author: WeiqunZhang Date: Mon Jul 22 09:45:52 2019 -0700 Merge pull request #527 from Alpine-DAV/task/2019_07_blueprint_updates bugfixes for conduit blueprint support commit 0defefb82c85cff78c99194a402a7ee6f9f71a92 Author: Ann Almgren Date: Sun Jul 21 16:07:07 2019 -0700 Fix spelling so 'git grep' searches will find the right thing Src/Particle/AMReX_ParticleContainerI.H commit 782aaa6f07d52d82ec8e53a343ae0be21f157b1a Merge: 631147387 28851a48b Author: mic84 Date: Fri Jul 19 18:28:39 2019 -0700 Merge pull request #526 from rupertnash/development CMake install step: make header modification more cross-platform commit 631147387cc478046a43a59883f13b261cba4fdf Merge: f55469c65 92b98d1f1 Author: Weiqun Zhang Date: Fri Jul 19 16:22:21 2019 -0700 Merge branch 'hackathon' into development commit 93f42c2bfa85c211e7773d631542f0dadbe2104a Merge: 7538d3d9a 7491ba037 Author: Andrew Myers Date: Fri Jul 19 14:45:37 2019 -0400 Merge branch 'mfix_hackathon' of github.com:AMReX-Codes/amrex into mfix_hackathon commit 7538d3d9a4f7b821106bf73f5a406c5a094b0529 Author: Andrew Myers Date: Fri Jul 19 14:45:06 2019 -0400 need to change where we are setting the number of neighbors from the remotes Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 6c95169d36a5dec2406f67830aecb89253593e14 Author: Cyrus Harrison Date: Fri Jul 19 10:11:31 2019 -0700 clarify comment Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp commit 92b98d1f1d076d4f12fc15abed2bb0c2380bec0d Merge: 8a3273ccc 6612b70d4 Author: Weiqun Zhang Date: Fri Jul 19 09:19:54 2019 -0700 Merge branch 'weiqun/hackathon' into hackathon commit 8a3273ccc29d4ff030f3e130ef056de9634d8472 Merge: 37e6ab242 b943eaa07 Author: Weiqun Zhang Date: Fri Jul 19 09:18:59 2019 -0700 Merge branch 'hackathon' of github.com:AMReX-Codes/amrex into hackathon commit 37e6ab24262dce6c04f55972f80d39443fe47cb9 Author: Weiqun Zhang Date: Fri Jul 19 06:23:21 2019 -0700 libamrex: move AMReX_Config.H inside include guard Tools/GNUMake/Make.rules commit 28851a48b5925fa223f582b7085da51aed034659 Author: Rupert Nash Date: Fri Jul 19 14:26:19 2019 +0100 insert include AMReX_Config.H within include guard Tools/CMake/modify_installed_headers.cmake commit 07eb2fa7e6d13e727774339161fd806e13b4141d Author: Rupert Nash Date: Fri Jul 19 13:17:57 2019 +0100 make header modification use cmake to be more cross-platform Tools/CMake/modify_installed_headers.cmake commit 03ae58294642a98fbf4a7acdbd634f5add2a429b Author: Andrew Myers Date: Fri Jul 19 03:41:19 2019 -0400 some towards fixing the mpi Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 2d2777fb2e2d3035bc0780d967ff4d434fadb742 Author: Andrew Myers Date: Thu Jul 18 19:41:52 2019 -0400 exchange the total number of rcv bytes Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit f889d61e1f79e09acc5102ed4103a0ce8f74df39 Author: Andrew Myers Date: Thu Jul 18 19:08:15 2019 -0400 fix proc_box_offsets Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit a380e2adf5ae0b7866fbe25fa6bcfb9282b841fb Author: Andrew Myers Date: Thu Jul 18 18:41:37 2019 -0400 taking out a print statement Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 7a5c2bfc11a57a867fb220c59cebb4d867a13a3f Author: Andrew Myers Date: Thu Jul 18 18:38:44 2019 -0400 computing proc ids and offsets Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit fdef8e6353417fc4f96e1e8d6de3d524294a19eb Author: Andrew Myers Date: Thu Jul 18 17:53:19 2019 -0400 pack particles into the send buffer such that all the boxes bound for the same proc id are together Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit cf84ab4230232f654eee2b31a3c772d6f5025274 Author: Andrew Myers Date: Thu Jul 18 17:25:54 2019 -0400 don't need to do any communication to figure out which procs sent what boxes to me Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 43df8b9084a2847b9adf007caf914722d5f5a18e Author: Andrew Myers Date: Thu Jul 18 16:46:18 2019 -0400 a test getBoxRcvCounts function Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 7491ba037ce4ff059939b0cf7dd631865080a8c7 Author: Ann Almgren Date: Thu Jul 18 09:54:55 2019 -0400 Fix printing so that we only print off the processor that owns grid 0 Tutorials/GPU/NeighborListUnitTest/main.cpp commit 2e4558dfc096f33d10575e5a14ad5f67f77d614d Merge: d9d8b9beb 7c32b7e97 Author: Ann Almgren Date: Thu Jul 18 09:45:15 2019 -0400 Merge branch 'mfix_hackathon' of https://github.com/amrex-codes/amrex into mfix_hackathon Conflicts: Tutorials/GPU/NeighborList/main.cpp commit d9d8b9beb995f2865386c524f79ff1d470008565 Author: Ann Almgren Date: Thu Jul 18 09:34:42 2019 -0400 Slight clean-up of main Tutorials/GPU/NeighborList/main.cpp commit 7c32b7e9737d559b3980aeeb199666df6667c710 Author: Andrew Myers Date: Thu Jul 18 00:05:12 2019 -0400 also look at particle positions in the neighbor list test Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.H Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp Tutorials/GPU/NeighborListUnitTest/main.cpp commit b737c7596ad29f9870bacd01b0eaab4e701c4016 Author: Andrew Myers Date: Wed Jul 17 23:31:02 2019 -0400 change some printing behavior Tutorials/GPU/NeighborList/MDParticleContainer.cpp Tutorials/GPU/NeighborList/inputs Tutorials/GPU/NeighborList/main.cpp commit 69751564ef932fe0d45b7ef76f92aa38e26573c6 Author: Andrew Myers Date: Wed Jul 17 23:21:05 2019 -0400 add a final call to redistribute Tutorials/GPU/NeighborList/main.cpp commit 866302f33311a3a4c3ff130cdf1214510fce8749 Author: Andrew Myers Date: Wed Jul 17 23:12:38 2019 -0400 don't print min dist unless requested Tutorials/GPU/NeighborList/main.cpp commit 4e0f352b2e6c3ef6f91bc895d0b2a847dc18d6b7 Author: Andrew Myers Date: Wed Jul 17 23:10:31 2019 -0400 don't print the neighbor list unless requested Tutorials/GPU/NeighborList/main.cpp commit b943eaa071c64a2b4b389edbf7e22ea53e179ec3 Author: kngott Date: Wed Jul 17 17:40:13 2019 -0700 Fix summit script flags for CUDA aware MPI. Tutorials/GPU/run.summit commit 814203250d0e7c6cc4cf7cb936b59b6997944030 Merge: 60121a99d 8716e0fb9 Author: Andrew Myers Date: Wed Jul 17 19:31:45 2019 -0400 merging. commit 60121a99d21cd75799fa10f3f12147410ee51268 Author: Andrew Myers Date: Wed Jul 17 19:26:25 2019 -0400 modify inputs for neighbor list test Tutorials/GPU/NeighborListUnitTest/inputs commit cb710281bb045c80df793cc9afabada86f27f109 Author: Andrew Myers Date: Wed Jul 17 19:24:30 2019 -0400 missed a box offset Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 8716e0fb9767618b1e7b97ccf415b74f6d3acaf8 Author: Ann Almgren Date: Wed Jul 17 19:16:13 2019 -0400 This has the CPU version of the checkParticles() version -- it gives the "correct" answer with 1 MPI process but not with 2 MPI processes. Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp commit 79ad9e3ed9462347b15b7d2c444b284369da9deb Author: Andrew Myers Date: Wed Jul 17 18:44:57 2019 -0400 src -> dst Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit ed1ac53a292462ec0dd299b93b547680a1dcc7f9 Author: Andrew Myers Date: Wed Jul 17 18:29:11 2019 -0400 implement update and Fill in terms of the new halo functions Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 3197ab40b50f78d19710d4b1ca59f4f0b66b601e Author: Ann Almgren Date: Wed Jul 17 18:19:08 2019 -0400 We need to explicitly call the sychronize before printing Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp commit 0b6015ccdc4ed11d5ba8cd822434bad6b3fe738f Author: Ann Almgren Date: Wed Jul 17 18:16:07 2019 -0400 Don't try to access "mine" when it's not actually set Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp commit 031c7f7f6903c5bf564e01739a6af0b46b752d28 Author: Ann Almgren Date: Wed Jul 17 18:12:41 2019 -0400 Actually lets use num_ppc = 1 Tutorials/GPU/NeighborListUnitTest/inputs commit d8c856be71f1342463d02e7c9b703dbea22aa37a Author: Ann Almgren Date: Wed Jul 17 18:12:08 2019 -0400 This is the inputs for this test Tutorials/GPU/NeighborListUnitTest/inputs commit 61f559c3a169480d6bb56474f54bafd1d596a86f Author: Ann Almgren Date: Wed Jul 17 18:10:53 2019 -0400 Change the print statements to work in parallel Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp commit 6ec34d49826744016595bbc1c468e4911689be53 Author: Weiqun Zhang Date: Wed Jul 17 15:08:26 2019 -0700 add optional shared memory to ParallelFor Src/Base/AMReX.cpp Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H commit f010ceb71d06ff52cb5dc92568d01df7b0eff5df Author: Andrew Myers Date: Wed Jul 17 17:15:21 2019 -0400 remove commented out code Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 046faa40d3741130dd9f216bace1258c33341d9c Author: Ann Almgren Date: Wed Jul 17 17:03:18 2019 -0400 This does all the testing on CPU even when the neighbor list is built on GPU. Tutorials/GPU/NeighborParticlesUnitTest/MDParticleContainer.cpp Tutorials/GPU/NeighborParticlesUnitTest/inputs Tutorials/GPU/NeighborParticlesUnitTest/main.cpp commit 1185a7dd8ea58a484bfd0854ee83584ad5257fca Merge: c2d1f9251 c061cb5a2 Author: Andrew Myers Date: Wed Jul 17 16:58:19 2019 -0400 Merge branch 'mfix_hackathon' of github.com:AMReX-Codes/amrex into mfix_hackathon commit c2d1f9251c351e3557bbce653dae92f28931c520 Author: Andrew Myers Date: Wed Jul 17 16:56:48 2019 -0400 apply periodic when packing the buffer Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit b42dc912c407906c4bb453d2940fcf37fc2a057f Author: Andrew Myers Date: Wed Jul 17 16:43:41 2019 -0400 compute the dst indices correctly Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit e0ad6bebf9f229e7524dd540f09cb94dd488bb14 Author: Andrew Myers Date: Wed Jul 17 16:14:09 2019 -0400 don't reset the counters inside the mfiter loop to sort the snd buffer by destination only Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit ef03ffccdc6c561cd35e1fd93c8728fda2dcb27e Author: Andrew Myers Date: Wed Jul 17 15:43:58 2019 -0400 implement pack and unpack Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit c061cb5a22752569f989597c6b8552b678e4b060 Author: Ann Almgren Date: Wed Jul 17 15:00:45 2019 -0400 New unit test for testing BuildNeighborList which creates particle-neighbor lists Tutorials/GPU/NeighborParticlesUnitTest/CMakeLists.txt Tutorials/GPU/NeighborParticlesUnitTest/CheckPair.H Tutorials/GPU/NeighborParticlesUnitTest/Constants.H Tutorials/GPU/NeighborParticlesUnitTest/GNUmakefile Tutorials/GPU/NeighborParticlesUnitTest/MDParticleContainer.H Tutorials/GPU/NeighborParticlesUnitTest/MDParticleContainer.cpp Tutorials/GPU/NeighborParticlesUnitTest/Make.package Tutorials/GPU/NeighborParticlesUnitTest/README.md Tutorials/GPU/NeighborParticlesUnitTest/inputs Tutorials/GPU/NeighborParticlesUnitTest/main.cpp Tutorials/GPU/NeighborParticlesUnitTest/script.sh commit 9142ef98d8c96bf10458998370dcbff43c11fcc3 Author: Andrew Myers Date: Wed Jul 17 15:00:45 2019 -0400 resize the snd_buffer to the appropriate size Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 5681a81f2ca5fb3a77f144bec6f0f58b2c727bfd Author: Cyrus Harrison Date: Wed Jul 17 11:45:38 2019 -0700 fix export of blueprint files for mult-domain, fix wrapping of multiple fields, add cycle info Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp commit 4f0b125d4a96df134cf7ffee7362ca5cc29f6acb Author: Andrew Myers Date: Wed Jul 17 14:34:37 2019 -0400 handle periodicity; compute box counts and offsets Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit a9ea3e17e35eab7aa6eb52a9d95679442022da9e Author: Andrew Myers Date: Wed Jul 17 14:10:54 2019 -0400 seperate out computing the halo particles and computing the copy plan Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit f55469c651808f7d2203687ffe8e556746fdb152 Author: Max Katz Date: Wed Jul 17 10:56:44 2019 -0700 Add option to change _device suffix for GPU pragma Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit ab04d2b4e29c5ede87e5a672d026905c9ddb46e1 Author: Max Katz Date: Wed Jul 17 10:01:13 2019 -0700 Add pragma gpu option to disable host version Tools/F_scripts/write_cuda_headers.py commit a5da9eafa0bba73bb594239970bb912809b11097 Author: Max Katz Date: Tue Jul 16 23:15:02 2019 -0700 Allow PGI -gopt to be disabled Tools/GNUMake/comps/pgi.mak commit 7359bc9eb1fce1d532f71566922b54f6b7143319 Author: Andrew Myers Date: Wed Jul 17 01:09:24 2019 -0400 some work towards reimplementing neighbor particle communication Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 42b7513c60d7e0be636900379c3a525b44fc5b9f Author: Ann Almgren Date: Tue Jul 16 20:43:48 2019 -0400 New unit test for FillNeighbors and UpdateNeighbors Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.H Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp Tutorials/GPU/NeighborListUnitTest/README.md Tutorials/GPU/NeighborListUnitTest/main.cpp commit 4df4b81f9958037c3372fe28b00fbddd983b9746 Author: Ann Almgren Date: Tue Jul 16 19:14:11 2019 -0400 add inputs Tutorials/GPU/NeighborListUnitTest/inputs commit 779c57b6cc5534ebe3c59408e29909b75e169720 Author: Ann Almgren Date: Tue Jul 16 19:13:55 2019 -0400 Starting point for new unit test Tutorials/GPU/NeighborListUnitTest/CMakeLists.txt Tutorials/GPU/NeighborListUnitTest/CheckPair.H Tutorials/GPU/NeighborListUnitTest/Constants.H Tutorials/GPU/NeighborListUnitTest/GNUmakefile Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.H Tutorials/GPU/NeighborListUnitTest/MDParticleContainer.cpp Tutorials/GPU/NeighborListUnitTest/Make.package Tutorials/GPU/NeighborListUnitTest/main.cpp Tutorials/GPU/NeighborListUnitTest/script.sh commit bb76dd6473e30bd78fcf8f2aa3b19a555796f2ba Author: Max Katz Date: Tue Jul 16 14:52:44 2019 -0700 Add attributes(host) attributes(device) macro Tools/GNUMake/Make.defs commit 738c5fbc989ca77bca28e1300163a4ce7239ce86 Author: Ann Almgren Date: Tue Jul 16 16:45:15 2019 -0400 Add run-time option to control whether we compute and print the minimum distance between particles Tutorials/GPU/NeighborList/inputs Tutorials/GPU/NeighborList/main.cpp commit 1c305c39985392557a486b2f98621bdd2cf17d0f Merge: 872b42930 66655c79c Author: Ann Almgren Date: Tue Jul 16 15:39:57 2019 -0400 Merge branch 'mfix_hackathon' of https://github.com/amrex-codes/amrex into mfix_hackathon Conflicts: Tutorials/GPU/NeighborList/main.cpp commit 872b429306fcf9da478b9e0a1385decb57569988 Author: Ann Almgren Date: Tue Jul 16 15:38:24 2019 -0400 Update this GPU neighborlist tutorial to make it closer to the MFiX-Exa conditions (2.5 particle diameters per grid cell, for example) Tutorials/GPU/NeighborList/Constants.H Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp Tutorials/GPU/NeighborList/README.md Tutorials/GPU/NeighborList/inputs Tutorials/GPU/NeighborList/main.cpp commit 15294deea3553117e7f4e7d11b04d425f7acba10 Author: Johannes Blaschke Date: Tue Jul 16 11:40:32 2019 -0700 need to skip ebfacets that coincide with cell boundaries when looking for eb-facet edges Src/EB/AMReX_EB_geometry.F90 commit 66655c79c825b66766f95fa84a93fbcfef9d8538 Author: Andrew Myers Date: Tue Jul 16 14:14:42 2019 -0400 remove extra set acceleration to 0.0 Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit 8232eced9349c53f209f6c054320bb37b5c91a0e Merge: 24f0ade3b f28006c19 Author: Andrew Myers Date: Tue Jul 16 13:56:40 2019 -0400 Merge branch 'mfix_hackathon' of github.com:AMReX-Codes/amrex into mfix_hackathon commit 24f0ade3bf4de4569c423b44afed439bcc1ea0b6 Author: Andrew Myers Date: Tue Jul 16 13:55:53 2019 -0400 add some more sanity checking Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H commit f28006c195c2edda7fe37484f7e0aab3c2deb2b8 Author: Michele Rosso Date: Tue Jul 16 13:46:17 2019 -0400 Make dt an input parameter and set it to a reasonable default value Tutorials/GPU/NeighborList/main.cpp commit 4f04a7dc8df01e188c38ebc903fffb7d5ad65fdb Author: Weiqun Zhang Date: Tue Jul 16 10:04:35 2019 -0700 return -1 as mask if particle id is negative Src/Particle/AMReX_Functors.H Src/Particle/AMReX_ParticleContainerI.H commit deb296cc5b7f75a279fc1877e612e0b81b763ea4 Author: Weiqun Zhang Date: Tue Jul 16 06:58:25 2019 -0700 add a new version of RealBox::contains Src/Base/AMReX_RealBox.H commit d273eaa9b033c6720898677e98c17b046861f556 Author: Andrew Myers Date: Tue Jul 16 04:05:14 2019 -0400 tweak inputs Tutorials/GPU/NeighborList/inputs commit 5ab9ec2e3079b2dc307d0475074e79f422f1712f Author: Andrew Myers Date: Tue Jul 16 04:05:01 2019 -0400 print out an error metric Tutorials/GPU/NeighborList/main.cpp commit 5cd7e6800c240adf52e5642ac0f9bc8d9109090f Author: Andrew Myers Date: Tue Jul 16 04:04:29 2019 -0400 function to print out the min distance between particles over the whole simulation Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit 1634cb65a48965efa13b8bfbd4cdbfa21a948452 Author: Andrew Myers Date: Tue Jul 16 04:03:58 2019 -0400 tweak CheckPair Tutorials/GPU/NeighborList/CheckPair.H commit 91f527209e52f6ccc9d98905caee18c20d3dc44e Author: Andrew Myers Date: Tue Jul 16 03:06:53 2019 -0400 fix typo Tutorials/GPU/NeighborList/main.cpp commit a37903ad06692f37903a07f97d872c27bd162c09 Author: Andrew Myers Date: Tue Jul 16 03:04:04 2019 -0400 parmparse rebuild int and num_ppc Tutorials/GPU/NeighborList/inputs Tutorials/GPU/NeighborList/main.cpp commit f6cf0ce9522f00dd169f15fa295292bfc5895edb Author: Andrew Myers Date: Mon Jul 15 20:59:25 2019 -0400 need to clear the neighbors before we re-generate the halo information Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 69a0b11aef6630807c0787eaebff932fdf210be4 Author: Michele Rosso Date: Mon Jul 15 17:22:13 2019 -0700 CMake: always link to Threads Src/Base/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in commit 4578ff6fd57b3a8bb43e5ab94a9d56e2e94b3622 Author: Andrew Myers Date: Mon Jul 15 17:47:29 2019 -0400 only count real particles Src/Particle/AMReX_ParticleContainerI.H commit 99ede46fb37ffebbb887ebba81e93b07dfc4d84c Author: Andrew Myers Date: Mon Jul 15 17:28:55 2019 -0400 don't include neighbor particles in ascii files Src/Particle/AMReX_ParticleContainerI.H commit 88a4090ab8728fb5dba44a42aa3e19f60f17faa9 Merge: 474c736ba a5aa5e654 Author: Ann Almgren Date: Mon Jul 15 15:05:25 2019 -0400 Merge branch 'mfix_hackathon' of https://github.com/amrex-codes/amrex into mfix_hackathon commit 474c736ba9a6bb26c059e85bf79a8f661ecd9c7b Author: Ann Almgren Date: Mon Jul 15 15:04:19 2019 -0400 Add flag to allow nvprof to work on ascent. Tutorials/GPU/NeighborList/script.sh commit a5aa5e6549e90e306b694de70315fadf7081111e Merge: 212b57213 9101ebd70 Author: Andrew Myers Date: Mon Jul 15 14:50:48 2019 -0400 Merge branch 'mfix_hackathon' of github.com:AMReX-Codes/amrex into mfix_hackathon commit 9101ebd709efc585413fc9e3f5fbf151ca58ac6d Author: Oscar Luis Antepara Zambrano Date: Mon Jul 15 14:49:23 2019 -0400 Increasing the number of particles by 8 per cell Tutorials/GPU/NeighborList/main.cpp commit 4999afb7ee25cc67ffb10dc811120b5ecb4325f1 Author: Oscar Luis Antepara Zambrano Date: Mon Jul 15 14:43:58 2019 -0400 adding a print statement for number of particles generated Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit 212b57213c62009327b843b387a995935cfda4ed Author: Andrew Myers Date: Mon Jul 15 14:38:56 2019 -0400 rebuild the neighbor list every 25 time steps Tutorials/GPU/NeighborList/main.cpp commit 2a6ae992cc4f8c679a7a6030857dfab2e6d380ee Author: Oscar Luis Antepara Zambrano Date: Mon Jul 15 14:30:30 2019 -0400 adding a print statement for number of particles generated Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit 1c9e80f1857fa160b8dded1c000c6c3b43724a74 Author: Andrew Myers Date: Mon Jul 15 12:17:43 2019 -0400 adding a run script for the hackathon Tutorials/GPU/NeighborList/script.sh commit 6612b70d4382848755cf3fce756fa55b68155bfc Author: Weiqun Zhang Date: Mon Jul 15 09:00:36 2019 -0700 check for nullptr after malloc Src/Base/AMReX_Arena.cpp commit 5dbf48e0f0c72dd90ee914ff6f1b3dc7aad86efb Author: Johannes Blaschke Date: Sun Jul 14 22:40:17 2019 -0700 ooops... forgot this Src/EB/AMReX_EB_levelset_F.F90 commit 2329c6d9135e2d5a0140287be1e9c0f862920c16 Author: Johannes Blaschke Date: Sun Jul 14 22:34:10 2019 -0700 fix off-by-epsilon error when filling level-set Src/EB/AMReX_EB_geometry.F90 Src/EB/AMReX_EB_levelset_F.F90 commit f386793a3cfcd78b1c99c745e44c839eec4ee6fe Author: Weiqun Zhang Date: Sun Jul 14 12:53:18 2019 -0700 replace usleep with std::this_thread::sleep_for Src/Base/AMReX_VisMF.cpp commit 1a2a7528d227956a683757f6907c017ec9948c12 Author: Weiqun Zhang Date: Sun Jul 14 07:07:32 2019 -0700 get around Cray Src/Particle/AMReX_ParticleContainerI.H commit 32bb14f8c5bf749a8dc63f2325bed882be2dca96 Author: Weiqun Zhang Date: Sat Jul 13 22:41:47 2019 -0700 fix for Cray Src/F_Interfaces/Base/AMReX_fab_mod.F90 commit 3eee258ef3439da203f9ab97b702071fc7213505 Author: Weiqun Zhang Date: Sat Jul 13 21:47:21 2019 -0700 fix a number of warnings Src/EB/AMReX_EB2_IF_Cylinder.H Src/EB/AMReX_EB2_IF_Scale.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit edca5b55f2f581278ebede1e966820e2c5b77d0c Author: Weiqun Zhang Date: Sat Jul 13 21:16:43 2019 -0700 remove old fortran amrex_eb2_build_cells Src/EB/AMReX_EB2_F.H Src/EB/AMReX_eb2_3d.F90 commit 2b2e3a27e420a9e5efe16627a717a0887f8d312b Author: Weiqun Zhang Date: Sat Jul 13 21:14:49 2019 -0700 wrong move Src/EB/AMReX_EB_LSCoreBase.cpp commit ae75f4bc8f7c93d1c57000d638271596dfcbc21c Author: Weiqun Zhang Date: Sat Jul 13 20:34:13 2019 -0700 fix bug in a new IOProcessor function Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_VisMF.cpp commit 97f01535d0396d2f60001278dc1f884f22b80456 Author: Weiqun Zhang Date: Sat Jul 13 20:29:00 2019 -0700 clean up Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunchFunctsC.H commit e4c5f6f1fa5af2f25d010225e25c6b1404069b50 Author: Weiqun Zhang Date: Sat Jul 13 19:44:45 2019 -0700 add a default constructor to DataDeleter Src/Base/AMReX_BaseFab.H commit 6bb1ed53c507ec8dc2025957c10bf3cf5f92afd5 Merge: 92af17530 354a126d2 Author: Weiqun Zhang Date: Sat Jul 13 18:11:12 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 92af1753077f977be6e4ae145b29fb57322022df Author: Weiqun Zhang Date: Sat Jul 13 18:10:50 2019 -0700 minor. std::async already creates a temporary in its internal buffer, so it's safe to use const& Src/Base/AMReX_VisMF.cpp commit 354a126d22ce9a0f800b6c87f8a030ed3b9b6af1 Merge: ace10bbae a8d6610d6 Author: atmyers Date: Sat Jul 13 17:12:21 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit ace10bbaef42ece6249618d1dc6da048fbf02e6c Author: atmyers Date: Sat Jul 13 17:12:09 2019 -0700 add remaining reduction operations (logical and and logical or) Src/Particle/AMReX_ParticleUtil.H commit a8d6610d6a9dc428ae0d086d67ecd484517f1dd3 Author: Weiqun Zhang Date: Sat Jul 13 13:45:16 2019 -0700 WriteAsync: tweak sleep time Src/Base/AMReX_VisMF.cpp Tests/VELOC/multifab/main.cpp commit e8a417af1ab6aacc9ca62a79a6af58b2933d121e Author: Weiqun Zhang Date: Sat Jul 13 10:28:14 2019 -0700 collect WriteAsyn status Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp Tests/VELOC/multifab/main.cpp commit c46349c6a3987f11654620de33e2da338200427d Author: Weiqun Zhang Date: Fri Jul 12 21:01:22 2019 -0700 make sure AMREX_CXX_* is properly included Src/Base/AMReX_TypeTraits.H commit 489acfe1fcf9947a0b2640d28dfb28a800452593 Merge: 079f2158d 3369cf716 Author: WeiqunZhang Date: Fri Jul 12 19:17:32 2019 -0700 Merge pull request #518 from eschnett/development Avoid warning about (safely) uninitialized variable commit 3369cf716ade4da0a5d5282e575c28ca16e1d49d Author: Erik Schnetter Date: Fri Jul 12 21:34:19 2019 -0400 Avoid warning about (safely) uninitialized variable Src/Base/AMReX_FabArrayCommI.H commit 079f2158dbf1622b49b9180147bbd8768aa176aa Merge: d5c5c8e32 8804af14f Author: Andrew Myers Date: Fri Jul 12 17:05:21 2019 -0700 Merge branch 'development' into particle_reductions commit d5c5c8e32933b8be56b78a1e0cf3f6b1394891dc Author: Andrew Myers Date: Fri Jul 12 17:02:10 2019 -0700 fix copy/paste errors Src/Particle/AMReX_ParticleUtil.H commit 162859d5efdc05a8025d358b5e4d332476a7776a Author: Andrew Myers Date: Fri Jul 12 16:57:26 2019 -0700 fix typo Src/Particle/AMReX_ParticleUtil.H commit 0e5494be5b5da099dd956d674a15eb74c49701fc Merge: 99eae6c63 2d44350a2 Author: Andrew Myers Date: Fri Jul 12 19:32:50 2019 -0400 Merge branch 'particle_reductions' of github.com:AMReX-Codes/amrex into particle_reductions commit 2d44350a243a1eea761e8350c5b8345a891627ce Author: Andrew Myers Date: Fri Jul 12 16:33:37 2019 -0700 use decltype instead of extra template parameter Src/Particle/AMReX_ParticleUtil.H commit 99eae6c6378346c2adad77131d17773fc7930659 Author: Andrew Myers Date: Fri Jul 12 19:32:29 2019 -0400 fix typos Src/Particle/AMReX_ParticleUtil.H commit 128938451ee10225f97b19d47fc4275b0d8ddc63 Author: Andrew Myers Date: Fri Jul 12 16:08:00 2019 -0700 simplifing Src/Particle/AMReX_ParticleUtil.H commit 0b0e3792e3b538d1e5f2b175089a85fb98081039 Author: Andrew Myers Date: Fri Jul 12 16:03:35 2019 -0700 also template on the lambda return type Src/Particle/AMReX_ParticleUtil.H commit ede635c9e0c7bed41bff04f35b2da24ebb920926 Author: Andrew Myers Date: Fri Jul 12 15:29:50 2019 -0700 add ReduceRealMax and ReduceRealMin functions as well. Src/Particle/AMReX_ParticleUtil.H commit 8804af14ff97a122c26e5c2c9550fa89831affc6 Author: Weiqun Zhang Date: Fri Jul 12 18:28:10 2019 -0400 fix for IBM compiler on summit that still use a very old gcc Src/Base/AMReX_Extension.H Src/Base/AMReX_TypeTraits.H commit 0205282e0c05588f2fbc76c7d34846c29fc0b528 Author: Andrew Myers Date: Fri Jul 12 14:45:55 2019 -0700 add a ReduceRealSum for particle data Src/Particle/AMReX_ParticleUtil.H commit 57b5ab9b3bd104fee24c73c738948724d2f77555 Merge: b9b65463b 57979cd17 Author: Michele Rosso Date: Fri Jul 12 14:34:04 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b9b65463bef2f408a4b639537cbff222a0a4d962 Author: Michele Rosso Date: Fri Jul 12 14:33:42 2019 -0700 CMake: add pthreads to dependency list for non-MPI builds Src/Base/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in commit 57979cd177c2584a07972a4f0b190b307bb756e7 Author: Weiqun Zhang Date: Fri Jul 12 14:30:06 2019 -0700 add -pthread to llvm Tools/GNUMake/comps/llvm.mak commit 2598329bfa991f00a2b82c89254a827a5e11a232 Author: Weiqun Zhang Date: Fri Jul 12 14:21:21 2019 -0700 add -pthread to intel Tools/GNUMake/comps/intel.mak commit cbf26980d2a98c1ed7dc3b8bbd4cb780dc0a5521 Author: Weiqun Zhang Date: Fri Jul 12 14:06:06 2019 -0700 pass -pthread to g++ Tools/GNUMake/comps/gnu.mak commit 2b6dd31a53b5a36b7bbc68739c03606c8a8e7b93 Author: Weiqun Zhang Date: Fri Jul 12 13:18:11 2019 -0700 more aggressive inline with AMREX_FORCE_INLINE Docs/sphinx_documentation/source/GPU.rst Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/Base/AMReX_Algorithm.H Src/Base/AMReX_BCRec.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_GpuRange.H Src/Base/AMReX_GpuReduce.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Src/Boundary/AMReX_InterpBndryData_1D_K.H Src/Boundary/AMReX_InterpBndryData_2D_K.H Src/Boundary/AMReX_InterpBndryData_3D_K.H Src/Boundary/AMReX_LOUtil_K.H Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_YAFluxRegister_1D_K.H Src/Boundary/AMReX_YAFluxRegister_2D_K.H Src/Boundary/AMReX_YAFluxRegister_3D_K.H Src/EB/AMReX_EB2_2D_C.H Src/EB/AMReX_EB2_3D_C.H Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_algoim_K.H Src/LinearSolvers/MLMG/AMReX_MG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLALap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLALap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLALap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H Src/Particle/AMReX_Particle_mod_K.H Tests/GPU/CudaGraphs/GraphBoundary/Prob.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.H Tutorials/GPU/Advection_AmrCore/Source/Tagging.H Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/mykernel.H Tutorials/GPU/Launch/MyKernel.H Tutorials/GPU/NeighborList/CheckPair.H Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H commit 3314a1b05bcbea8c8e564172aaf1ec187d962acf Author: Weiqun Zhang Date: Fri Jul 12 09:43:31 2019 -0700 modify the veloc test Tests/VELOC/multifab/main.cpp commit 2354d60c01f1be1c49a4422923bbf8352e143d40 Merge: d14fc1a8c 2919e6fa3 Author: Weiqun Zhang Date: Fri Jul 12 09:23:45 2019 -0700 Merge branch 'development' into weiqun/asynco commit 2919e6fa353c0f68b7dc7ad837a5140446757141 Merge: 778b1b56e b6688df3d Author: Weiqun Zhang Date: Fri Jul 12 09:22:12 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b6688df3d31bf71262d190ca3f13c6cfa3e2a06e Author: Stefan Vater Date: Fri Jul 12 16:43:06 2019 +0200 Doc update (#515) Doc update from @svater Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/BuildingAMReX.rst Docs/sphinx_documentation/source/BuildingAMReX_Chapter.rst Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/LinearSolvers.rst Docs/sphinx_documentation/source/LinearSolvers_Chapter.rst commit d39d96ef7840e77deebced05689e813a6ea1ff85 Author: Andrew Myers Date: Thu Jul 11 20:19:01 2019 -0700 also wrap thrust::exclusive_scan, providing CPU implementation Src/Base/AMReX_CudaContainers.H commit d14fc1a8cb2a98c4ccd6e31c274cde25d1d59914 Author: Weiqun Zhang Date: Thu Jul 11 19:34:33 2019 -0700 make the veloc test more general Tests/VELOC/multifab/GNUmakefile Tests/VELOC/multifab/main.cpp commit cad2c0c6b71065fd711cc2d838f1e86aaabb40aa Author: Weiqun Zhang Date: Thu Jul 11 19:10:03 2019 -0700 fix another bug in WriteAsync Src/Base/AMReX_VisMF.cpp commit d6f5eabd688d9e5a9f148a436f4a62bb9925f7e3 Merge: da04dbf64 bbe68d00a Author: Andrew Myers Date: Thu Jul 11 17:28:17 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit eee76630fd7fb6fbd1a33c440f7c31e0006d948e Merge: 1ad4f375d d6f5eabd6 Author: Christopher DeGrendele Date: Thu Jul 11 17:27:57 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit cd5d9ec8704dd028a30a26e9dc5ccbb575357e5a Author: Weiqun Zhang Date: Thu Jul 11 17:27:03 2019 -0700 fix index Src/Base/AMReX_VisMF.cpp commit da04dbf64f2fe074451ba3e3ec390fb35ec0ca2d Author: Andrew Myers Date: Thu Jul 11 17:26:44 2019 -0700 fix box_threads_and_blocks for AMREX_SPACEDIM < 3 Src/Base/AMReX_GpuDevice.cpp commit 1ad4f375deccb7c3d3a6970377cc47ba390b2233 Merge: aca194cf9 bbe68d00a Author: Christopher DeGrendele Date: Thu Jul 11 17:04:39 2019 -0700 merge with upstream commit 97efc66befb3941586608f6fbba8ecfe36054471 Author: Weiqun Zhang Date: Thu Jul 11 16:54:24 2019 -0700 VisMF::WriteAsync for multi cpus Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp Tests/VELOC/multifab/main.cpp commit aca194cf9a5a8022048fb7f8fa405fb2987cfe0b Author: Christopher DeGrendele Date: Thu Jul 11 16:42:45 2019 -0700 commented out Src/Base/AMReX_Utility.cpp commit abc04f6b2d4a5727abefc24e3bce5b92c4ddb6b6 Author: Christopher DeGrendele Date: Thu Jul 11 16:11:23 2019 -0700 temp Src/Base/#AMReX_GpuUtility.cpp# Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Tests/GPU/RandomNumberGeneration/GNUmakefile Tests/GPU/RandomNumberGeneration/launc_gpu.sh Tests/GPU/RandomNumberGeneration/main.cpp Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00000/Header Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00000/Level_0/Cell_D_00000 Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00000/Level_0/Cell_H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00100/Header Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00100/Level_0/Cell_D_00000 Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00100/Level_0/Cell_H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00183/Header Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00183/Level_0/Cell_D_00000 Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/plt00183/Level_0/Cell_H commit bbe68d00a81ad76bda43ade549c16d638d3752da Merge: 793403891 37cafcc83 Author: Ann Almgren Date: Thu Jul 11 15:07:23 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 793403891fcb1934a1b5d6b3a3919ec88c81de4a Author: Ann Almgren Date: Thu Jul 11 15:07:14 2019 -0700 fix formatting Src/Particle/AMReX_TracerParticles.cpp commit 37cafcc836e87185a683a5b94c391204ee337cab Author: kngott Date: Thu Jul 11 14:37:44 2019 -0700 Fix typo. Tutorials/GPU/run.summit commit dde53c330a4167b9ff540e9bc3556055b8023405 Merge: 699315780 927f5b1d6 Author: Christopher DeGrendele Date: Thu Jul 11 14:33:15 2019 -0700 Merge branch 'development' of https://github.com/ChrisDeGrendele/amrex into development commit 927f5b1d6c8366e867ec2f67d5b5d33aa6477c60 Author: Christopher Degrendele Date: Thu Jul 11 17:32:34 2019 -0400 CIC grid error - I pushed this earlier but I guess it didn't actually push Src/Particle/AMReX_TracerParticle_mod_K.H commit 4aa2a51797665759acbaa43d1ac062b6b3141f45 Merge: b797ee715 b2167ecc0 Author: Andrew Myers Date: Thu Jul 11 14:30:03 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b797ee7154c3c0e24a665c2d9fe3a03055445325 Author: Andrew Myers Date: Thu Jul 11 14:29:48 2019 -0700 a wrapper around thrust::inclusive_scan for portability between GPU and CPU codes Src/Base/AMReX_CudaContainers.H Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainerInit.cpp commit b2167ecc0ee79ab1766aedad109d1645a7a897d7 Author: Jean M. Sexton Date: Thu Jul 11 14:15:52 2019 -0700 Add nvprof profiler flags to run.summit script Tutorials/GPU/run.summit commit 23e7bd329d47d6625c043c4531bf9b84bff98fce Author: Christopher Degrendele Date: Thu Jul 11 17:04:19 2019 -0400 deleted unnecessary file Src/Particle/#AMReX_TracerParticles.H# commit dcd04709f5996bf385d62728ea359e0e9e7b5dd4 Author: Christopher Degrendele Date: Thu Jul 11 17:03:55 2019 -0400 Didn't mean to change this file Src/Particle/#AMReX_TracerParticles.H# Src/Particle/AMReX_ParticleContainerI.H commit 74d67c5114b8b72ac982ffb5b9b068be030fc392 Author: Andrew Myers Date: Thu Jul 11 11:53:41 2019 -0700 remove the 'unsigned short int' version of the atomicCAS wrapper, which we don't need and is only available in 10.1 Src/Base/AMReX_GpuUtility.H commit 7774ff9ebbef2c926cd7aa767eaee55cbdf2bd98 Author: Weiqun Zhang Date: Thu Jul 11 11:37:37 2019 -0700 finished VisMF::WriteAsync for single cpu Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_Utility.H Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp commit 32e4ea5812f4a8b789c77247ce271b62f0ea7afc Author: Weiqun Zhang Date: Thu Jul 11 11:36:26 2019 -0700 use memcpy to avoid potential alignment issue Src/Base/AMReX_FabConv.H Src/Base/AMReX_FabConv.cpp commit 6993157804653450a779aad027a59f1d5e76089b Merge: 53df7ea38 f5e81fc7e Author: Christopher DeGrendele Date: Thu Jul 11 10:05:56 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 4040930114eb8e4ca138ee38635542a19258a9c1 Merge: e7cec85f4 f5e81fc7e Author: Kevin Gott Date: Wed Jul 10 22:09:52 2019 -0400 Merge branch 'development' into kngott/cudaGraphs commit f5e81fc7ee1bf7a366c433f55a069df3ad0fd3d8 Author: Andrew Myers Date: Wed Jul 10 17:07:58 2019 -0700 fix indentation Src/Base/AMReX_GpuUtility.H commit edb287eee41d41e1ea9de939af3c5fa278e603c6 Author: Andrew Myers Date: Wed Jul 10 17:03:48 2019 -0700 add wrappers around Cuda's atomicCAS Src/Base/AMReX_GpuUtility.H commit 778b1b56e743cd6ca86c0e3cfb86ac839b7e8ff1 Author: Weiqun Zhang Date: Wed Jul 10 13:18:10 2019 -0700 use mlock on memory in The_Pinned_Arena when USE_CUDA=FALSE Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_DArena.H Src/Base/AMReX_DArena.cpp Src/Base/AMReX_EArena.H Src/Base/AMReX_EArena.cpp commit bb551984b72a36e732a5e0209f48488563f17a7a Author: Jean M. Sexton Date: Wed Jul 10 13:07:30 2019 -0700 Remove --pretty-print from AMReX_BLBackTrace.cpp since this gives an error on cori-gpu Src/Base/AMReX_BLBackTrace.cpp commit 5ff1ce247d4433625adf00063497e9c105b96254 Author: Weiqun Zhang Date: Wed Jul 10 10:49:01 2019 -0700 add optional communicator argument to some VisMF functions Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp commit 220f5ba5471e086fdadb90d1e986c65e64b577c5 Merge: c06f79b33 5b49394c1 Author: Weiqun Zhang Date: Tue Jul 9 14:16:57 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c06f79b332a2bb6ac11fd5b3a4776544b190d43b Author: Weiqun Zhang Date: Tue Jul 9 14:16:47 2019 -0700 use pinned memory Tests/VELOC/multifab/main.cpp commit 5b49394c1bc310d752cbbf45a51a9f5c741558f5 Merge: 6e869fadb 9774bdccc Author: Andrew Myers Date: Tue Jul 9 13:25:15 2019 -0700 Merge pull request #512 from KiranEiden/keiden/amrex Fix issues RealBox equality check commit 6e869fadbad3f4dd027e7b3dc92fc0d4b8a86a61 Merge: c7c919f5f 94ee36dbb Author: Weiqun Zhang Date: Tue Jul 9 13:17:50 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c7c919f5fd55835182fe1c98878083715b7ec23e Author: Weiqun Zhang Date: Tue Jul 9 13:17:09 2019 -0700 add BaseFab::release Src/Base/AMReX_BaseFab.H Tests/VELOC/multifab/GNUmakefile Tests/VELOC/multifab/inputs Tests/VELOC/multifab/main.cpp commit 9774bdcccb2462a347b2f33a561e3b10b1fb89ed Author: Kiran Eiden Date: Tue Jul 9 13:09:55 2019 -0700 Switched to <= for RealBox equality check Src/Base/AMReX_RealBox.cpp commit 5c724845069d518bd17f5b490e1606c5ad50e685 Author: Kiran Eiden Date: Tue Jul 9 12:34:38 2019 -0700 Revert to doing exact comparison by default Using machine epsilon to do inexact comparison is a bit confusing - it's probably better to have the user supply their own value if they want a tolerance. Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit 1ee5b42379c87185b8064da9da2e33a3b78609ea Author: Kiran Eiden Date: Tue Jul 9 11:54:23 2019 -0700 Switch to using machine epsilon Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit 94ee36dbbee9a19d7c7ee997c9ce8dedfed6d4b3 Author: Andrew Myers Date: Tue Jul 9 11:43:17 2019 -0700 make the default eps for contains be the roundoff error for Real Src/Base/AMReX_RealBox.H commit 41057f9fbe806b2d5417c5045a62803da4d742aa Merge: 3c5cf6395 8271a71c3 Author: Andrew Myers Date: Tue Jul 9 11:33:59 2019 -0700 Merge pull request #511 from KiranEiden/development Added function for checking RealBox equality commit 8271a71c3361a4fcc8ae626ada94a0f425cab304 Author: Kiran Eiden Date: Tue Jul 9 11:21:39 2019 -0700 Added exclamation point to comment for consistency Src/Base/AMReX_RealBox.H commit 885c2a053f74fa06f3c858eb944962426624ca21 Author: Kiran Eiden Date: Tue Jul 9 11:16:28 2019 -0700 Added function for checking RealBox equality Added the AlmostEqual function to the amrex namespace, which checks that the domains represented by two real boxes are the same within a tolerance. Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit 3c5cf63958bf2b6264cd34bcb3a775d8b66b2243 Merge: f6d2069fa c535309a3 Author: WeiqunZhang Date: Tue Jul 9 09:35:49 2019 -0700 Merge pull request #510 from AMReX-Codes/checkinput Enforce AMR validity checks on max_level commit f5a4a3528393507dbdd2114cad07a88ecf7cac05 Author: Weiqun Zhang Date: Tue Jul 9 09:24:10 2019 -0700 VeloC test: write and read MultiFab Tests/VELOC/multifab/GNUmakefile Tests/VELOC/multifab/Make.package Tests/VELOC/multifab/Readme Tests/VELOC/multifab/inputs Tests/VELOC/multifab/main.cpp Tests/VELOC/multifab/veloc.cfg commit 1e44675dd97bc5cd1100d0f1355b4c1a3c748e75 Author: Weiqun Zhang Date: Tue Jul 9 08:58:17 2019 -0700 add DistributionMappin::readFrom and writeOn Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit 5fef4dbf88b9b9fa077ea100d41ddbdc69dbc366 Author: Weiqun Zhang Date: Tue Jul 9 06:47:59 2019 -0700 dtoh_memcpy and htod_memcpy for MultiFabs Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MultiFabUtil.H commit c535309a3e9b403bfc6d884a3f990c27a6070242 Author: Max Katz Date: Mon Jul 8 19:27:50 2019 -0700 Enforce AMR validity checks on max_level The inputs validity check on the AMR quantities was not checking on max_level. So, e.g., if you had amr.max_level=0 then you could do things which would not make sense, like have amr.blocking_factor be larger than amr.max_grid_size. Src/Amr/AMReX_Amr.cpp commit 131d4333bdbcb53f3269bed3c0c04902878e86df Merge: 85177ce7c f6d2069fa Author: Weiqun Zhang Date: Mon Jul 8 16:33:46 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f6d2069fa4ce603b457e8c927acba1440e663f3d Author: Michele Rosso Date: Mon Jul 8 18:53:21 2019 -0400 CMake: make public the OpenMP flags passed to CUDA host compiler Tools/CMake/AMReX_Config.cmake commit 85177ce7c0601c04c888ad025f3a5eb789d4fa1a Author: Weiqun Zhang Date: Mon Jul 8 11:27:47 2019 -0700 use PhysBCFunctNoOp in amrex Tutorials/Particles/ElectrostaticPIC/main.cpp commit c25913e9ddb858439418effabd3efb4c5be95aec Merge: 3a6dc721f 8dd4568af Author: Weiqun Zhang Date: Mon Jul 8 10:44:57 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3a6dc721fd74c58acfbd558ecf8a70b2ef8e7ea8 Author: Weiqun Zhang Date: Mon Jul 8 10:44:47 2019 -0700 add a comment Src/EB/AMReX_EBCellFlag.H commit 8dd4568afe03aa4f5c5188cc1d6b9649caaee904 Author: Max Katz Date: Mon Jul 8 00:28:15 2019 -0700 Only write initial checkpoint if checkpoints are requested Src/Amr/AMReX_Amr.cpp commit 40cbab0fd2fcf52814f60ec1e20529b5a588b67c Merge: d7bd671f0 25c1a64a5 Author: Weiqun Zhang Date: Sun Jul 7 17:06:49 2019 -0700 Merge branch 'weiqun/dev' into development commit 25c1a64a5702e5aecc2fb87f39154a55f140662f Author: Weiqun Zhang Date: Sun Jul 7 16:49:31 2019 -0700 fix new index typo due to typo Src/EB/AMReX_EB2_3D_C.cpp commit 47d2c073cff4a77f66995994de44072af16f9c7e Author: Weiqun Zhang Date: Sun Jul 7 15:45:45 2019 -0700 build 3d eb cells on gpu Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_C.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EBCellFlag.H commit 8f5688b3fb406f207df5e18a2792d944dcec5841 Author: Weiqun Zhang Date: Sat Jul 6 22:31:26 2019 -0700 WIP: build 3d eb cells on gpu Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_C.H Src/EB/AMReX_EB2_Level.H commit d7bd671f0740b1c6a8fc9287136094eeb2519bb8 Merge: 3512030f9 cde14ca81 Author: Weiqun Zhang Date: Sat Jul 6 19:22:55 2019 -0700 Merge branch 'weiqun/dev' into development commit cde14ca81ae5804bf8dd3eaa564bd32bb10c6dae Author: Weiqun Zhang Date: Sat Jul 6 17:16:53 2019 -0700 3d EB: build faces on gpu Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_C.H Src/EB/AMReX_EB2_F.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_eb2_3d.F90 commit 3512030f924c8b9992aed0e62a9728159853b520 Author: Weiqun Zhang Date: Sat Jul 6 08:10:59 2019 -0700 assuming -lgomp only works gcc Tools/GNUMake/Make.defs Tools/GNUMake/comps/nvcc.mak commit bef4845741af2c8e2655af86eb373d1905f950e2 Merge: edd2e4397 97e0ef2c7 Author: Weiqun Zhang Date: Sat Jul 6 07:59:48 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 97e0ef2c72e466b51ab621894ca3168b7ba4b3d8 Author: Michele Rosso Date: Fri Jul 5 15:51:43 2019 -0700 CMake: fix bug in config file Tools/CMake/AMReXConfig.cmake.in commit af821107905ba1fcfa5ece54a52842ce0429cea9 Author: Michele Rosso Date: Fri Jul 5 14:30:33 2019 -0700 CMake: manually pass OpenMP flag to CUDA host compiler Tools/CMake/AMReX_Config.cmake commit 8950abd07f7336b13e6c16dce6b6a0dde0d363ed Author: Michele Rosso Date: Fri Jul 5 12:46:56 2019 -0700 CMake: use C++ bindings for MPI in addition to C bindings. This fixes bugs with certain MPI implementations still using C++ bindings. Src/Base/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in commit edd2e43971799f950a5404ebbda2b49cdb72edec Author: Weiqun Zhang Date: Fri Jul 5 12:10:35 2019 -0700 2d EB: build_cells on gpu Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_EB2_C.H Src/EB/AMReX_EB2_F.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_eb2_2d.F90 commit 932aefaa17a21f98087044da448c9183e042320c Author: Michele Rosso Date: Fri Jul 5 10:54:04 2019 -0700 CMake: allow builds with both CUDA and OMP Tools/CMake/AMReX_Options.cmake commit a323820d360f28dccacd5a908c8f54ac041faa95 Author: Andrew Myers Date: Fri Jul 5 13:43:36 2019 -0400 remove restriction that OMP and CUDA/HIP can't be enabled at the same time. Tools/GNUMake/Make.defs commit d57ddb3c020cb887295020ce8b9daa98d5212b5d Merge: 4fc3c4ddd 6eb20eaa3 Author: Weiqun Zhang Date: Fri Jul 5 10:41:57 2019 -0700 Merge branch 'development' into weiqun/dev commit 6eb20eaa39e3726c7008324fdbe3ed530c352733 Merge: b6ffd0bf8 6c43218a5 Author: Weiqun Zhang Date: Fri Jul 5 10:40:44 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4fc3c4dddb74a4cb0e7da3c8021a8acc78beea48 Author: Weiqun Zhang Date: Fri Jul 5 10:40:34 2019 -0700 EB: build_faces on gpu Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_eb2_2d.F90 commit 6c43218a5fdd57c7747b0a24880465c4c5cd04a9 Author: Andrew Myers Date: Fri Jul 5 10:33:47 2019 -0700 use value semantics instead of pointers for rhoarr Src/Particle/AMReX_ParticleContainerI.H commit fb087a265675311f1c51c7f2b2fd333ed7f4e25b Author: Andrew Myers Date: Fri Jul 5 10:14:31 2019 -0700 initialize rhoarr pointer to nullptr Src/Particle/AMReX_ParticleContainerI.H commit 9b9fa60913760fe7975da74ca0ed6763e74e8468 Author: Andrew Myers Date: Fri Jul 5 10:04:25 2019 -0700 update AssignCellDensitySingleLevel to handle the case where OMP and CUDA are on, but we are not in a launch region Src/Particle/AMReX_ParticleContainerI.H commit 65b6967001d506610483f51620db9529ede6cc89 Author: Weiqun Zhang Date: Fri Jul 5 08:10:10 2019 -0700 WIP: 2d compiles Src/EB/AMReX_EB2_C.H Src/EB/AMReX_EB2_Level.H commit 93dad44ef94ec1013bd60cafdc88c78e91ce511c Author: Weiqun Zhang Date: Fri Jul 5 07:55:31 2019 -0700 add LoopOnCpu to get rid of nvcc warnings Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_Loop.H Src/Base/CMakeLists.txt Src/Base/Make.package Src/EB/AMReX_EB2_GeometryShop.H commit 282a5f04f0c0bd70912af36ba159be9b4d361694 Author: Weiqun Zhang Date: Fri Jul 5 06:28:53 2019 -0700 WIP: EB2::build_faces on gpu Src/Base/AMReX_Box.H Src/EB/AMReX_EB2_2D_C.cpp Src/EB/AMReX_EB2_3D_C.cpp Src/EB/AMReX_EB2_C.H Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_Level.H Src/EB/CMakeLists.txt Src/EB/Make.package commit a8c8bd16537f24ff6f7f6afc38eebd21d9968324 Author: Ann Almgren Date: Thu Jul 4 19:01:20 2019 -0700 pass bottom_reltol and bottom_abstol through the MacProjector Src/LinearSolvers/MLMG/AMReX_MacProjector.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit b6ffd0bf89cbb4deff341793db021e5aac92d77a Author: Weiqun Zhang Date: Thu Jul 4 13:22:05 2019 -0700 EB: get intercepts on gpu if we can Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_Level.H commit d6f2212c9f28f43b668747e26da6000e96b556fb Author: Weiqun Zhang Date: Wed Jul 3 20:35:03 2019 -0700 old versions of eu-addr2line do not support pretty-print Src/Base/AMReX_BLBackTrace.cpp commit e2ec27e817fb74c1f2c053ed79f2432760977134 Merge: 0a0e97524 75642f91f Author: Weiqun Zhang Date: Wed Jul 3 18:42:35 2019 -0700 Merge branch 'development' into weiqun/dev commit 0a0e97524894fc9c98ab8fbc4e72af2e3b8fbd29 Author: Weiqun Zhang Date: Wed Jul 3 18:30:34 2019 -0700 around a possible gcc bug Src/Base/AMReX_BLBackTrace.cpp commit 75642f91f5754df9e4e73d857a29209b6331d9d5 Author: Ann Almgren Date: Wed Jul 3 17:11:47 2019 -0700 Need to only touch inverse_tags if enable_Inverse() is true Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit 69c5a9956694223fb1bad544c08b59deb495095d Author: Andrew Myers Date: Wed Jul 3 16:23:44 2019 -0700 Fix problem where the size of inverse_tags wasn't getting reset to 0 properly Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit 9223e448e8004525fa0ed1e2e52f3aa0c2d33e4f Author: Weiqun Zhang Date: Wed Jul 3 15:23:32 2019 -0700 fix typo Src/Base/AMReX_BLBackTrace.cpp commit d04fe88e773f0fa63229e0ae568e60ea459fbaff Author: Weiqun Zhang Date: Wed Jul 3 15:17:24 2019 -0700 use eu-addr2line if present Src/Base/AMReX_BLBackTrace.cpp commit 376886f4fc0180874237031520bb3947012ec732 Merge: 51757fccc 49796cf8b Author: Ann Almgren Date: Wed Jul 3 14:58:27 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 51757fcccb209d00e11c7883579f41589f42bb0c Author: Ann Almgren Date: Wed Jul 3 14:58:16 2019 -0700 default enable_inverse to false Src/Particle/AMReX_NeighborParticlesI.H commit 49796cf8b2f017c8b2db0b9677e151292bec2e9b Merge: 1afdbe658 196c1e80f Author: Andrew Myers Date: Wed Jul 3 17:17:26 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1afdbe6583e1a984c9fcdb759acf3d1dff8abe99 Author: Andrew Myers Date: Wed Jul 3 17:17:05 2019 -0400 workaround for compiler bug in gcc < 4.9 Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.cpp Src/Particle/AMReX_Particle.H commit 196c1e80f71243954c6dc8a86d2fa6c2da18bbaa Author: Michele Rosso Date: Wed Jul 3 14:13:41 2019 -0700 CMake: add -fimplicit-none to Fortran flags preset Tools/CMake/AMReXFlagsTargets.cmake commit 035e45bbc75deed9f4b582ad4a30e919d03a483f Author: Weiqun Zhang Date: Wed Jul 3 12:35:44 2019 -0700 GNU make: load Make.local-pre if present Tools/GNUMake/Make.defs commit d574e2ca67cd97ff964b9a40825bec1ba453b9a6 Author: Weiqun Zhang Date: Wed Jul 3 10:26:41 2019 -0700 fix warning for clang Src/Base/AMReX_TypeTraits.H commit b505bc08ba9ea1ce5d11c8c40c87e800908ecdda Author: Weiqun Zhang Date: Wed Jul 3 13:14:07 2019 -0400 workaround gcc 4 Src/Base/AMReX_BaseFab.H Src/Base/AMReX_TypeTraits.H commit d142f8cb4dddce15577e2e73449a5af204f8ee5e Author: Weiqun Zhang Date: Wed Jul 3 09:40:38 2019 -0700 add EXPORT_DYNAMIC to llvm-flag.mak Tools/GNUMake/comps/llvm-flang.mak commit 08aff0fed13b1f68ea58131f820efa4bc9f765b2 Author: Weiqun Zhang Date: Wed Jul 3 09:26:00 2019 -0700 Backtrace on mac: llvm is supported Src/Base/AMReX_BLBackTrace.cpp Tools/GNUMake/Make.defs Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/llvm.mak commit 5d3ff445a05ac3925d8fadb4238135ef32b40fbd Author: Weiqun Zhang Date: Wed Jul 3 07:22:03 2019 -0700 move dynamic load flags to gnu.mak Tools/GNUMake/Make.defs Tools/GNUMake/comps/gnu.mak commit 9af228dc7613a4938d2ff93cc772c42ff8e08bab Author: Weiqun Zhang Date: Wed Jul 3 07:02:33 2019 -0700 turn dynamic load by default for Darwin+gcc Tools/GNUMake/Make.defs commit 3ff591ec3e48a6eb3aa01e0a2f9f8a619cb6042e Author: Weiqun Zhang Date: Wed Jul 3 06:41:39 2019 -0700 use atos for backtrace on mac Src/Base/AMReX_BLBackTrace.cpp commit f3b66bc0f125905309f2606bb4721e48c20fb746 Merge: 6f255cc04 8e3340bb0 Author: Weiqun Zhang Date: Tue Jul 2 20:47:45 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6f255cc04c5a361e35f822b67537f3d17eff7150 Author: Weiqun Zhang Date: Tue Jul 2 20:47:28 2019 -0700 If available, print the tiny profiler stack when backtracing Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp commit 8e3340bb01c8a8bf1c712a594bf1f947071f3ba5 Author: Weiqun Zhang Date: Tue Jul 2 19:10:19 2019 -0700 set handler for SIGFPE Src/Base/AMReX.cpp commit 9fbe7b5730e413388f9cedca8e64cfa436b972d2 Author: Weiqun Zhang Date: Tue Jul 2 18:49:42 2019 -0700 For backtrace, do not omit frame pointer Src/Base/AMReX_BLBackTrace.cpp Tools/GNUMake/comps/gnu.mak commit c3054839d96ff00765d016a5fc2bb4d3c63f5610 Author: Weiqun Zhang Date: Tue Jul 2 18:23:53 2019 -0700 backtrace on Mac Src/Base/AMReX_BLBackTrace.cpp Tools/GNUMake/Make.defs Tools/GNUMake/comps/gnu.mak commit 7cd37bcd47fc98ac7df342f4266633056db83500 Author: Weiqun Zhang Date: Tue Jul 2 15:43:30 2019 -0700 enable floating pointer exception and backtrace for Mac Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.H Src/Base/AMReX_BLBackTrace.cpp commit e8439da97e6d6fe5d2eb5eabf6ce878e52c767c6 Author: Weiqun Zhang Date: Mon Jul 1 21:20:34 2019 -0700 fix 2d problem in my last commit Src/LinearSolvers/MLMG/AMReX_MLLinOp.H commit 221927e48ffa4b7d565670ce980523fa885ba0ee Author: Weiqun Zhang Date: Mon Jul 1 20:43:14 2019 -0700 Linear Solver: option to set non-zero domain bc locations Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMGBndry.H Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp commit 8b26185813970bed14d379827566aa7a48d0af77 Author: Weiqun Zhang Date: Mon Jul 1 19:07:45 2019 -0700 fix parse_bt.py Tools/Backtrace/parse_bt.py commit 785e653b7fa648a96f7f657fa2c5529bf7429091 Author: Weiqun Zhang Date: Mon Jul 1 18:50:37 2019 -0700 addr2line: skip libc.so because it causes troubles Src/Base/AMReX_BLBackTrace.cpp Tools/Backtrace/parse_bt.py commit 7ad1f74a64d6b7ec63a51759d30479b42026f60e Author: Weiqun Zhang Date: Mon Jul 1 18:33:05 2019 -0700 try to use the address in () for addr2line if we can Src/Base/AMReX_BLBackTrace.cpp commit 7fe1ba17e45dae3f379a8708eb48ccb14622f152 Author: Weiqun Zhang Date: Mon Jul 1 18:16:16 2019 -0700 Revert "backtrace: use the address returned by backtrace, not the one extraced from bactrace_symbols" This reverts commit daa3d2e8a3bbfd437524373dd2ef75a2f70649d0. Src/Base/AMReX_BLBackTrace.cpp Tools/Backtrace/parse_bt.py commit daa3d2e8a3bbfd437524373dd2ef75a2f70649d0 Author: Weiqun Zhang Date: Mon Jul 1 16:04:19 2019 -0700 backtrace: use the address returned by backtrace, not the one extraced from bactrace_symbols Src/Base/AMReX_BLBackTrace.cpp Tools/Backtrace/parse_bt.py commit 0021bd35c1f07284ee24b8895d74db82ea2af942 Merge: 36a98cdd9 12daa111a Author: Weiqun Zhang Date: Mon Jul 1 09:16:01 2019 -0700 Merge branch 'weiqun/dev' into development commit 36a98cdd937cafd7cbccd22b143a180dd27b87a3 Author: Weiqun Zhang Date: Mon Jul 1 09:13:27 2019 -0700 update CHANGES CHANGES commit 12daa111af200ca423e4f91f3a4c33b57dc617aa Author: Weiqun Zhang Date: Sat Jun 29 13:30:24 2019 -0700 fix warnings Src/Base/AMReX_PhysBCFunct.H Src/EB/AMReX_EBFluxRegister_2d.F90 Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_algoim.cpp Src/EB/AMReX_algoim_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit 7c38159afcfa5a074d489359689a8885304d9efd Author: Weiqun Zhang Date: Sat Jun 29 11:47:57 2019 -0700 option to turn off Wshadow because there are so many in thrust. fix some warnings Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_EArena.cpp Src/Base/AMReX_Lazy.cpp Src/Base/AMReX_Machine.cpp Tools/GNUMake/comps/gnu.mak Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/EBCNS/Source/CNS.cpp commit c61fa8297347e1bf028e8698342c5d85cc66bc7c Author: Weiqun Zhang Date: Sat Jun 29 11:05:06 2019 -0700 provide default constructor to EBCellFlag because nvcc cannot generate default device version Src/EB/AMReX_EBCellFlag.H commit 705d3d70717030107743435408a70f30bd134bda Author: Weiqun Zhang Date: Sat Jun 29 07:17:10 2019 -0700 put amrex::min and amrex::max in new file AMReX_Algorithm.H. add max_lbound and min_ubound functions Src/Base/AMReX_Algorithm.H Src/Base/AMReX_Box.H Src/Base/AMReX_Utility.H Src/Base/CMakeLists.txt Src/Base/Make.package Src/EB/AMReX_EB2_2D_C.H Src/EB/AMReX_EB2_3D_C.H commit 53df7ea38d06de9f2c0e188515977d126d075cc9 Author: Christopher DeGrendele Date: Fri Jun 28 14:48:40 2019 -0700 fixed the same indice error from before on CIC grids Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 35ae397c95c782dfff14424f8d7d1280d2d4bc0a Author: Weiqun Zhang Date: Fri Jun 28 10:32:02 2019 -0700 clean up Src/Base/AMReX_BaseFab.H Src/Particle/AMReX_ParticleContainerI.H commit 160ed2bb485515732b3b1f0a0ec028b1f8ce0d21 Author: Weiqun Zhang Date: Thu Jun 27 21:50:27 2019 -0700 for non-trivially_default_contructible types, do placement new on gpu to avoid touching memory on cpu. This will help BaseFab> and BaseFab. Src/Base/AMReX_BaseFab.H commit 0e70638008822e099a22365c04904bc4b95374e9 Merge: 8ee1554da 318df8ebe Author: Michele Rosso Date: Thu Jun 27 16:05:32 2019 -0700 Merge branch 'mr/cmake' into development commit 318df8ebe7b93a2953d269aa694a5f6e024de96b Author: Michele Rosso Date: Thu Jun 27 16:05:06 2019 -0700 CMake: add module to perform typecheck. Tools/CMake/AMReXTypecheck.cmake commit ba7c9fd40161e8b2e4aa4e71373158802fa921fe Author: Weiqun Zhang Date: Thu Jun 27 14:15:53 2019 -0700 update documentation and launch tutorial Docs/sphinx_documentation/source/AmrCore.rst Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/LoadBalancing.rst Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst commit d52691f0f0d63d8690fab4c4bf07186be1342400 Author: Weiqun Zhang Date: Thu Jun 27 13:22:25 2019 -0700 use amrex::Loop Tutorials/GPU/Launch/MyKernel.H Tutorials/GPU/Launch/main.cpp commit 8ee1554da33025eb0ecbfff10f77f302a7cc9940 Author: Weiqun Zhang Date: Thu Jun 27 12:43:17 2019 -0700 add amrex::Loop and amrex::LoopConcurrent Src/Base/AMReX_Box.H commit eb2a81cf11fdf8d8e1f5c880e20b902ff95652bc Author: Christopher Degrendele Date: Thu Jun 27 15:29:32 2019 -0400 Mac routine is now dimension agnostic. This is ready for testing Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 860c9ca8a35748180b0efedf5c9b7770e7112099 Merge: 3154a474c 505a94863 Author: Michele Rosso Date: Thu Jun 27 11:39:38 2019 -0700 Merge branch 'development' into mr/cmake commit 3154a474c819f883bce6b8980d130a8de3847032 Author: Michele Rosso Date: Thu Jun 27 11:14:12 2019 -0700 CMake: clean up Tools/CMake/AMReX_Utils.cmake commit 505a948635b08944d923450588424c4bdf7a1c7e Author: Ann Almgren Date: Thu Jun 27 08:11:27 2019 -0700 Fix typo Src/EB/CMakeLists.txt commit b48df45ad8791e230cc2febe2ecf195822af8882 Author: Weiqun Zhang Date: Thu Jun 27 07:49:55 2019 -0700 fix index bug Src/EB/AMReX_EBMultiFabUtil.cpp commit 41dc56fc27f0b0076247ca92a518d4de8dbe93ec Author: Weiqun Zhang Date: Thu Jun 27 07:47:43 2019 -0700 fix index bug Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit dba00a4daa7541cf68eeb70f00ebd7a5dd322f2b Author: Weiqun Zhang Date: Thu Jun 27 07:04:16 2019 -0700 fix cmake Src/EB/CMakeLists.txt Src/EB/Make.package commit eed6c3c7d0bd9dcec807de1ad8d1d9b7c68b3f9e Author: Weiqun Zhang Date: Wed Jun 26 20:45:34 2019 -0700 remove deprecated Fortran routine Src/EB/AMReX_eb2_3d.F90 commit ad5ee6913596d5671fe8a7b6ef238ce522a7c0f5 Author: Weiqun Zhang Date: Wed Jun 26 20:13:45 2019 -0700 EB: build types on gpu Src/EB/AMReX_EB2_2D_C.H Src/EB/AMReX_EB2_3D_C.H Src/EB/AMReX_EB2_C.H Src/EB/AMReX_EB2_F.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB2_MultiGFab.cpp Src/EB/AMReX_eb2_2d.F90 Src/EB/AMReX_eb2_3d.F90 Src/EB/CMakeLists.txt Src/EB/Make.package commit bd23a932205bd3e99c373d08e301e8a40e4cf402 Author: Weiqun Zhang Date: Wed Jun 26 15:54:44 2019 -0700 EB: fill leveset on gpu Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB_levelset.H commit a22849ec1a83a82a40dfbb2c355e4f39dc77e620 Author: Michele Rosso Date: Wed Jun 26 16:56:06 2019 -0700 CMake: update evaluate_genex Tools/CMake/AMReX_Utils.cmake commit 19e2cc351bb598a643061dca76375165f27c3dcc Merge: 2ff20c828 bdae54d6b Author: Weiqun Zhang Date: Wed Jun 26 13:42:34 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit bdae54d6b5d68d222a8dbca3cf15b94678ae5ebd Author: Weiqun Zhang Date: Wed Jun 26 13:40:27 2019 -0700 make sure we don't dereference nullptr Src/Base/AMReX_FabArray.H commit 92a5b6ded53125911d337fb9f005398323a41e0c Author: Christopher Degrendele Date: Wed Jun 26 16:12:12 2019 -0400 Fixed a bug and deleted unnecessary lines Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit d61683f8a6668acf476a404050cc39c55a293604 Author: kngott Date: Wed Jun 26 13:08:41 2019 -0700 Fix labels in launch test. Tests/GPU/FusedLaunches/main.cpp commit 2ff20c828793a18bd962d5cf97295c916c968228 Merge: e4ae24d84 3c737a5cf Author: Weiqun Zhang Date: Wed Jun 26 12:24:32 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e4ae24d849096964dcc37dd62ecbee99909438f5 Author: Weiqun Zhang Date: Wed Jun 26 12:18:24 2019 -0700 gpu: set covered cells and faces Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2D_C.H Src/EB/AMReX_EBMultiFabUtil_3D_C.H Src/EB/AMReX_EBMultiFabUtil_C.H Src/EB/AMReX_EBMultiFabUtil_F.H Src/EB/AMReX_EBMultiFabUtil_nd.F90 Src/EB/CMakeLists.txt Src/EB/Make.package Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 3c737a5cf081175972907b40cbcd35dbdea4eb2e Author: kngott Date: Wed Jun 26 11:49:40 2019 -0700 Updated launch tester. Tests/GPU/FusedLaunches/main.cpp commit eecacbe68ced3ccc350102a3de6848828ab8978d Author: Christopher Degrendele Date: Wed Jun 26 12:19:38 2019 -0400 removed unwanted files Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/Backtrace.0 commit 0210c0b3c62926dc93955342a7e7c146b332dddd Author: Weiqun Zhang Date: Wed Jun 26 09:05:11 2019 -0700 gpu: EBAmrUtil Src/EB/AMReX_EBAmrUtil.cpp Src/EB/AMReX_EBAmrUtil_F.H Src/EB/AMReX_EBAmrUtil_nd.F90 Src/EB/CMakeLists.txt Src/EB/Make.package commit 80d5ac7d70a5ab34ad06fe9b78a964b6ef22b729 Merge: 6876a3873 f437fdd3e Author: kngott Date: Tue Jun 25 19:47:07 2019 -0700 Merge branch 'development' into kngott/fused commit f437fdd3e4a0a40dc1d6f24f95a318cfe4ff031c Author: kngott Date: Tue Jun 25 19:46:48 2019 -0700 Adjust make system for Brian's new modules. Tools/GNUMake/sites/Make.nersc commit 45062a20fa1fcf730482b8399ee320fe9538aec3 Author: Weiqun Zhang Date: Tue Jun 25 17:13:08 2019 -0700 Fix nodal solver owner mask. This will break regression tests. Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 2850de0a99fd56f25848783fba58c93081edc89b Author: Andrew Myers Date: Tue Jun 25 16:07:01 2019 -0700 fix an off-by-one index error Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 1c926794d5199270bbc7042e4089997326dd0aad Author: Andrew Myers Date: Tue Jun 25 16:04:59 2019 -0700 change this variable name to keep yt happy Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 5aad842f3e11325052a1c9c698e128aa11609518 Merge: 43eef0b9c b99d5efc9 Author: Weiqun Zhang Date: Tue Jun 25 15:43:29 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 43eef0b9c2b8add6cc59ab66851578264da00827 Author: Weiqun Zhang Date: Tue Jun 25 15:43:19 2019 -0700 BoxList: make sure block size is not zero Src/Base/AMReX_BoxList.cpp commit b99d5efc9ac54e19643d86082ca7f7644a0d4e6f Merge: 61a178fdc 3f425b713 Author: WeiqunZhang Date: Tue Jun 25 15:33:45 2019 -0700 Merge pull request #508 from OscarAntepara/oscar Adding bottomSolver_maxIter and solver_maxIter to the MacProjector commit 3f425b713335bc90e7fb2d84e5f84e0dff188999 Author: Oscar Antepara Date: Tue Jun 25 15:03:29 2019 -0700 Adding bottomSolver_maxIter and solver_maxIter to the MacProjector Src/LinearSolvers/MLMG/AMReX_MacProjector.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit 61a178fdc36541b50d2941956b33d501028e8151 Author: Michele Rosso Date: Tue Jun 25 14:20:10 2019 -0700 Typechecker: add support for _Bool type Tools/typechecker/typechecker.py commit b078d47d75c5cd1f57086fda44df2dc5b42e9721 Merge: 2e04114f4 26ffd91d7 Author: Michele Rosso Date: Tue Jun 25 13:41:46 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 2e04114f42f1aadd2da9cd4fda331b65671e8c12 Author: Michele Rosso Date: Tue Jun 25 13:41:38 2019 -0700 Fix bug in doc that prevents latexpdf to compile Docs/sphinx_documentation/source/BuildingAMReX.rst commit f7bead79750aec0f9b148ff00f483e63e254c356 Author: Christopher Degrendele Date: Tue Jun 25 16:06:10 2019 -0400 f Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Header Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00000 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00001 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00002 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00003 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00004 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00005 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00006 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00007 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00008 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/chk00000/Level_0/phi_D_00009 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Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/plt00120/Level_2/Cell_H commit 5149c96f7a0e2b104f7861f921f1c700bed617c9 Author: Christopher Degrendele Date: Tue Jun 25 15:27:59 2019 -0400 Removed plotfile Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Header Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_0/Cell_D_00000 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_0/Cell_H Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_1/Cell_D_00000 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_1/Cell_H Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_2/Cell_D_00000 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Level_2/Cell_H Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Header Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Level_0/DATA_00000 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/plt00000/Tracer/Level_0/Particle_H 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Tue Jun 25 12:03:46 2019 -0700 fix jump to case label error Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp commit 8aa4e0ddacd552a7585cd4e4620020e578e0242c Author: Weiqun Zhang Date: Tue Jun 25 10:57:17 2019 -0700 add noexcept to some functions Src/Base/AMReX_PlotFileDataImpl.H Src/Base/AMReX_PlotFileDataImpl.cpp Src/Base/AMReX_PlotFileUtil.H commit b923ea663170870911911b58a3a5095011e2869d Author: Weiqun Zhang Date: Tue Jun 25 09:19:11 2019 -0700 add amrex_set_finest_level to amrex_amrcore_module Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 commit 2193b24d81ac180ee26f5ea7ffcdfa4c7c479c8a Author: Max Katz Date: Tue Jun 25 04:16:42 2019 -0700 Add more RegionTags to AmrLevel Src/Amr/AMReX_AmrLevel.cpp commit 6876a387346ca397e7a55c87744123c5837098ee Merge: 50a36155a 1a5e55fdc Author: kngott Date: Mon Jun 24 15:46:26 2019 -0700 Merge branch 'development' into kngott/fused commit 1a5e55fdc1f420a11c1d21643d0aba80b59ada68 Merge: 0ff36557b b23b7fd4b Author: Michele Rosso Date: Mon Jun 24 14:43:13 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 0ff36557b7f9756ff2bd2ff89095397d9d0a9670 Author: Michele Rosso Date: Mon Jun 24 14:43:01 2019 -0700 CMake: fix bug in OpenMP support Tools/CMake/AMReX_Config.cmake commit b23b7fd4bcda1e54c0dab18c096f42fb69a8d1bd Merge: 7fc20fb82 54200b20f Author: Weiqun Zhang Date: Mon Jun 24 12:52:11 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d0cdfa1727d398e841165068da2feb225b32f00b Author: Christopher Degrendele Date: Mon Jun 24 13:21:26 2019 -0400 CIC routine is now dimension agnostic, MAC routine has a bug Src/Particle/AMReX_Particle.H Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 7fc20fb82bd03842c84f1d36ec8b7b2ce29b4c6b Author: Weiqun Zhang Date: Mon Jun 24 08:24:42 2019 -0700 YAFluxRegister: no need to test fab ptr Src/Boundary/AMReX_YAFluxRegister.cpp commit 54200b20fbde5d37c37a77265ba7278707141d57 Author: Max Katz Date: Mon Jun 24 08:14:01 2019 -0700 Add statedata region tags Src/Amr/AMReX_AmrLevel.cpp commit 472369b1399c7d43cebc01107af60e976cce75b3 Author: Weiqun Zhang Date: Mon Jun 24 07:02:20 2019 -0700 need to BaseFab's DataAllocator ctors host and device Src/Base/AMReX_BaseFab.H commit 224f019e7688540be5f17e1765b9a96e402af997 Merge: e4357d781 6e299622f Author: Weiqun Zhang Date: Sun Jun 23 17:43:21 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e4357d781750bb7760d7ad92f5a622c2e79c9894 Author: Weiqun Zhang Date: Sun Jun 23 17:43:10 2019 -0700 make sure FabArray works for non-BaseFab FAB Src/Base/AMReX_FabArray.H commit 6e299622f1354812d1a1e2a7040ca2aaa2fdc267 Author: Andrew Myers Date: Sun Jun 23 19:57:05 2019 -0400 better to apply periodic shift for the remotes on the CPU, since they are to be copied off anyway Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit d261b77ea43cc0a0b60981c451e718367d4a4ac1 Author: Weiqun Zhang Date: Sun Jun 23 16:53:06 2019 -0700 minIndex and maxIndex for iMultiFab Src/Base/AMReX_iMultiFab.cpp commit 810ab0d4a42ab5f7fedd08c4e529b6398f64d053 Author: Andrew Myers Date: Sun Jun 23 19:19:38 2019 -0400 copy directly to pinned memory; use std::memcpy instead of cudaMemcpy Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 645849cfdaa880aaafbc86e86705ca2b5767fddd Author: Max Katz Date: Sun Jun 23 09:22:41 2019 -0700 Add StateData tag to MFs Src/Amr/AMReX_StateData.cpp commit c383e960612d47bbfc26e3c2313cd14666b6c7bf Author: Weiqun Zhang Date: Sun Jun 23 09:06:20 2019 -0700 fix for C++11 Src/Base/AMReX_BaseFab.H commit 89ac1bdb18431a16dc563d34b9a63c52f5fa468b Author: Weiqun Zhang Date: Sun Jun 23 07:31:30 2019 -0700 add MultiFab::queryMemUsage Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 7479af35e13e23d470e5e9edfffa3b65a1ca6884 Author: Weiqun Zhang Date: Sun Jun 23 07:12:18 2019 -0700 add tags to MultiFab/FabArray and use them to track memory usage Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 15aec70a779e2798a7144594b80e84e56ff59cc0 Merge: ccccc0d13 38e15113f Author: Weiqun Zhang Date: Sat Jun 22 22:38:30 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ccccc0d1350887a62c4b63d1ad796dd50bf33b05 Merge: b5ed712e1 d3a3799cf Author: Weiqun Zhang Date: Sat Jun 22 22:38:12 2019 -0700 Merge branch 'mlmg-2d' into development commit 38e15113f716274677118a184a1f33ffaf46e9fe Author: Max Katz Date: Sat Jun 22 21:41:01 2019 -0700 Add option to perform asynchronous MF prefetch Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MFIter.H commit c66ce820ac6c7194f425aa23b68e30bd579dcc43 Merge: 62d331f63 b5ed712e1 Author: Andrew Myers Date: Sat Jun 22 23:25:31 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 62d331f63f38f065f5e695ca58d0a8309614fc14 Author: Andrew Myers Date: Sat Jun 22 23:24:49 2019 -0400 use std::memcpy instead of cudaMemcpy for host-to-host transfers Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit b5ed712e17f00ffa4ecbf972ce7e6f411042b64b Author: Weiqun Zhang Date: Sat Jun 22 18:35:41 2019 -0700 use arena in FabArray Src/Base/AMReX_FabArray.H commit 0d77b47239d4a4d87b5174d7116e792fd21abeb4 Author: Weiqun Zhang Date: Sat Jun 22 17:56:46 2019 -0700 --no-edit Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabFactory.H Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_Mask.cpp Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBCellFlag.cpp Src/EB/AMReX_EBFArrayBox.H Src/EB/AMReX_EBFArrayBox.cpp Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_MultiCutFab.H commit 07d02af7dd4a3a50ac40bf98becb233757938b71 Author: Andrew Myers Date: Sat Jun 22 21:10:56 2019 -0400 also get rid of the transform when packing the MPI buffers Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 6481e0a7592e446017557ffa90d4b6a40a69b2fe Author: Andrew Myers Date: Sat Jun 22 20:26:44 2019 -0400 avoid the thrust::transform call, which is also blocking Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit c71c3f9b637a6089bd8db9fcf5292ee4deb4012c Author: Andrew Myers Date: Sat Jun 22 19:23:38 2019 -0400 use an async copy here instead of thrust::copy, which is blocking Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 258d8d93beda2ea9615387b7f3975489194dfe64 Author: Weiqun Zhang Date: Fri Jun 21 17:53:29 2019 -0700 BaseFab: remove allocator template paramter. instead make allocator base of BaseFab Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_TypeTraits.H commit 5b64348b4c208b670b592bbee22a1624caaea0ea Author: Weiqun Zhang Date: Fri Jun 21 17:09:33 2019 -0700 BaseFab no longer needs BaseFabData as base Src/Base/AMReX_BaseFab.H commit 3e146ad91fd219025ae50b2ff6f2ca65320fadae Author: Weiqun Zhang Date: Fri Jun 21 16:13:44 2019 -0700 remove asyncfab Src/Base/AMReX.cpp Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuAsyncFab.H Src/Base/AMReX_GpuAsyncFab.cpp Src/Base/AMReX_GpuAsyncFabImpl.H Src/Base/AMReX_GpuAsyncFabImpl.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 50b8bb01cadcb81cc27f946398527c328c4d67e0 Author: Weiqun Zhang Date: Fri Jun 21 16:11:02 2019 -0700 update license information Docs/sphinx_documentation/source/index.rst Docs/sphinx_tutorials/source/index.rst commit 705dc0d7b5b838a7dc7cdadca4f2f2256da595bd Merge: 0edb94dbd 449b915f6 Author: Andrew Myers Date: Fri Jun 21 15:32:35 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1c50ccb75646642ac1812e61a853a46441f967fd Merge: 1ab1f7a76 449b915f6 Author: Michele Rosso Date: Fri Jun 21 10:32:05 2019 -0700 Merge branch 'development' into mr/cmake commit 449b915f6d7edf84facce68632c88546c180eb6e Author: Weiqun Zhang Date: Thu Jun 20 17:11:35 2019 -0700 remove fab device ptr Docs/sphinx_documentation/source/BuildingAMReX.rst Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_FabAllocator.H Src/Base/AMReX_FabAllocator.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_FabFactory.H Src/Base/AMReX_GpuAsyncFabImpl.H Src/Base/AMReX_GpuAsyncFabImpl.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_VisMF.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_InterpBndryData.cpp Src/EB/AMReX_EB2_MultiGFab.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Tests/GPU/AsyncFab/GNUmakefile Tests/GPU/AsyncFab/Make.package Tests/GPU/AsyncFab/main.cpp Tests/GPU/libamrex_CUDA/main.cpp Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/GNUMake/Make.defs commit 0edb94dbddc7e3cd4cdab3736086f8d444eaa35b Merge: a8f723857 f2fa16d44 Author: Andrew Myers Date: Thu Jun 20 17:52:07 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f2fa16d445db7acebdb9aa0d1f9bd8b589e63b14 Merge: f5bb20302 6418732d6 Author: Marc Day Date: Thu Jun 20 13:56:41 2019 -0700 Merge pull request #505 from esclapez/dev_CleanDiffSameDomainRefined Clean the screen output of DiffSameDomainRefined. commit f5bb2030205d205ddd34fb4572fd2153b6113788 Author: Andrew Myers Date: Thu Jun 20 13:55:41 2019 -0700 Revert "change names in tutorial documentation and update license information" This reverts commit f24e91d024f4a2c0a38f5d94bc7d224c4d363873. Docs/sphinx_documentation/source/index.rst Docs/sphinx_tutorials/source/conf.py Docs/sphinx_tutorials/source/index.rst build_and_deploy.sh commit 6418732d61dce9527e85a7a66837bbcac8f72741 Author: Lucas Esclapez Date: Thu Jun 20 13:31:57 2019 -0700 Missing \n from previous commit ... Tools/C_util/Convergence/DiffSameDomainRefined.cpp commit f47d2e8aaa1583df10939f5cb6792ebd1d085763 Author: Lucas Esclapez Date: Thu Jun 20 13:20:40 2019 -0700 Clean the screen output of DiffSameDomainRefined. Tools/C_util/Convergence/DiffSameDomainRefined.cpp commit d99ec1d40dd33051415cf4ddf2f6d6ce53891171 Author: Weiqun Zhang Date: Thu Jun 20 11:12:22 2019 -0700 add amrex_set_boxarray, distromap and geometry to amrex_core_module Src/F_Interfaces/AmrCore/AMReX_amrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 commit a8f723857f1c4a5ce512d8f6b5bffed258daf67d Author: Andrew Myers Date: Thu Jun 20 13:14:26 2019 -0400 add early exit for EnforcePeriodicGPU at the end of RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H commit 5f6d5a2094add04f67dd89324b16071c47c6960d Author: Andrew Myers Date: Wed Jun 19 20:43:41 2019 -0400 change some HostToHost to HostToDevice Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 861b62d6bc6ade2d383d947c15ce09f9ddff7e6e Author: Andrew Myers Date: Wed Jun 19 20:29:08 2019 -0400 some optimizations for FillNeighborsGPU Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 1aed364542d21de1ee19383ce719b5d06c16669f Merge: 92e572bc9 88a1a98e6 Author: Christopher Degrendele Date: Wed Jun 19 18:56:04 2019 -0400 Merge branch 'development' of git://github.com/AMReX-Codes/amrex into development commit 92e572bc92afabb0d3537b89dfbe5abdb8fc447f Author: Chris DeGrendele Date: Wed Jun 19 15:03:15 2019 -0700 added umac interpolate function Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 88a1a98e63663d6ac55ec727b327d421a694010a Author: Weiqun Zhang Date: Wed Jun 19 13:45:29 2019 -0700 documentation: minor fix Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/InputsLoadBalancing.rst commit d205c1c181d8637d86cdf86419d8619995af40e3 Author: Weiqun Zhang Date: Wed Jun 19 13:31:58 2019 -0700 documentation: kernel launch Docs/sphinx_documentation/source/GPU.rst commit 59654eecfd4bc059a2783d3a6a3db646a4d27e3f Author: Weiqun Zhang Date: Wed Jun 19 13:24:39 2019 -0700 documentation: kernel launch Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/GPU.rst commit ef67087a356d588f795d7ab2ab8873107b15539e Author: Weiqun Zhang Date: Wed Jun 19 10:14:27 2019 -0700 documentation: AsyncArray and Elixir Docs/sphinx_documentation/source/GPU.rst commit 306ce37d4906c95d0066778575340295d6a2e3f4 Author: Weiqun Zhang Date: Tue Jun 18 16:18:02 2019 -0700 AMREX_OMP_OFFLOAD -> AMREX_USE_OMP_OFFLOAD. Remove AsyncFab from documentation Docs/sphinx_documentation/source/GPU.rst Tools/GNUMake/Make.defs Tutorials/GPU/Launch/MyKernel_F.F90 Tutorials/GPU/Launch/MyKernel_F.H Tutorials/GPU/Launch/main.cpp commit 3cdaf64b5de6ca167feaff855de73b1a2c0c6946 Author: Weiqun Zhang Date: Tue Jun 18 14:59:26 2019 -0700 documentation: update boundary Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/GPU_Chapter.rst commit eb8a5ba561b1049faf3f4dbbd1133735d005d887 Author: Weiqun Zhang Date: Tue Jun 18 14:55:51 2019 -0700 documentation: update boundary Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/LinearSolvers.rst commit 1ae99cf53f9b2ab01e234bfa478aea8a29d08115 Author: Weiqun Zhang Date: Tue Jun 18 14:37:08 2019 -0700 documentation: update kernel section Docs/sphinx_documentation/source/Basics.rst commit 60bb4a7ed64896632b190c8044e3c1b67e998a73 Author: Weiqun Zhang Date: Tue Jun 18 14:03:10 2019 -0700 documentation: update tiling section to use C++ Docs/sphinx_documentation/source/Basics.rst commit e5a9d749729327c4ae3149cc149057ee2cee0181 Author: Weiqun Zhang Date: Tue Jun 18 13:23:12 2019 -0700 add Array4::nComp and update documentation for Dim3 and Array4 Docs/sphinx_documentation/source/Basics.rst Src/Base/AMReX_Array4.H commit c6288932b4d33d529d59fb439386cd4bb706fdc9 Author: Andrew Myers Date: Wed Jun 19 13:00:52 2019 -0700 add some more verbosity to the build_and_deploy script to make it easier to debug build_and_deploy.sh commit 1e0920f874402954c990cde03a1827ebbca3ba8f Author: Andrew Myers Date: Wed Jun 19 14:27:11 2019 -0400 need to use different names for these derived type components Tutorials/Particles/NeighborList/neighbor_list_3d.f90 commit 50a36155a99a177a8d5cdade34f7ee0ed77a754b Author: kngott Date: Tue Jun 18 16:36:02 2019 -0700 Update for hip changes. Tests/GPU/FusedLaunches/main.cpp commit af94da9e2588d6c34ed7a429e87e1428a85cd99b Merge: 3fa645863 e73f42267 Author: kngott Date: Tue Jun 18 16:33:09 2019 -0700 Merge branch 'development' into kngott/fused commit d10101cbdb0f705b3bb39607f9e6d6ce6d0f78e8 Author: Andrew Myers Date: Tue Jun 18 16:02:17 2019 -0700 remove unused variable Src/Particle/AMReX_TracerParticles.cpp commit d039e9fc6a68cf64d09c3b80b73b48b5f0f35b2a Author: Andrew Myers Date: Tue Jun 18 15:55:26 2019 -0700 use different approach in interp_2 Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 0c81bfae9c331a514ab321d8c8abe815694c0f5d Author: Andrew Myers Date: Tue Jun 18 15:34:13 2019 -0700 add a debugging print Src/Particle/AMReX_TracerParticles.cpp commit 5fdb20e3d5356d415a8992ce07273be8ad288283 Author: Christopher DeGrendele Date: Tue Jun 18 15:30:21 2019 -0700 s Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 1ab1f7a76299803aad6328ec040e964494aed8d9 Merge: 06c653763 e73f42267 Author: Michele Rosso Date: Tue Jun 18 14:45:38 2019 -0700 Merge branch 'development' into mr/cmake commit e73f42267581177cb06b5dadee62042b4eaca3b3 Author: Michele Rosso Date: Tue Jun 18 14:36:23 2019 -0700 CMake: turn off tutorials by default CMakeLists.txt Docs/sphinx_documentation/source/BuildingAMReX.rst commit d47206a83fb18242fadda5007faf03febdfd881c Merge: d154c0e38 0a082d68f Author: Michele Rosso Date: Tue Jun 18 14:34:51 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d154c0e38e5758759cea6a1357983235d0f8da9d Author: Michele Rosso Date: Tue Jun 18 14:34:45 2019 -0700 CMake: allow user to build and install plotfile tools. Fixes issue #501 CMakeLists.txt Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/Plotfile/CMakeLists.txt commit e7cec85f4f15508de495994d4d6342ec7874de0d Author: kngott Date: Tue Jun 18 13:55:24 2019 -0700 Add timer regions to GraphBoundary test. Tests/GPU/CudaGraphs/GraphBoundary/main.cpp commit 4aecb0b957cd96c6bddfc6b7279824f2f6c4b682 Merge: b3650bc8d 0a082d68f Author: kngott Date: Tue Jun 18 13:53:37 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit 0a082d68fa63dcb806dae48f3196fb6a2773e1eb Author: kngott Date: Tue Jun 18 13:53:03 2019 -0700 Fix include guards. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H commit 2120ce7370d7ffa96347e43468231613450f5b35 Author: Christopher DeGrendele Date: Tue Jun 18 13:34:07 2019 -0700 revert back to no idx Src/Particle/#AMReX_TracerParticles.cpp# Src/Particle/.#AMReX_TracerParticles.cpp Src/Particle/AMReX_TracerParticle_mod_K.H commit 8cd9b0ac08b400d934248362ddb6735e0d70b482 Author: Christopher DeGrendele Date: Tue Jun 18 13:25:52 2019 -0700 cpu Src/Particle/#AMReX_TracerParticles.cpp# Src/Particle/.#AMReX_TracerParticles.cpp Src/Particle/AMReX_TracerParticle_mod_K.H commit 652b217c6b38766c190ce2f43e2c3c8168417a2c Author: kngott Date: Tue Jun 18 13:18:50 2019 -0700 Turn off OpenMP if GPU. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 61263d27e271378c8376a47d8a8c2af24ecc2668 Author: kngott Date: Tue Jun 18 12:51:08 2019 -0700 Update BCs and Patch calls for GPUs. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/Kernels_3d.H Tutorials/GPU/Advection_AmrCore/Source/Make.package Tutorials/GPU/Advection_AmrCore/Source/bc_fill.H Tutorials/GPU/Advection_AmrCore/Source/bc_fill_nd.F90 commit 7219680e2c85e66dabde6ef050499dac4f0faecb Author: kngott Date: Mon Jun 17 20:31:25 2019 -0700 Add GPU tagging. Tutorials/GPU/Advection_AmrCore/Exec/Make.Adv Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/Kernels_3d.H Tutorials/GPU/Advection_AmrCore/Source/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_nd/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_nd/Tagging_nd.f90 Tutorials/GPU/Advection_AmrCore/Source/Tagging.H commit d25ebbb32e2384849fb5d25300801a9356f0a5af Author: Christopher DeGrendele Date: Tue Jun 18 11:39:33 2019 -0700 This now compiles on CPUs Src/Particle/AMReX_TracerParticle_mod_K.H commit 2a74eeb3af2dcb3edd4dc96a44a00a40f11487e0 Author: Christopher DeGrendele Date: Tue Jun 18 11:29:13 2019 -0700 function parameters Src/Particle/#AMReX_ParGDB.H# Src/Particle/#AMReX_ParticleContainerI.H# Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 4dabc73a8f9f9661f8dceeedcf8f54e5587a15e1 Author: Ann Almgren Date: Tue Jun 18 10:53:36 2019 -0700 Remove unused variable Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit da7a35f4fe55ee0f7765b38648931febf6ebfec0 Author: Andrew Myers Date: Tue Jun 18 10:51:48 2019 -0700 change function signature of the interp function Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 1a25bea2391d72af127ef197f35cf459b49fd4bb Merge: f24e91d02 744a382b7 Author: WeiqunZhang Date: Tue Jun 18 10:48:42 2019 -0700 Merge pull request #504 from KiranEiden/keiden/amrex Fixed typo in print_backtrace_info commit 744a382b71d6cc79d51ac930f554e27d2b07a42f Author: Kiran Eiden Date: Tue Jun 18 10:40:46 2019 -0700 Fixed typo in print_backtrace_info Src/Base/AMReX_BLBackTrace.cpp commit 6d02591922fbae44799a52cd9ab0cfc6082fa7ab Author: Christopher DeGrendele Date: Tue Jun 18 10:33:59 2019 -0700 push Src/Particle/AMReX_Particle.H Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit f24e91d024f4a2c0a38f5d94bc7d224c4d363873 Author: Weiqun Zhang Date: Tue Jun 18 10:03:19 2019 -0700 change names in tutorial documentation and update license information Docs/sphinx_documentation/source/index.rst Docs/sphinx_tutorials/source/conf.py Docs/sphinx_tutorials/source/index.rst build_and_deploy.sh commit 688e5a174def29dfe0c02591bc569a5418309b33 Author: Weiqun Zhang Date: Tue Jun 18 09:16:38 2019 -0700 point to parse_bt.py in backtrace message Src/Base/AMReX_BLBackTrace.cpp Tools/Backtrace/parse_bt.py commit 716f890582f7bfc9a8aa424dac5555ce2a2741ec Merge: db2feda78 602bbf275 Author: WeiqunZhang Date: Tue Jun 18 08:48:46 2019 -0700 Merge pull request #503 from AMReX-Codes/mz increase precision of output commit 602bbf275a65ec29823dc23e1f45807b9343c1a9 Author: Michael Zingale Date: Tue Jun 18 11:38:51 2019 -0400 increase precision of output so we can use the results for mapping for problem inits to roundoff Tools/Plotfile/fextract.cpp commit 3ad6e7b4ccfedbfc3f3af215b8f927e732b2c1af Author: Christopher DeGrendele Date: Tue Jun 18 08:04:46 2019 -0700 testing Src/Particle/AMReX_TracerParticle_mod_K.H commit db2feda78066cff7e1617456a0e0b937306fb7cd Author: Weiqun Zhang Date: Mon Jun 17 20:43:27 2019 -0700 fix typecheck. It doesn't like __attribute__ Src/Base/AMReX_Extension.H Tools/GNUMake/Make.rules commit e1f523ae0d73d1c4965f7d20c8e7180eeb9603ec Merge: f41ba29a0 858fd5f5e Author: Andrew Myers Date: Mon Jun 17 20:21:21 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f41ba29a071f96f42e3405b14536def374b48731 Author: Andrew Myers Date: Mon Jun 17 20:21:02 2019 -0700 a better check for OpenMP < 3.1 Src/Particle/AMReX_Particle.H commit 858fd5f5eeaa81ebcce228c7191ab14bd6385e90 Merge: 7d3ba63ff 9de40b06b Author: Ann Almgren Date: Mon Jun 17 20:14:35 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 7d3ba63ffaa14087233bc05abd68d1ea8d1d7ebb Author: Ann Almgren Date: Mon Jun 17 20:11:07 2019 -0700 Need to test on apz(i,j,k+1) not apz(i,j,k) when testing the hi-side terms Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit b3650bc8d8258788ddbbd299f1f8d3d5415b21c6 Author: kngott Date: Mon Jun 17 18:04:30 2019 -0700 Fix header. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H commit 9de40b06b34bb1f86f208b66c21e6cb4222a6cb3 Author: Weiqun Zhang Date: Mon Jun 17 16:13:48 2019 -0700 fix omp race condition Src/Base/AMReX_BoxArray.cpp commit 15d3e78cb5aaf4dcd690a7b4be5e777529eda011 Author: Christopher DeGrendele Date: Mon Jun 17 15:06:06 2019 -0700 Trial 2 Src/Base/#AMReX_FArrayBox.H# Src/Base/#AMReX_FArrayBox.cpp# Src/Particle/#AMReX_ParGDB.H# Src/Particle/#AMReX_TracerParticles.cpp# Src/Particle/AMReX_Particle.H Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 283f26ae86e21aba1670813e5212c242d4a52967 Merge: 9dabc92e3 7fa5ef311 Author: Weiqun Zhang Date: Mon Jun 17 09:21:23 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9dabc92e32c8011a66cd4921fc16f835707a28a5 Author: Weiqun Zhang Date: Sun Jun 16 18:22:28 2019 -0700 add MacProjector::setBottomVerbose function Src/LinearSolvers/MLMG/AMReX_MacProjector.H commit 7fa5ef311e31efb7ded43f1d600f4919ef15888f Merge: 3fbd2a972 9a566efe6 Author: Andrew Myers Date: Sun Jun 16 17:31:31 2019 -0700 Merge branch 'development' into sum_neighbors commit 9a566efe6b4f761aff6ed35b9e450c4ccb9bc3be Author: Weiqun Zhang Date: Sat Jun 15 17:13:26 2019 -0700 make sure it works with OMP < 3.1 Src/Base/AMReX_MultiFab.cpp commit 3fbd2a972dd3608779ddb5b972df9d0e107f443d Author: Andrew Myers Date: Sat Jun 15 16:31:48 2019 -0700 add test integer comp to neighbor list tutorial Tutorials/Particles/NeighborList/NeighborListParticleContainer.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborList/inputs Tutorials/Particles/NeighborList/main.cpp Tutorials/Particles/NeighborList/neighbor_list_2d.f90 Tutorials/Particles/NeighborList/neighbor_list_3d.f90 commit a2613e5d2b62d4023b5a4ad05fe70c8ea7ae5a4b Author: Andrew Myers Date: Sat Jun 15 16:31:24 2019 -0700 add sumNeighbors for int comps too Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleContainerI.H commit db6e14d9c1ebae13a931259b76b29ad1233460d9 Merge: 16cb78b09 0bd6af517 Author: Weiqun Zhang Date: Sat Jun 15 16:25:12 2019 -0700 Merge branch 'hip' into development commit 42095c8e0ddcd3fc783ed4cd7b25c33e5f5f9760 Author: Andrew Myers Date: Sat Jun 15 16:16:47 2019 -0700 more descriptive variable name Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit 45df399e736b985fd711731305d29c1e4f985d2b Author: Andrew Myers Date: Sat Jun 15 16:15:00 2019 -0700 fix bug in sumNeighbors Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit 99f3559ac1a319b77b3591752ac5f30490972fa7 Author: Andrew Myers Date: Sat Jun 15 15:29:17 2019 -0700 unpack the communicated data Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_ParticleContainerI.H commit 59e310ef76bb28e3db6411858954ff476402c7aa Author: Andrew Myers Date: Sat Jun 15 15:28:46 2019 -0700 ignore this unused Src/Base/AMReX_FabArrayCommI.H commit 34c41ca8861090ba82d0e8598bc28da1e2a5d425 Author: Andrew Myers Date: Sat Jun 15 14:38:21 2019 -0700 minor formatting changes Src/Particle/AMReX_NeighborParticles.H commit 68348d7d93455dbcbb0f996cefebdf8e9a05157f Author: Andrew Myers Date: Sat Jun 15 14:35:55 2019 -0700 implementing MPI portion of sumNeighbors Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_ParticleContainerI.H commit 16cb78b098a6e9a38c8994504912240ed40b24c4 Merge: c93a3a8ba 7bb9bbfba Author: Weiqun Zhang Date: Sat Jun 15 14:12:20 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit aad7385eafbba4a41dbedb17f148a7826c17754f Author: Andrew Myers Date: Sat Jun 15 13:59:13 2019 -0700 implement local form of sumNeighbors Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit 7331ac04b35054055c74e1cf9b7bda26a64e6b1e Author: Andrew Myers Date: Sat Jun 15 13:32:10 2019 -0700 adding a level to the InverseCopyTag Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H commit 0f0c9b77093987e44b01b50e23d923f69508391f Author: Andrew Myers Date: Sat Jun 15 13:24:08 2019 -0700 starting to work on implementing the sumNeighbors MPI exchange Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H commit 0bd6af5177cd8bcdf92ab44397e09bb17f4aaeb0 Author: Weiqun Zhang Date: Sat Jun 15 13:04:55 2019 -0700 fix typo in interp 2d Src/AmrCore/AMReX_Interp_2D_C.H commit 9653057601ca68387e085ef28f8982764f3be2ab Merge: 27bb934de 0a10f69dc Author: Weiqun Zhang Date: Sat Jun 15 12:50:41 2019 -0700 Merge branch 'hip' of github.com:AMReX-Codes/amrex into hip commit 27bb934dec0edbe967a351c1c05ea7345f325370 Author: Weiqun Zhang Date: Sat Jun 15 11:49:30 2019 -0700 add lbound, ubound and length for Array4. remove fabPtr and AsyncFab from Interpolater Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_Interpolater.cpp Src/Base/AMReX_Array4.H commit 7bb9bbfbae415ef49a3ee1e67fb2c3fded36fca5 Author: Andrew Myers Date: Sat Jun 15 00:16:00 2019 -0400 fix off-by-one error Src/Particle/AMReX_ParticleContainerI.H commit 0a10f69dca40eb5965aadf82099267c73e3bc8d4 Author: atmyers Date: Fri Jun 14 20:26:52 2019 -0700 getting rid of some fabPtr in the particle classes Src/Particle/AMReX_Functors.H Src/Particle/AMReX_ParticleContainerI.H commit f48e6180ac6c31d5b6c72955b45db3e84ca2ebe7 Author: Weiqun Zhang Date: Fri Jun 14 18:43:57 2019 -0700 use Array4 in neighbor particles Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit e1c730810cd22d72db3114866e810fc90f1a330e Author: Weiqun Zhang Date: Fri Jun 14 18:43:06 2019 -0700 fix commit e65d50e9ba7d7dc Src/Amr/AMReX_AmrLevel.cpp commit 424ff4a03cc147073df36450aa935081a6deeb67 Author: Weiqun Zhang Date: Fri Jun 14 18:16:51 2019 -0700 put Array4 and Dim3 into their own files so that we can have Array4::operator() taking IntVect Src/Base/AMReX_Array.H Src/Base/AMReX_Array4.H Src/Base/AMReX_Box.H Src/Base/AMReX_Dim3.H Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_IntVect.H Src/Base/CMakeLists.txt Src/Base/Make.package commit dcb16862a1581cd854274aca11a212d27a09671e Author: Andrew Myers Date: Fri Jun 14 17:25:54 2019 -0700 fix compilation error in sumNeighbors Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit 18e75acb2b3bf6c8bfa0c1b31e2e7448ff91271d Author: Andrew Myers Date: Fri Jun 14 17:23:57 2019 -0700 fix comments Src/Particle/AMReX_NeighborParticles.H commit 9e92d38a747884db9a3078c45dc83bb25f542783 Author: Andrew Myers Date: Fri Jun 14 17:22:55 2019 -0700 output operator for InverseCopyTag Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit 5fbf9878ca02a7dd07b00525217ff58ad1b1392c Merge: eb75c4f7d c36b0c256 Author: Andrew Myers Date: Fri Jun 14 17:16:33 2019 -0700 Merge branch 'development' into sum_neighbors commit eb75c4f7d25c2d15544a3c0d0c60cef5b9ce9ece Author: Andrew Myers Date: Fri Jun 14 17:14:55 2019 -0700 use getter for enableInverse Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H commit eb2ce33a08e866cad4ac572da187eed9284f6339 Author: Andrew Myers Date: Fri Jun 14 17:12:33 2019 -0700 make enable_inverse static Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 3c6223be59ee9dc9792781df07f9494df7fff870 Author: Andrew Myers Date: Fri Jun 14 17:11:31 2019 -0700 getters / setters for enable inverse Src/Particle/AMReX_NeighborParticles.H commit f88bab0b65f576d3ffce2f127f619087233917c7 Author: Andrew Myers Date: Fri Jun 14 17:10:04 2019 -0700 abort if calling sumNeighbors without enable_inverse Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit 9f004f2e914e9422a40c311735b7752682ee5bea Author: Andrew Myers Date: Fri Jun 14 17:08:51 2019 -0700 remove Redistribute-based implementation of sumNeighbors Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit 5f6542a0af31318cc00b4b06b59324e649632054 Author: Andrew Myers Date: Fri Jun 14 17:08:13 2019 -0700 wrap the inverse neighbor particle stuff in a boolean flag Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H commit 14aa57859a78cdd8c557d419683d493b45de8356 Author: Christopher DeGrendele Date: Fri Jun 14 16:04:55 2019 -0700 not yet working gpu code Src/Particle/#AMReX_ParticleContainerI.H# Src/Particle/#AMReX_TracerParticles.cpp# Src/Particle/AMReX_Particle.H Src/Particle/AMReX_Particle_mod_K.H Src/Particle/AMReX_TracerParticle_mod_K.H Src/Particle/AMReX_TracerParticles.cpp commit 935f7fad0bf714ae54535d42f2d93411128d4cad Merge: e65d50e9b c93a3a8ba Author: Weiqun Zhang Date: Fri Jun 14 16:04:44 2019 -0700 Merge branch 'development' into hip commit e65d50e9ba7d7dc8810bbf1b508cd787a95472a2 Author: Weiqun Zhang Date: Fri Jun 14 16:03:59 2019 -0700 update Amr/ to avoid fabPtr Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AuxBoundaryData.H Src/Amr/AMReX_Extrapolater.cpp Src/AmrCore/AMReX_AmrParticles.H Src/AmrCore/AMReX_FillPatchUtil.cpp commit 38b19b8c8c19de8d12c0cc6b7a01f4d52c39312f Author: Andrew Myers Date: Fri Jun 14 12:53:05 2019 -0700 keep track of information needed to reverse the neighbor particle communication. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesI.H commit 3860655049c2d302ac343d0820b286b362e83880 Author: Andrew Myers Date: Fri Jun 14 11:10:38 2019 -0700 calling sumNeighbors in the main evolve loop Tutorials/Particles/NeighborList/main.cpp commit b6a775d7f36e90714a685c414f1d4898810e719c Author: Andrew Myers Date: Fri Jun 14 11:10:14 2019 -0700 add a test comp to the neighbor particle tutorial Tutorials/Particles/NeighborList/NeighborListParticleContainer.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborList/neighbor_list_2d.f90 Tutorials/Particles/NeighborList/neighbor_list_3d.f90 commit 06d69d6cf104e0f80574f20e19c99eda4685e3b8 Author: Andrew Myers Date: Fri Jun 14 11:08:57 2019 -0700 add Redistribute-based implementation of sumNeighbors Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit 7e4b3f862b6d90786abcf10538dc80ea7f2c1006 Author: Andrew Myers Date: Fri Jun 14 11:08:28 2019 -0700 add dispatch for CPU implementation of sumNeighbors Src/Particle/AMReX_NeighborParticlesI.H commit 42161e3da8a7066f69167784feab72663d40f850 Author: Andrew Myers Date: Fri Jun 14 11:07:48 2019 -0700 initialize a tmp PC from a known ParGDB Src/Particle/AMReX_Particles.H commit 0e7a6e58d836f936f9d453a4bd1f1a83007fcbfa Author: Andrew Myers Date: Fri Jun 14 11:07:18 2019 -0700 adding a sum neighbors method for the NeighborPC Src/Particle/AMReX_NeighborParticles.H commit c36b0c256a61cce36044a7e3318b4d62c031689e Author: Jean M. Sexton Date: Fri Jun 14 10:06:10 2019 -0700 Add GPU debugging section, make ReduceSum include function prototype in documentation Docs/sphinx_documentation/source/GPU.rst commit c93a3a8ba8ae6cfc712229c09f22ca78e8f25e3a Author: Weiqun Zhang Date: Fri Jun 14 09:31:53 2019 -0700 MLMG: fab Ptr to Array4 Src/Boundary/AMReX_MultiMask.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 36f1961fdd7ba705f31b6a07fb6a1143d2a87765 Author: Ann Almgren Date: Fri Jun 14 09:32:48 2019 -0700 Remove mfix-specific text Docs/sphinx_documentation/source/InputsProblemDefinition.rst commit 095b041a6dbbbd9afe903d17c99b154d93ea4aca Author: Weiqun Zhang Date: Fri Jun 14 09:23:28 2019 -0700 Mask: add constructors taking Array4 Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_MultiMask.cpp Src/Boundary/AMReX_YAFluxRegister.cpp commit d63d15c02a9cb3c4d6886248ec4660384881242b Author: Ann Almgren Date: Fri Jun 14 09:21:18 2019 -0700 Add default load balancing strategy Docs/sphinx_documentation/source/LoadBalancing.rst commit 89c204966d9bc2892dec73c9baad8a2aebb055f9 Merge: e8d59e161 be240fdd6 Author: Weiqun Zhang Date: Fri Jun 14 08:56:23 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit be240fdd6a361c2b56e533d0e03808d7666a1e21 Author: Jean M. Sexton Date: Thu Jun 13 16:03:02 2019 -0700 Add Run-time Inputs chapter based off amrex-specific portions of MFIX-Exa documentation Docs/sphinx_documentation/source/InputsCheckpoint.rst Docs/sphinx_documentation/source/InputsLoadBalancing.rst Docs/sphinx_documentation/source/InputsPlotFiles.rst Docs/sphinx_documentation/source/InputsProblemDefinition.rst Docs/sphinx_documentation/source/InputsTimeStepping.rst Docs/sphinx_documentation/source/Inputs_Chapter.rst Docs/sphinx_documentation/source/index.rst commit 0ad961e25d298a4882479bc0c6eb016dd06433e7 Author: Andrew Myers Date: Thu Jun 13 15:11:48 2019 -0700 remove outdated limitations from the GPU section Docs/sphinx_documentation/source/GPU.rst commit a2723446345f605246b5874c1b3c78d51302e1d8 Author: Andrew Myers Date: Thu Jun 13 15:06:59 2019 -0700 fix a formatting problem Docs/sphinx_documentation/source/Particle.rst commit 40ab2b73c7c0bcb464944578d45f71e2ccf38b35 Author: Andrew Myers Date: Thu Jun 13 15:03:15 2019 -0700 note the prefix for the amrex.use_gpu_aware_mpi flag Docs/sphinx_documentation/source/GPU.rst commit fb3767472c13b28df64df27496d11d83bfa12a3f Author: Andrew Myers Date: Thu Jun 13 14:47:35 2019 -0700 add some documentation about inputs parameters relevant for the behavior of amrex particles, including IO and GPU performance Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/Particle.rst commit e8d59e161f938723fe5c329071c1193acffb29e5 Merge: 276e61060 e4de829bc Author: Weiqun Zhang Date: Thu Jun 13 14:30:55 2019 -0700 Merge branch 'hip' into development commit e4de829bcc8b7225b13bd9bdd7673698bd4040f8 Author: Weiqun Zhang Date: Thu Jun 13 14:02:13 2019 -0700 PhysBCFunct: pass host fab to m_f Src/Base/AMReX_PhysBCFunct.H commit 276e6106053e3b27e205e2b6bee786cf05cf72f7 Merge: 30861bb61 c09dbcd79 Author: Andrew Myers Date: Thu Jun 13 13:43:28 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b5929471713f2f478402ff83b42e437f160a0976 Author: Weiqun Zhang Date: Thu Jun 13 13:39:41 2019 -0700 update amrex_avg_down* Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/runtime_common/AsyncMultiFabUtil.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_Perilla.cpp Src/Base/AMReX_MultiFabUtil_nd_C.H Src/EB/AMReX_EBMultiFabUtil.cpp Tests/Slice/main.cpp Tests/SliceWithInterp/main.cpp commit 6a2568b9135d3b2f97cfd83a09749a9cafd0bb7b Author: Weiqun Zhang Date: Thu Jun 13 13:27:19 2019 -0700 add noexcept Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_IArrayBox.H Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBCellFlag.cpp commit 30861bb610677ed4197afef12c32d441c232e044 Author: Andrew Myers Date: Thu Jun 13 12:55:32 2019 -0700 remove these now unimplemented functions - they are in the Gpu:: namespace directly now Src/Base/AMReX_GpuDevice.H commit c09dbcd79ece36a071e03939a0e8df69db8c23e4 Author: Andrew Myers Date: Thu Jun 13 12:55:21 2019 -0700 use explicit device-to-host copies here rather than relying on page faults Src/Particle/AMReX_ParticleContainerI.H commit 06c65376302e0688634e96f9766e2ce2a2492678 Author: Michele Rosso Date: Thu Jun 13 12:25:12 2019 -0700 CMake: update documentation. Docs/sphinx_documentation/source/GPU.rst commit cede2d99bb35dc79acaa21e4c85b63b3d7e2de18 Author: Michele Rosso Date: Thu Jun 13 12:14:01 2019 -0700 CMake: improve CUDA support. * Set C++ and CUDA required standard via CMake compile features * Force CUDA setup in application codes if ENABLE_CUDA=on Src/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_SetupCUDA.cmake Tutorials/GPU/NeighborList/CMakeLists.txt commit e3844d5cbcbe1fa2af2e890ba17f19de7c3ba576 Author: Weiqun Zhang Date: Thu Jun 13 11:33:54 2019 -0700 fab to array4 in a number of MultiFabUtil functions Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/runtime_common/AsyncMultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/Base/AMReX_MultiFabUtil_Perilla.cpp Src/EB/AMReX_EBMultiFabUtil.cpp Src/F_Interfaces/Octree/AMReX_octree_fi.cpp commit 9ad9c0190fcf96b1016000aeddafdb83f5f54dd0 Author: Weiqun Zhang Date: Thu Jun 13 09:38:53 2019 -0700 remove fabPtr from avg_cc_to_fc Src/Base/AMReX_BaseFab.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/Base/AMReX_Utility.H Tutorials/EB/Poisson/Poisson.cpp commit d3a3799cfaa57d5766a0b3e7f945f67e73ec8bb9 Merge: 06f1be5f7 bfad0e578 Author: Weiqun Zhang Date: Wed Jun 12 17:35:26 2019 -0700 Merge branch 'development' into mlmg-2d commit bfad0e578162b2bd0ce2f0dc2cf13cbdf81321e5 Author: Weiqun Zhang Date: Wed Jun 12 17:22:43 2019 -0700 Add IndexType to FArrayBox contructed from Array4 to avoid assertion failure Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_IArrayBox.H commit 79634850366c4a29c03400a9a553c458ac843c4b Merge: 67c7673d3 116468df3 Author: Michele Rosso Date: Wed Jun 12 16:01:53 2019 -0700 Merge branch 'development' into mr/cmake commit 06f1be5f7db8bc339d36912d32a16a840852b164 Merge: 0559612bb a313de181 Author: Weiqun Zhang Date: Wed Jun 12 14:17:46 2019 -0700 Merge branch 'development' into mlmg-2d commit 0559612bb188f27557b9cd310df649ace51cb449 Author: Weiqun Zhang Date: Tue Jun 11 21:15:37 2019 -0700 reimplement the treatment of metric terms in MLMG Src/LinearSolvers/MLMG/AMReX_MLALap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLALap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H commit 116468df3b5b21c64ce8ba7d527796e41d8b08bb Author: Michele Rosso Date: Wed Jun 12 11:08:21 2019 -0700 CMake: fix var_NOT-FOUND bug Tools/CMake/AMReX_Config.cmake commit 9f93ce821ea8669ad9091800c26bf062dcd1be7b Merge: d1744c100 a313de181 Author: Kevin Gott Date: Wed Jun 12 13:30:37 2019 -0400 Merge branch 'development' into kngott/cudaGraphs commit a313de1811fe529baef4dc4b9cd4ad263659e431 Author: Weiqun Zhang Date: Tue Jun 11 20:37:53 2019 -0700 fix enable_if Src/Particle/AMReX_Particles.H commit f30117a4df6bed1a8fd316c468833300927727d3 Merge: ea1623d05 4d575dba5 Author: Michele Rosso Date: Tue Jun 11 18:55:08 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit ea1623d0526cffddf6d2525c54fc7345e6719f35 Author: Michele Rosso Date: Tue Jun 11 18:54:22 2019 -0700 CMake: add nvToolsExt library to link line Tools/CMake/AMReX_Config.cmake commit 396d0423776d9d4d3e7850f559569d84a6305b8f Author: Michele Rosso Date: Tue Jun 11 18:41:37 2019 -0700 CMake: fix CUDA tutorials Tutorials/GPU/Launch/CMakeLists.txt Tutorials/GPU/NeighborList/CMakeLists.txt commit 2701b11260f0fdce20732463f080a626e48b2a8e Author: Michele Rosso Date: Tue Jun 11 18:30:05 2019 -0700 CMake: fix incorrect required Fortran flag for PGI compiler Tools/CMake/AMReXFlagsTargets.cmake commit 4d575dba55f626efcdbe44c43533308abb524775 Author: Andrew Myers Date: Tue Jun 11 20:57:08 2019 -0400 std::enable_if_t is C++14, using another approach Src/Particle/AMReX_Particles.H commit d1744c100328b34e3e123a2d1ad4f11f77d0ca4c Merge: a59b7d6f9 a7c163811 Author: Kevin Gott Date: Tue Jun 11 20:27:01 2019 -0400 Merge branch 'development' into kngott/cudaGraphs commit a59b7d6f900737e63f9353311e4b9dd1f0adee3c Author: kngott Date: Tue Jun 11 17:22:41 2019 -0700 Strictly define regions in test. Tests/GPU/CudaGraphs/GraphBoundary/main.cpp commit 947b28c4c3e148dcc8afec5a411d5bda8623ec38 Author: kngott Date: Tue Jun 11 17:09:14 2019 -0700 Move copyFromBuffer graph creation to try to get some additional overlap with MPI. Src/Base/AMReX_FabArrayCommI.H commit a7c163811d817047ad86361a3275ffe9e854f18d Author: Michele Rosso Date: Tue Jun 11 16:56:28 2019 -0700 CMake: enforce C++14 standard Tools/CMake/AMReX_Config.cmake commit 4fe57491f6b953bb132f54cc503c3e7440359f30 Author: kngott Date: Tue Jun 11 16:19:21 2019 -0700 Change FillBoundary graphs to include memcpy. Src/Base/AMReX_FabArrayCommI.H commit ac1334c7f23fabaf28f9eca92a6ae27cfcfccf4e Author: kngott Date: Tue Jun 11 15:51:54 2019 -0700 Add speedup calc to FillBoundary test. Tests/GPU/CudaGraphs/GraphBoundary/main.cpp commit 777cdb65de837b2f94aba8bc56787e6d73f01bde Author: kngott Date: Tue Jun 11 14:45:26 2019 -0700 Add check to memcpy if not added to the graph. Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp commit 67c7673d30d6d28893cbbca3d2a3f2e6d86dcdab Author: Michele Rosso Date: Tue Jun 11 15:03:33 2019 -0700 CMake: document latest changes Docs/sphinx_documentation/source/BuildingAMReX.rst Docs/sphinx_documentation/source/GPU.rst commit 08324925b4a9034f6c377b98cbd1db56029cd7f1 Author: Michele Rosso Date: Tue Jun 11 15:03:11 2019 -0700 CMake: use a component-centric approch in exported config file Tools/CMake/AMReXConfig.cmake.in commit d4cbbf2e5ae1485dd522542066adec10eea0344c Merge: 72c184330 ebe31dfe5 Author: WeiqunZhang Date: Tue Jun 11 13:41:31 2019 -0700 Merge pull request #497 from mattbement/master add an option to enable PIC to the configuration script commit 72c184330a56835570e1281793374e7ee371e6ba Merge: 491c6eb8f 9ff57aa24 Author: Andrew Myers Date: Tue Jun 11 13:29:17 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 491c6eb8f5b7ae28efd05c90d8472aaccdac0785 Author: Andrew Myers Date: Tue Jun 11 13:29:02 2019 -0700 prevent implicit conversion of 'const char *' to 'bool' from selecting this function overload Src/Particle/AMReX_Particles.H commit 9ff57aa24a8b540f129b9107d7d0f14d4ce3affa Merge: 18617a6ac 707312090 Author: Weiqun Zhang Date: Tue Jun 11 12:51:13 2019 -0700 Merge branch 'hip' into development commit 18617a6acb7f913840f582fd2a42cd59d536abca Merge: 34de71cd2 0868ed9ad Author: Weiqun Zhang Date: Tue Jun 11 12:51:01 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d04150f21fca0027a7784eaf0a6b300d44e7a265 Author: kngott Date: Tue Jun 11 12:23:39 2019 -0700 De-sync FB local copy graph. Src/Base/AMReX_FabArrayCommI.H commit 707312090fd21574de84030ef9001338ab97adef Author: Weiqun Zhang Date: Tue Jun 11 12:22:51 2019 -0700 fix make file for linking with mpif90 Tools/GNUMake/sites/Make.unknown commit ff491fc5e193e227b51d7362d2eb8c05bb6cbb62 Author: kngott Date: Tue Jun 11 12:15:46 2019 -0700 Change CudaGraph execute to use Gpu::Device function. Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp commit 9c6a94af608c4e9e363bb13838affedef79a56b4 Author: Weiqun Zhang Date: Tue Jun 11 11:20:59 2019 -0700 use omp atomic capture instead of critical Src/Base/AMReX_MultiFab.cpp commit 8cc3cbb82f13d130b541fc44f3bdb12d8776967d Author: Weiqun Zhang Date: Tue Jun 11 10:15:34 2019 -0700 MultiFabUtil: use Array4 Src/Base/AMReX_Geometry.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/EB/AMReX_EBMultiFabUtil.cpp commit f46a1b5c134507f53ab31a7f18a76ca16c04283d Merge: 6111a0a8a 0868ed9ad Author: Michele Rosso Date: Tue Jun 11 10:41:37 2019 -0700 Merge branch 'development' into mr/cmake commit c00947700470d8c29d4505bd43adcd181ef7b8ca Merge: ca299d34d 0868ed9ad Author: kngott Date: Tue Jun 11 10:32:13 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit f39adb9c6a8561a0725118431c602466306822d0 Author: Weiqun Zhang Date: Tue Jun 11 10:10:23 2019 -0700 fix for non-MPI Src/Base/AMReX_ccse-mpi.H commit 4f45439ab309a4753b2c89be939664e5bfedae37 Author: Weiqun Zhang Date: Tue Jun 11 09:45:18 2019 -0700 add Gpu::Atomic::Exch and reimplement MultiFab::minIndex and maxIndex Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_MultiFab.cpp commit ca299d34dbd3abba06bc0810a5d53c7aaf35c349 Author: kngott Date: Tue Jun 11 01:13:30 2019 -0700 Implement and test graph building with cudaEvents. Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Tests/GPU/CudaGraphs/GraphWithMemcpy/main.cpp commit d7eb6ad967f134ca842699d0b06e83abcd288963 Author: kngott Date: Tue Jun 11 01:09:36 2019 -0700 Properly order graphs to hide FB build. Tests/GPU/CudaGraphs/GraphBoundary/main.cpp commit 90c759ae4bf95bb9dfa0e3891498ccd9ebe20073 Author: kngott Date: Tue Jun 11 01:05:41 2019 -0700 Add additional graph building options to setVal graph test. Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp commit 0f86763ed62548c1cd5b78e58f36a947450e6abe Author: kngott Date: Tue Jun 11 01:02:22 2019 -0700 Turn off synchs in all graph creation loops in FillBoundary. Src/Base/AMReX_FabArrayCommI.H commit 6fa34588ce96ee508b364646d2259a5f266b4727 Author: kngott Date: Tue Jun 11 00:51:22 2019 -0700 Add StreamItInfo and option to turn off syncing. Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_GpuUtility.cpp commit eba83f629293ffaf6f92615c24564a72d05e5c94 Author: Weiqun Zhang Date: Mon Jun 10 18:37:37 2019 -0700 reimplement minIndex Src/Base/AMReX_MultiFab.cpp commit 0868ed9ad70dc73c771a68751e74a7a2a1f8e642 Author: Michele Rosso Date: Mon Jun 10 16:32:22 2019 -0700 Modify macro for consistency Src/Base/AMReX_Gpu.H commit ebe31dfe56294b7230f8082e1b72b55340af1d8a Author: Matt Bement Date: Mon Jun 10 14:49:22 2019 -0600 add an option to enable position independent code to the configuration script Tools/libamrex/configure.py commit b6d19b9f78f218c7fa721b4f136575b3d98c6895 Author: kngott Date: Mon Jun 10 13:38:54 2019 -0700 Add optional flag to make graphExecution asynchronous. Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp commit 34de71cd2c6a111c1c96d544ec3d016718283745 Author: Weiqun Zhang Date: Mon Jun 10 13:23:54 2019 -0700 add MultiFab::norminf Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 7d8e3a613d09c5ee78f0f39af1485f6fb3de1c3f Author: Weiqun Zhang Date: Mon Jun 10 13:22:43 2019 -0700 Box constructor for extracting Box from Array4 Src/Base/AMReX_Box.H commit 16190c8be8896c6699d78b1cb0b74516e74cde44 Author: Weiqun Zhang Date: Mon Jun 10 13:20:31 2019 -0700 remove const so that comiler generates operator= for BndryFuncArray Src/Base/AMReX_PhysBCFunct.H commit bb0a4c0ed968079acade0a85538f831f6a24df8d Author: Weiqun Zhang Date: Mon Jun 10 13:09:13 2019 -0700 fix DEBUG build Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_IArrayBox.H commit 43667c07b4278ad9dcd510d0cba8ec8b3dd30cc3 Author: Weiqun Zhang Date: Mon Jun 10 10:55:18 2019 -0700 add comment on initVal Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 449387477e3ac16d0aa16ddc3883bdf70ee3b858 Merge: 847991122 5cec696cf Author: kngott Date: Sun Jun 9 23:25:52 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit 430caf1fd1064ac8b8f358b677b130bd118d28c6 Author: Weiqun Zhang Date: Sun Jun 9 18:50:34 2019 -0700 update FArrayBox Src/Base/AMReX_FArrayBox.H commit 47438fcd2204d62e316f41284bd258f07bcd541d Author: Weiqun Zhang Date: Sun Jun 9 18:18:40 2019 -0700 update reduce for amd device Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuReduce.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 10fc78071639f8dd60770f8cc4ac27353e182b47 Author: Weiqun Zhang Date: Sun Jun 9 17:20:25 2019 -0700 avoid fabPtr in FabArrayUtility Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayUtility.H commit d190e37599f68daee6df5196cf6af54d2e0b2c10 Author: Weiqun Zhang Date: Sun Jun 9 15:57:05 2019 -0700 update Tutorials Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/EBCNS/Source/CNS_advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc.cpp Tutorials/GPU/Launch/MyKernel_F.F90 Tutorials/GPU/Launch/MyKernel_F.H Tutorials/GPU/Launch/main.cpp commit 9963851ab2ee40df0b891f4834240b2e8d88fb71 Author: Weiqun Zhang Date: Sun Jun 9 10:48:16 2019 -0700 add a new field int ncomp to Array4. add new constructor to fabs so that we can make fab from Array4 on device Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_IArrayBox.H Tutorials/GPU/Launch/main.cpp commit 5cec696cf475ba14007add4e721a21455a0fa2e5 Author: Weiqun Zhang Date: Sat Jun 8 21:04:56 2019 -0700 remove AsyncFab from StateData::FillBoundary Src/Amr/AMReX_StateData.cpp commit 2e78b664cfba9a3827fd44039e88cc10d724bc80 Author: Weiqun Zhang Date: Sat Jun 8 18:38:12 2019 -0700 update boundary fill functions to take Array4 instead of FArrayBox Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_FilCC_1D_C.H Src/Base/AMReX_FilCC_2D_C.H Src/Base/AMReX_FilCC_3D_C.H Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Tutorials/GPU/CNS/Source/CNS_bcfill.cpp Tutorials/GPU/EBCNS/Source/CNS_bcfill.cpp commit 7f501abca13d64d7234afc49741093230ff2f74a Merge: 2078ed142 acdde251f Author: Weiqun Zhang Date: Sat Jun 8 10:47:17 2019 -0700 Merge branch 'development' into hip commit acdde251ffa26fba5f6617dd182f8767595e48c7 Author: Weiqun Zhang Date: Sat Jun 8 10:46:42 2019 -0700 Fix the Poisson solver issue with dirichlet EB in periodic domain. It was mistakenly treated as singlular. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Tutorials/EB/Poisson/main.cpp commit 2078ed14211e3eac1d1f5a1bb94aa3e0eb84bde6 Author: Weiqun Zhang Date: Sat Jun 8 10:23:04 2019 -0700 update FillDomainBoundary for gpu Src/Base/AMReX_BCUtil.H Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_PhysBCFunct.H commit 8eeab192b896136e04b3694d0b632051ad3ae594 Author: Weiqun Zhang Date: Fri Jun 7 23:10:13 2019 -0700 allow z-direction cylinder in 2d Src/EB/AMReX_EB2.cpp Src/EB/AMReX_EB2_IF_Cylinder.H Tutorials/EB/Poisson/main.cpp commit 0dcceec29462daba1cc1c9d29725b16130614012 Author: Weiqun Zhang Date: Fri Jun 7 17:51:20 2019 -0700 BL_BACKTRACING -> AMREX_BACKTRACING Docs/Notes/Readme.backtrace Src/Base/AMReX_BLBackTrace.H Src/Base/AMReX_BLBackTrace.cpp Tools/GNUMake/Make.defs commit ad62c8398d66bc197bb26797a8a86e081623960e Author: Weiqun Zhang Date: Fri Jun 7 17:44:40 2019 -0700 BL_TESTING -> AMREX_TESTING Tools/GNUMake/Make.defs Tutorials/EB/CNS/Source/CNS_io.cpp Tutorials/GPU/EBCNS/Source/CNS_io.cpp commit ecdfa7bf5b03b21959f76d5362dde078d66a380d Author: Weiqun Zhang Date: Fri Jun 7 17:39:33 2019 -0700 BL_TINY_PROFILING -> AMREX_TINY_PROFILING Src/Base/AMReX_BLProfiler.H Tools/GNUMake/Make.defs commit 18e2ff6ab84761535709b4831e648b134493bb9a Author: Weiqun Zhang Date: Fri Jun 7 17:35:30 2019 -0700 BL_MEM_PROFILING -> AMREX_MEM_PROFILING Src/Amr/AMReX_Amr.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/Base/AMReX.cpp Src/Base/AMReX_BArena.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_MultiFab.cpp Src/EB/AMReX_EB_LSCoreBase.cpp Tools/GNUMake/Make.defs Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/SENSEI/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 6ed9a575567cefc3b8e0735f44d86487ea2cd5ba Author: Weiqun Zhang Date: Fri Jun 7 17:25:44 2019 -0700 make BArena use malloc and free directly, which is supposed to be for CPU memory Src/Base/AMReX_BArena.H Src/Base/AMReX_BArena.cpp commit 1179d1271ee726965e5e23d8e49b512577daf323 Author: Weiqun Zhang Date: Fri Jun 7 16:01:25 2019 -0700 update __CUDA_ARCH__ Src/Base/AMReX.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Extension.H Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuQualifiers.H commit 5c940cddd2bfbc7fda93ae10956e354a6db35f61 Author: Weiqun Zhang Date: Fri Jun 7 15:46:00 2019 -0700 hip: update Arena Src/Base/AMReX_Arena.cpp commit 6111a0a8aa56afa112f11f5714feb2f32b5a7d59 Merge: 601768332 07ebe4c22 Author: Michele Rosso Date: Fri Jun 7 15:07:36 2019 -0700 Merge branch 'development' into mr/cmake commit 07ebe4c22e8adedc9942f3868d20ef0ff0a9cab0 Author: Michele Rosso Date: Fri Jun 7 15:07:12 2019 -0700 CMake: add option to enable pinned memory Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake commit 8f63b7aa56f098c4150480eb5394e851b1645c3a Author: Michele Rosso Date: Fri Jun 7 14:42:02 2019 -0700 Revert "add AMREX_USE_GPU if ENABLE_CUDA" This reverts commit c1e23297b1b784e4cf45a68c5e5716357116ce95. AMREX_USE_GPU was already passed to the compiler for CUDA builds. Tools/CMake/AMReX_Defines.cmake commit 3768e1067a6ad6e8e4c32f33868bef5dbc7b10ba Author: Weiqun Zhang Date: Fri Jun 7 14:35:19 2019 -0700 add -DAMREX_FAB_IS_MANAGED Src/Base/AMReX_FabAllocator.cpp Tools/GNUMake/Make.defs commit 47fff5511ae94fc31f06de4661dae7a840bfe845 Author: atmyers Date: Fri Jun 7 12:53:54 2019 -0700 change the order of these loops to be cache-friendly Src/Particle/AMReX_Particle_mod_K.H commit e0f4e5a2d9761b3128e75618bcaaf00cfa4b7f8b Author: Weiqun Zhang Date: Fri Jun 7 12:12:56 2019 -0700 No need to use the legacy hipThreadIdx_* etc. Src/Base/AMReX_CudaReduce.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuLaunchMacrosG.H Src/Base/AMReX_GpuRange.H commit 63abf6d2cbfb50b1c867c9e29068b6e97d32d29a Author: atmyers Date: Fri Jun 7 10:37:29 2019 -0700 std::min/max -> amrex::min/max Src/Particle/AMReX_Particle_mod_K.H commit f5105f3cce31c8b9a31101392c96f80a71c9a4ab Merge: 28651c9cd 001c37bf2 Author: Weiqun Zhang Date: Fri Jun 7 07:47:13 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 001c37bf2a6c88b1eb0708c04bda6c9959f8cf93 Author: Weiqun Zhang Date: Thu Jun 6 19:17:08 2019 -0700 fix 1d nodal Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 commit 28651c9cd023f6d6aa9f84fb50f087f9fb21a5d0 Merge: 8976ac2ae 44ae36978 Author: Weiqun Zhang Date: Thu Jun 6 19:05:16 2019 -0700 Merge branch 'development' into hip commit 44ae3697841ad9580491cff233ca7908cd93e2e9 Author: Weiqun Zhang Date: Thu Jun 6 17:19:48 2019 -0700 simplify EB/Poisson tutorial Tutorials/EB/Poisson/Make.package Tutorials/EB/Poisson/Poisson.cpp Tutorials/EB/Poisson/Poisson_F.H Tutorials/EB/Poisson/main.cpp Tutorials/EB/Poisson/poisson.F90 commit 8976ac2ae09b2175cc75633e7026fc92ff6a96af Author: Weiqun Zhang Date: Thu Jun 6 14:34:46 2019 -0700 fix leading underscore Src/AmrCore/AMReX_AmrParticles.H Src/Base/AMReX_BLFort.H Src/Base/AMReX_MultiFabUtil_Perilla.H Src/EB/AMReX_EB_LSCore_F.H Src/Extern/ProfParser/AMReX_AVGDOWN_F.H Src/Extern/amrdata/AMReX_AmrData.H Src/Extern/amrdata/AMReX_AmrvisConstants.H Src/Extern/amrdata/AMReX_DataServices.H commit 74707f247a270f949daf211c698d4f608b900db6 Author: Weiqun Zhang Date: Thu Jun 6 14:14:06 2019 -0700 update launch macros and functions for hip Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_CudaReduce.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunch.cpp Src/Base/AMReX_GpuLaunchFunctsC.H Src/Base/AMReX_GpuLaunchFunctsG.H Src/Base/AMReX_GpuLaunchMacrosC.H Src/Base/AMReX_GpuLaunchMacrosG.H Src/Base/AMReX_GpuRange.H Src/Base/CMakeLists.txt Src/Base/Make.package Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp Tests/GPU/Test/main.cpp commit 0e82b71c96b9cecb791d3e4fe7ec446f33ccdaba Author: Weiqun Zhang Date: Thu Jun 6 13:18:39 2019 -0700 reorganize launch macros and functions Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuLaunch.cpp Src/Base/AMReX_GpuLaunchMacrosC.H Src/Base/AMReX_GpuLaunchMacrosG.H Src/Base/CMakeLists.txt Src/Base/Make.package commit d31a80e78cd404c969c20c6a104a78b5fe9a0b68 Author: Weiqun Zhang Date: Thu Jun 6 12:19:19 2019 -0700 update Range for hip Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuRange.H Src/Base/CMakeLists.txt Src/Base/Make.package commit cc1643b5fb54da606438be75025c4763bc37485f Merge: f3b5b6c34 ce3fbdf99 Author: WeiqunZhang Date: Thu Jun 6 12:09:28 2019 -0700 Merge pull request #495 from AMReX-Codes/mlcgfix fixed an error in the sxay function definition commit ce3fbdf99ac265c06361ebc88ec16d5f10098636 Author: Brandon Runnels Date: Thu Jun 6 12:46:49 2019 -0600 fixed an error in the sxay function definition Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit b2e4213b4e3e9ec016eb6e6c344a768c106516e2 Author: Weiqun Zhang Date: Thu Jun 6 11:19:07 2019 -0700 hip: CudaMemory -> GpuMemory Src/Base/AMReX_Box.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuMemory.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 9b156b419d7a949c5d6eb685d6bbfcc540672f41 Author: Weiqun Zhang Date: Thu Jun 6 10:28:46 2019 -0700 update Elixir for hip Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuElixir.H Src/Base/AMReX_GpuElixir.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit b665f144dcb0337157654bd8d99879f254e3b339 Author: Weiqun Zhang Date: Thu Jun 6 09:25:17 2019 -0700 remove unused variable Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit f3b5b6c34165452ff17292487b0842b4b89aecc0 Merge: 3915f8642 b784efaee Author: WeiqunZhang Date: Thu Jun 6 09:19:43 2019 -0700 Merge pull request #489 from AMReX-Codes/nodeghostcells-pr Merge nodeghostcells into development commit b784efaee2b42aa4fed582581cf30d15896d028c Author: Brandon Runnels Date: Wed Jun 5 16:03:38 2019 -0600 changed ncomp in fine_mask to 1 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 322c245a4e7ac4752bd9965e222f7ecb4ca31408 Author: Brandon Runnels Date: Wed Jun 5 15:54:10 2019 -0600 addressed weiqun's comments Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_F.H commit 85d99dca85a17de73262256687bf895adf659623 Merge: 56207ae00 3915f8642 Author: Brandon Runnels Date: Wed Jun 5 14:44:48 2019 -0600 Merge branch 'development' into nodeghostcells-pr commit 3915f8642ea1a79fb6d34248f3a4df09a77798d5 Merge: 76f130d1a 5a606682d Author: Weiqun Zhang Date: Tue Jun 4 22:04:06 2019 -0700 Merge branch 'hip' into development commit 76f130d1ad386736f7ad92007adfa65a18dbf7d2 Merge: a1fee8a50 d43204936 Author: Weiqun Zhang Date: Tue Jun 4 22:03:55 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 601768332c706e0b7d273466d822bb8a4cf84422 Author: Michele Rosso Date: Tue Jun 4 18:11:02 2019 -0700 CMake: add doc regarding exported targets Docs/sphinx_documentation/source/BuildingAMReX.rst commit 8479911226caca42ab682fcdc50cf275abb44165 Author: kngott Date: Tue Jun 4 16:22:29 2019 -0700 Add pinned std::vector allocator and Vector. Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaContainers.H commit d43204936a544023b33764fc40e87032d23c2689 Merge: 2cb6e1b34 685e1885d Author: Andrew Myers Date: Tue Jun 4 16:09:04 2019 -0700 Merge pull request #494 from AMReX-Codes/init_redist_gpu Init redist gpu commit d977768c1ff60292bbb92572b6015161628682b8 Author: kngott Date: Tue Jun 4 13:52:42 2019 -0700 Updating graph tests for hip. Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit 41c7f17a1107a73a15d5520328bccf88f0db03b2 Author: kngott Date: Tue Jun 4 13:45:41 2019 -0700 Adjust for hip merge. Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_GpuDevice.cpp Tests/GPU/CudaGraphs/GraphWithMemcpy/main.cpp commit 60d1f8025dedf8f8ab946c04ccf08bfb1115cb4b Author: kngott Date: Tue Jun 4 13:21:28 2019 -0700 Fix merge on GpuDevice Src/Base/AMReX_GpuDevice.cpp commit 76b769d20690b0e52738b4325ab17adadf89e5e7 Merge: 858c1b21e 5a606682d Author: kngott Date: Tue Jun 4 13:15:30 2019 -0700 Merge branch 'hip' into kngott/cudaGraphs commit 858c1b21ede4128c2f3cca27a01c1402d8a210ba Author: Weiqun Zhang Date: Mon Jun 3 17:06:06 2019 -0700 add AMREX_USE_GPU if ENABLE_CUDA Tools/CMake/AMReX_Defines.cmake commit 43c9de1dc3ade47aae00ee86f2378b0a64eb36c7 Author: Weiqun Zhang Date: Mon Jun 3 15:23:48 2019 -0700 add runtime boolean parameter `amrex.fpe_abort_on_out_of_gpu_memory` to address Issue #485. Src/Base/AMReX_Arena.cpp commit 3585101e3d9082373d323faff27777e4959f0346 Author: Cyrus Harrison Date: Fri May 31 10:57:41 2019 -0700 blueprint support: allow mpi tasks without mesh data Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp commit cb0e3c1c8763815ed48b0e1e597525abb343607e Author: Cyrus Harrison Date: Thu May 30 10:18:08 2019 -0600 use BL_SINGLE_PRECISION_PARTICLES to select particle data type Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H commit acfd6f369347a6d2a00f92a29173927b24fcf616 Author: kngott Date: Tue Jun 4 11:23:06 2019 -0700 [WIP]: currently breaks FB, working version in development -> test putting memcpy into cudaGraph. Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaGraph.H Tests/GPU/CudaGraphs/GraphWithMemcpy/GNUmakefile Tests/GPU/CudaGraphs/GraphWithMemcpy/Make.package Tests/GPU/CudaGraphs/GraphWithMemcpy/inputs_3d Tests/GPU/CudaGraphs/GraphWithMemcpy/main.cpp Tests/GPU/CudaGraphs/GraphWithMemcpy/run.corigpu commit 5a606682d5a06798beb8e8312e595876ef5bc9ec Author: Weiqun Zhang Date: Tue Jun 4 09:59:28 2019 -0700 fix the use of numCudaStreams Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp commit b5a47d4a735cc0db233fdf69d77b4fa02885b5a3 Author: Weiqun Zhang Date: Tue Jun 4 09:48:39 2019 -0700 fix merge Src/Base/AMReX_Arena.cpp commit 12674a740d290c78aa9bad11749d834557966c89 Merge: 870019f82 a1fee8a50 Author: Weiqun Zhang Date: Tue Jun 4 09:46:25 2019 -0700 Merge branch 'development' into hip commit a1fee8a507b95fdcf69c19d16675ba5b59ca3965 Merge: f21368e32 2cb6e1b34 Author: Weiqun Zhang Date: Tue Jun 4 09:38:58 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2cb6e1b34fbd2ede433585a5bbc2ac8cf5f30baa Merge: 6461054c8 0d7af3386 Author: WeiqunZhang Date: Tue Jun 4 09:36:27 2019 -0700 Merge pull request #476 from AMReX-Codes/kngott/cudaGraphs [WIP] Adding CUDA graph support to FillBoundary commit 685e1885d4f7c23229db0c6255e00fcd6505972e Author: Jean M. Sexton Date: Tue Jun 4 09:30:31 2019 -0700 Updated RedistributeMPI to use HostVector if AMREX_USE_CUDA=TRUE, fixed fortran indexing bug in particle test Src/Particle/AMReX_ParticleContainerI.H Tests/GPU/Particles/Redistribute/test_3d.F90 commit 1d7c3c028cd23cdbb59de78163c34e33d0e95b30 Author: Jean M. Sexton Date: Thu May 23 05:40:48 2019 -0700 Added HostVector to thrust::copy version of RedistributeMPI for the RedistributeCPU version Src/Particle/AMReX_ParticleContainerI.H commit f21368e320b441c98f00adca1681cfb51d7844e1 Merge: 6461054c8 0d7af3386 Author: Weiqun Zhang Date: Mon Jun 3 17:23:35 2019 -0700 Merge branch 'kngott/cudaGraphs' into development commit 870019f82595fbac854df1213498f662ceb63e60 Author: Weiqun Zhang Date: Mon Jun 3 17:16:42 2019 -0700 fix AMREX_HIP_OR_CUDA macro Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp commit 6461054c8ebee442d3b58936fa54a190cb96faea Author: Weiqun Zhang Date: Mon Jun 3 17:06:06 2019 -0700 add AMREX_USE_GPU if ENABLE_CUDA Tools/CMake/AMReX_Defines.cmake commit c1e23297b1b784e4cf45a68c5e5716357116ce95 Author: Weiqun Zhang Date: Mon Jun 3 17:06:06 2019 -0700 add AMREX_USE_GPU if ENABLE_CUDA Tools/CMake/AMReX_Defines.cmake commit d3693211379fbbe6706a10f77b54852c01ca41e1 Author: Weiqun Zhang Date: Mon Jun 3 16:49:54 2019 -0700 rename some Cuda* files to Gpu* Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaElixir.cpp Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuAsyncArray.H Src/Base/AMReX_GpuAsyncFab.H Src/Base/AMReX_GpuAsyncFab.cpp Src/Base/AMReX_GpuAsyncFabImpl.H Src/Base/AMReX_GpuAsyncFabImpl.cpp Src/Base/AMReX_GpuDevice.H Src/Base/AMReX_GpuDevice.cpp Src/Base/AMReX_GpuUtility.H Src/Base/CMakeLists.txt Src/Base/Make.package Tools/F_scripts/write_cuda_headers.py commit 148c5c11313865d6b2b22fe21b0ce788413bad27 Author: Weiqun Zhang Date: Mon Jun 3 16:33:30 2019 -0700 fix merge Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaGraph.H commit 3a90b2203170360d1a30597694324827ba461b8e Merge: e3cbe6680 0d7af3386 Author: Weiqun Zhang Date: Mon Jun 3 16:25:45 2019 -0700 Merge branch 'kngott/cudaGraphs' into hip commit 2ffe564e5bf0874bd3ab77ea1ee3524b3b7d4339 Author: Weiqun Zhang Date: Mon Jun 3 15:23:48 2019 -0700 add runtime boolean parameter `amrex.fpe_abort_on_out_of_gpu_memory` to address Issue #485. Src/Base/AMReX_Arena.cpp commit 0d7af338631711a7cc756a07b55a6a97e57b6fe8 Author: Weiqun Zhang Date: Mon Jun 3 12:59:06 2019 -0700 make cuda graph opt-in Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuControl.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 6a6e2f2af4b07004c990159ed7c1f773a20e044c Merge: 9e0a64055 be9b9def7 Author: Weiqun Zhang Date: Mon Jun 3 12:51:18 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit 9e0a64055811a07f0e0b1147e10aff5e70debfb1 Author: Weiqun Zhang Date: Mon Jun 3 12:39:53 2019 -0700 allow empty tags Src/Base/AMReX_FabArrayCommI.H commit 6e80ffa0bd8b99c722a19ffdebbd3e39292b80ec Author: Weiqun Zhang Date: Mon Jun 3 09:49:36 2019 -0700 check __cplusplus instead gcc version. add constexpr Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaGraph.H commit 2870127d6af5a9fc85953a7e69dfd1ea079ac42e Merge: be9b9def7 d6197cddb Author: WeiqunZhang Date: Mon Jun 3 09:20:59 2019 -0700 Merge pull request #491 from Alpine-DAV/task/2019_05_blueprint_updates conduit blueprint integration updates commit be9b9def7d6c2c1357bdce7b885483969c72f661 Merge: be09b67d6 ae4807a4a Author: Weiqun Zhang Date: Mon Jun 3 07:49:02 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit be09b67d618d8718dc6b6242c1816684de48bdc6 Merge: ca50d1467 586ea4491 Author: Weiqun Zhang Date: Mon Jun 3 07:47:35 2019 -0700 Merge branch 'master' into development commit ca50d1467f0382453b839a5007b9be0bc89a7132 Author: Weiqun Zhang Date: Sun Jun 2 09:16:51 2019 -0700 fix merge Src/AmrCore/AMReX_FluxReg_3D_C.H commit 35254317f5c7055f6953fc9c595c11ff83a2382b Merge: 956247907 1d249bb6e Author: Weiqun Zhang Date: Sun Jun 2 09:15:20 2019 -0700 Merge branch 'weiqun/dev' into development commit ae4807a4a2e372c996823a458e7625347de87cdf Author: Tan Nguyen Date: Sat Jun 1 16:55:31 2019 -0700 fix a memory deallocation bug Src/Amr/AMReX_Amr.cpp commit 6528aa97b8772ea248e5f3149a2ec1543d40f3b6 Merge: c43195122 fc46754ab Author: Tan Nguyen Date: Sat Jun 1 15:44:05 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c43195122c071c3a05d943bed5bc6ccc706a798b Author: Tan Nguyen Date: Sat Jun 1 15:43:41 2019 -0700 upcxx backend that survived a few production tests Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AsyncFillPatch.cpp Src/AmrTask/rts_impls/mpi/Makefile Src/AmrTask/rts_impls/mpi/PackageQueue.H Src/AmrTask/rts_impls/mpi/PackageQueue.cpp Src/AmrTask/rts_impls/mpi/Perilla.cpp Src/AmrTask/rts_impls/mpi/PerillaConfig.H Src/AmrTask/rts_impls/mpi/PerillaRts.H Src/AmrTask/rts_impls/mpi/PerillaRts.cpp Src/AmrTask/rts_impls/runtime_common/Perilla_common.cpp Src/AmrTask/rts_impls/runtime_common/RGIter.cpp Src/AmrTask/rts_impls/runtime_common/RegionGraph.H Src/AmrTask/rts_impls/runtime_common/RegionGraph.cpp Src/AmrTask/rts_impls/runtime_common/RegionQueue.H Src/AmrTask/rts_impls/runtime_common/RegionQueue.cpp Src/AmrTask/rts_impls/upcxx/Makefile Src/AmrTask/rts_impls/upcxx/PackageQueue.H Src/AmrTask/rts_impls/upcxx/PackageQueue.cpp Src/AmrTask/rts_impls/upcxx/Perilla.H Src/AmrTask/rts_impls/upcxx/Perilla.cpp Src/AmrTask/rts_impls/upcxx/PerillaConfig.H Src/AmrTask/rts_impls/upcxx/PerillaRts.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.mpi Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.mpi.omp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.upcxx Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/GNUmakefile Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/inputs Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv_advance.cpp Tools/GNUMake/Make.upcxx commit 1d249bb6e2df59c73561969b066432f40cca498c Author: Weiqun Zhang Date: Sat Jun 1 09:01:28 2019 -0700 fix calls to interp and protect Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AsyncFillPatch.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp Src/AmrTask/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_GpuControl.H Src/EB/AMReX_EBInterpolater.H Src/EB/AMReX_EBInterpolater.cpp commit db4fe217851770e1f9fa2e419156e40cfdd40026 Author: Weiqun Zhang Date: Sat Jun 1 08:15:07 2019 -0700 add RunOn parameter to virtual Interpolater::interp Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp commit 956247907aa233f820edf755c0d4bb98cdb1408a Merge: 8e2c570cf 4f638be78 Author: Weiqun Zhang Date: Sat Jun 1 07:56:22 2019 -0700 Merge branch 'weiqun/dev' into development commit 4f638be7886006b60a3c8658146380dfbb6d70bf Author: Weiqun Zhang Date: Fri May 31 22:13:30 2019 -0700 Add RunOn parameter to FluxRegister::FineAdd Src/AmrCore/AMReX_FluxReg_1D_C.H Src/AmrCore/AMReX_FluxReg_2D_C.H Src/AmrCore/AMReX_FluxReg_3D_C.H Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_advance.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp commit 8e2c570cfcf91c140d71c6318cbcd9fe57581616 Author: Weiqun Zhang Date: Fri May 31 22:13:30 2019 -0700 Add RunOn parameter to FluxRegister::FineAdd Src/AmrCore/AMReX_FluxReg_1D_C.H Src/AmrCore/AMReX_FluxReg_2D_C.H Src/AmrCore/AMReX_FluxReg_3D_C.H Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_advance.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp commit 44eaa4b655862acfb24e04e855d444f20ef99e1d Author: Weiqun Zhang Date: Fri May 31 15:36:00 2019 -0700 add RunOn parameter to some YAFluxRegister functions and fix MLMG Src/Base/AMReX_GpuControl.H Src/Boundary/AMReX_YAFluxRegister.H Src/Boundary/AMReX_YAFluxRegister.cpp Src/Boundary/AMReX_YAFluxRegister_1D_K.H Src/Boundary/AMReX_YAFluxRegister_2D_K.H Src/Boundary/AMReX_YAFluxRegister_3D_K.H Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBFluxRegister.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp commit 8304c79a612e809c8dc1c47291e1ce890e7af57f Merge: 1cbbdbb66 38dfa69df Author: Weiqun Zhang Date: Fri May 31 13:53:08 2019 -0700 Merge branch 'weiqun/attribute_weak' into development commit 1cbbdbb663acf09f25e4300361da964959670ba7 Merge: fc46754ab 73bee882d Author: Weiqun Zhang Date: Fri May 31 13:52:22 2019 -0700 Merge branch 'weiqun/amrex' into development commit 586ea4491d9920d4bb0b925cf3809cb1de1df493 Merge: 2699ef7a9 a3cead68b Author: Weiqun Zhang Date: Fri May 31 13:50:55 2019 -0700 Merge branch 'development' commit fc46754ab426f6325b3f8f1a31365b301c8ea56c Merge: a3cead68b fc5706e95 Author: Marc Day Date: Fri May 31 12:31:28 2019 -0700 Merge pull request #492 from burlen/development fix some issues w SENSEI tutorials commit fc5706e956b25e7aa0946f98efdc638411d4d664 Author: Burlen Loring Date: Fri May 31 12:06:56 2019 -0700 clean up SENSEI AmrLevel tutorial Build & run with sensei by default and fix path to source code Tutorials/SENSEI/Advection_AmrLevel/Exec/Make.Adv Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/inputs commit b18691f596ee7c10a128f0c4405b53f2f6e66598 Author: Burlen Loring Date: Fri May 31 12:01:44 2019 -0700 clean up SENSEI AmrCore tutorial Build & run with sensei by default and fix path to source code Tutorials/SENSEI/Advection_AmrCore/Exec/Make.Adv Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/GNUmakefile Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/inputs commit 25bb70bee8eb0306c0b9a68680dbd7e197b17379 Author: Burlen Loring Date: Fri May 31 10:58:34 2019 -0700 remove UniformVelocity from SENSEI AmrLevel tutorial Using SENSEI with amrex::Amr class is already covered in the SingleVortex tutorial. Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/Make.package Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_2d.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_3d.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/inputs Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/inputs.regt Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/probdata.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/probin commit a3cead68b29daa10b49ee094f277782d39ce5050 Author: kngott Date: Fri May 31 11:20:23 2019 -0700 Fix check for mvapich vs. openmpi on CoriGPU. Tools/GNUMake/sites/Make.nersc commit e3120bcca6387ac88b6c243176d3e983b41dff6e Author: Andrew Myers Date: Fri May 31 11:01:23 2019 -0700 test on particle_lvl_offset here, instead of dxi and pdxi Src/Particle/AMReX_ParticleContainerI.H commit 54715de6efd4b7115c1c774683ad1fa84712e827 Author: Andrew Myers Date: Fri May 31 10:59:23 2019 -0700 remove unused variables Src/Particle/AMReX_ParticleContainerI.H commit d6197cddbcb950d5d73e76729a23ea302c8acf3e Author: Cyrus Harrison Date: Fri May 31 10:57:41 2019 -0700 blueprint support: allow mpi tasks without mesh data Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp commit 1480be608565cb6ad887cc7b57c287f512218352 Author: Andrew Myers Date: Fri May 31 10:39:02 2019 -0700 make this runtime assertion into a compile-time one Src/Particle/AMReX_ParticleContainerI.H commit 2699ef7a9b2b00e6c2c3ba6e1971103aa208f63d Author: Weiqun Zhang Date: Fri May 31 08:04:29 2019 -0700 update CHANGES CHANGES commit e3cbe66800034236ddc277d3d3f22bdee36eddf9 Author: Weiqun Zhang Date: Thu May 30 15:51:08 2019 -0700 rename some Cuda* files to Gpu* Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuAsyncArray.H Src/Base/AMReX_GpuAsyncArray.cpp Src/Base/AMReX_GpuUtility.H Src/Base/AMReX_GpuUtility.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 0e994546d13dc513df628ace18848c141bf91b8e Author: Weiqun Zhang Date: Thu May 30 15:40:20 2019 -0700 add AMREX_DEVICE_COMPILE macro and update CudaUtility for hip Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_CudaUtility.cpp Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_GpuControl.H Src/Particle/AMReX_NeighborList.H commit 45269f6164dfcae5858dafdb206cad097b0d0ad7 Author: Weiqun Zhang Date: Thu May 30 14:00:04 2019 -0700 hip: update AsyncFab Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.H Src/Base/AMReX_CudaAsyncFabImpl.cpp commit 05e3984ebcbdd85d740ed87275946125d57a2adc Author: Weiqun Zhang Date: Thu May 30 13:31:23 2019 -0700 hip: update BaseFab and allow __managed__ when cuda is backend Src/Base/AMReX_BaseFab.H Src/Base/AMReX_GpuQualifiers.H commit e67ba0667d6f546146f81945a48fa92cf49fce5f Author: Weiqun Zhang Date: Thu May 30 12:38:38 2019 -0700 move some functions and classes to namespace amrex::Gpu. update Gpu::AsyncArray Docs/sphinx_documentation/source/GPU.rst Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncArray.cpp Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.cpp Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaElixir.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaUtility.cpp Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MFIter.cpp Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Tests/GPU/Test/main.cpp Tests/GPU/TestB/main.cpp Tests/GPU/TestC/main.cpp Tools/F_scripts/write_cuda_headers.py Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc.cpp commit ad7fdc2314fbe8b334f7551477c559215be57a98 Merge: d108b0532 1c59de7ae Author: Andrew Myers Date: Thu May 30 15:17:13 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d108b0532c5dfbd2008a9e63385c2fab5e725015 Author: Andrew Myers Date: Thu May 30 15:16:49 2019 -0400 need to call define on the particle tile when restarting and runtime soa components are in play Src/Particle/AMReX_ParticleContainerI.H commit 56207ae0002e99c6886c9f7715bf659a16c5a847 Merge: eddfdb614 1c59de7ae Author: Brandon Runnels Date: Thu May 30 11:44:27 2019 -0600 Merge branch 'development' into nodeghostcells-pr commit 8ee10e7071396b03c1342b7e16c04dde305bae80 Author: Cyrus Harrison Date: Thu May 30 10:18:08 2019 -0600 use BL_SINGLE_PRECISION_PARTICLES to select particle data type Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H commit b2025deaf2cd2bb44f085a4272f6271c34d54a43 Author: kngott Date: Thu May 30 00:42:14 2019 -0700 Seperate stopGraphRecording and setGraph. Src/Base/AMReX_FabArrayCommI.H commit 88198f0af86372b1de3b8155a4ce1a1eb5703166 Author: kngott Date: Thu May 30 00:07:24 2019 -0700 Change startRecord and stopRecord locations to work properly with Iter method. Src/Base/AMReX_FabArrayCommI.H commit 37ab0934e92751437887103c3a9d1ebffb7f786d Author: kngott Date: Wed May 29 23:20:16 2019 -0700 Fix initialization list for CopyMemory. Src/Base/AMReX_CudaGraph.H commit aa2a4327cf58c5f17d868cbb8c5f650dea1ce500 Author: kngott Date: Wed May 29 22:34:47 2019 -0700 Add instantiate error check to debug mode. Src/Base/AMReX_CudaDevice.cpp commit 51c3ad09d3a3325cf20816f88a6c1f57675b793e Author: kngott Date: Wed May 29 22:32:37 2019 -0700 DEBUG -> AMREX_DEBUG Src/Base/AMReX_MFIter.cpp commit f2a04d7dcf0c49227ba9e55e11625b54d9303318 Author: Weiqun Zhang Date: Wed May 29 17:25:14 2019 -0700 fix for cuda Src/Base/AMReX_CudaDevice.H commit 1a069a021b59a974c42a1ba0ac95f75c349cdf4b Author: Weiqun Zhang Date: Wed May 29 17:22:16 2019 -0700 add AMREX_HIP_OR_CUDA macro Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_GpuControl.H commit 203a5b016eff71f6e8ad6f8a9b5b6451fe4816ed Author: Weiqun Zhang Date: Wed May 29 16:51:44 2019 -0700 hip: Device::Finalize() Src/Base/AMReX_CudaDevice.cpp commit 8332b5f9fe2f42fc4c6ce3d27be754ec9558255d Merge: 6384415af 1c59de7ae Author: Weiqun Zhang Date: Wed May 29 16:30:45 2019 -0700 Merge branch 'development' into hip commit eddfdb614d11f4bca2d8c4949676a4dabf470b6e Author: Brandon Runnels Date: Wed May 29 17:28:42 2019 -0600 added additional residual correction Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit c33c28a049336b1d070410bccc1acc9ec07396a2 Author: Brandon Runnels Date: Wed May 29 17:27:05 2019 -0600 implemented compatibility enum in mlmg - running unit tests Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 1c59de7ae263f7076f1ecbd87f470ed145d35153 Author: Weiqun Zhang Date: Wed May 29 16:14:38 2019 -0700 MLNodeLaplacian: make normalization threshold a parameter and set the default to 1.e-10 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 746d3f5609e10005fbc38024b45a6be4180b459a Merge: c8a1b018e b3fab0920 Author: Weiqun Zhang Date: Wed May 29 14:51:24 2019 -0700 Merge branch 'algoim' into development commit c8a1b018e65cd3fdf80dc199b12fc2ed2a4d62d0 Merge: c9cf0d611 9e15061e2 Author: Weiqun Zhang Date: Wed May 29 14:49:32 2019 -0700 Merge branch 'algoim' into development commit c9cf0d611a7c81040001031cd143e8e4fe4880be Merge: b37e6fea7 08a4145aa Author: Weiqun Zhang Date: Wed May 29 14:49:21 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6384415af0b2a0214963b87b7e963248881f1c04 Author: Weiqun Zhang Date: Mon May 27 07:10:29 2019 -0700 hip: device and streams Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.cpp Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaElixir.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaUtility.cpp Src/Base/AMReX_FabArrayUtility.H Tools/F_scripts/write_cuda_headers.py commit 08a4145aa4e8abb24e2c0c480281819018c8a7e4 Author: Andrew Myers Date: Wed May 29 11:26:55 2019 -0700 fix a couple of bugs in the dx != particle_dx version of deposit_cic Src/Particle/AMReX_Particle_mod_K.H commit dae63dbfd10dfc9a906c13965425b17bad10a8c4 Author: Andrew Myers Date: Wed May 29 11:26:33 2019 -0700 remove unused variables Src/Particle/AMReX_ParticleContainerI.H commit 0b2e6ccd5f472d64c60210d182cbb795c177e472 Author: Weiqun Zhang Date: Wed May 29 10:50:56 2019 -0700 executeGraph can be const Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_FabArrayCommI.H commit 7e9bad849928d9552b23e385b4052eb6c2baa8af Author: Weiqun Zhang Date: Wed May 29 10:24:31 2019 -0700 Real --> value_type Src/Base/AMReX_FabArrayCommI.H commit 3fa645863e4fc00d6071b94799668088335f2ef2 Author: kngott Date: Tue May 28 17:25:59 2019 -0700 Reorganize into a function-based test to allow easy reading and easy scale testing of different launch strategies. Tests/GPU/FusedLaunches/main.cpp commit c20583444f7e5978cc80a630c7b13a739469f88a Author: kngott Date: Tue May 28 16:41:10 2019 -0700 Store cudaStream as cudaStream_t. Src/Base/AMReX_CudaDevice.cpp commit 919e990a83881d66b5b7e9ee225aa4062ea778a3 Merge: 2c73f99b8 02f94086f Author: Andrew Myers Date: Tue May 28 15:49:19 2019 -0700 Merge branch 'development' into pic_c++ commit b3fab0920907a2bef18c19c69c107eedf64d8383 Author: Michele Rosso Date: Tue May 28 15:28:54 2019 -0700 CMake: get rid of Algoim and Blitz (finally) Src/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_InstallExternalLibs.cmake Tools/CMake/AMReX_Options.cmake commit 2c73f99b84176ae3bd35cd91d7e7e68a69309a2c Author: Andrew Myers Date: Tue May 28 15:01:47 2019 -0700 fix AMREX_SPACEDIM Src/Particle/AMReX_Particle_mod_K.H commit b8c9accc5165a48aa22186b604d9510b1fe91008 Author: Andrew Myers Date: Tue May 28 15:01:26 2019 -0700 correct function signature for amrex_interpolate_cic Src/Particle/AMReX_ParticleContainerI.H commit 02f94086f6b94c13264650f8c41ac83080f83d97 Merge: b76bd6cc8 7c712e057 Author: WeiqunZhang Date: Tue May 28 14:33:26 2019 -0700 Merge pull request #486 from burlen/development fix SENSEI_INSITU build commit b97f9474d41ad61520c5ea41b7fe631c5e638e62 Author: Andrew Myers Date: Tue May 28 14:22:04 2019 -0700 implement these functions for AMREX_SPACEDIM != 3 Src/Particle/AMReX_Particle_mod_K.H commit 70082749670c44e36c0ad94249b9bd9e9c326917 Author: Andrew Myers Date: Tue May 28 14:21:47 2019 -0700 Fix this test for AMREX_SPACEDIM != 3 Tests/Particles/AssignDensity/main.cpp commit 12a380f185ac3e65e3865c5e2ac0b175a7e1dc4c Author: Weiqun Zhang Date: Tue May 28 14:02:00 2019 -0700 add explicit GraphSafeGuard Src/Base/AMReX_GpuControl.H commit 7c712e057ab142bf56c274db9fddbee5899b9681 Author: SENSEI SC18 VM Date: Tue May 28 14:01:33 2019 -0700 fix SENSEI_INSITU build Tools/GNUMake/Make.defs commit 3418323cea6766b5c098129551157dcabe87f526 Author: Weiqun Zhang Date: Tue May 28 13:58:42 2019 -0700 tidy Src/Base/AMReX_FabArrayCommI.H commit 65a26338a48dd6708612be5a842dd03c4f545b8b Merge: 62a7d997f b37e6fea7 Author: Weiqun Zhang Date: Tue May 28 13:53:34 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit 62a7d997ff2d8c773d10f31a5edc60f22061b818 Merge: 34c2d48ba 076ddfd60 Author: Weiqun Zhang Date: Tue May 28 13:42:02 2019 -0700 Merge branch 'kngott/cudaGraphs' of github.com:AMReX-Codes/amrex into kngott/cudaGraphs commit 547f9713e9126b1c6faf3cfb88651bafe6cc94cc Author: Andrew Myers Date: Tue May 28 13:25:03 2019 -0700 remove the OMP Deposition helper - this is done in BaseFab now Src/Particle/AMReX_OMPDepositionHelper_nd.F90 Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 7a069d8ec914de34783bc363187daa0a63e6ad5b Author: Andrew Myers Date: Tue May 28 13:19:15 2019 -0700 hardwired 1 -> ncomp Src/Particle/AMReX_ParticleContainerI.H commit efd0fd86418cec3b57a930155a4072e842d8f67f Author: Andrew Myers Date: Tue May 28 13:05:30 2019 -0700 remove now unused Fortran routines Src/Particle/AMReX_Particle_mod_1d.F90 Src/Particle/AMReX_Particle_mod_2d.F90 Src/Particle/AMReX_Particle_mod_3d.F90 Src/Particle/AMReX_Particles_F.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit f4ddce8d9401bcf5b4499ecd30ca0559ce7182fa Author: Andrew Myers Date: Tue May 28 12:45:27 2019 -0700 implement and use C++ versions of the particle deposition routines Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particle_mod_K.H Src/Particle/AMReX_Particles.H commit 8b204d4332a81e10f4fc71d758807156f682ef09 Merge: 8e7538dff b76bd6cc8 Author: Andrew Myers Date: Tue May 28 10:19:49 2019 -0700 Merge branch 'development' into pic_c++ commit 9e15061e2aaec10d8d9997345f9173c89e37da12 Author: Weiqun Zhang Date: Tue May 28 09:37:04 2019 -0700 update node eb solver test Tests/LinearSolvers/NodeEB/MyTest.cpp commit 54effab8ade361f520eec7e963fb2024c8cbcac8 Author: Weiqun Zhang Date: Tue May 28 09:21:40 2019 -0700 remove Src/Extern/Algoim and update documentation Docs/sphinx_documentation/source/BuildingAMReX.rst Src/Extern/Algoim/AMReX_algoim_integrals.H Src/Extern/Algoim/AMReX_algoim_integrals.cpp Src/Extern/Algoim/CMakeLists.txt Src/Extern/Algoim/Make.package Tests/Algoim/GNUmakefile Tests/LinearSolvers/NodeEB/GNUmakefile Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.algoim commit b37e6fea7563906796581a8dbbb2ab8145c94ebd Author: Weiqun Zhang Date: Mon May 27 22:07:27 2019 -0700 turn on omp for computing integrals using algoim Src/EB/AMReX_algoim.cpp commit b10e9bcf18bc6926ffcb7b753f1565933992da6b Author: Weiqun Zhang Date: Mon May 27 22:05:14 2019 -0700 switch to new algoim in 3d nodal solver Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit b76bd6cc8e7feb00d8b85ccdc181dbb511f87c3d Merge: 579d47e2c 9b59fa141 Author: Weiqun Zhang Date: Mon May 27 19:07:43 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 579d47e2c0232d0578f62c033b35516cd7ad9e63 Author: Weiqun Zhang Date: Mon May 27 18:58:42 2019 -0700 algoim: make it gpu ready Src/EB/AMReX_algoim.cpp Src/EB/AMReX_algoim_K.H commit 40e481659d1d13f5d44781afffd025a001de39e8 Author: Weiqun Zhang Date: Mon May 27 18:06:35 2019 -0700 algoim: add gpu qualifier, constexpr and inline Src/EB/AMReX_algoim_K.H Tests/Algoim/main.cpp commit 03e14ba2778c7c3944e6c56c1be82c65f796d714 Author: Weiqun Zhang Date: Mon May 27 17:53:45 2019 -0700 algoim: replace std::bitset with our own bitwise operation Src/EB/AMReX_algoim_K.H commit e09d3b9c3b9caf809b1594af926221ee543fc321 Author: Weiqun Zhang Date: Mon May 27 17:19:16 2019 -0700 algoim: use gpu friendly containers Src/EB/AMReX_algoim_K.H commit d8ecda29d5d28f0b6d586ab494b7a98edf433d56 Author: Weiqun Zhang Date: Mon May 27 16:51:57 2019 -0700 algoim: simplify BoundingBox Src/EB/AMReX_algoim_K.H commit b881686e4d4528e17477f29e9f6a6670b868bd8a Author: Weiqun Zhang Date: Mon May 27 16:38:44 2019 -0700 algoim: simplify Interval Src/EB/AMReX_algoim_K.H commit 6c706b82e51c7789e7555c678f59886e7e09a5e3 Author: Weiqun Zhang Date: Mon May 27 16:33:07 2019 -0700 algoim: use array instead of vector because the number of roots is at most 2 Src/EB/AMReX_algoim_K.H commit 23e8e5d59c2a42b874913014ecf44c15efc37ef4 Author: Weiqun Zhang Date: Mon May 27 16:21:12 2019 -0700 alogim: use fixed size array instead of vector because we know the maximal size it can get to. Src/EB/AMReX_algoim_K.H commit 1dcd8d88788c6dc52ca964522595ddc62d986382 Author: Weiqun Zhang Date: Mon May 27 12:37:41 2019 -0700 set precision in algoim test Tests/Algoim/main.cpp commit 36035ef54151f673a6a7ea8f3a8f8649671350e4 Author: Weiqun Zhang Date: Mon May 27 12:07:19 2019 -0700 test algoim performance Tests/Algoim/main.cpp commit 113bee1c9771ead24664f0506c9e227b4adf11b2 Author: Weiqun Zhang Date: Mon May 27 11:36:45 2019 -0700 update cmake to include algoim Src/EB/AMReX_algoim.cpp Src/EB/CMakeLists.txt Src/EB/Make.package commit 8a5581cc057ed7d4493fd364a62be765d3f0e4e0 Author: Weiqun Zhang Date: Mon May 27 11:03:01 2019 -0700 add algoim test Src/EB/AMReX_algoim_K.H Tests/Algoim/GNUmakefile Tests/Algoim/Make.package Tests/Algoim/main.cpp commit 9b59fa1415a99046c0ca9351226eb366ba36ffbc Author: Andrew Myers Date: Mon May 27 10:56:51 2019 -0700 add missing AMREX_D_TERM macros to fix SPACEDIM != 3 Src/Particle/AMReX_ParIterI.H commit 617f6f2879b343b45ff9247f866be72523446f9c Author: Weiqun Zhang Date: Mon May 27 07:50:57 2019 -0700 copy algoim to Src/EB and remove its dependency on blitz Src/EB/AMReX_algoim.H Src/EB/AMReX_algoim.cpp Src/EB/AMReX_algoim_K.H Src/EB/Make.package commit 8e7538dff79b4dcd830f75e7f395260748980347 Author: Andrew Myers Date: Fri May 24 14:18:51 2019 -0700 start C++ implementations of amrex pic routines Src/Particle/AMReX_Particle_mod_K.H commit 97045bf1f758e2c554def2489b7055c1ed96cd8a Author: Kevin Gott Date: Fri May 24 14:16:13 2019 -0700 Doc typo. Docs/sphinx_documentation/source/GPU.rst commit c5d7347640c1d70541624bdcc527e1f988ea77e3 Author: Andrew Myers Date: Fri May 24 13:43:21 2019 -0700 add missing stream sync Src/Particle/AMReX_ParIterI.H commit 500546ffd1d76df8e8670d0537c68652eb6bf10a Author: Andrew Myers Date: Fri May 24 13:19:33 2019 -0700 amrex_build_nl also doesn't exist any more Src/Particle/AMReX_Particles_F.H commit be033373a40aa723ce12c8a2bfde35b07f26dd6d Author: Andrew Myers Date: Fri May 24 13:18:53 2019 -0700 remove now un-used Fortran routines from the particle code Src/Particle/AMReX_Particle_mod_1d.F90 Src/Particle/AMReX_Particle_mod_2d.F90 Src/Particle/AMReX_Particle_mod_3d.F90 Src/Particle/AMReX_Particles_F.H commit 4385654eb2a2c106e95f56f2bfcec60556f8c94b Author: Andrew Myers Date: Fri May 24 13:18:32 2019 -0700 don't need these functors any more Src/Particle/AMReX_Functors.H commit d9fe1764072fccda6e4d2faa8a015529c6dea660 Author: Andrew Myers Date: Fri May 24 13:18:07 2019 -0700 switch to C++ in get/set particle position Src/Particle/AMReX_ParIterI.H commit 35d467cdd7e610a186d36e120d34b8f6eb5a50e2 Author: Weiqun Zhang Date: Thu May 23 17:07:27 2019 -0700 AMREX_CUDA_MAX_THREADS -> AMREX_GPU_MAX_THREADS Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_GpuControl.H Src/Base/AMReX_fort_mod.F90 Tools/CMake/AMReX_Defines.cmake Tools/GNUMake/Make.defs commit e7aa57f3368759722832fb4ff4bee6f5332fc343 Author: Weiqun Zhang Date: Thu May 23 17:02:29 2019 -0700 hip: error checking Src/Base/AMReX_Arena.cpp Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.cpp Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaElixir.cpp Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuError.H commit 3a7be1143610d838db371cc9e5d72a7ca7b50a7b Author: Weiqun Zhang Date: Thu May 23 15:25:39 2019 -0700 hip: inLaunchRegion Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.cpp Src/Base/AMReX_CudaContainers.H Src/Base/AMReX_CudaElixir.cpp Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuControl.cpp commit 6327843caebfbd78c5502b70967d42b5fbb0d674 Author: Andrew Myers Date: Thu May 23 15:13:45 2019 -0700 fix a few more warnings Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_AmrParticles.H Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/compute_flux_2d.f90 commit 076ddfd60267459c5342a796440fcf26d2fd8b22 Author: Kevin Gott Date: Thu May 23 17:51:14 2019 -0400 Adjustments for older GNU versions. Src/Base/AMReX_CudaGraph.H commit abf2cd7ff33baf1f9442d7053e545003c4ae96de Author: Kevin Gott Date: Thu May 23 17:50:15 2019 -0400 Add check for cuda version due to API change. Src/Base/AMReX_CudaDevice.cpp commit af8de8265c9f88c4c86fed08171e92fc8ff548bb Author: Weiqun Zhang Date: Thu May 23 14:47:30 2019 -0700 make: add HIP_PLATFORM Src/Base/AMReX_GpuQualifiers.H Tools/GNUMake/Make.defs Tools/GNUMake/comps/hip.mak commit c700ba356dbcbc38ef3204124aa878baeac9fec8 Merge: 54fa5d00f e8dc9a727 Author: Kevin Gott Date: Thu May 23 16:59:44 2019 -0400 Merge branch 'development' into kngott/cudaGraphs commit 6666e261f1a0f7e9380e32ba7ba3a1ac218c148c Author: Andrew Myers Date: Thu May 23 13:56:11 2019 -0700 fixing some more parameter shadowing / unused variable warnings Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_filcc_mod.F90 Src/Boundary/AMReX_BndryRegister.cpp Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit e8dc9a7272a94e4465eb8b1741379cb156b8640c Author: Andrew Myers Date: Thu May 23 13:21:32 2019 -0700 fix some parameter shadowing warnings Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H commit 67ad94f5cff39af6906f3d6df22bd94ac6450425 Author: Weiqun Zhang Date: Thu May 23 13:06:43 2019 -0700 start hip with nvcc as backend Tools/GNUMake/Make.defs Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/hip.mak commit c490d629eb070415e21ba035ac9731a81edbe809 Merge: 480dca22a 6548e1daf Author: Andrew Myers Date: Thu May 23 14:24:14 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 480dca22a62ec2868757bb986fe26703e74f85cb Author: Andrew Myers Date: Thu May 23 14:23:37 2019 -0400 correct this size of these vectors to account for possibly runtime-added components Src/Particle/AMReX_ParticleContainerI.H commit 9e1f4402140abd23e81698849b1a917a19f85524 Author: Andrew Myers Date: Thu May 23 14:03:26 2019 -0400 add assertion to catch problems earlier Src/Particle/AMReX_ParticleContainerI.H commit a245db9b97e893df1289bd06709ce2d3c2a6e1ad Author: Andrew Myers Date: Thu May 23 13:58:54 2019 -0400 fix size of comp_name and boolean write arrays Src/Particle/AMReX_ParticleContainerI.H commit 6548e1dafa136ad7a92d50a4025affbabb68237e Author: Weiqun Zhang Date: Thu May 23 10:48:22 2019 -0700 Tensor solver: fix periodic bc Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 6bb937235b35957279a3d15216e427847c7343b7 Author: Weiqun Zhang Date: Wed May 22 16:15:03 2019 -0700 remove explicit from ErrorFunc and ErrorFunc2 because codes rely on implicit conversion Src/AmrCore/AMReX_ErrorList.H commit 110494b7fe92994b25eb2110a9ca719b4f8ab2c5 Author: Weiqun Zhang Date: Wed May 22 16:10:21 2019 -0700 MLNodeLap: tweak normalization parameter to reduce the number of bicg iterations Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 9e16381ebae4e62c8dee90323ad0933e9c6bce7c Author: Weiqun Zhang Date: Wed May 22 16:07:56 2019 -0700 Allow implicit conversion from int to BoundCond. Src/Boundary/AMReX_BoundCond.H commit 30c7ace31233d31c7da30a5ad378879c71dcb008 Author: Weiqun Zhang Date: Wed May 22 15:24:50 2019 -0700 fix a bunch of warnings by cppcheck mostly on explicit ctor Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AuxBoundaryData.cpp Src/AmrCore/AMReX_AmrParGDB.H Src/AmrCore/AMReX_Cluster.H Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_Interpolater.H Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BoxIterator.H Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_CudaRange.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_GpuControl.H Src/Base/AMReX_Print.H Src/Base/AMReX_RealVect.H Src/Base/AMReX_TinyProfiler.H Src/Boundary/AMReX_BoundCond.H Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBInterpolater.H Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp commit 6b4dfc514111ce16919a90f6b9220bfd7dbb5251 Author: kngott Date: Wed May 22 14:49:40 2019 -0700 Updated fused Test. Tests/GPU/FusedLaunches/main.cpp commit 80f1c735441668d1f42dc2391fdad9e9392f6ca7 Author: kngott Date: Wed May 22 14:49:30 2019 -0700 Function to get num streams from Device. Src/Base/AMReX_CudaDevice.H commit 5242faf9f2cd8bbda37f21b99632a59518be0fe5 Author: Weiqun Zhang Date: Wed May 22 14:20:38 2019 -0700 initialize values so that static analysis tools don't complain Src/AmrCore/AMReX_AmrCore.cpp commit 58d27d5eea4bf7a70f6656f7aba4b8a77175fa68 Author: Weiqun Zhang Date: Wed May 22 13:51:43 2019 -0700 fix out of bound error for 1d Src/Base/AMReX_Geometry.cpp commit 0b23c23bb48df43018c8891f34b1113036846a82 Author: Weiqun Zhang Date: Wed May 22 14:42:09 2019 -0400 update nvml path on summit Tools/GNUMake/sites/Make.olcf commit 73bee882db6bbd388db0dc44b06fb96eda9d8b6f Author: Weiqun Zhang Date: Tue May 21 19:20:37 2019 -0700 FPinfo: pass the correct Geometry Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_Geometry.H Src/EB/AMReX_EB2.H Src/EB/AMReX_EB2_IndexSpaceI.H commit 31ea34b1610f6effa0d6b217e496aeb05e371594 Author: Weiqun Zhang Date: Tue May 21 16:44:04 2019 -0700 Geometry: functions to reset the default Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp commit fba16ecffd0697f7d2a2f32b03631bb39aa750e0 Author: Weiqun Zhang Date: Tue May 21 16:33:47 2019 -0700 Geometry default ctor: copy from AMReX stack if we can Src/Base/AMReX.H Src/Base/AMReX_Geometry.cpp commit 0c17f2b3d2fbc23e3746a55a9d53677a3dc525c3 Author: Weiqun Zhang Date: Tue May 21 16:08:00 2019 -0700 fix periodicity flags after Amr restart Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp commit 1e70ce59a1af8436db56398827ac399dfee59732 Author: Weiqun Zhang Date: Tue May 21 13:44:50 2019 -0700 add periodic to Geometry I/O Src/Base/AMReX_Geometry.cpp commit 4981fe9f00f9bc8b496720b033185bd3f578744e Author: Weiqun Zhang Date: Tue May 21 13:43:59 2019 -0700 add IntVector ctor taking Array as argument Src/Base/AMReX_IntVect.H commit 16e7c1a8aacde8d6aceab05ca63e31077d918806 Author: Weiqun Zhang Date: Tue May 21 13:43:28 2019 -0700 tidy Src/Base/AMReX_CoordSys.cpp commit 0df0d4856e64f9f3feeac69a0b819854d4d6903e Author: kngott Date: Tue May 21 12:38:18 2019 -0700 Fused Launches Test, first draft. Tests/GPU/FusedLaunches/GNUmakefile Tests/GPU/FusedLaunches/Make.package Tests/GPU/FusedLaunches/inputs_3d Tests/GPU/FusedLaunches/main.cpp Tests/GPU/FusedLaunches/run.corigpu commit 8277f4a8ce6929230ba42cb0ed05b3b4a209ea41 Author: Weiqun Zhang Date: Tue May 21 09:03:52 2019 -0700 fix a typo in documentation Docs/sphinx_documentation/source/Basics.rst commit 37086aa363d5b92a2e7990b3f3a32bac48b557b7 Author: Weiqun Zhang Date: Mon May 20 16:47:56 2019 -0700 DefaultGeometry: use the one at the top of AMReX stack. Src/Base/AMReX_Geometry.H commit 94b01a0d3490048c23cce9acf2dae8e03064e57c Merge: 846acd89c 24ca1f5a7 Author: Weiqun Zhang Date: Mon May 20 16:17:21 2019 -0700 Merge branch 'development' into weiqun/amrex commit 24ca1f5a722348632c8ae89ea7c58b3d2c70859d Author: Weiqun Zhang Date: Mon May 20 16:16:32 2019 -0700 added DefaultGeometry function Src/Base/AMReX_Geometry.H commit 846acd89c0253a6391bb1c64518acd5374af1a45 Merge: 3ac4a3eda d4bd3b9ec Author: Weiqun Zhang Date: Mon May 20 15:53:40 2019 -0700 Merge branch 'development' into weiqun/amrex commit d4bd3b9eca5f48e11732e3d83c6da9a4d4be8bf5 Author: Weiqun Zhang Date: Mon May 20 15:40:57 2019 -0700 MLEBABecLap: fix index bug Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 3ac4a3eda0f066d4c6472640726389885e1d07d0 Merge: 782b29dfd d52c86b92 Author: Weiqun Zhang Date: Mon May 20 15:26:51 2019 -0700 Merge branch 'development' into weiqun/amrex commit d52c86b922175faf29c6ef8fee0b23be88c63473 Author: Weiqun Zhang Date: Mon May 20 13:30:58 2019 -0700 added some geometry functions to help migration Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/Base/AMReX_Geometry.H commit 782b29dfdcc06423284dbbb5c92ade5136c53dc5 Author: Weiqun Zhang Date: Mon May 20 12:16:35 2019 -0700 fix an old tutorial OldTutorials/DataServicesTest0/DataServicesTest0.cpp commit a8b405d14721810c5ca6689419bbe3bf5d061850 Author: Weiqun Zhang Date: Mon May 20 11:26:53 2019 -0700 Geometry: fix tests and tutorials Docs/sphinx_documentation/source/Basics.rst Tests/LinearSolvers/CellEB/MyTest.cpp Tests/LinearSolvers/CellEB2/MyTest.cpp Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp Tests/LinearSolvers/EBflux_grad/MyTest.cpp Tests/LinearSolvers/NodeEB/MyTest.cpp Tools/C_util/WritePlotFile.cpp Tutorials/GPU/EBCNS/Source/CNS_init_eb2.cpp Tutorials/GPU/EBCNS/Source/CNS_io.cpp Tutorials/SENSEI/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 54fa5d00fb6edbecd6badd7739b8f6431a782d2e Author: kngott Date: Mon May 20 11:08:42 2019 -0700 Clean up copy with graphs test. 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Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Adv_io.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_io.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv_io.cpp Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.cpp Src/AmrTask/tutorials/MiniApps/HeatEquation/physbc.cpp commit 7fefcc72a5732de55dc3fc6f3beb6435d5041d61 Author: Weiqun Zhang Date: Mon May 20 10:22:10 2019 -0700 Geometry: update EB Src/EB/AMReX_EB2_Level.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_init_eb2.cpp Tutorials/EB/CNS/Source/CNS_io.cpp Tutorials/EB/CNS/Source/CNS_setup.cpp commit 4d934f2bc46d0607390659acd1f44adc3cadb600 Author: Weiqun Zhang Date: Mon May 20 09:55:07 2019 -0700 MLEBTensorOp: forgot to set scalars Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 769e989932d19bb1018b8cd8c19cdb398b0401e2 Author: Weiqun Zhang Date: Sun May 19 21:43:27 2019 -0700 Geometry: update Particle Src/Particle/AMReX_ParticleContainerI.H commit b58a65809446fedf4516a25b3eb9a73647ede560 Author: Weiqun Zhang Date: Sun May 19 21:33:43 2019 -0700 Geometry: update Amr Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit f6f063010cbf57dbda71438a19791fc70c6e4a3b Author: Weiqun Zhang Date: Sun May 19 18:59:59 2019 -0700 Geometry: put the first Geometry object to the top of AMReX stack and use arguments passed in whenever available. AmrMesh: repsect constructor parameters when building Geometry Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/Base/AMReX_Geometry.cpp commit 80dad487688a07b05e057c96cdf9fdc6af849219 Author: Weiqun Zhang Date: Sun May 19 17:16:45 2019 -0700 Geometry::define: fix comparison Src/Base/AMReX_Geometry.cpp commit c9cd0f84a7176211846477b29c07ce7d1c760dc8 Author: Weiqun Zhang Date: Sun May 19 14:34:40 2019 -0700 add scalars to Tensor solver Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 98ebaffb6acd309598d6fad3a248dd7f51b383f4 Author: Weiqun Zhang Date: Sun May 19 13:59:24 2019 -0700 Geometry: update AmrCore Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX_Geometry.H commit ee9e0f79aaa99f617636e50f3d21ca3931f84dde Author: Weiqun Zhang Date: Sun May 19 12:13:55 2019 -0700 Geometry: update linear solver Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMGBndry.H Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 0791f179c259f953bb6d0e2cff181182dc573929 Author: Weiqun Zhang Date: Sun May 19 11:41:10 2019 -0700 fix comments in inputs Tutorials/Basic/HeatEquation_EX2_C/Exec/inputs_2d Tutorials/Basic/HeatEquation_EX2_C/Exec/inputs_3d Tutorials/Basic/HeatEquation_EX3_C/Exec/inputs_2d Tutorials/Basic/HeatEquation_EX3_C/Exec/inputs_3d commit 9bbaed7a1e919fe6c515e227b910b201b3ca9b76 Author: Weiqun Zhang Date: Sun May 19 11:34:06 2019 -0700 Geometry: update F_Interfaces Src/F_Interfaces/Base/AMReX_geometry_fi.cpp Src/F_Interfaces/Octree/AMReX_octree_fi.cpp commit 8a1dded9c7f1f30f23198ba62f55ee957bf6cfd7 Author: Weiqun Zhang Date: Sun May 19 10:27:21 2019 -0700 removed static data from Geometry and updated Base Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PlotFileUtil.cpp commit 154697e73cfc6d542fdefc6ccfa3bf7f48356bd2 Author: Weiqun Zhang Date: Sat May 18 15:27:51 2019 -0700 WIP Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp commit 8f01bb994be7107428a6fb605645cd76ea209d90 Author: Weiqun Zhang Date: Sat May 18 14:36:38 2019 -0700 AMReX stack Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp commit 26ee936b4dd8163ba685e077d3b25353f930e775 Author: Weiqun Zhang Date: Sat May 18 09:25:36 2019 -0700 EB2::IndexSpace: make sure it's safe to push pointers that are already owned by the stack. Src/EB/AMReX_EB2.H Src/EB/AMReX_EB2.cpp commit eedeafe002fdb3b4615309c5a8a4281eb557d693 Author: Weiqun Zhang Date: Fri May 17 16:57:17 2019 -0700 MLMG: if the solution multifab has ghost cells, set them to zero, otherwise uninitialized values might get used. Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit ff5b7fefbb3e5f6c018729743c46da51dd171e9d Author: Weiqun Zhang Date: Fri May 17 14:50:36 2019 -0700 Nodal Poisson tutorial: multi-level Src/Base/AMReX_PhysBCFunct.H Tutorials/LinearSolvers/NodalPoisson/Make.package Tutorials/LinearSolvers/NodalPoisson/MyTest.H Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp Tutorials/LinearSolvers/NodalPoisson/MyTest_F.H Tutorials/LinearSolvers/NodalPoisson/init_prob.F90 commit 1f53266b482537f400e296533eb8bf00efbced5f Author: kngott Date: Fri May 17 14:12:35 2019 -0700 Small fix. Src/Base/AMReX_CudaDevice.cpp commit 8d84d7a41a0a7686cf7be1496695ff1b3fd50365 Author: kngott Date: Fri May 17 14:10:03 2019 -0700 Update BuildingGraphs for easier reading. Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp commit 9733620abf99dd1b5f0ac5f70fba00e68d7a8642 Author: Andy Nonaka Date: Fri May 17 09:50:22 2019 -0700 (more) cleanup only; make macros more readable/distinguishable from each other Src/Base/AMReX_ArrayLim.H commit dfbe0baece96cd2ffaf9fc6013492c1056f5b0a8 Merge: f97b08584 a643e2331 Author: Andy Nonaka Date: Fri May 17 09:48:39 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit f97b08584ae120e43c0248ec598d6534052fb4fe Author: Andy Nonaka Date: Fri May 17 09:48:15 2019 -0700 cleanup only; make macros more readable/distinguishable from each other Src/Base/AMReX_ArrayLim.H commit a643e2331e05793a8d3ee23c56b4dea50a610418 Merge: bd95c5c90 cdb437eac Author: Andrew Myers Date: Thu May 16 21:03:05 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit bd95c5c90a7e1a90a23d6734242f9678c83e10f4 Author: Andrew Myers Date: Thu May 16 20:47:53 2019 -0400 remove debug print Src/Particle/AMReX_ParIterI.H commit b95b65dfa68b72d4196411380e478c1ca8261ca1 Author: Andrew Myers Date: Thu May 16 20:34:16 2019 -0400 bug fix for set particle position, which wasn't properly copying the particles ids Src/Particle/AMReX_Functors.H Src/Particle/AMReX_ParIterI.H commit 5ebc4f76bf73c3743515d76bb472a4c149704c6a Author: Andrew Myers Date: Thu May 16 20:33:06 2019 -0400 format fix Src/Particle/AMReX_ParticleTile.H commit e92a9da3b74dc67658bef4a95276d62b7c3bcc06 Author: Andrew Myers Date: Thu May 16 20:32:51 2019 -0400 format fix Src/Particle/AMReX_StructOfArrays.H commit cdb437eac82633d9add487f9b1247a7a45741bb2 Author: Weiqun Zhang Date: Thu May 16 17:17:11 2019 -0700 EBTensor test: convergence test results Tests/LinearSolvers/EBTensor/results.org commit b53b005e4c906f1407f06f3c9136662084e42534 Author: Weiqun Zhang Date: Thu May 16 16:42:29 2019 -0700 MLEBTensor: fix bug Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit f2f96f4bc1fbd096e32429db305f50fe111d343f Author: Weiqun Zhang Date: Thu May 16 14:58:22 2019 -0700 EBTensorOp: fix bug Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit e42231c23428ca9794562a21b7873b0c604dd880 Author: Weiqun Zhang Date: Thu May 16 14:55:24 2019 -0700 EBTensor test Src/EB/AMReX_EBFabFactory.H Tests/LinearSolvers/EBTensor/GNUmakefile Tests/LinearSolvers/EBTensor/Make.package Tests/LinearSolvers/EBTensor/MyTest.H Tests/LinearSolvers/EBTensor/MyTest.cpp Tests/LinearSolvers/EBTensor/MyTestPlotfile.cpp Tests/LinearSolvers/EBTensor/MyTest_K.H Tests/LinearSolvers/EBTensor/inputs Tests/LinearSolvers/EBTensor/main.cpp commit 34c2d48bad95d31943e07ba6b166eccdbbd91d66 Author: Weiqun Zhang Date: Thu May 16 16:42:29 2019 -0700 MLEBTensor: fix bug Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 179631850e853dc41e8470ffa5a012c5360f3259 Author: Weiqun Zhang Date: Thu May 16 14:58:22 2019 -0700 EBTensorOp: fix bug Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit d2003dc3b104d9eea0bb93212c339aaaae7a78a5 Author: Weiqun Zhang Date: Thu May 16 14:55:24 2019 -0700 EBTensor test Src/EB/AMReX_EBFabFactory.H Tests/LinearSolvers/EBTensor/GNUmakefile Tests/LinearSolvers/EBTensor/Make.package Tests/LinearSolvers/EBTensor/MyTest.H Tests/LinearSolvers/EBTensor/MyTest.cpp Tests/LinearSolvers/EBTensor/MyTestPlotfile.cpp Tests/LinearSolvers/EBTensor/MyTest_K.H Tests/LinearSolvers/EBTensor/inputs Tests/LinearSolvers/EBTensor/main.cpp commit 85378ed5213742639b75e106e9a4f3d003e363a6 Author: Brandon Runnels Date: Thu May 16 13:05:06 2019 -0600 fixes error where solution only converges in mlmg with verbosity >= 0 - need a better solution Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit b3a8ffecf0cce5ccfcafc76407c75f1ed75493a7 Author: kngott Date: Wed May 15 23:49:14 2019 -0700 Additional graph fixing. Src/Base/AMReX_CudaDevice.cpp commit 8d766d0ae433af947b677ab06e2b3381d48fd61c Author: kngott Date: Wed May 15 20:51:25 2019 -0700 Add cudaGraph and cudaGraphExec destroy calls. Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaGraph.H commit b9e0ac4a131fb421538ab02c730df7c935526d5f Author: Weiqun Zhang Date: Wed May 15 14:59:37 2019 -0700 rm setGraphRegion call from linear solver tutorial Tutorials/LinearSolvers/ABecLaplacian_C/main.cpp commit 23dd87e4fa4068e54874cca461634a6b45848746 Author: Weiqun Zhang Date: Wed May 15 14:59:11 2019 -0700 add GraphSafeGuard Src/Base/AMReX_GpuControl.H commit 0c37e64889c3a5d4322457cd964fb564de864bfc Author: Weiqun Zhang Date: Wed May 15 14:51:44 2019 -0700 add AMReX_CudaGraph.H to cmake Src/Base/CMakeLists.txt commit 21686ef94c5a45d624cf321dd8687dbdfb31d08b Merge: 47f7a8c95 21788f7d9 Author: Weiqun Zhang Date: Wed May 15 14:48:04 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit 21788f7d96b3bbe3e0ff96dd083142b09ea03b51 Author: Weiqun Zhang Date: Wed May 15 11:04:45 2019 -0700 MLEBTensor: fix bug Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 303456cac4454d26cf12687da5fa2f5fdf747e77 Author: Weiqun Zhang Date: Tue May 14 16:33:23 2019 -0700 EB_average_down_boundaries: fix for multi-component Src/EB/AMReX_EBMultiFabUtil.cpp commit 47f7a8c95de9f96268f45a21beee4d107767fd00 Author: kngott Date: Tue May 14 15:33:18 2019 -0700 Tweak to be more consistent with non-graphed code. Src/Base/AMReX_FabArrayCommI.H commit 1f03b4b87c1ca52f3dfe516a4a23b6fa152c08b0 Author: Weiqun Zhang Date: Tue May 14 13:35:49 2019 -0700 MLEBTensor: fix sign Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 565a99f1fda550361aff36ee679c0d4d5061402a Author: Weiqun Zhang Date: Tue May 14 12:45:55 2019 -0700 Tensor solver: finish the coarsening of bulk viscosity Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit f25d353053c3b6a6aa504221a17400e3a3afa49d Author: atmyers Date: Mon May 13 17:02:12 2019 -0700 Make OK and Redistribute respect the launch region flag. Src/Particle/AMReX_ParticleContainerI.H commit c6bfe3bd094e3317f52a2bb7d4340c21ff93f03e Author: kngott Date: Mon May 13 15:26:39 2019 -0700 Fix GraphBoundary test error check to include user-specified number of components and ghost cells. Tests/GPU/CudaGraphs/GraphBoundary/main.cpp commit 1ac079b75f946b75c69c68a48c0edf82e9219bbe Author: kngott Date: Mon May 13 15:26:03 2019 -0700 Cleanup in Building test. Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp commit 5e50e2df58dacf4dae6d7bda5c1b41f02a398ea5 Merge: 7748e4323 c04fb7c0f Author: Andrew Myers Date: Mon May 13 15:45:29 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7748e43239e935797bd3bfb07fd76ca0ec512108 Author: Andrew Myers Date: Mon May 13 15:45:14 2019 -0400 these define calls are needed when using the runtime soa capability on the GPU Src/Particle/AMReX_ParticleContainerI.H commit c04fb7c0fc344ae6c4d2ab28f10b70d37b9d8eb7 Author: Weiqun Zhang Date: Mon May 13 12:03:31 2019 -0700 Noal RAP: don't renormalize if the diagonal component is too small compared to the global maximum Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 7cdffe9aacce77cc929c526932fedd9de6dc927b Author: Weiqun Zhang Date: Mon May 13 09:56:23 2019 -0700 MLEBTensorOp: fix EB flux Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 835f877238069c9f4a969fbc28612b992860a602 Merge: b8e66199a e0131f00c Author: Ann Almgren Date: Mon May 13 09:55:01 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit b8e66199a4c7d8278595df30a7d9f10a37bc7f01 Author: Ann Almgren Date: Mon May 13 09:54:32 2019 -0700 Set USE_MPI = FALSE in GNUMakefile since this version of diffmultifab only works in serial Tools/C_util/DiffMultiFab/GNUmakefile commit e0131f00c18496b2d67a3e676220b5e69fd0f555 Author: Weiqun Zhang Date: Mon May 13 09:20:08 2019 -0700 Edison is gone Src/Base/AMReX_Machine.cpp Tests/HDF5Benchmark/GNUmakefile Tests/Slice/GNUmakefile Tools/CMake/AMReX_Machines.cmake Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.nersc commit 2506a68a12d92946e19553cf02320fdb5a7a640f Merge: 772fc96c1 eed6d839b Author: Weiqun Zhang Date: Sun May 12 12:45:51 2019 -0700 Merge branch 'master' into development commit eed6d839b523051b0eb8ca0b71be7fb20bac7f3c Author: Weiqun Zhang Date: Sun May 12 12:45:23 2019 -0700 add citation to README.md README.md commit 772fc96c109f669078f46faa10507e39d4958815 Merge: 235011841 e17365efd Author: Weiqun Zhang Date: Sun May 12 10:47:41 2019 -0700 Merge branch 'master' into development commit e17365efd5c3cf1024dca00aa1304fff2610f976 Author: Weiqun Zhang Date: Sun May 12 10:40:19 2019 -0700 add JOSS status badge README.md commit ec1f0e69331bb0fc1f6a9ed250f21fc03a362795 Author: Weiqun Zhang Date: Sun May 12 08:37:51 2019 -0700 fix IAMR DOI paper/paper.bib commit 55bbd4f68f13ea901f71f78be8040d6735ecc383 Merge: 3d8ff225a 3712e149d Author: WeiqunZhang Date: Sun May 12 07:54:25 2019 -0700 Merge pull request #481 from kyleniemeyer/patch-4 Update paper.bib commit 3712e149d72f32b3d150a2e8feb8458a8306104f Author: Kyle Niemeyer Date: Sun May 12 00:41:03 2019 -0700 Update paper.bib paper/paper.bib commit 3d8ff225a5224d59d6362c152ebae41b8a4afc93 Merge: ca5a13c84 4203124ba Author: asalmgren Date: Sat May 11 20:59:53 2019 -0700 Merge pull request #480 from kyleniemeyer/patch-3 Update paper.bib commit ca5a13c84c93fd91828c8223b14ce5ed13425baa Merge: 2fca9b910 ffe309b26 Author: asalmgren Date: Sat May 11 20:55:25 2019 -0700 Merge pull request #479 from kyleniemeyer/patch-2 Fixes case of multiple references in paper commit 4203124ba1c4a0131b08624531403f76d77355d0 Author: Kyle Niemeyer Date: Sat May 11 20:51:33 2019 -0700 Update paper.bib paper/paper.bib commit ffe309b2673b99c75334bbc5c95d06604a6d8ec4 Author: Kyle Niemeyer Date: Sat May 11 20:43:01 2019 -0700 Fixes case of multiple references in paper paper/paper.md commit 2fca9b910efcd60453bf9487ea1d894856d62226 Author: Weiqun Zhang Date: Sat May 11 19:15:22 2019 -0700 paper: minor changes paper/paper.md commit d54ff71b72045f96ae7e77faddeefd0b1f86ad3d Author: Weiqun Zhang Date: Sat May 11 18:52:48 2019 -0700 spell out JCP paper/paper.bib commit c238df4c04feee99da7d6f8b814f9e0900c297a5 Author: Weiqun Zhang Date: Sat May 11 18:48:51 2019 -0700 Fix paper.bib paper/paper.bib paper/paper.md commit 5e4573c0429d5ba5a53f1317a580df6d0a4a5a7f Merge: c8949c78c 96f5d74b6 Author: Weiqun Zhang Date: Sat May 11 18:41:59 2019 -0700 Merge branch 'master' of github.com:AMReX-Codes/amrex commit c8949c78cd985cf56997cd4bcd060d95fde4b4e5 Author: Weiqun Zhang Date: Sat May 11 18:41:48 2019 -0700 Fix paper.bib paper/paper.bib commit 96f5d74b6b07ad8a93ecada5fa59904250e42662 Author: Ann Almgren Date: Sat May 11 17:37:22 2019 -0700 Update with many references. paper/paper.bib paper/paper.md commit 23501184140828cef7a9ad4cf1ce54d9e35effbd Merge: 651f423a8 29a4d3ff8 Author: Ann Almgren Date: Sat May 11 17:37:33 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 651f423a8c5842a01c3ee9bdda56d26b4c1b3252 Author: Ann Almgren Date: Sat May 11 17:37:22 2019 -0700 Update with many references. paper/paper.bib paper/paper.md commit 29a4d3ff82cc6741c71efa5408130ff424b31108 Merge: ad15a24c2 07d887e21 Author: Weiqun Zhang Date: Sat May 11 17:24:16 2019 -0700 Merge branch 'weiqun/mlmg' into development commit 07d887e214e944da4dcc8e580d483cfdd457dcff Author: Weiqun Zhang Date: Sat May 11 17:19:16 2019 -0700 MLEBTensor: calling cross terms Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 58d2d28cbee5db7501e37370c0faba377b32ecad Author: Weiqun Zhang Date: Sat May 11 16:46:38 2019 -0700 MLEBTensor: 2d cross terms Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 7eec0a71674c614aaa9d544376501b120bbccc28 Author: Weiqun Zhang Date: Sat May 11 15:31:23 2019 -0700 MLEBTensor: 3d cross terms Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 7b388baca09e16190a3db6d7d13ffcaee809dd6f Author: Ann Almgren Date: Fri May 10 17:12:49 2019 -0700 Add references for SUNDIALS, hypre, PETSc and xSDK. paper/paper.bib paper/paper.md commit db6c9cdf55097729c34a52ea213568ef14a24625 Author: Ann Almgren Date: Fri May 10 16:28:34 2019 -0700 Add city and country to the author affiliations. paper/paper.md commit ad15a24c25bc287bc28112d82a5e5a697a060773 Author: Ann Almgren Date: Fri May 10 17:12:49 2019 -0700 Add references for SUNDIALS, hypre, PETSc and xSDK. paper/paper.bib paper/paper.md commit 9f24d8cf493d0e358d9c9ff6cdac373f58c704ee Author: Weiqun Zhang Date: Fri May 10 17:08:48 2019 -0700 WIP: MLEBTensorOp Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 032e3124a4caac5b5942175d9bd7811285b4b784 Merge: 757e81d59 2269a986f Author: Ann Almgren Date: Fri May 10 16:28:52 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 757e81d59b41a30593e80ef84c98cdf9c82c9cbf Author: Ann Almgren Date: Fri May 10 16:28:34 2019 -0700 Add city and country to the author affiliations. paper/paper.md commit 3950bbe1bde5b6f5b21ee7b63d371b3055be27c2 Author: Weiqun Zhang Date: Fri May 10 15:39:01 2019 -0700 MLEBTensor: fill the corners of regular fabs too Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit 46d4bd53505f529a75bb818bbb8c947d08cf760a Author: Weiqun Zhang Date: Fri May 10 13:55:45 2019 -0700 MLEBTensor: save fluxes in MultiFab so that we don't have to have 2 ghost cells Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit b57616f15183d7661332832949f2d86bcb17e212 Merge: df41312c9 693f015fa Author: WeiqunZhang Date: Fri May 10 14:15:40 2019 -0700 Merge pull request #478 from kyleniemeyer/patch-1 Typographic edits in paper commit 693f015fac2983520df8ad4e5d3f2c495ecfc40b Author: Kyle Niemeyer Date: Fri May 10 14:13:34 2019 -0700 Typographic edits in paper paper/paper.md commit 8d1e5dcd9fcb83c5385fe803431a035e165e1f6b Author: Andrew Myers Date: Fri May 10 12:14:49 2019 -0700 size should be capacity here Src/Base/AMReX_PODVector.H commit 2269a986f8b95d5ca0ad16f90b6d110a24123729 Merge: 58087e086 28fd14a33 Author: Weiqun Zhang Date: Fri May 10 11:18:37 2019 -0700 Merge branch 'weiqun/mlmg' into development commit 28fd14a3310f6418a4007f9b260ecb08771e8d44 Author: Weiqun Zhang Date: Fri May 10 10:55:43 2019 -0700 MLEBABecLap: fix typo Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H commit 6a76c64fe1510544354907f9c306df64aa3833e6 Author: Weiqun Zhang Date: Fri May 10 09:42:08 2019 -0700 MLEBABecLap: fix new bug in mask Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H commit 0882f8ae9e1ac1ce6c79f064cf056cf2c791fca7 Author: Weiqun Zhang Date: Fri May 10 09:01:26 2019 -0700 WIP: MLEBTensor Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H commit 605aedda38e7de30a9016d17f8ced4863577a908 Author: Weiqun Zhang Date: Thu May 9 18:38:19 2019 -0700 MLEBTensor: cross term fluxes Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBCellFlag.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit e913ce83589191994d5feeff8267e07768824550 Author: kngott Date: Thu May 9 17:24:06 2019 -0700 Readme for CudaGraph tests. Tests/GPU/CudaGraphs/Readme.txt commit 9b812ee29f4b2233544f87d0ffb4b4843ff1941c Author: kngott Date: Thu May 9 17:15:53 2019 -0700 Clean up older, redundant graph tests. Tests/GPU/CudaGraphs/ArrayReuse/GNUmakefile Tests/GPU/CudaGraphs/ArrayReuse/Make.package Tests/GPU/CudaGraphs/ArrayReuse/inputs_3d Tests/GPU/CudaGraphs/ArrayReuse/main.cpp Tests/GPU/CudaGraphs/ArrayReuse/run.corigpu Tests/GPU/CudaGraphs/GraphCopy/GNUmakefile Tests/GPU/CudaGraphs/GraphCopy/Make.package Tests/GPU/CudaGraphs/GraphCopy/inputs_3d Tests/GPU/CudaGraphs/GraphCopy/main.cpp Tests/GPU/CudaGraphs/GraphCopy/run.corigpu Tests/GPU/CudaGraphs/GraphIterReuseCopy/GNUmakefile Tests/GPU/CudaGraphs/GraphIterReuseCopy/Make.package Tests/GPU/CudaGraphs/GraphIterReuseCopy/inputs_3d Tests/GPU/CudaGraphs/GraphIterReuseCopy/main.cpp Tests/GPU/CudaGraphs/GraphIterReuseCopy/run.corigpu commit b809d149518aac859ad2a9ff363faf8f97b8e0c5 Author: Andrew Myers Date: Thu May 9 16:08:24 2019 -0700 also use the PODVector on CPU code (for now, to test it) Src/Base/AMReX_CudaContainers.H commit f46861e8d51b459ce1269e0fb9aeee72e2cbbd56 Author: Weiqun Zhang Date: Thu May 9 15:15:26 2019 -0700 MLEBABecLap: prepare it for tensor solve Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_K.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_nd.F90 Src/LinearSolvers/MLMG/Make.package commit 58087e0860c5df5d1430606dfea04eff1b3d7d31 Author: Andrew Myers Date: Thu May 9 14:55:38 2019 -0700 correct the number of comps when writing particle data to plt files Src/Particle/AMReX_ParticleContainerI.H commit 464f4e828e9cd62639a2e258b5a105b994df02b5 Author: Weiqun Zhang Date: Thu May 9 12:45:57 2019 -0700 MLEBABecLap: switch to new gsrb with multi-component b coefficient Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit b092080f59f37f41b8777bc0419fe03e83d5c507 Author: Weiqun Zhang Date: Thu May 9 11:19:57 2019 -0700 simplification Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit 31b9fef50bd74a07333d9ec1b5ef65264b40f8a7 Author: Weiqun Zhang Date: Thu May 9 10:47:36 2019 -0700 WIP: MLEBTensorOp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 382cf29c2f6d1bcb2bffa03af4e9fce5f0a16037 Author: Weiqun Zhang Date: Thu May 9 09:03:28 2019 -0700 make some functions public for cuda Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H commit d809aeccd94d7fb7e849fb76b9873f4f4875fdde Author: Weiqun Zhang Date: Wed May 8 18:34:58 2019 -0700 MLEBABecLap: fix new bug introduced when removing HO EB Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 8da61e4ed19455dbaf21e3537d779d009e4c66f4 Author: Andrew Myers Date: Wed May 8 19:43:20 2019 -0400 mark these functions as noexcept, since we don't catch those ever Src/Base/AMReX_PODVector.H commit 116494b77630e5cfe13d7d9de7b150f4361a305a Author: Weiqun Zhang Date: Wed May 8 16:39:48 2019 -0700 MLEBTensorOp: add eb kappa Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H commit 2293195eaee42c5a2db80cf7e601b5d6f0b7072d Author: Andrew Myers Date: Wed May 8 19:25:52 2019 -0400 split this constructor for PODVector into two Src/Base/AMReX_PODVector.H commit 4a0d2576a772eabd4335f1a392ed5ed031ccae77 Author: Andrew Myers Date: Wed May 8 19:20:56 2019 -0400 don't need thrust::raw_pointer_cast anymore Src/Particle/AMReX_ParticleContainerI.H commit 3574bb75b433811ecbdfef038e3ce89e175bb2be Author: Weiqun Zhang Date: Wed May 8 15:48:07 2019 -0700 MLEBABecLap 2D: remove blend beta Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit 2e1ccbd6bfeb0f1f679b7c051a64a63b6e6edac0 Merge: 8e6d0eefc 4bee4f56f Author: Weiqun Zhang Date: Wed May 8 15:39:29 2019 -0700 Merge branch 'development' into weiqun/mlmg commit 4bee4f56fb10fd58319eef9dfa73634400a7284f Author: Weiqun Zhang Date: Wed May 8 15:38:23 2019 -0700 add a missing header Src/Base/AMReX_ParmParse.H commit 8e6d0eefc3c3ee8577f04f245cefeafa95a1060d Author: Weiqun Zhang Date: Wed May 8 15:00:24 2019 -0700 MLEBABecLap: update for multi-component Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_F.H Src/EB/AMReX_EBMultiFabUtil_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_nd.F90 commit 52923178ec2862573c27da6a3986772fa7c20246 Author: Andrew Myers Date: Wed May 8 18:08:38 2019 -0400 copying the grid start and stop indices using thrust_copy instead of the copy constructor Src/Particle/AMReX_ParticleContainerI.H commit 30123d14a5b5c6cd26580ae5c1a9ff3597c96129 Author: Kevin Gott Date: Wed May 8 16:32:16 2019 -0400 Fix run.summit script. -N = email, not number of nodes. Tutorials/GPU/run.summit commit d6a81ebed46d00465f66f9c6af8b6c1fef873e46 Author: Andrew Myers Date: Wed May 8 16:27:59 2019 -0400 remove debug print statement Src/Base/AMReX_PODVector.H commit 0efeb086b4fe010deecf3c7ef4179513c19a553f Author: Weiqun Zhang Date: Wed May 8 13:04:40 2019 -0700 MLEBABecLap: remove HO EB Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit d8f5b7f8d2badd0fb521304a759e3a03007ac147 Author: kngott Date: Wed May 8 12:47:05 2019 -0700 Proper CUDA Callback calls for CUDA 9 & CUDA 10, Part 2. Src/Base/AMReX_CudaAsyncFab.cpp commit 24f3a98b94454ca8e399143217045418712b58b1 Author: kngott Date: Wed May 8 12:41:55 2019 -0700 Proper CUDA Callback calls for CUDA 9 & CUDA 10. Src/Base/AMReX_CudaAsyncFab.cpp commit 168c3e76c9c887b89adb246acb8a1662fe5c11ec Author: kngott Date: Wed May 8 12:20:28 2019 -0700 Hide max_cuda_streams function when USE_CUDA=FALSE. Src/Base/AMReX_CudaDevice.H commit f35842fb095f454586b5ac4e8183ae4b5ee498f4 Author: Weiqun Zhang Date: Wed May 8 12:01:47 2019 -0700 MLTensor: limit kappa to mg level 0 Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 436e89302318ac007e989c10fe84b6b887369c26 Merge: b47e15032 f72952e55 Author: kngott Date: Wed May 8 11:49:01 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit c546ede052b29fc63277cea8f4100af54f0e4661 Author: Weiqun Zhang Date: Wed May 8 09:41:22 2019 -0700 MLTensor: move as much as possible into the laplacian Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit b47e15032453a0e121e57142de19cca6e69d3a4c Author: kngott Date: Wed May 8 11:47:25 2019 -0700 Clean up. Src/Base/AMReX_FabArrayCommI.H commit df41312c9566f1736263d93a731039bcb328c580 Author: Ann Almgren Date: Wed May 8 11:43:08 2019 -0700 Oops -- forgot to actually remove the text LICENSE commit f72952e55abe5ea16de6d7589df28a404b134f2f Author: Ann Almgren Date: Wed May 8 11:43:08 2019 -0700 Oops -- forgot to actually remove the text LICENSE commit 78bfa830555c5cec15a80635fb3e00a4e57bdc90 Author: kngott Date: Wed May 8 11:42:23 2019 -0700 Fix indentation in FillBoundary w/ Graphs. Src/Base/AMReX_FabArrayCommI.H commit 5b2b67d12d6e51970d53b7371b025c1b4cd772b8 Author: Ann Almgren Date: Wed May 8 11:40:17 2019 -0700 Update license.txt -> LICENSE and replace modified BSD by standard 3-clause BSD. LICENSE README.md commit 64e436fed185aaa7cb7136cb8a881c0d3aaeb5b4 Author: Ann Almgren Date: Wed May 8 11:40:17 2019 -0700 Update license.txt -> LICENSE and replace modified BSD by standard 3-clause BSD. LICENSE README.md commit 410a151e22ae1e93b3c3abddb9268cc1a0e0363c Merge: e3dffa05c a0a62c89e Author: kngott Date: Wed May 8 11:35:01 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit e3dffa05c32e46a31379afaf780beac95b0a23a4 Author: kngott Date: Wed May 8 11:34:18 2019 -0700 Add number of ghost cells and components to test inputs. Tests/GPU/CudaGraphs/GraphBoundary/inputs_3d commit 9540fa93dce0ad8bdd5ca3d82bab33972770fcaf Author: kngott Date: Wed May 8 11:32:55 2019 -0700 Add runtime flag to turn on/off graphs to LinearSolver Tutorial. Tutorials/LinearSolvers/ABecLaplacian_C/main.cpp commit 558238cf73e4002f151adadf7d1f735ff61e9cfa Author: kngott Date: Wed May 8 11:31:56 2019 -0700 Rename re-used timer. Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp commit 40b75ccdb70bcb5789b77a333834de8a5b2514fc Author: kngott Date: Wed May 8 11:31:22 2019 -0700 Clean up FillBoundary graph test. Tests/GPU/CudaGraphs/GraphBoundary/main.cpp commit 989ae7e6094c9e8a843cf9d9dc6f4c3d90b12c92 Merge: 84912ee98 a0a62c89e Author: Andrew Myers Date: Wed May 8 13:53:47 2019 -0400 Merge branch 'development' into atmyers/vector_memory_usage commit faff63fa11a4db0431522f8646b83539237808fa Author: Weiqun Zhang Date: Tue May 7 22:12:38 2019 -0700 MLTensor: apply the cross terms at all levels Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit fb2da0a448f73eccbb0d4b413aed5cf35062b6f5 Author: Weiqun Zhang Date: Tue May 7 19:34:45 2019 -0700 WIP: MLEBTensorOp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp commit a0a62c89e3b516732328433c5c1e5190a5c3ee4b Author: Ann Almgren Date: Tue May 7 18:06:28 2019 -0700 Add notes about being able to install amrex using spack. Docs/sphinx_documentation/source/BuildingAMReX_Chapter.rst Docs/sphinx_documentation/source/GettingStarted.rst commit 333a9bf5183faf81257c637c4f41ebbc619aa11e Author: Weiqun Zhang Date: Tue May 7 16:09:28 2019 -0700 MLEBTensorOp: stubs Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLEBTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLEBTensor_K.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/Make.package commit 949bcbe00bc8aa79a03178f1f854a4d96ecd6b07 Author: Weiqun Zhang Date: Tue May 7 15:54:36 2019 -0700 MLTensor: bc at corners Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 3ff85af3a1d7738e8c16b322a71498447fccda1e Author: Weiqun Zhang Date: Mon May 6 16:07:47 2019 -0700 MLMG: when using EB, the coarest domain size is now >= 4. Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 553054e9e30477c5ce3c9ae09e87ce0cb8c0137f Author: Weiqun Zhang Date: Mon May 6 14:46:07 2019 -0700 MLTensor: simplification Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 3b39fcedc22a4ac8a587ef6720846cfaa24a5b47 Author: Weiqun Zhang Date: Mon May 6 14:10:43 2019 -0700 MLTensor: include all cross terms Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit 93fd673f769a14e978a57eaac0dd2d8c58444446 Author: Ann Almgren Date: Sun May 5 15:57:15 2019 -0700 fix typos Docs/sphinx_documentation/source/GridCreation.rst Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst commit ebbc21bcde15f2fd633cddfec0a4af2de4e14620 Author: Ann Almgren Date: Sun May 5 15:42:35 2019 -0700 more on gridding Docs/sphinx_documentation/source/GridCreation.rst Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst commit a53ea77c8c5e9827c5536864f10b78f1a22cc666 Merge: cec41643e 08f5ec3f7 Author: Ann Almgren Date: Sun May 5 15:08:11 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit cec41643eeab2971ea3f07616dfc413a3fe788d7 Author: Ann Almgren Date: Sun May 5 15:07:59 2019 -0700 update to gridding stuff Docs/sphinx_documentation/source/DualGrid.rst Docs/sphinx_documentation/source/GridCreation.rst Docs/sphinx_documentation/source/LoadBalancing.rst Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst commit 08f5ec3f77e4ab2404cc6a3c68ed14ec18e21525 Merge: 9544fabca 610113bba Author: Weiqun Zhang Date: Sun May 5 13:53:12 2019 -0700 Merge branch 'weiqun/mlmg' into development commit 610113bbaec0e737567e562929b55d60825393bf Author: Weiqun Zhang Date: Sun May 5 13:52:57 2019 -0700 comments about the tensor solver Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H commit 9544fabca6396758b026766e3d8b9df32819e6f4 Author: Ann Almgren Date: Sun May 5 12:56:26 2019 -0700 fix formatting Docs/sphinx_documentation/source/LoadBalancing.rst commit 371e5d1a333ee4a07ac6fd1bd567de64811d0497 Author: Ann Almgren Date: Sun May 5 12:39:17 2019 -0700 Add short text about load balancing Docs/sphinx_documentation/source/DualGrid.rst Docs/sphinx_documentation/source/LoadBalancing.rst Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst commit 41dc5c930a802d617024a7e7e5ddc39455899fbc Author: Ann Almgren Date: Sat May 4 20:16:07 2019 -0700 Remove gridding from AmrCore now that it lives in its own section. Docs/sphinx_documentation/source/AmrCore.rst commit 00d7f91afd6e0bf19b62fa4933364266ab1dcd7e Author: Ann Almgren Date: Sat May 4 20:10:06 2019 -0700 fix typo Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst commit 8523085572c7a5e843f8b1f82bce21b55b28065c Author: Ann Almgren Date: Sat May 4 20:02:35 2019 -0700 Add text about dual gridding. Docs/sphinx_documentation/source/DualGrid.rst Docs/sphinx_documentation/source/GridCreation.rst Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst commit ad49b36289b19abe4d604661d97e52b58087d375 Author: Ann Almgren Date: Sat May 4 19:48:31 2019 -0700 More clarification Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst commit a49890cda3222f39b213a89558d4da1df998c030 Author: Ann Almgren Date: Sat May 4 19:27:58 2019 -0700 fix typo Docs/sphinx_documentation/source/ManagingGridHierarchy.rst commit 568cd1e53b80f9861b6ced3933f84761a41e5aaf Author: Ann Almgren Date: Sat May 4 19:26:46 2019 -0700 more fixes for grid creation Docs/sphinx_documentation/source/ManagingGridHierarchy.rst commit 038c21596e82ac37c06a32cd0b30ee509c28d88b Author: Ann Almgren Date: Sat May 4 19:21:39 2019 -0700 more grid creation update Docs/sphinx_documentation/source/ManagingGridHierarchy.rst commit d4c1426ffedbe33eca935cd74723662ef9ed4e36 Author: Ann Almgren Date: Sat May 4 19:03:44 2019 -0700 More detail Docs/sphinx_documentation/source/ManagingGridHierarchy.rst commit 9005459872d1876ef5de2fc1744508958668475b Author: Ann Almgren Date: Sat May 4 18:31:12 2019 -0700 Add refine_grid_layout Docs/sphinx_documentation/source/ManagingGridHierarchy.rst commit dd7bc35804f4d80b5930be70815f65e542d8728c Author: Ann Almgren Date: Sat May 4 18:16:08 2019 -0700 Fix oops re cpp use Docs/sphinx_documentation/source/ManagingGridHierarchy.rst commit 4f104341003e3014b89c4b0a4ce2aec8c96a2d04 Author: Ann Almgren Date: Sat May 4 18:14:15 2019 -0700 More update on grid creation Docs/sphinx_documentation/source/ManagingGridHierarchy.rst commit 0591a96fe6ecafc6e4de957cb077a7325dae5247 Author: Ann Almgren Date: Sat May 4 17:57:54 2019 -0700 More detail re grid creation Docs/sphinx_documentation/source/ManagingGridHierarchy.rst commit 85e7032c54c413fcf589d4fb34ee029c2c523ade Merge: 610af83c7 c1c8fc8aa Author: Ann Almgren Date: Sat May 4 11:20:02 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 610af83c7ae910a966e80777e36e0887fd969193 Author: Ann Almgren Date: Sat May 4 11:19:43 2019 -0700 Fix the headings for managing grid hierarchy Docs/sphinx_documentation/source/ManagingGridHierarchy.rst commit ea602a5205d4c782d12bf537381962efd8774598 Author: Weiqun Zhang Date: Sat May 4 09:04:31 2019 -0700 MLTensor: override apply instead of solutionResidual Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H commit b9e0cf89f39a0fc8afbeffb9cb25e431f0b68f3f Author: Weiqun Zhang Date: Fri May 3 21:48:06 2019 -0700 MLTensor: hide setScalars Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit c1c8fc8aafb61b7bcfe79e9867a603a157b1d0ba Merge: 22345ffd9 87a92ce86 Author: asalmgren Date: Fri May 3 18:21:47 2019 -0700 Merge pull request #475 from AMReX-Codes/docs-libamrex Expand section on building libamrex commit 87a92ce862dbbade55235e1f9f9bd580f7db9d1f Author: Donald E. Willcox Date: Fri May 3 18:04:42 2019 -0700 Expand section on building libamrex with details about how to set C++ flags and linker flags for the application code. Docs/sphinx_documentation/source/BuildingAMReX.rst commit 22345ffd9a9d62e8b8560538bd38079a69fcd692 Author: Ann Almgren Date: Fri May 3 17:57:58 2019 -0700 Add Chapter intro for ManagingGridHierarchy Docs/sphinx_documentation/source/ManagingGridHierarchy_Chapter.rst commit 315b636fbb1885f2bd784e4e2e0fb99f27ebfa9c Author: kngott Date: Fri May 3 17:28:20 2019 -0700 ifdefs to protect CUDA 10 features. Needs testing on Summit. Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayCommI.H commit 9bf8b2148e487859b023d75680277cea64854170 Merge: 0807d4699 d915ee787 Author: Ann Almgren Date: Fri May 3 17:00:50 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 0807d4699d4aefa4dc5cdeee65c8317f835df7a1 Author: Ann Almgren Date: Fri May 3 17:00:35 2019 -0700 add separate section on managing the grid hierarchy Docs/sphinx_documentation/source/ManagingGridHierarchy.rst Docs/sphinx_documentation/source/index.rst commit a8a0980d4834cb69ac09d3079fd07667e907cac6 Author: kngott Date: Fri May 3 16:00:31 2019 -0700 Update FillBoundary to switchable graph recording methods. Src/Base/AMReX_FabArrayCommI.H commit e3f3312cb66cee05a282888ad305f173bb03b4a2 Author: kngott Date: Fri May 3 15:59:08 2019 -0700 Add flag to switch graph recording methods and single start and stop function to choose. Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp commit 77c53699f76e1c7fd9bf64a74ce72032e5f7be08 Author: kngott Date: Fri May 3 15:57:29 2019 -0700 Reorganize and cleanup output. Tests/GPU/CudaGraphs/GraphBoundary/main.cpp commit 003af0e68836772836409e8b959e465692148243 Author: kngott Date: Fri May 3 15:56:12 2019 -0700 Whitespace cleanup. Src/Base/AMReX_GpuControl.H commit d915ee787fd0c91be3e9d82d30876f741a53f560 Author: Weiqun Zhang Date: Fri May 3 15:27:09 2019 -0700 Fix bndry for hypre and petsc Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 84912ee987d6ef4c29f229ca886abd2bda49e262 Author: Andrew Myers Date: Fri May 3 17:53:49 2019 -0400 fix move assignment operator Src/Base/AMReX_PODVector.H commit 20da97b5df6f4d7e81d2468cbc6eff43833eede4 Merge: 64e275ff1 5ff36d517 Author: Weiqun Zhang Date: Fri May 3 14:43:12 2019 -0700 Merge branch 'weiqun/mlmg' into development commit 5ff36d5176eab795107b08a8df9e151f3e215707 Author: Weiqun Zhang Date: Fri May 3 14:42:47 2019 -0700 MLTensor: add extra terms to residual Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/AMReX_MLTensor_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLTensor_K.H Src/LinearSolvers/MLMG/Make.package commit 756e704f1fa159e8acb29397003f185e693e4071 Author: Andrew Myers Date: Fri May 3 17:37:05 2019 -0400 implement erase, assign, insert Src/Base/AMReX_PODVector.H commit daa7fa8cc7501894fc6ba152fb50f78b556de952 Author: Weiqun Zhang Date: Fri May 3 12:59:25 2019 -0700 add computeGradient Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 13cba3c740562f5621f57753a65466b5bf1b95de Author: Andrew Myers Date: Fri May 3 13:55:06 2019 -0400 can implement these Vector using simple typedefs now Src/Base/AMReX_CudaContainers.H commit 912676ba3667384ca2b903da9d0aae0db34e547a Author: Andrew Myers Date: Fri May 3 13:54:20 2019 -0400 don't need this allocator to inherit from the thrust one Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_PODVector.H commit 946eb8b25555ec548a21c95b78b5ed1b759557e0 Author: Weiqun Zhang Date: Fri May 3 10:53:21 2019 -0700 MLTensorOp: prepareForSolve Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit 485e5204b5aa704b58a6355c6b27cf0eb3dcb6ff Author: Andrew Myers Date: Fri May 3 13:52:49 2019 -0400 use the wrapped version of Gpu::HostVector here Src/Particle/AMReX_ParticleContainerI.H commit e36ab664ecacf7f358362db84fe4edeb91421776 Author: Weiqun Zhang Date: Fri May 3 09:55:51 2019 -0700 MLEBABecLap: update for multi-component Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 64e275ff1fe7eecc24ca494e781ae218a63a52c7 Author: Weiqun Zhang Date: Fri May 3 07:15:37 2019 -0700 Fix FillPatch for EB Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArrayBase.H commit 2541da848d4cbbe3b395ecfd3dcfe00150d89458 Author: Maikel Nadolski Date: Fri May 3 10:49:21 2019 +0200 Link against the C version of MPI Src/Base/CMakeLists.txt commit 3a9dbdd41dc4b42be9f6bafea57c6ffa5a0ee53f Author: Marc Day Date: Thu May 2 19:19:36 2019 -0700 Fix WritePlotFile to allow few levels in output that in orig, based on length of mf data passed in Tools/C_util/WritePlotFile.cpp commit 9a142bf65ee11bbae0935073250e4156c4c62f4b Author: Marc Day Date: Thu May 2 18:50:57 2019 -0700 Update isoToVTK.py to be python3-compliant Tools/EBSurfaceTools/isoToVTK.py commit 740f38cd07f2d0b11afeb5aa4bf121361544b587 Author: Weiqun Zhang Date: Thu May 2 16:53:22 2019 -0700 MLCellLinOp: update for multi-component Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit d325bb1bbebad2b061ff5472fbaa70622818e090 Author: Weiqun Zhang Date: Thu May 2 16:38:54 2019 -0700 MLABecLap: update for multi-component Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit 9038424fb7544dc4244acc31f1c98cf05a6a3af8 Author: Andrew Myers Date: Thu May 2 19:00:38 2019 -0400 a vector implementation where we control the growth and reallocation strategy Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaContainers.H Src/Base/AMReX_PODVector.H Src/Base/CMakeLists.txt Src/Base/Make.package commit efb89649f8b8b656d3a51182bc7a5d2642e1e188 Author: Weiqun Zhang Date: Thu May 2 15:30:18 2019 -0700 MLMG: fine mask only needs to have 1 component. BaseFab::norinfmask now assumes the mask has only 1 component. Src/Base/AMReX_BaseFab.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit f753c13992d82e86df58f33c1a2ffa8e2263a606 Author: Weiqun Zhang Date: Thu May 2 13:51:48 2019 -0700 new version of contains_inf with IntVect argument for ghost cells Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 2cd342d657f0369b9bd37ff55035cfec3876078d Author: Weiqun Zhang Date: Thu May 2 13:46:21 2019 -0700 new version of SumBoundary with argument for number of ghost cells Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit d284917ff38db85e3eb82bf73168d08db545033f Author: Weiqun Zhang Date: Thu May 2 12:09:38 2019 -0700 Remove duplicated code in FillPatch Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit df3f4928cfd6ea972d66a1dde99e75c6d730d920 Author: Weiqun Zhang Date: Thu May 2 10:04:35 2019 -0700 MLMG nodal rap: change the number of ghost cells to 1 at the bottom Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 592f9433c38a29c03b8941583562c9952ff94561 Author: Andrew Myers Date: Thu May 2 13:21:50 2019 -0700 change the assert about the particle type to be even stronger Src/Particle/AMReX_ParticleContainerI.H commit e5f419bf5a57927c083b94bc1bd15782db0a2ac6 Author: Andrew Myers Date: Thu May 2 13:14:19 2019 -0700 let the constructor for the Particle struct be compiler-defined Src/Particle/AMReX_Particle.H commit bd985c84b1dde4e0f850dba96135d22edf41fe92 Merge: ed894c2cb ae63d370a Author: Andrew Myers Date: Thu May 2 10:04:21 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ed894c2cbae07a7b703634dded2854b212f54d3d Author: Andrew Myers Date: Thu May 2 10:03:58 2019 -0700 The pointer incrementing logic here was wrong due to the possibility of structure padding. Src/Particle/AMReX_NeighborParticlesCPUImpl.H commit e199498c25af95b180ed5c5508440ce5a8f576d6 Author: Maikel Nadolski Date: Thu May 2 17:58:33 2019 +0200 Do not require CXX libraries for MPI which are deprecated. CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in commit ae63d370abd38012c71e4a084717eb1b0d66f184 Author: Weiqun Zhang Date: Wed May 1 20:47:18 2019 -0700 fix symmetry issue of nodal rap stencil in 2D Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit ad961a579e41596480e7e12743a93abc769da4f9 Author: Weiqun Zhang Date: Wed May 1 19:13:18 2019 -0700 fix symmetry issue of nodal rap stencil Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 500b14b28ab45329175ad1bff84322156b8db4cc Merge: 27ec47ecd b78b4845f Author: kngott Date: Wed May 1 12:22:25 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit 27ec47ecd55d267ca02639dd7bacd5ea0315da15 Author: kngott Date: Wed May 1 12:21:36 2019 -0700 Output adjustment. Tests/GPU/CudaGraphs/GraphBoundary/main.cpp commit b78b4845fa328f0501497727cb594d78ed1ba906 Merge: 581ea816e 864a53bc7 Author: Andrew Myers Date: Wed May 1 10:10:46 2019 -0700 Merge pull request #471 from AMReX-Codes/particle_realdescriptor_fix bug fixes for particles when BL_FLOAT is used. commit 581ea816e3eb57e4c52dcd27f36f85b4c3797188 Merge: 9e3aaa705 358894a96 Author: WeiqunZhang Date: Wed May 1 10:07:28 2019 -0700 Merge pull request #472 from maikel/feature/FillPatch_IndexSpace EB: Add an additional overload for FillPatchTwoLevels. commit 27cddea41b00d3bff1f2dccf5232b53e5962c665 Author: Weiqun Zhang Date: Wed May 1 09:11:55 2019 -0700 MLMG: remove assertion to maintain backward compatibility Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 1eee82fea3fce9dfb86e8720eb280fe27d56c7b3 Merge: 16b471644 9e3aaa705 Author: Weiqun Zhang Date: Wed May 1 09:06:01 2019 -0700 Merge branch 'development' into weiqun/mlmg commit 9e3aaa7053499b9f7f0c786a92ef860c6322f10d Author: Weiqun Zhang Date: Wed May 1 09:04:52 2019 -0700 update CHANGES CHANGES commit 8e8143dd3264300f7bc510d2bea1f7abf30d00fb Merge: 637996a36 e4fcc5a1b Author: Weiqun Zhang Date: Wed May 1 08:44:20 2019 -0700 Merge branch 'development' commit e4fcc5a1b1c78e2a80c513401ac08f469f27e0ed Author: Tan Nguyen Date: Tue Apr 30 17:29:35 2019 -0700 factor upcxx backend code Src/AmrTask/rts_impls/mpi/Make.package Src/AmrTask/rts_impls/mpi/Perilla.cpp Src/AmrTask/rts_impls/mpi/perilla.mak Src/AmrTask/rts_impls/runtime_common/Make.package Src/AmrTask/rts_impls/runtime_common/Perilla_common.cpp Src/AmrTask/rts_impls/runtime_common/RGIter.cpp Src/AmrTask/rts_impls/runtime_common/RegionGraph.H Src/AmrTask/rts_impls/runtime_common/RegionGraph.cpp Src/AmrTask/rts_impls/runtime_common/WorkerThread.H Src/AmrTask/rts_impls/runtime_common/WorkerThread.cpp Src/AmrTask/rts_impls/runtime_common/perilla.mak Src/AmrTask/rts_impls/upcxx/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/upcxx/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/upcxx/Barrier.H Src/AmrTask/rts_impls/upcxx/Barrier.cpp Src/AmrTask/rts_impls/upcxx/LocalConnection.H Src/AmrTask/rts_impls/upcxx/Make.package Src/AmrTask/rts_impls/upcxx/Perilla.cpp Src/AmrTask/rts_impls/upcxx/PerillaConfig.H Src/AmrTask/rts_impls/upcxx/PerillaRts.H Src/AmrTask/rts_impls/upcxx/PerillaRts.cpp Src/AmrTask/rts_impls/upcxx/Perilla_common.cpp Src/AmrTask/rts_impls/upcxx/RGIter.H Src/AmrTask/rts_impls/upcxx/RGIter.cpp Src/AmrTask/rts_impls/upcxx/RegionQueue.H Src/AmrTask/rts_impls/upcxx/RegionQueue.cpp Src/AmrTask/rts_impls/upcxx/RemoteConnection.H Src/AmrTask/rts_impls/upcxx/WorkerThread.H Src/AmrTask/rts_impls/upcxx/WorkerThread.cpp Src/AmrTask/rts_impls/upcxx/mylock.h Src/AmrTask/rts_impls/upcxx/perilla.mak commit 16b4716446c48774cdaad26f44ca70206a900a51 Author: Weiqun Zhang Date: Tue Apr 30 17:04:10 2019 -0700 MLMGBndry: multi-component Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMGBndry.H Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp commit 1a636f070b2a5931b716e4eb2deca7ea8c9e5684 Author: Weiqun Zhang Date: Tue Apr 30 16:45:12 2019 -0700 MLMG: multi-component BndryCondLoc Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H commit d224feb1d63e9b1cac96e6deee9d458b1845adc6 Author: kngott Date: Tue Apr 30 16:19:01 2019 -0700 FillBoundary MPI graphed and tested on one node. CopyTo, Local & CopyFrom all graphed. Src/Base/AMReX_FabArrayCommI.H commit 864a53bc7fb4aa1596d0997a7e8b8dcea0a48d14 Author: Andrew Myers Date: Tue Apr 30 15:50:57 2019 -0700 make sure the format and order is consistent for each of the real conversion functions Src/Base/AMReX_FabConv.cpp commit 1396905f2eaba0d6830283a4c4bb4e7ae9b11200 Author: Andrew Myers Date: Tue Apr 30 15:26:03 2019 -0700 float -> double Src/Base/AMReX_FPC.cpp commit dcdb1f5e99bd19b726032172b39e7030678124de Author: Weiqun Zhang Date: Tue Apr 30 15:06:31 2019 -0700 make domain bc vector so that each component could have its own bc type Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H commit 08765ecd034828f845c8bbcd3de44fb25d9a0e61 Author: kngott Date: Tue Apr 30 14:57:41 2019 -0700 Get rid of StreamIter loops where not needed. Src/Base/AMReX_FabArrayCommI.H commit 799b93ca8998766ddc777fdf666d8a4260d82af6 Author: Weiqun Zhang Date: Tue Apr 30 14:40:43 2019 -0700 MLTensorOp: derive from MLABecLaplacian Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp commit cb4bcd2e7665f77ccc9f158ee7de7f2baa6860d2 Author: kngott Date: Tue Apr 30 14:38:16 2019 -0700 SendToBuffer Graphed Src/Base/AMReX_FabArrayCommI.H commit 5a7a71b6d44dac2c2d3bd1ec45c9b1f2ea84e116 Author: kngott Date: Tue Apr 30 14:36:33 2019 -0700 Better run script. Tests/GPU/CudaGraphs/GraphBoundary/run.corigpu commit aefcc35aff1c44f67ec6a8e19c8518cc9b3cfae4 Author: kngott Date: Tue Apr 30 14:36:16 2019 -0700 Small tweaks. Tests/GPU/CudaGraphs/GraphBoundary/main.cpp commit 09cc04b510cdbb5e1f028fb1ef11b118256dcbe9 Author: Tan Nguyen Date: Tue Apr 30 13:26:13 2019 -0700 delete duplicated codes Src/AmrTask/rts_impls/mpi/RegionGraph.H Src/AmrTask/rts_impls/mpi/RegionGraph.cpp commit 6fa22423ad1a1820e208eff88db1db0662dd5fe4 Author: Tan Nguyen Date: Tue Apr 30 13:24:12 2019 -0700 delete duplicated codes Src/AmrTask/rts_impls/mpi/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/mpi/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/mpi/Barrier.H Src/AmrTask/rts_impls/mpi/Barrier.cpp Src/AmrTask/rts_impls/mpi/LocalConnection.H Src/AmrTask/rts_impls/mpi/RGIter.H Src/AmrTask/rts_impls/mpi/RGIter.cpp Src/AmrTask/rts_impls/mpi/RegionQueue.H Src/AmrTask/rts_impls/mpi/RegionQueue.cpp Src/AmrTask/rts_impls/mpi/RemoteConnection.H Src/AmrTask/rts_impls/mpi/WorkerThread.H Src/AmrTask/rts_impls/mpi/WorkerThread.cpp Src/AmrTask/rts_impls/mpi/mylock.h commit 918c1efa87caba22fdec512c83a4e2f196664a81 Author: Weiqun Zhang Date: Tue Apr 30 10:23:43 2019 -0700 Start tensor solver Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLTensorOp.H Src/LinearSolvers/MLMG/AMReX_MLTensorOp.cpp Src/LinearSolvers/MLMG/Make.package commit 358894a96ac2f99313e76f5c44dba466b2dfa971 Author: Maikel Nadolski Date: Tue Apr 30 09:50:47 2019 +0200 Allows to create FPInfo objects with an associated EB2::IndexSpace. For enabled EB these changes allow to choose the EB2::IndexSpace which will be used for the interpolation regions in FillPatchTwoLevels. This commit also makes it possible to use FillPatchTwoLevels without any EB2::IndexSpace built at a prior stage. In this case it will do the same communication logic as if AMReX would not be built with enabled EB. Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/EB/AMReX_EB2.H Src/EB/AMReX_EB2.cpp commit 5ec0502580e28cd859cbabeb130b30eb52797568 Merge: 910bfa291 22309639f Author: Tan Nguyen Date: Mon Apr 29 21:52:39 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 910bfa291e346852434105d78f7a82aee1e2c0e2 Author: Tan Nguyen Date: Mon Apr 29 21:51:29 2019 -0700 factor codes in omp and pthreads backends Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/AmrTask/rts_impls/mpi/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/mpi/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/mpi/Barrier.H Src/AmrTask/rts_impls/mpi/Barrier.cpp Src/AmrTask/rts_impls/mpi/LocalConnection.H Src/AmrTask/rts_impls/mpi/Make.package Src/AmrTask/rts_impls/mpi/Makefile Src/AmrTask/rts_impls/mpi/PackageQueue.H Src/AmrTask/rts_impls/mpi/PackageQueue.cpp Src/AmrTask/rts_impls/mpi/Perilla.H Src/AmrTask/rts_impls/mpi/Perilla.cpp Src/AmrTask/rts_impls/mpi/PerillaConfig.H Src/AmrTask/rts_impls/mpi/PerillaRts.H Src/AmrTask/rts_impls/mpi/PerillaRts.cpp Src/AmrTask/rts_impls/mpi/RGIter.H Src/AmrTask/rts_impls/mpi/RGIter.cpp Src/AmrTask/rts_impls/mpi/RegionGraph.H Src/AmrTask/rts_impls/mpi/RegionGraph.cpp Src/AmrTask/rts_impls/mpi/RegionQueue.H Src/AmrTask/rts_impls/mpi/RegionQueue.cpp Src/AmrTask/rts_impls/mpi/RemoteConnection.H Src/AmrTask/rts_impls/mpi/WorkerThread.H Src/AmrTask/rts_impls/mpi/WorkerThread.cpp Src/AmrTask/rts_impls/mpi/mylock.h Src/AmrTask/rts_impls/mpi/perilla.mak Src/AmrTask/rts_impls/mpi_pthreads/Make.package Src/AmrTask/rts_impls/runtime_common/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/runtime_common/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/runtime_common/Barrier.H Src/AmrTask/rts_impls/runtime_common/Barrier.cpp Src/AmrTask/rts_impls/runtime_common/LocalConnection.H Src/AmrTask/rts_impls/runtime_common/Make.package Src/AmrTask/rts_impls/runtime_common/PerillaMemCheck.H Src/AmrTask/rts_impls/runtime_common/PerillaMemCheck.cpp Src/AmrTask/rts_impls/runtime_common/RGIter.H Src/AmrTask/rts_impls/runtime_common/RGIter.cpp Src/AmrTask/rts_impls/runtime_common/RegionQueue.H Src/AmrTask/rts_impls/runtime_common/RegionQueue.cpp Src/AmrTask/rts_impls/runtime_common/RemoteConnection.H Src/AmrTask/rts_impls/runtime_common/WorkerThread.H Src/AmrTask/rts_impls/runtime_common/WorkerThread.cpp Src/AmrTask/rts_impls/runtime_common/mylock.h Src/AmrTask/rts_impls/runtime_common/perilla.mak Src/AmrTask/rts_impls/upcxx/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/upcxx/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/upcxx/Barrier.H Src/AmrTask/rts_impls/upcxx/Barrier.cpp Src/AmrTask/rts_impls/upcxx/LocalConnection.H Src/AmrTask/rts_impls/upcxx/Make.package Src/AmrTask/rts_impls/upcxx/Makefile Src/AmrTask/rts_impls/upcxx/PackageQueue.H Src/AmrTask/rts_impls/upcxx/PackageQueue.cpp Src/AmrTask/rts_impls/upcxx/Perilla.H Src/AmrTask/rts_impls/upcxx/Perilla.cpp Src/AmrTask/rts_impls/upcxx/PerillaConfig.H Src/AmrTask/rts_impls/upcxx/PerillaRts.H Src/AmrTask/rts_impls/upcxx/PerillaRts.cpp Src/AmrTask/rts_impls/upcxx/Perilla_common.cpp Src/AmrTask/rts_impls/upcxx/RGIter.H Src/AmrTask/rts_impls/upcxx/RGIter.cpp Src/AmrTask/rts_impls/upcxx/RegionGraph.H Src/AmrTask/rts_impls/upcxx/RegionGraph.cpp Src/AmrTask/rts_impls/upcxx/RegionQueue.H Src/AmrTask/rts_impls/upcxx/RegionQueue.cpp Src/AmrTask/rts_impls/upcxx/RemoteConnection.H Src/AmrTask/rts_impls/upcxx/WorkerThread.H Src/AmrTask/rts_impls/upcxx/WorkerThread.cpp Src/AmrTask/rts_impls/upcxx/mylock.h Src/AmrTask/rts_impls/upcxx/perilla.mak commit 22309639f52247d9a3d91e5de2e167da52f7d115 Author: Johannes Blaschke Date: Mon Apr 29 21:23:53 2019 -0700 eb level's `fillLevelSet` needs to be public Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB_levelset.H commit 7ebe8be4fbfdb4a7ca6483efb6f47c33ba55bb05 Author: Weiqun Zhang Date: Mon Apr 29 16:55:32 2019 -0700 minor changes for format and consistence Src/AmrCore/AMReX_AmrMesh.cpp commit 71be12ce3796a76e815ca7575ebff64ad2d0bbbd Author: Weiqun Zhang Date: Mon Apr 29 16:44:49 2019 -0700 MLEBABecLap: loop fusion Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 182ed57a98fee1742fc8f1413e09f6207c924229 Author: kngott Date: Mon Apr 29 16:10:38 2019 -0700 CUDA Graphs API works for non-lambdas. Test later for lambdas? Tests/GPU/CudaGraphs/CrazyGraphs/main.cpp commit 7451a447e92c1f9f4f24af64086102735d80b734 Author: Maikel Nadolski Date: Tue Apr 30 00:06:21 2019 +0200 EB: Add an additional overload for FillPatchTwoLevels. * This adds an EB2::IndexSpace paramter to FillPatchTwoLevels. That way one can specify the exact EB2::IndexSpace for the interpolation region. * Add a defaulted FabFactory parameter to the constructor of FPInfo. Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 06e24c7b5805415d21e719579935732234b3601d Author: Andrew Myers Date: Mon Apr 29 11:01:33 2019 -0700 bug fixes for particles when BL_FLOAT is used. Src/Base/AMReX_FPC.H Src/Base/AMReX_FPC.cpp Src/Base/AMReX_FabConv.cpp Src/Particle/AMReX_Particles.H commit 544d679c5a38e271aaa2d58f365b36878e7449f7 Author: Weiqun Zhang Date: Mon Apr 29 08:58:24 2019 -0700 Fix NodeEB test Tests/LinearSolvers/NodeEB/MyTest.cpp commit 42c62961109a7603cfa48a7fd33718c33402764b Author: Max Katz Date: Sun Apr 28 21:32:18 2019 -0700 Add parameter for dynamic shared memory Tools/F_scripts/write_cuda_headers.py commit 6f1e4de8d425cf9a0b4fac90817537f60594c5bf Author: Max Katz Date: Sun Apr 28 17:04:14 2019 -0700 Use different format for passing box to pragma Tools/F_scripts/write_cuda_headers.py commit 0197802a5d61a6f95da3a60a07773c9487931091 Author: Max Katz Date: Sun Apr 28 15:57:19 2019 -0700 Allow the GPU pragma to accept information about the box Tools/F_scripts/write_cuda_headers.py commit ae8db34ec1135f49afd172c7ea3365efb019791f Author: Max Katz Date: Sun Apr 28 15:57:01 2019 -0700 Add version of grid stride calculation that uses box information Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp commit b57cf9df937731827b3bd1b91360c88176716302 Author: Max Katz Date: Sun Apr 28 15:56:26 2019 -0700 Add functions for shared memory reductions Src/Base/AMReX_fort_mod.F90 commit 4289ec4e84da7b97ed72541fb8c7e1cfe75714e1 Author: Weiqun Zhang Date: Sat Apr 27 11:04:54 2019 -0700 Change the default bottom solver to bicgcg for nodal RAP Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H commit bb63e1a636777758115320ef21bc96a6e5d56aee Author: Ann Almgren Date: Sat Apr 27 09:06:34 2019 -0700 Pass the mg_cg_verbose flag through the MacProjector Src/LinearSolvers/MLMG/AMReX_MacProjector.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit ce445b3740aa0d583b2369bfcb99378778a4f31b Author: Weiqun Zhang Date: Fri Apr 26 22:51:29 2019 -0700 MLMG bottom solver: add new types cgbicg and bicgcg. They will start with cg or bicg. If fails, it will switch to the other. If the alternative succeeds, the switch becomes permanent. Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 7252f34ccf209827d430c679330429a84588f14d Author: Weiqun Zhang Date: Fri Apr 26 22:03:29 2019 -0700 Fix omp bug in nodal solver with RAP Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit baa2f9cd2a3936e9a66635647c8b7638c203c1e4 Author: Weiqun Zhang Date: Fri Apr 26 19:28:57 2019 -0700 Remove use_hypre parameter from MLNodeLaplacian ctor Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 58d8b8e255b0e60b771e03e522ef2f0c69a11cdd Author: Michele Rosso Date: Fri Apr 26 20:38:58 2019 -0400 CMake: fix incorrect path Src/CMakeLists.txt commit 5d9f05836f70583d29e49b59016502aa58c21626 Author: Michele Rosso Date: Fri Apr 26 20:32:00 2019 -0400 CMake: fix printing of CUDA options Tools/CMake/AMReX_SetupCUDA.cmake commit e07a22c4d1576ea83a13b0369ec4d04a3aafc5d8 Author: kngott Date: Fri Apr 26 17:08:13 2019 -0700 Fix the indexes. Src/Base/AMReX_FabArrayCommI.H commit 613e26c968f26ff523a1416c592cdbd1530dfd9a Author: kngott Date: Fri Apr 26 17:07:24 2019 -0700 Free before allocing if resize a sized CudaGraph. Src/Base/AMReX_CudaGraph.H commit f3f88ebbda36bedf936f282e890804497acb4eef Author: Michele Rosso Date: Fri Apr 26 16:41:50 2019 -0700 CMake: move CUDA-specific options to AMReX_SetupCUDA.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_SetupCUDA.cmake commit f1391c25347dba337d75479f4a4c92a5f554d834 Merge: 02474f40c 23d011180 Author: Michele Rosso Date: Fri Apr 26 16:37:10 2019 -0700 Merge branch 'development' into mr/cmake commit ee3dacf3400b89bdd713b292475556e8e2efeea5 Author: kngott Date: Fri Apr 26 15:34:03 2019 -0700 Default run test case without nvprof. Tests/GPU/CudaGraphs/GraphBoundary/run.corigpu commit 7fa55dbb768f56bb2a2690aadca6ad9beb4f7c7b Author: kngott Date: Fri Apr 26 15:33:31 2019 -0700 Working test case comparing CPU, GPU and CudaGraph versions of FillBoundary. Tests/GPU/CudaGraphs/GraphBoundary/inputs_3d Tests/GPU/CudaGraphs/GraphBoundary/main.cpp commit e3e10f2264ad74f4cb8787a2dd12db092b175b91 Author: kngott Date: Fri Apr 26 15:32:29 2019 -0700 First working version of FillBoundary using Graphs with MPI = 1. Src/Base/AMReX_FabArrayCommI.H commit a625c123495c8e95b87b2af8c2d58c24a17bcddd Author: kngott Date: Fri Apr 26 15:32:00 2019 -0700 Change FB initialization to resize CudaGraphs. Src/Base/AMReX_FabArrayBase.cpp commit 07e653e2ffabe546a36f6af35cac4db05294a7ca Author: kngott Date: Fri Apr 26 15:31:26 2019 -0700 Clean up CudaGraph and allow resizing. Src/Base/AMReX_CudaGraph.H commit 83d5eefca87ebc0c2d00c598b6de7303d8d5d96c Author: kngott Date: Fri Apr 26 15:07:43 2019 -0700 Smarter GraphRegion checks and CPU version of functions. Src/Base/AMReX_GpuControl.H commit 23d011180f4c852a6d7ebab5d6880e1ecad80e30 Merge: 7c255a9b4 ce129bf56 Author: Andrew Myers Date: Fri Apr 26 14:27:58 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7c255a9b4bf16aecd381efbdc35f66cf4bbb6ad1 Author: Andrew Myers Date: Fri Apr 26 14:27:48 2019 -0700 methods for defining the number of runtime real and integer components in the particle container Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit a48116dfb923c463c51b7685f8e4de36f5fee6c1 Author: Andrew Myers Date: Fri Apr 26 14:24:13 2019 -0700 update struct-of-arrays test to include runtime-added components Tests/Particles/main.cpp commit ce129bf56c13cd68197734467c9d0e29c820815e Merge: c3c020faa 1c8efe7a1 Author: mic84 Date: Fri Apr 26 13:38:35 2019 -0700 Merge pull request #467 from mwm126/patch-5 Change FindPythonInterp (deprecated) to FindPython commit 76043467ea451197246750069fb03bed9130f880 Author: Andrew Myers Date: Fri Apr 26 13:03:18 2019 -0700 including the runtime added comps in the ParticleContainer functions Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 1c8efe7a11299bb7606f9efef779243416698307 Author: Mark Meredith Date: Fri Apr 26 15:54:31 2019 -0400 Change FindPythonInterp (deprecated) to FindPython Since CMake 3.12, FindPython is the preferred way of detecting Python. Also run makebuildinfo_C.py with the detected Python version (instead of assuming env python) Src/CMakeLists.txt commit ebe0acdd22c71ab485dbb9280426806587e617b4 Author: Andrew Myers Date: Fri Apr 26 12:24:57 2019 -0700 functions for adding runtime real and int components Src/Particle/AMReX_Particles.H commit e4dc62ca8adfba43d13017538e5f2fc61cd8edce Author: Andrew Myers Date: Fri Apr 26 12:21:25 2019 -0700 Have the particle container keep track of how many runtime comps it has Src/Particle/AMReX_Particles.H commit 3f160db93cf830971f715499397ef39fcba9a4c8 Author: Andrew Myers Date: Fri Apr 26 11:48:15 2019 -0700 adding runtime soa components to StructOfArrays Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_StructOfArrays.H commit c3c020faab93df225aa31f9aa4e7048c22090810 Author: kngott Date: Fri Apr 26 11:34:48 2019 -0700 Further summit script adjustment. Tutorials/GPU/run.summit commit 02474f40c8de135ed11d29129a22827c738a3117 Author: Michele Rosso Date: Fri Apr 26 10:32:30 2019 -0700 CMake: fix scope of Particle compile definitions Src/Particle/CMakeLists.txt commit 001405ff0dc01f37a7b3c0be8caf5780a0c7820c Merge: 601333a12 1c21e8456 Author: WeiqunZhang Date: Fri Apr 26 10:28:02 2019 -0700 Merge pull request #466 from maikel/feature/FabUtils_ngrow_IntVect Add more support for non-uniform grow vectors to MultiFab and FabArrayUtility commit 22e88aed16e2e0145ea60661bbfaaeecf55a374e Author: Michele Rosso Date: Fri Apr 26 10:02:17 2019 -0700 CMake: completely include AMReX_buildInfo.H into build tree. Src/CMakeLists.txt Tools/CMake/AMReXInstallHelpers.cmake commit 601333a128d5d8803983dd7a662e7b57242d7c4d Merge: 692f64091 0955bc390 Author: WeiqunZhang Date: Fri Apr 26 09:55:28 2019 -0700 Merge pull request #465 from maikel/feature/Improve_Move_Assignment Improve move assignment operators for BoxArray and DistributionMapping commit 692f64091933a63ffa9e45fc7c328941aa9a4214 Merge: e0073d88f 303c849a8 Author: WeiqunZhang Date: Fri Apr 26 09:19:10 2019 -0700 Merge pull request #464 from rhouim/development Added a trilinear interpolation option for 3D on cpu. This can be us… commit 1c21e84568159dad0b870cc4804bbd65a64ac82a Author: Maikel Nadolski Date: Fri Apr 26 13:19:29 2019 +0200 Add more support for non-uniform grow vectors to MultiFab and FabArrayUtility. Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 0955bc390f497a5910962b6fd4d11cf73316413c Author: Maikel Nadolski Date: Fri Apr 26 11:27:21 2019 +0200 Use rule of six to improve constructors of BoxArray and DistributionMapping Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit e0073d88f4732adde714f73438984142f73bd256 Merge: b8b20fe29 c3b32496b Author: WeiqunZhang Date: Thu Apr 25 21:58:15 2019 -0700 Merge pull request #463 from maikel/feature/AmrMesh_refrat Improve AmrCore and AmrMesh constructors. commit b8b20fe29465289d2250fe5b1dc6a8f3f53c6729 Merge: 3df331054 d8eea5807 Author: Andrew Myers Date: Thu Apr 25 19:57:47 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3df3310540ac6bd036f11436d0c5efb481ec0a2d Author: Andrew Myers Date: Thu Apr 25 19:57:30 2019 -0400 also apply the shift to the remote neighbors (gpu neighbor particles) Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit d8eea580713128fb3122ed1e897109224ee8ce42 Author: Weiqun Zhang Date: Thu Apr 25 16:36:08 2019 -0700 Remove debug lines Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 2c18f3df7bfd711d362aa1c076be507a0569633d Author: Weiqun Zhang Date: Thu Apr 25 16:33:48 2019 -0700 Nodal 2d solver: save some codes in comments Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 61defafc4b51b9751d6fec9ef50c8752b6426e44 Author: Andrew Myers Date: Thu Apr 25 18:51:51 2019 -0400 keep track of periodicity (gpu neighbor particles) Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit b39bef17fb9e64ef3c8d698fe4d5bade1741ec2d Author: Andrew Myers Date: Thu Apr 25 18:51:09 2019 -0400 nested struct for keeping track of neighbor tasks to perform Src/Particle/AMReX_NeighborParticles.H commit 845bf285b5259a97e7a93dcf1bdf7cc49a807077 Author: Andrew Myers Date: Thu Apr 25 18:50:39 2019 -0400 functor for shifting neighbor particles periodically so that naive distance calculation will return the shortest distance Src/Particle/AMReX_Functors.H commit 95790801796dc48765d05578e1e9589d3c817bc1 Author: Michele Rosso Date: Thu Apr 25 15:27:55 2019 -0700 CMake: add options to enable/disable tutorials CMakeLists.txt commit c23ce2995d63505e092ee5ca810f8de5f72a5d00 Author: Michele Rosso Date: Thu Apr 25 15:18:53 2019 -0700 CMake: change location of configuration files Src/CMakeLists.txt Tools/CMake/AMReXInstallHelpers.cmake commit 268feb1dbba3e6faf66fad1b18521fb464e09412 Merge: a6a729186 7e2140865 Author: Brandon Runnels Date: Thu Apr 25 15:46:20 2019 -0600 Merge branch 'development' into nodeghostcells commit 79b53183d9ad280329e41dd03e787a6743057189 Merge: 4751a0825 7e2140865 Author: Weiqun Zhang Date: Thu Apr 25 14:02:13 2019 -0700 Merge branch 'development' into weiqun/mlmg commit 4751a0825028ae4f59dbaa90448d7499f9d65df8 Author: Weiqun Zhang Date: Thu Apr 25 14:01:19 2019 -0700 Nodal RAP: fix R Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 7e21408659c00afef600f03a245a697c225c8047 Author: kngott Date: Thu Apr 25 12:41:28 2019 -0700 Update script for shared nodes. Will be important to get resources as more users are added to the system. Tutorials/GPU/run.corigpu commit 4c4ffa7880d3cfaff0b09e9339e043043a15aab3 Author: Andrew Myers Date: Thu Apr 25 13:48:46 2019 -0400 store information about the periodic shift in the grid map (gpu neighbor particles) Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 8cde53ce0ced58cece2db8fbe23366b77bd00baf Author: Ann Almgren Date: Thu Apr 25 07:12:57 2019 -0700 Revert "When we run the "bottom solver" at mglev = 0, we want to go ahead and" This reverts commit 38b925f70d1795f651a4de94e249f6e57f23d456. Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 38b925f70d1795f651a4de94e249f6e57f23d456 Author: Ann Almgren Date: Wed Apr 24 17:34:37 2019 -0700 When we run the "bottom solver" at mglev = 0, we want to go ahead and solve to completion, so we set the "bottom solver tolerance" to the tolerance specified in the solve call, rather than 1e-4. Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 303c849a836c7e076b5c1589636f74fdad9d1d4e Author: rhouim Date: Wed Apr 24 19:36:03 2019 -0400 Added a trilinear interpolation option for 3D on cpu. This can be used by using cell_bilinear_interp in the FillPatch routines. This was tested with the Advection_AmrCore tutorial and it behaved as expected. Src/AmrCore/AMReX_INTERP_3D.F90 Src/AmrCore/AMReX_Interpolater.cpp commit 4f6e559195c385e2e811fcf01dfaa86b0cdc9a8a Author: Ann Almgren Date: Wed Apr 24 16:32:56 2019 -0700 Change from cell-by-cell testing on volfrac to testing on flag Src/Extern/Algoim/AMReX_algoim_integrals.cpp commit c2efa0d2c68d7cd3854fa50d22d29b4bd39a27f9 Merge: b40c876fa 6452b0c18 Author: Weiqun Zhang Date: Wed Apr 24 14:11:30 2019 -0700 Merge branch 'development' into weiqun/mlmg commit 46ceb84768fdf74604a2dd0b97aaa844163d800c Author: kngott Date: Wed Apr 24 14:09:36 2019 -0700 WIP: Starting conversion of 1 Rank FillBoundary. Src/Base/AMReX_FabArrayCommI.H commit 7f421c2f99498d809ec17dd8dba9ce547baca1c2 Author: kngott Date: Wed Apr 24 14:09:16 2019 -0700 Add graphs to FB object Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 636fd7cb81512099830e18dcbbb7a0218e71ce8e Author: kngott Date: Wed Apr 24 14:08:40 2019 -0700 Add AMReX_CudaGraph.H to AMReX_Gpu.H and add bool declaring if graph is ready. Src/Base/AMReX_CudaGraph.H Src/Base/AMReX_Gpu.H commit e842cc850e0861760ed6a645187a7fdd8c519d77 Author: kngott Date: Wed Apr 24 14:07:09 2019 -0700 Label auto const's as Arrayk4's for clarity. Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit b40c876fae3f2429b8339967ed71ce7faafa50a9 Author: Weiqun Zhang Date: Wed Apr 24 13:54:44 2019 -0700 WIP: first pass of RAP coarsening Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 6452b0c189128831deb0886765de8405b874e194 Author: Michele Rosso Date: Wed Apr 24 11:33:49 2019 -0700 Change '#if AMREX_USE_GPU' to '#ifdef AMREX_USE_GPU' Src/Base/AMReX_FabArray.H commit 0ad3b400bdcb37c2fbce2406adc122de53eee58e Merge: f0b679622 025df4164 Author: Michele Rosso Date: Wed Apr 24 10:47:15 2019 -0700 Merge branch 'development' into mr/cmake commit 025df41646133d7c9dc14d12eb3b78d1581c071c Author: Ann Almgren Date: Wed Apr 24 10:32:07 2019 -0700 Revert "Don't set regular stencils when volfrac < 1e-12 -- go ahead and" This reverts commit bee3e24c26ff6c27d5e0021e3c3021c0977de275. Src/Extern/Algoim/AMReX_algoim_integrals.cpp commit bee3e24c26ff6c27d5e0021e3c3021c0977de275 Author: Ann Almgren Date: Wed Apr 24 09:29:53 2019 -0700 Don't set regular stencils when volfrac < 1e-12 -- go ahead and compute the integrals. Src/Extern/Algoim/AMReX_algoim_integrals.cpp commit c3b32496b2e9903e131462ab284159ec731b969d Author: Maikel Nadolski Date: Wed Apr 24 09:47:04 2019 +0200 Use std::move to avoid allocations. Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.cpp commit d44970c2f6c7a053e3243d0a430395dbab58747c Author: Maikel Nadolski Date: Wed Apr 24 09:32:08 2019 +0200 Improve AmrCore and AmrMesh constructors. Change the refinement ratio paramter of AmrMesh's constructor from std::vector to amrex::Vector to be more consistent with non-uniform refinement ratios. Add a refrat parameter to AmrCore's constructor. Before this change AmrMesh's refinment parameter was never set to this custom value. Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit 5a32196210f7a0d024fb2cd946dcd9edb3129206 Author: Weiqun Zhang Date: Tue Apr 23 16:54:49 2019 -0700 WIP: RAP stencil: add A matrix Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit d5d2f50e87c8560776ad2536e66de49581036579 Author: Weiqun Zhang Date: Tue Apr 23 16:19:19 2019 -0700 WIP: RAP stencil: P Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 9ed24023d5a0e15d78840ea4a8e97213690e763d Author: Andrew Myers Date: Tue Apr 23 16:12:48 2019 -0700 formatting fix Docs/sphinx_documentation/source/Testing.rst commit a48652e2289de797156718d6df7c5676eddb6a0e Author: Andrew Myers Date: Tue Apr 23 16:11:54 2019 -0700 remove redundant statement (test runner docs) Docs/sphinx_documentation/source/Testing.rst commit 76815c111f29791d10461f05a6a534f4a201f1cc Merge: 9290c666c 48f3eb00d Author: Andrew Myers Date: Tue Apr 23 16:09:12 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9290c666c2da4eab35f1c0817323e6a01a526155 Author: Andrew Myers Date: Tue Apr 23 16:09:00 2019 -0700 fix typo Docs/sphinx_documentation/source/Testing.rst commit f58130bd64ff6ea955287cb4e50fa591d6114f57 Author: kngott Date: Tue Apr 23 16:07:41 2019 -0700 Store void* in CopyMemory instead of Array4 Src/Base/AMReX_CudaGraph.H Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit 416d94d89b6a7970987217039fa8a8a5f330747d Author: Weiqun Zhang Date: Tue Apr 23 15:17:06 2019 -0700 WIP: RAP stencil: interp_from Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 161d7e6f148b06f4e9e5b68601553bb605776f20 Author: Weiqun Zhang Date: Tue Apr 23 15:01:19 2019 -0700 WIP: RAP stencil Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 77418b7131c69c571840cef4fbfd241264d2e4e8 Author: kngott Date: Mon Apr 22 19:49:12 2019 -0700 Move to Arenas. Src/Base/AMReX_CudaGraph.H Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit 91f4a3e4e769c8d169c5a7583233948471b66257 Author: kngott Date: Mon Apr 22 17:22:59 2019 -0700 Move AMReX_CudaGraph to Src/Base. Src/Base/AMReX_CudaGraph.H Src/Base/Make.package Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit 56077668a47532c9a3806b4cdc2eb993b57642fb Author: Weiqun Zhang Date: Tue Apr 23 13:16:32 2019 -0700 use Array4 in cuda graph Src/Base/AMReX_Array.H Tests/GPU/CudaGraphs/GraphReuseCopy/AMReX_CudaGraph.H Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit f0b679622942397b081193135cda14d8154fb5a6 Author: Michele Rosso Date: Tue Apr 23 11:52:16 2019 -0700 CMake: get interface properties rather than private properties for Flags targets Tools/CMake/AMReX_Config.cmake commit 48f3eb00d9b64fe19c7f4786f89a9d2d84987f58 Author: Weiqun Zhang Date: Tue Apr 23 11:24:57 2019 -0700 minor Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 1e64b8ed586e5d86176b84cdcb9776853f51b0b3 Author: Weiqun Zhang Date: Tue Apr 23 11:19:41 2019 -0700 No need to call FillBoundary on integrals because we compute them in ghost cells. Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit b3604ba1e2f0ed3e069a17bbc15e8653b8d1de18 Author: Weiqun Zhang Date: Tue Apr 23 10:57:38 2019 -0700 Use Array4 in computing integrals using algoim Src/Extern/Algoim/AMReX_algoim_integrals.H Src/Extern/Algoim/AMReX_algoim_integrals.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 436f754c05c7a52cec183dd5d8d56c908910e305 Author: Weiqun Zhang Date: Tue Apr 23 10:23:18 2019 -0700 Add Make.algoim. USE_ALGOIM -> AMREX_USE_ALGOIM. For hypre and petsc, both _DIR and _HOME are allowed. Src/Extern/Algoim/CMakeLists.txt Src/Extern/Algoim/Make.package Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tests/LinearSolvers/NodeEB/GNUmakefile Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.algoim Tools/GNUMake/packages/Make.hypre Tools/GNUMake/packages/Make.petsc commit c050a3d93c84821952ec5acd2615dab1afcda4a3 Author: Weiqun Zhang Date: Tue Apr 23 08:59:51 2019 -0700 FabArray: m_host_fabs_v is gone. Src/Base/AMReX_FabArray.H commit 706608af9e604fa3c938eb471f46d2fe6637eda8 Author: kngott Date: Mon Apr 22 17:07:38 2019 -0700 Remove un-needed MemCpy from CudaGraph. Tests/GPU/CudaGraphs/GraphReuseCopy/AMReX_CudaGraph.H commit 1fcb4e35dcc91d01f56b8fe01246e7b8c3fd3b6c Author: kngott Date: Mon Apr 22 17:01:40 2019 -0700 Update test for improved CudaGraph object. Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit fe225309b6e853c9475d279dc7176510137814d7 Author: Andrew Myers Date: Mon Apr 22 17:00:07 2019 -0700 adding some pages to the documentation about the regression testing Docs/sphinx_documentation/source/Regression_Testing_Chapter.rst Docs/sphinx_documentation/source/Testing.rst Docs/sphinx_documentation/source/index.rst commit fd4d15da2c5b1cde5dfab2be41b03619c310d0e2 Author: Andrew Myers Date: Mon Apr 22 15:51:49 2019 -0700 adding a sample .ini for running the amrex regression tests locally Tools/RegressionTesting/AMReX-tests.ini commit 9c0fcb6a481e10e79e158b47c389c6d1c481a1d0 Merge: 783deefb0 ac8fb6a72 Author: Weiqun Zhang Date: Mon Apr 22 15:41:27 2019 -0700 Merge branch 'development' into weiqun/mfdtor commit c2e57b347d0e6a86eac48fc984a1df2d7e540af2 Merge: b9a23594a ac8fb6a72 Author: kngott Date: Mon Apr 22 15:30:39 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit ac8fb6a7272d5e1c44d59a22df8154cc09b039f9 Author: kngott Date: Mon Apr 22 15:27:10 2019 -0700 Make Array4 Variables non-const. Src/Base/AMReX_Array.H commit b9a23594a09364666c9fefeffa84062e7baa559e Author: Weiqun Zhang Date: Mon Apr 22 15:11:05 2019 -0700 Tidy cuda graph classes Tests/GPU/CudaGraphs/GraphReuseCopy/AMReX_CudaGraph.H commit 7629e2068ceba11989cf3c1cea591d9217293ba6 Merge: ed650e27b 2bfe3a225 Author: Michele Rosso Date: Mon Apr 22 13:46:47 2019 -0700 Merge branch 'development' into mr/cmake commit 2bfe3a2255e13581235de58c6b88fe4d8d1eccd0 Author: Weiqun Zhang Date: Mon Apr 22 12:58:22 2019 -0700 Add prerequisites for building AMReX. This addresses comment #1 in Issue #458. Docs/sphinx_documentation/source/BuildingAMReX_Chapter.rst commit 348562f668fcaeba4b71e0b3d29b58213c199da6 Author: kngott Date: Mon Apr 22 12:41:21 2019 -0700 Separate CudaGraph object. Tests/GPU/CudaGraphs/GraphReuseCopy/AMReX_CudaGraph.H Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit 7ab43f9717fd1143bc4763e7360bf73c5f815b3a Merge: bf6e448c2 863515ea3 Author: Weiqun Zhang Date: Mon Apr 22 12:27:23 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit bf6e448c2a46281d1cc309313036b31ec170d70b Author: Weiqun Zhang Date: Mon Apr 22 12:27:16 2019 -0700 Update compilestesing.py for python 3 Tools/CompileTesting/compiletesting.py commit 637996a362d80103381ec726f26788717540f242 Author: Ann Almgren Date: Mon Apr 22 10:31:22 2019 -0700 Add John to core contributor list. README.md commit 863515ea30827e7205d6656c4fdb94b83be240bf Author: Ann Almgren Date: Mon Apr 22 10:31:22 2019 -0700 Add John to core contributor list. README.md commit 17ae359bf903ceacf0b549b500f87e276537064d Author: Ann Almgren Date: Mon Apr 22 06:48:04 2019 -0700 Fix oops in how we read in n_error_buf now that it is locally an IntVect Src/AmrCore/AMReX_AmrMesh.cpp commit 393e265d727c669a6f3184eaa9b3c603090fdf2b Author: kngott Date: Mon Apr 22 00:31:16 2019 -0700 First draft of working Graph object. Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit b53960c6b2941777650c12a7a139cb3771ab4682 Author: Ann Almgren Date: Sun Apr 21 13:18:53 2019 -0700 Add more detail about using GitHub issues. README.md commit 30ece45cb66a84ce4e1d11d7c85ee71faac8416b Author: Ann Almgren Date: Sun Apr 21 13:09:36 2019 -0700 Add list of current "core developers" to AMReX README README.md commit 123685425c31ab5fb6995996d5a4dbc36bd04d1a Author: Ann Almgren Date: Sun Apr 21 13:18:53 2019 -0700 Add more detail about using GitHub issues. README.md commit aecd721fa8cc1812d2b630f991cb71caa47ca851 Author: Ann Almgren Date: Sun Apr 21 13:09:36 2019 -0700 Add list of current "core developers" to AMReX README README.md commit 0bcbec1dbd8464ec983871b75a9a97a693666478 Author: Weiqun Zhang Date: Sat Apr 20 20:19:58 2019 -0700 Add optional argument for direction to AmrMesh::nErrorBuf function. Add IntVect version, nErrorBufVect. add optional argument for direction to FabArrayBase::nGrow Src/AmrCore/AMReX_AmrMesh.H Src/Base/AMReX_FabArrayBase.H commit 783deefb0068e55673055273a95c41237c87b562 Merge: ca282bf16 b4dcc2a4f Author: Weiqun Zhang Date: Sat Apr 20 18:37:00 2019 -0700 Merge branch 'development' into weiqun/mfdtor commit b4dcc2a4f3647184bda107f5530026c0a9387c61 Author: Weiqun Zhang Date: Sat Apr 20 18:03:42 2019 -0700 add a new BoxArray::growcoarsen function that takes IntVect as ngrow parameter and use it in TagBoxArray Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit d7d69522ad9eaa8fa3b7233b9b16c1684a55abcb Author: Weiqun Zhang Date: Sat Apr 20 17:59:58 2019 -0700 return IntVect from TagBoxArray::borderSize Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_IntVect.H commit ca282bf16a522e67df25da25bce330fe0f0042d8 Merge: 207359e3c 91340ee1c Author: Weiqun Zhang Date: Sat Apr 20 17:47:53 2019 -0700 Merge branch 'development' into weiqun/mfdtor commit 207359e3c1b26bf912f51d7a1b0f44630a966c4f Author: Weiqun Zhang Date: Sat Apr 20 17:47:04 2019 -0700 TagBoxArray: host ptr is the owner now Src/AmrCore/AMReX_TagBox.cpp commit 91340ee1c2ec0529f3a76539c6bcc48ee759796b Merge: b6201fd19 c8a6810aa Author: WeiqunZhang Date: Sat Apr 20 17:02:45 2019 -0700 Merge pull request #461 from chaw0023/HypreDeclaration Add missing declaration for hypre_int commit c8a6810aa721dc7e0b52a20d342fda4640e2ce89 Author: Saurabh Chawdhary Date: Sat Apr 20 17:57:45 2019 -0500 Add missing declaration for hypre_int Src/Extern/PETSc/AMReX_PETSc.cpp commit b6201fd19a989be5dc6ee8c35597dfd91b37d2c3 Author: Ann Almgren Date: Sat Apr 20 15:56:28 2019 -0700 Makes n_error_buf in AmrMesh class an IntVect rather than an int. Note that AmrCore-based codes can use this option by setting n_error_buf_x, n_error_buf_y, n_error_buf_z rather than setting simply n_error_buf in the inputs file, but setting n_error_buf will still work. AmrLevel-based applications are only able to use the int functionality since they don't currently have an errorEst routine that takes an IntVect. AmrCore-based apps may need to change based on this change; AmrLevel-based codes should not have to. Src/Amr/AMReX_Amr.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp commit 997547f60937437ec688d15049c6934bb6190db6 Merge: a23433996 46b457fd9 Author: Weiqun Zhang Date: Sat Apr 20 12:01:13 2019 -0700 Merge branch 'development' into weiqun/mfdtor commit 46b457fd98997bb83765b83c209318b1154fdfac Author: Weiqun Zhang Date: Sat Apr 20 12:00:36 2019 -0700 avoid fortran keyword Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit 1dde256e1f9b7684df62ec0f41cefd0513cf9a6c Author: Weiqun Zhang Date: Sat Apr 20 11:51:54 2019 -0700 shorten names Tests/Slice/GNUmakefile Tests/Slice/Make.package Tests/Slice/inputs Tests/Slice/main.H Tests/Slice/main.cpp Tests/SliceWithInterp/inputs Tests/SliceWithInterp/main.cpp commit a23433996c146526e3f9042dbc7c5782b3b14550 Author: Weiqun Zhang Date: Sat Apr 20 09:13:06 2019 -0700 Update the new fabDevicePtrAtLocalIdx and fabHostPtrAtLocalIdx functions because m_host_fabs_v has been removed Src/Base/AMReX_FabArray.H commit 31b6e0f8916ecbe40e1699a9dfeca22cb5ae8b81 Merge: 1117d77a7 5514d867b Author: Weiqun Zhang Date: Sat Apr 20 08:53:09 2019 -0700 Merge branch 'development' into weiqun/mfdtor commit 5514d867bfda0f93fb77911dfbf5024101522639 Merge: 7222ba2c2 94625cfb6 Author: WeiqunZhang Date: Fri Apr 19 20:22:37 2019 -0700 Merge pull request #459 from chaw0023/PetscSolveLS Petsc bottom solver in F_interface; update GNUmakefile commit 7222ba2c298ce47d7a9f44fb41045c00fdcc19d5 Author: Weiqun Zhang Date: Fri Apr 19 20:09:27 2019 -0700 add inputs.hypre and inputs.petsc to ABecLaplacian_C tutorial Tutorials/LinearSolvers/ABecLaplacian_C/inputs.hypre Tutorials/LinearSolvers/ABecLaplacian_C/inputs.petsc commit 8e589841aff3b399d71c3f315695185f580bc6d4 Author: Weiqun Zhang Date: Fri Apr 19 19:49:39 2019 -0700 PETSc: remove dependency on HYPRE Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/PETSc/AMReX_PETSc.H Src/Extern/PETSc/AMReX_PETSc.cpp Src/Extern/PETSc/AMReX_PETSc_fort_mod.F90 Src/Extern/PETSc/Make.package commit ed650e27b87020c2982b61f6d51f8555312f22ba Merge: 8b3d4e9d5 fb00c6fc6 Author: Michele Rosso Date: Fri Apr 19 17:35:40 2019 -0700 Merge branch 'development' into mr/cmake commit 8b3d4e9d5622565f1692a79550c8de909f77aad9 Author: Michele Rosso Date: Fri Apr 19 17:34:59 2019 -0700 CMake: clean up Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/TestManager.cmake Tools/CMake/select_gpu_arch.cmake commit f97eb34c4e6cf1499ce8d927aa57146f71f9639c Author: Michele Rosso Date: Fri Apr 19 17:31:38 2019 -0700 CMake: fix bug in CUDA flags due to recent changes Tools/CMake/AMReX_Config.cmake commit a9f9781195445dacedcc8e7ecaa1c7500bbe17fd Author: Michele Rosso Date: Fri Apr 19 17:17:01 2019 -0700 CMake: treat C++ and Fortran flags in a target-oriented fashion * Define INTERFACE targets for C++ and Fortran flags. * Export those targets so that app codes can use them. Src/CMakeLists.txt Tools/CMake/AMReXFlagsTargets.cmake Tools/CMake/AMReXInstallHelpers.cmake Tools/CMake/AMReX_Compilers.cmake commit 94625cfb60b733450ed7444115d9d9ae97aab926 Author: Saurabh Chawdhary Date: Fri Apr 19 18:25:25 2019 -0500 Add Particle fortran interface directory to Pdir GNUmakefile.in commit 3225aca3baa1ef125a4c40f530061a551ab3cce2 Author: Saurabh Chawdhary Date: Fri Apr 19 18:02:07 2019 -0500 Add option for using petsc as bottom solver Src/F_Interfaces/LinearSolvers/AMReX_multigrid_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90 commit f488568e17878b9e65a8f09973454dec2c135487 Author: Saurabh Chawdhary Date: Fri Apr 19 18:11:31 2019 -0500 Add option --enable-petsc to use PETSc as bottom solver GNUmakefile.in Tools/libamrex/configure.py commit fb00c6fc64b4148a76052cb655f3f272bf3a2155 Author: kngott Date: Fri Apr 19 15:52:48 2019 -0700 run.summit update #4. Tutorials/GPU/run.summit commit 4f91803860b92d2017f1c1df6055861dfa799338 Author: kngott Date: Fri Apr 19 15:40:21 2019 -0700 run.summit update #3. Tutorials/GPU/run.summit commit b4b17d40698584b5c3b4ed8596f0bc82ba2a281e Author: kngott Date: Fri Apr 19 14:03:30 2019 -0700 More Summit and CoriGPU script updates. Tutorials/GPU/run.corigpu Tutorials/GPU/run.summit commit 0d5e4d23cb18296e02ca21709eab98b1c7cbbae4 Merge: 73d6fb8d1 fa8334754 Author: Andrew Myers Date: Fri Apr 19 16:37:52 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 73d6fb8d11ead973ac36a935bcf59244bfde0ae5 Author: Andrew Myers Date: Fri Apr 19 16:37:40 2019 -0400 remove misleading timer from NeigborList::build Src/Particle/AMReX_NeighborList.H commit 4aca87f69252c8b2bc44badb1d27af24487a93e5 Author: Andrew Myers Date: Fri Apr 19 16:37:07 2019 -0400 change AMREX_ALWAYS_ASSERT to AMREX_ASSERT here Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit fa83347549d927dd0c18a22f3c9f1d396e803174 Author: kngott Date: Fri Apr 19 12:41:50 2019 -0700 Add Summit and jsrun specs to sample run script. Tutorials/GPU/run.summit commit 6629fae299a8367c4250d90151ed45b81905562a Author: Weiqun Zhang Date: Fri Apr 19 12:36:05 2019 -0700 amrex::Tuple is now an alias to std::tuple Src/Base/AMReX_Tuple.H commit 70dbf590b4ae8df2093e4c76cab056e0d70e060e Merge: d9a63cfa9 be836cf89 Author: Andrew Myers Date: Fri Apr 19 11:23:49 2019 -0700 Merge pull request #440 from RevathiJambunathan/SliceGenerationForDiagnostics_RJ Slice generation for diagnostics rj commit d9a63cfa9cdf2970a75c5f9df0bc573227199062 Author: Weiqun Zhang Date: Fri Apr 19 10:59:44 2019 -0700 AmrMesh: relax the assumption that the base level domain has even number of cells in each direction Src/AmrCore/AMReX_AmrMesh.cpp commit fa4643a2aa829dc85fa3428b24cbfbd935757665 Merge: 39735068c 1fba3a527 Author: Andy Nonaka Date: Fri Apr 19 10:36:09 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 39735068cc5ff4967b44945327302060e3a95edb Author: Andy Nonaka Date: Fri Apr 19 10:35:56 2019 -0700 minor tutorial notes Docs/sphinx_documentation/source/EB.rst Docs/sphinx_tutorials/source/EB_Tutorial.rst commit 2c80873a4f8a6a309c3469bf7d5c42061e6c507c Author: kngott Date: Fri Apr 19 10:14:40 2019 -0700 Graphs using Graph Class. WIP. Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit 1fba3a527594d7ac956ef5b1eaa735b03e99a4b7 Author: Weiqun Zhang Date: Fri Apr 19 09:32:20 2019 -0700 octree average down leaves: fix component index Src/F_Interfaces/Octree/AMReX_octree_mod.F90 commit 98344d3db3047f3398fb4d08178183626b4084fa Author: Andy Nonaka Date: Fri Apr 19 09:13:01 2019 -0700 EB/Poisson tutoral (enclosed sphere at zero potential with a point charge in the interior); fixed convergence issue - for now must specify Dirichlet domain boundary conditions, even if the fluid doesn't touch the domain boundary (AMReX was thinking the problem was singular) Tutorials/EB/Poisson/inputs Tutorials/EB/Poisson/main.cpp commit e3444f388b018040f1a3259dea8afb3118cdf75e Author: Andy Nonaka Date: Fri Apr 19 08:34:42 2019 -0700 init_data function Tutorials/EB/Poisson/Make.package Tutorials/EB/Poisson/Poisson.H Tutorials/EB/Poisson/Poisson.cpp Tutorials/EB/Poisson/Poisson_F.H Tutorials/EB/Poisson/main.cpp Tutorials/EB/Poisson/poisson.F90 commit be836cf89f7ba88bc2098e23275e0fc4a3410ff3 Author: RevathiJambunathan Date: Thu Apr 18 23:20:28 2019 -0700 Modified the diagnostic slice generation to inherent the index type of the underlying data. The code reads in lo and hi of the slice, and coarsening ratio. If the input for coarsening ratio is not an exponent of 2, then within the code, the ratio is modified to the nearest exponent of 2. The slice is generated in three steps. First, using the input lo and hi, the slice is generated with geom.CellSize() equal to the computational domain. Note that, in this test case, only one level of refinement is assumed. Next, if a 2D slice is extracted at a location where the data points are not available, then values are interpolated on the slice from the nearest points. Finally, if the coarsening ratio in any direction is > 1, then the data from the refine slice is averaged and stored on the coarsened slice ensuring that the box array sizes for both, refined and coarse slice are equal. I have assumed nghost > 0, since for interpolation, we need values from the ghost cells. The initial values for the baseline slice is such that the 0th,1st, and 2nd component correspond to x-pos y-pos, and z-pos, respectively. Tests/CreateSliceForDiagnosticsWithInterpolation_adjusttocoarsenIfrequired/inputs Tests/CreateSliceForDiagnosticsWithInterpolation_adjusttocoarsenIfrequired/main.cpp commit 18b2078821cba614af395108463f557e4d0466a9 Merge: 4a3322555 591856268 Author: Weiqun Zhang Date: Thu Apr 18 21:40:38 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4a332255586a0dfd9a4cf0c291e7d5e3bac7feb6 Author: Weiqun Zhang Date: Thu Apr 18 21:40:03 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development Src/Particle/AMReX_NeighborList.H Src/Particle/AMReX_ParticleContainerI.H Tutorials/EB/MacProj/GNUmakefile Tutorials/EB/MacProj/Make.package Tutorials/EB/MacProj/initEB.H Tutorials/EB/MacProj/initEB.cpp Tutorials/EB/MacProj/main.cpp Tutorials/EB/Poisson/GNUmakefile Tutorials/EB/Poisson/Make.package Tutorials/EB/Poisson/inputs Tutorials/EB/Poisson/main.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/GNUmakefile.libamrex Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainerInit.cpp commit f509cb16d7a24b3d83244d7fcc1f1038f3e5df65 Author: Weiqun Zhang Date: Thu Apr 18 21:36:25 2019 -0700 octree average_down: support for components and volume weighted Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Src/F_Interfaces/Octree/AMReX_octree_mod.F90 commit 2c6450848de3dd4b510d0d8df495afe17df27e41 Author: Weiqun Zhang Date: Thu Apr 18 21:04:16 2019 -0700 fix bug in octree leaf index array Src/F_Interfaces/Octree/AMReX_octree_fi.cpp commit 5fb9e7645a1844afd4358593f3b3333618d30591 Author: Weiqun Zhang Date: Thu Apr 18 20:44:56 2019 -0700 average down octree leaves Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Src/F_Interfaces/Octree/AMReX_octree_mod.F90 commit 92806ae87a384ff32d9778098e1a72380fc698d4 Author: Weiqun Zhang Date: Thu Apr 18 20:44:06 2019 -0700 add FabArray member functions for getting fab ptr given local index Src/Base/AMReX_FabArray.H commit 59185626809fdcd591c642fd678779f0fa05e835 Merge: 826d60c8f 56d98c8c5 Author: Andy Nonaka Date: Thu Apr 18 17:45:13 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 826d60c8fbc384a24547b191be2e672b04326e93 Author: Andy Nonaka Date: Thu Apr 18 17:44:27 2019 -0700 EB Poisson solver example. Needs a little tweaking still as the MG isn't converging well yet. Tutorials/EB/Poisson/GNUmakefile Tutorials/EB/Poisson/Make.package Tutorials/EB/Poisson/inputs Tutorials/EB/Poisson/main.cpp commit 56d98c8c57ad44bd5135e452ba60b5063bc017b0 Author: Andrew Myers Date: Thu Apr 18 19:58:32 2019 -0400 instruct thrust to use pooled memory for it's internal reduce operation in build neighbor list gpu Src/Particle/AMReX_NeighborList.H commit 281d8c0c80821851346c50f5c381a311e1ba63b4 Merge: 36dd49ed9 49836b6b8 Author: Andrew Myers Date: Thu Apr 18 19:10:23 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 36dd49ed92b9a495814c4dad2e8c004098088a0e Author: Andrew Myers Date: Thu Apr 18 19:09:34 2019 -0400 cache temporary variables in GPU NeighborList::build to save memory and avoid expensive cudaMalloc/cudaFree calls Src/Particle/AMReX_NeighborList.H commit 49836b6b83fac6a5c1729ed5a54e6fd9906286f5 Author: Andrew Myers Date: Thu Apr 18 12:34:13 2019 -0700 update PIC tutorial makefile Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/GNUmakefile.libamrex commit 52207e7292b9a51af0f2244f7872518d3b344b54 Author: Andrew Myers Date: Thu Apr 18 11:13:44 2019 -0700 dual grid particle restart - still need to skip if the header doesn't exist Src/Particle/AMReX_ParticleContainerI.H commit fe756d58a17f44354d8ac0905d9a11c8fe22c5b8 Author: Andrew Myers Date: Thu Apr 18 10:59:40 2019 -0700 fix typo Src/Particle/AMReX_ParticleContainerI.H commit cd515184e6d22ffd3c9c7b4d929ff43fd0a050c5 Author: Andrew Myers Date: Thu Apr 18 10:58:17 2019 -0700 in the particle restart, open the data file in binary mode. text mode is not sure to work for all implementations Src/Particle/AMReX_ParticleContainerI.H commit 93fe93138ce8c3c856129fa069951258320cf4c9 Author: Andrew Myers Date: Thu Apr 18 10:57:08 2019 -0700 fix logic in the dual grid restart to handle the case where not all levels have particles Src/Particle/AMReX_ParticleContainerI.H commit 656f310db34ae12d213e553964026fa601f3b5c0 Merge: 77c540b99 a637e5a04 Author: Andrew Myers Date: Thu Apr 18 10:52:13 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a637e5a040e36a81df7deeaece8d98a1e346dbed Merge: a7340027d aefa164e5 Author: Andrew Myers Date: Thu Apr 18 13:50:23 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 77c540b9931f9876190545aeb56152734f7be522 Author: Andrew Myers Date: Thu Apr 18 10:50:18 2019 -0700 fix whitespace errors in Makefile Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/GNUmakefile.libamrex commit a7340027d262d9342a7c49ddbef9520c301e66f9 Author: Andrew Myers Date: Thu Apr 18 13:49:59 2019 -0400 add missing file Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainerInit.cpp commit aefa164e55ffcf7995ab06476237ff4a21afb788 Merge: 5943fd5f7 88a2e78c1 Author: Andy Nonaka Date: Thu Apr 18 09:42:38 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 5943fd5f73179e78ad8d3f2b68c52117df9237f1 Author: Andy Nonaka Date: Thu Apr 18 09:42:26 2019 -0700 cleanup, comment tutorial Tutorials/EB/MacProj/GNUmakefile Tutorials/EB/MacProj/Make.package Tutorials/EB/MacProj/initEB.H Tutorials/EB/MacProj/initEB.cpp Tutorials/EB/MacProj/main.cpp commit e9913162027304110b8cca3a842aac94a310dc6c Author: Weiqun Zhang Date: Thu Apr 18 09:14:54 2019 -0700 octree: add BoxArray and DistributionMapping for leaf nodes only Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.H Src/F_Interfaces/AmrCore/AMReX_FAmrCore.H Src/F_Interfaces/Octree/AMReX_octree_fi.cpp commit 88a2e78c13eabc35f081cbc27aad4204347e29cf Author: Andrew Myers Date: Wed Apr 17 19:42:21 2019 -0400 move GNUmakefile.libamrex to the proper location Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/GNUmakefile.libamrex commit e3816db33b14db370f4fbaf7240b9669a7c79175 Merge: 0099cab65 4b9bd87f9 Author: Andrew Myers Date: Wed Apr 17 19:41:35 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0099cab65f84f49e40d50f06ffaf12eb4af539d0 Author: Andrew Myers Date: Wed Apr 17 19:41:11 2019 -0400 Adding a makefile, courtesy of Chris Daley and Weiqun, for building the PIC tutorial using a shared amrex library Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/GNUmakefile.libamrex commit d765b0e9ed766a857db68ec3defa858917b1c54b Author: Andrew Myers Date: Wed Apr 17 19:40:28 2019 -0400 add a few more options to the configure.py script for libamrex Tools/libamrex/configure.py commit 4b9bd87f95f2104360f3e1de04d697155178ab86 Merge: 2d3d15269 ce5208177 Author: Andy Nonaka Date: Wed Apr 17 15:37:15 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit ce5208177fb9e203938afb34dbec57a2e7dc0ce1 Merge: 715b6e56b ab0d7a90a Author: Andrew Myers Date: Wed Apr 17 18:36:44 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2d3d15269503b3f832c36f6337e53dafcfd46590 Author: Andy Nonaka Date: Wed Apr 17 15:36:31 2019 -0700 this tutorial now uses a mac projection to compute flow around a sphere given an initial velocity field of (1,0,0). There is also now a plotfile output that outputs the initial and final velocity and divergence Tutorials/EB/MacProj/main.cpp commit 715b6e56b627cc9c4e71d097635d94d28fd56f4b Author: Andrew Myers Date: Wed Apr 17 18:36:11 2019 -0400 use the share, gpu-enabled initialization routines for all the different versions of the EM PIC Tutorial Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Source/Make.package commit 6c1a86c90eb8a28dbc9e33afe60870c087793ac1 Author: Andrew Myers Date: Wed Apr 17 18:34:57 2019 -0400 update repo name in job submission script Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/script.sh commit 7a454be21b5b44fd35281cae4896f72ae8c00f7b Author: Andrew Myers Date: Wed Apr 17 18:14:05 2019 -0400 some tweaks and bug fixes to init particles Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp commit f306f29abf6456a3861a06f3506e575de2974601 Author: Andrew Myers Date: Wed Apr 17 18:06:36 2019 -0400 minor formatting change Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90 commit 27a2f9e421b5316c32412e898d696c2a2346a73d Author: Andrew Myers Date: Wed Apr 17 18:02:15 2019 -0400 correct CUDA version of gather_fields routine (EMPIC Tutorial) Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H commit 074f2f51d54d300711a93ca2b30520396a0aee3f Author: Andrew Myers Date: Wed Apr 17 15:00:39 2019 -0400 update python utility to look for the correct number of digits in the output Tools/Py_util/amrex_particles_to_vtp/amrex_binary_particles_to_vtp.py commit 1117d77a77c383158da1bf3ab0d2dc339b1b51cc Merge: 4deac7533 5973d4480 Author: Weiqun Zhang Date: Wed Apr 17 11:01:20 2019 -0700 Merge branch 'development' into weiqun/mfdtor commit 4deac75331a1429662fb815f90bccd542b2751de Author: Weiqun Zhang Date: Wed Apr 17 11:01:11 2019 -0700 no need to build device fabs for the temporary multifab in overridesync Src/Base/AMReX_FabArrayUtility.H commit 1e9edeeef6795d0686b6b9369c645c21258df8b5 Author: Andrew Myers Date: Wed Apr 17 13:44:32 2019 -0400 EM PIC Tutorial fix - need to convert this box so that it has the same type as jx (in check_langmuir_solution) Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.cpp commit 4f14cc7a55ad2a55d7140eeb1bd1abc52a0805d5 Author: Andrew Myers Date: Wed Apr 17 13:43:03 2019 -0400 mark these functions __host__ __device__ so they can also be run on the host for debugging Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H commit ab0d7a90a374887322bb1affb16117b2ff34d5b8 Author: Michele Rosso Date: Wed Apr 17 10:07:51 2019 -0700 CMake: add path to typechecker in export config file Tools/CMake/AMReXConfig.cmake.in commit 5973d4480a262897e18db2ff4681f0f95c8e742e Author: Andrew Myers Date: Wed Apr 17 07:47:47 2019 -0700 fix particle restart when finestLevel() goes down Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 8214977df6140ffc0cdba3eca396d797c4c42cc3 Author: Weiqun Zhang Date: Tue Apr 16 21:58:04 2019 -0700 fix a bug in tutorial Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 13817df5f960ab81c884302f890f07e9a828bae6 Author: Weiqun Zhang Date: Tue Apr 16 19:04:17 2019 -0700 fix alias FabArray Src/Base/AMReX_FabArray.H commit 8bfd3b6e8b22e87a002729c244a7f1c3491af0ad Author: Weiqun Zhang Date: Tue Apr 16 17:03:04 2019 -0700 fix data ptr consistence check Src/Base/AMReX_FabArray.H commit 4be754ebc7921f54d39c5b55eeb120f3b310daf3 Author: Weiqun Zhang Date: Tue Apr 16 16:56:53 2019 -0700 skip delete for nullptr Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabFactory.H commit 1f8162cf798fe749fe4780719b9a70a531c4741b Author: Weiqun Zhang Date: Tue Apr 16 14:43:33 2019 -0700 Option to not create device fabs Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.cpp commit ebfffb58e5a09ea62fea58f0219d0c153e6786ab Author: Weiqun Zhang Date: Tue Apr 16 14:25:23 2019 -0700 remove unused function Src/Base/AMReX_FabFactory.H commit 6578d600eb1e1d7bb7f7a64e5ea465ec78ace616 Author: Weiqun Zhang Date: Tue Apr 16 14:19:52 2019 -0700 make sure setFab only takes host fab. remove some deprecated functions in CoordSys Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_VisMF.cpp Src/EB/AMReX_EB2_MultiGFab.cpp Src/EB/AMReX_MultiCutFab.cpp commit fb6c7b96154e801bb0233c568bba7af34454e30f Author: Tan Nguyen Date: Tue Apr 16 14:00:53 2019 -0700 support on demand mode where an MFIter loop can be easily transformed into the async form Src/Amr/AMReX_Amr.cpp Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.cpp Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.cpp Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/pthreads_common/RGIter.H 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Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_3d/slope_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/._Adv_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/._Make.package Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/._Tagging_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/._tagging_params.f90 Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/Adv_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/Make.package Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/Tagging_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/Src_nd/tagging_params.f90 Src/AmrTask/tutorials/MiniApps/Adv_Async_OnDemand/Source/main.cpp Src/Base/AMReX_MultiFabUtil_Perilla.cpp commit 067ed424c0934fc7ed6b03cd8985d42d41f2b1b0 Author: Andrew Myers Date: Tue Apr 16 15:11:16 2019 -0400 formatting change Src/Particle/AMReX_Particles.H commit 225809167b0cb00308764165c30d3c685cc0b461 Author: Andrew Myers Date: Tue Apr 16 15:10:44 2019 -0400 offloading init particles in the CUDA version of the EM PIC Tutorial Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp commit aeecd78bba6fe99f5b597247f8fda01ae0eb4574 Author: Andrew Myers Date: Tue Apr 16 15:09:44 2019 -0400 add functions to StructOfArrays that return a GPU-accessible holder for the data pointers. Src/Particle/AMReX_StructOfArrays.H commit 4c71ce3e3486bff04d090d2e6502ec3d1341246d Author: Andrew Myers Date: Tue Apr 16 15:02:25 2019 -0400 implement GPU version of RandomNormal Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 63efdb7487ac29b104b424606ac4fc3883f39837 Author: Andrew Myers Date: Tue Apr 16 15:01:45 2019 -0400 automatically deallocate the random number arrays in amrex::Finalize Src/Base/AMReX.cpp Tests/GPU/RandomNumberGeneration/main.cpp commit 8432e342d34981b7ac7e36656340319d53dd8e1b Author: Weiqun Zhang Date: Tue Apr 16 10:30:13 2019 -0700 remove deprecated ctors Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_Mask.cpp Src/EB/AMReX_EBFArrayBox.H Src/EB/AMReX_EBFArrayBox.cpp commit 6c0334e0eb91ab39e1789e292b3ce7a0dfe5190b Merge: 2ccddfa70 c3f05b272 Author: Weiqun Zhang Date: Tue Apr 16 10:04:01 2019 -0700 Merge branch 'development' into weiqun/mfdtor commit 2ccddfa70bdcb1e601ed18099e2986c1faed2535 Author: Weiqun Zhang Date: Tue Apr 16 10:02:18 2019 -0700 FabArray: make host fab the main owner and device fab an alias. This will allow for not creating device fabs at all Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabFactory.H Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_Mask.cpp Src/EB/AMReX_EBFArrayBox.H Src/EB/AMReX_EBFArrayBox.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_MultiCutFab.H commit c3f05b2725c0bfadb0e46467b5cf2be9f32d676b Author: Weiqun Zhang Date: Tue Apr 16 12:59:30 2019 -0400 manually inline static constexpr member for device functions Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBCellFlag.cpp commit b30371b43db3419930d18a19fb371200073c16ed Author: Weiqun Zhang Date: Tue Apr 16 12:08:40 2019 -0400 std::max --> amrex::max in device function Src/EB/AMReX_EB2_IF_Cylinder.H commit b573e7a83ce77f2b8334fe6745ae34aac18e3062 Author: kngott Date: Tue Apr 16 08:25:52 2019 -0700 FAB* and Array4 versions both available. Array4 expected due to future unified memory flags. Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit 4ee9542ec29f971d961868ad24caad5a0c32816b Merge: 929e69347 f974bfe82 Author: Andrew Myers Date: Mon Apr 15 15:32:17 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 929e69347c62bf9ce34cd3b005ea98bcf690d0d8 Author: Andrew Myers Date: Mon Apr 15 15:32:08 2019 -0700 update the neighbor particle documentation to account for the fact that the neighbors are Vector, not Vector now. Docs/sphinx_documentation/source/Particle.rst commit f974bfe8266d17a5c820b3b6d71de5ed6ea1e649 Author: Max Katz Date: Mon Apr 15 12:25:28 2019 -0400 Add option to output fextract in scientific notation Tools/Plotfile/fextract.cpp commit 64e04a14b0e17eabfdaab5b134f8e194a8331e3e Author: Weiqun Zhang Date: Fri Apr 12 19:41:09 2019 -0700 put dx_eb computation in a function and use it to fix hypre Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 7d62eb59bcffbce7b5279868c1f526329824522f Author: Weiqun Zhang Date: Fri Apr 12 19:21:22 2019 -0700 fix the formular for dx_eb Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 6b7bad0c723cd9bb3802fbe26649fbc3922ab34a Author: Ann Almgren Date: Fri Apr 12 18:37:20 2019 -0700 oops - missed one declaration -- compiles now Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit 34415e6fd7a64d65644135a9cdb5e3a0d3946c76 Author: Ann Almgren Date: Fri Apr 12 18:29:20 2019 -0700 Update the stencil used for dphi/dn at EB walls when using Dirichlet bcs. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 09a347d5b63bc08d44e3586a0b7bf0bbf94decda Merge: 665c7aaf7 6a80d286f Author: Michele Rosso Date: Fri Apr 12 17:14:12 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 665c7aaf790355bac822460a4944925afd455714 Author: Michele Rosso Date: Fri Apr 12 17:14:06 2019 -0700 CMake: update documentation Docs/sphinx_documentation/source/BuildingAMReX.rst Docs/sphinx_documentation/source/GPU.rst commit 6a80d286f849a55d5f86111042f893199fe12186 Merge: a24c99169 873909694 Author: mic84 Date: Fri Apr 12 16:01:29 2019 -0700 Merge pull request #451 from mwm126/patch-2 Use " sed -i'' " for BSD sed on Mac commit 8739096940d52b278a59097527e0d08ed64ddc18 Merge: 52959e72c a24c99169 Author: mic84 Date: Fri Apr 12 16:01:17 2019 -0700 Merge branch 'development' into patch-2 commit 057bc4ed0844493273c15b203b526984122c5b57 Author: kngott Date: Fri Apr 12 15:41:08 2019 -0700 1 Graph per Iter methodology added. Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Tests/GPU/CudaGraphs/GraphIterReuseCopy/GNUmakefile Tests/GPU/CudaGraphs/GraphIterReuseCopy/Make.package Tests/GPU/CudaGraphs/GraphIterReuseCopy/inputs_3d Tests/GPU/CudaGraphs/GraphIterReuseCopy/main.cpp Tests/GPU/CudaGraphs/GraphIterReuseCopy/run.corigpu commit 52959e72cafb216be5004f29f52a60f45a3ebc2a Author: Mark Meredith Date: Fri Apr 12 18:26:29 2019 -0400 Use " sed -i'' " for BSD sed on Mac Tools/CMake/AMReX_InstallExternalLibs.cmake commit 5cef4dc03859c8cc910932ffd1a69d1d6c5d3e7f Author: kngott Date: Fri Apr 12 14:44:42 2019 -0700 Separate Instantiate Function. Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp commit e6eab706276d5a745772463136a2eee32f89fc61 Author: kngott Date: Fri Apr 12 14:34:55 2019 -0700 Change name of Graph functions to prepare for adding multiple capture methods. Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Tests/GPU/CudaGraphs/ArrayReuse/main.cpp Tests/GPU/CudaGraphs/GraphCopy/main.cpp Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit 00fdbe73963031d50704e46d20267c53338b3431 Author: kngott Date: Fri Apr 12 14:15:33 2019 -0700 Add proper free Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit 056aa13926b1fb19731f911df921e6a6363986a6 Author: kngott Date: Fri Apr 12 14:11:45 2019 -0700 Graph Reuse using Device Memory. Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit a19ce55234d392b61d11d73766c09417ee832197 Author: kngott Date: Fri Apr 12 13:39:06 2019 -0700 FAB lambda variation. Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit 1785d0ad9b29e74d436e204f3fdd0eb514baf831 Author: kngott Date: Fri Apr 12 13:28:10 2019 -0700 Array4 and FAB* methods for reusing graph on different MultiFabs. Tests/GPU/CudaGraphs/ArrayReuse/GNUmakefile Tests/GPU/CudaGraphs/ArrayReuse/Make.package Tests/GPU/CudaGraphs/ArrayReuse/inputs_3d Tests/GPU/CudaGraphs/ArrayReuse/main.cpp Tests/GPU/CudaGraphs/ArrayReuse/run.corigpu Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp commit 7b53b467f1e47ff288f1ff56dde257575475597c Author: kngott Date: Thu Apr 11 15:22:44 2019 -0700 Missed a noexcept. Src/Base/AMReX_CudaDevice.H commit defd405f02a8c6222c8c7a37ccc49d3bbed628cb Author: kngott Date: Thu Apr 11 15:22:25 2019 -0700 Update callback for Cuda 10. Src/Base/AMReX_CudaAsyncFab.cpp commit 6e1f818ff2fd58794168145df792a1883a6bbe9d Author: kngott Date: Thu Apr 11 15:22:04 2019 -0700 Sync Array fully with development. Src/Base/AMReX_Array.H commit e11dd4439dec8dcc9874acd8b583245fc78733c3 Author: kngott Date: Thu Apr 11 14:40:59 2019 -0700 Corrected CommI.H Src/Base/AMReX_FabArrayCommI.H commit 6e0cb2e5ff8a2e44e80cc13ad74b5cc08e7e5ce9 Merge: e7aeeba1e a24c99169 Author: kngott Date: Thu Apr 11 13:55:51 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit a24c99169876f2ade442f0415bd4106c7d962bc1 Author: Weiqun Zhang Date: Thu Apr 11 12:16:28 2019 -0700 make: when USE_CUDA, make sure comm and space are always defined before substition of compiler flags Tools/GNUMake/Make.defs commit 8489fba303b1f30fc893304c158ecfd12d1a594b Merge: da0c1442c f211d23ba Author: Weiqun Zhang Date: Thu Apr 11 12:07:37 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit da0c1442cdb89234e6466cb79ef0a95dfa755298 Author: Weiqun Zhang Date: Thu Apr 11 12:07:19 2019 -0700 hide errors in calling mpic++ -link_info Tools/GNUMake/sites/Make.nersc commit f211d23ba6d032808c794b6c75c089eb7d424b5b Merge: f1a41adb8 49b27f208 Author: Andrew Myers Date: Thu Apr 11 11:07:14 2019 -0700 Merge pull request #450 from AMReX-Codes/init_from_random_restart_gpu_friendly copy particles from host to device in one batch, 3 more funtions commit f1a41adb83b55b47c9c139ee0e9847198dc7c13e Author: Weiqun Zhang Date: Thu Apr 11 10:36:55 2019 -0700 option to fix -pthread for nvcc Tools/GNUMake/Make.defs commit 5c2ba97016ebf2df8499c1618d5834601b24cc9b Author: Weiqun Zhang Date: Thu Apr 11 07:52:06 2019 -0700 fix sign and unsigned comparison in 1d Src/Base/AMReX_CudaDevice.cpp commit 1d53b3c5ff9e12f73a9929ec7217ab0edda2488e Merge: c38638b6c 041e1ede6 Author: WeiqunZhang Date: Wed Apr 10 22:13:10 2019 -0700 Merge pull request #448 from AMReX-Codes/pgi-opt-fix Define PGI_OPT for any choice of AMREX_CCOMP and AMREX_FCOMP in pgi.mak commit c38638b6cdd260ac19c12efb6c5ed9685fcbd9ec Author: Weiqun Zhang Date: Wed Apr 10 21:54:33 2019 -0700 have to remove Werror=cross-execution-space-call because of cori Tools/GNUMake/comps/nvcc.mak commit 2db68bf770a7f568b4682438f9553b1649d6bf58 Author: Weiqun Zhang Date: Wed Apr 10 21:20:35 2019 -0700 simplify USE_HYPRE Tests/LinearSolvers/CellEB/GNUmakefile Tests/LinearSolvers/CellEB2/GNUmakefile Tests/LinearSolvers/EBConvergenceTest/GNUmakefile Tests/LinearSolvers/EBflux_grad/GNUmakefile Tests/LinearSolvers/MLMG/GNUmakefile Tests/LinearSolvers/NodeEB/GNUmakefile Tools/GNUMake/packages/Make.ascent Tools/GNUMake/packages/Make.hypre Tools/GNUMake/packages/Make.petsc Tutorials/EB/MacProj/GNUmakefile Tutorials/LinearSolvers/ABecLaplacian_C/GNUmakefile Tutorials/LinearSolvers/ABecLaplacian_F/GNUmakefile commit be8e18f40fdb7fb44fe42e5b41b023bda473f2a1 Author: Weiqun Zhang Date: Wed Apr 10 20:40:38 2019 -0700 if -> ifdef for consistence Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AsyncFillPatch.cpp Src/AmrCore/AMReX_TagBox.cpp Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp Src/Base/AMReX_CudaUtility.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_Machine.cpp Src/Base/AMReX_TypeTraits.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tests/C_BaseLib/tMF.cpp Tutorials/EB/CNS/Source/CNS_io.cpp Tutorials/GPU/CNS/Source/CNS_bcfill.cpp Tutorials/GPU/EBCNS/Source/CNS_bcfill.cpp Tutorials/GPU/EBCNS/Source/CNS_io.cpp commit 041e1ede6aed5621bb96ec2ddd72d56914cd0cba Author: Donald E. Willcox Date: Wed Apr 10 20:16:05 2019 -0700 Define PGI_OPT even if AMREX_CCOMP is not pgi in case AMREX_FCOMP is pgi. Tools/GNUMake/comps/pgi.mak commit 49b27f208b982d0bf5a5ab767b86a5dee27d98c2 Author: Jean Sexton Date: Wed Apr 10 21:48:39 2019 -0400 copy particles from host to device in one batch in InitRandom, InitNRandomPerCell, and Restart Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H commit a6a729186e9c6adc12ff9fdcc2a11ed848b3b3b3 Author: Brandon Runnels Date: Wed Apr 10 17:55:03 2019 -0600 added bottom abs tolerance Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 213ffaae3de3537b0dd4110dc152c9178787cf24 Author: Weiqun Zhang Date: Wed Apr 10 16:47:46 2019 -0700 remove .mod files in clean Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/GNUmakefile.libamrex commit ce789d0cd2c15496865d5b8a549d47440b501be4 Author: Weiqun Zhang Date: Wed Apr 10 16:33:52 2019 -0700 libamrex: add lib/pkgconfig/amrex.pc GNUmakefile.in Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/comps/cray.mak Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/ibm.mak Tools/GNUMake/comps/intel.mak Tools/GNUMake/comps/llvm-flang.mak Tools/GNUMake/comps/llvm.mak Tools/GNUMake/comps/nag.mak Tools/GNUMake/comps/nec.mak Tools/GNUMake/comps/pgi.mak Tools/libamrex/configure.py Tools/libamrex/mkpkgconfig.py Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/GNUmakefile.libamrex commit 498a82e89b6962f802fdbded545b0b4143d3a9c3 Merge: e424036a1 f52e5331a Author: Andrew Myers Date: Wed Apr 10 11:35:52 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e424036a109b173729f22b193e4861fbcfb1e4df Merge: 1f172bcf7 39bbdbe59 Author: Andrew Myers Date: Wed Apr 10 11:35:39 2019 -0700 Merge branch 'init_from_binary_gpu_friendly' into development commit 39bbdbe5941729c241a8436c19a43e7d9886b9be Author: Andrew Myers Date: Wed Apr 10 11:34:48 2019 -0700 add sync after InitFromBinary Src/Particle/AMReX_ParticleInit.H commit f52e5331a4fa9da0497efc2f51271eb31c7ce106 Author: Weiqun Zhang Date: Wed Apr 10 10:16:45 2019 -0700 configure: implement the allow_different_compiler option. Add an example makefile to heat equation OpenACC tutorial GNUmakefile.in Tools/libamrex/mkconfig.py Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/GNUmakefile.libamrex commit e7aeeba1e87855dc287f3ba84cbdb239f766ad39 Merge: 33cea5c4b 303f72eef Author: kngott Date: Tue Apr 9 17:14:43 2019 -0700 Merge branch 'development' into kngott/cudaGraphs commit 303f72eefffb55f4bc3ee8fb919bb9260119c959 Merge: 1f172bcf7 165e36b28 Author: WeiqunZhang Date: Tue Apr 9 17:03:06 2019 -0700 Merge pull request #446 from ghweber/master Add missing include for Conduit/Make.package and missing linker optio… commit 1f172bcf7a51c23b0c4bbc0c82519b0e1e0d4ae5 Merge: c8ac104bc eab42ef72 Author: Andrew Myers Date: Tue Apr 9 16:30:44 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit eab42ef72ed36fec536ac9de7c2e603a4e093734 Author: Weiqun Zhang Date: Tue Apr 9 15:58:07 2019 -0700 make Array4 is_trivially_copyable Src/Base/AMReX_Array.H commit c8ac104bca7d732dde316e3323f7b51893532a89 Author: Andrew Myers Date: Tue Apr 9 15:35:53 2019 -0700 add some overloads for backwards compatability Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 90c596d8c0463f3aff1140e7dd075c1cd616e074 Author: Andrew Myers Date: Tue Apr 9 13:37:50 2019 -0700 fix typo in assert statement Src/Particle/AMReX_ParticleContainerI.H commit 9ce41cb2a2d222700245a670377669f360c85a37 Author: Andrew Myers Date: Tue Apr 9 12:45:20 2019 -0700 fix logic error Src/Particle/AMReX_ParticleContainerI.H commit f33dd9e3b01feaaaca666d556f42918b7efd2c47 Author: Andrew Myers Date: Tue Apr 9 12:33:17 2019 -0700 update Checkpoint call in AssignDensity test Tests/Particles/AssignDensity/main.cpp commit 0bc4cca99e0415552e9f4b03d740edcac00c6de8 Author: Andrew Myers Date: Tue Apr 9 12:32:59 2019 -0700 update Header to reflect new num comps Src/Particle/AMReX_ParticleContainerI.H commit 45f9f16e5c38a5d26f7ed9d7bff2e81401691b19 Author: Michele Rosso Date: Tue Apr 9 12:16:37 2019 -0700 CMake: improve SUNDIALS support Src/Extern/SUNDIALS4/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/FindSUNDIALS.cmake commit 32b50503054afad890645c51d2eee962baa3156f Author: Andrew Myers Date: Tue Apr 9 11:52:42 2019 -0700 nuke is_checkpoint Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit b531acf7632129c265e6e946477aa3ba27164d22 Author: Andrew Myers Date: Tue Apr 9 11:29:42 2019 -0700 also add all those versions of WritePlotFile Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 40df9f69b432e2edc7d2b26c4f2e81d17c67953e Author: Andrew Myers Date: Tue Apr 9 11:17:33 2019 -0700 more formatting changes Src/Particle/AMReX_ParticleContainerI.H commit 7dd09da4c0c3e76ada1d15507cec02598565a3a9 Author: Andrew Myers Date: Tue Apr 9 11:15:48 2019 -0700 update ReadParticles to account for these changes Src/Particle/AMReX_ParticleContainerI.H commit 6176768bd673be2c4ce3167b4efd4aec106ddaf6 Author: Andrew Myers Date: Tue Apr 9 10:57:28 2019 -0700 update ReadParticles Function Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 8869a666706c78f32b358711b06ac1b8af787b64 Author: Andrew Myers Date: Tue Apr 9 10:54:42 2019 -0700 formatting changes Src/Particle/AMReX_ParticleContainerI.H commit 006f56148473ba615de3520689b185d90365d2cd Author: Andrew Myers Date: Tue Apr 9 10:52:42 2019 -0700 add a new Restart function, implement the specific one in terms of the general Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 7f11955c36340a403869ddde066229e43d744467 Merge: d665fd35a 09f0389a5 Author: Michele Rosso Date: Tue Apr 9 10:52:02 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d665fd35ae44e4a938c77774b8b0832355bef0b3 Author: Michele Rosso Date: Tue Apr 9 10:50:31 2019 -0700 CMake: improve HYPRE support * Add HYPRE detection to AMREX config file * Add minimum required version for HYPRE Src/Extern/HYPRE/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/FindHYPRE.cmake commit 7a7380b72b5582f0ee92b994c2eebb4a8645af2b Author: Andrew Myers Date: Tue Apr 9 10:48:53 2019 -0700 modify the WriteParticles method to only write out the requested components Src/Particle/AMReX_ParticleContainerI.H commit 905805653525f65cfe234a34708ec1e2d4e7cc97 Author: Andrew Myers Date: Tue Apr 9 10:35:19 2019 -0700 more formatting changes. Src/Particle/AMReX_Particles.H commit b69e5903d7aef5005e2a9a46e92ad7313769174a Author: Andrew Myers Date: Tue Apr 9 10:31:36 2019 -0700 implement the special Checkpoint functions in terms of the most general one. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit e313e8c2c264f064c775c3e4de1d8b1732edb8f0 Author: Andrew Myers Date: Tue Apr 9 10:15:24 2019 -0700 add overloaded versions of Checkpoint that allow for toggling IO on/off for specific particle components. Src/Particle/AMReX_Particles.H commit f25433a1bdf169e1f3c5b90d5120837d9e540eb7 Author: Andrew Myers Date: Tue Apr 9 10:05:40 2019 -0700 formatting changes Src/Particle/AMReX_ParticleContainerI.H commit 203cb0b817b8cf1b56604bde54d8df1ffa30c288 Author: Andrew Myers Date: Tue Apr 9 09:57:10 2019 -0700 copy particles from host to device in one batch Src/Particle/AMReX_ParticleInit.H commit 09f0389a52919f77aca7c55326f4e67e7ea98077 Merge: 46aa09194 80e6d666a Author: Andrew Myers Date: Mon Apr 8 21:35:23 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 165e36b28cdd5d9ab0448346a3bd8c2a8e7357f3 Author: Gunther H. Weber Date: Mon Apr 8 18:35:17 2019 -0700 Move include for conduit packages from Make.defs to Make.conduit Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.conduit commit 46aa091947e967ffc3a2803fecd14bba3cac816a Author: Andrew Myers Date: Mon Apr 8 21:35:04 2019 -0400 gpu neighbor list bug fix Src/Particle/AMReX_NeighborList.H commit 566fb12e7cf8d0982fe8a812533c776e1336e9d5 Author: Gunther H. Weber Date: Mon Apr 8 17:35:08 2019 -0700 Add missing include for Conduit/Make.package and missing linker options for Conduit/Ascent Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.ascent Tools/GNUMake/packages/Make.conduit commit 80e6d666ab77a471814faa59ac0500fdfe2a3d72 Author: Michele Rosso Date: Mon Apr 8 17:20:48 2019 -0700 CMake: add HYPRE support Src/CMakeLists.txt Src/Extern/HYPRE/CMakeLists.txt Tools/CMake/AMReX_Options.cmake Tools/CMake/FindHYPRE.cmake Tutorials/CMakeLists.txt Tutorials/LinearSolvers/ABecLaplacian_C/CMakeLists.txt commit 5180619f28df44d3474e5feef3f397a5e90ec662 Author: RevathiJambunathan Date: Mon Apr 8 12:31:08 2019 -0700 slicevalues are assigned based on the nearest grid point. Modified initialization of the multifabs such that the values represent the exact x,y,z location in the computational domain to assist with verification of the values assigned to the slice grid points. Tests/CreateSliceForDiagnostics/inputs Tests/CreateSliceForDiagnostics/main.cpp commit 16804ab0eded16d0a0e8fd1648d933a4f9fd269c Merge: 6d4bff37e 7b39f201b Author: Weiqun Zhang Date: Sat Apr 6 08:16:32 2019 -0700 Merge branch 'development' into weiqun/hypre-node commit 6d4bff37e241f7a0d11331f2ec142d8b3cae13ed Author: Weiqun Zhang Date: Sat Apr 6 08:12:39 2019 -0700 HypreNodeLap: 2d Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 39fdb400fed8c2d79f0dc6631964ab064e8464c1 Author: Weiqun Zhang Date: Fri Apr 5 21:37:15 2019 -0700 HypreNodeLap: switch to use RAP Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit de2cff267f22973bc49ced2120aadb05bbc73334 Author: Weiqun Zhang Date: Fri Apr 5 21:25:35 2019 -0700 HypreNodeLap: set use_hypre only once Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tests/LinearSolvers/NodeEB/MyTest.cpp commit a4106d137b02ed2faec42966cdb74baf063641ed Author: Weiqun Zhang Date: Fri Apr 5 16:37:54 2019 -0700 HypreNodeLap: fix id Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 7b39f201b106aa43056b39e5f5c9c350504653b1 Author: Michele Rosso Date: Fri Apr 5 16:36:05 2019 -0700 CMake: add back option I deleted by mistake Tools/CMake/AMReX_Options.cmake commit 9325058472e5bd07997c8b04431722ee6c8f59a3 Author: Weiqun Zhang Date: Fri Apr 5 13:25:26 2019 -0700 reorganize OverrideSync so that it can be used on any FabArray, not just MultiFab Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit 5bf667668c449628f165177d14c1e98b68689539 Merge: d7d90f098 36eb7d91b Author: RevathiJambunathan Date: Fri Apr 5 13:24:08 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into SliceGenerationForDiagnostics_RJ commit 36eb7d91ba4b8e8ff788e83f7dad2b6029fcb3d9 Merge: 0398c32a3 daeaa0022 Author: Michele Rosso Date: Fri Apr 5 11:54:59 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 0398c32a308034b68b520c9eabde0b045a03e286 Author: Michele Rosso Date: Fri Apr 5 11:54:47 2019 -0700 CMake: change how AMReX CUDA settings are passed to app codes Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_SetupCUDA.cmake commit daeaa002207368e99f915633b30c2ff12bdff72f Author: Marc Day Date: Thu Apr 4 20:32:02 2019 -0700 Put main code in local scope to avoid seg fault bug. Tools/Postprocessing/C_Src/HorizontalAvg.cpp Tools/Postprocessing/C_Src/IntegrateComp.cpp Tools/Postprocessing/C_Src/MultiFabToMatLab.cpp Tools/Postprocessing/C_Src/PlotfileToMatLab.cpp Tools/Postprocessing/C_Src/PtwisePltTransform.cpp commit a676b9c6768f0d1c5b5d869388a28a5ebdf06e3b Author: Michele Rosso Date: Thu Apr 4 17:08:55 2019 -0700 CMake: streamline CUDA setup Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_SetupCUDA.cmake commit 31949fd6e5dac680016d17cfcdd7c1fab951856e Author: Weiqun Zhang Date: Thu Apr 4 16:33:26 2019 -0700 HypreNodelap: implement loadVectors and getSolution Src/Extern/HYPRE/AMReX_HypreNodeLap.H Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp commit f3f046c46b5c98ff2219b686fe5a7a1d962a0cbd Merge: e8c486e6e 4eeb611e6 Author: Michele Rosso Date: Thu Apr 4 16:24:44 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 4eeb611e6ce6057693fd39c0b3e4647d763e5630 Merge: 1acc4e711 12b4834ce Author: Andrew Myers Date: Thu Apr 4 19:23:41 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1acc4e7118f47fc22b57b2e2a3c4e68dfbf25e07 Author: Andrew Myers Date: Thu Apr 4 19:23:22 2019 -0400 need to make a local copy of the particle struct pointer to pass into kernels when building the neighbor list Src/Particle/AMReX_NeighborList.H commit 12b4834ceeeadd2b4e92169d61902ed8c6786a8c Author: Ann Almgren Date: Thu Apr 4 16:06:35 2019 -0700 Change the default box_min_width for EB in the multigrid solves -- when AMREX_USE_EB make the min width 4 instead of 2 Src/LinearSolvers/MLMG/AMReX_MLLinOp.H commit 9b36ce98232b842299887e7d70adf71e9bff1f75 Author: Weiqun Zhang Date: Thu Apr 4 14:53:44 2019 -0700 HypreNodeLap: placeholder for loadVectors and getSolution Src/Extern/HYPRE/AMReX_HypreNodeLap.H Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 83c6db2f67cc816c1c27b4da5191105055715af8 Author: Weiqun Zhang Date: Thu Apr 4 14:40:17 2019 -0700 HypreNodeLap: setup amg solver Src/Extern/HYPRE/AMReX_HypreNodeLap.H Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit e8c486e6e2f5e690f33f62bbd5c4bae0555d7878 Merge: ca2943b83 1be04740c Author: Michele Rosso Date: Thu Apr 4 14:39:04 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 1be04740cc240bf6f6604f614625c63b99e79f70 Author: Michele Rosso Date: Thu Apr 4 14:26:44 2019 -0700 CMake: allow 1D builds. Fixes Issue 400 Docs/sphinx_documentation/source/BuildingAMReX.rst Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt commit f35533509cd99f69daf1b046f1c8b84b17551aaf Author: Michele Rosso Date: Thu Apr 4 13:58:17 2019 -0700 CMake: fix MPI search in config file Tools/CMake/AMReXConfig.cmake.in commit b69eb4da708fe85b8773a0b8f0b0e249084f45aa Author: Weiqun Zhang Date: Thu Apr 4 09:05:46 2019 -0700 MLNodeLaplacian: fill IJ matrix for non-EB Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit d7d90f09821029154a878a59ccdcb5e8d3e25d22 Author: RevathiJambunathan Date: Thu Apr 4 13:29:47 2019 -0700 modified main.cpp to generate error messages if cell size of slice is not an integer multiple of computational domain's cell size. Additional error messages include ensuring that the max_grid_size of box arrays are integer multiples of the coarsening ratio. Tests/CreateSliceForDiagnostics/inputs Tests/CreateSliceForDiagnostics/main.cpp commit a64dc49fc0829c9dd9c78c7bb19d2bb4e7f05eec Merge: e7c16b96c 4c1faf7da Author: WeiqunZhang Date: Thu Apr 4 12:26:59 2019 -0700 Merge pull request #442 from jrood-nrel/fix_fcompare3D_intel Fix fcompare3D for the Intel compiler commit e7c16b96c52e8c9b2e0799281925eebc1c248ea7 Author: Weiqun Zhang Date: Thu Apr 4 12:25:22 2019 -0700 EB: remove small cells with volume fraction less than 1.e-14 Src/EB/AMReX_eb2_2d.F90 Src/EB/AMReX_eb2_3d.F90 commit ca2943b838acd856345e6ef73beb7798737326a9 Author: Michele Rosso Date: Thu Apr 4 10:09:13 2019 -0700 CMake: remove obsolete check Tools/CMake/AMReX_SetupCUDA.cmake commit 4c1faf7da30bc47324f026af715a3082c531e304 Author: Jon Rood Date: Wed Apr 3 19:37:48 2019 -0600 Fixing line continuation in AMReX_FABUTIL_3D.F so that the Intel compiler can compile this file. Src/Extern/amrdata/AMReX_FABUTIL_3D.F commit 439cc171f414441efbbd9e6579a5bfd9b6394805 Author: RevathiJambunathan Date: Wed Apr 3 18:01:04 2019 -0700 corrected modification of max grid slice such that IntVect coarseslice can be an integer multiple for any dimension. Tests/CreateSliceForDiagnostics/main.cpp commit 5ff488b02c2560d53a2401b22d21d6f96a07dcd1 Author: RevathiJambunathan Date: Wed Apr 3 17:38:07 2019 -0700 modified max_grid_size for slice box array to enable slice generation such that the coarse IntVect can be any integer multiple of the baseline slice and not limited to a multiple of two. Tests/CreateSliceForDiagnostics/main.cpp commit 6d5b65028138ce3dadb5f7ad51554e9f814713cd Author: Weiqun Zhang Date: Wed Apr 3 16:41:29 2019 -0700 HypreNodeLap: ask MLNodeLaplacian to fill IJ matrix Src/Extern/HYPRE/AMReX_HypreNodeLap.H Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 20f567120930967e462bbb8dac0224249bffa535 Author: Weiqun Zhang Date: Wed Apr 3 15:45:33 2019 -0700 HyperNodeLap: set up node id Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreNodeLap.H Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tests/LinearSolvers/NodeEB/MyTest.cpp commit 33cea5c4b5f44ccc8e32a3be2ff3edbd96589288 Author: kngott Date: Wed Apr 3 14:59:06 2019 -0700 First draft of reusing copy graph on a different MultiFab. Tests/GPU/CudaGraphs/GraphReuseCopy/GNUmakefile Tests/GPU/CudaGraphs/GraphReuseCopy/Make.package Tests/GPU/CudaGraphs/GraphReuseCopy/inputs_3d Tests/GPU/CudaGraphs/GraphReuseCopy/main.cpp Tests/GPU/CudaGraphs/GraphReuseCopy/run.corigpu commit ada859949a4a8d548391cd1ac3b7964531398e27 Author: kngott Date: Wed Apr 3 14:55:59 2019 -0700 Adjust Array4 to allow needed access for CudaGraphs. Hopefully, a better way can be found later. Src/Base/AMReX_Array.H commit 9e9a783e1e161cbef29b8eee1988a122a9ef54dd Author: kngott Date: Wed Apr 3 14:54:13 2019 -0700 Adjust GraphRecordingStop to return the graph instead of take by reference. Also comment out graph log output for now. Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp commit 293be30a7c657fdb7b70c1224da46db503c0b3f1 Author: kngott Date: Wed Apr 3 14:52:05 2019 -0700 Turn off FillBoundary preliminary graphing. Need to test more, leave complete marker locations for now. Src/Base/AMReX_FabArrayCommI.H commit 8e76e2d8516a07b55b9b49b54006d7d97af1829f Author: Weiqun Zhang Date: Wed Apr 3 12:28:20 2019 -0700 start HypreNodeLap Src/Extern/HYPRE/AMReX_HypreNodeLap.H Src/Extern/HYPRE/AMReX_HypreNodeLap.cpp Src/Extern/HYPRE/Make.package Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tests/LinearSolvers/NodeEB/MyTest.cpp commit b560e52e8113e0cb2f51941f8138728fdf3b1e1b Merge: e456f0262 94ae28c65 Author: RevathiJambunathan Date: Wed Apr 3 12:17:06 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into SliceGenerationForDiagnostics_RJ commit e456f0262f74a418f1551bddf279848f5e32b161 Author: RevathiJambunathan Date: Wed Apr 3 12:16:47 2019 -0700 Adding test case to generate slice for diagnostics Tests/CreateSliceForDiagnostics/GNUmakefile Tests/CreateSliceForDiagnostics/Make.package Tests/CreateSliceForDiagnostics/inputs Tests/CreateSliceForDiagnostics/main.H Tests/CreateSliceForDiagnostics/main.cpp commit 94ae28c6563c32b2c59c4808f25533d9f66e61fb Author: Weiqun Zhang Date: Wed Apr 3 09:49:50 2019 -0700 fix memory issue related to using AsyncFab in non-launch region Src/Base/AMReX_CudaAsyncFabImpl.cpp commit e00ee5362dccfa6ea3562764e3ae82db465a3da8 Merge: 80b3e7e84 c124c5973 Author: Weiqun Zhang Date: Tue Apr 2 17:04:16 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 80b3e7e847ae7cbf4f31ce277118d0d4e0259fff Author: Weiqun Zhang Date: Tue Apr 2 17:04:05 2019 -0700 make it clear where LIBRARIES can be modified in make system Docs/sphinx_documentation/source/BuildingAMReX.rst commit c124c59733caba62b287ba2bd0b1bb6a0826b4e0 Merge: ba607885d aa9f2ddc5 Author: Ann Almgren Date: Tue Apr 2 15:44:12 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit ba607885d86f6f1e07f21914d7a108acf736f821 Author: Ann Almgren Date: Tue Apr 2 15:43:23 2019 -0700 Allow VisMF::Read to read an empty MultiFab without an error if and only if we pass in a flag (allow_empty_mf) that explicitly says its ok -- the default is still that it's not ok Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp commit aa9f2ddc5a62b63c16d89550a99e220a0c07e789 Author: Weiqun Zhang Date: Tue Apr 2 15:40:50 2019 -0700 write a debug chekcpoint file for MLNodeLaplaian Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_Utility.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit a9af990424d9f9b0f7d7ace2c79d984f75bc7a86 Author: Weiqun Zhang Date: Tue Apr 2 13:24:20 2019 -0700 fix a bug in 2d eb Src/EB/AMReX_eb2_2d.F90 commit 29ba0fc73865d20084a9c04f120230f409ac6618 Merge: e1a3b72ef 7ce0641c5 Author: Weiqun Zhang Date: Tue Apr 2 13:28:46 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e1a3b72efd2de40de5a68716f2100e1361060b7a Author: Weiqun Zhang Date: Tue Apr 2 13:24:20 2019 -0700 fix a bug in 2d eb Src/EB/AMReX_eb2_2d.F90 commit 7ce0641c516ad2d507a394fc2c4f47ac1cba8cde Merge: cdc1db367 8c4743a27 Author: Michele Rosso Date: Tue Apr 2 12:26:47 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit cdc1db3673fd09c19b36efbe0bed643c614e71f2 Author: Michele Rosso Date: Tue Apr 2 12:26:42 2019 -0700 CMake: find OpenMP dependency in AMReX export file Tools/CMake/AMReXConfig.cmake.in commit 8c4743a273f9d5a677f76478bae0719be1bee9d3 Merge: a0240cab1 bd6da4801 Author: Andrew Myers Date: Tue Apr 2 14:22:56 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a0240cab194762bb0b36620c5596b4ea59bfbe06 Author: Andrew Myers Date: Tue Apr 2 14:22:42 2019 -0400 need to fill the index sequence before using it... Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit bd6da4801691c58ee930358e9960c1afae720264 Author: Michele Rosso Date: Tue Apr 2 11:21:07 2019 -0700 CMake: add missing define for Algoim Src/Extern/Algoim/CMakeLists.txt commit 1105062387d9793ac3f5b14061878bea5bad0bf5 Author: Weiqun Zhang Date: Tue Apr 2 10:18:16 2019 -0700 change the interface of Interpolater::interp. Note that this is a virtual function, so it will break derived classes! Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp Src/EB/AMReX_EBInterpolater.H Src/EB/AMReX_EBInterpolater.cpp commit e6aec1f4026c2c2e97a89bd896bb766464c6d98d Author: Weiqun Zhang Date: Tue Apr 2 10:13:15 2019 -0700 fix default path to amrex Tools/Plotfile/GNUmakefile commit 3f922ab5358f1c5ba19ff6f2cdadc7977fb4eb93 Merge: 93f4b18b9 46e36a122 Author: Weiqun Zhang Date: Tue Apr 2 10:10:44 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 93f4b18b99cf724e99cee9dc4d127def602dacdd Author: Weiqun Zhang Date: Tue Apr 2 10:10:22 2019 -0700 remove C_Src/fcompare and fextract to avoid confusion Tools/Postprocessing/C_Src/GNUmakefile Tools/Postprocessing/C_Src/fcompare.cpp Tools/Postprocessing/C_Src/fextract.cpp commit 46e36a1220877e208305d06cc1aab379cc515170 Author: Andrew Myers Date: Mon Apr 1 20:50:17 2019 -0400 bail if cuda 9.2 used with USE_EB=TRUE Tools/GNUMake/comps/nvcc.mak commit 1dcf4a00aa631148ddff1c8b5802c095633cd135 Merge: 55d523d92 4a8ec6d6e Author: Andrew Myers Date: Mon Apr 1 20:20:41 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4a8ec6d6e0aa44d1ba35cdae922d5cb0281ab953 Merge: 21f3e9588 a66e94aba Author: Michele Rosso Date: Mon Apr 1 17:22:50 2019 -0700 Merge branch 'mr/cmake' into development commit a66e94aba302d856708f0a657833e2f15a112479 Author: Michele Rosso Date: Mon Apr 1 17:22:30 2019 -0700 CMake: bump up CMake minimum required version CMakeLists.txt commit 55d523d926079fb45ba72c56a8d8caac1f39f7d8 Author: Andrew Myers Date: Thu Mar 28 10:38:22 2019 -0700 mark EBCellFlag functions __host__ __device__ Src/EB/AMReX_EBCellFlag.H commit d78fa00137bb1d58188fd60913d035b707118280 Author: Andrew Myers Date: Thu Mar 28 19:37:13 2019 -0400 early exit for when neighbors don't need to be filled. Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit b58e823c0364cfc5709dff91ddf1f6668c94d94e Author: Andrew Myers Date: Mon Apr 1 20:18:23 2019 -0400 workaround for Thrust bug in Cuda 9.1 Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 6cfd06170bf44f1b61e779297713ba54d18905ad Author: Michele Rosso Date: Mon Apr 1 18:55:10 2019 -0400 Update doc Docs/sphinx_documentation/source/Fortran.rst commit 344b6d8a0693b7e0298b147ae00c47feccfb2c37 Author: Michele Rosso Date: Mon Apr 1 18:54:27 2019 -0400 CMake: return with error message if CUDA 9.2 is used whit ENABLE_EB=ON Tools/CMake/AMReX_SetupCUDA.cmake commit 21f3e95886b411294cecf6db199f869469f34377 Merge: 24f7b79cb 0a6afb5ec Author: Weiqun Zhang Date: Mon Apr 1 13:47:56 2019 -0700 Merge branch 'weiqun/gpu' of github.com:AMReX-Codes/amrex into weiqun/gpu commit 24f7b79cb47acdebbaf03d050c38c9fe9c25bf2a Author: Weiqun Zhang Date: Mon Apr 1 13:47:45 2019 -0700 Reduce: replace AsyncArray with DeviceScalar Src/Base/AMReX_FabArrayUtility.H commit 0a6afb5eca55ff14b889e54f7c52bef0bf7ad8f7 Author: Weiqun Zhang Date: Mon Apr 1 13:44:59 2019 -0700 fix UnionIF and IntersectionIF Src/EB/AMReX_EB2_IF_Intersection.H Src/EB/AMReX_EB2_IF_Union.H commit 0195f6944d9dcb2869cf60c3e0047aeafa1df844 Merge: a587c8f24 5f9987443 Author: Weiqun Zhang Date: Mon Apr 1 13:16:54 2019 -0700 Merge branch 'development' into weiqun/gpu commit 14d22dc36fd62d7634017d45b840e6ff286d38a5 Author: Michele Rosso Date: Mon Apr 1 11:18:10 2019 -0700 Fix #ifdef inconsistency Src/Base/AMReX_filcc_mod.F90 commit 5f9987443f04df963db0f3a7af7671e0c0cea597 Author: Michele Rosso Date: Mon Apr 1 11:18:10 2019 -0700 Fix #ifdef inconsistency Src/Base/AMReX_filcc_mod.F90 commit a587c8f24ea2261be91180d6a61c0b4b795f1de4 Author: Weiqun Zhang Date: Mon Apr 1 13:01:15 2019 -0700 UnionIF: fix typo Src/EB/AMReX_EB2_IF_Union.H commit df7aa4d4c6326b8b95904462d6ca6640be6695df Merge: d871ba204 7e07a40e2 Author: Weiqun Zhang Date: Mon Apr 1 12:33:32 2019 -0700 Merge branch 'development' into weiqun/gpu commit cf968fcf6ea7f55ff3fe6c592a059334757c9067 Author: Michele Rosso Date: Mon Apr 1 14:51:40 2019 -0400 Replace some #if with #ifdef Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_FabArray.H Src/Particle/AMReX_ParIterI.H commit 4037a5fe990759040ec4dc601517b8bc6ae99145 Author: Michele Rosso Date: Mon Apr 1 11:18:10 2019 -0700 Fix #ifdef inconsistency Src/Base/AMReX_filcc_mod.F90 commit d740974cd2dfe7ff10c23fbc3cc6e4435d123def Merge: aac0e7819 7e07a40e2 Author: Michele Rosso Date: Mon Apr 1 10:46:54 2019 -0700 Merge branch 'development' into mr/cmake commit 7e07a40e2d8a113f93db94606f5abb11234e6f14 Author: Weiqun Zhang Date: Mon Apr 1 09:07:43 2019 -0700 update changes CHANGES commit 7e68c299485b496babfa8de753f5165729eb74eb Merge: 1feaf93ce 71e6689e8 Author: Weiqun Zhang Date: Mon Apr 1 08:58:28 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 71e6689e862f039f485ce1348c1e77465c75b1c2 Author: Max Katz Date: Sat Mar 30 12:08:22 2019 -0700 Initialize xlcuf Src/Base/AMReX_CudaDevice.cpp commit bdbe5720ecdc474d3144e6ad34a38a9c920c2400 Author: Max Katz Date: Sat Mar 30 12:08:00 2019 -0700 Fix make syntax Tools/GNUMake/Make.rules commit 9401c943d4f9bd064fc45cad23c3be9b1f28f7ad Author: Max Katz Date: Sat Mar 30 11:29:29 2019 -0700 Generalize register capping to support xlf Tools/GNUMake/Make.rules commit 4ec099630a6cbf00952a5c367499f2e623e5a343 Author: Max Katz Date: Sat Mar 30 11:29:17 2019 -0700 Target the specific GPU arch for xlf Tools/GNUMake/comps/ibm.mak commit a8b12f2712bbbddbd7c9dfbafffa575ea82147ad Author: Max Katz Date: Sat Mar 30 10:31:40 2019 -0700 Disallow unrestricted private statements in the Fortran GPU script Tools/F_scripts/gpu_fortran.py commit 6cf7bc0b074d75ceaf849edeb2c06d0a0752e0c4 Author: Max Katz Date: Sat Mar 30 10:31:18 2019 -0700 Explicitly write out the device version of amrex_filccn Src/Base/AMReX_filcc_mod.F90 commit 1feaf93ce68014389bd5e0aeceb492caa01832d1 Author: Weiqun Zhang Date: Fri Mar 29 16:17:33 2019 -0700 User's Guide: parallel descriptor Docs/sphinx_documentation/source/Basics.rst commit aac0e7819c63548dbce3ab193f158b53ef17428b Merge: 6b36c1985 fe161deb7 Author: Michele Rosso Date: Fri Mar 29 15:39:20 2019 -0700 Merge branch 'development' into mr/cmake commit 6b36c198577928e492f46b0cd127a4d0ffc3db72 Author: Michele Rosso Date: Fri Mar 29 15:18:59 2019 -0700 CMake: start moving config and dependecies in the subdir where they are needed Src/Base/CMakeLists.txt Src/CMakeLists.txt Src/Extern/Algoim/CMakeLists.txt Src/Extern/Conduit/CMakeLists.txt Src/F_Interfaces/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_SetupThirdPartyLibs.cmake commit d871ba20470f1241ddd512bc2796f9873d81f2d2 Author: Weiqun Zhang Date: Fri Mar 29 13:25:41 2019 -0700 constexpr amrex::SpaceDim Src/Base/AMReX_SPACE.H commit fe161deb72c3c6fc3e9a223ce1f5d8c8f4b262cc Author: Weiqun Zhang Date: Fri Mar 29 13:13:40 2019 -0700 User's Guide: verbosity and make system Docs/sphinx_documentation/source/BuildingAMReX.rst Docs/sphinx_documentation/source/GettingStarted.rst commit 595238bf33d5e06e94fbd9d83a1a2f8b20b7b7c4 Author: Weiqun Zhang Date: Fri Mar 29 11:07:31 2019 -0700 make it easy to use python3 Docs/sphinx_documentation/Makefile commit 1a3f5a7a7c2f47e6b8f8ec0ee4a6d453fcf25709 Author: Weiqun Zhang Date: Fri Mar 29 08:31:52 2019 -0700 nvcc: error on calling host function from host device function Tools/GNUMake/comps/nvcc.mak commit 06c6c0e2777f105b538e154a3e8207b19f50b916 Author: Max Katz Date: Thu Mar 28 21:52:27 2019 -0700 Only cap registers if needed Tools/GNUMake/Make.rules commit ab9793fd4ef4d915fbfb79b6b847c19184a24006 Author: Weiqun Zhang Date: Thu Mar 28 17:28:42 2019 -0700 gpu: Intersection and Union IF Src/EB/AMReX_EB2_IF_Intersection.H Src/EB/AMReX_EB2_IF_Union.H commit ba009a7dc50859ccab2b284123522bdf66b67cea Merge: c7e58fe37 76d478783 Author: Tan Nguyen Date: Thu Mar 28 17:11:35 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c7e58fe375ef93a11af2ef36d1b57ef88a8f5b76 Author: Tan Nguyen Date: Thu Mar 28 17:11:18 2019 -0700 OpenMP backend for asyncMFIter Src/Amr/AMReX_Amr.cpp Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/mpi_omp/Barrier.cpp Src/AmrTask/rts_impls/mpi_omp/LocalConnection.H Src/AmrTask/rts_impls/mpi_omp/Make.package Src/AmrTask/rts_impls/mpi_omp/PackageQueue.H Src/AmrTask/rts_impls/mpi_omp/PackageQueue.cpp Src/AmrTask/rts_impls/mpi_omp/Perilla.H Src/AmrTask/rts_impls/mpi_omp/Perilla.cpp Src/AmrTask/rts_impls/mpi_omp/PerillaConfig.H Src/AmrTask/rts_impls/mpi_omp/PerillaRts.H Src/AmrTask/rts_impls/mpi_omp/PerillaRts.cpp Src/AmrTask/rts_impls/mpi_omp/RGIter.H Src/AmrTask/rts_impls/mpi_omp/RGIter.cpp Src/AmrTask/rts_impls/mpi_omp/RegionGraph.H Src/AmrTask/rts_impls/mpi_omp/RegionGraph.cpp Src/AmrTask/rts_impls/mpi_omp/RegionQueue.H Src/AmrTask/rts_impls/mpi_omp/RegionQueue.cpp Src/AmrTask/rts_impls/mpi_omp/RemoteConnection.H Src/AmrTask/rts_impls/mpi_omp/WorkerThread.H Src/AmrTask/rts_impls/mpi_omp/WorkerThread.cpp Src/AmrTask/rts_impls/mpi_omp/perilla.mak Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.H Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.cpp Src/AmrTask/rts_impls/pthreads_common/RGIter.H Src/AmrTask/rts_impls/pthreads_common/RGIter.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.mpi.omp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/GNUmakefile Src/Base/AMReX_MemPool.cpp commit 76d4787837d5b663b0dabce1c31c40cb1f8dc04a Merge: 0f96cd7bb ec3f2a23e Author: mic84 Date: Thu Mar 28 17:04:33 2019 -0700 Merge pull request #436 from balos1/development add SUNDIALS 4 support commit ef97ba76b583212e2134ae6d236d638b14da0561 Author: Weiqun Zhang Date: Thu Mar 28 19:10:48 2019 -0400 add __host__ __device__ to amrex::get for GpuTuple Src/Base/AMReX_Tuple.H commit 6aa4e2fec2aba919c60f955ae65bb51ae203661f Author: Michele Rosso Date: Thu Mar 28 15:37:50 2019 -0700 CMake: use add_subdirectory to include sub-folders into top-level CMakeLists. This change is made possible by CMake 3.13+. By doing so we can get rid of include(), use a more target-centric approach, and have a better localization of dependencies detail. Src/Amr/CMakeLists.txt Src/AmrCore/CMakeLists.txt Src/Base/CMakeLists.txt Src/Boundary/CMakeLists.txt Src/CMakeLists.txt Src/EB/CMakeLists.txt Src/Extern/Algoim/CMakeLists.txt Src/Extern/Conduit/CMakeLists.txt Src/Extern/ProfParser/CMakeLists.txt Src/Extern/SENSEI/CMakeLists.txt Src/Extern/SUNDIALS3/CMakeLists.txt Src/Extern/amrdata/CMakeLists.txt Src/F_Interfaces/CMakeLists.txt Src/LinearSolvers/CMakeLists.txt Src/Particle/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake commit f8344e2113a265383b1ec17faf02207a5424316b Author: Weiqun Zhang Date: Thu Mar 28 14:17:24 2019 -0700 Tuple: add constexpr Src/Base/AMReX_Tuple.H commit 168f2f912d660b970e648553e2bedc3522530efc Author: Weiqun Zhang Date: Thu Mar 28 13:52:45 2019 -0700 add makeTuple Src/Base/AMReX_Tuple.H commit ac4ff6a38508c76a228f973ab13b094b7d4990b7 Author: Weiqun Zhang Date: Thu Mar 28 13:33:35 2019 -0700 use amrex::Tuple in UnionIF and IntersectionIF Src/Base/AMReX_Tuple.H Src/EB/AMReX_EB2_IF_Intersection.H Src/EB/AMReX_EB2_IF_Union.H commit dda9b2b4f2f02895e8a2552b7d64adcafd3e4b4d Author: Weiqun Zhang Date: Thu Mar 28 10:36:50 2019 -0700 first pass of Tuple Src/Base/AMReX_IndexSequence.H Src/Base/AMReX_Tuple.H commit 0f96cd7bb644c0ac4c3067dbc9064172efdb6611 Author: Weiqun Zhang Date: Thu Mar 28 12:02:25 2019 -0700 fix for clang, thanks to Jon Rood Src/Amr/AMReX_StateDescriptor.H commit 9eb4f6dd0852c11ec93636a6b90532a017774adc Author: Andrew Myers Date: Thu Mar 28 10:40:33 2019 -0700 Revert "mark these functions AMREX_GPU_HOST_DEVICE so they can be used in device code" This reverts commit eb778611c7cbd256de870c783e7bb081ef40e4c4. Src/EB/AMReX_EBCellFlag.H commit add89e7a9b144ec2f9f9b6867c879085fd8d7477 Merge: eb778611c 8773ca0a8 Author: Andrew Myers Date: Wed Mar 27 19:56:39 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit eb778611c7cbd256de870c783e7bb081ef40e4c4 Author: Andrew Myers Date: Wed Mar 27 19:56:20 2019 -0400 mark these functions AMREX_GPU_HOST_DEVICE so they can be used in device code Src/EB/AMReX_EBCellFlag.H commit ec3f2a23e82844daf9e154b3ca02380d0119bf3c Author: Balos, Cody Joe Date: Wed Mar 27 16:13:15 2019 -0700 remove unused file from SUNDIALS4 Src/Extern/SUNDIALS4/farkode_butcher_mod.f90 Src/Extern/SUNDIALS4/fsunlinsol_dense.f90 Src/Extern/SUNDIALS4/fsunnonlinsol_mod.f90 commit c19f3c9443d9ff849619ebef406df7981448963e Author: Michele Rosso Date: Wed Mar 27 16:02:24 2019 -0700 CMake: clean-up output for algoim Tools/CMake/AMReX_InstallExternalLibs.cmake commit 8773ca0a895f7f589d0aeaf64785f732e84a6927 Author: Weiqun Zhang Date: Wed Mar 27 15:25:48 2019 -0700 removed the use of Tuple and old hypre interface OldTutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H OldTutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp OldTutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F OldTutorials/MultiGrid_C/HypreABecLap/HypreABec_F.H OldTutorials/MultiGrid_C/HypreABecLap/Make.package Src/Boundary/AMReX_BndryData.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG4/AMReX_ABec2.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.H Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_3D.F Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_F.H Tests/LinearSolvers/ComparisonTest/HypreABecLap/Make.package commit e5358db7f4684df54234d24f8a963f029414575b Merge: 0a8f7cc5c dc382c1d8 Author: Weiqun Zhang Date: Wed Mar 27 15:03:00 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8e02a2e40c865cbd5c253dfb6f7c67ab59ca0a5e Author: Michele Rosso Date: Wed Mar 27 14:52:50 2019 -0700 CMake: use configuration header to propagate definitions to application codes. * Generate and install AMReX_Config.H * Make defines (except Fortran ones) just a build requirement, i.e. not an install requirement * Modify installed headers to include AMReX_Config.H * Group install code into a single CMake modulex Src/CMakeLists.txt Tools/CMake/AMReXInstallHelpers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake Tools/CMake/modify_installed_headers.cmake commit dc382c1d80729292af75eadd5c302bd590c7230d Merge: 33c22300e 1b485769d Author: Ann Almgren Date: Wed Mar 27 14:10:48 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 0a8f7cc5c8dd3f8f8d4b33fdd89b3ef76d696556 Author: Weiqun Zhang Date: Wed Mar 27 14:01:41 2019 -0700 gpu: more on EB IF classes Src/EB/AMReX_EB2_IF.H Src/EB/AMReX_EB2_IF_Ellipsoid.H Src/EB/AMReX_EB2_IF_Extrusion.H Src/EB/AMReX_EB2_IF_Intersection.H Src/EB/AMReX_EB2_IF_Lathe.H Src/EB/AMReX_EB2_IF_Plane.H Src/EB/AMReX_EB2_IF_Rotation.H Src/EB/AMReX_EB2_IF_Scale.H Src/EB/AMReX_EB2_IF_Sphere.H Src/EB/AMReX_EB2_IF_Torus.H Src/EB/AMReX_EB2_IF_Translation.H commit 33c22300ea10f69173aba7977f6550b90bbe5684 Author: Ann Almgren Date: Wed Mar 27 13:59:44 2019 -0700 dudn --> dphidn for consistency Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 92eb4960207afa17c64e8d67b435d60845744fb0 Author: kngott Date: Wed Mar 27 13:24:12 2019 -0700 Comments to make reading graph method a little easier. Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp commit 6291ecbaf41dbef291f628c17eecfe0f3ec8b3ad Author: kngott Date: Wed Mar 27 13:23:37 2019 -0700 Label commented out section. Tests/GPU/CudaGraphs/GraphCopy/main.cpp commit e34e2dd24824ea2b51e349c261270c382aec2b2e Author: kngott Date: Wed Mar 27 13:04:13 2019 -0700 Add initial run to get clean timings and adjust timer names. Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp commit 6238b0e4aa2f99bb99306ac41905bfffeb11f27e Author: kngott Date: Wed Mar 27 12:49:13 2019 -0700 Implement the work as a function at the top to easily test Graphs on different MFIter loops. Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp commit 1b485769dfae81adb73e9c06df6b12046459ba50 Author: Weiqun Zhang Date: Wed Mar 27 12:07:07 2019 -0700 gpu: eb DifferenceIF Src/EB/AMReX_EB2_IF_Difference.H commit f75b0e8d1960412b17e592b5ebb158b811a72233 Author: kngott Date: Wed Mar 27 11:42:02 2019 -0700 Adjust graph timers. Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp commit 4fc6bec0551f6c662ddfded3bc97f826bd1d6c4f Author: Weiqun Zhang Date: Wed Mar 27 11:11:10 2019 -0700 use defaulted ctors Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_IF_Box.H Src/EB/AMReX_EB2_IF_Complement.H Src/EB/AMReX_EB2_IF_Cylinder.H commit c2ac17083597fe6f4bfe43c96abae40358e8482d Merge: 2d2173ccc a1f6ec0e0 Author: Balos, Cody Joe Date: Wed Mar 27 11:03:51 2019 -0700 Merge branch 'development' of https://github.com/amrex-codes/amrex into development commit 2d2173ccc36926459113ac6790d0b4d05938c550 Author: Balos, Cody Joe Date: Wed Mar 27 11:00:56 2019 -0700 add SUNDIALS 4 support cmake: support sundials 4 instead of 3 gnumake: support sundials 3 by default or optionally sundials 4 Src/CMakeLists.txt Src/Extern/SUNDIALS4/CMakeLists.txt Src/Extern/SUNDIALS4/Make.package Src/Extern/SUNDIALS4/arkode_interface.f90 Src/Extern/SUNDIALS4/cvode_interface.f90 Src/Extern/SUNDIALS4/farkode_arkstep_mod.f90 Src/Extern/SUNDIALS4/farkode_butcher_mod.f90 Src/Extern/SUNDIALS4/farkode_mod.f90 Src/Extern/SUNDIALS4/fcvode_mod.f90 Src/Extern/SUNDIALS4/fnvector_mod.f90 Src/Extern/SUNDIALS4/fnvector_serial_mod.f90 Src/Extern/SUNDIALS4/fsundials_types_mod.f90 Src/Extern/SUNDIALS4/fsunlinsol_dense.f90 Src/Extern/SUNDIALS4/fsunlinsol_dense_mod.f90 Src/Extern/SUNDIALS4/fsunlinsol_mod.f90 Src/Extern/SUNDIALS4/fsunmatrix_dense_mod.f90 Src/Extern/SUNDIALS4/fsunmatrix_mod.f90 Src/Extern/SUNDIALS4/fsunnonlinsol_mod.f90 Tools/CMake/AMReX_Options.cmake Tools/CMake/FindSUNDIALS.cmake Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.sundials4 Tutorials/CVODE/SUNDIALS4/EX_ark_analytic/GNUmakefile Tutorials/CVODE/SUNDIALS4/EX_ark_analytic/Make.package Tutorials/CVODE/SUNDIALS4/EX_ark_analytic/ark_analytic_f2003.f90 commit b9a66d75bdf9116ee5eb5f31905b44eb00bfdfee Author: Weiqun Zhang Date: Wed Mar 27 10:13:48 2019 -0700 gpu: eb cylinder Src/EB/AMReX_EB2_IF_Box.H Src/EB/AMReX_EB2_IF_Cylinder.H commit 4cc9a5b9974a2395fecc86eae518a9133bcc0af3 Author: Weiqun Zhang Date: Wed Mar 27 09:14:16 2019 -0700 include EB2_IF_Base.H in all IF headers Src/EB/AMReX_EB2_IF_Cylinder.H Src/EB/AMReX_EB2_IF_Difference.H Src/EB/AMReX_EB2_IF_Ellipsoid.H Src/EB/AMReX_EB2_IF_Extrusion.H Src/EB/AMReX_EB2_IF_Intersection.H Src/EB/AMReX_EB2_IF_Lathe.H Src/EB/AMReX_EB2_IF_Plane.H Src/EB/AMReX_EB2_IF_Polynomial.H Src/EB/AMReX_EB2_IF_Rotation.H Src/EB/AMReX_EB2_IF_Scale.H Src/EB/AMReX_EB2_IF_Spline.H Src/EB/AMReX_EB2_IF_Torus.H Src/EB/AMReX_EB2_IF_Translation.H Src/EB/AMReX_EB2_IF_Union.H commit a1f6ec0e083020950dfd2500068f1cfa1988b978 Author: Weiqun Zhang Date: Tue Mar 26 23:55:27 2019 -0400 option to disable device sync in MFIter Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 9e672929a4b058b0c27f7cf8b8b738f61c2d1df0 Author: Weiqun Zhang Date: Tue Mar 26 22:38:29 2019 -0400 add prefetch to AmrLevel::writePlotFile Src/Amr/AMReX_AmrLevel.cpp commit 6b11fc0d535fb2a97ec6886b40395eb99ae3f449 Author: Weiqun Zhang Date: Tue Mar 26 18:44:50 2019 -0700 add free functions prefetchToHost and prefetchToDevice for FabArray Src/Base/AMReX_FabArrayUtility.H Tutorials/GPU/EBCNS/Source/CNS_io.cpp commit fa965e623cacfb30f192e703179c9a12436a788c Author: Weiqun Zhang Date: Tue Mar 26 17:05:32 2019 -0700 fix enable_if Src/Base/AMReX_FabArray.H commit b2764d42eb4113ae16ddfb6e1c35330ee6ff1558 Merge: cdc91b563 714d12275 Author: Weiqun Zhang Date: Tue Mar 26 16:51:39 2019 -0700 Merge branch 'weiqun/gpu' into development commit e4439bfc37e2f008d2c7f1a83b7d7440fadfa82a Author: Michele Rosso Date: Tue Mar 26 16:28:58 2019 -0700 Replace #if with #ifdef as per Andrew's suggestion Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_ParallelDescriptor.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H Src/Particle/AMReX_ParticleContainerI.H commit 714d122759ed367e0db30f544b8699eda761dcfa Author: Weiqun Zhang Date: Tue Mar 26 16:27:37 2019 -0700 add README Tutorials/GPU/EBCNS/README commit 331a2c2696cccf75303f73c6fb81bc0cf108c696 Merge: f481dfc8a 4122aadfe Author: Weiqun Zhang Date: Tue Mar 26 16:24:58 2019 -0700 Merge branch 'development' into weiqun/gpu commit f481dfc8a094c0e15aebb17d5e7d325ece917d8e Author: Weiqun Zhang Date: Tue Mar 26 14:58:23 2019 -0700 fix enable_if and start gpu version of GeometryShop Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_IF.H Src/EB/AMReX_EB2_IF_Complement.H Src/EB/AMReX_EB2_IF_Sphere.H commit cdc91b56381d6942c80dab2742b57d13d262aada Author: Ann Almgren Date: Tue Mar 26 13:38:12 2019 -0700 Need to make the compute_dphidn* routines public Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 961d74f0d11e39b0d94940c45dc2c298f30b9738 Author: Ann Almgren Date: Tue Mar 26 13:25:50 2019 -0700 Make compute_dphidn hold the lower order stencil and create compute_dphidn_ho to hold the higher-order stencil. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit a62b4243648328b5ea9c3c3a670475d192d51e5d Author: Weiqun Zhang Date: Tue Mar 26 12:52:07 2019 -0700 gpu: BoxIF and ComplementIF Src/EB/AMReX_EB2_IF.H Src/EB/AMReX_EB2_IF_AllRegular.H Src/EB/AMReX_EB2_IF_Base.H Src/EB/AMReX_EB2_IF_Box.H Src/EB/AMReX_EB2_IF_Complement.H commit f194dffe7073620849798df1d9670c0f18ebb7de Author: Weiqun Zhang Date: Tue Mar 26 11:49:32 2019 -0700 gpu: copyMultiFabToMultiCutFab Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit e9bb22fb029a1d2398d93316d008f5f27c6ddd58 Merge: 4122aadfe 66392f8dc Author: WeiqunZhang Date: Tue Mar 26 09:18:15 2019 -0700 Merge pull request #435 from jared321/flash_tileID local tile index commit 66392f8dcf3689ac7d5ff81643e4ffa99a18fa89 Author: Jared O'Neal Date: Tue Mar 26 09:12:00 2019 -0500 Add local tile index to the MFIter's Fortran interface. Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit b10f929c5c01493337ef5ce75277ab556ab859a1 Author: Weiqun Zhang Date: Mon Mar 25 16:55:53 2019 -0700 noexcept and inline Src/Base/AMReX_Array.H Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit 2a9e4ce84f99bb4dfd20eb749d54beb4081fd39f Author: Weiqun Zhang Date: Mon Mar 25 16:35:28 2019 -0700 remove BoxLib MG and add noexcept Src/Amr/AMReX_Amr.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/EB/AMReX_EB2_Level.H commit ade8fe6ed5898f32b3c2bee57280981af1278378 Author: Michele Rosso Date: Mon Mar 25 19:16:17 2019 -0400 CMake: change how we set PUBLIC_HEADER and CUDA properties on sources Src/CMakeLists.txt commit 5b7e0c125f84362f0c24c96b505712880eebeba8 Merge: 5b628078c 4122aadfe Author: Michele Rosso Date: Mon Mar 25 17:30:19 2019 -0400 Merge branch 'development' into mr/cmake commit 16e1e06d30593b3b97c25014a951bab41b121bee Author: Weiqun Zhang Date: Mon Mar 25 13:18:45 2019 -0700 add struct XDim3 Src/Base/AMReX_Array.H commit f9ce57c9dc8ee1859b285e09d0b01ca6132e3108 Author: Weiqun Zhang Date: Mon Mar 25 13:03:44 2019 -0700 add struct GPUable that can be used as base for EB2's IF classes Src/EB/AMReX_EB2_IF.H Src/EB/AMReX_EB2_IF_Base.H Src/EB/AMReX_EB2_IF_Sphere.H Src/EB/CMakeLists.txt Src/EB/Make.package commit 363b0a505a685dc92c3f2afa5172c7fcdb0cf673 Author: Weiqun Zhang Date: Mon Mar 25 12:40:09 2019 -0700 update plotfile Tutorials/GPU/EBCNS/Exec/Sod/inputs Tutorials/GPU/EBCNS/Source/CNS.H Tutorials/GPU/EBCNS/Source/CNS.cpp Tutorials/GPU/EBCNS/Source/CNS_io.cpp commit 6dda2166dfbb4b6e7e9166b2b95b5d9726722e08 Author: Weiqun Zhang Date: Mon Mar 25 12:15:45 2019 -0700 fix makefile and add noexcept Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Tutorials/GPU/EBCNS/Exec/Make.CNS commit 4122aadfeab17c02218a7a76e445df945a38eaf5 Author: Weiqun Zhang Date: Mon Mar 25 09:15:27 2019 -0700 particle_compare: fix return type Tools/Postprocessing/C_Src/particle_compare.cpp commit 4f8f5f7f3a021fdc58f1fe9ff782d2e31c4b46d8 Author: Max Katz Date: Sun Mar 24 20:09:22 2019 -0700 Print out message that we are initializing CUDA This can take a long time on the P9 platform, so this message is there to reassure the user that in fact something is happening, not a hang. Src/Base/AMReX_CudaDevice.cpp commit d5b2c9fa0c82cc9c10cbf8f970950d280e8ba418 Author: Max Katz Date: Sun Mar 24 07:10:23 2019 -0700 Fix typo Src/Amr/AMReX_AmrLevel.cpp commit 3e2e1eb1379d62fa5d60c1f4554aba9d8c0c270f Merge: 99e8ebd38 084983de2 Author: WeiqunZhang Date: Sat Mar 23 16:25:42 2019 -0700 Merge pull request #434 from AMReX-Codes/convergence some clean ups to the Richardson convergence tool commit 084983de296346c26cf0e4e7e1837bc49e8e0047 Author: Michael Zingale Date: Sat Mar 23 13:53:19 2019 -0700 make the error files optional implement the verbose option Tools/C_util/Convergence/RichardsonConvergenceTest.cpp commit 99e8ebd382d533bc6525d9ac92d552a4f77a3b7c Merge: 136b2e299 845a7decd Author: WeiqunZhang Date: Sat Mar 23 13:30:35 2019 -0700 Merge pull request #433 from cgilet/development Make public interpolate_to_face_centroid() and interpolate_to_face_ce… commit 845a7decd47be7b8867f902d9a958740b577b951 Author: cgilet Date: Sat Mar 23 15:51:24 2019 -0400 Make public interpolate_to_face_centroid() and interpolate_to_face_centroid_per_cell() Src/EB/AMReX_EBMultiFabUtil_2d.F90 commit 136b2e299ae51586f0eb2fc006808ec3c8de27b4 Author: Max Katz Date: Sat Mar 23 14:21:15 2019 -0400 character variables should not be allocatable/managed Tools/F_scripts/write_probin.py commit de64576796ed24929a880703a153745dc4ae55c4 Author: Max Katz Date: Sat Mar 23 14:01:27 2019 -0400 Only CUDA header script copies files Tools/GNUMake/Make.rules commit 31b84a0b06f7554ac15cdfc01f9dc0bedb973e1c Author: Max Katz Date: Sat Mar 23 13:12:09 2019 -0400 Add some parallelism to the GPU header script Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.rules commit dfb29ccb26f8995f1753b425658ef1ceb8666ddd Author: Ann Almgren Date: Sat Mar 23 08:32:11 2019 -0700 Oops -- entered Friesen's ORCID wrong paper/paper.md commit daa75e3cea8d228eeeddd96939180ec7b809a148 Author: Ann Almgren Date: Sat Mar 23 08:32:11 2019 -0700 Oops -- entered Friesen's ORCID wrong paper/paper.md commit 4587cb067471eef99b87d384192b5a7491016f48 Merge: 795f60aae 6dcc2d807 Author: Weiqun Zhang Date: Fri Mar 22 21:48:44 2019 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 795f60aaef3b4c7feddd2086d455092ac1819068 Author: Weiqun Zhang Date: Fri Mar 22 21:41:17 2019 -0700 add cuda memory prefetch function Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H commit c4421d91479315c7ce56fa8cab2ee5720cac0249 Author: Ann Almgren Date: Fri Mar 22 16:51:15 2019 -0700 Fix some capitalization paper/paper.md commit 6dcc2d807014ab202207dbed21c4313646c8aa0e Author: Ann Almgren Date: Fri Mar 22 16:51:15 2019 -0700 Fix some capitalization paper/paper.md commit b61e0ba7f71511e533aeaa66fdb27934904d2104 Author: Ann Almgren Date: Fri Mar 22 16:47:15 2019 -0700 Moved JOSS stuff from Docs/JOSS to paper folder so reviewers can find it. paper/Makefile paper/paper.bib paper/paper.md commit 8d91613f3b6eecaf76ec44852501b45e25dda8d0 Author: Ann Almgren Date: Fri Mar 22 16:47:15 2019 -0700 Moved JOSS stuff from Docs/JOSS to paper folder so reviewers can find it. paper/Makefile paper/paper.bib paper/paper.md commit e4942f04109c3bfc98aaa1f38084e34f61b0418e Merge: a2d4c3546 26423be8e Author: Weiqun Zhang Date: Fri Mar 22 15:47:49 2019 -0700 Merge branch 'weiqun/data_allocator' into development commit a2d4c3546d2dc9330cc84ed3eb29e66cd3db0706 Merge: 192514b02 33bf6a42b Author: Weiqun Zhang Date: Fri Mar 22 18:40:58 2019 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 192514b02e014bd50bdbc723fd11f462b570597c Author: Weiqun Zhang Date: Fri Mar 22 18:40:19 2019 -0400 set CFLAGS_FROM_HOST to CXXFLAGS_FROM_HOST because nvcc -x cu compiles as C++ Tools/GNUMake/comps/nvcc.mak commit 1c479b6a74ad636fc5122ddef68a7988e3f4161e Author: kngott Date: Fri Mar 22 15:05:17 2019 -0700 Add Graphs to 1 MPI section of FillBoundary. Src/Base/AMReX_FabArrayCommI.H commit 847a571365176e8f9ba65f5d53b5c214cf5b18d8 Author: kngott Date: Fri Mar 22 15:04:27 2019 -0700 Add LaunchRegion and GraphRegion checks to Device::Graph calls. Src/Base/AMReX_CudaDevice.cpp commit dcf6922dab6cbd6ab5ba29cc6430629b3e02fa26 Author: kngott Date: Fri Mar 22 15:03:23 2019 -0700 Add static GraphRegion values for Graph Testing. Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuControl.cpp commit 26423be8e4e04710abde03d71753559963e77f13 Author: Weiqun Zhang Date: Fri Mar 22 14:49:09 2019 -0700 add The_Cpu_Arena and CpuDataAllocator. use CpuDataAllocator in parallelcopy meta-data processing Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArrayBase.cpp commit 86385fa4aea41e60dd98d041d5dc0bccbf86c8a2 Author: kngott Date: Fri Mar 22 12:24:57 2019 -0700 Rewrite with Device's graphs functions for testing. Tests/GPU/CudaGraphs/GraphCopy/main.cpp commit fbc343d915eeb93f723a2fb50bc2e518838c4ecb Author: kngott Date: Fri Mar 22 12:24:35 2019 -0700 Change GNUmakefile-s to work with reorganization. Tests/GPU/CudaGraphs/BuildingGraphs/GNUmakefile Tests/GPU/CudaGraphs/GraphBoundary/GNUmakefile Tests/GPU/CudaGraphs/GraphCopy/GNUmakefile commit de74f7f72b186763741dba951fa05d57938b7027 Author: kngott Date: Fri Mar 22 12:23:25 2019 -0700 Add first draft Graph functions to Device. Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Tests/GPU/CudaGraphs/BuildingGraphs/GNUmakefile Tests/GPU/CudaGraphs/BuildingGraphs/Make.package Tests/GPU/CudaGraphs/BuildingGraphs/inputs_3d Tests/GPU/CudaGraphs/BuildingGraphs/main.cpp Tests/GPU/CudaGraphs/BuildingGraphs/run.corigpu Tests/GPU/CudaGraphs/CrazyGraphs/GNUmakefile Tests/GPU/CudaGraphs/CrazyGraphs/main.cpp Tests/GPU/CudaGraphs/CrazyGraphs/run.corigpu Tests/GPU/CudaGraphs/GraphBoundary/GNUmakefile Tests/GPU/CudaGraphs/GraphBoundary/Make.package Tests/GPU/CudaGraphs/GraphBoundary/Prob.H Tests/GPU/CudaGraphs/GraphBoundary/inputs_3d Tests/GPU/CudaGraphs/GraphBoundary/main.cpp Tests/GPU/CudaGraphs/GraphBoundary/profile.sh Tests/GPU/CudaGraphs/GraphBoundary/run.corigpu Tests/GPU/CudaGraphs/GraphBoundary/run.summit Tests/GPU/CudaGraphs/GraphCopy/GNUmakefile Tests/GPU/CudaGraphs/GraphCopy/Make.package Tests/GPU/CudaGraphs/GraphCopy/inputs_3d Tests/GPU/CudaGraphs/GraphCopy/main.cpp Tests/GPU/CudaGraphs/GraphCopy/run.corigpu commit d76afa7775edee047e4d28165e9f562d01567df3 Author: Weiqun Zhang Date: Fri Mar 22 11:10:07 2019 -0700 add a default template paramter Allocator to BaseFab Src/Base/AMReX_BaseFab.H Src/Base/AMReX_TypeTraits.H commit 33bf6a42b60f5405d0eac8103252905df38799cb Merge: b6c3673c9 0119e469d Author: Ann Almgren Date: Fri Mar 22 10:49:49 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit b6c3673c9361844b8e4844778aca627275bf062c Author: Ann Almgren Date: Fri Mar 22 10:47:40 2019 -0700 1) Fixed bug in 3d version of amrex_eb_interpolate_to_face_centroid 2) Made 2d versions of amrex_eb_interpolate_to_face_centroid and amrex_eb_interpolate_to_face_centroid_per_cell Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 commit 0119e469d1d13d2581128eba640a8c49e3c455f3 Merge: 2fc5352d5 b2e933fcc Author: Andrew Myers Date: Fri Mar 22 10:16:45 2019 -0700 Merge pull request #432 from RevathiJambunathan/random_xorwow_RJ Random xorwow -- modified seed with mpi rank commit 2fc5352d5b685343ec6e0b0e85fd33d9cef912af Author: Weiqun Zhang Date: Fri Mar 22 10:12:18 2019 -0700 always use -Werror=return-type for gcc Tools/GNUMake/comps/gnu.mak commit ff8912a4b66d91230d69ec1dcbcb9241e9337def Author: Weiqun Zhang Date: Fri Mar 22 10:01:50 2019 -0700 comment out some profilers Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_VisMF.cpp Src/Particle/AMReX_ParticleContainerI.H commit 6553d972925b08a730fb72891b6c210c4ac2d896 Author: Ann Almgren Date: Fri Mar 22 08:06:54 2019 -0700 Add a per-cell interpolate to face centroid routine (taken from mfix). Src/EB/AMReX_EBMultiFabUtil_3d.F90 commit b628b06c1262198e72640657e007b06dc7a118b3 Author: Ann Almgren Date: Thu Mar 21 19:50:19 2019 -0700 Re-word the fork-join sentence Docs/JOSS/paper.md commit 10746be5d29ebed3dd54c548ce5264915170d7e0 Author: Ann Almgren Date: Thu Mar 21 19:43:10 2019 -0700 Fix more typos and remove "(AMR)" from the title. Docs/JOSS/paper.md commit e32bfd249038e4bea93fcf92745ed548e908cb5e Author: Max Katz Date: Thu Mar 21 21:39:43 2019 -0400 Typos Docs/JOSS/paper.md commit 7f04068914e195ef42f328fe5f7c03164d499554 Author: Max Katz Date: Thu Mar 21 21:37:36 2019 -0400 Change my name Docs/JOSS/paper.md commit 1930ad9048b18cef21df3bee3a1637ce23a8f74d Merge: 290903bad fbc72c3e5 Author: Ann Almgren Date: Thu Mar 21 18:02:59 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 290903badfacadf897160f60a53e227cecb84031 Author: Ann Almgren Date: Thu Mar 21 18:02:45 2019 -0700 Oops -- forgot John on the author list Docs/JOSS/paper.md commit fbc72c3e586511edc61fb79339e518ed570bf547 Author: Donald E. Willcox Date: Thu Mar 21 18:02:10 2019 -0700 Fix reference to Zingale et al 2018 Docs/JOSS/paper.md commit 38c8561e42ad4823ffe24a143b00db4c39e52e61 Author: Ann Almgren Date: Thu Mar 21 17:51:21 2019 -0700 updated references Docs/JOSS/paper.bib commit 59183dd9558da888df4a831040695dbe8672fb1a Author: Ann Almgren Date: Thu Mar 21 17:45:01 2019 -0700 updated with references Docs/JOSS/paper.md commit e7317e132519575528801d777943d86f42d86a6b Author: Ann Almgren Date: Thu Mar 21 17:22:42 2019 -0700 re-order sections Docs/JOSS/paper.md commit 6a46436e3a78b2713fc28111b3d3c6ec048c51f6 Author: Ann Almgren Date: Thu Mar 21 17:21:49 2019 -0700 Modify subsection headings Docs/JOSS/paper.md commit 5d1cc225b3b7f563e9de58a33cb371e6b0308557 Merge: 10163db6c bd7f69ff9 Author: Ann Almgren Date: Thu Mar 21 17:21:09 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 10163db6c4c2988b8b34ee1df10d90e78c6dc071 Author: Ann Almgren Date: Thu Mar 21 17:20:58 2019 -0700 This is getting closer... Docs/JOSS/paper.md commit b2e933fccea6cbead57d2946fda40c901d02add8 Author: RevathiJambunathan Date: Thu Mar 21 13:43:29 2019 -0700 cleaned rand, instead of using loc_rand Src/Base/AMReX_Utility.cpp commit 5e1988498841fe8e28fb251cf402381d205e48f8 Merge: 99e2f1b77 bd7f69ff9 Author: RevathiJambunathan Date: Thu Mar 21 13:31:38 2019 -0700 fixed the conflict with 1D threadId and the newly added 3D threadId in Utility.cpp after merging with development commit 99e2f1b7762f7e872250b4b726ffacfdd7a121c3 Author: RevathiJambunathan Date: Thu Mar 21 13:10:37 2019 -0700 Modified main.cpp in the test file to check for resize and ensuring that the seed generation is working properly for the grown vector Tests/GPU/RandomNumberGeneration/main.cpp commit 69d01eeebc6c73c5f34f4c588dbf7c5cb2a38c76 Author: RevathiJambunathan Date: Thu Mar 21 13:09:38 2019 -0700 Modified seed generation to depend on MyProc or mpi_rank, so that each GPU does not have the same seed. And within a GPU, given the same seed, the startsequence of random number generation is threadID dependent. Also, generalized the threadId calculation for 3D block Grid and 3D thread block. Finally, when resize is called, the seed generation is performed only for the newly added vector elements. Note that CheckSeedArraySizeAndResize() should be called to Resize() Src/Base/AMReX_Utility.cpp commit 3b978ba97d0a02b6dbbdb6f97cfd5dc616549384 Author: kngott Date: Thu Mar 21 12:57:18 2019 -0700 Add FillBoundary Test to repo. Tests/GPU/GraphBoundary/Prob.H Tests/GPU/GraphBoundary/inputs_3d Tests/GPU/GraphBoundary/main.cpp Tests/GPU/GraphBoundary/profile.sh Tests/GPU/GraphBoundary/run.corigpu Tests/GPU/GraphBoundary/run.summit Tests/GPU/GraphCopy/GNUmakefile Tests/GPU/GraphCopy/Make.package Tests/GPU/GraphCopy/inputs_3d Tests/GPU/GraphCopy/main.cpp Tests/GPU/GraphCopy/run.corigpu commit afd6aec629f10ae98f46dfb5b6f250509b5b8dd1 Author: kngott Date: Thu Mar 21 12:41:59 2019 -0700 Check changing memory layout on CudaGraphs. Tests/GPU/GraphBoundary/main.cpp commit 3124d1704338c9d6ec15fe051711578bf6bb515b Author: kngott Date: Thu Mar 21 00:11:20 2019 -0700 Light cleanup. Tests/GPU/GraphBoundary/main.cpp commit 6f6f073dfc02baf8cd424a5ed7eac4f5034ea887 Author: kngott Date: Wed Mar 20 23:17:10 2019 -0700 Test copy with cudaGraph. Tests/GPU/GraphBoundary/main.cpp commit bd7f69ff96622278f7b54d959e150e5b04574cd0 Author: Weiqun Zhang Date: Wed Mar 20 21:00:45 2019 -0700 fix host version of Random Src/Base/AMReX_Utility.cpp commit cd8c5660c180ff46935f8d36af376c21f87f9bab Author: Weiqun Zhang Date: Wed Mar 20 20:53:03 2019 -0700 add ifdef to cuda function call Src/Base/AMReX_Arena.cpp commit b717060fc03bb7456ba78cef1c12a0eecad676c2 Author: Weiqun Zhang Date: Wed Mar 20 16:12:14 2019 -0700 add init eb function Tutorials/GPU/EBCNS/Exec/Sod/GNUmakefile Tutorials/GPU/EBCNS/Exec/Sod/inputs Tutorials/GPU/EBCNS/Source/CNS_init_eb2.cpp Tutorials/GPU/EBCNS/Source/Make.package Tutorials/GPU/EBCNS/Source/main.cpp commit c511bb681dcd95d57072ddb21ef646e7ec23b863 Author: kngott Date: Wed Mar 20 17:43:33 2019 -0700 Cuda graph testing on lambda-less form of FillBoundary calls. Tests/GPU/GraphBoundary/GNUmakefile Tests/GPU/GraphBoundary/Make.package Tests/GPU/GraphBoundary/inputs_3d Tests/GPU/GraphBoundary/main.cpp Tests/GPU/GraphBoundary/run.corigpu commit 1a029724fd2176d6c9302ab5a7751f4be7241d60 Merge: c42e093db ba3d5d8e8 Author: Andrew Myers Date: Wed Mar 20 15:48:37 2019 -0700 Merge pull request #428 from RevathiJambunathan/random_xorwow_RJ Random number generator on GPU using CUDA - RJ commit c42e093db26da979ca92211aa23f1bc9d75f570e Merge: 40ff12886 f3a21370e Author: WeiqunZhang Date: Wed Mar 20 15:45:04 2019 -0700 Merge pull request #431 from dpgrote/development Added plot_log_per commit 46658d8f324f83f173cc249c59aedd92d1665353 Merge: 562a3e847 ba3d5d8e8 Author: RevathiJambunathan Date: Wed Mar 20 15:41:27 2019 -0700 Merge branch 'random_xorwow_RJ' of https://github.com/RevathiJambunathan/amrex into random_xorwow_RJ commit 562a3e847eec8532d894ddf84291506811f6cc3e Author: RevathiJambunathan Date: Wed Mar 20 15:40:44 2019 -0700 deleting main.H and instead added dependencies in main.cpp file of the in Tests/GPU/RandomNumberGeneration/ Tests/GPU/RandomNumberGeneration/main.H commit c212e45d8307612951e2a4bef042647d9321adf5 Author: Weiqun Zhang Date: Wed Mar 20 15:38:38 2019 -0700 start GPU/EBCNS Tutorials/GPU/EBCNS/Exec/Make.CNS Tutorials/GPU/EBCNS/Exec/Sod/GNUmakefile Tutorials/GPU/EBCNS/Exec/Sod/Make.package Tutorials/GPU/EBCNS/Exec/Sod/cns_prob.H Tutorials/GPU/EBCNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/EBCNS/Exec/Sod/cns_prob_parm.H Tutorials/GPU/EBCNS/Exec/Sod/inputs Tutorials/GPU/EBCNS/Source/CNS.H Tutorials/GPU/EBCNS/Source/CNS.cpp Tutorials/GPU/EBCNS/Source/CNSBld.cpp Tutorials/GPU/EBCNS/Source/CNS_K.H Tutorials/GPU/EBCNS/Source/CNS_advance.cpp Tutorials/GPU/EBCNS/Source/CNS_bcfill.cpp Tutorials/GPU/EBCNS/Source/CNS_derive.H Tutorials/GPU/EBCNS/Source/CNS_derive.cpp Tutorials/GPU/EBCNS/Source/CNS_index_macros.H Tutorials/GPU/EBCNS/Source/CNS_io.cpp Tutorials/GPU/EBCNS/Source/CNS_parm.H Tutorials/GPU/EBCNS/Source/CNS_parm.cpp Tutorials/GPU/EBCNS/Source/CNS_setup.cpp Tutorials/GPU/EBCNS/Source/CNS_tagging.H Tutorials/GPU/EBCNS/Source/Make.package Tutorials/GPU/EBCNS/Source/diffusion/Make.package Tutorials/GPU/EBCNS/Source/hydro/CNS_hydro_K.H Tutorials/GPU/EBCNS/Source/hydro/Make.package Tutorials/GPU/EBCNS/Source/main.cpp commit ba3d5d8e80f509b66b907eed5c68423f0d78a6bf Author: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com> Date: Wed Mar 20 15:38:25 2019 -0700 Delete main.H Tests/GPU/RandomNumberGeneration/main.H commit f3a21370e353f644bd22a23f8b0ac1568c62273e Author: Dave Grote Date: Tue Mar 19 10:46:18 2019 -0700 Added plot_log_per Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp commit 48debcf84ff8ece62e573e9b5fda01c3533b6c1e Author: RevathiJambunathan Date: Wed Mar 20 15:30:25 2019 -0700 removed main.H file that inluded AMReX header files and instead included them in the main.cpp file. Tests/GPU/RandomNumberGeneration/main.cpp commit 7930cd348e099094c556f678eae74f58bdd92cd0 Author: RevathiJambunathan Date: Wed Mar 20 15:18:37 2019 -0700 Tests/GPU/RandomNumberGeneration/main.cpp Tests/GPU/RandomNumberGeneration/main.cpp commit db7f4e98d01b9ef23c3b05ee745be20c1e49c832 Author: RevathiJambunathan Date: Wed Mar 20 15:05:16 2019 -0700 I had initialized array size with Nbuffer=N*2, but initialized seed with N in for loop, instead of Nbuffer. I have fixed it with Nbuffer. Also note that this array size is to prevent frequent call for resize. the size of array could even be 3*N or 1.5*N. I have put 2*N thinking that should be enough. Either way, user can call CheckSeedArraySizeAndResize() with the required number of CUDA threads launched (N). This function will resize dynamically. Src/Base/AMReX_Utility.cpp commit 3d0233825dd352bd78a85b05ad864fc5c67359e7 Author: RevathiJambunathan Date: Wed Mar 20 14:54:18 2019 -0700 adding the header file for testing random numbers Tests/GPU/RandomNumberGeneration/main.H commit aed416696f9bc9b278883f512027741281698d64 Author: RevathiJambunathan Date: Wed Mar 20 14:50:37 2019 -0700 adding the modified test file which calls the Random() function implemented in AMReX_Utility.cpp using either GPU or CPU. Tests/GPU/RandomNumberGeneration/main.cpp commit c02d0135611c62991ce46f73f0a5499afcfd7c7e Author: RevathiJambunathan Date: Wed Mar 20 14:49:32 2019 -0700 removed #include since it is not used in AMReX_Vector.H and instead included in AMReX_CudaUtility.H. Src/Base/AMReX_Vector.H commit bcad025b6a3b53b5f05fec944c48904fc66383bb Author: RevathiJambunathan Date: Wed Mar 20 14:48:02 2019 -0700 cleaned up utility.cpp such that it does not rely on using namespace amrex, or using namespace Gpu, instead using amrex:: or amrex::Gpu:: . Also included *glo_RandStates in an anonymous namespace. Finally, int NrandMax is removed as it is the size of the random seed vector. Instead, I have called dev_RandStates_Seed.size() Src/Base/AMReX_Utility.cpp commit 58334d7b708e18897539164f0bfb5faea856cfd9 Author: RevathiJambunathan Date: Wed Mar 20 14:45:08 2019 -0700 included curand_kernel.h in this file, instead of in AMReX_Vector.H file Src/Base/AMReX_CudaUtility.H commit 40ff1288626bdfdef7407fd1a412f5b2731e920b Merge: 8b9365b98 9846269b8 Author: WeiqunZhang Date: Wed Mar 20 13:46:08 2019 -0700 Merge pull request #430 from jrood-nrel/nrel_add_rhodes Adding some specific compiler flags for the Rhodes machine at NREL. commit 7656ba2b2e32aaf63602776d7ca3094ef4212a80 Author: RevathiJambunathan Date: Wed Mar 20 12:59:44 2019 -0700 deleted code (Hash_DistributionMap) in AMReX_Utility.H based on git diff random_xorwow_RJ and development Src/Base/AMReX_Utility.H commit 9846269b89d2d6302388b129b0e41d1946370257 Author: Jon Rood Date: Wed Mar 20 13:53:57 2019 -0600 Adding some specific compiler flags for the Rhodes machine at NREL. Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.nrel commit 2e8b9460926e1a18cf2860aadc8ef8ef44dab566 Merge: 1ebf6f067 8b9365b98 Author: RevathiJambunathan Date: Wed Mar 20 12:17:50 2019 -0700 Merge branch 'development' into random_xorwow_RJ commit 1ebf6f067849d30c20172ff37b1c8e173188b569 Author: RevathiJambunathan Date: Wed Mar 20 11:43:52 2019 -0700 modified Utility.cpp to generalize it for runs that do not use the CUDA flag Src/Base/AMReX_Utility.cpp commit 40a89049f4b089ba64dbd82cfacecf5bff3ecc69 Merge: dc703b384 5ecca63c8 Author: RevathiJambunathan Date: Wed Mar 20 10:55:43 2019 -0700 Merge branch 'random_xorwow_RJ' of https://github.com/RevathiJambunathan/amrex into random_xorwow_RJ commit dc703b38441cbd458092e74dccf74929212e43fb Author: RevathiJambunathan Date: Wed Mar 20 10:50:40 2019 -0700 modified Utility.cpp to generalize it for runs that do not use the CUDA flag Src/Base/AMReX_Utility.cpp commit 5ecca63c870ccfceb0ddd87caf4cc20303bf6f87 Author: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com> Date: Wed Mar 20 10:46:44 2019 -0700 Delete test1.out Tests/GPU/RandomNumberGeneration/test1.out commit 87cf6e6b23e48c8e273c8eda1947dff6396c57cd Author: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com> Date: Wed Mar 20 10:46:35 2019 -0700 Delete profilingdata_rndm.dat Tests/GPU/RandomNumberGeneration/profilingdata_rndm.dat commit 112c4b02b21003a603b893dccbfab31d198175a5 Author: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com> Date: Wed Mar 20 10:46:27 2019 -0700 Delete profile_without_skipahead.dat Tests/GPU/RandomNumberGeneration/profile_without_skipahead.dat commit 28f30a7464f4a3da15760f00bddb035dd1acc7b7 Author: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com> Date: Wed Mar 20 10:46:20 2019 -0700 Delete profile_with_skipahead.dat Tests/GPU/RandomNumberGeneration/profile_with_skipahead.dat commit b0f88d1875fc045def9f25733a9730701ad10ca7 Author: Revathi Jambunathan <41089244+RevathiJambunathan@users.noreply.github.com> Date: Wed Mar 20 10:46:04 2019 -0700 Delete Backtrace.0 Tests/GPU/RandomNumberGeneration/Backtrace.0 commit 8b9365b9812122c38e41ce93a9aa472a5363154d Merge: 829932ae2 2a06dcd84 Author: Weiqun Zhang Date: Wed Mar 20 10:37:40 2019 -0700 Merge branch 'weiqun/bestfit' into development commit 829932ae2827217e217f13c4ea5698dddd3dbafd Author: Weiqun Zhang Date: Wed Mar 20 13:35:11 2019 -0400 allocate 3/4 of global memory up front in the arena. this can be changed with parmparse parameter amrex.the_arena_init_size Src/Base/AMReX_Arena.cpp commit c932bb9f322d89ab69d1986aad4ad9349cbb27a7 Merge: fbeef499a f4da05bca Author: RevathiJambunathan Date: Tue Mar 19 18:29:10 2019 -0700 adding changes in Utility.H/.cpp after merging with the development branch commit 2a06dcd84001d2119f94f4531815771ece396efc Author: Weiqun Zhang Date: Tue Mar 19 16:41:06 2019 -0700 EArena: use lower bound Src/Base/AMReX_EArena.cpp commit fbeef499ac439b6cf407a7f23488b3b1141fd236 Author: RevathiJambunathan Date: Tue Mar 19 16:36:47 2019 -0700 adding changes made in Utility.H/.cpp to include random number generator for device Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Base/AMReX_Vector.H commit f4da05bca2382aba8fc257a606b335c3f897e086 Author: Andrew Myers Date: Tue Mar 19 18:33:06 2019 -0400 ReduceLongMax -> ReduceLongSum Src/Particle/AMReX_ParticleContainerI.H commit 9c8772b8607bd3320fb6f4a416682bce50912640 Author: Weiqun Zhang Date: Tue Mar 19 15:08:33 2019 -0700 EArena: memory allocator using best fit strategy Src/Base/AMReX_Arena.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_EArena.H Src/Base/AMReX_EArena.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 8a31d0355868ef62fa92012606a0722a869fe9c1 Author: Michael Zingale Date: Tue Mar 19 10:21:27 2019 -0400 fix makefile Docs/JOSS/Makefile commit cc30b10c28d6510d369d8a110cd14cbccc31f530 Author: Ann Almgren Date: Mon Mar 18 19:49:16 2019 -0700 Fix the author ordering so it shows correctly on the web page Docs/JOSS/paper.md commit d7ae6e8198092df61dadc236915d3bafc5e3c5c8 Author: Ann Almgren Date: Mon Mar 18 19:13:10 2019 -0700 Add mention of BoxLib and xSDK. Docs/JOSS/paper.md commit b85bd555ee8b5460367bf2bda0b867595deaa9f4 Author: Ann Almgren Date: Mon Mar 18 19:09:44 2019 -0700 A start of the JOSS paper and bibliography Docs/JOSS/Makefile Docs/JOSS/paper.bib Docs/JOSS/paper.md commit c5e98e07846f467dcf91003eb8e43abe9ea40fc8 Author: Ann Almgren Date: Mon Mar 18 18:52:47 2019 -0700 Remove "Overview" Docs/sphinx_documentation/source/ForkJoin.rst commit 8b5748e0124c423632ad940a20887a7117f5d82b Author: Ann Almgren Date: Mon Mar 18 18:48:40 2019 -0700 "framework library" --> "framework" Docs/sphinx_documentation/source/index.rst commit 3b382d37c8a462bf41099d6c518e54fa1d88b565 Merge: 2180b81a3 8813756dc Author: Ann Almgren Date: Mon Mar 18 18:41:04 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 2180b81a31eea71cf0faed2c001e94bfeed039fc Author: Ann Almgren Date: Mon Mar 18 18:40:45 2019 -0700 Add ForkJoin to the documentation (as well as the tutorials) Docs/sphinx_documentation/source/ForkJoin.rst Docs/sphinx_documentation/source/figs/fork_join_tasks.png Docs/sphinx_documentation/source/figs/nested_fork_join_tasks.png Docs/sphinx_documentation/source/index.rst commit 8813756dcaee5c9338ad0818e8cec3e286bf40e8 Author: Andrew Myers Date: Mon Mar 18 21:31:21 2019 -0400 keep the temporary variables around to save on memory usage with the Arena Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit c8caefd76ccf460d64c309c97cf6ff059e7dd950 Author: Andrew Myers Date: Mon Mar 18 21:30:40 2019 -0400 use the managed arena for thrust's interal calculations Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaAllocators.cpp commit 819afc65b99069eb608bb0ae43a1461158b9538b Merge: d2443edec ced520e4a Author: Ann Almgren Date: Mon Mar 18 14:52:11 2019 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit d2443edec41a4296f7e3dc941bcccc0df9bb50b8 Author: Ann Almgren Date: Mon Mar 18 14:50:45 2019 -0700 Add disclaimer re Macs Docs/sphinx_documentation/source/BuildingAMReX_Chapter.rst commit 38dfa69df8cd4c541c6d4765abef00b95a912a95 Author: Weiqun Zhang Date: Mon Mar 18 13:23:57 2019 -0700 attribute weak Src/Amr/AMReX_LevelBld.H Src/Amr/AMReX_PROB_AMR_F.H Src/Base/AMReX_Extension.H commit ced520e4a8a1c9ba71af2921cd9030cabf36ac12 Author: Weiqun Zhang Date: Mon Mar 18 13:22:51 2019 -0700 fix shadow warning Src/Base/AMReX_BCRec.H commit 816afbbf105c407b95e17d7c6b99944a2854dabd Author: Kevin Gott Date: Mon Mar 18 16:11:59 2019 -0400 Edit Scratchpad to compile on Summit. Tests/GPU/ScratchPad/main.cpp commit 6864211344d2df5e0067083779d8a6022f66c011 Merge: 05c7bee5a bc1832a62 Author: Weiqun Zhang Date: Mon Mar 18 16:06:38 2019 -0400 Merge branch 'weiqun/noexcept' into development commit bc1832a625bede9e927f8eda63a8e978c08d2113 Author: Weiqun Zhang Date: Mon Mar 18 16:06:13 2019 -0400 add noexcept to lambda functions Src/Base/AMReX_CudaLaunch.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_derive.cpp Tutorials/GPU/CNS/Source/CNS_tagging.H Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H commit 05c7bee5ae6f6a1eca36b485fceaf67e51a98f4e Merge: cb8bbd382 fc22930a1 Author: Weiqun Zhang Date: Mon Mar 18 12:27:19 2019 -0700 Merge branch 'weiqun/noexcept' of github.com:AMReX-Codes/amrex into weiqun/noexcept commit fc22930a179aeceb92e598c99e7b93c591976213 Merge: aabfca9b3 02aff8d8c Author: Weiqun Zhang Date: Mon Mar 18 15:25:48 2019 -0400 Merge branch 'development' into weiqun/noexcept commit cb8bbd3828a022c4c2087cb2fab63ecdfd32c4c0 Author: Weiqun Zhang Date: Mon Mar 18 12:24:46 2019 -0700 fix a warning Src/Amr/AMReX_StateDescriptor.H commit 02aff8d8cd61631905c2591767a573aae242e3c2 Author: Weiqun Zhang Date: Mon Mar 18 14:20:31 2019 -0400 fix make for olcf. Seems that cuda module no longer sets CUDAPATH. Tools/GNUMake/sites/Make.olcf commit aabfca9b3558e3d98f7c9632a040da201d404314 Author: Weiqun Zhang Date: Mon Mar 18 10:40:07 2019 -0700 add noexcept to TinyProfiler Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp commit fea04c8ee9ad59b60ce9c15b4627e1a9fc2ab3d3 Merge: 2a6734ed7 ff5b21f55 Author: Weiqun Zhang Date: Mon Mar 18 10:25:24 2019 -0700 Merge branch 'development' into weiqun/noexcept commit f2419baefdac71393046e2e8cf5604249e469d5c Author: kngott Date: Mon Mar 18 10:15:30 2019 -0700 Comment adjustments. Tests/GPU/CrazyGraphs/main.cpp commit 2a6734ed7755022c1b7516770dae981b49a8326b Author: Weiqun Zhang Date: Mon Mar 18 10:15:09 2019 -0700 add noexcept to Amr/ Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AuxBoundaryData.H Src/Amr/AMReX_AuxBoundaryData.cpp Src/Amr/AMReX_Derive.H Src/Amr/AMReX_Derive.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_AmrParGDB.H Src/AmrCore/AMReX_Cluster.H Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_ErrorList.cpp Src/AmrCore/AMReX_FluxReg_1D_C.H Src/AmrCore/AMReX_FluxReg_2D_C.H Src/AmrCore/AMReX_FluxReg_3D_C.H Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp commit 5420cfcb90aae2991547d01b3fbd25d8302e6416 Author: Weiqun Zhang Date: Fri Mar 15 17:00:19 2019 -0700 add noexcept to MLMG Src/LinearSolvers/MLMG/AMReX_MG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLALap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLALap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_3D_K.H Src/LinearSolvers/MLMG/AMReX_MacProjector.H commit 39fdcdd0a3efbc5636509777e3dc7c32ce45dc23 Author: kngott Date: Mon Mar 18 01:03:39 2019 -0700 Add lambda launch version. Still needs CUDA 10.1. Tests/GPU/CrazyGraphs/main.cpp commit 9d34ba257b21110492c895a4a535939879c96c78 Author: kngott Date: Mon Mar 18 01:03:19 2019 -0700 Add --expt-extended-lambda flag. Tests/GPU/CrazyGraphs/GNUmakefile commit bb35bdf115da661ec571b73136cd8ab1e5368a39 Author: kngott Date: Sun Mar 17 21:04:15 2019 -0700 Crazy Graphs. Attempt to reuse graphs with different parameters without re-instantiating. Needs CUDA 10.1 to test. Tests/GPU/CrazyGraphs/GNUmakefile Tests/GPU/CrazyGraphs/main.cpp Tests/GPU/CrazyGraphs/run.corigpu commit a204e6b58cc822c95c70133a31a20c5935b4765e Author: kngott Date: Fri Mar 15 16:58:17 2019 -0700 Reuse a graph. Tests/GPU/CudaGraphs/main.cpp commit ef2312dbc208c3d4176a0b61d70def50b35e49c1 Author: Weiqun Zhang Date: Fri Mar 15 16:40:53 2019 -0700 add noexcept to Boundary/ Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_BoundCond.H Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_FabSet.cpp Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_InterpBndryData_1D_K.H Src/Boundary/AMReX_InterpBndryData_2D_K.H Src/Boundary/AMReX_InterpBndryData_3D_K.H Src/Boundary/AMReX_LOUtil_K.H Src/Boundary/AMReX_MacBndry.H Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_Mask.cpp Src/Boundary/AMReX_MultiMask.H Src/Boundary/AMReX_YAFluxRegister.H Src/Boundary/AMReX_YAFluxRegister.cpp Src/Boundary/AMReX_YAFluxRegister_1D_K.H Src/Boundary/AMReX_YAFluxRegister_2D_K.H Src/Boundary/AMReX_YAFluxRegister_3D_K.H commit 85bc8de4c72f152e86893009c79d8ddba5ebf476 Author: kngott Date: Fri Mar 15 16:05:55 2019 -0700 Add linked graph over iterations. Tests/GPU/CudaGraphs/main.cpp commit 51a1fe4b26613918f37f1a818fe465aa226cfea0 Author: kngott Date: Fri Mar 15 15:30:11 2019 -0700 One linked MFIter graph & cleaned output. Tests/GPU/CudaGraphs/main.cpp commit 909d8608b360e8daaab090d238881c57e4aedcb6 Author: Weiqun Zhang Date: Fri Mar 15 15:21:17 2019 -0700 more noexcepts. remove BroadcastDistributionMap and BroadcastBoxArray Src/Base/AMReX_IndexType.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_Orientation.H Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_Periodicity.H Src/Base/AMReX_Periodicity.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Base/AMReX_Vector.H commit d0219a3d08f03dc3a41e830140df037258a6a86e Author: kngott Date: Fri Mar 15 14:17:00 2019 -0700 Individual timers. Tests/GPU/CudaGraphs/main.cpp commit cc8c58d755e240067f9892a734f4ea3c697562d3 Author: RevathiJambunathan Date: Fri Mar 15 14:14:18 2019 -0700 adding test directory for random no. generator on gpus - XORWOW Tests/GPU/RandomNumberGeneration/Backtrace.0 Tests/GPU/RandomNumberGeneration/GNUmakefile Tests/GPU/RandomNumberGeneration/Make.package Tests/GPU/RandomNumberGeneration/main.cpp Tests/GPU/RandomNumberGeneration/profile_with_skipahead.dat Tests/GPU/RandomNumberGeneration/profile_without_skipahead.dat Tests/GPU/RandomNumberGeneration/profilingdata_rndm.dat Tests/GPU/RandomNumberGeneration/test1.out commit 3152c11b416ed7f2bcef3ca3f2ea75b9f6ecbbc5 Author: Weiqun Zhang Date: Fri Mar 15 14:13:51 2019 -0700 more excepts and remove iMultiFab's own operator[] Src/Base/AMReX_COORDSYS_1D_C.H Src/Base/AMReX_COORDSYS_2D_C.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FilCC_1D_C.H Src/Base/AMReX_FilCC_2D_C.H Src/Base/AMReX_FilCC_3D_C.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuError.H Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/Base/AMReX_MultiFabUtil_nd_C.H Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit 28f490d40b76cccb1721e99c4a0513f126d91e8b Author: kngott Date: Fri Mar 15 13:11:52 2019 -0700 Touch the memory first to get a fair timing. Tests/GPU/CudaGraphs/main.cpp commit 7b1e52ccf5f9f122bc62b7b8ab80f2e6a7dc4e39 Author: Weiqun Zhang Date: Fri Mar 15 12:40:53 2019 -0700 more excepts Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_Array.H Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.H Src/Base/AMReX_CudaAsyncFabImpl.cpp Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaElixir.H Src/Base/AMReX_CudaElixir.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_CudaRange.H Src/Base/AMReX_CudaReduce.H Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_CudaUtility.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabFactory.H Src/Base/AMReX_LayoutData.H commit 384817f40cd35d5f011e663140f378957eda8b36 Author: kngott Date: Thu Mar 14 22:22:45 2019 -0700 Fix the indenting. Tests/GPU/CudaGraphs/main.cpp commit 00070c911de2ee2f260af738f9be02bc99c3a310 Author: kngott Date: Thu Mar 14 22:17:27 2019 -0700 Stream-based graph test. Tests/GPU/CudaGraphs/main.cpp commit 35bde2ddc178ba57ab78ac56a27128e111e0aa62 Author: kngott Date: Thu Mar 14 22:17:14 2019 -0700 Access maxCudaStreams for Stream based graph test. Src/Base/AMReX_CudaDevice.H commit fc2494f4d1b9062e6557a59a12844319995b1212 Author: kngott Date: Thu Mar 14 16:47:53 2019 -0700 First draft of CUDA graphs. Tests/GPU/CudaGraphs/GNUmakefile Tests/GPU/CudaGraphs/Make.package Tests/GPU/CudaGraphs/inputs_3d Tests/GPU/CudaGraphs/main.cpp Tests/GPU/CudaGraphs/run.corigpu commit d7a64c05b3e29bde947f804bb20acd039422995d Author: Weiqun Zhang Date: Thu Mar 14 16:40:29 2019 -0700 more noexcepts Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BaseFabUtility.H Src/Base/AMReX_Box.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxIterator.H Src/Base/AMReX_BoxIterator.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_IntVect.H commit ff5b21f5518a5aef24cad303781137f250c2c0e4 Merge: 890281e72 196631965 Author: Michele Rosso Date: Thu Mar 14 15:18:43 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 890281e72997428c8e6f4a88b0fcd452739f6b3b Author: Michele Rosso Date: Thu Mar 14 15:18:32 2019 -0700 CMake: enable linking against amrex in shared lib mode. Fixes Issue #425 Tools/CMake/AMReX_Config.cmake Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt commit 196631965f408cfb550c563a47b29be5d9145e50 Author: Kevin Gott Date: Thu Mar 14 17:37:36 2019 -0400 Convert relevant amrex::launch's to amrex::ParallelFor in Advection_AmrCore tutorial. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.H commit 0081789506427dd45120eb82771e2593978afd90 Author: Kevin Gott Date: Tue Mar 12 00:18:31 2019 -0400 Remove recursive header calls. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.H commit 378071778ff17ae1b17ff7efe3e6e2ac6a97d521 Merge: b4a778c4e e24c918b9 Author: Michele Rosso Date: Wed Mar 13 12:02:20 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b4a778c4e5c67f6ea2d41c69230663fc1085f218 Author: Michele Rosso Date: Wed Mar 13 11:53:41 2019 -0700 CMake: add support for SUNDIALS3 CMakeLists.txt Docs/sphinx_documentation/source/BuildingAMReX.rst Src/CMakeLists.txt Src/Extern/SUNDIALS3/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Options.cmake Tools/CMake/FindSUNDIALS.cmake Tutorials/CMakeLists.txt Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/CMakeLists.txt Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/main.cpp Tutorials/CVODE/SUNDIALS3_finterface/EX1/CMakeLists.txt Tutorials/CVODE/SUNDIALS3_finterface/EX1/main.cpp commit e24c918b9380242bc97224433ad2ae2b84cb037f Merge: 4381b5249 01f87dd5a Author: mic84 Date: Tue Mar 12 14:50:10 2019 -0700 Merge pull request #423 from Alpine-DAV/task/2019_03_ascent_and_conduit_cmake_support add amrex cmake support for including ascent and conduit commit 01f87dd5a6ad479ee71abc0fd454a4ef31a0dd67 Author: Cyrus Harrison Date: Tue Mar 12 14:24:41 2019 -0700 add cmake support for including ascent Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_SetupThirdpartyLibs.cmake commit 4381b524911266280a9150677768776e788484f0 Author: Weiqun Zhang Date: Tue Mar 12 09:15:40 2019 -0700 add include guard so that AMReX_Config.H can be included in C/Fortran codes Tools/libamrex/mkconfig.py commit 0cd354416760107cdbf7d61d5ab79c4c040db3bd Author: Kevin Gott Date: Mon Mar 11 19:28:12 2019 -0400 Change to simplified simple launch. Tests/GPU/Test/main.cpp Tests/GPU/TestB/main.cpp Tests/GPU/TestC/main.cpp commit 250ddad74ea3ff069474a888c785ce546220af63 Author: Kevin Gott Date: Mon Mar 11 15:41:48 2019 -0700 Add >= note to C++ loop discussion. Docs/sphinx_documentation/source/Basics.rst commit 58330314e939f9b9795f86a8157ca83de90ffe99 Author: Kevin Gott Date: Mon Mar 11 17:21:15 2019 -0400 Less than or equal to. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.H commit f12504a91fcd18ea01daa7827b2a13550cf92d43 Author: Max Katz Date: Sun Mar 10 15:49:08 2019 -0400 Make grid-stride loops better aware of numThreadsMin Src/Base/AMReX_CudaDevice.cpp commit 085335a9a86b01b6df3b88d5eade1e05a4b7ec4b Author: Max Katz Date: Sun Mar 10 15:48:40 2019 -0400 Specialize rule for AMReX_filcc_mod.F90 when using CUDA Src/Base/Make.package Tools/GNUMake/Make.rules commit 110d19aca9577691386509298084b7479999c766 Author: Max Katz Date: Sun Mar 10 08:58:24 2019 -0400 Echo which path we're taking for CUDA fortran compilation Tools/GNUMake/Make.rules commit 65cf70250191bbd83073ece40dd9ade3e4769406 Author: Max Katz Date: Sun Mar 10 05:07:57 2019 -0400 Add hook for setting Device::numThreadsMin Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp commit ccb1a3b672fb07b20e62712768f1d884aa58d56f Author: Max Katz Date: Sun Mar 10 03:31:49 2019 -0400 Get amrex_filccn going for the GPU pragma case Src/Base/AMReX_filcc_mod.F90 commit 12bedb4b8d3b418aa6f047f28b85cc220c52cd1b Author: Max Katz Date: Sun Mar 10 03:31:15 2019 -0400 Add a device sync in case the user code does bndryFill on the GPU Src/Amr/AMReX_StateData.cpp commit 79a9a2c0a5bde5a270ba6395051ab594f3aa90ed Author: Kevin Gott Date: Fri Mar 8 23:21:46 2019 -0500 Update Tests/GPU/Test: PinnedData idea. Tests/GPU/Test/main.cpp commit 68c79fdd49a1e37e0696131aae246c9cf9f6008a Author: Kevin Gott Date: Fri Mar 8 23:17:24 2019 -0500 Update Tests/GPU/TestC: Turning DeviceRegion on and off. Tests/GPU/TestC/main.cpp commit 93fc7d082666229a3392b0b3451106124074b8d7 Author: Kevin Gott Date: Fri Mar 8 22:56:44 2019 -0500 Update GPU/Test/TestB: Fortran return bug. (It's still a bug.) Tests/GPU/TestB/main.cpp commit 0134854893f3cf52b63bdfef35b85e304ba563bf Author: Kevin Gott Date: Wed Mar 6 19:28:10 2019 -0500 Macro based launches to function based launches. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit b2f10380f5008e4b5467156d59220d400d4016ee Author: Kevin Gott Date: Wed Mar 6 19:27:49 2019 -0500 Add USE_CUDA=TRUE to GPU tutorial makefile. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/GNUmakefile commit dd6007105408bc29fddd5d326aea8653b52c828c Merge: 6cf416c77 2d940e591 Author: Andrew Myers Date: Fri Mar 8 16:31:32 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6cf416c779b1de43ed4840a5320c42b000d13050 Author: Andrew Myers Date: Fri Mar 8 16:31:11 2019 -0800 need to include this header to compile with Cuda 10.1 Src/Base/AMReX_CudaAllocators.H commit 5b628078c031206b445bc15d2f8c683257077d63 Author: Michele Rosso Date: Fri Mar 8 18:31:44 2019 -0500 CMake: link to cuda only if ENABLE_CUDA is on Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.cmake commit 2d940e591f540ac7cddd64f5729e0d52b515dbca Author: Ann Almgren Date: Fri Mar 8 10:39:15 2019 -0800 1) Don't pass inhomogeneous flag into gsrb -- we are always in residual-correction form there 2) Make sure to use "integer, value, intent(in)" instead of just "integer, intent(in)" -- lesson learned! Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 5720d252f84f40e342e29db357f92df6f2f53647 Merge: 1e5ca6481 b40b22f0b Author: WeiqunZhang Date: Fri Mar 8 08:40:36 2019 -0800 Merge pull request #421 from AMReX-Codes/regrid_only Add optional flag to RegridOnly for disabling I/O commit b40b22f0b742aa81a63368e17a20d44a3aebddfc Author: Max Katz Date: Fri Mar 8 01:08:36 2019 -0500 Add optional flag to RegridOnly for disabling I/O RegridOnly is useful as a public interface to regridding for the user code to call. For cases where the user wants to call it during a simulation, rather than immediately after restart, the I/O options aren't meaningful, so this allows the user to disable that in their call to RegridOnly (while still potentially allowing it in other cases where plotfile_on_restart et al. are desired). Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp commit 72a3d156b0843bf00aad13adc3dea08ddda421c3 Merge: 0981654f8 1e5ca6481 Author: Cyrus Harrison Date: Thu Mar 7 21:36:26 2019 -0800 merge from development commit 0981654f8939f98696834415077799cd872ca21d Author: Cyrus Harrison Date: Thu Mar 7 21:30:00 2019 -0800 plumbing for cmake support for including ascent and conduit Src/CMakeLists.txt Src/Extern/Conduit/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_SetupThirdpartyLibs.cmake commit b41cebe4bdb46281b0aa7da7f9b9257e1fd612b5 Author: Michele Rosso Date: Thu Mar 7 20:34:39 2019 -0500 CMake: look for MPI in config file if required Tools/CMake/AMReXConfig.cmake.in commit 1263cbbf4b379103d2976091f7c563e4bbd6a68f Merge: ee4ddb0f4 1e5ca6481 Author: Michele Rosso Date: Thu Mar 7 18:56:04 2019 -0500 Merge branch 'development' into mr/cmake commit ee4ddb0f4e7e9f0eca5400c60141b087fca93326 Author: Michele Rosso Date: Thu Mar 7 18:55:13 2019 -0500 CMake: some clean-up CMakeLists.txt Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_SetupCUDA.cmake Tools/CMake/comps/AMReX_Cray.cmake Tools/CMake/comps/AMReX_GNU.cmake Tools/CMake/comps/AMReX_Intel.cmake Tools/CMake/comps/AMReX_NVIDIA.cmake Tools/CMake/comps/AMReX_PGI.cmake Tutorials/GPU/NeighborList/CMakeLists.txt commit 1e5ca6481023405aaea495e913353edb2220843c Author: Weiqun Zhang Date: Thu Mar 7 15:29:41 2019 -0800 add coarsen and refine to Geometry Src/Base/AMReX_Geometry.H commit 8b85de9e0d22cb6130fcdbb1befd8284ad964650 Merge: f607e4c8b e72cacca3 Author: Michele Rosso Date: Thu Mar 7 14:21:13 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit f607e4c8bd66d60880fef0f96877595f20099da5 Author: Michele Rosso Date: Thu Mar 7 14:20:51 2019 -0800 CMake: fix typo in configuration file. Tools/CMake/AMReXConfig.cmake.in commit e72cacca3456f312f665106dd1a948bcf7f041db Merge: 5e6e8afeb 27328435d Author: Andrew Myers Date: Thu Mar 7 13:23:16 2019 -0800 Merge pull request #420 from AMReX-Codes/marc/bad_rd_ptr_in_vismf Catch unhandled RealDescriptor logic in VisMf::Write commit 5e6e8afebedf52449a46b6ee355e33e6a7ba8b0c Author: sireeveslbl Date: Thu Mar 7 13:03:50 2019 -0800 Cleaned up diffmultifab's output, and got rid of segfault after amrex finalize Tools/C_util/DiffMultiFab/diffmultifab.cpp commit 1460aef9fb256a0e4c2caccac1b9b62923029155 Merge: 5b3c66c8a 6b53159af Author: Ann Almgren Date: Thu Mar 7 11:52:17 2019 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 5b3c66c8a30aacb1f279d3f32a418978b45c530a Author: Ann Almgren Date: Thu Mar 7 11:48:20 2019 -0800 Add support for higher order stencils at EB boundaries with Dirichlet bc's. This may be unstable so by default it is not used -- to use it you must call setEBHODirichlet() in addition to setEBDirichlet (or setEBHomogDirichlet). There should be no change to the default behavior of any AMReX-based code from this commit. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_nd.F90 commit 6b53159af7628abed84e7d73e5b46b8eab4d5d73 Author: sireeveslbl Date: Thu Mar 7 11:48:16 2019 -0800 Fixed the fix with DiffMultfab, doesn't work with MPI at the moment. Tools/C_util/DiffMultiFab/diffmultifab.cpp commit 27328435d004303c4e0c4d0a888c711b5257a66f Author: Marc Day Date: Thu Mar 7 11:15:34 2019 -0800 Catch unhandled RealDescriptor logic in VisMf::Write Src/Base/AMReX_VisMF.cpp commit 23c09ff9407c537c73de0ae51687d763560204bd Author: Michele Rosso Date: Thu Mar 7 10:40:57 2019 -0800 CMake: fix blitz dependency issue in configuration file. Fixes Issue #418 Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Options.cmake commit 8d54f8de195fa85909f1524808afc35dc722258f Merge: 989fba702 e6bbfdf82 Author: WeiqunZhang Date: Thu Mar 7 09:34:53 2019 -0800 Merge pull request #419 from maikel/bugfix/EB_LSCore Use AMREX_D_DECL for the 2D case. commit e6bbfdf824c8419da1e8304986e7d04a645e3115 Author: Maikel Nadolski Date: Thu Mar 7 15:00:18 2019 +0100 Use AMREX_D_DECL for the 2D case. Src/EB/AMReX_EB_LSCoreBase.cpp commit 989fba702d7a7687c5ec53490a43ddb751150a25 Merge: 133cdab11 1fe6643df Author: Andrew Myers Date: Wed Mar 6 19:39:49 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 133cdab119ebfcbac3cee31b6f699f06bd99d40e Author: Andrew Myers Date: Wed Mar 6 19:39:14 2019 -0500 do the same early exit in the neighbor particles as in redistribute Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit 1fe6643dfde54368ab4a9d7367cd3d13a2281f49 Merge: 8c8447e5f ce2f442cd Author: Andrew Myers Date: Wed Mar 6 16:15:36 2019 -0800 Merge pull request #374 from Alpine-DAV/task/2018_11_add_blueprint_particle_support add conduit blueprint support for particles commit 8c8447e5f069c5250446241bc50f26c6478966d9 Author: Andrew Myers Date: Wed Mar 6 19:05:59 2019 -0500 only include this file if using cuda Src/Particle/AMReX_NeighborParticles.H commit e5963a5ba3d5f4d6265163bb581055c11ce30ed2 Merge: 937806fe4 17c88dbe1 Author: Andrew Myers Date: Wed Mar 6 18:49:39 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 937806fe4f41ac62dfcebf016358be2c618edb8f Author: Andrew Myers Date: Wed Mar 6 18:49:17 2019 -0500 remove fortran neighbor list Src/Particle/AMReX_Particle_mod_3d.F90 commit aad250e03d2c48c19d37c52694a4e5d04bf62f9f Author: Andrew Myers Date: Wed Mar 6 18:22:18 2019 -0500 add missing files Src/Particle/AMReX_NeighborParticlesCPUImpl.H Src/Particle/AMReX_NeighborParticlesGPUImpl.H commit d810b1b74cb66144ea9946b79a3e8e9bb55d0dd3 Author: Andrew Myers Date: Wed Mar 6 18:21:50 2019 -0500 refactor neighbor list stuff so that it can be used in MFIX Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/CMakeLists.txt Src/Particle/Make.package Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp Tutorials/GPU/NeighborList/main.cpp commit 17c88dbe1143e429e43395d408339b0aaf9135c6 Author: Kevin Gott Date: Wed Mar 6 17:35:20 2019 -0500 Fix bugs in Advection_AmrCore GPU tutorial. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.H commit 2bf74d5cc1376d2a6ba036ff7f7d17ae98ebb1f1 Author: Kevin Gott Date: Mon Feb 18 14:53:53 2019 -0500 unresolved-symbols flag Tests/GPU/buildNotused/GNUmakefile commit ce2f442cd169dda3761eb6bf47a5916bfed24d02 Merge: 2d8c886e1 f6ded5d73 Author: Cyrus Harrison Date: Wed Mar 6 13:38:01 2019 -0800 complete merge from develop (3/6/19) commit 0eb9d007d46a4417051cec4cfd6474014dfc9268 Author: Kevin Gott Date: Wed Mar 6 13:37:21 2019 -0800 First draft of converting Advection_AmrCore to new GPU method. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Make.package Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp commit 2d8c886e1e4e364e06a43018b4e5001a57101669 Author: Cyrus Harrison Date: Wed Mar 6 13:31:37 2019 -0800 update ascent actions for plots to match current ascent api Tutorials/Blueprint/AssignMultiLevelDensity/main.cpp Tutorials/Blueprint/CellSortedParticles/main.cpp Tutorials/Blueprint/HeatEquation_EX1_C/Source/main.cpp commit fdf51201943fef3f90251fc7cd1054071cea3d79 Author: Cyrus Harrison Date: Wed Mar 6 13:30:59 2019 -0800 add logic to calc unique domain ids for particle tiles Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H commit f6ded5d73c17cc229cdce73d5de322dab76f3ee7 Author: Andrew Myers Date: Wed Mar 6 15:31:49 2019 -0500 remove missing include file Src/Particle/AMReX_NeighborList.H commit 5b2e8481e8e877d97d4fc8d734d3f44508eb4c97 Author: Weiqun Zhang Date: Wed Mar 6 09:14:30 2019 -0800 add noexcept Src/Base/AMReX_Arena.H Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp commit 0c875187fcec03d34651f99a4cb81437ae344be5 Merge: e565216fa 06a6419f9 Author: Andrew Myers Date: Tue Mar 5 18:49:48 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e565216fa5a53d67fed07c490b5c506f44cd9d55 Author: Andrew Myers Date: Tue Mar 5 18:49:32 2019 -0500 allow arbitrary numbers of grow cells in the gpu neighbor list tutorial Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit 06a6419f9bd8a799c5a84a4fd603296b9cbe83fa Author: Weiqun Zhang Date: Tue Mar 5 15:37:01 2019 -0800 print free gpu global memory Src/Base/AMReX_Arena.cpp Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp commit 1ab0eef9e802515b4af01d20ceb8b9f7371226c3 Author: Michele Rosso Date: Tue Mar 5 18:03:09 2019 -0500 CMake: fix Tutorials/GPU/neighborList Tutorials/GPU/NeighborList/CMakeLists.txt commit 93269c1f8ae8c3c97393b7923e23002238427b6a Merge: b38a71df8 f5f3723b1 Author: Michele Rosso Date: Tue Mar 5 17:34:52 2019 -0500 Merge branch 'development' into mr/cmake commit f5f3723b156e538e50c308e700cbfd741e64c180 Merge: 58943998f 0aabf455e Author: Weiqun Zhang Date: Tue Mar 5 14:29:42 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 58943998f399752cac724f16abb6bc8423ed1334 Merge: fb087ed65 6df265e2a Author: Weiqun Zhang Date: Tue Mar 5 14:27:59 2019 -0800 Merge branch 'weiqun/fb' into development commit b38a71df854ba4e812761cb366ebc9bc9a178bd3 Merge: f8ff0f7cc fc45ce327 Author: Michele Rosso Date: Tue Mar 5 17:08:49 2019 -0500 Merge branch 'mr/cmake' of https://github.com/AMReX-Codes/amrex into mr/cmake commit f8ff0f7cc87853d9f0d63001f0f01fcfb31c92e2 Merge: a73e2b8ce 0aabf455e Author: Michele Rosso Date: Tue Mar 5 17:08:23 2019 -0500 Merge branch 'development' into mr/cmake commit 0aabf455e2abca3da41960cda5dcde9d173eb730 Author: Weiqun Zhang Date: Tue Mar 5 12:57:48 2019 -0800 FillBoundary: tweak local copy Src/Base/AMReX_FabArrayCommI.H commit 6df265e2ac031b3160a952312eb39f4659d91706 Author: Weiqun Zhang Date: Tue Mar 5 13:10:05 2019 -0800 fix typo Src/Base/AMReX_FabArrayCommI.H commit 05885996d28a1dde73d3ff6555ba68ac39ed35bb Author: Weiqun Zhang Date: Tue Mar 5 12:57:48 2019 -0800 FillBoundary: tweak local copy Src/Base/AMReX_FabArrayCommI.H commit fb087ed65075a8222f4d786a0391ee60a814146c Author: sireeveslbl Date: Tue Mar 5 12:05:30 2019 -0800 Fixed bug in DiffMultiFab Tools/C_util/DiffMultiFab/diffmultifab.cpp commit e2be0b98d1bd0221ad4e7db050f4d7d19da24a39 Author: Andrew Myers Date: Tue Mar 5 14:06:13 2019 -0500 missed some device vectors Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 8254c0c55a4f3aac442203ef83bb4b3f713be3fb Merge: 3300b5c85 cc1321b52 Author: Andrew Myers Date: Tue Mar 5 13:37:54 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3300b5c854edb46f3af1cc0e25ea419cc9c5b9ac Author: Andrew Myers Date: Tue Mar 5 13:37:16 2019 -0500 switch the device allocator back to using device memory Src/Base/AMReX_CudaAllocators.H commit 2985fbbb8cc66b234d788cfe8f34938a423396a5 Author: Andrew Myers Date: Tue Mar 5 13:31:28 2019 -0500 more Gpu::DeviceVector -> Gpu::ManagedDeviceVector Src/Particle/AMReX_NeighborList.H Src/Particle/AMReX_ParticleContainerI.H commit 79b76f96fbc6ffdee258bb6ccec7612d00eb7f10 Author: Andrew Myers Date: Tue Mar 5 13:26:11 2019 -0500 Gpu::DeviceVector -> Gpu::ManagedDeviceVector in NeighborList Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit cc1321b520bb0cc2fe432558031f761c0ef7a210 Author: Weiqun Zhang Date: Mon Mar 4 12:50:21 2019 -0800 fix pointer consistence checking for non-BaseFab type Src/Base/AMReX_FabArray.H commit 14953314ebfdc0a6fec26eacfc5d3cb6d70a03da Author: Brandon Runnels Date: Mon Mar 4 11:31:32 2019 -0700 fixed missing nghost declaration Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 14d209996040e0ef7c6cfbcbcbd607873fc11cd3 Author: Brandon Runnels Date: Sun Mar 3 18:01:04 2019 -0700 updated to keep expected behavior for operators with nghost <= 1 Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit b1cc0f83bc182927182d0774199d10f85212693c Merge: fc2ccacb6 cce917ff8 Author: Brandon Runnels Date: Sun Mar 3 16:39:02 2019 -0700 Merge branch 'development' into nodeghostcells commit fc2ccacb60bdd4d277be432e18cc2ec865e97a5a Author: Brandon Runnels Date: Sun Mar 3 15:46:37 2019 -0700 fixed error causing assertion error in ABecLaplacian_C test by updating RHS fill Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 7bc6ca003500e3476cd89f9b53ff8fa1d2079194 Author: Weiqun Zhang Date: Sat Mar 2 12:49:11 2019 -0800 consistence of style README.md commit 884d3194c9d890fcd135e44ef48b8b9886d87c9c Merge: 5c4260319 cce917ff8 Author: Weiqun Zhang Date: Fri Mar 1 22:23:17 2019 -0800 Merge branch 'development' commit cce917ff87eaa23e4f62074c1c31646e26f7ce0f Author: Weiqun Zhang Date: Fri Mar 1 22:21:45 2019 -0800 fix gpu fillboundary Src/Base/AMReX_FabArrayCommI.H commit 7a990d68674db23d10742da2b27ffabd76518de1 Author: Weiqun Zhang Date: Fri Mar 1 21:09:39 2019 -0800 fix launch safe guard Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 63ae785291c19a9e81e2cf737b75831285d12602 Author: Weiqun Zhang Date: Fri Mar 1 20:09:27 2019 -0800 assert that the pointers in FabArray are consistent Src/Base/AMReX_BLassert.H Src/Base/AMReX_FabArray.H commit 5c4260319370353a875153576a766887b500f21d Author: Weiqun Zhang Date: Fri Mar 1 16:52:44 2019 -0800 fix FArrayBox I/O for gpu. resize is not safe. Src/Base/AMReX_FArrayBox.cpp commit e8841ac81388664158cd217c8ec7ef78f883223d Author: Weiqun Zhang Date: Fri Mar 1 16:52:44 2019 -0800 fix FArrayBox I/O for gpu. resize is not safe. Src/Base/AMReX_FArrayBox.cpp commit c81f8f3fd352b7fdba9c6d9d6012348f99dc5dfd Merge: 944478759 86f9cc096 Author: Weiqun Zhang Date: Fri Mar 1 08:49:56 2019 -0800 Merge branch 'development' into faballocator commit 86f9cc096de908c649a1b78acd20ca12a848b306 Author: Weiqun Zhang Date: Fri Mar 1 08:48:27 2019 -0800 update CHANGES CHANGES commit eae3b47d998d1a5225b285458de87c692fde31f7 Merge: 95f2cef66 c714fba7b Author: Andrew Myers Date: Thu Feb 28 22:13:35 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 95f2cef66a4ff16bde2211ada7acdfdee1ee1772 Author: Andrew Myers Date: Thu Feb 28 22:13:15 2019 -0500 switch the order of these resize operations - could in principle save memory when using the arena Src/Particle/AMReX_ParticleTile.H commit 9444787593f5732daa15cf9d42b22344bfc4e25c Author: Weiqun Zhang Date: Thu Feb 28 19:11:03 2019 -0800 CArena: use unordered_set for busy list Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp commit c714fba7b6d66a4eceb754eb9fe693c874e29280 Author: Weiqun Zhang Date: Thu Feb 28 16:00:41 2019 -0800 Arena: removed duplicated codes, and make the memory type hard to change to avoid mistakes. this also makes the DArena use preferred Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_DArena.H Src/Base/AMReX_DArena.cpp commit ea8879052bf828f13142eae162578de85b2a41ed Author: Weiqun Zhang Date: Thu Feb 28 15:16:43 2019 -0800 minor Src/Base/AMReX_FabAllocator.cpp commit 90bd72517f3241d5b13cb4abcaf2c8dba07487bb Merge: d9395fb42 5fb65eda2 Author: Weiqun Zhang Date: Thu Feb 28 14:33:02 2019 -0800 Merge branch 'faballocator' into development commit 5fb65eda277c314a4a0004d583e3c32e84ac53bf Author: Weiqun Zhang Date: Thu Feb 28 14:06:43 2019 -0800 special allocator for fab because they basically ahve the same size Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_FabAllocator.H Src/Base/AMReX_FabAllocator.cpp Src/Base/AMReX_FabArray.H Src/Base/CMakeLists.txt Src/Base/Make.package commit d9395fb422b180d00bfa756a4db809ad2af94909 Author: Andrew Myers Date: Thu Feb 28 15:41:31 2019 -0500 fix debug statement Src/Particle/AMReX_ParticleContainerI.H commit 41cb3affa22b67c1e8bb0f5b2d167cc6cd91a9e1 Merge: 2ca417dd0 206fd2c5e Author: Andrew Myers Date: Thu Feb 28 13:35:24 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2ca417dd0f3bdd62a26042034097b76b567b8e5b Author: Andrew Myers Date: Thu Feb 28 13:35:05 2019 -0500 add early exit in the loop over grids in RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H commit 206fd2c5e58eea85893ef7f354e2178434d695d9 Merge: 343eba415 5fdb2f74a Author: Andrew Myers Date: Thu Feb 28 08:20:31 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 343eba415aea228dbfcfd2af2f32adca0903e7d4 Author: Andrew Myers Date: Thu Feb 28 08:20:13 2019 -0800 fix for periodic boundary conditions for particles when single precision is used. Src/Particle/AMReX_ParticleContainerI.H commit 5fdb2f74a8cd02b309900563d8ab4838723a1bb3 Author: Weiqun Zhang Date: Wed Feb 27 20:44:49 2019 -0500 DArena: calculate free memory and print more information Src/Base/AMReX_DArena.H Src/Base/AMReX_DArena.cpp commit 4253a1157e3b79ac29779dc270d01eea41d09299 Merge: 91743dae1 9a192a52e Author: Weiqun Zhang Date: Wed Feb 27 16:11:36 2019 -0800 Merge branch 'development' into buddy-allocator commit 91743dae16532bf71c709b560a405bf76152e0b5 Author: Weiqun Zhang Date: Wed Feb 27 15:42:58 2019 -0800 DArena: add gpu support Src/Base/AMReX_Arena.cpp Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_DArena.H Src/Base/AMReX_DArena.cpp commit bef856f1d308583d0fca0cf93bf884d10bb02778 Author: Weiqun Zhang Date: Wed Feb 27 13:41:55 2019 -0800 buddy memory allocator Src/Base/AMReX_DArena.H Src/Base/AMReX_DArena.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 9a192a52e6a596b17e37dbe627a57d6a7970bc40 Merge: 1f955e7e4 cf637da31 Author: Andrew Myers Date: Wed Feb 27 15:18:36 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1f955e7e4cdd0caf57fe23012091ab542e90daea Author: Andrew Myers Date: Wed Feb 27 15:17:57 2019 -0500 use The_Arena for all the particle stuff for now. Src/Base/AMReX_CudaAllocators.H commit fc45ce327649583c8b5c4940bb5772d4d7aedcd1 Merge: c0b38c374 cf637da31 Author: Michele Rosso Date: Wed Feb 27 11:27:28 2019 -0800 Merge branch 'development' into mr/cmake commit c0b38c374376a4ed62472ea7fb4591747f80548b Author: Michele Rosso Date: Wed Feb 27 11:26:45 2019 -0800 CMake: require version 3.14 only is CUDA is enabled CMakeLists.txt commit cf637da31000cd83b1fdd19021b496c0eecd32ae Author: Max Katz Date: Tue Feb 26 00:06:10 2019 -0500 Correct spelling of fextrema Tools/Plotfile/GNUmakefile Tools/Plotfile/fextrema.cpp commit 89f1a49323768407bbef5e7dac52a7e720032729 Author: Weiqun Zhang Date: Mon Feb 25 13:40:17 2019 -0800 Vector version of FillBoundary: switch back to the old way. the new approach needs more works Src/Base/AMReX_MultiFab.cpp commit a08c792c95c0d8f63a85068395f669683aa59c18 Author: Max Katz Date: Mon Feb 25 13:01:20 2019 -0800 Update XL compiler locations at LLNL Tools/GNUMake/sites/Make.llnl commit c5242d698687e2c8412925362ece47c218783210 Author: Weiqun Zhang Date: Mon Feb 25 11:31:37 2019 -0800 add a new Geometry constructor for convenience Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp commit c452a0df721b89d82025daf83632774712f62ddb Merge: ad5e49e2d 0eb610a13 Author: Andrew Myers Date: Mon Feb 25 13:44:41 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ad5e49e2d4a613a4a97fb1a66a7cedb2028b9766 Author: Andrew Myers Date: Mon Feb 25 13:43:38 2019 -0500 NeighborList tutorial - seperate out sorting the particles from doing the copies, so we can re-use the same neighbor list for multiple time steps. Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit 0eb610a13ae3ab2828a81cd190784a759966e1a7 Author: Weiqun Zhang Date: Mon Feb 25 10:24:06 2019 -0800 no need to init/finalize fortran mpi anymore Src/Base/AMReX.cpp commit fddf08b976e13e8d291afea960bae9ac9c39607a Author: Weiqun Zhang Date: Mon Feb 25 10:20:52 2019 -0800 rm more Fortran BoxLib stuff Src/Base/AMReX.cpp Src/Base/AMReX_BLBoxLib_F.F90 Src/Base/AMReX_error_fi.cpp Src/Base/AMReX_error_mod.F90 Src/Base/CMakeLists.txt Src/Base/Make.package commit d90d53089878de6fdafbd54782eddd32b5fa242e Author: Weiqun Zhang Date: Mon Feb 25 09:38:30 2019 -0800 rm more Fortran BoxLib stuff Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BLassert.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_FPC.H Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_Utility.H commit 1b2933187e350039e6b3f12e1b8d5f1b137082b9 Merge: ecc269872 75f40f6e2 Author: Weiqun Zhang Date: Mon Feb 25 09:03:45 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ecc269872061692d396549b6f61ed82060bef2af Author: Weiqun Zhang Date: Mon Feb 25 09:02:15 2019 -0800 rm more deprecated files Src/Base/BL_mempool_f.f90 Src/Base/GPackage.mak commit 75f40f6e2b51de70c5975201136d84e93fbb99ea Author: Max Katz Date: Mon Feb 25 11:56:49 2019 -0500 Specialize some AMREX_USE_GPU to AMREX_USE_CUDA Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_FabArrayUtility.H commit 3022421f3dbce0b37a24a7e714f74697b0d7c1a5 Author: Max Katz Date: Mon Feb 25 03:47:06 2019 -0500 Specialize some AMREX_USE_GPU to AMREX_USE_GPU_PRAGMA Src/Base/AMReX_ArrayLim.H commit c1d7a8ff2aac73a7114cb8234223990190b4978e Author: Weiqun Zhang Date: Mon Feb 25 08:51:44 2019 -0800 include header Src/Base/AMReX_MemPool.H commit 8928e08ef800df9def57e6447cf33cb28a0369b4 Author: Ann Almgren Date: Mon Feb 25 08:32:29 2019 -0800 Remove F_BaseLib and parts of AMReX that used it. Docs/Doxygen/doxygen.conf Docs/sphinx_documentation/make_api.py Src/Base/AMReX.cpp Src/Base/AMReX_MemPool.H Src/Base/AMReX_MemPool.cpp Src/F_BaseLib/BLProfiler_f90.f90 Src/F_BaseLib/CMakeLists.txt Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/FParallelMG2.mak Src/F_BaseLib/FParallelMG_RNG.mak Src/F_BaseLib/GPackage.mak Src/F_BaseLib/MemProfiler_f.H Src/F_BaseLib/MemProfiler_f.cpp Src/F_BaseLib/MultiFab_C_F.H Src/F_BaseLib/MultiFab_C_F.cpp Src/F_BaseLib/amrex_fabio_c.f90 Src/F_BaseLib/amrex_fort_mod.f90 Src/F_BaseLib/amrex_timer_c.f90 Src/F_BaseLib/backtrace_c.cpp Src/F_BaseLib/backtrace_f.f90 Src/F_BaseLib/bc.f90 Src/F_BaseLib/bc_functions.f90 Src/F_BaseLib/bl_IO.f90 Src/F_BaseLib/bl_constants.f90 Src/F_BaseLib/bl_error.f90 Src/F_BaseLib/bl_mem_stat.f90 Src/F_BaseLib/bl_parmparse.f90 Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/bl_prof_stubs.f90 Src/F_BaseLib/bl_random_c.H Src/F_BaseLib/bl_random_c.cpp Src/F_BaseLib/bl_random_f.f90 Src/F_BaseLib/bl_space.f90 Src/F_BaseLib/bl_stream.f90 Src/F_BaseLib/bl_string.f90 Src/F_BaseLib/bl_system.f90 Src/F_BaseLib/bl_timer.f90 Src/F_BaseLib/bl_types.f90 Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/box_f.f90 Src/F_BaseLib/box_util.f90 Src/F_BaseLib/boxarray_f.f90 Src/F_BaseLib/boxlib_f.f90 Src/F_BaseLib/cc_restriction.f90 Src/F_BaseLib/cluster_f.f90 Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/cutcells.f90 Src/F_BaseLib/define_bc_tower.f90 Src/F_BaseLib/f2kcli.f90 Src/F_BaseLib/f2kcli_crayx1.f90 Src/F_BaseLib/f2kcli_nag.f90 Src/F_BaseLib/f2kcli_win32.f90 Src/F_BaseLib/fab.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c Src/F_BaseLib/filler.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/fourth_order_interp_coeffs.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/list_box.f90 Src/F_BaseLib/make_new_grids.f90 Src/F_BaseLib/memprof.f90 Src/F_BaseLib/ml_boxarray.f90 Src/F_BaseLib/ml_cc_restriction.f90 Src/F_BaseLib/ml_layout.f90 Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/ml_nd_restriction.f90 Src/F_BaseLib/ml_restrict_fill.f90 Src/F_BaseLib/mt19937ar.f90 Src/F_BaseLib/multifab_c.f90 Src/F_BaseLib/multifab_f.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 Src/F_BaseLib/multifab_physbc.f90 Src/F_BaseLib/multifab_physbc_edgevel.f90 Src/F_BaseLib/nodal_neumann_bcs.f90 Src/F_BaseLib/nodal_restriction.f90 Src/F_BaseLib/nodal_stencil_bc.f90 Src/F_BaseLib/omp.f90 Src/F_BaseLib/omp_stubs.f90 Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 Src/F_BaseLib/particles_f.f90 Src/F_BaseLib/pingpong.f90 Src/F_BaseLib/plotfile.f90 Src/F_BaseLib/ppm_util.f90 Src/F_BaseLib/ppm_util_c.c Src/F_BaseLib/regrid.f90 Src/F_BaseLib/sort_box.f90 Src/F_BaseLib/sort_d.f90 Src/F_BaseLib/sort_i.f90 Src/F_BaseLib/system_util_c.c Src/F_BaseLib/tag_boxes.f90 Src/F_BaseLib/timer_c.c Src/F_BaseLib/unittests/GNUmakefile Src/F_BaseLib/unittests/gr0_3d.1level Src/F_BaseLib/unittests/tests.f90 Src/F_BaseLib/vector_i.f90 Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak Tools/F_mk/Readme Tools/F_mk/comps/Darwin_ibm.mak Tools/F_mk/comps/Darwin_intel.mak Tools/F_mk/comps/Linux_cray.mak Tools/F_mk/comps/Linux_intel.mak Tools/F_mk/comps/Linux_lahey.mak Tools/F_mk/comps/Linux_nag.mak Tools/F_mk/comps/Linux_pathscale.mak Tools/F_mk/comps/Linux_pgi.mak Tools/F_mk/comps/Linux_sunstudio.mak Tools/F_mk/comps/aix.mak Tools/F_mk/comps/bgq.mak Tools/F_mk/comps/g95.mak Tools/F_mk/comps/gfortran.mak Tools/F_mk/comps/xlf.mak Tools/Postprocessing/F_Src/CMakeLists.txt Tools/Postprocessing/F_Src/GNUmakefile Tools/Postprocessing/F_Src/Palette Tools/Postprocessing/F_Src/TODO_GHOST Tools/Postprocessing/F_Src/faverage.f90 Tools/Postprocessing/F_Src/faverplot.f90 Tools/Postprocessing/F_Src/fboxinfo.f90 Tools/Postprocessing/F_Src/fcoarsen.f90 Tools/Postprocessing/F_Src/fcompare.f90 Tools/Postprocessing/F_Src/fdump.f90 Tools/Postprocessing/F_Src/fdumpdata2d.f90 Tools/Postprocessing/F_Src/fextract.f90 Tools/Postprocessing/F_Src/fextrema.f90 Tools/Postprocessing/F_Src/ffdcompare.f90 Tools/Postprocessing/F_Src/fintgvar2d.f90 Tools/Postprocessing/F_Src/fnan.f90 Tools/Postprocessing/F_Src/fsnapshot2d.f90 Tools/Postprocessing/F_Src/fsnapshot3d.f90 Tools/Postprocessing/F_Src/ftime.f90 Tools/Postprocessing/F_Src/fvarnames.f90 Tools/Postprocessing/F_Src/fwritecontents2d.f90 Tools/Postprocessing/F_Src/plt_compare_diff_grids.f90 Tools/Postprocessing/python/README Tools/Postprocessing/python/column_depth.py Tools/Postprocessing/python/conv_slopes.py Tools/Postprocessing/python/dumpparthistory.py Tools/Postprocessing/python/eos_data.txt Tools/Postprocessing/python/helmeos.py Tools/Postprocessing/python/parseparticles.py Tools/Postprocessing/python/test_helmeos.py Tools/Postprocessing/python/test_parseparticles.py Tools/Postprocessing/python/timestamp_00 Tools/Postprocessing/python/timestamp_02 Tools/Py_util/GNUmakefile Tools/Py_util/README Tools/Py_util/fsnapshot.f90 commit 999df87ae29312b09313f64c9993b93bf22dc4ad Author: Max Katz Date: Mon Feb 25 03:31:59 2019 -0500 Do not attempt to set CUDA_ARCH if not defined Tools/GNUMake/comps/pgi.mak commit f6d59f1fb784638e0e85f500c4a837a7299a7df2 Author: Weiqun Zhang Date: Sat Feb 23 15:23:39 2019 -0800 fix assert message Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit beedda6193deab67e169a4ed29a414276678ded9 Author: Weiqun Zhang Date: Sat Feb 23 12:51:14 2019 -0800 MLCellLinOp:: metric factor Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 commit f64fb942c7ed4bb157bb392ec552efba5c60849a Author: Weiqun Zhang Date: Sat Feb 23 12:36:53 2019 -0800 MLCellLinOp:: refactor Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 commit 4951558d0752119f0e74b1db18f606afa639732e Author: Weiqun Zhang Date: Sat Feb 23 10:32:01 2019 -0800 assertion no longer needed because of recent change in Array4 Src/Base/AMReX_BaseFab.H commit 3e3ffc22eb2ac5c5ed8ef897202b0aa73a5aa370 Author: Weiqun Zhang Date: Sat Feb 23 10:21:37 2019 -0800 pass by value Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/EB/AMReX_EB2_IF_Rotation.H commit bb6aeb6b0e7c62e8c960d2f27e6cabf67d7fd5fe Author: Weiqun Zhang Date: Sat Feb 23 07:52:38 2019 -0800 pass by value Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_LayoutData.H Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit ea9b22d5a7bad26659458f66fbab87e0005e7587 Author: Andrew Myers Date: Fri Feb 22 15:55:52 2019 -0800 remove f_baselib from the electrostatic pic tutorial Tutorials/Particles/ElectrostaticPIC/GNUmakefile Tutorials/Particles/ElectrostaticPIC/main.cpp commit 7253602a6c89813206b22f62db2d10f645b6117a Author: Andrew Myers Date: Fri Feb 22 15:30:54 2019 -0800 remove commented out code OldTutorials/PIC_C/solve_with_mlmg.cpp OldTutorials/TwoGrid_PIC_C/solve_with_mlmg.cpp commit b98d04f4f4f2e223cfc826bd7913412427c8f3b2 Merge: 245e1acf3 f4a3c9104 Author: Andrew Myers Date: Fri Feb 22 15:17:12 2019 -0800 Merge branch 'development' into f_baselib_particles_remove commit 245e1acf385ac854f62bccaff8eac2b094933595 Author: Andrew Myers Date: Fri Feb 22 15:16:25 2019 -0800 update TwoGrid_PIC_C for the removal of F_Baselib OldTutorials/PIC_C/main.cpp OldTutorials/TwoGrid_PIC_C/GNUmakefile OldTutorials/TwoGrid_PIC_C/Make.package OldTutorials/TwoGrid_PIC_C/main.cpp OldTutorials/TwoGrid_PIC_C/solve_for_accel.cpp OldTutorials/TwoGrid_PIC_C/solve_with_f90.cpp commit f4a3c9104ab5bb2acfe12b8bb63f452bd779eb74 Merge: a0efbaa51 e2ce5a520 Author: Andrew Myers Date: Fri Feb 22 15:04:15 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a0efbaa51dac07db3b62398fb5b770084f6ed370 Author: Andrew Myers Date: Fri Feb 22 15:03:27 2019 -0500 make the neighbor list build function templated on check_pair function Src/Particle/AMReX_NeighborList.H Tutorials/GPU/NeighborList/CheckPair.H Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp Tutorials/GPU/NeighborList/Make.package Tutorials/GPU/NeighborList/md_K.H commit e2ce5a520ac3b36106281d7133279fd48dfe5851 Merge: c80a2d2a0 42d2b3996 Author: Weiqun Zhang Date: Fri Feb 22 11:42:44 2019 -0800 Merge branch 'weiqun/gpu' into development commit 42d2b399623eb8e7f7da9220095b198f09a43bfb Author: Weiqun Zhang Date: Fri Feb 22 11:02:25 2019 -0800 fix bug in C++ apply bc Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H commit 167b0eff03c7d5e657030fb07e4dce94664d5f09 Author: Weiqun Zhang Date: Fri Feb 22 09:26:14 2019 -0800 MLCellLinOp: fix index Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H commit d77950fe236d6d28a34677d27dd3a346f3dc9416 Author: Weiqun Zhang Date: Fri Feb 22 08:00:36 2019 -0800 MLCellLinOP: coef0 on gpu Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H commit 4730498918618bcdf3bc465701fd302cf65eecaf Author: Weiqun Zhang Date: Thu Feb 21 22:02:07 2019 -0800 MLCellLinOp: applybc on gpu Src/Boundary/AMReX_BoundCond.H Src/Boundary/AMReX_FabSet.H Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_K.H Src/LinearSolvers/MLMG/Make.package commit c80a2d2a097dd9f3cea660cd81b23ab31d79fd08 Merge: 738097b47 89d262b6c Author: Andrew Myers Date: Thu Feb 21 20:31:33 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 738097b47335b11ac6f2819d33495431c37dd9fe Author: Andrew Myers Date: Thu Feb 21 20:31:13 2019 -0500 start migrating the neighbor list stuff into AMReX proper Src/Particle/AMReX_NeighborList.H Src/Particle/CMakeLists.txt Src/Particle/Make.package Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/Make.package commit bb56b8c5a98ce28050aeb452266d8a7c9a6b521b Author: Andrew Myers Date: Thu Feb 21 20:21:36 2019 -0500 pstruct[i] -> p Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit 7b8493e2e91b54c8279810b93cd0c60a7d024916 Author: Andrew Myers Date: Thu Feb 21 20:17:45 2019 -0500 allow the user to use range-based for loops for the neighbor list on the GPU Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp Tutorials/GPU/NeighborList/Make.package Tutorials/GPU/NeighborList/NeighborList.H Tutorials/GPU/NeighborList/NeighborList.cpp commit 89d262b6cee38e75467cd175204337be776356bd Author: Ann Almgren Date: Thu Feb 21 16:11:04 2019 -0800 Revert "Revert "CMake: change the way Algoim and Blitz are handled"" This reverts commit e6b3f2416241c5c6317ea79145cb112b5d38328b. CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_InstallExternalLibs.cmake commit b6ebe1b57736f5ad3dc9a2665a1ac47a5dcbda50 Author: Andrew Myers Date: Thu Feb 21 17:53:11 2019 -0500 start to add the NeighborList stuff into a discrete class Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp Tutorials/GPU/NeighborList/Make.package Tutorials/GPU/NeighborList/NeighborList.H Tutorials/GPU/NeighborList/NeighborList.cpp Tutorials/GPU/NeighborList/md_K.H commit 5e1659d86864da34ebbeb4c36062fd384de7d345 Author: Andrew Myers Date: Thu Feb 21 13:12:15 2019 -0800 remove the EBParticles OldTutorial OldTutorials/EBParticles/EBParticleContainer.H OldTutorials/EBParticles/EBParticleContainer.cpp OldTutorials/EBParticles/GNUmakefile OldTutorials/EBParticles/Make.package OldTutorials/EBParticles/ebparticles_2d.f90 OldTutorials/EBParticles/ebparticles_3d.f90 OldTutorials/EBParticles/ebparticles_F.H OldTutorials/EBParticles/inputs OldTutorials/EBParticles/main.cpp commit a73e2b8ceda3d2d817d2455d5b63218b1870b66c Author: Michele Rosso Date: Thu Feb 21 15:09:47 2019 -0500 CMake: fix GPU/NeighborList example Tutorials/GPU/NeighborList/CMakeLists.txt commit 60801cf8d364871f3aef81b8cb37e13d77bf1966 Merge: f170b0e19 f0d81c324 Author: Weiqun Zhang Date: Wed Feb 20 20:50:25 2019 -0800 Merge branch 'weiqun/fluxregister' into development commit f0d81c3242dc112aaf8441a7b3036b4771d9cee9 Author: Weiqun Zhang Date: Wed Feb 20 19:17:02 2019 -0800 allow different BoxArrays for average_down_nodal and average_down_edges. new versions of average_down_edges and average_down_faces for single direction Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit f170b0e1987605c66db5bed0b067a024a8f7df8f Merge: d356aa2c0 fab878800 Author: Daniel Ladiges Date: Wed Feb 20 18:54:52 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d356aa2c0af43e8b0a24f0dd98e08f277d3e291c Author: Daniel Ladiges Date: Wed Feb 20 18:49:30 2019 -0800 Made copy of .mak file in F_BaseLib so it has a sensible name before its death next week (and to keep consistency with FBoxLib). Src/F_BaseLib/FParallelMG_RNG.mak commit fab8788000015009657ac601037a09cf0b1f5f5c Author: Andrew Myers Date: Wed Feb 20 17:23:28 2019 -0800 do this interpolation from coarse in a different way. Src/AmrCore/AMReX_AmrParticles.H Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_PhysBCFunct.H commit 331c7227a5cbc71f12578a835662cea306605e57 Author: Weiqun Zhang Date: Wed Feb 20 16:29:09 2019 -0800 reflux for given direction Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp commit b74c17101afda68f3c73c509e4739c6832974fac Merge: 31273920e 77990a176 Author: Weiqun Zhang Date: Wed Feb 20 15:54:30 2019 -0800 Merge branch 'weiqun/gpu' into development commit 77990a1762c8c7f27386eb28b5c49ee6698c0bd8 Merge: 90174b0c3 e2ab935f0 Author: Weiqun Zhang Date: Wed Feb 20 16:12:34 2019 -0500 Merge branch 'weiqun/gpu' of github.com:AMReX-Codes/amrex into weiqun/gpu commit 90174b0c34bb56b2e0e01fb92001c19963d0a19e Author: Weiqun Zhang Date: Wed Feb 20 16:12:21 2019 -0500 Array4: add strides as members Src/Base/AMReX_Array.H commit e2ab935f0660504c2d444da11a4f10156ff1fe0c Author: Weiqun Zhang Date: Wed Feb 20 13:06:53 2019 -0800 Array4: use printf for device code Src/Base/AMReX_Array.H commit e9bc9286df099f35659f3f2ced5dd9eca2d6aa0c Author: Weiqun Zhang Date: Wed Feb 20 15:44:40 2019 -0500 Array4: constexpr and const Src/Base/AMReX_Array.H commit e5592392a9d3125a07a9b4418016622d2672cebd Author: Weiqun Zhang Date: Wed Feb 20 11:47:20 2019 -0800 print out bounds when access to Array4 is out of bounds Src/Base/AMReX_Array.H commit 19ad713be4c8cbadbb9bf4a66d97ec44c9659a46 Author: Andrew Myers Date: Wed Feb 20 14:20:08 2019 -0500 do the clear before Redistribute Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit 13fa03e7e63e19bb8ec833ca9e01a26d91225423 Author: Weiqun Zhang Date: Wed Feb 20 11:09:21 2019 -0800 addr2line pretty print Src/Base/AMReX_BLBackTrace.cpp commit 48f07fe8aed69475d20a9a5d98290168ed76862f Author: Weiqun Zhang Date: Wed Feb 20 11:06:13 2019 -0800 mlalaplacian on gpu Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLALap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLALap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLALap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLALap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLALap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLALap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLALap_F.H Src/LinearSolvers/MLMG/AMReX_MLALap_K.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/Make.package commit 31273920ebdd61166fa9aba7d75d382cc505e558 Author: Donald E. Willcox Date: Wed Feb 20 10:39:21 2019 -0800 Rename EX3-CUDA to EX-CUSOLVER Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/GNUmakefile Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/Make.CVODE Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/Make.package Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/README.md Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/extern_probin.template Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/inputs Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/inputs_128 Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/inputs_256 Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/inputs_32 Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/inputs_64 Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/main.cpp Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/make_cuda.sh Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/make_cuda_cusolver.sh Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/make_serial.sh Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/react_cuda.cpp Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/react_cuda_cusolver.cpp Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/react_serial.cpp Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/react_system.F90 Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/react_utils.F90 Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/test_react.H Tutorials/CVODE/SUNDIALS4/EX-CUSOLVER/test_react_F.H commit a8deba448082b4cd081646218977385750a1dbf0 Author: Donald E. Willcox Date: Wed Feb 20 10:38:01 2019 -0800 Remove unnecessary include line for FParallelMG Tutorials/CVODE/SUNDIALS4/EX3-CUDA/Make.CVODE commit 6bddb62a710763f23d3bd2de280eeadbeec605e7 Author: Andrew Myers Date: Tue Feb 19 19:45:01 2019 -0500 call clear and sort from inside fillNeighbors Tutorials/GPU/NeighborList/MDParticleContainer.cpp Tutorials/GPU/NeighborList/main.cpp commit efac4f44ac0de4da576d110710a3e7758f96a771 Merge: f6dadb262 68d909697 Author: Andrew Myers Date: Tue Feb 19 19:07:30 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f6dadb262efe74fb032017cefb15764bd191345c Author: Andrew Myers Date: Tue Feb 19 19:07:10 2019 -0500 adding and using wrappers around Cuda's atomicInc and atomicDec functions Src/Base/AMReX_CudaUtility.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp commit d3d2eda0d4ae3ae955435ed35bc9f17686c3b95b Author: Weiqun Zhang Date: Tue Feb 19 15:03:46 2019 -0800 mlpoisson: normalize Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_F.H Src/LinearSolvers/MLMG/Make.package commit 68d909697d32e6ce026ad330a11a85431b64262d Author: kngott Date: Tue Feb 19 14:22:01 2019 -0800 GPU docs. Docs/sphinx_documentation/source/GPU.rst commit 781294e7f293b6fd8bd033b60a979d2bd775285e Author: Weiqun Zhang Date: Tue Feb 19 14:14:04 2019 -0800 mlpoisson: gsrb Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_3D_K.H commit 273c1a40346f9236b460d13b87ea89e78ed5dcb8 Author: Andrew Myers Date: Tue Feb 19 12:45:03 2019 -0800 add a NoOpPhysBCFunct and use it in the amr assign density Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_PhysBCFunct.H commit 218613d76d97a5f42bee9838087f0214e06f1753 Author: Andrew Myers Date: Tue Feb 19 12:39:41 2019 -0800 version of InterpFromCoarseLevel that doesn't use enforce boundary conditions Src/AmrCore/AMReX_AmrParticles.H Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp commit 078c3dd49e4180a8af7893f710ac68719666ba66 Merge: a17c44399 c1b126b8d Author: WeiqunZhang Date: Tue Feb 19 10:36:40 2019 -0800 Merge pull request #411 from mwm126/patch-2 Fix USE_ACC error; refactor for readability commit a17c443996b1c7531c39d28937873c0646c71658 Author: Weiqun Zhang Date: Tue Feb 19 10:03:33 2019 -0800 warning instead of ignoring Tests/GPU/libamrex_CUDA/GNUmakefile commit 54885d5e680b17b14e1abb8da4ed4581001a4359 Author: Weiqun Zhang Date: Mon Feb 18 10:46:20 2019 -0800 an example of using libamrex with cuda Tests/GPU/libamrex_CUDA/GNUmakefile Tests/GPU/libamrex_CUDA/README.md Tests/GPU/libamrex_CUDA/main.cpp commit bf011401d524cc508e7356b4b45e31e8c748cfd1 Author: Weiqun Zhang Date: Mon Feb 18 09:24:12 2019 -0800 Elixir: add default constructor and move assignment Src/Base/AMReX_CudaElixir.H commit c1b126b8d16169f99ec30ce4dc4e0a5a110c4fb3 Author: Mark Meredith Date: Mon Feb 18 08:43:18 2019 -0500 Fix USE_ACC error; refactor for readability I noticed a typo: https://github.com/AMReX-Codes/amrex/blob/master/Tools/libamrex/configure.py#L98 should be "USE_ACC = TRUE". Writing each line in the Makefile with one line of source could help prevent errors like that. Tools/libamrex/configure.py commit e99e7f9657c34c275b39b33968717755d60a8dd8 Author: Max Katz Date: Sun Feb 17 15:49:08 2019 -0800 Generalize MFIter reduction to allow multiple reduce values Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 5b6808245f3f1908cfa0a00eeeac109178ac7a22 Author: Weiqun Zhang Date: Sun Feb 17 14:32:56 2019 -0800 MLPoisson: flux Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_3D_K.H commit 10dbe606c7013ca368ac6dd171173bf4e84feed0 Merge: ca573ae47 39c03e69c Author: WeiqunZhang Date: Sun Feb 17 12:42:41 2019 -0800 Merge pull request #406 from AMReX-Codes/plot_per_fix Add floating point awareness to the plot_per/check_per logic commit ca573ae47f449cf3f977b5bdda6b9180909fa497 Author: Weiqun Zhang Date: Sun Feb 17 12:28:21 2019 -0800 generalize FillPatch for non-uniform grow cells Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_PhysBCFunct.H commit 39c03e69c3718a9910e786e6d12671286931e7ae Author: Max Katz Date: Sun Feb 17 06:48:35 2019 -0800 Scale epsilon to the current simulation time Src/Amr/AMReX_Amr.cpp commit a4c454b23e821410f95a4347699dab792cd2d82f Merge: 2a66ac0f7 09f6ea280 Author: Max Katz Date: Sun Feb 17 06:32:58 2019 -0800 Merge branch 'development' into plot_per_fix commit fbb91394e0eedcc6c14fcda84f9bccd3807dc53a Author: Weiqun Zhang Date: Sat Feb 16 21:39:04 2019 -0800 minor change Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_3D_K.H commit ecd46a8a6fa69eefb7a3008a04249f7bfd43b9be Author: Weiqun Zhang Date: Sat Feb 16 21:14:12 2019 -0800 MLPoisson: adotx Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLPoisson_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_K.H Src/LinearSolvers/MLMG/Make.package commit 09f6ea28069094fd9efc332eec8e52a49333a63a Author: Ann Almgren Date: Sat Feb 16 19:27:11 2019 -0800 Add the option to call EB_set_covered with ngrow > 0 so we can cover ghost cells of each Fab. Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp commit b71ca303bd54731c5221425d39626317ea352007 Merge: 9557946e5 e6b3f2416 Author: Weiqun Zhang Date: Sat Feb 16 18:39:46 2019 -0800 Merge branch 'development' into weiqun/gpu commit 22e7de67ef2600e1c5ba5bbc4393115ed0e80226 Author: Brandon Runnels Date: Sat Feb 16 17:51:49 2019 -0700 Merge branch development into nodeghostcells Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit adb43e42816149a6ed291d7509c7ae5009f66647 Merge: 0cc8cc005 e6b3f2416 Author: Brandon Runnels Date: Sat Feb 16 17:33:51 2019 -0700 Merge branch 'development' into nodeghostcells commit 0cc8cc0051c5a31ae75212e8453fea6c7e3a0adb Author: Brandon Runnels Date: Sat Feb 16 17:33:24 2019 -0700 removed some superfluous functions to be implemented elsewhere Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H commit fe4eade0d1f1bb40ae365e10fb49a7f1e51f9b85 Author: Brandon Runnels Date: Sat Feb 16 16:23:39 2019 -0700 working - now cleaning up and updating Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit e6b3f2416241c5c6317ea79145cb112b5d38328b Author: Ann Almgren Date: Sat Feb 16 13:59:28 2019 -0800 Revert "CMake: change the way Algoim and Blitz are handled" This reverts commit 9b8390a6d3c14843692324ecad0a47f5fdf55f19. CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_InstallExternalLibs.cmake commit 9557946e50980885833e06a80ca007577f988dea Author: Weiqun Zhang Date: Sat Feb 16 12:10:54 2019 -0800 1d and 2d gsrb Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit fd5e14a1d746507fbc31aa3f73c5d3ca951171c5 Author: Max Katz Date: Sat Feb 16 01:25:58 2019 -0800 Add C++11 if PGI is nvcc host compiler Tools/GNUMake/comps/nvcc.mak commit 509152e50d22a882f7bfc8db2bfcedcd599fa37f Author: Weiqun Zhang Date: Fri Feb 15 23:06:51 2019 -0800 3d gsrb Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit dabb9cd5a2eef5fa6cbfd0a9b47e291aa3f0ccd1 Author: Weiqun Zhang Date: Fri Feb 15 21:18:18 2019 -0800 fix TagBox::coarsen for gpu Src/AmrCore/AMReX_TagBox.cpp commit f855cae564ec6ddc776966e1850023ee7f227ca0 Merge: df1cfbd8f 3ae67484c Author: Weiqun Zhang Date: Fri Feb 15 20:50:08 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5a9216b0150b4eb86806e37772ab8fcd1e4ce04a Author: Michele Rosso Date: Fri Feb 15 22:11:41 2019 -0500 CMake: add GPU/NeighborList test Tutorials/GPU/Launch/CMakeLists.txt Tutorials/GPU/NeighborList/CMakeLists.txt commit e39c42e0e76652ef50e01a862a5f947e00db7f85 Merge: 232b3c565 3ae67484c Author: Michele Rosso Date: Fri Feb 15 20:34:42 2019 -0500 Merge branch 'development' into mr/cmake commit 7102b1ced8cefec8ac245d8f9f56a610bf1a52df Merge: 20479915f da635ec8d Author: Brandon Runnels Date: Fri Feb 15 18:25:29 2019 -0700 Merge branch 'nodeghostcells' of https://github.com/AMReX-Codes/amrex into nodeghostcells commit 232b3c565bc24de4f461de420d9ae6860db56beb Author: Michele Rosso Date: Fri Feb 15 20:24:04 2019 -0500 CMake: fix GPU example Tools/CMake/AMReX_Config.cmake Tutorials/GPU/Launch/CMakeLists.txt commit 20479915fa82db4754510830a941616fb57e865a Author: Brandon Runnels Date: Fri Feb 15 18:22:42 2019 -0700 works for multiple grids in serial, need to determine why mpi does not work Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 3ae67484c3f22329dc28239f65f64999a5267c58 Merge: ea0ad89a1 47a4d0c16 Author: Andrew Myers Date: Fri Feb 15 19:56:03 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ea0ad89a18813e560f593c634af4c7be231785e9 Author: Andrew Myers Date: Fri Feb 15 19:55:32 2019 -0500 move the gpu neighbor list thing to Tutorials/GPU Tutorials/GPU/NeighborList/Constants.H Tutorials/GPU/NeighborList/GNUmakefile Tutorials/GPU/NeighborList/MDParticleContainer.H Tutorials/GPU/NeighborList/MDParticleContainer.cpp Tutorials/GPU/NeighborList/Make.package Tutorials/GPU/NeighborList/inputs Tutorials/GPU/NeighborList/main.cpp Tutorials/GPU/NeighborList/md_K.H commit df1cfbd8fc869378a7dee7d8d617817b40594a32 Merge: daa11fcf8 47a4d0c16 Author: Weiqun Zhang Date: Fri Feb 15 16:17:07 2019 -0800 Merge branch 'development' into weiqun/gpu commit 47a4d0c16ec04c6ddf36cd819bc23dee6b1283c9 Merge: d09950b4e e715f85aa Author: Weiqun Zhang Date: Fri Feb 15 15:00:56 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e715f85aaab69d9504ecaf716939a1f1c7098e52 Author: kngott Date: Fri Feb 15 14:59:53 2019 -0800 Add support for OpenMPI+UCX library on CoriGPU. Tools/GNUMake/sites/Make.nersc commit d09950b4ec9ce3d701b7db7e17a457c7b26dd157 Author: Weiqun Zhang Date: Fri Feb 15 14:55:34 2019 -0800 use always assert Src/Base/AMReX_Array.H Src/Base/AMReX_BLassert.H commit 267a70fc70e56c61ecb5d08ea5885ce3b3096b0b Author: Andrew Myers Date: Fri Feb 15 17:55:00 2019 -0500 removing files added by mistake Tutorials/Particles/NeighborList/AMReX_FPC.tsm Tutorials/Particles/NeighborList/AMReX_ForkJoin.tsm Tutorials/Particles/NeighborList/AMReX_NFiles.tsm Tutorials/Particles/NeighborList/AMReX_SPMD.tsm Tutorials/Particles/NeighborList/AMReX_VisMF.tsm Tutorials/Particles/NeighborList/NeighborListParticleContainer.tsm Tutorials/Particles/NeighborList/main.tsm commit 406ea8aff16d0da22cb1e225554d3f581e92a49a Author: Andrew Myers Date: Fri Feb 15 17:40:41 2019 -0500 also make the cpu version work with non-cubic domains Tutorials/Particles/NeighborList/AMReX_FPC.tsm Tutorials/Particles/NeighborList/AMReX_ForkJoin.tsm Tutorials/Particles/NeighborList/AMReX_NFiles.tsm Tutorials/Particles/NeighborList/AMReX_SPMD.tsm Tutorials/Particles/NeighborList/AMReX_VisMF.tsm Tutorials/Particles/NeighborList/GNUmakefile Tutorials/Particles/NeighborList/NeighborListParticleContainer.tsm Tutorials/Particles/NeighborList/inputs Tutorials/Particles/NeighborList/main.cpp Tutorials/Particles/NeighborList/main.tsm commit 20b6ede98b74ef34555d7c875f57358c24b8d229 Author: Andrew Myers Date: Fri Feb 15 17:32:38 2019 -0500 let this thing have a non-cubic domain Tests/Particles/GPUNeighborList/inputs Tests/Particles/GPUNeighborList/main.cpp commit 5c11c0368cf86d78fde8b6bc0a1b19c3a817e512 Author: Andrew Myers Date: Fri Feb 15 17:17:07 2019 -0500 fix another parallel bug Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 3d18248a5d9ddb1144143137b830485fae8e1c7e Author: Andrew Myers Date: Fri Feb 15 16:30:21 2019 -0500 parallel bug fix. Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit b9db30dbc3af718f293ff80a98c6e9748335e4b4 Merge: ad1c0c4f4 1f2ea4f98 Author: Brandon Runnels Date: Fri Feb 15 13:11:01 2019 -0700 Merge branch 'nodeghostcells-instr' into nodeghostcells commit ad1c0c4f4b7f8320ce91c47f8e6ccf83046e6e45 Author: Brandon Runnels Date: Fri Feb 15 13:06:54 2019 -0700 added nghost specification in linop Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 773292c317edbb013877256fb4914ccd0c3e3475 Author: Andrew Myers Date: Fri Feb 15 14:46:27 2019 -0500 don't write anything by default in inputs Tests/Particles/GPUNeighborList/inputs commit 1f2ea4f98788b8d88d9483680123ef8e1b0fcb80 Author: Brandon Runnels Date: Fri Feb 15 12:37:49 2019 -0700 WIP: fillboundary surgery Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 703705da86e6e464d117bd0634430bec687a5903 Merge: c2018408a aa75b41c6 Author: Andrew Myers Date: Fri Feb 15 14:34:17 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into gpu_neighbor_list commit c2018408a82e205f3d844cd884ac183db0a7c9ba Author: Andrew Myers Date: Fri Feb 15 14:32:33 2019 -0500 MPI for gpu fillNeighbors Tests/Particles/GPUNeighborList/GNUmakefile Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp Tests/Particles/GPUNeighborList/inputs Tests/Particles/GPUNeighborList/main.cpp commit 6736bc3050fef949a952b060a033f533695db784 Author: Brandon Runnels Date: Fri Feb 15 10:50:17 2019 -0700 re-instrumented and debugging fillboundary Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 commit b9710d835ebce911a9a637ce2bbb201d778590ca Author: Michele Rosso Date: Thu Feb 14 21:17:41 2019 -0500 CMake:semi-working CUDA support CMakeLists.txt Src/CMakeLists.txt Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_SetupCUDA.cmake Tools/CMake/AMReX_Utils.cmake Tools/CMake/comps/AMReX_GNU.cmake Tools/CMake/comps/AMReX_NVIDIA.cmake Tools/CMake/comps/AMReX_PGI.cmake Tutorials/CMakeLists.txt Tutorials/GPU/Launch/CMakeLists.txt Tutorials/GPU/Launch/MyKernel_F.F90 commit aa75b41c6085d9cb0c30ef16c9a9ddee4099dfe6 Author: kngott Date: Thu Feb 14 15:14:27 2019 -0800 Updated corigpu script. Tutorials/GPU/run.corigpu commit 63e1cb0aa8d616aa65dca00db0cca46ff576e929 Author: kngott Date: Thu Feb 14 13:37:00 2019 -0800 Add corigpu run script w/ environment & salloc instructions. Tutorials/GPU/run.corigpu commit de8b2127962387162d990b7c40e4f6b4d596bffb Merge: 38dba7d71 fffa4ad7b Author: Andrew Myers Date: Thu Feb 14 16:19:57 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into gpu_neighbor_list commit fffa4ad7b4d039b5b6cd2eb819dbfac22ae9a5a1 Merge: 863c3ce08 e932fc600 Author: Andrew Myers Date: Thu Feb 14 13:18:36 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 863c3ce08719f21c53b077013d326dfefab75b58 Author: Andrew Myers Date: Thu Feb 14 13:18:25 2019 -0800 routines for 3d neighbor list tutorial Tutorials/Particles/NeighborList/inputs Tutorials/Particles/NeighborList/main.cpp Tutorials/Particles/NeighborList/neighbor_list_3d.f90 commit 38dba7d719b0af5aa41314d788b461162102a910 Author: Andrew Myers Date: Thu Feb 14 15:39:07 2019 -0500 a few bug fixes Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit e932fc6007127b5b9813fa23ae8eac94118ebe0b Merge: 9b8390a6d d9a550eec Author: Michele Rosso Date: Thu Feb 14 11:47:11 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 9b8390a6d3c14843692324ecad0a47f5fdf55f19 Author: Michele Rosso Date: Thu Feb 14 11:47:02 2019 -0800 CMake: change the way Algoim and Blitz are handled CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_InstallExternalLibs.cmake commit d9a550eec244729b377f4bd2a16f351e7ba31665 Merge: 77bc33ad8 828e5ea16 Author: Weiqun Zhang Date: Thu Feb 14 09:55:01 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 77bc33ad8cbaadb7771a00acba1ac5d1a56f1738 Author: Weiqun Zhang Date: Thu Feb 14 09:54:22 2019 -0800 ParmParse: fix for IntVect Src/Base/AMReX_ParmParse.cpp commit 828e5ea161ac82ced786a9de36857210722266cd Author: Max Katz Date: Thu Feb 14 12:11:23 2019 -0500 Preprocess out -D defines in the CUDA script when searching for pragmas Tools/F_scripts/write_cuda_headers.py commit 4076ccbd8b8b71b3f11e7f40a41b7a737afff714 Merge: 281195a56 1a88f6deb Author: Weiqun Zhang Date: Thu Feb 14 08:21:06 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 281195a56987ed69d7677cee1b554352d3138c2f Author: Weiqun Zhang Date: Thu Feb 14 08:20:55 2019 -0800 fcompare: handle empty plotfile Src/Base/AMReX_PlotFileDataImpl.cpp Tools/Plotfile/fcompare.cpp commit 1a88f6deb08a8c18827aab95f240befbd518f49d Author: Kevin Gott Date: Wed Feb 13 17:50:07 2019 -0800 Updated GPU kernel launch docs. Docs/sphinx_documentation/source/GPU.rst commit 087012706fe32a30967c2ac12c4a2ba13ddd83c7 Author: Weiqun Zhang Date: Wed Feb 13 16:29:34 2019 -0800 remove space from variable names OldTutorials/MultiGrid_C/writePlotFile.cpp OldTutorials/Tiling_Heat_C/writePlotFile.cpp OldTutorials/WaveEquation_C/writePlotFile.cpp commit 7d829d3cbd093713ba8477fe83831c0b84f7abaf Author: Weiqun Zhang Date: Wed Feb 13 16:19:05 2019 -0800 add Palette Tools/Plotfile/Palette commit 05cbd13fd7207c7ea1a8fed41f255ce0af67dc45 Author: Andrew Myers Date: Wed Feb 13 18:47:10 2019 -0500 gpu neighbor list running with domain decomposition Tests/Particles/GPUNeighborList/MDParticleContainer.cpp Tests/Particles/GPUNeighborList/inputs Tests/Particles/GPUNeighborList/main.cpp commit 3d64b90e0417c1b7cbcef48567ac2760ebdad35d Author: Andrew Myers Date: Wed Feb 13 18:37:18 2019 -0500 make OKGPU() work in the presence of neighbor particles Src/Particle/AMReX_ParticleContainerI.H commit d5f79bf1d6be198577c2a9712757b2bb912cdb10 Author: Andrew Myers Date: Wed Feb 13 18:12:42 2019 -0500 make numParticles return the number of Real particles (excluding neighbors) Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_StructOfArrays.H commit 7e1edf97a1587cc221a73e7f0a0ecb7a134fa8e4 Author: Weiqun Zhang Date: Wed Feb 13 14:14:27 2019 -0800 fsnapshot: option to specify coordinates on slice Tools/Plotfile/fsnapshot.cpp commit 265f423be4bd102992588ba9f42779fc074f2e41 Author: Andrew Myers Date: Wed Feb 13 17:00:07 2019 -0500 add fillNeighbors and clearNeighbors Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp Tests/Particles/GPUNeighborList/inputs Tests/Particles/GPUNeighborList/main.cpp commit f4bf62f9725978f83cdcb8686807cf743d69387c Author: Weiqun Zhang Date: Wed Feb 13 13:11:55 2019 -0800 fsnapsht3d Tools/Plotfile/GNUmakefile Tools/Plotfile/fsnapshot.cpp Tools/Plotfile/fsnapshot2d.cpp commit 400a62485d3bf11be8c47f0bd545e7abc2862cf2 Author: Andrew Myers Date: Wed Feb 13 15:49:36 2019 -0500 copy neighbor particles to their destinations Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 11827cdaf94ed4a26aad8ee309f8d60f041854ff Author: Andrew Myers Date: Wed Feb 13 15:34:10 2019 -0500 starting to implement neighbor particle filling Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 3ba17f727aeb77abb4840086235e4955704984c6 Author: Andrew Myers Date: Wed Feb 13 15:33:51 2019 -0500 Add getters for numNeighbors Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_StructOfArrays.H commit 0e29da64deaf2b4c2df256039510e54a4225252f Author: Weiqun Zhang Date: Wed Feb 13 11:28:15 2019 -0800 fsnapshot2d Tools/Plotfile/AMReX_PPMUtil.H Tools/Plotfile/AMReX_PPMUtil.cpp Tools/Plotfile/GNUmakefile Tools/Plotfile/Make.package Tools/Plotfile/fcompare.cpp Tools/Plotfile/fextract.cpp Tools/Plotfile/fextreama.cpp Tools/Plotfile/fnan.cpp Tools/Plotfile/fsnapshot2d.cpp commit d64c4933448b75a4e1430a2a34e2e506f2ecbb5f Author: Weiqun Zhang Date: Wed Feb 13 09:40:05 2019 -0800 ParmParse: validate input by checking there are nothing left in the stream. For example 1.5.e7 is an invalid double. C++ istream will read it as 1.5 and leaves .e7 in the input stream. Src/Base/AMReX_ParmParse.cpp commit 1129559588e589b142385c254836d89ac5109a97 Author: Weiqun Zhang Date: Wed Feb 13 06:52:41 2019 -0800 Elixir: fix assertion in resize; don't own the pointer if not in gpu launch region Src/Base/AMReX_BaseFab.H commit 500413ee8ee2623a4229610305d37d21d583df9c Author: Andrew Myers Date: Tue Feb 12 20:12:30 2019 -0500 functions for setting the number of neighbor particles Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_StructOfArrays.H commit f9ee63ab6b8d24d75483f2ff268498a6b7abb3d9 Merge: 7aea4255a 2fc7c8c5b Author: Andrew Myers Date: Tue Feb 12 20:00:47 2019 -0500 Merge branch 'development' into gpu_neighbor_list commit 7aea4255a5c2c132c5b66e9cd602f45e43d71e4f Author: Andrew Myers Date: Tue Feb 12 19:58:10 2019 -0500 sorting the particles by which neighbor they need to be copied to Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp Tests/Particles/GPUNeighborList/inputs Tests/Particles/GPUNeighborList/main.cpp commit da635ec8d9a3b998c4af55ebe3ea2b366e2461bd Author: Brandon Runnels Date: Tue Feb 12 17:38:27 2019 -0700 removed instrumentation and cleanded up GNUmakefile Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 06f7342df94456a2df164643f3d4b96048c1685c Author: Andrew Myers Date: Tue Feb 12 18:34:50 2019 -0500 build mask data structure for sending particles to neighbors Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit f7883f842301be48390d7c3111eeaf55385a5da2 Author: Andrew Myers Date: Tue Feb 12 18:34:09 2019 -0500 distinction between real and ghost particles in ParticleTile Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_StructOfArrays.H commit 2fc7c8c5bdac3c444292d0264572662607b0d3aa Merge: 3391c5c9c d95d07215 Author: Weiqun Zhang Date: Tue Feb 12 14:20:40 2019 -0800 Merge branch 'plotfiletools' into development commit d95d0721583e3c8411084189a28f831d25be7461 Author: Weiqun Zhang Date: Tue Feb 12 14:20:21 2019 -0800 fextreama: make the output resemble fortran Src/Base/AMReX_CudaLaunch.H Tools/Plotfile/fextreama.cpp commit 6cefcedb845d781ebd052e831231dd368e52368b Author: Weiqun Zhang Date: Tue Feb 12 12:58:20 2019 -0800 fextract Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Tools/Plotfile/GNUmakefile Tools/Plotfile/fextract.cpp Tools/Plotfile/fextreama.cpp commit 96c09b428cc461910fc9927ed90fecec94e6d7ed Author: Brandon Runnels Date: Mon Feb 11 17:37:52 2019 -0700 initial working Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 3391c5c9cb322a82708d5b0025d2f9e367759d93 Author: Kevin Gott Date: Mon Feb 11 16:09:46 2019 -0800 Array4 const& Docs/sphinx_documentation/source/Basics.rst commit cf96ddcceb80aa6ab4329532fdcc380fe068d446 Author: Kevin Gott Date: Mon Feb 11 13:01:15 2019 -0800 Missing semicolon in example. Docs/sphinx_documentation/source/Basics.rst commit a242b41925b2d5fe49a631cae35c8a5885205ef0 Merge: 5683bf365 eb1a810ac Author: WeiqunZhang Date: Mon Feb 11 12:07:59 2019 -0800 Merge pull request #408 from mwm126/patch-1 Fix typos commit eb1a810ac39e18384f96e5a5bdf8a8750686e03f Author: Mark Meredith Date: Mon Feb 11 14:57:42 2019 -0500 Fix typos Docs/sphinx_documentation/source/BuildingAMReX.rst commit 5683bf3653b34f5bd69d82d8e0df1123ca1fe596 Author: Kevin Gott Date: Mon Feb 11 11:47:57 2019 -0800 Update docs from FabView to Array4 style. Docs/sphinx_documentation/source/Basics.rst commit 1a0859d60e6affe06b84dad1a3c4609bc9c04f88 Author: Weiqun Zhang Date: Mon Feb 11 14:21:17 2019 -0500 minor change of style Tutorials/GPU/CNS/Source/CNS_advance.cpp commit ed3979d9b1d9f3b406679caa3107bc85dc06e5f7 Author: Weiqun Zhang Date: Mon Feb 11 14:20:27 2019 -0500 elixir: make sure T is trivially dectructible Src/Base/AMReX_BaseFab.H commit 34bb28e19609a2ddc7c44a38d0484cea0dbf3920 Author: Weiqun Zhang Date: Mon Feb 11 14:00:07 2019 -0500 fix fab stats Src/Base/AMReX_BaseFab.H commit 8cc7c3de92291e9d37a941f8bc66274fca9108b1 Author: Andrew Myers Date: Mon Feb 11 13:34:53 2019 -0500 tweak inputs Tests/Particles/GPUNeighborList/MDParticleContainer.cpp Tests/Particles/GPUNeighborList/inputs commit 360d132f8aec861109deca039a560c7623e5b1cc Author: Weiqun Zhang Date: Sun Feb 10 11:00:01 2019 -0800 fix array initialization for C++11 Src/Base/AMReX_PlotFileDataImpl.H commit 0eb093f30af9047d0cdad153765834e6156d9df3 Author: Weiqun Zhang Date: Sun Feb 10 11:00:01 2019 -0800 fix array initialization for C++11 Src/Base/AMReX_PlotFileDataImpl.H commit a25e36766666921228314a42f2dd9f62342c342b Author: Weiqun Zhang Date: Sun Feb 10 09:54:20 2019 -0800 AsyncFab: add move ctor Src/Base/AMReX_CudaAsyncFab.H commit 8e4d02700fd4d05838237f96a96aceb48796434a Merge: 666130166 aa9f7ba30 Author: Weiqun Zhang Date: Sat Feb 9 22:36:53 2019 -0800 Merge branch 'plotfiletools' into development commit 6661301667432b1d4166c38eeb3dff16c2820f59 Author: Weiqun Zhang Date: Sat Feb 9 22:08:55 2019 -0800 elixir Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaElixir.H Src/Base/AMReX_CudaElixir.cpp Src/Base/AMReX_Gpu.H Src/Base/CMakeLists.txt Src/Base/Make.package commit c8f48f8fc3fba54c7455c66ad36537eb43e61368 Author: Max Katz Date: Sat Feb 9 21:43:49 2019 -0500 Add AsyncFab function to return the host data Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaAsyncFab.cpp commit aa9f7ba3053c8105bcb5425c045818966a655adb Author: Weiqun Zhang Date: Sat Feb 9 17:01:48 2019 -0800 fextreams Tools/Plotfile/GNUmakefile Tools/Plotfile/fextreama.cpp commit 6c664ead097a0d2cc6a9487347b6d97d14cbb8f7 Author: Weiqun Zhang Date: Sat Feb 9 15:02:15 2019 -0800 finish fcompare Tools/Plotfile/fcompare.cpp commit 21e436bb5c7743eb349db22f16e36ba75e691a47 Author: Max Katz Date: Sat Feb 9 17:10:40 2019 -0500 Skip plotfile if there's no variables to plot Src/Amr/AMReX_Amr.cpp commit 6311b5323d0a8189dd593bda76c1cc1618d2b266 Author: Max Katz Date: Sat Feb 9 17:04:33 2019 -0500 Symmetrize small plot with full plot Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp commit e44e96bf58416d3fedccc056a7d31deebff1bb4d Author: Weiqun Zhang Date: Sat Feb 9 13:02:04 2019 -0800 update to using PlotFileData in what we have so far Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_PlotFileDataImpl.H Src/Base/AMReX_PlotFileDataImpl.cpp Src/Base/AMReX_PlotFileUtil.H Tools/Plotfile/AMReX_AnyDimUtil.H Tools/Plotfile/AMReX_AnyDimUtil.cpp Tools/Plotfile/GNUmakefile Tools/Plotfile/Make.package Tools/Plotfile/fboxinfo.cpp Tools/Plotfile/fcompare.cpp Tools/Plotfile/fnan.cpp Tools/Plotfile/ftime.cpp Tools/Plotfile/fvarnames.cpp commit 2a66ac0f74567acef1c85339c6db03a4f00716e9 Author: Max Katz Date: Sat Feb 9 15:39:21 2019 -0500 Fix fp comparison logic using machine epsilon Src/Amr/AMReX_Amr.cpp commit 82dafd15a474e3168f6cf0c059aec8a31d79a6ab Author: Max Katz Date: Sat Feb 9 10:40:49 2019 -0800 Fix Cori build when linking with Fortran Tools/GNUMake/sites/Make.nersc commit c054a3b6422fddc52888a726137353bacb0fde43 Author: atmyers Date: Sat Feb 9 10:27:40 2019 -0800 add note that the GPU Vector classes now use the memory Arenas provided by AMReX. Docs/sphinx_documentation/source/GPU.rst commit 7d428cb321208d9fd501d42f4077c780a6ec76aa Author: Ann Almgren Date: Fri Feb 8 23:00:58 2019 -0800 Fix bug in 3D GSRB cell-centered solve. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 4eb4e7a25050ca83f02e551fcb9b8a591834395e Author: Ann Almgren Date: Fri Feb 8 23:00:58 2019 -0800 Fix bug in 3D GSRB cell-centered solve. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit db07868c85e9e62657922351be663d801fe12e1b Author: Weiqun Zhang Date: Fri Feb 8 20:47:41 2019 -0800 PlotFileData::get for single component Src/Base/AMReX_PlotFileDataImpl.H Src/Base/AMReX_PlotFileDataImpl.cpp Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_VisMF.H commit cbfd90359e43cc74af0e7609758762d97d7d9294 Author: Weiqun Zhang Date: Fri Feb 8 17:02:38 2019 -0800 revert changes to AmrData Src/Extern/amrdata/AMReX_AmrData.H Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_PlotfileData.H Src/Extern/amrdata/AMReX_PlotfileData.cpp Src/Extern/amrdata/CMakeLists.txt Src/Extern/amrdata/Make.package commit f4f264337c6e44342237640e152b663bff7519fb Author: Weiqun Zhang Date: Fri Feb 8 16:51:53 2019 -0800 add PlotFileData for reading plotfiles Src/Base/AMReX_PlotFileDataImpl.H Src/Base/AMReX_PlotFileDataImpl.cpp Src/Base/AMReX_PlotFileUtil.H Src/Base/CMakeLists.txt Src/Base/Make.package Tools/Plotfile/GNUmakefile Tools/Plotfile/ftime.cpp commit 116872d602347500cb2897eebda37ed0fa74c596 Author: Brandon Runnels Date: Fri Feb 8 17:49:46 2019 -0700 modifying avergedownandsync Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit aa1294e80753c94685ad51f4056ea74dc26f05b9 Merge: 1a8fefe26 29da11502 Author: Brandon Runnels Date: Fri Feb 8 17:17:52 2019 -0700 Merge branch 'development' into nodeghostcells commit 99f7226edf6505f2160c80d7274dadbc5643758a Merge: ed27fdba5 7633ccd2c Author: Weiqun Zhang Date: Fri Feb 8 13:43:17 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7633ccd2c4e8d53f014c3f1d4bfdf05e83869538 Author: Weiqun Zhang Date: Fri Feb 8 13:12:06 2019 -0800 fix Machine for cori gpu and clean up make Src/Base/AMReX_Machine.cpp Tools/GNUMake/sites/Make.nersc commit 407a6e4797edfd46ad116ad12de52d6d5f14d54d Author: Andrew Myers Date: Fri Feb 8 13:01:57 2019 -0800 don't need travis wait anymore .travis.yml commit 9ab2d191082cf2603316429aeda761c83835c06e Author: Andrew Myers Date: Fri Feb 8 12:44:53 2019 -0800 disable breathe for now build_and_deploy.sh commit 1a8fefe26ccf5b30087262de79c004b219dcf2b1 Author: Brandon Runnels Date: Fri Feb 8 13:36:27 2019 -0700 modified interpCorrection to NOT include ghost cells Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 29da1150278d56b093dfc9c1a0fe8c277c5df949 Author: Weiqun Zhang Date: Fri Feb 8 10:40:36 2019 -0800 WIP: make for cori gpu Tools/GNUMake/Make.defs Tools/GNUMake/sites/Make.nersc commit 64d5ff5bcc356ca852417069ac3cf2baed48d686 Author: Weiqun Zhang Date: Fri Feb 8 08:46:02 2019 -0800 fcompare wip Src/Base/AMReX.cpp Src/Extern/amrdata/AMReX_PlotfileData.H Src/Extern/amrdata/AMReX_PlotfileData.cpp Tools/Plotfile/GNUmakefile Tools/Plotfile/fcompare.cpp Tools/Plotfile/fnan.cpp Tools/Plotfile/ftime.cpp Tools/Plotfile/fvarnames.cpp commit 6a6d00ea00d489e243c3b548d9e3493cfc19ce77 Author: Max Katz Date: Fri Feb 8 11:41:13 2019 -0500 Add floating point awareness to the plot_per/check_per logic The current logic can be slightly erroneous due to floating point issues. For example, if the timestep is 0.01 and the plot_per is 0.1, you would expect plotfiles at steps that are multiples of 10, but due to roundoff errors the current logic will sometimes plot in the 11th step instead of the 10th. By adding a small number to both sides of the comparison, we can guarantee plotting on exactly the timestep we intended. Src/Amr/AMReX_Amr.cpp commit 1f1d21ccaa4d39466ae3494a445ed8e7ce075105 Merge: 49b9fadf4 630ebfc01 Author: Andrew Myers Date: Thu Feb 7 16:26:30 2019 -0800 Merge pull request #405 from MaxThevenet/development add tag to particles already split commit 630ebfc01d51f31a54ce6251e3d0600e6b00acef Author: Maxence Thevenet Date: Thu Feb 7 16:23:52 2019 -0800 add tag to particles already split Src/Particle/AMReX_Particle.H commit 49b9fadf43875f29fa9771b865ef904fa55a1b38 Author: Andrew Myers Date: Thu Feb 7 18:17:14 2019 -0500 remove unused variables Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit ac812c50d040f43dae59998b2f50a0df657abbc3 Author: Andrew Myers Date: Thu Feb 7 17:56:39 2019 -0500 make the nbor_list a map over tiles Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit b6676cb3e9c0f0f77316801ede80356792d927dc Author: Andrew Myers Date: Thu Feb 7 17:47:56 2019 -0500 copy the neigbor list to host before printing Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit c3a87d73bbfd64fe358348a88da25f284b225ad5 Author: Andrew Myers Date: Thu Feb 7 17:44:00 2019 -0500 read print_neighbor_list from inputs Tests/Particles/GPUNeighborList/inputs Tests/Particles/GPUNeighborList/main.cpp commit 3da5ad1bab09ffd3d1f4404782abecf52cae0243 Author: Andrew Myers Date: Thu Feb 7 17:41:19 2019 -0500 move printNeighborList to its own method Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit a9670d49e826069cf28d7a8dbc5f2f8d9bf0f54e Author: Andrew Myers Date: Thu Feb 7 17:38:05 2019 -0500 move computeForces to a separate method Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp Tests/Particles/GPUNeighborList/main.cpp commit ff82d228d01709feb3a991344700f319ae71e8e8 Author: Andrew Myers Date: Thu Feb 7 17:32:08 2019 -0500 make the neighbor list a class member Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 9bbdc7fafc6883a34432dc2a21f0e78ea43d5909 Author: Andrew Myers Date: Thu Feb 7 17:25:11 2019 -0500 thrust::raw_pointer_cast -> dataPtr() Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 057f5042062a1ad74123cbd20579a8d038525eaf Author: Andrew Myers Date: Thu Feb 7 17:21:18 2019 -0500 thrust::device_vector -> Gpu::DeviceVector Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 0af3ca4a90bfd2f2bddea260f792e92109545fd2 Merge: ca54c6f4d 565a8449d Author: Andrew Myers Date: Thu Feb 7 16:27:50 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ca54c6f4d4d872aa65380b19db5575dfa35137f5 Author: Andrew Myers Date: Thu Feb 7 16:19:47 2019 -0500 don't need a separate cached allocator now Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaAllocators.cpp commit e87e035fecbe69de9d3e04c154a94f3af272aa2b Author: Andrew Myers Date: Thu Feb 7 15:34:10 2019 -0500 remove the remaining device_vector members from ParticleContainer; temporaries now work fine. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit d94ed733a2dca5f4aa610fab960f3382dc4296dc Author: Andrew Myers Date: Thu Feb 7 15:01:35 2019 -0500 remove some more of the mutable thrust::device_vector members from the ParticleContainer Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 0cca265c6239d0ed93a1216603a3c36769df2fe7 Author: Andrew Myers Date: Thu Feb 7 14:52:32 2019 -0500 remove some of the mutable thrust::device_vector members from the ParticleContainer Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 12838ea2285227fbe46d10841e50cd8fac7fbea1 Author: Andrew Myers Date: Thu Feb 7 14:46:06 2019 -0500 thrust::device_vector -> Gpu::DeviceVector Src/Particle/AMReX_Particles.H commit 771000430adee5c3b1c6b8e389d789232bf91a33 Author: Andrew Myers Date: Thu Feb 7 14:34:27 2019 -0500 use the Arena in Gpu::DeviceVector Src/Base/AMReX_CudaContainers.H commit e3a4a63171569d1fedf1d124c8299e767138081b Author: Andrew Myers Date: Thu Feb 7 14:34:05 2019 -0500 add thrust allocators that are implemented in terms of AMReX's Arenas Src/Base/AMReX_CudaAllocators.H commit 24d73459b2e42b3fe084fe7b3b723e9003d50445 Author: Brandon Runnels Date: Thu Feb 7 11:12:56 2019 -0700 fixed mlcg to be consistent Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 565a8449d82f41aa225d65e15f4cfc8020c3f0a9 Author: Ann Almgren Date: Thu Feb 7 06:44:51 2019 -0800 Remove IMEX_Advec_Diff_C from the Tutorials documentation Docs/sphinx_tutorials/source/SDC_Tutorial.rst commit 1d53c0f0e28c7b243128f415c06eebf0ddcda119 Author: Ann Almgren Date: Thu Feb 7 06:44:07 2019 -0800 Remove IMEX_Advec_Diff_C per Minion's guidance -- this is deprecated. Tutorials/SDC/IMEX_Advec_Diff_C/GNUmakefile Tutorials/SDC/IMEX_Advec_Diff_C/Make.package Tutorials/SDC/IMEX_Advec_Diff_C/advance.cpp Tutorials/SDC/IMEX_Advec_Diff_C/advance_2d.f90 Tutorials/SDC/IMEX_Advec_Diff_C/init_phi_2d.f90 Tutorials/SDC/IMEX_Advec_Diff_C/init_phi_3d.f90 Tutorials/SDC/IMEX_Advec_Diff_C/inputs_2d Tutorials/SDC/IMEX_Advec_Diff_C/inputs_3d Tutorials/SDC/IMEX_Advec_Diff_C/main.cpp Tutorials/SDC/IMEX_Advec_Diff_C/myfunc.H Tutorials/SDC/IMEX_Advec_Diff_C/myfunc_F.H commit c16a286fa47b659ded31212cbb7b6192875d64f8 Author: Weiqun Zhang Date: Wed Feb 6 20:50:44 2019 -0800 clean up Src/Extern/amrdata/AMReX_PlotfileData.H Src/Extern/amrdata/AMReX_PlotfileData.cpp commit 5b192938c768ed560efa79c1278b844a6bd36851 Author: Weiqun Zhang Date: Wed Feb 6 17:55:57 2019 -0800 fnan Src/Extern/amrdata/AMReX_PlotfileData.H Src/Extern/amrdata/AMReX_PlotfileData.cpp Tools/Plotfile/GNUmakefile commit d8aa5f495950f03c110db482446bc3561ca276e4 Author: Weiqun Zhang Date: Wed Feb 6 16:30:33 2019 -0800 ftime Tools/GNUMake/Make.rules Tools/Plotfile/GNUmakefile Tools/Plotfile/fboxinfo.cpp Tools/Plotfile/ftime.cpp Tools/Plotfile/fvarnames.cpp commit 6245ecb708f17ca881ff92947ae706f6d39b3bac Author: Andrew Myers Date: Wed Feb 6 19:20:42 2019 -0500 restore cuda-aware mpi option to the particle container. Src/Particle/AMReX_Particles.H commit 269d67ea2ffedc06d6e1fa3f7c7221cc9a9726e9 Author: Andrew Myers Date: Wed Feb 6 19:20:25 2019 -0500 a vector based on same Src/Base/AMReX_CudaContainers.H commit a501651d0876625f266c728acb8c07dd7e066cac Author: Andrew Myers Date: Wed Feb 6 19:20:14 2019 -0500 a new allocator that can toggle between pinned and device memory at runtime Src/Base/AMReX_CudaAllocators.H commit 4d73dc704d83f7ea795690a66d75cd47b82b1de3 Author: Weiqun Zhang Date: Wed Feb 6 16:11:05 2019 -0800 fvarnames Tools/Plotfile/GNUmakefile Tools/Plotfile/fvarnames.cpp commit 4a4698c3e4b046e5e42f768448b0631c2194b5f8 Author: Weiqun Zhang Date: Wed Feb 6 15:47:18 2019 -0800 dimension agnostic fboxinfo Src/Extern/amrdata/AMReX_PlotfileData.H Src/Extern/amrdata/AMReX_PlotfileData.cpp Tools/Plotfile/AMReX_AnyDimUtil.H Tools/Plotfile/AMReX_AnyDimUtil.cpp Tools/Plotfile/GNUmakefile Tools/Plotfile/Make.package Tools/Plotfile/fboxinfo.cpp commit 186f6333908b28443323b4713f6abeeecc13d9c4 Author: Andrew Myers Date: Wed Feb 6 18:45:26 2019 -0500 some reorganization Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp Tests/Particles/GPUNeighborList/main.cpp commit b1638f1c15a6eba974ccbaef01782a1dbbb5e963 Author: Andrew Myers Date: Wed Feb 6 18:33:14 2019 -0500 fix bug Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit df4422828ad8eec996d02012c91faad2ed38ee9a Author: Andrew Myers Date: Wed Feb 6 18:06:33 2019 -0500 removing is_per Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 1507d265100126cd13b3c033a0e244cbd5802fcc Author: Andrew Myers Date: Wed Feb 6 18:06:00 2019 -0500 implement looping over the neighbor list and moving the particles Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit a136cb8e2f5f962cb6dc9e579104f8e4da628141 Author: Andrew Myers Date: Wed Feb 6 17:08:26 2019 -0500 hardwire nppc to (1, 1, 1) Tests/Particles/GPUNeighborList/inputs Tests/Particles/GPUNeighborList/main.cpp commit 5bf49ce7e3ffa91d9f5f731d90c9ac2cc46fcc57 Author: Andrew Myers Date: Wed Feb 6 17:07:49 2019 -0500 tweak cutoff Tests/Particles/GPUNeighborList/Constants.H commit 330d88c95dc7c18ecd1543e632eb269167fa830b Author: Andrew Myers Date: Wed Feb 6 16:28:05 2019 -0500 workaround for relaxed constexpr bug in cuda 9.2 Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit 5358ff056e79ef2acef1bf9db2dc1a2b52f4d5ff Author: Andrew Myers Date: Wed Feb 6 13:17:01 2019 -0800 tweak build and deploy build_and_deploy.sh commit 7e523e54bdf40a1dcaa5791370bdb28ab3c693a6 Author: Andrew Myers Date: Wed Feb 6 12:53:04 2019 -0800 add travis_wait before running the build script .travis.yml commit f891e1c9f513fc311d701707c83720c6b51e7ff2 Author: Andrew Myers Date: Wed Feb 6 12:27:42 2019 -0800 hide more output build_and_deploy.sh commit db944a4bad2d0a156e86f2121840a7d64ed2b5f8 Author: Andrew Myers Date: Wed Feb 6 11:56:05 2019 -0800 hide the doxygen output, which puts us over the log file length limit on Travis CI build_and_deploy.sh commit 811183ace1971501e338c848e9b3bae659945273 Author: Andrew Myers Date: Wed Feb 6 11:27:06 2019 -0800 restore stuff for latexpdf .travis.yml commit 09abf509e4adf60dc656767dbd9b3fdee7be2516 Author: Andrew Myers Date: Wed Feb 6 11:06:06 2019 -0800 don't specify python3.6 in the build_and_deploy script build_and_deploy.sh commit ff9aa423e48f124b1e35c074da32e6e9995e01e8 Author: Andrew Myers Date: Wed Feb 6 10:45:16 2019 -0800 also need libmpich-dev .travis.yml commit 034c4a1eff92a41d29503b8e91a59c643845da09 Author: Andrew Myers Date: Wed Feb 6 10:40:50 2019 -0800 remove extra addons entry .travis.yml commit dade31918536a7975d361f01493f40679258c349 Author: Andrew Myers Date: Wed Feb 6 10:22:08 2019 -0800 tweak installed packahed .travis.yml commit c3b0b359dfab752d80123aed46d87c24d106eddc Merge: 4c9450ab5 e9b906acf Author: Andrew Myers Date: Wed Feb 6 10:14:42 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4c9450ab50c05cdd042418251f0665da3e1f6158 Author: Andrew Myers Date: Wed Feb 6 10:14:30 2019 -0800 remove ubuntu-toolchain-r-test .travis.yml commit 499e9847d78846f1ceb39500de7da95fd268dc49 Author: Weiqun Zhang Date: Tue Feb 5 21:45:59 2019 -0800 add PlotfileData as a wrapper of DataServices Src/Extern/amrdata/AMReX_AmrData.H Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_PlotfileData.H Src/Extern/amrdata/AMReX_PlotfileData.cpp Src/Extern/amrdata/CMakeLists.txt Src/Extern/amrdata/Make.package commit e9b906acf3211e28b39c2835727f84c71d4e79a4 Merge: 7f96e550a 0f87676a5 Author: Andrew Myers Date: Tue Feb 5 21:29:11 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7f96e550a8d6a5f79d1dac74f74af9fab6fb23fc Merge: c05491c14 dec5ea386 Author: Andrew Myers Date: Tue Feb 5 21:28:47 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0f87676a5022e3581d52d7b81f384db1e1bfc99f Author: Marc Day Date: Tue Feb 5 18:28:38 2019 -0800 Add sig for WritePltFile that takes an alternative prob domain array Tools/C_util/WritePlotFile.H Tools/C_util/WritePlotFile.cpp commit c05491c1436375bf00fe81905e7408f4ea0dc281 Author: Andrew Myers Date: Tue Feb 5 21:28:28 2019 -0500 fix bug involving asynchronous mem copies with Cuda Src/Particle/AMReX_ParticleContainerI.H commit dec5ea3867a22e393d64137535e2967249c87028 Author: Andrew Myers Date: Tue Feb 5 17:53:04 2019 -0800 specify sources .travis.yml commit 1b1689f852b4c00711dfe1958fa142e115612c01 Author: Andrew Myers Date: Tue Feb 5 17:43:49 2019 -0800 add python to PATH .travis.yml commit 7bf0af89a6a48a965cdc91941701161dd0fbd837 Author: Andrew Myers Date: Tue Feb 5 17:37:49 2019 -0800 tweak pip install line .travis.yml commit c5e43f4fe302d439a11c3dcfcba9735adce9ae79 Author: Andrew Myers Date: Tue Feb 5 17:35:46 2019 -0800 change language. .travis.yml commit f0a900d22eb38243060145577c5b579ce8c3a350 Author: Andrew Myers Date: Tue Feb 5 17:30:25 2019 -0800 trying to fix the Travis build environment .travis.yml commit 6bc4fbfe92d581729182d9f73e79a876f52d9045 Merge: 976e652d3 9b051250b Author: Andrew Myers Date: Tue Feb 5 17:22:25 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9b051250b98062f5ecf4000425e4967359a3f99b Author: Kevin Gott Date: Tue Feb 5 20:15:36 2019 -0500 Get rid of 9.2.x limitation in GPU docs. Docs/sphinx_documentation/source/GPU_Chapter.rst commit 55b32ff45f673624afd316b729310498e679769a Merge: 5874c6538 2a64f44a9 Author: Ann Almgren Date: Tue Feb 5 17:10:00 2019 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 976e652d3a066a7fcc28919a7c47fdbc027e2ca9 Author: Andrew Myers Date: Tue Feb 5 17:08:06 2019 -0800 bump python version .travis.yml commit d39edf526c201680190bce56ec5c344708ae99bc Author: Brandon Runnels Date: Tue Feb 5 18:07:19 2019 -0700 wip - crude updates to allow ghost cell based reflux Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 2a64f44a92b2ec9af9bfc83557ca9354288b0d2c Merge: b4cc24130 0d6554c36 Author: Andrew Myers Date: Tue Feb 5 17:02:52 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b4cc2413004b7bb437278f25637a364c6244284e Author: Andrew Myers Date: Tue Feb 5 17:02:41 2019 -0800 mpich2 -> mpich .travis.yml commit 5874c6538a4f5ca5791828f8b16081d42064dd50 Author: Ann Almgren Date: Tue Feb 5 17:02:11 2019 -0800 Fix oops -- this now compiles. Src/EB/AMReX_EBMultiFabUtil_3d.F90 commit 0d6554c364d2d5b83e429755670b70b25820c0f0 Merge: 3da526daf 3c3fd622f Author: Ann Almgren Date: Tue Feb 5 16:58:56 2019 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 3da526dafa976fc98b30fdf03671dc00bdd3f777 Author: Ann Almgren Date: Tue Feb 5 16:58:19 2019 -0800 Move interpolate_to_face_centroid routine from mfix into amrex since it is completely general. Src/EB/AMReX_EBMultiFabUtil_3d.F90 commit 3c3fd622fc3770d99712f37cc9c8e7a4aec070aa Merge: 31847b83b cec6f7589 Author: Andrew Myers Date: Tue Feb 5 16:57:28 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 31847b83bd5d0f2016c6739b7cefa4fa8cf5638d Author: Andrew Myers Date: Tue Feb 5 16:57:14 2019 -0800 update ubuntu version used by travis .travis.yml commit cec6f758948f8cdee8145452ac7bc719506bfd43 Author: Kevin Gott Date: Tue Feb 5 19:40:09 2019 -0500 buildNotused, testing how to build AMReX as a library around user-defined functions. Tests/GPU/buildNotused/Extern.H Tests/GPU/buildNotused/GNUmakefile Tests/GPU/buildNotused/MyKernel.H Tests/GPU/buildNotused/MyKernel.cpp Tests/GPU/buildNotused/MyKernelB.H Tests/GPU/buildNotused/MyKernelB.cpp Tests/GPU/buildNotused/Notused.H Tests/GPU/buildNotused/Notused.cpp Tests/GPU/buildNotused/Readme Tests/GPU/buildNotused/main.cpp commit 6875f4c8b9245b2820fcdaa98e93ae56c17cca6f Author: Andrew Myers Date: Tue Feb 5 16:25:56 2019 -0800 add AddParticles method and implement copyParticles in terms of that. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 1c1298e51e882e0c21f80c9afed3738e21c389c8 Author: Andrew Myers Date: Tue Feb 5 18:32:48 2019 -0500 do custom partition by default Src/Particle/AMReX_ParticleContainerI.H commit c5d6f360a0453b6925a9041c5cbb5704330de8eb Author: Andrew Myers Date: Tue Feb 5 18:32:19 2019 -0500 add option to switch between versions of partition Src/Particle/AMReX_ParticleContainerI.H commit ed27fdba5911f1db6963dd9a02e61a31795c3595 Author: Weiqun Zhang Date: Tue Feb 5 14:45:39 2019 -0800 add Fortran 2003 style command argument functions Src/Base/AMReX.H Src/Base/AMReX.cpp commit a5f95054eeb4d5876865b392568dbc6d5fdad239 Author: Weiqun Zhang Date: Tue Feb 5 14:13:07 2019 -0800 fix merge Src/Particle/AMReX_Particles.H commit 4475e4f58d1855cd2f85b32018ad07b58cf0dcdc Author: Weiqun Zhang Date: Tue Feb 5 13:39:54 2019 -0800 fix merge Src/Particle/AMReX_Particles.H commit ada1baee2dc15999513816808f6d0cbe9713c5c8 Merge: 93ad1783c 1fefff037 Author: Weiqun Zhang Date: Tue Feb 5 13:32:47 2019 -0800 Merge branch 'development' into dev-tmp commit 1fefff037735b3c4b9fc6d620f8bc47b10d6cda9 Merge: 09e0d3951 355cc5730 Author: Weiqun Zhang Date: Tue Feb 5 13:29:14 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 93ad1783c973cc7203df192ce9c795d8b2357ebb Merge: 720756130 cdd7b44d5 Author: WeiqunZhang Date: Tue Feb 5 13:24:35 2019 -0800 Merge pull request #403 from harpolea/doxygen Doxygen commit 09e0d39514c20871b0cdeccb18d4208dcae6cfaa Author: Weiqun Zhang Date: Tue Feb 5 13:23:41 2019 -0800 add make option for multiple executables Tools/GNUMake/Make.rules commit 355cc5730c85c52b95c2c463d4bfd7ccc1bf9f84 Author: Ann Almgren Date: Tue Feb 5 12:53:46 2019 -0800 Add EB_set_covered call at end of reflux routine. Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit cdd7b44d5f92927898669c4e901873c0c54f5b11 Author: Alice Harpole Date: Tue Feb 5 15:36:19 2019 -0500 moves doxygen and breathe steps to build_and_deply Docs/Doxygen/doxygen.conf Docs/sphinx_documentation/Makefile Docs/sphinx_documentation/source/conf.py build_and_deploy.sh commit daa11fcf8660a664b380578d4f8c4cfbd6b23759 Merge: 8f61e2acb 64a5f55ed Author: Weiqun Zhang Date: Tue Feb 5 10:34:53 2019 -0800 Merge branch 'development' into weiqun/gpu commit 8f61e2acbef19601e1b345515b8b551d88b627e4 Author: Weiqun Zhang Date: Tue Feb 5 10:33:43 2019 -0800 MLMG on GPU: fix eb and put some comments Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 64a5f55edc87d874e94176d2819b14d7ffc4f4a1 Author: Ann Almgren Date: Tue Feb 5 09:57:01 2019 -0800 "OldMiniApps" was too old to be relevant. OldMiniApps/FillBoundary/GNUmakefile OldMiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp OldMiniApps/FillBoundary/README OldMiniApps/FillBoundary/qsub.ipm.bat OldMiniApps/MultiGrid_C/COEF_3D.F OldMiniApps/MultiGrid_C/COEF_F.H OldMiniApps/MultiGrid_C/GNUmakefile OldMiniApps/MultiGrid_C/Make.package OldMiniApps/MultiGrid_C/README OldMiniApps/MultiGrid_C/RHS_3D.F OldMiniApps/MultiGrid_C/RHS_F.H OldMiniApps/MultiGrid_C/main.cpp OldMiniApps/MultiGrid_C/qsub.ipm.bat commit 1958aa235378455e7788268743c49461e732f062 Author: Ann Almgren Date: Tue Feb 5 09:42:50 2019 -0800 Remove seriously old post-processing routines from Tools/Postprocessing/F_Src that were specific to certain applications. Tools/Postprocessing/F_Src/old_flame/GNUmakefile Tools/Postprocessing/F_Src/old_flame/fbubble_position.f90 Tools/Postprocessing/F_Src/old_flame/fbubble_position_3d.f90 Tools/Postprocessing/F_Src/old_flame/fcusp.f90 Tools/Postprocessing/F_Src/old_flame/fcylflame.f90 Tools/Postprocessing/F_Src/old_flame/fflamelength.f90 Tools/Postprocessing/F_Src/old_flame/finteg.f90 Tools/Postprocessing/F_Src/old_flame/fturbkin.f90 Tools/Postprocessing/F_Src/old_flame/fwidth.f90 Tools/Postprocessing/F_Src/tutorial/GNUmakefile Tools/Postprocessing/F_Src/tutorial/fspeciesmass2d.f90 Tools/Postprocessing/F_Src/tutorial/fwrite2d.f90 commit 1b68dd31ebf214046b2475671eb28ac36d72b64c Author: Weiqun Zhang Date: Tue Feb 5 09:33:53 2019 -0800 MLMG on GPU: flux Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/Make.package commit 92931676d88560e10e25f8d78c1f1aead798d1a6 Author: Weiqun Zhang Date: Tue Feb 5 08:34:22 2019 -0800 remove F_MG from inputs OldTutorials/MultiGrid_C/inputs OldTutorials/MultiGrid_C/inputs-rt-c-neu OldTutorials/MultiGrid_C/inputs-rt-c-ord2 OldTutorials/MultiGrid_C/inputs-rt-f-neu OldTutorials/MultiGrid_C/inputs-rt-f-ord2 OldTutorials/MultiGrid_C/inputs-rt-f-ord3 Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir-ord2 Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir-ord3 Tests/LinearSolvers/ComparisonTest/inputs-rt-Neu Tests/LinearSolvers/ComparisonTest/inputs.3d commit 9ee838bd8b98e9128d41738530259d884e5c1ded Merge: 4252ed123 22e73c07a Author: Andrew Myers Date: Mon Feb 4 20:46:07 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4252ed123c0199b878e87bb2fc013286087e5948 Author: Andrew Myers Date: Mon Feb 4 20:41:18 2019 -0500 fixing bug with freeing the snd_buffer for pinned memory in RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit fe90331210e2d5261f9ea2d7ee81d442b2c9bdcb Author: Andrew Myers Date: Mon Feb 4 20:40:36 2019 -0500 fixes for the ThrustPinnedAllocator Src/Base/AMReX_CudaAllocators.H commit 22e73c07a528101ed59db49db89348efea7e7ffd Merge: a3b5fee1d 9028db9e6 Author: Andrew Myers Date: Mon Feb 4 17:26:10 2019 -0800 Merge pull request #404 from ylunalin/new_heat_tutorials New heat tutorials commit a3b5fee1d27e0f0b873e04391a58b7c56c9e2223 Author: Kevin Gott Date: Mon Feb 4 20:13:53 2019 -0500 Clean up hybrid makefile. Tests/GPU/buildHybrid/GNUmakefile commit 24fb85140201c7373b8050b39fa8a89c8817822e Author: Andrew Myers Date: Mon Feb 4 20:11:01 2019 -0500 ifdef the PinnedDeviceVector to be a regular Vector if CUDA is off Src/Base/AMReX_CudaContainers.H commit 6ce88e79f370029db9427a4ebefafec50d409d20 Author: Kevin Gott Date: Mon Feb 4 20:10:48 2019 -0500 Bug fix and eliminate unneeded library and include lines when invoking nvcc and pgfortran. Tests/GPU/buildTest/GNUmakefile commit 9b08b9d9dd1282259ffddcab59f95de342a2b41e Author: Andrew Myers Date: Mon Feb 4 20:10:12 2019 -0500 add PinnedDeviceVector Src/Base/AMReX_CudaContainers.H commit 9028db9e692d1f83ec2f5a1046755c1b72333c48 Merge: 4e1a66ff3 0e64e8e1a Author: Luna Lin Date: Mon Feb 4 20:04:55 2019 -0500 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into new_heat_tutorials commit 4e1a66ff39ba974233147ecfcaa420a7f455a1f8 Author: Luna Lin Date: Mon Feb 4 20:04:29 2019 -0500 Fixed a typo in the CUDA version, and the multiple lines issue in mykernel.H Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/mykernel.H commit 2f9553a1ddd45475089cca0ce68c96a7619250d8 Author: Andrew Myers Date: Mon Feb 4 19:59:59 2019 -0500 templated pinned allocator that can be used with thrust::device_vector Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaAllocators.cpp commit b38418af137afaa87b2bcc85dd2e8e04df62660a Author: Andrew Myers Date: Mon Feb 4 19:22:10 2019 -0500 remove some private members that aren't used anymore from ThrustCachedAllocator Src/Base/AMReX_CudaAllocators.H commit 3c286fd647a1a7f836f7ed5b24dc41cb192bb5c9 Author: Andrew Myers Date: Mon Feb 4 19:18:02 2019 -0500 a Pinned allocator for use with Thrust Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaAllocators.cpp commit 0e64e8e1acd3552c18ad0b22c12ece2115af4321 Author: Ann Almgren Date: Mon Feb 4 13:01:38 2019 -0800 Remove F_BaseLib. Tests/LinearSolvers/ComparisonTest/GNUmakefile commit 21f1df0e7d284251ffb3e3a8ce9faaa8c9f67cc3 Author: Ann Almgren Date: Mon Feb 4 13:00:26 2019 -0800 Remove F_BaseLib. Tests/LinearSolvers/C_CellMG/GNUmakefile commit c098750243c8a2a157d379024ea16bfbb7357721 Author: Ann Almgren Date: Mon Feb 4 12:54:19 2019 -0800 Remove use of F_MG solvers OldTutorials/MultiGrid_C/GNUmakefile OldTutorials/MultiGrid_C/main.cpp OldTutorials/PIC_C/solve_with_f90.cpp OldTutorials/README_F commit 2aa75a2e2a3aa6212ac82eacb91c345221bca1b4 Author: Andrew Myers Date: Mon Feb 4 12:50:33 2019 -0800 rename solve_with_f90 OldTutorials/PIC_C/Make.package OldTutorials/PIC_C/solve_with_mlmg.cpp commit 3100be3ef8574ed34b4acfbd348d704497d8159f Merge: b2ef72422 12d2cd99f Author: Ann Almgren Date: Mon Feb 4 12:43:36 2019 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit b2ef724220b9936daae6e4dff703ba075e040a0c Author: Ann Almgren Date: Mon Feb 4 12:43:23 2019 -0800 Remove reference to F_MG or C_to_F_MG. Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit b57675cdb055e5eca57b3e8ecdaa78ece58ca1e5 Author: Andrew Myers Date: Mon Feb 4 12:34:09 2019 -0800 fix compilation / linking OldTutorials/PIC_C/GNUmakefile OldTutorials/PIC_C/main.cpp OldTutorials/PIC_C/single_level.cpp OldTutorials/PIC_C/solve_for_accel.cpp OldTutorials/PIC_C/solve_with_f90.cpp OldTutorials/PIC_C/two_level.cpp commit 01bf4b1b63830049516e72f970da4cfd0f18b0f0 Author: Andrew Myers Date: Mon Feb 4 11:12:15 2019 -0800 update GNUmakefile for new linear solver libraries. OldTutorials/PIC_C/GNUmakefile commit 12d2cd99f17d574951ac36a10ad2f5c0d40f514f Author: Andrew Myers Date: Mon Feb 4 11:01:29 2019 -0800 removed old CUDA Fortran example of PIC deposition. Tests/Particles/ManagedCUDADeposition/GNUmakefile Tests/Particles/ManagedCUDADeposition/Make.package Tests/Particles/ManagedCUDADeposition/MyParticleContainer.H Tests/Particles/ManagedCUDADeposition/MyParticleContainer.cpp Tests/Particles/ManagedCUDADeposition/cuda_deposit_3d.f90 Tests/Particles/ManagedCUDADeposition/deposit_3d.f90 Tests/Particles/ManagedCUDADeposition/deposit_F.H Tests/Particles/ManagedCUDADeposition/inputs Tests/Particles/ManagedCUDADeposition/main.cpp Tests/Particles/ManagedCUDADeposition/solve_for_accel.cpp Tests/Particles/ManagedCUDADeposition/solve_with_f90.cpp commit 68dda2aeeb2a91a5087257a5f93f500afe7c621c Author: Ann Almgren Date: Mon Feb 4 10:52:13 2019 -0800 Remove all use of F_MG solvers. Tests/LinearSolvers/ComparisonTest/GNUmakefile Tests/LinearSolvers/ComparisonTest/Make.package Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.H Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp Tests/LinearSolvers/F_MG/GNUmakefile Tests/LinearSolvers/F_MG/bc_interp.f90 Tests/LinearSolvers/F_MG/cc_edge_coeffs.f90 Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/cc_rhs.f90 Tests/LinearSolvers/F_MG/grids_2d_1lev Tests/LinearSolvers/F_MG/grids_2d_2lev Tests/LinearSolvers/F_MG/grids_3d_1lev Tests/LinearSolvers/F_MG/grids_3d_2lev Tests/LinearSolvers/F_MG/init_cell_coeffs.f90 Tests/LinearSolvers/F_MG/inputs.2d.fcycle Tests/LinearSolvers/F_MG/inputs.2d.fcycle.dir Tests/LinearSolvers/F_MG/inputs.2d.nodal.cross Tests/LinearSolvers/F_MG/inputs.2d.nodal.dense Tests/LinearSolvers/F_MG/inputs.2d.vcycle Tests/LinearSolvers/F_MG/inputs.2d.vcycle.dir Tests/LinearSolvers/F_MG/inputs.3d.fcycle Tests/LinearSolvers/F_MG/inputs.3d.fcycle.dir Tests/LinearSolvers/F_MG/inputs.3d.nodal.cross Tests/LinearSolvers/F_MG/inputs.3d.nodal.dense Tests/LinearSolvers/F_MG/inputs.3d.vcycle Tests/LinearSolvers/F_MG/inputs.3d.vcycle.dir Tests/LinearSolvers/F_MG/main.f90 Tests/LinearSolvers/F_MG/makefile Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/nodal_rhs.f90 Tests/LinearSolvers/F_MG/regression Tests/LinearSolvers/F_MG/t_smoother.f90 Tests/LinearSolvers/F_MG/t_stencil.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit a257467307d2fe0347eccc5aae10c3528b7f11d5 Author: Ann Almgren Date: Mon Feb 4 10:42:42 2019 -0800 Remove F_MG and C_to_F_MG. Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Src/LinearSolvers/C_to_F_MG/AMReX_stencil_types.H Src/LinearSolvers/C_to_F_MG/Make.package Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/coarsen_coeffs.f90 Src/LinearSolvers/F_MG/compute_defect.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_norm.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_applyop.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_enforce_dirichlet_rhs.f90 Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_newu.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_apply.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 Src/LinearSolvers/F_MG/nodal_sum.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 Src/LinearSolvers/F_MG/stencil_types.f90 Src/LinearSolvers/F_MG/stencil_util.f90 Src/LinearSolvers/F_MG/tridiag.f90 commit 720756130751c04935ff30be95c8a4d8d0bc1186 Author: Weiqun Zhang Date: Mon Feb 4 08:48:31 2019 -0800 BOUND_CHECK as an option Src/Base/AMReX_Array.H Tools/GNUMake/Make.defs commit 25cfedad12b08a9eacae799128e66510ffd9042a Author: Alice Harpole Date: Mon Feb 4 11:09:26 2019 -0500 fixed a few bugs and cleaned up Src/Base/AMReX_iMultiFab.H Src/Extern/CVODE/cvode_interface.f90 Src/Extern/CVODE/fnvector_serial.f90 Src/Extern/CVODE/sundials_fdlsmat.f90 Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_UTIL.F90 Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec4_2D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec4_3D.F90 Src/SDC/AMReX_SDCstruct.H commit ea2e9f2452d6ddaad39291f3cfd74eabbaba0824 Merge: dac9b474d 86269ec30 Author: Alice Harpole Date: Mon Feb 4 10:26:06 2019 -0500 fixed merge conflicts commit dac9b474d3f6af72539dfa41939241c94813cea0 Author: Alice Harpole Date: Mon Feb 4 10:23:41 2019 -0500 fixed bugs in AMReX_Particles.H Src/Particle/AMReX_Particles.H commit 78821da63aeedc7209cc95b0497c482009fb86dd Author: Weiqun Zhang Date: Sat Feb 2 16:52:02 2019 -0800 MLMG on GPU: normalize Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit abe38a80aa0bf13b4fe902859e7885480c1d18a6 Author: Weiqun Zhang Date: Sat Feb 2 15:49:38 2019 -0800 fix variable type and function name Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit b5b3b0bb24bcaa1e21943a3399dd225d7806630d Author: Weiqun Zhang Date: Sat Feb 2 15:05:40 2019 -0800 MLMG on GPU: MLABecLap A dot x Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLABecLap_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_3D_K.H Src/LinearSolvers/MLMG/Make.package commit 86269ec30720a181efbb17eb749b9c2e5e7e6422 Author: Weiqun Zhang Date: Sat Feb 2 14:03:22 2019 -0800 update tutorial documentation Docs/sphinx_tutorials/source/GPU_Tutorial.rst commit dd18243318cad4d9c9c1b5cb3b8ac80dedde3fbe Merge: 1d96e599c ad916fb0c Author: Luna Lin Date: Sat Feb 2 16:51:22 2019 -0500 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into new_heat_tutorials commit 1d96e599ceb39ef77ecdbd1b50ce3577673eec98 Author: Luna Lin Date: Sat Feb 2 16:50:49 2019 -0500 GNUMakefile needed to be tweaked to work with new directory organization. Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/GNUmakefile commit ad916fb0cb8887341fbc91d275d93a6ff769ef62 Author: Weiqun Zhang Date: Sat Feb 2 13:49:44 2019 -0800 fix 1d interpbndrydata Src/Boundary/AMReX_InterpBndryData_1D_K.H commit ae6f6a4e04a4ecfec035bdf1d57dd0f0aabfa69b Author: Weiqun Zhang Date: Sat Feb 2 13:49:44 2019 -0800 fix 1d interpbndrydata Src/Boundary/AMReX_InterpBndryData_1D_K.H commit fb927304cdb47835be7fbe3a15b2eba03370edce Author: Weiqun Zhang Date: Sat Feb 2 13:49:28 2019 -0800 MLMG on GPU: lin_cc_interp Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_F.H Src/LinearSolvers/MLMG/AMReX_MLMG_K.H Src/LinearSolvers/MLMG/Make.package commit b4690be1b3c3581ef780d0b2f6ec78f1d98550c2 Merge: c8cc366d0 b24944f59 Author: Weiqun Zhang Date: Sat Feb 2 08:51:32 2019 -0800 Merge branch 'development' into weiqun/gpu commit b24944f59763af18de89876fd8e9c3fd84b831cf Author: Weiqun Zhang Date: Sat Feb 2 11:51:08 2019 -0500 fix the version detection macro Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.cpp Tutorials/GPU/CNS/Source/CNS_K.H commit c8cc366d07e961af8d6052cd65be5a58b30d97c5 Author: Weiqun Zhang Date: Sat Feb 2 08:26:13 2019 -0800 use amrex::ParallelFor Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_derive.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp commit 506120153144a1420f3533206f6e313f0642b884 Merge: b52b38dd8 9d9414dce Author: Weiqun Zhang Date: Sat Feb 2 01:34:40 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b52b38dd894238147868fab8acfc26b48afebead Author: Weiqun Zhang Date: Sat Feb 2 00:32:29 2019 -0500 avoid using relaxed constexpr for nvcc 9.2 to get around its bug Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.cpp Tools/GNUMake/comps/nvcc.mak Tutorials/GPU/CNS/Source/CNS_K.H commit 9d9414dcee0b025087faf1392a9d362e029b0b01 Author: Andrew Myers Date: Fri Feb 1 19:58:26 2019 -0500 std::cout -> amrex::Print() Tests/Particles/GPUNeighborList/MDParticleContainer.cpp commit a4a7ea700f81bc9d63366b833b120a6405733b7e Author: Andrew Myers Date: Fri Feb 1 19:54:54 2019 -0500 add device function for checking a pair of particles Tests/Particles/GPUNeighborList/MDParticleContainer.cpp Tests/Particles/GPUNeighborList/Make.package Tests/Particles/GPUNeighborList/md_K.H commit 565daf1683b14ff0a003269270e18ddcac4da211 Merge: ea3a3308d 670a88067 Author: Andrew Myers Date: Fri Feb 1 19:40:49 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ea3a3308d478c95bf25b278b703fded1df0051cb Author: Andrew Myers Date: Fri Feb 1 19:40:30 2019 -0500 Test for building neighbor list data structure using CUDA/Thrust for Nvidia GPUs Tests/Particles/GPUNeighborList/Constants.H Tests/Particles/GPUNeighborList/GNUmakefile Tests/Particles/GPUNeighborList/MDParticleContainer.H Tests/Particles/GPUNeighborList/MDParticleContainer.cpp Tests/Particles/GPUNeighborList/Make.package Tests/Particles/GPUNeighborList/inputs Tests/Particles/GPUNeighborList/main.cpp commit 670a88067a3b6006f7a7facbeb21d5c43f61cbf5 Merge: e5cba96da 9ad96d3ac Author: Weiqun Zhang Date: Fri Feb 1 16:13:09 2019 -0800 Merge branch 'weiqun/gpu' into development commit 9ad96d3ace0183084cb2d66c4d32963aed5bbdf0 Author: Weiqun Zhang Date: Fri Feb 1 16:11:32 2019 -0800 change the default back to managed Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaAsyncFabImpl.H Src/Base/AMReX_CudaAsyncFabImpl.cpp Tools/GNUMake/Make.defs Tools/GNUMake/sites/Make.olcf commit 7a06ff43a2166572080e90d9370d7672bf3d7cee Author: Luna Lin Date: Fri Feb 1 18:13:15 2019 -0500 Added OpenACC + OpenMP versions to HeatEquation_EX1_C and reorganize the tutorial directory. Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/Make.package Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/mykernel.H Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/run.ascent Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/run.nocuda.script Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/run.summit Tutorials/GPU/HeatEquation_EX1_C/Exec/CUDA/run.summitdev Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/Make.package Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/myfunc_F.H Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/mykernel.F90 Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenACC/run.summitdev Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/Make.package Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/myfunc_F.H Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/mykernel.F90 Tutorials/GPU/HeatEquation_EX1_C/Exec/OpenMP/run.summitdev Tutorials/GPU/HeatEquation_EX1_C/Make.HEAT Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit a740f9b86f4bfbb9ad28e06da4a7125e66b7c252 Author: Weiqun Zhang Date: Fri Feb 1 15:04:42 2019 -0800 pinned version of AsyncFabImpl Src/Base/AMReX_CudaAsyncFabImpl.H Src/Base/AMReX_CudaAsyncFabImpl.cpp commit 4f063cc5889f719d01fd7edf86aa2a98a40e3a8b Author: WeiqunZhang Date: Fri Feb 1 14:11:22 2019 -0800 Add zenodo badge README.md commit 12f84640c4e17ccc2ba04d88b521e46e944784c0 Author: Alice Harpole Date: Fri Feb 1 17:00:20 2019 -0500 add breathe to .travis.yml file .travis.yml commit db29acd46f834ccc4f7a066280e807380508b3a9 Merge: eaa846041 e5cba96da Author: Alice Harpole Date: Fri Feb 1 16:56:05 2019 -0500 fixed merge conflicts commit eaa8460411c871c5133c2bbbfb174f4deaf4f31a Author: Alice Harpole Date: Fri Feb 1 16:48:16 2019 -0500 cleaned up some errors Src/Amr/AMReX_Derive.H Src/Amr/AMReX_Extrapolater.H Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateDescriptor.H Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_FluxReg_1D_C.H Src/AmrCore/AMReX_FluxReg_2D_C.H Src/AmrCore/AMReX_FluxReg_3D_C.H Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_TagBox.H Src/Base/AMReX_BCRec.H Src/Base/AMReX_NFiles.H Src/Base/AMReX_ParmParse.H Src/Base/AMReX_parstream.H Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_Mask.H Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_Tagging.F90 Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/Particle/AMReX_Particle.H commit 378ad53a4483c92fb32f6faa9f2da89f5e6d1974 Author: Weiqun Zhang Date: Fri Feb 1 13:15:02 2019 -0800 switch to use pinned memory for fab be default Src/Base/AMReX_BaseFab.H Tools/GNUMake/Make.defs commit e5cba96da276752f1da288294598d51037f64dea Merge: 2fa070459 27c11262d Author: Andrew Myers Date: Fri Feb 1 13:12:24 2019 -0800 Merge pull request #402 from MaxThevenet/splitting Add stuff for splitting commit 27c11262db0b09c304bbe5933ed04e749a2af7da Author: MaxThevenet Date: Fri Feb 1 12:59:58 2019 -0800 typo Src/Particle/AMReX_Particle.H commit df1cc103a293347f0ce18b42913a3a040ef51d97 Author: Alice Harpole Date: Fri Feb 1 15:43:50 2019 -0500 doxygenised fortran files already containing documentation Docs/sphinx_documentation/make_api.py Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_io_mod.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_LO_UTIL.F90 Src/EB/AMReX_EB_Tagging.F90 Src/EB/AMReX_EB_geometry.F90 Src/EB/AMReX_EB_levelset_F.F90 Src/Extern/CVODE/cvode_interface.f90 Src/Extern/CVODE/fnvector_serial.f90 Src/Extern/CVODE/integrator_stats.f90 Src/Extern/CVODE/sundials_fdlsmat.f90 Src/Extern/Conduit/AMReX_Conduit_Blueprint.H Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_UTIL.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec4_2D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec4_3D.F90 commit d933e35ac950857ecc801b461d5b91abf6f840e1 Author: Brandon Runnels Date: Fri Feb 1 13:20:22 2019 -0700 fixed error causing crse level to fail to converge Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit af7616af464bca2f02c150e2216a3cd0c3d6b967 Author: Alice Harpole Date: Fri Feb 1 14:41:47 2019 -0500 run on all header files (which already had some documentation) Docs/Doxygen/doxygen.conf Docs/sphinx_documentation/add_doxy_headers.py Docs/sphinx_documentation/make_api.py Src/Extern/amrdata/AMReX_DataServices.H Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_CellMG4/AMReX_ABec2.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/SDC/AMReX_SDCstruct.H commit 2fa070459ebdc27aa9af0e962889469bd765a1b8 Author: Ann Almgren Date: Fri Feb 1 11:34:06 2019 -0800 Fix name of file in CMakeLists.txt Src/Boundary/CMakeLists.txt commit 658af89cea4f87f32cb1e77076a8b9ddc6698a3c Merge: 44132463b 00bfaceaa Author: Weiqun Zhang Date: Fri Feb 1 14:16:09 2019 -0500 Merge branch 'development' into weiqun/gpu commit 00bfaceaa00a3bad47088fe9c0ac0bb20f06dcb4 Author: Weiqun Zhang Date: Fri Feb 1 14:15:44 2019 -0500 add -lmpi_ibm for summit Tools/GNUMake/sites/Make.olcf commit 44132463b990bd212d79031ef3c2d44671170911 Merge: 6f7c6d09e 6497c8137 Author: Weiqun Zhang Date: Fri Feb 1 13:52:48 2019 -0500 Merge branch 'development' into weiqun/summit-comm commit 6497c81373903c7fc3c355260c3f7764ca56bf04 Merge: e999e81d8 50706d7d7 Author: Weiqun Zhang Date: Fri Feb 1 10:50:48 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 50706d7d78c7d9b2553e6f8604b645758f2a4c55 Merge: 4a0433e56 ac4cb6c16 Author: Andrew Myers Date: Fri Feb 1 13:49:19 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4a0433e56da53822caa478ab4c0641bd989c09a3 Author: Andrew Myers Date: Fri Feb 1 13:49:02 2019 -0500 remove redundant code Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp commit e999e81d81d49b947bf0bd397bf9bcc7b2e01589 Author: Weiqun Zhang Date: Fri Feb 1 10:46:48 2019 -0800 use isGpuPtr instead of isHostPtr to allow BaseFab in pinned memory; some updates due to Array4 changes Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interpolater.cpp Src/Boundary/AMReX_InterpBndryData_1D_K.H Src/Boundary/AMReX_InterpBndryData_2D_K.H Src/Boundary/AMReX_InterpBndryData_3D_K.H Src/Boundary/AMReX_MultiMask.H Src/Boundary/AMReX_YAFluxRegister_1D_K.H Src/Boundary/AMReX_YAFluxRegister_2D_K.H Src/Boundary/AMReX_YAFluxRegister_3D_K.H Src/LinearSolvers/MLMG/AMReX_MG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H Tutorials/GPU/CNS/Source/CNS_bcfill.cpp commit 65a6028d77f49de5e492a4ce776631d173633488 Merge: ac4cb6c16 9274fb8ed Author: Weiqun Zhang Date: Fri Feb 1 10:01:09 2019 -0800 Merge branch 'weiqun/gpu' into development commit ac4cb6c164560d8a6ba8186f67a0b1c393300bd4 Author: Weiqun Zhang Date: Fri Feb 1 09:38:07 2019 -0800 fix the one that is supposed to use macro Tutorials/GPU/Launch/main.cpp commit 9e9ab758cf9786d00c192b6e27143f3b56befdef Merge: 262715e65 680b9ac0c Author: Weiqun Zhang Date: Fri Feb 1 09:23:01 2019 -0800 Merge branch 'weiqun/launch' into development commit 262715e6548a5e2fff161040c6cdbf5bfc3c3d27 Author: Weiqun Zhang Date: Fri Feb 1 09:00:51 2019 -0800 update CHANGES CHANGES commit ecb2ea1e35e8becafbac7d2c2a6324c1114c715b Merge: 8cc1f62d9 8ec473785 Author: Weiqun Zhang Date: Fri Feb 1 08:52:14 2019 -0800 Merge branch 'development' commit 038dee59900805978f860ba4faca1f920b2d4b48 Author: MaxThevenet Date: Fri Feb 1 08:22:35 2019 -0800 special id for splitting Src/Particle/AMReX_Particle.H Src/Particle/AMReX_Particles.H commit 8ec4737855cffa0f779327079486a51efa93d8c9 Merge: 530d36e9b 4ca00e575 Author: Johannes Blaschke Date: Thu Jan 31 17:53:54 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 530d36e9b10efb044d4f6e5fbce84b839d77fb61 Author: Johannes Blaschke Date: Thu Jan 31 17:53:49 2019 -0800 fix spelling Docs/sphinx_documentation/source/EB.rst commit 4ca00e575b82c485abf686f2eea82223a6395958 Merge: a710d3f57 bd2d36dad Author: Andrew Myers Date: Thu Jan 31 20:17:40 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a710d3f57337dadd5f6c8aedacf4308c3c96f7ef Author: Andrew Myers Date: Thu Jan 31 20:17:20 2019 -0500 use pinned memory for send / rcv buffers in Redistribute Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 680b9ac0c1fb3af2b9614c0e348d123d20558707 Author: Weiqun Zhang Date: Thu Jan 31 16:29:14 2019 -0800 change the const behavior of Array4 Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_COORDSYS_1D_C.H Src/Base/AMReX_COORDSYS_2D_C.H Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_FabArray.H Src/Boundary/AMReX_FabSet.H Tutorials/GPU/CNS/Exec/RT/cns_prob.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_tagging.H Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Source/mykernel.H Tutorials/GPU/Launch/main.cpp Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H commit bd2d36dad1fd7cba1939403ebc307ebc307aaf6d Author: Johannes Blaschke Date: Thu Jan 31 15:26:43 2019 -0800 thiis kind of manual buffering is not necessary Docs/sphinx_documentation/source/EB.rst Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp commit 660fd450f940977e28b3e5b83d7f4746de763042 Author: Alice Harpole Date: Thu Jan 31 17:41:55 2019 -0500 Ran on Particles folder Src/Particle/AMReX_LoadBalanceKD.H Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParGDB.H Src/Particle/AMReX_Particle.H Src/Particle/AMReX_Particles.H commit d8715ee08ae31fffaaeb55e2c4caab1c26cd22d2 Author: Alice Harpole Date: Thu Jan 31 17:29:27 2019 -0500 ran on EB folder Src/EB/AMReX_EB2_IF_Box.H Src/EB/AMReX_EB2_IF_Cylinder.H Src/EB/AMReX_EB2_IF_Ellipsoid.H Src/EB/AMReX_EB2_IF_Polynomial.H Src/EB/AMReX_EB2_IF_Spline.H Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBSupport.H Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.H commit d110e05ba8dec09ffb43831e808793283e5972e3 Merge: a0c21e62a f0e3c9b45 Author: Johannes Blaschke Date: Thu Jan 31 14:25:48 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit a0c21e62a224de3dfb552f5b664d11b9831145aa Author: Johannes Blaschke Date: Thu Jan 31 14:25:44 2019 -0800 move volfrac tagging out of levelset core Src/EB/AMReX_EBAmrUtil.H Src/EB/AMReX_EBAmrUtil.cpp Src/EB/AMReX_EBAmrUtil_F.H Src/EB/AMReX_EBAmrUtil_nd.F90 Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_Tagging.F90 commit 122900c70c565b5c0b7e5b69239f2c1c9a0db548 Author: Alice Harpole Date: Thu Jan 31 17:15:40 2019 -0500 ran on Boundary folder Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BoundCond.H Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_MacBndry.H Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_YAFluxRegister.H Src/EB/AMReX_distFcnElement.H commit e98e0fecf882211ff2e78380a1faad3287d754f1 Author: Alice Harpole Date: Thu Jan 31 16:58:05 2019 -0500 ran on Base folder Src/Base/AMReX_BLBackTrace.H Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseUmap.H Src/Base/AMReX_Box.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxDomain.H Src/Base/AMReX_BoxIterator.H Src/Base/AMReX_BoxList.H Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CudaContainers.H Src/Base/AMReX_CudaRange.H Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabConv.H Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_LayoutData.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_Machine.H Src/Base/AMReX_MemPool.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_NFiles.H Src/Base/AMReX_Orientation.H Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParmParse.H Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealVect.H Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_VisMF.H Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_parstream.H commit 030b6b9d7e1d38533f4adcb7f93d5c9dd56b36c1 Merge: e435b632b f0e3c9b45 Author: Weiqun Zhang Date: Thu Jan 31 16:47:32 2019 -0500 Merge branch 'development' into weiqun/launch commit f0e3c9b45ae447719329395f044e4f751d280fea Author: Andrew Myers Date: Thu Jan 31 16:27:41 2019 -0500 use the same cuda aware mpi flag as the mesh data Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 6f7c6d09ef2421d12c0857bf19aa36cd9667a626 Merge: dc91fbc9c 89ed30720 Author: Weiqun Zhang Date: Thu Jan 31 16:18:55 2019 -0500 Merge branch 'development' into weiqun/summit-comm Conflicts: Src/Base/AMReX_FabArrayBase.H commit 89ed30720a1324e65d030e19b53cb7c78316f84f Author: Weiqun Zhang Date: Thu Jan 31 13:13:37 2019 -0800 disabel cuda aware mpi by default Src/Base/AMReX_ParallelDescriptor.cpp commit 26d8f6a5a421b9eb3ba06bb4a06eba1194aac9fa Author: Weiqun Zhang Date: Thu Jan 31 15:59:48 2019 -0500 Cuda --> Gpu Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit fd51cfe0b4e545d51543a4a19b0930a049064992 Author: Weiqun Zhang Date: Thu Jan 31 15:54:29 2019 -0500 use pinned memory when amrex.use_cuda_aware_mpi is false Src/Base/AMReX.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit 32efa0c72f9d214f039fd1629c6d26369cc6e9c0 Author: Alice Harpole Date: Thu Jan 31 15:43:32 2019 -0500 ran on AmrCore folder Docs/sphinx_documentation/add_doxy_headers.py Docs/sphinx_documentation/make_api.py Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_Cluster.H Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_FluxReg_1D_C.H Src/AmrCore/AMReX_FluxReg_2D_C.H Src/AmrCore/AMReX_FluxReg_3D_C.H Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_TagBox.H commit 773ac11c7a10541de7c3ab2f0dd77ec9f43b268c Author: Alice Harpole Date: Thu Jan 31 15:05:06 2019 -0500 run script on Amr folder Docs/sphinx_documentation/add_doxy_headers.py Docs/sphinx_documentation/source/conf.py Src/Amr/AMReX_Amr.H Src/Amr/AMReX_AuxBoundaryData.H Src/Amr/AMReX_Derive.H Src/Amr/AMReX_LevelBld.H Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateDescriptor.H Src/Base/AMReX_FPC.cpp Src/Base/AMReX_RealVect.H commit dc91fbc9c09c1d34364c05271a3b9dcaf20295ee Author: Weiqun Zhang Date: Thu Jan 31 12:40:02 2019 -0500 clean up unused features in fabarray communications Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Tests/FillBoundaryComparison/main.cpp commit d0229e9bfb4a98cd1433197e261caaa7e148ea5f Author: Andrew Myers Date: Wed Jan 30 23:35:59 2019 -0500 add tupleAdd functor Src/Particle/AMReX_Functors.H Src/Particle/AMReX_ParticleContainerI.H commit 44da9dd9b653b220e0f59137d432eb21dae192e5 Author: Andrew Myers Date: Wed Jan 30 23:21:32 2019 -0500 fix non-CUDA compilation Src/Particle/AMReX_ParticleContainerI.H commit 95cdb55600fb623ea2d3c03b7f5f4aa50e8d04f7 Merge: c386c6b8a 022f111d1 Author: Andrew Myers Date: Wed Jan 30 22:19:01 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c386c6b8a7aaa409c760fe893df5873a48c40d51 Author: Andrew Myers Date: Wed Jan 30 22:13:53 2019 -0500 implement option for non cuda-aware mpi Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit afc67311339dd7e2fe6961bf2818c0e9df04d077 Author: Michele Rosso Date: Wed Jan 30 21:04:00 2019 -0500 CMake: replace function to evaluate genex Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake commit 1fdb55f49206e86de87a73ff45d2b448def775ca Author: Andrew Myers Date: Wed Jan 30 19:38:23 2019 -0500 remove some misleading timers from GPU routines. Src/Particle/AMReX_ParticleContainerI.H commit c65395e911b9a6481d4cfade7ccba23e892cf4d2 Merge: 51fed6a4e 022f111d1 Author: Michele Rosso Date: Wed Jan 30 17:53:09 2019 -0500 Merge branch 'development' into mr/cmake commit 2c197ad3d5276e471c306ebb783b0ec77ed4fff6 Author: Andrew Myers Date: Wed Jan 30 17:32:08 2019 -0500 some more async copy Src/Particle/AMReX_ParticleContainerI.H commit e435b632b7563c77fdac50e6146397cf943c5c8b Author: Weiqun Zhang Date: Wed Jan 30 13:32:47 2019 -0800 use auto; add profilers in launch tutorial Src/Base/AMReX_Array.H Src/Base/AMReX_CudaLaunch.H Tutorials/GPU/Launch/MyKernel_F.H Tutorials/GPU/Launch/main.cpp commit 6914821c7d79c4cc7ebcb089a97e4f0c02fdd648 Author: Alice Harpole Date: Wed Jan 30 16:25:35 2019 -0500 Fixed indentation of comments for add_doxy_headers so it now works almost correctly for Amr/AMReX_Derive.H Docs/sphinx_documentation/add_doxy_headers.py commit 2c7187b7870bde3e58bb1fd4fe24ad62afc427cd Author: Andrew Myers Date: Wed Jan 30 16:25:27 2019 -0500 use some Async mem copies Src/Particle/AMReX_ParticleContainerI.H commit b8423b87dc3babbb50a0673239b2957ebec73630 Author: Alice Harpole Date: Wed Jan 30 15:09:40 2019 -0500 make_api.py is now recursive so will work if directories have subdirectories Docs/sphinx_documentation/Makefile Docs/sphinx_documentation/make_api.py commit 022f111d15813839ae9b028e690ec070792cc419 Author: Kevin Gott Date: Wed Jan 30 14:24:22 2019 -0500 Bug fix. Tests/GPU/buildHybrid/GNUmakefile commit 52e21fe56b1e5ad1cd25471fe5f2b2a3f37e1075 Author: Weiqun Zhang Date: Wed Jan 30 11:17:02 2019 -0800 add force inline Src/Base/AMReX_CudaLaunch.H commit cd49be0195aec5d5f59a405c2113e07985df65cf Author: Andrew Myers Date: Wed Jan 30 13:53:35 2019 -0500 first attempt at a less thrust-intensive redistribute Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 51fed6a4e814237e5ee4aab37346824773aea86f Author: Michele Rosso Date: Wed Jan 30 13:03:11 2019 -0500 CMake: move handling of SENSEI lib to config function Src/Extern/SENSEI/CMakeLists.txt Tools/CMake/AMReX_Config.cmake commit 12ae5398e853ff514eda0565e235885e052d2ad1 Author: Alice Harpole Date: Wed Jan 30 12:14:39 2019 -0500 Added doxygen and breathe to docs build to autogenerate the API Docs/Doxygen/doxygen.conf Docs/sphinx_documentation/Makefile Docs/sphinx_documentation/make_api.py Docs/sphinx_documentation/source/conf.py Docs/sphinx_documentation/source/index.rst commit 913a912585f16b2dda20fb9badd064654e652962 Author: Weiqun Zhang Date: Tue Jan 29 21:15:35 2019 -0800 use rvalue in launch_host Src/Base/AMReX_CudaLaunch.H commit 3109c0f4a3864d98a2564739070ca3dc4b51cd88 Author: Weiqun Zhang Date: Tue Jan 29 20:49:16 2019 -0800 use rvalue reference for lambda parameter for cpu version Src/Base/AMReX_CudaLaunch.H Tutorials/GPU/Launch/main.cpp commit 60a481cb343eddbddde20f1d76f769820a2a0e15 Author: Weiqun Zhang Date: Tue Jan 29 19:56:12 2019 -0800 add amrex::launch, amrex::ParallelFor and amrex:For functions Src/Base/AMReX_CudaLaunch.H Tutorials/GPU/Launch/main.cpp commit 4c506c52b8b6ffa123b4211657083818170c1846 Merge: 485205d81 2c5c89c06 Author: Brandon Runnels Date: Tue Jan 29 17:59:46 2019 -0700 Merge branch 'nodeghostcells' of github.com:AMReX-Codes/amrex into nodeghostcells commit 485205d8155ca2ca9f8ffc5c51230a41c1c6b547 Author: Brandon Runnels Date: Tue Jan 29 17:59:21 2019 -0700 wip - implementing update of ghost cells Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit ff219c077f9bc93b9d2fb46530d94f15835db5a0 Author: Andrew Myers Date: Tue Jan 29 19:08:24 2019 -0500 remove empty entries from m_not_ours before calling RedistributeMPIGPU Src/Particle/AMReX_ParticleContainerI.H commit 9274fb8ed97b7a5e678f342a0f2833f25307392a Merge: dab1f0acb 5e9340795 Author: Weiqun Zhang Date: Tue Jan 29 15:40:23 2019 -0800 Merge branch 'development' into weiqun/gpu commit f6908ca1f7272c39a5124071fa2c20ff10fb1ae1 Author: Michele Rosso Date: Tue Jan 29 18:19:22 2019 -0500 CMake: refactor how compile definitions are handled. Src/CMakeLists.txt Src/EB/CMakeLists.txt Src/Extern/ProfParser/CMakeLists.txt Src/Extern/SENSEI/CMakeLists.txt Src/F_Interfaces/CMakeLists.txt Src/Particle/CMakeLists.txt Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_ThirdPartyProfilers.cmake Tools/CMake/AMReX_Utils.cmake commit dab1f0acbf800697ebf98d97df01d8eb7e1831b7 Author: Weiqun Zhang Date: Tue Jan 29 14:18:45 2019 -0800 2D InterpBndryData: make it the same as Fortran Src/Boundary/AMReX_InterpBndryData_2D_K.H Src/Boundary/AMReX_LOUtil_K.H Src/Boundary/CMakeLists.txt Src/Boundary/Make.package commit 5e9340795ac8b538a41a43ef367f070531cf196a Author: Kevin Gott Date: Tue Jan 29 16:11:15 2019 -0500 AMReX independent CUDA build tests: one using only C++ with lots of compiler options, one with hybrid Fortran & C++ that focuses on pgfortran, as done in AMReX. Tests/GPU/buildHybrid/GNUmakefile Tests/GPU/buildHybrid/MyKernel.H Tests/GPU/buildHybrid/MyKernel.cpp Tests/GPU/buildHybrid/MyKernelB.H Tests/GPU/buildHybrid/MyKernelB.cpp Tests/GPU/buildHybrid/MyKernel_F.F90 Tests/GPU/buildHybrid/MyKernel_F.H Tests/GPU/buildHybrid/Readme Tests/GPU/buildHybrid/main.cpp Tests/GPU/buildHybrid/run.script Tests/GPU/buildTest/GNUmakefile Tests/GPU/buildTest/MyKernel.H Tests/GPU/buildTest/MyKernel.cpp Tests/GPU/buildTest/MyKernelB.H Tests/GPU/buildTest/MyKernelB.cpp Tests/GPU/buildTest/Readme Tests/GPU/buildTest/main.cpp Tests/GPU/buildTest/run.script commit 96337e58054314ce1d3667d6c2b3a98a42e56b60 Author: Weiqun Zhang Date: Tue Jan 29 12:59:15 2019 -0800 InterpBndryData: fix a sign Src/Boundary/AMReX_InterpBndryData_3D_K.H commit 17deff46f11b22706d6882eeb08a2f123d5e4493 Author: Andrew Myers Date: Tue Jan 29 11:22:59 2019 -0800 add a private pure virtual function for doing custom behavior after a particle is location is Redistribute(). Will be used in WarpX to do particle splitting /merging. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit c9877df05f54cfa3f085d31a50d550f28b8d52c6 Author: Weiqun Zhang Date: Tue Jan 29 11:12:23 2019 -0800 InterpBndryData: fix bugs Src/Boundary/AMReX_InterpBndryData_2D_K.H Src/Boundary/AMReX_InterpBndryData_3D_K.H commit 5c9c34429f6d43d906a363b4d51847b316966f2e Author: Michele Rosso Date: Tue Jan 29 13:52:48 2019 -0500 CMake: more changes to support CUDA. * Add architecture detection * Split compiler flags over multiple files based on the compiler ID * Start adding GPU tests. WARNING: this commit still has a linking problem when CUDA is enabled. CMakeLists.txt Src/CMakeLists.txt Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_Utils.cmake Tools/CMake/comps/AMReX_Cray.cmake Tools/CMake/comps/AMReX_GNU.cmake Tools/CMake/comps/AMReX_Intel.cmake Tools/CMake/comps/AMReX_NVIDIA.cmake Tools/CMake/comps/AMReX_PGI.cmake Tools/CMake/select_gpu_arch.cmake Tutorials/GPU/Advection_AmrCore/CMakeLists.txt Tutorials/GPU/Launch/CMakeLists.txt commit 81326952efa4bbfba36be1d4c8545d954f0958c1 Author: Johannes Blaschke Date: Tue Jan 29 10:36:31 2019 -0800 cleanup Src/EB/AMReX_EB_LSCoreI.H commit 1de012cddab052ff8d9cdeade920082302f829d0 Author: Weiqun Zhang Date: Tue Jan 29 09:32:13 2019 -0800 InterpBndryData: pass component index to kernels Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_InterpBndryData_1D_K.H Src/Boundary/AMReX_InterpBndryData_2D_K.H Src/Boundary/AMReX_InterpBndryData_3D_K.H Src/Boundary/AMReX_YAFluxRegister.cpp Src/Boundary/AMReX_YAFluxRegister_1D_K.H Src/Boundary/AMReX_YAFluxRegister_2D_K.H Src/Boundary/AMReX_YAFluxRegister_3D_K.H commit c98a6aa046bd5dad80ae62a6e070d05ee340b917 Author: Weiqun Zhang Date: Tue Jan 29 09:11:19 2019 -0800 using Cuda::AsyncFab and CudaAsyncArray in amrex namespace Docs/sphinx_documentation/source/GPU.rst Src/Amr/AMReX_StateData.cpp Src/AmrCore/AMReX_Interpolater.cpp Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_PhysBCFunct.H Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp commit dfaf4a1e6cadb73e38d54501def34b25772eccb8 Author: Weiqun Zhang Date: Tue Jan 29 09:02:01 2019 -0800 operator<< for printing bounds of Array4 Src/Base/AMReX_Array.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp commit d1726a8d1f5186e6f86a4b711b419c42d3eb7449 Author: Weiqun Zhang Date: Mon Jan 28 21:04:30 2019 -0800 fix another bug in new InterpBndryData: refine is not always 2 Src/Boundary/AMReX_InterpBndryData_1D_K.H Src/Boundary/AMReX_InterpBndryData_2D_K.H Src/Boundary/AMReX_InterpBndryData_3D_K.H commit c5480f04d60f39d0086f15f2da17896f04e4436f Author: Weiqun Zhang Date: Mon Jan 28 18:53:53 2019 -0800 fix bug in new InterpBndryData Src/Boundary/AMReX_InterpBndryData.cpp commit 850752ffa5743f989f7f71a8be7f079fbb9691d4 Author: Weiqun Zhang Date: Mon Jan 28 18:42:23 2019 -0800 minor optimization by avoiding BoxArray's virtual function Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_MultiMask.cpp Src/Boundary/AMReX_YAFluxRegister.cpp commit b8aeda07da7eb43021a7281dd8389020530712d7 Author: Weiqun Zhang Date: Mon Jan 28 16:59:04 2019 -0800 InterpBndryData on gpu Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_F.H Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_InterpBndryData_1D_K.H Src/Boundary/AMReX_InterpBndryData_2D_K.H Src/Boundary/AMReX_InterpBndryData_3D_K.H Src/Boundary/AMReX_InterpBndryData_K.H Src/Boundary/AMReX_MacBndry.cpp Src/Boundary/AMReX_MultiMask.H Src/Boundary/CMakeLists.txt Src/Boundary/Make.package commit c30c1bb5af40464497dbd5e9d17c8613345dd81e Merge: 19c4b8eda a9f90d613 Author: Johannes Blaschke Date: Mon Jan 28 13:21:56 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 19c4b8edac7f46267ca2bd40468a65570dd92472 Author: Johannes Blaschke Date: Mon Jan 28 13:21:53 2019 -0800 finish documenting levelset Docs/sphinx_documentation/source/EB.rst commit a9f90d613a7cdff3f00c5fa2ecc9f59a2c61f278 Merge: bbf87ed4e 2796aa3aa Author: Andrew Myers Date: Mon Jan 28 10:50:07 2019 -0800 Merge pull request #401 from ylunalin/new_particle_tutorials Add OpenMP offloading directory in EMPIC. commit 1adf695a251ef804d8d29116d02d8f3a69d87ccc Author: Weiqun Zhang Date: Mon Jan 28 10:29:16 2019 -0800 hopefully make omp and cuda more compatible in MFIter Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 798909a1dd5968c9fc8f5e879b7b42ce1c3dbd73 Author: Weiqun Zhang Date: Sun Jan 27 17:43:40 2019 -0800 YAFluxRegister: fix tiling bug Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_YAFluxRegister.cpp commit e88f2b0f7e5fafc1ccf46bba4c2bdf6d9a84ccf6 Author: Weiqun Zhang Date: Sun Jan 27 15:38:21 2019 -0800 fix index bug in YAFluxRegister gpu kernel Src/Boundary/AMReX_YAFluxRegister_1D_K.H Src/Boundary/AMReX_YAFluxRegister_2D_K.H Src/Boundary/AMReX_YAFluxRegister_3D_K.H commit 5c473f96dfc71ac0c8945a61df22ede7371667ee Author: Weiqun Zhang Date: Sun Jan 27 13:31:24 2019 -0800 finish YAFluxRegister on gpu Src/Boundary/AMReX_YAFluxRegister.H Src/Boundary/AMReX_YAFluxRegister.cpp Src/Boundary/AMReX_YAFluxRegister_1D_K.H Src/Boundary/AMReX_YAFluxRegister_1d.F90 Src/Boundary/AMReX_YAFluxRegister_2D_K.H Src/Boundary/AMReX_YAFluxRegister_2d.F90 Src/Boundary/AMReX_YAFluxRegister_3D_K.H Src/Boundary/AMReX_YAFluxRegister_3d.F90 Src/Boundary/AMReX_YAFluxRegister_F.H Src/Boundary/AMReX_YAFluxRegister_K.H Src/Boundary/AMReX_YAFluxRegister_nd.F90 Src/Boundary/CMakeLists.txt Src/Boundary/Make.package Src/EB/AMReX_EBFluxRegister_nd.F90 commit bbf87ed4e6f3b814eae555f840db0499f8ab6230 Author: Ann Almgren Date: Sat Jan 26 20:07:02 2019 -0800 Revert "using async Iters for Nyx first attempt" This reverts commit 68e3eed7aeb8ed9d25df9a5e4b598f3cc6fbb725. Src/LinearSolvers/MLMG/AMReX_MacProjector.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit 461f3279c096dc1a4b8c2d2bf215902befe58b8b Author: Johannes Blaschke Date: Fri Jan 25 21:37:58 2019 -0800 added explanation on using fortran level-set modules Docs/sphinx_documentation/source/EB.rst commit 3a100440f955bba5f9f73cbf3d1efb429cd49dd5 Merge: b69bcba43 f8626ffb4 Author: Johannes Blaschke Date: Fri Jan 25 20:46:44 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b69bcba43e81bfe538970740f50ecaa2295c3cb9 Author: Johannes Blaschke Date: Fri Jan 25 20:43:20 2019 -0800 fix indentation Docs/sphinx_documentation/source/EB.rst commit f8626ffb4dfb5c4da3e63fad4e8106d551cded35 Merge: 4ca35b5f6 4d7f1a2bc Author: Johannes Blaschke Date: Fri Jan 25 20:42:40 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 4d7f1a2bcc6372787a65e099034041346a849f33 Merge: db64b5720 698d2f8c9 Author: Tan Nguyen 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Src/AmrTask/tutorials/Apps/Nyx_hydro/Util/sample_run_scripts/run_Nyx_LyA_Cori.sh Src/AmrTask/tutorials/Apps/Nyx_hydro/Util/zhi_converter/GNUmakefile Src/AmrTask/tutorials/Apps/Nyx_hydro/Util/zhi_converter/Make.package Src/AmrTask/tutorials/Apps/Nyx_hydro/Util/zhi_converter/main.cpp Src/AmrTask/tutorials/Apps/Nyx_hydro/copyright.txt Src/AmrTask/tutorials/Apps/Nyx_hydro/license.txt commit 698d2f8c92445dcd1d72a9f464f6e2e70f547f6a Merge: e83998dd7 68e3eed7a Author: Andrew Myers Date: Fri Jan 25 21:00:57 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e83998dd7e4562a7b450513c436c6ada7bf2ba30 Author: Andrew Myers Date: Fri Jan 25 21:00:39 2019 -0500 use the pooling memory allocator for thrust::gather calls as well Src/Particle/AMReX_ParticleContainerI.H commit 5da9d1716156384b2384734db0a8e3ebc3e18359 Author: Andrew Myers Date: Fri Jan 25 20:42:07 2019 -0500 cache grid_begin and grid_end arrays to avoid reallocation. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 0976e0bbc7e427b2f6dedf80dd305b29a69757e1 Author: Weiqun Zhang Date: Fri Jan 25 17:24:52 2019 -0800 YAFluxRegiser: more on gpu Src/Boundary/AMReX_YAFluxRegister.cpp commit 4ca35b5f6784fc07eeb246d70064bc0802c61220 Merge: efff562bb 68e3eed7a Author: Johannes Blaschke Date: Fri Jan 25 17:21:33 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit efff562bb28f0162e7c7ec963408c90aeaf820b3 Author: Johannes Blaschke Date: Fri Jan 25 17:21:25 2019 -0800 update level-set docs Docs/sphinx_documentation/source/EB.rst commit b5c54c281495784b568f1d6fa2711e64343036e9 Author: Weiqun Zhang Date: Fri Jan 25 16:27:19 2019 -0800 start YAFluxRegister on gpu Src/Boundary/AMReX_MultiMask.cpp Src/Boundary/AMReX_YAFluxRegister.cpp Src/Boundary/AMReX_YAFluxRegister_1D_K.H Src/Boundary/AMReX_YAFluxRegister_2D_K.H Src/Boundary/AMReX_YAFluxRegister_3D_K.H 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Src/AmrTask/tutorials/Apps/Nyx_hydro/Util/sample_run_scripts/run_Nyx_LyA_Cori.sh Src/AmrTask/tutorials/Apps/Nyx_hydro/Util/zhi_converter/GNUmakefile Src/AmrTask/tutorials/Apps/Nyx_hydro/Util/zhi_converter/Make.package Src/AmrTask/tutorials/Apps/Nyx_hydro/Util/zhi_converter/main.cpp Src/AmrTask/tutorials/Apps/Nyx_hydro/copyright.txt Src/AmrTask/tutorials/Apps/Nyx_hydro/license.txt commit cb7c327c00a86d12058dc16f7c6bcac915033ad9 Author: Weiqun Zhang Date: Fri Jan 25 15:24:20 2019 -0800 Mask on gpu Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_Mask.cpp Src/Boundary/AMReX_MultiMask.cpp commit 9732331f3d5c28d47ef8dad3248c09ba4477a80e Author: Johannes Blaschke Date: Fri Jan 25 14:59:57 2019 -0800 remove unused file Docs/sphinx_documentation/source/Tutorials_Chapter.rst commit f6cafe2db54939bad4c69d897cca88c9181f2b47 Merge: 13935cfba 3f204392a Author: Johannes Blaschke Date: Fri Jan 25 14:55:52 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 13935cfba537ab7ec8685484574c7de061546fa8 Author: Johannes Blaschke Date: Fri Jan 25 14:55:48 2019 -0800 1. add levelset doxygen, 2. clean up eb docs formatting, 3. fix gpu docs code highlighting Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/EB.rst Docs/sphinx_documentation/source/GPU.rst Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp commit 8cc1f62d9c3a924e4ea8a968567cb140f0d977fa Author: Ann Almgren Date: Fri Jan 25 14:45:02 2019 -0800 Last ORCID has been added .zenodo.json commit 721a8fff6fc57d28f1c50b9d3eb1b3647782ba90 Author: Ann Almgren Date: Fri Jan 25 14:38:17 2019 -0800 Add one more ORCID .zenodo.json commit 3f204392a3405423848b8a7628da889caf018442 Author: Weiqun Zhang Date: Fri Jan 25 13:05:42 2019 -0800 add missing grownnodaltilebox Src/Base/AMReX_MFIter.cpp commit a3939152f67e072dc74305695152f7c581e15190 Author: Weiqun Zhang Date: Fri Jan 25 12:38:54 2019 -0800 update FabSet and BndryRegister Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_FabSet.cpp commit 7652fef16944e7d6c85f0512118dae8e05cfb003 Author: Weiqun Zhang Date: Fri Jan 25 10:34:40 2019 -0800 fix compiler warning about shadow Src/Base/AMReX_RealBox.H commit 2796aa3aa3889fa4855aafe2df8dcae4b064e8e5 Author: Luna Lin Date: Fri Jan 25 13:05:15 2019 -0500 Add OpenMP offloading directory in EMPIC. Moved C++ header files to Source/ to be shared. Got rid of FTOC macro (use name binding), as well as function definition for PushParticlePosition (never used) in OpenACC/. Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/inputs Tutorials/Particles/ElectromagneticPIC/Exec/OpenMP/run.summitdev Tutorials/Particles/ElectromagneticPIC/Source/EMParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Source/Evolve.H Tutorials/Particles/ElectromagneticPIC/Source/Make.package commit edd1dc82660cdb4edaf7fe66c289471c3e4a84de Author: Weiqun Zhang Date: Thu Jan 24 16:12:29 2019 -0800 fix virtual override Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H commit 4fb96078524e95f51a32494ae6ca020d409332ac Author: Weiqun Zhang Date: Thu Jan 24 16:09:59 2019 -0800 some fixes Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 13d9cf7da79610d0359863c49bc0c627477a345a Author: Weiqun Zhang Date: Thu Jan 24 16:00:50 2019 -0800 make functions public for cuda Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H commit fb6d8d718f2832152f62bb2ee688e1caa10b3c35 Author: Ann Almgren Date: Thu Jan 24 15:24:31 2019 -0800 Re-add comma that I accidentally deleted .zenodo.json commit 96d17b9ad02e39e595b777421a377b0da6f55cca Merge: bbf111d07 ef7bf254e Author: Ann Almgren Date: Thu Jan 24 15:21:36 2019 -0800 Merge branch 'master' of https://www.github.com/amrex-codes/amrex commit bbf111d0733f0dd5bbf8ed8688cf5d9d592db759 Author: Ann Almgren Date: Thu Jan 24 15:19:53 2019 -0800 add more data .zenodo.json commit ef7bf254e68ac13908d9de7bdee42ef02efbcc71 Author: Weiqun Zhang Date: Thu Jan 24 15:12:53 2019 -0800 fix format .zenodo.json commit d0b275c69e2214490ffd9a86871d293254965687 Author: Ann Almgren Date: Thu Jan 24 15:06:43 2019 -0800 Updated with Graves, Williams and more ORCIDs .zenodo.json commit d2335e850c3e3c9c0b98f6cbe59295e2d9a95957 Merge: c35c342b5 24945e04e Author: Ann Almgren Date: Thu Jan 24 15:06:31 2019 -0800 Merge branch 'master' of https://www.github.com/amrex-codes/amrex commit 54264f60c6a54f583acfe434243df821037b99f7 Author: Weiqun Zhang Date: Thu Jan 24 15:01:51 2019 -0800 mg interp on gpu Src/LinearSolvers/MLMG/AMReX_MG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit c35c342b512e5b500ed30cd2d7900752cca12f06 Author: Ann Almgren Date: Thu Jan 24 12:01:01 2019 -0800 Update with names and ORCID .zenodo.json commit 24945e04e8a36876ba7e03c296644a0a130eed40 Author: Weiqun Zhang Date: Thu Jan 24 11:26:40 2019 -0800 add a link to license in README README.md commit e530915c6bb7173629ed885cd2b5f29fbfa65f71 Author: Weiqun Zhang Date: Thu Jan 24 11:26:40 2019 -0800 add a link to license in README README.md commit d91dd0169bf03828bb524d1062eb1254ee38403e Merge: 54aca57ed ff807ee2f Author: Weiqun Zhang Date: Thu Jan 24 11:20:25 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9f473e5487d9c833ddfcb5db549d4d913ecdb52e Author: Weiqun Zhang Date: Thu Jan 24 11:20:20 2019 -0800 mg_interp in C++ Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MG_1D_K.H Src/LinearSolvers/MLMG/AMReX_MG_2D_K.H Src/LinearSolvers/MLMG/AMReX_MG_3D_K.H Src/LinearSolvers/MLMG/AMReX_MG_K.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/Make.package commit cf9c3f560e85ff8352310f5197d2eceaa31893da Author: Ann Almgren Date: Thu Jan 24 11:15:38 2019 -0800 Update README README.md commit bb06a46ce7d05c8289de23a129e12ca6842a3773 Author: Ann Almgren Date: Thu Jan 24 11:13:25 2019 -0800 README.txt --> README.md README.txt commit ce2bc7465b668cfa75d8cabab4e7c893fa2cb5c4 Author: Ann Almgren Date: Thu Jan 24 11:09:48 2019 -0800 Update with information about being a "core developer" README.md commit ff807ee2fa3387cbb3c2776044daf15bf097f5c4 Author: Ann Almgren Date: Thu Jan 24 11:13:25 2019 -0800 README.txt --> README.md README.txt commit 38af517354d3331f05fb5b7f0571a4888f6d5443 Author: Ann Almgren Date: Thu Jan 24 11:09:48 2019 -0800 Update with information about being a "core developer" README.md commit 54aca57edddd52ca4b2c27154e6986f7745e01f4 Author: Weiqun Zhang Date: Thu Jan 24 10:00:37 2019 -0800 add assertion Src/Base/AMReX_Array.H commit bd609da88082df917acbf769432d0d7e7244c602 Author: Weiqun Zhang Date: Thu Jan 24 12:07:10 2019 -0500 ibm compiler flags and pragma Src/Base/AMReX_Extension.H Tools/GNUMake/comps/ibm.mak commit e1fb3cccbb386c07b9e29626b5274449ce8ad42d Author: Weiqun Zhang Date: Thu Jan 24 09:30:14 2019 -0800 add zenodo json .zenodo.json commit 72ac04c53936c051a63aea766c776567be89b32c Author: Michele Rosso Date: Wed Jan 23 19:58:16 2019 -0500 CMake: Fortran interfaces are now disabled by default Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/CMake/AMReX_Options.cmake commit e8af04416d5a401d82f034e4d7fd32fd5d8b4c29 Author: Weiqun Zhang Date: Wed Jan 23 14:38:15 2019 -0800 mismatched #if Src/Base/AMReX_Extension.H commit f1c0c9cf6a41fc5666e8cae5caa64b483a5b664e Author: Weiqun Zhang Date: Wed Jan 23 14:36:31 2019 -0800 comment out omp simd Src/Base/AMReX_Extension.H commit 069bf4f3231f37627de5688f64d5d897bd3a134a Author: Weiqun Zhang Date: Wed Jan 23 14:15:02 2019 -0800 add AMREX_PARALLEL_FOR_?D Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_GpuLaunch.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_derive.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/Launch/main.cpp Tutorials/LinearSolvers/ABecLaplacian_C/initProb.cpp Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.cpp commit a14e51fb19075bff6d60840ecb9be27269c214a9 Author: Kevin Gott Date: Wed Jan 23 13:11:08 2019 -0800 Docs rewording. Docs/sphinx_documentation/source/BuildingAMReX.rst commit c3288d891d2d313f17c3334c04f2df4f0258e6ec Author: Weiqun Zhang Date: Wed Jan 23 10:46:53 2019 -0800 fix the Poisson test Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H commit 19f13c9ba90efc0a9a597268d3431b0c4e40481f Author: Weiqun Zhang Date: Wed Jan 23 10:39:37 2019 -0800 fix bug in ProbHiArray Src/Base/AMReX_Geometry.H commit 0522b3363d917678b8fdb59d9f707ec16bf489e4 Merge: 26e83cd82 fa19a77e0 Author: Andrew Myers Date: Tue Jan 22 20:34:04 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit fa19a77e08bfed6dd504e5000f0ddcf984ec4af1 Author: Weiqun Zhang Date: Tue Jan 22 17:03:56 2019 -0800 some fixes for cuda Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H commit 26e83cd82dcc118adb2bc3a94848ab495662b7aa Author: Andrew Myers Date: Tue Jan 22 19:56:42 2019 -0500 swap data pointers instead of making temporary copies when reordering particles in RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 6d747fbb4fc1a633857359d8a3b0156ddfad0099 Author: Weiqun Zhang Date: Tue Jan 22 16:37:40 2019 -0800 update Tutorials/LinearSolvers/ABecLaplacian_C for gpu Tutorials/LinearSolvers/ABecLaplacian_C/Make.package Tutorials/LinearSolvers/ABecLaplacian_C/MyTest_F.H Tutorials/LinearSolvers/ABecLaplacian_C/initProb.cpp Tutorials/LinearSolvers/ABecLaplacian_C/initProb_K.H Tutorials/LinearSolvers/ABecLaplacian_C/init_prob.F90 commit f4b12fd12c6ef7d53aea6595f955ae5e516d1198 Merge: 43fc9ffe7 4923040b1 Author: Johannes Blaschke Date: Tue Jan 22 15:40:56 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 43fc9ffe748462ec8bbce72cabc86061dc92d477 Author: Johannes Blaschke Date: Tue Jan 22 15:40:48 2019 -0800 allow users to specify coarsening level when creating eblevels Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCoreI.H commit 4923040b1073a74ec3a6e08c806ca40a535b0eb1 Author: Weiqun Zhang Date: Tue Jan 22 15:05:46 2019 -0800 remove numpts from BaseFab. After dlen and numpts are removed, the size of BaseFab went down from 80 to 56 bytes Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseUmap.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FabArray.H Tests/BaseFabTesting/main.cpp Tests/C_BaseLib/tUMap.cpp commit eb8be3f73a8654b7f4c1f9b6616e79b0c930e8ab Author: Weiqun Zhang Date: Tue Jan 22 14:09:07 2019 -0800 remove dlen from BaseFab Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BaseFab.H commit a6cd626771b8dbadfa9f115a94d5fcd738d3f6b5 Author: Weiqun Zhang Date: Tue Jan 22 14:04:29 2019 -0800 fix some shadows Src/Base/AMReX_FabArrayCommI.H commit e3281bc9124ad029a9deb4e1c806077d7fc2b067 Author: Johannes Blaschke Date: Sun Jan 20 22:18:23 2019 -0800 fill boundary not needed Src/EB/AMReX_EB_levelset.cpp commit 05b81e6b5504311b681618cbb93a98fc02e84371 Author: Johannes Blaschke Date: Sun Jan 20 22:05:38 2019 -0800 added static level-set intersection Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 commit d2a6fdb290ef2847f5bbee910dc843f717a7f112 Author: Weiqun Zhang Date: Sat Jan 19 11:26:01 2019 -0800 add a new interface to InterpCrseFineBndryEMfield Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_Interpolater.cpp commit 5c565107ca8fdaf15119bfadab4c88d53fc4f874 Merge: ef2b8f522 b7c0ebaad Author: Weiqun Zhang Date: Fri Jan 18 23:05:26 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ef2b8f522111787ffbbad74ff302527e234ee979 Author: Weiqun Zhang Date: Fri Jan 18 23:05:01 2019 -0500 pic cuda: optimization and simplification Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H commit b7c0ebaade2a69bbeb0453f834ec2a40f8eac78d Author: Kevin Gott Date: Fri Jan 18 13:42:59 2019 -0800 AsyncArray example. Docs/sphinx_documentation/source/GPU.rst commit 7edc34a1278891860bfe191fbbb849efff5460a6 Author: Johannes Blaschke Date: Fri Jan 18 13:27:25 2019 -0800 make consistent fucntion signatures Src/Base/AMReX_MultiFabUtil.H commit c11d3c5b35b9e84801aa0d854df2560376fa5597 Merge: 1e145b73c bafb9d584 Author: Weiqun Zhang Date: Fri Jan 18 09:22:41 2019 -0800 Merge branch 'weiqun/pic_cuda' of github.com:AMReX-Codes/amrex into weiqun/pic_cuda commit bafb9d5842da3c129da866c566f610a75576f87f Author: Weiqun Zhang Date: Fri Jan 18 12:15:01 2019 -0500 add RedistributionLocal Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.H commit 60492c8629a390c8ff3fee45aa4689fd4b69d1c1 Merge: 63bdcfe7c d8dde2dc1 Author: Weiqun Zhang Date: Fri Jan 18 11:59:15 2019 -0500 Merge branch 'development' into weiqun/pic_cuda commit d8dde2dc19205b1ccc1d63a91e555354b0b6f026 Author: Andrew Myers Date: Fri Jan 18 01:38:26 2019 -0800 call local form of Redistribute in the pic tutorial Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Source/main.cpp commit 1e145b73c624259a5da450937aea30ed0d7a925d Author: Weiqun Zhang Date: Thu Jan 17 20:56:46 2019 -0800 rm Fortran files in the cuda version of empic Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Source/main.cpp commit 63bdcfe7cf6aeda3186edb1552ffc50ed62dece8 Author: Weiqun Zhang Date: Thu Jan 17 16:58:59 2019 -0800 forgot a new file Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_K.H commit b7caa133593cec57380731ce20048a3010559c1c Author: Weiqun Zhang Date: Thu Jan 17 16:52:05 2019 -0800 set cuda stream in particle iterator Src/Particle/AMReX_Particles.H commit 855c2b9fabd593e09c8f2655e447ca0bd2e30dd5 Author: Weiqun Zhang Date: Thu Jan 17 16:16:16 2019 -0800 current deposition on gpu Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp commit aaa789c601a0c78d953cc1830d297baa234f0155 Author: Weiqun Zhang Date: Thu Jan 17 15:37:40 2019 -0800 push e and b in cuda Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.cpp commit 5fc27c1e65de1858d97656d4a4e24784fc38c3dd Author: Weiqun Zhang Date: Thu Jan 17 15:17:14 2019 -0800 field gather and momentum push in cuda Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp commit b0c7c77784a3402aea90c085fdd8033783574215 Author: Weiqun Zhang Date: Thu Jan 17 15:16:45 2019 -0800 make functions in Paticle struct host and device Src/Particle/AMReX_Particle.H commit 6004dc8f9f1797b88aaa486daced907745cff641 Author: Michele Rosso Date: Thu Jan 17 14:44:13 2019 -0800 CMake: begin adding CUDA support CMakeLists.txt Src/CMakeLists.txt Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake commit ec0a20667c89523923a49c32b3ed99664b039c71 Merge: 660e429e9 d21cbd4b7 Author: Weiqun Zhang Date: Thu Jan 17 13:38:08 2019 -0800 Merge branch 'development' into weiqun/pic_cuda commit 22c4438916f883a58174fc92b9768832cf2c8ace Author: Kevin Gott Date: Thu Jan 17 13:31:09 2019 -0800 AsyncFab Example. Docs/sphinx_documentation/source/GPU.rst commit d21cbd4b7433e803f92b6ea17fed6e9e5e410d44 Author: Weiqun Zhang Date: Thu Jan 17 13:06:51 2019 -0800 simplification Src/Base/AMReX_MultiFabUtil.H commit 27ef77ef0eb9671239d40cf63f9f08532ae0d23a Author: Weiqun Zhang Date: Thu Jan 17 12:38:11 2019 -0800 EBFArrayBoxFactory cannot be used unless it's inside ifdef AMREX_USE_EB Src/Base/AMReX_MultiFabUtil.H commit 0a723f34f99f7f868541b90f2ff0b21087e370c4 Merge: 8335287a9 f0d04f6e3 Author: Weiqun Zhang Date: Thu Jan 17 15:21:44 2019 -0500 Merge branch 'weiqun/mpi' into development commit f0d04f6e3b7538ef983a50d8b7096ecea8cb2d9e Author: Weiqun Zhang Date: Thu Jan 17 15:20:46 2019 -0500 get around gcc-4 Src/Base/AMReX_ParallelDescriptor.cpp commit 8335287a96da1c236aa706e0dd3bf96caec657b0 Author: Johannes Blaschke Date: Thu Jan 17 12:18:05 2019 -0800 add helper functions fore regridding Src/Base/AMReX_MultiFabUtil.H commit 4d0afc3a4f924b1cf1d0ccbbd01eac1524a7e52b Merge: cfaa1de39 f835ce9c9 Author: Michele Rosso Date: Thu Jan 17 12:09:34 2019 -0800 Merge branch 'development' into mr/cmake commit 358d96c92edd2414992fe0b5bb4e922476bcb606 Author: Weiqun Zhang Date: Thu Jan 17 11:31:28 2019 -0800 new Mpi_typemap to replace the old implementation using removed MPI constructs Src/Base/AMReX_ParallelDescriptor.cpp commit 1065df71e3e4acc199387d9d31f65109c1199374 Author: Weiqun Zhang Date: Thu Jan 17 11:20:35 2019 -0800 missing amrex:: Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H commit f835ce9c90a757c8615bd75259dc77b566377696 Author: Weiqun Zhang Date: Wed Jan 16 20:47:23 2019 -0800 derive variables in AmrLevel and CNS tutorial Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_Derive.H Tutorials/GPU/CNS/Exec/Sod/inputs Tutorials/GPU/CNS/Source/CNS_derive.H Tutorials/GPU/CNS/Source/CNS_derive.cpp Tutorials/GPU/CNS/Source/CNS_setup.cpp Tutorials/GPU/CNS/Source/Make.package commit c064ae8232ba538c001f612534f07c72d5f18133 Author: Weiqun Zhang Date: Wed Jan 16 17:32:33 2019 -0800 add Fab version of derive function Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_Derive.H Src/Amr/AMReX_Derive.cpp commit 25d2f0a5da3b1ff3c0c65ee0fbb037d236b80627 Author: Weiqun Zhang Date: Wed Jan 16 15:42:01 2019 -0800 add fabPtr to AuxBoundaryData Src/Amr/AMReX_AuxBoundaryData.H commit 49869e16d5e8ae7177fbe400f5832edd0ce93a4d Author: Weiqun Zhang Date: Wed Jan 16 15:20:40 2019 -0800 add Gpu::notInLaunchRegion() Src/Amr/AMReX_AmrLevel.cpp commit cb1f9ab3a39d45d3b4e209304a0969027f48845f Merge: b15c3cc79 44808b3eb Author: Weiqun Zhang Date: Wed Jan 16 12:55:13 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b15c3cc7926356d2d49cf426612dce80eca1c248 Author: Weiqun Zhang Date: Wed Jan 16 12:55:06 2019 -0800 Revert "Readability adjustment." This reverts commit 4ab95611015372f3f16d58fc4d3aa43e2f026e28. Src/Base/AMReX_ParallelContext.H commit 9b6719d112d1ea31fe7cb46b0d4f6bbc15909b2c Merge: 461ad8c4e 4ab956110 Author: Weiqun Zhang Date: Wed Jan 16 12:51:46 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 44808b3eb7d569bea0bcad33806998b8906661e1 Author: Kevin Gott Date: Wed Jan 16 12:48:30 2019 -0800 Edit GPU Tutorials to explicitly cite correct the useable cuda modules on summit and summitdev. Docs/sphinx_tutorials/source/GPU_Tutorial.rst commit 461ad8c4e58876e58e61847eb3561a7cb92835d8 Author: Weiqun Zhang Date: Wed Jan 16 12:43:09 2019 -0800 more on amr gpu Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX_BaseFab.H Src/Boundary/AMReX_FabSet.H commit 4ab95611015372f3f16d58fc4d3aa43e2f026e28 Author: Kevin Gott Date: Wed Jan 16 11:30:11 2019 -0800 Readability adjustment. Src/Base/AMReX_ParallelContext.H commit 6ef7110fa695a65df032066f1415b4925742f854 Author: Kevin Gott Date: Wed Jan 16 11:29:52 2019 -0800 Bit more on ParallelContext. Docs/sphinx_documentation/source/Basics.rst commit 0cac8d30aebbb0530ebd5ea032ab931753e22463 Author: Kevin Gott Date: Wed Jan 16 11:28:37 2019 -0800 Edit GPU Tutorials Docs. Docs/sphinx_tutorials/source/GPU_Tutorial.rst commit bc4a285127e938bac50544d6dedb9bca11fd85e0 Author: Kevin Gott Date: Wed Jan 16 11:27:35 2019 -0800 Comment on ParallelContext. Docs/sphinx_documentation/source/Basics.rst commit 5bf70fcf6169171a0ef46dcc837ab6d84115215c Author: Andy Nonaka Date: Wed Jan 16 11:15:23 2019 -0800 typo Docs/sphinx_documentation/source/Particle.rst commit 7429e367252d7061aa07d47f39b0aa24219357ed Author: Weiqun Zhang Date: Wed Jan 16 13:23:05 2019 -0500 add ldg function for Array4 Src/Base/AMReX_Array.H Src/Base/AMReX_CudaUtility.H commit 66c7741f29e5fed332c1fa2a9b4ca169008cdc37 Author: Weiqun Zhang Date: Wed Jan 16 11:43:16 2019 -0500 add restrict the pointer member in Array4 and FabView Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H commit cfaa1de39a45976ba0658069e9c77853bd32861b Author: Michele Rosso Date: Tue Jan 15 21:12:24 2019 -0800 CMake: treat Algoim and Blitz as imported interfaces CMakeLists.txt Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_InstallExternalLibs.cmake commit cb4a4dfb682fb4973099025f1973d253a27f435d Author: Johannes Blaschke Date: Tue Jan 15 18:43:34 2019 -0800 make static interfaces more portable Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp commit ce284986b70f8f0b5ced05c62d854f24d7201878 Merge: d70586399 06b97375d Author: Johannes Blaschke Date: Tue Jan 15 17:17:01 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d70586399d3f9f7f6725476ec4b68785f6330140 Author: Johannes Blaschke Date: Tue Jan 15 17:16:58 2019 -0800 expose more LSCore as static functions Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_levelset.H commit 06b97375ddee04cc25b4cd2a7f200d0f165dbf8e Author: Weiqun Zhang Date: Tue Jan 15 16:46:48 2019 -0800 fix another new bug Src/Base/AMReX_FabArrayUtility.H commit 6abfcd5873532f4aa4577285256530fdb05b9855 Author: Weiqun Zhang Date: Tue Jan 15 16:27:12 2019 -0800 fix a new bug Src/Base/AMReX_MultiFab.cpp commit bbc9878fb38fe7c1c4db2b086623094973e5260a Merge: b79a449d5 4cd807e99 Author: Weiqun Zhang Date: Tue Jan 15 15:59:34 2019 -0800 Merge branch 'weiqun/gpu' into development commit b79a449d598d7fb49a995940deaf6383dd90728b Merge: 8a1cae6c5 92d495a71 Author: Weiqun Zhang Date: Tue Jan 15 15:59:23 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4cd807e99d67eef527f847d84ccacdff70a0894c Author: Weiqun Zhang Date: Tue Jan 15 15:54:18 2019 -0800 view -> array Tutorials/GPU/CNS/Source/CNS_K.H commit 15a4fb74475a12cb1840dea6ed9d7d11a4fd1334 Author: Weiqun Zhang Date: Tue Jan 15 14:32:00 2019 -0800 remove some duplicated codes in MultiFab and iMultiFab Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.cpp commit dc338fd95ddd1e4f5966f39164f92af977b5a6b5 Merge: 1e0cc1dc8 8a1cae6c5 Author: Weiqun Zhang Date: Tue Jan 15 13:14:00 2019 -0800 Merge branch 'development' into weiqun/gpu commit 1e0cc1dc853c48c9764661c0a82fcbc9eea49543 Author: Weiqun Zhang Date: Tue Jan 15 13:13:54 2019 -0800 update FillBoundary Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 8a1cae6c563ad934fd95d3a014dda3ac04b2b8d4 Author: Weiqun Zhang Date: Tue Jan 15 12:26:22 2019 -0800 update Geometry Src/Base/AMReX_COORDSYS_1D_C.H Src/Base/AMReX_COORDSYS_2D_C.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_Geometry.cpp commit 9ff6fce72a2b22a2a491e813f49b556419a16a09 Author: Weiqun Zhang Date: Tue Jan 15 11:58:37 2019 -0800 change Array4 so that it can be easily passed to Fortran Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H commit 92d495a71ffee8230823e36801622651c1da19fe Author: Kevin Gott Date: Tue Jan 15 11:11:34 2019 -0800 Update GPU docs: needs picture change & AsyncFab/AsyncArray examples (w.r.t. new Array4 style)? Docs/sphinx_documentation/source/GPU.rst commit 83c9d27801179848a1b0927e9874521f24dcfabf Author: Weiqun Zhang Date: Tue Jan 15 10:34:37 2019 -0800 add profilers Tutorials/GPU/Launch/main.cpp commit 2125d4e05ac687779a87c40aa48f25416c80e8bd Merge: ac6f246e1 b7eddc452 Author: Michele Rosso Date: Tue Jan 15 09:45:24 2019 -0800 Merge branch 'development' into mr/cmake commit ac6f246e12bf2bb53d39e94d79c16c806dbd5f4d Author: Michele Rosso Date: Tue Jan 15 09:32:55 2019 -0800 CMake: finalize move to CMake 3.11 Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake commit b7eddc452ba695f8740cc40e38ffc4e0d665b0ed Merge: 4a782e27e b8ae7684f Author: Weiqun Zhang Date: Mon Jan 14 20:09:39 2019 -0800 Merge branch 'weiqun/gpu' into development commit 3619b1531940bf56510343b7684f89366b3c428a Author: Michele Rosso Date: Mon Jan 14 16:47:09 2019 -0800 CMake: move to CMake 3.11 CMakeLists.txt Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tutorials/Amr/Advection_F/CMakeLists.txt Tutorials/Amr/Advection_octree_F/CMakeLists.txt commit 4a782e27eff751f4ee255b1eb29041dbaddd9835 Author: Weiqun Zhang Date: Mon Jan 14 15:57:31 2019 -0800 fix bug in AMREX_FOR Src/Base/AMReX_CudaLaunch.H commit b8ae7684f146b17c9fc9f2328902aa5a7f9b50ee Author: Weiqun Zhang Date: Mon Jan 14 15:57:31 2019 -0800 fix bug in AMREX_FOR Src/Base/AMReX_CudaLaunch.H commit 0a1e0b10a513a7ef1bc6cc673116316b4c6303e3 Author: Weiqun Zhang Date: Mon Jan 14 18:28:57 2019 -0500 use AMREX_FOR in ParallelCopy Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MultiFab.cpp commit bd0cf61754dd0ef8373861f485040040e9cfa851 Author: Weiqun Zhang Date: Mon Jan 14 13:58:12 2019 -0500 use AMREX_FOR Src/Base/AMReX_MultiFab.cpp commit 43cf0a7de440111239f1c5f7dfa4facf0173b609 Author: Weiqun Zhang Date: Mon Jan 14 10:54:04 2019 -0800 fix template for no BaseFab type Src/Base/AMReX_FabArray.H commit aabef6a869f9d2a9048789ac3df4f3be1e9a4ae0 Merge: 0055e59e8 6f90c1498 Author: Weiqun Zhang Date: Mon Jan 14 10:41:50 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0055e59e8bf0de97e695727bef21053db35b5145 Author: Weiqun Zhang Date: Mon Jan 14 10:41:42 2019 -0800 remove the unused buggy code for now Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 6f90c1498db7738c7ee78082772dc2aee90a970a Author: Kevin Gott Date: Mon Jan 14 08:47:25 2019 -0800 Comments on proper use of tilebox and dynamic tiling overview. Docs/sphinx_documentation/source/Basics.rst commit c09797378b82e6c02783a16d7193e08adb48b009 Author: Kevin Gott Date: Mon Jan 14 08:46:33 2019 -0800 Note on ~/amrex in GNUMakefile Docs/sphinx_documentation/source/BuildingAMReX.rst commit eb8cf9c1361e5fa5d3a1e71cf329c898d3a3334c Merge: 03beae5a2 4a37ba24e Author: Weiqun Zhang Date: Mon Jan 14 09:41:20 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 03beae5a2d6b03de98cfb30b37e61c0a341d3c63 Author: Weiqun Zhang Date: Mon Jan 14 09:41:12 2019 -0800 forgot a file Tutorials/GPU/HeatEquation_EX1_C/Source/mykernel.H commit 4a37ba24e9e283b8f5ca7d75872717b7b462b3ec Author: Tan Nguyen Date: Mon Jan 14 11:20:54 2019 -0600 update known limitations Docs/sphinx_documentation/source/AsyncIter.rst commit 4a7a2c6f79157f5b3798b20768f2855079c69217 Author: Tan Nguyen Date: Mon Jan 14 11:13:41 2019 -0600 update known limitation Docs/sphinx_documentation/source/AsyncIter.rst commit 50c0e87934d17619a15deca57e8754929c322ce7 Author: Tan Nguyen Date: Mon Jan 14 09:08:46 2019 -0800 add known limitation of the async runtime to the userguide Docs/sphinx_documentation/source/AsyncIter.rst commit d1ade0d389ed8a354ac1faa0e01f3ebca9ad47a4 Author: Weiqun Zhang Date: Mon Jan 14 06:51:06 2019 -0800 fix compilation Src/Base/AMReX_CudaAsyncFabImpl.cpp commit c01e7748e568364be978b3d25f32532407f7c093 Merge: eeda8e8c6 e842e4c55 Author: Weiqun Zhang Date: Sun Jan 13 20:51:10 2019 -0800 Merge branch 'weiqun/for' into development commit eeda8e8c6379a02d21de2113c85caf66405a6ba3 Author: Weiqun Zhang Date: Sun Jan 13 20:33:48 2019 -0800 Merge branch 'weiqun/for' into development Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.H Src/Base/AMReX_CudaAsyncFabImpl.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_IntVect.H Tutorials/GPU/CNS/Exec/RT/cns_prob.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_tagging.H Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H Tutorials/GPU/Launch/MyKernel.H Tutorials/GPU/Launch/main.cpp commit e842e4c55bdd9bcaad1a35bb3e848538f0cb11bb Author: Weiqun Zhang Date: Sun Jan 13 20:29:16 2019 -0800 update GPU heat equation example Src/Base/AMReX_FArrayBox.H Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H commit 20ebe72f487a7288cb1bc7e7a3e44d0d99f879bb Author: Weiqun Zhang Date: Sun Jan 13 14:42:30 2019 -0800 use AMREX_FOR in CNS tutorial Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H Tutorials/GPU/Launch/MyKernel.H commit 6b05cde316cc8b9ff60b132325e2a2d8f51a2b45 Author: Weiqun Zhang Date: Sun Jan 13 11:24:12 2019 -0800 simplification of AMREX_FOR and more examples in launch tutorial Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_GpuLaunch.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/Launch/main.cpp commit bb77c7b9824cb23e02c8efedb1944d81ee61ebc9 Author: Johannes Blaschke Date: Sun Jan 13 10:17:27 2019 -0800 expand implicit function filling Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp commit 732c186a03343ce36048c90d808f9413b8dca77f Author: Weiqun Zhang Date: Sat Jan 12 22:56:57 2019 -0800 start using AMREX_FOR in CNS tutorial Tutorials/GPU/CNS/Exec/RT/cns_prob.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_tagging.H commit 46502edbf2822721d8d2d219a233b537b6c6023b Author: Weiqun Zhang Date: Sat Jan 12 22:44:37 2019 -0800 update Launch Tutorials/GPU/Launch/main.cpp commit c5e0b4f083f86ee4718fa1be54e07369fb81621c Author: Weiqun Zhang Date: Sat Jan 12 22:44:13 2019 -0800 reorder BaseFabData structure Src/Base/AMReX_BaseFab.H commit 5b2b5ad41b411936c4e3f5481ee5954ff0d38a84 Author: Weiqun Zhang Date: Sat Jan 12 22:05:16 2019 -0800 AMREX_FOR_1D, 3D and 4D Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_GpuLaunch.H commit 56673a536ce2f182e84364b49bfeb75ddc94a2a8 Author: Weiqun Zhang Date: Sat Jan 12 18:31:03 2019 -0800 add AsyncFab::array and fix const of Array4 Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.H Src/Base/AMReX_CudaAsyncFabImpl.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_IntVect.H Tutorials/GPU/Launch/main.cpp commit 9b4fcc6fdef69d6e4610b807ec0bc28965b8b4b3 Author: Johannes Blaschke Date: Sat Jan 12 17:53:18 2019 -0800 cleanup Src/EB/AMReX_EB_LSCoreI.H commit c6f4196a2799860fd21c8a2d90aac8ff7afe1176 Author: Johannes Blaschke Date: Sat Jan 12 17:48:16 2019 -0800 expose ebis level building as a static template class Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCoreI.H commit cf8ffe2fcb4bf65659e304155356096aeafbf00a Author: Weiqun Zhang Date: Sat Jan 12 15:11:39 2019 -0800 AMREX_FOR: a new kernel launch approach Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_GpuLaunch.H Tutorials/GPU/Launch/main.cpp commit 8ead21ca94828cea573178b656f95eca66b3bb60 Author: Johannes Blaschke Date: Sat Jan 12 14:46:56 2019 -0800 fix eb_pad error Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/Donut/Exec/inputs commit 7bb5d656198d11bd28f4bc6ac8bd9254c18f2927 Author: Ann Almgren Date: Sat Jan 12 13:40:23 2019 -0800 Fix typo in push_position_boris -- we were using uxp for all directions instead of uxp, uyp, uzp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90 commit 4a311f0b2fd612106aee7bf838561ee425a7915c Author: Ann Almgren Date: Sat Jan 12 13:38:52 2019 -0800 Fix typo in push_position_boris code example. Docs/sphinx_documentation/source/GPU.rst commit d22c2d3e9bc5d0c9aec84df563ce672692f2290c Merge: 37daa4ecf cc5a51a34 Author: Johannes Blaschke Date: Sat Jan 12 12:21:52 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 37daa4ecf00537282ff887357fd2c35b1d9fff5b Author: Johannes Blaschke Date: Sat Jan 12 12:21:40 2019 -0800 add profiling Src/EB/AMReX_EB_LSCoreBase.cpp commit cc5a51a3446c0a2270134d042716757c405b33da Merge: f1a471c75 d19211acd Author: Ann Almgren Date: Sat Jan 12 11:51:18 2019 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit f1a471c756b9e4d78735cf071eee13eed17347c8 Author: Ann Almgren Date: Sat Jan 12 11:51:06 2019 -0800 Add brackets to fcompare.cpp as well. Tools/Postprocessing/C_Src/fcompare.cpp commit d19211acd3543b17dba4e0aa7b0e52176a3257fc Merge: 34fd76fb2 ea53a9314 Author: Johannes Blaschke Date: Sat Jan 12 11:49:30 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 34fd76fb22e8b1fd840dd6f5758b1798eafd59d8 Author: Johannes Blaschke Date: Sat Jan 12 11:49:27 2019 -0800 make sure boxarrays are nodal/cc and ensure this works when DIM!=3 Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H commit ea53a931474a5e70a59a507faf900a68e1765657 Author: Ann Almgren Date: Sat Jan 12 11:36:32 2019 -0800 Needed to add brackets between Initialize and Finalize so this doesn't segfault. Tools/Postprocessing/C_Src/fextract.cpp commit 660e429e900045681dc1538ee690971df3487616 Author: Weiqun Zhang Date: Fri Jan 11 22:53:01 2019 -0800 cuda: check solution and push e field Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.H Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Exec/CUDA/inputs Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Source/main.cpp commit dc3cb890be59ff9ed9ad00aec014ed56b32a5034 Author: Weiqun Zhang Date: Fri Jan 11 21:32:01 2019 -0800 fix memory leak in pic tutorial Tutorials/Particles/ElectromagneticPIC/Make.EMPIC Tutorials/Particles/ElectromagneticPIC/Source/main.cpp commit 254824ce0fd4578ed971d573def56e5e614047f3 Merge: 1fd5b3ac8 27b39baab Author: Weiqun Zhang Date: Fri Jan 11 19:43:28 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 27b39baabfd5c27bfa3cbd7b4d4fdff47d3e3ad3 Merge: d54e6e319 cff78ecc9 Author: Johannes Blaschke Date: Fri Jan 11 16:30:59 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d54e6e31906f313862c4c14338cf75adbea99b20 Author: Johannes Blaschke Date: Fri Jan 11 16:30:57 2019 -0800 expose multi-level filling Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H commit 156c85ab7d65455c3443325e09b33b2ed0a2d214 Author: Johannes Blaschke Date: Fri Jan 11 15:23:35 2019 -0800 static EBSearchBox, needed to expose multi-level filling Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp commit 1fd5b3ac8eca1ae1497a002722e4d3cf78275448 Merge: d112ec151 cff78ecc9 Author: Weiqun Zhang Date: Fri Jan 11 16:58:22 2019 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d112ec1512d72072c1b77556fa7cd28e880c77ac Author: Weiqun Zhang Date: Fri Jan 11 16:58:13 2019 -0500 add nvcc argument -maxrregcount Tools/GNUMake/comps/nvcc.mak commit cff78ecc9f961052a05d38049a6821927ea22c22 Author: Andrew Myers Date: Fri Jan 11 15:42:40 2019 -0500 turn off OMP_OFFLOAD by default Tutorials/GPU/Launch/GNUmakefile commit b7c9564a70c0d7b9cfa8d4ce00c072c1e0c30ddf Author: Andrew Myers Date: Fri Jan 11 15:42:02 2019 -0500 restoring the USE_OMP_OFFLOAD option and adding an example to the launch Tutorial Tools/GNUMake/Make.defs Tutorials/GPU/Launch/GNUmakefile Tutorials/GPU/Launch/MyKernel_F.F90 Tutorials/GPU/Launch/MyKernel_F.H Tutorials/GPU/Launch/main.cpp commit 081c2d73bd0f0d26508c1461457333f22b36d9bf Author: Weiqun Zhang Date: Fri Jan 11 09:22:27 2019 -0800 exclude initilizations including cuda and openacc that could take a long time from tiny profiler Src/Base/AMReX.cpp Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_TinyProfiler.cpp commit 2c5c89c06bd9ed0066ea00a77bc21f6fd3dcfaab Merge: 053a0b4f0 d614fa6b8 Author: Brandon Runnels Date: Fri Jan 11 09:46:32 2019 -0700 Merge branch 'development' into nodeghostcells commit d614fa6b845280d8a975f87b4505f51760301339 Author: Weiqun Zhang Date: Thu Jan 10 16:27:53 2019 -0800 inline some RealBox functions Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit bb799c57972b5264aa49947ca48ec7db9d87c7f6 Author: Weiqun Zhang Date: Thu Jan 10 16:12:50 2019 -0800 more constexpr Src/Base/AMReX_Orientation.H commit 960d9d84258f7258c1ac2fc37caab1e1b959f966 Author: Weiqun Zhang Date: Thu Jan 10 15:44:16 2019 -0800 make the implementation of print_state template Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MultiFabUtil.cpp commit 5c913d55f0364ea05e1273d61fe630c09ec3f79f Author: Weiqun Zhang Date: Thu Jan 10 15:24:16 2019 -0800 optional ghost cell argument in print_state Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 2fe13f081e8e93091d50c8ab1230eb39d68f762d Merge: 78cc5d5dc 6dc86bcbc Author: Michele Rosso Date: Thu Jan 10 15:43:30 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 78cc5d5dc7c3389235b0cd026db420b1b19713f6 Author: Michele Rosso Date: Thu Jan 10 15:43:19 2019 -0800 CMake: completely drop support for F_Baselib Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Options.cmake commit 6dc86bcbc0955c988d66b386bd404ec468d0f175 Author: Weiqun Zhang Date: Thu Jan 10 15:08:13 2019 -0800 amrex::cast for MultiFab kind types Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit cbe7d1341ac71f6444d17abb7ed0d72744addb52 Author: Weiqun Zhang Date: Thu Jan 10 14:40:30 2019 -0800 make some functions constexpr Src/Base/AMReX_Box.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H commit 2cf7dfa6f23bf9c7bb0410851fcd6ac4134a27f3 Author: Weiqun Zhang Date: Thu Jan 10 13:36:54 2019 -0800 rm deprecated functions Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp commit 21cbe2c60d286338474abe75dbc7ff95ce5ebbaa Author: Michele Rosso Date: Thu Jan 10 15:05:57 2019 -0800 CMake: change how the build type is set Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_InstallExternalLibs.cmake Tools/CMake/AMReX_Options.cmake commit b165ee89211f93d9fb04ce99d1f0177278be5274 Merge: 60d72f35e fbd1cb83a Author: Johannes Blaschke Date: Thu Jan 10 13:43:49 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit fbd1cb83a2da6e8d7dce77ca62388eb4fbffceb9 Author: Weiqun Zhang Date: Thu Jan 10 13:09:09 2019 -0800 use new BaseFab interface in various places Src/Base/AMReX_Box.H Src/Base/AMReX_CudaRange.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit e64943a852c83cabe1f8dde301a81a8190ec6c8c Author: Weiqun Zhang Date: Thu Jan 10 13:08:20 2019 -0800 mod gpu launch tutorial to show generic loop launch Tutorials/GPU/Launch/main.cpp commit b95ef42847819822055fdeef9b5c1eb60f322371 Author: Weiqun Zhang Date: Thu Jan 10 09:54:53 2019 -0800 safeguard some CoordSys functions Src/AmrCore/AMReX_Interpolater.cpp Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_GpuControl.H commit c8cfab36f0a1b4a79dbfd542e6c7e1052640b69d Author: Weiqun Zhang Date: Thu Jan 10 09:27:34 2019 -0800 inline setBC function Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp commit b78f9d043ad3b731f42bf64b837e303f95672aad Author: Weiqun Zhang Date: Thu Jan 10 09:17:53 2019 -0800 rm deprecated BaseIndex class and changed the interface of BaseFab cast Src/Base/AMReX_BaseFabUtility.H Src/Base/AMReX_BaseIndex.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit eb95c6568f5ef4bf57b1223ca15c00a59890d936 Merge: b8d6e8a3f 1d4969c85 Author: Weiqun Zhang Date: Wed Jan 9 19:28:16 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1d4969c8589d067434c22ecdaa88cafcd676998f Author: Ann Almgren Date: Wed Jan 9 17:37:57 2019 -0800 Make a link back from Tutorials to Documentation Docs/sphinx_documentation/source/index.rst Docs/sphinx_tutorials/source/index.rst commit 59ce97a0123203ef7bc50069e67bee4e9f76e6d2 Merge: 61e1aaffd d2df83446 Author: Ann Almgren Date: Wed Jan 9 17:33:46 2019 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 61e1aaffd771fb635c0b92092dfa8dbd4817f970 Author: Ann Almgren Date: Wed Jan 9 17:33:03 2019 -0800 Add link to Tutorials page from the front page. Docs/sphinx_documentation/source/index.rst commit 60d72f35ed01fd8f82bb9054fb3a08632dda5556 Author: Johannes Blaschke Date: Thu Jan 10 02:17:24 2019 +0100 exposed level-set and volfrac box tagging Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp commit b8d6e8a3ff5f9bbe434dbf6273c6540c95a33148 Author: Weiqun Zhang Date: Wed Jan 9 17:03:57 2019 -0800 compiles Src/Base/AMReX_BaseFab.H commit fbbea4eecebfa60a1fcf3a280d768b0bd95e0f1b Author: Weiqun Zhang Date: Wed Jan 9 16:49:31 2019 -0800 more on the new interface in BaseFab Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArrayBase.H commit d2df83446e68f2fd8ac7a8efab101d134657de33 Author: Weiqun Zhang Date: Wed Jan 9 12:02:14 2019 -0800 add missing atomic add Src/Base/AMReX_FabArrayUtility.H commit 25bdaa1f00393d8cecaf4ebbfa44dcedd4cbbfcc Author: Weiqun Zhang Date: Wed Jan 9 11:58:27 2019 -0800 optimization of reuction on summit Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_FabArrayUtility.H commit aece35f6a9c7131d12727268090e230a3d177f96 Author: Weiqun Zhang Date: Wed Jan 9 10:53:05 2019 -0800 add profilers and minor changes Src/Base/AMReX_CudaLaunch.H Tutorials/GPU/CNS/Source/CNS.cpp commit 03e7e796fec822c04dec564abaa856b8422b9bd0 Author: Weiqun Zhang Date: Wed Jan 9 10:50:34 2019 -0800 add copyToHost function to AsyncArray Src/Base/AMReX_CudaAsyncArray.H commit 1ed88de1b19240d8320044cb4c53d21713de61ea Merge: 57e34de9f ce68827cb Author: Weiqun Zhang Date: Wed Jan 9 10:30:26 2019 -0800 Merge branch 'weiqun/gpu' into development commit 57e34de9fb283a4f28eecf612ee1c0585640daa5 Merge: 509612a1b 3b692f6de Author: Guy Moore Date: Tue Jan 8 21:45:09 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 509612a1bad5d51cc86810ff5520d5fe713086b5 Author: Guy Moore Date: Tue Jan 8 21:43:58 2019 -0800 Corrected intersphinx with URL Docs/sphinx_documentation/source/conf.py Docs/sphinx_tutorials/source/conf.py commit 3b692f6de7b2b268c9365fe71fa0c2ad4479bd93 Merge: 9070d9aa5 09a9fdcbc Author: Ann Almgren Date: Tue Jan 8 17:41:58 2019 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 9070d9aa57f61ed065cc3ae04b49e2d8d5a85b2a Author: Ann Almgren Date: Tue Jan 8 17:35:25 2019 -0800 "to be ran" --> "to be run" Docs/sphinx_documentation/source/GPU.rst commit 09a9fdcbc260286d3290d6cfd0cb396121ef41b2 Merge: 4d0f6aa91 6c2fd673e Author: Guy Moore Date: Tue Jan 8 17:21:50 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 4d0f6aa9170409e3d7b44939e22079dba103237f Author: Guy Moore Date: Tue Jan 8 17:19:30 2019 -0800 Added intersphinx extension to cross-ref between sphinx_documentation and sphinx_tutorials Docs/sphinx_documentation/source/SWFFT.rst Docs/sphinx_documentation/source/Tutorials_Chapter.rst Docs/sphinx_documentation/source/conf.py Docs/sphinx_tutorials/source/SWFFT_Tutorial.rst Docs/sphinx_tutorials/source/conf.py Docs/sphinx_tutorials/source/index.rst commit 6c2fd673e6f39621d51a9fab8bd73154b313a793 Merge: 5ba26828f f1e993be3 Author: WeiqunZhang Date: Tue Jan 8 16:54:01 2019 -0800 Merge pull request #388 from AMReX-Codes/cy-perf Bunch of changes to support MLMG performance analysis and tuning commit 5ba26828fd43c8265f3ded5ac83a5e0450ec33f0 Author: Weiqun Zhang Date: Tue Jan 8 16:05:31 2019 -0800 use cuda driver api to avoid cuda-memcheck error Src/Base/AMReX_CudaUtility.H Tools/GNUMake/Make.defs commit dd73a27974f899bb965b1ce501d34a862b2e8fa6 Merge: c27978183 7f46e6c12 Author: Cy Chan Date: Tue Jan 8 14:26:21 2019 -0800 Merge branch 'development' into forkjoin commit c27978183724e4a088bd7fd1734a69b80ec770fa Author: Cy Chan Date: Tue Jan 8 14:14:51 2019 -0800 simplify ForkJoin interface a bit remove ngrow argument from reg_mf() number of grow cells in forked MultiFab now matches original MultiFab by default can customize after registration via modify_ngrow() function add overloads to modify_comp_split() and modify_ngrow() for no index argument Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp Tutorials/ForkJoin/MLMG/main.cpp Tutorials/ForkJoin/Simple/MyTest.cpp commit 7f46e6c1277c038ebb0393e075993b13991968e6 Author: Weiqun Zhang Date: Tue Jan 8 11:02:07 2019 -0800 add SafeLaunchGuard and use it in Interpolaters so that they work with old style FillPatch Src/AmrCore/AMReX_Interpolater.cpp Src/Base/AMReX_GpuControl.H commit 455486d41baf1f3f1a01dde98422962012911aa2 Merge: a4cb3dbb1 4717f7e8e Author: Tan Nguyen Date: Tue Jan 8 02:33:26 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a4cb3dbb16f5f0d3364d3db38671ddcb11081966 Author: Tan Nguyen Date: Tue Jan 8 02:33:18 2019 -0800 fix a bug in the upcxx banckend that could lead to deadlock Src/Amr/AMReX_Amr.cpp Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.cpp Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.cpp Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.cpp commit 4717f7e8ee99339bbd649bcb42ca30e0d2fff0c9 Merge: 755023861 36b548c54 Author: Andrew Myers Date: Mon Jan 7 17:36:20 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7550238614b969085ce9670b3d9e89a95d7addf0 Author: Andrew Myers Date: Mon Jan 7 17:36:10 2019 -0800 only allow this early exit in RedistributeGPU if allPeriodic Src/Particle/AMReX_ParticleContainerI.H commit 36b548c54e491c9cc48dc479ef58a4136ca020d3 Merge: 441adbb22 8ebd9ffde Author: Johannes Blaschke Date: Tue Jan 8 00:07:58 2019 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 441adbb226be19d68e2a7073e8a7b0e2b8417a5e Author: Johannes Blaschke Date: Tue Jan 8 00:07:33 2019 +0100 expand level-set documentation Docs/sphinx_documentation/source/EB.rst commit 8ebd9ffde3ebd0164cc7e3e8ead208418b4b80b2 Merge: cebfc7913 823140ab2 Author: Cy Chan Date: Mon Jan 7 14:19:15 2019 -0800 Merge branch 'development' into forkjoin commit cebfc791397d21fb888cdf5ecb3bc3b184013a3d Author: Cy Chan Date: Mon Jan 7 14:18:30 2019 -0800 ForkJoin Tutorial documentation edits and formatting Docs/sphinx_tutorials/source/AMR_Tutorial.rst Docs/sphinx_tutorials/source/ForkJoin_Tutorial.rst Docs/sphinx_tutorials/source/conf.py commit 96b8ba69bdafdbebf33150ddfae0cd7af692ac91 Author: Cy Chan Date: Mon Jan 7 11:41:43 2019 -0800 updates to ForkJoin/MLMG tutorial and documentation Docs/sphinx_tutorials/source/ForkJoin_Tutorial.rst Docs/sphinx_tutorials/source/figs/fork_join_tasks.png Docs/sphinx_tutorials/source/figs/mf_remap_hires.png Docs/sphinx_tutorials/source/figs/nested_fork_join_tasks.png Tutorials/ForkJoin/MLMG/inputs Tutorials/ForkJoin/MLMG/main.cpp commit 823140ab24fc993d9d35d4661a7f0acb7bbb5e65 Author: Johannes Blaschke Date: Mon Jan 7 20:09:03 2019 +0100 expand level-set documentation Docs/sphinx_documentation/source/EB.rst Src/EB/AMReX_EB_levelset.H commit 6af00cbeb1bd2cd6988fc6585fdfb6de80679d5c Merge: 76709e2a7 27b896530 Author: Johannes Blaschke Date: Mon Jan 7 19:16:41 2019 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 76709e2a78db888d4406c422516a1f7d86801c62 Author: Johannes Blaschke Date: Mon Jan 7 19:15:50 2019 +0100 start adding level-set documentation Docs/sphinx_documentation/source/EB.rst Docs/sphinx_documentation/source/EB/loc_ls_ex.png commit d0ad234d25324ab59d54a41aeda0e57163cb255a Author: Cy Chan Date: Mon Jan 7 10:04:30 2019 -0800 working on ForkJoin Tutorial Docs/sphinx_tutorials/source/ForkJoin_Tutorial.rst Tutorials/ForkJoin/Simple/MyTest.cpp commit 27b896530d2eeafdeb6c06e200e640bd68c35c27 Merge: e6ae5eed0 35ab62b94 Author: Weiqun Zhang Date: Mon Jan 7 08:56:01 2019 -0800 Merge branch 'weiqun/interp-3' into development commit e6ae5eed02d8a98de0ab2e7468cb8d2f152c1ccf Merge: 60dfa3c37 f094aed84 Author: Johannes Blaschke Date: Mon Jan 7 17:16:10 2019 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 60dfa3c37ca1b6d8b205d9f20ee821fafc4a6d52 Author: Johannes Blaschke Date: Mon Jan 7 17:16:04 2019 +0100 added more profiling Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp commit f094aed844058b50f244746c50c12cceb4cf5a1c Merge: 89054d418 807b01a19 Author: Andrew Myers Date: Mon Jan 7 06:48:29 2019 -0800 Merge pull request #395 from khou2020/ncmpi Add PnetCDF benchmark commit 807b01a198219221470cc34df4d1a4848bcb1b3a Merge: aeddee480 89054d418 Author: Kaiyuan Hou Date: Mon Jan 7 06:04:19 2019 -0600 Merge branch 'development' into ncmpi commit aeddee480a95a1548bbc3e5d7ede9ca9b3fdc4c6 Merge: 45704789d 2a75167fd Author: Kaiyuan Hou Date: Mon Jan 7 06:03:22 2019 -0600 Merge branch 'master' into ncmpi commit 89054d418601a6f50a58539cfda7af30bca1f049 Merge: 08d1d9857 78f5d8011 Author: Weiqun Zhang Date: Sun Jan 6 18:47:40 2019 -0800 Merge branch 'weiqun/interp-2' into development commit 08d1d9857913cd1d8d175ecc55acfc1faca368fc Merge: 80f401773 53761ce0b Author: Ann Almgren Date: Sun Jan 6 17:31:59 2019 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 80f401773b50c1ad8e1f07b3deef08fd3670b26c Author: Ann Almgren Date: Sun Jan 6 17:31:32 2019 -0800 Add non-const access functions for the level set arrays. Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_levelset.H commit 53761ce0b4947e02a35db733bd24ea2845378084 Author: Tan Nguyen Date: Sun Jan 6 17:25:26 2019 -0800 a small change in metadata extraction Src/Amr/AMReX_Amr.cpp commit c7c6f6d7e4546c29b9add83706c6bb8a68e2c35d Author: Tan Nguyen Date: Sun Jan 6 14:27:11 2019 -0800 fix a bug to avoid potential deadlocks Src/Amr/AMReX_Amr.cpp Src/AmrTask/rts_impls/mpi_pthreads/PackageQueue.H Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv.H commit bb3596507a374ce7362214e89d3563aa1e1b975b Author: Cy Chan Date: Sat Jan 5 21:29:26 2019 -0800 Move existing ForkJoin tutorial to Tutorials/ForkJoin/Simple demonstrates various ways of passing MultiFabs into forked tasks demonstrates setting task output directory Add second ForkJoin tutorial based on modified OldTutorials/MultiColor_C tutorial demonstrates reusing and nesting fork-joins demonstrates customizing component split across tasks for split MultiFabs Tutorials/ForkJoin/GNUmakefile Tutorials/ForkJoin/MLMG/GNUmakefile Tutorials/ForkJoin/MLMG/Make.package Tutorials/ForkJoin/MLMG/ff.f90 Tutorials/ForkJoin/MLMG/inputs Tutorials/ForkJoin/MLMG/main.cpp Tutorials/ForkJoin/Simple/GNUmakefile Tutorials/ForkJoin/Simple/Make.package Tutorials/ForkJoin/Simple/MyTest.H Tutorials/ForkJoin/Simple/MyTest.cpp Tutorials/ForkJoin/Simple/MyTest_F.H Tutorials/ForkJoin/Simple/inputs Tutorials/ForkJoin/Simple/main.cpp commit 1b9cec10d9f0164ffa39b0c6fe383406126bab94 Author: Cy Chan Date: Sat Jan 5 12:50:58 2019 -0800 modifications to ForkJoin: task_output_dir set through member function instead of constructor defaults to empty string (don't write task output files) dir created in fork_join invocation instead of constructor append to task output files instead of creating unique filenames simplify ComponentBounds() Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp Src/Base/AMReX_ParallelContext.H Tutorials/ForkJoin/MyTest.cpp commit ce68827cb299214f60478d55d7212785686cdc08 Author: Weiqun Zhang Date: Sat Jan 5 10:50:02 2019 -0800 rm performCopy because it is no longer used Src/Base/AMReX_BaseFab.H commit 9338b0c3de0642bf7884c15a5541b5b7cb918960 Author: Weiqun Zhang Date: Sat Jan 5 08:56:09 2019 -0800 start new BaseFab interface Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H commit 65047451c1652ca2f0238ecd0fa53eec4221432c Author: Johannes Blaschke Date: Sat Jan 5 15:46:12 2019 +0100 implicit function filling now also has the option to apply threshold Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_utils.cpp commit 61d230d5ed8c11ab906c1f9f375764ebc9307088 Merge: e860dee9b 2f3adfd4c Author: Johannes Blaschke Date: Sat Jan 5 12:18:47 2019 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 2f3adfd4c7d412eeb8c705113b319592fa483b69 Author: Andrew Myers Date: Fri Jan 4 16:12:42 2019 -0800 minor tweaks Docs/sphinx_tutorials/source/Particles_Tutorial.rst commit ec5ab53c76b57096feef4157a38116f8982237ca Merge: f061e5273 d05fcf2ef Author: Andrew Myers Date: Fri Jan 4 15:55:12 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f061e5273098a2407b3880f6d3a4eeb8eea0dfca Author: Andrew Myers Date: Fri Jan 4 15:54:59 2019 -0800 add description of the CellSortedParticles tutorial Docs/sphinx_tutorials/source/Particles_Tutorial.rst commit d05fcf2ef8d848ff51083ed70666ac8b516fb870 Merge: 1443b1339 e23d5421d Author: Andy Nonaka Date: Fri Jan 4 15:36:17 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 1443b13391aaa98ca0280e2e18c423aee9ee253f Author: Andy Nonaka Date: Fri Jan 4 15:36:00 2019 -0800 Tutorials/Amr README files copied into documentation Docs/sphinx_tutorials/source/AMR_Tutorial.rst Docs/sphinx_tutorials/source/Basic_Tutorial.rst commit e23d5421d0695a15f8f8e3a5a11037c6f7b07442 Merge: f54304faa 09022f7a2 Author: Andrew Myers Date: Fri Jan 4 15:04:51 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f54304faa93b9a8ceea148cac70ab6ccccfc2b39 Author: Andrew Myers Date: Fri Jan 4 15:00:10 2019 -0800 move LoadBalance from Tutorials to Tests - it's not really a full Tutorial. Tests/Particles/LoadBalance/GNUmakefile Tests/Particles/LoadBalance/Make.package Tests/Particles/LoadBalance/create_binary_particle_file.py Tests/Particles/LoadBalance/inputs Tests/Particles/LoadBalance/main.cpp Tests/Particles/LoadBalance/visualize_output.ipynb commit b3fd6d1946288f99b5e63131e9e26123544a7602 Author: Andrew Myers Date: Fri Jan 4 14:59:25 2019 -0800 minor changes Docs/sphinx_tutorials/source/Particles_Tutorial.rst commit d19a39976f31aabbf1589512fdb827819148cc22 Author: Andrew Myers Date: Fri Jan 4 14:50:31 2019 -0800 add a section on the ElectromagneticPIC tutorial Docs/sphinx_tutorials/source/Particles_Tutorial.rst commit 242bc17aae7b8df9a2b79844e8f7f9d20f4f29f8 Author: Andrew Myers Date: Fri Jan 4 14:21:03 2019 -0800 update sphinx documentation for particle tutorials Docs/sphinx_tutorials/source/Particles_Tutorial.rst commit f653b28c46cb194098474bb36f6aae20e4a428aa Author: Andrew Myers Date: Fri Jan 4 14:20:22 2019 -0800 merge the two NeighborList Tutorials into one 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Andy Nonaka Date: Fri Jan 4 13:15:21 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 8aea385cddf2603d1fe2331a99c5dd8f360b2460 Author: Andy Nonaka Date: Fri Jan 4 13:14:56 2019 -0800 add link to amrex documentation Docs/sphinx_tutorials/source/SWFFT_Tutorial.rst commit a73b82479070732308d744a910c2b16a00a71d62 Author: Weiqun Zhang Date: Fri Jan 4 11:15:31 2019 -0800 add a function to set the static data for periodicity in Geometry Src/Base/AMReX_Geometry.H commit e860dee9b18550a07e27aa91c756e83b5c92b779 Merge: 906d4cac8 431e9cb07 Author: Johannes Blaschke Date: Fri Jan 4 11:11:23 2019 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 431e9cb07247e8bca8d7a2f4ba668da16801b2cf Merge: c4cb0102e 68755c560 Author: Andrew Myers Date: Thu Jan 3 16:50:07 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c4cb0102e1c5c41108f63ffda0b0bfe71246d6e8 Author: Andrew Myers Date: Thu Jan 3 16:49:05 2019 -0800 add caveat about one of the code snippets in the GPU docs Docs/sphinx_documentation/source/GPU.rst commit e9b3d8a1ca7aa8b12f1787aeed761e8991382af1 Author: Andrew Myers Date: Thu Jan 3 16:43:12 2019 -0800 docs typo fix Docs/sphinx_documentation/source/GPU.rst commit 68755c56051e420828a58495161a2c878dfad313 Author: Weiqun Zhang Date: Thu Jan 3 15:20:47 2019 -0800 removed the unroll line I accidently left there Tutorials/GPU/Launch/MyKernel.H commit 0c687f0ad2e7a75928297dfea652f791e7b94600 Merge: 267643332 35ab62b94 Author: Weiqun Zhang Date: Thu Jan 3 14:55:30 2019 -0800 Merge branch 'weiqun/interp-3' into weiqun/gpu commit 267643332b59c77c531d6b2842ccae2a4fbdbc11 Merge: d110eaf5d 75e2ac89c Author: Weiqun Zhang Date: Thu Jan 3 14:55:16 2019 -0800 Merge branch 'development' into weiqun/gpu commit 75e2ac89cf240c9cd15cd11cb14f0e76eb71baac Author: Weiqun Zhang Date: Thu Jan 3 14:47:20 2019 -0800 minor changes to gpu documentation Docs/sphinx_documentation/source/GPU.rst commit 7675c8122d31302a3781244282fc2580147255d2 Author: Weiqun Zhang Date: Thu Jan 3 14:46:43 2019 -0800 add a new constructor to AsynArray so that it can be used as scratchpad Src/Base/AMReX_CudaAsyncArray.H commit c5a603e9fdcebbf1610c1857744d632c27b2ff63 Author: Tan Nguyen Date: Thu Jan 3 13:36:52 2019 -0800 minor changes in asyncIter guide Docs/sphinx_documentation/source/AsyncIter_Chapter.rst commit f1e993be3b7b9fd0bdaecbe743ae445297bb9a51 Author: Cy Chan Date: Thu Jan 3 12:58:49 2019 -0800 remove MLMG::Initialize/Finalize init MLLinOp the first time MLLinOp::define is called Src/Base/AMReX.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit d489bc34c6f40ef83e8bb6889c1f7fb87418f901 Merge: 1f28cbd76 97a5f8db0 Author: Andrew Myers Date: Thu Jan 3 13:00:43 2019 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1f28cbd760f07c2dede673a4e440c56e2d6ef335 Author: Andrew Myers Date: Thu Jan 3 13:00:27 2019 -0800 some double -> Real Tools/C_util/WritePlotFile.cpp commit 906d4cac82481d9ace9cd47d3414d2e7698b51e4 Merge: 1b838c4e6 97a5f8db0 Author: Johannes Blaschke Date: Thu Jan 3 21:21:57 2019 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 1b838c4e6a0e0c765b2c1c9deff321b7e46af9bd Author: Johannes Blaschke Date: Thu Jan 3 21:21:25 2019 +0100 clean up method naming convention and doxygen Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp commit 97a5f8db02bf192db882a01b356c6720b175bb6a Author: Kevin Gott Date: Thu Jan 3 10:42:23 2019 -0800 Profiling and summary GPU docs with pictures. Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/GPU/Streams.pdf Docs/sphinx_documentation/source/GPU/Streams.png Docs/sphinx_documentation/source/GPU/Streams.pptx Docs/sphinx_documentation/source/GPU/gpu_1.pdf Docs/sphinx_documentation/source/GPU/gpu_1.png Docs/sphinx_documentation/source/GPU/gpu_2.pdf Docs/sphinx_documentation/source/GPU/gpu_2.png Docs/sphinx_documentation/source/GPU/gpu_3.pdf Docs/sphinx_documentation/source/GPU/gpu_3.png commit 8ffc455134c12294394972e72709247a816baf3d Author: Kevin Gott Date: Thu Jan 3 10:41:25 2019 -0800 Doc warnings. Docs/sphinx_documentation/source/AmrCore.rst commit 9aa15a7cf406224c4a247e035875d10b2c669f44 Merge: 0dd74cf65 c3bfc420b Author: Weiqun Zhang Date: Thu Jan 3 09:55:55 2019 -0800 Merge branch 'weiqun/interp-1' into development commit 85f932820aa90c5e0d79a68580891673b95986b1 Author: Cy Chan Date: Wed Jan 2 17:48:02 2019 -0800 fix some issues with performance analysis / tuning features add MLMG::Initialize/Finalize move MLCellLinOp software performance counters to static class member clears counters on Finalize add MLLinOp::Initialize/Finalize use unique_ptr to manage comm_cache clears MPI communicator cache via destructor on Finalize add machine::Finalize use unique_ptr to manage machine object clears neighborhood cache via destructor on Finalize add optional argument to DistributionMapping::makeSFC to allow selecting old behavior Src/Base/AMReX.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_Machine.H Src/Base/AMReX_Machine.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/GNUmakefile Tests/LinearSolvers/MLMG/main.cpp commit 0dd74cf65a3a12646c3e927088fb123a3681f7cb Author: Tan Nguyen Date: Thu Jan 3 01:09:43 2019 -0800 update online guide for async Iters Docs/sphinx_documentation/source/AsyncIter.rst Docs/sphinx_documentation/source/AsyncIter_Chapter.rst commit 9477abdab118994177daff8ba0ce468d68c66396 Author: Andy Nonaka Date: Wed Jan 2 17:15:52 2019 -0800 some more details on ghost cells and fillpatch Docs/sphinx_documentation/source/AmrCore.rst Docs/sphinx_documentation/source/Basics.rst commit 4904d8f91c6d88b5d391b869142fa7a61395b100 Author: atmyers Date: Wed Jan 2 14:25:59 2019 -0800 adding another early exit to copyParticles Src/Particle/AMReX_ParticleContainerI.H commit bdcd2e307d486faf591a2c0f40c433bdce9ce8e2 Merge: 814b027ce 34984a372 Author: Cy P Chan Date: Wed Jan 2 12:51:02 2019 -0800 Merge pull request #393 from AMReX-Codes/weiqun/perf Weiqun/perf commit 34984a372e866e033ef484a4d543b993484518bb Merge: 6e2c32beb 814b027ce Author: WeiqunZhang Date: Wed Jan 2 12:12:52 2019 -0800 Merge branch 'cy-perf' into weiqun/perf commit 814b027ce0091ca90d7934280c00ded10287683b Merge: 3677d1f83 839bba4a1 Author: WeiqunZhang Date: Wed Jan 2 11:29:03 2019 -0800 Merge pull request #392 from AMReX-Codes/development Development commit 6e2c32bebb9f3dc5f3714257455257d1bc9183ea Author: Weiqun Zhang Date: Wed Jan 2 11:26:10 2019 -0800 minor changes: boost license, cmake, etc. Src/Base/AMReX_Machine.H Src/Base/AMReX_Machine.cpp Src/Base/AMReX_Utility.H Src/Base/CMakeLists.txt commit a37501507bf58cc9dc0864432231504ef6dd1e74 Merge: 3677d1f83 839bba4a1 Author: Weiqun Zhang Date: Wed Jan 2 10:11:26 2019 -0800 Merge branch 'development' into pr-388 commit 839bba4a149a1fb74de7ad3c861aad2737586720 Merge: 2a75167fd 4743ed44b Author: Weiqun Zhang Date: Wed Jan 2 10:08:52 2019 -0800 Merge branch 'weiqun/fluxregister' into development commit 2a75167fd3febd46e0090a89941e42793224ad15 Author: Weiqun Zhang Date: Wed Jan 2 10:06:55 2019 -0800 update changes CHANGES commit 053a0b4f0010f68847a984b4563b2c69bc04853b Author: Brandon Runnels Date: Wed Jan 2 10:46:27 2019 -0700 tidied up Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit e6292c5146f5487f36213e7f990e12627ad3aafc Merge: b1708cefd 557c5de1f Author: Brandon Runnels Date: Wed Jan 2 10:21:22 2019 -0700 Merge branch 'development' into nodeghostcells commit 557c5de1fce005f018c6c36acc693de28d8c2042 Author: Johannes Blaschke Date: Tue Jan 1 14:19:09 2019 +0100 add utility function automating levelset__eb_pad Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp commit e991da7e44177626617d8048aa0bc9c800ed45ea Author: Johannes Blaschke Date: Tue Jan 1 14:00:55 2019 +0100 update Doxygen Src/EB/AMReX_EB_levelset.H commit bcfb3f08f23b16e9336a26d8d3a5c90c51cb7185 Author: Johannes Blaschke Date: Sun Dec 30 17:44:46 2018 +0100 fix level-set thresholding Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp commit ba52db4f9053cf44d013eb2f7b85ee13e1a10300 Merge: 9e6b91436 f07d6c7c4 Author: Johannes Blaschke Date: Sun Dec 30 12:19:21 2018 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 9e6b91436513abc972d71d2804dca4ae4d5c156e Author: Johannes Blaschke Date: Sun Dec 30 12:19:17 2018 +0100 clean up function name and doxygen Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp commit f07d6c7c41e0872c27f0a2af3ee969ec48d282c3 Author: Tan Nguyen Date: Sat Dec 29 21:58:46 2018 -0800 remove async metadata at stop time Src/Amr/AMReX_Amr.cpp Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.cpp commit 798f0279177cf47d85eb76dd886e1e663f765bfc Author: Ann Almgren Date: Sat Dec 29 17:50:37 2018 -0800 Replace std::cout by amrex::Print() Src/Extern/Algoim/AMReX_algoim_integrals.cpp commit c0bbc307818bc7fccdf83969d400ab212043ca65 Author: Kevin Gott Date: Sat Dec 29 15:45:45 2018 -0800 Fix numbered list for GPU docs. Docs/sphinx_documentation/source/GPU.rst commit 6a4bfc13e81b84e978c0a9e7ee0712c216f465f1 Author: Tan Nguyen Date: Sat Dec 29 14:04:50 2018 -0800 fix a memory leak bug in the upcxx backend Src/Amr/AMReX_Amr.cpp Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.H Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.cpp Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.cpp Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.H Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.upcxx.pthreads commit 3c5c92f231dfa364ce39be7b5111a4a8b331b9fb Author: Johannes Blaschke Date: Sat Dec 29 15:45:28 2018 +0100 update level-set doxygen Src/EB/AMReX_EB_levelset.H commit 9b219390a1c7f72c03a7efa0254d0d9912479682 Author: Johannes Blaschke Date: Sat Dec 29 15:40:07 2018 +0100 fix sign error in local leve-set filling Src/EB/AMReX_EB_levelset.cpp commit 7f7f1a43bcf782f25c167105fa4b52cf805d0a04 Author: Johannes Blaschke Date: Sat Dec 29 15:21:53 2018 +0100 clean up LSFactory function names Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp commit 81d8ba0d214dc365594e754e5d18dc7b36910684 Author: Johannes Blaschke Date: Sat Dec 29 15:14:28 2018 +0100 profile LSFactory fill local Src/EB/AMReX_EB_levelset.cpp commit 3002590269b8507172e0c56f3d82921bb4b9c27a Author: Johannes Blaschke Date: Sat Dec 29 15:12:26 2018 +0100 document level-set doxygen Src/EB/AMReX_EB_levelset.H commit 40ae1781ccf8fc18192710d739f8c0a125fa5666 Author: Johannes Blaschke Date: Sat Dec 29 14:59:51 2018 +0100 make eb_facets public Src/EB/AMReX_EB_levelset.H commit d357fa84b1c9f47942e6aa1268ea34590cb6b886 Author: Johannes Blaschke Date: Sat Dec 29 12:09:37 2018 +0100 start adding profiling the level-set Src/EB/AMReX_EB_levelset.cpp commit 838cd775a814bb1b6ec72208c1c410c2c813b497 Author: Johannes Blaschke Date: Sat Dec 29 11:54:31 2018 +0100 continue documenting more level-set stuff Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp commit ed39914f2660117b2d5b54d60aabe463e071202a Author: Ann Almgren Date: Fri Dec 28 20:03:49 2018 -0800 Change so that we only print "Bottom solve failed" when mg_verbose > 1 not >= 1 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit a23fbae244879bd048818729ef9b4e77feb9cacd Author: Ann Almgren Date: Fri Dec 28 19:01:06 2018 -0800 If the BiCG bottom solver fails then sets the "solution" it found to 0 before going into the "bottom smooth" (if nub > 0). This enables certain solves to converge which don't otherwise. Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 00d23045be82aab53f36d2ca57acd3fa78d3e504 Author: Kevin Gott Date: Thu Dec 27 15:46:34 2018 -0800 Generic loop launch GPU streams docs. Docs/sphinx_documentation/source/GPU.rst commit 4743ed44b4f699cc4f0d061c696ec2947afba893 Author: Weiqun Zhang Date: Tue Dec 25 15:59:28 2018 -0800 gpu: BndryRegister Src/AmrCore/AMReX_FluxReg_2D_C.H Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp commit 6d08f6a76fa5dbf15eb6614695ab81e0e2e351eb Author: Weiqun Zhang Date: Tue Dec 25 12:57:16 2018 -0800 fix component index in FineAdd Src/AmrCore/AMReX_FluxReg_1D_C.H Src/AmrCore/AMReX_FluxReg_2D_C.H Src/AmrCore/AMReX_FluxReg_3D_C.H commit ecc7f8ac9dd6d19833653692236cf4e9bf2fb0a6 Author: Johannes Blaschke Date: Tue Dec 25 03:15:56 2018 -0800 this used to fail in debug, even though subsequent checks catch bad EB, this cange makes it safe in debug also Src/EB/AMReX_EB_levelset.cpp commit 86d9062f07884c8b4740515ff279d1b3e0421507 Author: Weiqun Zhang Date: Mon Dec 24 19:35:44 2018 -0800 gpu: FluxRegister in 1D and 2D Src/AmrCore/AMReX_FLUXREG_1D.F90 Src/AmrCore/AMReX_FLUXREG_2D.F90 Src/AmrCore/AMReX_FLUXREG_3D.F90 Src/AmrCore/AMReX_FLUXREG_F.H Src/AmrCore/AMReX_FluxReg_1D_C.H Src/AmrCore/AMReX_FluxReg_2D_C.H Src/AmrCore/AMReX_FluxReg_3D_C.H Src/AmrCore/CMakeLists.txt Src/AmrCore/Make.package commit 0826c3368a949a3f359f8bef9aad6d87496c5f05 Author: Weiqun Zhang Date: Mon Dec 24 18:04:21 2018 -0800 gpu: FluxRegister in 3D Src/AmrCore/AMReX_FluxReg_3D_C.H Src/AmrCore/AMReX_FluxRegister.cpp commit b1708cefdf8a65f10ef617f8c8c1008c0dcd6e91 Merge: cc0c0e3e8 096e7732c Author: Brandon Runnels Date: Mon Dec 24 16:05:47 2018 -0700 Merge branch 'development' into nodeghostcells commit cc0c0e3e83edf64ebdf846243146d186aa9682c0 Author: Brandon Runnels Date: Mon Dec 24 16:04:58 2018 -0700 removed unnecessary ghost cell copy for rhs fab GNUmakefile Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 096e7732c3c87fd23db4b406ed4dd42ae5c3db04 Author: Tan Nguyen Date: Mon Dec 24 02:09:16 2018 -0800 a few small updates on the upcxx backend Src/Amr/AMReX_Amr.cpp commit 45704789db59d6195b4a9dd2c2f38c138a56b3af Author: Kaiyuan Hou Date: Mon Dec 24 00:19:33 2018 -0600 add performance result Tests/PnetCDFBenchmark/ReadMe commit 08211da50a6a4793d512f64515940d2e6e44887d Author: Weiqun Zhang Date: Sun Dec 23 15:54:58 2018 -0800 WIP: FluxRegister::FineAdd on gpu Src/AmrCore/AMReX_FluxReg_1D_C.H Src/AmrCore/AMReX_FluxReg_2D_C.H Src/AmrCore/AMReX_FluxReg_3D_C.H Src/AmrCore/AMReX_FluxReg_C.H Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/CMakeLists.txt Src/AmrCore/Make.package commit d18c55b82cd5218944e98ea2571c789015444887 Merge: fa1bbf87d a25c1ce15 Author: Kevin Gott Date: Sun Dec 23 14:49:01 2018 -0800 Merge branch 'development' into gpu commit fa1bbf87d7d01e48f862f59fcdbb82c75ffd31c5 Author: Kevin Gott Date: Sun Dec 23 14:48:28 2018 -0800 Doc bugs fix. Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_tutorials/source/ForkJoin_Tutorial.rst Docs/sphinx_tutorials/source/MUI_Tutorial.rst Docs/sphinx_tutorials/source/SDC_Tutorial.rst commit f4533acc9955f6864359dd5a22b3f07428e64908 Author: Kevin Gott Date: Sun Dec 23 14:37:44 2018 -0800 GPU how-to tutorial doc. Docs/sphinx_tutorials/source/GPU_Tutorial.rst commit 6cd5eae47593b91b18781134ffd73daa72b16d59 Author: Kevin Gott Date: Sun Dec 23 14:37:18 2018 -0800 First draft of GPU docs. Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/GPU.rst commit a9773a33e7e383962ae687f0af0a38f9c14697cd Author: Kaiyuan Hou Date: Sun Dec 23 02:00:01 2018 -0600 add comment Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.cpp commit 2d9299d77f3d3f2f37fa919928fd977279d4da7c Author: Weiqun Zhang Date: Sat Dec 22 20:50:14 2018 -0800 WIP: FluxRegister on gpu Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/Boundary/AMReX_FabSet.H commit 75097b0aa3bcb1b321c589c01ef492e81c170681 Author: Weiqun Zhang Date: Sat Dec 22 16:40:22 2018 -0800 gpu: FabSet Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_FabSet.cpp commit a25c1ce154bca6202dda26de2662a17028d314d5 Merge: 3110cacc9 59b225f08 Author: Johannes Blaschke Date: Sat Dec 22 23:24:57 2018 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 3110cacc94e2f52e2989f2a83ebb8a2da12ef82f Author: Johannes Blaschke Date: Sat Dec 22 23:24:52 2018 +0100 expose level-set filling functions as static functions. This makes incorporating level-sets without LSFactory easier Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp commit 59b225f088034a66409306092c0d819ece4e2057 Author: Weiqun Zhang Date: Sat Dec 22 12:31:17 2018 -0800 add fabHostPtr and fabDevicePtr to FabArray and make fabPtr's return depends on whether it is in gpu launch region Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_iMultiFab.cpp commit 7f1384179c1ae0e43afa41efeb5f2a5a33fe6b31 Author: Kevin Gott Date: Sat Dec 22 01:13:24 2018 -0500 Add synch. Tutorials/GPU/Launch/main.cpp commit 2e218ad5c54ee83affca17845639e65e24970f82 Author: Kevin Gott Date: Sat Dec 22 01:11:40 2018 -0500 Loop lambda works. Remove check. Tutorials/GPU/Launch/main.cpp commit dbf9905e4065b5d420dced99fb1a8383caac30a6 Author: Weiqun Zhang Date: Fri Dec 21 20:25:17 2018 -0800 make stop time smaller Tutorials/GPU/CNS/Exec/RT/inputs commit 35ab62b94c1e7e296a47bbbec67c97753d5ea73c Merge: afdd73c13 78f5d8011 Author: Weiqun Zhang Date: Fri Dec 21 20:24:14 2018 -0800 Merge branch 'weiqun/interp-2' into weiqun/interp-3 commit 78f5d8011f90191b56e134d403dbf25bfd4f11e8 Merge: 012b7cf9c c3bfc420b Author: Weiqun Zhang Date: Fri Dec 21 20:23:19 2018 -0800 Merge branch 'weiqun/interp-1' into weiqun/interp-2 commit c3bfc420b6bdfa426c52561f9ede8a616fee778b Author: Weiqun Zhang Date: Fri Dec 21 20:22:46 2018 -0800 fix a new bug in interpolater Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H commit b21bdad0ae4307afc3ae514bbfebc966667fd377 Author: Kevin Gott Date: Fri Dec 21 17:37:33 2018 -0800 Loop launch example. Tutorials/GPU/Launch/main.cpp commit 501014c3031d910b6d0e37249fc93da68b45640d Author: Brandon Runnels Date: Fri Dec 21 17:14:52 2018 -0700 implemented amrex_mlmg_lin_nd_interp for 3D GNUmakefile Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 commit b03b18a7d082fa9645e8ebefcfcc3eecb89e4513 Merge: 543a67898 09ee73331 Author: Weiqun Zhang Date: Fri Dec 21 15:17:24 2018 -0800 Merge branch 'development' into weiqun/interp-1 commit 09ee73331316f1bda0547354d42ceaf869ead786 Author: Weiqun Zhang Date: Fri Dec 21 14:39:06 2018 -0800 Tutorials/GPU/CNS: compute T Tutorials/GPU/CNS/Exec/RT/inputs Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_parm.H Tutorials/GPU/CNS/Source/CNS_parm.cpp commit 6b4a9fe38ce2ff96577d0f1443f4564ea2a611a4 Author: Weiqun Zhang Date: Fri Dec 21 14:12:11 2018 -0800 Tutorials/GPU/CNS: store runtime parameters as managed variables Src/Base/AMReX_GpuQualifiers.H Tutorials/GPU/CNS/Exec/RT/Make.package Tutorials/GPU/CNS/Exec/RT/cns_prob.H Tutorials/GPU/CNS/Exec/RT/cns_prob.cpp Tutorials/GPU/CNS/Exec/RT/cns_prob_parm.H Tutorials/GPU/CNS/Exec/RT/inputs Tutorials/GPU/CNS/Exec/Sod/Make.package Tutorials/GPU/CNS/Exec/Sod/cns_prob.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/CNS/Exec/Sod/cns_prob_parm.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_parm.H Tutorials/GPU/CNS/Source/CNS_parm.cpp Tutorials/GPU/CNS/Source/Make.package Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H commit d30b06969ba14479c6502687afff265f87b68070 Author: Brandon Runnels Date: Fri Dec 21 15:01:11 2018 -0700 BR GNUmakefile commit d0a01e2ad54bea8f035bf25d52e8082c487b4858 Author: Weiqun Zhang Date: Fri Dec 21 12:50:09 2018 -0800 need to ifdef Src/AmrCore/AMReX_TagBox.cpp commit 07bbc35ac91af9e5a8ec50aa9f227ab851337021 Author: Weiqun Zhang Date: Fri Dec 21 12:48:35 2018 -0800 TagBox on gpu: we must coarsen both device and host fabs Src/AmrCore/AMReX_TagBox.cpp commit 2600464be0ef6b2c004d377a61c3b468b7cb59a2 Author: Weiqun Zhang Date: Thu Dec 20 17:04:58 2018 -0800 Tutorials/GPU/CNS: add RT test Tutorials/GPU/CNS/Exec/RT/GNUmakefile Tutorials/GPU/CNS/Exec/RT/Make.package Tutorials/GPU/CNS/Exec/RT/cns_prob.H Tutorials/GPU/CNS/Exec/RT/cns_prob.cpp Tutorials/GPU/CNS/Exec/RT/inputs commit 07ea653a2492e440da3fa719814278f40af66622 Author: Weiqun Zhang Date: Thu Dec 20 17:04:03 2018 -0800 Tutorials/GPU/CNS: add gravity Tutorials/GPU/CNS/Source/CNS.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp commit 43c833e1d9f02422629a47e1bac13474c7e7fd93 Author: Kaiyuan Hou Date: Fri Dec 21 03:21:35 2018 -0600 update to dev branch Tests/HDF5Benchmark/GNUmakefile Tests/PnetCDFBenchmark/ReadMe Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.cpp Tests/PnetCDFBenchmark/inputs Tests/PnetCDFBenchmark/main.cpp commit 136052781abe601a746b393f8a8a806e5e5d01d8 Merge: e13946693 766aa2052 Author: Kaiyuan Hou Date: Fri Dec 21 00:13:44 2018 -0600 Merge remote-tracking branch 'upstream/development' into ncmpi commit 3dd9faa830269848a048572f9af543d2c10c243a Author: Brandon Runnels Date: Thu Dec 20 18:12:45 2018 -0700 updated ghost cell copy and streamlined some of the code Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 commit d110eaf5d79db4f4daa5e3fe61a52d082ac5cb15 Author: Weiqun Zhang Date: Thu Dec 20 17:04:58 2018 -0800 Tutorials/GPU/CNS: add RT test Tutorials/GPU/CNS/Exec/RT/GNUmakefile Tutorials/GPU/CNS/Exec/RT/Make.package Tutorials/GPU/CNS/Exec/RT/cns_prob.H Tutorials/GPU/CNS/Exec/RT/cns_prob.cpp Tutorials/GPU/CNS/Exec/RT/inputs commit bc5133e87b665864c9df5030fbd49d1726318f73 Author: Weiqun Zhang Date: Thu Dec 20 17:04:03 2018 -0800 Tutorials/GPU/CNS: add gravity Tutorials/GPU/CNS/Source/CNS.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp commit afdd73c13cfe98f062c7afb96006c58034d87cb5 Author: Weiqun Zhang Date: Thu Dec 20 15:54:13 2018 -0800 clean up and comments Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/AmrCore/AMReX_INTERP_F.H Src/AmrCore/AMReX_Interpolater.cpp commit 55a82eabd947217b38dc8e1e628d41ccbcd000e8 Author: Weiqun Zhang Date: Thu Dec 20 15:31:32 2018 -0800 NodeBilinear on gpu Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_Interpolater.cpp commit 012b7cf9c47f60277fe0d0341e8d62d7c054137a Author: Weiqun Zhang Date: Thu Dec 20 11:14:15 2018 -0800 rm old fortran routines for pcinterp Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/AmrCore/AMReX_INTERP_F.H commit 90dd9f5fa832128406c2dd7bc7d51d894b73e0d0 Author: Weiqun Zhang Date: Thu Dec 20 11:08:18 2018 -0800 fix volume coordinates for 1d spherical coordinates. note that this is a long-standing issue we never bothered to fix. Src/Base/AMReX_CoordSys.cpp commit cb732a1a9e28ffb98c3c8569133d882f92d5beff Author: Weiqun Zhang Date: Thu Dec 20 10:45:51 2018 -0800 PCInterp on gpu Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_Interpolater.cpp commit 543a67898de1c5456d5ebede63ca3ca6036a2d15 Author: Weiqun Zhang Date: Thu Dec 20 10:32:30 2018 -0800 minor optimization Src/AmrCore/AMReX_Interp_3D_C.H commit 766aa20522d667922b3161799a89fb5a0713a712 Author: Johannes Blaschke Date: Thu Dec 20 17:27:50 2018 +0100 update gitignore .gitignore commit a3ee515b1843c5c4625d382d45f0567b8e9c09bb Author: Kevin Gott Date: Wed Dec 19 17:50:43 2018 -0800 Fix documentation warnings. Docs/sphinx_documentation/source/Tutorials_Chapter.rst Docs/sphinx_documentation/source/index.rst commit dc2632f340ae863bb5d8d43e879a01277ae00169 Merge: 92d6463f7 71c54b24e Author: Kevin Gott Date: Wed Dec 19 17:23:09 2018 -0800 Merge branch 'development' into gpu commit 92d6463f7d44698dcc8cd59a24306656f3d57c43 Author: Kevin Gott Date: Wed Dec 19 17:16:30 2018 -0800 Plane docs Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/GPU_Chapter.rst commit ade23a1813d035d7763016644f194b37d7180554 Merge: 2d687b4ff 71c54b24e Author: Weiqun Zhang Date: Wed Dec 19 16:53:01 2018 -0800 Merge branch 'development' into weiqun/interp-1 commit 71c54b24e55bdb87a3a9332a5bc3bab7c6e36048 Author: Andy Nonaka Date: Wed Dec 19 16:44:42 2018 -0800 bugfix in avgdown_faces... was only operating on component 0 Src/Base/AMReX_MultiFabUtil.cpp commit 32dbac07c887c1b36f22eff98cee8f174b3af657 Author: Brandon Runnels Date: Wed Dec 19 17:06:19 2018 -0700 initial working version in 2D Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 commit 42fd595bd0c40773cadfceedef6f80e9a83ed890 Author: Johannes Blaschke Date: Thu Dec 20 00:06:54 2018 +0100 act on Weiqun's advice Src/Base/AMReX_MultiFabUtil.H commit 7fc8e63e76084b2d3dc8f08e5828961adb112b7c Author: Johannes Blaschke Date: Thu Dec 20 00:06:36 2018 +0100 fix comment Src/Base/AMReX_MultiFabUtil.H commit 2d687b4ff8402eae5ee2e61434204faa812a94e6 Author: Weiqun Zhang Date: Wed Dec 19 14:57:08 2018 -0800 partially updated CellConservativeProtected Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/AmrCore/AMReX_INTERP_F.H Src/AmrCore/AMReX_Interpolater.cpp commit 0a6260d134b7134959204f212b4691089021534f Merge: 3205ba40e 70cbf86a9 Author: Johannes Blaschke Date: Wed Dec 19 23:40:41 2018 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 3205ba40e56eabb799cebcd0af03e2684b7751c0 Author: Johannes Blaschke Date: Wed Dec 19 23:40:36 2018 +0100 move multifab utils used by LSCore to a better place and document in doxygen Src/Base/AMReX_MultiFabUtil.H Src/EB/AMReX_EB_LSCoreBase.H commit 3677d1f8302550d0333ba77949cb891a99e82dc7 Author: Cy Chan Date: Wed Dec 19 13:55:52 2018 -0800 some cleanup Src/Base/AMReX_DistributionMapping.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit e49bfb3acb01542ab1d502a16a39ce99261e2dbb Author: Weiqun Zhang Date: Wed Dec 19 13:41:46 2018 -0800 linccinterp in 1d and 2d Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp Src/Base/AMReX_CoordSys.cpp commit 70cbf86a9b37c3b8946b2b92a22f9207d092b893 Author: Andrew Myers Date: Wed Dec 19 13:46:31 2018 -0800 Adding clearParticles and copyParticles method to ParticleContainer. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit c05273cf1021460d8a56bb7e0a09174017eda5a8 Merge: d18c06be6 ec573fe36 Author: Cy Chan Date: Wed Dec 19 13:29:35 2018 -0800 Merge branch 'development' into cy-perf commit d6861a144f06378342d635de3ddedd4a0496d035 Author: Brandon Runnels Date: Wed Dec 19 14:28:16 2018 -0700 updating C/F interpolation to update ghost cells as well as other cells Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 commit 981651a49b919efb1f7cf7220c23da0c7e3047bc Author: Weiqun Zhang Date: Wed Dec 19 12:35:03 2018 -0800 add some comments and clean up Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_Interpolater.cpp commit be0da1a69439e0b08fed5e6263c80ac348ddc777 Author: Weiqun Zhang Date: Wed Dec 19 11:13:04 2018 -0800 fix issues in 3D CellConservative Interpolater Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_Interpolater.cpp commit 3c6999c58df3cba6629eee8bcb1ac437401a9f06 Author: Johannes Blaschke Date: Wed Dec 19 18:12:37 2018 +0100 clean up comments and formatting Src/Base/AMReX_MultiFabUtil.H commit ec573fe367a068b32346a0eda97b9b892827fd7b Author: Tan Nguyen Date: Wed Dec 19 00:39:15 2018 -0800 partially fix a memory leak bug in the upcxx backend Src/Amr/AMReX_Amr.cpp Src/AmrTask/rts_impls/mpi_pthreads/PackageQueue.cpp Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.H Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/pthreads_common/LocalConnection.H Src/AmrTask/rts_impls/pthreads_common/PerillaMemCheck.cpp Src/AmrTask/rts_impls/pthreads_common/RemoteConnection.H Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.H Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.cpp Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.cpp Src/AmrTask/rts_impls/upcxx_pthreads/PerillaRts.cpp Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.H Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.cpp commit f92fbe20ee3ea0212bb55bade65dfda1b6963bd7 Author: Kevin Gott Date: Wed Dec 19 00:37:30 2018 -0800 WIP: GPU docs. Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/GPU_Chapter.rst commit f287e1a3358706478d014b5349e886a4c1801c8b Author: Weiqun Zhang Date: Tue Dec 18 21:15:58 2018 -0800 fix omp performance in atomicAdd Src/Base/AMReX_BaseFab.H commit f234852f473dc914eb204d98e131683134e043b5 Author: Kevin Gott Date: Tue Dec 18 20:24:10 2018 -0500 Add flag to script to turn off GPUDirect. Tutorials/GPU/run.summit commit d18c06be6e37e2cdef03832a95f0cdb8cd3d17fe Author: Cy Chan Date: Tue Dec 18 14:07:32 2018 -0800 clean up performance analysis a bit Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_Machine.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tests/LinearSolvers/MLMG/inputs Tools/Backtrace/parse_bt.py commit 00434689bd119d256605f4118bc15dd956feea49 Author: Andrew Myers Date: Tue Dec 18 13:48:24 2018 -0800 get the in and out file names from the command line Tools/Postprocessing/C_Src/cube_extract.cpp commit b4341be444362a69c58ff6ea9dae8099b5d5851f Author: Weiqun Zhang Date: Tue Dec 18 13:47:22 2018 -0800 3D CellConservative Interpolater on gpu Src/AmrCore/AMReX_INTERP_3D.F90 Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp commit cef7b115e7e3bbe1b0a8e5e2d4670bf8529a02e4 Author: Andrew Myers Date: Tue Dec 18 13:27:33 2018 -0800 a utility for extracting a sub-region from a plotfile. Tools/Postprocessing/C_Src/GNUmakefile Tools/Postprocessing/C_Src/cube_extract.cpp commit d84739688bb420d9abf6c29a2b4044b935f54c5f Merge: 50bc84011 900ce1f3b Author: Cy Chan Date: Tue Dec 18 13:14:55 2018 -0800 Merge branch 'development' into cy-perf commit 900ce1f3ba6c92b7ee14d5bbb658d4c89bda5e56 Author: Andrew Myers Date: Mon Dec 17 15:58:02 2018 -0800 tweak snippet slightly Docs/sphinx_documentation/source/GPU.rst commit 097a5f9c130a6c50db9b56247efc87eed7d885fb Author: Andrew Myers Date: Mon Dec 17 15:56:30 2018 -0800 add examples of Cuda::HostVector and Cuda::DeviceVector Docs/sphinx_documentation/source/GPU.rst commit 59a8c2348c29d66f778bb3e2deb447b27e4d3f11 Author: Andrew Myers Date: Mon Dec 17 15:39:17 2018 -0800 fix markdown Docs/sphinx_documentation/source/GPU.rst commit 21eccaff6ef7a17b9361d77ff7221e5d4871e991 Author: Andrew Myers Date: Mon Dec 17 15:38:38 2018 -0800 fix highlight section Docs/sphinx_documentation/source/GPU.rst commit 5d6cc3d35630cf23bb7e1567d29ed38116f895d0 Author: Andrew Myers Date: Mon Dec 17 15:36:31 2018 -0800 add OpenACC example to GPU documentation Docs/sphinx_documentation/source/GPU.rst commit 6d459567d990f3f3086ede73a282f74fd31c64b9 Author: Andrew Myers Date: Mon Dec 17 15:23:18 2018 -0800 remove Cuda Fortran version of EM PIC tutorial Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/inputs Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/script.sh commit bbf880fe5306655392f7c6edaa7bd053e91ae767 Merge: 9d5c71989 e1f547915 Author: Andrew Myers Date: Mon Dec 17 15:17:48 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9d5c71989f2f4b674513af109637d91b25c08557 Author: Andrew Myers Date: Mon Dec 17 15:00:09 2018 -0800 these variables are no longer managed Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90 commit 50bc840111cbe9b73ef6df579562846c62fa001f Author: Cy Chan Date: Mon Dec 17 14:34:12 2018 -0800 DistributionMapping: use ParallelAllGather functions Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_ParallelReduce.H commit 4eabf6fafaa0402fda8346acf728468a1f86a6de Author: Kevin Gott Date: Mon Dec 17 14:25:40 2018 -0800 WIP: GPU docs edit. Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/GPU_Chapter.rst commit a0d3372539957d3363b7809ec75e41e9427e0f5e Author: Kevin Gott Date: Thu Dec 13 15:32:26 2018 -0800 Adjust to remove warning in docs. Docs/sphinx_documentation/source/SWFFT.rst commit 1f202d7331ae76d97a4c8218cea28ac5ddb3ae60 Author: Cy Chan Date: Mon Dec 17 14:11:18 2018 -0800 add current subgroup ranks to comm cache hash key Src/Base/AMReX_Machine.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit df45733f3778a2b9028f5d138fa1bb716e61ecf4 Author: Weiqun Zhang Date: Mon Dec 17 13:59:43 2018 -0800 2d compiles Src/AmrCore/AMReX_Interpolater.cpp commit f27e4f58aa341246d4aea1bb227aa22ac7c02a13 Author: Andrew Myers Date: Mon Dec 17 13:51:34 2018 -0800 can't use ParticlesAt here Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp commit 3d7c6cf7f3d1089cfa79a15870f5b28e034b4cfa Author: Weiqun Zhang Date: Mon Dec 17 13:51:23 2018 -0800 fix assertion Src/AmrCore/AMReX_Interpolater.cpp commit 75ad8c5d570f9719483c583fabe2cd9fee5a4665 Author: Weiqun Zhang Date: Mon Dec 17 13:45:58 2018 -0800 fix 2d and minor tweak Src/AmrCore/AMReX_Interp_3D_C.H Src/Base/AMReX_IntVect.H commit 3093f89a9e45d7e03550dcc501dbee84e752024c Author: Andrew Myers Date: Mon Dec 17 13:45:07 2018 -0800 Tutorial compiles again Src/Particle/AMReX_Particles.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Source/main.cpp commit 36d3535f93dc41afd66c8d2c58cf8b5662ab767c Author: Andrew Myers Date: Mon Dec 17 13:02:59 2018 -0800 remove unused include Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.H commit 3bd07a0dc043c4bb1044c6fbac6cc4852c5cdcc7 Author: Cy Chan Date: Mon Dec 17 13:00:46 2018 -0800 move hash_combine() and hash_vector() to AMReX_Utility.H Src/Base/AMReX_Machine.cpp Src/Base/AMReX_Utility.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit ff4940125952ec492e0cc4d20cf8d73dd2968f8d Author: Andrew Myers Date: Mon Dec 17 12:58:27 2018 -0800 fix tabs / spaces issue in emacs Tutorials/Particles/ElectromagneticPIC/Make.EMPIC commit dfff9586e950d24a98b3e452cbc500077b17f8d7 Author: Cy Chan Date: Mon Dec 17 12:47:57 2018 -0800 move AMReX_Machine files Src/Base/AMReX_Machine.H Src/Base/AMReX_Machine.cpp Src/Base/Make.package Src/LinearSolvers/MLMG/Make.package commit ed2dd5c8c5062595a5bbd91ec82ef38617a1c41d Author: Andrew Myers Date: Mon Dec 17 12:46:09 2018 -0800 update fortran subroutines Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_F.H commit 4e9f1eb3a9dc72968729c6a86264b17a057233d4 Author: Weiqun Zhang Date: Mon Dec 17 12:37:25 2018 -0800 Unlimited 3D CellConservative Interpolater on gpu Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_IntVect.H commit 6b6fdea486eda47d38a2d0dec7fd7fd1759b2a9b Author: Andrew Myers Date: Mon Dec 17 12:22:19 2018 -0800 update EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp commit 82d11e853a0e2d20f5a0698d19d1419cddddbb18 Author: Andrew Myers Date: Mon Dec 17 11:57:02 2018 -0800 new form of ParticlesAt that is templated on Iterator type Src/Particle/AMReX_Particles.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp commit 1a1c248ee5fd242f72a97c3bf707092180c3bdb6 Author: Andrew Myers Date: Mon Dec 17 11:49:50 2018 -0800 use MakeMFIter instead of iterating over the mask Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp commit 5cfc36eac9a2bdd9563d8fd04e60de9d0d209b12 Author: Cy Chan Date: Mon Dec 17 11:47:47 2018 -0800 updates to support non-MPI build Src/LinearSolvers/MLMG/AMReX_Machine.cpp Tests/LinearSolvers/MLMG/inputs commit e659f9506f00e803d3c53409c1fd377ec266e1c4 Author: Andrew Myers Date: Mon Dec 17 11:25:40 2018 -0800 forgot namespace Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp commit b03f77ad38f3b6d06a67ab220a77bc94afb5ff3a Author: Andrew Myers Date: Mon Dec 17 11:22:37 2018 -0800 thrust::copy -> thrust_copy Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp commit 319f599b455c0bdd7a15f6851cfdb46e0e665ad9 Author: Andrew Myers Date: Mon Dec 17 11:15:15 2018 -0800 some renaming Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/EMParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Make.package Tutorials/Particles/ElectromagneticPIC/Source/main.cpp commit 9cad441d4f3a8a1e2d2306bb0e9cdc79afa9ed52 Author: Andrew Myers Date: Mon Dec 17 11:11:18 2018 -0800 add EMParIter Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H commit e1f547915158c59342f9526d5fc5210ad17054cd Merge: 62004898c 7d6616883 Author: Weiqun Zhang Date: Sun Dec 16 18:03:34 2018 -0800 Merge branch 'weiqun/gpu' into development commit 62004898cced1661774d4d05a4664a15975b7ca7 Author: Weiqun Zhang Date: Sat Dec 15 15:48:22 2018 -0500 add extra -lmpi_ibm on summitdev Tools/GNUMake/sites/Make.olcf commit 7d661688335f60d922cb217692e55e3f433ca7be Author: Weiqun Zhang Date: Fri Dec 14 22:18:16 2018 -0800 remove FabArray constructor that takes FAB::value_type Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/EB/AMReX_EB2_MultiGFab.cpp commit fb041279a96defaf91556dc47551fb7c2d17331e Author: Weiqun Zhang Date: Fri Dec 14 16:37:39 2018 -0800 add some empty files for interpolater in C++ Src/AmrCore/AMReX_Interp_1D_C.H Src/AmrCore/AMReX_Interp_2D_C.H Src/AmrCore/AMReX_Interp_3D_C.H Src/AmrCore/AMReX_Interp_C.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/CMakeLists.txt Src/AmrCore/Make.package commit 8a0c805821e24f8d6983cc29295b53c23d5ab0ef Author: Weiqun Zhang Date: Fri Dec 14 16:26:24 2018 -0800 put interpolation in time on gpu Src/AmrCore/AMReX_FillPatchUtil.cpp commit 14a6d85fed8811c348f5c42ba675dc341b423d8c Author: Weiqun Zhang Date: Fri Dec 14 15:57:35 2018 -0800 Tutorials/GPU/CNS: amr Tutorials/GPU/CNS/Exec/Sod/inputs Tutorials/GPU/CNS/Exec/Sod/inputs.amr Tutorials/GPU/CNS/Source/CNS.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_bcfill.cpp Tutorials/GPU/CNS/Source/CNS_io.cpp Tutorials/GPU/CNS/Source/CNS_setup.cpp Tutorials/GPU/CNS/Source/CNS_tagging.H Tutorials/GPU/CNS/Source/Make.package commit f8b2836d50f4952cb4157024df938750282eb38d Merge: e3f2fa5da 549d1032c Author: Kevin Gott Date: Fri Dec 14 18:22:43 2018 -0500 Merge branch 'development' into gpu commit e3f2fa5da3cc4cf50fb6ee80d0c18805338a3d12 Author: Kevin Gott Date: Fri Dec 14 18:19:37 2018 -0500 summit run script works. Turns off GPUDirect. Tutorials/GPU/run.summit commit 549d1032c19f0c4cb06a55fddd84bbd14ccdd320 Author: Ann Almgren Date: Fri Dec 14 14:56:46 2018 -0800 Oops -- forgot "Real" when I added the brackets. Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 422f88635223f7c9c59e342c8d5923784b294297 Author: Ann Almgren Date: Fri Dec 14 14:45:56 2018 -0800 Update "Amr Task" --> "Asynchronous Iterators (Amr Task)" Docs/sphinx_documentation/source/AsyncIter_Chapter.rst commit 70170984590e53417fb91e93a82aa12e4a7e89a7 Author: Weiqun Zhang Date: Fri Dec 14 14:06:39 2018 -0800 minor Src/Amr/AMReX_AmrLevel.H Tutorials/EB/CNS/Source/CNS_setup.cpp commit df420b19c7db3b61a445b4428a5bb80fab24acd8 Author: Ann Almgren Date: Fri Dec 14 13:50:32 2018 -0800 Change formatting of norm output when verbose >= 4. No change in functionality, only in output. Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit d2e0dab5fe7abf299b08148b74d6f67fcb0d3e28 Author: Ann Almgren Date: Fri Dec 14 13:44:34 2018 -0800 Zero out the "res" array right after we create it in the nodal solve so that we can use the ghost nodes as a convenience in the stencil (knowing they are now zero) Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 2089f9ea17c225a338c0a834ee8051f4ec5ef30e Author: Weiqun Zhang Date: Fri Dec 14 13:30:49 2018 -0800 get rid of some warnings Src/Base/AMReX_CoordSys.cpp commit 328f888ad2e42b69582a9b468c6246b25c820562 Author: Weiqun Zhang Date: Fri Dec 14 13:29:02 2018 -0800 variadic template for amrex::min and max Src/Base/AMReX_Utility.H commit 70b6656498288f9231412d04f723f1e7f6ed17e9 Merge: ad82ba680 515667495 Author: Andrew Myers Date: Fri Dec 14 11:58:09 2018 -0800 Merge pull request #386 from jrood-nrel/update_nrel_site Update makefiles for NREL machines commit ad82ba68089502be5f51f6379e0eee46042ee6a4 Author: Max Katz Date: Fri Dec 14 11:29:02 2018 -0800 Add Lassen @ LLNL Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.llnl commit d0b2e013741807642403985e76226bd7d68723b6 Author: Max Katz Date: Fri Dec 14 11:28:57 2018 -0800 Cuda -> CUDA Src/Base/AMReX_GpuError.H commit 5156674950fd0055e767ef282a2e5f329d1582dd Author: Jon Rood Date: Fri Dec 14 12:21:56 2018 -0700 Adding note about older compilers on NREL machines. Tools/GNUMake/sites/Make.nrel commit c9e04f70f36e6083f705b5912053f8a620a06022 Author: Jon Rood Date: Fri Dec 14 12:07:00 2018 -0700 Using same compiler flags for gcc, gnu, and llvm on NREL's Eagle machine. Tools/GNUMake/sites/Make.nrel commit a2d9de71de164b91f7a0e2541d03941957699e83 Author: Jon Rood Date: Fri Dec 14 11:49:42 2018 -0700 Updating makefiles for NREL machines. Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.nrel commit 791afa80b3499101afc168d365884123023ae613 Author: Ann Almgren Date: Fri Dec 14 09:49:25 2018 -0800 In the nodal solve -- if we set CoarseningStrategy to RAP rather than Sigma -- which is what we do when AMREX_USE_EB is defined -- then we should always use the restriction_rap routine (based on "sten") rather than the standard restriction which sees no geometric information Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 7a3a6b7a6135346b12b823fd0287d23fb9da610f Merge: b4a842f84 f19b676fe Author: Weiqun Zhang Date: Fri Dec 14 07:22:02 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b4a842f84b002e9746ac2377bc0a501b37a2056b Author: Weiqun Zhang Date: Fri Dec 14 07:21:32 2018 -0800 fix some AMREX_PRAGMA_SIMD issues Src/Base/AMReX_BaseFab.H Src/Base/AMReX_COORDSYS_1D_C.H commit f19b676fe32ae6701c4b3b410372d2998354a303 Merge: cb522a6e5 35c168382 Author: Andrew Myers Date: Thu Dec 13 16:50:44 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit cb522a6e54764480833fbaa75f4fa24531c80db2 Author: Andrew Myers Date: Thu Dec 13 16:50:24 2018 -0800 fix typo Docs/sphinx_documentation/source/index.rst commit dfd4ce41b0d3fb778a1f12aa8289cefe647cbb60 Author: Andrew Myers Date: Thu Dec 13 16:49:29 2018 -0800 rename chapters in sphinx documentation Docs/sphinx_documentation/source/AMReX_Profiling_Tools_Chapter.rst Docs/sphinx_documentation/source/AmrCore_Chapter.rst Docs/sphinx_documentation/source/AmrLevel_Chapter.rst Docs/sphinx_documentation/source/AsyncIter_Chapter.rst Docs/sphinx_documentation/source/Basics_Chapter.rst Docs/sphinx_documentation/source/BuildingAMReX_Chapter.rst Docs/sphinx_documentation/source/EB_Chapter.rst Docs/sphinx_documentation/source/External_Frameworks_Chapter.rst Docs/sphinx_documentation/source/External_Profiling_Tools_Chapter.rst Docs/sphinx_documentation/source/Fortran_Chapter.rst Docs/sphinx_documentation/source/GPU_Chapter.rst Docs/sphinx_documentation/source/GettingStarted_Chapter.rst Docs/sphinx_documentation/source/IO_Chapter.rst Docs/sphinx_documentation/source/LinearSolvers_Chapter.rst Docs/sphinx_documentation/source/Particle_Chapter.rst Docs/sphinx_documentation/source/Visualization_Chapter.rst Docs/sphinx_documentation/source/index.rst commit d5b6512c1a6b56319ea040bc5d1e918b81b869b8 Author: Andrew Myers Date: Thu Dec 13 16:31:40 2018 -0800 make corresponding changes to the OpenACC version Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.cpp commit 41c470d04fe296eaa9b61483763a3b137339cf53 Author: Andrew Myers Date: Thu Dec 13 15:47:27 2018 -0800 formatting changes Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp commit 35c1683828fd17230b61fad24b31279d5f8ad134 Author: Weiqun Zhang Date: Thu Dec 13 13:17:18 2018 -0800 small changes Src/Base/AMReX_BaseFab.H Src/EB/AMReX_EB2_GeometryShop.H commit 6c4bb54d3782c6470743bb54ab5a90007bd948cb Author: Andrew Myers Date: Thu Dec 13 12:29:29 2018 -0800 update generating initial conditions with the changes from WarpX Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp commit 888ab89fa3edcd7bde2054061c216010e0426616 Author: Andrew Myers Date: Thu Dec 13 12:17:45 2018 -0800 Just call the base class constructor. Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp commit f90d742cf8b3e4e3789253516e6e26774a26610a Author: Andrew Myers Date: Thu Dec 13 12:13:35 2018 -0800 move PIdx to the ParticleContainer subclass; do not need Particles.H any more Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Source/Particles.H commit ac99368de8d774625830ba1ee45452ff5b6e841f Author: Andrew Myers Date: Thu Dec 13 12:11:15 2018 -0800 Redistribute Strategy is not a thing any more. Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H commit 551476cb0c13d632a5a25dc41693d0b3d8a00019 Author: Andrew Myers Date: Thu Dec 13 12:09:20 2018 -0800 restoring the ElectromagneticPIC Tutorial Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/inputs Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/script.sh Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/inputs Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/script.sh Tutorials/Particles/ElectromagneticPIC/Make.EMPIC Tutorials/Particles/ElectromagneticPIC/Source/Constants.H Tutorials/Particles/ElectromagneticPIC/Source/IO.H Tutorials/Particles/ElectromagneticPIC/Source/IO.cpp Tutorials/Particles/ElectromagneticPIC/Source/Make.package Tutorials/Particles/ElectromagneticPIC/Source/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/Source/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/Source/Particles.H Tutorials/Particles/ElectromagneticPIC/Source/main.cpp commit 2e1558182d42608aaeffbc941bc6e04074b6b1c9 Merge: edd55d592 d291fc2ce Author: Weiqun Zhang Date: Thu Dec 13 11:09:25 2018 -0800 Merge branch 'development' into gpu commit d291fc2cef417e73cbc997752ab24c9f08deafd2 Author: Weiqun Zhang Date: Thu Dec 13 10:32:54 2018 -0800 no need to pass GeometryData if it is not needed Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/EB/AMReX_EBMultiFabUtil.cpp commit ba1ffef2494988119c850ddc3be342fa9b4c1a5c Author: Weiqun Zhang Date: Thu Dec 13 10:21:49 2018 -0800 rm functions we don't really need Src/Base/AMReX_COORDSYS_3D_C.H Src/Base/AMReX_CoordSys.cpp commit 37c8bbd57ad1b4428b6eea5b29d9ffdb6d6b8a0d Author: Weiqun Zhang Date: Thu Dec 13 10:11:34 2018 -0800 add Geometry::isPeriodicArray that returns gpu friendly array Src/Base/AMReX_Geometry.H commit 775c7129ce7741c2f4fc08961cb83d9444260036 Author: Weiqun Zhang Date: Thu Dec 13 10:00:33 2018 -0800 move AsyncFab dtor to header Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaAsyncFab.cpp commit 174ea540c2a693d60ee7ba0c125b100d49853b31 Author: Weiqun Zhang Date: Thu Dec 13 09:46:04 2018 -0800 add amrex_multifab_read Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Tools/CompileTesting/compiletesting.py commit c552cde95b3923d6d41f5410fc778f0ae1ceb848 Merge: 911d46f7d 6c66a68fb Author: Guy Moore Date: Thu Dec 13 07:42:23 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 911d46f7d9a9b91613c1ed7de5b0a030f68c623c Author: Guy Moore Date: Thu Dec 13 07:39:04 2018 -0800 Moved SWFFT tutorials into separate sub-directories, and updated documentation to reflect change Filled MUI documentation Docs/sphinx_documentation/source/SWFFT.rst Docs/sphinx_tutorials/source/MUI_Tutorial.rst Docs/sphinx_tutorials/source/SWFFT/iface_rect.png Docs/sphinx_tutorials/source/SWFFT_Tutorial.rst Tutorials/SWFFT/SWFFT_poisson/GNUmakefile Tutorials/SWFFT/SWFFT_poisson/Make.package Tutorials/SWFFT/SWFFT_poisson/README Tutorials/SWFFT/SWFFT_poisson/SWFFT_Test.H Tutorials/SWFFT/SWFFT_poisson/SWFFT_Test.cpp Tutorials/SWFFT/SWFFT_poisson/SWFFT_Test_F.F90 Tutorials/SWFFT/SWFFT_poisson/SWFFT_Test_F.H Tutorials/SWFFT/SWFFT_poisson/inputs.128 Tutorials/SWFFT/SWFFT_poisson/inputs.32 Tutorials/SWFFT/SWFFT_poisson/inputs.64 Tutorials/SWFFT/SWFFT_poisson/main.cpp Tutorials/SWFFT/SWFFT_poisson/run_me Tutorials/SWFFT/SWFFT_poisson/swfft_solver.cpp Tutorials/SWFFT/SWFFT_simple/GNUmakefile Tutorials/SWFFT/SWFFT_simple/Make.package Tutorials/SWFFT/SWFFT_simple/README Tutorials/SWFFT/SWFFT_simple/SWFFT_Test.H Tutorials/SWFFT/SWFFT_simple/SWFFT_Test.cpp Tutorials/SWFFT/SWFFT_simple/SWFFT_Test_F.F90 Tutorials/SWFFT/SWFFT_simple/SWFFT_Test_F.H Tutorials/SWFFT/SWFFT_simple/inputs.multipleGrids Tutorials/SWFFT/SWFFT_simple/inputs.oneGrid Tutorials/SWFFT/SWFFT_simple/main.cpp Tutorials/SWFFT/SWFFT_simple/run_me_2d Tutorials/SWFFT/SWFFT_simple/run_me_3d Tutorials/SWFFT/SWFFT_simple/swfft_compute.cpp commit 6c66a68fbe4f6dcec8209f8be758ee9d012a82bd Merge: 3c8a3938c 0e9af35d0 Author: Ann Almgren Date: Thu Dec 13 06:55:49 2018 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 3c8a3938c1b2106618e5b1f925cfec3e49738499 Author: Ann Almgren Date: Thu Dec 13 06:55:33 2018 -0800 Wrap EB_set_covered inside ifdef AMREX_USE_EB Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit edd55d59270912b2d1bd363842df49cca623c924 Author: Kevin Gott Date: Thu Dec 13 01:47:36 2018 -0500 Tweaks to get AmrCore compiling on Summit + making H files for converted Fortran->C++ functions. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Make.package Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.H Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/GPU/Advection_AmrCore/Source/Kernels_3d.H Tutorials/GPU/Advection_AmrCore/Source/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp commit a2b7572c6d08cbf22a8ebbb51d08761927501c38 Author: Kevin Gott Date: Thu Dec 13 01:42:57 2018 -0500 Add non const bracket operator to GpuArray. Src/Base/AMReX_Array.H commit 0e9af35d043b34271cfa8cc706e16cc19177359d Author: Tan Nguyen Date: Wed Dec 12 20:49:37 2018 -0800 add code to detect memory leak Src/AmrTask/rts_impls/mpi_pthreads/PackageQueue.cpp Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.cpp Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.H Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.cpp Src/AmrTask/rts_impls/pthreads_common/LocalConnection.H Src/AmrTask/rts_impls/pthreads_common/Make.package Src/AmrTask/rts_impls/pthreads_common/PerillaMemCheck.H Src/AmrTask/rts_impls/pthreads_common/PerillaMemCheck.cpp Src/AmrTask/rts_impls/pthreads_common/RemoteConnection.H Src/AmrTask/rts_impls/pthreads_common/perilla.mak Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/main.cpp commit 95d2bc1c52f1024d3fb7da28da6481d14de68452 Merge: d99bd0b92 27a825d50 Author: Tan Nguyen Date: Wed Dec 12 20:44:30 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 27a825d50af795b777516c0f5c2893c5a0bf17b9 Merge: daa511781 290a27b66 Author: Ann Almgren Date: Wed Dec 12 20:05:16 2018 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit daa5117817605b8a463f25e026108d5c1d543294 Author: Ann Almgren Date: Wed Dec 12 20:03:45 2018 -0800 1) Some clean-up of nodal restriction 2) Grow nodal domain by 1000 so that we don't double at Neumann boundaries in divu_cf_contrib when using CoarseningStrategy::RAP Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 290a27b667fb16ce3c32e20f5594e403b4f4a64a Merge: a44c5d07c 39d6c85cd Author: Andrew Myers Date: Wed Dec 12 17:09:34 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a44c5d07c40f92cb674b3bf06428f8415d67bc76 Author: Andrew Myers Date: Wed Dec 12 17:09:03 2018 -0800 Make sure to remove particles that leave the problem domain when running on the GPU. Src/Particle/AMReX_ParticleContainerI.H commit d99bd0b927aa9b0152368afa7fd2873929ad80da Merge: 4a03b2d9b 39d6c85cd Author: Tan Nguyen Date: Wed Dec 12 16:54:26 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 39d6c85cdf8a28906dfb5a186761411c6c1a0971 Merge: 913849408 15cae6e53 Author: Weiqun Zhang Date: Wed Dec 12 19:02:22 2018 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 913849408ff3956804edd374be82bb9cb2c979a5 Author: Weiqun Zhang Date: Wed Dec 12 19:01:59 2018 -0500 more inline Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/Base/AMReX_MultiFabUtil_nd_C.H commit 501082f87f76fd64f3840f3309f5551aa085adc4 Author: Weiqun Zhang Date: Wed Dec 12 18:41:41 2018 -0500 inline in FArrayBox Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp commit 229882ccd8695badb1699a8a658896ea1c3acbb4 Author: Weiqun Zhang Date: Wed Dec 12 18:29:01 2018 -0500 inline in Box Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit f3a32809a0dd29311f3da683c1d7e382ce55b7f3 Author: Weiqun Zhang Date: Wed Dec 12 17:50:03 2018 -0500 clean up Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_CudaReduce.H Src/Base/AMReX_FabArrayUtility.H commit cf58b03889c4a4baa32d1b34172192c0d09c723c Author: Weiqun Zhang Date: Wed Dec 12 16:53:32 2018 -0500 move MultiFabUtil kernels to headers for inline Src/Base/AMReX_MultiFabUtil_1D_C.H Src/Base/AMReX_MultiFabUtil_2D_C.H Src/Base/AMReX_MultiFabUtil_3D_C.H Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_nd_C.H Src/Base/CMakeLists.txt Src/Base/Make.package commit a4028844951d7f95b8016bee374887a10cb6fd9d Author: Weiqun Zhang Date: Wed Dec 12 16:22:21 2018 -0500 return by value to save registers Src/Amr/AMReX_StateData.cpp commit 76f4e015942edf0212ba758ec7957f5fb2a00feb Author: Weiqun Zhang Date: Wed Dec 12 16:05:06 2018 -0500 move CoordSys kernels to headers for inline Src/Base/AMReX_COORDSYS_1D_C.H Src/Base/AMReX_COORDSYS_2D_C.H Src/Base/AMReX_COORDSYS_3D_C.H Src/Base/AMReX_COORDSYS_C.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 9b81226de7ba7defc96384b40bf788df0bd3cdc6 Author: Weiqun Zhang Date: Wed Dec 12 15:47:26 2018 -0500 move FillCC to headers for inline Src/Base/AMReX_FilCC_1D_C.H Src/Base/AMReX_FilCC_2D_C.H Src/Base/AMReX_FilCC_3D_C.H Src/Base/AMReX_FilCC_C.H Src/Base/CMakeLists.txt Src/Base/Make.package Tutorials/GPU/CNS/Source/CNS_bcfill.cpp commit fc2b7a03beb681ae6ac6ac00044ea84bca6d2df4 Author: Weiqun Zhang Date: Wed Dec 12 15:06:31 2018 -0500 clean up Tutorials/GPU/CNS/Source/CNS_setup.cpp commit 4a03b2d9b76737e84c0e7ae4df0f057e62daa2cc Merge: c7b0e5d86 15cae6e53 Author: Tan Nguyen Date: Wed Dec 12 11:32:29 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ce40a97582a094a08400370966545f25f745a7cb Author: Weiqun Zhang Date: Wed Dec 12 13:08:19 2018 -0500 add AMREX_FORCE_INLINE macro Src/Base/AMReX_Extension.H commit 78ea4e4e27a92012d3f9643eb7381f78764e0732 Author: Weiqun Zhang Date: Wed Dec 12 12:59:47 2018 -0500 reorganize Tutorials/GPU/CNS for inline Tutorials/GPU/CNS/Exec/Sod/cns_prob.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_K.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/Make.package Tutorials/GPU/CNS/Source/hydro/CNS_hydro_K.H Tutorials/GPU/CNS/Source/hydro/Make.package Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp commit 15cae6e5342862eafec9997e1355db9d34845374 Author: atmyers Date: Wed Dec 12 08:04:11 2018 -0800 remove inconsistent definition of Real in AMReX_ParticleTile.H Src/Particle/AMReX_ParticleTile.H commit c7b0e5d8611bd4e8d27c32be0b5f4223ddc38db7 Merge: 047005c36 aefd341e1 Author: Tan Nguyen Date: Tue Dec 11 21:35:30 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit aefd341e113e3ff7b5836a5be44877786fe1b0f8 Author: Andrew Myers Date: Tue Dec 11 16:28:59 2018 -0800 want to tile this loop Src/Particle/AMReX_NeighborParticlesI.H commit 87ba82ce9bc4e0ad2dcc03e1a2810ea429d81435 Merge: 4ee591692 64dabee50 Author: Kevin Gott Date: Tue Dec 11 19:19:21 2018 -0500 Merge branch 'development' into gpu commit 64dabee5065f976decac1ee611bc7303ffc69138 Author: Andrew Myers Date: Tue Dec 11 15:43:47 2018 -0800 same thing here Src/Particle/AMReX_NeighborParticlesI.H commit 961c4716bb94231cac34f9721fc07bcd1bbcc02d Author: Andrew Myers Date: Tue Dec 11 15:39:21 2018 -0800 the relevant dmap here is the one associated with the dst level, not the src level Src/Particle/AMReX_NeighborParticlesI.H commit 047005c36261615129b7733ff7fc0b4b5c6a92df Merge: 75b8167db e5264a09b Author: Tan Nguyen Date: Tue Dec 11 14:48:50 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 75b8167db49c7f7b4a7111e3edc9903c4d9d49e0 Author: Tan Nguyen Date: Tue Dec 11 14:48:35 2018 -0800 abc Src/Amr/AMReX_Amr.cpp commit e5264a09bd943e2d99fff7e8af8127d49ad3dee9 Author: Johannes Blaschke Date: Tue Dec 11 14:46:23 2018 -0800 fix BA type Src/EB/AMReX_EB_LSCoreBase.cpp commit 6261525ee1a94b75f9adaf7def603907a938bf38 Author: Andrew Myers Date: Tue Dec 11 14:17:20 2018 -0800 add section label Docs/sphinx_documentation/source/GPU.rst commit 25cd200a2bb8918edc09822921d25f0c5639541f Author: Andrew Myers Date: Tue Dec 11 14:13:37 2018 -0800 use cpp formatting Docs/sphinx_documentation/source/GPU.rst commit 4d35070a5da95c78950fbd72b3f175ff9236979f Merge: 75047bd1a f0abc01f5 Author: Andrew Myers Date: Tue Dec 11 13:58:11 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 75047bd1af21d62eebc761612b56ea6a4818f048 Author: Andrew Myers Date: Tue Dec 11 13:57:57 2018 -0800 add section on GPU particles to the docs. Docs/sphinx_documentation/source/GPU.rst commit f0abc01f51ede8a15b773c8bbe722abe090a67a3 Merge: 491e3be78 e8b8cd2b7 Author: Johannes Blaschke Date: Tue Dec 11 13:22:08 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 491e3be7888f5543f9c353535bdd4407e53c23bb Author: Johannes Blaschke Date: Tue Dec 11 13:22:04 2018 -0800 LSCore uses a local level-set paradigm now Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset_F.F90 commit e8b8cd2b72bde36a66d24804c907869473bbd4fc Merge: aa535b72f 06e551108 Author: Andrew Myers Date: Tue Dec 11 12:40:17 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit aa535b72f9d8c1aa634ff670719c19a8912c4c6c Author: Andrew Myers Date: Tue Dec 11 12:39:40 2018 -0800 proofreading pass of GPU documentation Docs/sphinx_documentation/source/ChapterGPU.rst Docs/sphinx_documentation/source/GPU.rst commit 06e551108f3a44e7a8ac185aec43af14f3e9fa74 Author: Ann Almgren Date: Tue Dec 11 12:26:32 2018 -0800 Remove memory leak - changes per Weiqun's suggestion. Src/AmrCore/AMReX_Cluster.cpp commit 4ee59169264ff14c54cbf78dadab497651d5bb69 Author: Kevin Gott Date: Tue Dec 11 11:57:32 2018 -0800 Removed print statement. AmrCore GPU rewrite tutorial now works on CPUs. Tutorials/Amr/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp commit 221f8efb40bf829bcd70535a290870481f72a99d Author: Kevin Gott Date: Tue Dec 11 11:50:14 2018 -0800 inputs Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/inputs commit 94bf3b5d1dd53da94719cd0e9a5abebd6729a456 Author: Weiqun Zhang Date: Tue Dec 11 13:19:13 2018 -0500 add USE_FORCE_INLINE Src/Base/AMReX_Extension.H Tools/GNUMake/Make.defs commit 26359bdb672611fb73a2f0175f8640ee392c23f7 Merge: b8c56c544 ba4a1f4d1 Author: Johannes Blaschke Date: Mon Dec 10 21:41:15 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b8c56c544e35544561be15ea9132f7b5d3bbdf1b Author: Johannes Blaschke Date: Mon Dec 10 21:41:08 2018 -0800 implement tiling for local level-set creation Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.cpp commit 146ebe53514ea80138ddba2b4688c25a6a20b311 Author: Ann Almgren Date: Mon Dec 10 18:32:19 2018 -0800 Fix some bounds problems Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit e139466936c4f8c6afc8ce2436b79772ee291f2d Author: Kaiyuan Hou Date: Mon Dec 10 19:16:54 2018 -0600 update timer name Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.cpp commit c6855f1c011e99e5d4d094267031abb319531a1b Author: Kevin Gott Date: Mon Dec 10 17:09:03 2018 -0800 Turn off tiling in AmrCore tutorial for testing. Tutorials/Amr/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90 commit 82591ffcae7cb1a24c9dc2d3b51b335050164460 Author: Kevin Gott Date: Mon Dec 10 17:08:30 2018 -0800 Continuing to fix Core. Has prints. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/GNUmakefile Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/inputs Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp commit ba4a1f4d1118edb494cbe5a0b40e89856aa54869 Merge: 53edbed39 e9555bd0e Author: Andrew Myers Date: Mon Dec 10 16:35:57 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 53edbed3996cbef21cede6f6026d6e24a5c1eb51 Author: Andrew Myers Date: Mon Dec 10 16:35:47 2018 -0800 this needs to be 'class' instead of 'typename' to keep gcc < 5 happy Src/EB/AMReX_EB_LSCoreBase.H commit e9555bd0e33254a9195271bad6d2157c06537c03 Author: Weiqun Zhang Date: Mon Dec 10 16:16:23 2018 -0800 more gpu doc Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/LinearSolvers.rst commit 5eea46603a428adb2531534a130e52048508bf7c Author: Marc Day Date: Mon Dec 10 16:06:22 2018 -0800 Remove GPU macros prior to typecheck Tools/GNUMake/Make.rules commit 018b78d088f6e0051b85fb7303cd5d4e4ea17d22 Merge: 0a3fae573 fb3e848ff Author: Andrew Myers Date: Mon Dec 10 16:04:26 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0a3fae5738bb4c19d2087573620094d2a597fbd1 Author: Andrew Myers Date: Mon Dec 10 16:04:08 2018 -0800 fix Tutorial Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborList/main.cpp commit d773b177c44b3575c21843e368820b978609aa3e Author: Andrew Myers Date: Mon Dec 10 15:35:38 2018 -0800 also communicate the level information in the MPI send data for neighbor particles Src/Particle/AMReX_NeighborParticlesI.H commit fb3e848ff08f29bc21efd1cd7d69dcfe2b60a92c Author: Weiqun Zhang Date: Mon Dec 10 15:02:19 2018 -0800 minor fixes Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/EB.rst Docs/sphinx_documentation/source/GPU.rst commit 0a8a4262924a4e22aa138acd2c9058d1fde79cc0 Merge: e86416ad4 2a0d803ed Author: Ann Almgren Date: Mon Dec 10 14:12:30 2018 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit e86416ad43b9ae57a68ceaa2c2f0bafeac0c5b8b Author: Ann Almgren Date: Mon Dec 10 14:11:20 2018 -0800 Allow multilevel solves with CoarseningStrategy::RAP. Note there is a default assumption that the EB boundary does not cross the coarse-fine interface because the coarse-fine stencil is NOT defined using the EB-aware stencils. Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 8607a0dcc4f7bd95f5c88bc25831f8a8efdf3e62 Author: kngott Date: Mon Dec 10 13:45:10 2018 -0800 Ann found compute flux was wrong. Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp commit c09c5c9a93981e422d3cc6e80f369c214aaed4a2 Author: Weiqun Zhang Date: Mon Dec 10 16:07:00 2018 -0500 minor: add some consts Src/Base/AMReX_CudaLaunch.H commit 2a0d803eddbfec632827a308b30d8dc6e5cb7b94 Author: Weiqun Zhang Date: Mon Dec 10 12:43:47 2018 -0800 Tutorials/GPU/Launch: inline the C++ kernel Tutorials/GPU/Launch/Make.package Tutorials/GPU/Launch/MyKernel.H Tutorials/GPU/Launch/MyKernel.cpp commit 1e2325a029b70075d94c5d41c30255729b4c376a Author: kngott Date: Mon Dec 10 11:33:31 2018 -0800 Fixing errors in fluxes. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp commit a83358a95b2ca59b6fd9e2019b19e8f2469f3098 Author: Tan Nguyen Date: Mon Dec 10 00:35:57 2018 -0800 extend the upcxx backend to support RGIter Src/Amr/AMReX_Amr.cpp Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.H Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.cpp Src/AmrTask/rts_impls/upcxx_pthreads/PerillaConfig.H Src/AmrTask/rts_impls/upcxx_pthreads/Perilla_common.cpp Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.H Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.cpp commit d254d93f6e9fe9051a092c611e17be9ad53f7bf1 Author: Ann Almgren Date: Sun Dec 9 15:06:42 2018 -0800 Remove "mfix" from routine names Tutorials/EB/Donut/Src/EB_F.H Tutorials/EB/Donut/Src/eb_to_pvf.F90 Tutorials/EB/Donut/Src/main.cpp commit 4c67b88445466888851ea7d29338e597317af887 Merge: 299736c21 fb8db1b66 Author: Johannes Blaschke Date: Sun Dec 9 10:27:29 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 299736c21cea9b47ed1a033a0e94e2e5ef5ab39c Author: Johannes Blaschke Date: Sun Dec 9 10:27:22 2018 -0800 use tiling to fill level-set Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.cpp commit fb8db1b667b71b075061dfb38bf34944d68bea14 Author: Tan Nguyen Date: Sat Dec 8 22:41:44 2018 -0800 fit a small bug in the mpi backend Src/Amr/AMReX_Amr.cpp Src/AmrTask/rts_impls/mpi_pthreads/Perilla.H Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.cpp Src/AmrTask/rts_impls/pthreads_common/Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv_advance.cpp commit 28fc85e3f07e4215f77a0535dbcc57afa533642a Author: Weiqun Zhang Date: Sat Dec 8 21:38:44 2018 -0800 on limitations. this finishes my first pass of gpu documentation Docs/sphinx_documentation/source/GPU.rst commit ff1c4ff9a5173925f8da7679f6f02aa37b8ca5d4 Author: Weiqun Zhang Date: Sat Dec 8 21:19:34 2018 -0800 on assetion, error check and reduction Docs/sphinx_documentation/source/GPU.rst commit 6861cac76d7c9d71343718f416fad694068f3a78 Author: Weiqun Zhang Date: Sat Dec 8 20:44:53 2018 -0800 on AsyncFab Docs/sphinx_documentation/source/GPU.rst commit ed14ee8e5bd39274a2c726bdd30f2cd43b0ae048 Author: Michael Zingale Date: Sat Dec 8 22:11:41 2018 -0500 pout -> amrex::Print() Tools/C_util/Convergence/RichardsonConvergenceTest.cpp commit d33ba4e13afa7dfa2bd08d8713563f94fe2812f7 Author: Ann Almgren Date: Sat Dec 8 18:58:00 2018 -0800 Add error message if we reach the end of the new_chop routine without returning the new grids. Src/AmrCore/AMReX_Cluster.cpp commit f2f373c692e7e5d698b44c43c77a4810a0cd0d70 Author: Weiqun Zhang Date: Sat Dec 8 18:36:47 2018 -0800 try again Src/AmrCore/AMReX_Cluster.cpp commit 0864eba4d6a3773945505d37b718cffc3f88cc8f Author: Weiqun Zhang Date: Sat Dec 8 18:35:13 2018 -0800 not sure it's the right fix for ClusterList, but it compiles now Src/AmrCore/AMReX_Cluster.cpp commit 7ae312e136ff4a6eed065b1934f156cc87ddd740 Merge: a5c4441cd 17d085ff0 Author: Weiqun Zhang Date: Sat Dec 8 18:28:17 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a5c4441cd2200f5f679735ce332e1c6dd62bfa78 Author: Weiqun Zhang Date: Sat Dec 8 18:28:08 2018 -0800 rm FabArray::getDomain and comment out some debug code using it Src/Base/AMReX_FabArray.H Tools/C_util/Convergence/DebugOut.cpp commit 17d085ff0064bb0298cd244ed65d1be6dbfa36e0 Merge: 6335d8fd9 e0c8c55ea Author: Ann Almgren Date: Sat Dec 8 18:18:51 2018 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 6335d8fd97638fe4d9afca7c183838012c3f6efe Author: Ann Almgren Date: Sat Dec 8 18:17:01 2018 -0800 Update the creation of the grids for the level set by 1) removing the iteration -- we shoudln't need it 2) Introducting a modified "chop" function which doesn't accept cuts if they don't imporove the grid efficiency. This is available to all grid creation routines if they set the flag use_new_chop to true. The level set routines now do that by default. Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_Cluster.H Src/AmrCore/AMReX_Cluster.cpp Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H commit e0c8c55ea25f553c44b58da75a300f9147bf5001 Author: Weiqun Zhang Date: Sat Dec 8 13:21:44 2018 -0800 on gpu safe classes Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/GPU.rst commit dbd1935cc094caef3c67b5f3ba5220da71305178 Author: Weiqun Zhang Date: Sat Dec 8 12:02:30 2018 -0800 add writing C++ kernel Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/index.rst commit 50ccc26b22142bd6b541c0a8b98cfe602a18dc75 Author: Weiqun Zhang Date: Fri Dec 7 22:21:57 2018 -0800 Merge branch 'gpu-docs' into development Docs/sphinx_documentation/Makefile Docs/sphinx_documentation/source/AsyncIter.rst Docs/sphinx_documentation/source/ChapterGPU.rst Docs/sphinx_documentation/source/GPU.rst Docs/sphinx_documentation/source/index.rst Src/Base/AMReX_Arena.cpp Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BLFort.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_fort_mod.F90 Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak Tutorials/GPU/Launch/GNUmakefile Tutorials/GPU/Launch/Make.package Tutorials/GPU/Launch/MyKernel.H Tutorials/GPU/Launch/MyKernel.cpp Tutorials/GPU/Launch/MyKernel_F.F90 Tutorials/GPU/Launch/MyKernel_F.H Tutorials/GPU/Launch/Readme.md Tutorials/GPU/Launch/main.cpp commit 23d857adcfd386d858d22c72d23c42b1b122a3d9 Author: Andrew Myers Date: Fri Dec 7 18:10:27 2018 -0800 fix bug involving periodic boundary conditions and NeighborCopyTags Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit c28fa1cd7ab39c68d1d2b360c8f81efdc4086978 Author: Johannes Blaschke Date: Fri Dec 7 18:00:55 2018 -0800 change buffer Src/EB/AMReX_EB_LSCoreBase.cpp commit 58f7a604e48def6d4e954b53fac110dd88bf34c4 Author: Andrew Myers Date: Fri Dec 7 16:40:56 2018 -0800 need to remove duplicates whether or not mask is used. Src/Particle/AMReX_NeighborParticlesI.H commit e4f89d443fdfe3770d203742e50097a128a04233 Author: Andrew Myers Date: Fri Dec 7 16:38:54 2018 -0800 change order of output for << operator Src/Particle/AMReX_NeighborParticles.H commit be65d07a3fabfe0e8b72ef94693d27e2019b4497 Author: Johannes Blaschke Date: Fri Dec 7 15:22:44 2018 -0800 finished volfrac tagging Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCore_F.H Src/EB/AMReX_EB_Tagging.F90 commit 54c261e672353138051499dc2e8912068d0ef765 Author: Andrew Myers Date: Fri Dec 7 15:22:19 2018 -0800 add << operators for NeighborIndexMap and NeighborCommTag Src/Particle/AMReX_NeighborParticles.H commit da241e1193df19f1c1644fecc92a8137eaa3d311 Author: Andrew Myers Date: Fri Dec 7 14:24:01 2018 -0800 change the neighbor list print format Src/Particle/AMReX_NeighborParticlesI.H commit 301d736f02aa86c6d3fa8465a8b3974f80115794 Author: Johannes Blaschke Date: Fri Dec 7 13:39:06 2018 -0800 get ready for volfrac tagging Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp commit 106cd661d74633fb2e025b501845d0be08301f68 Author: Andrew Myers Date: Fri Dec 7 13:32:13 2018 -0800 need to always bin the particles for the nl on level 0 Src/Particle/AMReX_NeighborParticlesI.H commit 479f9baa6ad5c5d390c905e31755cb5ad3577247 Author: Andrew Myers Date: Fri Dec 7 13:28:37 2018 -0800 have printNeighborList take a prefix argument Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 7804497218a9de72a302b1db1f8c2a007fe8a32d Author: Andrew Myers Date: Fri Dec 7 13:20:11 2018 -0800 add method to print out nbor list for debugging. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit b115db7b1e61e0ea389f0022496f7c7addbc8e12 Author: kngott Date: Fri Dec 7 11:39:55 2018 -0800 Fix slope.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp commit a3f955334bd335f67308a917d8a009044fc8f534 Merge: 84f4b4c87 b38e9b742 Author: Andrew Myers Date: Fri Dec 7 11:36:21 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b38e9b742ffe1ed3d315624c54cd57e3d9e8c3e7 Author: Johannes Blaschke Date: Fri Dec 7 11:19:18 2018 -0800 level-set tagging now seperately declared as such Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCore_F.H Src/EB/AMReX_EB_Tagging.F90 commit a13b09a6285b993e57e9af1eb072ad9e54dac6f6 Merge: e38c6c99b cf4f78074 Author: Johannes Blaschke Date: Fri Dec 7 11:12:33 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit e38c6c99b6169e0c3932f841e75761fd60930bee Author: Johannes Blaschke Date: Fri Dec 7 11:12:26 2018 -0800 clean up tagging Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCore_F.H Src/EB/AMReX_EB_Tagging.F90 commit cf4f78074391cc3ad5d4c8b63a37e0b28d3333b9 Author: Weiqun Zhang Date: Fri Dec 7 10:25:11 2018 -0800 make AsyncFab copy constructor device function only and use_cuda=true only Src/Base/AMReX_CudaAsyncFab.H commit df4e8ddb6f5e22ccca6ddff055b8426b9ccb163e Author: Weiqun Zhang Date: Fri Dec 7 10:05:16 2018 -0800 Make AsyncFab interface nicer thanks to Marc's suggestion. AsyncFab can be captured by value and AsyncFab::fab() will return a reference to Fab. Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaAsyncFab.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp commit 755fdee3596dce4e36e8ce38053cfb3fcaee5018 Merge: 1e0f26f59 2fc648f2b Author: Andrew Myers Date: Thu Dec 6 16:56:12 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1e0f26f5927af1b2e06e44f3c7a2a143a83dcd7a Author: Andrew Myers Date: Thu Dec 6 16:55:59 2018 -0800 separate out the printing stuff from Arena::Finalize so it can be used for debugging. Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp commit 2fc648f2b7a9748a93b2ba8be09ead8aaa321345 Merge: d5f925a85 44d1aa689 Author: Weiqun Zhang Date: Thu Dec 6 16:45:11 2018 -0800 Merge branch 'weiqun/fabptr' into development commit 44d1aa689304da45eeef491c240898c80ebea0cf Merge: 1735cb9df 0a83a08fb Author: Weiqun Zhang Date: Thu Dec 6 19:32:21 2018 -0500 Merge branch 'weiqun/fabptr' of github.com:AMReX-Codes/amrex into weiqun/fabptr commit 0a83a08fb8c0352bd91ec6ba3ee62e0ee8f999f5 Author: Weiqun Zhang Date: Thu Dec 6 16:31:57 2018 -0800 update particle functors to use device ptr Src/Particle/AMReX_ParticleContainerI.H commit 9fb48b454ff9a3582f43319602a97516a7ec839a Author: Weiqun Zhang Date: Thu Dec 6 16:31:28 2018 -0800 add __FILE__ and __LINE__ as arguments ot Cuda::ErrorCheck Src/Base/AMReX_GpuError.H commit d5f925a85f5a8ec100356c4594b05fa359c57646 Author: Tan Nguyen Date: Thu Dec 6 16:29:11 2018 -0800 avg_down with region graph iterator Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv.H Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Adv_advance.cpp commit 84f4b4c8799f70518690e92e65f023bf8e678675 Author: Andrew Myers Date: Thu Dec 6 15:31:01 2018 -0800 this at least runs to completion in serial Src/Particle/AMReX_NeighborParticlesI.H commit aad8fd94bb2cc0026d94b6abd60acfb62e67d5cf Author: Johannes Blaschke Date: Thu Dec 6 15:23:53 2018 -0800 don't regrid LSCore if BA/DM don't change Src/EB/AMReX_EB_LSCoreBase.cpp commit 30b59d4aba050af46e12a50a4ac818506725b754 Author: Andrew Myers Date: Thu Dec 6 15:15:44 2018 -0800 fix bug that involved confusing the src level with the dst level Src/Particle/AMReX_NeighborParticlesI.H commit 0fbd493fbc3868f97c4ec4666515bd4b631dca0b Author: Cy Chan Date: Thu Dec 6 15:03:17 2018 -0800 add consolidation threshold parameter to MLLinOp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tests/LinearSolvers/MLMG/main.cpp commit 0d61aaaf1ef552232587373cf188537fb92189a1 Author: Andrew Myers Date: Thu Dec 6 14:35:57 2018 -0800 clean up resize containers Src/Particle/AMReX_NeighborParticlesI.H commit b2076101e93364df7a58ec2805ae31cfa85dbc1b Author: Andrew Myers Date: Thu Dec 6 14:33:19 2018 -0800 the buffer tag cache also needs to be an array over levels Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 08b8a83d7e099e1c346d0611d5dfbc8cb69549de Author: Andrew Myers Date: Thu Dec 6 14:04:42 2018 -0800 tweak inputs Tutorials/Particles/NeighborListMR/inputs commit f574f4296072366731e22459284be8cfb4054395 Author: Andrew Myers Date: Thu Dec 6 13:45:26 2018 -0800 remove some hard-coded 'const int lev = 0' Src/Particle/AMReX_NeighborParticlesI.H commit c66a7f5d4ea6341963f90dcf34991ec356bcc2aa Merge: 74dfa67f9 7d6e0deff Author: Ann Almgren Date: Thu Dec 6 13:33:23 2018 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 74dfa67f953cab0a37fca514deb38c2a838e5d6b Author: Ann Almgren Date: Thu Dec 6 13:30:26 2018 -0800 Abort in the case when the entire domain is covered. Previously this case ended up being viewed as "all_regular" Src/EB/AMReX_EB2_Level.H commit ccf2d9acef3f8d6d283840d939a712a02398bf6d Author: Andrew Myers Date: Thu Dec 6 13:12:51 2018 -0800 use the mask if max_level = 0 Src/Particle/AMReX_NeighborParticlesI.H commit 7d6e0deff711f761aa146ab9e935ef985c28063a Author: Johannes Blaschke Date: Thu Dec 6 13:12:05 2018 -0800 completed local level-set Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Exec/inputs Tutorials/EB/LevelSet/Src/make_cylinder.cpp commit 328c5e382552e48d91bf4753d5eeac71975e4c57 Author: Andrew Myers Date: Thu Dec 6 13:07:36 2018 -0800 remove unused stuff from NeighborListParticleContainer Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.H Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborListMR/inputs Tutorials/Particles/NeighborListMR/main.cpp commit 10aa0dcd50730c16a98484238dae70bb8839a3ef Author: Andrew Myers Date: Thu Dec 6 13:04:23 2018 -0800 fix and simplify periodic boundary adjustment for neighbors Src/Particle/AMReX_NeighborParticlesI.H commit 735ecee8453331d8e2099b494ab297f97dc60ea4 Author: Andrew Myers Date: Thu Dec 6 13:03:50 2018 -0800 overload << operator for NeighborCopyTag for ease of debugging Src/Particle/AMReX_NeighborParticles.H commit 92f11a35a0f5cc8605c130c975dc6fdf0fb25e86 Author: kngott Date: Thu Dec 6 13:02:02 2018 -0800 Properly use cell number. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp commit 015d1715dfb385e96571ca9efdf512c06f6a0980 Author: Andrew Myers Date: Thu Dec 6 12:39:12 2018 -0800 fixing a couple more bugs Src/Particle/AMReX_NeighborParticlesI.H commit 1735cb9df00e81d9b86323e9de6a9b4ab3be063a Merge: d05cc3dfd 8bd8d779a Author: Weiqun Zhang Date: Thu Dec 6 14:01:17 2018 -0500 Merge branch 'development' into weiqun/fabptr commit 800b1ab5ed73e3590b212f77a7d63133cba84a12 Author: Johannes Blaschke Date: Thu Dec 6 10:53:12 2018 -0800 fix typo Src/EB/AMReX_EB_levelset_F.F90 commit 004d224bce436d83bb6e18547148a4d9fc7d389d Author: Johannes Blaschke Date: Thu Dec 6 10:52:01 2018 -0800 fix level-set thresholding Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 commit 8bd8d779a57b60f012d9eabd671e6ae6db5f7b72 Author: Weiqun Zhang Date: Thu Dec 6 09:44:47 2018 -0800 make gcc happy Src/Base/AMReX_MultiFab.H commit 5792abb9f712808e1fbecd45893abb048aa6cb77 Author: Weiqun Zhang Date: Thu Dec 6 09:39:10 2018 -0800 get rid of warning in version checking when users set their own CXX Tools/GNUMake/comps/gnu.mak commit 9a4f0380840a791187920b45ccf823d864f79992 Author: Ann Almgren Date: Thu Dec 6 06:34:45 2018 -0800 Instead of IntVect{0,0,0} use IntVect{AMREX_DECL(0,0,0)} Src/EB/AMReX_EB_levelset.cpp commit 8b02ace0edda80e99613599ebb5708bdd94a5e54 Author: Ann Almgren Date: Thu Dec 6 06:10:16 2018 -0800 Need to return something from eb_facets routine Src/EB/AMReX_EB_levelset.cpp commit d9a0177026af3807f0dd82b21195a43ebca5236a Author: Tan Nguyen Date: Thu Dec 6 01:43:37 2018 -0800 Advection code using RGIter Src/AmrTask/rts_impls/pthreads_common/RGIter.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/._Exec Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/._README Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/._Source Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/._Make.Adv Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/._SingleVortex Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/._UniformVelocity Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.mpi.omp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.mpi.pthreads Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/Make.Adv.upcxx.pthreads Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._GNUmakefile Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._Prob.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._face_velocity_2d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._face_velocity_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._inputs Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/._probin Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Exec/SingleVortex/Backtrace.0 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Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_2d/slope_2d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/._Adv_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/._Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/._compute_flux_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/._slope_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/Adv_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/compute_flux_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_3d/slope_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/._Adv_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/._Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/._Tagging_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/._tagging_params.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/Adv_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/Tagging_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/Src_nd/tagging_params.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync_rgi/Source/main.cpp commit 7b44a0ad27e6676a13f17985e2e36fd0a42e368c Author: Johannes Blaschke Date: Wed Dec 5 21:50:40 2018 -0800 hack level-set threshold Src/EB/AMReX_EB_levelset_F.F90 commit 091fec3fe7354179a7035dc8d47f41b6011853f1 Author: Andrew Myers Date: Wed Dec 5 19:04:58 2018 -0800 use AMREX_D_TERM so this works in 2D Src/Particle/AMReX_NeighborParticles.H commit f16c01ede142973a541ce809c766a0a4d4272b2f Author: Andrew Myers Date: Wed Dec 5 19:00:53 2018 -0800 fix a couple of bugs Src/Particle/AMReX_NeighborParticlesI.H commit 96e554d82246baea5457934194cc539fc56c8bee Author: Johannes Blaschke Date: Wed Dec 5 18:37:43 2018 -0800 bug fixes for eb_search Src/EB/AMReX_EB_levelset.cpp commit d1d939e2589feb63ead97d21bdc0019cd2770e69 Merge: f4a374526 54fc8e952 Author: Johannes Blaschke Date: Wed Dec 5 18:06:08 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit f4a3745268bd4c62af2c0277051ba1d08391d22a Author: Johannes Blaschke Date: Wed Dec 5 18:06:04 2018 -0800 work on local level-set filling Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp commit d05cc3dfd5e11ed0235401d4cde08e7f064e4445 Merge: 50c6a75d0 844b24995 Author: Weiqun Zhang Date: Wed Dec 5 16:51:26 2018 -0800 Merge branch 'development' into weiqun/fabptr commit 50c6a75d0bb00b47657a178e91ecfe44709d712b Author: Weiqun Zhang Date: Wed Dec 5 16:51:14 2018 -0800 udpate gpu codes ot use fabPtr Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_iMultiFab.cpp Tests/GPU/AsyncFab/main.cpp Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit 54fc8e9523bfc0b83100d2c87604a03eaf22bfce Author: Andy Nonaka Date: Wed Dec 5 16:44:53 2018 -0800 add link to tutorial documentation Docs/sphinx_documentation/source/Chapter4a.rst Docs/sphinx_documentation/source/index.rst commit f6cbb3abaadfb794bad959f5fcbac163996bdae1 Author: Andrew Myers Date: Wed Dec 5 16:23:59 2018 -0800 finish non-mask version of GetNeighborCommTags Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit fb0bb60892059f2402d761544ad0ca54d41a230c Author: Andrew Myers Date: Wed Dec 5 16:10:26 2018 -0800 fix bug in computeRefFac Src/Particle/AMReX_NeighborParticlesI.H commit c193167511c124d0dc2b09614d2ae7f3fb384766 Author: Andrew Myers Date: Wed Dec 5 15:58:44 2018 -0800 add a numLevels() method to ParticleContainer and use it Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_Particles.H commit ad5138f90c21732fdee327c50c8dd559c4451e51 Author: Andrew Myers Date: Wed Dec 5 15:51:47 2018 -0800 function to compute net ref ratio between two levels Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 86cd2c99e563033c0630aabd7a058786c9b15062 Author: Cy Chan Date: Wed Dec 5 15:30:09 2018 -0800 fix bug in remap neighborhoods Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 844b24995aab5d55a06ac4ef667b8d67d7be2c8b Author: Weiqun Zhang Date: Wed Dec 5 14:26:20 2018 -0800 fix fortran function name so that the gpu script works Src/Base/AMReX_filcc_mod.F90 Src/Base/AMReX_fort_mod.F90 commit 7cb795f3c265b64fd5a544bec9bfbb16ea85ae92 Author: Weiqun Zhang Date: Wed Dec 5 14:14:33 2018 -0800 WIP: add host alias fabs to FabArray Src/Base/AMReX_FabArray.H commit bbf1c7c02c6266b9f90be0b731d44763f4458cb2 Author: Weiqun Zhang Date: Wed Dec 5 13:37:47 2018 -0800 add createHostAlias for fab Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabFactory.H Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_Mask.cpp Src/EB/AMReX_EBFArrayBox.H Src/EB/AMReX_EBFArrayBox.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_MultiCutFab.H commit b3af3c7216a88f17d439c7bd686762fbc4613019 Author: Andrew Myers Date: Wed Dec 5 12:57:05 2018 -0800 some more refactoring Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 6b428e22beedb86f5f1636069fc3ded69c32a947 Author: Ann Almgren Date: Wed Dec 5 12:36:03 2018 -0800 move Parallel/ForkJoin --> ForkJoin Tutorials/ForkJoin/GNUmakefile Tutorials/ForkJoin/Make.package Tutorials/ForkJoin/MyTest.H Tutorials/ForkJoin/MyTest.cpp Tutorials/ForkJoin/MyTest_F.H Tutorials/ForkJoin/inputs Tutorials/ForkJoin/main.cpp commit cecc20d2056aa93683a16b77e002d68f2e64526c Author: Andrew Myers Date: Wed Dec 5 12:25:15 2018 -0800 do_mask -> use_mask Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 9e3ce33f20a7d824c2932757a9a2d834f0ff134c Author: Andrew Myers Date: Wed Dec 5 12:04:47 2018 -0800 split up BuildMasks into two different methods Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 8322c23fd739d4149848a7b8f869c6c3e624b616 Author: Ann Almgren Date: Wed Dec 5 12:01:17 2018 -0800 1) Copy the current Tutorials that use SENSEI into a new Tutorials/SENSEI directory. 2) Remove mentions of SENSEI from Tutorials/Amr. 3) Add items in the sphinx documentation for each Tutorials subdirectory. Docs/sphinx_tutorials/source/Blueprint_Tutorial.rst Docs/sphinx_tutorials/source/Forkjoin_Tutorial.rst Docs/sphinx_tutorials/source/GPU_Tutorial.rst Docs/sphinx_tutorials/source/MUI_Tutorial.rst Docs/sphinx_tutorials/source/SDC_Tutorial.rst Docs/sphinx_tutorials/source/SENSEI_Tutorial.rst Docs/sphinx_tutorials/source/index.rst Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt Tutorials/Amr/Advection_AmrLevel/Exec/Make.Adv Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/inputs Tutorials/SENSEI/Advection_AmrCore/CMakeLists.txt Tutorials/SENSEI/Advection_AmrCore/Exec/Make.Adv Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/GNUmakefile Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/Make.package Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/Prob.f90 Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/inputs Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_catalyst.py Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.session Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.session Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml Tutorials/SENSEI/Advection_AmrCore/Exec/SingleVortex/sensei/write_vtk.xml Tutorials/SENSEI/Advection_AmrCore/README Tutorials/SENSEI/Advection_AmrCore/README_SENSEI.md Tutorials/SENSEI/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/SENSEI/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/SENSEI/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/SENSEI/Advection_AmrCore/Source/Make.package Tutorials/SENSEI/Advection_AmrCore/Source/Src_2d/Adv_2d.f90 Tutorials/SENSEI/Advection_AmrCore/Source/Src_2d/Make.package Tutorials/SENSEI/Advection_AmrCore/Source/Src_2d/compute_flux_2d.f90 Tutorials/SENSEI/Advection_AmrCore/Source/Src_2d/slope_2d.f90 Tutorials/SENSEI/Advection_AmrCore/Source/Src_3d/Adv_3d.f90 Tutorials/SENSEI/Advection_AmrCore/Source/Src_3d/Make.package Tutorials/SENSEI/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90 Tutorials/SENSEI/Advection_AmrCore/Source/Src_3d/slope_3d.f90 Tutorials/SENSEI/Advection_AmrCore/Source/Src_nd/Make.package Tutorials/SENSEI/Advection_AmrCore/Source/Src_nd/Tagging_nd.f90 Tutorials/SENSEI/Advection_AmrCore/Source/bc_fill_nd.F90 Tutorials/SENSEI/Advection_AmrCore/Source/main.cpp Tutorials/SENSEI/Advection_AmrLevel/CMakeLists.txt Tutorials/SENSEI/Advection_AmrLevel/Exec/Make.Adv Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/Make.package Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/Prob.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/inputs Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/inputs.tracers Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/probin Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_catalyst.py Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.session Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.session Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/render_libsim.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/SingleVortex/sensei/write_vtk.xml Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/Make.package Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_2d.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_3d.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/inputs Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/inputs.regt Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/probdata.f90 Tutorials/SENSEI/Advection_AmrLevel/Exec/UniformVelocity/probin Tutorials/SENSEI/Advection_AmrLevel/README Tutorials/SENSEI/Advection_AmrLevel/README_SENSEI.md Tutorials/SENSEI/Advection_AmrLevel/Source/Adv_F.H Tutorials/SENSEI/Advection_AmrLevel/Source/AmrLevelAdv.H Tutorials/SENSEI/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/SENSEI/Advection_AmrLevel/Source/LevelBldAdv.cpp Tutorials/SENSEI/Advection_AmrLevel/Source/Make.package Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/Make.package Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/compute_flux_2d.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_2d/slope_2d.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/Make.package Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/compute_flux_3d.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_3d/slope_3d.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_nd/Adv_nd.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_nd/Make.package Tutorials/SENSEI/Advection_AmrLevel/Source/Src_nd/Tagging_nd.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/Src_nd/tagging_params.f90 Tutorials/SENSEI/Advection_AmrLevel/Source/main.cpp commit e88a99e0421496e1a646988984d3208810c2bd70 Author: Andrew Myers Date: Wed Dec 5 11:57:26 2018 -0800 make BuildMasks protected Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 553ac85392d32539b44bd74dbe6cebe4524262ad Author: Andrew Myers Date: Wed Dec 5 11:32:44 2018 -0800 give NeighborCopyTag explicity default constructor as well Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit b34d0f5d1241c7009f1e68349c21265f5e665410 Author: Andrew Myers Date: Wed Dec 5 11:27:53 2018 -0800 finish implementation of non-mask getNeighborTag Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 488218b2ee65105fad4086f6aa3aceefdd578207 Author: Andrew Myers Date: Wed Dec 5 11:17:46 2018 -0800 give NeighborCopyTag a non-default constructor Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit c3069dabf14e57f717b7a5778ba84aef568d29aa Author: Andrew Myers Date: Wed Dec 5 11:13:42 2018 -0800 some work towards implementing the non-mask neighbor tag function Src/Particle/AMReX_NeighborParticlesI.H commit 74fb185d9e7b3391f6cf4d1aa349572890325700 Author: Andrew Myers Date: Wed Dec 5 10:55:06 2018 -0800 some refactoring Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit fc9eb17147e8bd44205f957de085dc792fafc0a8 Author: Ann Almgren Date: Wed Dec 5 10:52:09 2018 -0800 Remove HYPRE tutorial -- there isn't a separate one Docs/sphinx_tutorials/source/HYPRE_Tutorial.rst Docs/sphinx_tutorials/source/index.rst commit 4d0b529ec569977e7aee17a087a192cb3bf26191 Author: Ann Almgren Date: Wed Dec 5 10:35:56 2018 -0800 Update with the three specific Tutorial names. Docs/sphinx_tutorials/source/LinearSolvers_Tutorial.rst commit 64fb5db975b04aeb460d1fbb37647a229a2603f0 Author: Andrew Myers Date: Wed Dec 5 10:04:22 2018 -0800 correct comment Src/Particle/AMReX_NeighborParticlesI.H commit be8a7002984ec3936c1c6b9ec5d6025cf161d8be Author: Andrew Myers Date: Wed Dec 5 09:55:30 2018 -0800 selectively switch off building the mask Src/Particle/AMReX_NeighborParticlesI.H commit a2af55f423c6c2d9df28ab6c9f7407ff9d68f55b Author: Andrew Myers Date: Wed Dec 5 09:53:43 2018 -0800 add a static member variable to disable the mask approach Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 33ea069dd237cbb2c20f024cd287cd8b4126f18b Author: Weiqun Zhang Date: Wed Dec 5 09:15:35 2018 -0800 make distFcnElement2d pure virtual Src/EB/AMReX_distFcnElement.H Src/EB/AMReX_distFcnElement.cpp commit ca1b4f06754fa8edbd3dd9ae34a82ca149aeab17 Author: Weiqun Zhang Date: Wed Dec 5 09:00:22 2018 -0800 FabArray::fabPtr functions to return pointer to fab Src/Base/AMReX_FabArray.H commit 085ca1d8690d1464425093e2f32382625e305332 Author: kngott Date: Wed Dec 5 00:37:47 2018 -0800 Fix initialization error. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp commit f98431fe25836db90ed1ec11b4651529b4c3e08a Author: kngott Date: Tue Dec 4 15:49:34 2018 -0800 Fix boxes. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 2b8fc5e325b761896ebc4b88b7ab8e417e3d4428 Author: kngott Date: Tue Dec 4 15:48:32 2018 -0800 Fix conversion of single-plane psi into three dimensional loop. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp commit e7ecff9e146e0dc52949bdbee87619d396f9a999 Merge: 793bfd761 4e2f1d07e Author: Johannes Blaschke Date: Tue Dec 4 15:44:58 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 793bfd7616482dff5294a3038c226f71ca26c041 Author: Johannes Blaschke Date: Tue Dec 4 15:44:55 2018 -0800 make EBSearchBox compatible of infs and nans Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp commit 4e2f1d07e2b9677bbc440663fac925488de6be3e Author: Tan Nguyen Date: Tue Dec 4 14:45:50 2018 -0800 change RTS name Src/AmrTask/rts_impls/mpi_omp/PerillaRts.H Src/AmrTask/rts_impls/mpi_omp/PerillaRts.cpp Src/AmrTask/rts_impls/mpi_pthreads/Make.package Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.H Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.cpp Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/pthreads_common/Make.package Src/AmrTask/rts_impls/upcxx_pthreads/Make.package Src/AmrTask/rts_impls/upcxx_pthreads/PerillaRts.H Src/AmrTask/rts_impls/upcxx_pthreads/PerillaRts.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv.mpi.omp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv.mpi.pthreads Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv.upcxx.pthreads Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/main.cpp Src/Base/AMReX_MultiFabUtil_Perilla.cpp commit 034f3fff3a9b7f1be31b61efe8097726ddb9c424 Merge: 9b2ba32de 82027145d Author: Weiqun Zhang Date: Tue Dec 4 14:30:48 2018 -0800 Merge branch 'weiqun/comm' into development commit 9b2ba32de4ef72218bd0e0db45c3d087cf6188ad Author: Tan Nguyen Date: Tue Dec 4 14:06:50 2018 -0800 change directory name for rts backends Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/mpi_omp/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/mpi_omp/Barrier.H Src/AmrTask/rts_impls/mpi_omp/Barrier.cpp Src/AmrTask/rts_impls/mpi_omp/LocalConnection.H Src/AmrTask/rts_impls/mpi_omp/Make.package Src/AmrTask/rts_impls/mpi_omp/PackageQueue.H Src/AmrTask/rts_impls/mpi_omp/PackageQueue.cpp Src/AmrTask/rts_impls/mpi_omp/Perilla.H Src/AmrTask/rts_impls/mpi_omp/Perilla.cpp Src/AmrTask/rts_impls/mpi_omp/PerillaConfig.H Src/AmrTask/rts_impls/mpi_omp/PerillaRts.H Src/AmrTask/rts_impls/mpi_omp/PerillaRts.cpp Src/AmrTask/rts_impls/mpi_omp/RegionGraph.H Src/AmrTask/rts_impls/mpi_omp/RegionGraph.cpp Src/AmrTask/rts_impls/mpi_omp/RegionQueue.H Src/AmrTask/rts_impls/mpi_omp/RegionQueue.cpp Src/AmrTask/rts_impls/mpi_omp/RemoteConnection.H Src/AmrTask/rts_impls/mpi_omp/WorkerThread.H Src/AmrTask/rts_impls/mpi_omp/WorkerThread.cpp Src/AmrTask/rts_impls/mpi_omp/perilla.mak Src/AmrTask/rts_impls/mpi_pthreads/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/mpi_pthreads/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/mpi_pthreads/Barrier.H Src/AmrTask/rts_impls/mpi_pthreads/Barrier.cpp Src/AmrTask/rts_impls/mpi_pthreads/LocalConnection.H Src/AmrTask/rts_impls/mpi_pthreads/Make.package Src/AmrTask/rts_impls/mpi_pthreads/Makefile Src/AmrTask/rts_impls/mpi_pthreads/PackageQueue.H Src/AmrTask/rts_impls/mpi_pthreads/PackageQueue.cpp Src/AmrTask/rts_impls/mpi_pthreads/Perilla.H Src/AmrTask/rts_impls/mpi_pthreads/Perilla.cpp Src/AmrTask/rts_impls/mpi_pthreads/PerillaConfig.H Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.H Src/AmrTask/rts_impls/mpi_pthreads/PerillaRts.cpp Src/AmrTask/rts_impls/mpi_pthreads/RGIter.H Src/AmrTask/rts_impls/mpi_pthreads/RGIter.cpp Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.H Src/AmrTask/rts_impls/mpi_pthreads/RegionGraph.cpp Src/AmrTask/rts_impls/mpi_pthreads/RegionQueue.H Src/AmrTask/rts_impls/mpi_pthreads/RegionQueue.cpp Src/AmrTask/rts_impls/mpi_pthreads/RemoteConnection.H Src/AmrTask/rts_impls/mpi_pthreads/WorkerThread.H Src/AmrTask/rts_impls/mpi_pthreads/WorkerThread.cpp Src/AmrTask/rts_impls/mpi_pthreads/mylock.h Src/AmrTask/rts_impls/mpi_pthreads/perilla.mak Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/pthreads_common/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/pthreads_common/Barrier.H Src/AmrTask/rts_impls/pthreads_common/Barrier.cpp Src/AmrTask/rts_impls/pthreads_common/LocalConnection.H Src/AmrTask/rts_impls/pthreads_common/Make.package Src/AmrTask/rts_impls/pthreads_common/RGIter.H Src/AmrTask/rts_impls/pthreads_common/RGIter.cpp Src/AmrTask/rts_impls/pthreads_common/RegionQueue.H Src/AmrTask/rts_impls/pthreads_common/RegionQueue.cpp Src/AmrTask/rts_impls/pthreads_common/RemoteConnection.H Src/AmrTask/rts_impls/pthreads_common/WorkerThread.H Src/AmrTask/rts_impls/pthreads_common/WorkerThread.cpp Src/AmrTask/rts_impls/pthreads_common/mylock.h Src/AmrTask/rts_impls/pthreads_common/perilla.mak Src/AmrTask/rts_impls/upcxx_pthreads/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/upcxx_pthreads/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/upcxx_pthreads/Barrier.H Src/AmrTask/rts_impls/upcxx_pthreads/Barrier.cpp Src/AmrTask/rts_impls/upcxx_pthreads/LocalConnection.H Src/AmrTask/rts_impls/upcxx_pthreads/Make.package Src/AmrTask/rts_impls/upcxx_pthreads/Makefile Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.H Src/AmrTask/rts_impls/upcxx_pthreads/PackageQueue.cpp Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.H Src/AmrTask/rts_impls/upcxx_pthreads/Perilla.cpp Src/AmrTask/rts_impls/upcxx_pthreads/PerillaConfig.H Src/AmrTask/rts_impls/upcxx_pthreads/PerillaRts.H Src/AmrTask/rts_impls/upcxx_pthreads/PerillaRts.cpp Src/AmrTask/rts_impls/upcxx_pthreads/Perilla_common.cpp Src/AmrTask/rts_impls/upcxx_pthreads/RGIter.H Src/AmrTask/rts_impls/upcxx_pthreads/RGIter.cpp Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.H Src/AmrTask/rts_impls/upcxx_pthreads/RegionGraph.cpp Src/AmrTask/rts_impls/upcxx_pthreads/RegionQueue.H Src/AmrTask/rts_impls/upcxx_pthreads/RegionQueue.cpp Src/AmrTask/rts_impls/upcxx_pthreads/RemoteConnection.H Src/AmrTask/rts_impls/upcxx_pthreads/WorkerThread.H Src/AmrTask/rts_impls/upcxx_pthreads/WorkerThread.cpp Src/AmrTask/rts_impls/upcxx_pthreads/mylock.h Src/AmrTask/rts_impls/upcxx_pthreads/perilla.mak commit f3d96cb502ba6fed718e5c4aff69af8423f929e2 Author: kngott Date: Tue Dec 4 13:45:12 2018 -0800 Change inputs file for GPU testing. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/inputs commit 6fc4d9381c491c681fd65d86f0d461015f3b2016 Author: kngott Date: Tue Dec 4 13:44:51 2018 -0800 clean up false comment Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp commit 1a721f46057b8c90f844dedda3be98e2df120f64 Author: kngott Date: Tue Dec 4 13:44:30 2018 -0800 Fix swapped function arguments. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 5acc2f80dbc4bb4d14e2271911fcc335faf022a6 Author: Andrew Myers Date: Tue Dec 4 13:28:52 2018 -0800 change periodic shift logic to be more forgiving Src/Particle/AMReX_NeighborParticlesI.H commit ad06310da89845754862aa6164cf833ef19852e1 Author: Andrew Myers Date: Tue Dec 4 13:27:54 2018 -0800 use and IntVect for the periodic_shift member of NeighborCopyTag Src/Particle/AMReX_NeighborParticles.H commit 4d4f95cd0e61d8a99b2bb99ae26d56819fbf07a2 Author: Andrew Myers Date: Tue Dec 4 13:27:21 2018 -0800 change variable name to be more consistent Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 5f6ea6be841b632db975a718d7d7bada764f1efa Author: Johannes Blaschke Date: Tue Dec 4 13:09:13 2018 -0800 added std::move symmantics to regridding and tweake coarsening Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H commit 82027145d1b99602f820e585488d546cad4d852c Author: Weiqun Zhang Date: Tue Dec 4 15:10:02 2018 -0500 add profiler Src/Base/AMReX_FabArrayCommI.H commit 138f84a2f4a6a67fda8d90d298e70a73b280139f Author: Weiqun Zhang Date: Tue Dec 4 11:31:34 2018 -0800 AsyncArray: return earlier if size is zero Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_FabArrayCommI.H commit f7df47f6098c85263f3e120e680d78985bfff8ea Author: Weiqun Zhang Date: Tue Dec 4 11:13:48 2018 -0800 merged fillboundary: gpu version of local copy Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_GpuLaunch.H commit 31ea9f9c14c6ea702d196484aef08e83d576f18b Author: Weiqun Zhang Date: Tue Dec 4 10:27:31 2018 -0800 merged fillboundary: omp version of local copy Src/Base/AMReX_FabArrayCommI.H commit d0629364a979d02518a042328b29be9fab30fd72 Author: Weiqun Zhang Date: Tue Dec 4 10:05:38 2018 -0800 remove TagVols because they have not been used. gpu version copyFromMem in the new merged fillboundary Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H commit a3ea4fc2cab5b38495032badfc8564295ae4fdd5 Merge: 38ec07bfe 9491906a4 Author: Johannes Blaschke Date: Mon Dec 3 18:58:17 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 38ec07bfe0ad71c809fb79beb09ee15d83529467 Author: Johannes Blaschke Date: Mon Dec 3 18:58:10 2018 -0800 add regrid (i.e. update MF and DM of particular level) to LSCore Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp commit 9491906a4f4201380b39ba971a68d7a0f6bc0489 Author: Andrew Myers Date: Mon Dec 3 17:21:36 2018 -0800 != operator for NeighborCopyTag Src/Particle/AMReX_NeighborParticles.H commit 4b99c80b1d7af05c407e76c0676ba09674c18400 Author: Weiqun Zhang Date: Mon Dec 3 13:44:16 2018 -0800 first pass of merged FillBoundary Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit d65843d856a3a2da545108d736db06e2e4f8a4e2 Merge: e65d66552 82338f024 Author: Andrew Myers Date: Mon Dec 3 16:56:59 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e65d665521e181cc974ef0893ef10926106768bf Author: Andrew Myers Date: Mon Dec 3 16:56:42 2018 -0800 on-the-fly computation of neighbor particles in a multi-level setting. Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.H Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborListMR/inputs Tutorials/Particles/NeighborListMR/main.cpp commit 584073756c3ae49fd5d563be79be4b4cfc3918d0 Author: kngott Date: Mon Dec 3 16:50:47 2018 -0800 Primary MFIter loop done and compiling. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp commit 82338f0242e14af5301315241a19e15b332892b3 Author: rgrout Date: Mon Dec 3 16:44:12 2018 -0700 Replaces #375 Spline Implicit function for EB (#380) * Added Spline implicit function for EB2 * Testing the FORD Scorpion piston bowl generation * Cleaned up spline implicit function * Modified the case to test the spline functionality * Resolve conflicts and address @WeiqunZhang comments * add missing amrex namespace Src/EB/AMReX_EB2.cpp Src/EB/AMReX_EB2_IF.H Src/EB/AMReX_EB2_IF_Spline.H Src/EB/AMReX_distFcnElement.H Src/EB/AMReX_distFcnElement.cpp Src/EB/CMakeLists.txt Src/EB/Make.package Tutorials/EB/GeometryGeneration/main.cpp commit 258204865af0baa1c9b48ad3b0ba611895036d45 Author: Andrew Myers Date: Mon Dec 3 12:29:54 2018 -0800 don't forget to define the dmaps Tutorials/Particles/NeighborListMR/main.cpp commit 6ecaa6804cbbba6c7af222ba7a88ef2ec65024e4 Author: Andrew Myers Date: Mon Dec 3 12:28:05 2018 -0800 fix parameter shadowing Src/Particle/AMReX_NeighborParticlesI.H commit de2b701db2ef26a1ad4b7271824b56cf232b9f75 Author: Andrew Myers Date: Mon Dec 3 12:25:47 2018 -0800 update inputs file Tutorials/Particles/NeighborListMR/inputs commit 6d8e2c95b52dfe60e19e0416c2be5c062533abc2 Author: Andrew Myers Date: Mon Dec 3 12:24:32 2018 -0800 fix another typo. Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.cpp commit 43dbfbe77ad1462f33495f764a7c1c0149dbe585 Author: kngott Date: Mon Dec 3 12:23:17 2018 -0800 Advection broken into functions. Compute_flux & slope left. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.cpp commit 47b0de5451176a866f819fd8a4676a80bcbc4320 Merge: 57b017a4c c1dd3bec9 Author: Andrew Myers Date: Mon Dec 3 12:22:38 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 57b017a4c8668e3b6a5d055f9d7eb4214ac585dc Author: Andrew Myers Date: Mon Dec 3 12:22:06 2018 -0800 fix typo Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.cpp commit c1dd3bec9ec915de235a38136976e50b61ae52cd Author: Tan Nguyen Date: Mon Dec 3 11:56:06 2018 -0800 add ref guide for RegionGraph Iterator Docs/sphinx_documentation/source/AsyncIter.rst Docs/sphinx_documentation/source/Chapter6aa.rst commit 447f0d010be812b2a42c4248954f2d0a45c7c8ce Merge: b2580ad88 80e09a33a Author: Andrew Myers Date: Mon Dec 3 10:30:20 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b2580ad886d732b4aa2cfc85373e8b51be395e0c Author: Andrew Myers Date: Mon Dec 3 10:29:47 2018 -0800 fix issue involving component names Tests/HDF5Benchmark/main.cpp commit 3c894116ab368c1a8b6cb3b9cb5487ef5b880ed4 Author: Andrew Myers Date: Mon Dec 3 10:24:27 2018 -0800 fix assertion re: containing_bx in InitRandom. Src/Particle/AMReX_ParticleInit.H commit de31cb8f8db8ab38c3259d6f527bdfa4a106aa9b Author: Andrew Myers Date: Mon Dec 3 10:23:57 2018 -0800 remove unused variable Tests/HDF5Benchmark/main.cpp commit b682e2d2d06cb0a36adb0d9f1485c9a4f688ffef Merge: 94a17c84a 80e09a33a Author: Weiqun Zhang Date: Mon Dec 3 08:47:26 2018 -0800 Merge branch 'weiqun/gpu' into weiqun/comm commit 80e09a33a08f0ab49f63ee7d7f06f66e083cc9c7 Merge: ec579be7b 8baf1cccb Author: Weiqun Zhang Date: Mon Dec 3 08:46:01 2018 -0800 Merge branch 'weiqun/gpu' into development commit ec579be7bf1be1665a868441bb16dd432eaac49d Author: Weiqun Zhang Date: Mon Dec 3 08:44:35 2018 -0800 update CHANGES CHANGES commit ada0fb15545f7fc57926b1f46ee30819a3d8a26d Author: Johannes Blaschke Date: Sun Dec 2 22:21:50 2018 -0800 oopsie Src/EB/AMReX_EB_LSCoreBase.H commit 23d20fdefffb16c079935ba14058fe5ef94d2e5c Author: Johannes Blaschke Date: Sun Dec 2 22:15:38 2018 -0800 added valid flags to LSCore class Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H commit 3ae95dde12aa1f4382873fe030ec08e170399cf6 Author: Max Katz Date: Sun Dec 2 21:12:43 2018 -0500 Restore some code that was deleted in 70befea Src/Amr/AMReX_Amr.cpp commit 57c076cbae838343a61cda16067ac679f54f2a0a Author: Michael Zingale Date: Sun Dec 2 17:55:44 2018 -0500 make the extrema use a mask to find the true extrema in the domain (#378) closes #291 Tools/Postprocessing/F_Src/fextrema.f90 commit bcd5963ec6593de3a6d2af9a02edae0986829a19 Author: Michael Zingale Date: Sun Dec 2 13:31:02 2018 -0500 increase width of box and zone output Tools/Postprocessing/F_Src/fboxinfo.f90 commit 94a17c84a8d9ca741e868dd06799b62d1ad5aaeb Author: Weiqun Zhang Date: Sat Dec 1 19:08:00 2018 -0500 shift the lo box the big end and do copy too Src/Base/AMReX_FabArrayCommI.H commit 0957e4146a010f321d43606fcad392e6181c85d4 Author: Weiqun Zhang Date: Sat Dec 1 16:03:31 2018 -0500 add profilers Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 53e0aa67a7a87c50275711758c02a169146f6a57 Author: Weiqun Zhang Date: Sat Dec 1 15:32:51 2018 -0500 fewer kernels in FillBoundary Src/Base/AMReX_FabArrayCommI.H commit 6c890bf807f707d4e912f7bf032c4f575c143156 Author: Weiqun Zhang Date: Sat Dec 1 13:38:57 2018 -0500 fix typo Src/Base/AMReX_FabArray.H commit 31ba86098e8eb01b52d964f1fc0c59202e13e5d3 Merge: 8baf1cccb 6b69a6233 Author: Weiqun Zhang Date: Sat Dec 1 13:31:40 2018 -0500 Merge branch 'development' into weiqun/comm commit 6b69a623349da833d398b0c51e59fe1b0731079d Merge: 62c77d49a d80ea3fba Author: Weiqun Zhang Date: Sat Dec 1 13:24:28 2018 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 62c77d49a16047368567b39f8235e19787cb1354 Author: Weiqun Zhang Date: Sat Dec 1 13:23:56 2018 -0500 add function to help MPI progress Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 8baf1cccb1ccf957c32d027efc70f704cde2ea8f Author: Weiqun Zhang Date: Sat Dec 1 07:40:30 2018 -0800 filcc: multiple passes so that the corners can be dealt Src/Base/AMReX_PhysBCFunct.H commit aa33e0729700dc718adbb374605a8c6bd27290f5 Author: kngott Date: Fri Nov 30 18:08:32 2018 -0800 face velocities into MFIter loop. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit d80ea3fba27850bf44943295aa3c3b991f25e4d9 Merge: d96c01462 90e03d7a2 Author: Johannes Blaschke Date: Fri Nov 30 13:51:00 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d96c0146274babc458907e80785c6ae5af0990eb Author: Johannes Blaschke Date: Fri Nov 30 13:50:56 2018 -0800 updated amrex build info for macOS Docs/sphinx_documentation/source/BuildingAMReX.rst commit 44945c2591ad3168b99e9f5233a081f7e38a71d8 Author: Weiqun Zhang Date: Fri Nov 30 13:36:34 2018 -0800 add hoextrap to filcc3d Src/Base/AMReX_FilCC_3D_C.cpp commit 90e03d7a24697568c6dad67f4ff402d0d98444a7 Author: Tan Nguyen Date: Fri Nov 30 12:00:54 2018 -0800 ref guide for AMFIter Docs/sphinx_documentation/source/Chapter6aa.rst Docs/sphinx_documentation/source/index.rst commit 20bcb58b6ff29a7af6c2eea7409b2e6021dafb34 Author: Weiqun Zhang Date: Fri Nov 30 11:26:23 2018 -0800 filcc 2d Src/Base/AMReX_FilCC_1D_C.cpp Src/Base/AMReX_FilCC_2D_C.cpp commit 69ce86ca42425cb959d1190102980fa996d5de66 Author: kngott Date: Thu Nov 29 16:49:20 2018 -0800 Init and EstTimeDt Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 2fe8285b060c01e73f9626eb9ba1582f3f692627 Author: kngott Date: Thu Nov 29 16:49:00 2018 -0800 Init and EstTimeDt Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H commit 5b08907503df65c25f59ba33ad6d43897f3b2aa9 Author: kngott Date: Thu Nov 29 16:48:41 2018 -0800 Break apart face velocity. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp commit cc7a1cddf33d3fba828089c29752e75b6dad0262 Author: kngott Date: Thu Nov 29 16:47:09 2018 -0800 Clean up init function. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp commit f114ec215cd55c3ffbbd1a17bf8af04dc7c72bdd Author: Andrew Myers Date: Thu Nov 29 19:29:44 2018 -0500 add special case early exit to RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H commit a747825fe1a41777bddd381dd0de106d2c74c49b Author: Weiqun Zhang Date: Thu Nov 29 15:48:33 2018 -0800 fix bug Src/Base/AMReX_IntVect.H Src/Base/AMReX_MultiFabUtil_1D.cpp Src/Base/AMReX_MultiFabUtil_2D.cpp Src/Base/AMReX_MultiFabUtil_3D.cpp commit 4c54ae43798b6924ecf8d2170ab34fe1e09d84f4 Author: Cy Chan Date: Thu Nov 29 14:54:14 2018 -0800 added Backtrace parser script to Tools/Backtrace/ Tools/Backtrace/parse_bt.py commit 2347a0e0ef8e021c48640f625f73c1930ceb455b Author: Weiqun Zhang Date: Thu Nov 29 14:02:19 2018 -0800 make gcc on cori knl happy Src/Base/AMReX.H commit 65ead10e07b6cd7bb83fea9a37d228e98251609f Author: Weiqun Zhang Date: Thu Nov 29 13:43:55 2018 -0800 remove all fortran codes in EBMultiFabUtil Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2D.cpp Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3D.cpp Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_MultiFabUtil_Perilla.cpp Src/Base/AMReX_MultiFabUtil_nd.cpp Src/Base/AMReX_iMultiFab.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Src/EB/AMReX_EBMultiFabUtil.cpp commit 3ea33ff385f20e447ce66654014ddb6c8c4b9cd8 Merge: 2b9e0e251 22cee7fa9 Author: Weiqun Zhang Date: Thu Nov 29 13:31:42 2018 -0800 Merge branch 'development' into weiqun/gpu commit 2b9e0e2516bc798131220aded01e61e636852ec5 Author: Weiqun Zhang Date: Thu Nov 29 13:23:19 2018 -0800 get_loop_bounds -> amrex_get_loop_bounds for the c bind name because it's global Src/Base/AMReX_fort_mod.F90 commit 909732f20b838fb41c85144ae1e1c51fc85cd963 Author: Weiqun Zhang Date: Thu Nov 29 13:06:47 2018 -0800 gpu: amrex_avgdown_with_vol Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Perilla_omp/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Pthread_Common/AsyncMultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_MultiFabUtil_Perilla.cpp Src/EB/AMReX_EBMultiFabUtil.cpp commit 36fef10df061fcd5f898c8560e78166a7ae643d9 Author: Andrew Myers Date: Thu Nov 29 12:34:56 2018 -0800 start work on making BuildMasks multi-level Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 322fdd36a5b02a201c86e09798ac5948f0945443 Author: Weiqun Zhang Date: Thu Nov 29 12:16:41 2018 -0800 gpu: amrex_compute_divergence Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_F.H Src/EB/AMReX_EBMultiFabUtil.cpp commit 7ea65c0048ff1f29373f3a953e1ac1b86911df14 Author: Weiqun Zhang Date: Thu Nov 29 11:41:00 2018 -0800 gpu: amrex_avgdown and amrex_avgdown_nodes Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Perilla_omp/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Pthread_Common/AsyncMultiFabUtil.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_F.H Src/EB/AMReX_EBMultiFabUtil.cpp commit 22cee7fa9a7cddcfcf689738fee4bf112a37fdcc Author: Donald Willcox Date: Thu Nov 29 14:33:57 2018 -0500 Integrate to dt/2 then to dt to show example of reinitializing CVODE. Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_cuda_cusolver.cpp commit f28cc1ffd88f637f47816bc0094650af9709eeee Author: Andrew Myers Date: Thu Nov 29 11:30:25 2018 -0800 update Tutorial Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborListMR/main.cpp commit d89badd63d4cf3655f1724471cd55d4c62565ef3 Author: Andrew Myers Date: Thu Nov 29 11:30:15 2018 -0800 don't make the neighbor particle methods take a lev argument Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 8fbc63e072901a6519de53c25387d8fbced169fb Author: Weiqun Zhang Date: Thu Nov 29 10:52:10 2018 -0800 gpu: amrex_avgdown_edges Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_C.H commit 3727cf4ea401a97284b2e2d90a513c90435e966d Merge: f5192d875 37b39ba08 Author: Andrew Myers Date: Thu Nov 29 10:35:38 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f5192d875a99170cb4a7a626f704d8a5267f06f6 Author: Andrew Myers Date: Thu Nov 29 10:35:21 2018 -0800 add new Test for multi-level neighbor lists Tutorials/Particles/NeighborListMR/GNUmakefile Tutorials/Particles/NeighborListMR/Make.package Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.H Tutorials/Particles/NeighborListMR/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborListMR/inputs Tutorials/Particles/NeighborListMR/main.cpp Tutorials/Particles/NeighborListMR/neighbor_list_2d.f90 Tutorials/Particles/NeighborListMR/neighbor_list_F.H commit 3e78636ed75b4eab768e70f215c14fe472305343 Author: Weiqun Zhang Date: Thu Nov 29 10:33:42 2018 -0800 gpu: amrex_avgdown_faces Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_F.H Src/EB/AMReX_EBMultiFabUtil.cpp commit 9fcadf16b023aeec9516af6a2a0cd4868cb13ff6 Author: Andrew Myers Date: Thu Nov 29 10:32:56 2018 -0800 add additional constructor to NeighborParticleContainer Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 37b39ba082b64cd7829790be88aa271aaad92d0c Author: Weiqun Zhang Date: Thu Nov 29 13:14:47 2018 -0500 make BL_NO_FORT compile Src/Base/AMReX_iMultiFab.cpp commit a88c4888dc9e35a258a48b9ff0a93b0217c35c77 Merge: 5fd128017 92fe64e3f Author: Weiqun Zhang Date: Thu Nov 29 09:23:52 2018 -0800 Merge branch 'development' into weiqun/gpu commit 5fd1280172236880c12ed36b5dc41f59399173b2 Author: Weiqun Zhang Date: Wed Nov 28 16:59:02 2018 -0800 Revert "Tutorials/GPU/CNS: fuse launches" This reverts commit 707f735d4e3374e9655b1a13309d006b8a739c58. Tutorials/GPU/CNS/Source/CNS_advance.cpp commit 707f735d4e3374e9655b1a13309d006b8a739c58 Author: Weiqun Zhang Date: Wed Nov 28 16:25:12 2018 -0800 Tutorials/GPU/CNS: fuse launches Tutorials/GPU/CNS/Source/CNS_advance.cpp commit 6e2f7372c8d30286af6045eeb0fa685966f7c5bd Author: Weiqun Zhang Date: Wed Nov 28 16:24:37 2018 -0800 capability of fusing independent kernels Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_GpuLaunch.H commit 92fe64e3f1c247cfaefa2ad250e0374e790acffc Author: Andrew Myers Date: Wed Nov 28 14:30:10 2018 -0800 remove unused function Src/Base/AMReX_MFIter.H commit 2f65b1283319d61969d9373b75c078fcc7f11097 Author: kngott Date: Wed Nov 28 13:17:05 2018 -0800 cleanup Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.cpp commit fac777b90a4f22478854313be771e5cd1c0cd712 Author: kngott Date: Wed Nov 28 13:16:54 2018 -0800 Ignore TagBox for now. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H commit 1d928eb79a5e123659afcae922d5aeb926898567 Author: kngott Date: Wed Nov 28 13:16:00 2018 -0800 Add maxabs to BaseFab. Src/Base/AMReX_BaseFab.H commit a22446a39189fb343973b434af6c1fedc5c2db2c Author: Cy Chan Date: Wed Nov 28 13:12:53 2018 -0800 some performance analysis updates Src/Base/AMReX_DistributionMapping.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_Machine.cpp commit 44a68266598eeeb5834aa5f9e97de424fe5b67f8 Author: Weiqun Zhang Date: Wed Nov 28 11:59:10 2018 -0800 fix index bug Src/Base/AMReX_MultiFabUtil.cpp commit ce384a97f8ffb598115fb31156fe2f49004a0ba6 Author: Weiqun Zhang Date: Wed Nov 28 11:42:22 2018 -0800 renaming Src/Base/AMReX_Box.H Src/Base/AMReX_MultiFabUtil.cpp commit db3c756aae4a8c8da5542718a3f21b876b8d2882 Author: Weiqun Zhang Date: Wed Nov 28 10:36:43 2018 -0800 turn off simd for debug Src/Base/AMReX_Extension.H commit 6cfc7469072d48033c2569d4ba76bc5cbfa663e3 Author: Weiqun Zhang Date: Wed Nov 28 10:36:25 2018 -0800 fix bug in iMultiFab::sum Src/Base/AMReX_iMultiFab.cpp commit a2ff44f56b78acffc1e6b9038af0a85bc3e2dc57 Author: Weiqun Zhang Date: Wed Nov 28 10:28:58 2018 -0800 consolidate functions for casting from one type of fab to another Src/Base/AMReX_BaseFabUtility.H Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_nd_C.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit ecc11db0b5e9455bc8d5f194186d614c24660918 Author: Weiqun Zhang Date: Wed Nov 28 09:55:04 2018 -0800 add iMultiFab::sum to return long Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_nd_C.cpp Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit 89186eaff831c17d31fef84476f9f21298faddd1 Author: Weiqun Zhang Date: Tue Nov 27 23:05:34 2018 -0800 fix bug in case of tiling Src/Base/AMReX_Box.H Src/Base/AMReX_MultiFabUtil.cpp commit 8fd46592de2c6547c464afef536b1bb6daa89f96 Merge: b15759b0f a2b9040d9 Author: Weiqun Zhang Date: Tue Nov 27 16:41:16 2018 -0800 Merge branch 'weiqun/gpu' into development commit a2b9040d929b4559b24ee1fe5d2c9525cf09cc8e Author: Weiqun Zhang Date: Tue Nov 27 16:39:59 2018 -0800 gpu: amrex_avg_cc_to_fc Src/Base/AMReX_Box.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_F.H commit b15759b0f314875c10ef47d0b86e74b5d8cf30b2 Merge: d74e55aa4 27f32782b Author: Andrew Myers Date: Tue Nov 27 16:33:21 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 27f32782b778606e5ec88267471a2beaf6d90570 Author: Weiqun Zhang Date: Tue Nov 27 16:28:01 2018 -0800 avoid using omp simd with pgi Src/Base/AMReX_Extension.H commit aa843d2500bf6b685692e2d33d4a74fb874f2096 Author: Weiqun Zhang Date: Tue Nov 27 16:28:01 2018 -0800 avoid using omp simd with pgi Src/Base/AMReX_Extension.H commit d74e55aa473e87c381cb203a9875d41c9b05a222 Author: Andrew Myers Date: Tue Nov 27 16:17:35 2018 -0800 make the neighbors and neighbor_list protected Src/Particle/AMReX_NeighborParticles.H commit 4c4fa373b5ec06b106db8c2a05dd5f7b422b79ce Author: Andrew Myers Date: Tue Nov 27 16:16:49 2018 -0800 add some accessor functions for neighbors and neighbor lists Src/Particle/AMReX_NeighborParticles.H commit 3468ed9dbba429bf87bda9f55f0c06641af8051d Author: Cy Chan Date: Tue Nov 27 16:12:13 2018 -0800 Add neighborhood cache Add machine model input parameter parsing Add baseline score for neighborhood comparison Src/Base/AMReX.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_Machine.H Src/LinearSolvers/MLMG/AMReX_Machine.cpp commit a0f60c022fe43bb9d5d1979afeecc6cc3650a840 Author: Cyrus Harrison Date: Tue Nov 27 15:25:01 2018 -0800 add conduit blueprint support for particles Src/Extern/Conduit/AMReX_Conduit_Blueprint.H Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp Src/Extern/Conduit/AMReX_Conduit_Blueprint_ParticlesI.H Tutorials/Blueprint/AssignMultiLevelDensity/GNUmakefile Tutorials/Blueprint/AssignMultiLevelDensity/main.cpp Tutorials/Blueprint/CellSortedParticles/CellSortedPC.H Tutorials/Blueprint/CellSortedParticles/CellSortedPC.cpp Tutorials/Blueprint/CellSortedParticles/GNUmakefile Tutorials/Blueprint/CellSortedParticles/Make.package Tutorials/Blueprint/CellSortedParticles/cell_sorted_3d.F90 Tutorials/Blueprint/CellSortedParticles/cell_sorted_F.H Tutorials/Blueprint/CellSortedParticles/inputs Tutorials/Blueprint/CellSortedParticles/main.cpp Tutorials/Blueprint/README.txt commit f533e759ce05c234d0c77a87af6b68c9a67957b4 Author: Andrew Myers Date: Tue Nov 27 15:12:08 2018 -0800 add the level to the internal structs used for keeping track of copies Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit c3305e77a317f1afeae22a7a9560a359ea021e3c Author: Weiqun Zhang Date: Tue Nov 27 15:00:48 2018 -0800 fix eb and comp issues in two previous commits Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_C.H Src/EB/AMReX_EBMultiFabUtil.cpp commit 93c6211e86fb6c3e5a63e880999c163bdcf632b0 Author: Weiqun Zhang Date: Tue Nov 27 14:34:21 2018 -0800 gpu: amrex_avg_fc_to_cc Src/Base/AMReX_Geometry.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_RealBox.H commit b07d9b79ee0f57f030b186257154143114e14ae5 Author: kngott Date: Tue Nov 27 14:06:14 2018 -0800 Spelling error. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 22a6c94a3d10b61c06bec87a460154f5ea6edbb0 Author: Andrew Myers Date: Tue Nov 27 13:26:20 2018 -0800 also keep track of the level information in the mask Src/Particle/AMReX_NeighborParticlesI.H commit 337431702942e18a80b6cf4c7e948e7cef62bc8d Author: Andrew Myers Date: Tue Nov 27 13:22:21 2018 -0800 use an enum to keep mask comps straight Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit f11385e38b18050594dda92b071c66dfc4271433 Author: Andrew Myers Date: Tue Nov 27 13:12:37 2018 -0800 BL_ASSERT -> AMREX_ASSERT Src/Particle/AMReX_NeighborParticlesI.H commit c4f61746abf88ad1c8db987248887d8a7e89609a Author: kngott Date: Tue Nov 27 13:12:31 2018 -0800 Adjust for new PhysBCFunct. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit f6fddb620d8b3ee73eef31f9d2e8c0acf68eb9bf Author: Andrew Myers Date: Tue Nov 27 13:11:14 2018 -0800 some additional regrid functions Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 3f4635d422cd74a369a93395938da40e99833fa9 Author: kngott Date: Tue Nov 27 13:09:03 2018 -0800 DeviceFab -> AsyncFab Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp commit 162fb7c90b427ff28e1d2a716cf03793e24a5429 Author: Weiqun Zhang Date: Tue Nov 27 13:00:51 2018 -0800 gpu: amrex_avg_eg_to_cc Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_F.H commit c342ae4dda410c068276b6a9ccfb048dfa77da0c Author: Andrew Myers Date: Tue Nov 27 12:59:24 2018 -0800 minor Src/Particle/AMReX_NeighborParticlesI.H commit e6cae1e5bb6706374122c965a0319811a8e7a43f Author: Andrew Myers Date: Tue Nov 27 12:53:13 2018 -0800 include mask_ptr in the resizeContainers call Src/Particle/AMReX_NeighborParticlesI.H commit 283f9d5961598858069dd9495f5aafaf6a4ffc92 Author: Andrew Myers Date: Tue Nov 27 12:50:55 2018 -0800 also make the level mask structure multi-level Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 5e6bc065dda0e752a61acd1cee253e14108190cc Author: Andrew Myers Date: Tue Nov 27 12:32:01 2018 -0800 fix off-by-one error Src/Particle/AMReX_NeighborParticlesI.H commit 5495721b275c8b7b157f64e4173e34b344518d09 Author: Andrew Myers Date: Tue Nov 27 12:31:46 2018 -0800 fix scoping issue in Tutorial Tutorials/Particles/NeighborList/main.cpp commit e76d9ad2092488c8b53fc16d4c3c794077c35fa8 Author: Weiqun Zhang Date: Tue Nov 27 12:25:13 2018 -0800 fix the call to get Src/Base/AMReX_FabArrayCommI.H commit 05b189297d71ff53d7b9d4ca3ac1a8cb4e2145d8 Author: Andrew Myers Date: Tue Nov 27 12:21:46 2018 -0800 remove unused variable Src/Base/AMReX_PhysBCFunct.cpp commit 10d556985a79682713e9d19f064e1b1fcd681e32 Author: Andrew Myers Date: Tue Nov 27 12:18:07 2018 -0800 add call to resize containers to the appropriate size Src/Particle/AMReX_NeighborParticlesI.H commit a696343486d69a1dc33123fce2d75d9813d05462 Author: Andrew Myers Date: Tue Nov 27 12:10:59 2018 -0800 add method for syncing up the size of neighbors and neighbor_list Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 53b4b703622036ebe9f0300b48cb58123321cfe5 Author: Andrew Myers Date: Tue Nov 27 12:05:38 2018 -0800 remove the fortran version of buildNeighborList Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 9b40684f3f5d381858f1344d8c4bfba9d1966da0 Author: Andrew Myers Date: Tue Nov 27 12:03:23 2018 -0800 also update the neighbor_list structure for multilevel Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp commit 604b346d41404634584d45c1fb29093b428af841 Author: Andrew Myers Date: Tue Nov 27 11:56:20 2018 -0800 update Tutorial Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp commit 442f87268e5cd918736826831bce1997bf052bc6 Author: Andrew Myers Date: Tue Nov 27 11:55:34 2018 -0800 make the neighbor particle data structure a vector over levels Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit a0fc1d50718d770c5a9a2f57c8b2a522bfc434c8 Author: Weiqun Zhang Date: Tue Nov 27 11:54:01 2018 -0800 gpu: amrex_avg_nd_to_cc Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_C.H commit 8af96cff4d4b8bb14032673206b172b47d8323b0 Merge: 93a5653d9 4d4134648 Author: Marc Day Date: Tue Nov 27 10:40:16 2018 -0800 Merge pull request #369 from burlen/sensei_init_ghost_zones Sensei init ghost zones commit 93a5653d9a009da4fe1a5f863fda189af0aab8cf Merge: d98e0394f a90386b41 Author: WeiqunZhang Date: Tue Nov 27 10:28:16 2018 -0800 Merge pull request #372 from knutsvk/development use VisIt compatible plotfile heading commit a90386b415670b5dc2dee1151dd5341ddc388b34 Merge: 9d16204e0 d98e0394f Author: knutsvk Date: Tue Nov 27 18:07:40 2018 +0000 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 9d16204e0033ca6db80f56fa00fe52203dd3106b Author: knutsvk Date: Tue Nov 27 18:06:14 2018 +0000 use VisIt compatible plotfile heading Tutorials/EB/CNS/Source/CNS.H commit d98e0394fe88f5e8024fdf20cb8d4d67fc53363d Author: Johannes Blaschke Date: Mon Nov 26 22:49:33 2018 -0800 fix spelling mistake Src/Base/CMakeLists.txt commit 437dce0206c2fd4ddadd398a0cccc4593fd6334f Merge: c585d14f4 c88b75641 Author: Johannes Blaschke Date: Mon Nov 26 22:22:01 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit c585d14f4ff19c204c7dc2c9985ac86bac301351 Author: Johannes Blaschke Date: Mon Nov 26 22:21:56 2018 -0800 coarsen ghost cells as well Src/EB/AMReX_EB_levelset.cpp commit 6cc3879c42b32db5646547f36dfc2e8d3de6dd81 Author: kngott Date: Mon Nov 26 17:50:01 2018 -0800 Fix merge error. Src/Base/AMReX_BaseFab.H commit c88b75641a1beae9305bd8100d79684665a62333 Author: Weiqun Zhang Date: Mon Nov 26 17:48:23 2018 -0800 more inline Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H commit 59d2bb299033a77c5a10bc5697912069537ea345 Author: Weiqun Zhang Date: Mon Nov 26 17:42:43 2018 -0800 MultiFabUtil: fill slice on gpu Src/Base/AMReX_Geometry.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_MultiFabUtil_nd.F90 Src/Base/AMReX_MultiFabUtil_nd_C.cpp Src/Base/AMReX_RealBox.H Src/Base/CMakeLists.txt Src/Base/Make.package commit f407b2e146676c0e9db639903529bec04df9fc2b Author: Weiqun Zhang Date: Mon Nov 26 16:09:09 2018 -0800 MultiFabUtil: start gpu Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1D_C.cpp Src/Base/AMReX_MultiFabUtil_2D_C.cpp Src/Base/AMReX_MultiFabUtil_3D_C.cpp Src/Base/AMReX_MultiFabUtil_C.H Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_MultiFabUtil_nd.F90 Src/Base/AMReX_MultiFabUtil_nd_C.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 0109491620ec711793de5923db0ac4e4208a52b2 Merge: a34829755 8ec0fd690 Author: Weiqun Zhang Date: Mon Nov 26 18:05:32 2018 -0500 Merge branch 'weiqun/gpu' of github.com:AMReX-Codes/amrex into weiqun/gpu commit 8ec0fd6901cd626b4b969eb882e1d4c6e251ff3e Merge: 767340215 a4477286a Author: Weiqun Zhang Date: Mon Nov 26 14:52:50 2018 -0800 Merge branch 'weiqun/gpu' into development commit a4477286ac5e500e98ee05715326b67678a6a8ee Author: Weiqun Zhang Date: Mon Nov 26 13:45:58 2018 -0800 remove unused norm0 function Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit a34829755027f91bc4f7a52296dbfe7ea0fad616 Author: Weiqun Zhang Date: Mon Nov 26 16:04:50 2018 -0500 cudaMallocHost -> cudaHostAlloc Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CudaDevice.cpp commit 1c97b60679aca2f252472d19973704629fa5ad45 Author: Cy Chan Date: Mon Nov 26 12:41:14 2018 -0800 added remap neighborhoods to MLLinOp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_Machine.H Src/LinearSolvers/MLMG/AMReX_Machine.cpp Src/LinearSolvers/MLMG/Make.package Tests/LinearSolvers/MLMG/AMReX_Machine.H Tests/LinearSolvers/MLMG/Make.package Tests/LinearSolvers/MLMG/inputs Tests/LinearSolvers/MLMG/main.cpp commit b2078bee4ac065af057e2f57087502b88076ac22 Merge: b4d512644 856c92e85 Author: kngott Date: Mon Nov 26 12:06:18 2018 -0800 Merge branch 'weiqun/gpu' into gpu commit b4d5126445f2953baf3dffc20f0a3aadb1a9cae8 Author: kngott Date: Mon Nov 26 12:00:19 2018 -0800 Remove .f90. Now CPU compiling. (WIP). Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.f90 commit 9f5bd9b44a0af3516e03c6b1218ab39fd60ea2f6 Author: kngott Date: Mon Nov 26 11:51:50 2018 -0800 First attempt at slope_3d.cpp. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp commit 767340215715c48a6d8676eeccc340032c0fa59e Author: Ann Almgren Date: Mon Nov 26 11:32:41 2018 -0800 Add the brackets between amrex::Initialize() and amrex::Finalize() Tests/HDF5Benchmark/main.cpp commit 478344792199cd9bac51a70595a0113fa2a24db3 Author: Cy Chan Date: Mon Nov 26 10:36:50 2018 -0800 bug fixes and cleanup Tests/LinearSolvers/MLMG/AMReX_Machine.cpp commit 856c92e85f23886856310bba9afdb88af4717226 Author: Weiqun Zhang Date: Mon Nov 26 09:35:37 2018 -0800 change the interface of WriteMLMF to take Vector of MultiFab const* Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_PlotFileUtil.cpp commit a59d18ca6deb7acaa1d47f74e7c62d11c6624492 Author: Weiqun Zhang Date: Mon Nov 26 08:56:17 2018 -0800 rm iMultiFab norm funcitons Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit 721b25223730371bcdd358c058a4c13e9cfa1d4e Author: Weiqun Zhang Date: Mon Nov 26 11:32:40 2018 -0500 make: add USE_CUDA_FAST_MATH so that we could turn off fast math Tools/GNUMake/Make.defs Tools/GNUMake/comps/nvcc.mak commit 137a4867386aef4e4dcff4e55611625cc6507dcf Author: Weiqun Zhang Date: Mon Nov 26 11:23:51 2018 -0500 set shared memory bank size Src/Base/AMReX_CudaDevice.cpp commit 178d3783494e96e724e310ad2d315720a4ac51f0 Merge: 747cfc80e c67fabdf7 Author: WeiqunZhang Date: Mon Nov 26 08:09:05 2018 -0800 Merge pull request #273 from Alpine-DAV/task/2018_06_add_blueprint_and_ascent add optional blueprint and ascent support to AMReX commit 747cfc80e7c2f0a341251497fd1df62ffbc18f69 Merge: 4a808bd7f e3fd8549b Author: WeiqunZhang Date: Mon Nov 26 08:06:54 2018 -0800 Merge pull request #371 from knutsvk/development MLNodeLaplacian: overload define() with EBFArrayBoxFactory as input commit e3fd8549bb652f87b39b08c7b64e083115de2e96 Merge: 585197c97 4a808bd7f Author: knutsvk Date: Mon Nov 26 10:44:26 2018 +0000 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 9d7237b5a6a9c24b8d57ca5dfa76a4911fc1064d Author: Kaiyuan Hou Date: Sun Nov 25 23:56:27 2018 -0600 remove hdf5 code Tests/HDF5Benchmark/GNUmakefile Tests/PnetCDFBenchmark/GNUmakefile Tests/PnetCDFBenchmark/Make.package Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.cpp Tests/PnetCDFBenchmark/main.cpp commit fc089604b47df3469b116c495a3291f33327da02 Author: kngott Date: Sun Nov 25 20:03:26 2018 -0800 slope left (WIP). Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/GNUmakefile Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Make.package commit e0be6a3f8b72b799271c1806a2c21f8791bb8e2b Author: kngott Date: Sun Nov 25 19:59:19 2018 -0800 cpp versions Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.cpp commit 4a808bd7f6fcd7d61c10de4005b59f64fb5d0224 Merge: 4d7a76e60 f2666cb82 Author: Weiqun Zhang Date: Sun Nov 25 18:18:08 2018 -0800 Merge branch 'weiqun/comm' into development commit 4d7a76e604525d4a7d7b842306df91863edadf82 Author: Tan Nguyen Date: Sun Nov 25 16:42:13 2018 -0800 update destructors for AMFIter related classes Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AsyncFillPatch.cpp Src/AmrTask/rts_impls/Perilla/PackageQueue.cpp Src/AmrTask/rts_impls/Perilla/Perilla.H Src/AmrTask/rts_impls/Perilla/Perilla.cpp Src/AmrTask/rts_impls/Perilla/RegionGraph.H Src/AmrTask/rts_impls/Perilla/RegionGraph.cpp Src/AmrTask/rts_impls/Pthread_Common/LocalConnection.H commit f2666cb82e90527016a46af039ce7ff91e497c33 Author: Weiqun Zhang Date: Sun Nov 25 15:14:30 2018 -0800 fix bug: forgot for after omp parallel Src/Base/AMReX_FabArrayCommI.H commit 1c1af75d0d3676b78d533e5eefc56f1ab1a7c048 Author: Weiqun Zhang Date: Sun Nov 25 11:28:39 2018 -0800 fix bugs in the new ParallelCopy Src/Base/AMReX_FabArrayCommI.H commit 4a4a6fc9e57dd8eda4bfb3b417fd861b3efbf09e Merge: edc44492e b780552b3 Author: Johannes Blaschke Date: Sat Nov 24 22:01:54 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit edc44492e56b17e6f3788994863f7df35c99a3ce Author: Johannes Blaschke Date: Sat Nov 24 22:01:45 2018 -0800 some cleanup and fixing parameters Src/AmrCore/AMReX_FillPatchUtil.cpp Src/EB/AMReX_EB_LSCoreBase.cpp Tutorials/EB/Donut/Exec/inputs commit e7d41e59b5851dc65a623f1b119674b348a70245 Merge: 806760c27 b780552b3 Author: Weiqun Zhang Date: Sat Nov 24 21:17:11 2018 -0800 Merge branch 'development' into weiqun/comm commit b780552b31083ace4790b1698a38209a58456209 Author: Weiqun Zhang Date: Sat Nov 24 21:14:28 2018 -0800 add scope Tests/LinearSolvers/ComparisonTest/main.cpp commit d2aed8c06b8b67e765aca2c99630ff951d8193c4 Author: Johannes Blaschke Date: Sat Nov 24 21:07:47 2018 -0800 make use of BL_TO_FORTRAN macros Src/EB/AMReX_EB_LSCoreI.H Tutorials/EB/Donut/Exec/inputs commit c2888bae4e220010281eb87c674b608c535ce626 Author: Johannes Blaschke Date: Sat Nov 24 20:28:46 2018 -0800 higher blocking factor Tutorials/EB/Donut/Exec/inputs commit 806760c271ae14e4624cf18d07e5651e97d1fa5b Author: Weiqun Zhang Date: Sat Nov 24 19:40:04 2018 -0800 update ParallelCopy Src/Base/AMReX_FabArrayCommI.H commit d66db7a81b76d32d12bc454b6c2c86712c33725d Author: Johannes Blaschke Date: Sat Nov 24 18:14:36 2018 -0800 added adaptive mesh around donut Src/EB/AMReX_EB_LSCoreI.H Tutorials/EB/Donut/Exec/inputs Tutorials/EB/Donut/Src/main.cpp commit 02565c7ac9cf3eea2195521728156fbf7664c2ea Author: Weiqun Zhang Date: Sat Nov 24 18:11:10 2018 -0800 update FillBoundary Src/Base/AMReX_FabArrayCommI.H commit f4793327cdb15156098831302326659609dd63af Author: Weiqun Zhang Date: Sat Nov 24 17:03:25 2018 -0800 fix bug: unpacking must be consistent with packing Src/Base/AMReX_FabArrayCommI.H commit 8055a22fbda6c66cf2c3a083383f9423f0e8012d Author: Weiqun Zhang Date: Sat Nov 24 16:58:55 2018 -0500 wip: fix race condition in ParallelCopy unpacking Src/Base/AMReX_FabArrayCommI.H commit ca9166ffaa0751dc117ce50c7d0f5ee4a052fbd1 Author: Weiqun Zhang Date: Sat Nov 24 16:07:07 2018 -0500 clean up Src/Base/AMReX_FabArrayCommI.H commit 06002035ba829796c77852c01c66eccd94147e86 Author: Weiqun Zhang Date: Sat Nov 24 15:38:45 2018 -0500 split local copy in ParallelCopy into multiple versons Src/Base/AMReX_FabArrayCommI.H commit 7e254f695e0f61cf97d64c6fab277f45a4d69062 Author: Johannes Blaschke Date: Sat Nov 24 12:16:17 2018 -0800 added bite make to donut Tutorials/EB/Donut/Exec/inputs Tutorials/EB/Donut/Src/eb_to_pvf.F90 Tutorials/EB/Donut/Src/main.cpp commit 0a521a5f82d160d36ae1732b92cd4906a4957e12 Author: Weiqun Zhang Date: Sat Nov 24 14:41:22 2018 -0500 change operator< for locality Src/Base/AMReX_FabArrayBase.H commit b9c967a062492be6f6e6986f56b6060c8a6271a5 Author: Weiqun Zhang Date: Sat Nov 24 14:39:35 2018 -0500 print version Src/Base/AMReX.cpp commit 9cbf6208f88600886c05f9babda785434e4ff5ce Author: Johannes Blaschke Date: Fri Nov 23 23:20:52 2018 -0800 yay this is a donut... but some of the ebgrids are missing :( Tutorials/EB/Donut/Exec/inputs Tutorials/EB/Donut/Src/main.cpp commit 037d3436e9188fff02a75b6974ee4b8239bc2746 Author: Johannes Blaschke Date: Fri Nov 23 23:09:12 2018 -0800 added rudimentary inputs file Tutorials/EB/Donut/Exec/inputs commit 2171962ba2191507ae9e038a623e2870ac54d3a2 Author: Johannes Blaschke Date: Fri Nov 23 23:04:49 2018 -0800 debug donut example Src/EB/AMReX_EB2_IF_Torus.H Tutorials/EB/Donut/Exec/GNUmakefile Tutorials/EB/Donut/Src/Make.package Tutorials/EB/Donut/Src/main.cpp commit 286fb83f0f491c2d7a74df4a3fa6f13c944f1bfd Author: Weiqun Zhang Date: Sat Nov 24 01:47:40 2018 -0500 reorder local copy in ParallelCopy Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 3db42ef6513d624ebd87b7c7777d014260f2d5a6 Author: Johannes Blaschke Date: Fri Nov 23 22:42:16 2018 -0800 make use of BL_TO_FORTRAN macros Tutorials/EB/Donut/Src/main.cpp commit e073ffb0ebca07db8b80a135e4baf9e8a09f851b Merge: ba0746dbe c0c345176 Author: Johannes Blaschke Date: Fri Nov 23 22:34:22 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit ba0746dbe91ad5f17b61cef167764ac4ea187732 Author: Johannes Blaschke Date: Fri Nov 23 22:34:15 2018 -0800 start working on donut example Tutorials/EB/Donut/Exec/GNUmakefile Tutorials/EB/Donut/Src/EB_F.H Tutorials/EB/Donut/Src/Make.package Tutorials/EB/Donut/Src/eb_to_pvf.F90 Tutorials/EB/Donut/Src/main.cpp Tutorials/EB/LevelSet/Src/main.cpp commit c0c3451764b2c2f88bf3cb0dbb20de58d9b35ddb Merge: c284b72d6 89033d508 Author: Weiqun Zhang Date: Fri Nov 23 17:06:15 2018 -0800 Merge branch 'development' into weiqun/gpu commit 89033d5086c9b88d53603a9274cc125e0b7f0aa5 Author: Weiqun Zhang Date: Fri Nov 23 17:02:46 2018 -0800 rm using std::min and std::max Src/Extern/amrdata/AMReX_DataServices.cpp commit 51df3727f66f2de65c0aa362fa7e1d3b0c053465 Author: Weiqun Zhang Date: Fri Nov 23 17:00:55 2018 -0800 remove start_profiler Src/Amr/AMReX_Amr.cpp commit c284b72d6831882c00b7d52e621655c0105633e6 Author: Weiqun Zhang Date: Fri Nov 23 16:04:11 2018 -0800 ifdef cuda specific stuff Src/Base/AMReX_CudaMemory.H commit 4914edce868d167ee63c0ce44d0ed51e9895dab8 Author: Weiqun Zhang Date: Fri Nov 23 16:02:17 2018 -0800 gpu reduce in MultiFab Src/Base/AMReX_MultiFab.cpp commit f41e4957a40c26d8f6b88cdebb14400c7f64f533 Author: Weiqun Zhang Date: Fri Nov 23 15:38:50 2018 -0800 fix extern shared for templates Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_FabArrayUtility.H commit 45ae3fb36af2ff21673235e5329a890261247329 Author: Weiqun Zhang Date: Fri Nov 23 14:51:49 2018 -0800 Gpu reduce in iMultiFab. Removed norm functions from iMultiFab. don't think we need them. If they are indeed needed by codes, we will put them back. Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit f47b56755a421441c44f31d9c12ac28207ed5caf Author: Weiqun Zhang Date: Fri Nov 23 14:47:32 2018 -0800 remove init from reduce Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MultiFab.cpp Tutorials/GPU/CNS/Source/CNS.cpp commit b54302ef90187d8001173a97f41d8bb8031b7d9c Author: Weiqun Zhang Date: Fri Nov 23 13:34:46 2018 -0800 add more FabArray reduce and put them in FabArrayUtility Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayUtility.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.H Src/Base/CMakeLists.txt Src/Base/Make.package Tutorials/GPU/CNS/Source/CNS.cpp commit ea3f2f9998acae3aa0be629353d101c521ef7090 Author: Weiqun Zhang Date: Fri Nov 23 11:30:09 2018 -0800 add indentation when printing unused parmparse parameters Src/Base/AMReX_ParmParse.cpp commit c2cc40c5b19c51cec3e38d323598e31e6ac056f1 Author: Weiqun Zhang Date: Fri Nov 23 11:20:25 2018 -0800 print out a message after initialize and finalize Src/Base/AMReX.cpp commit 585197c975018d4d8beee9a979bde18267707e2f Author: knutsvk Date: Fri Nov 23 14:00:14 2018 +0100 use the ebfactory version of define in the ebfactory version of constructor Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 2eab5b1a939038aed4dfc3530af065eefd8f5a0b Author: knutsvk Date: Fri Nov 23 13:54:28 2018 +0100 use c++14 Tools/GNUMake/comps/llvm.mak commit d9bc46c4f1c04442380d820f81db794121076466 Merge: 2505cedf9 9b5cc802c Author: knutsvk Date: Fri Nov 23 13:53:39 2018 +0100 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 2505cedf9cb0b8611a8217ffd73f48b741ffcbdc Author: knutsvk Date: Fri Nov 23 13:53:19 2018 +0100 overload define() to work when given EBFArrayBoxFactory instead of FabFactory as input Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit f156676014877f3346953b0a84317fd17f7d5f06 Author: Weiqun Zhang Date: Wed Nov 21 21:33:40 2018 -0800 add typename Src/Base/AMReX_FabArray.H commit 0394f55afdd17359abbad1621a07c654a80b2fea Author: Weiqun Zhang Date: Wed Nov 21 20:57:21 2018 -0800 more FabArray::reduce* Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.cpp commit e4c8f72f31bcbe740d17624cfcea45adbe0a74e7 Author: Weiqun Zhang Date: Wed Nov 21 19:05:18 2018 -0800 move MultiFab reduction into FabArray templates Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.cpp Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_K.cpp commit 9b5cc802c47b2e55040ed59fe3f413c361eef584 Author: Ann Almgren Date: Wed Nov 21 18:49:20 2018 -0800 give more information before aborting Src/AmrCore/AMReX_AmrMesh.cpp commit 53c0d85e8f515b9691d6d0bc64ad278bf588adc2 Author: Weiqun Zhang Date: Wed Nov 21 16:39:23 2018 -0800 Tutorials/GPU/CNS: fast reduction Src/Amr/AMReX_AmrLevel.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.H Tutorials/GPU/CNS/Source/CNS.H Tutorials/GPU/CNS/Source/CNS.cpp commit d014b9fcb0439066d8327f63c15ee3fa09701ced Author: Weiqun Zhang Date: Wed Nov 21 16:06:22 2018 -0800 add more reduce functions Src/Base/AMReX_CudaReduce.H commit 70befea8415fbb8e894a91944462a2eba783d5fd Author: Tan Nguyen Date: Wed Nov 21 13:06:06 2018 -0800 extract metadata after regridding on a non-base AMR level Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AsyncFillPatch.cpp commit 7832675e2e5fff4d800061db8a41e088b6a0e0cf Author: kngott Date: Wed Nov 21 12:18:15 2018 -0800 Put changes into Src_3d until 3d and 2d combined. Tutorials/GPU/Advection_AmrCore/Source/Src/Adv_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src/Adv_3d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src/compute_flux_3d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src/slope_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src/slope_3d.f90 commit 6078d9f034b1c3c222128417116bdfdbfd1c8b01 Author: kngott Date: Wed Nov 21 12:15:03 2018 -0800 Wrap OpenMP pragma. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp commit e824b4261bf0aed01325595536e154726f4f5ea2 Merge: 120a9973e 5b53e4779 Author: Weiqun Zhang Date: Tue Nov 20 21:01:50 2018 -0500 Merge branch 'weiqun/gpu' into development commit 5b53e4779f1a3cff3959913e963d776dcb5e953d Author: Weiqun Zhang Date: Tue Nov 20 19:52:13 2018 -0500 back to use device pagable memory Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncArray.cpp Src/Base/AMReX_CudaAsyncFabImpl.H Src/Base/AMReX_CudaAsyncFabImpl.cpp commit c67fabdf7fee2d33be5541fe1039613f54a6c121 Merge: 4f200274f 120a9973e Author: Cyrus Harrison Date: Tue Nov 20 11:22:35 2018 -0800 Merge branch 'development' into task/2018_06_add_blueprint_and_ascent commit 120a9973ec590851fc610e94c9b4c96329134aad Author: dwillcox Date: Tue Nov 20 01:47:57 2018 -0500 Clarify CUDA and PGI versions as well as the make command in the Readme. Tutorials/CVODE/SUNDIALS4/EX3-CUDA/README.md commit 6651dfe2cbc6d3182f33f1982bb29f339f3ab670 Author: dwillcox Date: Tue Nov 20 01:38:03 2018 -0500 Update call to cv_cuSolver_SetLinearSolver to support additional arguments. Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_cuda_cusolver.cpp commit aa9c9b11ed3488897b324b226f8dd879c3999c7c Author: Max Katz Date: Mon Nov 19 22:46:01 2018 -0500 Write out small plotfile in addition to full plotfile Src/Amr/AMReX_Amr.cpp commit 0bfde6d6d3c55245eb66e7657b4f3a75c2583cde Author: Weiqun Zhang Date: Mon Nov 19 15:56:22 2018 -0800 split warpReduceSum into two versions Src/Base/AMReX_CudaReduce.H commit 4149cfaefd29119cc403be99564f05f9fabbc719 Merge: 955b96053 600e5b612 Author: Weiqun Zhang Date: Mon Nov 19 15:28:49 2018 -0800 Merge branch 'development' into weiqun/gpu commit 955b960538279f7b30da2a4c23285926d93593cd Author: Weiqun Zhang Date: Mon Nov 19 15:28:02 2018 -0800 preallocate some memory in amrex::Initialize; switch to using pinned memory for cudaMemcpyAsync Src/Base/AMReX_Arena.cpp Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncArray.cpp Src/Base/AMReX_CudaAsyncFabImpl.H Src/Base/AMReX_CudaAsyncFabImpl.cpp commit 600e5b612d8dc2a739604ba0117595bf5f09c62f Author: Weiqun Zhang Date: Mon Nov 19 10:50:29 2018 -0800 call __syncwarp for volta Src/Base/AMReX_CudaReduce.H commit 16ce30f8c791228c9b96bba793473192c0a916bb Author: Weiqun Zhang Date: Mon Nov 19 10:23:08 2018 -0800 ifdef Src/Base/AMReX_CudaLaunch.cpp commit b74be9040027d89acc81c1cc9c5cd57056c5542b Author: Ann Almgren Date: Mon Nov 19 09:41:34 2018 -0800 AMREX_CudaReduce.H --> AMReX_CudaReduce.H Src/Base/CMakeLists.txt commit a0ab2c6b19a14593df3221d02715a61d04902f32 Author: Weiqun Zhang Date: Mon Nov 19 09:20:17 2018 -0800 Tutorials/GPU/CNS: set USE_CUDA to TRUE by default Tutorials/GPU/CNS/Exec/Sod/GNUmakefile commit e2c38eef2fd3422a0050ebe017a46f03274e32b3 Merge: d666bd771 ceb0e0af3 Author: Weiqun Zhang Date: Mon Nov 19 08:53:16 2018 -0800 Merge branch 'weiqun/gpu' into development commit e2ca2ab0783b4e76b3ccf08a8255085b80681985 Author: kngott Date: Mon Nov 19 01:24:20 2018 -0800 Fix: phi -> psi. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp commit d666bd77129b51d721a63990a8408c07a6a98846 Author: Johannes Blaschke Date: Sun Nov 18 22:32:08 2018 -0800 LSCoreBase returns level-set data Src/EB/AMReX_EB_LSCoreBase.H commit ceb0e0af37773b74c3ee72af1d5956faa16bda0b Author: Weiqun Zhang Date: Sun Nov 18 21:46:55 2018 -0800 minor Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaReduce.H Src/Base/AMReX_MFIter.cpp commit 4d413464896d3226f3e825bf4301170d93147b6d Author: Burlen Loring Date: Fri Nov 16 12:55:14 2018 -0800 add option to pin mesh this forces mesh origin to 0,0,0. this works around a bug in visit enabling visualization of moving meshes it's off by deault. Src/Extern/SENSEI/AMReX_AmrDataAdaptor.H Src/Extern/SENSEI/AMReX_AmrDataAdaptor.cpp Src/Extern/SENSEI/AMReX_AmrInSituBridge.cpp Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.H Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.cpp Src/Extern/SENSEI/AMReX_AmrMeshInSituBridge.cpp Src/Extern/SENSEI/AMReX_InSituBridge.H Src/Extern/SENSEI/AMReX_InSituBridge.cpp commit c927f0ddf5459dd12aa96835a350ee0845820d0c Author: Burlen Loring Date: Thu Nov 15 04:50:13 2018 -0800 add functions to fill ghost cells in cell centering conversions Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit aeb0d638586ee3a6c0825c8357d99cbe155bd9ed Author: Kaiyuan Hou Date: Sun Nov 18 00:19:45 2018 -0600 single thread Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.cpp commit b1eeb6a6542ff178994703c3eb6ce2876091b1d1 Author: Johannes Blaschke Date: Sat Nov 17 15:04:48 2018 -0800 add note for macOS users Tools/CMake/AMReX_InstallExternalLibs.cmake commit dd0b2365bd418de956a10ff9f13d25325a17d78e Author: Weiqun Zhang Date: Sat Nov 17 13:27:20 2018 -0800 redo reduction in MultiFab::sum Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_CudaReduce.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuControl.H Src/Base/AMReX_MultiFab.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 68c1e87a04b340b33dca3f3a55edfc7c0eb956c6 Author: Kevin Gott Date: Sat Nov 17 12:28:56 2018 -0800 Begin cpp version of Src Tutorials/GPU/Advection_AmrCore/Source/Src/Adv_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src/Adv_3d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src/compute_flux_3d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src/slope_3d.cpp Tutorials/GPU/Advection_AmrCore/Source/Src/slope_3d.f90 commit 32314df834fef408e1b75e63304385cbed5db875 Author: Kevin Gott Date: Sat Nov 17 12:26:52 2018 -0800 Adjustments. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H commit 5ed794b0acea00106526b8dbe5d838fc3efbf651 Author: Kevin Gott Date: Sat Nov 17 12:25:20 2018 -0800 Clean up face_velocity. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90 commit e6b8a27a1d1938674aed03233c6ca0526c4b50c5 Author: Kaiyuan Hou Date: Fri Nov 16 23:50:23 2018 -0600 compile passed Tests/PnetCDFBenchmark/GNUmakefile Tests/PnetCDFBenchmark/Make.package Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.H Tests/PnetCDFBenchmark/WritePlotfilePnetCDF.cpp Tests/PnetCDFBenchmark/inputs Tests/PnetCDFBenchmark/main.cpp commit 5b2d0651e9f9c4183d56cc0befab5a7fe62afdd1 Author: Johannes Blaschke Date: Fri Nov 16 20:40:15 2018 -0800 enable ls core to read external tag-levels (needed for mfix) Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp commit f5455443cb8d489a5771c19b9ce37f2b9c5fcc2c Merge: ad67d0abb ba40fb506 Author: Johannes Blaschke Date: Fri Nov 16 19:10:06 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit ad67d0abb901a65a8388c3b9541c2689d3536649 Author: Johannes Blaschke Date: Fri Nov 16 19:09:31 2018 -0800 no longer need to store extra level_set_cc mf vector Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H Tutorials/EB/LevelSet/Src/main.cpp commit 42aa3481d01272932ebc2a203bd3f3ccdf65109e Author: Weiqun Zhang Date: Fri Nov 16 20:44:04 2018 -0500 add some inline Src/Base/AMReX_CudaUtility.H commit 83c8c07e8869d0d9f740fe726c24cb33ed6d74a5 Author: Weiqun Zhang Date: Fri Nov 16 16:20:33 2018 -0800 put setComplement on gpu Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_BoxList.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_PhysBCFunct.H commit ba40fb506aaef4286f5f1fb6d48aa3c51b95542b Author: Andrew Myers Date: Fri Nov 16 14:25:56 2018 -0800 fix makefile logic Tools/GNUMake/comps/pgi.mak commit 5d9e2af76f36a54b591f253f1f27484e529510d9 Author: Cy Chan Date: Fri Nov 16 13:24:47 2018 -0800 add local neighborhood calculation Tests/LinearSolvers/MLMG/AMReX_Machine.H Tests/LinearSolvers/MLMG/AMReX_Machine.cpp Tests/LinearSolvers/MLMG/main.cpp commit 9092a4ac36b82c09f9bd12aff52252cb231d7319 Merge: d83573b24 37f722f0d Author: Andrew Myers Date: Fri Nov 16 14:10:20 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d83573b24ca031203494a8d8057d8e6cb447b126 Author: Andrew Myers Date: Fri Nov 16 14:10:12 2018 -0800 fix merge error Tools/GNUMake/comps/pgi.mak commit 37f722f0dbd62cafb99b2276951a59cc5e272f57 Author: Johannes Blaschke Date: Fri Nov 16 13:57:29 2018 -0800 get rid of unused variable Src/EB/AMReX_EB_levelset.cpp commit da7e544936a8600b1e3987a8d68d632526af2b75 Merge: daa5a07f9 5de1c7c9e Author: Andrew Myers Date: Fri Nov 16 13:16:34 2018 -0800 merging commit daa5a07f9831c8bbc5d929d775958e1c349771ce Author: Andrew Myers Date: Fri Nov 16 13:14:27 2018 -0800 turn on c++14 for pgi if the gcc version is new enough Tools/GNUMake/comps/pgi.mak commit 723dd0205cf4ea14f99f41d7ac01234963012dc6 Author: Andrew Myers Date: Fri Nov 16 12:49:32 2018 -0800 also parse pgi major and minor version numbers in pgi.mak Tools/GNUMake/comps/pgi.mak commit 5de1c7c9e6e093616c826a5b5abe8cb0a1412504 Merge: b15fb1802 f3c4db991 Author: Andrew Myers Date: Fri Nov 16 12:04:49 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b15fb180281ad9c8276915c9740221576d68c961 Author: Andrew Myers Date: Fri Nov 16 12:04:34 2018 -0800 do not serialize the initial conditions in the HDF5 benchmark Tests/HDF5Benchmark/main.cpp commit f3c4db9919ad0242da284f769d660315d05092fe Merge: 748a52609 a55bdf533 Author: Johannes Blaschke Date: Fri Nov 16 10:40:46 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 748a52609ad540ad3bcb97f1381ccfb65d0ed7df Author: Johannes Blaschke Date: Fri Nov 16 10:40:39 2018 -0800 fix pointer pass-by-reference Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_Tagging.F90 Tutorials/EB/LevelSet/Exec/inputs Tutorials/EB/LevelSet/Src/main.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp Tutorials/EB/LevelSet/Src/make_shapes.H commit a55bdf5337df5329a624339ebcffbe3949620355 Author: Michele Rosso Date: Fri Nov 16 09:32:49 2018 -0800 Add absolute tolerance to MAC projector Src/LinearSolvers/MLMG/AMReX_MacProjector.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit 42d99eead6b34fc3a2373a3333ea19e41f18689e Author: Weiqun Zhang Date: Thu Nov 15 22:58:51 2018 -0800 move the change to libraries to the end of Make.defs Tools/GNUMake/Make.defs Tools/GNUMake/comps/nvcc.mak commit 42ee5a4fa30016e56ed65ffca4ac504cbb72dd43 Author: Weiqun Zhang Date: Thu Nov 15 22:53:31 2018 -0800 fix linking with nvcc Tools/GNUMake/Make.rules Tools/GNUMake/comps/nvcc.mak commit 31b76485d42cfcff8b66f4bb354bade72a5e323a Author: Cy Chan Date: Thu Nov 15 17:55:13 2018 -0800 performance analysis: added AMReX_Machine.H/.cpp utilities to determine location on machine Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tests/LinearSolvers/MLMG/AMReX_Machine.H Tests/LinearSolvers/MLMG/AMReX_Machine.cpp Tests/LinearSolvers/MLMG/GNUmakefile Tests/LinearSolvers/MLMG/Make.package Tests/LinearSolvers/MLMG/main.cpp commit 6080db1e5756f0de7221c5823745633b15127fe6 Author: Weiqun Zhang Date: Thu Nov 15 16:32:10 2018 -0800 respect NVCC_HOST_COMP Tools/GNUMake/Make.defs Tools/GNUMake/comps/nvcc.mak commit 13e2853aba4b5de117e267a7c9c313aca1715636 Author: Weiqun Zhang Date: Thu Nov 15 18:03:35 2018 -0500 fix ibm.mak Tools/GNUMake/comps/ibm.mak commit 8b73bc3d14741f5fcb61395d9cd8deedc6bc4dd2 Author: Weiqun Zhang Date: Thu Nov 15 14:56:47 2018 -0800 rename for clarity and update make help Tools/GNUMake/Make.rules commit e1b14f3b6590e32ff16ba5cc3fa29b16a7a6797e Merge: b57559673 0fcabd296 Author: Weiqun Zhang Date: Thu Nov 15 14:45:07 2018 -0800 Merge branch 'development' into weiqun/gpu commit 0fcabd296257704eec33a9dfc9d0afd45905e881 Merge: 72fe56099 db19bbe8b Author: Weiqun Zhang Date: Thu Nov 15 14:44:01 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b575596733a154c0e8db2ec2b9d0cb62e26794db Author: Weiqun Zhang Date: Thu Nov 15 14:37:35 2018 -0800 add openacc to ignore list Tools/F_scripts/dep.py commit bd6b03f7e0669af5c7593b14d052388fb3b4a78c Author: Weiqun Zhang Date: Thu Nov 15 13:55:56 2018 -0800 modify make so that we can compile with nvcc+gcc without pgi or ibm Src/Base/AMReX_fort_mod.F90 Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/ibm.mak Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak commit 340ef295b4ccb20a1638907ecf8d58c38c459113 Author: Weiqun Zhang Date: Thu Nov 15 11:30:35 2018 -0800 a bug in make Tools/GNUMake/comps/nvcc.mak commit d1d5be2f422fa881ea69c966e842e1fc56dc9188 Author: Weiqun Zhang Date: Thu Nov 15 11:19:27 2018 -0800 add --ptxas-options=-O3 Tools/GNUMake/comps/nvcc.mak commit 74efda15ac77fae4e68f0c6c1efc071ecb15eaae Author: Weiqun Zhang Date: Thu Nov 15 11:18:22 2018 -0800 add comments Tools/GNUMake/sites/Make.unknown commit db19bbe8b70f95d9c2614072148af43d738d6984 Merge: c7c66cc52 50fd11678 Author: Andrew Myers Date: Thu Nov 15 10:18:30 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c7c66cc52d79accf7545db044038f394b34fdc9c Author: Andrew Myers Date: Thu Nov 15 10:17:52 2018 -0800 whitelist nec compiler as well Tools/libamrex/configure.py Tools/libamrex/mkconfig.py commit ca3c1eaeeed1f0d32f61c4d401f2d34512861cbe Author: Weiqun Zhang Date: Thu Nov 15 09:47:18 2018 -0800 typo Src/Base/AMReX_CudaDevice.cpp commit b5272afe231d5a88fcd5c3e547c554f8a0b1b7b6 Author: Weiqun Zhang Date: Thu Nov 15 09:46:31 2018 -0800 move openacc stuff into fortran Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_acc_mod.F90 Src/Base/CMakeLists.txt Src/Base/Make.package commit aead304ed350e941dde31f13ea77586718a7e91e Author: Weiqun Zhang Date: Thu Nov 15 09:23:40 2018 -0800 update script Tools/F_scripts/write_cuda_headers.py commit deba7d0183f12a31606eba86012df9ea238007d7 Author: Weiqun Zhang Date: Thu Nov 15 09:00:06 2018 -0800 move the initialiation and finalization of arenas to amrex::Initialize and Finalize so that these arenas will be deleted before cuda shuts down its runtime Src/Base/AMReX.cpp Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp commit 50fd116781b97720674a17ffab3b39afd94e96ce Merge: 4589aeb5e 1de4fe03e Author: Johannes Blaschke Date: Wed Nov 14 21:44:40 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 4589aeb5eed4e4299613f6b6d514fa3938939467 Author: Johannes Blaschke Date: Wed Nov 14 21:44:29 2018 -0800 modernizing ls core tutorial Tutorials/EB/LevelSet/Exec/inputs Tutorials/EB/LevelSet/Src/main.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp Tutorials/EB/LevelSet/Src/make_shapes.H commit ed8f5c6cae96596a014503e2ee3e186f14a97b2f Author: Weiqun Zhang Date: Wed Nov 14 16:49:30 2018 -0800 migrated fortran function threads_and_blocks Src/Base/AMReX_CudaDevice.cpp commit ca87b3760f3f6757f2ab1515504570f62a071f0d Author: Weiqun Zhang Date: Wed Nov 14 15:51:14 2018 -0800 remove AMReX_CudaFort.F90 Src/Base/AMReX_CudaFort.F90 Src/Base/Make.package commit 7757529a6cfd67f4f0a69c1472d68b088b6f413f Author: Weiqun Zhang Date: Wed Nov 14 15:50:15 2018 -0800 remove dependence on cuda fortran Src/Amr/AMReX_Amr.cpp Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_BArena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaFort.F90 Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaUtility.cpp Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_fort_mod.F90 commit 1de4fe03ee650146c9bf1f822670e6ae7cc87d38 Author: Andrew Myers Date: Wed Nov 14 17:42:59 2018 -0500 support ibm compiler for libamrex Tools/GNUMake/Make.rules Tools/libamrex/configure.py Tools/libamrex/mkconfig.py commit dc4909ac0e6c9fe17bfbdf86ac7de914ec1a59fa Author: Guy Moore Date: Wed Nov 14 13:51:42 2018 -0800 fix sphynx error message Docs/sphinx_tutorials/source/AMR_Tutorial.rst Docs/sphinx_tutorials/source/Basic_Tutorial.rst Docs/sphinx_tutorials/source/Tutorials/Tutorials.rst Docs/sphinx_tutorials/source/_static/theme_overrides.css Docs/sphinx_tutorials/source/index.rst commit 6d857e9a3e77eb44d35bca57195a5414e5954161 Author: Weiqun Zhang Date: Wed Nov 14 13:28:16 2018 -0800 initialize device in C++ Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.cpp Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaRange.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuError.H Src/Base/CMakeLists.txt Src/Base/Make.package Tools/GNUMake/Make.defs commit 28eff992dedc605c69db09e888b37a2ee32c3131 Merge: 6a5823674 aacb1aec4 Author: Guy Moore Date: Wed Nov 14 12:30:27 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 6a5823674c6904df79fd236be3283e8c4abfed95 Author: Guy Moore Date: Wed Nov 14 12:27:38 2018 -0800 Fixed LaTex equation for building HTML Docs/sphinx_documentation/source/SWFFT.rst commit aacb1aec42f153da510a455f23ab745377e721af Author: Weiqun Zhang Date: Wed Nov 14 09:00:17 2018 -0800 don't include EB_LSCore* in 2D because it doesn't compile. cmake not fixed Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCoreBase.H Src/EB/Make.package commit 96fa560a852ab2e4feacfe9cc54e88ebe86d0f57 Author: Johannes Blaschke Date: Wed Nov 14 08:06:39 2018 -0800 update AMReX CMake system Src/EB/CMakeLists.txt commit 0c12fc4dd0b8aa67226cdba3de63f7f388706abe Author: Johannes Blaschke Date: Tue Nov 13 22:31:16 2018 -0800 LSCore accepts amr parameters during initialization Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H commit 48ac82abf31f1bec2b372d379f53b824bb6e2b22 Author: Guy Moore Date: Tue Nov 13 19:56:10 2018 -0800 Updated SWFFT documentation, and moved SWFFT and CVODE documentation into a single chapter titled "External Frameworks" Docs/sphinx_documentation/source/CVODE.rst Docs/sphinx_documentation/source/CVODE_top.rst Docs/sphinx_documentation/source/Chapter14.rst Docs/sphinx_documentation/source/SUNDIALS3.rst Docs/sphinx_documentation/source/SWFFT.rst Docs/sphinx_documentation/source/SWFFT/figs/grid_1x4x2.png Docs/sphinx_documentation/source/SWFFT/figs/grid_2x2x2.png Docs/sphinx_documentation/source/SWFFT/figs/grid_4x1x2.png Docs/sphinx_documentation/source/SWFFT/figs/grid_4x2x1.png Docs/sphinx_documentation/source/SWFFT/figs/grid_4x4x4.png Docs/sphinx_documentation/source/SWFFT/figs/grid_8x8x1.png Docs/sphinx_tutorials/source/SWFFT_Tutorial.rst commit abc9cf9e06841f09a4cffb377d9fdac353744909 Author: Johannes Blaschke Date: Tue Nov 13 16:32:49 2018 -0800 store ls checkpoint Src/EB/AMReX_EB_LSCoreBase.H Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp commit 72fe560996fc7ea501f6568264284f6dca37768b Author: Weiqun Zhang Date: Tue Nov 13 16:25:16 2018 -0800 some name changes for xSDK Src/Base/AMReX.cpp Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.cpp Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaLaunch.H Tools/F_scripts/write_cuda_headers.py commit 9753aad412ea3e9100a8858012d59b579ca76701 Merge: 0263ecf17 f692ab251 Author: Johannes Blaschke Date: Tue Nov 13 16:20:34 2018 -0800 Merge branch 'development' into jpb/ls-core commit 0263ecf1758e7f79b10b25b9f29e8018657a767f Author: Johannes Blaschke Date: Tue Nov 13 16:19:52 2018 -0800 update inputs Tutorials/EB/LevelSet/Exec/inputs commit 9faafa0f5a68d3acb8a0fc528bd0559bcd75a2b6 Author: Weiqun Zhang Date: Tue Nov 13 15:33:40 2018 -0800 remove some unused stuff Src/Base/AMReX_BLFort.H Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaFort.F90 commit f692ab2512be55d096733f48d6516544baffc3f0 Author: Weiqun Zhang Date: Tue Nov 13 14:40:53 2018 -0800 in BndryFuncArray, we need to loop over components Src/Base/AMReX_PhysBCFunct.cpp commit ea0dc1d033665b2a0bef3ad2a276bf5532dfd87a Author: kngott Date: Tue Nov 13 13:49:23 2018 -0800 AMREX_RESTRICT non SIMD BaseFab loops. Try dot and sum for now to test. Src/Base/AMReX_BaseFab.H commit cc76e9f205f1de10fd153b9c301a59870fd1a8e5 Author: kngott Date: Tue Nov 13 13:07:44 2018 -0800 Clear DeviceFab pointer after use. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp commit cd683be53ac88470f5c161301b76c1488faef395 Author: Weiqun Zhang Date: Tue Nov 13 12:45:16 2018 -0800 fix a new bug in PhysBCFunct Src/Base/AMReX_PhysBCFunct.H commit 5f82cde4ac22edb09bae84e3cb3cdbc6df6764a8 Author: Johannes Blaschke Date: Tue Nov 13 11:47:10 2018 -0800 update levelset amr to be compatible with new changes Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit dedae103e191ef38873ca30c4255ee6372d36fbe Merge: 4db7b2b58 5aa3c1e5d Author: Johannes Blaschke Date: Tue Nov 13 11:15:25 2018 -0800 Merge branch 'development' into jpb/ls-core commit 5aa3c1e5d9f70f8cf864476ff97fe77f80eeff9c Merge: 63887f2f4 f4613b60a Author: Weiqun Zhang Date: Tue Nov 13 11:14:11 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f4613b60aa66d3b2a7c39ed1b73b9b4f39eb9492 Merge: e59622750 fd2f527cb Author: Michele Rosso Date: Tue Nov 13 11:13:31 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit e59622750a7a8ee8ae25556dd490eab97f4c47b4 Author: Michele Rosso Date: Tue Nov 13 11:13:22 2018 -0800 Algoim: output runtime info only in debug mode Src/Extern/Algoim/AMReX_algoim_integrals.cpp commit 63887f2f4aca103a1648eb3641323abe09e31d58 Merge: 9c97f0224 671f3fef3 Author: Weiqun Zhang Date: Tue Nov 13 10:10:45 2018 -0800 Merge branch 'weiqun/gpu' into development commit 9c97f0224fc96eb0c719c7e7f2d8fe5d22411ab8 Merge: 9dd2a8d63 fd2f527cb Author: Weiqun Zhang Date: Tue Nov 13 10:08:19 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 671f3fef3eba27e76ccd860b4957d2c151b2fab3 Author: Weiqun Zhang Date: Tue Nov 13 10:07:54 2018 -0800 fix out of bound Src/Base/AMReX_CudaDevice.cpp commit fd2f527cbd757adab8f73fe54c6622ca640f3e27 Merge: 4f8afdbe4 9fc668a32 Author: WeiqunZhang Date: Tue Nov 13 08:51:32 2018 -0800 Merge pull request #366 from AMReX-Codes/SDC cleaning up redundant MG assignments commit 4db7b2b5809ef4af5055c8d7814574913032c8af Author: Johannes Blaschke Date: Mon Nov 12 23:16:02 2018 -0800 Updated fortran subroutine names to match amrex convention Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCore_F.H Src/EB/AMReX_EB_Tagging.F90 Src/EB/AMReX_EB_bc_fill_nd.F90 commit efe7c3fcbe8ffbff45d8cb0387000fd2b0e385e6 Merge: 0f9b93cce 4f8afdbe4 Author: Johannes Blaschke Date: Mon Nov 12 22:57:54 2018 -0800 Merge branch 'development' into jpb/ls-core commit 0f9b93cce917fe1007b33ac4c1ef08269969f3bc Author: Johannes Blaschke Date: Mon Nov 12 22:56:30 2018 -0800 clean up Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_utils.H Src/EB/AMReX_EB_utils.cpp Src/EB/Make.package commit 8afdff893128fb636ffe06780ed5a89c21e1be74 Author: Johannes Blaschke Date: Mon Nov 12 15:14:41 2018 -0800 yay, fixed performance problem Src/Base/AMReX_Box.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_ParallelDescriptor.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Exec/inputs commit 48382f6b6111234ad686edb262b6fb7052368557 Author: kngott Date: Mon Nov 12 14:40:51 2018 -0800 Implement deviceFab. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp commit 4f8afdbe4ed70aef3942fbd3cb8de654d87ea348 Author: Tan Nguyen Date: Mon Nov 12 14:25:04 2018 -0800 fixing a memory leak bug in the upcxx backend Src/AmrTask/rts_impls/Perilla_upc++/PackageQueue.H Src/AmrTask/rts_impls/Perilla_upc++/PackageQueue.cpp Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.H Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.cpp commit 9fc668a32685b4faf4c9173a8fbdca48707425fc Author: Lawrence Minion Date: Mon Nov 12 14:12:00 2018 -0800 cleaning up redundant MG assignments Tutorials/SDC/MISDC_ADR_2d/Exec/inputs_2d Tutorials/SDC/MISDC_ADR_2d/README Tutorials/SDC/MISDC_ADR_2d/Source/SDC_sweeper.cpp Tutorials/SDC/MISDC_ADR_2d/Source/main.cpp commit 3ddca080959b46c2eb4c3dadde55d2447c8357df Author: Tan Nguyen Date: Mon Nov 12 13:37:09 2018 -0800 fixing a memory leak bug Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/AmrTask/rts_impls/Perilla/PackageQueue.H Src/AmrTask/rts_impls/Perilla/PackageQueue.cpp Src/AmrTask/rts_impls/Perilla/RegionGraph.H Src/AmrTask/rts_impls/Perilla/RegionGraph.cpp Src/AmrTask/rts_impls/Pthread_Common/LocalConnection.H Src/AmrTask/rts_impls/Pthread_Common/RGIter.cpp Src/AmrTask/rts_impls/Pthread_Common/RegionQueue.H Src/AmrTask/rts_impls/Pthread_Common/RegionQueue.cpp Src/AmrTask/rts_impls/Pthread_Common/RemoteConnection.H Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/inputs Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.H Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.cpp commit e328b6f8a7ad282d105bae38e666a501f1b436aa Author: Weiqun Zhang Date: Mon Nov 12 12:34:56 2018 -0800 white spaces Src/Amr/AMReX_AmrLevel.cpp commit c01eb9540020c03e7d5f2d4d46f757419372415b Author: Weiqun Zhang Date: Mon Nov 12 12:25:53 2018 -0800 filcc 1D Src/Base/AMReX_FilCC_1D_C.cpp Src/Base/AMReX_FilCC_3D_C.cpp commit c74b35ced20ac8c4478d3675d7ccb00fbf7e2dce Author: kngott Date: Mon Nov 12 09:32:39 2018 -0800 c++ version of face_velocity compiles. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 348af9b982919c69d1ac1286f913f5591ed5ee3b Author: kngott Date: Mon Nov 12 09:31:07 2018 -0800 Protect Prob.cpp. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp commit 8b6d8552ea76b8fe48a2b45cd71f3f7ba624a56a Author: Kevin Gott Date: Sun Nov 11 21:50:29 2018 -0800 First attempt at C++ version of face_velocity. Not compile tested. WIP. Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Make.package Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H commit f792081d111283d3a6353d13190be844a16912a5 Author: Johannes Blaschke Date: Sun Nov 11 17:47:24 2018 -0800 sync wip Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H commit 0787918b09b78e5063c7ccf3bb3076655dea955d Author: Johannes Blaschke Date: Sun Nov 11 17:15:55 2018 -0800 work on improving performance of multi-level level-set Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_MultiFab.H Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Exec/inputs commit 5c1dc182a434b71dfc1e9782e9cef422a31a00e5 Author: Johannes Blaschke Date: Sun Nov 11 13:59:13 2018 -0800 fix problem where eb_padding wil to small... this does not perform well though Src/AmrCore/AMReX_AmrMesh.cpp Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Exec/inputs commit 81882353d396ce1268a2a2f9e1a1421c807fa224 Author: Weiqun Zhang Date: Sun Nov 11 16:54:06 2018 -0500 use functor instead of function pointer so that we can pass user provided function to kernels Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Tutorials/GPU/CNS/Source/CNS_bcfill.cpp commit 0f03bebd13f1f3984dc2758976347aa03793ee0c Author: kngott Date: Sun Nov 11 11:08:50 2018 -0800 Define C version of get_face_velocity. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H commit 347ecddbb27f37829489ca5d32efd1c49e2ec436 Author: Weiqun Zhang Date: Sun Nov 11 01:00:02 2018 -0500 have to create a local copy of the member variable for the lambda to capture Src/Base/AMReX_PhysBCFunct.cpp commit 90e88c7f53ca3079fe91c398d8aa05e30ad6ec55 Author: Weiqun Zhang Date: Sat Nov 10 23:13:43 2018 -0500 no need to use mutex in AsynArray anymore because carena has one Src/Base/AMReX_CudaAsyncArray.cpp commit cc358c9ff92d41452ef06b0499a8c4486c01b789 Author: Weiqun Zhang Date: Sat Nov 10 23:10:21 2018 -0500 fix mutex in AsyncFab Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.H Src/Base/AMReX_CudaAsyncFabImpl.cpp commit 0b66130965fddab8f1545306dcabd90cd6e14bff Author: Weiqun Zhang Date: Sat Nov 10 22:57:47 2018 -0500 mutex in CArean Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp commit 320d925a430f2eafb2399172b81a50dede087d51 Author: Weiqun Zhang Date: Sat Nov 10 22:47:27 2018 -0500 avoid using fab.box() in assertion Src/Amr/AMReX_StateData.cpp commit 7b7a20bfcd6ac0bc7c27f4be61b77ae5c2e4b8aa Author: Weiqun Zhang Date: Sat Nov 10 22:46:21 2018 -0500 comment out set nan on gpu for now. will move it to multifab in the future. Src/Base/AMReX_FArrayBox.cpp commit 5a2b5c7153a939f87eac6b4b1227d4c2249fa248 Author: Weiqun Zhang Date: Sat Nov 10 19:13:41 2018 -0500 StateData: option to fill domain bc on gpu Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_FilCC_3D_C.cpp Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuControl.cpp commit 3f2ad8e84e8b21f0a5f6715355eef166692e4e68 Author: Weiqun Zhang Date: Sat Nov 10 16:53:49 2018 -0500 first pass of filcc in 3d w/o high-order extrapolation Src/Base/AMReX_FilCC_3D_C.cpp commit b9af50543d94a0130a4b319c65e03ee021b5bd0a Author: Johannes Blaschke Date: Sat Nov 10 13:34:27 2018 -0800 going to nodal level-set Src/AmrCore/AMReX_AmrMesh.H Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_Tagging.F90 commit eaa37d7572c4fafabeea9984cc61fb6444f93a86 Author: Weiqun Zhang Date: Sat Nov 10 16:21:23 2018 -0500 inline some BCRec functions Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp commit 076f97b4b04a3114f4acaca58b31d687b5465643 Author: Weiqun Zhang Date: Sat Nov 10 01:27:04 2018 -0500 more work on GpuBndryFuncFab Src/Base/AMReX_FilCC_1D_C.cpp Src/Base/AMReX_FilCC_2D_C.cpp Src/Base/AMReX_FilCC_3D_C.cpp Src/Base/AMReX_FilCC_C.H Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit e413b72175f0392b1b84a4802f6d5412f4f2889a Author: Weiqun Zhang Date: Sat Nov 10 00:12:02 2018 -0500 add ___host__ __device__ to BCRec Src/Base/AMReX_BCRec.H commit 4a9a3b5d2f3368db014e1f06249699f64e2bac0c Author: Weiqun Zhang Date: Fri Nov 9 23:53:45 2018 -0500 make sure nvcc use the same std version as gcc in case gcc version > 5 Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/nvcc.mak commit 38c922223bbdef9def542d9cb722a430e764fa87 Author: kngott Date: Fri Nov 9 19:48:40 2018 -0800 Define new initprob and change implementation. Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H commit 852f807db97068af7f41f0416536e88333f80ac6 Author: kngott Date: Fri Nov 9 19:46:47 2018 -0800 Update make system. Tutorials/GPU/Advection_AmrCore/Exec/Make.Adv Tutorials/GPU/Advection_AmrCore/Source/Make.package commit 0e1e38ab95afd99cf831f71d63200244623bea10 Author: kngott Date: Fri Nov 9 19:31:52 2018 -0800 C++ version of Prob Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.f90 commit 24ca8ad17d7f60a43ea9c0066dd77df76180d778 Author: kngott Date: Fri Nov 9 19:27:16 2018 -0800 Remove exec. Tutorials/GPU/Advection_AmrCore/Source/a.out commit a9a689ba999656e483c51e7c44c27fb008aa6c27 Author: Andrew Myers Date: Fri Nov 9 16:46:44 2018 -0800 use --std=c++14 when using gcc as the host compiler if the gcc version is new enough Tools/GNUMake/comps/nvcc.mak commit 81f716e91e9298bc02dcc7b033adca7e342b0658 Author: Johannes Blaschke Date: Fri Nov 9 15:19:04 2018 -0800 sync wip while debug Src/AmrCore/AMReX_Interpolater.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_Tagging.F90 Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Exec/inputs commit 063dbc403c44e82219c30b46b0117d5ece4a270d Author: Weiqun Zhang Date: Fri Nov 9 14:23:13 2018 -0800 GpuBndryFuncFab WIP Src/Base/AMReX_PhysBCFunct.cpp commit d5595203ed27ed5fb53ab30183daebf7ad8ae50c Merge: 2a793646b 7a809e032 Author: Andrew Myers Date: Fri Nov 9 14:00:04 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ef199fc338e2f63c2eb3cc9f4c6f7d2004dd38b3 Author: Weiqun Zhang Date: Fri Nov 9 13:54:31 2018 -0800 some work on CpuBndryFuncFab Src/Amr/AMReX_StateDescriptor.H Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Tutorials/GPU/CNS/Source/CNS.H Tutorials/GPU/CNS/Source/CNS_bcfill.cpp Tutorials/GPU/CNS/Source/CNS_setup.cpp commit 2a793646bdd4f10a8fe8b26138b29a0e90c0a04f Author: Andrew Myers Date: Fri Nov 9 13:33:06 2018 -0800 correct neighbor size in NeighborListParticleContainer.cpp Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp commit 480c1913a40f892131497c00c50d936534c735f4 Author: Andrew Myers Date: Fri Nov 9 13:10:55 2018 -0800 switch the neighbor list structure to use ParticleType instead of char Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 2a5de399ddaa51fc47f23c09a550f20f6a1a3a98 Author: Andrew Myers Date: Fri Nov 9 13:08:01 2018 -0800 remove neighbor_t from the NeighborList tutorial Tutorials/Particles/NeighborList/neighbor_list_3d.f90 commit 5a8a8e8653ff4ab37c76899a00e80f21402fa7d7 Author: Weiqun Zhang Date: Fri Nov 9 10:08:01 2018 -0800 add default constructor for StateDescriptor::BndryFunc Src/Amr/AMReX_StateDescriptor.H commit 7794be7772348a25bb86cd1ba678e9d3b1946559 Author: Weiqun Zhang Date: Fri Nov 9 09:50:52 2018 -0800 clean up Src/Amr/AMReX_StateDescriptor.H Src/AmrCore/AMReX_AmrParticles.H Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 75c6d1f103f3e5d2022fbdcfb7efccb85bcf9b73 Merge: b2ddabb82 9dd2a8d63 Author: Weiqun Zhang Date: Fri Nov 9 08:40:31 2018 -0800 Merge branch 'development' into weiqun/gpu commit 9dd2a8d638d56724a90dbc851eb50e57593c242d Merge: 91d89b639 7a809e032 Author: Weiqun Zhang Date: Fri Nov 9 08:37:18 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ebf9099a8f6ad98aad858b15764e325b8a5f1229 Author: Johannes Blaschke Date: Thu Nov 8 22:51:12 2018 -0800 yay! level-sets Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H Tutorials/EB/LevelSet/Exec/inputs Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp commit f7b4e5e21591e041da8b6b0c4a7fd36847acc527 Author: Johannes Blaschke Date: Thu Nov 8 21:53:13 2018 -0800 split basic amr core behaviour and specialized eb-geometry Src/AmrCore/AMReX_AmrCore.H Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCoreBase.H Src/EB/AMReX_EB_LSCoreBase.cpp Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_LSCore_F.H Src/EB/AMReX_EB_bc_fill_nd.F90 Src/EB/Make.package Tutorials/EB/LevelSet/Exec/inputs Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp commit b2ddabb82f2847528721e27d80cb4e7d82a10180 Author: Weiqun Zhang Date: Thu Nov 8 21:51:54 2018 -0800 update due to change in FillPatch Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/AmrCore/AMReX_AmrParticles.H Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/Base/AMReX_FPhysBC.H Src/F_Interfaces/Base/AMReX_FPhysBC.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex Tutorials/Amr/ScalarAdvectionDiffusion/Doc/references.bib Tutorials/Amr/ScalarAdvectionDiffusion/Doc/working_notes.tex Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Make.Adv.Diff Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/inputs Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/inputs.tracers Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/probin Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/debug.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/face_velocity_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/face_velocity_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/init.2d.convtest.sh Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/init.3d.convtest.sh Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/probdata.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/probin Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/face_velocity_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/face_velocity_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/inputs Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/probdata.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/probin Tutorials/Amr/ScalarAdvectionDiffusion/README Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugDump.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugOut.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugOut.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/LevelBldAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/slope_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/slope_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Adv_nd.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Tagging_nd.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/tagging_params.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/main.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/fourthOrderCFInterpTest.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/test.inputs Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_mpi_driver.py Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_serial_driver.py Tutorials/Particles/ElectrostaticPIC/main.cpp commit 3a64c9f48ab0b559a4d1e0c33554ccfb68ce6108 Author: Johannes Blaschke Date: Thu Nov 8 20:24:12 2018 -0800 LSCore needs to be a template class (so that it can hold gshop objects) .gitignore Src/EB/AMReX_EB2_IF_Intersection.H Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCoreI.H Src/EB/AMReX_EB_levelset.H commit 7a809e03241f4c1d562129ab3c366abc9de60bae Author: Ann Almgren Date: Thu Nov 8 18:07:51 2018 -0800 Fix error statements to correctly reflect the routine they're from Src/Particle/AMReX_ParticleContainerI.H commit 21a1a5f6df7821407c5e9cc5b24b6ccd163bfec0 Author: Weiqun Zhang Date: Thu Nov 8 16:45:05 2018 -0800 Redo the FillPatch interface. The change is not backward compatible for AmrCore based codes that use FillPatch Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 4df63d6fad46656c88a0530cec6e25e2d82e41ec Author: Johannes Blaschke Date: Thu Nov 8 13:57:40 2018 -0800 sync wip Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCore.cpp commit 2fd1f4d04f7a234555b7cda05327bac93fe7b967 Author: Kevin Gott Date: Thu Nov 8 16:23:19 2018 -0500 AdvCore added to Tutorials/GPU and being worked on. Tutorials/GPU/Advection_AmrCore/CMakeLists.txt Tutorials/GPU/Advection_AmrCore/Exec/Make.Adv Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/GNUmakefile Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Make.package Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.cpp Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/Prob.f90 Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/inputs Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_catalyst.py Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.session Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.session Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml Tutorials/GPU/Advection_AmrCore/Exec/SingleVortex/sensei/write_vtk.xml Tutorials/GPU/Advection_AmrCore/README Tutorials/GPU/Advection_AmrCore/README_SENSEI.md Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/GPU/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/GPU/Advection_AmrCore/Source/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_2d/Adv_2d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_2d/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_2d/compute_flux_2d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_2d/slope_2d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Adv_3d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_3d/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_3d/slope_3d.f90 Tutorials/GPU/Advection_AmrCore/Source/Src_nd/Make.package Tutorials/GPU/Advection_AmrCore/Source/Src_nd/Tagging_nd.f90 Tutorials/GPU/Advection_AmrCore/Source/a.out Tutorials/GPU/Advection_AmrCore/Source/bc_fill_nd.F90 Tutorials/GPU/Advection_AmrCore/Source/main.cpp commit ec4b8204115062a6911e9fbcfddd0df81964a353 Author: Kevin Gott Date: Thu Nov 8 16:22:14 2018 -0500 fix .x issue Src/Base/AMReX_COORDSYS_2D.cpp commit 8993f36dfe04f325c521fa9b1a2b9d000f7f1cbf Merge: 2db12ffb1 50a22c82e Author: Johannes Blaschke Date: Thu Nov 8 10:20:00 2018 -0800 Merge branch 'development' into jpb/ls-core commit 50a22c82ebbb2ffa0132bc0529de884525db68b8 Merge: 4bbe220b7 40f129709 Author: WeiqunZhang Date: Thu Nov 8 09:32:11 2018 -0800 Merge pull request #362 from AMReX-Codes/f2py-microphysics Add compile flags for building a code using the AMReX build system as an f2py library commit 2db12ffb1f33c55722f152915400b6e21e88ee2b Author: Johannes Blaschke Date: Wed Nov 7 21:16:15 2018 -0800 added first pass at AMR for level-set Src/EB/AMReX_EB_LSCore.H Src/EB/AMReX_EB_LSCore.cpp Src/EB/AMReX_EB_LSCore_F.H Src/EB/AMReX_EB_Tagging.F90 Src/EB/AMReX_EB_bc_fill_nd.F90 commit cda9450fed9a2476b4f1cf4db71d758cacb12491 Author: Weiqun Zhang Date: Wed Nov 7 21:15:03 2018 -0800 DeviceFab -> AsyncFab Src/Base/AMReX.cpp Src/Base/AMReX_CudaAsyncFab.H Src/Base/AMReX_CudaAsyncFab.cpp Src/Base/AMReX_CudaAsyncFabImpl.H Src/Base/AMReX_CudaAsyncFabImpl.cpp Src/Base/AMReX_CudaFab.H Src/Base/AMReX_Gpu.H Src/Base/CMakeLists.txt Src/Base/Make.package Tests/GPU/AsyncFab/GNUmakefile Tests/GPU/AsyncFab/Make.package Tests/GPU/AsyncFab/main.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp commit 02b2174e95a924cbfaef78e7dc8c32a923cecb41 Author: Weiqun Zhang Date: Wed Nov 7 21:03:27 2018 -0800 fix bug in CudaAsyncArray Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncArray.cpp commit 4bbe220b7fe2b8046aba6d926caa150c273a676e Merge: 1bb6078bd 7c61e745e Author: Johannes Blaschke Date: Wed Nov 7 20:55:53 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 1bb6078bdaed7e00a090540fb96f3c1cb3d4f67e Author: Johannes Blaschke Date: Wed Nov 7 20:54:48 2018 -0800 these aren't needed after all Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp commit 7c61e745e5e77a230e1bb79064bc85c503c3e0f1 Merge: 00cc23d0c 250056522 Author: Michele Rosso Date: Wed Nov 7 17:26:58 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 00cc23d0c9df8242b42249c4ead940795bb5d654 Author: Michele Rosso Date: Wed Nov 7 17:26:23 2018 -0800 CMake: add hack to compile blitz on nersc machines Tools/CMake/AMReX_InstallExternalLibs.cmake commit 40f1297094cac431c511cc874484614938560322 Author: Donald E. Willcox Date: Mon Oct 22 21:59:11 2018 -0700 Support for building StarKiller Microphysics as a library with f2py. WIP support for building StarKiller Microphysics as a library with f2py. Add default setting USE_COMPILE_PIC?=FALSE Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/comps/gnu.mak commit ec2a5af3e54de5ba46c3087cf95833fcef6c4b86 Author: Michele Rosso Date: Wed Nov 7 17:01:11 2018 -0800 CMake: fix mispelled variable Tools/CMake/AMReX_Machines.cmake commit 91d89b6394d93bb359c99226d7b4f97c9b115c52 Author: Weiqun Zhang Date: Wed Nov 7 17:00:07 2018 -0800 Gpu::AsyncArray Src/Base/AMReX_CudaAsyncArray.H Src/Base/AMReX_CudaAsyncArray.cpp Src/Base/AMReX_CudaFab.cpp Src/Base/AMReX_Gpu.H Src/Base/CMakeLists.txt Src/Base/Make.package Tutorials/GPU/CNS/Source/CNS_bcfill.cpp commit 2500565223741a820d23ff29e49fdb9b9f98ed06 Merge: 6da90a772 cac20db4c Author: Johannes Blaschke Date: Wed Nov 7 15:46:35 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 1bf7b7c85dfb4dae8ce53c5336d0e5907986b33e Author: Weiqun Zhang Date: Wed Nov 7 14:57:46 2018 -0800 new bndry fill function in StateData Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/Base/AMReX_BCRec.cpp commit 6da90a772c64ddd9349883b14d421cac5b9b54e4 Author: Johannes Blaschke Date: Wed Nov 7 14:09:09 2018 -0800 added FillPatch operations for constant-in-time MFs Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp commit 0a692aed36ff87fa32c3d5a1fbed5ccf269fcf58 Author: Kevin Gott Date: Wed Nov 7 17:07:48 2018 -0500 protected_divide with zeros BaseFab test. Tests/BaseFabTesting/main.cpp commit 7e93f251c4b3b4a2195036bafa44920ef699098a Author: kngott Date: Wed Nov 7 13:38:16 2018 -0800 Convert remaining stridedPtr to FabView. Src/Base/AMReX_COORDSYS_1D.cpp Src/Base/AMReX_COORDSYS_2D.cpp Src/Base/AMReX_COORDSYS_3D.cpp Src/Boundary/AMReX_Mask.cpp Src/EB/AMReX_EB2_GeometryShop.H commit 244b51157747ca3899b4ea6944882d4cf574f127 Author: Kevin Gott Date: Wed Nov 7 15:53:21 2018 -0500 Merge errors. Src/Base/AMReX_BaseFab.H commit f8d6386c7dba6d73b206179b6dd2e3a418e766cd Merge: 7288d56b0 968d21e04 Author: Kevin Gott Date: Wed Nov 7 15:32:54 2018 -0500 Merge branch 'weiqun/gpu' into gpu Conflicts: Src/Base/AMReX_BaseFab.H commit 968d21e0400cb7e175006cc7f2bab88c35f15f19 Author: Kevin Gott Date: Wed Nov 7 15:30:28 2018 -0500 BaseFab with FabView. Src/Base/AMReX_BaseFab.H commit cac20db4cc05c54b02b06b426ef3d44a79a80ce8 Merge: 5acf72db9 17f6ffac9 Author: Andrew Myers Date: Wed Nov 7 12:09:49 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5acf72db9bd1d4dab68c2f9af2cd66a21f74a8ad Author: Andrew Myers Date: Wed Nov 7 12:09:33 2018 -0800 when running with CUDA, construct the neighbor on the host, then copy it into managed memory. Src/Particle/AMReX_NeighborParticlesI.H commit 17f6ffac9ca6628720dc31a77e1a39a2a89a2e34 Author: Weiqun Zhang Date: Wed Nov 7 14:24:45 2018 -0500 fix set_covered for nodal Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H commit d82851308915a602750d0d130d6f1ec585165962 Merge: 1896de9dc ba587b7d8 Author: Andrew Myers Date: Wed Nov 7 14:00:10 2018 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1896de9dcf1809fb838fcc73eb79e522d82f7832 Author: Andrew Myers Date: Wed Nov 7 13:59:43 2018 -0500 remove uneccesary casts from these thrust calls. Src/Particle/AMReX_ParticleContainerI.H commit 08e9124e007302e2cd23eb6c44981486d090f510 Author: Andrew Myers Date: Wed Nov 7 13:32:15 2018 -0500 prettify thrust calls Src/Particle/AMReX_ParticleContainerI.H commit ba587b7d8792d39f336dc5ed81df549d032acc38 Author: Weiqun Zhang Date: Wed Nov 7 13:31:33 2018 -0500 setVal: return if Box is not ok. This is the traditional behavior Src/Base/AMReX_BaseFab.H commit e91f4804ad368390be99fab92a2167d5afe3aa1b Merge: 9ee3679f6 0ba75635d Author: Weiqun Zhang Date: Wed Nov 7 09:07:17 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0ba75635d3b79a814caab7a2c54749ee51bffc05 Author: Weiqun Zhang Date: Wed Nov 7 09:06:33 2018 -0800 fix omp Src/Base/AMReX_MultiFab.cpp commit 7edb86960a42110461b7df0d3090c66045bdaa45 Author: Weiqun Zhang Date: Wed Nov 7 08:53:26 2018 -0800 include cmath Src/EB/AMReX_EB2_IF.H Src/EB/AMReX_EB2_IF_Torus.H commit 9ee3679f6eba992f6f69757d91a4d723a6a75124 Author: Weiqun Zhang Date: Wed Nov 7 08:51:46 2018 -0800 include cmath Src/EB/AMReX_EB2_IF.H Src/EB/AMReX_EB2_IF_Torus.H commit 8913ef23e056ae8df148e349a6484b0c468703a8 Merge: 45bdb9528 a6ed9fa6c Author: Weiqun Zhang Date: Wed Nov 7 07:18:14 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a6ed9fa6cf88a9d547141ebfdd756e616a297eaa Author: Ann Almgren Date: Wed Nov 7 06:51:44 2018 -0800 sqrt --> std::sqrt Src/EB/AMReX_EB2_IF_Torus.H commit a0f953dbd52ce9e2a1e1a8c26540d5b4d7c38e95 Author: Tan Nguyen Date: Wed Nov 7 02:40:10 2018 -0800 fixing a memory leak bug Src/Amr/AMReX_AmrLevel.cpp commit 374cb85df40ba94922c307738c884e15c091929d Author: Tan Nguyen Date: Wed Nov 7 02:24:05 2018 -0800 fixing a few memory leak bugs Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp commit a2e25aeaa066b763fb263573f540efd89a6539e7 Merge: 65aeade51 34512fd4b Author: Ann Almgren Date: Tue Nov 6 17:45:45 2018 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 65aeade51c813e21819cc4382a5d1f14ca0f3186 Author: Ann Almgren Date: Tue Nov 6 17:45:22 2018 -0800 Add torus Src/EB/AMReX_EB2.cpp Src/EB/AMReX_EB2_IF_Torus.H Src/EB/Make.package commit 34512fd4bf61a6cf822125e326b45f881cb47638 Merge: d13627acb 921999aca Author: Michele Rosso Date: Tue Nov 6 17:37:55 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d13627acb34f1b4249a4ec9a060b9d9df0b18459 Author: Michele Rosso Date: Tue Nov 6 17:37:49 2018 -0800 CMake: update documentation Docs/sphinx_documentation/source/BuildingAMReX.rst commit 48fbb6359a4513b8b7e58c8e01e7700058ecf0a9 Author: Michele Rosso Date: Tue Nov 6 17:25:36 2018 -0800 Cmake: implement small improvements Src/CMakeLists.txt Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_InstallExternalLibs.cmake commit 45bdb9528d7410f19bf8510789522216c9b5fee4 Author: Weiqun Zhang Date: Tue Nov 6 17:12:24 2018 -0800 add Fab version of Bndry Func Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Tutorials/GPU/CNS/Exec/Sod/inputs Tutorials/GPU/CNS/Source/CNS_bcfill.cpp Tutorials/GPU/CNS/Source/CNS_setup.cpp Tutorials/GPU/CNS/Source/Make.package commit 3a689942263c0248fbe967fd6e6a91739c9eb5d6 Author: Michele Rosso Date: Tue Nov 6 16:53:56 2018 -0800 CMake: add support for 3D nodal projection. Add support for Algoim and Blitz libraries if nodal projection is required. CMake will download and install these libraries if no installation paths is given for them. CMakeLists.txt Src/CMakeLists.txt Src/Extern/Algoim/CMakeLists.txt Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_InstallExternalLibs.cmake Tools/CMake/AMReX_Options.cmake commit e3eb98e47040c7e7434df09c5a034b8ae886d884 Author: Michele Rosso Date: Tue Nov 6 16:49:26 2018 -0800 CMake: refactor CMakeLists hierarchy in Extern subdir Src/CMakeLists.txt Src/Extern/CMakeLists.txt Src/Extern/ProfParser/CMakeLists.txt Src/Extern/amrdata/CMakeLists.txt commit 921999aca9956d5c9f3adcaa5a28ba54971e1f43 Author: Weiqun Zhang Date: Tue Nov 6 14:36:15 2018 -0800 remove some unused print functions Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/Base/AMReX_PhysBCFunct.cpp commit 7bbee07ec545ca82b4ac183ac30f4884224712cc Author: Weiqun Zhang Date: Tue Nov 6 14:07:13 2018 -0800 fix a bug in StateData FillBoundary Src/Amr/AMReX_StateData.cpp commit e5cd19abce7ef8f081e791279573c448ea8b7554 Author: Weiqun Zhang Date: Tue Nov 6 12:52:32 2018 -0800 fix omp Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_MultiFab.cpp Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90 commit 65d3283fc465b1aaf08e8ae49e3bce874bd41cd0 Author: Kevin Gott Date: Tue Nov 6 15:31:56 2018 -0500 First draft of GPU minIndex and maxIndex. Needs atomic IntVect assignment to complete thread-safety. Src/Base/AMReX_MultiFab.cpp commit 082c2929733d083fdb653b1e9f947a10e6bbfa2d Author: Kevin Gott Date: Tue Nov 6 15:29:27 2018 -0500 Change DeviceScalar from is_pod to is_trivially_copyable. Src/Base/AMReX_CudaMemory.H commit 0bdbe1f53c3d6be7be454e9d9ad86a740f3d5ee1 Author: Kevin Gott Date: Tue Nov 6 15:28:49 2018 -0500 BaseFab::indexFromValue. Need tolerance checking. Src/Base/AMReX_BaseFab.H commit 15a031411ec8c0bfb5c28698a761e164a21f24e4 Author: Kevin Gott Date: Mon Nov 5 19:37:26 2018 -0500 Thin wrapper around thrust::copy. Src/Base/AMReX_CudaContainers.H commit 4f25e5885f48e90baf1a3720306be9a274918c62 Author: Kevin Gott Date: Mon Nov 5 18:54:14 2018 -0500 Cuda -> Gpu & first attempt at minIndex. Src/Base/AMReX_MultiFab.cpp commit 938696829fc2defee110b1044c465edb0af9c893 Author: Kevin Gott Date: Mon Nov 5 13:12:35 2018 -0500 Remaining norm Multifab funcs outlined. Won't compile with USE_CUDA=FALSE until thrust::copy is wrapped. Src/Base/AMReX_MultiFab.cpp commit dbafce0b26fbdcdc40672352509258820c5884e3 Author: Weiqun Zhang Date: Tue Nov 6 10:52:19 2018 -0800 use amrex::min and max Src/Base/AMReX_Utility.H Tutorials/GPU/CNS/Source/CNS_K.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp commit f25f62a96323a53cef6aedd853050875abd18a13 Merge: b8b285840 7288d56b0 Author: Weiqun Zhang Date: Tue Nov 6 09:55:14 2018 -0800 Merge branch 'gpu' into development commit b8b2858408263f7dfadc5921d38a0d6e2dbe0dba Merge: b9fb7eebb 696d43119 Author: WeiqunZhang Date: Tue Nov 6 09:38:39 2018 -0800 Merge pull request #356 from AMReX-Codes/SDC Sdc commit b9fb7eebbae4b31dfbc5b3400228f9403979bece Author: Andrew Myers Date: Mon Nov 5 18:31:53 2018 -0800 missed a few. Tools/Postprocessing/C_Src/fcompare.cpp commit ed6798a0b547d1914ca65858aba0cdf501d8f1b8 Merge: b547fb80e c555a00ac Author: Andrew Myers Date: Mon Nov 5 18:27:40 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b547fb80eab0bc88108746bcca4f406b56a32fca Author: Andrew Myers Date: Mon Nov 5 18:27:21 2018 -0800 specifiy amrex::min and amrex::max Tools/Postprocessing/C_Src/fcompare.cpp commit c555a00acaf40b10e749f2fa864b4848924602f8 Author: Ann Almgren Date: Mon Nov 5 17:56:17 2018 -0800 print out the maximum discrepancy in volume fraction but don't abort when the volume fraction or centroids don't match. Src/Extern/Algoim/AMReX_algoim_integrals.cpp commit 7288d56b04c485312216b11ca51c99dd139f7e4b Author: Weiqun Zhang Date: Mon Nov 5 16:08:53 2018 -0800 bug fixes Src/Base/AMReX_BaseFab.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp commit 696d43119763ec931a31592becdc827353e4c36c Merge: 2911a010b 15aca4b7e Author: Minion Date: Mon Nov 5 14:58:55 2018 -0800 Merge branch 'SDC' of https://github.com/AMReX-Codes/amrex into SDC commit 2911a010be3fbdff82ce1f30a423db9c2602d1b6 Author: Minion Date: Mon Nov 5 14:57:43 2018 -0800 fixing size of quad matrices Src/SDC/AMReX_SDCstruct.cpp commit 0e8f194986baaf1b9a67ec31b47b426cdbc256ed Author: Weiqun Zhang Date: Mon Nov 5 14:54:19 2018 -0800 fix bound checking Src/Base/AMReX_BaseFab.H commit 0432b7e20041941eb5587b5c0d5c87f418108fbb Merge: a0d53567a 52d8c89a1 Author: Ann Almgren Date: Mon Nov 5 14:36:32 2018 -0800 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit a0d53567aa50b39bb183eb3539679908ca033d49 Author: Ann Almgren Date: Mon Nov 5 14:36:24 2018 -0800 Fix typos in comments Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H commit 52d8c89a135a5277edbcf4e02523ad9b27b73a7d Author: Andrew Myers Date: Mon Nov 5 16:50:02 2018 -0500 and use the new utility functions in the getParticleTile function Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_ParticleUtil.cpp commit f8a11d9f74ee35a7781cbb7b616dd3c71b0f7eb2 Author: Andrew Myers Date: Mon Nov 5 16:49:23 2018 -0500 add min and max utility functions that work in both host and device code Src/Base/AMReX_Utility.H commit 2dbee854a7502231592981be375671623541fa2f Author: Weiqun Zhang Date: Mon Nov 5 13:43:18 2018 -0800 ostream for Dim3 Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp commit ca0f955c72562e0f82c86acf8a797e0ace4277a7 Author: Weiqun Zhang Date: Mon Nov 5 13:38:32 2018 -0800 Riemann solver and reset eint Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_K.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp commit 15aca4b7ecc929a4b90628bce06239c07013fedc Merge: 04b5e71e4 c1bd29b4f Author: Lawrence Minion Date: Mon Nov 5 12:07:59 2018 -0800 Merge branch 'SDC' of https://github.com/AMReX-Codes/amrex into SDC commit 04b5e71e48336ac62ba262606b58a6b90c80b6f5 Author: Lawrence Minion Date: Mon Nov 5 12:06:56 2018 -0800 removing outdated example Tutorials/Basic/SDCAdvDiffusion_C/Exec/.#advance.cpp Tutorials/Basic/SDCAdvDiffusion_C/Exec/GNUmakefile Tutorials/Basic/SDCAdvDiffusion_C/Exec/inputs_2d Tutorials/Basic/SDCAdvDiffusion_C/Source/Make.package Tutorials/Basic/SDCAdvDiffusion_C/Source/advance.cpp Tutorials/Basic/SDCAdvDiffusion_C/Source/advance_2d.f90 Tutorials/Basic/SDCAdvDiffusion_C/Source/init_phi_2d.f90 Tutorials/Basic/SDCAdvDiffusion_C/Source/init_phi_3d.f90 Tutorials/Basic/SDCAdvDiffusion_C/Source/inputs_3d Tutorials/Basic/SDCAdvDiffusion_C/Source/main.cpp Tutorials/Basic/SDCAdvDiffusion_C/Source/myfunc.H Tutorials/Basic/SDCAdvDiffusion_C/Source/myfunc_F.H Tutorials/Basic/SDCAdvDiffusion_C/Source/pf_quadrature.f90 commit a5c20708b7f1f57e9dffe57b8530cb8a36982206 Author: Weiqun Zhang Date: Mon Nov 5 11:22:47 2018 -0800 GPU/CNS: slopes Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_K.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp commit 06f6cc1725c5d829293d39bfd73d88d6288ebb5a Author: Ann Almgren Date: Mon Nov 5 09:45:36 2018 -0800 Update the ALGOIM stuff to be in AMReX namespace and change the convention so ALGOIM_HOME points to the external Algoim directory. Src/Extern/Algoim/AMReX_algoim_integrals.H Src/Extern/Algoim/AMReX_algoim_integrals.cpp Src/Extern/Algoim/Make.package Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tests/LinearSolvers/NodeEB/GNUmakefile Tests/LinearSolvers/NodeEB/MyTest.cpp commit f47e18811b37d527639af6bd6939c6640ffc8f50 Author: Weiqun Zhang Date: Sun Nov 4 17:55:41 2018 -0500 add Dim3 struct and this helps pgi in vectorization Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_IntVect.H Tests/Vectorization/kc.H commit 0e1bf5a256fe8cd93e34e4106236d7dd3809c7de Author: Weiqun Zhang Date: Sun Nov 4 17:19:27 2018 -0500 use the correct pragma for pgi Src/Base/AMReX_Extension.H commit d291935c0c654a0c47b51f7609c9c05c0044e550 Author: Weiqun Zhang Date: Sun Nov 4 13:13:56 2018 -0800 minor tweak Tests/Vectorization/kc.H commit 23ebf8526b134ac163fee43939fa10afa4ec8ce8 Author: Weiqun Zhang Date: Sun Nov 4 11:04:28 2018 -0800 use FabView Tests/Vectorization/kc.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/CNS/Source/CNS_K.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_index_macros.H Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp commit 79b4db257953fad46291e5c14c6ffd9cef93b75f Author: Weiqun Zhang Date: Sun Nov 4 13:37:57 2018 -0500 rewrite ctoprim Tests/Vectorization/kc.H commit dd39b0b2cd9dbd0ef80fc08628395e921bd16c38 Author: Weiqun Zhang Date: Sat Nov 3 21:19:46 2018 -0700 use the new version Tests/Vectorization/kc.H commit fdc36806121794d983bf88483ada7e509be73331 Author: Weiqun Zhang Date: Sat Nov 3 21:16:32 2018 -0700 FabView: clean up and add bound checking in debug Src/Base/AMReX_BaseFab.H commit 3471613152fddb8d76037e3b631f403d7b6dfe3a Author: Weiqun Zhang Date: Sat Nov 3 16:48:27 2018 -0700 fix intel deprecaion warning Src/Base/AMReX_Extension.H commit 565e6c2e947869e6bddc3f6a46a86c9bbe5d3726 Author: Ann Almgren Date: Sat Nov 3 16:47:27 2018 -0700 Update the regression tests so we test 2d and 3d -- in 3d we test cylinder with the axis in three coordinate directions Tests/LinearSolvers/NodeEB/GNUmakefile Tests/LinearSolvers/NodeEB/MyTest.H Tests/LinearSolvers/NodeEB/MyTest.cpp Tests/LinearSolvers/NodeEB/inputs Tests/LinearSolvers/NodeEB/inputs.rt.2d Tests/LinearSolvers/NodeEB/inputs.rt.3d.x Tests/LinearSolvers/NodeEB/inputs.rt.3d.y Tests/LinearSolvers/NodeEB/inputs.rt.3d.z commit b912973803e916534c70441c016fadcdfad4345f Author: Ann Almgren Date: Sat Nov 3 16:45:56 2018 -0700 Had to change the coarsening since the stencils pointing to the faces are 0 for regular cells when dx = dy = dz. This messes with the coarsening when a full cell is near an almost full cell. We should probably make the same change in the interpolation but for now this works on simple test cases (ie cylinders) Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit e636f202ada3d72eeb2f38e13570afeef4d0d23b Author: Ann Almgren Date: Sat Nov 3 16:45:24 2018 -0700 Remove extra printing Src/Extern/Algoim/Algoim_integrals.cpp commit a4950f92e993736e95be03123d5e190a4402deeb Merge: def64bb26 3511c3a6e Author: Ann Almgren Date: Sat Nov 3 15:05:12 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit def64bb2623181d02f9184d0e7d3409e27bb3962 Author: Ann Almgren Date: Sat Nov 3 15:04:49 2018 -0700 Comment out print statement and setprecision statement Src/Extern/Algoim/Algoim_integrals.cpp commit 3511c3a6e740670fc368866d5426dee940481e66 Author: Max Katz Date: Sat Nov 3 17:20:44 2018 -0400 Fix some divide by zero issues in DistributionMapping Src/Base/AMReX_DistributionMapping.cpp commit d622b0810d0845efadac34f16bb8c5e4d4657355 Author: Weiqun Zhang Date: Sat Nov 3 13:33:49 2018 -0700 add warm up to the test Tests/Vectorization/main.cpp commit 726dea8fabb696951325f6b3c2bfe1b7b8ad0d1b Author: Weiqun Zhang Date: Sat Nov 3 13:01:04 2018 -0700 new headers Tests/Vectorization/kc.H Tests/Vectorization/kdecl.H commit 6bc8f365d007e2a0280c4bec138b28f8b48773c0 Author: Weiqun Zhang Date: Sat Nov 3 12:57:50 2018 -0700 add ctoprim test Tests/Vectorization/kf.F90 Tests/Vectorization/main.cpp commit 64efcfa03bdc4a60688d17d4c9f954994b3b2286 Author: Weiqun Zhang Date: Sat Nov 3 12:06:37 2018 -0700 add non-simd version Tests/Vectorization/GNUmakefile Tests/Vectorization/Make.package Tests/Vectorization/kc.cpp Tests/Vectorization/main.cpp commit 0a559d26a6f1a9526e222cd5aa3bbac1896c6822 Author: Weiqun Zhang Date: Sat Nov 3 11:35:18 2018 -0700 minor Tests/Vectorization/main.cpp commit 2a3e605f3c77f643e55e76ef6b50cc39954df190 Author: Weiqun Zhang Date: Sat Nov 3 11:32:46 2018 -0700 compiler extension macros Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaFab.cpp Src/Base/AMReX_Extension.H Src/Base/AMReX_REAL.H Src/Base/AMReX_RESTRICT.H Src/Base/CMakeLists.txt Src/Base/Make.package Tools/GNUMake/comps/gnu.mak commit 2863b6b904349c63a17f8dce9f028b6bc0684ff9 Merge: 5f6827ae3 1eb1ea1d2 Author: Ann Almgren Date: Sat Nov 3 10:54:17 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 5f6827ae3596519b180a82fa8cfa01dddeb2a790 Author: Ann Almgren Date: Sat Nov 3 10:53:36 2018 -0700 Fix indexing problem in 3D EB nodal restriction operator. (There is still a different issue but this does fix some problems) Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 1eb1ea1d248613621cbcad424aa5a94326f30711 Merge: 1cc028db9 7319fe527 Author: WeiqunZhang Date: Sat Nov 3 10:45:10 2018 -0700 Merge pull request #359 from AMReX-Codes/mkatz/last_checkpoint Fill in last_checkpoint/last_plotfile after a restart commit 1cc028db99547da2b99792e8da56c18824ecf29b Merge: ac5ab03e6 8612e00ef Author: WeiqunZhang Date: Sat Nov 3 10:43:03 2018 -0700 Merge pull request #358 from AMReX-Codes/mkatz/minimalbox_overflow_fix Fix a potential numerical overflow in BoxArray::minimalBox commit 7319fe5270ddd8586e1e87c2fe516c7c699138b9 Author: Max Katz Date: Sat Nov 3 03:05:46 2018 -0400 Fill in last_checkpoint/last_plotfile after a restart Castro and Nyx have logic in main.cpp that says to only dump a checkpoint if the coarse timestep of the last checkpoint is older than the current coarse timestep. In the edge case where the simulation doesn't actually take any timesteps after a restart, this results in a checkpoint and plotfile being written from the same data we restarted from, which unnecessarily clobbers the old data and creates a duplicate checkpoint/plotfile. If the user explicitly wants a new checkpoint on restart, perhaps because they are doing some kind of transformation, they can still take advantage of the flags checkpoint_on_restart and plotfile_on_restart. Src/Amr/AMReX_Amr.cpp commit 5238e6cce46bb8ca38bd73d746753f1b5f8cffb3 Author: Weiqun Zhang Date: Fri Nov 2 23:10:12 2018 -0700 vectorization test Tests/Vectorization/GNUmakefile Tests/Vectorization/Make.package Tests/Vectorization/kc.cpp Tests/Vectorization/kf.F90 Tests/Vectorization/main.cpp commit 88d30002be822cb4f87045b0e043ddb68807e1ff Author: Weiqun Zhang Date: Fri Nov 2 23:03:34 2018 -0700 AMREX_PRAGMA_SIMD Src/Base/AMReX_RESTRICT.H Tools/GNUMake/comps/ibm.mak Tools/libamrex/configure.py Tools/libamrex/mkconfig.py commit dada09ea8463efbfa6b27feae7cf160515b79fed Author: Weiqun Zhang Date: Fri Nov 2 23:02:13 2018 -0700 FabView Src/Base/AMReX_BaseFab.H commit 8612e00ef852f90e5f18943d2ae1903029f00a4e Author: Max Katz Date: Sat Nov 3 00:11:07 2018 -0400 Fix a potential numerical overflow in BoxArray::minimalBox If the number of points per dimension N is such that N^3 is larger than a 32-bit integer (or N^2, for 2D), then this implementation of minimalBox will overflow when accumulating into an n_pts variable. Solved by replacing the value holding the number of points with a long, which is consistent with similar calculations elsewhere in BoxArray. Fixes #357 Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.cpp commit b10af54c31f5739027a46947500937c23e49600d Author: Weiqun Zhang Date: Fri Nov 2 16:31:32 2018 -0700 flux to dudt Tutorials/GPU/CNS/Source/CNS.H Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp commit ac5ab03e650a385be49c10c451460ff449e76c3a Author: Weiqun Zhang Date: Fri Nov 2 15:27:26 2018 -0700 std::isnan and isinf -> amrex::isnan and isinf Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp commit 6e51633e90166360dfdc8c4d10d16974192c92ec Author: Weiqun Zhang Date: Fri Nov 2 15:25:26 2018 -0700 ptxas info Tools/GNUMake/comps/nvcc.mak commit 947008102af7345cbb73ae5b653f74bcf74dc185 Author: Weiqun Zhang Date: Fri Nov 2 14:48:12 2018 -0700 fix omp Src/Base/AMReX_MultiFab.cpp commit 70949172d769b9f4a0decfbbc91f92e1cf5008c0 Author: Kevin Gott Date: Fri Nov 2 15:02:33 2018 -0400 Turn off OpenMP+GPU in contains_inf/nan. Src/Base/AMReX_MultiFab.cpp commit 34cf9c02ab2bf7122d48a0a47e6e02ce387bc33e Author: Kevin Gott Date: Fri Nov 2 14:54:32 2018 -0400 MultiFab::contains_nan and contains_inf to gpu. Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_MultiFab.cpp commit 77afe4ca7dbdd1b4982ab07b74093e841c1ae5d3 Author: Weiqun Zhang Date: Fri Nov 2 11:11:49 2018 -0700 add AMREX_LAUNCH_DEVICE_LAMBDA_BOXIV Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_GpuLaunch.H commit dd2205cb04cf4c28c8ec93fc4826be0b3b1278a9 Author: Weiqun Zhang Date: Fri Nov 2 12:28:58 2018 -0400 fix merge Src/Base/AMReX_BaseFab.H commit 2ad4777695fdfda1fb5eb3e199fb6d35684ff37a Merge: df9ce56be b43c2ba1f Author: Weiqun Zhang Date: Fri Nov 2 12:26:42 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development Conflicts: Src/Base/AMReX_BaseFab.H commit df9ce56bea4c593d4218ec53a9747f7bf2a7bbaa Author: Weiqun Zhang Date: Fri Nov 2 12:23:08 2018 -0400 hopefully mfic can now compile with USE_CUDA=TRUE Src/Base/AMReX_BaseFab.H Src/EB/AMReX_EBCellFlag.H commit b43c2ba1f9727e58d97d3c973a19d12ec2a09afa Merge: 81c1a06d2 49a3b05ab Author: Weiqun Zhang Date: Fri Nov 2 09:15:27 2018 -0700 Merge branch 'development' into weiqun/merge-b-devicefab commit 49a3b05abb56feb035fa79a48e0fa31bcdc9ec79 Author: Weiqun Zhang Date: Thu Nov 1 21:05:00 2018 -0700 in debug mode, add -Werror=return-type to gcc Tools/GNUMake/comps/gnu.mak commit 0b2fa86a9884bb742a5ac0849526aa9efa410451 Author: Weiqun Zhang Date: Thu Nov 1 21:00:34 2018 -0700 fix a bug Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp commit 874e8b5ebd33d2d4c0a3c9f41a68dd5422de5040 Author: Andrew Myers Date: Thu Nov 1 20:30:07 2018 -0400 use thrust::sort here if running with Cuda Src/Particle/AMReX_NeighborParticlesI.H commit 119dcba4c631911b3d5241f16e8bb8dd3e07f78c Author: Weiqun Zhang Date: Thu Nov 1 17:25:25 2018 -0700 add ctoprim Src/Amr/AMReX_Amr.cpp Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/CNS/Exec/Sod/inputs Tutorials/GPU/CNS/Source/CNS.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_K.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_index_macros.H Tutorials/GPU/CNS/Source/CNS_io.cpp Tutorials/GPU/CNS/Source/Make.package Tutorials/GPU/CNS/Source/hydro/Make.package Tutorials/GPU/CNS/Source/hydro/cns_hydro.cpp commit d88aa6729cb284a3dad11c47ee3e4e5683b5fbeb Merge: 395af60a2 6cb4623e0 Author: Andrew Myers Date: Thu Nov 1 18:44:50 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 395af60a2aee4063d49672da6566d3252017498a Author: Andrew Myers Date: Thu Nov 1 18:40:10 2018 -0400 remove the index conversion stuff for now. Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_ParticleUtil.cpp commit 71131379dbb447c153fcc50b1aee0bca95645029 Author: Weiqun Zhang Date: Thu Nov 1 15:26:57 2018 -0700 fix sum Tutorials/GPU/CNS/Source/CNS.cpp commit f7416dbc005dbf0a93ad2f856f7084923af8a6c0 Author: Weiqun Zhang Date: Thu Nov 1 15:20:59 2018 -0700 estimate dt Src/Base/AMReX_CoordSys.H Src/Base/AMReX_Geometry.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/CNS/Exec/Sod/inputs Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_K.cpp Tutorials/GPU/CNS/Source/CNS_io.cpp Tutorials/GPU/CNS/Source/CNS_setup.cpp Tutorials/GPU/CNS/Source/Make.package commit ec51de4aff007da6ae19f728d8d74253d8eeb659 Author: Andrew Myers Date: Thu Nov 1 17:45:33 2018 -0400 fix compilation error Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit f93b3b10ca8dead382ee67e6c3398d5111e5ac3e Author: Andrew Myers Date: Thu Nov 1 17:45:15 2018 -0400 forgot to add these files. Src/Particle/AMReX_ParticleUtil.H Src/Particle/AMReX_ParticleUtil.cpp commit e8cea75c2f986efadf83e78b676c294f34052906 Author: Andrew Myers Date: Thu Nov 1 17:30:11 2018 -0400 pass the bin start and stop indices into the SortParticlesByBin method Src/Particle/AMReX_ParticleContainerI.H commit 3d7fbabc57e3e73eb603baafa111494016143fdc Author: Weiqun Zhang Date: Thu Nov 1 14:10:44 2018 -0700 vectorization Src/Base/AMReX_BaseFab.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp commit 96cac23e66c3045f906e6700e8e824f0af065feb Author: Andrew Myers Date: Thu Nov 1 17:07:17 2018 -0400 add stub for SortParticlesByBin Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 40e9eefc2e8ad4628531a009c0d3f6dbb40fa913 Author: Andrew Myers Date: Thu Nov 1 16:58:56 2018 -0400 add new functor for binning particles on a sub-grid basis Src/Particle/AMReX_Functors.H commit 81c1a06d2483d5f29953f1e4b18bf24b5a311c2f Author: Weiqun Zhang Date: Thu Nov 1 13:46:44 2018 -0700 comment out resize because it contains cuda api calls thus not safe as callback. add mutex in delete to protect the memory pool Src/Base/AMReX_CudaFab.H Src/Base/AMReX_CudaFab.cpp commit 21a8695d612bd84543456272019d77777272d20b Author: Weiqun Zhang Date: Thu Nov 1 13:46:44 2018 -0700 comment out resize because it contains cuda api calls thus not safe as callback. add mutex in delete to protect the memory pool Src/Base/AMReX_CudaFab.H Src/Base/AMReX_CudaFab.cpp commit 78c6f55c20119eca33f56652ac4014fa5f113068 Author: Andrew Myers Date: Thu Nov 1 16:06:15 2018 -0400 move getTileIndex to a separate file, make it run on both host and device Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 50ea830583d0f158fe2b16343b02737d434c58e7 Author: Andrew Myers Date: Thu Nov 1 15:06:47 2018 -0400 mark getTileIndex as __host__ __device__ Src/Particle/AMReX_Particles.H commit 627abba7953dfc82f1d7b5accd7d4c274dfbfb63 Author: Andrew Myers Date: Thu Nov 1 15:05:46 2018 -0400 refactor getTileIndex to not use static members so that it can be called from device code. Src/Particle/AMReX_ParticleContainerI.H commit 6cb4623e06cd0eaaec95c31fe66340a45095e96f Author: Kevin Gott Date: Thu Nov 1 12:00:41 2018 -0700 Reset minIndex. Src/Base/AMReX_MultiFab.cpp commit ccc079ae976a0b8c7f89dc9fbc09531a4c43186d Author: Kevin Gott Date: Thu Nov 1 14:58:23 2018 -0400 Continuing to convert MultiFab functions. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_MultiFab.cpp commit dcbe6b8641af335edebd3dc9a6d1668599f310cc Author: Weiqun Zhang Date: Thu Nov 1 11:05:22 2018 -0700 add cns_initdata Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/CNS/Exec/Sod/inputs Tutorials/GPU/CNS/Source/CNS.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNS_K.H Tutorials/GPU/CNS/Source/CNS_index.H Tutorials/GPU/CNS/Source/CNS_setup.cpp Tutorials/GPU/CNS/Source/Make.package commit 716d57dec1adad263055fdb1219481faec948ebe Merge: 1980702fd 41aab2c48 Author: Andrew Myers Date: Thu Nov 1 10:00:41 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1980702fd2cd88a2cb9265362fbbc37b6f70163a Author: Andrew Myers Date: Thu Nov 1 10:00:31 2018 -0700 remove unused variables Src/Particle/AMReX_Particles.H commit 68f5caf7b30ad5f8b424757e1d5d75cadd17fe88 Author: Weiqun Zhang Date: Thu Nov 1 09:06:02 2018 -0700 DeviceFab:: add async clear and resize Src/Base/AMReX_CudaFab.H Src/Base/AMReX_CudaFab.cpp Src/Base/AMReX_CudaFabImpl.cpp commit 64a29a129c71dec35166d292a5bdb0177285b271 Author: Weiqun Zhang Date: Thu Nov 1 09:06:02 2018 -0700 DeviceFab:: add async clear and resize Src/Base/AMReX_CudaFab.H Src/Base/AMReX_CudaFab.cpp Src/Base/AMReX_CudaFabImpl.cpp commit e95a08277bb7a06bb480c696237cbfc9ae2377e6 Merge: 694e288db 0ece4fc65 Author: Weiqun Zhang Date: Thu Nov 1 08:40:17 2018 -0700 Merge branch 'development' into weiqun/gpu commit 0ece4fc651d9e404f7c3355632cb0988392f9ad0 Merge: c54384dea f033c9774 Author: Weiqun Zhang Date: Thu Nov 1 08:39:40 2018 -0700 Merge branch 'weiqun/merge-a-coord' into development commit 41aab2c480411a2bc444078d012550c0b7dc432c Merge: 6a39666fb 0ece4fc65 Author: Ann Almgren Date: Thu Nov 1 08:38:50 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 6a39666fb693a8159cb7e8a496fa40fd1197d0e0 Author: Ann Almgren Date: Thu Nov 1 08:38:37 2018 -0700 Remove VisMF::Write call. Src/Extern/Algoim/Algoim_integrals.cpp commit c54384dea796c6a836cbf1b1ebab6744ba87cb24 Author: Weiqun Zhang Date: Thu Nov 1 08:38:20 2018 -0700 update CHANGES CHANGES commit 3ad2b25ff9209da59fb217fa1cafc43b895a2ee6 Author: Ann Almgren Date: Thu Nov 1 08:30:50 2018 -0700 Fix typo in 3d version of mknewu_eb Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit b256a7f58911d839e52a5d5eec573279436a64d8 Author: Ann Almgren Date: Thu Nov 1 07:15:42 2018 -0700 Make sure to enforce periodicity of 3d nodal EB integrals Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit a6571badce486ac5bb463ee10ea31e36fbcdca3a Merge: f4cd3dcb1 c004d364c Author: Ann Almgren Date: Thu Nov 1 07:13:44 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit f4cd3dcb1a82024f63830be49653dfef87741c06 Author: Ann Almgren Date: Wed Oct 31 21:16:12 2018 -0700 Fix some sign errors and the scaling of the 3D EB nodal stencil Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 54105bfef870bafa790bf393d4ede9e07dea029c Author: Ann Almgren Date: Wed Oct 31 18:19:24 2018 -0700 Initialize the ghost cells of the intg array elements as well Src/Extern/Algoim/Algoim_integrals.cpp commit c004d364c3a51f07538a2a419c8b01a82040faae Author: Kevin Gott Date: Wed Oct 31 19:40:40 2018 -0400 Update HeatEquation GPU example. Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H commit f033c9774da77c0973f2472f6fd9674c35181c65 Merge: 3b5495f15 ef9811401 Author: Weiqun Zhang Date: Wed Oct 31 16:29:24 2018 -0700 Merge branch 'development' into weiqun/merge-a-coord commit ef981140198a4abd3b913d3bb50c1899b4a1a6b9 Author: Andrew Myers Date: Wed Oct 31 16:24:52 2018 -0700 remove now-unused file Src/Particle/AMReX_RedistributeStrategy.H commit 1cfe9fde6288c53dcde2dab34fc39b012b649006 Author: Andrew Myers Date: Wed Oct 31 16:18:37 2018 -0700 remove broken tutorials - will fix these and add them back later. Tutorials/GPU/ElectromagneticPIC/Constants.H Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.H Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/Evolve.H Tutorials/GPU/ElectromagneticPIC/Evolve.cpp Tutorials/GPU/ElectromagneticPIC/GNUmakefile Tutorials/GPU/ElectromagneticPIC/IO.H Tutorials/GPU/ElectromagneticPIC/IO.cpp Tutorials/GPU/ElectromagneticPIC/Make.package Tutorials/GPU/ElectromagneticPIC/NodalFlags.H Tutorials/GPU/ElectromagneticPIC/NodalFlags.cpp Tutorials/GPU/ElectromagneticPIC/Particles.H Tutorials/GPU/ElectromagneticPIC/StructOfArrays.H Tutorials/GPU/ElectromagneticPIC/em_pic_3d.F90 Tutorials/GPU/ElectromagneticPIC/em_pic_F.H Tutorials/GPU/ElectromagneticPIC/inputs Tutorials/GPU/ElectromagneticPIC/main.cpp Tutorials/GPU/ElectromagneticPIC/script.nompi.sh Tutorials/GPU/ElectromagneticPIC/summit.sh Tutorials/GPU/ElectromagneticPIC/summitdev.sh Tutorials/GPU/ElectromagneticPIC/test.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/inputs Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/script.sh Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/inputs Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/script.sh Tutorials/Particles/ElectromagneticPIC/Make.EMPIC Tutorials/Particles/ElectromagneticPIC/Source/Constants.H Tutorials/Particles/ElectromagneticPIC/Source/IO.H Tutorials/Particles/ElectromagneticPIC/Source/IO.cpp Tutorials/Particles/ElectromagneticPIC/Source/Make.package Tutorials/Particles/ElectromagneticPIC/Source/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/Source/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/Source/Particles.H Tutorials/Particles/ElectromagneticPIC/Source/main.cpp commit 76e1d5eade440c280c8dddcec3a96a577f1fa4b6 Author: Andrew Myers Date: Wed Oct 31 16:07:07 2018 -0700 remove debug print statement Src/Particle/AMReX_ParticleContainerI.H commit 43d0b56ad367bd0ab30927633cff967a6c74b18f Author: Andrew Myers Date: Wed Oct 31 16:03:27 2018 -0700 force rebuilding the redistribute mask when you ask for more ghost cells than it currently has Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 3b5495f15cb893a035fbeb9295f8c030f062316d Author: Weiqun Zhang Date: Wed Oct 31 12:59:21 2018 -0700 fix offset Src/Base/AMReX_COORDSYS_1D.cpp Src/Base/AMReX_COORDSYS_2D.cpp commit 694e288db246188be0853355a3380ca06ddd53e7 Author: Weiqun Zhang Date: Wed Oct 31 11:04:36 2018 -0700 minor Tutorials/GPU/CNS/Exec/Sod/GNUmakefile commit ffd1eaf025d5ab9e08a1d4270500f27a87c61286 Author: Weiqun Zhang Date: Wed Oct 31 10:32:46 2018 -0700 skelton for CNS Tutorials/GPU/CNS/Exec/Make.CNS Tutorials/GPU/CNS/Exec/Sod/GNUmakefile Tutorials/GPU/CNS/Exec/Sod/Make.package Tutorials/GPU/CNS/Exec/Sod/cns_prob.H Tutorials/GPU/CNS/Exec/Sod/cns_prob.cpp Tutorials/GPU/CNS/Exec/Sod/inputs Tutorials/GPU/CNS/Source/CNS.H Tutorials/GPU/CNS/Source/CNS.cpp Tutorials/GPU/CNS/Source/CNSBld.cpp Tutorials/GPU/CNS/Source/CNS_advance.cpp Tutorials/GPU/CNS/Source/CNS_io.cpp Tutorials/GPU/CNS/Source/CNS_setup.cpp Tutorials/GPU/CNS/Source/Make.package Tutorials/GPU/CNS/Source/diffusion/Make.package Tutorials/GPU/CNS/Source/hydro/Make.package Tutorials/GPU/CNS/Source/main.cpp commit fe129b1524ad8e41d95a8b42e99aad51b6cfa203 Author: Tan Nguyen Date: Wed Oct 31 01:49:47 2018 -0700 refactoring AMFIter codes Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Perilla/Barrier.H Src/AmrTask/rts_impls/Perilla/Barrier.cpp Src/AmrTask/rts_impls/Perilla/LocalConnection.H Src/AmrTask/rts_impls/Perilla/Make.package Src/AmrTask/rts_impls/Perilla/PackageQueue.H Src/AmrTask/rts_impls/Perilla/PackageQueue.cpp Src/AmrTask/rts_impls/Perilla/Perilla.cpp Src/AmrTask/rts_impls/Perilla/PerillaRts.cpp Src/AmrTask/rts_impls/Perilla/RGIter.H Src/AmrTask/rts_impls/Perilla/RGIter.cpp Src/AmrTask/rts_impls/Perilla/RegionQueue.H Src/AmrTask/rts_impls/Perilla/RegionQueue.cpp Src/AmrTask/rts_impls/Perilla/RemoteConnection.H Src/AmrTask/rts_impls/Perilla/WorkerThread.H Src/AmrTask/rts_impls/Perilla/WorkerThread.cpp Src/AmrTask/rts_impls/Perilla/mylock.h Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Perilla_upc++/Barrier.H Src/AmrTask/rts_impls/Perilla_upc++/Barrier.cpp Src/AmrTask/rts_impls/Perilla_upc++/LocalConnection.H Src/AmrTask/rts_impls/Perilla_upc++/Make.package Src/AmrTask/rts_impls/Perilla_upc++/Perilla.H Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp Src/AmrTask/rts_impls/Perilla_upc++/PerillaRts.cpp Src/AmrTask/rts_impls/Perilla_upc++/Perilla_common.cpp Src/AmrTask/rts_impls/Perilla_upc++/RGIter.H Src/AmrTask/rts_impls/Perilla_upc++/RGIter.cpp Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.H Src/AmrTask/rts_impls/Perilla_upc++/RegionQueue.H Src/AmrTask/rts_impls/Perilla_upc++/RegionQueue.cpp Src/AmrTask/rts_impls/Perilla_upc++/RemoteConnection.H Src/AmrTask/rts_impls/Perilla_upc++/WorkerThread.H Src/AmrTask/rts_impls/Perilla_upc++/WorkerThread.cpp Src/AmrTask/rts_impls/Perilla_upc++/mylock.h Src/AmrTask/rts_impls/Perilla_upc++/perilla.mak Src/AmrTask/rts_impls/Pthread_Common/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/Pthread_Common/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Pthread_Common/Barrier.H Src/AmrTask/rts_impls/Pthread_Common/Barrier.cpp Src/AmrTask/rts_impls/Pthread_Common/LocalConnection.H Src/AmrTask/rts_impls/Pthread_Common/Make.package Src/AmrTask/rts_impls/Pthread_Common/RGIter.H Src/AmrTask/rts_impls/Pthread_Common/RGIter.cpp Src/AmrTask/rts_impls/Pthread_Common/RegionQueue.H Src/AmrTask/rts_impls/Pthread_Common/RegionQueue.cpp Src/AmrTask/rts_impls/Pthread_Common/RemoteConnection.H Src/AmrTask/rts_impls/Pthread_Common/WorkerThread.H Src/AmrTask/rts_impls/Pthread_Common/WorkerThread.cpp Src/AmrTask/rts_impls/Pthread_Common/mylock.h Src/AmrTask/rts_impls/Pthread_Common/perilla.mak commit c66db4aa57bc4ae0753e548c32642b94bc61f849 Author: Weiqun Zhang Date: Tue Oct 30 20:51:40 2018 -0700 forgot to add files Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaFab.H Src/Base/AMReX_CudaFab.cpp Src/Base/AMReX_CudaFabImpl.H Src/Base/AMReX_CudaFabImpl.cpp commit c8a19ef4b87f6af07e1a0a409137d431b71cafc4 Author: Ann Almgren Date: Tue Oct 30 18:31:48 2018 -0700 Fix oops Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 5c40964565eebb68813c6783dec6f0e013765f65 Author: Ann Almgren Date: Tue Oct 30 18:30:17 2018 -0700 Remove extra print Src/Extern/Algoim/Algoim_integrals.cpp commit a0ee1013509291d365fe3d6f525601fee4bf5534 Merge: c5345f915 c106386b3 Author: Ann Almgren Date: Tue Oct 30 18:29:21 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit c5345f9154c0c05792ee6973c533cd1d05073684 Author: Ann Almgren Date: Tue Oct 30 18:28:53 2018 -0700 In preparation for being able to use Algoim to construct the 3d EB nodal integrals for use in the 3d nodal projection Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/Extern/Algoim/Algoim_integrals.H Src/Extern/Algoim/Algoim_integrals.cpp Src/Extern/Algoim/Make.package Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit b4f1121f9254b529c149e66294cd3a65f0b6cf10 Author: Weiqun Zhang Date: Tue Oct 30 18:08:58 2018 -0700 add an example of using DeviceFab Tests/GPU/DeviceFab/GNUmakefile Tests/GPU/DeviceFab/Make.package Tests/GPU/DeviceFab/main.cpp commit c1bd29b4f004a4e2558591b6105deb14c5cd4b8f Author: Minion Date: Tue Oct 30 17:03:16 2018 -0700 Moving files to look like other tutorials Tutorials/SDC/MISDC_ADR_2d/Exec/GNUmakefile Tutorials/SDC/MISDC_ADR_2d/Exec/inputs_2d Tutorials/SDC/MISDC_ADR_2d/README Tutorials/SDC/MISDC_ADR_2d/Source/Make.package Tutorials/SDC/MISDC_ADR_2d/Source/SDC_sweeper.cpp Tutorials/SDC/MISDC_ADR_2d/Source/functions_2d.f90 Tutorials/SDC/MISDC_ADR_2d/Source/init_phi_2d.f90 Tutorials/SDC/MISDC_ADR_2d/Source/main.cpp Tutorials/SDC/MISDC_ADR_2d/Source/myfunc.H Tutorials/SDC/MISDC_ADR_2d/Source/myfunc_F.H commit 4140ab4bc1b81bbd5c6337f25f88ef132c8d148b Author: Minion Date: Tue Oct 30 16:46:50 2018 -0700 made Nnodes adjustable and cleaner quadrature matrices Src/SDC/AMReX_SDCstruct.H Src/SDC/AMReX_SDCstruct.cpp commit 66c28074a74c58f2f638a8931beb2d0dd046f7fb Author: Weiqun Zhang Date: Tue Oct 30 16:39:14 2018 -0700 DeviveFab: add new constructor for the omp fab resize idiom Src/Base/AMReX_CudaFab.H Src/Base/AMReX_CudaFab.cpp Src/Base/AMReX_CudaFabImpl.H Src/Base/AMReX_CudaFabImpl.cpp commit 4ede0759b96454126701d2714cbc8221126133b6 Author: Weiqun Zhang Date: Tue Oct 30 18:54:52 2018 -0400 add profiler to CudaFab Src/Base/AMReX_CudaFab.cpp Src/Base/AMReX_CudaFabImpl.cpp commit c106386b3b2a742b7721048b3019512800193a19 Author: Jean Sexton Date: Tue Oct 30 18:31:28 2018 -0400 Remove old example Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/GNUmakefile Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/Make.package Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/SetIC.f90 Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/inputs Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/main.cpp Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/myfunc_F.H Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/ode_mod.f90 commit ec188f084e32e892030f1c83ca87fd6a35dde213 Author: Cy Chan Date: Tue Oct 30 14:03:15 2018 -0700 add flag to turn on/off new features for A/B comparison within the same run want to compare under same node assignment from job scheduler print SLURM_NODELIST in MLLinOp Src/Base/AMReX_DistributionMapping.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit f9001a7b11625cb2d114c4390c36639e4a688c78 Author: Kevin Gott Date: Tue Oct 30 13:55:22 2018 -0700 Add to documentation: Fortran cannot be instrumented when using Tiny Profiling. Docs/sphinx_documentation/source/AMReX_Profiling_Tools.rst commit e4acbdeb12a65f32e410e44253cd4cd00d779387 Merge: 7eeb6c85f 19c76c581 Author: Weiqun Zhang Date: Tue Oct 30 16:38:10 2018 -0400 Merge branch 'weiqun/gpu' of github.com:AMReX-Codes/amrex into weiqun/gpu commit 19c76c581a3bf61fd70da9559951881ed2d9f90f Merge: 39bf92507 d9aaff042 Author: Weiqun Zhang Date: Tue Oct 30 13:38:19 2018 -0700 Merge branch 'development' into weiqun/gpu commit 39bf925072b86e96c5ce900fbcb1ea6b7c5c1fe0 Author: Weiqun Zhang Date: Tue Oct 30 13:24:49 2018 -0700 fix non-cuda build Src/Base/AMReX_CudaFabImpl.cpp commit 7eeb6c85fd335fead31ea75a5676da2796dd1257 Merge: 49b575057 39bf92507 Author: Weiqun Zhang Date: Tue Oct 30 16:24:47 2018 -0400 Merge branch 'weiqun/gpu' of github.com:AMReX-Codes/amrex into weiqun/gpu commit 49b575057ca01a8053717810e8951d51afa6deea Author: Weiqun Zhang Date: Tue Oct 30 16:16:33 2018 -0400 use AMREX_CUDA_MAX_THREADS instead of hardwired number 256 Src/Base/AMReX_CudaDevice.cpp commit 9d921899f75417a174f1b2b9489aef90122ecfc2 Author: Weiqun Zhang Date: Tue Oct 30 13:11:44 2018 -0700 implement DeviceFab Src/Base/AMReX.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaFab.H Src/Base/AMReX_CudaFab.cpp Src/Base/AMReX_CudaFabImpl.H Src/Base/AMReX_CudaFabImpl.cpp Src/Base/AMReX_CudaUtility.H Src/Base/CMakeLists.txt Src/Base/Make.package commit d9aaff042c73cb7bc9c63db6479c8b4b1c5700bd Author: atmyers Date: Tue Oct 30 06:49:03 2018 -0700 use resize instead of clear Src/Particle/AMReX_ParticleContainerI.H commit c48a300c697bddd066589e91a6cb14e4ccdd069f Author: atmyers Date: Tue Oct 30 06:29:11 2018 -0700 need to clear ghosts / virtuals after adding them Src/Particle/AMReX_ParticleContainerI.H commit 7a72ea52e74a4c00ab0ae11f3a9dff756ec72791 Author: Tan Nguyen Date: Tue Oct 30 01:13:29 2018 -0700 correct AMFIter metadata after regridding Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AsyncFillPatch.cpp Src/AmrTask/rts_impls/Perilla/Perilla.H Src/AmrTask/rts_impls/Perilla/Perilla.cpp Src/AmrTask/rts_impls/Perilla/PerillaRts.cpp Src/AmrTask/rts_impls/Perilla/RGIter.cpp Src/AmrTask/rts_impls/Perilla_upc++/Perilla_common.cpp commit 1c84d8ea34cd10ba1757513d12cd4665a4ce64ea Author: Lawrence Minion Date: Mon Oct 29 23:39:35 2018 -0700 fix mfi ordering bug Src/SDC/AMReX_SDCstruct.cpp commit f343a140599f66417f601b64aaf972fdf6341d00 Author: Lawrence Minion Date: Mon Oct 29 23:10:49 2018 -0700 Adding MISDC example with exact solution Tutorials/SDC/MISDC_ADR_2d/GNUmakefile Tutorials/SDC/MISDC_ADR_2d/Make.package Tutorials/SDC/MISDC_ADR_2d/SDC_sweeper.cpp Tutorials/SDC/MISDC_ADR_2d/functions_2d.f90 Tutorials/SDC/MISDC_ADR_2d/init_phi_2d.f90 Tutorials/SDC/MISDC_ADR_2d/inputs_2d Tutorials/SDC/MISDC_ADR_2d/main.cpp Tutorials/SDC/MISDC_ADR_2d/myfunc.H Tutorials/SDC/MISDC_ADR_2d/myfunc_F.H commit b5eb8b749eed5a3c5cb0b679219ebaa5f4b2c62c Author: Weiqun Zhang Date: Mon Oct 29 18:06:00 2018 -0700 make BaseFab's data trivially copyable Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaFab.H Src/Base/AMReX_CudaFab.cpp Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_Gpu.H Src/Base/CMakeLists.txt Src/Base/Make.package commit d59e0d08b8a1848be1cb0626c3b08f3a1382d112 Merge: 39d65fbc9 d4166f5b0 Author: Ann Almgren Date: Mon Oct 29 17:33:18 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 39d65fbc9efa0b9cc147af9fa70c5cf718c1c50e Author: Ann Almgren Date: Mon Oct 29 17:33:04 2018 -0700 Remove unused "auto sfab = ..." lines Src/EB/AMReX_EBAmrUtil.cpp Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EB_levelset.cpp commit d4166f5b0622718219a66ab0ae75290a081a813d Merge: 506200fdd 0a6668d06 Author: Andrew Myers Date: Mon Oct 29 20:30:54 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 506200fddcc2878e3bca575e5d65d5635653b6cd Author: Andrew Myers Date: Mon Oct 29 20:30:11 2018 -0400 changes needed for Nyx to compile with USE_CUDA=TRUE Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H commit 0a6668d06a9c056f565bfcaa8b938b2b60dc7d37 Author: Kevin Gott Date: Mon Oct 29 20:00:56 2018 -0400 Consolidate and cleanup GPU tutorials. Tests/GPU/ScratchPad/GNUmakefile Tests/GPU/ScratchPad/Make.package Tests/GPU/ScratchPad/inputs_3d Tests/GPU/ScratchPad/main.cpp Tests/GPU/ScratchPad/run.script Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/Evolve.cpp Tutorials/GPU/ElectromagneticPIC/inputs Tutorials/GPU/ElectromagneticPIC/summitdev.sh Tutorials/GPU/ElectromagneticPIC_1/Constants.H Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.H Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_1/Evolve.H Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_1/GNUmakefile Tutorials/GPU/ElectromagneticPIC_1/IO.H Tutorials/GPU/ElectromagneticPIC_1/IO.cpp Tutorials/GPU/ElectromagneticPIC_1/Make.package Tutorials/GPU/ElectromagneticPIC_1/NodalFlags.H Tutorials/GPU/ElectromagneticPIC_1/NodalFlags.cpp Tutorials/GPU/ElectromagneticPIC_1/Particles.H Tutorials/GPU/ElectromagneticPIC_1/StructOfArrays.H Tutorials/GPU/ElectromagneticPIC_1/em_pic_3d.F90 Tutorials/GPU/ElectromagneticPIC_1/em_pic_F.H Tutorials/GPU/ElectromagneticPIC_1/inputs Tutorials/GPU/ElectromagneticPIC_1/main.cpp Tutorials/GPU/ElectromagneticPIC_1/make.out Tutorials/GPU/ElectromagneticPIC_1/summit.sh Tutorials/GPU/ElectromagneticPIC_1/summitdev.sh Tutorials/GPU/ElectromagneticPIC_1/test.cpp Tutorials/GPU/ElectromagneticPIC_2/Constants.H Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.H Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_2/Evolve.H Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_2/GNUmakefile Tutorials/GPU/ElectromagneticPIC_2/IO.H Tutorials/GPU/ElectromagneticPIC_2/IO.cpp Tutorials/GPU/ElectromagneticPIC_2/Make.package Tutorials/GPU/ElectromagneticPIC_2/NodalFlags.H Tutorials/GPU/ElectromagneticPIC_2/NodalFlags.cpp Tutorials/GPU/ElectromagneticPIC_2/Particles.H Tutorials/GPU/ElectromagneticPIC_2/StructOfArrays.H Tutorials/GPU/ElectromagneticPIC_2/em_pic_3d.F90 Tutorials/GPU/ElectromagneticPIC_2/em_pic_F.H Tutorials/GPU/ElectromagneticPIC_2/inputs Tutorials/GPU/ElectromagneticPIC_2/main.cpp Tutorials/GPU/ElectromagneticPIC_2/script.nompi.sh Tutorials/GPU/ElectromagneticPIC_2/summit.sh Tutorials/GPU/ElectromagneticPIC_2/summitdev.sh Tutorials/GPU/ElectromagneticPIC_2/test.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Exec/run.ascent Tutorials/GPU/HeatEquation_EX1_C/Exec/run.nocuda.script Tutorials/GPU/HeatEquation_EX1_C/Exec/run.summit Tutorials/GPU/HeatEquation_EX1_C/Exec/run.summitdev Tutorials/GPU/HeatEquation_EX1_C/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Make.package Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H Tutorials/GPU/HeatEquation_EX1_C/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/init_phi_2d.f90 Tutorials/GPU/HeatEquation_EX1_C/init_phi_3d.f90 Tutorials/GPU/HeatEquation_EX1_C/inputs_2d Tutorials/GPU/HeatEquation_EX1_C/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/main.cpp Tutorials/GPU/HeatEquation_EX1_C/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H Tutorials/GPU/HeatEquation_EX1_C/physbc.cpp Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/run_summit_1node.sh Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/Make.package Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/advance_2d.f90 Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/advance_3d.f90 Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/init_phi_2d.f90 Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/init_phi_3d.f90 Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/myfunc.H Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/myfunc_F.H Tutorials/GPU/Readme.txt commit 2c2f779f371425ba325e2a487abceb6b036baf08 Author: Cy Chan Date: Mon Oct 29 14:31:35 2018 -0700 MLMG: add cache for bottom-solve MPI sub-communicators MPI_Comm_create() is expensive and is called for every gravity solve remove some BL_PROFILE_REGION Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 90daca52c65dda8bfbcd30d0332ddb3f30c53e15 Merge: 67384a33d 8faebca49 Author: Guy Moore Date: Mon Oct 29 16:38:38 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 67384a33d2d62934af1bd788d710fdefac1e0622 Author: Guy Moore Date: Mon Oct 29 16:36:44 2018 -0700 First commit of MUI-coupling tutorial Tutorials/MUI/Exec_01/GNUmakefile Tutorials/MUI/Exec_02/GNUmakefile Tutorials/MUI/Exec_coupled/cmd_mpirun Tutorials/MUI/Exec_coupled/inputs Tutorials/MUI/Source_01/Make.package Tutorials/MUI/Source_01/init_phi_3d.f90 Tutorials/MUI/Source_01/main_01.cpp Tutorials/MUI/Source_01/myfunc.H Tutorials/MUI/Source_01/myfunc_F.H Tutorials/MUI/Source_02/Make.package Tutorials/MUI/Source_02/main_02.cpp Tutorials/MUI/Source_02/myfunc.H Tutorials/MUI/doc/GNUmakefile Tutorials/MUI/doc/MUIcouplingNotes.tex Tutorials/MUI/doc/iface_rect.png Tutorials/MUI/doc/vis_interface.m commit 71dafe50f2ec780e19db7b515b42380701b70bb5 Author: Cy Chan Date: Mon Oct 29 14:29:43 2018 -0700 change makeSFC() to use box volume instead of just 1.0 for weights should improve load balancing for consolidated multigrid levels Src/Base/AMReX_DistributionMapping.cpp commit 3808405a6a51a4a29235b5c897f5e7cf0ddeb8ed Author: Lawrence Minion Date: Mon Oct 29 14:12:56 2018 -0700 Added multi-implicit capability Src/SDC/AMReX_SDCstruct.H Src/SDC/AMReX_SDCstruct.cpp commit 8faebca4988624a8bba8afe196afbfe4c9aaae90 Author: Ann Almgren Date: Mon Oct 29 12:22:37 2018 -0700 "conn" in 3d has 27 not 12 components Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 5151270cce8c80d6235b5b7b334e335215505a8a Author: Ann Almgren Date: Mon Oct 29 12:22:06 2018 -0700 Formatting for easier reading Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit efda8adbd37a120594284769f2f6f237846b4aa5 Author: Ann Almgren Date: Mon Oct 29 12:21:49 2018 -0700 Fix typo: "coarest" --> "coarsest" Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 9253860d1913c6d807d54cf860182913a25f6331 Merge: 2ebb5b5eb ffce8dd68 Author: Ann Almgren Date: Mon Oct 29 12:20:58 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 2ebb5b5eb9d6fd18363e317d24818d407126491a Author: Ann Almgren Date: Mon Oct 29 12:20:15 2018 -0700 1) Fix typo in newu -- should be (i,j,k,2) not (i,j,2,k) 2) add eps to the denominator when we create sten(i,j,k,ist_inv) -- mimicing 2d Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 8861eec1e4bd9e90385880aba7f04d4b5a9dba04 Author: Weiqun Zhang Date: Mon Oct 29 11:54:09 2018 -0700 update Src/Base/AMReX_Box.H Src/Base/AMReX_COORDSYS_1D.cpp Src/Base/AMReX_COORDSYS_2D.cpp Src/Base/AMReX_COORDSYS_3D.cpp Src/Base/AMReX_COORDSYS_C.H Src/Base/AMReX_CoordSys.cpp commit ffce8dd6825a86a9191c208fca2256b33f38be90 Author: Michele Rosso Date: Mon Oct 29 10:30:39 2018 -0700 Fix typo in Makefile Src/Particle/Make.package commit 38e50ecc98eabf388dd821c0bab58b0fc73900eb Merge: 55268c973 d8d2b4f37 Author: Ann Almgren Date: Mon Oct 29 10:18:09 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 55268c973f89cd3d68cb831034dcecfc0c78e62e Author: Ann Almgren Date: Mon Oct 29 10:17:45 2018 -0700 Make sure that the direction of a cylinder is in the range [0:AMREX_SPACEDIM-1] not [0:AMREX_SPACEDIM] Src/EB/AMReX_EB2.cpp commit d8d2b4f37a5efcaef22187ec0bfad455312d1789 Author: Andrew Myers Date: Mon Oct 29 09:55:32 2018 -0700 fix restart Src/Particle/AMReX_ParticleContainerI.H commit 6fb2d3eecc35d78db25a312e9abc7c4d33fb211b Merge: 53d95a4b5 0c568ccd3 Author: Weiqun Zhang Date: Mon Oct 29 09:50:43 2018 -0700 Merge branch 'development' into weiqun/gpu commit 55eb9c58db32f2116b1c1693b926b5e1ba2ac473 Author: Ann Almgren Date: Sun Oct 28 20:21:29 2018 -0700 Add the 3D EB nodal stencil. Note that we haven't yet computed the integrals -- this just goes from the 19 core integrals to "conn" to "sten" -- we still need to include the computation of the vol, S_x, S_x^2 integrals etc. Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 0c568ccd3857d29374f4605e7d7282e824851889 Merge: 7fbc66c4e 765e93c09 Author: Weiqun Zhang Date: Sat Oct 27 20:39:37 2018 -0700 Merge branch 'gpu-merge-test' into development commit 765e93c095c81c67418a875cbae5c7a03ba84f66 Author: Weiqun Zhang Date: Sat Oct 27 20:30:25 2018 -0700 udpate build Src/Base/CMakeLists.txt Tools/libamrex/configure.py commit 6236953c9793e7b1b9615ac0fea23d5e1eb4ff1f Author: Weiqun Zhang Date: Sat Oct 27 23:17:28 2018 -0400 simplification Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_GpuLaunch.H commit 39f5fa9b35e180836a9dd59077523f8d09595b51 Author: Weiqun Zhang Date: Sat Oct 27 21:16:57 2018 -0400 add cpu and device version for the range macro Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_GpuLaunch.H commit 2a9b3972d80ca49dec80ae91c6217a3fc57b5dd6 Author: Weiqun Zhang Date: Sat Oct 27 17:57:26 2018 -0700 add Cuda::Range so that we can use the same macro for int and Box Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaRange.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuLaunch.H Src/Base/CMakeLists.txt Src/Base/Make.package commit cb94ca9f609e10f8c28ec0f12a264c8634248e10 Author: Weiqun Zhang Date: Sat Oct 27 11:50:47 2018 -0700 some renaming Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.cpp commit b18cdae149120db47010c35bb94a214dad6cb8e8 Author: Lawrence Minion Date: Fri Oct 26 17:18:29 2018 -0700 Nuking old Heat Equation Example Tutorials/SDC/HeatEquation_EX1_C/GNUmakefile Tutorials/SDC/HeatEquation_EX1_C/Make.package Tutorials/SDC/HeatEquation_EX1_C/advance.cpp Tutorials/SDC/HeatEquation_EX1_C/advance_2d.f90 Tutorials/SDC/HeatEquation_EX1_C/advance_3d.f90 Tutorials/SDC/HeatEquation_EX1_C/init_phi_2d.f90 Tutorials/SDC/HeatEquation_EX1_C/init_phi_3d.f90 Tutorials/SDC/HeatEquation_EX1_C/inputs_2d Tutorials/SDC/HeatEquation_EX1_C/inputs_3d Tutorials/SDC/HeatEquation_EX1_C/main.cpp Tutorials/SDC/HeatEquation_EX1_C/myfunc.H Tutorials/SDC/HeatEquation_EX1_C/myfunc_F.H Tutorials/SDC/HeatEquation_EX1_C/pf_quadrature.f90 commit a832e81015429843797f1be47a20137291b28a32 Author: Lawrence Minion Date: Fri Oct 26 17:16:13 2018 -0700 Changing example name to reflect IMEX advection diffusion Tutorials/SDC/IMEX_Advec_Diff_C/GNUmakefile Tutorials/SDC/IMEX_Advec_Diff_C/Make.package Tutorials/SDC/IMEX_Advec_Diff_C/advance.cpp Tutorials/SDC/IMEX_Advec_Diff_C/advance_2d.f90 Tutorials/SDC/IMEX_Advec_Diff_C/init_phi_2d.f90 Tutorials/SDC/IMEX_Advec_Diff_C/init_phi_3d.f90 Tutorials/SDC/IMEX_Advec_Diff_C/inputs_2d Tutorials/SDC/IMEX_Advec_Diff_C/inputs_3d Tutorials/SDC/IMEX_Advec_Diff_C/main.cpp Tutorials/SDC/IMEX_Advec_Diff_C/myfunc.H Tutorials/SDC/IMEX_Advec_Diff_C/myfunc_F.H commit 13ca64a783647f7c0c2695b32e7a43e876fa21b1 Author: Lawrence Minion Date: Fri Oct 26 17:14:27 2018 -0700 Reworked Tutorial to have a modular SDC form Src/SDC/AMReX_SDCquadrature.F90 Src/SDC/AMReX_SDCstruct.H Src/SDC/AMReX_SDCstruct.cpp Src/SDC/Make.package Tutorials/SDC/HeatEquation_EX3_C/Make.package Tutorials/SDC/HeatEquation_EX3_C/advance.cpp Tutorials/SDC/HeatEquation_EX3_C/advance_2d.f90 Tutorials/SDC/HeatEquation_EX3_C/init_phi_2d.f90 Tutorials/SDC/HeatEquation_EX3_C/inputs_2d Tutorials/SDC/HeatEquation_EX3_C/main.cpp Tutorials/SDC/HeatEquation_EX3_C/myfunc.H Tutorials/SDC/HeatEquation_EX3_C/myfunc_F.H commit 7fbc66c4e2d3935f2ef736880083c090f291398a Merge: 1e5a3fe9c ffcbf4f44 Author: Ann Almgren Date: Fri Oct 26 16:52:39 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 1e5a3fe9cf5c525aa6264544a23b38863c677947 Author: Ann Almgren Date: Fri Oct 26 16:45:52 2018 -0700 Cleaned up notation a little -- no functional change Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit ffcbf4f44251e8db10ea962a0d96bec2e4675f4e Author: Weiqun Zhang Date: Fri Oct 26 16:25:28 2018 -0700 add regression test inputs Tests/LinearSolvers/NodeEB/inputs.rt.2d commit 6164cc521ec926c5230c261dd9a04e0221f462ef Author: Weiqun Zhang Date: Fri Oct 26 16:08:36 2018 -0700 Nodal EB test Tests/LinearSolvers/NodeEB/GNUmakefile Tests/LinearSolvers/NodeEB/Make.package Tests/LinearSolvers/NodeEB/MyTest.H Tests/LinearSolvers/NodeEB/MyTest.cpp Tests/LinearSolvers/NodeEB/initEB.cpp Tests/LinearSolvers/NodeEB/inputs Tests/LinearSolvers/NodeEB/main.cpp commit 70d83427535d98b918a10dc536f598e37c2e8fe4 Merge: ac9ac4fe1 a685ebe0b Author: WeiqunZhang Date: Fri Oct 26 13:41:30 2018 -0700 Merge pull request #333 from AMReX-Codes/gpu-merge-test gpu-mm branch into development. commit a685ebe0b4f611912408ae89db3d017302b44d43 Author: Weiqun Zhang Date: Fri Oct 26 16:34:03 2018 -0400 fix include in BLFort.H Src/Base/AMReX_BLFort.H commit 75c3501849f8d6d288a1584011c0af2e2d3e27ce Author: Weiqun Zhang Date: Fri Oct 26 12:43:05 2018 -0700 fix some remaining issues of the reorganization Src/Base/AMReX_CudaContainers.H Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_GpuLaunch.H commit 61c498d2a326cc77e5f05da24774b9e911a57901 Author: Weiqun Zhang Date: Fri Oct 26 11:17:45 2018 -0700 update cuda qualifier Src/Base/AMReX_CudaUtility.H commit 309dd1a9f14e110e8590a86a66de37354b33369f Author: Weiqun Zhang Date: Fri Oct 26 11:14:22 2018 -0700 update the cuda script Tools/F_scripts/write_cuda_headers.py commit 56cce79c0d51be9ad2e67b6740e7ab2b569f8507 Author: Weiqun Zhang Date: Fri Oct 26 10:54:51 2018 -0700 fix the merge Src/Base/AMReX_Geometry.H Src/Particle/AMReX_Functors.H commit c398a6b48286fccf9ecd7d15d49f239a788c7e37 Merge: 5cb5b7a8f 9fbff2b57 Author: Weiqun Zhang Date: Fri Oct 26 10:51:21 2018 -0700 Merge branch 'gpu-merge-test2' into gpu-merge-test commit 5cb5b7a8f7e93e0eda92f7aef809b827ca48b4ab Author: Weiqun Zhang Date: Fri Oct 26 10:48:43 2018 -0700 add namespace alias Gpu and hide the name cuda from users Src/Base/AMReX_GpuControl.cpp commit 89a32cf2116277362cb2980d066f6838f8c9a94b Author: Weiqun Zhang Date: Fri Oct 26 10:42:23 2018 -0700 add namespace alias Gpu and hide the name cuda from users Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_GpuControl.H commit c57a165f27753158dbc958dae012eb265e342eec Author: Weiqun Zhang Date: Fri Oct 26 10:34:18 2018 -0700 add namespace alias Gpu and hide the name cuda from users Src/Amr/AMReX_Amr.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_Array.H Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BArena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_Cuda.H Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaContainers.H Src/Base/AMReX_CudaDevice.H Src/Base/AMReX_CudaDevice.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_CudaQualifiers.H Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_CudaUtility.cpp Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_Gpu.H Src/Base/AMReX_GpuControl.H Src/Base/AMReX_GpuControl.cpp Src/Base/AMReX_GpuLaunch.H Src/Base/AMReX_GpuQualifiers.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_Orientation.H Src/Base/AMReX_RealBox.H Src/Base/AMReX_iMultiFab.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Src/EB/AMReX_MultiCutFab.H Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_Particle.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_StructOfArrays.H Tests/GPU/TestC/main.cpp Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.defs Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/main.cpp Tutorials/GPU/HelloWorld_C/main.cpp commit 9fbff2b57d15688e2b2a5482707cff3c73a1c068 Merge: 523c86ba5 6255c37d2 Author: Andrew Myers Date: Fri Oct 26 10:50:25 2018 -0400 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit 523c86ba50dbf41daedf5e7514a4c5840bd65cf0 Author: Andrew Myers Date: Fri Oct 26 10:50:03 2018 -0400 start to work on particle tiling for GPU Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_ParticleContainerI.H commit 6255c37d2512eb382346bf021604aca5400dcaba Author: atmyers Date: Thu Oct 25 23:35:23 2018 -0400 fix NumberOfParticlesAtLevel Src/Particle/AMReX_ParticleContainerI.H commit 94710fac5624846ddbe9ef0d93e7eaa07e1b1121 Author: Andrew Myers Date: Thu Oct 25 23:00:05 2018 -0400 remove functors from AMReX_Particles.H Src/Particle/AMReX_Particles.H commit 5ac787888c199d5bba35e2db1bef921ce95a5f73 Author: Andrew Myers Date: Thu Oct 25 22:52:11 2018 -0400 template the setPosition functor on particle type Src/Particle/AMReX_ParIterI.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 860f4c88cb581ccfc357395c4d92e01583a77db7 Author: Andrew Myers Date: Thu Oct 25 22:51:40 2018 -0400 move functors to separate file Src/Particle/AMReX_Functors.H commit c0d30e018379f90f4b6baf3fdeac1a44a29a7853 Author: Andrew Myers Date: Thu Oct 25 22:51:11 2018 -0400 fix bug introduced Src/Particle/AMReX_ParticleContainerI.H commit 316539153bf0af44072f86e55671e4fa560e869c Author: Andrew Myers Date: Thu Oct 25 22:11:31 2018 -0400 use the new managed objects in the thrust functors Src/Particle/AMReX_ParticleContainerI.H commit 48de6feaab5ce99e07136ec1e0ab2f60f6894f50 Author: Andrew Myers Date: Thu Oct 25 22:11:14 2018 -0400 add isPeriodic to GeometryData Src/Base/AMReX_Geometry.H commit 29182d9e1a0e892bef85b7de09e9f30e62c8b821 Author: Andrew Myers Date: Thu Oct 25 21:25:32 2018 -0400 use the AMREX_CUDA_HOST_DEVICE macro Src/Particle/AMReX_ParticleContainerI.H commit 3e3458a432662ee604b7159889eeab205b9b5b85 Author: Weiqun Zhang Date: Thu Oct 25 17:39:44 2018 -0700 tidy Src/Base/AMReX_Arena.cpp commit 41bd87262672d01b560163973087d525f3b19a5e Merge: 8e21373da 90c477529 Author: Weiqun Zhang Date: Thu Oct 25 20:25:44 2018 -0400 Merge branch 'gpu-merge-test2' into gpu-merge-test commit 8e21373da351fd6c17996fc4aa87f38e04a209e1 Merge: 1b4fa0932 ac9ac4fe1 Author: Weiqun Zhang Date: Thu Oct 25 20:25:33 2018 -0400 Merge branch 'development' into gpu-merge-test commit 90c4775297c61575ee33007b8e02dc413eec9899 Author: Weiqun Zhang Date: Thu Oct 25 20:24:03 2018 -0400 reorganize arenas. Managed class uses the managed arena. remove BaseFab Fortran functions Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_CudaMemory.H Src/Base/Make.package commit 537b8bc1bb2f6cee9e323b9833a1d0f849a6cfd0 Author: Andrew Myers Date: Thu Oct 25 16:01:25 2018 -0400 do not sort the grids here. Src/Particle/AMReX_ParticleContainerI.H commit bfc0fa5bcd267c99d226dc5dedce51eb0aaefbae Author: Andrew Myers Date: Thu Oct 25 15:41:48 2018 -0400 function to sort particles be cell if desired Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 7295a6d377f9ce6307e65ea96859572047cf2d20 Author: Andrew Myers Date: Thu Oct 25 10:32:43 2018 -0400 also use it in the call to sort_by_dest Src/Particle/AMReX_ParticleContainerI.H commit c5f02c1fccb8281e7f70bb97c495e2f213b75bf4 Author: Andrew Myers Date: Thu Oct 25 10:32:24 2018 -0400 simply use The_Cuda_Arena() internally for thrust Src/Base/AMReX_CudaAllocators.H commit f6d27a51c218afaa5c82cd4d01935e42133b70b6 Author: Weiqun Zhang Date: Wed Oct 24 14:44:53 2018 -0700 make sure communication work with non-cuda-aware mpi Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit b8bf689a998fcfc764eaa8d4753afd29de66caa8 Author: Weiqun Zhang Date: Wed Oct 24 14:27:06 2018 -0700 arena reorganization Src/Base/AMReX.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 65be25d3d36fdbfbf151767063e478dba6e0e157 Author: Weiqun Zhang Date: Wed Oct 24 16:49:42 2018 -0400 the cuda arena based on CArena and cudaMalloc Src/Base/AMReX_Arena.H Src/Base/AMReX_FabArrayBase.cpp commit fc0a642c83d71187766bb42b5958cc05bb677704 Author: Minion Date: Wed Oct 24 13:35:45 2018 -0700 Creating SDCstruct library in Src Src/SDC/AMReX_SDCstruct.H Src/SDC/AMReX_SDCstruct.cpp Src/SDC/Make.package commit 62cf619a1c9b909d1a8a4e964e013ebba1af12d0 Author: Minion Date: Wed Oct 24 13:34:25 2018 -0700 moving SDC arrays into struct Tutorials/SDC/HeatEquation_EX3_C/GNUmakefile Tutorials/SDC/HeatEquation_EX3_C/Make.package Tutorials/SDC/HeatEquation_EX3_C/SDCstruct.H Tutorials/SDC/HeatEquation_EX3_C/advance.cpp Tutorials/SDC/HeatEquation_EX3_C/main.cpp Tutorials/SDC/HeatEquation_EX3_C/myfunc.H commit 967a220b2aff75f0ee3e5de2d9dcfd70bb581970 Author: Andrew Myers Date: Wed Oct 24 16:21:01 2018 -0400 also keep the recv buffers around to avoid cudaMalloc costs Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit ac9ac4fe11dcbb7e563bc034525ca28de35848fd Author: Tan Nguyen Date: Wed Oct 24 12:44:50 2018 -0700 regular AMFiter update Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AsyncFillPatch.cpp Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Perilla/Barrier.cpp Src/AmrTask/rts_impls/Perilla/Make.package Src/AmrTask/rts_impls/Perilla/Perilla.H Src/AmrTask/rts_impls/Perilla/Perilla.cpp Src/AmrTask/rts_impls/Perilla/PerillaConfig.H Src/AmrTask/rts_impls/Perilla/PerillaRts.H Src/AmrTask/rts_impls/Perilla/PerillaRts.cpp Src/AmrTask/rts_impls/Perilla/RGIter.H Src/AmrTask/rts_impls/Perilla/RGIter.cpp Src/AmrTask/rts_impls/Perilla/RegionGraph.H Src/AmrTask/rts_impls/Perilla/RegionGraph.cpp Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/Perilla_upc++/Barrier.cpp Src/AmrTask/rts_impls/Perilla_upc++/Make.package Src/AmrTask/rts_impls/Perilla_upc++/Perilla.H Src/AmrTask/rts_impls/Perilla_upc++/PerillaConfig.H Src/AmrTask/rts_impls/Perilla_upc++/RGIter.H Src/AmrTask/rts_impls/Perilla_upc++/RGIter.cpp Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.H Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/GNUmakefile Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.cpp Src/Base/AMReX_MultiFabUtil_Perilla.cpp commit 74cb6ab1e506203146a90694213735c4efdc27a9 Author: Lawrence Minion Date: Wed Oct 24 11:51:28 2018 -0700 making constructor for SDCstruct Tutorials/SDC/HeatEquation_EX3_C/SDCstruct.H Tutorials/SDC/HeatEquation_EX3_C/advance.cpp Tutorials/SDC/HeatEquation_EX3_C/main.cpp Tutorials/SDC/HeatEquation_EX3_C/myfunc.H Tutorials/SDC/HeatEquation_EX3_C/myfunc_F.H commit 8832b2c8c5629fa34371e321f4ed217037cd13fa Merge: 63f719d71 0438f560c Author: Andrew Myers Date: Wed Oct 24 13:30:34 2018 -0400 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit 63f719d71504c19b4addd8cd5931118aec7aab51 Author: Andrew Myers Date: Wed Oct 24 13:30:00 2018 -0400 fix DEBUG build for gpu Src/Particle/AMReX_ParticleContainerI.H commit 0438f560c9f7ea95e937d364598d0c790c19b445 Author: Kevin Gott Date: Wed Oct 24 13:27:59 2018 -0400 Wrap nvvp naming with appropriate directives. Src/Base/AMReX.H Src/Base/AMReX.cpp commit 826e9f269ca57d66c7790328e0aeeb830bb292f8 Merge: b83a116e0 9f99a1c67 Author: Andrew Myers Date: Wed Oct 24 13:21:35 2018 -0400 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit b83a116e05b5549425c6fc53ab5eb47817255f58 Author: Andrew Myers Date: Wed Oct 24 13:18:49 2018 -0400 fix circular includes Src/Base/AMReX_CudaAllocators.H commit 9f99a1c67880c5fc68465d235385616a5d8b404b Author: Weiqun Zhang Date: Wed Oct 24 08:41:23 2018 -0700 check thread safety when using cuda Src/Base/AMReX_FabArrayBase.cpp commit 63bc8312cbaf1e40baa9c062d08074710fea198e Author: Weiqun Zhang Date: Wed Oct 24 08:41:00 2018 -0700 these static functions are host only Src/Base/AMReX_BaseFab.H commit 8b2b99c7c464e73101e475fee48cb5890673e975 Author: Weiqun Zhang Date: Wed Oct 24 08:35:10 2018 -0700 remove unused variable Src/Base/AMReX_FabArrayBase.cpp commit 92a1b84de41dfa0841d757f2edbdb83293be2334 Author: Kevin Gott Date: Wed Oct 24 11:44:19 2018 -0400 Add profiler wrapper to Device's init to clearly identify Cuda driver and Cuda API startups in nvvp. Src/Base/AMReX.H Src/Base/AMReX.cpp commit eb5dde28a2c6701858df41a624488416340150f5 Author: Andrew Myers Date: Wed Oct 24 11:20:51 2018 -0400 clean up a little bit. Src/Base/AMReX_CudaAllocators.cpp commit 48ed7472cdb79291c760bc8624ab4a0a654fcc7f Author: Andrew Myers Date: Wed Oct 24 11:10:06 2018 -0400 comments Src/Base/AMReX_CudaContainers.H commit a06eb9f571a15c096187ec06ca3b099b79f5aa5a Author: Andrew Myers Date: Wed Oct 24 11:07:32 2018 -0400 restore the managed version of std::vector (could be useful elsewhere) Src/Base/AMReX_CudaContainers.H commit 0cb3608d69a0f2c721eefbbf102de95ffd9cf5c7 Author: Andrew Myers Date: Wed Oct 24 11:02:29 2018 -0400 rename ManagedVector -> ManagedDeviceVector Src/Base/AMReX_CudaContainers.H Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_StructOfArrays.H commit 0a29562201ab2e8a32942f70e8ee58717d13daa5 Author: Andrew Myers Date: Wed Oct 24 10:55:49 2018 -0400 add missing ifdef Src/Base/AMReX_CudaAllocators.cpp commit 557a9a76a307e4da8f7db96578ec0054f427a48b Author: Andrew Myers Date: Wed Oct 24 10:49:06 2018 -0400 add stub from compiling fcompare in Tools/Postprocessing/C_Src Tools/Postprocessing/C_Src/GNUmakefile commit 903e77cca560dfc489873ca4528743cffb733ada Author: Andrew Myers Date: Wed Oct 24 10:42:01 2018 -0400 use preallocated buffer for mpi communication in RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit f90fe630f4f2f4e6101bbf1999012ef311cc20b3 Author: Andrew Myers Date: Wed Oct 24 10:40:57 2018 -0400 use the ThrustManagedAllocator in the Thrust calls in RedistributeGPU Src/Base/AMReX.cpp Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaAllocators.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit b6131ba1b6248fc37c45ec675c335d94c9a57bae Author: Andrew Myers Date: Wed Oct 24 10:03:52 2018 -0400 adding a ThrustCachedAllocator for calls to thrust::sort and thrust::partition Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaContainers.H commit d1ce3e7f80ea8fa5b9814468f63db076c207b69f Author: Weiqun Zhang Date: Tue Oct 23 21:36:45 2018 -0700 fix thread safety Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_CudaUtility.cpp Src/Base/AMReX_FabArrayCommI.H commit 1629d511d857ffecad77c92bae17b0063825a4b2 Author: Weiqun Zhang Date: Tue Oct 23 17:00:58 2018 -0700 fix omp for StreamIter Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_CudaUtility.cpp Src/Base/AMReX_FabArrayCommI.H commit c24fb524352c2b3bb3b8ad0d154a4780c58986a6 Merge: c3b307b93 0e6efde14 Author: Andrew Myers Date: Tue Oct 23 19:32:36 2018 -0400 Merge branch 'gpu-fb' into gpu-merge-test2 commit c3b307b9358b428692cb471411d10202ceadf72b Author: Andrew Myers Date: Tue Oct 23 19:31:16 2018 -0400 make The_FA_Arena used the managed CArena (from weiqun) Src/Base/AMReX_FabArrayBase.cpp commit 0e6efde141eafca0ac373fe3a658daf848529f70 Author: Weiqun Zhang Date: Tue Oct 23 15:24:35 2018 -0700 use one buffer for all send data Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H commit cfa0eaae30bb45a7bfd459dfa011bfc82a1d47b0 Merge: feacbc658 40ead55e1 Author: Lawrence Minion Date: Tue Oct 23 14:50:20 2018 -0700 Merge branch 'SDC' of https://github.com/AMReX-Codes/amrex into SDC commit feacbc65867ed76d108b6eaaf06527daa865560d Author: Lawrence Minion Date: Tue Oct 23 14:49:42 2018 -0700 changing example size Tutorials/SDC/HeatEquation_EX1_C/GNUmakefile Tutorials/SDC/HeatEquation_EX1_C/inputs_2d commit b7f3fc328a3e59b27d848befdcff55ba9d4f100e Author: Weiqun Zhang Date: Tue Oct 23 14:44:56 2018 -0700 use one buffer for all recv data Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit b454232ae53a9344ea95876b0fbfb6ce1ef53c8c Merge: e61209937 717aefe9e Author: Weiqun Zhang Date: Tue Oct 23 14:20:06 2018 -0700 Merge branch 'gpu-comm-malloc' into gpu-fb commit 717aefe9e4bb96fb60825ede45f5d87d0b2c7136 Merge: 5de1483b2 b6de7a841 Author: Weiqun Zhang Date: Tue Oct 23 14:17:15 2018 -0700 Merge branch 'gpu-merge-test2' into gpu-comm-malloc commit b6de7a841fa9595ae2faf4a59fbc4770d5150284 Author: Andrew Myers Date: Tue Oct 23 16:15:56 2018 -0400 changes needed by the new Cuda::ManagedVector Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_TracerParticles.cpp commit b87b9301b53074c8d2164fa59d2a369887e2e498 Author: Andrew Myers Date: Tue Oct 23 16:14:55 2018 -0400 use thrust as the underlying container type for Cuda::ManagedVector Src/Base/AMReX_CudaContainers.H commit 03f081a63d960bb31c17f07f011d85b0607719e7 Author: Andrew Myers Date: Tue Oct 23 16:14:17 2018 -0400 add custom allocator for use with thrust::device_vector Src/Base/AMReX_CudaAllocators.H commit 67518a4f8735e78864e0ede8b10fc1c5b1c63cf3 Author: Kevin Gott Date: Tue Oct 23 16:10:08 2018 -0400 Revert "Async FillBoundary kernel calls. Further testing/tweaking required." This reverts commit e97874816bccf9c426b192fe22100d6e185f2cd2. Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit a78779eafd3ea737d23faae6e12ab4d433a34255 Author: Kevin Gott Date: Tue Oct 23 16:09:46 2018 -0400 Revert "Revert "Add first draft of ASYNC macro and CPU versions of other macros."" This reverts commit e15f53cbdad4384d63298fab0cf33983216dd871. Src/Base/AMReX_CudaLaunch.H commit e15f53cbdad4384d63298fab0cf33983216dd871 Author: Kevin Gott Date: Tue Oct 23 16:07:23 2018 -0400 Revert "Add first draft of ASYNC macro and CPU versions of other macros." This reverts commit d5186eb8c5051a0463e64ce8fe8c48fe8626c7fe. Src/Base/AMReX_CudaLaunch.H commit e61209937ed4aec73e142c73dbf30ee8e9481754 Author: Weiqun Zhang Date: Tue Oct 23 15:54:07 2018 -0400 remove _async Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 1b26cb4daeb975ad16203417c932b416c292b530 Author: Weiqun Zhang Date: Tue Oct 23 15:29:58 2018 -0400 WIP: StreamIter Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_FabArrayCommI.H commit e97874816bccf9c426b192fe22100d6e185f2cd2 Author: Kevin Gott Date: Tue Oct 23 12:32:49 2018 -0400 Async FillBoundary kernel calls. Further testing/tweaking required. Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit d5186eb8c5051a0463e64ce8fe8c48fe8626c7fe Author: Kevin Gott Date: Tue Oct 23 12:31:10 2018 -0400 Add first draft of ASYNC macro and CPU versions of other macros. Src/Base/AMReX_CudaLaunch.H commit 842a711be6466015d6f137d28149aaf048d93c00 Author: Kevin Gott Date: Tue Oct 23 12:29:59 2018 -0400 GPU-ize another norm function. Src/Base/AMReX_MultiFab.cpp commit 13b5f19b75db5fa0cfd187b544665f61c83fcf91 Merge: eedcf1d17 c23349772 Author: Andrew Myers Date: Tue Oct 23 00:04:26 2018 -0400 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit eedcf1d1750aa9e452fe7526b3200af0135c1d81 Author: Andrew Myers Date: Tue Oct 23 00:03:42 2018 -0400 further reduce the number of memory allocations in RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 53d95a4b59491e321c731edd55c5a9e61af63ab9 Author: Weiqun Zhang Date: Mon Oct 22 18:15:47 2018 -0700 update header name Src/Base/AMReX_CoordSys.cpp commit c8586b61ad75a7d2edd8ce2b6a59711fc02841cd Author: Weiqun Zhang Date: Mon Oct 22 18:15:07 2018 -0700 rename for typecheck Src/Base/AMReX_COORDSYS_C.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 814b8773616d954d91356bdfb3a2cb659e85cf0c Author: Weiqun Zhang Date: Mon Oct 22 17:58:51 2018 -0700 CoordSys: Fortran -> C++ and GPU Src/Base/AMReX_Box.H Src/Base/AMReX_COORDSYS_1D.F90 Src/Base/AMReX_COORDSYS_1D.cpp Src/Base/AMReX_COORDSYS_2D.F90 Src/Base/AMReX_COORDSYS_2D.cpp Src/Base/AMReX_COORDSYS_3D.F90 Src/Base/AMReX_COORDSYS_3D.cpp Src/Base/AMReX_COORDSYS_F.H Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_Geometry.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit ddee8db74e6a3bb49f016fd7ce9d9b25cc335a45 Merge: ad376e6ce 221c5a255 Author: Marc Day Date: Mon Oct 22 17:31:29 2018 -0700 Merge pull request #351 from burlen/sensei_adaptor_bugfix sensei data adaptor fixes commit 221c5a255302e7206dcf047122a0db6611622c86 Author: Burlen Loring Date: Mon Oct 22 15:15:27 2018 -0700 sensei data adaptor fixes * set data set origin, fixes issue with simulations where the lower left corner in physical space is not at 0,0,0 * fix a memory leak in AmrMeshDataAdaptor * let simulations set control parameters explicilty * validate control parameters during initialization Src/Extern/SENSEI/AMReX_AmrDataAdaptor.cpp Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.cpp Src/Extern/SENSEI/AMReX_InSituBridge.H Src/Extern/SENSEI/AMReX_InSituBridge.cpp commit c23349772678299dfb6577422c8c7b31ec7fcda4 Author: Kevin Gott Date: Mon Oct 22 17:31:09 2018 -0400 First attempt at a triple macro for (i, j, k) equivalent flux calls. Src/Base/AMReX_CudaLaunch.H commit d7799ee3d171e5c707eda56bf4052e28d3831785 Merge: b051fff63 b580f51d9 Author: Andrew Myers Date: Mon Oct 22 16:15:32 2018 -0400 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit b051fff6371899f56ebe69198b1189af6aecfa27 Author: Andrew Myers Date: Mon Oct 22 16:15:08 2018 -0400 avoid repeatedly reallocating memory on the GPU Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 5de1483b2931314733afa90ce5d8f97c165f43e5 Author: Weiqun Zhang Date: Mon Oct 22 13:08:25 2018 -0700 rm deprecated upc++ stuff OldTutorials/PGAS_HEAT/GNUmakefile OldTutorials/PGAS_HEAT/Make.package OldTutorials/PGAS_HEAT/advance_3d.f90 OldTutorials/PGAS_HEAT/init_phi_3d.f90 OldTutorials/PGAS_HEAT/inputs_3d OldTutorials/PGAS_HEAT/main.cpp OldTutorials/PGAS_HEAT/test-mpi3/main.cpp OldTutorials/PGAS_HEAT/writePlotFile.H OldTutorials/PGAS_HEAT/writePlotFile.cpp Src/Base/AMReX.cpp Src/Base/AMReX_BLPgas.H Src/Base/AMReX_BLPgas.cpp Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Tests/FillBoundaryComparison/GNUmakefile Tests/FillBoundaryComparison/main.cpp commit 622b4886e007bf8a5a4e5daf4e278bcd09342f16 Author: Andrew Myers Date: Mon Oct 22 14:57:49 2018 -0400 remove page faults from RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H commit ad376e6ce33b5af896fd6e0510f548c8154056d9 Author: Weiqun Zhang Date: Mon Oct 22 11:10:08 2018 -0700 fix a bug in 1d interpolation thanks to Zhonglin Li Src/AmrCore/AMReX_INTERP_1D.F90 commit b580f51d93eb7ba0860b854a298f5e58e70a6529 Author: Kevin Gott Date: Mon Oct 22 12:55:59 2018 -0400 Fix MultiFab reduction locations in some functions. Src/Base/AMReX_MultiFab.cpp commit eba26e1b87bcdee08a82ddbf1293bc5001d352c1 Author: Kevin Gott Date: Mon Oct 22 12:45:34 2018 -0400 Add Cuda namespace to HeatEquation & add script for OLCF Ascent. Tutorials/GPU/HeatEquation_EX0_C/Exec/run.ascent Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp commit f0522d233060090007f2ee6de1d645ac1bd1aa34 Author: Weiqun Zhang Date: Mon Oct 22 09:23:17 2018 -0700 fix typo Src/Base/AMReX_CudaLaunch.H commit dfd2a06a7cf9847e00b84272f4fd43bfc17de3e8 Author: Ann Almgren Date: Sun Oct 21 17:50:23 2018 -0700 Add the gradient operation for 3D EB nodal -- this is in the mknewu routine. Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 78698624591ac90c23e0e380cf55d263d0466354 Author: Ann Almgren Date: Sun Oct 21 13:44:05 2018 -0700 Add the 3D EB divergence stencil Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 5952cd8706c1d95c2590ba5e277334491ee72047 Merge: 50b168a12 3effacd61 Author: Weiqun Zhang Date: Sun Oct 21 13:22:08 2018 -0700 Merge branch 'gpu-merge-test3' into gpu-merge-test2 commit 3effacd61be9ec1f7d27ffbdf96b6376f786f6f4 Author: Weiqun Zhang Date: Sun Oct 21 16:15:46 2018 -0400 tweak threading trying to be more page friendly Src/Base/AMReX_CudaLaunch.H commit 50b168a12af0d818db0df27afff56f1b255c48f5 Author: Kevin Gott Date: Sun Oct 21 13:15:16 2018 -0400 Small, partial changes. Src/Base/AMReX_MultiFab.cpp commit 3145dcb7a79bb20645adf093621f8d18303754fc Author: Weiqun Zhang Date: Sat Oct 20 13:38:35 2018 -0700 rm Managed as Base of Box and RealBox. namespace reorganization: amrex::Cuda::Atomic::Add etc. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_RealBox.H commit 1cfd6f6e70d724821e1c4379db74d0e8f377b81e Author: Weiqun Zhang Date: Sat Oct 20 10:46:13 2018 -0700 try to avoid potential name conflict Src/Base/AMReX_CudaLaunch.H commit c3b85aff79d51946760c4d672dc11ea1d6b8b3da Author: Weiqun Zhang Date: Sat Oct 20 10:42:49 2018 -0700 put Strategy and getThreadBox into namespace Cuda Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_FArrayBox.cpp commit 272c5f695410b4af9c761d6a33ad7ae140cf4515 Author: Weiqun Zhang Date: Fri Oct 19 21:52:02 2018 -0700 int -> long and inline Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp commit f3496ee8b6f015d474b35896b110f3181823fae7 Merge: 11a138912 9a7850d44 Author: Kevin Gott Date: Fri Oct 19 22:17:33 2018 -0400 Merge branch 'gpu-merge-test3' of https://github.com/AMReX-Codes/amrex into gpu-merge-test3 commit 11a138912b5480e7ee16539c23dd153e887a98c4 Author: Kevin Gott Date: Fri Oct 19 22:17:25 2018 -0400 Better/(fixed(?)) version of the 1D thread box. Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp commit ef6746b65a474180e719340c899d461e94615220 Merge: c9de04b6b 8416218ae Author: Marc Day Date: Fri Oct 19 17:44:31 2018 -0700 Merge pull request #346 from burlen/amrmesh_bug_fix fix a bug in sensei AmrMeshDataAdaptor commit 9a7850d449316a404718e2a46b4d62bccd817af7 Merge: 73bac1d4b 9fae0a04c Author: Weiqun Zhang Date: Fri Oct 19 17:39:03 2018 -0700 Merge branch 'gpu-merge-test2' into gpu-merge-test3 commit 9fae0a04cedc44206683579f51cc36111e49b223 Author: Andrew Myers Date: Fri Oct 19 17:23:53 2018 -0700 make ManagedVector::assign run either on the CPU or GPU depending on Cuda::inLaunchRegion Src/Base/AMReX_CudaContainers.H commit 511bb792b34ae4be94f07e9656f7c88cac62961c Author: Andrew Myers Date: Fri Oct 19 17:21:18 2018 -0700 double -> Real Src/Particle/AMReX_Particles.H commit bd6b0f6b920d9b6b80e463257bf92690ff51fed7 Author: Andrew Myers Date: Fri Oct 19 17:15:41 2018 -0700 fix get / set particles for 2D Src/Particle/AMReX_Particles.H commit 2a3c5898766f7e5fb1b365651c6613ee27f2a1eb Author: Andrew Myers Date: Fri Oct 19 16:56:22 2018 -0700 use Cuda::ManagedVector in Particles Src/Base/AMReX_CudaContainers.H Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_StructOfArrays.H commit 8416218aef70d73c3702202c4bef3aa2b7ddeb99 Author: Burlen Loring Date: Fri Oct 19 16:53:08 2018 -0700 fix a bug in sensei AmrMeshDataAdaptor ref ratios may be empty if only 1 level, and cleanup some code in the tutorial that should not have been committed. Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 333bb4050f6182d8df0d12bb959fe1a884594789 Author: Andrew Myers Date: Fri Oct 19 16:32:35 2018 -0700 add HostVector and ManagedVector, move to a different file. Src/Base/AMReX_Cuda.H Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_CudaContainers.H Src/Base/AMReX_Vector.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 91326c5e8ee36eb63a01ed98cb1d0336b2de236a Author: Andrew Myers Date: Fri Oct 19 16:27:51 2018 -0700 remove executable permissions from these source files. Src/Base/AMReX_MultiFabUtil_Perilla.H Src/Base/AMReX_MultiFabUtil_Perilla.cpp commit 5b3fbd0f7f41420c4f01f73b03a7865c18c37469 Author: Andrew Myers Date: Fri Oct 19 16:16:39 2018 -0700 add dataPtr() wrapper to ArrayOfStructs Src/Particle/AMReX_ArrayOfStructs.H commit 35586c4839633a5e1e83e35badbe76b9a32c2c26 Author: Andrew Myers Date: Fri Oct 19 15:59:09 2018 -0700 use a template function to reduce code duplication Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit b5a55b0235d467e20f21c4e40c220a168ed0ae67 Author: Andrew Myers Date: Fri Oct 19 15:55:37 2018 -0700 mn -> mx again Src/Base/AMReX_MultiFab.cpp commit aa2284aea9b3acaebf3fee65b136a7bcbf0c49e1 Author: Andrew Myers Date: Fri Oct 19 15:55:13 2018 -0700 mn -> mx Src/Base/AMReX_MultiFab.cpp commit 4e23aa2432ff8b0abde2de1a28b3854b950492cf Author: Andrew Myers Date: Fri Oct 19 15:54:45 2018 -0700 add missing if Src/Base/AMReX_MultiFab.cpp commit a72c44636fa55974944cd4e7b051b5cf133a90ab Merge: 86ddc9845 5e6f81c78 Author: Andrew Myers Date: Fri Oct 19 15:53:22 2018 -0700 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit 73bac1d4bfc2a3dd37f6eaa37b4ddfc8b5c73964 Merge: 04b9866de 5e6f81c78 Author: Weiqun Zhang Date: Fri Oct 19 15:14:53 2018 -0700 Merge branch 'gpu-merge-test2' into gpu-merge-test3 commit 04b9866de714ef21b7aa5d0943b56e66cc2e4051 Author: Kevin Gott Date: Fri Oct 19 18:12:26 2018 -0400 fix launches. Src/Base/AMReX_CudaLaunch.H commit 86ddc98456ba2da67f69f735f52081cc5a78e8e5 Author: Andrew Myers Date: Fri Oct 19 14:52:31 2018 -0700 give DeviceVector an assign method Src/Base/AMReX_Vector.H commit de4aed5058d95c1a0486d815e96b8fc2d54713b4 Author: Kevin Gott Date: Fri Oct 19 17:47:29 2018 -0400 Launch macros with striding. Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp commit 5e6f81c7876e3c69760db1c9945c32065c1e5f87 Merge: aae00b159 3663e3556 Author: Weiqun Zhang Date: Fri Oct 19 14:40:42 2018 -0700 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit 789ec15f2f3b00e03082161c917aa9ca3281a01b Author: Andrew Myers Date: Fri Oct 19 14:31:22 2018 -0700 give both device and managed versions of Get / Set Position to ParIter Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit 032a6e9abd45b7f73a6b230c40b88b7ac29fd62f Author: Andrew Myers Date: Fri Oct 19 14:08:07 2018 -0700 use DeviceVector in the ParIter Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit c77f544cb7cb5db60792d1e0474b64b837cbf7e4 Author: Andrew Myers Date: Fri Oct 19 14:07:34 2018 -0700 add a wrapper around thrust::device_vector that does the raw_pointer_cast for you Src/Base/AMReX_Vector.H commit 83e88bc291ea473cc89488802387eef02e1b59f4 Merge: ad9b2422d c9de04b6b Author: Cy Chan Date: Fri Oct 19 13:57:02 2018 -0700 Merge branch 'development' into cy-perf commit ad9b2422d41a06de524313640efd52fd139347f2 Author: Cy Chan Date: Mon Oct 15 16:22:54 2018 -0700 add verbose_mapper flag and detailed messages for DistributionMapping Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_ParallelContext.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 3663e3556fcb693030c75d4651950569de7f82a4 Author: Kevin Gott Date: Fri Oct 19 16:31:54 2018 -0400 Testing safe for USE_CUDA=FALSE Tutorials/GPU/HelloWorld_C/main.cpp commit 6e928cda2515a3f93fb14e8e18a180f79aeab623 Author: Kevin Gott Date: Fri Oct 19 16:30:09 2018 -0400 Starting MultiFab::norm conversions with norm0. Src/Base/AMReX_MultiFab.cpp commit 0181e1ffa0ef0039f3b627b39953875839bcf605 Author: Weiqun Zhang Date: Fri Oct 19 16:19:46 2018 -0400 new strategy Src/Base/AMReX_Box.H Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp commit aae00b1593adff0e32f7796ab4a4ca12b0017265 Author: Weiqun Zhang Date: Fri Oct 19 10:52:32 2018 -0700 add AMReX_Cuda.H so that the user only needs to include this one header. add operator<< for printing dim3. Src/Base/AMReX_Cuda.H Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_CudaUtility.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 663a0ccda84f293c103b5b49c29626d62af709c3 Merge: f4b98ac39 d7763752c Author: Andrew Myers Date: Thu Oct 18 21:22:55 2018 -0400 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit f4b98ac395d991347e91791f74e011f8361c469f Author: Andrew Myers Date: Thu Oct 18 21:22:28 2018 -0400 add a nice hack to the Ascent makefile so you don't have to mess with CPATH to build Tools/GNUMake/sites/Make.olcf commit d7763752c955374e021fd4ac9741041cf46c9527 Author: Weiqun Zhang Date: Thu Oct 18 17:40:31 2018 -0700 move ptr identification functions to amrex::Cuda:: in AMReX_CudaUtility.H Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 77e413592db6b454a6dcfcda767e9c797f77d797 Merge: f8336006e 34279d587 Author: Andrew Myers Date: Thu Oct 18 17:19:46 2018 -0700 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit 34279d587b305bcaa3e93e7356ec379a573ed37e Author: Weiqun Zhang Date: Thu Oct 18 13:31:06 2018 -0700 fix bugs Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_Device.cpp commit f8336006efa9d9ab89d7cbcf1234b70074cfef3e Author: Andrew Myers Date: Thu Oct 18 17:15:38 2018 -0700 only use thrust::device_vector in Get / Set Position if Cuda is on. Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit ec4a8db5772117cdda281fa1e32c6df828c9b1d7 Author: Kevin Gott Date: Thu Oct 18 19:51:53 2018 -0400 Wrap Utility for USE_CUDA=FALSE Src/Base/AMReX_CudaUtility.H commit fa0c021a0807540103dcd5aaca616791a57c37e8 Author: Kevin Gott Date: Thu Oct 18 19:50:57 2018 -0400 Fix DeviceScalar. Src/Base/AMReX_CudaMemory.H commit 65f17202f3dba8def313a2272c0138a4bd1ab38f Author: Kevin Gott Date: Thu Oct 18 19:30:41 2018 -0400 Max and Min changes and test case. Src/Base/AMReX_MultiFab.cpp Tutorials/GPU/HelloWorld_C/main.cpp commit fccc7da68dff5f23da8b8511b26bca3233ed2646 Author: Weiqun Zhang Date: Thu Oct 18 09:35:21 2018 -0700 add inline so that it compiles Src/Base/AMReX_CudaUtility.H commit a357913fddb967b9f520d44024ea9d8039ef58eb Author: Weiqun Zhang Date: Thu Oct 18 09:32:41 2018 -0700 fix typo Src/Base/AMReX_CudaUtility.H commit 1b6e52296808a8ea2dbb29087a7e29465c9c16e7 Author: Kevin Gott Date: Thu Oct 18 03:17:15 2018 -0400 First draft of GPU MultiFab::min and max. Needs testing. Fix in sum. Src/Base/AMReX_MultiFab.cpp commit 850ca7b99d27c6a7bb4038f174d13c972535d140 Author: Kevin Gott Date: Thu Oct 18 03:15:13 2018 -0400 atomicMin and atomicMax for float and double. Src/Base/AMReX_CudaUtility.H commit c8548e91b34ca265b86aefe989fa30b75009095d Author: Kevin Gott Date: Wed Oct 17 20:12:39 2018 -0400 GPU versions of Dot, Dotmask, initVal and Sum. Src/Base/AMReX_MultiFab.cpp commit 8b28c2b9a4422232273678b74e11a5dbddd92fdf Author: Andrew Myers Date: Wed Oct 17 17:04:38 2018 -0700 Device::inLaunchRegion() -> Cuda::inLaunchRegion() Src/Base/AMReX_MultiFab.cpp commit 1d6ae19d0c6c5743a0c971df199428e1f5571103 Author: Andrew Myers Date: Wed Oct 17 19:55:20 2018 -0400 use macro instead of template thing here Src/Base/AMReX_TypeTraits.H Src/Particle/AMReX_ParticleContainerI.H commit 5d8e28d67b9242a8e1b9a2c18f099476c320297f Merge: 3cc671420 552f0252f Author: Andrew Myers Date: Wed Oct 17 16:42:46 2018 -0700 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit 3cc671420414e414c24ec9d73ed7a6ef1fa136ef Author: Andrew Myers Date: Wed Oct 17 16:42:21 2018 -0700 always have this compile-time check return true if the gcc version is too old to support it Src/Base/AMReX_TypeTraits.H commit 552f0252fb104cbd2fbe4514699f208bc5bd2b66 Author: Weiqun Zhang Date: Wed Oct 17 16:14:03 2018 -0700 put FabArray::initVal on GPU Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.cpp commit c770bc52070b7f1afdc7db2717c8d3e89bfa2019 Author: Weiqun Zhang Date: Wed Oct 17 16:12:50 2018 -0700 int -> long in 1d Strategy Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit f8433622c712dbe49b0aa5d1d28b4319bc04d557 Merge: cee4866cc 1b4fa0932 Author: Weiqun Zhang Date: Wed Oct 17 15:40:51 2018 -0700 Merge branch 'gpu-merge-test' into gpu-merge-test2 commit 1b4fa0932bed42f242ed72b0a170360c079ac992 Merge: 1c6c2c543 c9de04b6b Author: Weiqun Zhang Date: Wed Oct 17 15:40:28 2018 -0700 Merge branch 'development' into gpu-merge-test commit c9de04b6bc954eeeab467fbc221db0f5e7a87420 Author: Weiqun Zhang Date: Wed Oct 17 15:38:09 2018 -0700 CArena: make sure memory blocks from different allocations are not coalesced, otherwise cuda complains about invalid argument in cudaMemcpy. Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp commit cee4866ccc65968b89c57083e19b6d9ef35f9ea1 Author: Weiqun Zhang Date: Wed Oct 17 15:38:09 2018 -0700 CArena: make sure memory blocks from different allocations are not coalesced, otherwise cuda complains about invalid argument in cudaMemcpy. Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp commit 474fdf549b9325be5cd1dd47864b4e767249f1fc Author: Weiqun Zhang Date: Wed Oct 17 11:31:04 2018 -0700 add some Cuda error checks Src/Base/AMReX_CudaLaunch.H commit b2bd5bd71669421e2870fc62fcb4ffb481f9a824 Author: Ann Almgren Date: Wed Oct 17 15:07:45 2018 -0700 Fix a problem that was causing us to lose particles in a triply periodic domain. In the case that required this fix, which used single precision particles, the particle's location was only slightly outside the low domain, but the periodic shift put the particle exactly on the high boundary. The solution is to move the particle to the low boundary when the domain is periodic and the particle lies exactly on the high boundary. The particle will then live in the first cell along the low boundary rather than being labeled as out of bounds outside the high boundary. Src/Particle/AMReX_ParticleContainerI.H commit acacbab977bb7596c6149af640b83fc4984e72b1 Author: Andrew Myers Date: Wed Oct 17 15:06:03 2018 -0700 fix typo in new constructor Src/Particle/AMReX_Particles.H commit cb4c5faa794dd04499288bbbe36a2ec7ea034d69 Merge: cffcd15ba 45138fbd4 Author: Andrew Myers Date: Wed Oct 17 14:13:08 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit cffcd15bab274b3b4e412dc5260d91bb7390a4e9 Author: Andrew Myers Date: Wed Oct 17 14:12:55 2018 -0700 add some ifdefs for when HDF5 is not on Tests/HDF5Benchmark/WritePlotfileHDF5.H Tests/HDF5Benchmark/WritePlotfileHDF5.cpp Tests/HDF5Benchmark/main.cpp commit 45138fbd4a2d4bb8a4e471a21660d26fbaf92e4b Author: Andrew Myers Date: Wed Oct 17 14:03:52 2018 -0700 read nppc from inputs file Tests/HDF5Benchmark/inputs commit 1f0a379555637124a40da161d994b1f96e979967 Author: Andrew Myers Date: Wed Oct 17 14:01:53 2018 -0700 change default compiler to intel Tests/HDF5Benchmark/GNUmakefile commit 9556b63c262223946fbfde56be7a54f5d042a58e Author: Andrew Myers Date: Wed Oct 17 14:00:35 2018 -0700 add Particle IO to the HDF5Benchmark Tests/HDF5Benchmark/GNUmakefile Tests/HDF5Benchmark/main.cpp commit ec02d203a8f02ce016d8f559788ce298086bdff5 Author: Andrew Myers Date: Wed Oct 17 14:00:17 2018 -0700 add new constructor to ParticleContainer Src/Particle/AMReX_Particles.H commit 90b279922532e4c1f05cabcabc6e7ad85ad06657 Merge: 5ee51995a 1aca796ae Author: Andrew Myers Date: Wed Oct 17 15:14:01 2018 -0400 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit 5ee51995a5b14489060ccd896affb6013b3f2954 Author: Andrew Myers Date: Wed Oct 17 15:13:33 2018 -0400 also assert that the particle type is trivially copyable Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 6d887f3b40d1c60eea1c58d4cefaab22532160a5 Author: Andrew Myers Date: Wed Oct 17 15:13:12 2018 -0400 add a new template to work around the fact that gcc < 5 doesn't have std::is_trivially_copyable Src/Base/AMReX_TypeTraits.H commit 077141f4cd6e0e1c1e8973dc32b44cce020a4206 Merge: bef95aee8 1d78ad5f9 Author: WeiqunZhang Date: Wed Oct 17 10:25:36 2018 -0700 Merge pull request #344 from jared321/intersectionInFortran Intersection in fortran commit 1aca796aef4c24c1a2ab9f65a6baba10f1125f64 Author: Weiqun Zhang Date: Wed Oct 17 10:03:45 2018 -0700 change strides back to 1 again Src/Base/AMReX_CudaLaunch.H commit 5b18bffc1eca1c57af848961fc54477fe227abec Author: Weiqun Zhang Date: Wed Oct 17 09:38:05 2018 -0700 shift the box so that the smallend is zero. this will make threading consistent for same size boxes Src/Base/AMReX_CudaLaunch.H commit 1d78ad5f9866957126be3aadc06c0d29c713baaa Author: Jared O'Neal Date: Wed Oct 17 11:31:31 2018 -0500 Intersection is no longer done by using C++ routines. It is handled directly in the Fortran box module. Src/F_Interfaces/Base/AMReX_box_fi.cpp Src/F_Interfaces/Base/AMReX_box_mod.F90 commit c993c1b5d0e383cb91c03e1332fe974cbf5be695 Author: Weiqun Zhang Date: Wed Oct 17 00:13:38 2018 -0400 change strides to 1 till we fix the bug Src/Base/AMReX_CudaLaunch.H commit 40d9cdb19982422c58f6be48308143c5599b5f75 Author: Weiqun Zhang Date: Tue Oct 16 17:25:31 2018 -0700 new Strategy giving more work to threads Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_MultiFab.cpp Tutorials/GPU/HelloWorld_C/inputs_3d Tutorials/GPU/HelloWorld_C/main.cpp commit afec298e37620f67d6dbf25d4d5614aa3b0326c6 Merge: 97eb06a5a 1c6c2c543 Author: Andrew Myers Date: Tue Oct 16 20:08:31 2018 -0400 Merge branch 'gpu-merge-test' into gpu-merge-test2 commit 97eb06a5ae75b233e66e70e5a8ab836f7ef8d0e6 Merge: 542762a68 2b42f69dc Author: Andrew Myers Date: Tue Oct 16 19:54:12 2018 -0400 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit 542762a68f0c72e99333546c5016a60955eba256 Author: Andrew Myers Date: Tue Oct 16 19:53:41 2018 -0400 relax the assumption that the particle type must be POD Src/Particle/AMReX_ParticleContainerI.H commit 32840f308ba21930321a317a11c7de7fb330c888 Author: Andrew Myers Date: Tue Oct 16 19:53:20 2018 -0400 give particle a constructor marked host/device Src/Particle/AMReX_Particle.H commit 2b42f69dc920288dd0fc2d48e122889a085c65e5 Author: Kevin Gott Date: Tue Oct 16 19:42:04 2018 -0400 Correct inputs for Dot test. Tutorials/GPU/HelloWorld_C/inputs_3d Tutorials/GPU/HelloWorld_C/inputs_geometry commit 706e81e7b32c150885153fe17c26d131b0536196 Author: Kevin Gott Date: Tue Oct 16 19:39:27 2018 -0400 Dot test. Tutorials/GPU/HelloWorld_C/main.cpp Tutorials/GPU/HelloWorld_C/run.script commit 85d28b4d011f4c536dd8e77ffa75f187912bca62 Author: Weiqun Zhang Date: Tue Oct 16 15:21:19 2018 -0700 update DeviceScalar so that it works outside launch region Src/Base/AMReX_CudaMemory.H commit 977490bee138aaaffe6a0a20ab9de2f7f323ba8a Author: Weiqun Zhang Date: Tue Oct 16 15:16:32 2018 -0700 Device::inLaunchRegion -> Cuda::inLaunchRegion so that we can access the flag without including AMReX_Device.H Src/Base/AMReX_CudaControl.H Src/Base/AMReX_CudaControl.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Tools/F_scripts/write_cuda_headers.py commit bef95aee815d4a5b3a374753a276a555cf323f23 Merge: ec10bcd50 6c4502f31 Author: Marc Day Date: Tue Oct 16 14:57:25 2018 -0700 Merge pull request #339 from burlen/sensei_insitu_development Sensei insitu development commit 46ce15270972adede511b8b4071f35253f4364e4 Author: Andrew Myers Date: Tue Oct 16 17:33:28 2018 -0400 make MultiFab::OverrideSync() launchable Src/Base/AMReX_MultiFab.cpp commit dc0a172a2b63ce21cb8cab24a711954de774beff Merge: bac5a1517 bd26abbe3 Author: Andrew Myers Date: Tue Oct 16 17:23:30 2018 -0400 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit bd26abbe385f1fa6367faac6e7819bba820010bc Author: Weiqun Zhang Date: Tue Oct 16 13:08:39 2018 -0700 remove HostDeviceScalar Src/Base/AMReX_CudaMemory.H commit 7ba2891dc0b8d34b1910f4d0a4397279a6df49b8 Author: Jared O'Neal Date: Tue Oct 16 15:04:39 2018 -0500 Added box intersection routine in Fortran interface. Src/F_Interfaces/Base/AMReX_box_fi.cpp Src/F_Interfaces/Base/AMReX_box_mod.F90 commit bac5a1517b548d2170678436276a9f80880d008d Author: Andrew Myers Date: Tue Oct 16 15:59:12 2018 -0400 fix parameter shadowing Src/Particle/AMReX_ParticleContainerI.H commit ed5302819a64ef6fbd4c950e21ae80f23fe2e10b Author: Andrew Myers Date: Tue Oct 16 14:30:22 2018 -0400 remove AtomicAccumulate method from ParticleContainer in favor of the one from BaseFab. Src/Particle/AMReX_Particles.H commit 694d60e5dd8e6f85ba856be7d7152f5e88d0c967 Author: Andrew Myers Date: Tue Oct 16 14:27:27 2018 -0400 fix atomicAdd implementation Src/Base/AMReX_BaseFab.H commit 14f48a1c6485cce5f40338862a01a5e360324aac Author: Andrew Myers Date: Tue Oct 16 14:24:24 2018 -0400 finish implementing atomicAdd for BaseFab Src/Base/AMReX_BaseFab.H commit f2fa505f07865d706cb7aef274e204048c1db74d Author: Andrew Myers Date: Tue Oct 16 14:16:43 2018 -0400 start to implement atomicAdd for BaseFab Src/Base/AMReX_BaseFab.H commit 260b53169badaa760b91dfc60ea6b2ea3d9ccf06 Author: Michele Rosso Date: Mon Oct 15 15:09:23 2018 -0700 CMake: fix bug in STRIP macro Tools/CMake/AMReX_Utils.cmake commit 5a5d8727ed77d662573e8e5c31f52edc43f47921 Merge: 1339cfbd2 6a9d88715 Author: Andrew Myers Date: Tue Oct 16 13:56:58 2018 -0400 Merge branch 'gpu-merge-test' into gpu-merge-test2 commit 1339cfbd2fa0586c355ecabc94d16ee13d16a7d8 Author: Weiqun Zhang Date: Tue Oct 16 10:52:51 2018 -0700 move atomics to CudaUtility.H, add DeviceScalar, and simplify reduction for MultiFab::Dot Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_TypeTraits.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 6a9d88715bf57f1619697a441785ea377d39cd2c Author: Andrew Myers Date: Tue Oct 16 02:11:40 2018 -0400 more timers in Multifab Src/Base/AMReX_MultiFab.cpp commit a38cbc60ce533ebf4bcfd6a795307242c12c6638 Author: Andrew Myers Date: Tue Oct 16 00:24:53 2018 -0400 C++ version of amrex_atomic_accumulate Src/Particle/AMReX_Particles.H commit 1c6c2c5432dc5dabbe1dd6abb4820180b561c60c Merge: 66c214a96 b8fe354b5 Author: Weiqun Zhang Date: Mon Oct 15 17:50:28 2018 -0700 Merge branch 'gpu-merge-test' of github.com:AMReX-Codes/amrex into gpu-merge-test commit 66c214a96c59e82c627aee0f68df270971912874 Author: Weiqun Zhang Date: Mon Oct 15 17:50:12 2018 -0700 add some Device:synchronize calls to the two step version of parallel copy Src/Base/AMReX_FabArrayCommI.H commit b8fe354b5627348ccc31e49a1c865b5b3bde3236 Author: Kevin Gott Date: Mon Oct 15 20:28:30 2018 -0400 Preliminary GNUMake system for Ascent. Just copy of summit for now. Tools/GNUMake/Make.machines Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/sites/Make.olcf commit ec10bcd50884367156bb763d7949e9bb8dfb00bb Merge: 5733c76f1 ab070f507 Author: Jean M. Sexton Date: Mon Oct 15 17:21:14 2018 -0700 Merge branch 'development' of github.com:amrex-codes/amrex into development commit 5733c76f17dd724503e433f88cfe2edf9e9ae41d Author: Jean M. Sexton Date: Mon Oct 15 17:20:34 2018 -0700 Add basic documentation for new flags Docs/sphinx_documentation/source/CVODE.rst Docs/sphinx_documentation/source/SUNDIALS3.rst commit ab070f5072cacdaf2ab2a205612325eae19c110d Author: Andy Nonaka Date: Mon Oct 15 17:09:25 2018 -0700 wrote a helpful debugging utility, "WriteMLMF" that writes a multilevel plotfile to disk given only: -plotfile name -vector of MultiFabs -vector of Geometrys variable names are written as "Var0", "Var1", etc. refinement ratio is computed from the Geometry vector "time" and "level_steps" are set to zero Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_PlotFileUtil.cpp commit a94c915413c792cf7afe8a0d2bd691d1f421a38c Merge: 955a5f404 0dd78397b Author: Jean M. Sexton Date: Mon Oct 15 17:04:25 2018 -0700 Merge branch 'development' of github.com:amrex-codes/amrex into development commit 955a5f40436f591cfd43601e0b493c8aaf346bbf Author: Jean M. Sexton Date: Mon Oct 15 17:04:18 2018 -0700 Updated make system with new sundials compile flags Src/Extern/SUNDIALS3/Make.package Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.cvode Tools/GNUMake/packages/Make.sundials3 Tutorials/CVODE/SUNDIALS2_finterface/EX1/GNUmakefile Tutorials/CVODE/SUNDIALS2_finterface/EX2/GNUmakefile Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/GNUmakefile Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/main.cpp Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/GNUmakefile Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/main.cpp Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/GNUmakefile Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/SetIC.f90 Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/main.cpp Tutorials/CVODE/SUNDIALS3_finterface/EX1/GNUmakefile Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/GNUmakefile Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/Make.package Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_fp/GNUmakefile Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns/GNUmakefile Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_sys_dns_jac/GNUmakefile Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_brusselator_dns/GNUmakefile commit 0dd78397b1853a9d2b943781d592f69193d8d0cf Author: Michele Rosso Date: Mon Oct 15 15:50:43 2018 -0700 Replace macro D_DECL() with AMREX_D_DECL to comply with XSDK defaults Src/Base/AMReX_ForkJoin.H commit e8179196c88981689b84e62fae9bec3d03701a46 Author: Cy Chan Date: Mon Oct 15 15:43:22 2018 -0700 added software performance counters for MLMG operations smooth, apply, restrict, interpolate turn on with -DAMREX_SOFT_PERF_COUNTERS added some profiling regions for detailed MLMG analysis regions used to tag sends/receives when used with amrprofvis -srlist separate out different MG levels Src/Base/AMReX_MultiFabUtil.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 0f5856290ca27801f0137839f6a24b5ad2fc7785 Author: Weiqun Zhang Date: Mon Oct 15 15:44:57 2018 -0700 add addFromMem and use it for FabArray::ADD Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArrayCommI.H commit 36cec267a68ada9ecd6ea2a5f2ac9c52e5a290b2 Author: Michele Rosso Date: Mon Oct 15 15:09:23 2018 -0700 CMake: fix bug in STRIP macro Tools/CMake/AMReX_Utils.cmake commit aa6f45e6071aa0463c1353e1b72524b2c253b04a Author: Jean M. Sexton Date: Mon Oct 15 14:37:25 2018 -0700 Rearranged Sundials tutorials Tutorials/CVODE/SUNDIALS2_finterface/EX1/GNUmakefile Tutorials/CVODE/SUNDIALS2_finterface/EX1/Make.package Tutorials/CVODE/SUNDIALS2_finterface/EX1/inputs Tutorials/CVODE/SUNDIALS2_finterface/EX1/integrate_ode.f90 Tutorials/CVODE/SUNDIALS2_finterface/EX1/main.cpp Tutorials/CVODE/SUNDIALS2_finterface/EX1/myfunc_F.H Tutorials/CVODE/SUNDIALS2_finterface/EX1/ode_mod.f90 Tutorials/CVODE/SUNDIALS2_finterface/EX2/GNUmakefile Tutorials/CVODE/SUNDIALS2_finterface/EX2/Make.package Tutorials/CVODE/SUNDIALS2_finterface/EX2/inputs Tutorials/CVODE/SUNDIALS2_finterface/EX2/integrate_ode_no_jac.f90 Tutorials/CVODE/SUNDIALS2_finterface/EX2/integrate_ode_with_jac.f90 Tutorials/CVODE/SUNDIALS2_finterface/EX2/main.cpp Tutorials/CVODE/SUNDIALS2_finterface/EX2/myfunc_F.H Tutorials/CVODE/SUNDIALS2_finterface/EX2/ode_mod.f90 Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/GNUmakefile Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/Make.package Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/SetIC.f90 Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/inputs Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/main.cpp Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/myfunc_F.H Tutorials/CVODE/SUNDIALS3_cppversion/EX1_CUDA_NVEC/ode_mod.f90 Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/GNUmakefile Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/Make.package Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/SetIC.f90 Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/inputs Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/main.cpp Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/myfunc_F.H Tutorials/CVODE/SUNDIALS3_cppversion/EX1_GPU_PRAGMA/ode_mod.f90 Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/GNUmakefile Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/Make.package Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/inputs Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/inputs_2box Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/inputs_non_vectorized Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/main.cpp Tutorials/CVODE/SUNDIALS3_cppversion/EX1_SERIAL_NVEC/myfunc_F.H Tutorials/CVODE/SUNDIALS3_finterface/EX1/GNUmakefile Tutorials/CVODE/SUNDIALS3_finterface/EX1/Make.package Tutorials/CVODE/SUNDIALS3_finterface/EX1/inputs Tutorials/CVODE/SUNDIALS3_finterface/EX1/integrate_ode.f90 Tutorials/CVODE/SUNDIALS3_finterface/EX1/main.cpp Tutorials/CVODE/SUNDIALS3_finterface/EX1/myfunc_F.H Tutorials/CVODE/SUNDIALS3_finterface/EX1/ode_mod.f90 Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/GNUmakefile Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/Make.package Tutorials/CVODE/SUNDIALS3_finterface/EX_ark_analytic_fp/ark_analytic_fp.f90 Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_fp/GNUmakefile Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_analytic_fp/Make.package 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Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_brusselator_dns/cv_brusselator_dns.f90 Tutorials/CVODE/SUNDIALS3_finterface/EX_cv_brusselator_dns/cv_brusselator_dns.out Tutorials/CVODE/SUNDIALS4/EX3-CUDA/GNUmakefile Tutorials/CVODE/SUNDIALS4/EX3-CUDA/Make.CVODE Tutorials/CVODE/SUNDIALS4/EX3-CUDA/Make.package Tutorials/CVODE/SUNDIALS4/EX3-CUDA/README.md Tutorials/CVODE/SUNDIALS4/EX3-CUDA/extern_probin.template Tutorials/CVODE/SUNDIALS4/EX3-CUDA/inputs Tutorials/CVODE/SUNDIALS4/EX3-CUDA/inputs_128 Tutorials/CVODE/SUNDIALS4/EX3-CUDA/inputs_256 Tutorials/CVODE/SUNDIALS4/EX3-CUDA/inputs_32 Tutorials/CVODE/SUNDIALS4/EX3-CUDA/inputs_64 Tutorials/CVODE/SUNDIALS4/EX3-CUDA/main.cpp Tutorials/CVODE/SUNDIALS4/EX3-CUDA/make_cuda.sh Tutorials/CVODE/SUNDIALS4/EX3-CUDA/make_cuda_cusolver.sh Tutorials/CVODE/SUNDIALS4/EX3-CUDA/make_serial.sh Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_cuda.cpp Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_cuda_cusolver.cpp Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_serial.cpp Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_system.F90 Tutorials/CVODE/SUNDIALS4/EX3-CUDA/react_utils.F90 Tutorials/CVODE/SUNDIALS4/EX3-CUDA/test_react.H Tutorials/CVODE/SUNDIALS4/EX3-CUDA/test_react_F.H commit d3e7d2fa241862ee6378f7f4e0481544b040ccfd Merge: ed1a621ee 0b0b6ee61 Author: Kevin Gott Date: Mon Oct 15 17:15:07 2018 -0400 Merge branch 'gpu-merge-test' of https://github.com/AMReX-Codes/amrex into gpu-merge-test commit ed1a621ee5461ff445410e69edd08479b2d2ac03 Author: Kevin Gott Date: Mon Oct 15 17:14:50 2018 -0400 Update tutorials to new macros and library names. All successfully compile. Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/GNUmakefile commit 0b0b6ee614313337a6625db94d68f4465d0aab4e Merge: 5c94039ce 254d8c1b2 Author: Andrew Myers Date: Mon Oct 15 16:41:01 2018 -0400 Merge branch 'gpu-merge-test' of github.com:AMReX-Codes/amrex into gpu-merge-test commit 254d8c1b29c57edd3cc98160308ebcccd6c27197 Author: Kevin Gott Date: Mon Oct 15 16:24:44 2018 -0400 AMReX_Device.H included in AMReX_CudaAllocators.H Src/Base/AMReX_CudaAllocators.H commit 5c94039ce9ee08f0e3bea3e5ba5d59c60b5871be Merge: f0c06bcbe 8a3ccfb8f Author: Andrew Myers Date: Mon Oct 15 16:05:39 2018 -0400 Merge branch 'development' into gpu-merge-test commit 8a3ccfb8f259eb1904e78b49b90a93ed36a68615 Merge: 20d365936 a1c1a5e6b Author: Andrew Myers Date: Mon Oct 15 15:43:18 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 20d3659361c4f007a6ad5101c1c4d67fc9adebda Author: Andrew Myers Date: Mon Oct 15 15:42:51 2018 -0400 add a few dimension macros to silence unused variable warnings. Src/Base/AMReX_BaseFab.H commit f0c06bcbe12b31b41b9b8cb0485039e739bdbbca Merge: 63c9754f8 43668dbca Author: Weiqun Zhang Date: Mon Oct 15 12:11:15 2018 -0700 Merge branch 'gpu-merge-test2' into gpu-merge-test commit 43668dbcade3b6fdc01da825bbcfb99522c9568b Author: Weiqun Zhang Date: Mon Oct 15 12:10:46 2018 -0700 fix the_FA_arena initializaiton Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit f27cb8316d2833cbc5b771f5623a6a438c8e9524 Author: Weiqun Zhang Date: Mon Oct 15 11:58:17 2018 -0700 back to the usual version Src/Base/AMReX_FabArrayCommI.H commit 21a5eaf1e8dd9c0beb12e4db06bc2d1f5d6ab34b Author: Weiqun Zhang Date: Mon Oct 15 10:39:19 2018 -0700 add NOBOX version of launch macro Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_FabArrayCommI.H commit 6c4502f316c345c38b6e4a1bb9c8a0ab064b86df Author: Burlen Loring Date: Thu Oct 11 15:09:26 2018 -0700 SENSEI sphinx documentation Docs/sphinx_documentation/source/Visualization.rst Docs/sphinx_documentation/source/Visualization/rt_2048_paraview_000500.png Docs/sphinx_documentation/source/Visualization/rt_2048_visit_000500.png Docs/sphinx_documentation/source/Visualization/sensei_amrex_arch_sm_824.png commit bd5eca87996fb79848bd26227736a500f5967e29 Author: Burlen Loring Date: Thu Apr 19 15:47:10 2018 -0700 SENSEI Integrates the SENSEI in situ framework with AMReX. Adds SENSEI data adaptors, and bridge codes for Amr and AmrMesh classes, and is demonstrated through the Advection AmrLevel and AmrCore SingleVortex Tutorial. .gitignore GNUmakefile.in Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/AmrCore/Make.package Src/CMakeLists.txt Src/Extern/SENSEI/AMReX_AmrDataAdaptor.H Src/Extern/SENSEI/AMReX_AmrDataAdaptor.cpp Src/Extern/SENSEI/AMReX_AmrInSituBridge.H Src/Extern/SENSEI/AMReX_AmrInSituBridge.cpp Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.H Src/Extern/SENSEI/AMReX_AmrMeshDataAdaptor.cpp Src/Extern/SENSEI/AMReX_AmrMeshInSituBridge.H Src/Extern/SENSEI/AMReX_AmrMeshInSituBridge.cpp Src/Extern/SENSEI/AMReX_InSituBridge.H Src/Extern/SENSEI/AMReX_InSituBridge.cpp Src/Extern/SENSEI/AMReX_InSituUtils.H Src/Extern/SENSEI/AMReX_InSituUtils.cpp Src/Extern/SENSEI/CMakeLists.txt Src/Extern/SENSEI/Make.package Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/GNUMake/Make.defs Tools/GNUMake/sites/Make.nersc Tools/GNUMake/tools/Make.sensei Tools/libamrex/configure.py Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Amr/Advection_AmrCore/Exec/Make.Adv Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_catalyst.py Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.session Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.session Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/sensei/write_vtk.xml Tutorials/Amr/Advection_AmrCore/README_SENSEI.md Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt Tutorials/Amr/Advection_AmrLevel/Exec/Make.Adv Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_catalyst.py Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.py Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_2d.xml Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.py Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_catalyst_3d.xml Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.session Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_2d.xml Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.session Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_iso_libsim_3d.xml Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/render_libsim.xml Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/sensei/write_vtk.xml Tutorials/Amr/Advection_AmrLevel/README_SENSEI.md Tutorials/Amr/Advection_AmrLevel/Source/main.cpp commit a1c1a5e6b36f30e60babed681746c811be9878f9 Author: Max Katz Date: Mon Oct 15 05:50:06 2018 -0700 Catch errors in the launch configuration Tools/F_scripts/write_cuda_headers.py commit c8e73c069af2dc2aaddd9b1583567c77a9107a85 Author: Weiqun Zhang Date: Sat Oct 13 16:50:11 2018 -0700 wrap atomic min and max Src/Base/AMReX_CudaLaunch.H commit a084436d79def743d9c2a2011b8419a876a89508 Author: Weiqun Zhang Date: Sat Oct 13 19:01:39 2018 -0400 abort if not in launch region Src/Base/AMReX_CudaLaunch.H commit 5eeb655d8b4af570e77808b2980df6efcca1d697 Author: Weiqun Zhang Date: Sat Oct 13 13:35:55 2018 -0700 add some ifdef AMREX_USE_CUDA so that it compiles without cuda Src/Base/AMReX_CudaMemory.H commit f470da94764575ba0b3a32f482015ee7dd3a61d3 Author: Weiqun Zhang Date: Sat Oct 13 13:19:29 2018 -0700 add a helper function for reduction Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaMemory.H Src/Base/AMReX_MultiFab.cpp commit 84026f1096ae0fe7eaeb45a16cba7dfd9aee6a9b Author: Weiqun Zhang Date: Sat Oct 13 12:29:58 2018 -0700 more gpu stuff to MultiFab and iMultiFab Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.cpp commit 11a6bae96de0f454521cc0467cd716d465eec266 Author: Weiqun Zhang Date: Sat Oct 13 11:17:45 2018 -0700 fix typo; avoid new when copying Src/Base/AMReX_FabArrayCommI.H commit 5cafd447fd3c7645ea98abf7eb824569b6be1ce3 Author: Weiqun Zhang Date: Sat Oct 13 10:18:02 2018 -0700 simplification: as long as we pack and unpack the same way, the buffer does not have to preserve the order in memory Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 5acb45e74323ef8537c2b18495dd11bb31af187a Author: Weiqun Zhang Date: Sat Oct 13 10:00:53 2018 -0700 fix EB CutFab Src/EB/AMReX_MultiCutFab.H commit 64709e1ee51b7efa5eec36b7bb575e5d83f67e58 Author: Weiqun Zhang Date: Sat Oct 13 00:08:04 2018 -0700 FArrayBox -> FAB in template Src/Base/AMReX_FabArrayCommI.H commit 63c9754f88586f11568ef9cfcc0fb1e3a7223f12 Merge: d652ecdab e116d5de1 Author: Weiqun Zhang Date: Sat Oct 13 00:03:15 2018 -0700 Merge branch 'development' into gpu-merge-test commit e116d5de1c7597ca0480a0bdd2eb183779920481 Author: Weiqun Zhang Date: Sat Oct 13 00:01:45 2018 -0700 fix particle for 1 and 2d Src/Particle/AMReX_ParIterI.H commit 053e52f836b845dbf59e60aa0ea77f0371f557bc Author: Weiqun Zhang Date: Sat Oct 13 00:01:45 2018 -0700 fix particle for 1 and 2d Src/Particle/AMReX_ParIterI.H commit 0bed3e5b09bbe3d4397bde69fda865f8d8faaf15 Author: Weiqun Zhang Date: Sat Oct 13 00:01:27 2018 -0700 fix macro name Src/Base/AMReX_FabArrayCommI.H commit 2897d46c3d476dab009d4570152414af31d48330 Author: Weiqun Zhang Date: Fri Oct 12 23:39:42 2018 -0700 finish FabCommI Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 235bf656b6bf2e8e5b9afaf6e9d69c4a3d21e5b6 Merge: a57c5a179 d489b822c Author: Weiqun Zhang Date: Fri Oct 12 21:51:32 2018 -0700 Merge branch 'gpu-merge-test2' of github.com:AMReX-Codes/amrex into gpu-merge-test2 commit a57c5a17999ba1de4cf5ca297338b67bef66ddce Author: Weiqun Zhang Date: Fri Oct 12 21:50:48 2018 -0700 add AMREX_LAUNCH_HOST_DEVICE_LAMBDA Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MultiFab.cpp commit d489b822c563d99f876ac2be144cbe0fa6bc2d2e Author: Kevin Gott Date: Fri Oct 12 17:03:50 2018 -0400 First version of ManagedMemory object for testing. Src/Base/AMReX_CudaMemory.H commit 5e47ce93a5569693c57e178accb8bc7a0e7e16bc Author: Kevin Gott Date: Thu Oct 11 19:31:18 2018 -0400 AMReX_CudaManaged.H -> AMReX_CudaMemory.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_CudaMemory.H Src/Base/CMakeLists.txt Src/Base/Make.package Tests/GPU/Test/main.cpp Tests/GPU/TestB/main.cpp Tests/GPU/TestC/main.cpp commit e154aa7ed3ef7e0782d2565cbc71a62793d04736 Merge: d963236da d652ecdab Author: Weiqun Zhang Date: Fri Oct 12 16:41:07 2018 -0700 Merge branch 'gpu-merge-test' into gpu-merge-test2 commit d652ecdabdf2b87e183803e3952000943309122b Merge: 6ff9981b5 ea1b5802d Author: Weiqun Zhang Date: Fri Oct 12 16:40:26 2018 -0700 Merge branch 'development' into gpu-merge-test commit d963236da799f4e30567e61fc1cd6b9e4e597511 Author: Kevin Gott Date: Fri Oct 12 19:32:34 2018 -0400 Fix MultiFab::Dot launch macro name. Src/Base/AMReX_MultiFab.cpp commit 5ce0145b53e29d0675696b0a7e9329d3022cf8e6 Author: Kevin Gott Date: Fri Oct 12 19:31:10 2018 -0400 First draft of MultiFab::Dot. Included test in GPU/HelloWorld. Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_MultiFab.cpp Tutorials/GPU/HelloWorld_C/main.cpp Tutorials/GPU/HelloWorld_C/run.script commit 9214a0527a6b986e162f465533cc96963cc889a7 Author: Weiqun Zhang Date: Fri Oct 12 19:28:37 2018 -0400 rename launch macros and add AMREX_USE_BASEFAB_CPP Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MultiFab.cpp commit ea1b5802d7ec0dc44e589c32f4567665e555185d Author: Andrew Myers Date: Fri Oct 12 18:26:58 2018 -0400 a testbed for profiling the particle redistribute on GPUs Tests/GPU/Particles/Redistribute/Constants.H Tests/GPU/Particles/Redistribute/GNUmakefile Tests/GPU/Particles/Redistribute/Make.package Tests/GPU/Particles/Redistribute/TestParticleContainer.H Tests/GPU/Particles/Redistribute/TestParticleContainer.cpp Tests/GPU/Particles/Redistribute/inputs Tests/GPU/Particles/Redistribute/main.cpp Tests/GPU/Particles/Redistribute/test_3d.F90 Tests/GPU/Particles/Redistribute/test_F.H commit 55af278d5d15c64af1aac94949e8dfc572296491 Author: Andrew Myers Date: Fri Oct 12 17:48:21 2018 -0400 cut down on the number of temporary memory allocations in RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H commit 1b6c143420f0c8133f8550a0231781fdcdcfb101 Author: Andrew Myers Date: Fri Oct 12 17:35:41 2018 -0400 add finer-grained profiling information to RedistributeGPU Src/Particle/AMReX_ParticleContainerI.H commit 53e85598e2f4ff5fc487e536ba83af3853bf5725 Author: Andrew Myers Date: Fri Oct 12 17:34:52 2018 -0400 minor Src/Particle/AMReX_ParIterI.H commit a863f2b1746d41a8422b152fde69a810a86fb8fa Author: Andrew Myers Date: Fri Oct 12 17:34:15 2018 -0400 use cudaMemAdvise to set the preferred location of managed vector data to the GPU Src/Base/AMReX_CudaAllocators.H commit 6ff9981b50c6332642a0a2896e378d6868d1d12b Author: Kevin Gott Date: Fri Oct 12 17:03:50 2018 -0400 First version of ManagedMemory object for testing. Src/Base/AMReX_CudaMemory.H commit 703d1c1bd48272553253e63addec73268210c4d1 Author: Weiqun Zhang Date: Fri Oct 12 16:12:30 2018 -0400 use ThreadBox instead of ThreadComponentBox Src/Base/AMReX_FabArrayCommI.H commit 8fbd56efac4099d6c22cf60c3ea6adf0a83daaf5 Author: Weiqun Zhang Date: Fri Oct 12 14:33:53 2018 -0400 lambda launch setVal Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_FabArray.H commit ed5baeb6aac91e97a6211f745076cac1183e66da Author: Weiqun Zhang Date: Fri Oct 12 13:33:43 2018 -0400 new ThreadComponentBox function Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_Device.cpp commit 503c9d26b17835950719bf33e14c563d630e4742 Author: Weiqun Zhang Date: Fri Oct 12 01:38:11 2018 -0400 ComponentBox Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_FabArrayCommI.H commit 3968ca2909705c95002e0271cb07334562550875 Author: Weiqun Zhang Date: Thu Oct 11 22:34:12 2018 -0700 fix plus Src/Base/AMReX_FabArrayCommI.H commit 1d06eb512bc935ff09a2cc274d588628d82d43f2 Author: Kevin Gott Date: Thu Oct 11 19:31:18 2018 -0400 AMReX_CudaManaged.H -> AMReX_CudaMemory.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_CudaMemory.H Src/Base/CMakeLists.txt Src/Base/Make.package Tests/GPU/Test/main.cpp Tests/GPU/TestB/main.cpp Tests/GPU/TestC/main.cpp commit 36b963a58a68729b266764e38fc22e337bbb9dbc Author: Weiqun Zhang Date: Thu Oct 11 16:09:35 2018 -0700 use C++ copy Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayCommI.H commit cb7b7663d094cfed70acc656df4579b8ec98a9bd Merge: 9078c3f99 5bd899bfe Author: Andrew Myers Date: Thu Oct 11 18:21:16 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9078c3f99b79139c3f4f2d061965b942e9f9f463 Author: Andrew Myers Date: Thu Oct 11 18:20:50 2018 -0400 GPU-enabled version of get / set particle position Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit d20ef2a3cf02b61cd7b3011a459f3b1041820bbe Author: Andrew Myers Date: Thu Oct 11 17:19:10 2018 -0400 early exit if there are no particles to redistribute Src/Particle/AMReX_ParticleContainerI.H commit 682a1151061f676600550eacc516e552729165ac Merge: c06b9eabb 5bd899bfe Author: Weiqun Zhang Date: Thu Oct 11 11:01:34 2018 -0700 Merge branch 'development' into gpu-merge-test commit 5bd899bfed68f130024535a7265e1e153c041e06 Author: Weiqun Zhang Date: Thu Oct 11 10:55:17 2018 -0700 fix OMP Src/F_Interfaces/Base/AMReX_fab_mod.F90 Tutorials/Amr/Advection_F/Source/compute_dt_mod.F90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 Tutorials/Amr/Advection_octree_F/Source/compute_dt_mod.F90 Tutorials/Amr/Advection_octree_F/Source/evolve_mod.F90 commit ce1bc9871d7cba1ba34fc991cb490d5702a57f1b Merge: 42e928358 6da8d37c9 Author: Andrew Myers Date: Wed Oct 10 19:38:03 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 42e928358b05f0a3125544537d6103e1975d1d5e Author: Andrew Myers Date: Wed Oct 10 19:29:17 2018 -0400 remove early exits, they are wrong Src/Particle/AMReX_ParticleContainerI.H commit c98eb4d1aa741c58e3d8723891b9d929f6578ed1 Author: Andrew Myers Date: Wed Oct 10 19:28:43 2018 -0400 correct for domain offset in assignParticle(), for consistency with CPU version Src/Particle/AMReX_ParticleContainerI.H commit c06b9eabb8984e60ea3c3a0e3dff82af0ee39bcb Author: Weiqun Zhang Date: Wed Oct 10 12:41:52 2018 -0700 fix omp compilation Src/Base/AMReX_Device.cpp Src/Base/Make.package commit 570817d2b761a7d7363a387b4fa6b5cede83248f Author: Andrew Myers Date: Wed Oct 10 15:39:46 2018 -0400 fix copy/paste error Src/Particle/AMReX_ParticleContainerI.H commit 999e02e94beb09d251dd24cf615b00cade1a7565 Author: Weiqun Zhang Date: Wed Oct 10 12:06:03 2018 -0700 fix fortran boxlib compilation Src/Base/AMReX_CArena.cpp commit e824d6d0e002c0f46f40de2eab247d27bc214014 Author: Weiqun Zhang Date: Wed Oct 10 12:00:58 2018 -0700 revert change to TinyProfiler Src/Base/AMReX_TinyProfiler.cpp commit fdecce49f2dc3d9f4593072df38c7902226526cb Merge: 278248839 6da8d37c9 Author: Weiqun Zhang Date: Wed Oct 10 11:57:41 2018 -0700 Merge branch 'development' into gpu-merge-test commit 6da8d37c9ad93a8f81ca666da23a14dfb175b3ca Author: Johannes Blaschke Date: Wed Oct 10 09:56:37 2018 -0700 fix fortran fcompare crash when given nComp=0 plotfile Src/F_BaseLib/bl_IO.f90 Src/F_BaseLib/plotfile.f90 Tools/Postprocessing/C_Src/fcompare.cpp Tools/Postprocessing/F_Src/GNUmakefile Tools/Postprocessing/F_Src/fcompare.f90 commit 9673d70e47191b5d0d58395a4f4f21e2862c4940 Merge: 2b47bf4f5 8204cc067 Author: Andrew Myers Date: Tue Oct 9 20:35:43 2018 -0700 Merge pull request #334 from RemiLehe/cuda_system Set SYSTEM_CUDA_PATH for unknown machine commit 8204cc06763144ffbb34bded77414d836c3c1d1b Author: Remi Lehe Date: Tue Oct 9 20:14:40 2018 -0700 Set SYSTEM_CUDA_PATH for unknown machine Tools/GNUMake/sites/Make.unknown commit 2b47bf4f58b84f7041152b6bfcc544645939f44f Merge: eb41871a3 fa8dd15a0 Author: Johannes Blaschke Date: Tue Oct 9 19:19:13 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit eb41871a387e4c0788f6c4d353bdfb74fc156cd2 Author: Johannes Blaschke Date: Tue Oct 9 19:19:10 2018 -0700 Add feature to write 'just' the header files <- helpful for postprocessing particle-only plotfiles Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp commit fa8dd15a08e3cdcce5c643b4a36e5f084beaca51 Author: Andrew Myers Date: Tue Oct 9 21:17:06 2018 -0400 make sure the requested device number gets passed in to acc_set_device Src/Base/AMReX_CUDA.F90 commit 9b8120ce81558cfb9684e83a282e99707333c593 Author: Andrew Myers Date: Tue Oct 9 21:09:26 2018 -0400 fix RedistributeMPIGPU. Src/Particle/AMReX_ParticleContainerI.H commit 1044002820cfa48eb48173f5df50460a001abf30 Merge: f376bc9cc 28a17a959 Author: Donald E. Willcox Date: Tue Oct 9 20:14:46 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f376bc9cc9e406c9e63f42afdfa38e8d0b1057d8 Author: Donald E. Willcox Date: Tue Oct 9 20:14:29 2018 -0400 Add sample compile lines. Tutorials/CVODE/EX3-CUDA/make_cuda.sh Tutorials/CVODE/EX3-CUDA/make_cuda_cusolver.sh Tutorials/CVODE/EX3-CUDA/make_serial.sh commit 8c2df241bd0f820b1a9aca624e3c42be7b98376d Author: Donald E. Willcox Date: Tue Oct 9 20:14:13 2018 -0400 Add a react example using cuSolver linear algebra for CUDA CVODE. Tutorials/CVODE/EX3-CUDA/GNUmakefile Tutorials/CVODE/EX3-CUDA/Make.CVODE Tutorials/CVODE/EX3-CUDA/Make.package Tutorials/CVODE/EX3-CUDA/README.md Tutorials/CVODE/EX3-CUDA/react_cuda.cpp Tutorials/CVODE/EX3-CUDA/react_cuda_cusolver.cpp Tutorials/CVODE/EX3-CUDA/react_serial.cpp Tutorials/CVODE/EX3-CUDA/test_react.H Tutorials/CVODE/EX3-CUDA/test_react_F.H commit 6dde8c81a8283c3a7c9bcf82c8a51d1b5ac2acbf Author: Donald E. Willcox Date: Tue Oct 9 19:31:44 2018 -0400 Add optional Fortran RHS or C++ RHS to mimic the Fortran RHS interface in StarKiller Microphysics. Tutorials/CVODE/EX3-CUDA/Make.package Tutorials/CVODE/EX3-CUDA/react_cuda.cpp Tutorials/CVODE/EX3-CUDA/react_system.F90 Tutorials/CVODE/EX3-CUDA/react_utils.F90 Tutorials/CVODE/EX3-CUDA/test_react_F.H commit 24bfc3d81c3f3868ecc8d3aa76bb4cc32190734d Author: Donald E. Willcox Date: Tue Oct 9 19:30:44 2018 -0400 Add CVODE libraries to rpath. Define CPP_RHS. Tutorials/CVODE/EX3-CUDA/GNUmakefile Tutorials/CVODE/EX3-CUDA/Make.CVODE commit 27824883905f6478d77e6ad18729ee62c303455c Author: Weiqun Zhang Date: Tue Oct 9 16:14:08 2018 -0700 rm Arena_Initialize from amrex::Initialize Src/Base/AMReX.cpp commit 03e61ad58135e8cb8f8fa6a954d447d3551fba10 Author: Weiqun Zhang Date: Tue Oct 9 16:09:55 2018 -0700 revert changes to the_arena Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp commit 9f97e50fb02c458a8c3c308f2f04dffe59029539 Author: Weiqun Zhang Date: Tue Oct 9 15:35:09 2018 -0700 fix cmake Src/Base/CMakeLists.txt commit 62435cc50b83a31bb59ab96dc85e524631def285 Author: Weiqun Zhang Date: Tue Oct 9 15:16:11 2018 -0700 fix typo Tools/GNUMake/Make.defs commit 2c4e0ce9a8c0fd925cdd7db9e096ca18358c2d50 Author: Weiqun Zhang Date: Tue Oct 9 15:07:03 2018 -0700 move device finalization later after memory poll finalization Src/Base/AMReX.cpp commit 400f7c0e408939d6512ed5fc24f4774ed6e0f489 Author: Weiqun Zhang Date: Tue Oct 9 15:01:03 2018 -0700 comment out a version of getThreadBox Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_FabArrayCommI.H Tutorials/GPU/ElectromagneticPIC/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp commit 6eaa7b8848dfdd606b17d3a3d0ab8ffc7a248bf4 Author: Weiqun Zhang Date: Tue Oct 9 14:42:39 2018 -0700 Revert "Adjust Box+Type launch to match surroundingNodes method." This reverts commit 99cafc8df10acc7f84ec6404bee0dcb6ac41a81c. Src/Base/AMReX_CudaLaunch.cpp commit e4271c5186debc374a4bb41d639238ee1ca231fa Author: Weiqun Zhang Date: Tue Oct 9 14:25:51 2018 -0700 add more AMREX_CUDA_HOST_DEVICE Src/Base/AMReX_Box.H commit 99cafc8df10acc7f84ec6404bee0dcb6ac41a81c Author: Kevin Gott Date: Tue Oct 9 16:16:35 2018 -0400 Adjust Box+Type launch to match surroundingNodes method. Src/Base/AMReX_CudaLaunch.cpp commit 931d561ec567410893c249a1f71e00c36789374f Author: Weiqun Zhang Date: Tue Oct 9 12:51:22 2018 -0700 update ThreadComponentBox Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_Device.cpp Src/Base/AMReX_FabArrayCommI.H commit 4a779682bbbc1bee0da9cdb99b6b3193fcec6b32 Author: Weiqun Zhang Date: Tue Oct 9 11:24:06 2018 -0700 add another simple Strategy Src/Base/AMReX_CudaLaunch.H commit 63946a0c40857ee2a320fdfe766f0042f8ff6870 Author: Weiqun Zhang Date: Tue Oct 9 10:21:39 2018 -0700 fix copy between fab and buffer in FillBoundary Src/Base/AMReX_FabArrayCommI.H commit 6ac0f288617e378b5f02829c8427f92fe1ea0aa0 Author: Weiqun Zhang Date: Tue Oct 9 10:01:51 2018 -0700 for clarity add () Src/Base/AMReX_FabArrayCommI.H commit 0ee5d4ac76390a45794a7654d6534c0a0d6dc223 Merge: 1022620a0 3477509d2 Author: Kevin Gott Date: Tue Oct 9 12:38:27 2018 -0400 Merge branch 'gpu-merge-test' of https://github.com/AMReX-Codes/amrex into gpu-merge-test commit 1022620a01414b70047430eb8c07ce0efe5dce92 Author: Kevin Gott Date: Tue Oct 9 12:38:06 2018 -0400 Add both boxes to the check. Instead add an initial ASSERT or is that done elsewhere? Src/Base/AMReX_FabArrayCommI.H commit 3477509d263d4ab89bdbdd39a5ae54333dae342b Author: Weiqun Zhang Date: Tue Oct 9 09:18:27 2018 -0700 We can still do OMP and tiling if not in launch region and not using pragma gpu Src/Base/AMReX_Device.cpp Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MultiFab.cpp commit 1be78ff2e3e72ecc0be0e4532f4e55d5d7077b1b Author: Kevin Gott Date: Tue Oct 9 11:41:17 2018 -0400 Add missed Box checks to kernel launch functions. Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MultiFab.cpp commit 28a17a95904916c3422b377e0bd6fdcc84e29540 Author: Ann Almgren Date: Mon Oct 8 18:45:58 2018 -0700 Update the nodal linear solvers so that we can now call the operator to compute the multilevel nodal divergence, and can call MLMG::getFluxes for nodal as well as cell-centered data. Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H commit b47268d97d269aad3ea4ac5c04a0c4ef408d5c2b Author: Kevin Gott Date: Mon Oct 8 20:25:30 2018 -0400 Update Function tutorial with new version of launch macro. Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp commit 057d608d55e422465ca89ca2a146cd4ac4093aa0 Author: Weiqun Zhang Date: Mon Oct 8 17:17:07 2018 -0700 AMREX_CUDA_LAUNCH_FUNCTION -> AMREX_CUDA_LAUNCH_GLOBAL Src/Base/AMReX_CudaLaunch.H commit 81f4d323c9f89544f4347db1851de8ccceb3f7c4 Author: Kevin Gott Date: Mon Oct 8 20:11:17 2018 -0400 Changing lambda launch function. Src/Base/AMReX_CudaLaunch.H commit 040a87e3bb09c9d800b5a4eaedf1749cce286222 Author: Kevin Gott Date: Mon Oct 8 20:10:52 2018 -0400 More changes to Tutorials. Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_1/make.out Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp commit 7c7bb57d9fb60ba97ffb07dbbe0f4c68ab364149 Author: Weiqun Zhang Date: Mon Oct 8 16:07:19 2018 -0700 Simplify launching macros Src/Base/AMReX_CudaLaunch.H Src/Base/AMReX_CudaLaunch.cpp Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MultiFab.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 5f7ad33367f465370329a1124268cbd1649b3a1d Author: Kevin Gott Date: Mon Oct 8 17:25:31 2018 -0400 Adjust GPU tutorials for new changes and update Readme. Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/Evolve.cpp Tutorials/GPU/ElectromagneticPIC/em_pic_3d.F90 Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_1/em_pic_3d.F90 Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_2/em_pic_3d.F90 Tutorials/GPU/Readme.txt commit 6fbd4b6a724d06d3508b3c6f0aadd4a4df830dea Author: Kevin Gott Date: Mon Oct 8 17:05:06 2018 -0400 Fix HeatEquation0. Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp commit b7c12407e844e3e98cee68609551e0add6f2f9c1 Author: Kevin Gott Date: Mon Oct 8 17:03:48 2018 -0400 Add threading strategy to FillBoundary lambda calls. Src/Base/AMReX_FabArrayCommI.H commit 4488705e3a243a6da3af3cec0897298c11668133 Author: Kevin Gott Date: Mon Oct 8 17:02:53 2018 -0400 Add map to Allocators Src/Base/AMReX_CudaAllocators.H commit de0ff2c7f6451cf478ce969060899714936d8ad1 Author: Kevin Gott Date: Mon Oct 8 16:59:47 2018 -0400 verbose fortran attributes Tools/GNUMake/Make.defs commit e62c61b4950a099e4344807127c1bd607d42261b Merge: 818ae0bac 90b67ec60 Author: Kevin Gott Date: Mon Oct 8 15:47:06 2018 -0400 Merge branch 'gpu-merge-test' of https://github.com/AMReX-Codes/amrex into gpu-merge-test commit 818ae0bacbc686d3edcd5834e600a5af1efb0437 Author: Kevin Gott Date: Mon Oct 8 15:46:49 2018 -0400 AMREX_CUDA_DEVICE to AMREX_CUDA_HOST_DEVICE for lambda launches. Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MultiFab.cpp commit 90b67ec60d474a1030107c7a8fe0e33afdf26dc0 Author: Weiqun Zhang Date: Mon Oct 8 12:05:50 2018 -0700 minor Src/Base/AMReX_Device.H Tools/F_scripts/write_cuda_headers.py commit d93c7f84a1e79de290bc927872370cf6ddcbe154 Author: Kevin Gott Date: Mon Oct 8 14:53:35 2018 -0400 Add threading strategy to all MultiFab functions currently using lambdas. Src/Base/AMReX_MultiFab.cpp commit f06533b08f94bf29e1e8b198786f185d1394a339 Author: Weiqun Zhang Date: Mon Oct 8 10:41:52 2018 -0700 TilingIfNotGPU() Src/Base/AMReX_MFIter.H Src/Base/AMReX_MultiFab.cpp commit 47f47efe7342bdeece2064c68241ad57d351bd86 Author: Weiqun Zhang Date: Mon Oct 8 10:33:35 2018 -0700 remove RunOn Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MultiFab.cpp Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Tests/C_BaseLib/tFB.cpp commit e864202d9ebd4602f881c8693bd944fe6581682a Author: Weiqun Zhang Date: Mon Oct 8 09:47:58 2018 -0700 more reorganization Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_CudaFort.F90 Src/Base/AMReX_CudaManaged.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 3909f8e942ac3ab3c2fd142569bd63d9ddc245f6 Author: Weiqun Zhang Date: Mon Oct 8 09:33:25 2018 -0700 reorganization Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Array.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CudaQualifiers.H Src/Base/AMReX_CudaUtility.H Src/Base/AMReX_CudaUtility.cpp Src/Base/AMReX_Device.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_Managed.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_Orientation.H Src/Base/CMakeLists.txt Src/Base/Make.package Tools/F_scripts/write_cuda_headers.py commit 239a48ad36de99fb8aeecaf85c91877ee8b60de6 Author: Weiqun Zhang Date: Sun Oct 7 12:24:16 2018 -0700 move SetPreferred to where the arena is built now Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BaseFab.cpp commit 7ea2b4e7450059d4094faf4a44d8791d22bf0663 Author: Weiqun Zhang Date: Sat Oct 6 22:36:07 2018 -0700 fix omp Src/Base/AMReX_FabArrayCommI.H commit 4578fe4d817cc529888434283763061d4aac39be Author: Weiqun Zhang Date: Sat Oct 6 22:09:52 2018 -0700 fix some warnings Src/Base/AMReX.cpp Src/Base/AMReX_BaseFab.cpp commit dd3307a7facf5c78fa10b16302625ecd10c3d27e Author: Weiqun Zhang Date: Sat Oct 6 21:49:49 2018 -0700 put OKGPU inside AMREX_USE_CUDA Src/Particle/AMReX_ParticleContainerI.H commit 5dce3ada07cf07aea542a43a55727f6a7d38ffef Author: Weiqun Zhang Date: Sat Oct 6 21:49:49 2018 -0700 put OKGPU inside AMREX_USE_CUDA Src/Particle/AMReX_ParticleContainerI.H commit 248fcc4694c10f79ba0e2db2d749ae32cba63020 Author: Weiqun Zhang Date: Sat Oct 6 21:31:09 2018 -0700 fix compilation for USE_CUDA=FALSE Src/Base/AMReX_CUDA_Utility.H Src/Base/AMReX_Managed.H commit aae70ef8facb4df3e65d8d1d47b073dd78ce9c66 Merge: 56c23968b a5312d657 Author: Weiqun Zhang Date: Sat Oct 6 21:22:55 2018 -0700 Merge branch 'development' into gpu-merge-test commit 56c23968b92472fcfb542092966c25a40c4ed30c Author: Weiqun Zhang Date: Sat Oct 6 21:21:41 2018 -0700 revert some changes to Arena Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_FabArrayBase.cpp commit 591165fd3c05766710f2514d3df1ba33c1eb8a68 Author: Weiqun Zhang Date: Sat Oct 6 17:43:07 2018 -0700 minor changes for easy comparison Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp commit 5882b9199b012ae4e064ca17b198d1938c67a21a Author: Weiqun Zhang Date: Sat Oct 6 17:29:23 2018 -0700 return old value when set Src/Base/AMReX.H Src/Base/AMReX.cpp commit ffce78411488db2a68f24aa568f9506c4aac6a4f Author: Weiqun Zhang Date: Sat Oct 6 17:27:07 2018 -0700 function to set where to run Src/Base/AMReX.H Src/Base/AMReX.cpp commit 3a71e5495f46660c0aecde3c3fe144e82ba2486c Author: Weiqun Zhang Date: Sat Oct 6 17:08:03 2018 -0700 WhereToRunDefault -> WhereToRun Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_FabArray.H Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Tests/C_BaseLib/tFB.cpp commit 6fe12e10eb5a59299a2c4cec65b8a91370349edc Author: Weiqun Zhang Date: Sat Oct 6 16:41:07 2018 -0700 simplify Geometry::data Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp commit a5312d6577b83f88199d73cbe60ed01b13311b4b Merge: e812b6113 9b6dffe22 Author: Weiqun Zhang Date: Sat Oct 6 16:33:24 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e812b6113f358d7cc8bae8fab5ac1b5df2f4304a Author: Kevin Gott Date: Mon Oct 1 20:41:06 2018 -0400 toLower and toUpper Utility functions. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit fafb6d00ef660666db8e024cd6c562536cafa298 Author: Weiqun Zhang Date: Sat Oct 6 15:47:19 2018 -0700 minor changes for readability Src/Base/AMReX_Array.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_Orientation.H commit 0bb7558a2d6fb4e89d59797bc94cbbc997ffc383 Author: Weiqun Zhang Date: Sat Oct 6 14:29:48 2018 -0700 Managed: remove the device version Src/Base/AMReX_Managed.H commit f38c8bf1ec869bbd619223c96f2c7a89040158b1 Author: Weiqun Zhang Date: Sat Oct 6 11:30:13 2018 -0700 reorganization Src/Base/AMReX_Box.H Src/Base/AMReX_CUDA_Utility.H Src/Base/AMReX_CUDA_Utility.cpp Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_Managed.H commit 9b6dffe22240b94daf93f59a7bd4718d50fb7fca Merge: d96fb1fc0 9a34444c3 Author: Andrew Myers Date: Sat Oct 6 13:50:17 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d96fb1fc00ed03dead033470651f76f70053b38e Author: Andrew Myers Date: Sat Oct 6 13:49:48 2018 -0400 correctly enforce periodic boundary conditions in the GPU form of Redistribute() Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 9ff5186db106317340367968f5b1f93d55f4405d Merge: 37a99eca6 f72817118 Author: Weiqun Zhang Date: Fri Oct 5 21:00:43 2018 -0700 Merge branch 'gpu-merge-test' of github.com:AMReX-Codes/amrex into gpu-merge-test commit 37a99eca62219557579ee045e58355106888ddfd Author: Weiqun Zhang Date: Fri Oct 5 20:58:54 2018 -0700 fix conflict Tutorials/GPU/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H commit 0f6a6036fc60c8ebc1f5f867fcd6ed61cff31f22 Author: Weiqun Zhang Date: Fri Oct 5 20:54:08 2018 -0700 fix conflict Tutorials/Particles/ElectromagneticPIC/Particles.H Tutorials/Particles/ElectromagneticPIC/StructOfArrays.H Tutorials/Particles/ElectromagneticPIC/script.sh Tutorials/Particles/ElectromagneticPIC/test.cpp commit f728171185d2af4cfefdd7ec19a1d47f27b24049 Author: Kevin Gott Date: Fri Oct 5 20:30:20 2018 -0400 Add threading strategy for copy to match Castro's Sedov. Rest of MultiFab to come soon. Src/Base/AMReX_MultiFab.cpp commit 296c0cb81682680801e8a6951fc497679cde71c2 Author: Weiqun Zhang Date: Fri Oct 5 15:13:51 2018 -0700 hide some codes from Fortran BoxLib Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BArena.cpp Src/Base/GPackage.mak commit 9f27079b97613cd748842d5be62ce0924b1f9e2e Author: Kevin Gott Date: Fri Oct 5 17:35:40 2018 -0400 Library adjustments. Src/Base/AMReX_Arena.cpp Src/Base/AMReX_CArena.cpp commit 71c76174c8cfdf8d1f4e6d9198aeabe54ad43825 Author: Andrew Myers Date: Fri Oct 5 16:22:04 2018 -0400 implement OK() routine that can be run on either the GPU or the CPU. Src/Particle/AMReX_ParticleContainerI.H commit c836e5024f180cf51a5d720bedd99d97de06f2e7 Author: Andrew Myers Date: Fri Oct 5 16:21:39 2018 -0400 make these data members mutable Src/Particle/AMReX_Particles.H commit 9a34444c332c6f6c6d1ee0c74b9d9270d4280a34 Merge: afa5d328a 70091733e Author: Jean Sexton Date: Fri Oct 5 13:57:21 2018 -0400 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit afa5d328ad1f7166d2eded46cf4928d83fd5e138 Author: Jean Sexton Date: Fri Oct 5 13:56:58 2018 -0400 Single cell successfully passed through to f90 device function Tutorials/SUNDIALS3/EX1_CUDA_NVEC/Make.package Tutorials/SUNDIALS3/EX1_CUDA_NVEC/main.cpp Tutorials/SUNDIALS3/EX1_CUDA_NVEC/myfunc_F.H Tutorials/SUNDIALS3/EX1_CUDA_NVEC/ode_mod.f90 commit 3f64d828ca476e1160a8e1cd93b5d7ac71cd1f9b Author: Jean Sexton Date: Fri Oct 5 13:55:39 2018 -0400 c rhs calls user-defined kernel Tutorials/SUNDIALS3/EX1_CUDA_NVEC/main.cpp commit 70091733e9f9a4586c573e1039d9250565bb3af1 Merge: 165ec1073 b8d7fa82c Author: WeiqunZhang Date: Fri Oct 5 10:46:26 2018 -0700 Merge pull request #331 from AMReX-Codes/mc-nodelinop Mc nodelinop commit b8d7fa82ce71c7e731b50d847233ae19080f508a Author: Brandon Runnels Date: Fri Oct 5 11:40:28 2018 -0600 Update AMReX_MLMG.cpp Removed `setVal` Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 165ec1073be3835ed562613270b91ed99b323adc Merge: 24f6e1c9c a2f6e352f Author: Jean Sexton Date: Fri Oct 5 13:07:00 2018 -0400 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 24f6e1c9ce5b5a023ace519d3f8845c1b29de893 Author: Jean Sexton Date: Fri Oct 5 13:06:50 2018 -0400 Added serial C++ driven version of EX1, differences between vectorized version and non-vectorized approaches precision level as tolerances are tightened Tutorials/SUNDIALS3/EX1_CUDA_NVEC/main.cpp Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/GNUmakefile Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/Make.package Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/inputs Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/inputs_2box Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/inputs_non_vectorized Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/main.cpp Tutorials/SUNDIALS3/EX1_SERIAL_NVEC/myfunc_F.H commit 0ba8578cf2b8cb137cb192cfb8b00201790b8bdc Author: Brandon Runnels Date: Fri Oct 5 11:03:53 2018 -0600 Update AMReX_MLMG.cpp bug fix Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit edf3af4b21f2e44805461a92f9ce323bf180d900 Author: Brandon Runnels Date: Fri Oct 5 10:54:49 2018 -0600 Update AMReX_MLLinOp.cpp Removed setVal Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit a5ec72d206674f796b8769aab14edd3de2a910dc Author: Brandon Runnels Date: Fri Oct 5 10:53:35 2018 -0600 Update AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 51ccd7a70b17b25794cfba218c71ca665bd5138a Author: Brandon Runnels Date: Fri Oct 5 10:39:44 2018 -0600 Made n inside loop Src/LinearSolvers/MLMG/AMReX_MLNodeLap_nd.F90 commit a2f6e352f0d0414f4a16fab76d9daa3602936dd3 Merge: ac4e409ef 55ea9f123 Author: sireeveslbl Date: Fri Oct 5 09:26:58 2018 -0700 Merge branch 'mlmg' of https://github.com/AMReX-Codes/amrex into development commit 55ea9f12316161732a7c177a591c60b4e05f0df8 Author: sireeveslbl Date: Fri Oct 5 09:19:45 2018 -0700 Commented out unnecessary subtractions Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit ac4e409ef8714918dc9f4657befd9f0669159546 Author: Ann Almgren Date: Fri Oct 5 08:04:56 2018 -0700 Revert "Put the makeSolvable (ie subtract off the mean) back into the BiCG solver - this" This reverts commit f0f2a15fa9f0ce1ef82a5f41d8367e672f6016de. Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit acac718cc2d6feed65a5c788b338b673d785ad22 Merge: 0e5ba95f0 f0f2a15fa Author: sireeveslbl Date: Thu Oct 4 18:00:27 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mlmg commit 0e5ba95f0acb3d9824bd2c796e5f4fa7ac94f7eb Author: sireeveslbl Date: Thu Oct 4 17:59:15 2018 -0700 Changed MLCG makeSolvable to MLMG makeSolvable, changed computeVolInv to kill bug that was not inverting volume for use EB but all_Regular geometry Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit f0f2a15fa9f0ce1ef82a5f41d8367e672f6016de Author: Ann Almgren Date: Thu Oct 4 17:55:54 2018 -0700 Put the makeSolvable (ie subtract off the mean) back into the BiCG solver - this should help. Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit c609c026326e4f3ff3762adca36bdbd6715817f5 Merge: e48a263be be8ef9dc0 Author: Weiqun Zhang Date: Thu Oct 4 17:41:51 2018 -0700 Merge branch 'development' into gpu-merge-test commit be8ef9dc07252d3ecd1b4f3e42250d13f1c97fd4 Merge: 3e0f6acea e5bfc8f7f Author: Weiqun Zhang Date: Thu Oct 4 17:05:46 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3e0f6aceac00387db1f14050fb91bac0effc03dd Author: Weiqun Zhang Date: Thu Oct 4 17:02:20 2018 -0700 Call mlmg's makeSolvable. Calls are commented out because it may not work. Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit e5bfc8f7f4066cddf863ce42b66970d9ff016a25 Author: Jean Sexton Date: Thu Oct 4 20:01:06 2018 -0400 Cleaned up some comments Tutorials/SUNDIALS3/EX1_CUDA_NVEC/main.cpp Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/GNUmakefile Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/Make.package Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/SetIC.f90 Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/inputs Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/main.cpp Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/myfunc_F.H Tutorials/SUNDIALS3/EX1_GPU_PRAGMA/ode_mod.f90 commit 26263474a9d1fcd37822f26ea9c9093e87abfec0 Author: Weiqun Zhang Date: Thu Oct 4 16:58:04 2018 -0700 make MLCGSolver a friend of MLMG and pass MLMG pointer into MLCGSolver ctor Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 16705a37b7f62a8bde4cb19d93eee3db52fe812e Author: Jean Sexton Date: Thu Oct 4 19:56:38 2018 -0400 Updated sundials library include statements, seperated N_Vector cuda example from AMREX_GPU_PRAGMA example Src/Extern/SUNDIALS3/Make.package Tools/GNUMake/packages/Make.sundials3 Tutorials/SUNDIALS3/EX1/GNUmakefile Tutorials/SUNDIALS3/EX1/integrate_ode.f90 Tutorials/SUNDIALS3/EX1/ode_mod.f90 Tutorials/SUNDIALS3/EX1_CUDA_NVEC/GNUmakefile Tutorials/SUNDIALS3/EX1_CUDA_NVEC/Make.package Tutorials/SUNDIALS3/EX1_CUDA_NVEC/SetIC.f90 Tutorials/SUNDIALS3/EX1_CUDA_NVEC/inputs Tutorials/SUNDIALS3/EX1_CUDA_NVEC/main.cpp Tutorials/SUNDIALS3/EX1_CUDA_NVEC/myfunc_F.H Tutorials/SUNDIALS3/EX1_cuda/GNUmakefile Tutorials/SUNDIALS3/EX1_cuda/Make.package Tutorials/SUNDIALS3/EX1_cuda/SetIC.f90 Tutorials/SUNDIALS3/EX1_cuda/main.cpp Tutorials/SUNDIALS3/EX1_cuda/myfunc_F.H Tutorials/SUNDIALS3/EX_ark_analytic_fp/GNUmakefile Tutorials/SUNDIALS3/EX_cv_analytic_fp/GNUmakefile Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns/GNUmakefile Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns_jac/GNUmakefile Tutorials/SUNDIALS3/EX_cv_brusselator_dns/GNUmakefile commit b700751e8cefe64c86861d8085db2d95ec4d0205 Merge: b30c565ff d61ea5edb Author: Andrew Myers Date: Thu Oct 4 19:34:51 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b30c565ffcb6739d93afce2c960af1d05310cdfc Author: Andrew Myers Date: Thu Oct 4 19:34:23 2018 -0400 dispatch redistribute to the GPU when possible when compiling with AMREX_USE_CUDA=TRUE Src/Particle/AMReX_ParticleContainerI.H commit d61ea5edb1ffdaa7906a6d2ffa97b0240937953f Author: Weiqun Zhang Date: Thu Oct 4 16:23:55 2018 -0700 comment out some new codes Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit 94b1db4b57d3a7da8ff668c9e02d38aa9322b49b Merge: b6ba5f43c b2ee31a58 Author: sireeveslbl Date: Thu Oct 4 15:32:48 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b6ba5f43c8c9900773c3abef611f5e2a47b7ef6d Author: sireeveslbl Date: Thu Oct 4 15:32:27 2018 -0700 Some clean up in AMReX_MLCGSolver.cpp. Removed leftovers from debugging bicgstab Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit b2ee31a5803ba85e44d83208169efa39d79af852 Merge: e46f1ce47 debc6f3da Author: Andrew Myers Date: Thu Oct 4 15:32:18 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e46f1ce47b095e38e068a9b10ad5a32effb8be6c Author: Andrew Myers Date: Thu Oct 4 15:32:04 2018 -0700 work-around for pgi in how we handle OMP in the particle container Src/Particle/AMReX_ParticleContainerI.H commit debc6f3daa772bf9669f76176f37766353e28600 Merge: ce5d30d09 eaef6b7eb Author: sireeveslbl Date: Thu Oct 4 15:29:14 2018 -0700 Merge branch 'mlmg' of https://github.com/AMReX-Codes/amrex into development commit ce5d30d09d090be5bbc280bfa681262693e5ef2d Merge: 87e055c7a 92174343a Author: sireeveslbl Date: Thu Oct 4 15:17:57 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit eaef6b7eba63ef2404e41be74dfc30f729d92b27 Merge: b42789355 92174343a Author: sireeveslbl Date: Thu Oct 4 15:17:44 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mlmg commit b42789355af42d6a36c44e9766241a304a38838a Author: sireeveslbl Date: Thu Oct 4 15:16:59 2018 -0700 Changed BiCGStab to include subtracting out the Mean residual for singular linear operators only. This solved the issue with the sinusoidal RHS on the 5x5x5 problem. I also tested it with the classic CellEB problems, that the original BiCGstab solved. Each test yeilded good results. Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit e48a263beb55363e9b499c38212f82bf2d6f8852 Author: Weiqun Zhang Date: Thu Oct 4 14:20:01 2018 -0700 make more device functions Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Managed.H Src/Base/AMReX_TinyProfiler.cpp commit 92174343a3a59c3cdf36d4d2291bb2d72639ef6f Merge: e4c681c65 953c10b3c Author: Andrew Myers Date: Thu Oct 4 16:49:03 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e4c681c65dd391d13d859f0d1412a7d26d712b13 Author: Andrew Myers Date: Thu Oct 4 16:32:41 2018 -0400 disambiguate timer Src/Particle/AMReX_ParticleContainerI.H commit c2718943209d18bf7bf309bf8dd96f166abce34e Author: Andrew Myers Date: Thu Oct 4 16:30:00 2018 -0400 a thrust particle redistribute for both soa and aos data Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 369405607081dad8a0b495809af2fba3e4cda5d3 Merge: 210a88c3d 953c10b3c Author: Brandon Runnels Date: Thu Oct 4 13:59:06 2018 -0600 Merge branch 'development' into mc-nodelinop commit 87e055c7a3ac1f4d9da458a4851abb0a6e728ed6 Merge: f8c85d079 953c10b3c Author: sireeveslbl Date: Thu Oct 4 12:48:32 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into mlmg commit f8c85d079761fe9a97e49d32fb6623ba843fb696 Author: sireeveslbl Date: Thu Oct 4 12:31:06 2018 -0700 Changed BiCGStab to subtract out the mean residual, solves the periodic 5x5x5 problem along with the regular problems. Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit 852df5db6fafeaa4d53f6b18de7605cd6bc06e73 Author: Weiqun Zhang Date: Thu Oct 4 12:10:35 2018 -0700 add AMREX_CUDA_HOST_DEVICE to more functions Src/Base/AMReX_Box.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_Orientation.H commit 953c10b3c07a914973aea6e8c6bad69b9cbcd88d Author: Michele Rosso Date: Thu Oct 4 11:33:45 2018 -0700 CMake: start GPU support Src/Base/CMakeLists.txt Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake commit ad48a7228c30f54101659d89e498916793f7a2b3 Author: Weiqun Zhang Date: Thu Oct 4 10:38:38 2018 -0700 Fix for codes with Fortran main. Add AMREX_CUDA_HOST_DEVICE to some functions Src/Base/AMReX_Box.H Src/Base/AMReX_IntVect.H Tools/GNUMake/comps/pgi.mak commit 3935349c0bd917dc3d3b514924dc0335e9b588e5 Author: Weiqun Zhang Date: Thu Oct 4 10:37:39 2018 -0700 make amrex::Assert host and device function Src/Base/AMReX.H Src/Base/AMReX.cpp commit b7f87e11efd68fed6b8404fd934ed8ebbbd34d61 Author: Michele Rosso Date: Thu Oct 4 09:52:35 2018 -0700 CMake: fix misspelled file name Src/Particle/CMakeLists.txt commit c1ac9ace874984fcc5a4b86a3ecccafd3102cf75 Merge: dcda64455 b3f484b7d Author: Weiqun Zhang Date: Thu Oct 4 09:20:12 2018 -0700 Merge branch 'development' into gpu-merge-test commit b3f484b7d2f39373fbd9ea517d67fb00855ff3ed Merge: fbc42fb28 334f37853 Author: WeiqunZhang Date: Thu Oct 4 09:19:13 2018 -0700 Merge pull request #315 from AMReX-Codes/devirtualize-fab Devirtualize fab commit dcda64455e8eb315fbfdb7bcb99986fa6c04227c Author: Weiqun Zhang Date: Wed Oct 3 22:06:05 2018 -0700 fix some tests Tests/C_BaseLib/tFB.cpp Tests/FillBoundaryComparison/main.cpp commit 6c1f5fd2d6e44cc8d28b2eff1a3a2f42df720ab0 Author: Weiqun Zhang Date: Wed Oct 3 21:44:50 2018 -0700 pragma gpu script: add call to device function Tools/F_scripts/write_cuda_headers.py commit e40dbec38b7eed737150f0190aceee47f117f22b Author: Weiqun Zhang Date: Wed Oct 3 21:42:03 2018 -0700 comment out a specialization Src/Base/AMReX_BaseFab.H commit 845eeeba85ce70d0b84e7e2173920a1767f71122 Author: Weiqun Zhang Date: Wed Oct 3 21:29:49 2018 -0700 remove duplicated declarations and fix missing definition of variable Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Device.cpp commit 9dc98d4f1eda7f2b5cc8335d4a4af7764352be91 Author: Weiqun Zhang Date: Wed Oct 3 21:16:58 2018 -0700 rm BF_init. we initialize The Arena in amrex::Initialize Src/Base/AMReX_BaseFab.H commit 2ebe82e886d94e2b55b94b855eae2d427955d688 Author: Weiqun Zhang Date: Wed Oct 3 21:08:42 2018 -0700 remove a number of BaseFab Fortran calls because they don't use gpu pragama anyway. so we can simpply use c++ versions Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp commit 0223a41d86cb0b2c986de46dd60d42a0a299aa04 Author: Weiqun Zhang Date: Wed Oct 3 17:30:51 2018 -0700 more fixes Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BoxArray.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 882d8371211affc2f8a6304e8483a85052f05994 Author: Andrew Myers Date: Wed Oct 3 20:19:50 2018 -0400 start porting over the thrust redistribute from the tutorial Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 20b8371e74550cf8dbb0615c73efcfbe4a70210a Author: Andrew Myers Date: Wed Oct 3 20:19:15 2018 -0400 add a wrapper around resize for the ArrayOfStructs Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_ParticleTile.H commit 8252d3be81253e2d51f7e15ef933e2438619cbb4 Author: Weiqun Zhang Date: Wed Oct 3 16:47:25 2018 -0700 fix ArrayLim Src/Base/AMReX_ArrayLim.H commit 662eab153ddf8a0661782d83fa667414f3401129 Author: Weiqun Zhang Date: Wed Oct 3 16:19:26 2018 -0700 fix some FillBoundary arguments Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit 6d1804c453d3d4f5971b888eaecb5589e89bb7e8 Author: Weiqun Zhang Date: Wed Oct 3 16:05:49 2018 -0700 fix F_Interfaces Src/F_Interfaces/Base/AMReX_multifab_fi.cpp commit cd0fc7f7c8352968e16005bf5e9e41d7bc2ea1e0 Author: Weiqun Zhang Date: Wed Oct 3 16:00:38 2018 -0700 HelloWorld compiles Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_ForkJoin.H commit f5308036863cdf5819ce68cb627f68065b13d5d0 Author: Kevin Gott Date: Wed Oct 3 15:42:21 2018 -0700 Fix namespace brackets. Src/Base/AMReX_BaseFab.cpp commit cc5ac2a40022662f3354ed8160fd5f74dc0309f5 Author: Kevin Gott Date: Wed Oct 3 15:38:50 2018 -0700 Add back TrueUnlessGPU. Src/Base/AMReX_MFIter.H commit eb8e21ba2380aa5b2f4219c9fa00a57d22998e55 Merge: d897ea302 334f37853 Author: Weiqun Zhang Date: Wed Oct 3 15:29:15 2018 -0700 Merge branch 'devirtualize-fab' into gpu-merge-test commit 334f37853fb4dd2bb1605ee51b1e1493b4a48237 Merge: 219195023 fbc42fb28 Author: Weiqun Zhang Date: Wed Oct 3 15:26:15 2018 -0700 Merge branch 'development' into devirtualize-fab commit d897ea3027fa57030a0949ecc019a1fd36ae464b Author: Kevin Gott Date: Wed Oct 3 18:25:30 2018 -0400 Adjust arena to match both branches. Src/Base/AMReX_Arena.H commit 0c6782ad08bd27ebd3ed862f29e848b8a99e3080 Author: Kevin Gott Date: Wed Oct 3 18:12:13 2018 -0400 Wrap Device::synchronizes. Src/Base/AMReX_FabArrayCommI.H commit d2e1a875d169848a7626ebb25c9668d6fe21e378 Author: Kevin Gott Date: Wed Oct 3 18:09:38 2018 -0400 Add missing commas to macros. Src/Base/AMReX_Managed.H commit 31b509687232ec0d0e173812ec5b88e76841596f Author: Weiqun Zhang Date: Wed Oct 3 13:50:20 2018 -0700 fix conflicts in Base Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCUtil.H Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_CudaAllocators.H Src/Base/Make.package commit 83858a30bfd281d4528ec20ff3e60ad42d8f4c03 Author: Weiqun Zhang Date: Wed Oct 3 13:23:06 2018 -0700 fix conflicts in make Src/Particle/AMReX_NeighborParticlesI.H Tools/F_mk/GMakedefs.mak Tools/GNUMake/Make.defs Tools/GNUMake/Make.local.template Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/packages/Make.cvode Tools/GNUMake/tools/Make.craypat Tools/GNUMake/tools/Make.vtune commit fbc42fb28884d43f8cca0005c05206bfeb46cb26 Author: Jean Sexton Date: Wed Oct 3 15:51:12 2018 -0400 Added SUNDIALS3 EX1 tutorial using CVODE Cuda N_Vector and amrex copyToMem Src/Extern/SUNDIALS3/cvode_interface.f90 Tools/GNUMake/packages/Make.sundials3 Tutorials/SUNDIALS3/EX1_cuda/GNUmakefile Tutorials/SUNDIALS3/EX1_cuda/Make.package Tutorials/SUNDIALS3/EX1_cuda/SetIC.f90 Tutorials/SUNDIALS3/EX1_cuda/inputs Tutorials/SUNDIALS3/EX1_cuda/main.cpp Tutorials/SUNDIALS3/EX1_cuda/myfunc_F.H Tutorials/SUNDIALS3/EX1_cuda/ode_mod.f90 commit dc7e5d178250981b3a858ce48688fb0e1148c076 Author: Donald E. Willcox Date: Wed Oct 3 15:24:04 2018 -0400 Add CUDA CVODE example EX3-CUDA. Tutorials/CVODE/EX3-CUDA/GNUmakefile Tutorials/CVODE/EX3-CUDA/Make.CVODE Tutorials/CVODE/EX3-CUDA/Make.package Tutorials/CVODE/EX3-CUDA/README.md Tutorials/CVODE/EX3-CUDA/extern_probin.template Tutorials/CVODE/EX3-CUDA/inputs Tutorials/CVODE/EX3-CUDA/inputs_128 Tutorials/CVODE/EX3-CUDA/inputs_256 Tutorials/CVODE/EX3-CUDA/inputs_32 Tutorials/CVODE/EX3-CUDA/inputs_64 Tutorials/CVODE/EX3-CUDA/main.cpp Tutorials/CVODE/EX3-CUDA/react_cuda.cpp Tutorials/CVODE/EX3-CUDA/react_serial.cpp Tutorials/CVODE/EX3-CUDA/react_utils.F90 Tutorials/CVODE/EX3-CUDA/test_react.H Tutorials/CVODE/EX3-CUDA/test_react_F.H commit 3ea34f6b320e115263b2c0f1faf2faf8cbdb6bbf Merge: 0debf4672 cd2d1974a Author: Kevin Gott Date: Wed Oct 3 15:13:55 2018 -0400 Merge branch 'development' into gpu-merge-test Conflicts: Src/Base/AMReX_Arena.H Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BArena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_fort_mod.F90 Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Tests/Particles/StructOfArrays/GNUmakefile Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_pgi.mak Tools/GNUMake/Make.defs Tools/GNUMake/Make.machines Tools/GNUMake/Make.rules Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/ibm.mak Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak Tools/GNUMake/sites/Make.llnl Tools/GNUMake/sites/Make.olcf Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Evolve.H Tutorials/Particles/ElectromagneticPIC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/inputs Tutorials/Particles/ElectromagneticPIC/main.cpp commit cd2d1974af3f3e0fac37ea6359db961774b35c87 Merge: 0d37b7018 b2ea0899f Author: Andrew Myers Date: Wed Oct 3 13:15:32 2018 -0400 merging. commit b2ea0899f5f0877cad640ae0ad8833b6eca0f267 Author: Weiqun Zhang Date: Wed Oct 3 10:00:27 2018 -0700 put Nvar_Arena into AMREX_USE_GPU_PRAGMA Src/Base/AMReX_Arena.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp commit 0debf467219b97db857890122a2f8c1c22ebe6dc Author: Kevin Gott Date: Wed Oct 3 12:33:09 2018 -0400 Rename for runOn variable for easy searching/renaming later. Src/Base/AMReX_FabArray.H commit 233249a4bf63b7476065ab6e6f343c3c783a1489 Author: Weiqun Zhang Date: Wed Oct 3 08:56:36 2018 -0700 fix cmake Src/Particle/CMakeLists.txt commit f444578adb74961897da4968898af368efb208f2 Author: Kevin Gott Date: Wed Oct 3 11:48:48 2018 -0400 FillBoundary and EnforcePeriodicity converted to RunOn selection. Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit 210a88c3d8994cb9d1645dee28d9bb02ee9a047b Merge: dbad922a6 230386b12 Author: Brandon Runnels Date: Wed Oct 3 07:41:58 2018 -0600 Merge branch 'development' into mc-nodelinop commit 0d37b70186095c90ca2ce9de1f5bef78e28baf02 Merge: 0c75eb190 230386b12 Author: Andrew Myers Date: Tue Oct 2 20:02:40 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 230386b1270a3a3122486437994b106090d7cc2e Merge: 2c73850b8 adef2262f Author: Marc Day Date: Tue Oct 2 16:41:06 2018 -0700 Merge branch 'marc/forkjoin_dev' into development commit adef2262fd189a5e8707b200776326c0d49dca3d Merge: eea81a253 2c73850b8 Author: Marc Day Date: Tue Oct 2 16:39:14 2018 -0700 resolve trivial conflict commit eea81a253aed94b0a30708b3a818c8423120e7dc Author: Marc Day Date: Tue Oct 2 16:37:21 2018 -0700 Remove commented code lines Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp commit 2c73850b8ea68b7aab42ad980eacb4fb0cd43d3c Author: Weiqun Zhang Date: Tue Oct 2 16:34:13 2018 -0700 add NVCC_HOST_COMP Tools/GNUMake/comps/nvcc.mak commit bdaaa2f684b632bf3c2a624e26eb1f09f68a6c37 Author: Marc Day Date: Tue Oct 2 16:32:26 2018 -0700 Add some functionality to the test code Tutorials/Parallel/ForkJoin/MyTest.H Tutorials/Parallel/ForkJoin/MyTest.cpp commit f0d799a3e74e9530d58f584be22112c8b3ab075a Author: Marc Day Date: Tue Oct 2 16:20:31 2018 -0700 Add name of output folder to fj ctr, allow to be empty string and to overwrite existing output Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp commit d3147168110ba07ccb48f2cb476c95e895ceb895 Author: Kevin Gott Date: Tue Oct 2 18:52:16 2018 -0400 Slight renaming. Src/Base/AMReX.cpp commit a1504b496a4d80681ed9aefe15bc30fca014088d Author: Weiqun Zhang Date: Tue Oct 2 15:40:51 2018 -0700 use linop getFluxes Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 0c75eb1904e11beff025a231e22754231dbdf363 Merge: 41df4737c fc8006968 Author: Andrew Myers Date: Tue Oct 2 18:13:29 2018 -0400 Merge branch 'atmyers-gpu_particles_reorg' into development commit 41df4737c3f3953e098fa47caf094e1ae6ac8d51 Merge: 6c3e75f57 3aecf683b Author: Weiqun Zhang Date: Tue Oct 2 14:46:41 2018 -0700 Merge branch 'gpu' into development commit 414375f32ebb15579c18857b5f2c03aa6ea6706b Merge: 769c6c513 6c3e75f57 Author: Kevin Gott Date: Tue Oct 2 17:43:34 2018 -0400 Merge branch 'development' into gpu-mm commit 3c73c35ace600e800b5e9ba925ac7b35df9c8e60 Merge: 99e3ddc9e 6c3e75f57 Author: Marc Day Date: Tue Oct 2 14:30:24 2018 -0700 Merge branch 'development' into marc/forkjoin_dev commit 6c3e75f5726372819ade8b54a57fccc1f652d6d4 Merge: 2ebd40238 ccb519cf0 Author: Marc Day Date: Tue Oct 2 14:28:33 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 769c6c513a8346f0c5aa7a37c2a4ada30a3905bf Merge: 150705e01 ccb519cf0 Author: Kevin Gott Date: Tue Oct 2 17:06:31 2018 -0400 Merge branch 'development' into gpu-mm commit 3aecf683bb4ecd1fd2ca8a2e7edd7b461727b734 Merge: 5560aec9f ccb519cf0 Author: Weiqun Zhang Date: Tue Oct 2 14:01:36 2018 -0700 Merge branch 'development' into gpu commit ccb519cf083ed4c1713c5001e1872eb1ca6296c8 Author: Weiqun Zhang Date: Tue Oct 2 13:59:54 2018 -0700 remove some old unused functions Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 5560aec9fcc67f3f5d4bd61e6103a91a5be110e4 Author: Weiqun Zhang Date: Tue Oct 2 13:35:57 2018 -0700 fix cmake Src/Base/AMReX_BaseFab_nd.F90 Src/Base/CMakeLists.txt commit 150705e013ad3a4078326d582a232105e8946ee6 Author: Kevin Gott Date: Tue Oct 2 16:33:30 2018 -0400 Reorganize FillBoundary and EnforcePeriodicity calls. Src/Base/AMReX_FabArray.H commit e0ce2946abbd2f6c863235ac9f1f565a817bda42 Merge: 785d6b7d0 e8248d3d7 Author: Weiqun Zhang Date: Tue Oct 2 13:15:23 2018 -0700 Merge branch 'development' into gpu commit 785d6b7d0b744ea3e9ddc74542f6f41ba6e27666 Author: Weiqun Zhang Date: Tue Oct 2 12:25:00 2018 -0700 minor changes in MFIter Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit cb2beeda3c9acb5ed6dbd16e408a78c57441145d Author: Kevin Gott Date: Tue Oct 2 15:26:17 2018 -0400 Move RunOn and CopyFromTo to AMReX.H Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Managed.H commit ea0c6cfa09ac0b9fd8fa9b9659542bb0f545313e Author: Kevin Gott Date: Tue Oct 2 15:19:31 2018 -0400 Make AMReX_Managed.H called under any circumstances. Src/Base/AMReX_Array.H Src/Base/AMReX_MultiFab.cpp commit 7818a0172acdbf9bf764075be25fb8d290421dcb Author: Kevin Gott Date: Tue Oct 2 15:18:43 2018 -0400 Addition of runOn/CopyFromTo runtime default and slight renaming. Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Managed.H commit fc80069684dfa30c0a161af8da862e1da228f671 Author: Andrew Myers Date: Tue Oct 2 15:12:48 2018 -0400 remove variadic tuple stuff from particle tile - taking a different approach Src/Particle/AMReX_ParticleTile.H commit dc1d7fc163c8a890e5fe5f53f2afaf8e77c8a962 Author: Andrew Myers Date: Tue Oct 2 15:07:34 2018 -0400 using the managed particle vector in Redistribute Src/Particle/AMReX_ParticleContainerI.H commit 8ba121b44005ada3621aedaae108df5ff63d3ae2 Author: Andrew Myers Date: Tue Oct 2 15:06:47 2018 -0400 use managed vectors in the particle iterator for get / set position Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit e8248d3d745f739542f1a88dc05d624bece5df3c Merge: 1fe401cc1 4b3b33ccd Author: Tan Nguyen Date: Tue Oct 2 11:59:32 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1fe401cc1d32e87efe6b1b5812556bcbe3372a57 Author: Tan Nguyen Date: Tue Oct 2 11:58:50 2018 -0700 update asyncFP Src/Amr/AMReX_AsyncFillPatch.cpp commit 067e9e9708f525058c330db93161ffed9cab8d0a Author: Weiqun Zhang Date: Tue Oct 2 10:49:46 2018 -0700 use AMREX_USE_GPU_PRAGMA in the script Tools/F_scripts/gpu_fortran.py Tools/F_scripts/write_cuda_headers.py commit da910af96c8ba4df8167be7e8c63ca35eb105b09 Author: Weiqun Zhang Date: Mon Oct 1 18:10:50 2018 -0700 make make have the old behavior when USE_GPU_PRAGMA is not TRUE Src/Base/AMReX_fort_mod.F90 Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 4b3b33ccd267036262a37d625764856a1cb01ca0 Author: Weiqun Zhang Date: Mon Oct 1 18:17:31 2018 -0700 fix compilation Src/Amr/AMReX_AsyncFillPatch.cpp commit b141e7f88d4254043f9032d4a3ccb4cdc0524498 Author: Kevin Gott Date: Mon Oct 1 20:41:06 2018 -0400 toLower and toUpper Utility functions. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 2a32f206cf84fc258cb67602a32a4c4e15fbf324 Author: Kevin Gott Date: Mon Oct 1 20:40:44 2018 -0400 Small fix. Src/Base/AMReX.cpp commit 1a5460d010ed5cb448470015fe494c8b72ec926f Author: Kevin Gott Date: Mon Oct 1 20:35:00 2018 -0400 Temporary fill of RunOn in lambdas to allow compile testing while default and function interfaces are adjusted. Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MultiFab.cpp commit ab605debe629b59e28a10e2f876af4a3a470d55b Author: Tan Nguyen Date: Mon Oct 1 15:28:29 2018 -0700 create a separate file for asyncMFIter code Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AsyncFillPatch.cpp Src/Amr/Make.package commit d8ef12ae8a62efa43554782176cb939195a39df8 Author: Kevin Gott Date: Mon Oct 1 15:51:03 2018 -0400 Small GPU Readme to remind difference between tutorials. Tutorials/GPU/Readme.txt commit 1c0e03c7d90f9272d3f25412d3b7b33efa79f8e9 Author: Kevin Gott Date: Mon Oct 1 15:37:29 2018 -0400 First pass at runtime selection of location of lambdas. Should run poorly with HeatEquation_EX0 (lambda version). Src/Base/AMReX.cpp Src/Base/AMReX_Managed.H Tests/GPU/TestC/main.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp commit 21828270092961a053533bbdb95be31ff28e920a Author: Andrew Myers Date: Mon Oct 1 15:32:01 2018 -0400 add some useful typedefs to the ParIter Src/Particle/AMReX_Particles.H commit 4b02af10b9d5798ea4fc829cae97e1a200e8a449 Merge: 9af14f5ef 185a1cfc1 Author: Weiqun Zhang Date: Mon Oct 1 12:25:41 2018 -0700 Merge branch 'eb-grow' into development commit 185a1cfc1045ae0e419f9841a101a90c5974a392 Author: Weiqun Zhang Date: Mon Oct 1 12:18:48 2018 -0700 update CellEB2 test Tests/LinearSolvers/CellEB2/MyTest.cpp commit 4c0cdaf3ef3a7e0169b8e180fb0ced8d11560a7b Author: Weiqun Zhang Date: Mon Oct 1 12:02:17 2018 -0700 update EB doc Docs/sphinx_documentation/source/EB.rst Tutorials/EB/CNS/Source/CNS_init_eb2.cpp commit c48e8cc7c435c6ab979b1cef614b2dc1003a6111 Author: Weiqun Zhang Date: Mon Oct 1 11:10:28 2018 -0700 finish implementation of ngrow for eb Src/EB/AMReX_EB2.H Src/EB/AMReX_EB2_IndexSpaceI.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB2_Level.cpp commit 9af14f5ef064fcc90b649a4d90b18981b7cddf60 Merge: 8663e8d4d d37a266c3 Author: Guy Moore Date: Mon Oct 1 09:18:10 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d37a266c38092e1174096e245326e9eead1f4e03 Author: Weiqun Zhang Date: Mon Oct 1 08:52:00 2018 -0700 update CHANGES CHANGES commit 7099057e70a363413c04a919d09fbb83df604c1e Merge: 88120db47 8ddb10347 Author: Weiqun Zhang Date: Mon Oct 1 08:51:10 2018 -0700 Merge branch 'development' commit 820a056d757cc9dffd4ae4229aca320431f2639e Author: Weiqun Zhang Date: Sun Sep 30 16:40:43 2018 -0700 add aoptional ngrow argument to EB2::Build and start implementation Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/EB/AMReX_EB2.H Src/EB/AMReX_EB2.cpp Src/EB/AMReX_EB2_IndexSpaceI.H Src/EB/AMReX_EB2_Level.H commit 724e9de81ac48270f56374f01531a1906d6def10 Merge: 15242cc40 8ddb10347 Author: Weiqun Zhang Date: Sat Sep 29 11:24:50 2018 -0700 Merge branch 'development' into mlmg commit 8ddb10347af60125bf0589762211f46867c70f10 Author: Weiqun Zhang Date: Sat Sep 29 11:24:33 2018 -0700 Merge branch 'mlmg' into development Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 15242cc406b8656b12281825ac567e94b7006674 Author: Weiqun Zhang Date: Sat Sep 29 11:23:34 2018 -0700 fix hypre: make sure to exclude non-valid cells Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 8663e8d4dfca430e5875a8ce9ebbf8c491f35cb3 Merge: 624bac4ee b58eb2915 Author: Guy Moore Date: Fri Sep 28 16:32:19 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 624bac4eea8875fe99e184d911a785c80fc17f29 Author: Guy Moore Date: Fri Sep 28 16:29:12 2018 -0700 Added more comments to README Tutorials/SWFFT_simple/README commit ec56db81c6c2ded85e613dc525848a8724d2e75d Merge: 8fac85696 b58eb2915 Author: Kevin Gott Date: Fri Sep 28 18:53:06 2018 -0400 Merge branch 'development' into gpu-mm commit 8fac8569671dfb1a04480947ffae69226cbd28be Author: Kevin Gott Date: Fri Sep 28 18:48:59 2018 -0400 AMREX_CUDA_HOST_DEVICE added. Src/Base/AMReX_Array.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_CUDA_Utility.H Src/Base/AMReX_CUDA_Utility.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_Managed.H Src/Base/AMReX_RealBox.H commit 521025199d2823670bf056df962c84c953d44a0b Author: Guy Moore Date: Fri Sep 28 14:53:27 2018 -0700 Added scaling comment to README Tutorials/SWFFT_simple/README commit b69e23143b88fb1479951d9e786007e51d986506 Author: Guy Moore Date: Fri Sep 28 14:48:56 2018 -0700 Confirmed FFT scaling Tutorials/SWFFT_simple/SWFFT_Test.cpp Tutorials/SWFFT_simple/SWFFT_Test_F.F90 Tutorials/SWFFT_simple/inputs.multipleGrids Tutorials/SWFFT_simple/inputs.oneGrid commit b58eb2915bd6e89301fdbed515a98ca6d4404b90 Author: Andrew Myers Date: Fri Sep 28 14:46:06 2018 -0700 Revert "use git pull instead of clone to avoid polluting the download statistics" This reverts commit d98ba486285950f512e0050a7a2c460748da11f3. build_and_deploy.sh commit a0398299a3556834c502b39e448bf1be0869c626 Merge: d98ba4862 b9d64035a Author: Andrew Myers Date: Fri Sep 28 14:36:55 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d98ba486285950f512e0050a7a2c460748da11f3 Author: Andrew Myers Date: Fri Sep 28 14:32:45 2018 -0700 use git pull instead of clone to avoid polluting the download statistics build_and_deploy.sh commit b9d64035ab504bd4b81f1332b8b3cc99921b43e3 Author: Weiqun Zhang Date: Fri Sep 28 14:26:14 2018 -0700 port BoxArray DistributionMapping version of MFIter constructor to Fortran Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 33635666f41238532f119769cce6bdd5a00d9998 Author: Andrew Myers Date: Fri Sep 28 14:19:19 2018 -0700 fix typo build_and_deploy.sh commit a3077d36650d8273d9d994a3cfbe890cbfe6e4b0 Author: Andrew Myers Date: Fri Sep 28 14:07:03 2018 -0700 generate pdf and copy it into source before building html build_and_deploy.sh commit 056bfacd8b34efdc6ab68840959dd28fb9b53f92 Author: Andrew Myers Date: Fri Sep 28 13:43:36 2018 -0700 build pdf of the docs and link to it from the html version on every commit to development .travis.yml Docs/sphinx_documentation/source/index.rst Docs/sphinx_tutorials/source/index.rst build_and_deploy.sh commit 8a05a8d6ac3c5f48c3de390f2110905bb2868301 Author: Weiqun Zhang Date: Fri Sep 28 13:38:55 2018 -0700 attempt to set computability with deviceQuery Tools/GNUMake/sites/Make.unknown commit 255e15c760592722d0ca07140dda929024d1a99f Author: Weiqun Zhang Date: Fri Sep 28 13:37:36 2018 -0700 make sure C++ standards are consistently set Tools/GNUMake/comps/nvcc.mak commit 19fde6b1b2487b260df3ab1974e617b7e5c3f6df Author: Weiqun Zhang Date: Fri Sep 28 13:29:26 2018 -0700 fix shadows Src/Base/AMReX_BArena.cpp Src/Base/AMReX_Device.H commit 9f1f6d820cdb06b81c07acdf5e63530cda31c8cf Author: Guy Moore Date: Fri Sep 28 12:39:53 2018 -0700 Updated README Tutorials/SWFFT_simple/README Tutorials/SWFFT_simple/SWFFT_Test.cpp commit e8cfe6486565367990f8033c5e129fcb3160fb9b Merge: 5cf21b1c4 121d9c0bd Author: Guy Moore Date: Fri Sep 28 12:06:13 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 5cf21b1c48e5f476fb0d791289a5b4124ca1f16b Author: Guy Moore Date: Fri Sep 28 12:04:24 2018 -0700 Adapted for 2D Tutorials/SWFFT_simple/SWFFT_Test.H Tutorials/SWFFT_simple/SWFFT_Test.cpp Tutorials/SWFFT_simple/SWFFT_Test_F.F90 Tutorials/SWFFT_simple/SWFFT_Test_F.H Tutorials/SWFFT_simple/run_me Tutorials/SWFFT_simple/run_me_2d Tutorials/SWFFT_simple/run_me_3d Tutorials/SWFFT_simple/swfft_compute.cpp commit a0090cfd73fe8117d7bb544dd858b2752e6e9db9 Author: Kevin Gott Date: Fri Sep 28 14:16:54 2018 -0400 Adjust C+ BaseFab merge to get GPU HeatEquation Running. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_Box.H commit 121d9c0bd059567a508de0d891e4e1ba98c4e8d3 Author: Andrew Myers Date: Fri Sep 28 11:15:10 2018 -0700 Fix VisMF for the case where the number of ghost cells can be different in each direction Src/Base/AMReX_VisMF.cpp commit 8d342d42bd34c712067ac2e0f059164496ecca6b Author: Guy Moore Date: Fri Sep 28 10:53:59 2018 -0700 Cleaned up SWFFT_simple - removed unecessary code from original SWFFT tutorial Tutorials/SWFFT_simple/Make.package Tutorials/SWFFT_simple/README Tutorials/SWFFT_simple/SWFFT_Test.H Tutorials/SWFFT_simple/SWFFT_Test.cpp Tutorials/SWFFT_simple/SWFFT_Test_F.F90 Tutorials/SWFFT_simple/SWFFT_Test_F.H Tutorials/SWFFT_simple/inputs.multipleGrids Tutorials/SWFFT_simple/main.cpp Tutorials/SWFFT_simple/swfft_compute.cpp commit 62be6d6affd053b9a4f130a8d4fc662693c3c5ce Author: Guy Moore Date: Fri Sep 28 10:11:00 2018 -0700 First commit of SWFFT_simple tutorial, in which only a forward FFT is performed Tutorials/SWFFT_simple/GNUmakefile Tutorials/SWFFT_simple/Make.package Tutorials/SWFFT_simple/README Tutorials/SWFFT_simple/SWFFT_Test.H Tutorials/SWFFT_simple/SWFFT_Test.cpp Tutorials/SWFFT_simple/SWFFT_Test_F.F90 Tutorials/SWFFT_simple/SWFFT_Test_F.H Tutorials/SWFFT_simple/inputs.multipleGrids Tutorials/SWFFT_simple/inputs.oneGrid Tutorials/SWFFT_simple/main.cpp Tutorials/SWFFT_simple/run_me Tutorials/SWFFT_simple/swfft_solver.cpp commit 2a6cc3ae37d1ed74e67f2f10152433845224c9ca Merge: e086a6dfb ca424826b Author: Kevin Gott Date: Thu Sep 27 20:21:26 2018 -0400 Merge branch 'development' into gpu-mm: cpp versions of BaseFab funcs Conflicts: Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit e086a6dfbe5ea61b8ab915d25fd34623b2099e2a Author: Kevin Gott Date: Thu Sep 27 13:08:22 2018 -0400 Move GPU tests from Tutorials to Test. Tests/GPU/Test/GNUmakefile Tests/GPU/Test/Make.package Tests/GPU/Test/main.cpp Tests/GPU/Test/run.exitcode Tests/GPU/Test/run.script Tests/GPU/TestB/GNUmakefile Tests/GPU/TestB/Make.package Tests/GPU/TestB/main.cpp Tests/GPU/TestB/return_test.F90 Tests/GPU/TestC/GNUmakefile Tests/GPU/TestC/Make.package Tests/GPU/TestC/main.cpp Tests/GPU/TestC/run.summit Tests/GPU/TestC/run.summitdev commit ca424826bf266655a50546dc083e7d0bbd2f02f8 Author: Weiqun Zhang Date: Wed Sep 26 18:11:14 2018 -0700 add an assertion Src/Base/AMReX_BaseFab.H commit 56979db722ffdbbbdfb49c215d8d082cdfe91b36 Author: Max Katz Date: Wed Sep 26 14:02:31 2018 -0400 Prefix CUDA_MAX_THREADS with AMREX Src/Base/AMReX_CUDA.F90 Tools/GNUMake/Make.defs commit 3fd8df894308fdbd3e640ba2ae4a342d0988921d Author: Max Katz Date: Wed Sep 26 13:57:48 2018 -0400 Prefix GPUS_PER_SOCKET/NODE with AMREX Src/Base/AMReX_Device.cpp Tools/GNUMake/Make.defs commit 32bc96f5d0006430d6f3e4ea41c943ba49f27b0e Author: Max Katz Date: Wed Sep 26 13:56:07 2018 -0400 Remove CUDA_UM Src/Base/AMReX_BArena.cpp Tools/GNUMake/Make.defs commit 919cbd5d129b9ac301ac2ff4887d601c739266f7 Author: Max Katz Date: Wed Sep 26 13:54:25 2018 -0400 Remove unused OMP_OFFLOAD Tools/GNUMake/Make.defs commit f9ee1dcf86042562e505ee0cdba921863c9709be Author: Weiqun Zhang Date: Wed Sep 26 10:48:15 2018 -0700 make sure global operators are used Src/Base/AMReX_BArena.cpp commit 7a34a97a3293b9f72f8be794b40f25b2038d72b5 Author: Weiqun Zhang Date: Wed Sep 26 10:44:17 2018 -0700 remove unused variables Src/Base/AMReX_MultiFab.cpp commit d8be47241364208e8887f52f75d97819696a046d Author: Weiqun Zhang Date: Wed Sep 26 10:40:37 2018 -0700 remove unused variable Src/Base/AMReX_FabArray.H commit e68f67a684be0ab51b748e7af667620b0af532da Author: Max Katz Date: Tue Sep 25 20:10:21 2018 -0400 Free local communicator Src/Base/AMReX_Device.cpp commit 2b6b20403f14b796ce8d6225da3058bf9b217986 Author: Max Katz Date: Tue Sep 25 20:03:39 2018 -0400 Use PD Communicator Src/Base/AMReX_Device.cpp commit 51e078eec9311ccb427b5b75ee5531d67ac9e212 Author: Max Katz Date: Tue Sep 25 20:00:43 2018 -0400 Remove unused variable Src/Base/AMReX_Device.H commit 1dd184209fed7848a4b03dec2583cf4ae0c2562e Author: Max Katz Date: Tue Sep 25 19:59:56 2018 -0400 Add a definition for max_cuda_streams Src/Base/AMReX_Device.cpp commit e76cc4031aaa71bc34b7d89a73bd0a9262a9d907 Merge: 01a4ac424 cfead3cb9 Author: Andrew Myers Date: Tue Sep 25 15:26:31 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 01a4ac4249302e6a8d19402b4b1c70ca0b19fc70 Author: Andrew Myers Date: Tue Sep 25 15:26:12 2018 -0700 add ba / dmap access functions to EBFArrayBoxFactory Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp commit cfead3cb93b186c4f709cea5a13f0c3b2b6343c9 Author: Tan Nguyen Date: Tue Sep 25 14:33:04 2018 -0700 update async version of FillPatchIter Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Base/AMReX_MultiFabUtil_Perilla.H Src/Base/AMReX_MultiFabUtil_Perilla.cpp commit 0adfc2d409071e5ce0350c07f64335e2f044c927 Merge: 14aee912a 7c0b43f32 Author: Weiqun Zhang Date: Tue Sep 25 12:56:33 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 14aee912a1d05f56d40b805edf5a887213ce5e37 Author: Weiqun Zhang Date: Tue Sep 25 12:54:24 2018 -0700 EB: fix roundoff error issues Src/EB/AMReX_eb2_3d.F90 commit 7c0b43f32b258da45f27c0cac337f057ec5e7788 Merge: b42886c01 9f3e47def Author: WeiqunZhang Date: Tue Sep 25 12:11:21 2018 -0700 Merge pull request #324 from zingale/development work around intel compiler crash commit 9f3e47defef515291acae8ff882f6fab2d4f9b00 Author: Michael Zingale Date: Tue Sep 25 11:54:47 2018 -0700 work around intel compiler crash Tools/F_scripts/write_probin.py commit b42886c011559ded9e20255bd8f3d655797ee813 Merge: 85ea48afe 89ff1b368 Author: WeiqunZhang Date: Tue Sep 25 09:23:03 2018 -0700 Merge pull request #322 from wolfram-schmidt/development Development commit dbad922a63dfaa45a6954fef211e3c0df424f7fd Merge: f61963323 85ea48afe Author: Brandon Runnels Date: Tue Sep 25 09:58:04 2018 -0600 Merge branch 'development' into mc-nodelinop commit f619633233fdd7e915bfd8f872032655615f500b Author: Brandon Runnels Date: Tue Sep 25 09:57:36 2018 -0600 updated MLMG solver for multicomponent solve Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 89ff1b368dec291b0b7fa54c60940875f9c4f3c1 Author: Wolfram Schmidt Date: Tue Sep 25 11:52:20 2018 +0200 Cleaned up nec.mak Tools/GNUMake/comps/nec.mak commit 021e3887788848d568bc437f6a59f14e45eddcca Merge: b2dc22a13 85ea48afe Author: Wolfram Schmidt Date: Tue Sep 25 10:14:15 2018 +0200 Merge remote-tracking branch 'upstream/development' into development commit 85ea48afedf511d0035fcd0ac4bce4c4f5d56a1c Author: Jean M. Sexton Date: Mon Sep 24 17:53:47 2018 -0700 Added ARKODE interface for Sundials 3.X from CVODE interface, used with USE_ARKODE=TRUE and USE_SUNDIALS3=TRUE Docs/sphinx_documentation/source/SUNDIALS3.rst Src/Extern/SUNDIALS3/Make.package Src/Extern/SUNDIALS3/arkode_interface.f90 Src/Extern/SUNDIALS3/farkode.f90 Tools/GNUMake/packages/Make.sundials3 Tutorials/SUNDIALS3/EX_ark_analytic_fp/GNUmakefile Tutorials/SUNDIALS3/EX_ark_analytic_fp/Make.package Tutorials/SUNDIALS3/EX_ark_analytic_fp/ark_analytic_fp.f90 commit 3c6a51dfd6ecf5aaf88aba4ffff73dbd9d5a2927 Author: Jean M. Sexton Date: Mon Sep 24 14:00:08 2018 -0700 Added initial documentation for added Sundials version 3.X support Docs/sphinx_documentation/source/CVODE.rst Docs/sphinx_documentation/source/Chapter14.rst Docs/sphinx_documentation/source/SUNDIALS3.rst commit c28b1e5f4adb2cb921aeff54b55fbe2a686f07c6 Author: Jean M. Sexton Date: Mon Sep 24 13:18:34 2018 -0700 USE_SUNDIALS3=TRUE links in David's updated fcvode interface for Sundials 3.X, 5 new example added to Tutorials Src/Extern/SUNDIALS3/Make.package Src/Extern/SUNDIALS3/cvode_interface.f90 Src/Extern/SUNDIALS3/fcvode.f90 Src/Extern/SUNDIALS3/fnvector_serial.f90 Src/Extern/SUNDIALS3/fnvector_serial_fprefix.f90 Src/Extern/SUNDIALS3/fsunlinsol_dense.f90 Src/Extern/SUNDIALS3/fsunmat_dense.f90 Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.sundials3 Tutorials/SUNDIALS3/EX1/GNUmakefile Tutorials/SUNDIALS3/EX1/Make.package Tutorials/SUNDIALS3/EX1/inputs Tutorials/SUNDIALS3/EX1/integrate_ode.f90 Tutorials/SUNDIALS3/EX1/main.cpp Tutorials/SUNDIALS3/EX1/myfunc_F.H Tutorials/SUNDIALS3/EX1/ode_mod.f90 Tutorials/SUNDIALS3/EX_cv_analytic_fp/GNUmakefile Tutorials/SUNDIALS3/EX_cv_analytic_fp/Make.package Tutorials/SUNDIALS3/EX_cv_analytic_fp/cv_analytic_fp.f90 Tutorials/SUNDIALS3/EX_cv_analytic_fp/cv_analytic_fp.out Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns/GNUmakefile Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns/Make.package Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns/cv_analytic_sys_dns.f90 Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns/cv_analytic_sys_dns.out Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns_jac/GNUmakefile Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns_jac/Make.package Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns_jac/cv_analytic_sys_dns_jac.f90 Tutorials/SUNDIALS3/EX_cv_analytic_sys_dns_jac/cv_analytic_sys_dns_jac.out Tutorials/SUNDIALS3/EX_cv_brusselator_dns/GNUmakefile Tutorials/SUNDIALS3/EX_cv_brusselator_dns/Make.package Tutorials/SUNDIALS3/EX_cv_brusselator_dns/cv_brusselator_dns.f90 Tutorials/SUNDIALS3/EX_cv_brusselator_dns/cv_brusselator_dns.out commit b2dc22a1323683dcb314dae78ad1188381cdab88 Merge: 23d55db77 87fecafe9 Author: Wolfram Schmidt Date: Mon Sep 24 12:19:18 2018 +0200 Merge remote-tracking branch 'upstream/development' into development commit 23d55db77fd1672b1cd1d668a06dcdb95006299e Author: Wolfram Schmidt Date: Mon Sep 24 12:18:31 2018 +0200 Another fix for NEC. Src/F_BaseLib/fabio_c.c Tools/GNUMake/sites/Make.hs commit ce6518915bf7d1c637c7d11fdcae58a39ee10ddd Merge: 9d79af8d4 87fecafe9 Author: Max Katz Date: Sat Sep 22 09:21:02 2018 -0400 Merge branch 'development' into gpu commit 87fecafe9e4d129429b45a0df9b1c25baa77d575 Author: Kevin Gott Date: Sat Sep 22 02:06:51 2018 -0400 Fix timer. Tests/BaseFabTesting/main.cpp commit cd32a15b912ffc1e03f2f2c9c44051592e16a61c Author: Kevin Gott Date: Sat Sep 22 01:55:30 2018 -0400 Small change to BaseFabTest. Tests/BaseFabTesting/main.cpp commit 750884a083365e65e4659dab1fa0606942632ac5 Merge: 20fa1d364 1c5f001a8 Author: kngott Date: Fri Sep 21 22:48:07 2018 -0700 Merge branch 'development' of https://github.com/AMReX-codes/amrex into development commit 20fa1d3645857e23979fe64fd3b5fd8fb792e137 Author: kngott Date: Fri Sep 21 22:47:55 2018 -0700 BaseFab edit for 1 iter. Tests/BaseFabTesting/inputs Tests/BaseFabTesting/main.cpp commit 1c5f001a82bdc9244ad952366e8d4c2a5070fea1 Author: Tan Nguyen Date: Fri Sep 21 14:18:17 2018 -0700 update RGIter Src/Base/AMReX_FabArrayBase.H commit 9c511332eb82a8e2c165b5020a1d08441d81112f Merge: e8de6e431 cb49c42d5 Author: Tan Nguyen Date: Fri Sep 21 13:43:39 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e8de6e43110a332a9aa8123bcc4a5fe548167b92 Author: Tan Nguyen Date: Fri Sep 21 13:43:25 2018 -0700 update AsyncFillPatchIter Src/AmrTask/rts_impls/Perilla/Perilla.H Src/AmrTask/rts_impls/Perilla/Perilla.cpp Src/AmrTask/rts_impls/Perilla/PerillaConfig.H Src/AmrTask/rts_impls/Perilla/RegionGraph.H Src/Base/AMReX_MultiFabUtil_Perilla.H Src/Base/AMReX_MultiFabUtil_Perilla.cpp Src/Base/Make.package commit cb49c42d59d8df605ae75060e5a7c2b4093ffb95 Author: kngott Date: Fri Sep 21 12:40:03 2018 -0700 Update to BaseFabTest: some results fixed and masks set randomly. Tests/BaseFabTesting/main.cpp commit 6d4d2c1630e43c561dd637385756aa3c14596c7f Author: Weiqun Zhang Date: Fri Sep 21 10:51:34 2018 -0700 For portability, static_cast std::streampos to std::streamoff for comparison with long Src/Base/AMReX_VisMF.cpp commit f9c36dc1b37a4e50d0d1b48b96cac00c4f69ed3a Author: Andrew Myers Date: Fri Sep 21 13:32:36 2018 -0400 wip - beging reorg of gpu particle code Src/Particle/AMReX_ArrayOfStructs.H Src/Particle/AMReX_Particle.H Src/Particle/AMReX_ParticleTile.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_StructOfArrays.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 9d79af8d46745f0db98a089d051c495c0943908a Author: Max Katz Date: Fri Sep 21 10:33:01 2018 -0400 Use PGI as host compiler when using OpenACC Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak commit 5f01b8a8e5f5d0cc4476c719069efc68b4f1c8be Merge: d4ab5da69 17fa3737c Author: Wolfram Schmidt Date: Fri Sep 21 12:01:19 2018 +0200 Merge remote-tracking branch 'upstream/development' into development commit 2191950236b8f3afd92882b6e7a53e78f2202ba6 Merge: e843ef37a 17fa3737c Author: Weiqun Zhang Date: Thu Sep 20 21:15:04 2018 -0700 Merge branch 'development' into devirtualize-fab commit 17fa3737c9b5ec8879cb8aeaaca0f04cdf88ea86 Merge: 56b1039f3 ddf4807bc Author: Weiqun Zhang Date: Thu Sep 20 21:13:52 2018 -0700 Merge branch 'development' into basefab_T commit ddf4807bc1803686cf980fe0a2536865fc4896f4 Merge: ec04f3fe7 928e8a5f1 Author: Weiqun Zhang Date: Thu Sep 20 18:01:15 2018 -0700 Merge branch 'development' into mlmg commit ec04f3fe743cd4b4e93d87da97dd9609c1090fe0 Author: sireeveslbl Date: Thu Sep 20 15:53:30 2018 -0700 Fixed PETSC Src/Extern/PETSc/AMReX_PETSc.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 928e8a5f1214c8969ada1b570a054f45d9393d9c Merge: 1c06400dc b8b3da920 Author: Johannes Blaschke Date: Thu Sep 20 15:51:12 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 1c06400dc9b19dcddb30dcca20f057725c555713 Author: Johannes Blaschke Date: Thu Sep 20 15:51:10 2018 -0700 levelset factory now outputs eb-geometry Src/EB/AMReX_EB_levelset.H commit 99e3ddc9e4aae9ab30b1c73203fc41409cdf76f6 Author: Marc Day Date: Thu Sep 20 15:36:29 2018 -0700 pass flux call down to linop Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 56b1039f305ac8f26cbdda63bea7cfaeb6e35125 Author: kngott Date: Thu Sep 20 15:24:16 2018 -0700 remove whitespace Tests/BaseFabTesting/inputs commit 760663448a9374beebe075de57120ea01c7a555b Merge: 97560a325 2ebd40238 Author: Marc Day Date: Thu Sep 20 15:13:06 2018 -0700 Merge branch 'development' into marc/forkjoin_dev commit 2ebd40238fe38bb52f42fdae024c80689e279fee Author: Marc Day Date: Thu Sep 20 15:12:32 2018 -0700 Add a getFluxes function that takes a solution rather than using the internal one, which may not exist unless solve is called. Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit a1884b8e39f533671b3a0c3d2446cfc0a44a21f1 Author: kngott Date: Thu Sep 20 14:34:34 2018 -0700 mask fix Tests/BaseFabTesting/inputs Tests/BaseFabTesting/main.cpp commit af8dbbdd0185c14446c75dcd77fa32ed5c488dd1 Author: kngott Date: Thu Sep 20 13:43:52 2018 -0700 More BaseFabTest adjustments. Tests/BaseFabTesting/main.cpp commit 5a2b3c99deb75b30984c52a0fc14bf52a2a49267 Author: kngott Date: Thu Sep 20 13:37:35 2018 -0700 Less iterations, all basefab routines. Tests/BaseFabTesting/inputs Tests/BaseFabTesting/main.cpp commit e89addee8935f821d2e2f2ea3763ce33ef0c331c Merge: 3cf9be60c 6177caca8 Author: Weiqun Zhang Date: Thu Sep 20 13:25:49 2018 -0700 Merge branch 'basefab_T' of github.com:AMReX-Codes/amrex into basefab_T commit 773997eddebe446c65a0b0a8d7cd11cce2fecaae Merge: e5272a82f b8b3da920 Author: Max Katz Date: Thu Sep 20 16:14:19 2018 -0400 Merge branch 'development' into gpu commit b8b3da920dc0ddb18c41e409aa0d9bcf1471c3c1 Author: Max Katz Date: Thu Sep 20 16:11:34 2018 -0400 Add template for max reduction Src/Base/AMReX_BLFort.H commit e5272a82f8684d1ab2800586e19efe5aaa14e936 Author: Max Katz Date: Thu Sep 20 16:10:23 2018 -0400 Add max reduction Src/Base/AMReX_BLFort.H commit 3cf9be60c1cee4dd559aed229fda59208092d113 Author: Weiqun Zhang Date: Thu Sep 20 12:54:02 2018 -0700 minor Src/Boundary/AMReX_Mask.cpp Src/EB/AMReX_EB2_GeometryShop.H commit 415a8a0086e72165eb4c8a872d568b8dcdc3a4b6 Author: Max Katz Date: Thu Sep 20 15:21:54 2018 -0400 Split up kernel launch line Tools/F_scripts/write_cuda_headers.py commit dfb95920fb25b41fee2a1430fec8b39bd10db072 Author: Max Katz Date: Thu Sep 20 15:10:08 2018 -0400 Throw an error if not using PGI or XL with CUDA Tools/GNUMake/Make.defs commit 6177caca8213b5d3a8ac8927806b05ea2c79e63f Author: kngott Date: Thu Sep 20 11:41:46 2018 -0700 Clean up prints. Tests/BaseFabTesting/main.cpp commit 9e3e723f7ba4b41229d513658b1510f0b7953b46 Author: kngott Date: Thu Sep 20 11:28:03 2018 -0700 Partial test update. Tests/BaseFabTesting/main.cpp commit 1ddc5b2cc6c9b0a4899954b132227fcfa414ebe6 Author: Weiqun Zhang Date: Thu Sep 20 11:17:57 2018 -0700 fix uninitialized value Src/Base/AMReX_BaseFab.H commit 7b0fbd276822b1a2ea4e5d25bbfebfdb5111a3a5 Author: Weiqun Zhang Date: Thu Sep 20 10:18:12 2018 -0700 add StridedPtr and use it Src/Base/AMReX_BaseFab.H commit 9ed0650832d9c400a46dcfe96f39b1830a13fc76 Author: Donald E. Willcox Date: Thu Sep 20 10:18:18 2018 -0400 preserve case for gpu targets in public statements Tools/F_scripts/gpu_fortran.py commit 38ea4e77a0058259e19451bfd9cf6924d1394500 Author: Alice Harpole Date: Thu Sep 20 09:19:09 2018 -0400 Add charstring compiler flag (#321) Adds -Mcuda=charstring flag to pgi.mak. This is needed for offloading some of the gravity routines to GPU in Castro. Tools/GNUMake/comps/pgi.mak commit afed15270ed58609866a69886bc87eb6af71d8fd Merge: 57be1050a 991eab98f Author: Weiqun Zhang Date: Wed Sep 19 21:54:56 2018 -0700 Merge branch 'basefab_T' of github.com:AMReX-Codes/amrex into basefab_T commit 57be1050a2e6bd769609c70e1e7be0d14f0b25ed Author: Weiqun Zhang Date: Wed Sep 19 21:54:07 2018 -0700 clean up Src/Base/AMReX_BaseFab.H commit 0b269ac566f33eb6a571a423d3fd2a410a0d1a35 Author: Weiqun Zhang Date: Wed Sep 19 21:39:19 2018 -0700 new version of BaseFab function templates Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_c.H Src/Base/AMReX_BaseFab_c.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 991eab98fe4c6f8a709bd7504bb37822d2487be8 Author: Kevin Gott Date: Wed Sep 19 23:45:23 2018 -0400 Compile worked on BaseFab test. Tests/BaseFabTesting/GNUmakefile Tests/BaseFabTesting/inputs Tests/BaseFabTesting/main.cpp commit 8ce5ecd7dbf1335f55a907b3748ddb28e3202d99 Author: Kevin Gott Date: Wed Sep 19 20:47:35 2018 -0400 Add number of components to test. Tests/BaseFabTesting/inputs Tests/BaseFabTesting/main.cpp commit 552af8241010354126edd98022c7df31e540602c Author: Tan Nguyen Date: Wed Sep 19 16:52:04 2018 -0700 add asyncFillPatchIter Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/Perilla/Perilla.H Src/AmrTask/rts_impls/Perilla/Perilla.cpp Src/AmrTask/rts_impls/Perilla/RGIter.H Src/AmrTask/rts_impls/Perilla/RGIter.cpp commit 00b27ac091cef8de3647497d044fa0c1a7f2dc47 Merge: 70ed8cb76 d2869ab98 Author: Weiqun Zhang Date: Wed Sep 19 16:39:58 2018 -0700 Merge branch 'basefab_c' into basefab_T commit 70ed8cb76f3ea85fcdfd92f3841c292be06bff95 Author: Weiqun Zhang Date: Wed Sep 19 16:38:07 2018 -0700 another version of linComb Src/Base/AMReX_BaseFab.H commit 7d9f62944a7456098b985bc7b52a4b5b7868b019 Author: Brandon Runnels Date: Wed Sep 19 17:01:20 2018 -0600 minor changes to fix NAN errors Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 92e952a00020251c2164d24dd530eeb70970e03a Author: Max Katz Date: Wed Sep 19 18:46:17 2018 -0400 Fix macros Src/Base/AMReX_ArrayLim.H commit 826b23c08a9e0fdc9eb1822e13fdb8dcc6cfd1eb Author: Weiqun Zhang Date: Wed Sep 19 15:42:31 2018 -0700 an alternative version of linComb Src/Base/AMReX_BaseFab.H commit d4e956eda3257514787a2350e500d2ecd3c62451 Author: Weiqun Zhang Date: Wed Sep 19 15:02:12 2018 -0700 fix bug Src/Base/AMReX_BaseFab.H commit fb668653ffdfe594e5a1aa75376643a10e193dd0 Author: Ann Almgren Date: Wed Sep 19 14:27:33 2018 -0700 Add the option to set the bottom_solver_type through the MacProjector. Src/LinearSolvers/MLMG/AMReX_MacProjector.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit 8df7e4b41be58074ab65e3bbcf3376ae529b90f1 Author: Weiqun Zhang Date: Wed Sep 19 13:14:30 2018 -0700 first pass to template implementation Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_REAL.H Src/Base/AMReX_RESTRICT.H Src/Base/CMakeLists.txt Src/Base/Make.package commit ec5fe31f02ac81414bc4beaee86412f42382dad7 Author: Andrew Myers Date: Wed Sep 19 16:44:04 2018 -0400 Revert "Respect the COMP choice when compiling with CUDA" This reverts commit ff00b18c80682a5f9de44f7e22e0ab883e2b2305. Tools/GNUMake/comps/nvcc.mak commit fda299797705f6e721143b8f456ff5d3621969ed Author: Andrew Myers Date: Wed Sep 19 16:22:24 2018 -0400 remove un-needed boilerplate from CudaManagedAllocator; let compiler define constructors Src/Base/AMReX_CudaAllocators.H commit d2869ab9836eaf0a401f5f2276b34efbcf452718 Author: kngott Date: Wed Sep 19 12:14:30 2018 -0700 Working BaseFab test suite. Tests/BaseFabTesting/GNUmakefile Tests/BaseFabTesting/inputs Tests/BaseFabTesting/main.cpp commit 0b965fc36be5b9605edd23d4d25933223bbcedbe Merge: 8dce409e6 d91e3c5b8 Author: Brandon Runnels Date: Wed Sep 19 12:46:59 2018 -0600 Merge branch 'development' into mc-nodelinop commit 8dce409e67c771ba1bf4b967f8438b64b7916a8d Author: Brandon Runnels Date: Wed Sep 19 12:46:25 2018 -0600 updated MLMG for multicomponent solve Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit bfc628da256ba2a3a263918e8aef1d3b720533cc Author: kngott Date: Wed Sep 19 11:32:57 2018 -0700 First draft of BaseFab Test. Tests/BaseFabTesting/GNUmakefile Tests/BaseFabTesting/Make.package Tests/BaseFabTesting/main.cpp commit d91e3c5b879ce7ce4443a745e586a69881b22d5a Author: Andrew Myers Date: Wed Sep 19 11:30:07 2018 -0700 protect against floating point exceptions in DistributionMapping::makeKnapSack Src/Base/AMReX_DistributionMapping.cpp commit ff00b18c80682a5f9de44f7e22e0ab883e2b2305 Author: Max Katz Date: Wed Sep 19 13:02:42 2018 -0400 Respect the COMP choice when compiling with CUDA Tools/GNUMake/comps/nvcc.mak commit f532c44f946958cc39355ed6931b1b90f938851b Author: Max Katz Date: Wed Sep 19 13:01:59 2018 -0400 Always use gcc for the preprocessing Tools/GNUMake/Make.rules commit fc4b7f01b7d084d547f1706cb96365f062b3388f Author: Weiqun Zhang Date: Wed Sep 19 08:52:07 2018 -0700 expose MLMG and LinOp from MacProjector Src/LinearSolvers/MLMG/AMReX_MacProjector.H commit d4ab5da6933ba92f525b553e8f9d5f7ef75cd101 Author: Wolfram Schmidt Date: Wed Sep 19 17:21:11 2018 +0200 Added configuration for NEC Aurora (only serial) to GNUMake and excluded GNU extensions not supported by NEC compiler via __NEC__ preprocessor symbol. Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.H Src/Base/AMReX_BLBackTrace.cpp Src/F_BaseLib/backtrace_c.cpp Src/F_BaseLib/fabio_c.c Tools/GNUMake/Make.defs Tools/GNUMake/Make.machines Tools/GNUMake/comps/nec.mak Tools/GNUMake/sites/Make.hs commit 20790814b01bbd1a0587148c29419aadd8742818 Author: Max Katz Date: Wed Sep 19 11:10:33 2018 -0400 Catch numbers in subroutine names Tools/F_scripts/write_cuda_headers.py commit 310ffbf104842929c723603d4a9fdd31144ae87f Author: Weiqun Zhang Date: Tue Sep 18 21:28:39 2018 -0700 rm slowCopy Src/Base/AMReX_BaseFab.H commit 01a2d92387a4f3b962b00b628a7012bda9044c7e Author: Weiqun Zhang Date: Tue Sep 18 21:08:00 2018 -0700 ifdef out specialization Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp commit f28ee981b4ce45c57009a2197c227a28f0d2e4b5 Author: Weiqun Zhang Date: Tue Sep 18 20:28:09 2018 -0700 remove trailing space Tools/GNUMake/Make.defs commit 2fd22c8b3a770aff9f74df92632f027496230b81 Merge: 41db4e235 229cb6d31 Author: Weiqun Zhang Date: Tue Sep 18 20:26:19 2018 -0700 Merge branch 'basefab_c' of github.com:AMReX-Codes/amrex into basefab_c commit 41db4e2354844fdc3241dce0d99974bd0f692d08 Author: Weiqun Zhang Date: Tue Sep 18 20:26:05 2018 -0700 c -> cpp Src/Base/AMReX_BaseFab_c.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 91ec9a71e350f4d82338f17eccc538832c914488 Author: Weiqun Zhang Date: Tue Sep 18 20:18:20 2018 -0700 add AMREX_RESTRICT Src/Base/AMReX_BaseFab_c.H Src/Base/AMReX_BaseFab_c.c Src/Base/AMReX_REAL.H commit 229cb6d310e03acb559c4178e2930796b9d062c3 Author: Kevin Gott Date: Tue Sep 18 20:18:31 2018 -0400 Add USE_GPU_PRAGMA option to GNUMakefile. Tools/GNUMake/Make.defs commit f6d5c1126cca1c9a260d611ec7bd1c3a5e8e5b57 Author: Weiqun Zhang Date: Tue Sep 18 17:14:43 2018 -0700 fix a test Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 380d5a19434060995f10bce9a722b103bfd30bc0 Author: Weiqun Zhang Date: Tue Sep 18 16:41:24 2018 -0700 missing fabs Src/Base/AMReX_BaseFab_c.c commit 83d693fa651b2af7f234ce23ff629a53835b1d3e Merge: 39ea73594 deca90b22 Author: Brandon Runnels Date: Tue Sep 18 15:41:06 2018 -0600 Merge branch 'development' into mc-nodelinop commit 39ea73594ec6872d88da8599e291ce81e868e3cf Author: Brandon Runnels Date: Tue Sep 18 15:38:16 2018 -0600 initial update of mllinop for multicomponent solves Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 995acb2b91f4178412d83d810de999aedcb848a9 Author: Weiqun Zhang Date: Tue Sep 18 14:17:41 2018 -0700 removed some BL_NO_FORT's Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_MultiFab.cpp commit b6083a89ffea3f55d3851a77458b986d9ee928e6 Merge: b26def87f deca90b22 Author: Kevin Gott Date: Tue Sep 18 17:03:50 2018 -0400 Merge branch 'development' into gpu-mm Conflicts: Src/Base/AMReX_BaseFab_nd.F90 commit 61980308b13a8db3ad874dbb1641b063542d7a47 Author: Weiqun Zhang Date: Tue Sep 18 14:02:24 2018 -0700 update setval_ifnot Src/Base/AMReX_BaseFab.cpp commit b26def87fd980a576762c564faf5ce9586c14025 Author: Kevin Gott Date: Tue Sep 18 16:56:43 2018 -0400 Remove CPU versions of now Device functions. Src/Base/AMReX_Managed.H commit 2cfcb81e5922b95838c05372d3d406c8cc673a3b Merge: f0db9e99d 53bd120ce Author: Weiqun Zhang Date: Tue Sep 18 13:54:03 2018 -0700 Merge branch 'development' into basefab_c commit 53bd120ce750886b33d3478a5f81c0da60aa3a6a Author: Weiqun Zhang Date: Tue Sep 18 13:49:38 2018 -0700 add BaseFab::setValIfNot Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_MultiFab.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit f0db9e99d43a54ca1badfb1a503a913d556bf4dd Author: Weiqun Zhang Date: Tue Sep 18 13:19:10 2018 -0700 use c versions in BaseFab Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_c.H Src/Base/AMReX_BaseFab_c.c Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 commit ee0f3775fed2645c6f0237ce9cf70a4483a96354 Merge: 2fc2f8e43 5e3d0608d Author: Donald E. Willcox Date: Tue Sep 18 20:06:31 2018 +0000 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 2fc2f8e432ce495d8dd33b2b753cbddf949b3a88 Author: Donald E. Willcox Date: Tue Sep 18 20:06:26 2018 +0000 AMREX_ARLIM_ARG with CUDA always returns 3 arguments. Src/Base/AMReX_ArrayLim.H commit 5e3d0608d225749262afb05ee86744771c22dcec Author: dwillcox Date: Tue Sep 18 15:47:28 2018 -0400 Replace procedure with procedure_device, preserving the case of procedure. Tools/F_scripts/gpu_fortran.py commit 151591f0a4584f50f5e46c43966ea6e2ea7db046 Author: Weiqun Zhang Date: Tue Sep 18 11:34:01 2018 -0700 tidy Src/Base/AMReX_BaseFab_c.c commit d6faa268c40e2e41faae905b4362174a0fe7de89 Author: Weiqun Zhang Date: Tue Sep 18 11:21:20 2018 -0700 first pass Src/Base/AMReX_BaseFab_c.H Src/Base/AMReX_BaseFab_c.c Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_MultiFab.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit deca90b22f50857cb517e2f07bfcc057c259d34d Author: Weiqun Zhang Date: Tue Sep 18 10:40:51 2018 -0700 eb: add more protection against roundoff errors Src/EB/AMReX_eb2_3d.F90 commit c08ad19cfbcfc69fda1718487c74e44dfe88b732 Merge: 63632196e b3f2725aa Author: Max Katz Date: Tue Sep 18 12:43:47 2018 -0400 Merge branch 'development' into gpu commit 63632196e9e5700fc531061e532a6b10b1d985a6 Author: dwillcox Date: Tue Sep 18 12:31:34 2018 -0400 Fix a subroutine-detecting bug. Tools/F_scripts/gpu_fortran.py commit b3f2725aa632d2860ea4ef68f4f39db13258843b Merge: dd9e391e2 f5c68e313 Author: WeiqunZhang Date: Tue Sep 18 09:09:00 2018 -0700 Merge pull request #311 from AMReX-Codes/statedata Statedata commit dcbe6deeb5becf3f3ca4f9fd7a0f9d0aa12077e1 Merge: b0ba1c547 8f20d5130 Author: Donald E. Willcox Date: Tue Sep 18 05:52:48 2018 +0000 Merge branch 'gpu-fortran-update' into gpu to support StarKiller Microphysics. commit 8f20d5130f35c5d769cbf82c58b94964a9bc6501 Author: Donald E. Willcox Date: Tue Sep 18 05:52:27 2018 +0000 GPU Fortran preprocessing script supports StarKiller. Tools/F_scripts/gpu_fortran.py commit c2e9a0bdabe5569a467bdacf555832431ead0759 Author: Weiqun Zhang Date: Mon Sep 17 22:04:47 2018 -0700 more on BaseFab C functions Src/Base/AMReX_BaseFab_c.H Src/Base/AMReX_BaseFab_c.c Src/Base/AMReX_BaseFab_f.H commit dd9e391e2f15cfd77a920f5be4cd7b22457acaf3 Author: Tan Nguyen Date: Mon Sep 17 17:12:49 2018 -0700 regular updates Src/AmrTask/rts_impls/Perilla/PackageQueue.cpp Src/AmrTask/rts_impls/Perilla/PerillaConfig.H Src/AmrTask/rts_impls/Perilla_upc++/PerillaConfig.H Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/GNUmakefile commit b976cead5a5f0517defc8680f62ad0b5442195f9 Author: Kevin Gott Date: Mon Sep 17 20:05:18 2018 -0400 Test showing Fortran return problem. Tutorials/GPU/TestB/GNUmakefile Tutorials/GPU/TestB/Make.package Tutorials/GPU/TestB/main.cpp Tutorials/GPU/TestB/return_test.F90 commit 8f7255047d8464a7a70dcf8b22fc57234735c996 Author: Weiqun Zhang Date: Mon Sep 17 16:59:18 2018 -0700 tweak macros Src/Base/AMReX_BaseFab_c.c commit 5b22ac305e7bb55d0f39d0905d6f906a77b58957 Author: Kevin Gott Date: Mon Sep 17 19:30:44 2018 -0400 Missed parenthesis. Src/Base/AMReX_MultiFab.cpp commit b0ba1c5475705a64c7ebe3629909d85bbed2004d Author: Max Katz Date: Mon Sep 17 17:15:57 2018 -0400 Function signatures should be case sensitive in C++ Tools/F_scripts/write_cuda_headers.py commit f43f16cb37bbe3fcafd60adc6adb98e283258efd Author: Weiqun Zhang Date: Mon Sep 17 13:48:44 2018 -0700 tidy and check in new files Src/Base/AMReX_BaseFab_c.H Src/Base/AMReX_BaseFab_c.c commit 85e68ce79dcef853e61d89a6c37dc38b9c26fe8a Author: Weiqun Zhang Date: Mon Sep 17 13:24:10 2018 -0700 start BaseFab_c Src/Base/AMReX_BaseFab.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit d73d9b995a98da777eb3c067b2daa56474e56604 Author: Tan Nguyen Date: Mon Sep 17 12:46:06 2018 -0700 just regular updates Src/AmrTask/rts_impls/Perilla/PackageQueue.cpp Src/AmrTask/rts_impls/Perilla/Perilla.cpp Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/GNUmakefile Src/Base/AMReX_MemPool.cpp commit b91ae7fd7dd6856c820d4b441598825f3e4c9c36 Merge: 1a6c653f9 3d701d39f Author: Weiqun Zhang Date: Mon Sep 17 11:15:04 2018 -0700 Merge branch 'mlmg' into development commit 1a6c653f9f44ae80dcbb5e03bcd9203db70644ee Merge: bab0ae7b9 74071026e Author: Weiqun Zhang Date: Mon Sep 17 11:14:55 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3d701d39f64e5c7d6c125936ed3fce97f02fb7da Author: Weiqun Zhang Date: Mon Sep 17 11:13:02 2018 -0700 CellEB2 test: more general at boundary Tests/LinearSolvers/CellEB2/MyTest.cpp Tests/LinearSolvers/CellEB2/MyTest_F.H Tests/LinearSolvers/CellEB2/mytest_f.F90 commit 2e39720bd140f0705021f0e0ae88e3713f613f53 Author: dwillcox Date: Mon Sep 17 14:01:59 2018 -0400 Update GPU script for StarKiller Microphysics. Tools/F_scripts/gpu_fortran.py commit 74071026e5a1b26c62dcf6c19a68dc4be3f65c18 Author: Andrew Myers Date: Mon Sep 17 10:54:51 2018 -0700 adding overloaded versions of get_particles, num_particles, and add_particle to the Fortran interfaces Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 commit bab0ae7b93dd02195b77943a03b8b1464b7dc965 Author: Weiqun Zhang Date: Mon Sep 17 09:38:58 2018 -0700 add a new geometry type to CellEB2 test Tests/LinearSolvers/CellEB2/initEB.cpp commit cbfcd9b0083fd2a4933c6ac7f1ae397ff7da1136 Author: Weiqun Zhang Date: Sun Sep 16 15:43:55 2018 -0700 fix path Tools/CompileTesting/compiletesting.py commit d1ad2ce60c0a89176dfb87ae1912b0c3420f163f Author: Weiqun Zhang Date: Sun Sep 16 15:38:30 2018 -0700 update compile testing Tools/CompileTesting/compiletesting.py commit f3abf6e02581576f0ff62a7eff5f4f6de233f366 Author: Weiqun Zhang Date: Sun Sep 16 15:21:48 2018 -0700 inputs for new EB regression tests Tests/LinearSolvers/CellEB/inputs.rt.2d Tests/LinearSolvers/CellEB/inputs.rt.2d.petsc Tests/LinearSolvers/CellEB/inputs.rt.3d commit b26a042de089fcc357d50b1238a27e7a93ba36b9 Author: Weiqun Zhang Date: Sun Sep 16 15:17:29 2018 -0700 fix return Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 3e968376f2e709925e37892853ef8cb25bd32989 Author: Weiqun Zhang Date: Sat Sep 15 23:08:56 2018 -0700 writePlotfile Tests/LinearSolvers/CellEB/MyTest.H Tests/LinearSolvers/CellEB/MyTest.cpp Tests/LinearSolvers/CellEB/main.cpp commit 5e22baa229fa1ae1193a01033ad0c0d18f5c2e4a Author: Weiqun Zhang Date: Sat Sep 15 21:32:36 2018 -0700 inputs for new EB regression tests Tests/LinearSolvers/CellEB2/inputs.rt.2d Tests/LinearSolvers/CellEB2/inputs.rt.3d Tests/LinearSolvers/CellEB2/inputs.rt.hypre commit 8aff4457d84491fae6b9f3d87760e79774bcd7b8 Author: Weiqun Zhang Date: Sat Sep 15 21:10:59 2018 -0700 add a test for BL_NO_FORT Tests/NoFort/GNUmakefile Tests/NoFort/Make.package Tests/NoFort/main.cpp commit 2794ccca02cbbaeb8dd4cd0da79cb5ff968ba307 Author: Weiqun Zhang Date: Sat Sep 15 18:13:06 2018 -0700 doc: make it clear the command line argument is optional. Docs/sphinx_documentation/source/GettingStarted.rst commit f5c68e3131061498fe92c7b1571303797fb8944a Author: Weiqun Zhang Date: Sat Sep 15 18:13:06 2018 -0700 doc: make it clear the command line argument is optional. Docs/sphinx_documentation/source/GettingStarted.rst commit 3ca992f0e1732a4ebfdc0b6c8cd6026de3a9710d Author: Weiqun Zhang Date: Sat Sep 15 11:43:08 2018 -0700 more changes for NEC Src/Base/AMReX_ParallelDescriptor_F.F90 Src/Base/AMReX_parmparse_mod.F90 commit bc203b5549b96cde060dc663127c2df6980337cc Author: dwillcox Date: Sat Sep 15 13:30:23 2018 -0400 Hack for importing functions and logic for distinguishing function calls. Tools/F_scripts/gpu_fortran.py commit af2467b5dc1f988a8aefeae5e54fd132f8e9bf79 Author: Weiqun Zhang Date: Sat Sep 15 07:31:13 2018 -0700 fix missing prefix Src/Base/AMReX_BaseFab_nd.f90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90 commit 11c81834513540ab46d6e613beb352b676a5053a Merge: 7f00168b4 99a6d7f58 Author: WeiqunZhang Date: Fri Sep 14 22:54:51 2018 -0700 Merge pull request #313 from kweide/development More changes for per-fab fluxregister fineadd use from FLASH commit e843ef37aa2fcd8a3f896951ca5ad840803a17eb Author: Weiqun Zhang Date: Fri Sep 14 21:47:40 2018 -0700 fix more casts Src/EB/AMReX_EBAmrUtil.cpp Src/EB/AMReX_EBFluxRegister.cpp commit 279603fdfd84a12b377916f20e961c5323b5fc12 Author: Weiqun Zhang Date: Fri Sep 14 21:33:33 2018 -0700 fix cast Tutorials/EB/CNS/Source/CNS.cpp commit 56ff25928f590b2c3ab24e94d7f4671eb8068821 Author: Weiqun Zhang Date: Fri Sep 14 21:22:26 2018 -0700 explicitly write move constructor for StateData hoping to make NEC happy Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp commit f12257f38fdd9a0379e0f1b388f1a9680b0d7d62 Merge: f4f400f29 7f00168b4 Author: Weiqun Zhang Date: Fri Sep 14 21:08:30 2018 -0700 Merge branch 'development' into statedata commit c13472ab908abcf3e4fbb71ebea6cecffd2acd08 Merge: 927fe48ee 7f00168b4 Author: Weiqun Zhang Date: Fri Sep 14 21:03:04 2018 -0700 Merge branch 'development' into devirtualize-fab commit 7f00168b406f5b933c0d181c3f77ecacc6a1b75d Merge: a5d7b435c 87ac3b5b0 Author: Weiqun Zhang Date: Fri Sep 14 21:01:00 2018 -0700 Merge branch 'development' into mlmg commit 5efb8456973abbd17f8c4f6dd412297f55bfe4cd Author: Kevin Gott Date: Fri Sep 14 21:45:34 2018 -0400 BaseFab add, subtract, multiply and divide GPU-ized, including Multifab calls. Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_MultiFab.cpp commit a5d7b435c980bece82f149000ae210e8f4ce9017 Author: Weiqun Zhang Date: Fri Sep 14 18:02:04 2018 -0700 use dx_eb from module Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 6a9d908c1ee6f0b571b92f543623d1d039a22003 Merge: f57613995 aff8d7421 Author: Weiqun Zhang Date: Fri Sep 14 17:56:19 2018 -0700 Merge branch 'mlmg' of github.com:AMReX-Codes/amrex into mlmg commit f576139954e1e4b4dba2d48ce3c9d406b45920bd Author: Weiqun Zhang Date: Fri Sep 14 17:56:14 2018 -0700 add makePETSc Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit aff8d742102925331e3f49453b3e4d6331a819f6 Author: sireeveslbl Date: Fri Sep 14 17:29:13 2018 -0700 Hypre Routines for EB Dirichlet complete. Works for 2D and 3D Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit fa7b9eb6de8a9a40c5499bbad8762f0ed1325020 Author: Kevin Gott Date: Fri Sep 14 19:23:12 2018 -0400 Make HeatEquation0 lambdas inlined. EmPIC keeps the separate lambdas/macro example. Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp commit d553aeb73888d59fe82bc451c09f30c3f9de389a Author: Kevin Gott Date: Fri Sep 14 19:17:07 2018 -0400 Change Remaining BaseFab -> FArrayBox Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit 253e363f7cce40acb2fb14fd03cf50e50cd1f80d Author: Kevin Gott Date: Fri Sep 14 19:02:27 2018 -0400 Rename and distinguish run scripts. Tutorials/GPU/HeatEquation_EX0_C/Exec/run.summit Tutorials/GPU/HeatEquation_EX0_C/Exec/run.summitdev commit 83ce8eade8a63b3b64d55ecf1075aa9e22bb9ac0 Author: Kevin Gott Date: Fri Sep 14 19:01:45 2018 -0400 Change BaseFab to FArrayBox for lambda capture. First test. Need to explicitly label all FArrayBox functions that use static class objects AMREX_DEVICE_HOST for safety. Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp commit 8e815ab798d0e816c3b911b481155d167023a3a2 Author: Kevin Gott Date: Fri Sep 14 19:00:43 2018 -0400 Variable and test to turn tiling off if on GPU. Src/Base/AMReX_MFIter.H Src/Base/AMReX_MultiFab.cpp commit a68552eb66db1ff6b525e6b3dde0bc1de766e263 Author: Kevin Gott Date: Fri Sep 14 18:59:23 2018 -0400 First Multifab function to GPU: copy. HeatEquation now has negligible page faults. Src/Base/AMReX_MultiFab.cpp commit fe3ab6c42a17112bc884b3ed3e88e51c2057c84b Author: Kevin Gott Date: Fri Sep 14 18:57:35 2018 -0400 Change inputs Tutorials/GPU/HeatEquation_EX0_C/Exec/inputs_3d commit 79a58cada1b7a9cba486ce12bf2a18faefa21a09 Author: Kevin Gott Date: Fri Sep 14 18:56:46 2018 -0400 EmPIC with Lambdas inlined. Tutorials/GPU/ElectromagneticPIC_2/Constants.H Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.H Tutorials/GPU/ElectromagneticPIC_2/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_2/Evolve.H Tutorials/GPU/ElectromagneticPIC_2/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_2/GNUmakefile Tutorials/GPU/ElectromagneticPIC_2/IO.H Tutorials/GPU/ElectromagneticPIC_2/IO.cpp Tutorials/GPU/ElectromagneticPIC_2/Make.package Tutorials/GPU/ElectromagneticPIC_2/NodalFlags.H Tutorials/GPU/ElectromagneticPIC_2/NodalFlags.cpp Tutorials/GPU/ElectromagneticPIC_2/Particles.H Tutorials/GPU/ElectromagneticPIC_2/StructOfArrays.H Tutorials/GPU/ElectromagneticPIC_2/em_pic_3d.F90 Tutorials/GPU/ElectromagneticPIC_2/em_pic_F.H Tutorials/GPU/ElectromagneticPIC_2/inputs Tutorials/GPU/ElectromagneticPIC_2/main.cpp Tutorials/GPU/ElectromagneticPIC_2/script.nompi.sh Tutorials/GPU/ElectromagneticPIC_2/summit.sh Tutorials/GPU/ElectromagneticPIC_2/summitdev.sh Tutorials/GPU/ElectromagneticPIC_2/test.cpp commit ca8494e7cf1f97abb31760d8d0474753cd7fbbeb Author: Kevin Gott Date: Fri Sep 14 18:43:16 2018 -0400 CUDA ifdef wrapper fix. Src/Base/AMReX_Device.cpp commit 845b6c56af0859616e381b9ee2d53a7f133cfdfa Author: Weiqun Zhang Date: Fri Sep 14 13:58:10 2018 -0700 explicitly use final override. makeHypre linop Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H commit 040c226e8a3019932b2fe9ab9747aa9a4bddf765 Author: Weiqun Zhang Date: Fri Sep 14 11:33:32 2018 -0700 move getFluxes from MLMG to MLCellABecLap Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 3b5deb3ba0648997681535b9a8a1ee1b67ad3c27 Author: Weiqun Zhang Date: Fri Sep 14 10:52:32 2018 -0700 add abstract MLCellABecLap class Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.H Src/LinearSolvers/MLMG/AMReX_MLCellABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/Make.package commit ed2d373b8aa2c805879b160aee5887e1cbbf6480 Author: Weiqun Zhang Date: Fri Sep 14 09:28:54 2018 -0700 fix typo Src/Extern/HYPRE/AMReX_HABEC_2D.F90 commit 97560a325151085babaea6d40d7393dc24fbe32a Merge: 0f4c084a0 87ac3b5b0 Author: Marc Day Date: Thu Sep 13 23:45:13 2018 -0700 Merge branch 'development' into marc/forkjoin_dev commit 87ac3b5b0dd4cd6e344c56dc9437cbbe4d9965d8 Author: Cy Chan Date: Thu Sep 13 23:10:50 2018 -0700 added ForkJoin::set_task_output_file() enabled appending to task output files enabled changing task output files in the middle of tasks updates to MultiColor_C OldTutorials/MultiColor_C/main.cpp Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ParallelContext.cpp commit 0f4c084a08ff5992b76084d5755c4e3e6ea71e3a Author: Marc Day Date: Thu Sep 13 19:41:36 2018 -0700 Make C_CellMG collectives Fork-Join friendly Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp commit 551c93b3e38d4c8b3443c2dbdf7a2033b119cafb Author: Marc Day Date: Thu Sep 13 18:28:01 2018 -0700 Add not-equal for BERec Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp commit cfa1aa40cf55016330bbe94cf8a783f628ddd714 Author: Weiqun Zhang Date: Thu Sep 13 17:19:16 2018 -0700 add use_petsc Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H Src/Extern/PETSc/AMReX_PETSc.H Src/Extern/PETSc/AMReX_PETSc.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/CellEB2/GNUmakefile Tests/LinearSolvers/CellEB2/MyTest.H Tests/LinearSolvers/CellEB2/MyTest.cpp commit 62640744a59be3bb84755761ba02bb64e99a668b Merge: 4894efe1c a689085d5 Author: Weiqun Zhang Date: Thu Sep 13 16:20:58 2018 -0700 Merge branch 'development' into mlmg commit a689085d5e8baa1a6ccdb8a2e96ec26df4be1ea5 Author: Weiqun Zhang Date: Thu Sep 13 16:20:38 2018 -0700 fix a bug in test set up Tests/LinearSolvers/CellEB2/mytest_f.F90 commit c8721ee4aec4842e1f93f67029f01b19377614a2 Author: Kevin Gott Date: Thu Sep 13 19:08:01 2018 -0400 script and input adjustments Tutorials/GPU/ElectromagneticPIC/summitdev.sh Tutorials/GPU/HeatEquation_EX0_C/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX0_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX0_C/Exec/run.script Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script commit 3ca865739c66d466538e88cdd29e67edfc4c3edd Author: Kevin Gott Date: Thu Sep 13 19:00:14 2018 -0400 Addition of non-sync cudaMemcpy wrappers. Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 4692fc987a563403187961424f75a4df6efcbab2 Author: Kevin Gott Date: Thu Sep 13 18:51:52 2018 -0400 Additional Device::synch Src/Base/AMReX_FabArrayCommI.H commit 6c63cfe392ca17616792ee5de67ee2d3399f96c0 Author: Kevin Gott Date: Thu Sep 13 18:51:15 2018 -0400 CUDA wrapper adjustment. Src/Base/AMReX_fort_mod.F90 commit 4204e75e7f518bbc3b1eca28d6899fd5d5abfed1 Author: Kevin Gott Date: Thu Sep 13 18:49:19 2018 -0400 include fix Src/Base/AMReX_CudaAllocators.H commit 86f8e6fda4c16f06e724bb68e465bb415b0a8e45 Author: Kevin Gott Date: Thu Sep 13 18:47:24 2018 -0400 amrex_malloc and amrex_free library fix. Src/Base/AMReX_CUDA_Utility.cpp commit 4894efe1c32f060f073c90739f0a37af79697d67 Author: Weiqun Zhang Date: Thu Sep 13 15:16:32 2018 -0700 fix a few things Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit edf385a6516f134a880628675a29a9a8c0af4532 Author: Weiqun Zhang Date: Thu Sep 13 13:04:21 2018 -0700 some clean up Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit b7f0e6a68e1dd9aa2781e30a1e595a92bc9ce228 Merge: 1940e64fa 017bab3cf Author: Marc Day Date: Thu Sep 13 13:16:47 2018 -0700 Merge remote-tracking branch 'origin/development' into marc/forkjoin_dev commit 017bab3cf58b4f469688910badb210fd84e4e39d Author: Andrew Myers Date: Thu Sep 13 13:08:50 2018 -0700 tweak .travis.yml again... .travis.yml commit 42314c66af1ecc412fb597f528f851eec734d1ce Merge: 702260635 5edc18251 Author: Andrew Myers Date: Thu Sep 13 13:03:55 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 702260635f682e4f9d8411c71011db2f7f8a22e5 Author: Andrew Myers Date: Thu Sep 13 13:03:44 2018 -0700 assume 'yes' to queries since this is happening in a script .travis.yml commit 5edc18251fe8e64d9287001f0875f7a240c6106d Author: Marc Day Date: Thu Sep 13 13:03:30 2018 -0700 Add (another) multifab diff tool that includes grow cells Tools/C_util/DiffMultiFab/GNUmakefile Tools/C_util/DiffMultiFab/diffmultifab.cpp commit 75a151285a9afbb484a5dc76859951cfb86e4d60 Author: Andrew Myers Date: Thu Sep 13 12:55:18 2018 -0700 try to use 3.6 instead of 3.4 .travis.yml build_and_deploy.sh commit 8bfff3d54f9c8733af2b31e88829d81e019b291e Author: Weiqun Zhang Date: Thu Sep 13 12:54:40 2018 -0700 pass EB b coefficients to hypre Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 6b719eea6fcdaf2130a2f613123e01601ae33898 Merge: 6f74e6fd1 52fb9a07c Author: Andrew Myers Date: Thu Sep 13 12:30:46 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6f74e6fd1f097639ba1fd0476093efe14f7bd795 Author: Andrew Myers Date: Thu Sep 13 12:30:28 2018 -0700 specifiy that we want python3 in the build_and_deploy script build_and_deploy.sh commit 323d0653f3cf5bf402c9be09ef7163bb4a645cc2 Merge: b993fca41 52fb9a07c Author: Weiqun Zhang Date: Thu Sep 13 12:27:03 2018 -0700 Merge branch 'development' into mlmg commit 52fb9a07ced778f04a6b94316a9e09a25865e9d7 Merge: 854ae4eb1 eb22724a0 Author: Weiqun Zhang Date: Thu Sep 13 12:24:18 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 854ae4eb1f5d8aaf1cea7ff81b4bd2afe5f07d5a Author: Weiqun Zhang Date: Thu Sep 13 12:24:10 2018 -0700 add a tutorial for geometry generation Tutorials/EB/GeometryGeneration/GNUmakefile Tutorials/EB/GeometryGeneration/Make.package Tutorials/EB/GeometryGeneration/main.cpp commit eb22724a05ed80f7b31e5e9ce55ff11d484d7036 Merge: 744ba179e 72c131f91 Author: Andrew Myers Date: Thu Sep 13 12:18:39 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f252f875aa8bb3bbcb0bc0ba9f19233453d3c11e Author: Weiqun Zhang Date: Thu Sep 13 12:18:36 2018 -0700 add functions for writing plotifles with EB Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_PlotFileUtil.cpp commit 744ba179ebb079154438ea3af476d487b3919915 Author: Andrew Myers Date: Thu Sep 13 12:18:22 2018 -0700 try explicitly using pip3 .travis.yml commit 72c131f9187ad247eb9082f622f0ddbded64dfe3 Merge: dd22ee965 85945ea91 Author: Andrew Myers Date: Thu Sep 13 12:03:13 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit dd22ee96584de28d0ecee69eab2793364d833e9e Author: Andrew Myers Date: Thu Sep 13 12:02:54 2018 -0700 turn on TINY_PROFILING Tests/HDF5Benchmark/GNUmakefile commit a7882e4eb21505a25edfac0c481fd1391f25e224 Author: Andrew Myers Date: Thu Sep 13 12:02:43 2018 -0700 also add the native write plot file to the benchmark Tests/HDF5Benchmark/main.cpp commit 85945ea91c38252af6a00a52d5ea4442eb7913f6 Author: Andrew Myers Date: Thu Sep 13 11:28:06 2018 -0700 tweak travis.yml again .travis.yml commit 99a6d7f58700211ecc8d2b8cc440d05f2466ffcc Author: Klaus Weide Date: Thu Sep 13 13:27:00 2018 -0500 add short comment and cleanup Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp commit f652cae8e734281907836721aff11ee84a5b41ab Author: Andrew Myers Date: Thu Sep 13 11:14:05 2018 -0700 switch to using python 3 with travis .travis.yml commit 9ea4c20a72fe2ca020145efa76a95d9aa3db47df Merge: 99d050e04 ae97e5166 Author: Andrew Myers Date: Thu Sep 13 11:06:23 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 99d050e048a4dbf87d5c1634382800467f910f8f Author: Andrew Myers Date: Thu Sep 13 11:06:12 2018 -0700 change python version in travis config .travis.yml commit 741d3df63b76f110205c1ab423ded95cd6c4e298 Author: Klaus Weide Date: Thu Sep 13 12:59:56 2018 -0500 Changes for per-FAB fluxregister use from Fortran Added optional argument to amrex_fluxregister_fineadd_1fab for requesting zeroing of the coresponding fluxregister data storage before flux data from the current fab are added. Added FineSetVal method to FluxRegister class. Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90 commit ae97e5166b24e9200291004332b6964fc5c81409 Merge: d61749462 fcdf621bc Author: Andrew Myers Date: Thu Sep 13 10:52:55 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d617494626d3ebb72f4645205d5b725eb52789e5 Author: Andrew Myers Date: Thu Sep 13 10:52:43 2018 -0700 add an HDF5 IO Benchmark test, based on the writer fron Nyx Tests/HDF5Benchmark/GNUmakefile Tests/HDF5Benchmark/Make.package Tests/HDF5Benchmark/WritePlotfileHDF5.H Tests/HDF5Benchmark/WritePlotfileHDF5.cpp Tests/HDF5Benchmark/inputs Tests/HDF5Benchmark/main.cpp commit 48b8caed39f802a695bea3dcabd1c061c176a069 Merge: 96dd09460 fcdf621bc Author: Weiqun Zhang Date: Thu Sep 13 09:26:39 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit fcdf621bc57451cf1d5a7f27324dcadf5f0cbfb0 Author: Weiqun Zhang Date: Thu Sep 13 09:20:41 2018 -0700 CylinderIF: fix sign bug and clean up Src/EB/AMReX_EB2.cpp Src/EB/AMReX_EB2_IF_Cylinder.H commit 96dd09460030991fa52d2be9e8c36f77cfc95f1a Author: Weiqun Zhang Date: Wed Sep 12 21:16:15 2018 -0700 add Difference and Extrusion for EB Src/Base/AMReX_Array.H Src/EB/AMReX_EB2_IF.H Src/EB/AMReX_EB2_IF_Complement.H Src/EB/AMReX_EB2_IF_Difference.H Src/EB/AMReX_EB2_IF_Extrusion.H Src/EB/AMReX_EB2_IF_Lathe.H Src/EB/AMReX_EB2_IF_Rotation.H Src/EB/AMReX_EB2_IF_Scale.H Src/EB/CMakeLists.txt Src/EB/Make.package Tests/LinearSolvers/CellEB/initEB.cpp Tests/LinearSolvers/CellEB2/initEB.cpp Tutorials/EB/CNS/Source/CNS_init_eb2.cpp Tutorials/EB/MacProj/initEB.cpp commit 57d7bfd5ebbf79a2451cb5b038cf604de1ecede9 Merge: 1ad468341 e33d35cb6 Author: Johannes Blaschke Date: Wed Sep 12 21:07:32 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 1ad468341e5b4edf374f6f0702fa69bdba432c21 Author: Johannes Blaschke Date: Wed Sep 12 21:07:29 2018 -0700 added infinite CylinderIF by overloading constructor Src/EB/AMReX_EB2.cpp Src/EB/AMReX_EB2_IF_Cylinder.H commit e33d35cb688dcd422e094ea05d00f86c1f49b0d4 Author: Andrew Myers Date: Wed Sep 12 13:58:39 2018 -0700 always have at least ref_ratio ghost cells for the fine levels in AssignDensity Src/AmrCore/AMReX_AmrParticles.H commit 8e18378077dc5ce077ec03cd40c882a2da9c988e Merge: 812204412 124db5ef0 Author: Andrew Myers Date: Wed Sep 12 12:33:34 2018 -0700 merging commit 8122044125f9de48735079f89538f74c0bee51d3 Author: Andrew Myers Date: Wed Sep 12 12:25:54 2018 -0700 allow callers to pass in an ngrow parameter into AssignDensity Src/AmrCore/AMReX_AmrParticles.H Src/Particle/AMReX_Particles.H commit c060fc26041ff5e8bf3a0e999f4abd2b5638bfc9 Author: Max Katz Date: Wed Sep 12 13:46:42 2018 -0400 Add CUDA initialization output Src/Base/AMReX_Device.cpp commit b993fca41560d481dcb40106fff3e3408cbe9090 Author: sireeveslbl Date: Wed Sep 12 10:28:43 2018 -0700 Hypre Dirichlet main routines compile, but need to get the eb_b multifab. Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit a98ba2a392317425ee9c26107372b161ee5ade98 Merge: 67144df5a 7b4b7f3ac Author: Max Katz Date: Wed Sep 12 12:56:39 2018 -0400 Merge branch 'development' into gpu commit 124db5ef04b28b0795a0028159a669120023c1c3 Author: Weiqun Zhang Date: Wed Sep 12 09:23:38 2018 -0700 because C++ has double pow(double base, int iexp), there is no reason we don't use it Src/EB/AMReX_EB2_IF_Polynomial.H commit d0bb78e6e478d021a79fbbb385c12098ffcc5286 Author: Weiqun Zhang Date: Wed Sep 12 08:57:26 2018 -0700 more ParallelDescriptor::second -> amrex::second Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AuxBoundaryData.cpp Src/Base/AMReX_VisMF.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_TracerParticles.cpp Tutorials/Amr/Advection_AmrCore/Source/main.cpp Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/Amr/Advection_AmrLevel/Source/main.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/main.cpp Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX2_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX3_C/Source/main.cpp Tutorials/CVODE/EX1/main.cpp Tutorials/CVODE/EX2/main.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/main.cpp commit 86568eb046d4cb2fb48b8dfecabedf14e30a190b Author: Weiqun Zhang Date: Wed Sep 12 08:21:05 2018 -0700 ParallelDescriptor::second -> amrex::second in profiler Src/Base/AMReX_BLProfiler.cpp commit f836ba8801e6752c3f6586b816e95dda50dc7cf3 Author: Weiqun Zhang Date: Wed Sep 12 08:17:36 2018 -0700 update doc Docs/sphinx_documentation/source/GettingStarted.rst commit c6a72fa2109d56e44c249e969164645b113a8fdc Author: Weiqun Zhang Date: Wed Sep 12 08:08:56 2018 -0700 turn on verbosity by default Src/Base/AMReX.cpp Src/Base/AMReX_Utility.cpp commit 5860aaa1ee6a5d7a5e2279320d8ec32668b45dc5 Author: Weiqun Zhang Date: Tue Sep 11 22:10:02 2018 -0700 use double in tiny profiler Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp commit 9a9c2cb9231b28c0388eb918547449a1168d4d61 Merge: d7de271b3 51915efeb Author: Weiqun Zhang Date: Tue Sep 11 21:07:54 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d7de271b37171ae58f193951edc7d81eab829c45 Author: Weiqun Zhang Date: Tue Sep 11 20:54:01 2018 -0700 double precision -> real(amrex_real) Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/Prob.f90 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/slope_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_nd/Tagging_nd.f90 commit 67144df5a4c1f9bf2cdc5be8b7880313f209cab9 Author: Max Katz Date: Tue Sep 11 23:33:21 2018 -0400 Fix string concatenation Src/Base/AMReX_Device.cpp commit 191c687ba711221f97e12e1e72b791d3a0e2a531 Author: sireeveslbl Date: Tue Sep 11 16:04:03 2018 -0700 Still working on Hypre EB Dirichlet. Some more compilation errors to work out. Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit 51915efeb21a78407ed2d7b6b85538940cae352e Merge: 146f052b9 6c418708f Author: Johannes Blaschke Date: Tue Sep 11 15:04:23 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 146f052b93da9ea7926f72e532c84d67c7938448 Author: Johannes Blaschke Date: Tue Sep 11 15:04:13 2018 -0700 elaborate on gcc and cmake Docs/sphinx_documentation/source/BuildingAMReX.rst Docs/sphinx_documentation/source/Visualization.rst commit 6c418708f938608f033d87fd71b61bef4794988e Merge: 1ab2188fc c47603c7a Author: WeiqunZhang Date: Tue Sep 11 14:37:00 2018 -0700 Merge pull request #310 from kweide/development Fortran build routine for non-owning fab commit c47603c7ab9b3525571aa1c1721ecbea73509a23 Author: Klaus Weide Date: Tue Sep 11 16:34:23 2018 -0500 Use amrex_error not ERROR STOP Src/F_Interfaces/Base/AMReX_fab_mod.F90 commit 1ab2188fc527fa719bb8f08fd2d1887659440422 Author: Johannes Blaschke Date: Tue Sep 11 14:19:46 2018 -0700 rephrase homebrew install isntructions slightly Docs/sphinx_documentation/source/BuildingAMReX.rst commit 926033f69142179986f0eda28951f88c86cb9b53 Author: Johannes Blaschke Date: Tue Sep 11 14:10:18 2018 -0700 elaborate more on gcc install for macOS Docs/sphinx_documentation/source/BuildingAMReX.rst commit 072c214c04faed8ffca518c44de3dbebcc2486d1 Author: Johannes Blaschke Date: Tue Sep 11 14:05:15 2018 -0700 elaborate more on Amrvis install for macOS Docs/sphinx_documentation/source/Visualization.rst commit 770ac2327155e8a858f5d6622b146120600410c3 Author: Johannes Blaschke Date: Tue Sep 11 13:53:37 2018 -0700 update docs to give more info about building on macOS Docs/sphinx_documentation/source/BuildingAMReX.rst Docs/sphinx_documentation/source/GettingStarted.rst Docs/sphinx_documentation/source/Visualization.rst commit 140912c21a97f980b9f73ed031408c23af4f41d8 Author: Klaus Weide Date: Tue Sep 11 13:27:17 2018 -0500 rename a Fortran routine, add argument error checking Changed specific name from amrex_fab_build to amrex_fab_build_alloc. Added some argument size error checking, subject to ifdef AMREX_DEBUG; uses ERROR STOP. Src/F_Interfaces/Base/AMReX_fab_mod.F90 commit f4f400f292403770e18c6e35e8816e32ea5b5554 Author: Weiqun Zhang Date: Tue Sep 11 11:20:16 2018 -0700 StateData: use unique_ptr internally; declare all five explicitly Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp commit a66c2db182fed0fd5ae64221c0e3ad7a7dc85798 Author: Andrew Myers Date: Tue Sep 11 11:11:45 2018 -0700 fix AssignDensity for ref_ratio != 2 Src/AmrCore/AMReX_AmrParticles.H commit 66bab144507df416ee7cabd5faff8f43a8bb4db4 Author: Klaus Weide Date: Tue Sep 11 09:25:12 2018 -0500 Add amrex_fab_build_install New specific subroutine that builds a non-owning (Fortran) FAB from a given (Fortran) data pointer. Src/F_Interfaces/Base/AMReX_fab_mod.F90 commit 92bcecb7c395b6a8bb29fef7b9607d6b3711d18a Author: Tan Nguyen Date: Tue Sep 11 01:43:07 2018 -0700 fix a synchronization bug Src/AmrTask/rts_impls/Perilla/Barrier.H Src/AmrTask/rts_impls/Perilla/Barrier.cpp Src/AmrTask/rts_impls/Perilla/PackageQueue.H Src/AmrTask/rts_impls/Perilla/Perilla.cpp Src/AmrTask/rts_impls/Perilla/PerillaConfig.H Src/AmrTask/rts_impls/Perilla/RegionGraph.H Src/AmrTask/rts_impls/Perilla/RegionGraph.cpp Src/AmrTask/rts_impls/Perilla/RegionQueue.H Src/AmrTask/rts_impls/Perilla/RegionQueue.cpp Src/AmrTask/rts_impls/Perilla/WorkerThread.H Src/AmrTask/rts_impls/Perilla/WorkerThread.cpp Src/AmrTask/rts_impls/Perilla_omp/Perilla.cpp Src/AmrTask/rts_impls/Perilla_omp/RegionGraph.H Src/AmrTask/rts_impls/Perilla_omp/RegionGraph.cpp Src/AmrTask/rts_impls/Perilla_upc++/Barrier.H Src/AmrTask/rts_impls/Perilla_upc++/Barrier.cpp Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv.mpi.omp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv.mpi.pthreads Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv.upcxx.pthreads Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/GNUmakefile Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_advance.cpp commit 0d9b14e867d94585ce4ff8c7dbb58d1943066728 Author: Klaus Weide Date: Mon Sep 10 19:56:01 2018 -0500 The 1-FAB fineadd now takes a 0-based boxno (aka gridIdx) argument Don't convert from a 1-based to a zero-based index. The new behavior is more consistent with other multifab functions in the Fortran interface that either take or return a grid_index. Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90 commit 291f8c47fe703f79041f57d3a43a0e13e629e02d Merge: e576f1413 3bee1ad0c Author: Andrew Myers Date: Mon Sep 10 10:33:59 2018 -0700 Merge pull request #309 from AMReX-Codes/endian use __BYTE_ORDER__ to detect endianess commit e576f1413f9e2bec1f69aaf82dc25974f4ce2a07 Merge: c4f32d1c6 9b5cfc32b Author: Weiqun Zhang Date: Mon Sep 10 10:30:10 2018 -0700 Merge branch 'pr-308' into development commit c4f32d1c654f5337b41c4640556b6e76e51d2bc6 Merge: 7b4b7f3ac 334d74e18 Author: WeiqunZhang Date: Mon Sep 10 10:30:00 2018 -0700 Merge pull request #308 from kweide/development Add per-fab version of FineAdd to fluxregister's Fortran interface commit 9b5cfc32baa8f433c158166482e93737ab049456 Author: Weiqun Zhang Date: Mon Sep 10 10:29:15 2018 -0700 cleanup Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp commit 3bee1ad0c0fcc592b5d826fd3daabb157e1297dc Author: Weiqun Zhang Date: Mon Sep 10 09:45:19 2018 -0700 use __BYTE_ORDER__ to detect endianess Src/Base/AMReX_FPC.cpp Src/F_BaseLib/fabio_c.c commit 2aac05efc1a8bd2e06abe74aff2d908dd847b0eb Author: Michael Zingale Date: Sun Sep 9 10:05:31 2018 -0400 remove ref to interface block Tools/F_scripts/gpu_fortran.py commit 26fec164f8eef160eee091daa5199356eb9f8ef5 Author: Max Katz Date: Sun Sep 9 09:58:16 2018 -0400 Update comments for gpu_fortran.py Tools/F_scripts/gpu_fortran.py commit 4f0ff97dc38479b5b339873a1114fde86c85c632 Author: Kevin Gott Date: Sun Sep 9 00:53:00 2018 -0400 Add NVML to Summit, Sierra. Tools/GNUMake/sites/Make.llnl Tools/GNUMake/sites/Make.olcf commit 1cb8044996f3c1e5d2ae61e9fdec760504dbff63 Author: Kevin Gott Date: Sun Sep 9 00:47:25 2018 -0400 String comparison fix. Src/Base/AMReX_Device.cpp commit 7b4b7f3acdaeac0c6585f66e2fd22f94f1a54fd0 Merge: f7e21f72a 49de74f2f Author: Weiqun Zhang Date: Sat Sep 8 20:50:54 2018 -0700 Merge branch 'streampos' into development commit f7e21f72a4b05f002ed1b34cebc30770f3b58a33 Author: Weiqun Zhang Date: Sat Sep 8 18:57:21 2018 -0700 minor cleanup Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp commit e7422089cc2d544dcc1431a103e9e456725888d8 Author: Weiqun Zhang Date: Sat Sep 8 18:43:56 2018 -0700 add ErrorHandler Src/Base/AMReX.H Src/Base/AMReX.cpp commit b8c20ca5c291e7b14c5e1acbb14d1626afb9ea35 Author: Weiqun Zhang Date: Sat Sep 8 18:06:10 2018 -0700 clean up Print Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit e7a5e150f8c5da1911a3f5b43119b439b722b633 Author: Weiqun Zhang Date: Sat Sep 8 17:44:35 2018 -0700 rm unused Serialize/UnSerialize functions Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit a2e015903d61896c4b25df367324ecf65273b3ff Author: Weiqun Zhang Date: Sat Sep 8 17:30:18 2018 -0700 change tolerance of nodal Poisson solver test Tutorials/LinearSolvers/NodalPoisson/MyTest.H Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp commit a84b3405d62b4bd1d93a7e69dec0fcfc0090508c Author: Weiqun Zhang Date: Sat Sep 8 17:28:48 2018 -0700 add amrex::SetVerbose function Src/Base/AMReX.H Src/Base/AMReX.cpp commit 42aab349841e34676c91a87047ad895236cab155 Author: Weiqun Zhang Date: Sat Sep 8 11:41:17 2018 -0700 Nodal Poisson solver tutorial Tutorials/LinearSolvers/NodalPoisson/GNUmakefile Tutorials/LinearSolvers/NodalPoisson/Make.package Tutorials/LinearSolvers/NodalPoisson/MyTest.H Tutorials/LinearSolvers/NodalPoisson/MyTest.cpp Tutorials/LinearSolvers/NodalPoisson/MyTest_F.H Tutorials/LinearSolvers/NodalPoisson/init_prob.F90 Tutorials/LinearSolvers/NodalPoisson/main.cpp commit c691f5b10e9e06f5b0beb6060449f6bf843c2dd9 Author: Max Katz Date: Sat Sep 8 11:20:02 2018 -0700 Add warning if oversubscribing GPUs Src/Base/AMReX_Device.cpp commit 57e0bc9834cad25be101b86a630808e3734b81d6 Author: Max Katz Date: Sat Sep 8 10:39:45 2018 -0700 Simplify and make more robust the logic for mapping ranks to GPUs Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit c7cf9b2746194a249b4bf99d4e66130323d552c7 Author: Max Katz Date: Sat Sep 8 10:39:21 2018 -0700 Provide GPU configuration on known systems Tools/GNUMake/Make.defs Tools/GNUMake/sites/Make.llnl Tools/GNUMake/sites/Make.olcf commit a17626a37738fc467aef3af2482cab2557842d2f Author: Max Katz Date: Sat Sep 8 07:03:54 2018 -0700 Move Sierra to the rolling MPI release Tools/GNUMake/sites/Make.llnl commit a37d6137d7847390aab947632a552466376fe8c6 Author: Max Katz Date: Sat Sep 8 07:03:45 2018 -0700 Add NVML to Summit, Sierra Tools/GNUMake/sites/Make.llnl Tools/GNUMake/sites/Make.olcf commit ad762b5dade33480b2d2044482062982fd5c8f35 Author: Max Katz Date: Sat Sep 8 07:02:23 2018 -0700 Fix string comparison issue Src/Base/AMReX_Device.cpp commit f47220b129f11e307681a35c19adcb10cdca46a9 Merge: 217f28ade bdbf3e685 Author: Weiqun Zhang Date: Fri Sep 7 22:26:08 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 217f28adee4853b1288b4f1c1740394d37157ff0 Author: Weiqun Zhang Date: Fri Sep 7 22:25:54 2018 -0700 fix due to change of average_center_to_face Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp commit bdbf3e6858e92de0d27ba459eee536cc1aafa36a Author: Weiqun Zhang Date: Fri Sep 7 22:23:13 2018 -0700 fix new typo Src/Base/AMReX_mempool_mod.F90 commit 07aa1e69fb1ede76ab2601d31195ce109b46deb1 Author: Weiqun Zhang Date: Fri Sep 7 22:11:42 2018 -0700 use pointer bound remapping to avoid an intel compiler bug Src/Base/AMReX_mempool_mod.F90 Src/Base/BL_mempool_f.f90 Src/Base/CMakeLists.txt Src/Base/GPackage.mak Src/Base/Make.package commit 0a61d7874670ef2b80340ddd5db7e9d54c894232 Author: Weiqun Zhang Date: Fri Sep 7 15:06:04 2018 -0700 remove duplication Src/Base/AMReX_MultiFabUtil.cpp commit 12a7b67ef2a214b2200b675264593e4e69fb700d Merge: 7b61710a4 d999f8441 Author: Weiqun Zhang Date: Fri Sep 7 14:06:35 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7b61710a4795fdfcfd95aab01447485ba16aed09 Author: Weiqun Zhang Date: Fri Sep 7 14:05:48 2018 -0700 avoid calling popen when intel is used with omp Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp commit d999f8441bf8ad1bc8ed86967ac98371306f0b8e Merge: d703a46aa abc809d38 Author: Andrew Myers Date: Fri Sep 7 12:11:46 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit abc809d3828aaf2258cfdad4b51c4b164823d7e8 Author: Michele Rosso Date: Fri Sep 7 12:11:53 2018 -0700 Add ome more conversion subroutine for vector of array of ptrs Src/Base/AMReX_Array.H Src/Base/AMReX_Vector.H commit d703a46aa3fbb35ebb4f0e2eedcbebc2075bfb6a Author: Andrew Myers Date: Fri Sep 7 12:11:30 2018 -0700 only allow this version of GetArrOfPtrs to be chosen if T has a FABType Src/Base/AMReX_Array.H commit 63dbc95df8e363136a1b95d7631dc252556bb81d Merge: cebcc92df 1134b64b2 Author: Kevin Gott Date: Fri Sep 7 15:06:45 2018 -0400 Merge remote-tracking branch 'origin/development' into gpu-mm commit 1940e64fa6690753aaa0628a70a259930fddd247 Merge: 658e5404c 1134b64b2 Author: Marc Day Date: Fri Sep 7 11:15:10 2018 -0700 Merge branch 'development' into marc/forkjoin_dev commit 1134b64b2201e8c681c8032a0bd0b549426aa246 Merge: 7e46c5cb2 410724a96 Author: Michele Rosso Date: Fri Sep 7 11:12:36 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 7e46c5cb23d81446f02f1c28eac86191f4b3aaf7 Author: Michele Rosso Date: Fri Sep 7 11:12:31 2018 -0700 Add signature for average_cellcenter_to_face() Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 658e5404cc12498257699e88dca80b064d0121f8 Merge: 57ee2c92a 410724a96 Author: Marc Day Date: Thu Sep 6 23:35:38 2018 -0700 Merge branch 'development' into marc/forkjoin_dev commit 57ee2c92a834a13b2d44c9ec43f9633741b5d18b Author: Marc Day Date: Thu Sep 6 23:34:56 2018 -0700 Add profiling info for ForkJoin overhead Src/Base/AMReX_ForkJoin.cpp commit 410724a9619908bd71c0ff7505331c0038003ff3 Author: Andrew Myers Date: Thu Sep 6 17:24:02 2018 -0700 add additional constructor for MakeMFIter that knows about dynamic scheduling. Src/Particle/AMReX_Particles.H commit d6e5646e30a72bc39252d6418ce3d1d9e5954860 Author: sireeveslbl Date: Thu Sep 6 16:00:18 2018 -0700 More work on Dirichlet Hypre, not finished yet. Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 334d74e18484c7e26b81f0ee0f17a708781214fd Author: Klaus Weide Date: Thu Sep 6 14:24:33 2018 -0500 add amrex_fluxregister_fineadd_1fab implementation This is a fineadd method for amrex_fluxregister that adds fluxes from only one fab to a fluxregister. Currently an amrex_fab has to be constructed by the caller and passed, as well as a box number (grid_index, more or less). Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90 commit 927fe48eea74a4330223e85ce163028d3f396cf3 Author: Weiqun Zhang Date: Thu Sep 6 09:29:06 2018 -0700 use factory to delete FAB Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabFactory.H Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp commit cebcc92df5e4ef47695b52d0f4886ede5558b02d Author: Kevin Gott Date: Thu Sep 6 05:29:40 2018 -0400 Threading strategy fix. Src/Base/AMReX_BaseFab.cpp commit a3465150cd44a85ec3f455eb988f8e53fc2ce4c7 Author: Weiqun Zhang Date: Wed Sep 5 21:27:05 2018 -0700 const_cast for MPI-2 Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_ParallelReduce.H commit c15ee3cbc578294d7839105f6327f92d15c5c152 Author: Michele Rosso Date: Wed Sep 5 17:38:25 2018 -0700 Add signature for GetArrOfConstPtrs() Src/Base/AMReX_Array.H commit ce4c25a56482d57828a0578b38ec0ccc5d4c7456 Author: Weiqun Zhang Date: Wed Sep 5 16:58:23 2018 -0700 remove vitual from BaseFab Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_IArrayBox.H Src/EB/AMReX_EBAmrUtil.cpp Src/EB/AMReX_EBFArrayBox.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBInterpolater.cpp Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_MultiCutFab.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_nd.F90 commit 939c571443e0901584762d8930641f43ce79b4f1 Author: sireeveslbl Date: Wed Sep 5 16:00:10 2018 -0700 Changed Makefile to reflect location in amrex download Tests/LinearSolvers/CellEB2/GNUmakefile commit 4f6af1982d851ddea9fac6e995f4a2a9be87a4ab Author: sireeveslbl Date: Wed Sep 5 15:55:59 2018 -0700 More progress on Hypre EB-dirichlet. Bogus compiler flags are included as to not break anything Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 4f200274fccc8e37c90d8fca8d902120a524c7da Author: Cyrus Harrison Date: Wed Sep 5 15:37:27 2018 -0700 restore missing endif Tools/GNUMake/Make.defs commit ea9ba1cdd0986f3f378490387e6f66965c87f828 Merge: 35b737fbf b79c23c77 Author: Cyrus Harrison Date: Wed Sep 5 15:33:53 2018 -0700 merge development branch and resolve conflict commit 35b737fbf78559967cd4e43b452f72392091a00d Author: Cyrus Harrison Date: Wed Sep 5 15:28:46 2018 -0700 add build system var for ascent Tools/GNUMake/Make.defs commit e3d68706946ac8b59a71555ddac0095d36c2c3db Author: Cyrus Harrison Date: Wed Sep 5 15:22:24 2018 -0700 move blueprint support Src/Base/Make.package Src/Extern/Conduit/AMReX_Conduit_Blueprint.H Src/Extern/Conduit/AMReX_Conduit_Blueprint.cpp Src/Extern/Conduit/Make.package Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.ascent Tools/GNUMake/packages/Make.conduit Tutorials/Blueprint/AssignMultiLevelDensity/GNUmakefile Tutorials/Blueprint/HeatEquation_EX1_C/Exec/GNUmakefile commit b79c23c77dc7dc6fbb3a0fbaec498c4e824a3c87 Author: Weiqun Zhang Date: Wed Sep 5 14:16:21 2018 -0700 rm SPMD Src/Base/AMReX_FabArray.H Src/Base/AMReX_SPMD.H Src/Base/AMReX_SPMD.cpp Src/Base/AMReX_SPMDI.H Src/Base/AMReX_parstream.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit b3244f3ed46ae62e49d256bf3c2471486a1c78dd Author: Weiqun Zhang Date: Wed Sep 5 13:55:04 2018 -0700 simplification Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp commit dbb1077733c0099e89b52776a3dbf468d4f692f6 Author: Weiqun Zhang Date: Wed Sep 5 13:13:03 2018 -0700 pass by value so that it support both rvalue and lvalue Src/Base/AMReX_ParallelReduce.H commit db6edb7dcfb1106d1687401fc7ac13dfa77d694b Author: Kevin Gott Date: Wed Sep 5 15:24:15 2018 -0400 Mistype. Src/Base/AMReX_BaseFab.cpp commit a8b71fa5c3140a2c242b00d1605d238a860c10f2 Merge: 8c3f56ff8 41ced5b3d Author: Kevin Gott Date: Wed Sep 5 15:19:23 2018 -0400 Merge remote-tracking branch 'origin/development' into gpu-mm Conflicts: Src/Base/AMReX_ArrayLim.H Src/Particle/AMReX_ParticleContainerI.H commit 8c3f56ff80b74763c0970b4c72a552c29a6d345f Author: Kevin Gott Date: Wed Sep 5 15:03:45 2018 -0400 FillBoundary rewritten onto GPUs. Src/Base/AMReX_FabArrayCommI.H commit 9c3fca60c1cd12e2c3b2a82fe543afb0d15fd869 Author: Kevin Gott Date: Wed Sep 5 14:48:40 2018 -0400 Threading strategy for copy, copyTo and copyFrom. Src/Base/AMReX_BaseFab.cpp commit 2d6927f3782edb5eebb3e3fdbafb4a1fcc178a8c Author: Kevin Gott Date: Wed Sep 5 14:27:16 2018 -0400 Changes to GPU data class thingee. Tutorials/GPU/Test/main.cpp commit 2653cd9d8faff3a4eeb5bfae7ac0de1c83aa3d60 Author: Steven Date: Wed Sep 5 10:17:50 2018 -0700 Forgot this one Src/Extern/HYPRE/AMReX_Hypre.cpp commit ce728bc49aa7760b4a548a44b691f534a68567ab Author: Steven Date: Wed Sep 5 10:16:42 2018 -0700 Hypre Dirichlet Additions, not complete Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit 49de74f2feee32ba5daec788b2e633de1a766234 Author: Weiqun Zhang Date: Wed Sep 5 10:10:26 2018 -0700 try to fix portablity issue of std::streampos Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_VisMF.cpp commit 3746b45dc428401e654a8cfcf5765eefaecc27a8 Author: Cyrus Harrison Date: Wed Sep 5 09:59:37 2018 -0700 move Blueprint examples from Test to Tutorials Tutorials/Blueprint/AssignMultiLevelDensity/GNUmakefile Tutorials/Blueprint/AssignMultiLevelDensity/Make.package Tutorials/Blueprint/AssignMultiLevelDensity/inputs Tutorials/Blueprint/AssignMultiLevelDensity/main.cpp Tutorials/Blueprint/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/Blueprint/HeatEquation_EX1_C/Exec/inputs_2d Tutorials/Blueprint/HeatEquation_EX1_C/Exec/inputs_3d Tutorials/Blueprint/HeatEquation_EX1_C/Source/Make.package Tutorials/Blueprint/HeatEquation_EX1_C/Source/advance.cpp Tutorials/Blueprint/HeatEquation_EX1_C/Source/advance_2d.f90 Tutorials/Blueprint/HeatEquation_EX1_C/Source/advance_3d.f90 Tutorials/Blueprint/HeatEquation_EX1_C/Source/init_phi_2d.f90 Tutorials/Blueprint/HeatEquation_EX1_C/Source/init_phi_3d.f90 Tutorials/Blueprint/HeatEquation_EX1_C/Source/main.cpp Tutorials/Blueprint/HeatEquation_EX1_C/Source/myfunc.H Tutorials/Blueprint/HeatEquation_EX1_C/Source/myfunc_F.H Tutorials/Blueprint/README.txt commit d508dd45165f149c6eb389429bd570bd1ee0c3b9 Author: Kevin Gott Date: Wed Sep 5 12:31:59 2018 -0400 Fortran functions for amrex_gpu_malloc and amrex_gpu_free. Src/Base/AMReX_fort_mod.F90 commit c61e858780f58946228093a71a1133065b50406b Author: Kevin Gott Date: Wed Sep 5 12:31:24 2018 -0400 Initial attempt at Box+component threading strategy. Still need to account for very large kernels (thread > max number of threads). Src/Base/AMReX_CUDA_Utility.H Src/Base/AMReX_CUDA_Utility.cpp Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_Managed.H commit fedb7704de7e774aa157b982a4a59aba66fb5011 Author: Kevin Gott Date: Wed Sep 5 12:19:56 2018 -0400 amrex_gpu_alloc, amrex_gpu_free and cudaMemCpy wrappers. Src/Base/AMReX_CUDA_Utility.H Src/Base/AMReX_CUDA_Utility.cpp Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 205afa5e4499414634d01182fa769f1b4d153aae Author: Kevin Gott Date: Wed Sep 5 12:08:19 2018 -0400 Additional Box device functions. Src/Base/AMReX_Box.H commit 27419a34ea5fef8dead32662d2bec305cd75143c Author: Kevin Gott Date: Wed Sep 5 12:07:36 2018 -0400 Make main FillBoundary function public to allow kernels. Src/Base/AMReX_FabArray.H commit 2d69658452a4fa73b5e99f73b87aada10d0a8302 Author: Steven Date: Wed Sep 5 07:48:59 2018 -0700 EB Dirichlet Hypre Started. Going through Dirichlet MLMG and adapting it to the Hypre format. Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp commit e1da443aa7972aeaffaaca9aebd678298e5a156a Author: Kevin Gott Date: Wed Sep 5 02:37:21 2018 -0400 Add error checking to BArena. Src/Base/AMReX_BArena.cpp commit 41ced5b3dd927a7f5b18a3f811fb3e2e61feb38b Author: Weiqun Zhang Date: Tue Sep 4 17:17:47 2018 -0700 add a number of BL_NO_FORTs so that part of Base can be built without Fortran Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_MFCopyDescriptor.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_ParmParse.cpp Src/Base/Make.package commit 88120db4736c325a2d3d2c291adacaffd3bf224b Author: Michele Rosso Date: Tue Sep 4 11:58:18 2018 -0700 CMake:some modification to comply with SPACK requirements Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_Utils.cmake Tools/CMake/MakefileConfig.export.in Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt commit 9ed611aabb2e0e5a10dfcdb126921a53a3a93fb3 Merge: 3606f59b2 2abf9db9b Author: Weiqun Zhang Date: Tue Sep 4 12:31:47 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3606f59b245f3674a6d66b024cf0ffcbbcb004f5 Author: Weiqun Zhang Date: Tue Sep 4 11:30:50 2018 -0700 MLMG: cell-centered fluxes Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 2abf9db9b8b3c10bdba23e29a3f3eb109f79c249 Author: Michele Rosso Date: Tue Sep 4 11:58:18 2018 -0700 CMake:some modification to comply with SPACK requirements Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_Utils.cmake Tools/CMake/MakefileConfig.export.in Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt commit 47c74fac3f4c47e4a45bb56cf6ccdd7a5b155baf Merge: 6be160f84 6f2191f5f Author: Weiqun Zhang Date: Mon Sep 3 13:54:44 2018 -0700 Merge branch 'mlmg' into development commit 6f2191f5f522b3620518a9ec6e04a7af7aea0026 Merge: 81c1ddcd0 b139f059d Author: Weiqun Zhang Date: Mon Sep 3 13:54:24 2018 -0700 Merge branch 'petsc' into mlmg commit b139f059defdd099bba691f282647eb0a8a93eeb Author: Weiqun Zhang Date: Mon Sep 3 13:53:28 2018 -0700 follow convention in Extern/HYPRE Src/Extern/PETSc/AMReX_PETSc.cpp commit 8f9a33add396bdfcfe3c4316de5fcf2bdd8b3e77 Author: Weiqun Zhang Date: Mon Sep 3 13:44:04 2018 -0700 set one row at a time Src/Extern/PETSc/AMReX_PETSc.cpp commit 581c5af99d72e343bdf24216820daa09494b8753 Author: Weiqun Zhang Date: Mon Sep 3 13:34:44 2018 -0700 white space Src/Extern/PETSc/AMReX_PETSc.cpp commit b9a55172be3307b21b8baf7127abb747481ce927 Author: Weiqun Zhang Date: Mon Sep 3 13:32:48 2018 -0700 Not sure we can assume these petsc calls are omp thread safe. Src/Extern/PETSc/AMReX_PETSc.cpp commit d7a1a68728005eaf64a12ad84f35dd621783fd4d Author: Weiqun Zhang Date: Mon Sep 3 13:30:01 2018 -0700 adjust petsc preallocatoin. (note that the estimate is for per row, not for all rows in a process.) Src/Extern/PETSc/AMReX_PETSc.cpp commit efa1e89949d51d4c798189f7cc5618f550c660c1 Author: Weiqun Zhang Date: Mon Sep 3 12:48:19 2018 -0700 static assert hypre and petsc have the same int Src/Extern/PETSc/AMReX_PETSc.cpp commit 29b62c80ec6f5a5a9679064cfa9c173ed5a7511b Author: Weiqun Zhang Date: Mon Sep 3 12:43:40 2018 -0700 comment out KSPSetFromOptions Src/Extern/PETSc/AMReX_PETSc.cpp commit 81c1ddcd0039b18c34bc5c665ab386d1e7b8b0f9 Author: Weiqun Zhang Date: Mon Sep 3 12:32:47 2018 -0700 update MLPoisson:FFlux Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 6be160f841ac2b1413b0e7c0cadcde96baae22e6 Author: Weiqun Zhang Date: Mon Sep 3 12:32:47 2018 -0700 update MLPoisson:FFlux Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 2256d4d86e2a64bbcc3e3c9d15d43da7ec2f5681 Author: Weiqun Zhang Date: Mon Sep 3 12:33:09 2018 -0700 remove HYPRE_DIR/include from petsc Tools/GNUMake/packages/Make.petsc commit bf8f4a742cc8221d005eed36a8eee791c501e3d4 Author: Weiqun Zhang Date: Mon Sep 3 12:32:47 2018 -0700 update MLPoisson:FFlux Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 6464384b1e8bbb8d40d65765d944de4e1dbf16b0 Author: Weiqun Zhang Date: Mon Sep 3 12:16:59 2018 -0700 fix link to petsc on NERSC Tests/LinearSolvers/CellEB/MyTest.cpp Tools/GNUMake/packages/Make.petsc commit b2b534c6618d8cc0bbc49d00e647d41fc7949928 Author: Weiqun Zhang Date: Mon Sep 3 12:10:15 2018 -0700 the link flags for various petsc stuff have to be inside ifdef otherwise it won't compile on say NERSC because they want different flags Tests/LinearSolvers/CellEB/inputs Tools/GNUMake/packages/Make.hypre Tools/GNUMake/packages/Make.petsc commit 387ed47fdcca4e2725c34a5b037c7e0a0b82989f Author: Weiqun Zhang Date: Mon Sep 3 11:51:42 2018 -0700 remove hardwired path to petsc Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/CellEB/GNUmakefile commit aa201fce71d252dec54c4572be45fc5dcfde51cc Author: Weiqun Zhang Date: Mon Sep 3 11:43:50 2018 -0700 use forward declaration Src/LinearSolvers/MLMG/AMReX_MLMG.H Tutorials/EB/MacProj/GNUmakefile commit d4cb9228802dc233746ca513237c5ec479fd10a9 Merge: 0730549a7 ff84fdd6d Author: Weiqun Zhang Date: Mon Sep 3 09:40:40 2018 -0700 Merge branch 'mlmg' into petsc commit ff84fdd6d8568374497cd74a0f1313ed3e026cfd Merge: ad95a796b a3ad049f6 Author: Weiqun Zhang Date: Mon Sep 3 09:39:19 2018 -0700 Merge branch 'development' into mlmg commit a3ad049f66699ae26d3b25a9fb1fc2c2a6d7ceff Merge: cfa91bcd6 b412bd3fc Author: WeiqunZhang Date: Mon Sep 3 09:36:56 2018 -0700 Merge pull request #270 from AMReX-Codes/forkjoin Forkjoin commit b412bd3fc264d102b3a26bba707ace092dd46805 Author: Weiqun Zhang Date: Mon Sep 3 09:35:53 2018 -0700 move -> forward Src/Base/AMReX_ParallelReduce.H commit cfa91bcd624666c2c9e73be957b4250348f27fcd Merge: de9ddd380 af3d41da3 Author: Weiqun Zhang Date: Mon Sep 3 09:31:41 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit af3d41da360184211ff809a512d82da46d9e19fe Merge: 73649f2c4 545b1b204 Author: Weiqun Zhang Date: Mon Sep 3 09:30:51 2018 -0700 Merge branch 'master' into development commit 545b1b204cf40f13ba0af97bcedc157b8e5a985c Author: Weiqun Zhang Date: Mon Sep 3 09:29:50 2018 -0700 update CHANGES CHANGES commit fe2832048af33c55a12ef21797d18755af1a7a65 Merge: a152a2921 73649f2c4 Author: Michael Zingale Date: Mon Sep 3 12:19:14 2018 -0400 Merge branch 'development' into gpu commit a152a29210c871bc5251e1386dbec7156698383a Author: Michael Zingale Date: Mon Sep 3 12:18:59 2018 -0400 sync encodings Tools/F_scripts/preprocess.py commit 73649f2c40c91d36595252fc89c45448e43d032b Author: Michael Zingale Date: Mon Sep 3 12:15:45 2018 -0400 remove unneeded module Tools/F_scripts/dep.py commit f1677c7d36555d3017da5892160864f4b7bb7bad Author: Michael Zingale Date: Mon Sep 3 12:13:50 2018 -0400 split out preprocess like we do in GPU Tools/F_scripts/dep.py Tools/F_scripts/preprocess.py commit 144fac9401c6ecebb8a5276a5847b4ed1ebec3fa Author: Max Katz Date: Mon Sep 3 11:56:16 2018 -0400 Insert a device sync in CrseInit Src/AmrCore/AMReX_FluxRegister.cpp commit ad95a796b14e9e36447a4a5fd04327dacbb4222f Author: Weiqun Zhang Date: Sun Sep 2 11:30:56 2018 -0700 MLMG: clean up flux and grad Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 12defb1e4e043b9b0cb29cdbbc35704495f00f51 Author: Klaus Weide Date: Sun Sep 2 00:44:44 2018 -0500 flailing around Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90 commit 4d0fea2b36968e3a6328ad698c8ffb2674df305a Author: Max Katz Date: Sat Sep 1 19:28:23 2018 -0400 Don't do MFIter reductions if not executing on device Src/Base/AMReX_MFIter.cpp commit ab87ed54fef50ae7159d24e3d40c15fc81391279 Author: Max Katz Date: Sat Sep 1 19:28:09 2018 -0400 Write amrex_max, etc. device versions by hand Src/Base/AMReX_fort_mod.F90 commit 66fb3be2476142c760ff4caf860d2649f57b63bf Author: Max Katz Date: Sat Sep 1 19:27:37 2018 -0400 Start in device launch region Src/Base/AMReX_Device.cpp commit e5582e3a01d0a2bc9ed6cb96553ea3e87c51fd21 Author: Max Katz Date: Sat Sep 1 18:34:27 2018 -0400 Add an option to disable the device offload Tools/F_scripts/write_cuda_headers.py commit 4faaa20955663ae875efbc7629b985f52bfda4bc Author: Max Katz Date: Sat Sep 1 18:17:36 2018 -0400 Write out the host function signature Tools/F_scripts/write_cuda_headers.py commit 1680006d2c5da2f91053088c90f9669f5749cdf0 Author: Max Katz Date: Sat Sep 1 18:04:31 2018 -0400 Add a device synchronize in debug mode Tools/F_scripts/write_cuda_headers.py commit c567d40bf917071f1e98a596e5b3b5c74fda393d Author: Weiqun Zhang Date: Sat Sep 1 14:21:33 2018 -0700 implement the locatio option for grad phi Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 1e3ba848e05fa71848987b2a4e0fb46cd34cd987 Merge: 090beb27d 830698efa Author: Klaus Weide Date: Sat Sep 1 16:08:55 2018 -0500 Merge branch 'development' of github.com:kweide/amrex into kw-development commit b5ebb4eed8da50ac006007c6aae184b7e67e4289 Author: Weiqun Zhang Date: Sat Sep 1 13:49:27 2018 -0700 implement the locatio option for flux Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 206c474b1463e6cea9a94de87ab66469564a222b Author: Weiqun Zhang Date: Sat Sep 1 08:24:47 2018 -0700 add Location in preparation for getting fluxes at different locations Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit e5011f4cde0ed48095131cdbae4d7f1ab0922c6c Author: Weiqun Zhang Date: Sat Sep 1 07:49:55 2018 -0700 simplification Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit c1232d8d6b8dea0e717c471a5c4ec90c2f443148 Author: Marc Day Date: Fri Aug 31 17:26:27 2018 -0700 Modify reductions to use parallel context comm Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp commit fb03b2387f456144769ed9e1273ecc085e09fd22 Author: Marc Day Date: Fri Aug 31 16:45:58 2018 -0700 Add grow cells to ForkJoin registration. Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp Tutorials/Parallel/ForkJoin/MyTest.cpp commit c2dbb38959144c7ed9b21f53d9d1290d17e054bf Author: Weiqun Zhang Date: Fri Aug 31 15:59:31 2018 -0700 CellEB2 test: fix the setup of prob type 2 Tests/LinearSolvers/CellEB2/mytest_f.F90 commit b53691d3234267e4d1b4541647fe6f4b2b10709c Author: Marc Day Date: Fri Aug 31 14:46:40 2018 -0700 Use ComponentSet instead of std::pair, and use Redistribute instead of copy. Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp Tutorials/Parallel/ForkJoin/MyTest.cpp commit badfafcee7977494120c4b958b398de83a13dfee Author: Weiqun Zhang Date: Fri Aug 31 14:44:59 2018 -0700 CellEB2 test: add option for composite or level by level solve Tests/LinearSolvers/CellEB2/MyTest.H Tests/LinearSolvers/CellEB2/MyTest.cpp Tests/LinearSolvers/CellEB2/inputs commit de9ddd3807a5d0da987de1cf28a14da545021337 Author: Weiqun Zhang Date: Fri Aug 31 13:50:33 2018 -0700 cell centered EB solver: multi-level works Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 3f9b894b3304841226d5d4730030e1ab496f6d0e Author: Weiqun Zhang Date: Fri Aug 31 13:43:24 2018 -0700 MLMG: add StateMode so that we can properly apply EB bc Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 090beb27d1248a961930c9105ad9ccb242e4fe0f Author: atmyers Date: Fri Aug 31 12:39:29 2018 -0700 restore some debugging changes I introduced. Tools/F_scripts/dep.py commit b3e32913542aacd625b3ee42add5cf77c942925c Author: atmyers Date: Fri Aug 31 12:38:05 2018 -0700 fix some Python 3 / Unicode issues in dep.py Tools/F_scripts/dep.py commit 0730549a7ec09ffad6579a3e359bc69b6412107b Author: sireeveslbl Date: Fri Aug 31 11:24:25 2018 -0700 PETSC looks ok Src/Extern/PETSc/AMReX_PETSc.H Src/Extern/PETSc/AMReX_PETSc.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 05c999f36532598890e6ee9e1c5c0d3efb764a5a Author: Weiqun Zhang Date: Fri Aug 31 10:46:15 2018 -0700 EB dirichlet: average down for multi amr levels Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 7f0c7f4b925683152e5404eab4d92780883764d2 Author: Weiqun Zhang Date: Fri Aug 31 10:28:37 2018 -0700 add Array versions of various average down functions Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp commit f878a4db1319ec01175c8c0bf130da1f0fd44451 Merge: 38edde91e eed28bbeb Author: Marc Day Date: Thu Aug 30 19:09:25 2018 -0700 Merge branch 'marc/forkjoin_dev' of github.com:AMReX-Codes/amrex into marc/forkjoin_dev commit 38edde91ee1e7010b548784eff857138fad06fde Author: Marc Day Date: Thu Aug 30 12:07:22 2018 -0700 Fix bug in tutorial. Tutorials/Parallel/ForkJoin/MyTest.cpp commit 77d753896336274c9f9705c74160076e7e26ffa5 Author: Marc Day Date: Thu Aug 30 12:01:28 2018 -0700 Add a simple ForkJoin Tutorial, add a function to the fj class. Tutorial currently gives weird result for duplicated multifabs. Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp Tutorials/Parallel/ForkJoin/GNUmakefile Tutorials/Parallel/ForkJoin/Make.package Tutorials/Parallel/ForkJoin/MyTest.H Tutorials/Parallel/ForkJoin/MyTest.cpp Tutorials/Parallel/ForkJoin/MyTest_F.H Tutorials/Parallel/ForkJoin/inputs Tutorials/Parallel/ForkJoin/main.cpp commit 0ae12cf86c40ba3887e8eb559f3184b6c406c414 Merge: a5aca977c 8da75a422 Author: Marc Day Date: Thu Aug 30 18:59:44 2018 -0700 Merge remote-tracking branch 'origin/development' into forkjoin commit 8da75a422387409ed86d1d3a73d56fd3f4345143 Author: Weiqun Zhang Date: Thu Aug 30 16:43:13 2018 -0700 clean up GNUmakefile.in OldTutorials/EBParticles/GNUmakefile Src/Base/AMReX_BCRec.cpp Src/EB/AMReX_EB2.H Src/EB/AMReX_EB2.cpp Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Src/EB/CMakeLists.txt Src/EB/Make.package Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tests/LinearSolvers/CellEB/GNUmakefile Tests/LinearSolvers/CellEB2/GNUmakefile Tests/LinearSolvers/EBConvergenceTest/GNUmakefile Tests/LinearSolvers/EBflux_grad/GNUmakefile Tutorials/EB/CNS/Exec/Make.CNS Tutorials/EB/LevelSet/Exec/inputs_eb2 Tutorials/EB/LevelSet/Src/main.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp Tutorials/EB/LevelSet/Src/make_poly.cpp Tutorials/EB/LevelSet/Src/make_shapes.H Tutorials/EB/MacProj/GNUmakefile commit a828e688419d1a29461ddaf59633b72b53e23f6b Author: Weiqun Zhang Date: Thu Aug 30 16:26:04 2018 -0700 removed old EB Docs/Doxygen/doxygen.conf Docs/sphinx_documentation/source/EB.rst OldTutorials/EBParticles/EBParticleContainer.H OldTutorials/EBParticles/EBParticleContainer.cpp OldTutorials/EBParticles/GNUmakefile OldTutorials/EBParticles/Make.package OldTutorials/EBParticles/ebparticles_2d.f90 OldTutorials/EBParticles/ebparticles_3d.f90 OldTutorials/EBParticles/ebparticles_F.H OldTutorials/EBParticles/inputs OldTutorials/EBParticles/main.cpp OldTutorials/GeometryGeneration/exec/GNUmakefile OldTutorials/GeometryGeneration/exec/coveredSlabs.cpp OldTutorials/GeometryGeneration/exec/coveredslabs.inputs OldTutorials/GeometryGeneration/exec/parabolaWithSphere.cpp OldTutorials/GeometryGeneration/exec/parabolaWithSphere.inputs OldTutorials/GeometryGeneration/exec/sphere.cpp OldTutorials/GeometryGeneration/exec/sphere.inputs OldTutorials/GeometryGeneration/exec/surfaceOfRevolution.cpp OldTutorials/GeometryGeneration/exec/surfaceOfRevolution.inputs OldTutorials/GeometryGeneration/src/CommonCode.H OldTutorials/GeometryGeneration/src/CommonCode.cpp OldTutorials/GeometryGeneration/src/Make.package OldTutorials/GeometryGeneration/src/WriteEBPlotFile.H OldTutorials/GeometryGeneration/src/WriteEBPlotFile.cpp Src/Amr/AMReX_StateData.H Src/CMakeLists.txt Src/EB/AMReX_EB2.H Src/EB/AMReX_EB2.cpp Src/EB/AMReX_EB2_F.H Src/EB/AMReX_EB2_GeometryShop.H Src/EB/AMReX_EB2_Graph.H Src/EB/AMReX_EB2_IF_AllRegular.H Src/EB/AMReX_EB2_IF_Box.H Src/EB/AMReX_EB2_IF_Complement.H Src/EB/AMReX_EB2_IF_Cylinder.H Src/EB/AMReX_EB2_IF_Ellipsoid.H Src/EB/AMReX_EB2_IF_Intersection.H Src/EB/AMReX_EB2_IF_Lathe.H Src/EB/AMReX_EB2_IF_Plane.H Src/EB/AMReX_EB2_IF_Polynomial.H Src/EB/AMReX_EB2_IF_Rotation.H Src/EB/AMReX_EB2_IF_Scale.H Src/EB/AMReX_EB2_IF_Sphere.H Src/EB/AMReX_EB2_IF_Translation.H Src/EB/AMReX_EB2_IF_Union.H Src/EB/AMReX_EB2_IndexSpaceI.H Src/EB/AMReX_EB2_Level.H Src/EB/AMReX_EB2_Level.cpp Src/EB/AMReX_EB2_MultiGFab.H Src/EB/AMReX_EB2_MultiGFab.cpp Src/EB/AMReX_eb2_2d.F90 Src/EB/AMReX_eb2_3d.F90 Src/EB/CMakeLists.txt Src/EB/Make.package Src/EB2/CMakeLists.txt Src/EB2/Make.package Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Src/EBAMRTools/AMReX_DivergenceOp.H Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_EBCFInterp.H Src/EBAMRTools/AMReX_EBCFInterp.cpp Src/EBAMRTools/AMReX_EBCoarseAverage.H Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_EBFastFR.H Src/EBAMRTools/AMReX_EBFastFR.cpp Src/EBAMRTools/AMReX_EBFineInterp.H Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/EBAMRTools/AMReX_EBFortND_F.H Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/EBAMRTools/AMReX_GradientOp.H Src/EBAMRTools/AMReX_GradientOp.cpp Src/EBAMRTools/AMReX_MeshRefine.H Src/EBAMRTools/AMReX_MeshRefine.cpp Src/EBAMRTools/Make.package Src/GeometryShop/AMReX_AggStencil.H Src/GeometryShop/AMReX_AggStencilI.H Src/GeometryShop/AMReX_AllRegularService.H Src/GeometryShop/AMReX_AllRegularService.cpp Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H Src/GeometryShop/AMReX_AnisotropicIF.H Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_BaseEBCellFactory.H Src/GeometryShop/AMReX_BaseEBFaceFAB.H Src/GeometryShop/AMReX_BaseEBFaceFABI.H Src/GeometryShop/AMReX_BaseIF.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFAB.cpp Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_BaseIFFactory.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_CH_EBIS_ORDER.H Src/GeometryShop/AMReX_CellEdge.H Src/GeometryShop/AMReX_CellEdge.cpp Src/GeometryShop/AMReX_ComplementIF.H Src/GeometryShop/AMReX_ComplementIF.cpp Src/GeometryShop/AMReX_ConstrainedLS.H Src/GeometryShop/AMReX_ConstrainedLS.cpp Src/GeometryShop/AMReX_CoordinateSystem.H Src/GeometryShop/AMReX_CoordinateSystemImplem.H Src/GeometryShop/AMReX_CoveredSlabs.H Src/GeometryShop/AMReX_CoveredSlabs.cpp Src/GeometryShop/AMReX_CutCellMoments.H Src/GeometryShop/AMReX_CutCellMoments.cpp Src/GeometryShop/AMReX_CutCellMomentsImplem.H Src/GeometryShop/AMReX_DivNormalRefinement.H Src/GeometryShop/AMReX_DivNormalRefinementImplem.H Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_EBCellFAB.H Src/GeometryShop/AMReX_EBCellFAB.cpp Src/GeometryShop/AMReX_EBCellFactory.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBDataFactory.H Src/GeometryShop/AMReX_EBDataVarMacros.H Src/GeometryShop/AMReX_EBDebugDump.H Src/GeometryShop/AMReX_EBDebugOut.H Src/GeometryShop/AMReX_EBDebugOut.cpp Src/GeometryShop/AMReX_EBFaceFAB.H Src/GeometryShop/AMReX_EBFaceFAB.cpp Src/GeometryShop/AMReX_EBFluxFAB.H Src/GeometryShop/AMReX_EBFluxFAB.cpp Src/GeometryShop/AMReX_EBFluxFactory.H Src/GeometryShop/AMReX_EBFluxFactory.cpp Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISBox.H Src/GeometryShop/AMReX_EBISBox.cpp Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_EBLevelGrid.H Src/GeometryShop/AMReX_EBLevelGrid.cpp Src/GeometryShop/AMReX_EBLevelRedist.H Src/GeometryShop/AMReX_EBLevelRedist.cpp Src/GeometryShop/AMReX_EBLoHiCenter.H Src/GeometryShop/AMReX_EBLoHiCenter.cpp Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.H Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp Src/GeometryShop/AMReX_EB_TYPEDEFS.H Src/GeometryShop/AMReX_Ellipsoid.cpp Src/GeometryShop/AMReX_EllipsoidIF.H Src/GeometryShop/AMReX_EllipsoidIF.cpp Src/GeometryShop/AMReX_ExtrudeIF.H Src/GeometryShop/AMReX_ExtrudeIF.cpp Src/GeometryShop/AMReX_FabArrayIO.H Src/GeometryShop/AMReX_FabArrayIO.cpp Src/GeometryShop/AMReX_FaceIndex.H Src/GeometryShop/AMReX_FaceIndex.cpp Src/GeometryShop/AMReX_FaceIterator.H Src/GeometryShop/AMReX_FaceIterator.cpp Src/GeometryShop/AMReX_Factorial.H Src/GeometryShop/AMReX_FixedRefinement.H Src/GeometryShop/AMReX_FixedRefinementImplem.H Src/GeometryShop/AMReX_FlatPlateGeom.H Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_GenericArithmetic.H Src/GeometryShop/AMReX_GenericArithmeticI.H Src/GeometryShop/AMReX_GeomIntersectUtils.H Src/GeometryShop/AMReX_GeomIntersectUtils.cpp Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryService.cpp Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_GraphNode.H Src/GeometryShop/AMReX_GraphNode.cpp Src/GeometryShop/AMReX_IFData.H Src/GeometryShop/AMReX_IFData.cpp Src/GeometryShop/AMReX_IFDataImplem.H Src/GeometryShop/AMReX_IFSlicer.H Src/GeometryShop/AMReX_IFSlicer.cpp Src/GeometryShop/AMReX_IFSlicerImplem.H Src/GeometryShop/AMReX_IndexTM.H Src/GeometryShop/AMReX_IndexTMI.H Src/GeometryShop/AMReX_IndexedMoments.H Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntVectSet.cpp Src/GeometryShop/AMReX_IntersectionIF.H Src/GeometryShop/AMReX_IntersectionIF.cpp Src/GeometryShop/AMReX_IrregFAB.H Src/GeometryShop/AMReX_IrregFAB.cpp Src/GeometryShop/AMReX_IrregFABFactory.H Src/GeometryShop/AMReX_IrregFABFactory.cpp Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_IrregNode.cpp Src/GeometryShop/AMReX_KDStruct.H Src/GeometryShop/AMReX_KDTree.H Src/GeometryShop/AMReX_KDTree.cpp Src/GeometryShop/AMReX_LSProblem.H Src/GeometryShop/AMReX_LSProblem.cpp Src/GeometryShop/AMReX_LSProblemImplem.H Src/GeometryShop/AMReX_LSquares.H Src/GeometryShop/AMReX_LSquares.cpp Src/GeometryShop/AMReX_LatheIF.H Src/GeometryShop/AMReX_LatheIF.cpp Src/GeometryShop/AMReX_LoHiSide.H Src/GeometryShop/AMReX_LoHiSide.cpp Src/GeometryShop/AMReX_MetaPrograms.H Src/GeometryShop/AMReX_MinimalCCCM.H Src/GeometryShop/AMReX_MinimalCCCM.cpp Src/GeometryShop/AMReX_MinimalCCCMImplem.H Src/GeometryShop/AMReX_MomentIterator.H Src/GeometryShop/AMReX_MomentIteratorImplem.H Src/GeometryShop/AMReX_Moments.H Src/GeometryShop/AMReX_Moments.cpp Src/GeometryShop/AMReX_MonomialPowers.H Src/GeometryShop/AMReX_MultiIndex.H Src/GeometryShop/AMReX_MultiIndexImplem.H Src/GeometryShop/AMReX_NoRefinement.H Src/GeometryShop/AMReX_NoRefinementImplem.H Src/GeometryShop/AMReX_NormalDerivative.H Src/GeometryShop/AMReX_NormalDerivative.cpp Src/GeometryShop/AMReX_NormalDerivativeNew.H Src/GeometryShop/AMReX_Notation.H Src/GeometryShop/AMReX_PXStuff.H Src/GeometryShop/AMReX_PXStuff.cpp Src/GeometryShop/AMReX_PlaneIF.H Src/GeometryShop/AMReX_PlaneIF.cpp Src/GeometryShop/AMReX_PolyGeom.H Src/GeometryShop/AMReX_PolyGeom.cpp Src/GeometryShop/AMReX_PolynomialIF.H Src/GeometryShop/AMReX_PolynomialIF.cpp Src/GeometryShop/AMReX_RedistStencil.H Src/GeometryShop/AMReX_RedistStencil.cpp Src/GeometryShop/AMReX_RefinementCriterion.H Src/GeometryShop/AMReX_STLAsciiReader.H Src/GeometryShop/AMReX_STLAsciiReader.cpp Src/GeometryShop/AMReX_STLBox.H Src/GeometryShop/AMReX_STLBox.cpp Src/GeometryShop/AMReX_STLExplorer.H Src/GeometryShop/AMReX_STLExplorer.cpp Src/GeometryShop/AMReX_STLIF.H Src/GeometryShop/AMReX_STLIF.cpp Src/GeometryShop/AMReX_STLMesh.H Src/GeometryShop/AMReX_STLMesh.cpp Src/GeometryShop/AMReX_STLReader.H Src/GeometryShop/AMReX_STLUtil.H Src/GeometryShop/AMReX_STLUtil.cpp Src/GeometryShop/AMReX_SmoothAbsoluteValue.H Src/GeometryShop/AMReX_SmoothAbsoluteValue.cpp Src/GeometryShop/AMReX_SmoothIntersection.H Src/GeometryShop/AMReX_SmoothIntersection.cpp Src/GeometryShop/AMReX_SmoothUnion.H Src/GeometryShop/AMReX_SmoothUnion.cpp Src/GeometryShop/AMReX_SphereIF.H Src/GeometryShop/AMReX_SphereIF.cpp Src/GeometryShop/AMReX_Stencils.H Src/GeometryShop/AMReX_Stencils.cpp Src/GeometryShop/AMReX_TransformIF.H Src/GeometryShop/AMReX_TransformIF.cpp Src/GeometryShop/AMReX_UnionIF.H Src/GeometryShop/AMReX_UnionIF.cpp Src/GeometryShop/AMReX_VoFIterator.H Src/GeometryShop/AMReX_VoFIterator.cpp Src/GeometryShop/AMReX_VolIndex.H Src/GeometryShop/AMReX_VolIndex.cpp Src/GeometryShop/AMReX_WrappedGShop.H Src/GeometryShop/AMReX_WrappedGShop.cpp Src/GeometryShop/AMReX_ZCylinder.H Src/GeometryShop/AMReX_ZCylinder.cpp Src/GeometryShop/CMakeLists.txt Src/GeometryShop/Make.package Src/GeometryShop/_save/AMReX_GeometryShop.H Src/GeometryShop/_save/AMReX_GeometryShop.cpp Tests/EBAMRTools/README Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/Make.package Tests/EBAMRTools/regression/aggpwlfp.inputs Tests/EBAMRTools/regression/aggpwlfpTest.cpp Tests/EBAMRTools/regression/divergenceOpTest.cpp Tests/EBAMRTools/regression/divop.inputs Tests/EBAMRTools/regression/ebCoarseAveTest.cpp Tests/EBAMRTools/regression/ebCoarseAveTestFace.cpp Tests/EBAMRTools/regression/ebFineInterpTest.cpp Tests/EBAMRTools/regression/ebcoarave.inputs Tests/EBAMRTools/regression/ebfineinterp.inputs Tests/EBAMRTools/regression/fluxRegTest.cpp Tests/EBAMRTools/regression/fluxreg.inputs Tests/EBAMRTools/regression/gradientOpTest.cpp Tests/EBAMRTools/regression/gradop.inputs Tests/EBAMRTools/regression/meshref.inputs Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp Tests/EBAMRTools/regression/nwoebquadcfi.inputs Tests/EBAMRTools/regression/regFluxRegTest.cpp Tests/EBAMRTools/regression/runalltests.mpi.sh Tests/EBAMRTools/regression/runalltests.serial.sh Tests/EBAMRTools/regression/simpleMeshRefine.cpp Tests/EBAMRTools/regression/sphere.inputs Tests/EBEB2/GNUmakefile Tests/EBEB2/Make.package Tests/EBEB2/MyTest.H Tests/EBEB2/MyTest.cpp Tests/EBEB2/initEB.cpp Tests/EBEB2/inputs Tests/EBEB2/main.cpp Tests/EBbcent/GNUmakefile Tests/EBbcent/Make.package Tests/EBbcent/main.cpp Tests/GeometryShop/README Tests/GeometryShop/STLGeom/GNUmakefile Tests/GeometryShop/STLGeom/bad.cylinder.inputs Tests/GeometryShop/STLGeom/bad.reactor.inputs Tests/GeometryShop/STLGeom/cylinder.stl Tests/GeometryShop/STLGeom/good.cylinder.inputs Tests/GeometryShop/STLGeom/good.reactor.inputs Tests/GeometryShop/STLGeom/good.sphere.inputs Tests/GeometryShop/STLGeom/reactor.stl Tests/GeometryShop/STLGeom/sphere.stl Tests/GeometryShop/STLGeom/stl.inputs Tests/GeometryShop/STLGeom/stlgeom.cpp Tests/GeometryShop/ebgraphDistributed/GNUmakefile Tests/GeometryShop/ebgraphDistributed/Make.package Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp Tests/GeometryShop/ebgraphDistributed/sphere.inputs Tests/GeometryShop/ebgraphSingleGrid/GNUmakefile Tests/GeometryShop/ebgraphSingleGrid/Make.package Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp Tests/GeometryShop/ebgraphSingleGrid/sphere.inputs Tests/GeometryShop/flatPlate/GNUmakefile Tests/GeometryShop/flatPlate/Make.package Tests/GeometryShop/flatPlate/flatPlateTest.cpp Tests/GeometryShop/flatPlate/flatplate.inputs Tests/GeometryShop/ramp/GNUmakefile Tests/GeometryShop/ramp/Make.package Tests/GeometryShop/ramp/inputs Tests/GeometryShop/ramp/main.cpp Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/Make.package Tests/GeometryShop/regression/dataArith.cpp Tests/GeometryShop/regression/dataarith.inputs Tests/GeometryShop/regression/ebio.2.inputs Tests/GeometryShop/regression/ebio.cpp Tests/GeometryShop/regression/ebio.inputs Tests/GeometryShop/regression/ebnormalizeTest.cpp Tests/GeometryShop/regression/ebnormtest.inputs Tests/GeometryShop/regression/fabfromif.cpp Tests/GeometryShop/regression/fabio.cpp Tests/GeometryShop/regression/fabio.inputs Tests/GeometryShop/regression/levelRedistTest.cpp Tests/GeometryShop/regression/levelredist.inputs Tests/GeometryShop/regression/momentConvTest.cpp Tests/GeometryShop/regression/momentconvtest.inputs Tests/GeometryShop/regression/multicelllev.cpp Tests/GeometryShop/regression/multicelllev.inputs Tests/GeometryShop/regression/runalltests.mpi.sh Tests/GeometryShop/regression/runalltests.serial.sh Tests/GeometryShop/regression/serialization.cpp Tests/GeometryShop/regression/serialization.inputs Tests/GeometryShop/regression/simpleMomentExample.cpp Tests/GeometryShop/regression/simplemomentexample.inputs Tests/GeometryShop/runalltests.mpi.sh Tests/GeometryShop/runalltests.serial.sh Tests/GeometryShop/sparseDataSingleGrid/GNUmakefile Tests/GeometryShop/sparseDataSingleGrid/Make.package Tests/GeometryShop/sparseDataSingleGrid/sparseDataSG.cpp Tests/GeometryShop/sparseDataSingleGrid/sphere.inputs Tests/GeometryShop/sphere/GNUmakefile Tests/GeometryShop/sphere/Make.package Tests/GeometryShop/sphere/sphere.inputs Tests/GeometryShop/sphere/sphereConvTest.cpp Tests/GeometryShop/sphere/sphereTest.cpp Tests/GeometryShop/sphereEBISBox/GNUmakefile Tests/GeometryShop/sphereEBISBox/Make.package Tests/GeometryShop/sphereEBISBox/sphere.inputs Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp Tests/GeometryShop/stencilTestbed/exec/GNUmakefile Tests/GeometryShop/stencilTestbed/exec/Make.package Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/dirichletTest_F.H Tests/GeometryShop/stencilTestbed/exec/sphere.inputs Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD_3d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD_F.H Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.H Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp Tests/GeometryShop/stencilTestbed/src/Make.package Tests/GeometryShop/stencilTestbed/src/lapl_nd.F90 Tests/GeometryShop/stencilTestbed/src/lapl_nd_F.H Tests/GeometryShop/vofStructures/AMReX_EBRedist.H Tests/GeometryShop/vofStructures/AMReX_EBStruct.H Tests/GeometryShop/vofStructures/AMReX_ebstruct_mod.F90 Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/README.txt Tests/GeometryShop/vofStructures/flatplate.inputs Tests/GeometryShop/vofStructures/nbrsTest.cpp Tests/GeometryShop/vofStructures/nbrsTest_mod.F90 Tests/GeometryShop/vofStructures/nbrsTest_nd.f90 Tests/GeometryShop/vofStructures/sphere.inputs Tests/GeometryShop/vofStructures/umapTest.H Tests/GeometryShop/vofStructures/umapTest.cpp Tests/GeometryShop/vofStructures/umapTest_mod.f90 Tests/GeometryShop/vofStructures/umapTest_nd.f90 Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/EBSurfaceTools/GNUmakefile Tools/GNUMake/Make.defs Tutorials/EB/CNS/Exec/Make.CNS Tutorials/EB/LevelSet/Exec/GNUmakefile commit 709648e92f38216f6ca9c0ff76d7826b0e0107e7 Author: sireeveslbl Date: Thu Aug 30 16:10:43 2018 -0700 odd stencil behavior for generating the matrix. Some regions do not have the penta-diagonal design it should have. Looking to investigate this. Src/Extern/PETSc/AMReX_PETSc.cpp commit e81287afe1376ae6c713b92e1f97d1d6b92f96a3 Author: Ray Grout Date: Thu Aug 30 16:10:01 2018 -0600 Change how vfrac threshold is written out so that amrvis and visit are both happy Tutorials/EB/CNS/Source/CNS_io.cpp commit 1f7656f9a9c9e2b828d4823af1723c9f13b5c0d8 Author: Weiqun Zhang Date: Thu Aug 30 13:46:38 2018 -0700 CellEB2: add fine grids Src/EB2/AMReX_EB2_Level.H Tests/LinearSolvers/CellEB2/MyTest.H Tests/LinearSolvers/CellEB2/MyTest.cpp Tests/LinearSolvers/CellEB2/inputs commit 643509674776052123936ab34ad7a250849a6c64 Author: Weiqun Zhang Date: Thu Aug 30 13:32:33 2018 -0700 add CellEB2 test for Dirichlet bc Tests/LinearSolvers/CellEB2/GNUmakefile Tests/LinearSolvers/CellEB2/Make.package Tests/LinearSolvers/CellEB2/MyEB.H Tests/LinearSolvers/CellEB2/MyTest.H Tests/LinearSolvers/CellEB2/MyTest.cpp Tests/LinearSolvers/CellEB2/MyTest_F.H Tests/LinearSolvers/CellEB2/initEB.cpp Tests/LinearSolvers/CellEB2/inputs Tests/LinearSolvers/CellEB2/main.cpp Tests/LinearSolvers/CellEB2/mytest_f.F90 commit eed28bbeb53f6f2dee4a30be3d2d07397eb4681d Author: Marc Day Date: Thu Aug 30 12:07:22 2018 -0700 Fix bug in tutorial. Tutorials/Parallel/ForkJoin/MyTest.cpp commit ea6fa99f9a0a7a61abc207e05c1946e1778cfed4 Author: Marc Day Date: Thu Aug 30 12:01:28 2018 -0700 Add a simple ForkJoin Tutorial, add a function to the fj class. Tutorial currently gives weird result for duplicated multifabs. Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp Tutorials/Parallel/ForkJoin/GNUmakefile Tutorials/Parallel/ForkJoin/Make.package Tutorials/Parallel/ForkJoin/MyTest.H Tutorials/Parallel/ForkJoin/MyTest.cpp Tutorials/Parallel/ForkJoin/MyTest_F.H Tutorials/Parallel/ForkJoin/inputs Tutorials/Parallel/ForkJoin/main.cpp commit 44e9af1c70862d81d9c1b473aa1335afa22a6aeb Merge: 38054bf01 fefa27a73 Author: Marc Day Date: Thu Aug 30 10:34:44 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 38054bf013726790a25938ed60ae8322895e216c Author: Marc Day Date: Thu Aug 30 10:34:41 2018 -0700 Add == op for BCRec Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp commit fefa27a73c32d8b214d7536f6ce97174f5c532f4 Author: Weiqun Zhang Date: Thu Aug 30 10:29:14 2018 -0700 new iMultiFab constructor taking IntVect ngrow Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit a5aca977c7a329889e827d2d79931919c310eb26 Author: Cy Chan Date: Wed Aug 29 22:05:39 2018 -0700 ParallelReduce.H: for MPI_Op lookup, change unordered_map to array Src/Base/AMReX_ParallelReduce.H commit ec5f92caf73f1a464f95a7fea155793e4681e016 Author: sireeveslbl Date: Wed Aug 29 16:02:57 2018 -0700 Matrix appears to be correctly populating. However, the KSB solver is throwing a floating point exception. Will continue to debug. Possible culprits: RHS and Sol vectors not correctly being loaded, petsc not being correctly initialized, or something I haven't thought of. Src/Extern/PETSc/AMReX_PETSc.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 14c7589340cc397fb57c83b5213ebd1827b36508 Author: Weiqun Zhang Date: Wed Aug 29 15:59:00 2018 -0700 put limit on eb max coarsening level Src/EB2/AMReX_EB2_IndexSpaceI.H commit 383ec3f996be26470f85299c8414eefaf0195986 Merge: 18a918819 1043881a3 Author: Weiqun Zhang Date: Tue Aug 28 17:15:27 2018 -0700 Merge branch 'development' into mlmg commit 18a9188191c8428b1aaa33a7a7a6837267b532b6 Author: Weiqun Zhang Date: Tue Aug 28 17:15:08 2018 -0700 remove unused variables Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit a876aa21d75df39d46f789ddc0b0eb1898cf5242 Author: Weiqun Zhang Date: Tue Aug 28 16:08:34 2018 -0700 3d eb dirichlet: gsrb and normalize Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 520065595c5eb9860eae17cdb5d447c798be568c Author: sireeveslbl Date: Tue Aug 28 15:59:47 2018 -0700 Removed unneeded function Src/Extern/PETSc/AMReX_PETSc.H commit fa7adeb898eaddce869247ca8aea94929ab7a6a8 Author: sireeveslbl Date: Tue Aug 28 15:57:23 2018 -0700 Wrote the function to connect applications and PETSc routines. There are bugs in the execution that will need to be flushed out. Src/Extern/PETSc/AMReX_PETSc.H Src/Extern/PETSc/AMReX_PETSc.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 5e7ad67a03df0e99b686250495b86acf8348e83e Author: Weiqun Zhang Date: Tue Aug 28 15:45:34 2018 -0700 3d eb dirichlet a dot x Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit cdfabe1c5f582be8026143201756655c559f376e Author: sireeveslbl Date: Tue Aug 28 14:26:48 2018 -0700 Proper build of Petsc, returned Make.petsc to previous version, single include directory. KSP solver not converging, need to iron out bugs. Tests/LinearSolvers/CellEB/GNUmakefile Tests/LinearSolvers/CellEB/inputs Tools/GNUMake/packages/Make.petsc commit 6f66f5a50b1bde6a26df8874dda477b99107da45 Author: sireeveslbl Date: Tue Aug 28 13:32:55 2018 -0700 Switched things a bit Tests/LinearSolvers/CellEB/GNUmakefile Tools/GNUMake/packages/Make.petsc commit e2e2a0e49ca5316c75f97c84050b249d008fc3e2 Author: Weiqun Zhang Date: Tue Aug 28 13:28:15 2018 -0700 update normalize Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 38489804162cc2df2aaa4cf29040ac328ca6ecd1 Author: Weiqun Zhang Date: Tue Aug 28 13:03:33 2018 -0700 eb dirichlet: use the simple version Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit acb27634fba830f26bce0625ddbdcd8049a4007b Author: sireeveslbl Date: Tue Aug 28 13:02:59 2018 -0700 AMReX with PETSC bottom solve works. Going to go through and remove any unneccessary links/ directories Src/Extern/PETSc/AMReX_PETSc.cpp Tests/LinearSolvers/CellEB/GNUmakefile Tools/GNUMake/packages/Make.petsc commit c31a704acbb36935c90053dfe6dafd01963ad317 Author: sireeveslbl Date: Mon Aug 27 14:16:51 2018 -0700 Killing compilation issues, got the proper linkage. However now am having pointer issues. Will try and fix those. Note this does not compile yet for USE_PETSC=TRUE Src/Extern/PETSc/AMReX_PETSc.cpp Tests/LinearSolvers/CellEB/MyTest.H Tests/LinearSolvers/CellEB/MyTest.cpp Tests/LinearSolvers/CellEB/inputs commit 1043881a346d9ecb87aac47cdb21e4feec0aaf1c Merge: 5571d6518 1618960ee Author: Weiqun Zhang Date: Mon Aug 27 12:30:38 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5571d651869ad5bdcf92d313b3ba100ce256b788 Author: Weiqun Zhang Date: Mon Aug 27 12:28:30 2018 -0700 VisMF::Read can read lower-dimensional files with ghost cells Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_VisMF.cpp commit 464b372c849956fe9758ea87c9581862cb85660a Author: Weiqun Zhang Date: Mon Aug 27 12:27:25 2018 -0700 mfiter: support no IntVect number of ghost cells Src/Base/AMReX_MFIter.cpp commit 1618960ee2bb21ef7586c715cdd627f2a2ab0a92 Author: Tan Nguyen Date: Mon Aug 27 12:24:17 2018 -0700 fix a small buf in the custom Barrier Src/AmrTask/rts_impls/Perilla/Barrier.cpp Src/AmrTask/rts_impls/Perilla_upc++/Barrier.cpp commit 04f8fb95f182a9b6ce43441ed5dcfc7d1b99a3e7 Author: Weiqun Zhang Date: Mon Aug 27 10:34:07 2018 -0700 make IntVect operator>> work for data of any dimensions Src/Base/AMReX_IntVect.cpp commit ae7e840f2c21b7274c6fb31ef839e29ac5fd70f8 Author: Max Katz Date: Sat Aug 25 15:45:15 2018 -0700 Fix up the heat equation GPU tutorial Tutorials/GPU/HeatEquation_EX1_C/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/advance.cpp commit efd541e50d65cfdbb68fe265d0ec877a8b7a6fd8 Author: Max Katz Date: Sat Aug 25 15:33:42 2018 -0700 Fix typo Tools/F_mk/GMakeMPI.mak commit b1a5265aff081f7ff76c4e49e3b4122cb9b88989 Author: Max Katz Date: Sat Aug 25 15:30:35 2018 -0700 Sync up some more with development Src/Base/AMReX.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_Geometry.cpp commit b7551f2d0402dd7b139aaa2acbea1685a513b632 Merge: df38fe032 c391a6b37 Author: Max Katz Date: Sat Aug 25 14:42:40 2018 -0700 Merge branch 'development' into gpu Conflicts: Src/Base/AMReX_ArrayLim.H commit df38fe03235e2fff53f518406d7450b5fa7444c7 Author: Max Katz Date: Sat Aug 25 14:35:04 2018 -0700 Sync up RealBox with development Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit 265d5c62c91fea96ed15ad4d4a3e77ca05959df1 Author: Weiqun Zhang Date: Sat Aug 25 13:54:00 2018 -0700 dirichlet eb: clean up Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit bb825ce97b7b0460cfcfc9c40deff6ad4a17b78a Author: Weiqun Zhang Date: Sat Aug 25 11:09:55 2018 -0700 eb dirichlet: version that avoids extrapolation Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit 046ebb0be1e88ed886554b211b4992d50b57dcef Author: Weiqun Zhang Date: Fri Aug 24 22:30:10 2018 -0700 CellEB test: print out the smallest cut cell's volume fraction Tests/LinearSolvers/CellEB/MyTest.cpp commit 87be0e337d2b9498af56e18e17817cd11ab65333 Author: Weiqun Zhang Date: Fri Aug 24 22:03:49 2018 -0700 eb dirichlet: tweak parameters Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit 3a85382433e7ecbbce99f6ea280e5f9fe1a17f12 Author: Weiqun Zhang Date: Fri Aug 24 21:40:24 2018 -0700 eb dirichlet: fix blend function Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Tests/LinearSolvers/CellEB/MyTest.cpp commit db5906154b6b2bb62f74fabd41ae8b1acb32d4eb Author: Weiqun Zhang Date: Fri Aug 24 17:15:51 2018 -0700 eb dirichlet: 2d gsrb Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit 06d313e0d0bc54b17e92aab4de352756f6688813 Author: Weiqun Zhang Date: Fri Aug 24 17:15:38 2018 -0700 CellEB test: add parameters for scalars Tests/LinearSolvers/CellEB/MyTest.H Tests/LinearSolvers/CellEB/MyTest.cpp commit fa3b32e073d489e592c8b53e207eb434a9b1f0b6 Author: sireeveslbl Date: Fri Aug 24 15:57:28 2018 -0700 Linking issues between PETSc HYPRE and AMReX. Will route out the problem. Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Tests/LinearSolvers/CellEB/GNUmakefile Tools/GNUMake/packages/Make.petsc commit 1d4290d2f38db54ccb2dbfb95a955cee67b2ab37 Author: Weiqun Zhang Date: Fri Aug 24 15:53:30 2018 -0700 pass dirichlet information into gsrb Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit bf481d47d7a21ce436cf060174f9d829142459df Author: Weiqun Zhang Date: Fri Aug 24 15:43:59 2018 -0700 change the CellEB test initial data Tests/LinearSolvers/CellEB/MyTest.cpp commit 1121f9007282bfd1229b28c62bca43daeb24c766 Author: Weiqun Zhang Date: Fri Aug 24 15:17:11 2018 -0700 eb dirichlet: a dot x Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit c391a6b37c611da604d00fde8e63dc99cf47d1c2 Author: sireeveslbl Date: Fri Aug 24 13:48:16 2018 -0700 Typo fix Docs/sphinx_documentation/source/EB.rst commit 818bf6d0034d8a8ab4fda9ce1b3b693c7a1048b7 Author: sireeveslbl Date: Fri Aug 24 13:45:35 2018 -0700 Use Vec functions from PETSc Src/Extern/PETSc/AMReX_PETSc.cpp commit 0802a66b2b0ee34d03e7aa401196cc08e03e7f3c Author: Cy Chan Date: Fri Aug 24 01:27:33 2018 -0700 fixed issue in ParallelReduce for non-integer MPI_Op implementations Src/Base/AMReX_ParallelReduce.H commit 608274b33196e20702a8757ef182efbd2e4028e7 Author: Weiqun Zhang Date: Thu Aug 23 17:53:10 2018 -0700 WIP: eb dirichlet Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 760b87f6ee413ff5d2425ba430c7d66a2618490e Author: Johannes Blaschke Date: Thu Aug 23 17:47:38 2018 -0700 fix problem with levelset bcs and avoid unncessary tiling Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Src/main.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp commit fd18fa29478f03a3e4b9dd5ee33d478cd4c85ec4 Author: sireeveslbl Date: Thu Aug 23 16:03:31 2018 -0700 Working on PETSc availability for the bottom solve. Currently am preallocating based on the stencil for our problem. Might be an over estimate, but could also be cheaper than looping through the solution to dictate what is in the diagonal blocks and what is not. Load vector and get solution vector is being modeled after the HYPRE ones, but will change to utilize the PETSc routines. Src/Extern/PETSc/AMReX_PETSc.cpp commit a0b9e650596c87fbb464ea0b03a131d328dd67a3 Author: Weiqun Zhang Date: Thu Aug 23 14:57:44 2018 -0700 pass eb area and beta coefficient into Fortran Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 34ea5522f8a9cb1582ef3af0d5d0be68478a0ade Merge: ad4f8df68 bbbd62fe3 Author: Weiqun Zhang Date: Thu Aug 23 13:37:26 2018 -0700 Merge branch 'development' into forkjoin commit 67914d65b3cbb48eeae66ecf4394913d1dff3601 Author: Weiqun Zhang Date: Thu Aug 23 10:23:13 2018 -0700 add a blend function for EB dirichlet Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit bbbd62fe30625e5da44b1ad02468fc294cec4e5d Author: Johannes Blaschke Date: Thu Aug 23 10:11:21 2018 -0700 bug fix: EB tutorial now works without DAMREX_USE_GEOMETRYSHOP Src/EB2/AMReX_EB2_IF_Polynomial.H Tutorials/EB/LevelSet/Src/main.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp Tutorials/EB/LevelSet/Src/make_poly.cpp Tutorials/EB/LevelSet/Src/make_shapes.H commit 95f30560c551f12d0020ac67821f18fae18acbdc Author: Kevin Gott Date: Thu Aug 23 13:03:38 2018 -0400 Pinned allocator adjustment. Src/Base/AMReX_CudaAllocators.H commit d3f68bae3bf28bae2312397f16d4aba6c668f244 Author: Kevin Gott Date: Thu Aug 23 13:01:55 2018 -0400 PinnedData object draft. Tutorials/GPU/Test/GNUmakefile Tutorials/GPU/Test/main.cpp Tutorials/GPU/Test/run.script commit f535cd4940c3d23fc08941639e0735617d0c3290 Author: Johannes Blaschke Date: Wed Aug 22 21:56:32 2018 -0700 update level set tutorial => user can specify eb or eb2 Src/EB/AMReX_EBTower.H Tutorials/EB/LevelSet/Exec/inputs_eb2 Tutorials/EB/LevelSet/Src/main.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp Tutorials/EB/LevelSet/Src/make_poly.cpp Tutorials/EB/LevelSet/Src/make_shapes.H commit 3b5efc731f33b19af16bb66f8efa33c0afa5cc8e Author: Johannes Blaschke Date: Wed Aug 22 17:49:35 2018 -0700 replace pow function in IF_Polynomial with integer-specific version Src/EB2/AMReX_EB2_GeometryShop.H Src/EB2/AMReX_EB2_IF_Plane.H Src/EB2/AMReX_EB2_IF_Polynomial.H Tutorials/EB/LevelSet/Exec/inputs Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp commit 77ed7663f2a8fc4431bc2b61b5c6fc2cc95677c7 Author: Weiqun Zhang Date: Wed Aug 22 11:21:31 2018 -0700 fix bug Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 1fe1f1bf8f62ee6c58af0680f3e5eeb1d10dd349 Merge: 07f054abd d193bea63 Author: Johannes Blaschke Date: Wed Aug 22 10:48:03 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 07f054abdcaa52995e5ba679e4d559da7aa632bf Author: Johannes Blaschke Date: Wed Aug 22 10:47:54 2018 -0700 upgrade LSFactory to work with EB2 Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2_IF_Plane.H Src/EB2/AMReX_EB2_IF_Polynomial.H Src/EB2/AMReX_EB2_IF_Translation.H Src/EB2/AMReX_EB2_IF_Union.H Src/EB2/AMReX_EB2_IndexSpaceI.H Src/EB2/CMakeLists.txt Src/EB2/Make.package Src/GeometryShop/AMReX_EBIndexSpace.cpp Tutorials/EB/LevelSet/Src/main.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp Tutorials/EB/LevelSet/Src/make_shapes.H commit d193bea63e806a9f653b5969f5eab236648569e2 Author: sireeveslbl Date: Wed Aug 22 10:40:31 2018 -0700 Last of the EB proofreading. Docs/sphinx_documentation/source/EB.rst commit b5ab6e0943881fbac83ce3ea8c5d9745fb892bef Author: Ann Almgren Date: Wed Aug 22 06:35:40 2018 -0700 GEOMETRY_SHOP-->GEOMETRYSHOP Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake commit 85138a3a4aac0237d28e5a9313fc08e286195787 Author: Ann Almgren Date: Wed Aug 22 06:31:32 2018 -0700 USE_GEOMETRY_SHOP --> USE_GEOMETRYSHOP Tools/GNUMake/Make.defs commit dd3a90424a7f805fa9d10de2c684de33e4ecfac5 Author: Max Katz Date: Tue Aug 21 23:50:43 2018 -0700 Fix some variable definitions for nvcc.mak Tools/GNUMake/comps/nvcc.mak commit 0e2798c5fe02c932598dbacd34dc0128c5fc3571 Author: Max Katz Date: Tue Aug 21 21:53:23 2018 -0700 Move the fortran preprocessing to the actual compile rule Tools/GNUMake/Make.rules commit 878b100c0fdab1221c1e770a58bce95785c3650f Author: Max Katz Date: Tue Aug 21 21:11:56 2018 -0700 We no longer need the Fortran passed to the CUDA script Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.rules commit 7cadcadda6d24129de9a7eb5c35d3dcae2bb8949 Author: Weiqun Zhang Date: Tue Aug 21 17:01:01 2018 -0700 eb avgdown boundaries Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 1e64ce7dc8d6f7125112f8f56673cb3165575911 Author: Weiqun Zhang Date: Tue Aug 21 16:27:14 2018 -0700 add boundary area to eb factory Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H commit 9ca4216b58cb970527886268761d76fec50cb6aa Author: sireeveslbl Date: Tue Aug 21 16:06:49 2018 -0700 Proof read edits to new EB documentation. Still working through it. Docs/sphinx_documentation/source/EB.rst commit 8f4b1dcbe6eb371b20c5ef15c5f6f45767b3d4a3 Author: Weiqun Zhang Date: Tue Aug 21 15:53:16 2018 -0700 add function to pass Dirichlet data for EB Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_nd.F90 Tests/LinearSolvers/CellEB/MyTest.H Tests/LinearSolvers/CellEB/MyTest.cpp commit 4846ceb6287140bcb0682d7756e1c716d1d31b65 Author: Max Katz Date: Tue Aug 21 15:18:59 2018 -0700 cuda header script should also depend on CEXE_sources Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.rules commit a4332294408dc73e8be6caf98141480899f18d55 Merge: 628d75676 f09217428 Author: Weiqun Zhang Date: Tue Aug 21 14:29:32 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 628d7567618643b530a62b5e906df7a8232e50fa Author: Weiqun Zhang Date: Tue Aug 21 14:26:34 2018 -0700 EB documentation Docs/sphinx_documentation/source/EB.rst commit f09217428bf5ffb67d19596a8d12fa08c6bc758d Merge: 7db8c4073 ae3865684 Author: kngott Date: Tue Aug 21 13:12:43 2018 -0700 Merge branch 'development' of https://github.com/AMReX-codes/amrex into development commit 7db8c407373c52e5e05e5a9bc46909bf0aab4433 Author: kngott Date: Tue Aug 21 13:12:15 2018 -0700 Profiler adjustment to allow compile. Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp commit ae3865684bb04f23e6fa692c641c8c29b5665ba2 Author: Ann Almgren Date: Tue Aug 21 12:55:15 2018 -0700 Need to add flags for using GeometryShop directory Tools/GNUMake/Make.defs commit 0bd72466a806009870c687c57293f1438c49c46e Author: sireeveslbl Date: Tue Aug 21 10:04:12 2018 -0700 Consistency in pronouns Docs/sphinx_documentation/source/EB.rst commit 219e3aed3b3305f7be46c2245951c6bff13d7d72 Merge: adc1a2313 9a2b6692e Author: Weiqun Zhang Date: Mon Aug 20 17:25:08 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit adc1a231387982e3bd7479a77397bd307775f4e3 Author: Weiqun Zhang Date: Mon Aug 20 17:25:02 2018 -0700 WIP: EB documentation Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/EB.rst Docs/sphinx_documentation/source/EB/EB_example.fig.bak Docs/sphinx_documentation/source/EB/eb_fluxes.fig.bak Docs/sphinx_documentation/source/EB/parabsphere.pdf Docs/sphinx_documentation/source/EB/parabsphere.png Docs/sphinx_documentation/source/EB/parabsphere.ps Docs/sphinx_documentation/source/EB/revolution.pdf Docs/sphinx_documentation/source/EB/revolution.png Docs/sphinx_documentation/source/EB/revolution.ps Src/EB2/AMReX_EB2_IF_Scale.H commit ad4f8df687d0a7efc855d2b6c64736f62b8df878 Merge: b43e7decf 9a2b6692e Author: Cy Chan Date: Mon Aug 20 15:32:54 2018 -0700 Merge branch 'development' into forkjoin commit b43e7decf9c03fb0a49f9b8f56c10f4b9506cf8e Author: Cy Chan Date: Mon Aug 20 15:24:46 2018 -0700 create directory for fork-join task output files Src/Base/AMReX_ForkJoin.cpp commit 9a2b6692e3094bcfa63e8f76535d5aba7f376303 Author: sireeveslbl Date: Mon Aug 20 14:49:44 2018 -0700 Further Documentation Editing, reviewed Linear Solvers, will do EB next Docs/sphinx_documentation/source/LinearSolvers.rst commit c2b4aba9f08a75a88b96c5c366a4fe6764eb620e Author: Andrew Myers Date: Mon Aug 20 11:31:39 2018 -0700 bugfix to the fill_slice interpolation routine Src/Base/AMReX_MultiFabUtil_nd.F90 commit f4a89f644d45ce6d00e7578404eb2b040c98ab8b Author: Max Katz Date: Mon Aug 20 03:19:20 2018 -0400 Clean up lineinfo/debug differences for CUDA Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak commit 5ad73a1009a0dfd16149d9f21ab2a5f14f9badac Author: Max Katz Date: Sun Aug 19 13:28:18 2018 -0400 Sync up write_probin.py with gpu branch Tools/F_scripts/write_probin.py commit 9a2ec79e4a8cdab222887ac15356b86852f29242 Author: Max Katz Date: Sun Aug 19 13:25:23 2018 -0400 Clean whitespace Tools/F_scripts/write_probin.py commit cae6e8617735ce9438de920a4c1e12d1517c1806 Author: Michael Zingale Date: Sun Aug 19 11:04:44 2018 -0400 fix typo in macro Src/Base/AMReX_ArrayLim.H commit 0c92e0d7bcfab4a645993644661d9b9daee39bb7 Author: Max Katz Date: Sat Aug 18 23:56:43 2018 -0700 Remove get_fortran_pointer Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_MFIter.H commit 891b36b3e2d522af3cef1d751d7120c8efa5d358 Author: Max Katz Date: Sat Aug 18 23:55:38 2018 -0700 Remove registerRealBox Src/Base/AMReX_MFIter.H commit ccc2c8e6d588051e778c19f871e60cefb6d2151d Author: Max Katz Date: Sat Aug 18 23:25:14 2018 -0700 Add rzansel @ LLNL Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.llnl commit e33904777c6f4e2eb513ef62f77f21266a3e270a Author: Max Katz Date: Sun Aug 19 01:15:49 2018 -0400 Re-enable optimizations for PGI with CUDA Tools/GNUMake/comps/pgi.mak commit 350b2bca656c7670ac92bbee2469ef123a028669 Author: Max Katz Date: Sat Aug 18 21:06:56 2018 -0700 Switch to arch specification, default cc35 Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_pgi.mak Tools/GNUMake/Make.defs Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak Tools/GNUMake/sites/Make.llnl Tools/GNUMake/sites/Make.olcf commit 24fbf9e8d284370fbaa321d2c71bd07f44ab4a55 Author: Max Katz Date: Sat Aug 18 21:01:03 2018 -0700 Add debug flags for nvcc Tools/GNUMake/comps/nvcc.mak commit e138ef2d02377043c43302fff9fd19661232fca5 Author: Max Katz Date: Sat Aug 18 22:04:12 2018 -0400 Take the physical boundary fill off the GPU for now Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_filcc_f.H Src/Base/AMReX_filcc_mod.F90 commit 0a5edd60d12a9a2a8d512c5156c90a2d83261c21 Author: Max Katz Date: Sat Aug 18 22:03:35 2018 -0400 Take the derives off the GPU for now Src/Amr/AMReX_AmrLevel.cpp commit 683a7843db4fefb9cb41f99c42c6b634f760c4bd Author: Max Katz Date: Sat Aug 18 21:45:13 2018 -0400 Create a preprocessed version of the C++ files for diagnostic uses Tools/F_scripts/write_cuda_headers.py commit 24854df385c372b918a4b85495458c1504457c66 Author: Max Katz Date: Sat Aug 18 21:23:02 2018 -0400 ZFILL -> AMREX_ZFILL Src/Base/AMReX_ArrayLim.H commit a9fb4ef56515d05d54084e3118a958fe07e78867 Merge: b0d89f7da 554094a4b Author: Max Katz Date: Sat Aug 18 20:13:04 2018 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 554094a4b44a56bcb96f8ff0f0adbc388a9121d7 Author: Max Katz Date: Sat Aug 18 19:56:24 2018 -0400 Fix nvcc version check Tools/GNUMake/comps/nvcc.mak commit b0d89f7da8a1075ce644b6cddf2f742a8e0a0eba Author: Max Katz Date: Sat Aug 18 19:44:17 2018 -0400 Replace mfi.get_fortran_pointer with macro Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_ArrayLim.H commit 2eec9a2d74907e16d88289abcc4c54f4b2adb39c Merge: 4c3be4bdd 11b516bd0 Author: Weiqun Zhang Date: Sat Aug 18 13:59:17 2018 -0700 Merge branch 'development' into petsc commit 11b516bd03944643f6cd5f67a583839656cc0efb Author: Weiqun Zhang Date: Sat Aug 18 13:58:28 2018 -0700 no need to include GeometryShop in Tutorials Docs/README.md Tests/LinearSolvers/CellEB/GNUmakefile Tests/LinearSolvers/CellEB/inputs Tests/LinearSolvers/EBConvergenceTest/GNUmakefile Tests/LinearSolvers/EBConvergenceTest/inputs Tests/LinearSolvers/EBflux_grad/GNUmakefile Tests/LinearSolvers/EBflux_grad/inputs Tutorials/EB/CNS/Exec/Combustor/inputs Tutorials/EB/CNS/Exec/Combustor/inputs.regt Tutorials/EB/CNS/Exec/Make.CNS Tutorials/EB/CNS/Exec/Pulse/inputs Tutorials/EB/CNS/Exec/Pulse/inputs.regt Tutorials/EB/CNS/Exec/ShockRef/inputs Tutorials/EB/CNS/Exec/ShockRef/inputs.amr Tutorials/EB/CNS/Exec/ShockRef/inputs.regt Tutorials/EB/CNS/Exec/Sod/inputs Tutorials/EB/CNS/Source/main.cpp Tutorials/EB/MacProj/GNUmakefile commit 51e8982993a6cd8f3c434f10a824c425522befc4 Author: Weiqun Zhang Date: Sat Aug 18 13:42:20 2018 -0700 put some notes into subdirectory Docs/Notes/Notes.io_implementation Docs/Notes/Readme.backtrace Docs/Notes/Readme.io Docs/Notes/Readme.profiling Docs/Notes/Readme.typecheck Docs/README.md Docs/Readme.sphinx commit 33dd9839bfa2eda1a869987ae7f06af4c37a580f Author: Weiqun Zhang Date: Sat Aug 18 13:33:28 2018 -0700 reset hypre solver in case the solver is reused Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 6456880d6c8d939ea2ae6075501e1d1b55d08325 Merge: 722bd10e1 ce6b671ff Author: Weiqun Zhang Date: Sat Aug 18 13:18:00 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 722bd10e164093f553d349913cbc84feb6e9bf47 Author: Weiqun Zhang Date: Sat Aug 18 13:16:25 2018 -0700 ZFILL -> AMREX_ZFILL Src/Base/AMReX_ArrayLim.H commit 921700285f364f5511b354a5794e7376277c9aa0 Author: Weiqun Zhang Date: Sat Aug 18 13:14:09 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development Src/Base/AMReX_ArrayLim.H commit 0683a5f84dddfd6638b55d7227fdee2d5c62677f Author: Weiqun Zhang Date: Sat Aug 18 13:08:43 2018 -0700 cleanup Src/EB/AMReX_ebinterp_2d.F90 Src/EB2/AMReX_eb2_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 723653b904381c272389ae87f6b5fd0e6058f99b Author: Weiqun Zhang Date: Sat Aug 18 13:06:58 2018 -0700 fix return Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H commit a76d7b5c966d630595df045847698c6a493d8499 Author: Max Katz Date: Sat Aug 18 15:58:40 2018 -0400 Create fewer streams to shorten initialization time Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H commit abc67e6c4ef33ae398b0ecd9c41119a6dc5c0c20 Author: Weiqun Zhang Date: Sat Aug 18 12:48:02 2018 -0700 save parent in factory Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_Level.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit d21b1777107e0ef30373d6008a6b30c761c994f5 Author: Weiqun Zhang Date: Sat Aug 18 08:47:33 2018 -0700 use AMREX_USE_GEOMETRYSHOP. add parent information to EB2::Level and Factory Src/Amr/AMReX_StateData.H Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IndexSpaceI.H Src/EB2/AMReX_EB2_Level.H commit 7839385de6af4be1e862f6af6c7d99af48e88896 Author: Max Katz Date: Sat Aug 18 06:18:48 2018 -0400 GPU script learns about AMREX_REAL_ANYD Tools/F_scripts/write_cuda_headers.py commit af6235eacf4be6168122809d0051d8f4d9a25910 Author: Max Katz Date: Sat Aug 18 06:18:30 2018 -0400 Add AMREX_REAL_ANYD Src/Base/AMReX_ArrayLim.H commit 251b88feea7f068e88f68b169a2c43601fc01051 Merge: 6cf7f43fa ce6b671ff Author: Max Katz Date: Sat Aug 18 05:39:07 2018 -0400 Merge branch 'development' into gpu commit ce6b671ff2ae968ba81c3274e8c64247d0202ee4 Author: Max Katz Date: Sat Aug 18 05:23:01 2018 -0400 Add macros for compatibility with GPU branch Src/Base/AMReX_ArrayLim.H commit 6cf7f43fa311df39f0f7b9f361162a07aa55c53a Author: Max Katz Date: Sat Aug 18 05:08:11 2018 -0400 Remove MFIter::registerBox Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 73af76577c8efcc5be3d93d6d26bcb6f267c7188 Author: Max Katz Date: Sat Aug 18 05:01:19 2018 -0400 Sync up Box class with development Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit 5bc3eb51735919810ae5f58bd0e52a1af2511b98 Author: Max Katz Date: Sat Aug 18 05:01:07 2018 -0400 Add some missing includes Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.H commit 6a92f6c976439618e393ed83013741b50157f95e Author: Max Katz Date: Sat Aug 18 04:49:38 2018 -0400 Pass intvect by value for several common macros Src/Base/AMReX_ArrayLim.H Tools/F_scripts/write_cuda_headers.py commit 58d931885d11deafd66d790e29eeb7e18e8e3d3a Author: Max Katz Date: Sat Aug 18 03:29:15 2018 -0400 AMREX_ARLIM_ARG -> AMREX_INT_ANYD Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_BaseFab.cpp Tutorials/GPU/HeatEquation_EX1_C/advance.cpp commit ce5f373d8f827fa0a7a2ffe1b3fd0154fa9c844b Author: Max Katz Date: Sat Aug 18 03:24:23 2018 -0400 Make GPU script aware of BL_TO_FORTRAN Tools/F_scripts/write_cuda_headers.py commit f9f51cb0c3d00adc892a490419ac38eb7a8db8f9 Author: Weiqun Zhang Date: Fri Aug 17 18:44:41 2018 -0700 MLMG reuse for EB too Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit ecf336175baba90a43b2ec4224b585cccdcc62fd Author: Weiqun Zhang Date: Fri Aug 17 18:38:09 2018 -0700 allow MLMG being reused Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 7f518734f15ddaddb86a86baedf38c59a06fad90 Author: Andrew Myers Date: Fri Aug 17 17:09:46 2018 -0400 change the default value of USE_CUDA in the OMP HeatEquation example. Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/GNUmakefile commit 85f50783ebde9ae99803aab76e1e33ece27cf13a Author: Andrew Myers Date: Fri Aug 17 17:09:16 2018 -0400 no longer need to do special memory allocation for OMP_OFFLOAD Src/Base/AMReX_BArena.cpp commit d0661bba80b5a94ca17d8873aa49b4b9d2eb6a8e Author: Weiqun Zhang Date: Fri Aug 17 13:54:40 2018 -0700 make EB2 the default Src/EB2/AMReX_EB2.cpp commit a40a90525631d5c663444dfce089fed3dd3f6d62 Merge: ae3e64c28 f7b22e11f Author: Weiqun Zhang Date: Fri Aug 17 13:48:08 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c2c8a366b960297dcef08da4ac3ed3916a47fae1 Merge: a8a67d7ee 5c91340a7 Author: Andrew Myers Date: Fri Aug 17 16:44:27 2018 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit a8a67d7ee28d333e7108911451d3c764a506d614 Author: Andrew Myers Date: Fri Aug 17 16:44:05 2018 -0400 add in missing cudaDeviceSynchronize to FillBoundary (bug only affected NProcs = 1) Src/Base/AMReX_FabArrayCommI.H commit ae3e64c2895512cc8b3524dc223df7c843ec734b Author: Weiqun Zhang Date: Fri Aug 17 13:41:49 2018 -0700 use the new GetVecOfArrOfPtrs Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp Tutorials/EB/MacProj/main.cpp commit bd6aeacc62fd8526142dbccba1193bd984a8f64d Author: Weiqun Zhang Date: Fri Aug 17 13:37:57 2018 -0700 fix the new GetVecOfArrOfPtrs with enable_if Src/Base/AMReX_Vector.H commit 6eb922fd1d536f7f2d30f715922d5e0afbbd76e2 Author: Weiqun Zhang Date: Fri Aug 17 13:36:32 2018 -0700 add IsFabArray type traits Src/Base/AMReX_TypeTraits.H commit 9cb5874c3453506474d04d868f3e496e6e4fd458 Author: Cy Chan Date: Fri Aug 17 13:06:48 2018 -0700 fix bug in ParallelReduce.H for USE_MPI=FALSE Src/Base/AMReX_ParallelReduce.H commit f7b22e11feedbeeba494f7bfdc22ee144a7fbf6e Author: Ann Almgren Date: Fri Aug 17 11:05:24 2018 -0700 Update CMake stuff to take AMREX_ENABLE_GEOMETRY_SHOP option through CMake and convert it to AMREX_USE_GEOMETRY_SHOP flag Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake commit 96cf74fb421384c43183a2159f55c36ac1e36c6c Author: Weiqun Zhang Date: Fri Aug 17 10:55:35 2018 -0700 fix bug in my last commit Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit 052f43b00337e999da38431cf7a4a67ef6dea323 Author: Weiqun Zhang Date: Fri Aug 17 10:47:23 2018 -0700 MacProjector: support regular geometry too Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit 3c21310cd784ed8771c5679b202a6ad399019e81 Author: Weiqun Zhang Date: Fri Aug 17 10:41:03 2018 -0700 comment out VisMF::Write Tutorials/EB/MacProj/main.cpp commit 000eaa5978772d17045f1c78a1aefb7a32c0cc5c Merge: 64fe6c261 6ff658002 Author: WeiqunZhang Date: Fri Aug 17 10:33:59 2018 -0700 Merge pull request #301 from jared321/flash_fluxcorrection Flux correction changes needed for FLASH commit b9f4872e39bd79f003ee744e53f79ec6319929c0 Author: Kevin Gott Date: Fri Aug 17 13:03:27 2018 -0400 Test program. Tutorials/GPU/Test/GNUmakefile Tutorials/GPU/Test/Make.package Tutorials/GPU/Test/main.cpp Tutorials/GPU/Test/run.exitcode Tutorials/GPU/Test/run.script commit 5c91340a774fb7c46da55e5fe645c8bfc4518eed Author: Max Katz Date: Fri Aug 17 03:36:18 2018 -0400 GPU script now passes AMREX_INT_ANYD wrapped IntVects by value Still needs work; there is an incompatibility between the argument positions in the C++ and the preprocessed headers. Src/Base/AMReX_ArrayLim.H Tools/F_scripts/write_cuda_headers.py commit 404e6e08ffa61e5d0eb3ceb6e23cf1b5327836d5 Author: Max Katz Date: Fri Aug 17 02:33:59 2018 -0400 Add capability for script to detect argument location of macros Tools/F_scripts/write_cuda_headers.py commit 64fe6c261266289e07723765da3825b57ad06ed2 Author: Weiqun Zhang Date: Thu Aug 16 21:44:12 2018 -0700 switch to IAMR sign convention Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp Tutorials/EB/MacProj/main.cpp commit e0a41c3094099f612a5785ed53dec1d9dec9fd58 Author: Weiqun Zhang Date: Thu Aug 16 21:35:10 2018 -0700 add EB2::useEB2 function to update the use_eb2 flag Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp commit 28ec121a66b66ff73c45aef189c24baae3608525 Author: Weiqun Zhang Date: Thu Aug 16 18:32:12 2018 -0700 finish MacProjector and tutorial Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_F.H Src/EB/AMReX_EBMultiFabUtil_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MacProjector.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp Tutorials/EB/MacProj/main.cpp commit 3656567fe7d8b25ea4c4c0174ef4e6cd458bcfae Author: Weiqun Zhang Date: Thu Aug 16 17:24:12 2018 -0700 remove some debug lines Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit 694351c218fe547eb79e4fd0425d3d25a25848f7 Author: Weiqun Zhang Date: Thu Aug 16 17:23:35 2018 -0700 have to remove the new GetVecOfArrOfPtrs because it breaks the old one Src/Base/AMReX_Vector.H commit 7623ee837f7e829f445b02cd37182b13314cf2c5 Author: Weiqun Zhang Date: Thu Aug 16 17:15:06 2018 -0700 add new files Src/LinearSolvers/MLMG/AMReX_MacProjector.H Src/LinearSolvers/MLMG/AMReX_MacProjector.cpp commit ced3486ca6231e5726a35231fa34d51200583ddd Author: Kevin Gott Date: Thu Aug 16 20:10:09 2018 -0400 Change HeatEquation_EX1 to GPU global functions version. Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit 1004c7eaae54c7c5f6e674cf203e0078faff460a Author: Kevin Gott Date: Thu Aug 16 20:05:17 2018 -0400 Remove un-needed in linear solver heat equation tutorial... for now. Tutorials/GPU/HeatEquation_EX2_C/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX2_C/Exec/inputs_2d Tutorials/GPU/HeatEquation_EX2_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX2_C/Source/Make.package Tutorials/GPU/HeatEquation_EX2_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX2_C/Source/advance_2d.f90 Tutorials/GPU/HeatEquation_EX2_C/Source/advance_3d.f90 Tutorials/GPU/HeatEquation_EX2_C/Source/init_phi_2d.f90 Tutorials/GPU/HeatEquation_EX2_C/Source/init_phi_3d.f90 Tutorials/GPU/HeatEquation_EX2_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX2_C/Source/myfunc.H Tutorials/GPU/HeatEquation_EX2_C/Source/myfunc_F.H commit 471818267e056ad5e936f62c8339322844db236d Author: Kevin Gott Date: Thu Aug 16 19:59:23 2018 -0400 Adjustment to GPU Box distribution strategy. Src/Base/AMReX_Box.H Src/Base/AMReX_CUDA_Utility.cpp Src/Base/AMReX_IndexType.H commit decd6550378970e25930d720c9e0605c264f644e Merge: 03aa29f81 6ebe2e8c1 Author: Weiqun Zhang Date: Thu Aug 16 16:55:31 2018 -0700 Merge branch 'development' into mlmg commit 6ebe2e8c1ca06502c43869c7afcf10aaab6177e0 Merge: 93a747106 f6d000bbd Author: Weiqun Zhang Date: Thu Aug 16 16:54:51 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 93a7471065fda9447bf9edac6ead0ef8ad2b3426 Author: Weiqun Zhang Date: Thu Aug 16 16:54:39 2018 -0700 MacProjector: compute rhs and then solve Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_F.H Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Tutorials/EB/MacProj/inputs commit f6d000bbda48c12f3e203970f4c3f14fb8a8c66f Author: sireeveslbl Date: Thu Aug 16 16:00:11 2018 -0700 Fixed some document typos + some rewording for clarity. Docs/sphinx_documentation/source/Basics.rst commit 3790604432c1a86a4eea6c81b4683e5c8ba8b63a Author: Tan Nguyen Date: Thu Aug 16 14:59:33 2018 -0700 fix a small bug Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp commit a02933a1e890a77d8a6f8cdfe15a2713819d3f74 Author: Weiqun Zhang Date: Thu Aug 16 14:58:47 2018 -0700 start MacProjector Src/EB2/AMReX_EB2.cpp Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/Make.package Tutorials/EB/MacProj/GNUmakefile Tutorials/EB/MacProj/Make.package Tutorials/EB/MacProj/initEB.H Tutorials/EB/MacProj/initEB.cpp Tutorials/EB/MacProj/inputs Tutorials/EB/MacProj/main.cpp commit 74628ab0ea38459e676cc1a77439c1c9a9c0d7e0 Merge: ff2cf30c2 baf5edfa8 Author: kngott Date: Thu Aug 16 14:01:42 2018 -0700 Merge branch 'development' of https://github.com/AMReX-codes/amrex into development commit 03aa29f814cdccbe5dee858f690ac7d5795ef5ec Author: sireeveslbl Date: Thu Aug 16 13:39:25 2018 -0700 GetVecOfArrOfPtrs implemented for regular class T Src/Base/AMReX_Vector.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Tests/LinearSolvers/EBflux_grad/MyTest.H Tests/LinearSolvers/EBflux_grad/MyTest.cpp commit baf5edfa89dce5261490a3df658608ab827bcce5 Author: Tan Nguyen Date: Thu Aug 16 13:29:27 2018 -0700 fix a mem leak bug in the runtime backend Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp commit ff2cf30c2c850875dddcf1d0c0c7dbdbbc28ed45 Author: kngott Date: Thu Aug 16 13:17:01 2018 -0700 int to long in Profiler to accomodate very large profiling jobs. More similar fixes to likely come later. Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp commit 6ff658002cfb76e8bbc16dd0f9f635f15b6357b4 Author: Jared O'Neal Date: Thu Aug 16 14:42:35 2018 -0500 Fixed bug in OverwriteFlux routine. The code was coarsening the grid in the FluxRegister constructor and in the OverwriteFlux function. It now just coarsens at construction. For FLASH, we only need to do flux correction at fine/coarse boundaries. Therefore, altered code to ignore physical boundaries. Src/AmrCore/AMReX_FLUXREG_nd.F90 Src/AmrCore/AMReX_FluxRegister.cpp commit 8c2ab4035d1ef0be2af7a737a8f79e10fa16bf6e Author: Weiqun Zhang Date: Thu Aug 16 12:28:27 2018 -0700 documentation Docs/sphinx_documentation/source/EB.rst Docs/sphinx_documentation/source/EB/eb_fluxes.eps Docs/sphinx_documentation/source/EB/eb_fluxes.fig Docs/sphinx_documentation/source/EB/eb_fluxes.fig.bak Docs/sphinx_documentation/source/EB/eb_fluxes.pdf Docs/sphinx_documentation/source/EB/eb_fluxes.png Docs/sphinx_documentation/source/LinearSolvers.rst commit d491d7d45c2edb82ff48beb31462a769c7ea7d16 Author: sireeveslbl Date: Thu Aug 16 10:12:19 2018 -0700 Killed the 3D bug. EB Grad and Flux work for 2D and 3D Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Tests/LinearSolvers/EBflux_grad/MyTest.cpp commit b0e110fe9a927e4d6abfed7cc811decd2ff6c65a Merge: d09fb0c6b 5f10806a1 Author: Weiqun Zhang Date: Wed Aug 15 18:19:26 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d09fb0c6b3c73c5aafee926cfa3bfded8761f555 Author: Weiqun Zhang Date: Wed Aug 15 18:19:05 2018 -0700 linear solver documentation Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/Chapter7.rst Docs/sphinx_documentation/source/LinearSolvers.rst Src/LinearSolvers/MLMG/AMReX_MLLinOp.H commit 5f10806a1c9e606f76bc5e8847bb3f3d9714376e Author: Johannes Blaschke Date: Wed Aug 15 17:26:40 2018 -0700 If you try to build and EBTower 'over' another, the second one is ingored. This is a misleading design pattern => throw error if trying to build EBTower twice (without clearing the old one first) Src/EB/AMReX_EBTower.cpp commit 83683a4e23e030eb4312d3cc55c6dcda8b0bafb8 Author: sireeveslbl Date: Wed Aug 15 16:20:34 2018 -0700 Flux and Grad 2D are working, flux 3D is working. Debugging Grad 3D Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Tests/LinearSolvers/EBflux_grad/GNUmakefile Tests/LinearSolvers/EBflux_grad/Make.package Tests/LinearSolvers/EBflux_grad/MyEB.H Tests/LinearSolvers/EBflux_grad/MyTest.H Tests/LinearSolvers/EBflux_grad/MyTest.cpp Tests/LinearSolvers/EBflux_grad/initEB.cpp Tests/LinearSolvers/EBflux_grad/inputs Tests/LinearSolvers/EBflux_grad/main.cpp commit a6b193b5c9579b478961533b371c9046e4c50067 Author: Weiqun Zhang Date: Wed Aug 15 14:55:16 2018 -0700 std::array --> Array Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMGBndry.H Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp commit 593538e2c9788db7ae439d8dba970edc49220384 Author: sireeveslbl Date: Wed Aug 15 11:32:25 2018 -0700 amrex_mlebabeclap_flux/grad compile for both 2D and 3D Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit d477f16cee15fd4ece0a9b578ffea66af3da836f Author: Ann Almgren Date: Wed Aug 15 10:04:21 2018 -0700 Don't use ls_ba as a local variable when it's defined in the .H file Src/EB/AMReX_EB_levelset.cpp commit 54ada627642587bbaedb2cceb741582628c38a42 Author: Weiqun Zhang Date: Tue Aug 14 18:13:05 2018 -0700 remove using namespace amrex from headers Tutorials/Basic/HeatEquation_EX1_C/Source/advance.cpp Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc.H Tutorials/Basic/HeatEquation_EX2_C/Source/advance.cpp Tutorials/Basic/HeatEquation_EX2_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX2_C/Source/myfunc.H Tutorials/Basic/HeatEquation_EX3_C/Source/advance.cpp Tutorials/Basic/HeatEquation_EX3_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX3_C/Source/myfunc.H commit d733339089b971c697e4c5dce18dad28b4ca4963 Author: Weiqun Zhang Date: Tue Aug 14 18:04:40 2018 -0700 update documentation Docs/sphinx_documentation/source/AmrCore.rst Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/Visualization.rst Src/Base/AMReX.cpp commit 79c9e2f13755a6a0e38b311b70e9a0b3d4b041ce Author: sireeveslbl Date: Tue Aug 14 17:39:21 2018 -0700 Get Gradient of solution implemented for 2D Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 9e9786090613c51d1f06407f3799e4b7471cac89 Author: Ann Almgren Date: Tue Aug 14 16:04:05 2018 -0700 Remove unused variables Src/EB/AMReX_EBFluxRegister_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 commit 3d362b059d5b6439ca8e4bb0b1bc951aa68c346e Merge: cd10a23f5 4265d480a Author: Ann Almgren Date: Tue Aug 14 16:02:56 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit cd10a23f5fb11b58e2f4787c1365ed8dcbaba388 Author: Ann Almgren Date: Tue Aug 14 16:02:32 2018 -0700 Remove unused variable Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 4265d480a1dfc943329152c3a95c9507ae036ee1 Author: Weiqun Zhang Date: Tue Aug 14 16:00:59 2018 -0700 update documentation Docs/Readme.typecheck Docs/sphinx_documentation/source/Basics.rst commit 5d133848773b7db2deca9971062ed1e70e7c916a Author: Kevin Gott Date: Tue Aug 14 17:21:15 2018 -0400 Setup for larger comparison testing. Src/Base/AMReX_Box.H Src/Base/AMReX_CUDA_Utility.cpp Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/inputs Tutorials/GPU/ElectromagneticPIC/summitdev.sh Tutorials/Particles/ElectromagneticPIC/Evolve.cpp commit 4a78bc70523698eb96b7e08b8dd8442b1359b1a2 Author: Weiqun Zhang Date: Tue Aug 14 13:49:20 2018 -0700 set dt_level after building bldFineLevels Src/Amr/AMReX_Amr.cpp commit 6b0a54e6abaeeaa00db2004ada21ab14ff08f1da Author: Kevin Gott Date: Tue Aug 14 16:13:31 2018 -0400 Global function version of ElectromagneticPIC. Tutorials/GPU/ElectromagneticPIC_1/Constants.H Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.H Tutorials/GPU/ElectromagneticPIC_1/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC_1/Evolve.H Tutorials/GPU/ElectromagneticPIC_1/Evolve.cpp Tutorials/GPU/ElectromagneticPIC_1/GNUmakefile Tutorials/GPU/ElectromagneticPIC_1/IO.H Tutorials/GPU/ElectromagneticPIC_1/IO.cpp Tutorials/GPU/ElectromagneticPIC_1/Make.package Tutorials/GPU/ElectromagneticPIC_1/NodalFlags.H Tutorials/GPU/ElectromagneticPIC_1/NodalFlags.cpp Tutorials/GPU/ElectromagneticPIC_1/Particles.H Tutorials/GPU/ElectromagneticPIC_1/StructOfArrays.H Tutorials/GPU/ElectromagneticPIC_1/em_pic_3d.F90 Tutorials/GPU/ElectromagneticPIC_1/em_pic_F.H Tutorials/GPU/ElectromagneticPIC_1/inputs Tutorials/GPU/ElectromagneticPIC_1/main.cpp Tutorials/GPU/ElectromagneticPIC_1/summit.sh Tutorials/GPU/ElectromagneticPIC_1/summitdev.sh Tutorials/GPU/ElectromagneticPIC_1/test.cpp commit 3ffe41790fab95c869a2af2a6877a3e8ebb2f81a Author: Kevin Gott Date: Tue Aug 14 16:11:06 2018 -0400 Fix size check. Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp commit 3b1c7e948a8aa9574a4392bbdde6a50ae3b9f0bc Author: Kevin Gott Date: Tue Aug 14 16:10:42 2018 -0400 Adjusting GPU box setup. Src/Base/AMReX_CUDA_Utility.cpp commit 1dedd3cbcc70536ec6242f0c014275826ea56c75 Merge: 2d23cd4ad 0b0316db2 Author: Tan Nguyen Date: Tue Aug 14 12:45:35 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2d23cd4ad4199777539cc15fe7cc21b0052b9fc8 Author: Tan Nguyen Date: Tue Aug 14 12:45:27 2018 -0700 first demo of the upcxx backend Src/Amr/AMReX_Amr.cpp commit 069a10cc1743fe75c8d59611e2a1cf0df8511f67 Author: Tan Nguyen Date: Tue Aug 14 12:35:13 2018 -0700 a demo version of the upcxx backend Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp Src/Base/AMReX.cpp commit 0b0316db228190c70b2bbe0bf042175d871e3f17 Author: Weiqun Zhang Date: Tue Aug 14 12:26:14 2018 -0700 update documentation Docs/sphinx_documentation/source/Basics.rst Docs/sphinx_documentation/source/BuildingAMReX.rst Docs/sphinx_documentation/source/Chapter3.rst commit e102fdb3d7e5c1f34c6d915ac19f9e79e030abbb Author: Max Katz Date: Tue Aug 14 01:54:05 2018 -0400 Catch a corner case in device function naming Tools/F_scripts/gpu_fortran.py commit b8603d7c98e60dea88b101b6490dfb781f605a6a Author: Weiqun Zhang Date: Mon Aug 13 18:19:55 2018 -0700 move heat equation example to the end of the chapter on base so that the readers have seen names like MultiFab, BoxArray, etc. at that time Docs/sphinx_documentation/source/Basics.rst Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp commit 79571416140d546bf21cc408e80972e5c703dab9 Author: Kevin Gott Date: Mon Aug 13 20:43:15 2018 -0400 Improved GPU thread distribution method. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CUDA_Utility.cpp Tutorials/GPU/ElectromagneticPIC/Evolve.cpp commit e3e150c16c1a91ac78c70e8843c4f5366cbea653 Author: Weiqun Zhang Date: Mon Aug 13 17:41:07 2018 -0700 update documentation Docs/sphinx_documentation/source/BuildingAMReX.rst commit f04dfe47a5350336476849de3f71024a431cc61c Author: Weiqun Zhang Date: Mon Aug 13 17:40:44 2018 -0700 add hypre to libamrex GNUmakefile.in Tools/libamrex/configure.py commit 967b6fd2145db4b55c2e3374080e658b550f20cc Author: Weiqun Zhang Date: Mon Aug 13 17:22:21 2018 -0700 add EB to libamrex.a as optional feature GNUmakefile.in Src/Amr/AMReX_StateData.H Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Tools/libamrex/configure.py Tutorials/EB/CNS/Exec/Make.CNS Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp commit f33092bbbaded26bbd3f2dbad84668a26266b471 Author: Kevin Gott Date: Mon Aug 13 20:02:03 2018 -0400 Implement ParticlesData. Src/Base/AMReX_Box.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/Particles.H commit cc24985d12d619daae3fe9d224733a1fee024b6b Author: Weiqun Zhang Date: Mon Aug 13 16:46:26 2018 -0700 update documentation Docs/sphinx_documentation/source/BuildingAMReX.rst Docs/sphinx_documentation/source/Chapter3.rst Docs/sphinx_documentation/source/GettingStarted.rst Docs/sphinx_documentation/source/Introduction.rst commit 15f341cd1ab8d5fcc17a880e6ff4fa00932d94e8 Author: sireeveslbl Date: Mon Aug 13 16:10:44 2018 -0700 Flux routine for 2D and 3D compile. Will need to test them. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Tests/LinearSolvers/EBConvergenceTest/bcoef.F90 commit 9a066df3ee7c5a7804689fdf6350f85ab6cb80e0 Author: Weiqun Zhang Date: Mon Aug 13 15:27:14 2018 -0700 less verbose Src/Base/AMReX.cpp Src/Base/AMReX_FabArrayBase.cpp commit 8a633c8e66f2569f487a22a4629f64f8ae8d5230 Author: sireeveslbl Date: Mon Aug 13 14:54:34 2018 -0700 Did 2D comp flux for EB. Didn't break anything. Now for 3D. Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Tests/LinearSolvers/EBConvergenceTest/Results/ConvergencePlot2D.m commit ff31f3770b3984139ea6770bcf5ca909179f44ee Merge: 7a5a3037e 4d4a6f15e Author: Weiqun Zhang Date: Mon Aug 13 14:45:28 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7a5a3037e7ad79c644307493187da14073dfcfbc Author: Weiqun Zhang Date: Mon Aug 13 14:45:01 2018 -0700 fix a bug 3d gsrb for eb Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 4d4a6f15ed394d82c8f9bb8f986eb3e084c8a364 Merge: b259148f9 155115d5c Author: Daniel Ladiges Date: Mon Aug 13 13:28:52 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b259148f9423149dcbca1b334d2e8d7fce797b1d Author: Daniel Ladiges Date: Mon Aug 13 13:25:50 2018 -0700 Added seperate FParallelMG2.mak file for AMReX-FHDeX, to avoid conflict with existing LLNS code Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/FParallelMG2.mak commit 155115d5c617c02dc617304839af5238919bd60c Merge: 70ab883e8 67232ffff Author: Weiqun Zhang Date: Mon Aug 13 12:33:02 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 70ab883e81f3bf3a9d6f30defaa9eb8e1cf3a60d Author: Weiqun Zhang Date: Mon Aug 13 12:30:23 2018 -0700 weight by volume fraction in computing max-norm error Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 1eb48d8c659ab060e2c26775581511850a1e59ab Author: Weiqun Zhang Date: Mon Aug 13 10:47:59 2018 -0700 EB linear solver test: add periodic test Tests/LinearSolvers/CellEB/MyTest.H Tests/LinearSolvers/CellEB/MyTest.cpp commit 67232ffff098b05625551788322588864a8c307f Merge: 82138c3c4 d5b2a6f69 Author: asalmgren Date: Mon Aug 13 09:34:27 2018 -0700 Merge pull request #298 from AMReX-Codes/initial_dt_fix Do not initialize dt_level on levels that do not yet exist commit 98a532001e92da33e5d84f8a01aa416ada1d3298 Author: Brian Friesen Date: Sun Aug 12 02:39:47 2018 -0700 Add OpenMP GPU offload version of HeatEquation_EX1_C tutorial (#296) * Tools: add Piz Daint at CSCS to list of sites/machines * GNUmake: add OpenMP GPU offload flags for XL on Summit/summitdev * Tutorials: create HeatEquation_EX1_C using OpenMP 4.5 GPU offloading Src/Base/AMReX_BArena.cpp Tools/GNUMake/Make.defs Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.cscs Tools/GNUMake/sites/Make.olcf Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX1_C_OMP/Exec/run_summit_1node.sh Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/Make.package Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/advance_2d.f90 Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/advance_3d.f90 Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/init_phi_2d.f90 Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/init_phi_3d.f90 Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/myfunc.H Tutorials/GPU/HeatEquation_EX1_C_OMP/Source/myfunc_F.H commit d5b2a6f693b5438ce16906d163015cd238a5f98c Author: Max Katz Date: Sun Aug 12 05:23:07 2018 -0400 Do not initialize dt_level on levels that do not yet exist This initialization is problematic if the level 0 timestep when the simulation starts is significantly different from the timestep later on in the simulation when we add refinement. In particular, this will happen if the simulation code shrinks the initial timestep by some factor. If the fine levels are only added later on once the timestep has caught back up to its normal limited level, then the first timestep on the fine level will be effectively limited by the initial level 0 timestep, which can sharply decrease the timestep for no reason. Src/Amr/AMReX_Amr.cpp commit 2d69e5ae9f3149c9edc286d4cb9ce8612978a5fc Author: Weiqun Zhang Date: Fri Aug 10 18:28:31 2018 -0700 effectively remove the floor on target relative tolerance so that it's easy for testing how small the residual can be Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 82138c3c40583b696b356a72a2586306b5187aca Author: Marc Day Date: Fri Aug 10 17:13:18 2018 -0700 Rewrite this AmrData function in terms of mesh and data that might be provided by something like SENSEI, e.g. (although fake it using plotfile data) Tools/Postprocessing/C_Src/IntegrateComp.cpp commit 27729495d34424e1bce7be257ebf6f6aa710d6ed Author: Weiqun Zhang Date: Fri Aug 10 16:38:10 2018 -0700 typo in profiler name Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 50d2b75d5322d0f07eb9a4c0f3ad64553799bd0c Author: Marc Day Date: Fri Aug 10 16:00:25 2018 -0700 Add a simple AmrData-based integrate function. Tools/Postprocessing/C_Src/IntegrateComp.cpp commit 66f6c3325a7464d9bdf1af4be7d2085c9edaf462 Author: sireeveslbl Date: Fri Aug 10 14:17:06 2018 -0700 Forgot to add RHS Tests/LinearSolvers/EBConvergenceTest/RHS.F90 commit a93753c6b67c735806fcf9c2c5bb11810f709eaa Author: sireeveslbl Date: Fri Aug 10 14:04:56 2018 -0700 EB convergence testing complete. Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp Tests/LinearSolvers/EBConvergenceTest/RHS.F90 Tests/LinearSolvers/EBConvergenceTest/Results/ConvergencePlot2D.m Tests/LinearSolvers/EBConvergenceTest/bcoef.F90 commit 4c3be4bddbe53baa056530676898925676af0e9e Author: Weiqun Zhang Date: Thu Aug 9 16:53:43 2018 -0700 must re-assign m_factory because rhs must be a different multifab Src/Extern/PETSc/AMReX_PETSc.cpp commit bf9234962a054a1295beb92a6088152f757480da Author: Weiqun Zhang Date: Thu Aug 9 16:52:35 2018 -0700 hypre: must re-assign m_factory because rhs must be a different multifab Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit b463c90ee3166f340175db420af228bcf05fca9e Author: sireeveslbl Date: Thu Aug 9 16:05:38 2018 -0700 Solution is a little off at the physical boundary. Need to fix before moving on. Tests/LinearSolvers/EBConvergenceTest/Make.package Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp Tests/LinearSolvers/EBConvergenceTest/MyTest_F.H Tests/LinearSolvers/EBConvergenceTest/RHS.F90 Tests/LinearSolvers/EBConvergenceTest/acoef.F90 Tests/LinearSolvers/EBConvergenceTest/bcoef.F90 commit 6b4d4a586b284ae34098df52131473e773142f80 Author: Weiqun Zhang Date: Thu Aug 9 16:00:56 2018 -0700 EB solvability Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit be9247ad4e22f1a79f5b0f0fe16b30d46fe7ba30 Author: sireeveslbl Date: Thu Aug 9 08:32:06 2018 -0700 Corrected Convergence script, and Octave scprit. 3D constant coefficient shows 2nd Order convergence. Tests/LinearSolvers/EBConvergenceTest/Convergence_Data_Gen.sh Tests/LinearSolvers/EBConvergenceTest/Results/ConvergencePlot3D.m commit 06285cc3519f8d361042dbf6902e9e5da2ecb4f4 Author: sireeveslbl Date: Wed Aug 8 19:34:41 2018 -0700 Still ironing out some bugs. Looks like the analytic solution isn't being generated correctly for the error calculation in 3D test case. Tests/LinearSolvers/EBConvergenceTest/BC.F90 Tests/LinearSolvers/EBConvergenceTest/Convergence_Data_Gen.sh Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp Tests/LinearSolvers/EBConvergenceTest/RHS_2D.F90 Tests/LinearSolvers/EBConvergenceTest/Results/ConvergencePlot3D.m Tests/LinearSolvers/EBConvergenceTest/Results/mfread2.m Tests/LinearSolvers/EBConvergenceTest/Results/mfread3.m commit d9ec7cebda29312b244e22dbce6336922f70a7f4 Merge: f02665628 ee533db0f Author: Andrew Myers Date: Wed Aug 8 16:13:12 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f026656283afd4d9668e4044c1a1effe3a26f428 Author: Andrew Myers Date: Wed Aug 8 16:13:03 2018 -0700 update these function names Tests/Particles/AssignDensity/main.cpp Tests/Particles/AssignMultiLevelDensity/main.cpp commit ee533db0fd60ced11fb952ea984195f92b0e27b8 Author: Weiqun Zhang Date: Wed Aug 8 16:11:20 2018 -0700 update documentation Docs/sphinx_documentation/source/IO.rst commit c06609bb38399e840dffc9470c2fb0274b5a0c23 Author: Andrew Myers Date: Wed Aug 8 15:39:22 2018 -0700 reverse the order of the IOBuffer and fstream variables. Src/Base/AMReX_NFiles.H Src/Base/AMReX_PlotFileUtil.cpp Src/Extern/ProfParser/AMReX_BLWritePlotFile.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_TracerParticles.cpp Tools/C_util/dbgTools/crsGrids.cpp Tools/C_util/dbgTools/intersectGrids.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 49a525f7e9e294a863af5c99b3aec4e35e3848d8 Author: Kevin Gott Date: Wed Aug 8 17:48:41 2018 -0400 MultiFab to iMultiFab + Deviceifying BaseFab functions Src/Base/AMReX_BaseFab.H Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.H Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/inputs commit 52f41cdd3fcfbcadac712e941f695a55d02a5892 Author: Kevin Gott Date: Wed Aug 8 14:39:24 2018 -0400 Added simple overall timer and option to output error at each step. Tutorials/GPU/ElectromagneticPIC/main.cpp commit bc43affff8b58de0a60978b4e2f5ee09ed9204bb Author: Weiqun Zhang Date: Wed Aug 8 11:08:09 2018 -0700 call pubsetbuf before fstream is opened, otherwise it has no effect for some compilers Docs/Readme.sphinx Docs/sphinx_documentation/source/IO.rst Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_VisMF.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 7a8c068e96d948577005b9d3c11e44511b184f0f Author: Kevin Gott Date: Wed Aug 8 13:30:53 2018 -0400 Convert emPIC to use BaseFab Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp commit 8ec8581d6253bebea8397fa8e5ef367690a940a4 Author: sireeveslbl Date: Tue Aug 7 22:08:27 2018 -0700 3D MyTest now produces results that visually look like the analytical solution. Fixed MultiFabToMatlab 3D so now the binary files aren't garbage. Updated Bash script so user can specify spacedim of test. Todo - Matlab/Octave script for 3D scaling plot. Tests/LinearSolvers/EBConvergenceTest/BC_3D.F90 Tests/LinearSolvers/EBConvergenceTest/Convergence_Data_Gen.sh Tools/Postprocessing/C_Src/MultiFabToMatLab.cpp commit 10854617b7e5f8f7a0bbb0d2c716a9c8d8c66c10 Author: sireeveslbl Date: Tue Aug 7 16:12:38 2018 -0700 Working on 3D Problem. There are some kinks to work out still. Tests/LinearSolvers/EBConvergenceTest/BC_2D.F90 Tests/LinearSolvers/EBConvergenceTest/BC_3D.F90 Tests/LinearSolvers/EBConvergenceTest/Make.package Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp Tests/LinearSolvers/EBConvergenceTest/MyTest_F.H Tests/LinearSolvers/EBConvergenceTest/RHS.F90 commit 897b63be3e172d2c0c18392253e595b57b8bac6d Author: Kevin Gott Date: Tue Aug 7 18:21:41 2018 -0400 DeviceBox and DeviceDomain replaced with standard AMReX objects. Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/summit.sh Tutorials/GPU/ElectromagneticPIC/summitdev.sh commit 12f505d3c2de614cbe29680d832882214d69143d Merge: 777a7c424 235e00105 Author: Ann Almgren Date: Tue Aug 7 14:08:46 2018 -0700 Merge branch 'master' into development commit 235e001052a690d442f7e41e5d6758c3f8a785c2 Author: Ann Almgren Date: Tue Aug 7 13:41:41 2018 -0700 We have added a new flag -- system::regtest_reduction -- that controls whether or not we use the OpenMP reduction. In AMReX_MultiFab we have replaced "pragma omp parallel reduction(+:sm)" by "pragma omp parallel if (!system::regtest_reduction) reduction(+:sm)" so that if you set system.regtest_reduction = 1 in your inputs file (or command line), you will not see the OpenMP-related variability in MultiFab sum and norm1. You can also use this in your application code. Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_MultiFab.cpp commit d70e98974990038e8df13e96db3c7b3f7c384811 Author: sireeveslbl Date: Mon Aug 6 16:18:53 2018 -0700 Convergence test for 2D constant coefficient successfully illustrates second order convergence. Convergence_Data_Gen.sh is a script that generates the EB solution for 32X32 to 1024x1024 grids. In the Results folder, there is an octave script that generates a scaling plot and saves it as a .png for later viewing. Tests/LinearSolvers/EBConvergenceTest/BC.F90 Tests/LinearSolvers/EBConvergenceTest/Convergence_Data_Gen.sh Tests/LinearSolvers/EBConvergenceTest/RHS_2D.F90 Tests/LinearSolvers/EBConvergenceTest/Results/ConvergencePlot2D.m Tests/LinearSolvers/EBConvergenceTest/Results/mfread.m Tests/LinearSolvers/EBConvergenceTest/inputs commit 777a7c4241cb82437e06aabd7dfe0a32d44ef936 Author: Andrew Myers Date: Mon Aug 6 15:28:15 2018 -0700 fix typo in assert Src/Base/AMReX_Geometry.cpp commit 9947c338f3542f55d98f83042dd01163c61a0c68 Author: Kevin Gott Date: Mon Aug 6 14:39:16 2018 -0400 Corrected run script for summitdev, different version for summit. Tutorials/GPU/ElectromagneticPIC/summit.sh Tutorials/GPU/ElectromagneticPIC/summitdev.sh commit 340b5c888d4a213e7def53fda2d1e268254a74ca Author: Andrew Myers Date: Mon Aug 6 09:59:52 2018 -0700 if there is no information about the particle box array in the checkpoint file (true for old checkpoints), assume dual_grid = false. Src/Particle/AMReX_ParticleContainerI.H commit c723b1d08668bf8940a86338296e6651addb7aff Merge: 4bb9a2f7a 0828c263b Author: Andrew Myers Date: Mon Aug 6 10:00:01 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4bb9a2f7a656443f57248a4f620f1872d694b801 Author: Andrew Myers Date: Mon Aug 6 09:59:52 2018 -0700 if there is no information about the particle box array in the checkpoint file (true for old checkpoints), assume dual_grid = false. Src/Particle/AMReX_ParticleContainerI.H commit 5edad1fd3a72740d9bc03298710162f590f212fb Author: sireeveslbl Date: Mon Aug 6 09:10:03 2018 -0700 The BCs appear to be fixed. Tests/LinearSolvers/EBConvergenceTest/BC.F90 Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp commit 52bf2dff4d44a5d3204648a6ad44d6d296475ae8 Author: sireeveslbl Date: Sun Aug 5 20:23:45 2018 -0700 Seems to be correct, but odd error for small n_cell. Need to find the answer to this problem. Tests/LinearSolvers/EBConvergenceTest/BC.F90 Tests/LinearSolvers/EBConvergenceTest/Make.package Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp Tests/LinearSolvers/EBConvergenceTest/MyTest_F.H commit 0828c263b8169c59e4cd9b53a163f25639347e5a Merge: 84d785d49 c24144fa8 Author: Weiqun Zhang Date: Sat Aug 4 09:31:02 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 84d785d49c75d93084367e071960547838207b05 Author: Weiqun Zhang Date: Sat Aug 4 09:30:49 2018 -0700 make sure MLMG works when AMREX_USE_EB is defined but EB indexspace is not defined Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit c24144fa891e956efd97bf02afa2ed3f3aa11dda Merge: 82e31a6b5 f70afe3f8 Author: Tan Nguyen Date: Sat Aug 4 02:06:27 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 82e31a6b594f5fa5114640e64aed142944d0a537 Author: Tan Nguyen Date: Sat Aug 4 02:06:02 2018 -0700 upcxx backend Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/Perilla_upc++/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Perilla_upc++/Barrier.H Src/AmrTask/rts_impls/Perilla_upc++/Barrier.cpp Src/AmrTask/rts_impls/Perilla_upc++/LocalConnection.H Src/AmrTask/rts_impls/Perilla_upc++/Make.package Src/AmrTask/rts_impls/Perilla_upc++/Makefile Src/AmrTask/rts_impls/Perilla_upc++/PackageQueue.H Src/AmrTask/rts_impls/Perilla_upc++/PackageQueue.cpp Src/AmrTask/rts_impls/Perilla_upc++/Perilla.H Src/AmrTask/rts_impls/Perilla_upc++/Perilla.cpp Src/AmrTask/rts_impls/Perilla_upc++/PerillaConfig.H Src/AmrTask/rts_impls/Perilla_upc++/PerillaRts.H Src/AmrTask/rts_impls/Perilla_upc++/PerillaRts.cpp Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.H Src/AmrTask/rts_impls/Perilla_upc++/RegionGraph.cpp Src/AmrTask/rts_impls/Perilla_upc++/RegionQueue.H Src/AmrTask/rts_impls/Perilla_upc++/RegionQueue.cpp Src/AmrTask/rts_impls/Perilla_upc++/RemoteConnection.H Src/AmrTask/rts_impls/Perilla_upc++/WorkerThread.H Src/AmrTask/rts_impls/Perilla_upc++/WorkerThread.cpp Src/AmrTask/rts_impls/Perilla_upc++/mylock.h Src/AmrTask/rts_impls/Perilla_upc++/perilla.mak commit 02a2dd52bb61e3303fa7fa8f8d599e17e0d7765c Author: Andrew Myers Date: Fri Aug 3 14:30:41 2018 -0700 streamline particle restart when dual-grid is enabled. Src/Particle/AMReX_ParticleContainerI.H commit f70afe3f8fe02e4a81762a92580d4fc59f7ce57b Author: Andrew Myers Date: Fri Aug 3 17:26:17 2018 -0700 remove a debug print. Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp commit 5f786d77aaa08bb4b37d7d56a43a12fbc518c387 Author: Andrew Myers Date: Fri Aug 3 17:13:13 2018 -0700 add a bunch of debugging functions to the CellSortedPC Tutorials/Particles/CellSortedParticles/CellSortedPC.H Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp commit a0cfd9a4933ece49788669cbe12b0619f04c59fe Author: Andrew Myers Date: Fri Aug 3 14:45:52 2018 -0700 fix parameter shadowing Src/Particle/AMReX_ParticleContainerI.H commit 69f26df30f39eca0b1468b708c2e86919b0051fb Merge: 3f94b472b 25ffe806c Author: Andrew Myers Date: Fri Aug 3 14:33:55 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3f94b472b24ccb0598f4385a63a82f30285729a9 Author: Andrew Myers Date: Fri Aug 3 14:33:38 2018 -0700 some work on enabling caching of the cell vectors for the DSMC code Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Tutorials/Particles/CellSortedParticles/CellSortedPC.H Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp Tutorials/Particles/CellSortedParticles/cell_sorted_3d.F90 Tutorials/Particles/CellSortedParticles/main.cpp commit 25ffe806cda0c8392367bee150a5e8e4a6122a42 Author: Andrew Myers Date: Fri Aug 3 14:30:41 2018 -0700 streamline particle restart when dual-grid is enabled. Src/Particle/AMReX_ParticleContainerI.H commit 620330305c50c399dba5a92baf06fdfbe5943e99 Author: Kevin Gott Date: Fri Aug 3 09:49:16 2018 -0400 emPIC working on Summitdev w one rank. Src/Base/AMReX_CUDA_Utility.cpp Src/Base/AMReX_Device.cpp Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/Evolve.cpp Tutorials/GPU/ElectromagneticPIC/GNUmakefile Tutorials/GPU/ElectromagneticPIC/em_pic_3d.F90 Tutorials/GPU/ElectromagneticPIC/script.nompi.sh Tutorials/GPU/ElectromagneticPIC/script.sh commit 2e0750f6f918688782dea12032730be17e282b53 Author: sireeveslbl Date: Thu Aug 2 11:09:18 2018 -0700 added inputs Tests/LinearSolvers/EBConvergenceTest/inputs commit b73f2d4e4e7f2260fa39ea6b783ed90b4727595b Author: Weiqun Zhang Date: Wed Aug 1 18:16:15 2018 -0700 WIP: PETScABecLap Src/Extern/PETSc/AMReX_PETSc.cpp commit 289e81f7dde2cf4693c5a8f0815f19e583a45624 Author: Weiqun Zhang Date: Wed Aug 1 16:56:21 2018 -0700 WIP: PETScABecLap Src/Extern/HYPRE/Make.package Src/Extern/PETSc/AMReX_PETSc.H Src/Extern/PETSc/AMReX_PETSc.cpp Src/Extern/PETSc/Make.package commit 5b737f217eee471f2a3e3426efda17c09899e79d Author: Andrew Myers Date: Wed Aug 1 19:26:11 2018 -0400 some reorganization Src/Particle/AMReX_RedistributeStrategy.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Source/Particles.H commit 89ca43b5ab3c8bb8016477f19533ae0be7e63b7d Merge: ab26897d8 6d29b6d2c Author: Andrew Myers Date: Wed Aug 1 15:53:55 2018 -0700 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit ab26897d8cea5d1bdeec50cde1a35d30bd1c202e Author: Andrew Myers Date: Wed Aug 1 15:49:29 2018 -0700 fix compilation problem on Travis build Src/Particle/AMReX_RedistributeStrategy.H Src/Particle/AMReX_RedistributeStrategyCPU.cpp Src/Particle/AMReX_RedistributeStrategyGPU.cpp Src/Particle/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.cpp commit c1e88b4c2698c09591f3168953bbeebe5c04c811 Author: Marc Day Date: Wed Aug 1 14:18:43 2018 -0700 Make sure define is called when reading a coordsys Src/Base/AMReX_CoordSys.cpp commit 4af7c1fa61d0beee1985438be86b463b9133d66e Author: Ann Almgren Date: Wed Aug 1 14:29:35 2018 -0700 Add the MLMG path to the new files added to CMakeLists.txt which are only included if ENABLE_EB is on. Src/LinearSolvers/CMakeLists.txt commit b956ea85cbb1eee66b7e9614688ba74727d38575 Author: Marc Day Date: Wed Aug 1 14:18:43 2018 -0700 Make sure define is called when reading a coordsys Src/Base/AMReX_CoordSys.cpp commit 7071cf6d4f29210bbb24058f6b3cbedfc7f96d87 Author: Weiqun Zhang Date: Wed Aug 1 13:07:34 2018 -0700 add Make.petsc Tools/GNUMake/packages/Make.petsc commit f0b8abb5aa0006330ca0573b32847437b8b32bcd Merge: 09ada901c 525ee4de6 Author: Weiqun Zhang Date: Wed Aug 1 13:03:53 2018 -0700 Merge branch 'development' into petsc commit 6d29b6d2ccbccf884835f8e8e8e94a08712a765c Merge: ab02053e9 c725a104c Author: Andrew Myers Date: Wed Aug 1 12:51:00 2018 -0700 Merge pull request #295 from ylunalin/gpu Added collapse clause to acc directives on the triple do loops. commit 525ee4de627e393de5c253d0eb980fb48f4b9eed Author: Weiqun Zhang Date: Wed Aug 1 12:18:15 2018 -0700 minor optimization: use mfi instead of int index Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit c725a104c75fcc0623801dc142be2dc0df17f553 Author: Luna Lin Date: Wed Aug 1 15:14:05 2018 -0400 Added collapse clause to acc directives on the triple do loops. Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90 commit 3b145eb7abe4364498fbfa08241f510d837997dc Author: Weiqun Zhang Date: Wed Aug 1 11:14:49 2018 -0700 MLMG: for multiple components, we only need to to do one allreduce Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 7679874d89eeee5a672c9e4d0892998acbf71811 Merge: a63d729e5 25b57ac80 Author: Weiqun Zhang Date: Wed Aug 1 11:01:51 2018 -0700 Merge branch 'development' into hypre commit 25b57ac80971e5722a8dfa5988a9ee98864ffe63 Author: Weiqun Zhang Date: Wed Aug 1 11:00:23 2018 -0700 update CHANGES CHANGES commit 0c363cbead5424e9916a6b7951d43191b22a37a5 Author: Weiqun Zhang Date: Tue Jul 31 23:18:25 2018 -0700 reimplement LayoutData copy ctor and assignment op Src/Base/AMReX_LayoutData.H commit a63d729e568313f143efd51f825a4374de68b00a Author: Weiqun Zhang Date: Tue Jul 31 21:34:20 2018 -0700 add boomeramg parameters Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp commit af97e4e4655a4644c457d8b7514b3b4282c9193f Author: Weiqun Zhang Date: Tue Jul 31 21:31:08 2018 -0700 clean up Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 769bcadc79ad11f6d8da45fca5fd366b40f9dbb7 Author: Weiqun Zhang Date: Tue Jul 31 18:24:15 2018 -0700 remove bd key from LayoutData Src/Base/AMReX_LayoutData.H commit ab02053e9249aa8151c4d539c9f0aee4ab95c1ca Author: Andrew Myers Date: Tue Jul 31 20:20:52 2018 -0400 put shared code into a Source directory Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Constants.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/IO.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/IO.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Particles.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/main.cpp Tutorials/Particles/ElectromagneticPIC/Make.EMPIC Tutorials/Particles/ElectromagneticPIC/Source/Constants.H Tutorials/Particles/ElectromagneticPIC/Source/IO.H Tutorials/Particles/ElectromagneticPIC/Source/IO.cpp Tutorials/Particles/ElectromagneticPIC/Source/Make.package Tutorials/Particles/ElectromagneticPIC/Source/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/Source/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/Source/Particles.H Tutorials/Particles/ElectromagneticPIC/Source/main.cpp commit 27e0ce09d6b8f3c7c3ddc5c5000365de0abc603d Author: Andrew Myers Date: Tue Jul 31 19:53:50 2018 -0400 move the Cuda and OpenACC problem directories into Exec Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Constants.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/IO.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/IO.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/Particles.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/inputs Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/main.cpp Tutorials/Particles/ElectromagneticPIC/Exec/Cuda/script.sh Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Constants.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/IO.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/IO.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Make.package Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/Particles.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/inputs Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/main.cpp Tutorials/Particles/ElectromagneticPIC/Exec/OpenACC/script.sh commit e1b7db165c7a4f1ff88375aad886e762a7500627 Author: Andrew Myers Date: Tue Jul 31 19:49:01 2018 -0400 some slight renaming Tutorials/Particles/ElectromagneticPIC/Cuda/Constants.H Tutorials/Particles/ElectromagneticPIC/Cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/Cuda/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Cuda/Evolve.H Tutorials/Particles/ElectromagneticPIC/Cuda/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/Cuda/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Cuda/IO.H Tutorials/Particles/ElectromagneticPIC/Cuda/IO.cpp Tutorials/Particles/ElectromagneticPIC/Cuda/Make.package Tutorials/Particles/ElectromagneticPIC/Cuda/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/Cuda/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/Cuda/Particles.H Tutorials/Particles/ElectromagneticPIC/Cuda/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/Cuda/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/Cuda/inputs Tutorials/Particles/ElectromagneticPIC/Cuda/main.cpp Tutorials/Particles/ElectromagneticPIC/Cuda/script.sh Tutorials/Particles/ElectromagneticPIC/OpenACC/Constants.H Tutorials/Particles/ElectromagneticPIC/OpenACC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/OpenACC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/OpenACC/Evolve.H Tutorials/Particles/ElectromagneticPIC/OpenACC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/OpenACC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/OpenACC/IO.H Tutorials/Particles/ElectromagneticPIC/OpenACC/IO.cpp Tutorials/Particles/ElectromagneticPIC/OpenACC/Make.package Tutorials/Particles/ElectromagneticPIC/OpenACC/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/OpenACC/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/OpenACC/Particles.H Tutorials/Particles/ElectromagneticPIC/OpenACC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/OpenACC/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/OpenACC/inputs Tutorials/Particles/ElectromagneticPIC/OpenACC/main.cpp Tutorials/Particles/ElectromagneticPIC/OpenACC/script.sh commit 6cd98f1caa81cf615140c610681e077fbcf8abbe Author: Andrew Myers Date: Tue Jul 31 19:45:16 2018 -0400 remove the original directory Tutorials/Particles/ElectromagneticPIC/orig/Constants.H Tutorials/Particles/ElectromagneticPIC/orig/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/orig/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/orig/Evolve.H Tutorials/Particles/ElectromagneticPIC/orig/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/orig/GNUmakefile Tutorials/Particles/ElectromagneticPIC/orig/IO.H Tutorials/Particles/ElectromagneticPIC/orig/IO.cpp Tutorials/Particles/ElectromagneticPIC/orig/Make.package Tutorials/Particles/ElectromagneticPIC/orig/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/orig/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/orig/Particles.H Tutorials/Particles/ElectromagneticPIC/orig/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/orig/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/orig/inputs Tutorials/Particles/ElectromagneticPIC/orig/main.cpp Tutorials/Particles/ElectromagneticPIC/orig/script.sh commit b8005751fd1aeed6b3da93976ea65fbd78e81d2d Author: Andrew Myers Date: Tue Jul 31 19:44:37 2018 -0400 finish off the merge between my stuff and Luna's Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/cuda/ElectromagneticParticleContainer.cpp commit 03384d118a3e2d8b999d820c3f733d991096f827 Merge: 4cad1fdb3 2221e56fe Author: Andrew Myers Date: Tue Jul 31 19:19:55 2018 -0400 merging gpu_particles_refactor into gpu commit 4cad1fdb3549256b5fd864033545b8f359f2266e Merge: ff395b5aa bcc7563eb Author: Andrew Myers Date: Tue Jul 31 16:11:18 2018 -0700 Merge pull request #294 from ylunalin/gpu Try again to merge new GPU particles EMPIC tutorial in. commit bcc7563ebebe52bb81ddbc63db70fd590d8a4889 Author: Luna Lin Date: Tue Jul 31 18:40:51 2018 -0400 Fixed the fortran subroutine name binding issue. Tutorials/Particles/ElectromagneticPIC/acc/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/acc/inputs Tutorials/Particles/ElectromagneticPIC/orig/inputs commit 2221e56fec1b6175946e45be50dad07a208e8c28 Author: Andrew Myers Date: Tue Jul 31 17:59:07 2018 -0400 move the GPU particle redistribute code into Src/Particle Src/Particle/AMReX_RedistributeStrategy.H Src/Particle/AMReX_RedistributeStrategyCPU.cpp Src/Particle/AMReX_RedistributeStrategyGPU.cpp Src/Particle/Make.package Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Make.package commit b123487a95fc1fb5d11ee2dc33ea38ac99e88c94 Author: Weiqun Zhang Date: Tue Jul 31 14:32:46 2018 -0700 Remove deprecated Tutorial. We now use hypre through MLMG. Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tutorials/HYPRE/ABecLaplacian/ABL.H Tutorials/HYPRE/ABecLaplacian/ABL.cpp Tutorials/HYPRE/ABecLaplacian/ABL_F.F90 Tutorials/HYPRE/ABecLaplacian/ABL_F.H Tutorials/HYPRE/ABecLaplacian/GNUmakefile Tutorials/HYPRE/ABecLaplacian/Make.package Tutorials/HYPRE/ABecLaplacian/inputs Tutorials/HYPRE/ABecLaplacian/main.cpp commit d9a3c75da0cc0084f115592fa9dbeb082aeb0364 Author: Andrew Myers Date: Tue Jul 31 14:24:18 2018 -0700 use pair index to store particles tiles even when using the GPU Tutorials/Particles/ElectromagneticPIC/AMReX_RedistributeStrategy.H Tutorials/Particles/ElectromagneticPIC/AMReX_RedistributeStrategyCPU.cpp Tutorials/Particles/ElectromagneticPIC/AMReX_RedistributeStrategyGPU.cpp Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp commit ff395b5aaff4e763fe832b464c108444451170ca Author: Max Katz Date: Tue Jul 31 17:19:49 2018 -0400 Fix a typo in the IBM makefile Tools/GNUMake/comps/ibm.mak commit 348104b5511aed739e9385bc6e496ed6dd4e8d36 Author: Andrew Myers Date: Tue Jul 31 14:10:19 2018 -0700 seperate out the implementation strategy of Redistribute from the ParticleContainer code Tutorials/Particles/ElectromagneticPIC/AMReX_RedistributeStrategy.H Tutorials/Particles/ElectromagneticPIC/AMReX_RedistributeStrategyCPU.cpp Tutorials/Particles/ElectromagneticPIC/AMReX_RedistributeStrategyGPU.cpp Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Make.package commit 38a9a93d20ad01dec3673c104f7f487416293f0a Author: sireeveslbl Date: Tue Jul 31 13:48:17 2018 -0700 Testing MultiFab to MatLab converter Tools/Postprocessing/C_Src/GNUmakefile Tools/Postprocessing/C_Src/MultiFabToMatLab.cpp commit 03c4f4c0d9950941a7cc583d5e86983c9ccc45e7 Author: Weiqun Zhang Date: Tue Jul 31 13:35:14 2018 -0700 fix memory leak in HypreABecLap Src/Extern/HYPRE/AMReX_HypreABecLap.cpp commit 4ebc4635fdfd99c456debd5aba50fed4144a64a8 Author: Weiqun Zhang Date: Tue Jul 31 13:19:29 2018 -0700 HypreABecLap2: avoid memory leak due to hypre bug. Because HypreABecLap memory leak is not fixed yet, switch to HypreABecLap2 in MLMG Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H commit 99f2eda289158a5b6c6c5050a93d7dbb4e30d3aa Author: Max Katz Date: Tue Jul 31 15:15:58 2018 -0400 Make defines consistent Src/Base/AMReX_filcc_mod.F90 commit 2d0a42380a0fdc60e8b475c9154ade097b03af82 Author: Max Katz Date: Tue Jul 31 15:02:58 2018 -0400 Use unmodified C++ defines for the CUDA script We always use g++ for host compiling when USE_CUDA=TRUE, so we want to use the -D defines, not the -WF defines when COMP=IBM. Tools/GNUMake/Make.rules commit 97b65b7749615f80e857d86b3ddf32c30719e275 Author: Weiqun Zhang Date: Tue Jul 31 11:14:03 2018 -0700 normalize matrix for regular hypre too Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit 4167a3732e4374f9b212cd8abb214f1029b9663b Author: Luna Lin Date: Tue Jul 31 09:35:53 2018 -0700 Strip trailing whitespaces in cuda/ and orig/. Tutorials/Particles/ElectromagneticPIC/cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/cuda/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/cuda/Evolve.H Tutorials/Particles/ElectromagneticPIC/cuda/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/cuda/IO.H Tutorials/Particles/ElectromagneticPIC/cuda/IO.cpp Tutorials/Particles/ElectromagneticPIC/cuda/Make.package Tutorials/Particles/ElectromagneticPIC/cuda/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/cuda/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/cuda/Particles.H Tutorials/Particles/ElectromagneticPIC/cuda/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/cuda/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/cuda/main.cpp Tutorials/Particles/ElectromagneticPIC/orig/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/orig/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/orig/Evolve.H Tutorials/Particles/ElectromagneticPIC/orig/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/orig/IO.H Tutorials/Particles/ElectromagneticPIC/orig/IO.cpp Tutorials/Particles/ElectromagneticPIC/orig/Make.package Tutorials/Particles/ElectromagneticPIC/orig/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/orig/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/orig/Particles.H Tutorials/Particles/ElectromagneticPIC/orig/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/orig/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/orig/main.cpp commit d0af9c20a9d174984507612d653cccf9de791214 Author: Luna Lin Date: Tue Jul 31 09:32:27 2018 -0700 Convert push_electric(magnetic)_field_x(y,z) subroutine to OpenACC version. Strip whitesopaces in acc/. Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/acc/Evolve.H Tutorials/Particles/ElectromagneticPIC/acc/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/acc/IO.H Tutorials/Particles/ElectromagneticPIC/acc/IO.cpp Tutorials/Particles/ElectromagneticPIC/acc/Make.package Tutorials/Particles/ElectromagneticPIC/acc/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/acc/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/acc/Particles.H Tutorials/Particles/ElectromagneticPIC/acc/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/acc/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/acc/main.cpp commit f50fd483bf8aa55e3619f4db8675a6a883aacedb Author: Luna Lin Date: Tue Jul 31 08:23:24 2018 -0700 Convert to AMREX_FORT_LAUNCH_PARTICLES functions to OpenACC. Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/acc/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/acc/em_pic_F.H commit 2d9b899bf53fa0d8cf24d9d8cc1c734d90e83099 Author: Weiqun Zhang Date: Mon Jul 30 17:51:06 2018 -0700 refactor hypre classes to reuse the solver for different x and b Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.H Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp commit 761afebd3cc54b8d640cd7135e558eca6e2b778c Merge: 88c53c6e3 93b68d527 Author: Andrew Myers Date: Mon Jul 30 19:45:02 2018 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 88c53c6e30493b3d46d8aca17b5943d36510cc91 Merge: 50a5d1281 98b67a839 Author: Andrew Myers Date: Mon Jul 30 19:42:00 2018 -0400 fixing merge conflict commit 98b67a8395f50aafed0905a40c9fd1fddd83a022 Author: Max Katz Date: Mon Jul 30 19:32:52 2018 -0400 Need to add source to INCLUDE_LOCATIONS Tutorials/Basic/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/Basic/HeatEquation_EX2_C/Exec/GNUmakefile Tutorials/Basic/HeatEquation_EX3_C/Exec/GNUmakefile commit 3cf447221bde95aa5a0c8389bd44f15e13d00bfe Merge: 29c34af95 93b68d527 Author: Luna Lin Date: Mon Jul 30 19:27:33 2018 -0400 Merge remote-tracking branch 'upstream/gpu' into gpu commit 93b68d527a2819b01bae00c3af67daa725ab8adb Author: Max Katz Date: Mon Jul 30 19:18:50 2018 -0400 These flags only belong on Fortran Tools/GNUMake/comps/ibm.mak commit 271a8778e4edfaa42fb5792d8cf08a2b34ac0c8e Merge: 4290cba32 d1cbbd343 Author: sireeveslbl Date: Mon Jul 30 15:33:41 2018 -0700 Merge branch 'mlmg' of https://github.com/AMReX-Codes/amrex into mlmg commit 4290cba32edee1d61aadce49f8680d081ab3e301 Author: sireeveslbl Date: Mon Jul 30 15:33:21 2018 -0700 MLMG to generate solution for testing convergence of EB solver. Going to change PlotFile->matlab to use multifabs to illustrate convergence. The RHS is for the function phi = (x-1/2)/sqrt((x-1/2)^2+(y-1/2)^2), and should be used with the sphere geometry in 2D only, with location 1/2,1/2 and radius 0.25. Tests/LinearSolvers/EBConvergenceTest/GNUmakefile Tests/LinearSolvers/EBConvergenceTest/Make.package Tests/LinearSolvers/EBConvergenceTest/MyEB.H Tests/LinearSolvers/EBConvergenceTest/MyTest.H Tests/LinearSolvers/EBConvergenceTest/MyTest.cpp Tests/LinearSolvers/EBConvergenceTest/MyTest_F.H Tests/LinearSolvers/EBConvergenceTest/RHS_2D.F90 Tests/LinearSolvers/EBConvergenceTest/initEB.cpp Tests/LinearSolvers/EBConvergenceTest/inputs Tests/LinearSolvers/EBConvergenceTest/main.cpp commit 29c34af95434c06224828ee3386b248fc01da8e9 Author: Luna Lin Date: Mon Jul 30 17:03:10 2018 -0400 Added OpenACC only version of the tutorial. Tutorials/Particles/ElectromagneticPIC/acc/Constants.H Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/acc/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/acc/Evolve.H Tutorials/Particles/ElectromagneticPIC/acc/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/acc/GNUmakefile Tutorials/Particles/ElectromagneticPIC/acc/IO.H Tutorials/Particles/ElectromagneticPIC/acc/IO.cpp Tutorials/Particles/ElectromagneticPIC/acc/Make.package Tutorials/Particles/ElectromagneticPIC/acc/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/acc/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/acc/Particles.H Tutorials/Particles/ElectromagneticPIC/acc/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/acc/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/acc/inputs Tutorials/Particles/ElectromagneticPIC/acc/main.cpp Tutorials/Particles/ElectromagneticPIC/acc/script.sh commit 50a5d1281495e3d0451042d1ef5af6ceabddd79b Author: Andrew Myers Date: Mon Jul 30 16:22:19 2018 -0400 wrap these thrust things in AMREX_USE_CUDA Src/Particle/AMReX_StructOfArrays.H commit a6f0b41246587d51c436614aae5c654b3d545e47 Author: Luna Lin Date: Mon Jul 30 15:43:27 2018 -0400 Fixed a few AMREX_USE_CUDA left behind. Tutorials/Particles/ElectromagneticPIC/cuda/em_pic_3d.F90 commit 801fa23a90a1dfc6bde3555d6d6e6b787afcfe7c Author: Luna Lin Date: Mon Jul 30 14:55:31 2018 -0400 Moved tutorial files to orig/ subdirectory, create cuda/ subdir, and separate out only cuda enabled codes into it. Tutorials/Particles/ElectromagneticPIC/cuda/Constants.H Tutorials/Particles/ElectromagneticPIC/cuda/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/cuda/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/cuda/Evolve.H Tutorials/Particles/ElectromagneticPIC/cuda/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/cuda/GNUmakefile Tutorials/Particles/ElectromagneticPIC/cuda/IO.H Tutorials/Particles/ElectromagneticPIC/cuda/IO.cpp Tutorials/Particles/ElectromagneticPIC/cuda/Make.package Tutorials/Particles/ElectromagneticPIC/cuda/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/cuda/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/cuda/Particles.H Tutorials/Particles/ElectromagneticPIC/cuda/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/cuda/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/cuda/inputs Tutorials/Particles/ElectromagneticPIC/cuda/main.cpp Tutorials/Particles/ElectromagneticPIC/cuda/script.sh Tutorials/Particles/ElectromagneticPIC/inputs Tutorials/Particles/ElectromagneticPIC/orig/Constants.H Tutorials/Particles/ElectromagneticPIC/orig/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/orig/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/orig/Evolve.H Tutorials/Particles/ElectromagneticPIC/orig/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/orig/GNUmakefile Tutorials/Particles/ElectromagneticPIC/orig/IO.H Tutorials/Particles/ElectromagneticPIC/orig/IO.cpp Tutorials/Particles/ElectromagneticPIC/orig/Make.package Tutorials/Particles/ElectromagneticPIC/orig/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/orig/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/orig/Particles.H Tutorials/Particles/ElectromagneticPIC/orig/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/orig/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/orig/inputs Tutorials/Particles/ElectromagneticPIC/orig/main.cpp Tutorials/Particles/ElectromagneticPIC/orig/script.sh commit d1cbbd3437a7bae21440be1b8b825cce846c556e Merge: 0ab42684b 3441d979b Author: Weiqun Zhang Date: Sun Jul 29 21:32:28 2018 -0700 Merge branch 'development' into hypre commit 0ab42684b84bfb898b703ff5a84236ec301e6dd5 Author: Weiqun Zhang Date: Sun Jul 29 21:23:06 2018 -0700 minor change to get rid of a compiler warning Src/EB2/AMReX_EB2_IF_Rotation.H commit 89f95aa6495b4ca7a6f07225d03ec25584e3aebd Author: Weiqun Zhang Date: Sat Jul 28 18:24:08 2018 -0700 normalize matrix for hypre Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit 155e39707d281d1279fed52b35b7a9cb4b68efbc Author: Kevin Gott Date: Sat Jul 28 04:46:20 2018 -0400 Test program update. Tutorials/GPU/HelloWorld_C/main.cpp Tutorials/GPU/HelloWorld_C/run.script commit f6298152582205c8c23e7887b6e774539409dfbe Author: Kevin Gott Date: Sat Jul 28 04:45:52 2018 -0400 ElectromagneticPIC, Lamdba version. Work breakdown needs debugging. Tutorials/GPU/ElectromagneticPIC/Constants.H Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.H Tutorials/GPU/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/GPU/ElectromagneticPIC/Evolve.H Tutorials/GPU/ElectromagneticPIC/Evolve.cpp Tutorials/GPU/ElectromagneticPIC/GNUmakefile Tutorials/GPU/ElectromagneticPIC/IO.H Tutorials/GPU/ElectromagneticPIC/IO.cpp Tutorials/GPU/ElectromagneticPIC/Make.package Tutorials/GPU/ElectromagneticPIC/NodalFlags.H Tutorials/GPU/ElectromagneticPIC/NodalFlags.cpp Tutorials/GPU/ElectromagneticPIC/Particles.H Tutorials/GPU/ElectromagneticPIC/StructOfArrays.H Tutorials/GPU/ElectromagneticPIC/em_pic_3d.F90 Tutorials/GPU/ElectromagneticPIC/em_pic_F.H Tutorials/GPU/ElectromagneticPIC/inputs Tutorials/GPU/ElectromagneticPIC/main.cpp Tutorials/GPU/ElectromagneticPIC/script.sh Tutorials/GPU/ElectromagneticPIC/test.cpp commit 6fd4c98f5c5456b0d70d92b000f50fa622caba51 Author: Kevin Gott Date: Sat Jul 28 04:42:57 2018 -0400 ElectromagneticPIC function version. Conversion in progress. Need Particles wrapper for GPUs. Tutorials/Particles/ElectromagneticPIC/CudaManagedAllocator.H Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Particles.H Tutorials/Particles/ElectromagneticPIC/StructOfArrays.H Tutorials/Particles/ElectromagneticPIC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/inputs Tutorials/Particles/ElectromagneticPIC/script.sh commit 02c6d56723a8717e2ca27e4efb55843ed095ce9c Author: Kevin Gott Date: Sat Jul 28 04:38:00 2018 -0400 Adjustments for ElectromagneticPIC. Src/Base/AMReX_Box.H Src/Base/AMReX_CUDA_Utility.H Src/Base/AMReX_CUDA_Utility.cpp Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H commit 0cd7b4e31639eba4c28e6627eabddb7325d35f27 Author: Weiqun Zhang Date: Fri Jul 27 21:16:49 2018 -0700 bug fix in eb apply bc Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_nd.F90 commit d57b5d83cd629194684bc0ede250c88a1ff386de Author: Weiqun Zhang Date: Fri Jul 27 18:36:39 2018 -0700 2d high order Src/Extern/HYPRE/AMReX_HABEC_2D.F90 commit 711643e52c8323eed93010de1b64e66a2a59ef55 Author: Weiqun Zhang Date: Fri Jul 27 18:32:08 2018 -0700 change the parameter of two spheres so that it doesn't have multi-cuts in 3d Tests/LinearSolvers/CellEB/initEB.cpp Tests/LinearSolvers/CellEB/inputs commit 45a9a938bbd83a39853a236528cfce4d22896e60 Author: Weiqun Zhang Date: Fri Jul 27 18:31:34 2018 -0700 high order bc Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit 3441d979bacf05d1478ba85af376e75a95befc9f Author: Andrew Myers Date: Fri Jul 27 17:25:00 2018 -0700 remove these functions for getting all particle data on a single proc - these are inefficient and not needed. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 419872e082b2bbc740af7a4cb7d05959a8e72520 Author: Andrew Myers Date: Fri Jul 27 16:52:52 2018 -0700 also provide interfaces to get the particle id and cpu number when initializing particles from Fortran Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob_2d.f90 Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob_3d.f90 commit 589fff3f71cbe4d6b670953ef47036eed7b9337e Author: Weiqun Zhang Date: Fri Jul 27 16:52:22 2018 -0700 eb apply bc Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 Src/LinearSolvers/MLMG/Make.package commit efadcb6d52ef66476e1c5c43c4b5138900728f64 Author: Andrew Myers Date: Fri Jul 27 16:38:41 2018 -0700 remove deprecated particle initialization style from the F_Interfaces Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 commit 8f74237075429d5118c6790a3f165f2a9c5393d3 Author: Andrew Myers Date: Fri Jul 27 16:33:33 2018 -0700 add new wrappers to the F_Interfaces and set the Advection_F Tutorial to use them Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob_2d.f90 Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob_3d.f90 Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 Tutorials/Amr/Advection_F/Source/initdata.F90 commit 6d9568af0c81aafd8b9efc6fa052dcbf4ae893e8 Author: Weiqun Zhang Date: Thu Jul 26 18:39:22 2018 -0700 fix bug Src/EB/AMReX_EBMultiFabUtil_3d.F90 commit e7d4c9c2af937a48515b25fc4a9122af088b341c Merge: d35aa1a28 412af911e Author: Andrew Myers Date: Thu Jul 26 20:52:43 2018 -0400 Merge branch 'development' into gpu commit d35aa1a28256068b9bd1ca99715055d233e2ff02 Merge: 13d05f705 28e147310 Author: Andrew Myers Date: Thu Jul 26 20:52:03 2018 -0400 merging development into gpu commit 412af911e4b3f3f763c68f4bc5826e2b3e54c221 Author: Andrew Myers Date: Thu Jul 26 17:50:23 2018 -0700 removed unused variable Src/Particle/AMReX_ParticleContainerI.H commit 28e1473106ac6507a669301deff5c98115318708 Merge: b9dfcb149 0273af52d Author: Andrew Myers Date: Thu Jul 26 17:42:03 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b9dfcb14961c0467b888bc86cdfd9962a76f6ef3 Author: Andrew Myers Date: Thu Jul 26 17:41:51 2018 -0700 rename these functions to reflect the fact that there are no longer C++ and Fortran versions. Src/AmrCore/AMReX_AmrParticles.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 533065b1e5038073d4ae869f0923aa91eb9b958f Author: Andrew Myers Date: Thu Jul 26 17:30:41 2018 -0700 minor. Src/Particle/AMReX_ParticleContainerI.H commit 01974359fdcde0fafe732b180c85a17c72eb7bc6 Author: Andrew Myers Date: Thu Jul 26 17:26:01 2018 -0700 minor. Src/Particle/AMReX_ParticleContainerI.H commit 52767010bbade11d9518f4b7feb98147f7261db9 Author: Weiqun Zhang Date: Thu Jul 26 15:33:07 2018 -0700 tweak gsrb near the intersection of eb and domain boundary Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 2cd038b898ed5734d5d3716a041f5e3bf2bb6fe0 Author: Weiqun Zhang Date: Thu Jul 26 12:18:37 2018 -0700 fix corner cases Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit 13d05f7055f79fbf176362190a1016a9db155cad Author: Andrew Myers Date: Thu Jul 26 14:53:36 2018 -0400 put the detail stuff from StructOfArrays into the amrex namespace. Src/Particle/AMReX_StructOfArrays.H commit 74a6431b869ac8ec92e7787910c1c17056d6a39c Author: Andrew Myers Date: Thu Jul 26 14:51:16 2018 -0400 use the IndexSequence stuff Weiqun added to Base instead of rolling my own. Src/Particle/AMReX_StructOfArrays.H commit ccdabdfb59a442d804234f45ffdda21e0514fbbc Author: Weiqun Zhang Date: Thu Jul 26 10:27:20 2018 -0700 add MLMG::setBottomTolerance Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/CellEB/MyTest.H Tests/LinearSolvers/CellEB/MyTest.cpp commit 23c8a20c32e3ab026340010c3af119a80b9d4e01 Author: Weiqun Zhang Date: Thu Jul 26 10:18:39 2018 -0700 tweak hypre parameter Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 2fc6f35688cc194f0c756d9daff5494133a60775 Author: Weiqun Zhang Date: Thu Jul 26 09:16:46 2018 -0700 need to cal EB_average_down_faces Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_F.H commit f4d938f2b63e55d0d4579db21076578164647194 Merge: de5972ec4 267ff7bcc Author: Weiqun Zhang Date: Thu Jul 26 07:59:18 2018 -0700 Merge branch 'hypre' into mlmg commit 267ff7bcc735cf50ce2ad699f7330a402131a3e7 Author: Weiqun Zhang Date: Thu Jul 26 07:58:22 2018 -0700 fix bug Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit d4a478006fe7accc131f71bd95fcd38e9ac2855f Author: Weiqun Zhang Date: Wed Jul 25 16:55:49 2018 -0700 fix bug Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit ca0fafc7e977804484095e74f05f0a763bfe4213 Author: Weiqun Zhang Date: Wed Jul 25 16:21:30 2018 -0700 for eb, b coefficients must have one ghost Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 658f25a308373eea629b39fc6e814dc043b104c2 Author: Weiqun Zhang Date: Wed Jul 25 16:10:31 2018 -0700 ij matrix for 3d eb Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit 0273af52de2dcd1ae9436f65df4b350264de822b Author: Emmanuel Motheau Date: Wed Jul 25 15:36:47 2018 -0700 Exiting properly the AugmentPlotfile tool if we already have divergence and vorticity already computed, and avoiding useless copy-paste of data Tools/C_util/AugmentPlotfile/AugmentPlotfile.cpp commit e1c99e78405a178a163f8dbe30a76c0be0f555f1 Merge: 373b6fcf3 0c370472e Author: Andrew Myers Date: Wed Jul 25 15:04:09 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 914395fb1cf5f7d654cb4be627953e94b8dc8f81 Author: Weiqun Zhang Date: Wed Jul 25 13:59:39 2018 -0700 ij matrix for 3d all_regular eb Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Tests/LinearSolvers/CellEB/inputs commit 373b6fcf3bc6e903f89f95adb57e2ce67c2ab6c7 Author: Andrew Myers Date: Wed Jul 25 13:48:42 2018 -0700 optimize the 'remove_if' logic in ParticleContainer::Redistribute() - note that this will affect the order of particles on the tiles and therefore will cause roundoff differences in the tests. Src/Particle/AMReX_ParticleContainerI.H commit 64015a3b4d813173494271ad01db968f60fa802b Author: Weiqun Zhang Date: Wed Jul 25 12:41:47 2018 -0700 tweak hypre parameters Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 424870a7fc6ca67a31bcae60d98ba339e206ca58 Author: Weiqun Zhang Date: Wed Jul 25 11:34:13 2018 -0700 add rotated box to CellEB test Tests/LinearSolvers/CellEB/initEB.cpp Tests/LinearSolvers/CellEB/inputs commit 382cdda6084605d5238562fef228d2c747786fd0 Author: Weiqun Zhang Date: Wed Jul 25 10:35:09 2018 -0700 fix typo Src/Extern/HYPRE/AMReX_HABEC_2D.F90 commit 5de0c99c2c130537de909294ebb9f569cb537bab Author: Weiqun Zhang Date: Tue Jul 24 18:34:25 2018 -0700 add linop_maxorder option to CellEB test Tests/LinearSolvers/CellEB/MyTest.H Tests/LinearSolvers/CellEB/MyTest.cpp commit dcdd83ae0df53988fc96c15f1c56b4784f3a2c97 Author: Weiqun Zhang Date: Tue Jul 24 17:11:33 2018 -0700 fix bug Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit f42815d353d53679a66fa694e348ae12f3a09ee4 Author: Weiqun Zhang Date: Tue Jul 24 17:00:15 2018 -0700 WIP: ij matrix for 2d eb Src/Extern/HYPRE/AMReX_HABEC_2D.F90 commit 0c370472eec89a53e3a444ff9960ce43b6f1d240 Author: Weiqun Zhang Date: Tue Jul 24 13:11:34 2018 -0700 move the computation of indexArray and ownerShip to DistributionMapping Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArrayBase.cpp commit b59efaa89ae3aabef2b7a4a9eb41021cb5c1f020 Author: Weiqun Zhang Date: Tue Jul 24 12:31:25 2018 -0700 WIP: hypre for eb Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit 7bedbea4a6d26576e59309ccda43ed9e07fd1e0b Merge: bb4ec0f33 c9911e3bb Author: Andrew Myers Date: Tue Jul 24 12:14:07 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit bb4ec0f33564a5f759237ba3d9135222c1f59464 Author: Andrew Myers Date: Tue Jul 24 12:13:58 2018 -0700 Allow for the creation of multiple particle container instances when using the Fortran interfaces. Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 Tutorials/Amr/Advection_F/Source/amr_data_mod.F90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 Tutorials/Amr/Advection_F/Source/initdata.F90 Tutorials/Amr/Advection_F/Source/my_amr_mod.F90 Tutorials/Amr/Advection_F/Source/plotfile_mod.F90 commit c6ae786df7123d1c3e973f6f5b305b8553846d02 Merge: ef8211ad0 c9911e3bb Author: Andrew Myers Date: Mon Jul 23 21:48:24 2018 -0400 Merge branch 'development' into gpu commit c9911e3bba0174ea16b1fc51daef61bed60cb1a1 Author: Andrew Myers Date: Mon Jul 23 21:47:29 2018 -0400 remove unused code from Src/Particle Src/Particle/AMReX_Particles_1D.F Src/Particle/AMReX_Particles_2D.F Src/Particle/AMReX_Particles_3D.F Src/Particle/AMReX_Particles_F.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit ef8211ad0a63a0f89b6e3c0e3c5697e6662d02d5 Merge: 8e6b9b46e 807115b20 Author: Andrew Myers Date: Mon Jul 23 21:44:24 2018 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 8e6b9b46e6306f9af03b6c5805fc0ee80fbc8b0a Author: Andrew Myers Date: Mon Jul 23 21:36:20 2018 -0400 move the thrust-aware struct-of-arrays to Particles so it can be reused elsewhere. Src/Particle/AMReX_Particles.H Src/Particle/AMReX_StructOfArrays.H Src/Particle/CMakeLists.txt Src/Particle/Make.package Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Particles.H commit 807115b20f54b65aac1a0e605fb87e3adee743e9 Author: Michael Zingale Date: Mon Jul 23 21:09:16 2018 -0400 remove old function Tools/F_scripts/write_cuda_headers.py commit db75016594a0283fc762001852eabcc403cd4d21 Merge: 07404eef7 5ae9071ec Author: Andrew Myers Date: Mon Jul 23 21:06:16 2018 -0400 merging development into gpu commit 07404eef74220f3b239d6511edcbbb116707d52a Merge: 432620e15 34a8aaee8 Author: Andrew Myers Date: Mon Jul 23 20:44:53 2018 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 432620e1506a5d810c289ab975827fd41ffdd2f7 Author: Andrew Myers Date: Mon Jul 23 20:41:03 2018 -0400 install the CudaAllocators Header in Base Src/Base/Make.package commit 62eef0ba0ff8e42503f92d615459efdac13117fe Author: Andrew Myers Date: Mon Jul 23 20:35:05 2018 -0400 update Make.packages Src/Base/Make.package Src/Particle/Make.package commit 10cd7d2490b28821acb101bf0b3f27982882e1c3 Author: Andrew Myers Date: Mon Jul 23 20:34:39 2018 -0400 use the Base version of the CudaManagedAllocator Src/Particle/AMReX_Particles.H commit fd2c370d7d71efd609631433b5c942d0b3e44281 Author: Andrew Myers Date: Mon Jul 23 20:29:28 2018 -0400 remove old deposition example Tests/Particles/CUDADeposition/GNUmakefile Tests/Particles/CUDADeposition/Make.package Tests/Particles/CUDADeposition/MyParticleContainer.H Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/cuda_deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_F.H Tests/Particles/CUDADeposition/inputs Tests/Particles/CUDADeposition/main.cpp Tests/Particles/CUDADeposition/solve_for_accel.cpp Tests/Particles/CUDADeposition/solve_with_f90.cpp commit 5c263cc3bd71dc11000b273e7e97ef569cd70bdf Author: Andrew Myers Date: Mon Jul 23 20:28:52 2018 -0400 fix deposition test Tests/Particles/ManagedCUDADeposition/deposit_F.H Tests/Particles/ManagedCUDADeposition/main.cpp Tests/Particles/ManagedCUDADeposition/solve_for_accel.cpp Tests/Particles/ManagedCUDADeposition/solve_with_f90.cpp commit 34a8aaee8642fd0b9897650a0bdcb62d429d6786 Author: Michael Zingale Date: Mon Jul 23 20:08:36 2018 -0400 find the fortran targets from the C++ pragmas Tools/F_scripts/write_cuda_headers.py commit 194d9f580979955023ba845e8d69785a4694b8f5 Author: Weiqun Zhang Date: Mon Jul 23 16:50:57 2018 -0700 HYPRE_BoomerAMGSetup only needs to be called once Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 87aad53ed3811da1eb5eb8a070f8aaed3a9ee066 Author: Weiqun Zhang Date: Mon Jul 23 16:31:27 2018 -0700 fix bct and bcl Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit 9aede95a245e0971b8e656e8502aaeec2a7f2108 Author: Andrew Myers Date: Mon Jul 23 19:21:24 2018 -0400 some Array->Vector Src/Particle/AMReX_CudaManagedAllocator.H Tests/Particles/CUDADeposition/main.cpp Tests/Particles/CUDADeposition/solve_for_accel.cpp Tests/Particles/CUDADeposition/solve_with_f90.cpp commit 680989e31a422bd71180164f756f32aa4115ae15 Author: Kevin Gott Date: Mon Jul 23 19:19:19 2018 -0400 HeatEq1 uses standard functions. HeatEq0 uses lambda launchers. Tutorials/GPU/HeatEquation_EX0_C/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX0_C/Exec/inputs_2d Tutorials/GPU/HeatEquation_EX0_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX0_C/Exec/run.nocuda.script Tutorials/GPU/HeatEquation_EX0_C/Exec/run.script Tutorials/GPU/HeatEquation_EX0_C/Source/Make.package Tutorials/GPU/HeatEquation_EX0_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/advance_2d.F90 Tutorials/GPU/HeatEquation_EX0_C/Source/advance_3d.F90 Tutorials/GPU/HeatEquation_EX0_C/Source/init_phi_2d.F90 Tutorials/GPU/HeatEquation_EX0_C/Source/init_phi_3d.F90 Tutorials/GPU/HeatEquation_EX0_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX0_C/Source/myfunc.H Tutorials/GPU/HeatEquation_EX0_C/Source/myfunc_F.H commit 0c9d5caadf25743add5527f5172648545671ce7f Author: Kevin Gott Date: Mon Jul 23 19:11:58 2018 -0400 Done playing with lambdas in HeatEq1. Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H commit e6e0153e80a0bf912c1ffee211d8ee4d737b3e9d Author: Weiqun Zhang Date: Mon Jul 23 15:54:24 2018 -0700 2d ij matrix Src/Extern/HYPRE/AMReX_HABEC_2D.F90 commit de5972ec4ca0f88e4c37d84db54915660de6aea4 Author: sireeveslbl Date: Mon Jul 23 14:36:51 2018 -0700 EB Avgdown faces works in 2D and 3D Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 00e9cb6044379a35e3b4e470dca93eb54546b346 Author: Weiqun Zhang Date: Mon Jul 23 13:41:13 2018 -0700 clean up Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit b9d2989ea1a5b11c9c7238c9f2788cc6f9af4364 Author: Andrew Myers Date: Mon Jul 23 16:37:31 2018 -0400 move the cuda allocator for std::vector into Base so that it may be re-used (not really particle specific) Src/Base/AMReX_CudaAllocators.H Tutorials/Particles/ElectromagneticPIC/CudaManagedAllocator.H Tutorials/Particles/ElectromagneticPIC/StructOfArrays.H commit 4d3e8445203bcfe21572b6a7abe0fe72ce58423f Author: Weiqun Zhang Date: Mon Jul 23 13:33:58 2018 -0700 fix more bugs Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp commit d670a560fe7cec0b516ea7ec07a98b2226604e70 Author: Kevin Gott Date: Mon Jul 23 16:27:38 2018 -0400 1st version of Lambda kernel wrappers. May want to rename later. Src/Base/AMReX_Managed.H Tools/GNUMake/comps/nvcc.mak commit 0f4235cd754c49616efed5e639b27ea9957f1503 Author: Weiqun Zhang Date: Mon Jul 23 12:36:14 2018 -0700 bug fixes Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit 03f6ff791a6ee7dd57098e23ac4c421c48915326 Author: Max Katz Date: Mon Jul 23 11:49:28 2018 -0700 Merge particle support into GPU branch (#290) Adds GPU particle support to AMReX, along with several Tutorials. Src/Base/AMReX_BLFort.H Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_Vector.H Src/Particle/AMReX_CudaManagedAllocator.H Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Src/Particle/Make.package Tests/Particles/CUDADeposition/GNUmakefile Tests/Particles/CUDADeposition/Make.package Tests/Particles/CUDADeposition/MyParticleContainer.H Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/cuda_deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_F.H Tests/Particles/CUDADeposition/inputs Tests/Particles/CUDADeposition/main.cpp Tests/Particles/CUDADeposition/solve_for_accel.cpp Tests/Particles/CUDADeposition/solve_with_f90.cpp Tests/Particles/ManagedCUDADeposition/GNUmakefile Tests/Particles/ManagedCUDADeposition/Make.package Tests/Particles/ManagedCUDADeposition/MyParticleContainer.H Tests/Particles/ManagedCUDADeposition/MyParticleContainer.cpp Tests/Particles/ManagedCUDADeposition/cuda_deposit_3d.f90 Tests/Particles/ManagedCUDADeposition/deposit_3d.f90 Tests/Particles/ManagedCUDADeposition/deposit_F.H Tests/Particles/ManagedCUDADeposition/inputs Tests/Particles/ManagedCUDADeposition/main.cpp Tests/Particles/ManagedCUDADeposition/solve_for_accel.cpp Tests/Particles/ManagedCUDADeposition/solve_with_f90.cpp Tests/Particles/StructOfArrays/CudaManagedAllocator.H Tests/Particles/StructOfArrays/GNUmakefile Tests/Particles/StructOfArrays/Make.package Tests/Particles/StructOfArrays/StructOfArrays.H Tests/Particles/StructOfArrays/main.cpp Tools/GNUMake/comps/pgi.mak Tutorials/Particles/ElectromagneticPIC/CudaManagedAllocator.H Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Evolve.H Tutorials/Particles/ElectromagneticPIC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Particles.H Tutorials/Particles/ElectromagneticPIC/StructOfArrays.H Tutorials/Particles/ElectromagneticPIC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/inputs Tutorials/Particles/ElectromagneticPIC/main.cpp Tutorials/Particles/ElectromagneticPIC/script.sh commit 892b4b72c5cf09e97df4469eab10a69e0c344373 Author: Weiqun Zhang Date: Mon Jul 23 10:51:19 2018 -0700 WIP: load vectors and get solution Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 752d0e25fbd7bd9e6345e9583e533198e92b1c02 Author: Weiqun Zhang Date: Sun Jul 22 18:02:02 2018 -0700 WIP: finish matrix setup Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit 76307f580638d57a6daa316d53ee0de14dbf1668 Author: Weiqun Zhang Date: Sun Jul 22 08:37:47 2018 -0700 WIP: prepare ij matrix Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 5ae9071ec99c7abb1342aeb244aa33a71aee2d42 Author: Tan Nguyen Date: Sat Jul 21 23:53:42 2018 -0700 add a routine into Perilla WorkerThread Src/AmrTask/rts_impls/Perilla/WorkerThread.H Src/AmrTask/rts_impls/Perilla_omp/WorkerThread.H commit 06b14123e050285707db963dd67499118497ba46 Author: Tan Nguyen Date: Sat Jul 21 23:34:57 2018 -0700 extend the memory pool to make it compatible with Perilla Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_advance.cpp Src/Base/AMReX_MemPool.cpp commit a113d4809d8f2450499437918311903291761dcd Author: Weiqun Zhang Date: Sat Jul 21 21:47:32 2018 -0700 WIP: prepare the solver Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 507957415d315883bfb12191fa7c43e6f76b9f9c Author: Max Katz Date: Sat Jul 21 12:15:57 2018 -0400 Fix incorrect GPU parameter Src/Amr/AMReX_AmrLevel.cpp commit 9008c5f2912d38edb930517127c0309867bd4029 Author: Kevin Gott Date: Fri Jul 20 19:42:00 2018 -0400 Playing with lambdas. Tutorials/GPU/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H commit 74c389700754570c2ac284346f249bf473198b97 Merge: e41f308e5 326de99b8 Author: Michele Rosso Date: Fri Jul 20 13:09:34 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 326de99b8512bb35c0b9e2f29de2cdd53db15e34 Author: Weiqun Zhang Date: Fri Jul 20 06:39:45 2018 -0700 #ifdef so that Vector.H is safe for BoxLib Fortran Src/Base/AMReX_Vector.H commit e310740ae369906f1b1fcf2595877f57df5bdcbc Author: Andrew Myers Date: Thu Jul 19 17:38:54 2018 -0700 remove const I just added Src/Base/AMReX_Array.H commit e41f308e5ffba26b2da7a21f06f019829780b2dd Merge: 820ecb425 67dba6f56 Author: Michele Rosso Date: Thu Jul 19 17:10:52 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 67dba6f56ce82c04f222a9f5be4920926a673466 Merge: ec79ce5be f3ccbe5cf Author: Andrew Myers Date: Thu Jul 19 17:07:28 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ec79ce5be8561f6f10bd6c3af4b90f8e2b15dee2 Author: Andrew Myers Date: Thu Jul 19 17:07:22 2018 -0700 function for converting from unique_ptr to ptr in the kind of containers used by MLMG to store fluxes and gradients. Src/Base/AMReX_Array.H Src/Base/AMReX_Vector.H commit 5fb73550ed1190d00697cfa680fff6459f80b789 Author: Weiqun Zhang Date: Thu Jul 19 16:13:58 2018 -0700 use HYPRE_Int Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.H Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_Hypre_fort_mod.F90 Src/Extern/HYPRE/Make.package Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp commit 1bfae3b567c4df987b0a1bd1a3c6ac9d1fc4c67f Author: Weiqun Zhang Date: Thu Jul 19 14:33:58 2018 -0700 WIP: ij matrix Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.H Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit adc8774bd5007688cf6d616001b55a239d4170f5 Author: Kevin Gott Date: Thu Jul 19 16:16:46 2018 -0400 Fixing namespaces. Src/Base/AMReX_Array.H Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_Managed.H commit 3ed3c2e12b4f8d80deeb853e84d3bc016ca848de Author: Weiqun Zhang Date: Thu Jul 19 12:49:03 2018 -0700 option to choose hypre_interface Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp commit eb77c4269df3757efaf33b285b44550d380e133a Author: Weiqun Zhang Date: Thu Jul 19 12:33:39 2018 -0700 clean up semi-structed hypre Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.H Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit da10cfadaa3ac5a9ab4ed8b7e0bdd5c178fc1c7a Merge: 4fa43c06f f3ccbe5cf Author: Kevin Gott Date: Thu Jul 19 14:26:41 2018 -0400 Merge branch 'development' into gpu-mm Conflicts: Src/Base/CMakeLists.txt commit 820ecb425f27921aaadd37d044c9834feaec0608 Merge: 2a264f232 f3ccbe5cf Author: Michele Rosso Date: Thu Jul 19 11:24:24 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 4fa43c06f888fb278fb74d42dced941bf3b5e9cc Author: Kevin Gott Date: Thu Jul 19 14:11:10 2018 -0400 Various small changes for GPU C++ particles. Src/Base/AMReX_Array.H Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_fort_mod.F90 commit 9f45e1aea13aa842cddd6a2bc5400872961f3059 Author: Weiqun Zhang Date: Thu Jul 19 11:02:00 2018 -0700 2d structed Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit 2eff0155b80f73c10ba7a6ef1bfd0ecf1459dfa7 Author: Weiqun Zhang Date: Thu Jul 19 07:09:17 2018 -0700 set hypre logging and limit linop maxorder Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 6d4a8832bc9d2f812080e1d7dc7d4fff78a9a1fa Author: Weiqun Zhang Date: Thu Jul 19 06:48:58 2018 -0700 match boundary maxorder Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.H Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 commit ac332ef7ac7a3548085700a7708ceef61bf4d04f Author: Weiqun Zhang Date: Wed Jul 18 22:38:49 2018 -0700 WIP: clean up Src/Extern/HYPRE/AMReX_HABEC_2D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.H Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit f4097bdcc8a6ca298ab3371494bd931c9ded7e93 Author: Weiqun Zhang Date: Wed Jul 18 17:01:34 2018 -0700 make structed grid interface work Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.H Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit 40ead55e1c1690587343e3f02b14e0786a943c09 Author: Minion Date: Wed Jul 18 16:04:42 2018 -0700 input variables v and nu, fix multi-block error, improve modularity, clean up advance.dpp Tutorials/Basic/SDCAdvDiffusion_C/Exec/GNUmakefile Tutorials/Basic/SDCAdvDiffusion_C/Exec/inputs_2d Tutorials/Basic/SDCAdvDiffusion_C/Source/advance.cpp Tutorials/Basic/SDCAdvDiffusion_C/Source/advance_2d.f90 Tutorials/Basic/SDCAdvDiffusion_C/Source/init_phi_2d.f90 Tutorials/Basic/SDCAdvDiffusion_C/Source/main.cpp Tutorials/Basic/SDCAdvDiffusion_C/Source/myfunc.H Tutorials/Basic/SDCAdvDiffusion_C/Source/myfunc_F.H commit ad610c94a322c4931f20febb7ff5240b93185f2f Author: Weiqun Zhang Date: Wed Jul 18 15:33:34 2018 -0700 start refactoring Hypre Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_3D.F Src/Extern/HYPRE/AMReX_HypreABec_F.H Src/Extern/HYPRE/Make.package Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp Tutorials/LinearSolvers/ABecLaplacian_C/inputs Tutorials/LinearSolvers/ABecLaplacian_C/inputs-rt-abeclap-com Tutorials/LinearSolvers/ABecLaplacian_C/inputs-rt-poisson-lev commit b01a997c8484adfd65ba958f20b79a49e2f26497 Author: Weiqun Zhang Date: Tue Jul 17 18:19:25 2018 -0700 back to use HypreABecLap2 because HypreABecLap3 doesn't work yet Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/GNUmakefile Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit f73cc77e8b0aad7d9f4273c06fcc8d86328f793a Author: Weiqun Zhang Date: Tue Jul 17 17:06:55 2018 -0700 expand some macros Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit 14ef3b031e43cebbe0869eedeaa9f176e41c26b1 Merge: e012c6611 e25107061 Author: Weiqun Zhang Date: Tue Jul 17 16:55:29 2018 -0700 Merge branch 'mlmg' into hypre commit e012c661112b387dc9e51acef4943c2030575d36 Merge: 531f1310c 82f6835de Author: WeiqunZhang Date: Tue Jul 17 16:41:00 2018 -0700 Merge pull request #246 from shashankNREL/sy/hypre Sy/hypre - HYPRE IJ matrix interface commit e2510706171aaccf17fc3af719b181f8842a52a6 Author: Weiqun Zhang Date: Tue Jul 17 16:40:04 2018 -0700 fix gsrb when eb crosses domain Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit f3ccbe5cfde43464f47b779fb0e1ded6375e9710 Merge: 049b432dd 48d428fd0 Author: WeiqunZhang Date: Tue Jul 17 16:31:32 2018 -0700 Merge pull request #288 from cdaley/development Add a makefile fragment for Clang/Flang commit 48d428fd04645d82d22638fbeac06820f2c434d2 Author: cdaley Date: Tue Jul 17 16:11:31 2018 -0700 Add a makefile fragment for Clang/Flang Tools/GNUMake/Make.defs Tools/GNUMake/comps/llvm-flang.mak commit 2777513969f905bda35a402b4f65a89db5a872c9 Author: Weiqun Zhang Date: Tue Jul 17 15:39:33 2018 -0700 use mask for EB and domain bc crosses Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 049b432dd72b98f118d8ca84ae1971210f1756f5 Author: Weiqun Zhang Date: Tue Jul 17 15:10:26 2018 -0700 fix omp bug in ABecLaplacian_F tutorial Tutorials/LinearSolvers/ABecLaplacian_F/init_prob.F90 commit 980398b4ce2d8d0428c4eb69f94867360e391b73 Author: Weiqun Zhang Date: Tue Jul 17 15:04:34 2018 -0700 fix make Tutorials/LinearSolvers/ABecLaplacian_F/GNUmakefile commit 9505fed62919d0c47f30f6fde925ba5ebe4dc916 Author: Weiqun Zhang Date: Tue Jul 17 15:04:20 2018 -0700 avoid using null as variable name Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit c6861b5dd0d47832cf299246d136092fec55623e Author: Minion Date: Tue Jul 17 14:56:39 2018 -0700 IMEX advection diffusion example. This works as long as there is only one box Tutorials/Basic/SDCAdvDiffusion_C/Exec/.#advance.cpp Tutorials/Basic/SDCAdvDiffusion_C/Exec/GNUmakefile Tutorials/Basic/SDCAdvDiffusion_C/Exec/inputs_2d Tutorials/Basic/SDCAdvDiffusion_C/Source/Make.package Tutorials/Basic/SDCAdvDiffusion_C/Source/advance.cpp Tutorials/Basic/SDCAdvDiffusion_C/Source/advance_2d.f90 Tutorials/Basic/SDCAdvDiffusion_C/Source/init_phi_2d.f90 Tutorials/Basic/SDCAdvDiffusion_C/Source/init_phi_3d.f90 Tutorials/Basic/SDCAdvDiffusion_C/Source/inputs_3d Tutorials/Basic/SDCAdvDiffusion_C/Source/main.cpp Tutorials/Basic/SDCAdvDiffusion_C/Source/myfunc.H Tutorials/Basic/SDCAdvDiffusion_C/Source/myfunc_F.H Tutorials/Basic/SDCAdvDiffusion_C/Source/pf_quadrature.f90 commit a803b3d82c40ed525a82e1e460ea3d5db4d691a8 Merge: 45d0d5b38 61ee04090 Author: Minion Date: Mon Jul 16 19:55:12 2018 -0700 Merge branch 'SDC' of https://github.com/AMReX-Codes/amrex into SDC commit 45d0d5b386997ae191d417be69e84901c71afc83 Author: Minion Date: Mon Jul 16 19:52:36 2018 -0700 changing to match new tutorial style Tutorials/SDC/HeatEquation_EX1_C/GNUmakefile Tutorials/SDC/HeatEquation_EX1_C/advance.cpp Tutorials/SDC/HeatEquation_EX1_C/init_phi_2d.f90 Tutorials/SDC/HeatEquation_EX1_C/inputs_2d Tutorials/SDC/HeatEquation_EX1_C/main.cpp Tutorials/SDC/HeatEquation_EX1_C/myfunc_F.H commit dfdbe126aea9c8963431587222d38b58c64197df Author: Weiqun Zhang Date: Mon Jul 16 18:24:22 2018 -0700 pass mask to Fortran Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit b18eb8a28513d0a1ca194c42d05cfaf7c862c8d5 Merge: 52b198cd4 8be6f356b Author: Weiqun Zhang Date: Mon Jul 16 18:11:01 2018 -0700 Merge branch 'mlmg' of github.com:AMReX-Codes/amrex into mlmg commit 52b198cd45b12a2eea527aff890370e991470501 Author: Weiqun Zhang Date: Mon Jul 16 18:10:25 2018 -0700 add cc mask Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 5a2b6ddc8b2016a2eafbbf4b1e72b8bef581e95c Merge: 79776f577 a515281a2 Author: Minion Date: Mon Jul 16 17:58:59 2018 -0700 Merge branch 'development' into SDC commit ed3b7738b29b0238ae3b83c4dc2445f0e1e0c217 Author: Weiqun Zhang Date: Mon Jul 16 17:45:26 2018 -0700 simplification Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 8be6f356b32830ba1cb1a085d2b9a959292266c3 Merge: 65472b901 5a6506e04 Author: sireeveslbl Date: Mon Jul 16 14:03:49 2018 -0700 Merge branch 'mlmg' of https://github.com/AMReX-Codes/amrex into mlmg commit 65472b901a3a3c872ea4c6493d733bf76a29f83c Author: sireeveslbl Date: Mon Jul 16 14:03:47 2018 -0700 myTest for merging Tests/LinearSolvers/CellEB/MyTest.cpp commit 509d81b59ee38f2ce7ccc239ce14fa637792432e Author: sireeveslbl Date: Mon Jul 16 14:01:19 2018 -0700 Some changes, need to investigate some bugs, put it back to non-EB face averaging for now Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 5a6506e04572d46493870ac1a1679be10e02a0ad Author: Weiqun Zhang Date: Mon Jul 16 13:37:59 2018 -0700 3d mlebabeclap and over relaxation Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit a515281a22a12272ddbe6a0ec886584755ee2acd Author: Tan Nguyen Date: Mon Jul 16 12:45:26 2018 -0700 fix a compile error in the OMP backend of perilla Src/AmrTask/rts_impls/Perilla_omp/Perilla.cpp Src/AmrTask/rts_impls/Perilla_omp/RegionGraph.H Src/AmrTask/rts_impls/Perilla_omp/RegionGraph.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/inputs commit 1fbe33e5204d084c8c118ded7ed3569e9600906a Author: Weiqun Zhang Date: Mon Jul 16 12:10:31 2018 -0700 2d mlebabeclap Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit 8411fddf20009056ffe8ea101d9426d46718be7f Merge: 3560ae55d 8f9c9de99 Author: Weiqun Zhang Date: Mon Jul 16 10:29:58 2018 -0700 Merge branch 'development' into mlmg commit 8f9c9de99b31f988257ae00ee530a4d686820818 Merge: 3ca96758e c066e7d11 Author: Weiqun Zhang Date: Mon Jul 16 10:29:19 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3ca96758e1222602e605943906234f4cb3415412 Author: Weiqun Zhang Date: Mon Jul 16 10:28:50 2018 -0700 move GeometryGeneration to OldTutorials OldTutorials/GeometryGeneration/exec/GNUmakefile OldTutorials/GeometryGeneration/exec/coveredSlabs.cpp OldTutorials/GeometryGeneration/exec/coveredslabs.inputs OldTutorials/GeometryGeneration/exec/parabolaWithSphere.cpp OldTutorials/GeometryGeneration/exec/parabolaWithSphere.inputs OldTutorials/GeometryGeneration/exec/sphere.cpp OldTutorials/GeometryGeneration/exec/sphere.inputs OldTutorials/GeometryGeneration/exec/surfaceOfRevolution.cpp OldTutorials/GeometryGeneration/exec/surfaceOfRevolution.inputs OldTutorials/GeometryGeneration/src/CommonCode.H OldTutorials/GeometryGeneration/src/CommonCode.cpp OldTutorials/GeometryGeneration/src/Make.package OldTutorials/GeometryGeneration/src/WriteEBPlotFile.H OldTutorials/GeometryGeneration/src/WriteEBPlotFile.cpp commit c066e7d1119cf07471e0c5ba6f481dbdb03c9971 Merge: 130ac3536 2f51703bd Author: WeiqunZhang Date: Mon Jul 16 10:23:01 2018 -0700 Merge pull request #287 from zingale/development close math mode in latex table commit 82f6835de6a06bd3223b35b9e3ae7baf6f5ac8d3 Author: shashankNREL Date: Mon Jul 16 08:15:28 2018 -0600 Accomodating suggestions from Weiqun on the PR Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Tests/LinearSolvers/MLMG/GNUmakefile commit 130ac3536719876276ffb237825f4f88d7833e21 Author: Tan Nguyen Date: Mon Jul 16 01:32:52 2018 -0700 add perilla source code Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/Perilla/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Perilla/Barrier.H Src/AmrTask/rts_impls/Perilla/Barrier.cpp Src/AmrTask/rts_impls/Perilla/LocalConnection.H Src/AmrTask/rts_impls/Perilla/Make.package Src/AmrTask/rts_impls/Perilla/Makefile Src/AmrTask/rts_impls/Perilla/PackageQueue.H Src/AmrTask/rts_impls/Perilla/PackageQueue.cpp Src/AmrTask/rts_impls/Perilla/Perilla.H Src/AmrTask/rts_impls/Perilla/Perilla.cpp Src/AmrTask/rts_impls/Perilla/PerillaConfig.H Src/AmrTask/rts_impls/Perilla/PerillaRts.H Src/AmrTask/rts_impls/Perilla/PerillaRts.cpp Src/AmrTask/rts_impls/Perilla/RegionGraph.H Src/AmrTask/rts_impls/Perilla/RegionGraph.cpp Src/AmrTask/rts_impls/Perilla/RegionQueue.H Src/AmrTask/rts_impls/Perilla/RegionQueue.cpp Src/AmrTask/rts_impls/Perilla/RemoteConnection.H Src/AmrTask/rts_impls/Perilla/WorkerThread.H Src/AmrTask/rts_impls/Perilla/WorkerThread.cpp Src/AmrTask/rts_impls/Perilla/mylock.h Src/AmrTask/rts_impls/Perilla/perilla.mak Src/AmrTask/rts_impls/Perilla_omp/AsyncMultiFabUtil.H Src/AmrTask/rts_impls/Perilla_omp/AsyncMultiFabUtil.cpp Src/AmrTask/rts_impls/Perilla_omp/Barrier.H Src/AmrTask/rts_impls/Perilla_omp/Barrier.cpp Src/AmrTask/rts_impls/Perilla_omp/LocalConnection.H Src/AmrTask/rts_impls/Perilla_omp/Make.package Src/AmrTask/rts_impls/Perilla_omp/PackageQueue.H Src/AmrTask/rts_impls/Perilla_omp/PackageQueue.cpp Src/AmrTask/rts_impls/Perilla_omp/Perilla.H Src/AmrTask/rts_impls/Perilla_omp/Perilla.cpp Src/AmrTask/rts_impls/Perilla_omp/PerillaConfig.H Src/AmrTask/rts_impls/Perilla_omp/PerillaRts.H Src/AmrTask/rts_impls/Perilla_omp/PerillaRts.cpp Src/AmrTask/rts_impls/Perilla_omp/RegionGraph.H Src/AmrTask/rts_impls/Perilla_omp/RegionGraph.cpp Src/AmrTask/rts_impls/Perilla_omp/RegionQueue.H Src/AmrTask/rts_impls/Perilla_omp/RegionQueue.cpp Src/AmrTask/rts_impls/Perilla_omp/RemoteConnection.H Src/AmrTask/rts_impls/Perilla_omp/WorkerThread.H Src/AmrTask/rts_impls/Perilla_omp/WorkerThread.cpp Src/AmrTask/rts_impls/Perilla_omp/perilla.mak Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/._Exec Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/._README Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/._Source Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/._Make.Adv Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/._SingleVortex Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/._UniformVelocity Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/Make.Adv Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._GNUmakefile Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._Prob.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Exec/SingleVortex/._face_velocity_2d.f90 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Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/README Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv.H Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._AdvBld.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv_F.H Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv_advance.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv_dt.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv_io.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Adv_setup.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Src_2d Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Src_3d Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._Src_nd Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/._main.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.H Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/AdvBld.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_F.H Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_advance.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_dt.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_io.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Adv_setup.cpp Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/._Adv_2d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/._Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/._compute_flux_2d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/._slope_2d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/Adv_2d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/compute_flux_2d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_2d/slope_2d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/._Adv_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/._Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/._compute_flux_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/._slope_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/Adv_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/compute_flux_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_3d/slope_3d.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/._Adv_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/._Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/._Tagging_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/._tagging_params.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/Adv_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/Make.package Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/Tagging_nd.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/Src_nd/tagging_params.f90 Src/AmrTask/tutorials/MiniApps/Adv_phaseAsync/Source/main.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 3560ae55d0739a805d6c8a58ed4894b547f8dedc Author: Weiqun Zhang Date: Sat Jul 14 12:58:36 2018 -0700 make EB2::maxCoarsening more general Src/Base/AMReX_Box.H Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tests/LinearSolvers/CellEB/MyTest.cpp commit cec46dc541f186ab998072eb56235d74ce38de68 Author: Weiqun Zhang Date: Sat Jul 14 11:38:06 2018 -0700 use EB_average_down for solution too Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 55b55e3eb55a82efa8c39d60c786a12016148cde Merge: f9e823bfa 3a9355814 Author: Weiqun Zhang Date: Sat Jul 14 11:33:59 2018 -0700 Merge branch 'mlmg' of github.com:AMReX-Codes/amrex into mlmg commit 3a935581486f221f9e2485e7ee9b9bb21919c011 Author: sireeveslbl Date: Fri Jul 13 16:18:02 2018 -0700 Changed one arguement Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp commit f61b6dae717acb74c9059863164b075c8ec97083 Author: sireeveslbl Date: Fri Jul 13 16:00:57 2018 -0700 EB average down faces compiles, and doesn't break code. Still need to test Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H commit f9e823bfa5952d6181853a02695ff6ee829ddd32 Merge: 6a7c3dfbf 691517ce6 Author: Weiqun Zhang Date: Fri Jul 13 15:06:00 2018 -0700 Merge branch 'development' into mlmg commit 691517ce6f3b60da31d9e186c26d9667f19151e8 Author: Weiqun Zhang Date: Fri Jul 13 15:05:41 2018 -0700 simplication Src/EB2/AMReX_EB2.cpp commit 2ed93da32aefec3d5609ffe1da8b0935a5b0eb97 Author: Weiqun Zhang Date: Fri Jul 13 15:02:23 2018 -0700 ParmParse: get and query using std::array Src/Base/AMReX_ParmParse.H commit ecd25ef050e4f0223e08519772e6cadbd679816e Author: Weiqun Zhang Date: Fri Jul 13 14:07:22 2018 -0700 remove old EB from EB/CNS Tutorials/EB/CNS/Exec/Combustor/benchmark.inputs Tutorials/EB/CNS/Exec/Combustor/inputs Tutorials/EB/CNS/Exec/Combustor/inputs.regt Tutorials/EB/CNS/Exec/Combustor/inputs.testing Tutorials/EB/CNS/Exec/Combustor/inputs_combustor Tutorials/EB/CNS/Exec/Pulse/inputs.regt Tutorials/EB/CNS/Exec/ShockRef/aniso.inputs Tutorials/EB/CNS/Exec/ShockRef/inputs Tutorials/EB/CNS/Exec/ShockRef/inputs.amr Tutorials/EB/CNS/Exec/ShockRef/inputs.regt Tutorials/EB/CNS/Source/CNS_init_eb.cpp Tutorials/EB/CNS/Source/CNS_init_eb2.cpp Tutorials/EB/CNS/Source/Make.package Tutorials/EB/CNS/Source/main.cpp commit 6a7c3dfbf92ac848323a39dc228605a64c362736 Author: sireeveslbl Date: Thu Jul 12 22:18:32 2018 -0700 More work on EB average down faces Src/EB/AMReX_EBMultiFabUtil.cpp commit eb5c62e5fc5ded20067110cce89b109318de0e64 Merge: 927826862 dad6ae5ca Author: Weiqun Zhang Date: Thu Jul 12 22:10:24 2018 -0700 Merge branch 'development' into eb2 commit 09ada901c51782f0d71facad83b10659ee4935bb Author: Weiqun Zhang Date: Thu Jul 12 18:43:48 2018 -0700 start petsc based bottom solver Src/Extern/PETSc/AMReX_PETSc.H Src/Extern/PETSc/Make.package Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.hypre Tutorials/LinearSolvers/ABecLaplacian_C/GNUmakefile Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp commit 2f51703bd89e80e5cf977d02378a36188c6e1a77 Author: Michael Zingale Date: Thu Jul 12 20:28:28 2018 -0400 close math mode in latex table Tools/C_util/Convergence/RichardsonConvergenceTest.cpp commit ced95389b25918fbabb5a63e7a43a7e31e141b8b Author: sireeveslbl Date: Thu Jul 12 14:48:33 2018 -0700 EB Average Down Faces not finished yet, but code compiles Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp commit 927826862920a545ad64f5112e7c5f812ea1c27b Author: Weiqun Zhang Date: Thu Jul 12 11:16:03 2018 -0700 change inputs back to sphere Tutorials/EB/CNS/Exec/Sod/inputs commit dad6ae5caca1fcf5e8a49c15c8d08fc25110ff83 Author: Weiqun Zhang Date: Wed Jul 11 21:42:27 2018 -0700 update inputs Tutorials/EB/CNS/Exec/ShockRef/inputs.regt commit e9058a1fa2a1dc6d513c5ca8cf7e47c36486db01 Author: Weiqun Zhang Date: Wed Jul 11 18:26:19 2018 -0700 fix corner case of BoxArray::maxSize Src/Base/AMReX_BoxArray.cpp commit 9a5a5f57aa63bf7498a5c6b75a979c5ba1e5f769 Merge: d0519d23d 2a78ea8ac Author: Weiqun Zhang Date: Wed Jul 11 17:37:53 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d0519d23d287bb5c9aa3b070ed2bc0781f65c544 Author: Weiqun Zhang Date: Wed Jul 11 17:37:40 2018 -0700 turn off SIGTERM handling by default to avoid generating tons of Backtrace files after going over the queue time limit Src/Base/AMReX.cpp commit 10dfb13851e078345daa1ad97653c728d5f69825 Author: sireeveslbl Date: Wed Jul 11 16:20:57 2018 -0700 Working on EB average down faces. Not complete yet. Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp commit 2a78ea8accce37560f45a07b2756701528cbc9f5 Merge: 8430a292c 5778f465c Author: Weiqun Zhang Date: Wed Jul 11 16:05:30 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8430a292c4dd8081037d61e7d6e8fa932aaa24a1 Author: Weiqun Zhang Date: Wed Jul 11 16:05:12 2018 -0700 fix a bug in PhysBCFunct Src/Base/AMReX_PhysBCFunct.cpp commit 5778f465c602ea9b1dbf8150711bb09d301a54a9 Author: Weiqun Zhang Date: Wed Jul 11 13:05:02 2018 -0700 avoid conflict with PROFILE Src/Base/AMReX_TinyProfiler.cpp commit 512c5a249a4c6fd5e7f88e2ff4e723ad323bf77a Merge: a7dfcacb6 552db3088 Author: Marc Day Date: Wed Jul 11 12:27:01 2018 -0700 Merge pull request #286 from AMReX-Codes/valentina/timer added timer for MLMG::Solve commit 552db308896838dec075173dce4d01ca8a329cdc Author: Valentina Ricchiuti Date: Wed Jul 11 12:04:11 2018 -0700 added timer for MLMG::Solve Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit f53d2ebfd5a86db00835310948f6a1e043903403 Author: sireeveslbl Date: Wed Jul 11 11:01:54 2018 -0700 Moved to a 4 point interpolation for fluxes Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit b57ec0bab1a5de2c21a3fb78635fa01b2bfe9d82 Author: Weiqun Zhang Date: Tue Jul 10 18:01:48 2018 -0700 add ghost cells to A coefficient Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit a7dfcacb63d8f35b9367c5d1b9e7feab06f4ea14 Merge: 572339b01 fda1c2b6f Author: Andrew Myers Date: Tue Jul 10 17:24:33 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 572339b013728150092909f470d07110d0f3e8a1 Author: Andrew Myers Date: Tue Jul 10 17:10:48 2018 -0700 remove the allow_particles_near_boundaries parameter - no longer needed. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit e1183ab2381106b596b6779690d54dd8009284cf Author: Andrew Myers Date: Tue Jul 10 16:50:16 2018 -0700 remove old multi-level deposition routines (aren't used any more) Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit defab885cf874c55607f6fec28c5a7545c7ecbd6 Merge: 955d0f229 fda1c2b6f Author: Weiqun Zhang Date: Tue Jul 10 16:07:37 2018 -0700 Merge branch 'development' into mlmg commit fda1c2b6f8f081f65a3cc0eb6d9b7586a693283d Author: Weiqun Zhang Date: Tue Jul 10 16:07:13 2018 -0700 compile with PRECISION=FLOAT Src/EB/AMReX_EB_levelset_F.F90 Src/EB2/AMReX_EB2_GeometryShop.H Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_GeometryShop.cpp commit 955d0f2294b377ca0ab8bf131c51f204cfc37d3e Author: sireeveslbl Date: Tue Jul 10 15:32:03 2018 -0700 Other Functions with centroid interpolation Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 7736e114152ccec29760d3723971d41a4c063afe Merge: f243786b7 0e567a6b0 Author: Weiqun Zhang Date: Tue Jul 10 15:12:57 2018 -0700 Merge branch 'eb2' into development commit b3eb51b1de06a715e292adef42813f7c328a6734 Merge: cc222af75 b4d88a9d5 Author: sireeveslbl Date: Tue Jul 10 14:49:05 2018 -0700 Merge branch 'mlmg' of https://github.com/AMReX-Codes/amrex into mlmg commit cc222af7584214038e76c8dfcdaec2c730693f40 Author: sireeveslbl Date: Tue Jul 10 14:49:02 2018 -0700 merging Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit b4d88a9d5524285d3aaf2f683a110ffed21bd7f4 Author: Weiqun Zhang Date: Tue Jul 10 13:54:23 2018 -0700 fix bugs in adotx Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 49dee18fbf93a34643177da05907981e0cbe0834 Author: sireeveslbl Date: Tue Jul 10 13:01:48 2018 -0700 Interpolating on a*phi in 'A dot x', utilizing the centroid data Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit f243786b77ab00a34a381d274e215cf827cc12c3 Merge: d07bbeb35 9f710245a Author: Weiqun Zhang Date: Mon Jul 9 17:50:46 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d07bbeb350786e591771d4152c3d2669630a630b Author: Weiqun Zhang Date: Mon Jul 9 17:17:04 2018 -0700 catch SIGTERM Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp commit 0e567a6b0ff836d822a045f6f37ead5cdb54ccd1 Author: Weiqun Zhang Date: Mon Jul 9 17:47:55 2018 -0700 need to parallel reduce the error code Src/EB2/AMReX_EB2_Level.cpp commit 559b9e25e148c14a2f8eadf22d5d54592c03a8ca Author: Weiqun Zhang Date: Mon Jul 9 17:17:04 2018 -0700 catch SIGTERM Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp commit c5ec7423b18284cbdba2edfe9159c002cc484b7a Author: Weiqun Zhang Date: Mon Jul 9 17:47:55 2018 -0700 need to parallel reduce the error code Src/EB2/AMReX_EB2_Level.cpp commit 393c066ec3ee14c2c172a4d38e2a7ceef36ca231 Author: Weiqun Zhang Date: Mon Jul 9 17:17:04 2018 -0700 catch SIGTERM Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp commit 9f710245ae599ea2ee5c8369b5e31cdd026b99cc Merge: fc6d1990e 542cab184 Author: Emmanuel Motheau Date: Mon Jul 9 16:49:25 2018 -0700 Merge pull request #282 from johnpwakefield/augtool Augtool commit e34e6e65f6099d9c60977d3b5dac000dd3188a0e Author: Weiqun Zhang Date: Mon Jul 9 16:45:07 2018 -0700 increase max_coarsening_level Tests/LinearSolvers/CellEB/MyTest.H Tests/LinearSolvers/CellEB/initEB.cpp commit 94fc9d91bc4a2bd2d1f0d33c767acac3038482e7 Merge: c254a0975 228dea15b Author: Weiqun Zhang Date: Mon Jul 9 16:35:01 2018 -0700 Merge branch 'mlmg' of github.com:AMReX-Codes/amrex into mlmg commit c254a097541d2657ab2a8e82e048f18e2d1183cd Merge: 28205b983 841cbb71d Author: Weiqun Zhang Date: Mon Jul 9 16:34:57 2018 -0700 Merge branch 'eb2' into mlmg commit 841cbb71d53bc528358206f2451db3eb67adab89 Merge: 651b95644 fc6d1990e Author: Weiqun Zhang Date: Mon Jul 9 16:34:25 2018 -0700 Merge branch 'development' into eb2 commit fc6d1990ef90ad15eb6c3702559539f5a7a665d0 Author: Weiqun Zhang Date: Mon Jul 9 16:34:08 2018 -0700 cannot call MPI_Group_free after MPI_Finalize Src/Base/AMReX_ParallelDescriptor.cpp commit 28205b9830a4112fcd15761d852e0f180abae701 Author: Weiqun Zhang Date: Mon Jul 9 16:28:42 2018 -0700 when using EB, limit max coarsening level Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 228dea15be34961de9bab728cc3b530d15f5d9c8 Merge: 42035035f b1f56aafc Author: sireeveslbl Date: Mon Jul 9 16:26:19 2018 -0700 Merge branch 'mlmg' of https://github.com/AMReX-Codes/amrex into mlmg commit 42035035f0e90930d5aa946b1f55ef710b7b7f31 Author: sireeveslbl Date: Mon Jul 9 16:25:57 2018 -0700 Wrong dx in interpolation in 2D for a, 3D non-zero alpha now supported. Works with sphere test. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit b1f56aafce8bd3a95776114bebfd580b74adb91a Merge: 846f5aaa5 651b95644 Author: Weiqun Zhang Date: Mon Jul 9 15:46:42 2018 -0700 Merge branch 'eb2' into mlmg commit 651b956443f48333997fc3abe3502c8f42d536b4 Merge: a9db80e1d e7d7ee1ba Author: Weiqun Zhang Date: Mon Jul 9 15:46:17 2018 -0700 Merge branch 'weiqun/eb2' into eb2 commit a9db80e1deee1425e96f3a482fb3da914bba8a10 Merge: f85db4c8e 6a2dc8b85 Author: Weiqun Zhang Date: Mon Jul 9 15:45:58 2018 -0700 Merge branch 'development' into eb2 commit e7d7ee1bab282024c75a8f2757301637d5a5a793 Author: Weiqun Zhang Date: Mon Jul 9 15:44:57 2018 -0700 make sure fine grids are coarsenable Src/EB2/AMReX_EB2_Level.cpp commit 846f5aaa5863c6fa34af7cd9c8fa781bccc76fd7 Author: sireeveslbl Date: Mon Jul 9 14:30:18 2018 -0700 Minor change Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit e5351432e1b2c9fe30bda6ae71694adf2aa3c8d7 Author: Weiqun Zhang Date: Mon Jul 9 13:41:48 2018 -0700 rm old comment Src/EB2/AMReX_EB2_Level.H commit c7e9bb0cd3cef59040a449288799c3e210750b70 Author: Weiqun Zhang Date: Mon Jul 9 13:24:16 2018 -0700 EB2: fix maxCoarseningLevel Src/EB2/AMReX_EB2.H commit f60d786037f2d801276fdf79005d0c4cb09192da Author: Weiqun Zhang Date: Mon Jul 9 13:09:26 2018 -0700 finished implementation of coarsening to different grids Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Tests/EBEB2/MyTest.cpp commit 6a2dc8b85974cb0c54aa2fc9d774ed6008e769ae Author: Weiqun Zhang Date: Mon Jul 9 10:57:00 2018 -0700 push communicator to ParallelContext stack earlier so that Abort could work properly Src/Base/AMReX_ParallelDescriptor.cpp commit 236294e064d209b1be6ce8f24da5c7bb8a1eb673 Author: sireeveslbl Date: Mon Jul 9 10:42:49 2018 -0700 Fixed Erroneous Arithmetic Error, and convergence, non-zero alpha is working for 2D. Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit da0d632dd280e0c7dcbca33947f6f542d0e367ae Author: Weiqun Zhang Date: Sun Jul 8 08:38:58 2018 -0700 MPI_TAG_UB may only be obtained with MPI_COMM_WORLD Src/Base/AMReX_ParallelDescriptor.cpp commit a36694f639ca6799baba9fd41d5d827a1aec25d1 Author: Weiqun Zhang Date: Sat Jul 7 11:09:35 2018 -0700 Fix a bug. Even if boxarray is empty, we may still need to clear various cache. Src/Base/AMReX_FabArrayBase.cpp commit 2a264f23285fa73758eb63161432a21b78014676 Author: Michele Rosso Date: Fri Jul 6 17:58:37 2018 -0700 CMake: add test_install to be XSDK compliant CMakeLists.txt Tutorials/Basic/HeatEquation_EX1_C/CMakeLists.txt Tutorials/CMakeLists.txt commit 004caa4ee2c28d4ac6fb0d68a7716d9a0ccd3ee9 Author: Kevin Gott Date: Fri Jul 6 20:13:52 2018 -0400 Add Summit's no CUDA-aware flag. Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script commit d1ff6424b0694f079a20676020f835b50890a696 Author: Kevin Gott Date: Fri Jul 6 18:48:18 2018 -0400 run script with GPUDirect off flag. Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script commit 8b7da5177b10f54dde8d3d5a8cfed0edf9e75b3d Author: Kevin Gott Date: Fri Jul 6 18:44:00 2018 -0400 Rename kernel Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit 797a9b44d8ace781f8e6937e9c1cec94c8442e25 Author: sireeveslbl Date: Fri Jul 6 15:26:57 2018 -0700 Testing Nonzero Alpha for 2D EB MLMG Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Tests/LinearSolvers/CellEB/MyTest.cpp commit 3546209b79672225ca6b9ee141da7741d59f17df Author: Weiqun Zhang Date: Fri Jul 6 10:57:24 2018 -0700 remove optional nmax argument from SFC Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit 4604b968412d4a3602c3a9725506ab9c46809c32 Merge: b02d00bc0 16d087f90 Author: Michele Rosso Date: Fri Jul 6 10:34:39 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b02d00bc02bd5ee2eb2ac469cc67d6a7a7064807 Author: Michele Rosso Date: Fri Jul 6 10:34:34 2018 -0700 CMake: strip MPI and OpenMP variables before using them Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake commit 16d087f900dc6eb441a2c1df2e016ef7e46c4bcf Author: Weiqun Zhang Date: Thu Jul 5 18:57:26 2018 -0700 special fix for cray, don't know why it works Src/Base/AMReX_DistributionMapping.cpp commit fc0af66e48009713b1e4d2cacc815590c09c2097 Author: Michele Rosso Date: Thu Jul 5 17:01:28 2018 -0700 CMake: fix setting for Cray compiler Tools/CMake/AMReX_Config.cmake commit 5690ba52bf0540efef9dd003734d6d3121041b0f Merge: d93039084 8382ab61d Author: Michele Rosso Date: Thu Jul 5 13:37:09 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d93039084ec5bed6f2e0b40bd51d2da3268224fb Author: Michele Rosso Date: Thu Jul 5 13:37:02 2018 -0700 CMake: fix problem with AppleClang compiler Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake commit c4d8cf91685fdb6bc7e482d93260f98caf766af7 Author: Kevin Gott Date: Thu Jul 5 01:18:14 2018 -0400 Reorganization and small adjustments. Src/Base/AMReX_Box.H Src/Base/AMReX_CUDA_Utility.H Src/Base/AMReX_CUDA_Utility.cpp Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_MFIter.H Src/Base/AMReX_Managed.H Src/Base/Make.package Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit 9a25037bdf66a69afec318964291533fe5f4313c Author: Weiqun Zhang Date: Wed Jul 4 18:34:58 2018 -0700 WIP: coarsen to different grids Src/EB2/AMReX_EB2_IndexSpaceI.H Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp commit 3307cb83e7f8d979dd23945faee93eb0c974698c Merge: ebb1c1b58 f85db4c8e Author: Weiqun Zhang Date: Wed Jul 4 07:24:13 2018 -0700 Merge branch 'eb2' into mlmg commit f85db4c8e1874b570d1c955539dffd2c38b49378 Author: Weiqun Zhang Date: Wed Jul 4 07:17:47 2018 -0700 finish 3d version of amrex_eb2_check_mvmc Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit 64ba238415fcffe4d2325bb01c1018b76e36702e Author: Weiqun Zhang Date: Tue Jul 3 22:06:40 2018 -0700 start 3d version of amrex_eb2_check_mvmc Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit f60d9717ccd0e431e0454dfc0e3c775b5f51ae76 Author: Weiqun Zhang Date: Tue Jul 3 22:05:34 2018 -0700 init IArrayBox to INT_MAX in debug/test mode Src/Base/AMReX_IArrayBox.cpp commit ebb1c1b582c47cb14c28afc0a90583198aaee869 Author: Weiqun Zhang Date: Wed Jul 4 07:17:47 2018 -0700 finish 3d version of amrex_eb2_check_mvmc Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit bd6f03b18079b6883a8fdadc9303f3983a5e17e4 Author: Weiqun Zhang Date: Tue Jul 3 22:06:40 2018 -0700 start 3d version of amrex_eb2_check_mvmc Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit 0d79f5b576f5e79f13a05158c36f34067df71927 Author: Weiqun Zhang Date: Tue Jul 3 22:05:34 2018 -0700 init IArrayBox to INT_MAX in debug/test mode Src/Base/AMReX_IArrayBox.cpp commit 8382ab61d08c2044d8d6955238eb242ac9aedbbd Author: atmyers Date: Tue Jul 3 18:31:00 2018 -0700 Don't warn when particles are removed at non-periodic boundaries, even with verbose=true. Src/Particle/AMReX_ParticleContainerI.H commit f9703d80b8c35167c05d5151d996d33011a6338f Merge: bbcd2696f 164f0a732 Author: Michele Rosso Date: Tue Jul 3 17:26:52 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit bbcd2696fa405e4ca030eaab3b57cc9c69962fc4 Author: Michele Rosso Date: Tue Jul 3 17:26:39 2018 -0700 CMake: provide AMReX versioning even when .git is not present CMakeLists.txt Src/CMakeLists.txt commit 164f0a732f8069763e03e6c1bd4c5a4532136d07 Author: Weiqun Zhang Date: Tue Jul 3 17:20:34 2018 -0700 only print when verbose is true Src/Particle/AMReX_ParticleContainerI.H commit c36c7f25874b236f701b4811279cd108e5560120 Merge: 94b6ce6d3 260a5d47f Author: Weiqun Zhang Date: Tue Jul 3 17:15:16 2018 -0700 Merge branch 'eb2' into mlmg commit 260a5d47f65bdefe26223c7dbd59941931c364ed Merge: b75d5148a d8924b227 Author: Weiqun Zhang Date: Tue Jul 3 17:11:25 2018 -0700 Merge branch 'development' into eb2 commit 94b6ce6d3df64263ae3d516075f9415d8752fdff Merge: b2b033b38 b75d5148a Author: Weiqun Zhang Date: Tue Jul 3 17:00:03 2018 -0700 Merge branch 'eb2' into mlmg commit b2b033b38e0e44e8ef6bd87cfca3c35eeef28aae Author: Weiqun Zhang Date: Tue Jul 3 16:59:44 2018 -0700 don't let linear solver's max_coarsening_level exceed EB2's Tests/LinearSolvers/CellEB/MyTest.cpp commit d8924b227bbe8bb170011513bafbb992026a4621 Author: Michele Rosso Date: Tue Jul 3 16:49:11 2018 -0700 CMake: fix bug Tools/CMake/AMReX_Options.cmake commit 52bcf493a3eb1eb0dc505db77626b090888ac4ce Merge: 9dcb04a00 34a7c2a58 Author: Weiqun Zhang Date: Tue Jul 3 16:48:30 2018 -0700 Merge branch 'mlmg' of github.com:AMReX-Codes/amrex into mlmg commit b75d5148a36ea321d14cee89046f6e8305369f25 Author: Weiqun Zhang Date: Tue Jul 3 16:45:03 2018 -0700 fix m_ok Src/EB2/AMReX_EB2_Level.H commit 9b80fdefcbaf843c705e099121025f8c9ddac6c6 Author: Weiqun Zhang Date: Tue Jul 3 16:35:50 2018 -0700 function to return max coarsening level Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IndexSpaceI.H Src/EB2/AMReX_EB2_Level.H commit ae3a33af15546154dfa272ea3a00232847adaf96 Author: Weiqun Zhang Date: Tue Jul 3 15:31:32 2018 -0700 check for multi-cuts and multi-values Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit 9dcb04a00ebbb9339400f8bb366d9e55d9b623d9 Author: Weiqun Zhang Date: Tue Jul 3 16:45:03 2018 -0700 fix m_ok Src/EB2/AMReX_EB2_Level.H commit 629445959075a908e67898ddda7982002320c271 Author: Weiqun Zhang Date: Tue Jul 3 16:35:50 2018 -0700 function to return max coarsening level Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IndexSpaceI.H Src/EB2/AMReX_EB2_Level.H commit 89fb725224878784203ec3193a750f7f7954aacb Author: Weiqun Zhang Date: Tue Jul 3 15:31:32 2018 -0700 check for multi-cuts and multi-values Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit 9b03ef620f9b153c281280b55358057127b94344 Merge: b39fd01ea 44deb6cec Author: Michele Rosso Date: Tue Jul 3 14:48:39 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b39fd01ea97a037176b01fb93c9ca7dce252e7f9 Author: Michele Rosso Date: Tue Jul 3 14:48:04 2018 -0700 CMake: one more change Src/CMakeLists.txt commit 34a7c2a58e2c427d982e12e08770e59b26a8bb4b Author: sireeveslbl Date: Tue Jul 3 13:11:35 2018 -0700 Fixed Another Bug, for regular convergence Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 8621380e17be754ede57dada277a81f1bd1b90e2 Merge: 342ee9bb6 299bdb6ec Author: Weiqun Zhang Date: Tue Jul 3 13:03:42 2018 -0700 Merge branch 'mlmg' of github.com:AMReX-Codes/amrex into mlmg commit 44deb6cec4d4aa616d9e182def520f722127190e Merge: 8846a9637 b5ad64e66 Author: Marc Day Date: Tue Jul 3 12:57:28 2018 -0700 Merge pull request #279 from jrood-nrel/update_nrel_makefile Update makefile for NREL site to get higher vectorization from the Intel compiler commit b5ad64e661526ca3bf4722b406dd4c1b3a727c32 Author: Jon Rood Date: Tue Jul 3 13:37:40 2018 -0600 Update makefile for NREL site to get higher vectorization from the Intel compiler. Tools/GNUMake/sites/Make.nrel commit 8846a963766a06631f8529f3a4f3a16f44aa6fa1 Author: Michele Rosso Date: Tue Jul 3 12:06:56 2018 -0700 CMake: some more improvements Src/CMakeLists.txt Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake commit 299bdb6ec94c1737d61c1e34578681320b8b5f5b Author: sireeveslbl Date: Tue Jul 3 10:12:26 2018 -0700 MyTest Changed to allow for 3D Tests/LinearSolvers/CellEB/MyTest.cpp commit 3f979b055ee47c6c2308f16d2fd0ec6411ffdfae Author: sireeveslbl Date: Tue Jul 3 10:10:18 2018 -0700 Bug Killed, Test Case works for Sphere Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 8516211a54365bb57aef52f599c24fdb27c62e1f Author: Michele Rosso Date: Mon Jul 2 16:19:37 2018 -0700 CMake: bug fix Tools/CMake/AMReX_Config.cmake commit 408f52fc973b26a36634001f33c7150beedd6339 Author: Kevin Gott Date: Mon Jul 2 18:56:02 2018 -0400 strip USE_CUDA in make file Tools/GNUMake/Make.defs commit 77a20533a94a08ed51ec35139a8fc7bff35482d1 Author: Kevin Gott Date: Mon Jul 2 18:52:47 2018 -0400 Add CUDA streams to MFIter. Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 6e375fe703b69e6b0a22ec8176c6290e1007e096 Author: Kevin Gott Date: Mon Jul 2 18:50:08 2018 -0400 Adjust Device for AMREX_USE_CUDA=FALSE. Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/Make.package commit 4f6b0d847f8325e538f68aef1ffec31fac0aa2d8 Author: Michele Rosso Date: Mon Jul 2 15:49:31 2018 -0700 CMake: update Doc Docs/sphinx_documentation/source/BuildingAMReX.rst commit be077d818d3c42c9a24909bfdce42123d8d778db Author: Kevin Gott Date: Mon Jul 2 18:45:17 2018 -0400 Add using CudaAllocators = std allocator for USE_CUDA=FALSE. Src/Base/AMReX_CudaAllocators.H commit 86b36224e2dfb22226166f10a868d701e82937a5 Merge: 4c97e88e4 3db026077 Author: Michele Rosso Date: Mon Jul 2 15:28:58 2018 -0700 Merge branch 'development' into mr/cmake commit 4c97e88e41b7ea8a93245fc770004f6e54685eb2 Author: Michele Rosso Date: Mon Jul 2 15:22:22 2018 -0700 CMake: complete transition to 'Modern CMake' CMakeLists.txt Src/CMakeLists.txt Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Machines.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_Utils.cmake Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt commit 3db026077b0d4ad989e9eb72c1ce1cefeeb33bc5 Merge: 8cf3bfeb0 fbedfc53f Author: Johannes Blaschke Date: Mon Jul 2 13:38:42 2018 -0700 :Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 8cf3bfeb0a4ed59bd10761f4046ed22baa169966 Author: Johannes Blaschke Date: Mon Jul 2 13:38:38 2018 -0700 remove meaningless const Src/EB/AMReX_EB_levelset.H commit fbedfc53fb3d01c3383faf4c59a5358455b92576 Author: Johannes Blaschke Date: Mon Jul 2 13:11:54 2018 -0700 fixed dummy variable and meaningless const Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset_F.F90 commit c10251c76a7062355a1647b147a6bf9e017016e5 Author: Weiqun Zhang Date: Mon Jul 2 10:46:08 2018 -0700 makeSFC: switch the order of optional arguments Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit 6953a91f00229ce957b1e1d692fc30f60574b92a Merge: 900cee71e 65a6e8ded Author: Weiqun Zhang Date: Mon Jul 2 10:42:01 2018 -0700 Merge branch 'sfc' into development commit 900cee71eb6d4dde7560cbcb1ed386942e3ec0b2 Merge: 8174212e8 913731ccf Author: Weiqun Zhang Date: Mon Jul 2 10:41:34 2018 -0700 Merge branch 'knapsack' into development commit 8174212e898677d6413cf5e4db44148a52b4b732 Author: Weiqun Zhang Date: Mon Jul 2 10:40:21 2018 -0700 update CHANGES CHANGES commit 342ee9bb659836fa894fc71ebb46e214f03941e4 Merge: 4e40b3032 4d005d53d Author: Weiqun Zhang Date: Fri Jun 29 18:33:28 2018 -0700 Merge branch 'eb2' into mlmg commit 4d005d53d789eb3816285d765232524639bf1a6f Author: Weiqun Zhang Date: Fri Jun 29 18:08:26 2018 -0700 detect mutli-values in 2d Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit 4e40b3032010c00e8fd570ad0bf749c025418c88 Author: sireeveslbl Date: Fri Jun 29 16:37:01 2018 -0700 Bugs somewhere, maybe in the interp. Gotta buscar! Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit aa8d66789ecec0c25e7a177fe5c20af0bac05a9c Author: sireeveslbl Date: Fri Jun 29 15:11:45 2018 -0700 MLEBABecLap_3d compiles, fixed interpolation to multi-D. Needs testing Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 60e0efbd39f4c6e3e87e3e44ff4115046e463cf8 Merge: de3223719 f632781c8 Author: WeiqunZhang Date: Fri Jun 29 14:15:38 2018 -0700 Merge pull request #276 from AMReX-Codes/bugfix_Convergence_tools fix convergence tools in 1D commit de32237196cb00a9eb9ce4edf147a72ad4a6b635 Author: Weiqun Zhang Date: Fri Jun 29 13:45:31 2018 -0700 IntVect version of iMultiFab::define Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit c21b0b05b4df36dfc2c8d69b2b2458154d3dc360 Author: Michele Rosso Date: Thu Jun 28 17:59:26 2018 -0700 CMake: bug fixes Src/Extern/CMakeLists.txt Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake commit 7c2be80f44a881dd981e47b2dce14eb719d6ffcc Merge: 4b3052099 e89c0e501 Author: Michele Rosso Date: Thu Jun 28 17:01:19 2018 -0700 Merge branch 'development' into mr/cmake commit 4b305209953d1a037214ad973dbcfdbd0b0e98e4 Author: Michele Rosso Date: Thu Jun 28 16:37:10 2018 -0700 CMake: improve installation step Src/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake commit 913731ccfce832980b646421f7fe5e50ccf97a0e Author: Weiqun Zhang Date: Thu Jun 28 16:34:16 2018 -0700 knapsack: minor cleanup Src/Base/AMReX_DistributionMapping.cpp commit 68a2b1d5980b47dd05b2ce07b465d493cda8f14c Author: Weiqun Zhang Date: Thu Jun 28 16:04:04 2018 -0700 knapsack swap: only need to check the end Src/Base/AMReX_DistributionMapping.cpp commit f632781c859b9231f065aa487bb2df85d5cfe3fa Author: Emmanuel Motheau Date: Thu Jun 28 13:50:07 2018 -0700 fix convergence tools in 1D Src/Extern/ProfParser/AMReX_AVGDOWN_1D.F Tools/C_util/Convergence/GNUmakefile commit 64d19f573cc20d97f1535a1a5d966b444b99a7d9 Author: sireeveslbl Date: Thu Jun 28 13:44:42 2018 -0700 First function compelete Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 commit 24a5e6cf630d3478a39287a907b37afcf25c9161 Author: Michele Rosso Date: Thu Jun 28 11:01:00 2018 -0700 CMake: use generator expressions when setting compiler flags Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake commit aa8594474637b79e2dc62e91b615c24ea9f6f1e4 Author: Weiqun Zhang Date: Thu Jun 28 10:59:02 2018 -0700 knapsack: timer and assertion Src/Base/AMReX_DistributionMapping.cpp commit e89c0e501b9e25168c0bc5595379ec6a4f06efb8 Merge: 4af9e54ec 5be100875 Author: Johannes Blaschke Date: Thu Jun 28 10:18:38 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 4af9e54ec6b7c3242e69c6fc23f3914af76533c2 Author: Johannes Blaschke Date: Thu Jun 28 10:18:34 2018 -0700 boundary level-set initialization ignored periodic directions (filled using FillBoundary anyway) Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 commit c4623ea386f5ba570244a8424ece92fa409ad447 Author: Weiqun Zhang Date: Thu Jun 28 07:32:34 2018 -0700 knapsack: if the top has only one Box, there is no need to check swapping Src/Base/AMReX_DistributionMapping.cpp commit 427358d98ecee440b53e8526af6eddd055642584 Author: Weiqun Zhang Date: Thu Jun 28 07:21:41 2018 -0700 knapsack: switch order for performance Src/Base/AMReX_DistributionMapping.cpp commit 1e85acf730a8962222660c3c9d9c6313bea1a399 Author: Weiqun Zhang Date: Thu Jun 28 07:02:39 2018 -0700 knapsack: list -> vector Src/Base/AMReX_DistributionMapping.cpp commit 5be100875d02dad228d5657bfb6351439e62c3c9 Merge: 5aec30ac9 abba84eb1 Author: Marc Day Date: Wed Jun 27 19:30:53 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5aec30ac98edcde310082c4fdfeb1a5594e1ecb6 Author: Marc Day Date: Wed Jun 27 19:30:26 2018 -0700 Add a utility to append stuff to plotfiles...requires some care to use. following instructions on screen after plotfile modified this way. Tools/C_util/AppendToPlotFile.H Tools/C_util/AppendToPlotFile.cpp commit abba84eb16b79571067cbb4ebb18fc371b4936a9 Merge: 5320e87b8 d4fa5f694 Author: Andrew Myers Date: Wed Jun 27 18:47:10 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5320e87b86c031d134a376f5e629482a7891d178 Author: Andrew Myers Date: Wed Jun 27 18:46:40 2018 -0700 force it to rebuild the CellVectors every time Redistribute is called. Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp commit 87cd8881735975bea3869b7a88a59876c743b116 Author: Andrew Myers Date: Wed Jun 27 18:44:20 2018 -0700 lower dt Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp commit 747cfbe6bdb24099dc28f0c220954814a3a6bdd5 Author: Andrew Myers Date: Wed Jun 27 18:43:55 2018 -0700 make this loop work with tiling Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp Tutorials/Particles/CellSortedParticles/cell_sorted_3d.F90 Tutorials/Particles/CellSortedParticles/cell_sorted_F.H Tutorials/Particles/CellSortedParticles/main.cpp commit debfe3f492d9cd8d3c4793762b2f7d4b187d265b Author: Andrew Myers Date: Wed Jun 27 18:38:26 2018 -0700 typo fix Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp commit 068328093fe4d94a7dc02f1ce811f0f705e7381d Author: Michele Rosso Date: Wed Jun 27 17:56:22 2018 -0700 CMake: update tutorials Tools/CMake/AMReX_Compilers.cmake Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt Tutorials/Amr/Advection_F/CMakeLists.txt Tutorials/Amr/Advection_F/Source/my_amr_mod.F90 Tutorials/Amr/Advection_octree_F/CMakeLists.txt Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90 Tutorials/CMakeLists.txt commit d4fa5f69481f2efd7b10d912b8d3a4a9131af4e3 Author: Ann Almgren Date: Wed Jun 27 17:22:12 2018 -0700 Remove IOIOI cout statements for precreating directory struture Src/Amr/AMReX_Amr.cpp commit 2b7853b3fc69eac342b49f37f7c38573c2b8e7e7 Author: Michele Rosso Date: Wed Jun 27 16:16:07 2018 -0700 CMake: set manually C++ std flags to enable transitive dependencies on this property CMakeLists.txt Tools/CMake/AMReX_Compilers.cmake commit cf5f46fedd43c3d0ffd91f98e0d232a2a7e47592 Author: Michele Rosso Date: Wed Jun 27 15:02:41 2018 -0700 CMake: some modifications to support different scenarios Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_ThirdPartyProfilers.cmake commit e1440db2a60a8a79b536e47ca8622ecfc186dccb Author: Kevin Gott Date: Wed Jun 27 17:27:28 2018 -0400 Remove blockSize from particle blocks_and_threads. Src/Base/AMReX_Device.cpp commit b7e971e8382771f8f100430ea468830756c4a51b Author: Johannes Blaschke Date: Wed Jun 27 14:06:05 2018 -0700 only manually fill valid non-periodic boundaries Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 commit 229aaf4adf595a6acd745f50c4fab5367e4ac2b9 Author: Johannes Blaschke Date: Wed Jun 27 13:30:29 2018 -0700 almost done eliminating all the copy-and-paste bits Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 commit b739a7d953f7a5e7b776e5a7a1822d6427528dd4 Author: Kevin Gott Date: Wed Jun 27 15:18:01 2018 -0400 Direct, unedited copy of tutorial from gpu_particles. Tutorials/Particles/ElectromagneticPIC/CudaManagedAllocator.H Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Evolve.H Tutorials/Particles/ElectromagneticPIC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/Particles.H Tutorials/Particles/ElectromagneticPIC/StructOfArrays.H Tutorials/Particles/ElectromagneticPIC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/inputs Tutorials/Particles/ElectromagneticPIC/main.cpp Tutorials/Particles/ElectromagneticPIC/script.sh Tutorials/Particles/ElectromagneticPIC/test.cpp commit 9c2978a9015f29244eccc957d01e4d5f8324d20e Author: Michele Rosso Date: Wed Jun 27 10:40:36 2018 -0700 CMake: some bug fixes Tools/CMake/AMReX_Config.cmake commit 81d1f64ce7430d900c8e66fbcc8cea903db3bae7 Author: Weiqun Zhang Date: Wed Jun 27 10:34:32 2018 -0700 add inputs Tests/LinearSolvers/CellEB/inputs commit aeca530f9ac3ea6f1cbb54aa066ca530c05974b8 Merge: b847eb27e 6eea83171 Author: Johannes Blaschke Date: Wed Jun 27 10:09:14 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b847eb27e015935a5815be647b05224ad9b2fa67 Author: Johannes Blaschke Date: Wed Jun 27 10:08:49 2018 -0700 some more cleaning and removing unncessary arguments Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 commit 21868dd5526c03c2854b39f32d33dc1a3e902df9 Author: Johannes Blaschke Date: Tue Jun 26 21:57:16 2018 -0700 more cleaning up Src/EB/AMReX_EB_levelset_F.F90 commit 1540a51f0c005c4ff4282d092b962c2eed0ad4cf Author: Johannes Blaschke Date: Tue Jun 26 18:48:27 2018 -0700 working on cleaning copy-and-paste Src/EB/AMReX_EB_levelset_F.F90 commit 6eea831713a0b04fa1a222e9d9e0a1f4ad2ded0f Merge: c1953bfc2 4a8c19660 Author: Andrew Myers Date: Tue Jun 26 17:52:20 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c1953bfc2db88ee99734d1f4d82764e72938e99c Author: Andrew Myers Date: Tue Jun 26 17:52:02 2018 -0700 periodic shift should *repeatedly* shift the particle until it is inside. Src/Particle/AMReX_ParticleContainerI.H commit 35c965eb4527625dc44e439f9ebdf5777549981b Author: Michele Rosso Date: Tue Jun 26 17:49:11 2018 -0700 CMake: further improvements Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake commit 4a8c19660ee8f019490b3a5e0ec4835d376b4fa4 Author: Johannes Blaschke Date: Tue Jun 26 17:36:10 2018 -0700 fill level set manually in boundary points Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 commit 36da80fb4d6d4530da229e5ff5f9e4feea6f81a8 Author: Michele Rosso Date: Tue Jun 26 15:51:44 2018 -0700 CMake: continue transition to 'modern CMake' CMakeLists.txt Src/CMakeLists.txt Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_ThirdPartyProfilers.cmake commit 52d1fde3500c403572118d4cca1c6b602c22a64d Author: Andrew Myers Date: Mon Apr 23 19:10:18 2018 -0400 add macro and helper routine for launching particle kernels Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_Managed.H commit 457a7859380af97f029565e047cbafdb2ac43ffd Author: Ann Almgren Date: Wed Jun 6 14:56:11 2018 -0400 Add CharVector that can be CUDA memory managed and make neighbors now be managed the way particles are. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_Particles.H commit 4ffce6495043a506735ccca4d4702c29429ad02e Author: Andrew Myers Date: Wed Dec 20 14:59:45 2017 -0800 finish fixing gpu_particles branch Src/Particle/AMReX_Particles.H commit cdaf8d8655ecf2396309e766a60b23da230b5585 Author: Andrew Myers Date: Wed Dec 20 10:24:15 2017 -0800 some work on fixing the gpu_particles branch. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 25bb6ba8974a9191206be10bb2f348b385d7e0d5 Author: sireeveslbl Date: Tue Jun 26 14:38:33 2018 -0700 Pulse Inputs to use EB2 stuff Tutorials/EB/CNS/Exec/Pulse/inputs commit a97d0c4aac8e250a750ad84ee697a18b42d0ca52 Author: sireeveslbl Date: Tue Jun 26 14:26:55 2018 -0700 MyTest.cpp Tests/EBEB2/MyTest.cpp commit 51c8d238b6398d2c66cae3fb90e981a0ca91e5de Author: sireeveslbl Date: Tue Jun 26 14:14:43 2018 -0700 Minor Format Change Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit 22f861875f4afb2d0eb9e58140203cac8447a23f Author: sireeveslbl Date: Tue Jun 26 14:11:52 2018 -0700 Wrote combustor function for EB1 to follow same params as EB2. Edited initialize_EBIS to take additional Geometry argument, for the effective construction of the flattened corner. Removed the old polygon_revolution params in input. Tutorials/EB/CNS/Exec/Combustor/inputs Tutorials/EB/CNS/Source/CNS_init_eb.cpp Tutorials/EB/CNS/Source/main.cpp commit ebe364855a673cc36b91874c3965544eecbb2377 Author: Kevin Gott Date: Tue Jun 26 16:54:07 2018 -0400 Fix after merge. Tools/GNUMake/sites/Make.olcf commit f1695ed675eb3da64bcfc2ef9a8ea1db03133783 Merge: af292b9eb bb5f93267 Author: Kevin Gott Date: Tue Jun 26 16:44:37 2018 -0400 Merge with development. commit af292b9ebec171ab03098f17b369e4ac66d718c6 Author: Kevin Gott Date: Tue Jun 26 15:34:50 2018 -0400 HeatEquation Inputs and run.script Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script commit fd3e6175a60ad678af510d602fcbe564ac55b1bd Author: Max Katz Date: Tue Jun 26 03:03:35 2018 -0700 Automatically generate both host and device functions Tools/F_scripts/gpu_fortran.py Tools/F_scripts/write_cuda_headers.py commit 2176c523d711eb473a2348db85ca66fa59806462 Author: Max Katz Date: Tue Jun 26 01:26:51 2018 -0700 Move module use statements into subroutines Src/Base/AMReX_BaseFab_nd.F90 commit 134a6af9a7c1d5f493eb231e5dfc3a0fb4eeb3c0 Author: Kevin Gott Date: Mon Jun 25 22:13:52 2018 -0400 Split work on GPU to 1 grid cell per GPU thread. Src/Base/AMReX_Box.H Src/Base/AMReX_Managed.H Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp commit a9133655a4b41479c2ff693b1bbea8fea3084bd9 Author: sireeveslbl Date: Mon Jun 25 16:52:17 2018 -0700 Combustor Inputs returned to original problem Tutorials/EB/CNS/Exec/Combustor/inputs commit bb5f93267650e30b7d574cd68b6a99ebc999f3df Author: Andrew Myers Date: Mon Jun 25 16:31:18 2018 -0700 update the Tests and the Tutorials Tests/Particles/AssignDensity/GNUmakefile Tests/Particles/AssignMultiLevelDensity/main.cpp Tests/Particles/GNUmakefile Tutorials/Particles/CellSortedParticles/GNUmakefile Tutorials/Particles/ElectromagneticPIC/GNUmakefile Tutorials/Particles/NeighborList/GNUmakefile commit e0b22e8c62e51f67b4fc0b82d7dd7fe57371a97e Author: Andrew Myers Date: Mon Jun 25 16:30:13 2018 -0700 don't need these includes any more Src/Particle/AMReX_Particles.H commit 045af09e52070f79fa3ae8f355b43f5dc4040e57 Author: Andrew Myers Date: Mon Jun 25 16:29:56 2018 -0700 ... and actually remove it from Src/Particles Src/Particle/AMReX_ParticleContainerI.H commit a164f1c55fdf9330de3a1aa1d84429ca14ac47f5 Author: Andrew Myers Date: Mon Jun 25 16:29:24 2018 -0700 move implementation of multi-level assign density into Src/AmrCore Src/AmrCore/AMReX_AmrParticles.H commit 26ec8d6ee28255fd0d97ebcd5e47b60bfc033f12 Author: sireeveslbl Date: Mon Jun 25 16:17:25 2018 -0700 Changed inputs for working EB2, need to translate old EB to work with new inputs Tutorials/EB/CNS/Exec/Combustor/inputs Tutorials/EB/CNS/Exec/ShockRef/inputs commit 58179529033d81fc16174c385c0609e3fcea9c50 Author: Weiqun Zhang Date: Mon Jun 25 16:05:19 2018 -0700 test for CC EB solver Tests/LinearSolvers/CellEB/GNUmakefile Tests/LinearSolvers/CellEB/Make.package Tests/LinearSolvers/CellEB/MyEB.H Tests/LinearSolvers/CellEB/MyTest.H Tests/LinearSolvers/CellEB/MyTest.cpp Tests/LinearSolvers/CellEB/initEB.cpp Tests/LinearSolvers/CellEB/main.cpp commit 93c0b0af33b679a076d487c48451be1950462325 Author: Weiqun Zhang Date: Mon Jun 25 15:45:35 2018 -0700 add 3d version of amrex_mlmg_eb_cc_interp to public Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 commit af6961665b7f1e46e193db03256c51de83c91b4d Author: sireeveslbl Date: Mon Jun 25 13:14:18 2018 -0700 CNS combustor is finished for EB2, user defines locations of planes, boxes etc Tutorials/EB/CNS/Exec/Combustor/inputs Tutorials/EB/CNS/Source/CNS_init_eb2.cpp commit 8ea591253a95d4f3487ee60535697124dfc82061 Author: Andrew Myers Date: Mon Jun 25 12:15:40 2018 -0700 we need to include EB2 to build now. Tutorials/Particles/EBParticles/GNUmakefile commit c74f9e3bfe6222bc45ebf6947a96099e3524430d Merge: 364176273 5780c1456 Author: Andrew Myers Date: Mon Jun 25 10:48:55 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 36417627385487b5fb38f25a35e37a4f3386b310 Author: Andrew Myers Date: Mon Jun 25 10:48:36 2018 -0700 break this timer into two Src/Particle/AMReX_ParticleContainerI.H commit ed72074cf91668f4deb64d906093d983fe5f08f8 Author: Max Katz Date: Mon Jun 25 01:26:58 2018 -0700 Write out the actual CUDA code instead of using the macro Tools/F_scripts/write_cuda_headers.py commit 94ad6a05908aa163dfda3fa91dea656730258a86 Author: Max Katz Date: Mon Jun 25 01:14:17 2018 -0700 Also capture Fortran functions Tools/F_scripts/gpu_fortran.py commit ec1ee2cfafd4b3a066953dc8ea9aefc7779d6602 Author: Max Katz Date: Mon Jun 25 01:07:37 2018 -0700 Replace with attributes(device) instead of AMREX_DEVICE Tools/F_scripts/gpu_fortran.py Tools/F_scripts/write_cuda_headers.py commit 9007ac8981b5fdcf6031db645c6c983bc6ef0b7f Author: Max Katz Date: Sun Jun 24 23:52:37 2018 -0700 Update script info Tools/F_scripts/write_cuda_headers.py commit 9876a3e02aea3619324a9236394204d7d7d5591e Merge: c13812215 58352bbf5 Author: Max Katz Date: Sun Jun 24 23:46:44 2018 -0700 Merge branch 'gpu' into gpu-gpu commit 58352bbf574a1dd70f212503612682571318de96 Author: Max Katz Date: Sun Jun 24 23:37:32 2018 -0700 Preprocess CUDA files to look for !$gpu Tools/F_scripts/gpu_fortran.py Tools/GNUMake/Make.rules commit 50a66c416eddd52703e9dbb483817364dc1ac5cc Author: Max Katz Date: Sun Jun 24 23:32:32 2018 -0700 Only do the CUDA header work in the tempdir Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.rules commit bba205e101c150030cc3c8a07e26edf3eb6b850a Author: Max Katz Date: Sun Jun 24 22:56:05 2018 -0700 Really fix source term copying Tools/GNUMake/Make.rules commit ba50538c9455a522a7615c541fddb1677001474e Author: Max Katz Date: Sun Jun 24 22:39:08 2018 -0700 Fix source file copying Tools/GNUMake/Make.rules commit 49fa39c881a48b4eb3572557c5b0959fafd0e142 Author: Max Katz Date: Sun Jun 24 16:19:57 2018 -0700 Use the srcTempDir for the dependency generation Tools/GNUMake/Make.rules commit 81e149a2977374e5c70c8765842de721d298a452 Author: Max Katz Date: Sun Jun 24 16:03:43 2018 -0700 Fix tmpbuilddir logic Tools/GNUMake/Make.rules commit edc8b63c5b21bd5609d9d48b3175d5cc232e3e85 Author: Max Katz Date: Sun Jun 24 16:00:32 2018 -0700 Add a missing @ Tools/GNUMake/Make.rules commit ddfdd08c1325c54ac1596969d8ee4e38c9c15268 Author: Max Katz Date: Sun Jun 24 15:17:27 2018 -0700 Always include the temp build directory first Tools/GNUMake/Make.defs commit f31f3b7a944d2bf56d14d24dfefcaf14c1e61d95 Author: Max Katz Date: Sun Jun 24 15:02:59 2018 -0700 Reverse order so that source copies occur first Tools/GNUMake/Make.rules commit 02885810e4f3edcb0f28745e12f4c27c206d2820 Author: Max Katz Date: Sun Jun 24 14:20:48 2018 -0700 Copy all source files to a temp build directory before compilation Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit c138122157f50b686838bb949717ed1ac819baf1 Author: Max Katz Date: Sat Jun 23 21:21:03 2018 -0700 [WIP] Update the CUDA script description Tools/F_scripts/write_cuda_headers.py commit 2b6ff9ec802ccc817375681205d7dac40cf7971e Author: Max Katz Date: Sat Jun 23 21:19:21 2018 -0700 [WIP] Update the CUDA script description Tools/F_scripts/write_cuda_headers.py commit 262fb1a559c2e0d11abe237d6f5f6fbb5c2c20d1 Author: Max Katz Date: Sat Jun 23 21:14:37 2018 -0700 Replace AMREX_DEVICE with !$gpu Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_filcc_mod.F90 Src/Base/AMReX_fort_mod.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 commit ff4b7b4712060de05d0f25b40b3085403fbae014 Author: Max Katz Date: Sat Jun 23 20:28:24 2018 -0700 Add some more GPU defines Tools/GNUMake/Make.defs commit bc885152c1887b7846cfebdefd1396a22791f637 Merge: 05dd46855 5780c1456 Author: Max Katz Date: Sat Jun 23 14:45:39 2018 -0700 Merge branch 'development' into gpu Conflicts: Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BLFort.H Tools/GNUMake/sites/Make.olcf commit 5780c14567e6f69111e6f2f910444eec0f55bba3 Author: Max Katz Date: Sat Jun 23 14:38:28 2018 -0700 Add reduction macros Src/Base/AMReX_BLFort.H commit 05dd46855a65c93c3c37b344f3211fd27a0d651c Author: Max Katz Date: Sat Jun 23 14:13:48 2018 -0700 Fix logic on the nvcc version check Src/Base/AMReX_BLFort.H commit 78c6fb9e4382c0238dffdcef0062da519ee79ece Author: Max Katz Date: Sat Jun 23 15:36:18 2018 -0400 Remove legacy non-CUDA 8 code Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.cpp Tools/GNUMake/Make.defs Tools/GNUMake/sites/Make.olcf commit ddb41a270d0a3182ec908d805650c78621597e18 Author: Max Katz Date: Sat Jun 23 12:16:01 2018 -0700 Disallow CUDA toolkit versions <= 8.0 Tools/GNUMake/comps/nvcc.mak commit 4c1dc83bcd53bfc43e319cb27609efd24d3f8f63 Author: Max Katz Date: Sat Jun 23 12:12:01 2018 -0700 bl_error -> amrex_error for CUDA Src/Base/AMReX_CUDA.F90 commit 5a2473d75284154469d94b04c6a44bce593c292f Author: Max Katz Date: Sat Jun 23 14:20:59 2018 -0400 Capture NVCC version Tools/GNUMake/comps/nvcc.mak commit 91aeecd30aa0c603f13770f1c773d5e9cd5b8166 Author: Michele Rosso Date: Fri Jun 22 18:15:30 2018 -0700 CMake: start transition to 'modern CMake' Src/Amr/CMakeLists.txt Src/AmrCore/CMakeLists.txt Src/Base/CMakeLists.txt Src/Boundary/CMakeLists.txt Src/CMakeLists.txt Src/EB/CMakeLists.txt Src/EB2/CMakeLists.txt Src/Extern/CMakeLists.txt Src/F_Interfaces/CMakeLists.txt Src/GeometryShop/CMakeLists.txt Src/LinearSolvers/CMakeLists.txt Src/Particle/CMakeLists.txt Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_Utils.cmake Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/CMakeLists.txt commit 61ee04090a6f4ba68c36720c56cce106945beea2 Author: Lawrence Minion Date: Fri Jun 22 18:05:33 2018 -0700 Getting implicit example in SDC tutorials Tutorials/SDC/HeatEquation_EX3_C/GNUmakefile Tutorials/SDC/HeatEquation_EX3_C/Make.package Tutorials/SDC/HeatEquation_EX3_C/advance.cpp Tutorials/SDC/HeatEquation_EX3_C/advance_2d.f90 Tutorials/SDC/HeatEquation_EX3_C/init_phi_2d.f90 Tutorials/SDC/HeatEquation_EX3_C/init_phi_3d.f90 Tutorials/SDC/HeatEquation_EX3_C/inputs_2d Tutorials/SDC/HeatEquation_EX3_C/inputs_3d Tutorials/SDC/HeatEquation_EX3_C/main.cpp Tutorials/SDC/HeatEquation_EX3_C/myfunc.H Tutorials/SDC/HeatEquation_EX3_C/myfunc_F.H Tutorials/SDC/HeatEquation_EX3_C/pf_quadrature.f90 commit fc73420cb538873fe419ee7ce824534bbe182788 Author: Andrew Myers Date: Fri Jun 22 16:55:58 2018 -0700 use std::memcpy here instead of reinterpret_cast Src/Particle/AMReX_ParticleContainerI.H commit e60720e27d15e1440485ae0bae2c048da8d8738c Author: Andrew Myers Date: Fri Jun 22 16:15:08 2018 -0700 simplify timers Src/Particle/AMReX_ParticleContainerI.H commit 3fc59a5150bd4fe311786f7080b6c0b9a4a1953b Author: Andrew Myers Date: Fri Jun 22 16:11:40 2018 -0700 remove code that isn't needed any more Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 02e956c7cf321d477c22ac1f5612d5baea8d6e3d Author: Andrew Myers Date: Fri Jun 22 16:09:32 2018 -0700 remove an un-needed copy Src/Particle/AMReX_ParticleContainerI.H commit 0954f5eb57d47bc1d419200c374da27d4786e7fe Author: Andrew Myers Date: Fri Jun 22 13:48:20 2018 -0700 Some systems require flush calls here for the particle io to work correctly. There is a similar work-around in AMReX_FArrayBox.cpp. Src/Particle/AMReX_ParticleContainerI.H commit 1e3abb7cdb0e66c49ccfdb65ee21bd2fb5d543b3 Merge: d4dc46906 5d2cd984c Author: Andrew Myers Date: Fri Jun 22 13:04:24 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d4dc46906337f9421282f1ee1a26db8f837cd9f5 Author: Andrew Myers Date: Fri Jun 22 12:01:57 2018 -0700 try threading only the locate Src/Particle/AMReX_ParticleContainerI.H commit 02c3b57e037c8e4c7b6f17729538a5865ed4e4be Author: Andrew Myers Date: Fri Jun 22 11:43:27 2018 -0700 add some more timers Src/Particle/AMReX_ParticleContainerI.H commit 56013d6b3e1b3e1c1f4ebccdeb257e4e4a982a47 Author: Andrew Myers Date: Fri Jun 22 11:32:25 2018 -0700 adding threading to the unpack Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 5d2cd984c5ac4d3d8089488f872aa35031eb3696 Author: Weiqun Zhang Date: Fri Jun 22 07:15:47 2018 -0700 need to test the fortran function ptr in interp hook Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp commit ef177c4afea9152bc4c27e952170a50d06f28ca4 Merge: 7f6e92b94 5f2252313 Author: Weiqun Zhang Date: Thu Jun 21 18:13:40 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7f6e92b94368eb3b4d58582c56c82271b7ca1365 Author: Weiqun Zhang Date: Thu Jun 21 18:13:28 2018 -0700 minor Src/AmrCore/AMReX_FillPatchUtil.H commit 3ded97f3a21695023c6e933d96668ccba47a6955 Author: Weiqun Zhang Date: Thu Jun 21 18:06:15 2018 -0700 show how to use interploation hooks in tutorial Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 Tutorials/Amr/Advection_octree_F/Source/fillpatch_mod.F90 commit 4df91e601f79d4c6797a7cebd519d9c834d0f7c8 Author: Weiqun Zhang Date: Thu Jun 21 17:50:41 2018 -0700 add pre- and post-interp hooks in fillpatch for flash Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 commit 16f7ae07a894345c2ed9e3f8ac1bbde03d3a9faf Author: Andrew Myers Date: Thu Jun 21 17:41:50 2018 -0700 update test Tests/Particles/test.py commit fba1b37305443adb9060ba0bcc5490984d6b1423 Author: Andrew Myers Date: Thu Jun 21 17:41:36 2018 -0700 start threading unpacking the particle data in RedistributeMPI Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit f4e27b17634c2c973b1c4142d848824e01a74898 Author: Michael Zingale Date: Thu Jun 21 18:38:16 2018 -0400 remove duplicate signatures from the list of targets Tools/F_scripts/write_cuda_headers.py commit 5f2252313f3e8649d04c6610a58dc115cd79d5d0 Author: Johannes Blaschke Date: Thu Jun 21 10:54:39 2018 -0700 Avoid FillBoundary in recursive step Src/EB/AMReX_EB_levelset.cpp commit 8e22adeb4ec27df5af2fe93ceed6f210e8b27458 Merge: 738c26784 a5bbdfeea Author: Michele Rosso Date: Thu Jun 21 09:57:21 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 738c26784bec58a2687181a9b56d36660df13862 Author: Michele Rosso Date: Thu Jun 21 09:57:12 2018 -0700 CMake: add NDEBUG only in non-XSDK mode Tools/CMake/AMReX_Defines.cmake commit 927113373a8c5ea5b9a227a94a687e06fb794088 Author: Max Katz Date: Thu Jun 21 09:36:09 2018 -0700 Do reductions on host when not offloading Src/Base/AMReX_BaseFab.cpp commit 4e60ffff0fc5584ce4f27839591a06a3dfb3c144 Author: Max Katz Date: Thu Jun 21 08:00:46 2018 -0700 Add flag to disable device offload Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_filcc_mod.F90 Src/Base/AMReX_fort_mod.F90 Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit a5bbdfeea2e425da1b3d0dfb2820e7188f35e2de Author: Weiqun Zhang Date: Wed Jun 20 21:54:44 2018 -0700 NDEBUG -> AMREX_DEBUG Src/Amr/AMReX_StateDescriptor.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/Base/AMReX.H Src/Base/AMReX_BLassert.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_IArrayBox.cpp Src/Boundary/AMReX_LO_UTIL.F90 Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp Tools/C_util/Convergence/Add.cpp Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameDomainRefinedComposite.cpp Tools/C_util/Convergence/DiffSameDomainRefinedFD.cpp Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGrid2.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileNormB.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/Convergence/RichardsonConvergenceTest.cpp Tools/C_util/Statistics/PltFileFluxAve.cpp Tools/C_util/Statistics/PltFileList.cpp Tools/C_util/Statistics/PltFileStat.cpp Tools/C_util/Statistics/PltFileXAve.cpp Tools/GNUMake/Make.defs commit 9c335c03dc072ce464a41bbc00d701f41c403c43 Author: Weiqun Zhang Date: Wed Jun 20 17:59:48 2018 -0700 compiles Src/Base/AMReX.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp commit afd782057cba77cdcb12aa2a4de158e06f39cbf4 Author: Kevin Gott Date: Wed Jun 20 20:39:05 2018 -0400 Broken Arena Change Src/Base/AMReX.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BArena.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_CArena.H commit f6c2b8912231488b47128bc50bfb06836ea35527 Author: sireeveslbl Date: Wed Jun 20 17:09:12 2018 -0700 Ramp written for EB2, with both regular plane arguments and slope-point args. tested with Sod, will test Shock Reflection Tutorials/EB/CNS/Exec/Sod/inputs Tutorials/EB/CNS/Source/CNS_init_eb.cpp Tutorials/EB/CNS/Source/CNS_init_eb2.cpp commit 18dc754790d113f6ac8b47ab78e6a5302b8993e5 Author: Johannes Blaschke Date: Wed Jun 20 17:02:00 2018 -0700 change the way `valid` is populated... this should perform better if n_pad is large Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 commit 8adb5fab047f9a7d2ef0c9fee97b3b22a4cd3de1 Author: Kevin Gott Date: Wed Jun 20 18:41:11 2018 -0400 Update inputs files. Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d commit 7c6a21033d9390c03822761134aea8ef8c8d2bd4 Author: Kevin Gott Date: Wed Jun 20 17:52:52 2018 -0400 Addition of Device & CUDA from Max's branch. Devices initialize & finalize added to AMReX.cpp. Arenas adjusted to work with multiple MPI ranks. Src/Base/AMReX.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_BArena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_Managed.H Src/Base/Make.package Tutorials/GPU/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HelloWorld_C/main.cpp commit 79776f577e9dbbc219a966f31f7318af62321a17 Author: Minion Date: Wed Jun 20 12:34:08 2018 -0700 moving SDC tutorials into separate directory Tutorials/SDC/HeatEquation_EX1_C/GNUmakefile Tutorials/SDC/HeatEquation_EX1_C/Make.package Tutorials/SDC/HeatEquation_EX1_C/advance.cpp Tutorials/SDC/HeatEquation_EX1_C/advance_2d.f90 Tutorials/SDC/HeatEquation_EX1_C/advance_3d.f90 Tutorials/SDC/HeatEquation_EX1_C/init_phi_2d.f90 Tutorials/SDC/HeatEquation_EX1_C/init_phi_3d.f90 Tutorials/SDC/HeatEquation_EX1_C/inputs_2d Tutorials/SDC/HeatEquation_EX1_C/inputs_3d Tutorials/SDC/HeatEquation_EX1_C/main.cpp Tutorials/SDC/HeatEquation_EX1_C/myfunc.H Tutorials/SDC/HeatEquation_EX1_C/myfunc_F.H Tutorials/SDC/HeatEquation_EX1_C/pf_quadrature.f90 commit 7c12aeb057b0a8990e1877bb553b9bd9dcb46233 Merge: 948c8f0d6 bc2d9887a Author: Minion Date: Wed Jun 20 12:29:11 2018 -0700 Merge branch 'SDC' of https://github.com/AMReX-Codes/amrex into SDC commit 948c8f0d6391d981ae910748f88c06bef1cc3578 Author: Minion Date: Wed Jun 20 12:28:28 2018 -0700 starting to clean up SDC structures Tutorials/Basic/SDCHeat_Equation_EX1_C/GNUmakefile Tutorials/Basic/SDCHeat_Equation_EX1_C/Make.package Tutorials/Basic/SDCHeat_Equation_EX1_C/advance.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/init_phi_2d.f90 Tutorials/Basic/SDCHeat_Equation_EX1_C/inputs_2d Tutorials/Basic/SDCHeat_Equation_EX1_C/main.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc.H Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc_F.H Tutorials/Basic/SDCHeat_Equation_EX1_C/pf_quadrature.f90 commit 716a3718bc3a43f3bb8dc12dffa762be5c158bd6 Author: Johannes Blaschke Date: Wed Jun 20 11:41:51 2018 -0700 fix naming convention for fortran module Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset_F.F90 commit 65a6e8ded89fd357db1fa906917ffacd962673c2 Author: Weiqun Zhang Date: Wed Jun 20 09:52:11 2018 -0700 add an argument to makeSFC to limit the maximal number of boxes a process can get Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit b6fc415c4ab64a6fd5116645703fbd1d50cf9b18 Author: Michael Zingale Date: Wed Jun 20 12:13:01 2018 -0400 fix the ability to compile normal after CUDA w/o headers getting in the way Tools/GNUMake/Make.rules commit ea8a1c29f7c78eb983eb56b79979fa967148325d Author: Weiqun Zhang Date: Wed Jun 20 07:59:21 2018 -0700 update make Src/EB2/CMakeLists.txt Src/EB2/Make.package commit 9dd51e13223790f30908dc143c9104350463af74 Author: Max Katz Date: Tue Jun 19 19:53:30 2018 -0700 Generalize the IBM config so it is not OLCF specific Tools/GNUMake/comps/ibm.mak Tools/GNUMake/sites/Make.olcf commit 8931e024a0be42e6af706e451a48cfdcb1ef8260 Author: Max Katz Date: Tue Jun 19 19:51:16 2018 -0700 Update LLNL MPI setup Tools/GNUMake/sites/Make.llnl commit ee930f2239a9d7ad4ac66e7277aa0450441bb07f Author: Weiqun Zhang Date: Tue Jun 19 18:07:48 2018 -0700 RotationIF: fix 2d compilation; add std:: to cos and sin for portability; fix the sign in rotation matrix because we are rotating the object. Src/EB2/AMReX_EB2_IF_Rotation.H commit 8ef62675430553a3213f7d35602ca053896a4707 Author: Weiqun Zhang Date: Tue Jun 19 17:27:45 2018 -0700 fix typo Src/AmrCore/AMReX_INTERP_2D.F90 commit 8ce8c4ec60c662f26fb06891bf04d2f973b3dcec Merge: ce4a1e8f4 dc0a67301 Author: Weiqun Zhang Date: Tue Jun 19 17:15:42 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ce4a1e8f4690faafea8f5a88c956db27b62ac591 Author: Weiqun Zhang Date: Tue Jun 19 17:15:29 2018 -0700 xSDK: fix some Fortran print Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/Base/AMReX_COORDSYS_2D.F90 Src/Base/AMReX_COORDSYS_3D.F90 Src/EB2/AMReX_eb2_3d.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90 Src/Particle/AMReX_Particle_mod_1d.F90 Src/Particle/AMReX_Particle_mod_2d.F90 Src/Particle/AMReX_Particle_mod_3d.F90 commit bc2d9887a271a01276417662b28e9ea510f8b2de Author: Weiqun Zhang Date: Tue Jun 19 17:03:47 2018 -0700 typo Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc_F.H commit 5c51b14f445598dc88bfc188989e58860ad382c8 Author: Weiqun Zhang Date: Tue Jun 19 16:38:09 2018 -0700 xSDK: print Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_AmrCore.H Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_BoxDomain.cpp Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_Utility.cpp Src/Base/AMReX_VisMF.cpp Src/EB2/AMReX_EB2_GeometryShop.H Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H commit 21acc34cc59532a774a32369858b539334756653 Author: sireeveslbl Date: Tue Jun 19 16:24:22 2018 -0700 Rotation about the origin axes Src/EB2/AMReX_EB2_IF_Rotation.H commit dc0a673017563442de035fdb7bec9da098a07dc1 Merge: 2d7ac068b a8c8f6c92 Author: Johannes Blaschke Date: Tue Jun 19 16:08:45 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 2d7ac068b40497fe55671c3230efc0c913570d9a Author: Johannes Blaschke Date: Tue Jun 19 16:08:42 2018 -0700 update EB level-set to reflect recent changes in mfix Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_geometry.F90 Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 Src/EB/AMReX_compute_normals.F90 commit a8c8f6c925785646d8baee893ecb949e5217d57b Author: Weiqun Zhang Date: Tue Jun 19 15:17:42 2018 -0700 turn off print unless verbose is true Src/Base/AMReX_Utility.cpp commit 3ae44cced42c05ec438a6c5eb32b1975c0b65c60 Author: Weiqun Zhang Date: Tue Jun 19 15:17:02 2018 -0700 add amrex::RuntimeError and amrex.throw_exception ParmParse parameter Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Exception.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 1ffaf412ab49c3c09309ccdf027ad2d4b8dca15c Author: Andrew Myers Date: Tue Jun 19 12:26:45 2018 -0700 some clean up / comments Tutorials/Particles/CellSortedParticles/CellSortedPC.H Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp commit dab45fa9c4e58fb076491ea34ae72d1e00b8446e Author: Andrew Myers Date: Tue Jun 19 12:20:51 2018 -0700 store vectors directly instead of unique_ptr to vectors Tutorials/Particles/CellSortedParticles/CellSortedPC.H Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp commit ccc9384966f528963f4c50bbd6d6276c87294a7a Merge: a85a18029 e6babd503 Author: Andrew Myers Date: Tue Jun 19 10:52:02 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a85a18029177dd151e8f836e8cc5438a60bf1605 Author: Andrew Myers Date: Tue Jun 19 10:51:45 2018 -0700 remove another unused variable. Src/Base/AMReX_NFiles.cpp commit d4bf2e8ca4e2139aa205598263a1586ff4baafa3 Author: Andrew Myers Date: Tue Jun 19 10:47:31 2018 -0700 remove unused variables. Src/Base/AMReX_MultiFabUtil_nd.F90 commit e6babd5032243cd4f42b289601b96cc8a4a7b991 Author: Andrew Myers Date: Tue Jun 19 09:50:10 2018 -0700 adding an additional Timer to RedistributeMPI Src/Particle/AMReX_ParticleContainerI.H commit 2269adf1d58df09687c3cbebd3d6a504e8efc232 Author: Andrew Myers Date: Mon Jun 18 16:33:31 2018 -0700 remove need to explicitly update the structure of the cell vectors. Tutorials/Particles/CellSortedParticles/CellSortedPC.H Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp Tutorials/Particles/CellSortedParticles/main.cpp commit 8528478be7dc081e1196012072e4524ae1d502ac Merge: 691d1f1ba 62887687a Author: Andrew Myers Date: Mon Jun 18 15:40:55 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 691d1f1baefbe97294e82a9dc3d49f518dda09ab Author: Andrew Myers Date: Mon Jun 18 15:40:41 2018 -0700 starting to track to the ref of the BA and DM that the cell vectors are defined on. Tutorials/Particles/CellSortedParticles/CellSortedPC.H Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp commit 34f5fe07499a4cfd2425ea30d919c2daed9034ce Author: Michael Zingale Date: Mon Jun 18 10:21:50 2018 -0400 have the python preprocessor remove unwanted preprocessor directives Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.rules commit 8e2330f086cd10f52fd6a7cc6e60286398936c3d Author: Michael Zingale Date: Mon Jun 18 10:09:11 2018 -0400 fix CUDA flags Tools/GNUMake/Make.rules commit 62887687a8144c0eb701b589e49d4e2771ab48e5 Author: Michael Zingale Date: Sun Jun 17 22:18:47 2018 -0400 add some macros to sync with what is happening on the gpu branch this gives us CPU compatibility Src/Base/AMReX_ArrayLim.H commit 603c5530763c1690c17baa125513abe7caa7c02c Author: Max Katz Date: Sun Jun 17 13:03:24 2018 -0400 Handle MPICH with CUDA Tools/GNUMake/Make.defs commit f5bf40b484cdaaba3f618a9666862af5cb83beef Author: Michael Zingale Date: Sun Jun 17 11:41:01 2018 -0400 don't pass the MPI preprocessor directives into the CUDA stuff Tools/GNUMake/Make.rules commit 339a1f0071a2618c1792cc09c5ee3e8ea5b7cb53 Author: Lawrence Minion Date: Sat Jun 16 19:24:44 2018 -0700 optimal SDC order for heat equation Tutorials/Basic/SDCHeat_Equation_EX1_C/advance.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/init_phi_2d.f90 Tutorials/Basic/SDCHeat_Equation_EX1_C/inputs_2d Tutorials/Basic/SDCHeat_Equation_EX1_C/main.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc.H Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc_F.H Tutorials/Basic/SDCHeat_Equation_EX1_C/pf_quadrature.f90 commit c5b2b5ad71e6008320e43485418ae22841caac8e Author: Andrew Myers Date: Fri Jun 15 16:52:42 2018 -0700 enable OpenMP in some loops Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp commit ceb063b6ef02d53248826d43547327f2cc1a9365 Author: Andrew Myers Date: Fri Jun 15 16:45:54 2018 -0700 turn on mpi Tutorials/Particles/CellSortedParticles/GNUmakefile commit f834e1fec4ec3168f203da60e2e0a5ecbd71907a Author: Andrew Myers Date: Fri Jun 15 16:44:28 2018 -0700 keeping track of which particle in which cell as they move around. Tutorials/Particles/CellSortedParticles/CellSortedPC.H Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp Tutorials/Particles/CellSortedParticles/cell_sorted_3d.F90 Tutorials/Particles/CellSortedParticles/cell_sorted_F.H Tutorials/Particles/CellSortedParticles/main.cpp commit f6c9e08c6147bbc1a20b8fc096072966a3852e5f Author: Andrew Myers Date: Fri Jun 15 14:57:56 2018 -0700 use the fortran to link when using intel with a Fortran main. Tools/GNUMake/comps/intel.mak Tutorials/Amr/Advection_F/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/GNUmakefile Tutorials/Basic/HeatEquation_EX1_F/GNUmakefile Tutorials/Basic/HelloWorld_F/GNUmakefile Tutorials/Basic/main_F/GNUmakefile Tutorials/LinearSolvers/ABecLaplacian_F/GNUmakefile commit 13280073f0312f47c710eae11fec91bd92e52b77 Author: Andrew Myers Date: Fri Jun 15 12:52:04 2018 -0700 start working on cell-sorted particles for DSMC Tutorials/Particles/CellSortedParticles/CellSortedPC.H Tutorials/Particles/CellSortedParticles/CellSortedPC.cpp Tutorials/Particles/CellSortedParticles/GNUmakefile Tutorials/Particles/CellSortedParticles/Make.package Tutorials/Particles/CellSortedParticles/cell_sorted_3d.F90 Tutorials/Particles/CellSortedParticles/cell_sorted_F.H Tutorials/Particles/CellSortedParticles/inputs Tutorials/Particles/CellSortedParticles/main.cpp commit 11a9f00e068e01187fcf4220713073ac46895a68 Author: Andrew Myers Date: Fri Jun 15 12:50:58 2018 -0700 give ParticleContainer a virtual destructor. Src/Particle/AMReX_Particles.H commit 89e28083c23c1bfcf090c4405aedcc62462013ed Author: Michael Zingale Date: Thu Jun 14 19:47:10 2018 -0400 add back in the c99 standard Tools/GNUMake/Make.rules commit aad97cad436118b326bff8b669ac4033f1a40076 Author: Weiqun Zhang Date: Thu Jun 14 16:05:24 2018 -0700 EB MLMG: add interp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 6a5807843701d47452f7c9a070d29a3fc96542a2 Author: Kevin Gott Date: Thu Jun 14 18:29:50 2018 -0400 Redesign GeometryData object and data function to prevent caching. Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit 00d636f0363337074e4729718bc67d685fa6cfe4 Author: Michael Zingale Date: Thu Jun 14 18:17:16 2018 -0400 remove the check on the gcc return code for now it works for gcc > 6.4.0 but not earlier Tools/F_scripts/preprocess.py commit 5715c828ef026fa546e9a35324a3ee7940f308d6 Author: Weiqun Zhang Date: Thu Jun 14 14:57:39 2018 -0700 EB MLMG: fix bug Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 commit 0fc81c4e50e2be246ae8ae7658dbeb0d83e7daa2 Author: Weiqun Zhang Date: Thu Jun 14 14:22:43 2018 -0700 EB MLMG: interp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_F.H commit db71bf6850e292e01f7da8017a9ef7ab91eeddc7 Author: Michael Zingale Date: Thu Jun 14 17:08:31 2018 -0400 don't restrict to python3 Tools/F_scripts/write_cuda_headers.py commit 7dc2d066238e7aa6b8bc892d0c026e0cb4a33d30 Author: Max Katz Date: Thu Jun 14 16:11:05 2018 -0400 Fix IBM MPI library Tools/GNUMake/sites/Make.olcf commit 6a6e6fcfed36de568f2214a315ac965c1f327cfe Author: Michael Zingale Date: Thu Jun 14 16:03:22 2018 -0400 this works Tools/F_scripts/write_cuda_headers.py commit 7a5b3259f867b8def48ceb305c3fddaab66b1835 Author: Michael Zingale Date: Thu Jun 14 15:07:55 2018 -0400 this is mostly right, but somewhat wrong Tools/F_scripts/write_cuda_headers.py commit ce17d0859327591a66e8f7a4688352cb9fe447e6 Author: Weiqun Zhang Date: Thu Jun 14 11:22:02 2018 -0700 add a new eb_average_down Src/Base/AMReX_FabArray.H Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 6b4fa3926cfcc3cfd873af6d623a8da84713fcb2 Author: Michael Zingale Date: Thu Jun 14 13:24:49 2018 -0400 fix the case where a sig is on a line to itself Tools/F_scripts/write_cuda_headers.py commit 9bcaeaac67c55724324db58f996339d242752e35 Author: Weiqun Zhang Date: Thu Jun 14 10:10:32 2018 -0700 EB MLMG: normalize Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 98f07f8bdf61808edc70b6365288ee8651accd2d Author: Michael Zingale Date: Thu Jun 14 11:53:48 2018 -0400 restore file that my script overwrote :( Src/Base/AMReX_BaseFab_f.H commit a1c3b6ebe9702afcf5cbc13f64f1f15e0fe9e6c4 Author: Michael Zingale Date: Thu Jun 14 11:50:25 2018 -0400 weren't storing preprocessed headers Src/Base/AMReX_BaseFab_f.H Tools/F_scripts/write_cuda_headers.py commit 81a89ccd4baf4c6e1122ab55e16e572b71746905 Author: Michael Zingale Date: Thu Jun 14 10:27:18 2018 -0400 fix the preprocessing Tools/F_scripts/preprocess.py Tools/GNUMake/Make.rules commit 790fbfa82e734d82c4ab8b257914d965f697851a Author: Michael Zingale Date: Wed Jun 13 21:49:08 2018 -0400 the new preprocess version of the script. Doesn't work yet Tools/F_scripts/preprocess.py Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.rules commit 0920e3eb813c9f63a2a2639801c44c5964442e18 Merge: 3ad37a483 977b56196 Author: Andrew Myers Date: Wed Jun 13 17:32:50 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3ad37a4838e3271bd95ce66e0186e064b02eea9a Author: Andrew Myers Date: Wed Jun 13 17:32:38 2018 -0700 update NeighborList Tutorial Tutorials/Particles/NeighborList/NeighborListParticleContainer.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp commit eb2534b73a961b4c5801bdd6fa67c4e6e2bcc13a Author: Andrew Myers Date: Wed Jun 13 17:32:18 2018 -0700 use a template rather than a virtual function for checking particle pairs. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 7378fc21f92f9fdbee4eb6ea374d50fd2043db06 Author: Weiqun Zhang Date: Wed Jun 13 17:03:37 2018 -0700 EB MLMG: gsrb Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 9c654f7b2da0f1bce7cc40027bdeff597293d83d Author: Kevin Gott Date: Wed Jun 13 19:06:56 2018 -0400 HeatEquation_EX_1 works with USE_CUDA=FALSE in 2D and 3D, with global kernels in C and passing by value. Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit a9cc14447239973c762309114f09878051189ca7 Author: Kevin Gott Date: Wed Jun 13 19:02:37 2018 -0400 Remove unnecessary #ifdefs around GeometryData object. Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp commit d3bd569284f405e6d6d0267ca2c26c901a06bb4f Author: Kevin Gott Date: Wed Jun 13 19:01:34 2018 -0400 CUDA function wrappers for USE_CUDA=FALSE. Src/Base/AMReX_Managed.H commit 097bf738c6983e0e7bb02d2fcefb7da18755d18d Author: Kevin Gott Date: Wed Jun 13 19:00:57 2018 -0400 Creation and implementation of amrex_simpleArray to allow HOST DEVICE function declaration on macros. Src/Base/AMReX_ArrayLim.H commit ba0c9fb1f76759197410de144fadb7fffbeb5126 Author: Weiqun Zhang Date: Wed Jun 13 13:59:01 2018 -0700 EB MLMG: adotx and factories Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit d9eb28e33fb9ea73c7d28607b6c25d6cff8bb394 Author: Michael Zingale Date: Wed Jun 13 15:48:06 2018 -0400 split the preprocessor out for reuse Tools/F_scripts/dep.py Tools/F_scripts/preprocess.py commit 977b5619619c3da501d4e5dfac1d3bfec64d31bc Author: Weiqun Zhang Date: Wed Jun 13 12:20:10 2018 -0700 eb/cns: more udpates of inputs Tutorials/EB/CNS/Exec/Pulse/inputs Tutorials/EB/CNS/Exec/Pulse/inputs.regt Tutorials/EB/CNS/Exec/ShockRef/aniso.inputs Tutorials/EB/CNS/Exec/Sod/inputs commit d35a4e5067f20cafe06f492422650288aa68e903 Merge: 04549eae4 de0ec91c7 Author: Weiqun Zhang Date: Wed Jun 13 11:21:28 2018 -0700 Merge branch 'eb2' into weiqun/mlmg commit de0ec91c7de95f7fccbb991fc96e0e74f3dbae7b Author: Weiqun Zhang Date: Wed Jun 13 11:20:22 2018 -0700 eb/cns: update inputs Tutorials/EB/CNS/Exec/Combustor/benchmark.inputs Tutorials/EB/CNS/Exec/Combustor/inputs Tutorials/EB/CNS/Exec/Combustor/inputs.regt Tutorials/EB/CNS/Exec/Combustor/inputs.testing Tutorials/EB/CNS/Exec/Combustor/inputs_combustor Tutorials/EB/CNS/Exec/Pulse/inputs Tutorials/EB/CNS/Exec/Pulse/inputs.regt Tutorials/EB/CNS/Exec/ShockRef/aniso.inputs Tutorials/EB/CNS/Exec/ShockRef/inputs Tutorials/EB/CNS/Exec/ShockRef/inputs.amr Tutorials/EB/CNS/Exec/ShockRef/inputs.regt commit 18edc0d6b7c097e3626281393bfdd707f32abe92 Author: Weiqun Zhang Date: Wed Jun 13 09:55:26 2018 -0700 Fortran: add max_coarsening_level Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_poisson_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_poisson_mod.F90 Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit 30e9cb1233f08015f438af5a88c2af119480505b Author: Weiqun Zhang Date: Wed Jun 13 09:45:34 2018 -0700 Fortran: add multigrid % set_bottom_solver Src/F_Interfaces/LinearSolvers/AMReX_multigrid_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90 Tutorials/LinearSolvers/ABecLaplacian_F/GNUmakefile Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit 04549eae4d8a710ac05a7d5b42b8e4e9c5f3c406 Merge: d649d542d 8d1159da6 Author: Weiqun Zhang Date: Wed Jun 13 08:59:22 2018 -0700 Merge branch 'eb2' into weiqun/mlmg commit 8d1159da68cdf7347c996cea6d771fa1bcdf0f00 Author: Weiqun Zhang Date: Wed Jun 13 08:58:49 2018 -0700 fix typo Src/AmrTask/tutorials/MiniApps/HeatEquation/myfunc_F.H Tests/ProfTests/HeatEquation_EX1_C/Source/myfunc_F.H Tests/ProfTests/ThirdParty/Source/myfunc_F.H Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc_F.H Tutorials/Basic/HeatEquation_EX2_C/Source/myfunc_F.H Tutorials/Basic/HeatEquation_EX3_C/Source/myfunc_F.H Tutorials/CVODE/EX1/myfunc_F.H Tutorials/CVODE/EX2/myfunc_F.H commit de68b939f6550a60357adb0271a663c719f94533 Author: Weiqun Zhang Date: Wed Jun 13 08:54:36 2018 -0700 add init eb2 in a new file Tutorials/EB/CNS/Source/CNS_init_eb2.cpp commit d649d542d499f8888d0be997f9e4333424a33174 Merge: fb9301b0e e9ef06614 Author: Weiqun Zhang Date: Tue Jun 12 20:49:41 2018 -0700 Merge branch 'eb2' into weiqun/mlmg commit e9ef066148dd3bb4d6491fb6f2702249fc13b5ec Author: Weiqun Zhang Date: Tue Jun 12 20:49:09 2018 -0700 add required coarsening level Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IndexSpaceI.H Tests/EBEB2/MyTest.cpp Tutorials/EB/CNS/Source/main.cpp commit 1e792ca0550ec89521d9b91486f33c0e541bcdb5 Merge: 92b8b2880 c91327992 Author: Max Katz Date: Tue Jun 12 20:12:43 2018 -0700 Merge branch 'development' into gpu commit 92b8b28806454216c000aa2805fadedbff7bdd8f Author: Michael Zingale Date: Tue Jun 12 22:53:40 2018 -0400 can't have CPP_sources be a dependency for write_cuda_headers.py since it now writes the CPP sources in a new location Tools/GNUMake/Make.rules commit 75747e5e7ee449f572cdd80a69f70729ee416e41 Author: Michael Zingale Date: Tue Jun 12 21:42:26 2018 -0400 this does the C++ #pragma expansion still need to hook it into the vpath Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.rules commit fb9301b0eadb39adb2dbce3b886800a48c03726c Author: Weiqun Zhang Date: Tue Jun 12 17:13:05 2018 -0700 EBABecLap: start adotx Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H commit 808daab0d4de60344db433acd82ec0f9cae3428d Author: Max Katz Date: Tue Jun 12 15:41:50 2018 -0700 Use #pragma gpu Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_BaseFab.cpp Tutorials/GPU/HeatEquation_EX1_C/advance.cpp commit 6a53de62c46d7058d6af2c85c35bb04d09e4a106 Author: Weiqun Zhang Date: Tue Jun 12 14:56:50 2018 -0700 EBABecLap: prepare for solve Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 7758b651c66e0446accb43e16ca8cafe9a0b68b0 Author: Weiqun Zhang Date: Tue Jun 12 13:58:43 2018 -0700 stubs Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp commit 00ca0c1e48ba0e384db4632fba7a511370a6f30b Author: Kevin Gott Date: Tue Jun 12 16:26:54 2018 -0400 Pass GeometryData by class. Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit 12af51db2f3a87eac4be3df32c1770f3ccb6d371 Author: Kevin Gott Date: Tue Jun 12 16:13:19 2018 -0400 Add Pinned version of memory for passing small constant objects to kernels. Used on GeometryData. Src/Base/AMReX_Geometry.H Src/Base/AMReX_Managed.H commit 455251da435651e334dfe8d76bc20360e5a6b598 Author: Weiqun Zhang Date: Tue Jun 12 13:04:08 2018 -0700 it's possible to have only one cut Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit 37fa21318a530540d507f00df910d1ae6f67de68 Author: Weiqun Zhang Date: Tue Jun 12 13:04:08 2018 -0700 it's possible to have only one cut Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit 3b3d9768a335afc0d1acba87793363a4f3d025a3 Merge: 6e47684b1 1a65e4f40 Author: Weiqun Zhang Date: Tue Jun 12 12:27:51 2018 -0700 Merge branch 'weiqun/eb2' into weiqun/mlmg commit 6e47684b153ab6273e7db2daf9038c314bb97935 Merge: a418fc420 c91327992 Author: Weiqun Zhang Date: Tue Jun 12 12:27:35 2018 -0700 Merge branch 'development' into weiqun/mlmg commit a8dd4a119a666ae56ffc35bfba9dcb96dd04e6ef Author: Kevin Gott Date: Tue Jun 12 15:20:17 2018 -0400 Change HeatEquation_EX1 to pass Box by class to C++ based wrapper kernel. Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.f90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.f90 Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H commit 981703ab025b15fcc77b891e5de1a0c55aa322e4 Author: Kevin Gott Date: Tue Jun 12 15:18:30 2018 -0400 Testing passing Box into kernel by class. Tutorials/GPU/HelloWorld_C/main.cpp commit 1a65e4f403a34072b2de19045fc00d29eb8915fe Author: Weiqun Zhang Date: Tue Jun 12 12:18:14 2018 -0700 EB/CNS: set support level before initializing EB2 Tutorials/EB/CNS/Exec/Sod/inputs Tutorials/EB/CNS/Source/main.cpp commit 2838926ffaaa1833d9870c731f6d35286ea30473 Author: Kevin Gott Date: Tue Jun 12 15:17:43 2018 -0400 Declaring a few more function __host__ __device__. Src/Base/AMReX_Geometry.H Src/Base/AMReX_RealBox.H commit 4f4c38f70a47b218d67918e81ff83e0e0e6b4e3d Author: Max Katz Date: Tue Jun 12 14:27:15 2018 -0400 AMREX_ARLIM_VAL is no longer required Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_filcc_f.H Tools/F_scripts/write_cuda_headers.py Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H commit c913279929d9d4cf50678cc47051c088aa2c11d4 Merge: a3c05a5e8 28f4871bf Author: Weiqun Zhang Date: Tue Jun 12 10:42:36 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 28f4871bfde5ce3a4822dc7784788ee3f3d8da50 Merge: ea2111e49 c86968ee7 Author: Andrew Myers Date: Tue Jun 12 10:27:30 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ea2111e498a22fa22af83feeb42c59470406511b Author: Andrew Myers Date: Tue Jun 12 10:27:12 2018 -0700 just have Make.ccse refer to Make.unknown - should work on both updgraded and non-updated ccse machines. Tools/GNUMake/sites/Make.ccse commit a3c05a5e852db9f5b1ba1137a35c0b0452879d42 Author: Weiqun Zhang Date: Tue Jun 12 10:15:54 2018 -0700 fix make of the eb levelset test Tutorials/EB/LevelSet/Exec/GNUmakefile commit c808597bc4ba2380bc74c038818339fe18cc46bb Author: Weiqun Zhang Date: Tue Jun 12 09:48:20 2018 -0700 no need to have USE_EB2 Tools/GNUMake/Make.defs commit 52e39f36ae94ab3bbdbed66746deedbc4c0ee20b Author: Weiqun Zhang Date: Tue Jun 12 09:39:38 2018 -0700 add EB2 to cmake Src/CMakeLists.txt Src/EB2/CMakeLists.txt commit 82399816546a78e1df9fdcf8a8ccb23eb23ae7fc Author: Max Katz Date: Tue Jun 12 12:24:19 2018 -0400 Move a device sync to the right place Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H commit 0dee977490481c228f1ac5c42a5a60a10c5be352 Merge: 47212bd47 c86968ee7 Author: Weiqun Zhang Date: Tue Jun 12 09:19:07 2018 -0700 Merge branch 'development' into weiqun/eb2 commit 45d2dad864c68b005cd231f63bf2b4218ca900c2 Author: Max Katz Date: Tue Jun 12 11:57:58 2018 -0400 Cover some more Box functions, for safety Src/Base/AMReX_Box.H commit 8e5ffefa29527fde99e032895844e8c66be8e7e5 Author: Max Katz Date: Tue Jun 12 11:48:12 2018 -0400 Use the FA arena Src/Base/AMReX_FabArrayCommI.H commit e07b2b399cb804403b994ec3e237a2565f3d766b Author: Max Katz Date: Mon Jun 11 20:38:33 2018 -0400 Fix indexing issue in copyfrommem Src/Base/AMReX_BaseFab_nd.F90 commit 47212bd47b0798231cf836aa3eb6a1c98420f004 Author: Weiqun Zhang Date: Mon Jun 11 17:28:13 2018 -0700 add all_regular Src/AmrCore/AMReX_AmrMesh.cpp Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IF_AllRegular.H Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/Make.package Tutorials/EB/CNS/Exec/Sod/inputs Tutorials/EB/CNS/Source/CNS_init_eb.cpp Tutorials/EB/CNS/Source/Make.package Tutorials/EB/CNS/Source/main.cpp commit e0aa9e149c90a667b27a00046ab1a815a58e898f Author: Max Katz Date: Mon Jun 11 18:28:05 2018 -0400 Fix offsets in copytomem/copyfrommem Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit 57400ede3ba9290984705b2b60b5c9a59b9267f9 Merge: 62b824e13 799306734 Author: Weiqun Zhang Date: Mon Jun 11 15:47:41 2018 -0700 Merge branch 'development' into weiqun/eb2 commit b91ab9e6733edd5f7284fbb670cc40ca20eb4ea8 Author: Max Katz Date: Mon Jun 11 17:14:27 2018 -0400 Use AMREX_ARLIM_3D Src/Base/AMReX_ArrayLim.H commit c86968ee71904d28f1faf79adad705910366de11 Merge: 799306734 f8d5ffcb9 Author: WeiqunZhang Date: Mon Jun 11 13:39:54 2018 -0700 Merge pull request #274 from jaharris87/development Add interface for character bcast to F_BaseLib commit 3ece180c5a8bacda771f40bfba8359c253d8f5b5 Merge: 1009ee6ed 0bfa3a4ed Author: Max Katz Date: Mon Jun 11 16:26:50 2018 -0400 Merge branch 'development' into gpu commit 62b824e1312c574a927512f5e9e5b53728e6b5dc Author: Weiqun Zhang Date: Mon Jun 11 13:20:41 2018 -0700 coarsen valid cells only Src/EB/AMReX_EBCellFlag.H Src/EB2/AMReX_EB2_Level.cpp Tests/EBEB2/inputs commit 7993067348a411a4a4bff7714cf1952bb82989cd Merge: 035837741 0bfa3a4ed Author: Andrew Myers Date: Mon Jun 11 13:14:03 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 03583774129f8c56e5c37e2df6524ef075f4e0f2 Author: Andrew Myers Date: Mon Jun 11 13:13:52 2018 -0700 clean up CreateGhost and CreateVirtualParticles Src/Particle/AMReX_ParticleContainerI.H commit 76cc65b31d16b2e8285e291f638669f6415ecf49 Author: Andrew Myers Date: Mon Jun 11 13:11:15 2018 -0700 remove unused static member of RealVect Src/Base/AMReX_RealVect.H commit 3667e65281d6789d657455bca44f339b7e8e1d9a Author: Andrew Myers Date: Mon Jun 11 13:01:10 2018 -0700 silence another warning Src/Particle/AMReX_ParticleContainerI.H commit 3196211a503862d25ac39204664645c695a5d2fc Author: Andrew Myers Date: Mon Jun 11 12:58:14 2018 -0700 silence unused variable compiler warning Src/Particle/AMReX_ParticleContainerI.H commit f8d5ffcb922cf50bfbc9226e831eb80420c5e452 Author: Harris, James Austin Date: Mon Jun 11 15:25:22 2018 -0400 Add interface for character bcast to F_BaseLib Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit 0bfa3a4eddc66bb4e82234e06347b153a946ea71 Merge: 8c77a1f24 15316047f Author: Daniel Ladiges Date: Mon Jun 11 10:36:05 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 8c77a1f24e76ebcc47774225c4941c4b98a17779 Author: Daniel Ladiges Date: Mon Jun 11 10:30:45 2018 -0700 Added bl_random_.f90 bl_random_c.cpp bl_random_c.H to make package Src/F_BaseLib/FParallelMG.mak commit 24bb21d11e1d8340533d443cf8f198f3924ae839 Author: Kevin Gott Date: Mon Jun 11 00:37:42 2018 -0400 GeomData into all kernels. Requires non-const Geometry in advance.cpp function call in current form. Src/Base/AMReX_Geometry.H Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H commit 1009ee6ed5d2a8942512ed2345a958ba511544e5 Author: Max Katz Date: Sun Jun 10 21:48:45 2018 -0400 Sync up with the original heat equation example Tutorials/GPU/HeatEquation_EX1_C/main.cpp Tutorials/GPU/HeatEquation_EX1_C/physbc.cpp commit 5e5b8d08dff46e60c5a777ff01393bac5ad25a50 Author: Max Katz Date: Sun Jun 10 21:43:27 2018 -0400 Complete removal of amrex_fort_launch (except PIC) Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_filcc_f.H Src/Base/AMReX_filcc_mod.F90 Tutorials/GPU/HeatEquation_EX1_C/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H commit 8adc4080466783a8ac345183aa824a24622bcccb Author: Max Katz Date: Sun Jun 10 21:17:19 2018 -0400 Finish BaseFab Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit c008c3fd4c96f7de0f10bbabee1e12329b9f05e6 Author: Max Katz Date: Sun Jun 10 20:49:33 2018 -0400 Convert more BaseFab to new launch mechanism Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit 75b7fbffdc0b2f2772914ca533913aeb63ccb407 Author: Weiqun Zhang Date: Sat Jun 9 13:58:44 2018 -0700 fix bug in 3d cell flag Src/EB2/AMReX_eb2_3d.F90 Tests/EBEB2/MyTest.cpp commit 2966ec2e3e0c94d30a3e0a401e378ee7754af4f1 Author: Weiqun Zhang Date: Sat Jun 9 13:16:56 2018 -0700 ignore cells outside domain for cellflagfab type Src/EB2/AMReX_EB2_Level.cpp Tests/EBEB2/GNUmakefile commit 15316047fb4f84c0f4fb3790da808147ed089906 Merge: 5c7dfc136 da5a679b7 Author: WeiqunZhang Date: Sat Jun 9 12:24:21 2018 -0700 Merge pull request #266 from AMReX-Codes/f_interfaces_particles Adding some particle support to the F_Interfaces commit a50b4b57b840167e4c28b54249e294d0c4da442c Author: Weiqun Zhang Date: Fri Jun 8 22:53:05 2018 -0700 typo Tests/EBEB2/GNUmakefile Tests/EBEB2/initEB.cpp commit 8f28fe5acbff1beb3c24b745f320cb1151b8b7ab Author: Weiqun Zhang Date: Fri Jun 8 22:10:08 2018 -0700 set default value fo boundary centroid to -1 for consistence with the old implementation Tests/EBEB2/MyTest.cpp Tests/EBEB2/inputs commit da5a679b7d8dee82cb759405c27bb21ba2e7ca74 Merge: f24f2f36f d9d9cbfa2 Author: Andrew Myers Date: Fri Jun 8 21:54:10 2018 -0700 Merge branch 'f_interfaces_particles' of github.com:AMReX-Codes/amrex into f_interfaces_particles commit f24f2f36f8261e6deba8b1b0dbba35f6f72fa84d Author: Andrew Myers Date: Fri Jun 8 21:53:00 2018 -0700 simplify logic in advection kernels Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_F/Source/Src_3d/Adv_3d.f90 commit e82689d44bc8341eb73e02a2334ac5cd684b5259 Author: Weiqun Zhang Date: Fri Jun 8 21:49:06 2018 -0700 zero out neighbors for covered cells Src/EB/AMReX_EBCellFlag.H commit f6e64e193c53a34d49158f34626d020fad58f41b Author: Cyrus Harrison Date: Fri Jun 8 17:07:17 2018 -0700 initial ascent integration Src/Base/AMReX_Conduit_Blueprint.cpp Tests/Blueprint/AssignMultiLevelDensity/GNUmakefile Tests/Blueprint/AssignMultiLevelDensity/main.cpp Tests/Blueprint/HeatEquation_EX1_C/Exec/GNUmakefile Tests/Blueprint/HeatEquation_EX1_C/Source/main.cpp commit d65187b60ddb74ba27a2aabfc6069fd8ced93c69 Author: Weiqun Zhang Date: Fri Jun 8 17:06:28 2018 -0700 fix the check for multi-cuts Src/EB2/AMReX_eb2_2d.F90 commit ac9186e515c9161c80a164cbe5f01804cb025fca Author: Weiqun Zhang Date: Fri Jun 8 16:33:45 2018 -0700 add plane to test Tests/EBEB2/initEB.cpp Tests/EBEB2/inputs commit 107a8a34b09adace462aa63199e337b09892fc4e Author: Weiqun Zhang Date: Fri Jun 8 16:08:44 2018 -0700 buid cell flags from aperture Src/EB/AMReX_ebcellflag_mod.F90 Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 Tests/EBEB2/MyTest.cpp commit 3c6f973e4fe8a15628ed25bd7770fac2008a78ed Author: Weiqun Zhang Date: Fri Jun 8 14:30:14 2018 -0700 fix coarsening Src/EB2/AMReX_eb2_2d.F90 commit a573f92a41e266ef63c729542d4032352a666d99 Author: Weiqun Zhang Date: Fri Jun 8 14:20:19 2018 -0700 bug fix Src/EB/AMReX_EBTower.cpp Src/EB2/AMReX_eb2_2d.F90 Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Tests/EBEB2/MyTest.H Tests/EBEB2/MyTest.cpp Tests/EBEB2/initEB.cpp Tests/EBEB2/inputs commit 079c2071c6a218bac855a9e4a9a688f25b61a0e2 Author: Andrew Myers Date: Fri Jun 8 12:32:15 2018 -0700 convert this logical to a c_int Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 commit 626bb836d3a89e4de5faa2fdd12a6563e26b9227 Author: Andrew Myers Date: Fri Jun 8 12:26:48 2018 -0700 use nullptr instead of NULL Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp commit 610c19f5123d8f0a6315064644ec972eaf0ed20e Author: Andrew Myers Date: Fri Jun 8 12:24:34 2018 -0700 this doesn't need to be a target Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 commit 9dc6f43547d6b59529cd3ddb8df26bc37b3b92b9 Author: Andrew Myers Date: Fri Jun 8 12:21:15 2018 -0700 change name of these variables so as not to clash with Fortran built-ins Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 commit ceee7dbcc697f5817caf58e385a70d5e54ebe556 Author: Weiqun Zhang Date: Fri Jun 8 11:13:05 2018 -0700 avoid comparing domain boundary cells Src/EB2/AMReX_eb2_2d.F90 Tests/EBEB2/MyTest.cpp commit ae3e6beba77fc0df5b479a5adffa1259795ce194 Author: Max Katz Date: Fri Jun 8 11:02:46 2018 -0700 Start porting BaseFab to use the new launch mechanism Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit 314114acbdfd9f42b67170e142a32b2507b998e4 Author: Weiqun Zhang Date: Fri Jun 8 10:51:03 2018 -0700 zero out number of vofs for covered cell Src/EB/AMReX_ebcellflag_mod.F90 commit 9fe2e112155a393f9e00e44f1b849a5aaad99bec Author: Weiqun Zhang Date: Fri Jun 8 10:40:04 2018 -0700 change the default value of EBCellFlag in 2d for comparison Src/EB/AMReX_EBCellFlag.H commit 1e7be019484caa3f79e9de423a9790ca59de2006 Author: Cyrus Harrison Date: Fri Jun 8 10:34:19 2018 -0700 initial blueprint support Src/Base/AMReX_Conduit_Blueprint.H Src/Base/AMReX_Conduit_Blueprint.cpp Src/Base/Make.package Tests/Blueprint/AssignMultiLevelDensity/GNUmakefile Tests/Blueprint/AssignMultiLevelDensity/Make.package Tests/Blueprint/AssignMultiLevelDensity/inputs Tests/Blueprint/AssignMultiLevelDensity/main.cpp Tests/Blueprint/HeatEquation_EX1_C/Exec/GNUmakefile Tests/Blueprint/HeatEquation_EX1_C/Exec/inputs_2d Tests/Blueprint/HeatEquation_EX1_C/Exec/inputs_3d Tests/Blueprint/HeatEquation_EX1_C/Source/Make.package Tests/Blueprint/HeatEquation_EX1_C/Source/advance.cpp Tests/Blueprint/HeatEquation_EX1_C/Source/advance_2d.f90 Tests/Blueprint/HeatEquation_EX1_C/Source/advance_3d.f90 Tests/Blueprint/HeatEquation_EX1_C/Source/init_phi_2d.f90 Tests/Blueprint/HeatEquation_EX1_C/Source/init_phi_3d.f90 Tests/Blueprint/HeatEquation_EX1_C/Source/main.cpp Tests/Blueprint/HeatEquation_EX1_C/Source/myfunc.H Tests/Blueprint/HeatEquation_EX1_C/Source/myfunc_F.H Tests/Blueprint/README.txt Tools/GNUMake/Make.defs commit 060daa4023954e81039d7a917bd0368f52932ef3 Author: Weiqun Zhang Date: Fri Jun 8 10:32:39 2018 -0700 fix bug Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_eb2_2d.F90 commit 4453a0e6aa62e036895b4bdaeae17f8de58c5710 Author: Max Katz Date: Fri Jun 8 10:23:05 2018 -0700 16x16 seems to be better Src/Base/AMReX_Device.cpp commit 06b534962bc611b7d347a74e3da7726d556d5c65 Author: Kevin Gott Date: Fri Jun 8 13:21:55 2018 -0400 Initial GeometryData tests and implementation in HeatEquation_EX_1. Tutorials/GPU/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/run.script Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HelloWorld_C/GNUmakefile Tutorials/GPU/HelloWorld_C/inputs_geometry Tutorials/GPU/HelloWorld_C/main.cpp Tutorials/GPU/HelloWorld_C/run.script Tutorials/GPU/run.script commit c26e09047571ea7e0f1555424843b45bf0a5c78b Author: Kevin Gott Date: Fri Jun 8 13:19:56 2018 -0400 GeometryData object for CUDA managed memory. Src/Base/AMReX_Box.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_RealBox.H commit 1f906aceddb3e39f68513f20aff2d96943007ad7 Author: Max Katz Date: Fri Jun 8 09:47:37 2018 -0700 Switch to 32x8 thread layout Src/Base/AMReX_Device.cpp commit b3275961aa0d6d2a1c9e3ba497dcad6118cd4599 Author: Weiqun Zhang Date: Fri Jun 8 09:46:08 2018 -0700 for consistence, set boundary centroid to -1 for regular and cover cells Src/EB/AMReX_EBTower.cpp Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 Tests/EBEB2/MyTest.H Tests/EBEB2/MyTest.cpp Tests/EBEB2/initEB.cpp Tests/EBEB2/inputs commit 1d43380f0a648dd8aabaaf602bbc9d73f80891be Author: Max Katz Date: Thu Jun 7 20:33:20 2018 -0400 Need to pass an int by value Src/Base/AMReX_BaseFab_nd.F90 commit 60aeaea631b0675d816f7d9db701698ec5d54098 Author: Weiqun Zhang Date: Thu Jun 7 17:11:06 2018 -0700 parameter eb2.use_eb2 and function makeEBFabFactory Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArrayBase.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Tutorials/EB/CNS/Exec/Make.CNS commit 5c7dfc13652e52f93c824858f646b52634360682 Merge: 40dc889f6 554046be6 Author: Michele Rosso Date: Thu Jun 7 16:27:51 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 40dc889f658b504bed36c50006a11948b4f3c6a6 Author: Michele Rosso Date: Thu Jun 7 16:27:45 2018 -0700 Add C++ versions of fcompare and fextract Tools/Postprocessing/C_Src/fcompare.cpp Tools/Postprocessing/C_Src/fextract.cpp commit 542cab184722fadfa60e2143f5010ce3bd34490a Author: John Wakefield Date: Thu Jun 7 16:19:00 2018 -0700 Changed SWFFT max_sizes to be at least as large as inputs. Tutorials/SWFFT/inputs.128 commit d3f5782bd8de101ca7bb8f28e4392c431b7bdda4 Author: John Wakefield Date: Thu Jun 7 16:18:39 2018 -0700 Changed SWFFT max_sizes to be at least as large as inputs. Tools/C_util/AugmentPlotfile/AugFolder.sh Tools/C_util/AugmentPlotfile/GNUmakefile Tutorials/SWFFT/inputs.32 Tutorials/SWFFT/inputs.64 Tutorials/SWFFT/swfft_solver.cpp commit e86ac7f5fa329834b151b5bd007a8ecded161bce Author: Max Katz Date: Thu Jun 7 19:12:31 2018 -0400 Fix the block/thread override Src/Base/AMReX_Device.cpp commit 745fa508a53b4792cd949ff81027507b2c196735 Author: Weiqun Zhang Date: Thu Jun 7 15:52:03 2018 -0700 scale Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IF_Scale.H Src/EB2/Make.package Tests/EBEB2/MyTest.cpp commit bd18e0ba8e9cbd19ee9f502e3961307e0a023901 Author: Weiqun Zhang Date: Thu Jun 7 15:09:02 2018 -0700 add ellipsoid Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IF_Ellipsoid.H Src/EB2/Make.package commit 554046be6849eaab5ac54796416ee6d3049afdfb Author: Ann Almgren Date: Thu Jun 7 14:45:11 2018 -0700 Moved files from amrex/Tools/Postprocessing/F_Src/MAESTRO* into MAESTRO/Diagnostics. Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/fsubchandra.f90 Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/fsubchandra_mod.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_tests/fgaussianpulse.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/fmlcompare.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/fmlconverge.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/fnorm.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_wdconvect/feint.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fthermo.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fthermo_driver.py Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fwdconvect.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_xrb/fad_excess.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fbuoyancy.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fconv_slopes.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/frates.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fspec_total_mass.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fspeciesmass.f90 commit 4ec3a2c80cdb667dd734c4a1f41ce376edc731b3 Merge: 5149dd46e f68f76892 Author: Ann Almgren Date: Thu Jun 7 14:37:22 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 5149dd46e80d4f165e80c6f4767be1b4d641c5df Author: Ann Almgren Date: Thu Jun 7 14:36:49 2018 -0700 Moved amrex/Tools/Postprocessing/F_Src/CASTRO_radiation files out of amrex and into Castro itself Tools/Postprocessing/F_Src/CASTRO_radiation/GNUmakefile Tools/Postprocessing/F_Src/CASTRO_radiation/fgaussianpulse.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/flgt_frnt1d.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradshock.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradsource.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradsphere.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/frhdshocktube.f90 commit 9ba9ca24a646d0ce0ef4fb337eec5edfc942087f Author: Weiqun Zhang Date: Thu Jun 7 14:29:27 2018 -0700 some modification for comparison of the two implementations Src/EB/AMReX_EBTower.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Tests/EBEB2/inputs commit 9705234f3dc9ae0f9c2bd0a008484ffa9f5b046f Author: Weiqun Zhang Date: Thu Jun 7 13:56:00 2018 -0700 function to covert MultiCutFab to MultiFab Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp Tests/EBEB2/MyTest.cpp commit 75d05dae73abb2e2f2594873bb32df3f25410092 Author: Weiqun Zhang Date: Thu Jun 7 13:27:45 2018 -0700 fix return type Src/EB/AMReX_EBCellFlag.cpp Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp commit 3702230719cde4e62fe3d9a3c1889e4092fc4855 Author: Weiqun Zhang Date: Thu Jun 7 13:25:40 2018 -0700 fill boundary centroid, area fraction and face centtroid Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_WrappedGShop.cpp Tests/EBEB2/MyTest.cpp commit dd30c16bea6160e5524784550ac03e07c5fc732c Author: Max Katz Date: Thu Jun 7 12:48:15 2018 -0700 Handle the OpenMPI + CUDA case generally, not just for CORAL Tools/GNUMake/Make.defs Tools/GNUMake/sites/Make.llnl Tools/GNUMake/sites/Make.olcf commit b7632e1550908c53ce1b8359d73fb5918b9398ca Author: Weiqun Zhang Date: Thu Jun 7 12:38:36 2018 -0700 fix # of components for face centroid Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit 4baa5823c558d88a93f8328af763fe4659e0de1e Author: Weiqun Zhang Date: Thu Jun 7 12:01:31 2018 -0700 fix # of components Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBTower.cpp commit 7e24d35dfe055a603fcde83b57f25c099d65956f Author: Weiqun Zhang Date: Thu Jun 7 11:59:00 2018 -0700 fill centroid Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Tests/EBEB2/MyTest.H Tests/EBEB2/MyTest.cpp commit aa9be833d3e796e2022a506f10a29946d3857809 Author: Max Katz Date: Thu Jun 7 14:07:41 2018 -0400 Fix capitalization in a macro Src/Base/AMReX_Device.cpp commit 33d290bb4b6c3d5a37a68a0b02a9c97e9b717ef7 Author: Weiqun Zhang Date: Thu Jun 7 10:35:18 2018 -0700 fill cell flags Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBCellFlag.cpp Src/EB/AMReX_EBDataCollection.cpp Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Tests/EBEB2/MyTest.cpp commit f68f768929feb0dda9b5bc540de94f711e8e2e49 Merge: 1a9b49829 e6595fff3 Author: Brandon Runnels Date: Thu Jun 7 11:17:49 2018 -0600 Merge pull request #271 from AMReX-Codes/corner-fill-update updated corner fill for non-cross stencil to work in 3D as well as 2D commit e6595fff334ca5dfd0b8520047c91db829a47b0c Author: Brandon Runnels Date: Thu Jun 7 12:08:19 2018 -0500 updated corner fill for non-cross stencil to work in 3D as well as 2D Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 commit 6496b8dd8d811c0dddcdb360a7e1cffbffe4949c Author: Weiqun Zhang Date: Thu Jun 7 09:11:47 2018 -0700 make EB2:max_grid_size a ParmParse parameter Src/Base/AMReX.cpp Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IndexSpaceI.H Tests/EBEB2/MyTest.cpp commit 0c3284c99c758294a8a50d8192327f6f2050cde3 Author: Max Katz Date: Thu Jun 7 08:52:31 2018 -0700 Disable calls to memadvise for unsupported GPUs Src/Base/AMReX_Device.cpp commit f9084bd59d5edfc27f3a78cf502251001d840646 Author: Max Katz Date: Thu Jun 7 08:52:17 2018 -0700 Collect the CUDA device properties in C++ Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit ede1220858e68a8deb4b911e5235d7e9ab121d63 Author: Max Katz Date: Wed Jun 6 23:42:58 2018 -0400 Remove some more dependences on the tile box Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit d5809436dd115b86fdffe0b4da4e72cd225c0191 Author: Max Katz Date: Wed Jun 6 23:23:23 2018 -0400 Rewrite fab copy to avoid dependence on lo Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit dcfdedfef382a9e85d4f12144b338cbf13e9b9fd Merge: 887a2f4ed 1a9b49829 Author: Max Katz Date: Wed Jun 6 20:49:19 2018 -0400 Merge branch 'development' into gpu commit 887a2f4ed5f0b8cc0278d339b89a60657879c6b1 Merge: 2981d914f 5553b6af6 Author: Max Katz Date: Wed Jun 6 20:40:36 2018 -0400 Merge commit '5553b6af63da745ef13ecdb51654b72ec1cca544' into gpu commit d2ab5ad3d7f6524da5acd2717ae3152489c185ef Author: Weiqun Zhang Date: Wed Jun 6 17:40:11 2018 -0700 new EB factory Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Tests/EBEB2/MyTest.H Tests/EBEB2/MyTest.cpp Tests/EBEB2/initEB.cpp Tests/EBEB2/inputs commit c2a4f9e29d917f73737979b94c9cb833eefaa233 Author: Weiqun Zhang Date: Wed Jun 6 17:07:26 2018 -0700 move initEB to a new file Tests/EBEB2/Make.package Tests/EBEB2/MyTest.cpp Tests/EBEB2/initEB.cpp commit c94c9129dfc247351fb4ef6404f970107701ca57 Author: Weiqun Zhang Date: Wed Jun 6 16:15:27 2018 -0700 2d compiles Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_eb2_2d.F90 Tests/EBEB2/MyTest.H Tests/EBEB2/MyTest.cpp commit 1e6f92df26bbe7adc5a1f697f2d5c591b5417a86 Author: Weiqun Zhang Date: Wed Jun 6 15:18:39 2018 -0700 coarsen geometry Src/EB/AMReX_ebcellflag_mod.F90 Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_IndexSpaceI.H Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/AMReX_EB2_MultiGFab.H Src/EB2/AMReX_EB2_MultiGFab.cpp Src/EB2/AMReX_eb2_3d.F90 Tests/EBEB2/MyTest.H Tests/EBEB2/MyTest.cpp Tests/EBEB2/inputs commit 54315194d35e884eca51199e26b98914771c5024 Author: Kevin Gott Date: Wed Jun 6 17:58:48 2018 -0400 Turn on advance and change bc vector to HostAllocator. Tutorials/GPU/HeatEquation_EX2_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX2_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX2_C/Source/myfunc.H commit 3f9ea83fe13ad2b1dfc11a9b8c584a611d88b56a Author: Kevin Gott Date: Wed Jun 6 17:58:10 2018 -0400 Add CudaHostAllocator for cudaMallocHost based Vectors. Src/Base/AMReX_BCRec.H Src/Base/AMReX_CudaAllocators.H commit 2981d914f073e16090190a4649ff3451da75c067 Author: Max Katz Date: Wed Jun 6 14:47:24 2018 -0700 Add a registerBox hook for new growntilebox Src/Base/AMReX_MFIter.cpp commit fffe5c5be22d6189187ea42e5b3810fab5169243 Author: Kevin Gott Date: Wed Jun 6 17:03:22 2018 -0400 HeatEquation_EX2_C with BCs and managed vector running with small problem. Also awaiting features for further improvement. Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCUtil.H Src/Base/AMReX_BCUtil.cpp Tutorials/GPU/HeatEquation_EX2_C/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX2_C/Exec/inputs_2d Tutorials/GPU/HeatEquation_EX2_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX2_C/Source/Make.package Tutorials/GPU/HeatEquation_EX2_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX2_C/Source/advance_2d.f90 Tutorials/GPU/HeatEquation_EX2_C/Source/advance_3d.f90 Tutorials/GPU/HeatEquation_EX2_C/Source/init_phi_2d.f90 Tutorials/GPU/HeatEquation_EX2_C/Source/init_phi_3d.f90 Tutorials/GPU/HeatEquation_EX2_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX2_C/Source/myfunc.H Tutorials/GPU/HeatEquation_EX2_C/Source/myfunc_F.H commit d04171640ab69916ceba80014e3d35ce6e14762a Author: Max Katz Date: Wed Jun 6 14:01:21 2018 -0700 Avoid non amrex-prefixed macros Src/Amr/AMReX_Amr.cpp Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_FILCC_1D.F90 Tools/F_scripts/write_cuda_headers.py commit 2eb3d4cf6bd2742229651e7da4342853deec06fe Author: Kevin Gott Date: Wed Jun 6 16:59:49 2018 -0400 CudaAllocators for Vector CUDA memory management. Src/Base/AMReX_CudaAllocators.H Src/Base/AMReX_Vector.H Src/Base/Make.package commit 75ded4a7d065bee7c09ae9b1b412817174d338f3 Author: Kevin Gott Date: Wed Jun 6 16:56:56 2018 -0400 Improved HeatEquation_EX_1 for larger problem. Awaiting features for further improvement. Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit 5153fcb2110e5b0ded6f7f0886ce43adeeacf050 Author: Max Katz Date: Wed Jun 6 10:36:44 2018 -0700 Correct summitdev MPI setup in F_mk Tools/F_mk/GMakeMPI.mak commit 32445f53499b9ed24c46af27afcfc034b9f27fab Author: Max Katz Date: Wed Jun 6 10:35:38 2018 -0700 Update LLNL MPI setup Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.llnl commit 3489ff1c2a854e33481a87ba094216b805bf1382 Author: Kevin Gott Date: Wed Jun 6 13:02:07 2018 -0400 Clean up Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit 9b4f9a0ac209623e8c764596e35f8fbd16898f39 Author: Weiqun Zhang Date: Wed Jun 6 08:43:31 2018 -0700 eb cell flags Src/EB/AMReX_ebcellflag_mod.F90 Src/EB2/AMReX_EB2_MultiGFab.H Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 Tests/EBEB2/MyTest.cpp commit 73af4e4c223a0890e51bb2188fcb0eaf1054236e Author: Kevin Gott Date: Wed Jun 6 11:40:09 2018 -0400 HeatEquation_EX1 first draft. Running with kernels. Needs threads and blocks setup. Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.f90 Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H commit 9cc89f72e35f8f2828d41ec47828925c251ec913 Author: Max Katz Date: Tue Jun 5 19:31:57 2018 -0400 Include amrex_ macros Tools/F_scripts/write_cuda_headers.py commit 858e18b0430bf082f734fc4a94ed2379b3c8ca76 Author: Max Katz Date: Tue Jun 5 19:31:37 2018 -0400 Use basename to avoid bug in find_files_vpath Tools/F_scripts/find_files_vpath.py commit 3b2480477c6aeff46a08a306ddeb9e7c5d5ca54c Author: Max Katz Date: Tue Jun 5 19:00:54 2018 -0400 Catch amrex_arlim_val too Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.rules commit 3c40fe4dc5b3cecfd3cf1babd328096fa8452527 Author: Max Katz Date: Tue Jun 5 18:57:35 2018 -0400 Fix the header class for basefab Src/Base/Make.package commit 2aea7658705b00d5150ae652195ec7d7458e4af9 Author: Max Katz Date: Tue Jun 5 18:57:11 2018 -0400 Add amrex_arlim_rep Src/Base/AMReX_ArrayLim.H commit 86f108e999bbe6c58981f2f4a372320b643568bc Author: dwillcox Date: Tue Jun 5 18:31:28 2018 -0400 Pass IFABs by value in write_cuda_headers.py Tools/F_scripts/write_cuda_headers.py commit c2e8fcb0847ff3fb7391faeeeb9d8fb7fe6eeca9 Merge: 789707522 72ad4d351 Author: dwillcox Date: Tue Jun 5 18:17:58 2018 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 7897075225b77ee75135c7017437ddecc3065e90 Author: dwillcox Date: Tue Jun 5 18:17:53 2018 -0400 Fix bound subroutine searching in write_cuda_headers.py Tools/F_scripts/write_cuda_headers.py commit 1a9b498295d9a5411881798aead2bcbae439ee0a Merge: dd8a3ec84 fc4f6aa90 Author: Weiqun Zhang Date: Tue Jun 5 15:12:45 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit dd8a3ec845bad1535ca83a80304b3ab471eb6b33 Author: Weiqun Zhang Date: Tue Jun 5 15:11:36 2018 -0700 fix a new bug in amrex_pd_bcast Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParallelDescriptor_F.F90 commit 9cdf5f52c49f72139a58a2d52df00f098e4ca2e6 Author: Weiqun Zhang Date: Tue Jun 5 15:11:36 2018 -0700 fix a new bug in amrex_pd_bcast Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParallelDescriptor_F.F90 commit 72ad4d351afe019ff3ae64088d3dc45a66785197 Merge: 73bd3882b 54bc01a08 Author: Max Katz Date: Tue Jun 5 17:58:11 2018 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 54bc01a0897ffb00282aa19e5a9f456038389f67 Author: dwillcox Date: Tue Jun 5 17:19:38 2018 -0400 Fix target finding bug in write_cuda_headers.py Tools/F_scripts/write_cuda_headers.py commit 3699fc25f5b2d2514051bc16e099623286df1ae4 Author: dwillcox Date: Tue Jun 5 17:17:28 2018 -0400 Make the function signature error verbose for write_cuda_headers.py Tools/F_scripts/write_cuda_headers.py commit 73bd3882be8ab3cc9e061a43cb70897ff0ddb2f9 Merge: 5ca335268 bd6b94802 Author: Max Katz Date: Tue Jun 5 15:34:29 2018 -0400 Merge commit 'bd6b948020e9dbce9c347fd66aead8da6cfcfe39' into gpu commit 5ca3352688f5610593a378cecc8dec9e6ace8dc1 Merge: 5b3672b26 ce70eec0b Author: Max Katz Date: Tue Jun 5 15:25:04 2018 -0400 Merge commit 'ce70eec0b05dd8fc390ee14b578702323263d082' into gpu commit 2d73758c9bd31bf627d1d13128d24aeea3353151 Merge: 6a1376b3e fc4f6aa90 Author: Cy Chan Date: Tue Jun 5 12:19:55 2018 -0700 Merge branch 'development' into forkjoin commit 6a1376b3e7398cb4c23354dbf2bee8bab2924776 Author: Cy Chan Date: Mon May 14 15:56:40 2018 -0700 forkjoin: modify Print.H to redirect task output to files default behavior unchanged added ParallelContext frame ID, IO filename, and ostream pointer OldTutorials/MultiColor_C/main.cpp Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelContext.cpp Src/Base/AMReX_Print.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit fc4f6aa90fcf0f915208823f50994da44fbe8cca Author: Ann Almgren Date: Tue Jun 5 11:43:34 2018 -0700 1) Replace . by --> (gnu allowed this but pgi caught it) 2) remove unused variable Src/GeometryShop/AMReX_IFSlicerImplem.H Src/GeometryShop/AMReX_WrappedGShop.cpp commit 1d4655bc6d840d72017ab8442c05590c205f70d1 Author: Kevin Gott Date: Tue Jun 5 14:26:48 2018 -0400 HeatEqu cleanup Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp commit 5b3672b2630959e8ac81082ed20b5a07e79cac99 Author: Max Katz Date: Tue Jun 5 13:00:54 2018 -0400 Temp headers depend on all Fortran sources Tools/GNUMake/Make.rules commit 7224b6903dcbb1bcf3c95b6bb3efc402515955f9 Author: Kevin Gott Date: Tue Jun 5 12:16:48 2018 -0400 First draft of kernel in HeatConduction Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 Tools/GNUMake/Make.defs Tutorials/GPU/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_2d Tutorials/GPU/HeatEquation_EX1_C/Exec/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/Source/Make.package Tutorials/GPU/HeatEquation_EX1_C/Source/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/advance_2d.f90 Tutorials/GPU/HeatEquation_EX1_C/Source/advance_3d.f90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_2d.f90 Tutorials/GPU/HeatEquation_EX1_C/Source/init_phi_3d.f90 Tutorials/GPU/HeatEquation_EX1_C/Source/main.cpp Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/Source/myfunc_F.H Tutorials/GPU/HelloWorld_C/main.cpp commit b3a34e31b51ba17c9d8261b42722630a2dc143e9 Author: Max Katz Date: Tue Jun 5 10:59:52 2018 -0400 Really always re-execute the temp CUDA header rule, and also avoid infinite loops Tools/GNUMake/Make.rules commit 1bc1a6751c0f35deaadc95dc50f600df63705551 Author: Max Katz Date: Tue Jun 5 10:50:44 2018 -0400 Revert "Always re-execute the temp CUDA header rule" This reverts commit 71bb5df8d167dd78b95113c7f108112af280df2c. Tools/GNUMake/Make.rules commit 71bb5df8d167dd78b95113c7f108112af280df2c Author: Max Katz Date: Tue Jun 5 10:33:50 2018 -0400 Always re-execute the temp CUDA header rule Tools/GNUMake/Make.rules commit c8dbb1867d6e7e0f75c7f9c6efe9670a68c83296 Author: Max Katz Date: Tue Jun 5 00:05:44 2018 -0400 Fix the device launch macro token concatenation Src/Base/AMReX_BLFort.H commit a3c064ec60993d4f8e0f4a08958a00dd1566607d Author: Weiqun Zhang Date: Mon Jun 4 17:08:03 2018 -0700 combustor Src/EB2/AMReX_EB2_IF_Intersection.H Src/EB2/AMReX_EB2_IF_Union.H Src/EB2/AMReX_eb2_3d.F90 Tests/EBEB2/MyTest.cpp commit ca2934f1bdf0a7587b332b90f288e3006863214a Author: Weiqun Zhang Date: Mon Jun 4 16:34:18 2018 -0700 lathe and translate Src/EB2/AMReX_EB2_IF_Lathe.H Src/EB2/AMReX_EB2_IF_Translation.H Src/EB2/Make.package Tests/EBEB2/MyTest.cpp Tests/EBEB2/inputs commit 2b3ceeb526771f5ce5e2dbfcd6019e0e2a95b190 Author: Max Katz Date: Mon Jun 4 18:25:11 2018 -0400 Fix the macros so CPU code works Src/Base/AMReX_ArrayLim.H commit d104333a0aeb875789f1bb000d9361be759ac06a Author: Weiqun Zhang Date: Mon Jun 4 15:22:59 2018 -0700 translation Src/EB2/AMReX_EB2_IF_Box.H Src/EB2/AMReX_EB2_IF_Complement.H Src/EB2/AMReX_EB2_IF_Translation.H Src/EB2/Make.package Tests/EBEB2/MyTest.cpp commit 17b6bdd13b6087af5600d3d8ed4465c3681476c1 Author: Max Katz Date: Mon Jun 4 18:16:03 2018 -0400 Fix up the CUdA header generation Tools/F_scripts/find_files_vpath.py Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit eed9d4442369e4db5fe19af245f0339dcd34d969 Author: Weiqun Zhang Date: Mon Jun 4 15:10:25 2018 -0700 add Complement Src/EB2/AMReX_EB2_IF_Box.H Src/EB2/AMReX_EB2_IF_Complement.H Src/EB2/AMReX_EB2_IF_Cylinder.H Src/EB2/AMReX_EB2_IF_Plane.H Src/EB2/AMReX_EB2_IF_Sphere.H Src/EB2/Make.package Tests/EBEB2/MyTest.cpp commit f60d7cd64292395c98407b0b4d53c6caed3298cf Author: Weiqun Zhang Date: Mon Jun 4 13:22:48 2018 -0700 add two arguments versions of amrex_error Src/Base/AMReX_error_mod.F90 commit c137508c6cba681d435664871833774398fbdc0d Merge: 448b6a768 5e4caed34 Author: Weiqun Zhang Date: Mon Jun 4 12:22:05 2018 -0700 Merge branch 'development' into weiqun/eb2 commit 5e4caed3456e0da35630d2b155e25976fbee8e69 Author: Weiqun Zhang Date: Mon Jun 4 12:05:33 2018 -0700 add amrex_io_module Src/Base/AMReX_io_mod.F90 Src/Base/CMakeLists.txt Src/Base/Make.package commit 49944257b1d5ca1fa7aa8218dbf61254f3f49ee8 Author: Weiqun Zhang Date: Mon Jun 4 11:59:50 2018 -0700 add amrex_pd_wtime Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParallelDescriptor_F.F90 commit 2d91c484363810aa51b79ea53e4f72cb537a5b20 Author: Max Katz Date: Mon Jun 4 14:26:18 2018 -0400 Move CUDA header script over from StarLord Tools/F_scripts/write_cuda_headers.py Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 5e520e3020eb462640b1bc15bb9070a5527c624e Author: Max Katz Date: Mon Jun 4 13:40:21 2018 -0400 Add an apparently necessary device synchronize Src/Base/AMReX_FabArray.H commit 448b6a7686f54cbbae0501a8ed45c7c12dd1a509 Author: Weiqun Zhang Date: Sun Jun 3 16:50:05 2018 -0700 Union and intersection Src/Base/AMReX_IndexSequence.H Src/Base/CMakeLists.txt Src/Base/Make.package Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2_GeometryShop.H Src/EB2/AMReX_EB2_IF_Intersection.H Src/EB2/AMReX_EB2_IF_Union.H Src/EB2/AMReX_EB2_IndexSpaceI.H Src/EB2/Make.package Tests/EBEB2/MyTest.cpp commit 36e9925e3e480e5760bde573c60efa8649d5f559 Author: Weiqun Zhang Date: Sun Jun 3 07:35:35 2018 -0700 clean up Src/EB2/AMReX_EB2.cpp commit 025079ecc4f06734ad98de3c1d7cc2f436f80b3e Author: Weiqun Zhang Date: Sun Jun 3 07:32:46 2018 -0700 add PlaneIF Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IF_Box.H Src/EB2/AMReX_EB2_IF_Cylinder.H Src/EB2/AMReX_EB2_IF_Plane.H Src/EB2/Make.package commit 641bcae975e4aa21fc2d6123099bb8782c3c8f73 Author: Ann Almgren Date: Sat Jun 2 17:53:53 2018 -0700 Replace dp_t by rt Tools/F_scripts/write_probin.py commit 224281866cc43416a8e5ead05f80526d0a2924ad Author: Weiqun Zhang Date: Sat Jun 2 16:36:47 2018 -0700 add Box Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IF_Box.H Src/EB2/AMReX_EB2_IF_Cylinder.H Src/EB2/Make.package commit ae0bcc59372583134c4238fbe741955e7ea7da8d Author: Weiqun Zhang Date: Sat Jun 2 15:50:39 2018 -0700 rename so that all implicit function files start with AMReX_EB2_IF_ Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IF_Cylinder.H Src/EB2/AMReX_EB2_IF_Sphere.H Src/EB2/Make.package commit 3127af379b305c60b3ac03b28404c23c267d2b4d Author: Weiqun Zhang Date: Sat Jun 2 15:23:07 2018 -0700 function to fill volume fraction Src/EB2/AMReX_EB2_Level.cpp Tests/EBEB2/MyTest.cpp commit d9d9cbfa2a51676c7aafd7933712ee8e35ede185 Author: Weiqun Zhang Date: Sat Jun 2 14:05:19 2018 -0700 fix omp compilation Tutorials/Amr/Advection_F/Source/evolve_mod.F90 commit 96aa3d88904b216361d0aecf49f6301394c54231 Author: Weiqun Zhang Date: Sat Jun 2 08:56:19 2018 -0700 add getLevel Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IndexSpaceI.H Tests/EBEB2/MyTest.cpp commit ff5d98b67075020e165ad5273ba3ea0895121e8d Author: Weiqun Zhang Date: Sat Jun 2 08:38:49 2018 -0700 cleanup Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_IndexSpaceI.H commit 52f9e7fce471904e397c8dc933b10e768958d420 Author: Weiqun Zhang Date: Sat Jun 2 08:03:00 2018 -0700 add base Level class Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2_IndexSpaceI.H Src/EB2/AMReX_EB2_Level.H Src/EB2/AMReX_EB2_Level.cpp Src/EB2/Make.package commit c9f431c50fb42220345af6f8a3672f29f9b8c71e Author: Weiqun Zhang Date: Sat Jun 2 07:31:33 2018 -0700 add a new test Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2_ISLevel.H Tests/EBEB2/GNUmakefile Tests/EBEB2/Make.package Tests/EBEB2/MyTest.H Tests/EBEB2/MyTest.cpp Tests/EBEB2/inputs Tests/EBEB2/main.cpp commit bdabea589f8b2c93d1c558352eebaecda112b630 Author: Kevin Gott Date: Sat Jun 2 00:01:34 2018 -0400 BaseFab buildable on GPU with all constructors except copy. Test included. Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_Managed.H Tutorials/GPU/HelloWorld_C/main.cpp commit 3f59ba0dd9685ad79735a348a16266806ac014e0 Merge: d3f139557 649a1a49f Author: Weiqun Zhang Date: Fri Jun 1 17:06:44 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d3f1395573faaa76292c46d024b52c5978616352 Author: Weiqun Zhang Date: Fri Jun 1 17:06:15 2018 -0700 add bast to amrex_paralleldescriptor_module Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParallelDescriptor_F.F90 commit 366d40a9b2fe4ac91cfda6b5112af49521f991e9 Author: Weiqun Zhang Date: Fri Jun 1 14:47:23 2018 -0700 finish 2d cells Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_eb2_2d.F90 commit 60606ed0ee7dd6292bc659331c3fac41e8d83e06 Author: Weiqun Zhang Date: Fri Jun 1 13:13:30 2018 -0700 assert there are no multiple cuts in 2d Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_eb2_2d.F90 commit 649a1a49f624333cbaa89b946cdb104514abcaf8 Merge: 20f83a184 649f62967 Author: Andrew Myers Date: Fri Jun 1 10:39:17 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 20f83a18401b0cfdd1c59b46f97015197d88cd76 Author: Andrew Myers Date: Fri Jun 1 10:38:53 2018 -0700 adding an Electromagnetic PIC tutorial to development Tutorials/Particles/ElectromagneticPIC/Constants.H Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.H Tutorials/Particles/ElectromagneticPIC/ElectromagneticParticleContainer.cpp Tutorials/Particles/ElectromagneticPIC/Evolve.H Tutorials/Particles/ElectromagneticPIC/Evolve.cpp Tutorials/Particles/ElectromagneticPIC/GNUmakefile Tutorials/Particles/ElectromagneticPIC/IO.H Tutorials/Particles/ElectromagneticPIC/IO.cpp Tutorials/Particles/ElectromagneticPIC/Make.package Tutorials/Particles/ElectromagneticPIC/NodalFlags.H Tutorials/Particles/ElectromagneticPIC/NodalFlags.cpp Tutorials/Particles/ElectromagneticPIC/em_pic_3d.F90 Tutorials/Particles/ElectromagneticPIC/em_pic_F.H Tutorials/Particles/ElectromagneticPIC/inputs Tutorials/Particles/ElectromagneticPIC/main.cpp commit 649f629677290cf6c8400225d0b9e99ff6bd3c1f Merge: 101cb0526 b999bb1ac Author: WeiqunZhang Date: Fri Jun 1 09:50:17 2018 -0700 Merge pull request #267 from cgilet/master Fix --ghost option. Do not advance farg in case(--ghost) section bec… commit b999bb1ac23636bf472f690ecb939f9ce2de3bc0 Author: cgilet Date: Fri Jun 1 12:40:08 2018 -0400 Fix --ghost option. Do not advance farg in case(--ghost) section because --ghost does not take any arguments. Tools/Postprocessing/F_Src/fcompare.f90 commit 101cb05262687ef7b8f452e84f4753565571aabe Author: Weiqun Zhang Date: Fri Jun 1 09:33:11 2018 -0700 remove some old Fortran BoxLib tutorials OldTutorials/AMR_Adv_F/Exec/SingleVortex/GNUmakefile OldTutorials/AMR_Adv_F/Exec/SingleVortex/GPackage.mak OldTutorials/AMR_Adv_F/Exec/SingleVortex/init_phi.f90 OldTutorials/AMR_Adv_F/Exec/SingleVortex/inputs_2d OldTutorials/AMR_Adv_F/Exec/SingleVortex/inputs_3d OldTutorials/AMR_Adv_F/Exec/SingleVortex/set_velocity.f90 OldTutorials/AMR_Adv_F/Exec/UniformVelocity/GNUmakefile OldTutorials/AMR_Adv_F/Exec/UniformVelocity/GPackage.mak OldTutorials/AMR_Adv_F/Exec/UniformVelocity/init_phi.f90 OldTutorials/AMR_Adv_F/Exec/UniformVelocity/inputs_2d OldTutorials/AMR_Adv_F/Exec/UniformVelocity/inputs_3d OldTutorials/AMR_Adv_F/Exec/UniformVelocity/set_velocity.f90 OldTutorials/AMR_Adv_F/Source/GPackage.mak OldTutorials/AMR_Adv_F/Source/advance.f90 OldTutorials/AMR_Adv_F/Source/compute_flux.f90 OldTutorials/AMR_Adv_F/Source/main.f90 OldTutorials/AMR_Adv_F/Source/slope.f90 OldTutorials/AMR_Adv_F/Source/tag_boxes.f90 OldTutorials/AMR_Adv_F/Source/update_phi.f90 OldTutorials/AMR_Adv_F/Source/write_plotfile.f90 OldTutorials/Exp_CNS_NoSpec_F/CNSEquations.tex OldTutorials/Exp_CNS_NoSpec_F/GNUmakefile OldTutorials/Exp_CNS_NoSpec_F/GPackage.mak OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.c OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.h OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/GNUmakefile OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/bench.c OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/timer.h OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/timer.x86.c OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/Make.package OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/timer_c.c OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/Make.package OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/README OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/advance.f90 OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/main.f90 OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/README OldTutorials/Exp_CNS_NoSpec_F/README OldTutorials/Exp_CNS_NoSpec_F/advance.f90 OldTutorials/Exp_CNS_NoSpec_F/init_data.f90 OldTutorials/Exp_CNS_NoSpec_F/inputs.jbb OldTutorials/Exp_CNS_NoSpec_F/inputs_3d OldTutorials/Exp_CNS_NoSpec_F/main.f90 OldTutorials/Exp_CNS_NoSpec_F/write_plotfile.f90 OldTutorials/GettingStarted_F/GNUmakefile OldTutorials/GettingStarted_F/GPackage.mak OldTutorials/GettingStarted_F/main.f90 OldTutorials/GettingStarted_F/work_on_data.f90 OldTutorials/HeatEquation_EX1_F/GNUmakefile OldTutorials/HeatEquation_EX1_F/GPackage.mak OldTutorials/HeatEquation_EX1_F/advance.f90 OldTutorials/HeatEquation_EX1_F/init_phi.f90 OldTutorials/HeatEquation_EX1_F/inputs_2d OldTutorials/HeatEquation_EX1_F/inputs_3d OldTutorials/HeatEquation_EX1_F/main.f90 OldTutorials/HeatEquation_EX1_F/write_plotfile.f90 OldTutorials/HeatEquation_EX2_F/GNUmakefile OldTutorials/HeatEquation_EX2_F/GPackage.mak OldTutorials/HeatEquation_EX2_F/advance.f90 OldTutorials/HeatEquation_EX2_F/define_bc_tower.f90 OldTutorials/HeatEquation_EX2_F/init_phi.f90 OldTutorials/HeatEquation_EX2_F/inputs_2d OldTutorials/HeatEquation_EX2_F/inputs_3d OldTutorials/HeatEquation_EX2_F/main.f90 OldTutorials/HeatEquation_EX2_F/multifab_physbc.f90 OldTutorials/HeatEquation_EX2_F/write_plotfile.f90 OldTutorials/HeatEquation_EX3_F/GNUmakefile OldTutorials/HeatEquation_EX3_F/GPackage.mak OldTutorials/HeatEquation_EX3_F/advance.f90 OldTutorials/HeatEquation_EX3_F/define_bc_tower.f90 OldTutorials/HeatEquation_EX3_F/init_phi.f90 OldTutorials/HeatEquation_EX3_F/inputs_2d OldTutorials/HeatEquation_EX3_F/inputs_3d OldTutorials/HeatEquation_EX3_F/main.f90 OldTutorials/HeatEquation_EX3_F/multifab_physbc.f90 OldTutorials/HeatEquation_EX3_F/write_plotfile.f90 OldTutorials/HeatEquation_EX4_F/GNUmakefile OldTutorials/HeatEquation_EX4_F/GPackage.mak OldTutorials/HeatEquation_EX4_F/advance.f90 OldTutorials/HeatEquation_EX4_F/define_bc_tower.f90 OldTutorials/HeatEquation_EX4_F/init_phi.f90 OldTutorials/HeatEquation_EX4_F/inputs_2d OldTutorials/HeatEquation_EX4_F/inputs_3d OldTutorials/HeatEquation_EX4_F/main.f90 OldTutorials/HeatEquation_EX4_F/multifab_physbc.f90 OldTutorials/HeatEquation_EX4_F/write_plotfile.f90 OldTutorials/HeatEquation_EX5_F/GNUmakefile OldTutorials/HeatEquation_EX5_F/GPackage.mak OldTutorials/HeatEquation_EX5_F/advance.f90 OldTutorials/HeatEquation_EX5_F/define_bc_tower.f90 OldTutorials/HeatEquation_EX5_F/init_phi.f90 OldTutorials/HeatEquation_EX5_F/inputs-rt OldTutorials/HeatEquation_EX5_F/inputs-rt-expl OldTutorials/HeatEquation_EX5_F/inputs-rt-impl OldTutorials/HeatEquation_EX5_F/inputs_2d OldTutorials/HeatEquation_EX5_F/inputs_3d OldTutorials/HeatEquation_EX5_F/main.f90 OldTutorials/HeatEquation_EX5_F/multifab_physbc.f90 OldTutorials/HeatEquation_EX5_F/write_plotfile.f90 OldTutorials/MultiGrid_F/GNUmakefile OldTutorials/MultiGrid_F/README OldTutorials/MultiGrid_F/constants.f90 OldTutorials/MultiGrid_F/cycle_tower.f90 OldTutorials/MultiGrid_F/fmg_cycle.f90 OldTutorials/MultiGrid_F/init_coeffs.f90 OldTutorials/MultiGrid_F/init_rhs.f90 OldTutorials/MultiGrid_F/inputs_fmg_lin_2d OldTutorials/MultiGrid_F/inputs_fmg_lin_3d OldTutorials/MultiGrid_F/inputs_fmg_pc_2d OldTutorials/MultiGrid_F/inputs_fmg_pc_3d OldTutorials/MultiGrid_F/inputs_v_lin_2d OldTutorials/MultiGrid_F/inputs_v_lin_3d OldTutorials/MultiGrid_F/inputs_v_pc_2d OldTutorials/MultiGrid_F/inputs_v_pc_3d OldTutorials/MultiGrid_F/main.f90 OldTutorials/MultiGrid_F/solve.f90 OldTutorials/MultiGrid_F/traverse.f90 OldTutorials/MultiGrid_F/v_cycle.f90 OldTutorials/Random_F/GNUmakefile OldTutorials/Random_F/GPackage.mak OldTutorials/Random_F/main.f90 OldTutorials/Tiling_Heat_F/GNUmakefile OldTutorials/Tiling_Heat_F/GPackage.mak OldTutorials/Tiling_Heat_F/advance.f90 OldTutorials/Tiling_Heat_F/init_phi.f90 OldTutorials/Tiling_Heat_F/inputs_3d OldTutorials/Tiling_Heat_F/main.f90 OldTutorials/Tiling_Heat_F/results.txt OldTutorials/Tiling_Heat_F/results/babbage_omp.run OldTutorials/Tiling_Heat_F/results/results.txt OldTutorials/Tiling_Heat_F/results/t1a.txt OldTutorials/Tiling_Heat_F/results/t1b.txt OldTutorials/Tiling_Heat_F/results/t2a.txt OldTutorials/Tiling_Heat_F/results/t2b.txt OldTutorials/Tiling_Heat_F/results/t3a.txt OldTutorials/Tiling_Heat_F/results/t3b.txt OldTutorials/Tiling_Heat_F/results/t4a.txt OldTutorials/Tiling_Heat_F/results/t4b.txt OldTutorials/Tiling_Heat_F/results/t5a.txt OldTutorials/Tiling_Heat_F/results/t5b.txt OldTutorials/Tiling_Heat_F/results/t6a.txt OldTutorials/Tiling_Heat_F/results/t6b.txt OldTutorials/Tiling_Heat_F/results/t7a.txt OldTutorials/Tiling_Heat_F/results/t7b.txt OldTutorials/Tiling_Heat_F/write_plotfile.f90 OldTutorials/WaveEquation_F/GNUmakefile OldTutorials/WaveEquation_F/GPackage.mak OldTutorials/WaveEquation_F/advance.f90 OldTutorials/WaveEquation_F/init_data.f90 OldTutorials/WaveEquation_F/inputs_2d OldTutorials/WaveEquation_F/inputs_3d OldTutorials/WaveEquation_F/main.f90 OldTutorials/WaveEquation_F/write_plotfile.f90 commit 5128c36448b6dd9d5a7438f90fda155c16c3ab40 Author: Weiqun Zhang Date: Fri Jun 1 09:31:23 2018 -0700 rename OldMiniApps/FillBoundary/GNUmakefile OldMiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp OldMiniApps/FillBoundary/README OldMiniApps/FillBoundary/qsub.ipm.bat OldMiniApps/MultiGrid_C/COEF_3D.F OldMiniApps/MultiGrid_C/COEF_F.H OldMiniApps/MultiGrid_C/GNUmakefile OldMiniApps/MultiGrid_C/Make.package OldMiniApps/MultiGrid_C/README OldMiniApps/MultiGrid_C/RHS_3D.F OldMiniApps/MultiGrid_C/RHS_F.H OldMiniApps/MultiGrid_C/main.cpp OldMiniApps/MultiGrid_C/qsub.ipm.bat Tools/CompileTesting/compiletesting.py commit 771afadba97a62f812813c2a7fd9ee5288f5c21c Author: Weiqun Zhang Date: Fri Jun 1 09:21:52 2018 -0700 remove some old mini apps MiniApps/PGAS_SMC/GNUmakefile MiniApps/PGAS_SMC/LiDryer.c MiniApps/PGAS_SMC/Make.package MiniApps/PGAS_SMC/SMC.H MiniApps/PGAS_SMC/SMC.cpp MiniApps/PGAS_SMC/SMC_F.H MiniApps/PGAS_SMC/SMC_advance.cpp MiniApps/PGAS_SMC/SMC_init.cpp MiniApps/PGAS_SMC/SMC_io.cpp MiniApps/PGAS_SMC/chemistry_module.f90 MiniApps/PGAS_SMC/derivative_stencil.f90 MiniApps/PGAS_SMC/init_data.f90 MiniApps/PGAS_SMC/kernels.f90 MiniApps/PGAS_SMC/main.cpp MiniApps/PGAS_SMC/make_plot.f90 MiniApps/PGAS_SMC/transport_properties.f90 MiniApps/PGAS_SMC/variables.f90 MiniApps/SMC/GNUmakefile MiniApps/SMC/GPackage.mak MiniApps/SMC/LiDryer.c MiniApps/SMC/_parameters MiniApps/SMC/advance.f90 MiniApps/SMC/chemistry_module.f90 MiniApps/SMC/derivative_stencil.f90 MiniApps/SMC/init_data.f90 MiniApps/SMC/initialize.f90 MiniApps/SMC/inputs_SMC MiniApps/SMC/kernels.f90 MiniApps/SMC/main.f90 MiniApps/SMC/make_plotfile.f90 MiniApps/SMC/probin.template MiniApps/SMC/smc.f90 MiniApps/SMC/smcdata.f90 MiniApps/SMC/time.f90 MiniApps/SMC/transport_properties.f90 MiniApps/SMC/variables.f90 commit 15f44bf733be8cecd96441c72f986d6ddbab4338 Merge: 9c283eb41 8d5c7a376 Author: Weiqun Zhang Date: Fri Jun 1 08:49:25 2018 -0700 Merge branch 'development' into weiqun/eb1 commit 8d5c7a37695e7dc899386bfd1f6ac28221984976 Author: Weiqun Zhang Date: Fri Jun 1 08:47:53 2018 -0700 update CHANGES CHANGES commit 9c283eb41300010943465ecb7588357c961170b7 Author: Weiqun Zhang Date: Thu May 31 17:32:11 2018 -0700 more on 2d Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_GeometryShop.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_EB2_MultiGFab.H Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit 7360a5df38e55f2ab624f77296f8fcee4fae8148 Author: Weiqun Zhang Date: Thu May 31 14:44:28 2018 -0700 add a new EB2::Initialize with simple geometries Src/Base/AMReX_Array.H Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp commit fd0d71b5c573f6ecd8d357d552f45809ae299078 Author: Weiqun Zhang Date: Thu May 31 14:04:25 2018 -0700 no need to use least square in 2d Src/EB2/AMReX_eb2_3d.F90 commit 10a251c4d55abce520bff04ea4a8e9f2762cc628 Author: Kevin Gott Date: Thu May 31 15:46:19 2018 -0400 BaseFab::copy, copyToMem and copyFromMem tested and working. std::min and std::max in IntVect written out to avoid namespace conflict. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_Box.H Src/Base/AMReX_IntVect.H Tutorials/GPU/HelloWorld_C/main.cpp commit ac25ad176c0fb9a61e8942f936bf464ae400ec84 Author: Andrew Myers Date: Thu May 31 11:31:59 2018 -0700 move the if np == 0 checks to inside the fortran subroutines. Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_F/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 commit 6f09d3d35c150304d8a372090722007d8f711139 Author: Andrew Myers Date: Thu May 31 11:19:08 2018 -0700 make this a bit less hard-coded for tracers Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_F/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 Tutorials/Amr/Advection_F/Source/initdata.F90 Tutorials/Amr/Advection_F/Source/my_amr_mod.F90 Tutorials/Amr/Advection_F/Source/plotfile_mod.F90 commit 376f45c9cb38533640406d7048bdb2e546eb6d45 Author: Andrew Myers Date: Thu May 31 11:08:53 2018 -0700 rename particle container module files Src/F_Interfaces/Particle/AMReX_particlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_particlecontainer_mod.F90 Src/F_Interfaces/Particle/Make.package commit 81e63a6f3aa37ad8462990e5dccc0faae2252a28 Author: Andrew Myers Date: Thu May 31 10:57:35 2018 -0700 implement 3d Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_F/Source/Src_3d/Adv_3d.f90 commit 5c641dfd99b947fd073e883138af291de595f150 Author: Andrew Myers Date: Thu May 31 10:30:42 2018 -0700 refactor advect_particles into a loop over spacedim Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 commit 7448480e15f9d938005ae0ceaefd33c56d879d78 Author: Andrew Myers Date: Thu May 31 10:07:09 2018 -0700 advection tutorial working with particles Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 commit 0463d512ac7c32e9b51e8b63fe553d00c07edcd8 Author: Weiqun Zhang Date: Thu May 31 09:33:29 2018 -0700 compute centroid Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_eb2_3d.F90 commit 08c02d81cb249e279e11f851c6eed5938afe632c Author: Andrew Myers Date: Thu May 31 09:28:56 2018 -0700 some bug fixes Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 Tutorials/Amr/Advection_F/Source/initdata.F90 commit 1a6e961241a3db2001a050be5f6601a2e333e604 Merge: fde7de3dc cea880e9b Author: WeiqunZhang Date: Thu May 31 08:47:23 2018 -0700 Merge pull request #265 from jameslehoux/patch-1 Updated SingleVortex GNUmakefile commit cea880e9b3f0c4960ffd5c856faf753b82389a6b Author: jameslehoux <37665786+jameslehoux@users.noreply.github.com> Date: Thu May 31 14:49:27 2018 +0100 Updated SingleVortex GNUmakefile Corrected AMREX_HOME to allow it to be built (should be 5 levels up, was 4 levels) Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile commit 39137b5c825d193b59d73dfced989974ec1084eb Author: Andrew Myers Date: Wed May 30 20:58:10 2018 -0700 implement advect_particles in 2D Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 Tutorials/Amr/Advection_F/Source/plotfile_mod.F90 commit ab86318efbcb27de3fbf8105dc07b53fb3ac45ee Author: Andrew Myers Date: Wed May 30 18:21:21 2018 -0700 3D version of advect particles Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_F/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 commit 57883dc9c01cbc9acc7e9a2cddbdc9bc6ccc29cf Author: Andrew Myers Date: Wed May 30 18:11:56 2018 -0700 wrap the call to c_to_f_pointer in amrex_get_particles Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 commit 87b22b00241280f8e055e3a4628137ba6e8ecd87 Author: Andrew Myers Date: Wed May 30 17:51:03 2018 -0700 also pass the velocity data into advect_particles Tutorials/Amr/Advection_F/Source/evolve_mod.F90 commit fde7de3dcbd4bdf7bd41a10c3a2f11b98b54e43e Author: Weiqun Zhang Date: Wed May 30 16:26:57 2018 -0700 MFIter dynamic scheduling: must call barrier before setting the staic variable Src/Base/AMReX_MFIter.cpp commit d401fc1b509165f3b2dcf94cdd6d841230434b4f Author: John Wakefield Date: Wed May 30 15:49:12 2018 -0700 Added skipping of existing components. Tools/C_util/AugmentPlotfile/AugmentPlotfile.cpp Tools/C_util/AugmentPlotfile/inputs commit e3b574cf2d16eb5541474338cdb09b4d2787c625 Author: Kevin Gott Date: Wed May 30 16:23:26 2018 -0400 Fix fortran bind name. Src/Base/AMReX_BaseFab_nd.F90 commit c3a2cb26b9213737ce94fa297c29896387b455c8 Author: Kevin Gott Date: Wed May 30 13:41:30 2018 -0400 Intermediate commit before working on std::min and std::max. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_Box.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Tutorials/GPU/HelloWorld_C/main.cpp commit 39e91665747be4773e287241c929ad9bf3de2824 Author: Andrew Myers Date: Tue May 29 20:07:46 2018 -0700 starting to implement advection kernel for tracer particles in Fortran Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 commit a2566d6271481af2081f612b12483eed6ff3a089 Author: Weiqun Zhang Date: Tue May 29 15:52:54 2018 -0700 compute 2nd moments on faces Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_eb2_3d.F90 commit 33cb2fdd6e080d448f6f03205fe7a6269841e603 Author: Kevin Gott Date: Tue May 29 19:26:02 2018 -0400 BaseFab setval tests. Working fine. Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CArena.cpp Tutorials/GPU/HelloWorld_C/main.cpp commit c0fe3926e6ccffd16366d24451d8d75773851ded Author: atmyers Date: Tue May 29 16:14:30 2018 -0700 add routine to recalculate superparticle size Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 14806cdc75f9e22490da17837575975ef188b6bd Author: Kevin Gott Date: Tue May 29 18:53:55 2018 -0400 Change macros to have prefix AMREX_CUDA_ Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_Box.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_Managed.H Tutorials/GPU/HelloWorld_C/main.cpp commit 468363463dc141d3181d099f570eb1a46fab95ac Author: John Wakefield Date: Tue May 29 14:02:22 2018 -0700 Augmentplotfile working in parallel Tools/C_util/AugmentPlotfile/AugmentPlotfile.cpp Tools/C_util/AugmentPlotfile/GNUmakefile commit a3f60c88765a8149f9c403a38864e6906ba684c3 Author: Kevin Gott Date: Tue May 29 16:34:27 2018 -0400 BaseFab setVal running on both host and device. Small make system tweak for OpenMP. Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 Tools/GNUMake/sites/Make.olcf Tutorials/GPU/HelloWorld_C/main.cpp commit 6224bedb38eb3b07e971f1d97947556bd490d652 Author: John Wakefield Date: Tue May 29 13:29:01 2018 -0700 Augment plotfile functional in serial. Tools/C_util/AugmentPlotfile/AugmentPlotfile.cpp Tools/C_util/AugmentPlotfile/AugmentPlotfile_F.H Tools/C_util/AugmentPlotfile/AugmentPlotfile_F.f90 Tools/C_util/AugmentPlotfile/GNUmakefile Tools/C_util/AugmentPlotfile/inputs commit d869e93ac7c96bd18e1965657a416fcef1e09766 Author: John Wakefield Date: Tue May 29 13:26:58 2018 -0700 Added cell size getter. Src/Extern/amrdata/AMReX_AmrData.H commit aa3d533004ca199e198ee42d4f2e953a7c049ed2 Author: Andrew Myers Date: Tue May 29 11:33:38 2018 -0700 fix amrex_get_particles and add a function for returning the number of particles in a tile. Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 commit 990bac5e11ed914048dde2157576ab4ea6eb9547 Author: Andrew Myers Date: Tue May 29 10:51:58 2018 -0700 initialize the tracer particle velocities to zero instead of the weird thing it was doing before Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 4755ed4b93bf1d34287c32197f272aa9ddf949c1 Author: Andrew Myers Date: Tue May 29 10:47:13 2018 -0700 add a function for getting the particls on a tile in fortran. Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 commit 92fb39f25272796c97f1074e481d2ba659770c5d Author: Weiqun Zhang Date: Tue May 29 10:24:11 2018 -0700 add cylinder Src/EB2/AMReX_EB2_CylinderIF.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_EB2_SphereIF.H Src/EB2/AMReX_eb2_3d.F90 Src/EB2/Make.package commit a76cb7e02a2c7a87b09bc378722dc51a1369deb1 Author: Kevin Gott Date: Mon May 28 20:17:53 2018 -0400 First edit of BArena to allocate BaseFab data. Need to edit CArena as well for COALESCE_FABS. Src/Base/AMReX_Arena.H Src/Base/AMReX_BArena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_Managed.H Tools/GNUMake/Make.defs Tutorials/GPU/HelloWorld_C/main.cpp Tutorials/GPU/HelloWorld_C/outline.cpp commit 98ae7b21dec154fffc9f4ef3c4a90628ebea1210 Author: Weiqun Zhang Date: Sat May 26 18:55:44 2018 -0700 compute volume fraction, and boundary norm, centrold and area Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_eb2_3d.F90 commit d3fc116f038ac5635c73ba9e9e342546ff04202d Author: Weiqun Zhang Date: Sat May 26 17:34:07 2018 -0700 fix small cells and almost regular cells Src/EB2/AMReX_eb2_3d.F90 commit 8a345af99a376357a0eae7be122395cb2bb251c2 Author: Andrew Myers Date: Fri May 25 16:46:42 2018 -0700 some bug fixes. Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90 commit 344284a765052de2997844412d1bb328cba002e9 Author: Andrew Myers Date: Fri May 25 16:46:26 2018 -0700 put the calls to amrex_particle_redistribute in the right place in the update loop. Tutorials/Amr/Advection_F/Source/evolve_mod.F90 commit f8982835e32c0ca9f94a6c362cdbd4a78d980203 Author: Andrew Myers Date: Fri May 25 16:01:42 2018 -0700 wrap Redistribute. Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90 commit 9f5e1ba81174467a9f7c9856f3566fcad5a67913 Author: Andrew Myers Date: Fri May 25 15:27:18 2018 -0700 writing plot files. Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90 Tutorials/Amr/Advection_F/Source/fmain.F90 Tutorials/Amr/Advection_F/Source/initdata.F90 Tutorials/Amr/Advection_F/Source/my_amr_mod.F90 Tutorials/Amr/Advection_F/Source/plotfile_mod.F90 commit 9eaba3d223be16c89cbc61d2b8778711c42a9a88 Author: Andrew Myers Date: Fri May 25 14:07:23 2018 -0700 also wrap InitOnePerCell Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90 Tutorials/Amr/Advection_F/Source/fmain.F90 commit c2d916db1f3ed67f633597a58e98efdb24cf6a6c Author: Andrew Myers Date: Fri May 25 13:48:23 2018 -0700 showing that I can initialize a tracer particle container from Fortran Src/AmrCore/AMReX_AmrCore.cpp Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90 Tutorials/Amr/Advection_F/Source/fmain.F90 commit 8242d1474213e1aca0e9f482ecd37867d2d0761a Author: Weiqun Zhang Date: Fri May 25 13:42:31 2018 -0700 compute area fraction and face centroids for y and z-faces Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_eb2_3d.F90 commit 0aa6214f27ed3fc12325abd74e141f3189b7c5b4 Author: Weiqun Zhang Date: Fri May 25 12:42:41 2018 -0700 compute area fraction and face centroids for x-faces Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_GeometryShop.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_eb2_3d.F90 commit 10422a13cb50c63dcfbe9a07a2375d9d604289c7 Author: Andrew Myers Date: Fri May 25 11:46:56 2018 -0700 first attempt at wrapping the AmrTracerParticleContainer for use with the Fortran interfaces. Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_fi.cpp Src/F_Interfaces/Particle/AMReX_amrtracerparticlecontainer_mod.F90 Tutorials/Amr/Advection_F/Exec/Make.Adv Tutorials/Amr/Advection_F/Exec/SingleVortex/GNUmakefile commit 5dc6d8f5479f9c43810d1e11b41f827f3953924f Merge: 9652772a5 cc23ba73a Author: Andrew Myers Date: Thu May 24 11:00:09 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9652772a5ccdcdd6e4142b26e98f349291294dc8 Author: Andrew Myers Date: Thu May 24 10:59:51 2018 -0700 fix timer name Src/Particle/AMReX_ParticleContainerI.H commit a0c2470a4b33050d6c7c244baa6fa99daac929df Author: Weiqun Zhang Date: Thu May 24 10:25:41 2018 -0700 3d build_types Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_EB2_MultiGFab.H Src/EB2/AMReX_EB2_MultiGFab.cpp Src/EB2/AMReX_eb2_2d.F90 Src/EB2/AMReX_eb2_3d.F90 commit a4b1c76a7a291b5d525e937a4437d7aae9fe55ac Merge: fb92b6d61 cc23ba73a Author: Weiqun Zhang Date: Wed May 23 12:38:28 2018 -0700 Merge branch 'development' into weiqun/eb2 commit fb92b6d619b3d00e947c9b4c26b6a51d7c56d45f Author: Weiqun Zhang Date: Wed May 23 12:38:22 2018 -0700 fix typo and add an alias IntVect::hasher Src/Base/AMReX_Box.H Src/Base/AMReX_IntVect.H Src/EB2/AMReX_EB2_Graph.H commit cc23ba73a872653e712d217ad286c469a0be988f Author: Weiqun Zhang Date: Wed May 23 10:51:15 2018 -0700 fix non-mpi build Src/Base/AMReX_FabArrayCommI.H commit f8833938e0e2d7b42f5e3d3069fc575dcab95b92 Author: Weiqun Zhang Date: Wed May 23 10:38:52 2018 -0700 non-blocking parallel copy Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H commit a06c2180631a6e5e0ea0d33c9d4683f8238e7927 Author: Kevin Gott Date: Wed May 23 12:53:29 2018 -0400 Test update. Tutorials/GPU/HelloWorld_C/GNUmakefile Tutorials/GPU/HelloWorld_C/main.cpp commit bf0281d50a9b767bf676c533a5370a683a652b25 Author: Kevin Gott Date: Tue May 22 21:52:47 2018 -0400 compiler no longer complaining Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab_nd.F90 Src/Base/CMakeLists.txt Src/Base/Make.package Tutorials/GPU/HelloWorld_C/main.cpp commit a3b30bb519d51696626b118b8b8437446c804f65 Merge: bed95c8f6 e0961fcca Author: Weiqun Zhang Date: Tue May 22 11:15:07 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit bed95c8f646342c5f533fffdd47cfce41676bbb1 Author: Weiqun Zhang Date: Tue May 22 11:15:00 2018 -0700 rm a profiler Src/Particle/AMReX_ParticleContainerI.H commit 669a3cd10f949d35dddc56e860b3a812874712b7 Author: Kevin Gott Date: Tue May 22 10:59:23 2018 -0400 setVal working. Src/Base/AMReX_BaseFab.H Tools/GNUMake/comps/nvcc.mak commit e0961fcca6f9612a990e430f98f209762fb3dcf8 Author: Andy Nonaka Date: Mon May 21 17:20:22 2018 -0700 endl -> std::endl so this compiles Tools/C_util/Convergence/RichardsonConvergenceTest.cpp commit adadfb1e146eb19718ef98602df580d9b364b7f3 Author: Weiqun Zhang Date: Mon May 21 17:04:48 2018 -0700 SumBoundary: use IntVect version of Copy Src/Base/AMReX_MultiFab.cpp commit f6ee003195b66408225b4c98492803174700fd36 Author: Max Katz Date: Mon May 21 16:14:02 2018 -0700 Fix MPI compilation at LLNL Tools/GNUMake/sites/Make.llnl commit fb67229899189cbfef776bde24889224a035039a Author: Weiqun Zhang Date: Mon May 21 16:11:06 2018 -0700 fix tiling bug in nodal linear solver Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit aef815aaaaa5da78b98d60d450195452f1d76430 Author: Kevin Gott Date: Mon May 21 17:21:24 2018 -0400 BaseFab::setVal prepped except for 'ForEach' Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_Box.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_Managed.H Tutorials/GPU/HelloWorld_C/main.cpp commit 3fcbc53ec08537f54fa74322a0ccbdc1ad62e5e2 Merge: 6be81c63a b6100bcdd Author: Weiqun Zhang Date: Mon May 21 13:04:33 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b6100bcdd33197599255f6b9c8b9e37f15ce37c6 Merge: bbda74a8a c7b581f08 Author: Marc Day Date: Mon May 21 11:45:46 2018 -0700 Merge pull request #263 from knutsvk/development add pp.query for unstable_criterion commit c7b581f087e220d9606186e53179217b84430349 Author: knutsvk Date: Mon May 21 13:35:43 2018 +0100 add pp.query for unstable_criterion Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp commit 6be81c63a3d7cc98dd836b2e8021f13ff9343a52 Author: Weiqun Zhang Date: Sat May 19 17:20:29 2018 -0700 fix single precision for 2d too Src/AmrCore/AMReX_FillPatchUtil_2d.F90 commit bbda74a8a8942c6a5ce3f159874f656c4367da32 Author: Michele Rosso Date: Fri May 18 16:11:27 2018 -0700 Fix single precision issue in AmrCore Src/AmrCore/AMReX_FillPatchUtil_3d.F90 commit be1f05b7224025c3b92e38c7306d021f34fff564 Author: Max Katz Date: Fri May 18 18:26:53 2018 -0400 FORT_LAUNCH -> AMREX_FORT_LAUNCH, DEVICE_LAUNCH -> AMREX_DEVICE_LAUNCH Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_filcc_f.H Tutorials/GPU/HeatEquation_EX1_C/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H commit 328dd188e61ac9888efb6a1f7d4a632ceb949b47 Merge: 2fa903df4 670ceda20 Author: Max Katz Date: Fri May 18 17:50:50 2018 -0400 Merge commit '670ceda20bb5aa4f2945ec31578d951fe196e95f' into gpu commit 2fa903df4d077e7863d42a2ab2829a6c903d9fb5 Merge: 62b45d4c8 1f1ac7799 Author: Max Katz Date: Thu May 17 22:19:20 2018 -0400 Merge commit '1f1ac77996a4753a378be86ec207017ca8903af2' into gpu commit 62b45d4c8bb5d36c456de2771c0f365c175a6ff1 Merge: f00e07022 e556a7f9a Author: Max Katz Date: Thu May 17 21:39:01 2018 -0400 Merge commit 'e556a7f9a5ee8abe7ffb8f223c0adc3c463af84c' into gpu commit f00e070228bb74fc1f7abc3a36be7a9b648a3b63 Merge: f34127acf 8de1a0e58 Author: Max Katz Date: Thu May 17 21:38:44 2018 -0400 Merge commit '8de1a0e585f30114133a8b47e64292f50be1d489' into gpu commit f6b088129b5d3fd006be0ad81a7b5fe012bd1fe3 Author: Weiqun Zhang Date: Thu May 17 14:00:16 2018 -0700 ignore .nfs* files .gitignore commit 474499fc77315a83af2f928ae9533df22c09bd4a Author: Weiqun Zhang Date: Thu May 17 13:56:49 2018 -0700 rm .nfs file Tutorials/GPU/HelloWorld_C/.nfs0000000002226f1d00001727 commit 6328de0f048d52b7454ad9131ce639420ea0ddd6 Merge: 614043a49 62f99798f Author: Weiqun Zhang Date: Thu May 17 09:52:18 2018 -0700 Merge branch 'development' into weiqun/eb1 commit f34127acfdfee1c790c810bba07e65c87a98eacf Merge: 2c2f6bda6 9f51cd259 Author: Max Katz Date: Thu May 17 11:50:38 2018 -0400 Merge commit '9f51cd25986ee55af04d34ef53d5fc70625238c7' into gpu commit 2c2f6bda6983ab1a91fedbe229ed8416029dfad4 Merge: 9d99c8ab0 66a2edee2 Author: Max Katz Date: Thu May 17 11:47:30 2018 -0400 Merge commit '66a2edee2371a4d3bfca8344b75040976bf77e4f' into gpu commit 9d99c8ab0879e93dd776e737bbc322c1bd177615 Merge: 77906cea9 2f4d3a871 Author: Max Katz Date: Thu May 17 11:43:09 2018 -0400 Merge commit '2f4d3a871c771236e3c74089c3cbc173f861aae1' into gpu commit 77906cea9c1273c14d5b009823d8b43f7083bf75 Merge: d326565e1 aca077b4b Author: Max Katz Date: Thu May 17 11:42:55 2018 -0400 Merge commit 'aca077b4b6c5b748ad00163befa09b4e727c29b2' into gpu commit d326565e13a172bc1268a2379facaee96772a555 Merge: 9d8e09b4b 2481bcd3d Author: Max Katz Date: Thu May 17 11:32:11 2018 -0400 Merge commit '2481bcd3def8af7e52b02fb9a0341e2590c95d48' into gpu commit 9d8e09b4b59f6921f12f800d2f2497b85c8a930f Merge: 41dce0448 1815971bb Author: Max Katz Date: Thu May 17 11:28:39 2018 -0400 Merge commit '1815971bbae8844fb29813c1cb8f587c4b63e6da' into gpu commit 41dce04483bd63bc3ca4b72de7d61ee1ba92dd60 Merge: cdf883955 1ef9f08f3 Author: Max Katz Date: Thu May 17 11:17:34 2018 -0400 Merge commit '1ef9f08f3089538d7f31d6861e9214d5e5415e07' into gpu commit cdf88395599a5c6c6a470f23d75a43339a17f192 Merge: e9ca8365c 4a3729fad Author: Max Katz Date: Thu May 17 11:16:10 2018 -0400 Merge commit '4a3729fad1fb67376b43fd84bb61b745af405b4b' into gpu commit e9ca8365c7bd6fa52a95e96a6d7c4ada084c5519 Merge: 5d84061d5 fdff649e6 Author: Max Katz Date: Thu May 17 10:51:27 2018 -0400 Merge commit 'fdff649e6e74d78abdb6f9df85bb1b9ff513fc95' into gpu commit 5d84061d5599ab82145628355a074f24477dc3bf Author: Max Katz Date: Wed May 16 20:56:23 2018 -0400 Allow runtime overriding of strided grid/block size Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 5cc62bc19639e15ba59aa15c01201c1999ba57da Author: Max Katz Date: Wed May 16 16:09:32 2018 -0400 sharedmemcarveout is only in 9.1+ Src/Base/AMReX_BLFort.H commit fc54699ff0c212a9691178ce6b4eae630c18c5be Author: Max Katz Date: Wed May 16 11:38:15 2018 -0400 Set the default register count to 255 Tools/GNUMake/Make.defs commit 0595022d91ab314fc027fa385afe95fb9751935d Author: Max Katz Date: Wed May 16 11:37:45 2018 -0400 Cap filcc at 128 registers Src/Base/Make.package commit f5ba5a1bb3e3821287d1be1497c7a77d113067a1 Author: Max Katz Date: Wed May 16 11:36:44 2018 -0400 Add the ability to do a file-specific register maximum Tools/GNUMake/Make.rules commit 2343cc4490f45d19d9b92712d9f581ad17379d08 Author: Max Katz Date: Wed May 16 07:21:13 2018 -0400 Compare correct y and z dimensions Src/Base/AMReX_CUDA.F90 commit c172d518693dac5b71b4f2225eb256091ebac118 Author: Max Katz Date: Wed May 16 07:19:37 2018 -0400 Correct the sanity check on too many threads Src/Base/AMReX_CUDA.F90 commit e3174d5454c7073d0bd10cca46b03a7789a1860f Author: Max Katz Date: Wed May 16 05:27:22 2018 -0400 Limit to 256 threads per block Tools/GNUMake/Make.defs commit 8a8cb9b0fdf7f4d2ed4229a23669aa89e0783f0e Author: Max Katz Date: Tue May 15 20:12:26 2018 -0400 Add more macros for the GPU script Src/Base/AMReX_ArrayLim.H commit 62f99798f674afc1dedb83b82abddf19c7a4a002 Merge: ea796e234 d75e7496f Author: Michael Zingale Date: Tue May 15 20:06:40 2018 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/AMReX into development commit ea796e2341770023f62265f84483e0dfb1d6196b Author: Michael Zingale Date: Tue May 15 20:06:13 2018 -0400 make this importable Tools/F_scripts/find_files_vpath.py commit 8f547d7a5f1bc9faccaaeae422caa91e7248e8b4 Author: Kevin Gott Date: Tue May 15 17:11:29 2018 -0400 IntVect managed memory start. Need AMReX_Vector to keep going. Src/Base/AMReX_IntVect.H commit 596c443b39d09b83ddcc08669635b143294fe8c2 Author: Kevin Gott Date: Tue May 15 17:10:42 2018 -0400 First outline of managed memory class and macros. Src/Base/AMReX_Managed.H Src/Base/Make.package Tutorials/GPU/HelloWorld_C/.nfs0000000002226f1d00001727 Tutorials/GPU/HelloWorld_C/GNUmakefile Tutorials/GPU/HelloWorld_C/Make.package Tutorials/GPU/HelloWorld_C/main.cpp Tutorials/GPU/HelloWorld_C/outline.cpp commit 43cfc87a9cd5a536e4f57c0c42119faba7077d87 Author: Kevin Gott Date: Tue May 15 17:09:57 2018 -0400 Copy of GPU build system from gpu branch. Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_pgi.mak Tools/GNUMake/Make.defs Tools/GNUMake/Make.local.template Tools/GNUMake/Make.machines Tools/GNUMake/Make.rules Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/ibm.mak Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak Tools/GNUMake/packages/Make.cvode Tools/GNUMake/sites/Make.llnl Tools/GNUMake/sites/Make.olcf Tools/GNUMake/tools/Make.craypat Tools/GNUMake/tools/Make.vtune commit d75e7496fd415a2ec4e7e09837abf478bcdda0ac Merge: aa749e905 ae262bdae Author: Andrew Myers Date: Tue May 15 13:08:21 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit aa749e9055926b66fafbac9825e2bc6df2b19253 Author: Andrew Myers Date: Tue May 15 13:08:08 2018 -0700 add option to interpolate in space when using amrex::get_slice_data Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_MultiFabUtil_nd.F90 commit 614043a49836eb585cc404e663a43f63d6ed26a9 Author: Weiqun Zhang Date: Tue May 15 12:23:09 2018 -0700 find intercept using Brent method Src/Base/AMReX_Box.H Src/EB2/AMReX_EB2_GeometryShop.H Src/EB2/AMReX_EB2_Graph.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_eb2_2d.F90 commit 62326b55345f8f5c17ef51b3bdf0b70379f1f9cf Author: Weiqun Zhang Date: Mon May 14 10:10:35 2018 -0700 build types Src/EB2/AMReX_EB2_GeometryShop.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_EB2_MultiGFab.H Src/EB2/AMReX_EB2_MultiGFab.cpp Src/EB2/AMReX_EB2_SphereIF.H Src/EB2/AMReX_eb2_2d.F90 commit cb9278db25b212160b6f86dfac5699ecc200fde7 Author: Weiqun Zhang Date: Sun May 13 07:29:09 2018 -0700 add fortran function stub for building types Src/Base/AMReX_LayoutData.H Src/EB2/AMReX_EB2_F.H Src/EB2/AMReX_EB2_GeometryShop.H Src/EB2/AMReX_EB2_Graph.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_EB2_MultiGFab.H Src/EB2/AMReX_EB2_MultiGFab.cpp Src/EB2/AMReX_eb2_2d.F90 Src/EB2/Make.package commit a7ff0bb8d386a9add964d18990af84886ec3b495 Author: Weiqun Zhang Date: Sat May 12 08:26:04 2018 -0700 keep cut boxes only Src/EB2/AMReX_EB2_GeometryShop.H Src/EB2/AMReX_EB2_Graph.H Src/EB2/AMReX_EB2_ISLevel.H commit 516bdc4ef17a8ceaef0a9b90272f100aa451c9b2 Author: Weiqun Zhang Date: Fri May 11 18:32:38 2018 -0700 start EB2:Graph Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2_GeometryShop.H Src/EB2/AMReX_EB2_Graph.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_EB2_IndexSpaceI.H Src/EB2/AMReX_EB2_SphereIF.H Src/EB2/Make.package commit ae262bdae615bc42e4e4b12ca75d9b307b32f18f Merge: f7167f0b0 c8710b70e Author: Michele Rosso Date: Fri May 11 15:07:24 2018 -0700 Merge branch 'mr/cmake' into development commit f7167f0b0ba6f9092130117730dad1c97d78214d Author: Marc Day Date: Fri May 11 14:42:52 2018 -0700 Remove debugging output. Src/GeometryShop/AMReX_EBISLevel.cpp commit 719bfef9b87b32bba2149ad1ec15d77d8c381c2d Author: Cy Chan Date: Fri May 11 13:46:31 2018 -0700 ForkJoin: remove task_rank_n member field since split_bounds duplicates information add forkjoin.verbose input parameter make MyTask and NTasks public OldTutorials/MultiColor_C/inputs OldTutorials/MultiColor_C/main.cpp Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp commit 1d0ea9a10da5f5717adc73c7b7a44a69dd83b6bd Author: Cy Chan Date: Fri May 11 13:06:07 2018 -0700 some clean up OldTutorials/MultiColor_C/inputs OldTutorials/MultiColor_C/main.cpp Src/Base/AMReX_ForkJoin.cpp commit 8eee5ba5f7b13db20f3601407346acbd28c8f559 Merge: 8decffa5c 27e03befa Author: Andrew Myers Date: Fri May 11 12:45:04 2018 -0700 Merge pull request #260 from nataraj2/master Advection_F generalized to 2d and 3d commit fa7284660cde3661f60dbc5e5d446dbb2c435f13 Author: Cy Chan Date: Fri May 11 12:36:45 2018 -0700 changed MultiFab collectives to use ParallelContext subcommunicator instead of ParallelDescriptor added Parallel(All)Reduce Or and And added ParallelAllGather and ParallelGather functions updates to MultiFab::(min/max)Index() remove broadcast, replace with allgather, everyone does reduction OldTutorials/MultiColor_C/main.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelReduce.H commit c8710b70ee1e663fcdb7a7e264b310a29607a86d Author: Michele Rosso Date: Fri May 11 11:58:40 2018 -0700 Fix namespace in export file Tools/CMake/AMReXConfig.cmake.in commit d221271e7c420af566e9b0bac5fab2fa9c008ac2 Author: Michele Rosso Date: Fri May 11 11:55:52 2018 -0700 Disable linear solver legacy components by default Docs/sphinx_documentation/source/BuildingAMReX.rst Src/LinearSolvers/CMakeLists.txt Tools/CMake/AMReX_Options.cmake commit 8decffa5c572aeab64a9d2c4b587a2d753affd1d Author: Andrew Myers Date: Fri May 11 11:05:12 2018 -0700 make this link go directly to the issues page. Docs/sphinx_documentation/source/index.rst commit a203b6defe75efb9595e23f9d8eacc42576d4ab1 Author: Andrew Myers Date: Fri May 11 11:03:49 2018 -0700 remove duplicated link Docs/sphinx_documentation/source/Introduction.rst commit 5be01ac2e1e6616f1606d210f0dec1eed4e068d4 Author: Andrew Myers Date: Fri May 11 11:02:39 2018 -0700 remove duplicated information between the introduction and main landing page for the docs. Docs/sphinx_documentation/source/Introduction.rst Docs/sphinx_documentation/source/index.rst commit 205ea4b475226e142ba1724b9c65bf3907ee9a9c Author: Andrew Myers Date: Fri May 11 11:00:49 2018 -0700 use hyperlink targets instead of including the entire test of links in the text. Docs/sphinx_documentation/source/index.rst commit fb5bf066e0905e19eb3d675e27d167da33dc0bfe Author: Andrew Myers Date: Fri May 11 10:49:03 2018 -0700 include a link to the Doxygen API docs on the main page for the long-form documentation. Docs/sphinx_documentation/source/index.rst commit f0e6a2b54161a919c534c8fb8eccece51f46f21b Author: Andrew Myers Date: Fri May 11 10:47:03 2018 -0700 some clarifying remarks in the documenation Docs/sphinx_documentation/source/Introduction.rst Docs/sphinx_documentation/source/index.rst commit 2784f86e4c29989e7115f13c70428ecf165503c0 Author: Weiqun Zhang Date: Thu May 10 21:02:35 2018 -0700 fix MLMG nodal solver in case there is no coarsening at all Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 104c9710c546a3639c4478ada37e6647e509a0b1 Author: Weiqun Zhang Date: Thu May 10 17:28:26 2018 -0700 start EB2 and set up IndexSpace Src/Base/AMReX_Array.H Src/EB2/AMReX_EB2.H Src/EB2/AMReX_EB2.cpp Src/EB2/AMReX_EB2_GeometryShop.H Src/EB2/AMReX_EB2_ISLevel.H Src/EB2/AMReX_EB2_IndexSpaceI.H Src/EB2/AMReX_EB2_SphereIF.H Src/EB2/Make.package Tools/GNUMake/Make.defs commit dafd0ea54155a73ab008472a6e3c1816840f832e Merge: 9fcc59c65 3840d8578 Author: Michael Zingale Date: Thu May 10 16:44:32 2018 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/AMReX into development commit 9fcc59c6584572d50ed0412211bebdf87f536d96 Author: Michael Zingale Date: Thu May 10 16:44:17 2018 -0400 allow for multiple specific variables to be output Tools/Postprocessing/F_Src/fextrema.f90 commit 12e3797fe32d86621bcc996bea5f369aa2a21c0d Author: Cy Chan Date: Thu May 10 11:47:48 2018 -0700 add support for custom MultiFab component split across tasks OldTutorials/MultiColor_C/inputs OldTutorials/MultiColor_C/main.cpp Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp commit 3840d8578086b53144cfc8c3b8955d8383717082 Author: Ann Almgren Date: Thu May 10 11:30:38 2018 -0700 Remove ifdef from around void setCoarseningStrategy so that we can call it even with EB defined. Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H commit 8854f37ad0313e53d1bd92a3b5d3d44f2f9a4f11 Author: Michael Zingale Date: Thu May 10 12:28:52 2018 -0400 GCC 8.x introduces more options for the sanitizers -- enable them is we are building with GCC >= 8 Tools/GNUMake/comps/gnu.mak commit dca72d8e991daf6dfeedcd61c5ebac44b5101657 Author: Weiqun Zhang Date: Thu May 10 08:45:14 2018 -0700 makeFineMask works for any index types as long as they are consistent Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit a07eb6741589ba8b4855e3a58898bd16d4e09162 Merge: 94a9b23f5 e401426be Author: Andrew Myers Date: Wed May 9 17:38:42 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 94a9b23f584c1469ada19d12e1322435a92f941f Author: Andrew Myers Date: Wed May 9 17:38:27 2018 -0700 add a function to test for the intersection of two RealBoxes Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit 518e80fc7e66859a3dff700e308e8e64faecb9c8 Author: Cy Chan Date: Wed May 9 15:41:40 2018 -0700 forkjoin: add some error checking OldTutorials/MultiColor_C/inputs OldTutorials/MultiColor_C/main.cpp Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp commit e401426be3f883be051081d79ae792f1236aaec8 Author: Weiqun Zhang Date: Wed May 9 14:46:56 2018 -0700 makeFineMask function Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 3848dc62ce80530ec8d43bbab94b6ad8282971bf Author: Weiqun Zhang Date: Wed May 9 14:45:44 2018 -0700 enable iMultiFab operator= for rvalue rhs Src/Base/AMReX_iMultiFab.H commit a418fc420a6e6276e59a3383ae1ec79cc19e234d Merge: 1cfe35871 9636f10f7 Author: Weiqun Zhang Date: Wed May 9 10:02:26 2018 -0700 Merge branch 'development' into weiqun/mlmg commit 9636f10f7a9635ad6daf7032398dc90c211db51f Author: Weiqun Zhang Date: Wed May 9 09:24:04 2018 -0700 ParmParse: support FILE=probin where probin is a Fortran namelist file Src/Base/AMReX_parmparse_mod.F90 commit 3af5e45b4b8ed2fd38850703ab5728670ea3efad Author: Ann Almgren Date: Tue May 8 17:32:05 2018 -0700 Add AMReX_CoveredSlabs* to CMakeLists.txt Src/GeometryShop/CMakeLists.txt commit f30e2bbf5a59e650d88562ad0260dfa5c7941912 Author: Weiqun Zhang Date: Tue May 8 17:24:57 2018 -0700 amrex namespace and prefix Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_geometry.F90 Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 Src/EB/AMReX_compute_normals.F90 Tutorials/EB/LevelSet/Src/main.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp Tutorials/EB/LevelSet/Src/make_shapes.H commit cb61a8aeda77867ea22580ba5a57ca96ee615149 Author: Weiqun Zhang Date: Tue May 8 16:58:54 2018 -0700 EB levelset: make 2d compile Src/EB/AMReX_EB_levelset.cpp Tutorials/EB/LevelSet/Src/main.cpp commit a1ec71b0b918662e85abcf9f3e65d4376ffd50fb Merge: cc3a943da 341f16fad Author: Weiqun Zhang Date: Tue May 8 15:37:13 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit cc3a943da1d6fe39cb1ebef2bc9b3067ef36afb7 Author: Weiqun Zhang Date: Tue May 8 15:37:04 2018 -0700 define USE_EB=TRUE and simplify GNUmakefile Tutorials/EB/LevelSet/Exec/GNUmakefile commit 341f16fad7d002dc652b703e4663305722aafb1f Merge: 8d495ec9d 049918e40 Author: Johannes Blaschke Date: Tue May 8 15:31:02 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 8d495ec9dd83835cc30efc12de0e3878d5cdd3d3 Author: Johannes Blaschke Date: Tue May 8 15:30:55 2018 -0700 cleanup Tutorials/EB/LevelSet/Src/Make.package commit 049918e40bf98f66978bd38eb7d9da7dbec9890a Merge: 7495c2124 5b395e9fb Author: Weiqun Zhang Date: Tue May 8 15:06:17 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7495c21247da5527e3ec6c95c39c34afe236e260 Author: Weiqun Zhang Date: Tue May 8 15:06:13 2018 -0700 ParmParse now reads Fortran namelist blocks in inputs file and saves them in amrex_namelist in amrex_parmparse_module. This allows mixing ParmParse parameters and Fortran namelist parameters in a single inputs file. Note that namelist is not stored in ParmParse database. Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_parmparse_mod.F90 commit 3bc1e33a8dc8c4770613a725e6cccb27e03129f2 Author: Max Katz Date: Tue May 8 17:43:28 2018 -0400 Remove a stray variadic arg Src/Base/AMReX_BLFort.H commit 5b395e9fbdd8dfe4bdbfb2b35d69e1383076e53c Author: Johannes Blaschke Date: Tue May 8 14:19:32 2018 -0700 moved level-set source into AMReX Src/EB Src/EB/AMReX_EB_F.H Src/EB/AMReX_EB_geometry.F90 Src/EB/AMReX_EB_levelset.H Src/EB/AMReX_EB_levelset.cpp Src/EB/AMReX_EB_levelset_F.F90 Src/EB/AMReX_compute_normals.F90 Src/EB/CMakeLists.txt Src/EB/Make.package Tutorials/EB/LevelSet/Src/Make.package Tutorials/EB/LevelSet/Src/make_eb.cpp Tutorials/EB/LevelSet/Src/make_shapes.H commit 7c607b33b99ca07b02269ccf409890284b91f333 Merge: b93bb65fd 4284f48bc Author: Johannes Blaschke Date: Tue May 8 13:35:42 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b93bb65fd5b403fb150f8f31413a7c4a991e5ff5 Author: Johannes Blaschke Date: Tue May 8 13:35:26 2018 -0700 Fix level-set tutorial Tutorials/EB/LevelSet/Exec/inputs Tutorials/EB/LevelSet/Src/main.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp Tutorials/EB/LevelSet/Src/make_poly.cpp Tutorials/EB/LevelSet/Src/make_shapes.H commit 4284f48bcfc206de7d4130a4eb0f1c0b84843670 Merge: 995b968dc 64e427098 Author: dtgraves Date: Tue May 8 13:15:25 2018 -0700 Merge pull request #259 from AMReX-Codes/dtg_branch added CoveredSlab geometry generation per Marc's request so we can ha… commit 49608874e9399165a3de464631631d714a3fd8bb Author: Michael Zingale Date: Thu Apr 26 15:45:29 2018 -0400 fix PGI compilation PGI complains that with the 'pure' keyword here: PGF90-S-0074-Illegal number or type of arguments to heapsort_indirect_d - arguments of greater_d and cmp do not agree (/home/zingale/development/AMReX//Src/F_BaseLib/knapsack.f90: 85) Src/F_BaseLib/knapsack.f90 commit 5aedce6d8a4b3aaa240919ce76d01edaa2674f45 Author: Max Katz Date: Tue May 8 16:14:06 2018 -0400 PGI now uses a different variable for the CUDA toolkit Tools/GNUMake/comps/pgi.mak commit 64e427098d7f41b91f62b7445ef9753b0a22accf Author: dtgraves Date: Tue May 8 13:13:22 2018 -0700 added CoveredSlab geometry generation per Marc's request so we can have geometries with sharp corners. Src/GeometryShop/AMReX_CoveredSlabs.H Src/GeometryShop/AMReX_CoveredSlabs.cpp Src/GeometryShop/Make.package Tutorials/EB/GeometryGeneration/exec/GNUmakefile Tutorials/EB/GeometryGeneration/exec/coveredSlabs.cpp Tutorials/EB/GeometryGeneration/exec/coveredslabs.inputs commit 995b968dcfdb64c9305038141629c20974b67ec3 Merge: 9a28a5ef9 0a3620607 Author: Weiqun Zhang Date: Tue May 8 10:45:38 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9a28a5ef9fd717e9a8ab0a383c0d45f85f19b458 Author: Weiqun Zhang Date: Tue May 8 10:45:30 2018 -0700 MLMG: refactor grids agglomeration so that it works even if the argument grids is not directly coarsenable. Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 0a36206075ae341df959604caf69b4400538f4c4 Author: Ann Almgren Date: Tue May 8 10:37:02 2018 -0700 Add Tutorials/EB/LevelSet to demonstrate how to generate level set from EB specification. Tutorials/EB/LevelSet/Exec/GNUmakefile Tutorials/EB/LevelSet/Exec/inputs Tutorials/EB/LevelSet/Src/Make.package Tutorials/EB/LevelSet/Src/compute_normals.f90 Tutorials/EB/LevelSet/Src/eb_F.H Tutorials/EB/LevelSet/Src/eb_geometry.f90 Tutorials/EB/LevelSet/Src/eb_levelset.H Tutorials/EB/LevelSet/Src/eb_levelset.cpp Tutorials/EB/LevelSet/Src/eb_levelset_f.f90 Tutorials/EB/LevelSet/Src/main.cpp Tutorials/EB/LevelSet/Src/make_cylinder.cpp Tutorials/EB/LevelSet/Src/make_eb.cpp Tutorials/EB/LevelSet/Src/make_poly.cpp Tutorials/EB/LevelSet/Src/make_shapes.H commit bab8e3fe8e16116f2645014c34130040383e6165 Author: Weiqun Zhang Date: Mon May 7 17:34:18 2018 -0700 MLMG: assert grids are coarsenable Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit cb1959a5522c931274f059918314c839ded7bc5c Merge: 0f5b5110f 9ca38ccfb Author: Ann Almgren Date: Mon May 7 17:18:43 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 0f5b5110ff6e539c2409bcb7d5ff6fd9be03fa4b Author: Ann Almgren Date: Mon May 7 17:18:37 2018 -0700 Revert "Allow face-based arrays to coarsen even if the boxes don't quite line up right (eg if a fine" This reverts commit 2832ad001c06a2e2ef0106e43a81620084e9dcb0. Src/Base/AMReX_MultiFabUtil.cpp commit 9ca38ccfb2235876ad4929dbd5eaa99afd6c9a70 Merge: a42f0fcf1 2832ad001 Author: Weiqun Zhang Date: Mon May 7 17:10:40 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a42f0fcf16e3ee4743393afbdb1a24db85ae52a4 Author: Weiqun Zhang Date: Mon May 7 17:10:36 2018 -0700 fix print in TinyProfiler Src/Base/AMReX_TinyProfiler.cpp commit 2832ad001c06a2e2ef0106e43a81620084e9dcb0 Author: Ann Almgren Date: Mon May 7 16:56:03 2018 -0700 Allow face-based arrays to coarsen even if the boxes don't quite line up right (eg if a fine 32x32 domain is broken into boxes 15-wide and 17-wide but the coarse boxes are 8x8) Src/Base/AMReX_MultiFabUtil.cpp commit 1a6e616469f53b8615fa3fd2006910e1e01dbaae Author: Weiqun Zhang Date: Mon May 7 16:49:42 2018 -0700 avoid using cout and cerr directly Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_TracerParticles.cpp commit 341add6033565375a56d74a79e0c9daedb7205ac Author: Weiqun Zhang Date: Mon May 7 15:37:23 2018 -0700 avoid using cout and cerr directly in Base/ Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_TinyProfiler.cpp Src/Base/AMReX_Utility.cpp Src/Base/AMReX_VisMF.cpp commit 542d31777de94d211f8d91c7cfe6cf5ec96d30dc Author: Max Katz Date: Mon May 7 18:07:45 2018 -0400 Indent make.olcf for clarity Tools/GNUMake/sites/Make.olcf commit b6575d1c5cdbb1d05950c128ef8cdac17a4d0a4c Author: Weiqun Zhang Date: Mon May 7 15:01:05 2018 -0700 add amrex::ErrorStream and remove cout and cerr from Amr/ Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateDescriptor.cpp Src/Base/AMReX.H Src/Base/AMReX.cpp commit 27e03befaf24683958b61970c224038191e9c05b Author: Mahesh Natarajan Date: Mon May 7 17:46:46 2018 -0400 Advection_F generalized to 2d and 3d Tutorials/Amr/Advection_F/Exec/SingleVortex/movie.visit commit 89bd7139c3e8d01958b77bfce195739e8be04f53 Author: Mahesh Natarajan Date: Mon May 7 17:44:57 2018 -0400 Advection_F generalized to 2d and 3d Tutorials/Amr/Advection_F/Exec/SingleVortex/.GNUmakefile.swp commit ba70d9e628b37da14400b58c174beac2d706b86c Author: Mahesh Natarajan Date: Mon May 7 17:44:37 2018 -0400 Advection_F generalized to 2d and 3d Tutorials/Amr/Advection_F/Exec/SingleVortex/.inputs.swp commit 4e966878f9ef3f7c98cb97836497f339b6aabb25 Author: Mahesh Natarajan Date: Mon May 7 17:43:32 2018 -0400 Advection_F generalized to 2d and 3d Tutorials/Amr/Advection_F/Exec/SingleVortex/.GNUmakefile.swp Tutorials/Amr/Advection_F/Exec/SingleVortex/.inputs.swp Tutorials/Amr/Advection_F/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_F/Exec/SingleVortex/Make.package Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob_2d.f90 Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob_3d.f90 Tutorials/Amr/Advection_F/Exec/SingleVortex/face_velocity_3d.F90 Tutorials/Amr/Advection_F/Exec/SingleVortex/movie.visit Tutorials/Amr/Advection_F/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_F/Source/Src_3d/Make.package Tutorials/Amr/Advection_F/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/Advection_F/Source/Src_3d/slope_3d.f90 commit 06eaed2beb9331268f43c88c42dadf3a1c0e9222 Author: Max Katz Date: Mon May 7 16:30:37 2018 -0400 Fix MPI compilation on summitdev Tools/GNUMake/sites/Make.olcf commit 5c7bce4c60e960e3e348acaad96be61b494f6881 Author: dtgraves Date: Mon May 7 11:51:17 2018 -0700 added a bit about using WrappedGShop for generating higher order EB moments. Docs/sphinx_documentation/source/EB.rst commit 5d6890c8aacd024fe56a58e57a94ecf849db1693 Author: dtgraves Date: Mon May 7 10:32:20 2018 -0700 added derivative functions for Union, Intersection and Complement implicit functions. Src/GeometryShop/AMReX_ComplementIF.H Src/GeometryShop/AMReX_ComplementIF.cpp Src/GeometryShop/AMReX_IntersectionIF.H Src/GeometryShop/AMReX_IntersectionIF.cpp Src/GeometryShop/AMReX_UnionIF.H Src/GeometryShop/AMReX_UnionIF.cpp commit 0655db9d6930d09deaeeb8ae49b3985afab9278d Author: Weiqun Zhang Date: Mon May 7 09:45:25 2018 -0700 add geom_type box to Tests/EBbcent Tests/EBbcent/main.cpp commit c6643db6ba5f5793b7f164847d0241d21cd3e562 Author: Max Katz Date: Sun May 6 17:49:57 2018 -0400 Use the new shared mem carveout attribute for CUDA 9 Src/Base/AMReX_BLFort.H commit 2300ff35304dafa3d73b40fd2ec02a50db0c7e0a Author: Max Katz Date: Sun May 6 17:27:48 2018 -0400 Always do strided DEVICE_LAUNCH Src/Base/AMReX_BLFort.H commit d943f1cec124ae1a1de0dfdd0d8481b7f44f68e0 Author: Max Katz Date: Sun May 6 17:27:38 2018 -0400 Note minimum number of threads Src/Base/AMReX_Device.cpp commit 666254963df18e84e413960b2c024f1260a3d65b Author: Max Katz Date: Sun May 6 16:35:40 2018 -0400 Update the grid strided loop layout Src/Base/AMReX_Device.cpp commit bf8264d4b9d62462a5e1b3975739b5277e3af623 Author: Max Katz Date: Sun May 6 15:12:43 2018 -0400 Add a grid-strided device launch macro Src/Base/AMReX_BLFort.H commit 9ed8c45c6f2bc819a0918adb621c467281ecad54 Author: Max Katz Date: Sun May 6 07:06:24 2018 -0400 Add a function for doing a grid-stride kernel Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit e6be561268a7ae18cf08ba886f58dc72fa78f119 Author: Max Katz Date: Sun May 6 07:05:11 2018 -0400 Add function to return number of device SMs Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H commit 5dbc6d6760df516cbd19e4691b15054897fec373 Author: Max Katz Date: Sat May 5 20:08:15 2018 -0400 Add a DEVICE_LAUNCH macro Src/Base/AMReX_BLFort.H commit 7d82c30df5c2a2cb17ea1acdf1decc8a090008cd Author: Max Katz Date: Sat May 5 19:37:32 2018 -0400 Move nvcc code to a unique file Tools/GNUMake/comps/ibm.mak Tools/GNUMake/comps/nvcc.mak Tools/GNUMake/comps/pgi.mak commit 1e2593cc4fc87560d1184dee241cd6863fdd4024 Author: Max Katz Date: Sat May 5 19:31:13 2018 -0400 Sync up IBM compile flags with PGI Tools/GNUMake/comps/ibm.mak commit ac485943486854a46dee54084a3b95c04fe6a2cc Author: Max Katz Date: Sat May 5 17:14:42 2018 -0400 Nullify a function template for CUDA Src/Base/AMReX_BLFort.H commit aae7b9489ca16bbcbdfd8b0c1e7ecc13c076b455 Merge: 0989da352 3d8360328 Author: Max Katz Date: Sat May 5 16:36:30 2018 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 0989da3521068eddf7a4e69fee239ecdf2f98dce Author: Max Katz Date: Sat May 5 16:36:25 2018 -0400 Do not link device code until final link Src/Base/AMReX_BLFort.H Tools/GNUMake/comps/pgi.mak commit f881fe22e747ef21fa219238522509df22690777 Author: Max Katz Date: Sat May 5 16:36:08 2018 -0400 get_loop_bounds is a device call Src/Base/AMReX_Device.H commit 48cd1e42126f0b983dd9e7de6c184f410123009a Merge: 12b94b74c 771d94899 Author: WeiqunZhang Date: Fri May 4 16:07:08 2018 -0700 Merge pull request #256 from AMReX-Codes/cg-mulicomponent updated CG solver for multicomponent solves commit 771d94899fb645eb46ac14cd48f0edf8e2affc3f Author: Brandon Runnels Date: Fri May 4 17:04:33 2018 -0600 updated CG solver for multicomponent solves Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit 12b94b74cba673f38edd912f2be6e14532301ab9 Author: Weiqun Zhang Date: Fri May 4 15:37:02 2018 -0700 add FabArray::Redistribute function that redistributes FabArray data from one to another with the same BoxArray but different DistributionMapping Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H commit 3d83603287bf4231484b540fadcf1544e45cbc35 Merge: 80c2d3da1 e4ad5c2ba Author: Andrew Myers Date: Fri May 4 17:16:21 2018 -0400 Merge branch 'gpu' of https://github.com/AMReX-Codes/amrex into gpu commit 80c2d3da1013860e8a30cb0e78540e1e6b0b272f Author: Andrew Myers Date: Fri May 4 17:15:44 2018 -0400 pass the allocator template parameter in to all uses of the base class in Vector. Src/Base/AMReX_Vector.H commit ca4514d762e45072e78598c9a7d6bebbca72f132 Author: Andrew Myers Date: Fri May 4 16:17:32 2018 -0400 make swapBytes a regular, non-template function. Src/Base/AMReX_IntConv.H Src/Base/AMReX_IntConv.cpp commit a5590c9365e8e07f2dff07c703bd063f1cd978c4 Merge: 504031a76 034aa4584 Author: Andrew Myers Date: Fri May 4 12:18:38 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 504031a76c463f435df9020a277aa7e89731954b Author: Andrew Myers Date: Fri May 4 12:18:09 2018 -0700 merging. Src/GeometryShop/AMReX_IndexedMoments.H Src/GeometryShop/AMReX_IrregNode.cpp Tests/EBbcent/GNUmakefile Tests/EBbcent/Make.package Tests/EBbcent/main.cpp commit b0eff8d4853962edd3434942f142adc6392325c7 Author: Andrew Myers Date: Fri May 4 12:14:00 2018 -0700 make the swapBytes function templated on size rather than type to make it work on Titan with cce Src/Base/AMReX_IntConv.H Src/Base/AMReX_IntConv.cpp commit 034aa4584b251d917e956051f8bf4023a75b55f9 Merge: 6b0ef2675 7879dd3e1 Author: dtgraves Date: Fri May 4 11:00:15 2018 -0700 Merge pull request #255 from AMReX-Codes/eb-bcent bug fix in higher order moments commit 7879dd3e1c58152cf9b3ad665367f4957b66532e Author: dtgraves Date: Fri May 4 10:57:53 2018 -0700 added fix for where EBMoments get the wrong sign Src/GeometryShop/AMReX_IndexedMoments.H Src/GeometryShop/AMReX_IrregNode.cpp Tests/EBbcent/main.cpp commit 6b0ef2675a4476b999b9539215e0c5ca45c8fb03 Author: Andrew Myers Date: Fri May 4 10:13:34 2018 -0700 fix loop bounds problem in BndryRegister. Src/Boundary/AMReX_BndryRegister.cpp commit 93e77c8a69f4ec7c435da63c6291b92e1a5304ef Author: Andrew Myers Date: Fri May 4 10:04:52 2018 -0700 simplify the logic here a bit. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 6cee5a02a19ef658b2242ea6fcae45e1de438fe7 Author: Weiqun Zhang Date: Fri May 4 09:56:47 2018 -0700 test for debugging Tests/EBbcent/GNUmakefile Tests/EBbcent/Make.package Tests/EBbcent/main.cpp commit ff68f170034a833989e0cd4e0845131a3e9efd11 Merge: ef4cee103 041050c05 Author: atmyers Date: Thu May 3 21:00:51 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit ef4cee103563d12b1a2442ef9819a95ee98c788c Author: atmyers Date: Thu May 3 21:00:28 2018 -0700 remove the version of amrex::ResetRandomSeed that set all the threads to have the same seed. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 041050c059e507d0fb7724e1df12843d23ef118f Merge: 56b970b3d 579b2a8a0 Author: Weiqun Zhang Date: Thu May 3 15:00:47 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 56b970b3d41b7a6fc2dae600b6183483d3435af2 Author: Weiqun Zhang Date: Thu May 3 14:57:36 2018 -0700 add cg to MLMG Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 755edb0a1ba816ce34821bfb551139d968a1c90b Author: Weiqun Zhang Date: Thu May 3 13:50:28 2018 -0700 clean up SPMD.H Src/Base/AMReX_SPMD.H Src/Base/AMReX_SPMD.cpp Src/Base/AMReX_SPMDI.H Src/Base/AMReX_parstream.cpp Src/GeometryShop/AMReX_FabArrayIO.H Tests/GeometryShop/regression/levelRedistTest.cpp commit 579b2a8a02e1882c7ed0257c1f8c7d877a6595ac Author: Andy Nonaka Date: Thu May 3 13:49:05 2018 -0700 MultiFab is_nodal test for a single direction Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit e4ad5c2ba8273ea8513dc6449b2816698feffcf1 Author: Max Katz Date: Thu May 3 13:34:35 2018 -0700 Update to new SMPI at LLNL Tools/GNUMake/sites/Make.llnl commit c8a715d8e60143411f880369416579ae55ccb104 Author: Weiqun Zhang Date: Thu May 3 13:24:00 2018 -0700 change pout basename to amrex_pout and use ParmParse instead of environment variable for specifying output interval Src/Base/AMReX_parstream.H Src/Base/AMReX_parstream.cpp commit 5ac4735c2b06cea32c8cf729a7f197488f52aaff Author: Weiqun Zhang Date: Thu May 3 12:47:11 2018 -0700 amrex::Initialize can now take an std::ostream argument for amrex::Print() to use Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_Print.H commit c86f2231918c050baa18d713683e50c8de48bf79 Author: Max Katz Date: Thu May 3 11:59:52 2018 -0700 Sync up LLNL build system Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.llnl commit 062b01d3bdfff4574b770d9a0758f3466eb0775d Merge: c0c376258 c53e284bd Author: Max Katz Date: Thu May 3 11:59:19 2018 -0700 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit c265cbe95b817db2a94caad52fe6150730f850a0 Author: Weiqun Zhang Date: Wed May 2 16:14:45 2018 -0700 rm EBAMRElliptic Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H Src/EBAMRElliptic/AMReX_BaseBCFuncEval.H Src/EBAMRElliptic/AMReX_BiCGStabSolver.H Src/EBAMRElliptic/AMReX_ConductivityBaseDomainBC.H Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.cpp Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRElliptic/AMReX_EBEllipticFort.F90 Src/EBAMRElliptic/AMReX_EBEllipticFort_F.H Src/EBAMRElliptic/AMReX_EBMultiGrid.H Src/EBAMRElliptic/AMReX_EBSimpleSolver.H Src/EBAMRElliptic/AMReX_EBSimpleSolver.cpp Src/EBAMRElliptic/AMReX_LinearSolver.H Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.H Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.cpp Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.H Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.cpp Src/EBAMRElliptic/AMReX_NoOpSolver.H Src/EBAMRElliptic/AMReX_VCAggStencil.H Src/EBAMRElliptic/AMReX_VCAggStencil.cpp Src/EBAMRElliptic/Make.package Tests/EBAMRElliptic/exec/GNUmakefile Tests/EBAMRElliptic/exec/cond.inputs Tests/EBAMRElliptic/exec/conductivitySolve.cpp commit a18a9ba9855d16d1d938cee0ca34c8660583cdac Author: Weiqun Zhang Date: Tue May 1 11:23:39 2018 -0700 minor update INSTALL commit 5553b6af63da745ef13ecdb51654b72ec1cca544 Author: Weiqun Zhang Date: Tue May 1 09:32:44 2018 -0700 update CHANGES CHANGES commit b2c6a638d1e27cf8be2f453d88f5041c6b9f4046 Author: Kevin Gott Date: Fri Apr 27 17:39:20 2018 -0700 MemCheck versions of flush for testing after timeSteps. Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp commit 21d32773eab0737d7b6dcff96682b8eebae58b81 Author: Kevin Gott Date: Fri Apr 27 14:45:35 2018 -0700 BL_PROFILE_FLUSH() allows user-specified profiling database writes. input flag 'blprofiler.prof_flushprint' can be set to false to remove intermediate std::cout outputs. Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp Tests/ProfTests/HeatEquation_EX1_C/Exec/GNUmakefile Tests/ProfTests/HeatEquation_EX1_C/Exec/inputs_2d Tests/ProfTests/HeatEquation_EX1_C/Exec/inputs_3d Tests/ProfTests/HeatEquation_EX1_C/Source/Make.package Tests/ProfTests/HeatEquation_EX1_C/Source/advance.cpp Tests/ProfTests/HeatEquation_EX1_C/Source/advance_2d.f90 Tests/ProfTests/HeatEquation_EX1_C/Source/advance_3d.f90 Tests/ProfTests/HeatEquation_EX1_C/Source/init_phi_2d.f90 Tests/ProfTests/HeatEquation_EX1_C/Source/init_phi_3d.f90 Tests/ProfTests/HeatEquation_EX1_C/Source/main.cpp Tests/ProfTests/HeatEquation_EX1_C/Source/myfunc.H Tests/ProfTests/HeatEquation_EX1_C/Source/myfunc_F.H commit a6872238056e639b6c4135971ddaf9ceb9c386ca Merge: c3b0d7e3f 5af5cde5b Author: Michael Zingale Date: Fri Apr 27 08:39:20 2018 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c3b0d7e3f570a3a9b4bde2367755f0f041cf8a03 Author: Michael Zingale Date: Fri Apr 27 08:38:45 2018 -0400 only warn if not all variables are present still send a success code so tests pass when we add new variables Tools/Postprocessing/F_Src/fcompare.f90 commit 5af5cde5b6fe47ceba7c54da718c73d0772d5ff7 Author: Weiqun Zhang Date: Thu Apr 26 22:33:15 2018 -0700 get aroung a compiler bug? Src/Base/AMReX_Box.H commit 3cf8767320a186a22a26dee9764f37f4d930852d Author: Weiqun Zhang Date: Thu Apr 26 15:57:04 2018 -0700 remove a number of function level static variables that may not be thread safe Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_IndexType.H Src/Base/AMReX_IndexType.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp commit 66fb57dba5f13d848d570de0b96d0c0861b099e6 Author: Weiqun Zhang Date: Thu Apr 26 15:33:13 2018 -0700 tidy Src/Base/AMReX_Box.H commit f3ed96383f67ce5da957801227fe6215b137ac60 Author: Weiqun Zhang Date: Thu Apr 26 13:36:27 2018 -0700 fix new Box bug and revert my revert Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit bbf478ec0d564bada752839bd784ac0a3a4e54ef Author: Weiqun Zhang Date: Thu Apr 26 13:31:26 2018 -0700 fix omp compilation Src/Boundary/AMReX_YAFluxRegister.cpp commit 3b078ac423a85e308e3320f681bd541007ae1273 Author: Weiqun Zhang Date: Thu Apr 26 13:22:36 2018 -0700 revert my change in Box due to a bug Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit 6474448fe41da6afa4982396699e387cf4b05f52 Merge: 14fd7e3c8 e2af6e6a5 Author: Weiqun Zhang Date: Thu Apr 26 13:00:46 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 14fd7e3c86975116e326d2f6ce5b18e80889c3c9 Author: Weiqun Zhang Date: Thu Apr 26 13:00:43 2018 -0700 omp in in YAFluxRegister::define Src/Boundary/AMReX_YAFluxRegister.cpp commit e2af6e6a5c85332b9b40c21bc322c6193e59d45b Merge: 68bba833e e5734db5d Author: WeiqunZhang Date: Thu Apr 26 12:54:12 2018 -0700 Merge pull request #252 from AMReX-Codes/pgi fix PGI compilation commit e5734db5d003b76aaca6fe816f4940a0372ab2ec Author: Michael Zingale Date: Thu Apr 26 15:45:29 2018 -0400 fix PGI compilation PGI complains that with the 'pure' keyword here: PGF90-S-0074-Illegal number or type of arguments to heapsort_indirect_d - arguments of greater_d and cmp do not agree (/home/zingale/development/AMReX//Src/F_BaseLib/knapsack.f90: 85) Src/F_BaseLib/knapsack.f90 commit 68bba833e0a0d8fba8d6a2f71246f71d199377ba Merge: 8fea0d1e7 bd6b94802 Author: Ann Almgren Date: Thu Apr 26 12:16:23 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit 8fea0d1e7f4f4a674cbc6fb5313d5a931bf79dae Author: Ann Almgren Date: Thu Apr 26 12:14:48 2018 -0700 Remove unused variables Src/GeometryShop/AMReX_GeometryShop.cpp commit 93f4fc171fe1cfa41867639822f8a0370529d5ab Author: Weiqun Zhang Date: Thu Apr 26 11:12:28 2018 -0700 optimization in YAFluxRegister::define Src/Boundary/AMReX_YAFluxRegister.cpp commit 3f3764c7fa5fa40abd52c7d86f8773c7cbfbd3db Author: Weiqun Zhang Date: Thu Apr 26 11:10:04 2018 -0700 inline most of IntVect and Box functions Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_IndexType.H Src/Base/AMReX_IndexType.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp commit bd6b948020e9dbce9c347fd66aead8da6cfcfe39 Author: Weiqun Zhang Date: Wed Apr 25 22:13:20 2018 -0700 when BoxArray is cell-centered and its coarse ratio is 1, use the internal Box data directly Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.H commit 30fd2c465e794247100150f71a1dbcfc4427eeb1 Author: Weiqun Zhang Date: Wed Apr 25 16:41:46 2018 -0700 add Tests/complementIn Src/Base/AMReX_VisMF.cpp Tests/complementIn/GNUmakefile Tests/complementIn/Make.package Tests/complementIn/grids/grids_1 Tests/complementIn/grids/grids_10 Tests/complementIn/grids/grids_2 Tests/complementIn/grids/grids_3 Tests/complementIn/grids/grids_4 Tests/complementIn/grids/grids_5 Tests/complementIn/grids/grids_6 Tests/complementIn/grids/grids_7 Tests/complementIn/grids/grids_8 Tests/complementIn/grids/grids_9 Tests/complementIn/main.cpp commit be7ab93f5e0738b822b23846181787b245067b28 Author: Andrew Myers Date: Wed Apr 25 16:09:07 2018 -0700 replace sed with perl here. Tools/GNUMake/Make.rules commit ea1fe034c49c48c2ad4ba890829af2aad0e61502 Merge: 5528a3ec7 312177a52 Author: atmyers Date: Wed Apr 25 15:40:19 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 5528a3ec789d97133847253054bbaa4f910b0393 Author: atmyers Date: Wed Apr 25 15:40:08 2018 -0700 add this newline in a way that works with OS X sed. Tools/GNUMake/Make.rules commit 312177a5293d9b698eccd4b6045a5f3b3a3a3eab Merge: 01b1554df 77b78b0c4 Author: Weiqun Zhang Date: Wed Apr 25 15:13:08 2018 -0700 Merge branch 'development' into weiqun/complementIn commit 01b1554df6e779d5c604e740f27d70e94388be94 Author: Weiqun Zhang Date: Wed Apr 25 13:53:42 2018 -0700 fix assertion Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.cpp commit f8e8a57d01b048de780133deea1b2420de790a8c Author: Weiqun Zhang Date: Wed Apr 25 13:37:22 2018 -0700 more optimization on using complementIn Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxDomain.cpp Src/Particle/AMReX_ParticleContainerI.H commit 4840c15e93517ad255bb105aaeb26885fd667ba8 Author: Weiqun Zhang Date: Wed Apr 25 13:03:30 2018 -0700 optimization of BoxList::complementIn Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.cpp commit 77b78b0c484d9f6fc38ed6269a149fef72ceee61 Merge: 22f683129 111be5f60 Author: Michele Rosso Date: Wed Apr 25 11:23:47 2018 -0700 Merge branch 'mr/cmake' into development commit 22f6831291a5dc0f95b1bf8a893717ba246727b4 Author: atmyers Date: Wed Apr 25 10:39:51 2018 -0700 remove the newline here, as Mac's sed doesn't like it. Tools/GNUMake/Make.rules commit 2b99334edebe45bf75d08ff6e7dd69b5dc78f60d Author: atmyers Date: Wed Apr 25 10:22:48 2018 -0700 include missing header in AMReX_IntVect.H Src/Base/AMReX_IntVect.H commit 49447802658c3c5a0a6ba74cc315a9d5c4a3a324 Author: Weiqun Zhang Date: Tue Apr 24 14:57:10 2018 -0700 profiling BoxList::complementIn Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_BoxList.cpp commit 111be5f60825f5f5f98315da59724a3735f41556 Merge: a73f28375 d1cda11a4 Author: Michele Rosso Date: Tue Apr 24 11:35:28 2018 -0700 Merge branch 'development' into mr/cmake commit a73f283752aa92d024f254b867823f28d1bc76f3 Author: Michele Rosso Date: Tue Apr 24 11:30:27 2018 -0700 CMake:update docs Docs/sphinx_documentation/source/BuildingAMReX.rst Tools/CMake/AMReX_Config.cmake commit 7ad844e7f440bacac57b95d2bcc3f9fc5e400ad1 Author: Weiqun Zhang Date: Tue Apr 24 11:06:51 2018 -0700 BoxList::complementIn calls BoxArray::complementIn Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit d1cda11a49096835ad9416c21a894600294c43fd Author: Weiqun Zhang Date: Tue Apr 24 07:46:49 2018 -0700 fix typos Src/Base/AMReX_MultiFab.cpp commit e0d439155dee08047b0a14beecc9d4e3e26fe442 Author: Marc Day Date: Mon Apr 23 22:04:56 2018 -0700 Initialize fab ptr array with nullptr, allowing safe call to delete whether or not data allocated, then remove FabArray::ok() test in AmrData::FlushGrids, allowing FlushGrids to clear fabs even if not allocated. Add AmrData::FlushGrids() function to clear all variables. Src/Base/AMReX_FabArray.H Src/Extern/amrdata/AMReX_AmrData.H Src/Extern/amrdata/AMReX_AmrData.cpp commit 30f45deb470e4f78c2f1bdefc30cfbb874ca4886 Author: Weiqun Zhang Date: Mon Apr 23 17:08:30 2018 -0700 add some functions in MultiFab to deal with IntVect ghost cells Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit f0c4b170dde81ba06c6d5719f2792077d3dcac15 Author: Weiqun Zhang Date: Mon Apr 23 13:24:23 2018 -0700 add some profilers Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit 6a2a73ea6156730816c37d5861a96184af5eb59f Merge: a706ee742 d878fe0e1 Author: Weiqun Zhang Date: Mon Apr 23 13:21:14 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a706ee7421d62febc35e8ee1bc1430876e2c717d Author: Weiqun Zhang Date: Mon Apr 23 13:20:50 2018 -0700 BoxList::reserve is bad if it is used in a loop! Src/Base/AMReX_BoxList.cpp commit d878fe0e13c0f760e58a470c1a390735c5fa070b Merge: e3f5a4177 a5d5660b6 Author: Andrew Myers Date: Mon Apr 23 11:27:39 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e3f5a41778fa34f300ed8b6c302645a78d999016 Author: Andrew Myers Date: Mon Apr 23 11:23:16 2018 -0700 refactor the CreateVirtualParticles code so that we don't create the buffer if we're not doing Cell aggregation. Src/Particle/AMReX_ParticleContainerI.H commit d37679f6c8160df0d58bfb7c5276482c82e5e233 Author: Andrew Myers Date: Mon Apr 23 10:53:52 2018 -0700 use a C++-style cast here. Src/Particle/AMReX_ParticleContainerI.H commit a5d5660b645a82adebe50675409e3b956f2fdb60 Author: Weiqun Zhang Date: Sat Apr 21 18:38:47 2018 -0700 add --enable-xsdk-defaults to configure Tools/GNUMake/Make.defs Tools/libamrex/configure.py commit b1db263331fadaef7ef99de49acb2f78a7c61366 Author: Weiqun Zhang Date: Sat Apr 21 18:02:08 2018 -0700 some amrex prefix in EB Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_IrregNode.cpp Src/GeometryShop/AMReX_NormalDerivative.cpp Src/GeometryShop/AMReX_SmoothIntersection.cpp Src/GeometryShop/AMReX_TransformIF.cpp Tutorials/EB/CNS/Exec/Combustor/bc_fill_nd.F90 Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/EB/CNS/Source/fortran/bc_fill_nd.F90 commit f2547bad2e931f0fffc27ffd837120a7607030da Author: Weiqun Zhang Date: Sat Apr 21 17:37:13 2018 -0700 do not build with unused old particles fortran routines Src/Particle/AMReX_Particles_1D.F Src/Particle/AMReX_Particles_2D.F Src/Particle/AMReX_Particles_3D.F Src/Particle/AMReX_Particles_F.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 5052604452c166d50d4f0d6e7c822f78f0180ae1 Author: Weiqun Zhang Date: Sat Apr 21 17:25:59 2018 -0700 AMREX_XSDK: Particle/ Src/Particle/AMReX_LoadBalanceKD.H Src/Particle/AMReX_LoadBalanceKD.cpp Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_Particles_F.H commit aa0e54d87828a423ffeca6170fdce01243c09031 Author: Weiqun Zhang Date: Sat Apr 21 15:55:03 2018 -0700 AMREX_XSDK: C_CellMG/ Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp commit 162bff367c73cec49dd75a138441b5842bf88235 Author: Weiqun Zhang Date: Sat Apr 21 15:31:29 2018 -0700 some amrex_ in LinearSovlers/ Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp commit e007f99754dd0eab2fc5a168128f6e9db5b08c60 Author: Weiqun Zhang Date: Sat Apr 21 14:34:52 2018 -0700 AMREX_XSDK: Boundary/ Src/Base/AMReX_BaseFab.H Src/Boundary/AMReX_INTERPBNDRYDATA_F.H Src/Boundary/AMReX_LO_BCTYPES.H Src/Boundary/AMReX_MacBndry.cpp Src/Boundary/AMReX_Mask.cpp Src/Boundary/AMReX_YAFluxRegister.H commit 91e86836ce1aa838a32709933489c30d70b31221 Author: Weiqun Zhang Date: Sat Apr 21 14:04:54 2018 -0700 amrex prefix in Amr/ Src/Amr/AMReX_Extrapolater.cpp Src/Amr/AMReX_extrapolater_1d.f90 Src/Amr/AMReX_extrapolater_2d.f90 Src/Amr/AMReX_extrapolater_3d.f90 commit cb60a3940241fe0790922fffb7f0a1d2134aef4f Merge: ce70eec0b 39d1e7537 Author: Weiqun Zhang Date: Sat Apr 21 10:48:48 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ce70eec0b05dd8fc390ee14b578702323263d082 Author: Weiqun Zhang Date: Sat Apr 21 10:47:09 2018 -0700 Merge branch 'weiqun/ng' into development Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_TagBox.cpp Src/AmrTask/AMFIter/AMReX_AmrTask.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_iMultiFab.cpp Tools/CompileTesting/compiletesting.py commit ca83d229516cb7f35289b2554ae23f92d1c5d274 Author: Michele Rosso Date: Fri Apr 20 17:37:41 2018 -0700 CMake:generate AMReX_BuildInfo.cpp and include it in the build Src/CMakeLists.txt Tools/CMake/AMReX_CMakeVariables.cmake commit e38a7136a4fbb7719e8ccae96ae0cee27e26765a Author: Michele Rosso Date: Fri Apr 20 15:56:04 2018 -0700 CMake:fix CMakeLists bugs Src/LinearSolvers/CMakeLists.txt commit c53e284bd5ae66b8bcd01544f8a91f9bc5250d7a Author: Max Katz Date: Fri Apr 20 18:46:10 2018 -0400 Sync up Titan build properties for CUDA Tools/GNUMake/sites/Make.olcf commit 8461af813f8ceb46b31d61f909f9437d0d6187f3 Author: Max Katz Date: Fri Apr 20 18:45:52 2018 -0400 Guard against using CUDA 8 when unavailable Src/Base/AMReX_Device.cpp commit 39d1e7537af60f65ef3bede08cc344c59d99035e Merge: b88060155 a86ea2314 Author: atmyers Date: Fri Apr 20 15:27:17 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b88060155c4b29187934939b2a6f79ed06bc004d Author: atmyers Date: Fri Apr 20 15:09:47 2018 -0700 be more conservative with writing output files in this tutorial by default. Tutorials/Particles/ElectrostaticPIC/inputs Tutorials/Particles/ElectrostaticPIC/main.cpp commit a86ea2314f5f07a926424cf013be488bca91b646 Author: Weiqun Zhang Date: Fri Apr 20 14:53:46 2018 -0700 for typecheck Src/Boundary/AMReX_INTERPBNDRYDATA_F.H commit a62dfa12c8699fdc8b350a418a09b200c53fdf61 Merge: b59eb2627 55b3f9aa9 Author: Ann Almgren Date: Fri Apr 20 14:00:41 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit b59eb2627d2cb68c5469cf880d7b695884e7d29d Author: Ann Almgren Date: Fri Apr 20 14:00:12 2018 -0700 Move distribution.h to distribution_c.h Src/Extern/SWFFT/Distribution.H Src/Extern/SWFFT/Make.package Src/Extern/SWFFT/distribution.c Src/Extern/SWFFT/distribution_c.h commit 1cfe35871c704c75eb7a8839721eaf2293136af2 Author: Weiqun Zhang Date: Fri Apr 20 11:14:43 2018 -0700 fix makefile Src/LinearSolvers/MLMG/Make.package commit a5b33c3c8ac3fae338eb738e0993887d74889fd8 Merge: 400f5d26f 55b3f9aa9 Author: Weiqun Zhang Date: Fri Apr 20 11:11:22 2018 -0700 Merge branch 'development' into weiqun/mlmg commit 55b3f9aa91dc7dcac2d4c3ff4892b14066877451 Author: Weiqun Zhang Date: Fri Apr 20 11:04:03 2018 -0700 AMREX_CRSEGRNDOMP Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp Tutorials/EB/CNS/Exec/Make.CNS commit a6f687cb040be85e03920b6f783164204a5a2c44 Author: Weiqun Zhang Date: Fri Apr 20 10:54:11 2018 -0700 minor Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_StateData.cpp commit dcafcf9eba81bf57f3399d2713e1bab00411ccd5 Author: Michele Rosso Date: Fri Apr 20 10:44:39 2018 -0700 CMake:more xSDK stuff Src/CMakeLists.txt Src/F_BaseLib/CMakeLists.txt Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit 8e10f0625357d31c5c6786ae25619d8d3cf24f18 Author: Weiqun Zhang Date: Fri Apr 20 10:30:34 2018 -0700 add anonymous namespace to some file scope classes Src/AmrCore/AMReX_Cluster.cpp commit b770a6df9ca6b36df9004168da130139a99f97d5 Author: Weiqun Zhang Date: Fri Apr 20 09:57:53 2018 -0700 use amrex_bc_types_module instead of AMReX_bc_types.fi Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 commit 18006c1d807b92eb140edd9195eb494c08d8f4b9 Author: Weiqun Zhang Date: Fri Apr 20 09:35:51 2018 -0700 remove some old tutorials OldTutorials/GettingStarted_C/GNUmakefile OldTutorials/GettingStarted_C/Make.package OldTutorials/GettingStarted_C/main.cpp OldTutorials/GettingStarted_C/work_on_data_2d.f90 OldTutorials/GettingStarted_C/work_on_data_3d.f90 OldTutorials/HeatEquation_EX2_C/FILCC_2D.F OldTutorials/HeatEquation_EX2_C/FILCC_3D.F OldTutorials/HeatEquation_EX2_C/GNUmakefile OldTutorials/HeatEquation_EX2_C/Make.package OldTutorials/HeatEquation_EX2_C/advance_2d.f90 OldTutorials/HeatEquation_EX2_C/advance_3d.f90 OldTutorials/HeatEquation_EX2_C/bc_fill_nd.F90 OldTutorials/HeatEquation_EX2_C/init_phi_2d.f90 OldTutorials/HeatEquation_EX2_C/init_phi_3d.f90 OldTutorials/HeatEquation_EX2_C/inputs_2d OldTutorials/HeatEquation_EX2_C/inputs_3d OldTutorials/HeatEquation_EX2_C/main.cpp OldTutorials/HeatEquation_EX2_C/myfunc_F.H OldTutorials/HeatEquation_EX2_C/writePlotFile.H OldTutorials/HeatEquation_EX2_C/writePlotFile.cpp commit ec4c73fd3ddb23c1ce595a50378b10ec250f8f19 Author: Weiqun Zhang Date: Fri Apr 20 09:30:42 2018 -0700 add AMREX_ Src/Extern/ProfParser/AMReX_AVGDOWN_2D.F Src/Extern/ProfParser/AMReX_AVGDOWN_3D.F Src/Extern/amrdata/AMReX_FABUTIL_1D.F Src/Extern/amrdata/AMReX_FABUTIL_2D.F Src/Extern/amrdata/AMReX_FABUTIL_3D.F Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit 400f5d26f89a4cb7023e1a4e438c5d20d5ed273f Author: Weiqun Zhang Date: Fri Apr 20 09:04:17 2018 -0700 start MLEBABecLap Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.H Src/LinearSolvers/MLMG/AMReX_MLEBABecLap.cpp Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLEBABecLap_F.H Src/LinearSolvers/MLMG/Make.package commit eb2f3a9f4c68d4dc2d893869a651d828164f0df6 Author: Marc Day Date: Thu Apr 19 18:00:42 2018 -0700 Add a simple AmrData-based function to computer (weighted) horizontal averages of plotfile variables. Tools/Postprocessing/C_Src/HorizontalAvg.cpp commit 735b0817690d7ae7afb22cb98fff2a177cf4e775 Author: Michele Rosso Date: Thu Apr 19 15:03:14 2018 -0700 CMake:one step closer to xSDK compliance Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_CompilersFlags.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake commit 6757f9057a15e0cdea4a7e3312b8e475e20019e4 Merge: 5cf25428a 9377350b0 Author: atmyers Date: Thu Apr 19 12:40:49 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5cf25428a2f1b223d8f693bb9f3e8361f677e010 Author: atmyers Date: Thu Apr 19 12:40:37 2018 -0700 move these function out of an anonymous namepsace and into a separate file to avoid compiler warnings. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleMPIUtil.H Src/Particle/AMReX_ParticleMPIUtil.cpp Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 1a3b0134e33a4e0bd09f2660a1559208a8e83b42 Merge: 8b098b3d6 9377350b0 Author: Weiqun Zhang Date: Thu Apr 19 11:36:23 2018 -0700 Merge branch 'development' into weiqun/mlmg commit b86b03823106cbbbc0d2f748c75186a1f094a63a Author: atmyers Date: Thu Apr 19 11:23:06 2018 -0700 remove some unused variables from the ElectrostaticPIC particle container Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/main.cpp commit 9377350b053d062498b3d172eb57110f1ddf710f Author: Weiqun Zhang Date: Thu Apr 19 11:08:07 2018 -0700 amrex prefix in LinearSolver/ Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H Src/LinearSolvers/C_CellMG/AMReX_LO_F.H Src/LinearSolvers/C_CellMG/AMReX_LP_F.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MG_F.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp Tests/LinearSolvers/C_CellMG/COEF_F.H Tests/LinearSolvers/C_CellMG/MACOPERATOR_F.H Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 3c96a022754d4e23196249a6bc2d712de696aa22 Author: Weiqun Zhang Date: Thu Apr 19 10:49:44 2018 -0700 amrex prefix in Amr/ and Particle/ etc. Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_Derive.H Src/Amr/AMReX_StateDescriptor.cpp Src/Extern/ProfParser/AMReX_AVGDOWN_F.H Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp Src/Extern/ProfParser/BLProfParser.y Src/Extern/amrdata/AMReX_AmrData.cpp Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp Src/Particle/AMReX_ParticleContainerI.H Tests/C_BaseLib/tUMap.cpp Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 6d5184e5529f89dacbd19426796776ae6fc1a75b Merge: a603506e9 97444ff82 Author: atmyers Date: Thu Apr 19 10:42:31 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a603506e96feb105ade36261af93b56f48dec74c Author: atmyers Date: Thu Apr 19 10:42:19 2018 -0700 remove the ShortRangeParticles tutorial, as that stuff is all included in the NeighborList tutorial now. Tutorials/Particles/ShortRangeParticles/GNUmakefile Tutorials/Particles/ShortRangeParticles/Make.package Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.H Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp Tutorials/Particles/ShortRangeParticles/inputs Tutorials/Particles/ShortRangeParticles/main.cpp Tutorials/Particles/ShortRangeParticles/short_range_2d.f90 Tutorials/Particles/ShortRangeParticles/short_range_3d.f90 Tutorials/Particles/ShortRangeParticles/short_range_F.H commit c54dbb53991de2178c4219b8e0cd7a9b2a11d418 Author: atmyers Date: Thu Apr 19 10:40:46 2018 -0700 some minor tweaks to the particle documentation. Docs/sphinx_documentation/source/Chapter8.rst Docs/sphinx_documentation/source/Particle.rst commit bcef2ec62714231bc3fea438e6740bb86c9ff8b2 Author: atmyers Date: Thu Apr 19 10:40:11 2018 -0700 add some info about the particle tutorials Docs/sphinx_tutorials/source/Particles_Tutorial.rst commit 29aa16d89d78d32345820ac94344251d5ef7c114 Author: atmyers Date: Thu Apr 19 10:39:44 2018 -0700 fix typo Docs/sphinx_tutorials/source/Basic_Tutorial.rst commit 8b098b3d6fddbd1a5fb2419bbb5fe8727cd73d25 Merge: 569fbb7e9 97444ff82 Author: Weiqun Zhang Date: Thu Apr 19 10:15:27 2018 -0700 Merge branch 'development' into weiqun/mlmg commit 97444ff82e68152dfbe23683c7351fb64ae60b86 Author: Weiqun Zhang Date: Thu Apr 19 09:05:20 2018 -0700 fix the conflict between macro and enum type Src/Base/AMReX_BC_TYPES.H Src/Boundary/AMReX_MacBndry.cpp commit 9f51a2411effe7f9825792f40786b1bb09f81f56 Author: Weiqun Zhang Date: Thu Apr 19 08:56:19 2018 -0700 remove preprocessor directive form AMReX_bc_types.fi Src/Base/AMReX_bc_types.fi commit 44f4e62b87aa66649821cf0c4f2133478b32b66a Author: Weiqun Zhang Date: Wed Apr 18 22:03:50 2018 -0700 amrex prefix in AmrCore and Boundary Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_ErrorList.cpp Src/AmrCore/AMReX_FLUXREG_F.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_INTERP_F.H Src/AmrCore/AMReX_Interpolater.cpp Src/Boundary/AMReX_INTERPBNDRYDATA_F.H Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_MacBndry.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrCore/Source/bc_fill_nd.F90 commit ed3114726281c6c8a83d0dd32ea86f751818bbb3 Author: Weiqun Zhang Date: Wed Apr 18 17:02:23 2018 -0700 D_DECL --> AMREX_D_DECL Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp commit 8ae4df53765566c6927d40d6779f15448269cdda Author: Weiqun Zhang Date: Wed Apr 18 16:57:23 2018 -0700 AMREX_XSDK: bc types and filcc Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_filcc_mod.F90 commit 9d5c692a9e18614187bf3ed52cbd04a35ba6e853 Author: Weiqun Zhang Date: Wed Apr 18 14:56:52 2018 -0700 make sure enum base type is int in BC_TYPES.H Src/Base/AMReX_BC_TYPES.H commit 2175e85d8e83c51b173e0e58f54f70db05612788 Author: Weiqun Zhang Date: Wed Apr 18 14:31:30 2018 -0700 AMREX_XSDK: BC_TYPES.H Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BC_TYPES.H Src/Base/AMReX_bc_types_mod.F90 commit 339c5f7d712d6906f63bbe7521cd1bbe9ed70362 Author: Weiqun Zhang Date: Wed Apr 18 14:06:10 2018 -0700 add amrex_random and amrex_random_int and AMREX_XSDK old fortran interface to amrex::Random Src/Base/AMReX_RealVect.cpp Src/Base/AMReX_Utility.cpp Src/Base/AMReX_fort_mod.F90 commit bb970363e5ad3abb5a1552bb0951df63f85f9501 Author: Michele Rosso Date: Wed Apr 18 15:31:52 2018 -0700 CMake:fix tutorials link issue Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt commit b7e10e2c7f1890830f4c50264e2b62dfcb066211 Author: Michele Rosso Date: Wed Apr 18 13:05:17 2018 -0700 CMake:forgot to include Fortran-only defines Tools/CMake/AMReX_CompilersFlags.cmake commit ebf787d99bb1301fc8a187140dba3cbc89af6a2e Author: dtgraves Date: Wed Apr 18 11:33:05 2018 -0700 added some const_cast calls so that ParallelContext will continue to compile with old versions of MPI. Src/Base/AMReX_ParallelContext.cpp commit b0b41cd7578a456afa64ed37aee80762a278c638 Merge: 362d97cdd 6e6c7438c Author: dtgraves Date: Wed Apr 18 11:16:16 2018 -0700 Merge pull request #249 from AMReX-Codes/dtg_branch moment convergence test good to go. commit 6e6c7438ced05773f6bd9b163abacad21950d186 Author: dtgraves Date: Wed Apr 18 11:14:56 2018 -0700 fixed another test that got broken by an interface change. Moment convergence test works fine. Tests/GeometryShop/regression/fabfromif.cpp Tests/GeometryShop/regression/simplemomentexample.inputs commit db577d9eb4a17e71f71cbb67bb249e3fcb612ce8 Author: Michele Rosso Date: Wed Apr 18 11:11:41 2018 -0700 CMake: modify how compiler flags are handled Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_CompilersFlags.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit 362d97cddf7e91d9fb31143064021149432c4c6a Author: Weiqun Zhang Date: Wed Apr 18 11:03:41 2018 -0700 fix a test Tests/C_BaseLib/tUMap.cpp commit f12b2c1d0f92142187f9ad55f845cd0f4633ddb7 Merge: ad9c33b56 99feb1f8f Author: dtgraves Date: Wed Apr 18 10:54:49 2018 -0700 Merge branch 'development' into dtg_branch commit 99feb1f8fe04262cec2e8ce32f96556f1c09e0fb Author: Weiqun Zhang Date: Wed Apr 18 10:27:17 2018 -0700 mempool_module --> amrex_mempool_module Docs/sphinx_documentation/source/Basics.rst Src/AmrCore/AMReX_FillPatchUtil_2d.F90 Src/AmrCore/AMReX_FillPatchUtil_3d.F90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_2d/slope_2d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_3d/slope_3d.f90 Src/Base/AMReX_mempool_f.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/vector_i.f90 Src/F_Interfaces/Base/AMReX_base_mod.F90 Src/F_Interfaces/Base/AMReX_fab_mod.F90 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/slope_3d.f90 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_3d/slope_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/slope_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/slope_3d.f90 Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90 commit 3697f0ef75361d0102c196242bbf805a16890b10 Author: Weiqun Zhang Date: Wed Apr 18 10:00:24 2018 -0700 AMREX_XSDK: filcc Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 Tutorials/Basic/HeatEquation_EX2_C/Source/AMReX_FILCC_2D.F Tutorials/Basic/HeatEquation_EX2_C/Source/AMReX_FILCC_3D.F commit 670ceda20bb5aa4f2945ec31578d951fe196e95f Author: Weiqun Zhang Date: Tue Apr 17 14:48:01 2018 -0700 use new ArrayLim macros in Base Src/Amr/AMReX_AmrLevel.cpp Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_COORDSYS_F.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp commit 1f1ac77996a4753a378be86ec207017ca8903af2 Author: Weiqun Zhang Date: Tue Apr 17 14:34:55 2018 -0700 FORTRAN_BOXLIB --> AMREX_FORTRAN_BOXLIB; add amrex prefix a BaseFab Fortran functions; add amrex prefix to macros in AMReX_ArrayLim.H. Src/Base/AMReX_Array.H Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BLassert.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_MemPool.cpp Src/F_BaseLib/backtrace_c.cpp Tools/F_mk/GMakedefs.mak commit b64321e18c2c2e767586534159b5049c706c7d9e Author: Weiqun Zhang Date: Tue Apr 17 17:28:26 2018 -0700 put subroutine filcc inside #ifndef AMREX_XSDK Src/Base/AMReX_BLBoxLib_F.F90 Src/Base/AMReX_BLProfiler_F.F90 Src/Base/AMReX_BLutil_F.F90 Src/Base/AMReX_BaseUmap_f.H Src/Base/AMReX_BaseUmap_nd.f90 Src/Base/AMReX_FILCC_1D.F90 commit e1307eed39a43750f8056325f64dd652679e42c3 Author: Weiqun Zhang Date: Tue Apr 17 17:08:19 2018 -0700 add missing std:: Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 8c73047c59c85bdca40abdd41d4b9db7fa34eb04 Author: Weiqun Zhang Date: Tue Apr 17 16:23:10 2018 -0700 D_* -> AMREX_D_* macros in Base/ Src/Base/AMReX_IntVect.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_SPACE.H Src/Base/AMReX_SPMD.H Src/Base/AMReX_SPMDI.H Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp commit 774cd6bad1887f30dede73c9a1342e8e2c3dc5ce Author: Weiqun Zhang Date: Tue Apr 17 15:54:43 2018 -0700 put some variables inside #ifndef AMREX_XSDK Src/Base/AMReX_CONSTANTS.H Src/Base/AMReX_REAL.H Src/Base/AMReX_bc_types.fi Src/Base/AMReX_bc_types_mod.F90 commit 85a4e2b00f3360d1b4bb97204e1230435710aeb6 Author: Weiqun Zhang Date: Tue Apr 17 15:43:12 2018 -0700 more namespace/prefix changes in Base/ Src/Base/AMReX_BLFort.H Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BaseUmap_f.H Src/Base/AMReX_PhysBCFunct.H Tests/ProfTests/ThirdParty/Source/main.cpp commit 891e590eb85ef939af6e081dca33b014cd48602b Author: Johannes Blaschke Date: Tue Apr 17 17:13:41 2018 -0700 fillNodalMultifab: allignment factor could be ratio => int -> Real Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp commit ad9c33b56edae74a64309047a2ea2f0ed9b2b826 Author: dtgraves Date: Tue Apr 17 17:04:03 2018 -0700 added moment convergence test. Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/momentConvTest.cpp Tests/GeometryShop/regression/momentconvtest.inputs commit 30f207076f657dca3e9f41cad5a99945849bf0ad Author: Weiqun Zhang Date: Tue Apr 17 11:09:47 2018 -0700 amrex prefix for include guards Src/AmrCore/AMReX_AmrParGDB.H Src/Boundary/AMReX_InterpBndryData.H Src/GeometryShop/AMReX_AggStencil.H Src/GeometryShop/AMReX_AggStencilI.H Src/GeometryShop/AMReX_AllRegularService.H Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H Src/GeometryShop/AMReX_AnisotropicIF.H Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_BaseEBCellFactory.H Src/GeometryShop/AMReX_BaseEBFaceFAB.H Src/GeometryShop/AMReX_BaseEBFaceFABI.H Src/GeometryShop/AMReX_BaseIF.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_CH_EBIS_ORDER.H Src/GeometryShop/AMReX_CellEdge.H Src/GeometryShop/AMReX_ComplementIF.H Src/GeometryShop/AMReX_ConstrainedLS.H Src/GeometryShop/AMReX_CoordinateSystem.H Src/GeometryShop/AMReX_CoordinateSystemImplem.H Src/GeometryShop/AMReX_CutCellMoments.H Src/GeometryShop/AMReX_CutCellMomentsImplem.H Src/GeometryShop/AMReX_DivNormalRefinement.H Src/GeometryShop/AMReX_DivNormalRefinementImplem.H Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBCellFAB.H Src/GeometryShop/AMReX_EBCellFactory.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBDataVarMacros.H Src/GeometryShop/AMReX_EBDebugDump.H Src/GeometryShop/AMReX_EBDebugOut.H Src/GeometryShop/AMReX_EBFaceFAB.H Src/GeometryShop/AMReX_EBFluxFAB.H Src/GeometryShop/AMReX_EBFluxFactory.H Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBISBox.H Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBLevelGrid.H Src/GeometryShop/AMReX_EBLevelRedist.H Src/GeometryShop/AMReX_EBLoHiCenter.H Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.H Src/GeometryShop/AMReX_EB_TYPEDEFS.H Src/GeometryShop/AMReX_EllipsoidIF.H Src/GeometryShop/AMReX_ExtrudeIF.H Src/GeometryShop/AMReX_FabArrayIO.H Src/GeometryShop/AMReX_FaceIndex.H Src/GeometryShop/AMReX_FaceIterator.H Src/GeometryShop/AMReX_Factorial.H Src/GeometryShop/AMReX_FixedRefinement.H Src/GeometryShop/AMReX_FixedRefinementImplem.H Src/GeometryShop/AMReX_FlatPlateGeom.H Src/GeometryShop/AMReX_GenericArithmetic.H Src/GeometryShop/AMReX_GenericArithmeticI.H Src/GeometryShop/AMReX_GeomIntersectUtils.H Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GraphNode.H Src/GeometryShop/AMReX_IFData.H Src/GeometryShop/AMReX_IFDataImplem.H Src/GeometryShop/AMReX_IFSlicer.H Src/GeometryShop/AMReX_IFSlicerImplem.H Src/GeometryShop/AMReX_IndexTM.H Src/GeometryShop/AMReX_IndexTMI.H Src/GeometryShop/AMReX_IndexedMoments.H Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntersectionIF.H Src/GeometryShop/AMReX_IrregFAB.H Src/GeometryShop/AMReX_IrregFABFactory.H Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_KDStruct.H Src/GeometryShop/AMReX_KDTree.H Src/GeometryShop/AMReX_LSProblem.H Src/GeometryShop/AMReX_LSProblemImplem.H Src/GeometryShop/AMReX_LSquares.H Src/GeometryShop/AMReX_LatheIF.H Src/GeometryShop/AMReX_LoHiSide.H Src/GeometryShop/AMReX_MetaPrograms.H Src/GeometryShop/AMReX_MinimalCCCM.H Src/GeometryShop/AMReX_MinimalCCCMImplem.H Src/GeometryShop/AMReX_MomentIterator.H Src/GeometryShop/AMReX_MomentIteratorImplem.H Src/GeometryShop/AMReX_Moments.H Src/GeometryShop/AMReX_MonomialPowers.H Src/GeometryShop/AMReX_MultiIndex.H Src/GeometryShop/AMReX_MultiIndexImplem.H Src/GeometryShop/AMReX_NoRefinement.H Src/GeometryShop/AMReX_NoRefinementImplem.H Src/GeometryShop/AMReX_NormalDerivative.H Src/GeometryShop/AMReX_NormalDerivativeNew.H Src/GeometryShop/AMReX_Notation.H Src/GeometryShop/AMReX_PXStuff.H Src/GeometryShop/AMReX_PlaneIF.H Src/GeometryShop/AMReX_PolyGeom.H Src/GeometryShop/AMReX_PolynomialIF.H Src/GeometryShop/AMReX_RedistStencil.H Src/GeometryShop/AMReX_RefinementCriterion.H Src/GeometryShop/AMReX_STLAsciiReader.H Src/GeometryShop/AMReX_STLBox.H Src/GeometryShop/AMReX_STLExplorer.H Src/GeometryShop/AMReX_STLIF.H Src/GeometryShop/AMReX_STLMesh.H Src/GeometryShop/AMReX_STLReader.H Src/GeometryShop/AMReX_STLUtil.H Src/GeometryShop/AMReX_SmoothAbsoluteValue.H Src/GeometryShop/AMReX_SmoothIntersection.H Src/GeometryShop/AMReX_SmoothUnion.H Src/GeometryShop/AMReX_SphereIF.H Src/GeometryShop/AMReX_Stencils.H Src/GeometryShop/AMReX_TransformIF.H Src/GeometryShop/AMReX_UnionIF.H Src/GeometryShop/AMReX_VoFIterator.H Src/GeometryShop/AMReX_VolIndex.H Src/GeometryShop/AMReX_WrappedGShop.H Src/GeometryShop/AMReX_ZCylinder.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_LO_F.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_MG_F.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_CellMG4/AMReX_ABec2.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/AMReX_MCLO_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H Src/LinearSolvers/C_to_F_MG/AMReX_stencil_types.H Tools/GNUMake/Make.defs commit b8f396ec0cfb0e877e72186654f0b1ad81c617ac Merge: b44b81aed 2d132dab7 Author: dtgraves Date: Tue Apr 17 12:36:51 2018 -0700 Merge pull request #248 from AMReX-Codes/dtg_branch adding simple higher order moments example commit 2d132dab7dfd663855302e967d061035f56cf094 Author: dtgraves Date: Tue Apr 17 12:34:43 2018 -0700 added simple example that illustrates moment stuff. I also fixed a test whose interface had moved out from under it. Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/fabfromif.cpp Tests/GeometryShop/regression/momentConvTest.cpp Tests/GeometryShop/regression/simpleMomentExample.cpp Tests/GeometryShop/regression/simplemomentexample.inputs Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp commit 32eafac9ccb933cafa8a05acbd2fa3a0c7d941c7 Author: Michele Rosso Date: Tue Apr 17 11:48:06 2018 -0700 CMake:start implementation of xSDK guidelines Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake commit b44b81aede83fbd6c64982b89228f2b0fa996a93 Author: atmyers Date: Tue Apr 17 11:40:52 2018 -0700 allow the passing of a number of ghost cells when constructing the redistribute mask Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit e556a7f9a5ee8abe7ffb8f223c0adc3c463af84c Merge: 70a230f97 68a935f67 Author: Johannes Blaschke Date: Mon Apr 16 18:03:48 2018 -0700 Merge remote-tracking branch 'origin/development' into jpb/fill-nodal commit 70a230f9734349beb459c0d3dbb88068bf65929e Author: Johannes Blaschke Date: Mon Apr 16 18:03:14 2018 -0700 allow filling nodal MF with different refinement than EBIndexSpace's dx Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp commit 92fe4596f2e16adc74ae3bf72d738fb42c0f5d29 Author: shashankNREL Date: Mon Apr 16 14:05:12 2018 -0600 Modification of MLMG to use IJ matrix interface Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/GNUmakefile Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 68a935f67ba536a39b7ae45847eaf2da52fd155e Author: Weiqun Zhang Date: Mon Apr 16 10:25:01 2018 -0700 restore previous exception trap status in amrex::Finalize Src/Base/AMReX.cpp commit e522d40b4d0a51ec6dc9ed9b67af096866772365 Author: Weiqun Zhang Date: Mon Apr 16 09:51:09 2018 -0700 add amrex.call_addr2line parameter so that the call to add2rline can be skipped Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp commit ef0c670b5e85dc14ad7f179e956d4e5137c98bd2 Author: Weiqun Zhang Date: Mon Apr 16 09:15:07 2018 -0700 move SIG_DFL to the beginning of handler Src/Base/AMReX_BLBackTrace.cpp commit 8de1a0e585f30114133a8b47e64292f50be1d489 Author: Weiqun Zhang Date: Sun Apr 15 13:31:41 2018 -0700 add a Fortran module for ParallelDescriptor Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParallelDescriptor_F.F90 Src/Base/CMakeLists.txt Src/Base/Make.package commit 1e2e572904876e8751e1cb23b221ef6d2cc17d40 Author: Michael Zingale Date: Sat Apr 14 13:15:23 2018 -0400 simple script to report git describe/hashes Tools/C_scripts/describe_sources.py commit 9f51cd25986ee55af04d34ef53d5fc70625238c7 Author: Weiqun Zhang Date: Thu Apr 12 17:58:13 2018 -0700 This is weird. GCC 7 with certain combination of flags requires explicitly defining these std::allocator's otherwise it fails at link time. Note that we have seen this before. Src/Base/AMReX.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_ParallelReduce.H Src/F_Interfaces/Base/AMReX_plotfile_fi.cpp commit f2ef816b6cf449230d09ceb09e21b38a9651bdf1 Author: Weiqun Zhang Date: Thu Apr 12 17:38:01 2018 -0700 Comment out everything in Make.local.template. It was meant just to show things that can be done in Make.local, not meant for people to simply copy it to Make.local Tools/GNUMake/Make.local.template commit e4267a4b6bba3fcce6419a2e20089c5b01463065 Author: Michele Rosso Date: Thu Apr 12 17:06:21 2018 -0700 CMake: fix bug in site recognition Tools/CMake/AMReX_Machines.cmake Tools/CMake/AMReX_ThirdPartyProfilers.cmake commit 2c6c68900a84adf027b967e863ac0e516774f035 Author: Michele Rosso Date: Thu Apr 12 15:41:10 2018 -0700 CMake: add support for third party profiler tools Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Machines.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_ThirdPartyProfilers.cmake commit 976c62c64632b1e92dff3696a03c022113000a57 Author: Michele Rosso Date: Thu Apr 12 14:22:23 2018 -0700 CMake: add host infos and third party profiling options Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Machines.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_Utils.cmake commit 870c5313061d79bab638afd74853348c865aa924 Merge: 00d14a954 8367fb069 Author: Michele Rosso Date: Thu Apr 12 10:41:56 2018 -0700 Merge branch 'development' into mr-cmake commit 00d14a954d4c6251810f8beffd82c9ec3bfb89df Author: Michele Rosso Date: Thu Apr 12 10:40:10 2018 -0700 CMake: turn off verbosity by default CMakeLists.txt commit 4c9177ccb69370e5aa8f290fdc85bb2e04dddb6b Author: Michele Rosso Date: Thu Apr 12 10:30:37 2018 -0700 CMake: slightly modify setup CMakeLists.txt Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Compilers.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_Utils.cmake Tools/CMake/AMReX_Version.cmake commit 87877ab6123b097f845747a60b1da08962a9a621 Author: shashankNREL Date: Thu Apr 12 10:44:23 2018 -0600 Removed some additional unused variables Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp commit ad995706cc25b033a149ccb825d4cfc48368f1e2 Author: shashankNREL Date: Thu Apr 12 10:39:48 2018 -0600 Optimized the IJ matrix interface Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit 8367fb069b35feda18e5fd2d693ac56425c01ca7 Author: Weiqun Zhang Date: Thu Apr 12 08:36:26 2018 -0700 fix AMREX_DIMENSION_AGNOSTIC Tools/GNUMake/Make.defs commit 312c3ce7096992cbebc62a085c1b50789ca3a77b Author: Weiqun Zhang Date: Wed Apr 11 16:53:23 2018 -0700 add AMREX_NO_STRICT_PREFIX Tools/CMake/AMReX_Defines.cmake Tools/GNUMake/Make.defs commit 66a2edee2371a4d3bfca8344b75040976bf77e4f Author: Weiqun Zhang Date: Wed Apr 11 16:05:27 2018 -0700 update cmake for AMREX_DEBUG and AMREX_PARTICLES Tools/CMake/AMReX_Defines.cmake commit 4e275142d32b64014e7cdab5036845d0429b8c71 Author: Weiqun Zhang Date: Wed Apr 11 15:41:07 2018 -0700 DEBUG --> AMREX_DEBUG Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArrayCommI.H Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_NFiles.cpp Src/Extern/ProfParser/AMReX_BLProfStats.cpp Tools/GNUMake/Make.defs commit fe79f26cbb094260962f42a1c1704edaa48a3396 Author: Weiqun Zhang Date: Wed Apr 11 13:37:03 2018 -0700 DIMENSION_AGNOSTIC --> AMREX_DIMENSION_AGNOSTIC Src/Amr/AMReX_Amr.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Tools/GNUMake/Make.defs commit ac2cfc2be8956e96d1209d35e8268119bb87e7d0 Author: Weiqun Zhang Date: Wed Apr 11 13:32:27 2018 -0700 add AMREX_ version of BL_* definitions Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 0c3df7da9bacc0aa104f38116979450aba18f55c Author: Weiqun Zhang Date: Wed Apr 11 12:59:39 2018 -0700 USE_CVODE --> AMREX_USE_CVODE Tools/GNUMake/packages/Make.cvode commit dd4f343a0aa6fb91ba0ba7d5649dc96c2ced7313 Author: Weiqun Zhang Date: Wed Apr 11 11:38:29 2018 -0700 PARTICLES and USE_PARTICLES --> AMREX_PARTICLES Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.H Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.cpp Src/Particle/AMReX_NeighborParticles.H Tools/GNUMake/Make.defs Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.H Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit f7182adb215f8afd2d7fd4a1063e1db5242d2813 Author: kngott Date: Wed Apr 11 14:23:15 2018 -0700 Adjust third party profiling macros to 'AMREX_name'. Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_ThirdPartyProfiling.H Tools/GNUMake/Make.defs Tools/GNUMake/tools/Make.craypat Tools/GNUMake/tools/Make.forge Tools/GNUMake/tools/Make.vtune commit 5fff2799856996b6f675b85d00619056004a2798 Author: Ann Almgren Date: Mon Apr 9 17:54:33 2018 -0700 Add link to original SWFFT source code Docs/sphinx_tutorials/source/SWFFT_Tutorial.rst commit d65019bfd9de77077ed87edac06f97da6f7d9021 Author: Ann Almgren Date: Mon Apr 9 17:50:44 2018 -0700 Update the sample inputs files in Tutorials/SWFFT. Tutorials/SWFFT/inputs.128 Tutorials/SWFFT/inputs.32 Tutorials/SWFFT/inputs.64 Tutorials/SWFFT/run_me Tutorials/SWFFT/swfft_solver.cpp commit dc39d17dc9296e9b1be3b759e778142c4f664367 Author: Ann Almgren Date: Mon Apr 9 17:19:04 2018 -0700 Adding source code for SWFFT so that the Tutorial can run. Src/Extern/SWFFT/AlignedAllocator.h Src/Extern/SWFFT/COPYING Src/Extern/SWFFT/CheckDecomposition.c Src/Extern/SWFFT/Dfft.H Src/Extern/SWFFT/DfftC.cpp Src/Extern/SWFFT/Distribution.H Src/Extern/SWFFT/DistributionC.cpp Src/Extern/SWFFT/Error.h Src/Extern/SWFFT/Make.package Src/Extern/SWFFT/README Src/Extern/SWFFT/TimingStats.h Src/Extern/SWFFT/complex-type.h Src/Extern/SWFFT/distribution.c Src/Extern/SWFFT/distribution.h commit 8b0b40a9ad68dc9f5ee1261c748a0aec72252223 Author: Ann Almgren Date: Mon Apr 9 16:54:21 2018 -0700 Update SWFFT Tutorial. Docs/sphinx_tutorials/source/SWFFT_Tutorial.rst commit d7564aa11352757675d70de419236e1d257264f8 Merge: 98ee66be7 696e6f78d Author: Michael Zingale Date: Mon Apr 9 16:16:30 2018 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 98ee66be7ca14e211aed700300b2e819ff2759ca Author: Michael Zingale Date: Mon Apr 9 16:16:03 2018 -0400 fextrema was a little misleading, since it was not giving the extrema over the whole domain. Now it does by looping over all levels Tools/Postprocessing/F_Src/fextrema.f90 commit 590c54e513b1eedaf23b66a25bad1d425264d50a Merge: 0bf5fd545 ce095dfb2 Author: shashankNREL Date: Mon Apr 9 12:52:08 2018 -0600 Added the IJ solver call to amrex_hypre.cpp commit 696e6f78de4cfc06db81bd23c8b1b31bdfddb846 Author: Andrew Myers Date: Mon Apr 9 11:33:43 2018 -0700 Remove FORTH from AMReX_CONSTANTS.H as well. Src/Base/AMReX_CONSTANTS.H commit 0bf5fd545a1a1193b9e5d786f8bd1110ae2ceafe Author: shashankNREL Date: Mon Apr 9 12:02:02 2018 -0600 Moved the HYPRE IJ calls to Fortran; Works well on the HYPRE tutorial case and compares well against the SStruct interface Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H Src/Extern/HYPRE/Make.package commit 782f7e07c249f1d5cbce62e4680fd89164ea6291 Author: Andrew Myers Date: Mon Apr 9 10:33:48 2018 -0700 replace 'forth' with 'fourth' Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 commit f79a83d66f47df66fe6923dccb5dac7087dbfc23 Author: Andrew Myers Date: Mon Apr 9 10:25:27 2018 -0700 remove redundant definition of 1/4 in AMReX_constants_mod.f90 Src/Base/AMReX_constants_mod.f90 commit 80a2fe91fd05b9c63ce7ae342c568093ead0007a Author: Weiqun Zhang Date: Sun Apr 8 18:29:20 2018 -0700 add Fortran interface to FluxRegister::OverwriteFlux Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90 commit cb5c4179ebf2846df60960ae79d859e93d024b7f Author: Weiqun Zhang Date: Sun Apr 8 18:00:20 2018 -0700 add FluxRegister::OverwriteFlux Src/AmrCore/AMReX_FLUXREG_F.H Src/AmrCore/AMReX_FLUXREG_nd.F90 Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/CMakeLists.txt Src/AmrCore/Make.package commit f9c19f056624a3826b1f87363731b004c477d239 Author: Ann Almgren Date: Sun Apr 8 09:00:37 2018 -0700 Link back to documentation Docs/sphinx_tutorials/source/CVODE_Tutorial.rst commit d4a18bffdcc2d7c28de00c077c0c1ee85ebd421c Author: Ann Almgren Date: Sun Apr 8 08:42:05 2018 -0700 Try to fix link. Docs/sphinx_documentation/source/CVODE.rst commit c46db76139cc0ec14f9e565a4dfffbab958314b2 Author: Ann Almgren Date: Sun Apr 8 08:14:17 2018 -0700 update link Docs/sphinx_documentation/source/CVODE.rst commit b086d2037e455f317ef922b503dd48805fa73036 Author: Ann Almgren Date: Sun Apr 8 08:06:27 2018 -0700 Move the CVODE Tutorial description into the Tutorials section Docs/sphinx_documentation/source/CVODE.rst Docs/sphinx_tutorials/source/CVODE_Tutorial.rst commit 6c5731c7016e7251a36c672f4ce053b5cd2a5d9e Author: Ann Almgren Date: Sun Apr 8 07:54:56 2018 -0700 Update Basics_Tutorials page Docs/sphinx_tutorials/source/Basic_Tutorial.rst commit a1468e59ef12964fb4bcf327c1a8970f89ccc8f9 Author: Ann Almgren Date: Sat Apr 7 18:05:15 2018 -0700 Start to fill in the Tutorials documentation. Docs/sphinx_tutorials/source/Basic_Tutorial.rst Docs/sphinx_tutorials/source/index.rst commit 27d8192e8b3949158531104a2a387ef868f95b35 Author: Weiqun Zhang Date: Sat Apr 7 16:55:03 2018 -0700 add mising conf.py Docs/sphinx_tutorials/source/conf.py commit 39de9d874283a874afe78c54fd7a6e9c693575ea Author: Weiqun Zhang Date: Sat Apr 7 16:38:20 2018 -0700 rm old ParmParse Fortran Src/Base/AMReX_BLParmParse_F.F90 Src/Base/AMReX_ParmParse.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 523769701f5f165d3b95282dd9c04a2fec002990 Author: Weiqun Zhang Date: Sat Apr 7 16:32:58 2018 -0700 rm AMReX_bl_flush.f Src/Base/AMReX_bl_flush.f commit 7f64c1110c6e58402e5a5ab0de88553c7a9e5b23 Author: Weiqun Zhang Date: Sat Apr 7 16:29:38 2018 -0700 rm AMReX_SPACE_F.H Src/Base/AMReX_SPACE_F.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 044f4eefadb64715aa3cc013da911dfb421e5360 Author: Weiqun Zhang Date: Sat Apr 7 16:20:35 2018 -0700 add a wrapper to polyintercoeff for tensormg Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/C_TensorMG/AMReX_DV_2D.F Src/LinearSolvers/C_TensorMG/AMReX_MCLO_2D.F Src/LinearSolvers/C_TensorMG/AMReX_MCLO_3D.F Src/LinearSolvers/C_TensorMG/Make.package Src/LinearSolvers/C_TensorMG/amrex_tmg_util.F90 commit 6f56bdc9846d1898cc5b8770c833c909cb7d2c2b Author: Weiqun Zhang Date: Sat Apr 7 14:11:21 2018 -0700 C_CellMG4: .F files to .F90 files OldTutorials/MultiGrid_C/GNUmakefile Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2_2D.F Src/LinearSolvers/C_CellMG4/AMReX_ABec2_2D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec2_3D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec2_F.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4_2D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec4_3D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec4_F.H Src/LinearSolvers/C_CellMG4/Make.package commit 192b51d0d71b36186a8dfd93c2909973cfa47733 Author: Weiqun Zhang Date: Sat Apr 7 10:44:46 2018 -0700 remove AMREX_REAL.H from Fortran 90 files Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_LO_UTIL.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_UTIL.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90 Src/LinearSolvers/C_CellMG4/AMReX_ABec2_2D.F Src/LinearSolvers/C_CellMG4/AMReX_ABec2_3D.F Src/LinearSolvers/C_TensorMG/AMReX_DV_2D.F Src/LinearSolvers/C_TensorMG/AMReX_MCLO_2D.F Src/LinearSolvers/C_TensorMG/AMReX_MCLO_3D.F Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 commit 3207c8982b1b30275b923a73e780e93c18bb4650 Merge: 2a0d31e81 bad5c0ce4 Author: Marc Day Date: Sat Apr 7 15:40:37 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2a0d31e8129f68ac2831a3a4c2c1d90f6eefd531 Author: Marc Day Date: Sat Apr 7 15:40:25 2018 -0700 Fix bugs in postprocessing codes, add matlab .m script files that can read the output generated by PlotfileToMatLab.cpp Tools/C_util/WritePlotFile.cpp Tools/Postprocessing/C_Src/GNUmakefile Tools/Postprocessing/C_Src/PtwisePltTransform.cpp Tools/Postprocessing/C_Src/binread.m Tools/Postprocessing/C_Src/mk2d.m commit bad5c0ce4f14a696705db2d4805f2fa9fb1ce0c8 Author: Ann Almgren Date: Sat Apr 7 15:18:47 2018 -0700 Move tutorials.rst to index.rst Docs/sphinx_tutorials/source/index.rst commit f10b23e410bdcf809149caa7ca399f573bbd5e2d Author: Ann Almgren Date: Sat Apr 7 15:09:13 2018 -0700 Try to build tutorials_html separately from docs_html Docs/sphinx_documentation/Makefile Docs/sphinx_documentation/source/AMReX_Profiling_Tools.rst Docs/sphinx_documentation/source/AmrCore.rst Docs/sphinx_documentation/source/AmrCore/figs/Adv1.pdf Docs/sphinx_documentation/source/AmrCore/figs/Adv1.png Docs/sphinx_documentation/source/AmrCore/figs/Adv2.pdf Docs/sphinx_documentation/source/AmrCore/figs/Adv2.png 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Zhang Date: Fri Apr 6 18:00:36 2018 -0700 expand typedef for typecheck and fix type problems Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_F.H commit 190ffb8b91a9a57bc8234dc03816fd04b18bdd1e Author: Weiqun Zhang Date: Fri Apr 6 17:56:35 2018 -0700 rename for typecheck Src/AmrCore/AMReX_FLUXREG_1D.F90 Src/AmrCore/AMReX_FLUXREG_2D.F90 Src/AmrCore/AMReX_FLUXREG_3D.F90 Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/Base/AMReX_COORDSYS_1D.F90 Src/Base/AMReX_COORDSYS_2D.F90 Src/Base/AMReX_COORDSYS_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 commit 57bfcde1ba3540526aff68bfb743b4341a876226 Author: Weiqun Zhang Date: Fri Apr 6 17:38:59 2018 -0700 break up some really long lines Src/AmrCore/AMReX_FLUXREG_2D.F90 Src/AmrCore/AMReX_FLUXREG_3D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/Base/AMReX_COORDSYS_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 commit 40da472801fcc1c1cf3c4455071f2af26bcf4b3c Author: Weiqun Zhang Date: Fri Apr 6 17:19:01 2018 -0700 filcc: remove AMReX_REAL.H Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 commit 334e8598f7c6258348100c1f2d1815d206049ec5 Author: Weiqun Zhang Date: Fri Apr 6 17:03:46 2018 -0700 linear solver routines: module and c binding Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_F.H Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_F.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_F.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Src/LinearSolvers/C_CellMG/AMReX_lo_bctypes.fi Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit 923ebed36996838784e775dc29b4d2e1bf0074ba Merge: 98355c7a8 539b2af9b Author: Marc Day Date: Fri Apr 6 16:44:57 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 98355c7a898ec5975f57e7eab91b11bff230a4a1 Author: Marc Day Date: Fri Apr 6 16:44:49 2018 -0700 Add a simple AmrData-based post-processing function Tools/C_util/WritePlotFile.H Tools/C_util/WritePlotFile.cpp Tools/Postprocessing/C_Src/GNUmakefile Tools/Postprocessing/C_Src/Make.package Tools/Postprocessing/C_Src/PtwisePltTransform.cpp Tools/Postprocessing/C_Src/PtwisePltTransform_nd.f90 commit 56e7007ee1918e0727d4aa3b69499a0bd65a7742 Author: Weiqun Zhang Date: Fri Apr 6 16:02:03 2018 -0700 put interpbndrydata routine into module and add c binding Src/Base/AMReX_constants_mod.f90 Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_F.H Src/Boundary/AMReX_InterpBndryData.cpp commit 36d3e53db35c0e640fa25ee8e872085829d9f6db Author: Weiqun Zhang Date: Fri Apr 6 14:44:23 2018 -0700 put coordsys routines into module Src/Base/AMReX_COORDSYS_1D.F90 Src/Base/AMReX_COORDSYS_2D.F90 Src/Base/AMReX_COORDSYS_3D.F90 Src/Base/AMReX_COORDSYS_F.H Src/Base/AMReX_CoordSys.cpp commit ebb652d4a995a3d5dcdbda0fe62ba221ba257f97 Author: Weiqun Zhang Date: Fri Apr 6 14:25:20 2018 -0700 put interpolation routines into module Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/AmrCore/AMReX_INTERP_F.H Src/AmrCore/AMReX_Interpolater.cpp commit 539b2af9b2feae503a60834cd61aa5c9926fbee0 Author: Andrew Myers Date: Fri Apr 6 14:13:16 2018 -0700 fix the ParticleContainer::Restart routine to work when levels are lost on restart.' Src/Particle/AMReX_ParticleContainerI.H commit 74f114f08b08494001f992902711bb73afae6ac1 Author: Weiqun Zhang Date: Fri Apr 6 13:37:17 2018 -0700 put flux register fortran code into module Src/AmrCore/AMReX_FLUXREG_1D.F90 Src/AmrCore/AMReX_FLUXREG_2D.F90 Src/AmrCore/AMReX_FLUXREG_3D.F90 Src/AmrCore/AMReX_FLUXREG_F.H Src/AmrCore/AMReX_FluxRegister.cpp commit 1366727211c0dbb260c242a1227d09bf79215856 Author: Weiqun Zhang Date: Fri Apr 6 12:50:42 2018 -0700 replace DIM[123] Src/AmrCore/AMReX_INTERP_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 commit b15579d4423082481d6e82950035c8a85e71bdf6 Author: Weiqun Zhang Date: Fri Apr 6 12:48:00 2018 -0700 move ARRAYLIM_?D.F90 to IAMR Src/Amr/AMReX_ARRAYLIM_1D.F90 Src/Amr/AMReX_ARRAYLIM_2D.F90 Src/Amr/AMReX_ARRAYLIM_3D.F90 Src/Amr/CMakeLists.txt Src/Amr/Make.package commit 22fa11d229e58f5fc30708a026e2cb95677e3def Author: Weiqun Zhang Date: Fri Apr 6 11:17:44 2018 -0700 remove AMReX_ArrayLim.H from F90 files Src/Amr/AMReX_ARRAYLIM_1D.F90 Src/Amr/AMReX_ARRAYLIM_2D.F90 Src/Amr/AMReX_ARRAYLIM_3D.F90 Src/AmrCore/AMReX_FLUXREG_1D.F90 Src/AmrCore/AMReX_FLUXREG_2D.F90 Src/AmrCore/AMReX_FLUXREG_3D.F90 Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/Base/AMReX_COORDSYS_1D.F90 Src/Base/AMReX_COORDSYS_2D.F90 Src/Base/AMReX_COORDSYS_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F90 commit c038c8eb545410794d30f896a0bbf8434c27494e Author: Weiqun Zhang Date: Fri Apr 6 11:10:21 2018 -0700 replace ARG_L1, ARG_L2, ... etc. Src/Amr/AMReX_ARRAYLIM_1D.F90 Src/Amr/AMReX_ARRAYLIM_2D.F90 Src/Amr/AMReX_ARRAYLIM_3D.F90 Src/AmrCore/AMReX_FLUXREG_1D.F90 Src/AmrCore/AMReX_FLUXREG_2D.F90 Src/AmrCore/AMReX_FLUXREG_3D.F90 Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/Base/AMReX_COORDSYS_1D.F90 Src/Base/AMReX_COORDSYS_2D.F90 Src/Base/AMReX_COORDSYS_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 commit 328d37aef25f0d2b99cae303e9dd0e1834b96d9a Author: Weiqun Zhang Date: Fri Apr 6 11:04:39 2018 -0700 replace DIM1, DIM2 and DIM3 Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 commit be01dfe557b1dfe9abfe0e2da819a98eaaa9d45e Author: Weiqun Zhang Date: Fri Apr 6 11:00:10 2018 -0700 replace DIMV Src/AmrCore/AMReX_FLUXREG_1D.F90 Src/AmrCore/AMReX_FLUXREG_2D.F90 Src/AmrCore/AMReX_FLUXREG_3D.F90 Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/Base/AMReX_COORDSYS_1D.F90 Src/Base/AMReX_COORDSYS_2D.F90 Src/Base/AMReX_COORDSYS_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F90 commit 8d2a14e41345f41608d042e741af711e15fc3797 Author: Weiqun Zhang Date: Fri Apr 6 10:55:55 2018 -0700 replace DIMDEC in F90 files Src/Amr/AMReX_ARRAYLIM_1D.F90 Src/Amr/AMReX_ARRAYLIM_2D.F90 Src/Amr/AMReX_ARRAYLIM_3D.F90 Src/AmrCore/AMReX_FLUXREG_1D.F90 Src/AmrCore/AMReX_FLUXREG_2D.F90 Src/AmrCore/AMReX_FLUXREG_3D.F90 Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/Base/AMReX_COORDSYS_1D.F90 Src/Base/AMReX_COORDSYS_2D.F90 Src/Base/AMReX_COORDSYS_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F90 commit e0cd1585c461fb1685b735164d4d2b0811bd7a22 Author: Weiqun Zhang Date: Fri Apr 6 10:53:39 2018 -0700 replace DIMS in F90 files Src/Amr/AMReX_ARRAYLIM_1D.F90 Src/Amr/AMReX_ARRAYLIM_2D.F90 Src/Amr/AMReX_ARRAYLIM_3D.F90 Src/AmrCore/AMReX_FLUXREG_1D.F90 Src/AmrCore/AMReX_FLUXREG_2D.F90 Src/AmrCore/AMReX_FLUXREG_3D.F90 Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/Base/AMReX_COORDSYS_1D.F90 Src/Base/AMReX_COORDSYS_2D.F90 Src/Base/AMReX_COORDSYS_3D.F90 Src/Base/AMReX_FILCC_3D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F90 commit 5cbd0eb3263acec7e26eabf1f877e858e4c7cf96 Author: Marc Day Date: Fri Apr 6 10:52:19 2018 -0700 Remove commented out code, clean up slightly. Tools/Postprocessing/C_Src/PlotfileToMatLab.cpp commit aca077b4b6c5b748ad00163befa09b4e727c29b2 Author: Weiqun Zhang Date: Thu Apr 5 14:18:25 2018 -0700 add AMREX prefix to some include guards Src/Amr/AMReX_Amr.H Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AuxBoundaryData.H Src/Amr/AMReX_Derive.H Src/Amr/AMReX_Extrapolater.H Src/Amr/AMReX_LevelBld.H Src/Amr/AMReX_PROB_AMR_F.H Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateDescriptor.H Src/AmrCore/AMReX_Cluster.H Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_FLUXREG_F.H Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_INTERP_F.H Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_TagBox.H Src/AmrTask/AMFIter/AMReX_AmrTask.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/Amr/AMReX_AmrLevelTask.H Src/AmrTask/AmrCore/AMReX_FillPatchUtil.H Src/Base/AMReX_BCRec.H Src/Base/AMReX_BC_TYPES.H Src/Base/AMReX_BLBackTrace.H Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseIndex.H Src/Base/AMReX_BaseUmap_f.H Src/Base/AMReX_COORDSYS_F.H Src/Base/AMReX_CoordSys.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_Periodicity.H Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_RealBox.H Src/Base/AMReX_SPMD.H Src/Base/AMReX_SPMDI.H Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_parstream.H Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BoundCond.H Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_INTERPBNDRYDATA_F.H Src/Boundary/AMReX_LO_BCTYPES.H Src/Boundary/AMReX_MacBndry.H Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_MultiMask.H Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABec_F.H Src/Particle/AMReX_ParGDB.H Src/Particle/AMReX_Particles.H commit 8bfff3d88a67e3a081a977f9d659d3e3bf54ce99 Merge: a691b6283 dbcfdb6a9 Author: asalmgren Date: Wed Apr 4 14:21:27 2018 -0700 Merge pull request #240 from AMReX-Codes/add_matlab_conv Add plotfile-to-Matlab converter. commit a691b628362c4269f4c463ab12d13b279e68a69c Author: kngott Date: Wed Apr 4 12:06:13 2018 -0700 Adjustment to RStartStop profiling object to reomve padding and eliminate valgrind warning message. Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp commit ce095dfb2c87430c82c17ebcdbad1f7393d194eb Author: shashankNREL Date: Wed Apr 4 12:56:17 2018 -0600 Added call to the IJ solver in the hypre solver constructor Src/Extern/HYPRE/AMReX_Hypre.cpp commit 569fbb7e9015b0819a49f976f84905ff5a842f3a Merge: cfa145c7f f6113ab5f Author: Weiqun Zhang Date: Wed Apr 4 09:24:03 2018 -0700 Merge branch 'development' into weiqun/mlmg commit dbcfdb6a9bba3865aa0446168b1a7c7030593c84 Author: Marc Day Date: Tue Apr 3 11:25:43 2018 -0700 Add plotfile-to-Matlab converter. Tools/Postprocessing/C_Src/GNUmakefile Tools/Postprocessing/C_Src/Make.package Tools/Postprocessing/C_Src/PlotfileToMatLab.cpp commit f6113ab5fce6cc2bdad93ba58f5c2d12254d3525 Author: Johannes Blaschke Date: Tue Apr 3 11:19:21 2018 -0700 just to be _really_ clear about how to open flow fields with paraview Docs/sphinx/source/Visualization.rst commit 8d407ca90a9e0985ae82481a01f2e5c9d4584a08 Author: Johannes Blaschke Date: Tue Apr 3 11:16:50 2018 -0700 Fix some small problems with the documentation Docs/sphinx/source/Basics.rst Docs/sphinx/source/Visualization.rst commit 2481bcd3def8af7e52b02fb9a0341e2590c95d48 Author: Weiqun Zhang Date: Tue Apr 3 10:56:19 2018 -0700 fix a typo Src/Base/AMReX_ParallelContext.H commit a385bac3c9ea0ecff4f668ff3ed3781f35bc4a81 Author: Weiqun Zhang Date: Tue Apr 3 10:06:57 2018 -0700 Make amrex::Array an alias of std::array instead of amrex::Vector. This may break some codes. But warning was given 4 months ago. Src/Base/AMReX_Array.H commit df19368a88cb2c6b20c1d72d83fac77d39f0b083 Author: Andrew Myers Date: Tue Apr 3 09:40:35 2018 -0700 remove a debug print statement from ParticleContainer::Checkpoint Src/Particle/AMReX_ParticleContainerI.H commit a18d01f087987521c97ce93c4951e7360b27b608 Merge: 172d60f2a f55f567c1 Author: Weiqun Zhang Date: Mon Apr 2 18:57:56 2018 -0700 Merge branch 'forkjoin' into development commit f55f567c16eaf525b930ce52c32dbed14d1e77a7 Author: Weiqun Zhang Date: Mon Apr 2 18:40:45 2018 -0700 Merge branch 'development' into forkjoin Docs/sphinx/source/EB.rst Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ThirdPartyProfiling.H Src/Base/Make.package Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Tests/ProfTests/ThirdParty/Exec/GNUmakefile Tests/ProfTests/ThirdParty/Exec/inputs_2d Tests/ProfTests/ThirdParty/Exec/inputs_3d Tests/ProfTests/ThirdParty/Source/Make.package Tests/ProfTests/ThirdParty/Source/advance.cpp Tests/ProfTests/ThirdParty/Source/advance_2d.f90 Tests/ProfTests/ThirdParty/Source/advance_3d.f90 Tests/ProfTests/ThirdParty/Source/init_phi_2d.f90 Tests/ProfTests/ThirdParty/Source/init_phi_3d.f90 Tests/ProfTests/ThirdParty/Source/main.cpp Tests/ProfTests/ThirdParty/Source/myfunc.H Tests/ProfTests/ThirdParty/Source/myfunc_F.H Tools/GNUMake/Make.defs Tools/GNUMake/tools/Make.forge Tools/GNUMake/tools/Make.vtune commit 172d60f2ae614c72010cc5c979509dba1da30c16 Merge: 8c624245d 81d27e507 Author: Johannes Blaschke Date: Mon Apr 2 17:30:05 2018 -0700 Merge branch 'development' into jpb/fill-nodal commit 8c624245d20f1b2764f438910514bbc24d427f23 Author: Johannes Blaschke Date: Mon Apr 2 17:21:10 2018 -0700 fix double-scaling if fillNodalArrays from AnisotropicIF Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp commit 81d27e5076645af5b551dc383094d73f6a9f9561 Merge: c35c1c987 3a5110040 Author: kngott Date: Mon Apr 2 16:07:07 2018 -0700 Merge branch 'kngott_tpp' into development commit 3a5110040c8b64616b57096af9cff80c2ded5022 Merge: 64f4a36e1 bd6c2b9e2 Author: kngott Date: Mon Apr 2 16:03:46 2018 -0700 Merge branch 'development' into kngott_tpp commit 64f4a36e182460c15435296d157d5f1a7591082a Author: kngott Date: Mon Apr 2 15:56:06 2018 -0700 Final Third Party Version Src/Base/AMReX_BLProfiler.H Tests/ProfTests/ThirdParty/Exec/GNUmakefile Tests/ProfTests/ThirdParty/Exec/inputs_2d Tests/ProfTests/ThirdParty/Exec/inputs_3d Tests/ProfTests/ThirdParty/Source/Make.package Tests/ProfTests/ThirdParty/Source/advance.cpp Tests/ProfTests/ThirdParty/Source/advance_2d.f90 Tests/ProfTests/ThirdParty/Source/advance_3d.f90 Tests/ProfTests/ThirdParty/Source/init_phi_2d.f90 Tests/ProfTests/ThirdParty/Source/init_phi_3d.f90 Tests/ProfTests/ThirdParty/Source/main.cpp Tests/ProfTests/ThirdParty/Source/myfunc.H Tests/ProfTests/ThirdParty/Source/myfunc_F.H Tutorials/Basic/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp commit c35c1c987595ded5006e1285e3440b4c451d48b3 Merge: 00458add9 bd6c2b9e2 Author: dtgraves Date: Mon Apr 2 15:14:15 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 00458add9ab70989b5fe430184c212f41c7c1ce8 Author: dtgraves Date: Mon Apr 2 15:13:55 2018 -0700 added a bit about EBIndexSpace::read and EBIndexSpace::write into the User's guide. Docs/sphinx/source/EB.rst commit bd6c2b9e25f490beadf70ab69ba8b0a8c33ccad9 Author: kngott Date: Mon Apr 2 15:13:19 2018 -0700 Eliminate extra padding in ReadAndBcastFile. Src/Base/AMReX_ParallelDescriptor.cpp commit 6a5d71ba078e1db93410c3af0a762cdea7761740 Author: shashankNREL Date: Mon Apr 2 13:44:01 2018 -0600 Added HYPRE Matrix IJ Interface Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_HypreABecLap3.H Src/Extern/HYPRE/AMReX_HypreABecLap3.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit 7e18b3e1706b8311726bcb5ded4aa229f511c86b Merge: 1815971bb f6a0e9bba Author: Weiqun Zhang Date: Mon Apr 2 09:40:32 2018 -0700 Merge branch 'development' into forkjoin commit f6a0e9bbad2e1798ea0d0aeac83ae5a2bd3368e4 Author: Weiqun Zhang Date: Mon Apr 2 09:38:03 2018 -0700 update changes CHANGES commit 56b5e2cfb0be32d2cccbfee51932b49844af0441 Author: Ann Almgren Date: Sun Apr 1 09:32:02 2018 -0700 Add pointers to individual files Docs/sphinx/source/tutorials.rst commit 4757958d8f7385da698c7c5396ec4ed601303cbe Author: Ann Almgren Date: Sun Apr 1 09:31:47 2018 -0700 Add file for each Tutorial directory Docs/sphinx/source/AMR_Tutorial.rst Docs/sphinx/source/Basic_Tutorial.rst Docs/sphinx/source/CVODE_Tutorial.rst Docs/sphinx/source/EB_Tutorial.rst Docs/sphinx/source/HYPRE_Tutorial.rst Docs/sphinx/source/LinearSolvers_Tutorial.rst Docs/sphinx/source/Particles_Tutorial.rst Docs/sphinx/source/SWFFT_Tutorial.rst commit d13f46540e9b82d8d8b2ce2e0a77148b619f127f Author: Ann Almgren Date: Sun Apr 1 09:18:49 2018 -0700 Trying to set up tutorals link Docs/sphinx/source/tutorials.rst commit 36806bd26f907605a82846f4ea29e32247bbaa27 Author: Ann Almgren Date: Sun Apr 1 09:09:32 2018 -0700 Add Tutorials.rst for first start at Tutorials link from amrex io page. Docs/sphinx/source/Tutorials/Tutorials.rst commit 3372c293eaf1bb181e862f2bf0783ee0b7474f44 Author: Weiqun Zhang Date: Sat Mar 31 14:32:00 2018 -0700 replace HUGE with numeric_limits constexpr functions Src/GeometryShop/AMReX_ConstrainedLS.cpp Src/GeometryShop/AMReX_LSProblemImplem.H commit a52116410dd9dd8f1163fb10efaeb7f247dacb8e Merge: cfa841c5f 4919e62f9 Author: Andrew Myers Date: Fri Mar 30 16:32:07 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit cfa841c5fd7459822d4d676ea942357ee12eedb7 Author: Andrew Myers Date: Fri Mar 30 16:31:57 2018 -0700 add some parentheses here to silence compiler warnings. Src/Base/AMReX_MultiFabUtil.cpp commit 4919e62f91e1c3c74121aa2131f379895fa64256 Author: Ann Almgren Date: Fri Mar 30 14:51:37 2018 -0700 Modify the AssignDensity routine here (and the interfaces and calling routines in Nyx) so that we can pass in the number of grow cells used to define the array that will hold the particle deposition. Some previous calls defaulted to 1 ghost cell which is not big enough if valid particles live in ghost cells themselves (eg if starting the second level 1 solve of a subcycled level 0-1-2 simulation.) Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 1fd17792050f0edc4309f1d0c9021c960362d4fc Author: Andrew Myers Date: Fri Mar 30 14:18:17 2018 -0700 Removing RegressionTesting from the amrex repo. These live at https://github.com/AMReX-Codes/regression_testing now. Tools/RegressionTesting/AMReX-tests.ini Tools/RegressionTesting/README Tools/RegressionTesting/example-tests.ini Tools/RegressionTesting/gen_compile_test.sh Tools/RegressionTesting/params.py Tools/RegressionTesting/reg_test_gc.py Tools/RegressionTesting/regtest.py Tools/RegressionTesting/repo.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py Tools/RegressionTesting/test_util.py commit 7203fc1167fa2f2736559d9c69a7433f9d0f8ca6 Merge: c10861ae3 e45eaac99 Author: Andrew Myers Date: Thu Mar 29 16:43:14 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c10861ae38c0e75f5e56d67d0b188b503bc45b9e Author: Andrew Myers Date: Thu Mar 29 16:42:22 2018 -0700 improve omp scaling of CacheNeighborInfo Src/Particle/AMReX_NeighborParticlesI.H commit e45eaac99114deda0a097c086604cdf20f19b1f0 Author: Ann Almgren Date: Thu Mar 29 16:06:09 2018 -0700 Fix typo in init_rhs and make sure the rhs sums to 0 Tutorials/SWFFT/SWFFT_Test.cpp Tutorials/SWFFT/SWFFT_Test_F.F90 Tutorials/SWFFT/swfft_solver.cpp commit 1815971bbae8844fb29813c1cb8f587c4b63e6da Author: Weiqun Zhang Date: Thu Mar 29 14:42:11 2018 -0700 split some FabArray communciation functions into a separate file Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayCommI.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 1ef9f08f3089538d7f31d6861e9214d5e5415e07 Author: Weiqun Zhang Date: Thu Mar 29 13:53:40 2018 -0700 use move when possible OldTutorials/MultiFabTests_C/MultiFabFillBoundary.cpp OldTutorials/MultiFabTests_C/MultiFabReadWrite.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_ForkJoin.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_VisMF.cpp Src/Boundary/AMReX_YAFluxRegister.cpp Src/Extern/amrdata/AMReX_AmrData.cpp Src/F_Interfaces/Base/AMReX_distromap_fi.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit e21775031bb1ccf2f3fa56177dc6db3ffd8d8548 Author: Weiqun Zhang Date: Thu Mar 29 13:05:48 2018 -0700 add new constructor that moves Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelContext.cpp commit 24c0b8fd0aa5e8905f12bc601026255bf4a8a10a Author: Weiqun Zhang Date: Thu Mar 29 12:56:06 2018 -0700 MLMG: fix subcommunicator Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit b1f3cddd31ade7cc09c6baf5b6f947fa03b970e1 Author: Weiqun Zhang Date: Thu Mar 29 12:34:01 2018 -0700 MLMG: update for fork/join Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelContext.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 4a3729fad1fb67376b43fd84bb61b745af405b4b Author: Weiqun Zhang Date: Thu Mar 29 11:23:59 2018 -0700 add ParallelReduce, rename some functions and use MLMG in MultiColor_C OldTutorials/MultiColor_C/GNUmakefile OldTutorials/MultiColor_C/main.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_ForkJoin.cpp Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelContext.cpp Src/Base/AMReX_ParallelReduce.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit a6c2b37131a1b7260b63e201b4158874d32477d4 Merge: 4732ee219 beb7f6035 Author: Weiqun Zhang Date: Thu Mar 29 10:09:20 2018 -0700 Merge branch 'development' into forkjoin Conflicts: Src/Amr/AMReX_AmrLevel.cpp commit 4732ee219e2e93a1a3a1a7dfdf6605e928013cd7 Author: Weiqun Zhang Date: Thu Mar 29 10:07:21 2018 -0700 store groups to avoid repeatedly creating groups in rank translation Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelContext.cpp commit ccdaf208b6b25608cd4377581e3c08927172ba45 Author: Weiqun Zhang Date: Thu Mar 29 09:34:29 2018 -0700 fix MultiColor_C Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp Src/Base/AMReX_ParallelContext.cpp commit fd3a10a27c0897ec3a3f165c5e1d79bf988b4121 Author: Weiqun Zhang Date: Thu Mar 29 08:52:19 2018 -0700 rename Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_ForkJoin.cpp Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelContext.cpp commit beb7f6035bf9f6128f5485dc9e29571d60765d63 Author: Ann Almgren Date: Thu Mar 29 08:28:33 2018 -0700 Change name from solver_itself to swfft_solver Tutorials/SWFFT/SWFFT_Test.cpp Tutorials/SWFFT/swfft_solver.cpp commit 5fec56db159ddddfed07a069fd99fe7e0d5093f0 Author: Ann Almgren Date: Thu Mar 29 08:02:44 2018 -0700 Modify so that the interface to the solver isn't part of the testing class, but a stand alone routine that takes the rhs multifab and geometry and returns the soln multifab. Tutorials/SWFFT/Make.package Tutorials/SWFFT/SWFFT_Test.H Tutorials/SWFFT/SWFFT_Test.cpp Tutorials/SWFFT/SWFFT_Test_F.F90 Tutorials/SWFFT/SWFFT_Test_F.H Tutorials/SWFFT/main.cpp Tutorials/SWFFT/swfft_solver.cpp commit 1bdba3e68010a77be4e9929c1432c5fb94dce0cc Author: Ann Almgren Date: Wed Mar 28 21:22:21 2018 -0700 Update the call to the solver so it correctly handles the case where we decompose a cubic grid into different numbers of grids in each direction, eg a 32^3 grid decomposed into 32x16x16 boxes. Tutorials/SWFFT/SWFFT_Solver.cpp Tutorials/SWFFT/SWFFT_Solver_F.F90 Tutorials/SWFFT/SWFFT_Solver_F.H Tutorials/SWFFT/inputs.32 commit 7fd82f78f06cd35ac6ced49a5c0c4208369de582 Merge: c038c7623 a21915c48 Author: Ann Almgren Date: Wed Mar 28 20:36:15 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit c038c7623a5152651b4073645cb3ae813488d71d Author: Ann Almgren Date: Wed Mar 28 20:35:23 2018 -0700 Change the user interface so that for both max_grid_size and n_cell you can enter one value, which would set the values in all directions to that value, or it can take in 3 values, one for each direction (in 3d) Tutorials/SWFFT/SWFFT_Solver.H Tutorials/SWFFT/SWFFT_Solver.cpp commit a21915c4856e2079b30f7a4ed960bf89f5dbe9af Merge: 3f6cf17d2 238cc9b9a Author: Brandon Runnels Date: Wed Mar 28 17:39:56 2018 -0700 Merge pull request #235 from AMReX-Codes/MLLinOp_Fix MLLinop Corner Fix commit 238cc9b9a6fdc20570de3e2488262186e77e4ceb Author: Brandon Runnels Date: Wed Mar 28 19:27:39 2018 -0500 removed mask condition and added support for mixed bcs Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 commit 4350a9e364551783759685350b83b478f38f2942 Author: Weiqun Zhang Date: Wed Mar 28 17:00:06 2018 -0700 update DistributionMapping for fork/join Src/Base/AMReX_DistributionMapping.cpp commit baa719b536d68dccf588dd068de1ccbc2d6ff57d Author: Weiqun Zhang Date: Wed Mar 28 12:41:42 2018 -0700 update FabArray communication for fork/join Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_ParallelReduce.H commit 3f6cf17d229c7f66ec181bafec14ba55ec6810e2 Author: Weiqun Zhang Date: Wed Mar 28 10:58:52 2018 -0700 add Sod test to EB/CNS Tutorials/EB/CNS/Exec/Sod/GNUmakefile Tutorials/EB/CNS/Exec/Sod/Make.package Tutorials/EB/CNS/Exec/Sod/cns_prob.F90 Tutorials/EB/CNS/Exec/Sod/inputs commit fde840993ccd8caf4a2b95d0e7795b7226ee78bc Author: Weiqun Zhang Date: Wed Mar 28 09:32:36 2018 -0700 use the global communicator in ParallelDescriptor Src/AmrTask/AMFIter/AMReX_AmrTask.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_Print.H commit ae930c0ad89415c4ab2bb7d471cfea1f8b314ae7 Merge: f604154ce 0048b022c Author: Andrew Myers Date: Wed Mar 28 09:51:38 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f604154ce1a6c262bfbf574471dca22cadfa0a9f Author: Andrew Myers Date: Wed Mar 28 09:51:22 2018 -0700 remove AllReduce from RedistributeMPI Src/Particle/AMReX_ParticleContainerI.H commit 1782220f8532d6e3b06bbe3977c2c19deb7b0af4 Author: Weiqun Zhang Date: Wed Mar 28 09:21:38 2018 -0700 MLMG bottom: use ParallelContext Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 0048b022ccc13ae997af28241a3d90c1b0a0e475 Merge: df5f2fd14 a74c439b2 Author: WeiqunZhang Date: Wed Mar 28 08:59:23 2018 -0700 Merge pull request #234 from AMReX-Codes/MLCellLinOp_NCompFix Enable multicomponent flux registers commit a74c439b245a8aac738c7d82ef31814b8c807def Author: Brandon Runnels Date: Wed Mar 28 11:28:40 2018 -0400 removed extra comment Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit 88ddeca67bbb4070a18d5e7076c554f30084896e Author: Brandon Runnels Date: Wed Mar 28 11:27:23 2018 -0400 fixed bug caused by assuming single component flux registers Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit 22a34bf49065dc2ffccf207792ce54ec789770fd Author: Weiqun Zhang Date: Tue Mar 27 16:27:29 2018 -0700 simplify SeqNum() Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit 60b3b4a62c8641370bd37ac316d20255dea46023 Author: Weiqun Zhang Date: Tue Mar 27 14:48:38 2018 -0700 fix a new bug Src/Base/AMReX_ParallelDescriptor.cpp commit 5c2164c982ba0c43b52bc19ab05f394831d72e2c Merge: b7da79d31 df5f2fd14 Author: Max Katz Date: Tue Mar 27 16:54:25 2018 -0400 Merge branch 'development' into gpu commit f043b0128982c44e3ade9617f58888d667e97829 Author: Weiqun Zhang Date: Tue Mar 27 13:54:01 2018 -0700 fix non-MPI Src/Base/AMReX_ParallelDescriptor.cpp commit df5f2fd148c6e9c4da18a38f637470db86620992 Author: Max Katz Date: Tue Mar 27 16:29:45 2018 -0400 Add IBM MPI lib for Fortran on Summit Tools/GNUMake/sites/Make.olcf commit 4adac05d5d0c799cb8d2f3e41ca0aae88e94f6c5 Author: Weiqun Zhang Date: Tue Mar 27 11:56:38 2018 -0700 rm BroadCast DistributionMapping and BoxArray Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 5337b21ab74e4fa39c214e2e0b94fd87453c9eee Author: Weiqun Zhang Date: Tue Mar 27 11:51:52 2018 -0700 rm PFC Src/Amr/AMReX_Amr.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit fdff649e6e74d78abdb6f9df85bb1b9ff513fc95 Author: Weiqun Zhang Date: Tue Mar 27 11:36:51 2018 -0700 rm FAPId Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 920d32731fc3a09e97d0fccb0ab2e66d823e846e Author: Weiqun Zhang Date: Tue Mar 27 11:25:27 2018 -0700 rm FAPointers Src/Base/AMReX_FabArray.H commit a12c116052d9c834b4cacbd3b5a338bb362e00ce Author: Weiqun Zhang Date: Tue Mar 27 11:16:32 2018 -0700 rm MoveFabs OldTutorials/MultiFabTests_C/GNUmakefile OldTutorials/MultiFabTests_C/GridMoveTest.cpp OldTutorials/MultiFabTests_C/Make.package OldTutorials/MultiFabTests_C/MoveAllFabsTest.cpp Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H commit e566971964a69663dfe2ed71cb0c9d97080ab7a9 Author: Weiqun Zhang Date: Tue Mar 27 11:05:43 2018 -0700 rm AddProcsToComp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_FabSet.H commit 976562234296392bf5a72c05a20d493b96709193 Author: Weiqun Zhang Date: Tue Mar 27 10:57:48 2018 -0700 rm more sidecar stuff OldTutorials/DataServicesTest0/GNUmakefile Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_MemProfiler.H Src/Base/AMReX_MemProfiler.cpp Tests/IOBenchmark/GNUmakefile commit 3b496bb34880e8f45129a79cb28b62c0ea9fc461 Author: Weiqun Zhang Date: Tue Mar 27 10:29:23 2018 -0700 first pass of removing sidecar Docs/Readme.sidecars OldTutorials/Sidecar_EX1/DestMFTest.cpp OldTutorials/Sidecar_EX1/GNUmakefile OldTutorials/Sidecar_EX1/GridMoveTest.cpp OldTutorials/Sidecar_EX1/InTransitAnalysis.H OldTutorials/Sidecar_EX1/InTransitAnalysis.cpp OldTutorials/Sidecar_EX1/Make.package OldTutorials/Sidecar_EX1/NSidecarsTest.cpp OldTutorials/Sidecar_EX1/SidecarResizeTest.cpp OldTutorials/Sidecar_EX1/TestRankSets.cpp OldTutorials/Sidecar_EX1/inputs_3d OldTutorials/Sidecar_EX1/inputs_sc OldTutorials/Sidecar_EX1/run.sh Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/AmrTask/AMFIter/AMReX_AmrTask.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_ParallelContext.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_Print.H Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 Tests/C_BaseLib/BcastClasses/BcastClasses.cpp Tests/C_BaseLib/BcastClasses/GNUmakefile Tools/CompileTesting/compiletesting.py commit 62e8a6befd43eed6553991721ece6553c6f9a9dc Author: Ann Almgren Date: Tue Mar 27 09:16:25 2018 -0700 Get rid of more IOIOIO:CD writes Src/Amr/AMReX_AmrLevel.cpp commit 55a4b3dfd274934b27d4c06e4fba6ce9685f9bac Author: Ann Almgren Date: Tue Mar 27 09:15:19 2018 -0700 Get rid of all those IOIOIOI write statements Src/Amr/AMReX_Amr.cpp commit 8678e800d189ec8fb9a3024bffd4a894cc99feab Author: Weiqun Zhang Date: Mon Mar 26 15:52:44 2018 -0700 c bind for hoextraptocc Src/Base/AMReX_filcc_f.H Src/Base/AMReX_filcc_mod.F90 commit 3a1046a3e79ccb737a610235199264d256ca6be6 Author: Ann Almgren Date: Mon Mar 26 13:22:40 2018 -0700 Remove the IOIOIOIO print statements Src/Particle/AMReX_ParticleContainerI.H commit 9a1e92c892da319b2e74b368092429db3f79a247 Merge: 6bfda8c3f 059bd9ed0 Author: Weiqun Zhang Date: Mon Mar 26 12:26:38 2018 -0700 Merge branch 'development' into forkjoin Conflicts: Src/Base/AMReX.cpp Src/Base/AMReX_ParallelDescriptor.cpp commit 059bd9ed003d3d71513e9813d9f6eaaab3862ad3 Author: dtgraves Date: Mon Mar 26 10:53:44 2018 -0700 removed slabservice-- an unused geometry service. Src/GeometryShop/AMReX_SlabService.H Src/GeometryShop/AMReX_SlabService.cpp Src/GeometryShop/CMakeLists.txt commit 16593ef75981c1d0b3c537638f5f314920281351 Merge: 2cec4f57e 3573b890b Author: dtgraves Date: Mon Mar 26 10:43:35 2018 -0700 merging stuff commit 3573b890b1dd139db8ec3d2093acc98ae181fdbb Author: dtgraves Date: Mon Mar 26 10:36:59 2018 -0700 updated CMakeLists.txt Src/GeometryShop/CMakeLists.txt commit 2cec4f57e1ef9f485241a115622fdc756e38ce80 Author: Weiqun Zhang Date: Mon Mar 26 10:24:39 2018 -0700 nodal solvability: fix a bug Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit e6b0297b5edc5f99a82da6e2dbec2d7ac62f4129 Merge: 4bcd19a58 6e34bbce8 Author: Weiqun Zhang Date: Mon Mar 26 09:05:27 2018 -0700 Merge branch 'development' into nd_solvability commit 6e34bbce857954d3873ea6690955dfb49ce73f67 Author: Ann Almgren Date: Mon Mar 26 07:26:43 2018 -0700 Missed another one Src/GeometryShop/CMakeLists.txt commit abe8ecde00529a1e71eca6a439f8e9464bb70d46 Author: Ann Almgren Date: Mon Mar 26 07:22:43 2018 -0700 Fix typo Src/GeometryShop/CMakeLists.txt commit e6fc9ccea9acd85baf0883abd83ce726184efcb7 Author: Ann Almgren Date: Mon Mar 26 07:18:21 2018 -0700 Missed another one... Src/GeometryShop/CMakeLists.txt commit 7ba6e9a6af848cc06b163ca40a544bf009fa3631 Author: Ann Almgren Date: Mon Mar 26 07:14:52 2018 -0700 Fix typo Src/GeometryShop/CMakeLists.txt commit 3ed832f6b116fe73b098bca1dd1fc2307348cf09 Author: Ann Almgren Date: Mon Mar 26 07:12:26 2018 -0700 I think I got the rest of them... Src/GeometryShop/CMakeLists.txt commit f863857780abac37701b5e6e598e9bc5bf1ebfc8 Author: Ann Almgren Date: Mon Mar 26 07:04:02 2018 -0700 Add AMReX_IndexedMoments.H to CMakeLists.txt Src/GeometryShop/CMakeLists.txt commit bf76d0fd9f30fae599367b0acea7170ecdeb7549 Author: Weiqun Zhang Date: Sun Mar 25 16:19:47 2018 -0700 some minor additions to Finalize Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_Geometry.cpp commit 574c973274ba03fd8d6e150c1ffd42a77353d322 Author: Weiqun Zhang Date: Sun Mar 25 15:09:14 2018 -0700 Tests/ThirdPartiLib: solve Poisson GNUmakefile.in Src/Base/AMReX_ParallelDescriptor.cpp Tests/ThirdPartyLib/bar.F90 Tests/ThirdPartyLib/foo.cpp commit 620143a045b22cce08e1248e2d30003ecf68138e Author: Weiqun Zhang Date: Sat Mar 24 23:57:38 2018 -0700 reentrant: AMReX.cpp Src/Base/AMReX.cpp Src/Base/AMReX_MemPool.H Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_MemProfiler.H Src/Base/AMReX_MemProfiler.cpp Src/Base/AMReX_ParmParse.cpp commit 46891b4d45bad67101e5ef7d411da445fdbbd860 Author: Weiqun Zhang Date: Sat Mar 24 21:38:34 2018 -0700 add a test for using amrex as a third-party library Tests/ThirdPartyLib/GNUmakefile Tests/ThirdPartyLib/Readme Tests/ThirdPartyLib/bar.F90 Tests/ThirdPartyLib/foo.cpp Tests/ThirdPartyLib/main.c commit 608e64715d072f6cd6520191dccc4b4ba306a9f6 Author: Weiqun Zhang Date: Sat Mar 24 19:58:30 2018 -0700 no longer print # of MPI processes and OMP threads if verbose is not on Src/Base/AMReX.cpp commit e4fb06f4701c6d58c2347a5233c255dfb7771a8b Author: Weiqun Zhang Date: Sat Mar 24 19:43:51 2018 -0700 MPI_Comm is now safe if AMReX is initialized and then finalized repeated Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_ParallelDescriptor.cpp Src/F_Interfaces/Base/AMReX_init_fi.cpp Src/F_Interfaces/Base/AMReX_parallel_mod.F90 commit 42214c3d6afc053241443d279f4e70cfa945e3a5 Author: Weiqun Zhang Date: Sat Mar 24 19:36:00 2018 -0700 rm F_BaseLib and F_MG from libamrex GNUmakefile.in commit 9628ba528326753c9ba7e83cc48aa0f8fc8f13f1 Author: Weiqun Zhang Date: Sat Mar 24 14:52:29 2018 -0700 amrex::Initialize is now OK with argc=0. do not stop if get_command fails Src/Base/AMReX.cpp Src/F_Interfaces/Base/AMReX_init_mod.F90 commit fa80db71d2891635071493d9dd4a27dc06f72dc8 Author: Weiqun Zhang Date: Sat Mar 24 13:09:20 2018 -0700 if the communicator given is MPI_COMM_WORLD, we should go ahead calling MPI_Init Src/F_Interfaces/Base/AMReX_parallel_mod.F90 commit b7da79d31af22e15119e8f4101c8136510f00109 Merge: 5a2a1f007 4477d44f4 Author: Max Katz Date: Sun Mar 25 13:17:36 2018 -0400 Merge branch 'development' into gpu commit 5a2a1f007dad9842711fc77487a2fd95145aca0f Author: Max Katz Date: Sun Mar 25 12:57:33 2018 -0400 Use built-in F90 link when compiling with CUDA Tools/GNUMake/Make.rules Tools/GNUMake/comps/pgi.mak commit 4477d44f44f9aef297a4c5ae133a88838774bb5f Author: Ann Almgren Date: Sat Mar 24 11:21:10 2018 -0700 Updated the SWFFT Tutorial so 1) It correctly solves the Poisson equation on a single grid, 2) it creates a version of the DistributionMapping to pass to dfft. Tutorials/SWFFT/README Tutorials/SWFFT/SWFFT_Solver.H Tutorials/SWFFT/SWFFT_Solver.cpp Tutorials/SWFFT/SWFFT_Solver_F.F90 Tutorials/SWFFT/SWFFT_Solver_F.H Tutorials/SWFFT/inputs.128 Tutorials/SWFFT/inputs.32 Tutorials/SWFFT/inputs.64 commit 4bcd19a585ece4cea2dda0f91d90e0d03d80af95 Author: Weiqun Zhang Date: Fri Mar 23 20:36:59 2018 -0700 merge two mfiter loops Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit c2a23fa765706bb08a2ad86b5741d6ceffbc6668 Author: Weiqun Zhang Date: Fri Mar 23 18:05:16 2018 -0700 solve nodal solvability Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/Make.package commit c679774b31a583bcb034fe9ca1567b88f531a029 Author: Ann Almgren Date: Fri Mar 23 16:44:42 2018 -0700 This version seems to work. Tutorials/SWFFT/SWFFT_Solver.H Tutorials/SWFFT/SWFFT_Solver.cpp commit 0ba2f34fccd28ef239ca6b31b2ed51414b926835 Merge: f2df4d965 2cb8b1110 Author: Ann Almgren Date: Fri Mar 23 15:49:51 2018 -0700 Merge branch 'development' of https://www.github.com/amrex-codes/amrex into development commit f2df4d9655052aa27631e5785467d3466305b35a Author: Ann Almgren Date: Fri Mar 23 15:49:40 2018 -0700 Save this before I accidentally delete it Tutorials/SWFFT/SWFFT_Solver.cpp commit 2cb8b111014a434bdf60ddd6ea448f2ba01ff0bc Merge: fc7131e1a aea781ee9 Author: dtgraves Date: Fri Mar 23 13:54:12 2018 -0700 Merge pull request #232 from AMReX-Codes/dtg/high_order_moments added higher order moment infrastructure commit aea781ee9a6d7cf4765bb07c2e830c70de284b99 Merge: a359680c1 fc7131e1a Author: dtgraves Date: Fri Mar 23 13:51:48 2018 -0700 Merge branch 'development' into dtg/high_order_moments commit a359680c173b4d7e8fa70607473e24fda90959b5 Author: dtgraves Date: Fri Mar 23 13:50:42 2018 -0700 geometry generation with higher order moments now passes all the regression tests. Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBLevelGrid.cpp Tests/GeometryShop/regression/ebio.cpp commit 1a4bc48b2ecb1ac0c0f769e4d981d7b9665275e0 Author: dtgraves Date: Fri Mar 23 10:38:36 2018 -0700 fixed eb data serialization. all serial regression tests pass now. on to mpi testing Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_FabArrayIO.H Tests/GeometryShop/regression/serialization.cpp commit fc7131e1a25f80fda7f77e9feba5b5cbfbb3ab1a Author: Weiqun Zhang Date: Fri Mar 23 09:01:19 2018 -0700 fix non-mpi build Src/Base/AMReX_ParallelDescriptor.cpp commit 6bfda8c3f6a836a661febe7cb549242769173a71 Author: Weiqun Zhang Date: Fri Mar 23 08:55:41 2018 -0700 array version of rank translation Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelContext.cpp commit cb6cf2836247cd0644af95f5326350e4e1e47433 Author: Kevin Gott Date: Thu Mar 22 16:27:25 2018 -0700 Fix ParallelDescriptor::Waitany and update all other MPI_Wait calls to use the ParallelDescriptor versions. Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Tools/AMRProfParser/TestCodes/ProfWaitTest.cpp commit 355ff02990d43c200c9a798ae7dd64217b0ff708 Author: Andrew Myers Date: Thu Mar 22 15:56:22 2018 -0700 use the ParallelDescriptor version of Waitall in the particle communication routines. Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleContainerI.H commit 724711f7bdeba40e132796e264bca7f2d896d5e5 Merge: 3ff43498f 963ea1b61 Author: Andrew Myers Date: Thu Mar 22 14:49:04 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3ff43498fe2e74305f343a27735a21229f2ddbbe Author: Andrew Myers Date: Thu Mar 22 14:48:55 2018 -0700 fix omp shared variable list in plt_compare_diff_grids Tools/Postprocessing/F_Src/plt_compare_diff_grids.f90 commit 95dfd1fd64e529b602816526fef0e041e01956a3 Author: Weiqun Zhang Date: Thu Mar 22 14:44:58 2018 -0700 use MyProcAll instead of MyProc in some places; if the current context is the global communicator, no need to call translate Src/Amr/AMReX_AmrLevel.cpp Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_ParallelContext.cpp Src/Base/AMReX_Print.H commit 963ea1b613754f72c2f33fbd38e890df33368436 Author: Kevin Gott Date: Thu Mar 22 14:21:47 2018 -0700 Profiling added to the MPI Wait call wrappers. Simple test case also included. Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_ParallelDescriptor.cpp Tools/AMRProfParser/TestCodes/GNUmakefile Tools/AMRProfParser/TestCodes/ProfWaitTest.cpp commit 8c420f5f6fda449627d617e51a3b4213315c66f4 Author: Andrew Myers Date: Thu Mar 22 13:28:04 2018 -0700 add extra newline Tools/RegressionTesting/test_report.py commit 070987c65b86ddc2014cf8222965a4232f469129 Author: Andrew Myers Date: Thu Mar 22 12:50:16 2018 -0700 protect against pcomp_line being None. Tools/RegressionTesting/test_report.py commit 45e881e80b50764cd556db9394da28a37af9389f Author: Weiqun Zhang Date: Thu Mar 22 12:44:41 2018 -0700 use ParallelContext in ParallelDescriptor Src/Base/AMReX.cpp Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelContext.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit 9ed947205cbe1b134d4a9c16abd7dbc5c3efa868 Merge: 6a3dac17f 64682b080 Author: Andrew Myers Date: Thu Mar 22 12:09:55 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6a3dac17fb1951841d93d36b59bbe9179dbf84dc Author: Andrew Myers Date: Thu Mar 22 12:09:44 2018 -0700 hack the test suite to print out the particle comparison command. Tools/RegressionTesting/test_report.py commit 9c74ef01f34373898fed6ae8759d57d27805ecdd Merge: c33e04b02 64682b080 Author: Weiqun Zhang Date: Thu Mar 22 09:43:34 2018 -0700 Merge branch 'development' into forkjoin commit 64682b08084d84303323d21d72ed25ccadd43627 Author: Kevin Gott Date: Wed Mar 21 19:41:07 2018 -0700 Add empty Wait wrappers for cases without MPI. Src/Base/AMReX_ParallelDescriptor.cpp commit 3524b0bd7536d1e9a6fcb01f90be96e0fd17b9f6 Author: Weiqun Zhang Date: Wed Mar 21 17:18:35 2018 -0700 need to call MPI_Comm_free even wehn bl_fortran_mpi_comm_free has been called because the one in Fortran is a duplicate Src/Base/AMReX_ParallelDescriptor.cpp commit a3feb8150cc3ee972e1836898750dc4877721187 Author: kngott Date: Wed Mar 21 16:21:48 2018 -0700 AMReX wrappers for all MPI Wait functions. Profiling to be added and tested. Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Tools/AMRProfParser/TestCodes/GNUmakefile Tools/AMRProfParser/TestCodes/ProfWaitTest.cpp commit 45b74a497ab14d71369e99b5b480122afef27b05 Author: kngott Date: Wed Mar 21 16:10:13 2018 -0700 Make.allinea file rename to Make.forge Tools/GNUMake/tools/Make.forge commit 75cf2977c8f7339b2ea611b4df4419d119887b01 Author: kngott Date: Wed Mar 21 16:08:33 2018 -0700 TPP header file Src/Base/AMReX_ThirdPartyProfiling.H commit f0aa5816921477ebfd0137cc1ac7d31fc1a05cd6 Author: kngott Date: Wed Mar 21 16:05:51 2018 -0700 Third Party Profiling First Attempt Src/Base/AMReX_BLProfiler.H Src/Base/Make.package Tools/GNUMake/Make.defs Tools/GNUMake/tools/Make.vtune Tutorials/Basic/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp commit 014f1a00dadfc9d0ffac2ce30b0df513f66a61d8 Author: dtgraves Date: Wed Mar 21 14:51:46 2018 -0700 serialization still broken for higher order but all the other tests pass Src/GeometryShop/AMReX_EllipsoidIF.H Src/GeometryShop/AMReX_EllipsoidIF.cpp Src/GeometryShop/AMReX_PlaneIF.cpp Tests/GeometryShop/regression/fabio.cpp Tests/GeometryShop/regression/levelRedistTest.cpp Tests/GeometryShop/regression/multicelllev.cpp Tests/GeometryShop/regression/multicelllev.inputs Tests/GeometryShop/regression/runalltests.serial.sh commit 6c1482f9c93327772b099c25cc4816c77c3c89f7 Author: Johannes Blaschke Date: Wed Mar 21 13:30:48 2018 -0700 fix over-zealous deletions build_and_deploy.sh commit 7839b345485c5d6ea1e9d24be3099ca189efc6dd Author: dtgraves Date: Wed Mar 21 11:57:53 2018 -0700 fixed more tests so they also run with WrappedGShop. Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp Tests/GeometryShop/regression/dataArith.cpp Tests/GeometryShop/regression/ebio.cpp Tests/GeometryShop/regression/ebnormalizeTest.cpp Tests/GeometryShop/regression/fabfromif.cpp Tests/GeometryShop/regression/serialization.cpp commit f867f5d295d6a9ada4cb56d4598d08c9fb824276 Author: Johannes Blaschke Date: Wed Mar 21 11:48:41 2018 -0700 fix broken link in the docs (to Amrvis profiling) Docs/sphinx/source/AMReX_Profiling_Tools.rst Docs/sphinx/source/GettingStarted.rst commit b6750a6ad1a48ceed214db32be5d1ad826788b0e Author: Johannes Blaschke Date: Wed Mar 21 11:06:26 2018 -0700 debugging travis script build_and_deploy.sh commit fa8efd3728f18892af0f55015758167d5e955f7e Author: Johannes Blaschke Date: Wed Mar 21 10:52:32 2018 -0700 update travis to reflect new web root for docs build_and_deploy.sh commit 347baabf55de25c4eaf09f822793a0f2be49e726 Author: dtgraves Date: Tue Mar 20 16:28:40 2018 -0700 More tests are passing. Higher order stuff coming along. Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_IrregNode.cpp Src/GeometryShop/AMReX_PlaneIF.H Src/GeometryShop/AMReX_PlaneIF.cpp Src/GeometryShop/AMReX_WrappedGShop.H Src/GeometryShop/AMReX_WrappedGShop.cpp Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp Tests/GeometryShop/ramp/main.cpp commit a7d05ef985651fff2ce8bdf90b70e0c66abe179a Author: Weiqun Zhang Date: Tue Mar 20 13:32:38 2018 -0700 EBFluxRegister: fix a bug when tile size is odd Src/EB/AMReX_EBFluxRegister.cpp commit 24cd1247bf82644f304c1b3a738d5315e9245d8b Author: dtgraves Date: Tue Mar 20 10:58:21 2018 -0700 first higher order test passed. I still have to put in the new bits that fix regular next to covered and add more derivative methods to the implicit function classes. Src/Base/AMReX_IntVect.H Src/GeometryShop/AMReX_SphereIF.H Src/GeometryShop/AMReX_SphereIF.cpp Src/GeometryShop/AMReX_WrappedGShop.cpp commit 8d323b7de68bb62ffcef9fcae468ddf2ef78aa0e Merge: 2ec8b903b 93346b296 Author: Andrew Myers Date: Tue Mar 20 10:20:34 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2ec8b903b9d7faf40a88fdd1b499711f5712ab84 Author: Andrew Myers Date: Tue Mar 20 10:20:22 2018 -0700 wrap this variable in a BL_USE_MPI ifdef Src/Base/AMReX_ParallelDescriptor.cpp commit 93346b296977acef7f1d2020e0091462506284e0 Merge: c5014969e b098b233a Author: WeiqunZhang Date: Tue Mar 20 09:20:22 2018 -0700 Merge pull request #229 from JBlaschke/development GNUMake used by Tools/F_mk and Tools/Postprocessing/C_Src should respect settings in Make.local commit 84d93217d732d04772cb292aa0c9d1a4d5c25548 Merge: e074eeae8 c5014969e Author: dtgraves Date: Mon Mar 19 15:46:24 2018 -0700 merging with dev branch commit e074eeae8e90b55aab44d27cf3c31298348e7a79 Author: dtgraves Date: Mon Mar 19 15:44:03 2018 -0700 more fixes. I am not sure how to get Marc's intersection information in the new context. Still need to fix a bunch of implicit function so they produce their derivatives. Src/GeometryShop/AMReX_BaseIF.H Src/GeometryShop/AMReX_WrappedGShop.H Src/GeometryShop/AMReX_WrappedGShop.cpp Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp commit c5014969e01cecf0ff119ee9489ed056ee32e622 Author: Weiqun Zhang Date: Mon Mar 19 15:39:26 2018 -0700 move amrex_malloc and amrex_free to cpp file so that linker can find them for Fortran code Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit ce1b12f99563b3461589bf0dae99628dd71606e5 Author: dtgraves Date: Mon Mar 19 15:01:39 2018 -0700 Serialization of higher order moments is written and compiles. On to testing. Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFAB.cpp Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBData.cpp commit 8f4f41e0bd0350a42d5b5ed3d048a8d25e79422f Author: dtgraves Date: Mon Mar 19 11:33:35 2018 -0700 put Weiqun's isnan code into a template specialization so BaseIFFAB can work with other data types Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFAB.cpp Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBISBox.H Src/GeometryShop/Make.package commit b098b233a5aeba553eb7f8111b81d00cc15097e1 Author: Johannes Blaschke Date: Sun Mar 18 21:39:25 2018 -0700 fix typo in docs Docs/sphinx/source/BuildingAMReX.rst commit 368e659ae91feeb165623b0feb970c2e947a1b4c Author: Johannes Blaschke Date: Sun Mar 18 21:30:45 2018 -0700 GNUMake used by Tools/F_mk and Tools/Postprocessing/C_Src now respects compiler options in Make.local Tools/F_mk/comps/gfortran.mak Tools/Postprocessing/C_Src/GNUmakefile commit e825bca923d4c51824f910b38372637f581d0938 Merge: fc0e60c89 b7941e09a Author: WeiqunZhang Date: Fri Mar 16 17:25:42 2018 -0700 Merge pull request #227 from AMReX-Codes/MultiComponentMLMG Multi component mlmg commit b7941e09a4a7177cbc2ab7f40bc944c7696360be Author: Weiqun Zhang Date: Fri Mar 16 16:38:07 2018 -0700 multi-component solvability fix for cell-centered solve Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 518555ba841347ebd2d8bd057f1fc528890c7589 Author: dtgraves Date: Fri Mar 16 16:15:55 2018 -0700 integration with EBIS is complete except for the serialization stuff. This is very much like saying that except for the hundred year war, it was a heck of a century. Src/GeometryShop/AMReX_BaseIF.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBDataFactory.H Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_WrappedGShop.H Src/GeometryShop/AMReX_WrappedGShop.cpp commit c9dc246f95c104f522072c0b8c40bd5f3acdeab1 Merge: cff0a9011 9f30f358d Author: Brandon Runnels Date: Fri Mar 16 15:47:15 2018 -0700 Merge pull request #228 from AMReX-Codes/MCMLMG_bc Add isCrossStencil virtual function to MLCellLinOp. For non-cross st… commit fc0e60c8968e848fea72fe9a16311229a9e145e5 Author: Andrew Myers Date: Fri Mar 16 14:28:17 2018 -0700 grow by an additional cell here (can be needed even if all particles are in the right place due to roundoff errors). Src/Particle/AMReX_NeighborParticlesI.H commit 4651a3a1910b464250b11ae16a58a0630d90d67b Author: Andrew Myers Date: Fri Mar 16 14:26:50 2018 -0700 add some debug-mode asserts to help catch problems earlier. Src/Particle/AMReX_NeighborParticlesI.H commit edaafc88797e4779449657935804b99a5ec5c768 Author: Andrew Myers Date: Fri Mar 16 14:06:15 2018 -0700 use an explicit cast here to shut up compiler warnings. Src/Particle/AMReX_ParticleContainerI.H commit 9f30f358dec75c71e76f22a7616953fa2dd0275a Author: Weiqun Zhang Date: Fri Mar 16 12:23:58 2018 -0700 Add isCrossStencil virtual function to MLCellLinOp. For non-cross stencil, extend mask to corners and extrpolation is done only for non-covered corner cells. Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 commit cff0a90116873bfb96540e99680badb1ec289ba4 Author: Weiqun Zhang Date: Fri Mar 16 11:03:38 2018 -0700 use double precision Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 commit 26e56749782072996fb4b4efec7c174bfc7ed856 Author: Weiqun Zhang Date: Fri Mar 16 10:26:58 2018 -0700 no need to have overriding virtual function getNComp in MLCellLinop because a default implementation already exists in its base class MLLinOp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit d899969b3690b5a7422d7cae0ec8ad898bcecd90 Author: Weiqun Zhang Date: Fri Mar 16 10:16:11 2018 -0700 minor Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit 35e7ae7479b613835bfb0eef73c166cedf48b233 Author: Weiqun Zhang Date: Fri Mar 16 10:05:24 2018 -0700 no need to call linop.prepareForSolve in cases it has been called Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 5e60830c1f01b41f5787fc061df85145c974e7f8 Author: Weiqun Zhang Date: Fri Mar 16 09:37:34 2018 -0700 fix type mismatch Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 commit 854b0defd9e44ac1ba4ec9f4635e7e447a531623 Author: Weiqun Zhang Date: Fri Mar 16 09:30:14 2018 -0700 fix typos in 1d Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90 commit ad0ecda01d42a3771a8df1a4925f6f902b1f5cde Author: Brandon Runnels Date: Thu Mar 15 17:59:24 2018 -0600 reverted bndrydata Src/Boundary/AMReX_BndryData.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 commit 733b30097014146982307b4790bbfa600d2979b7 Author: Brandon Runnels Date: Thu Mar 15 17:49:01 2018 -0600 reverted ncomp changes Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit 86cc2bc3488a9e38b444b0742068f056afd086e2 Author: Brandon Runnels Date: Thu Mar 15 16:39:37 2018 -0600 fixed 3d error Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 commit fc19b8b4da663a1e788e23b64d47778afc10bd2e Author: Brandon Runnels Date: Thu Mar 15 16:14:09 2018 -0600 minor fixes to MLCG norm and to the number of components for masks in MLCellLinOp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit 6a2cf6376ce4effe23246a3ca074bd20666b858f Merge: 652de4337 33983cf09 Author: Brandon Runnels Date: Thu Mar 15 15:55:57 2018 -0600 Merge branch 'development' into MultiComponentMLMG commit 652de43370e4c8531b6a1cce8c5229b33c9f95b3 Author: Brandon Runnels Date: Thu Mar 15 15:47:19 2018 -0600 removed printout statement Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit c33e04b022b53765e06add9ef4b4f6cc18b6f9e0 Author: Weiqun Zhang Date: Thu Mar 15 14:22:37 2018 -0700 move task splitting stuff from ParallelContext into ForkJoin Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelContext.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ccse-mpi.H commit 9e5c7f4e45e6dbc85a7639eafc3ee863dd30bada Author: dtgraves Date: Thu Mar 15 11:10:16 2018 -0700 port of higher order moment infrastructure is complete. Now I need to integrate it into EBIndexSpace and all that. Src/GeometryShop/AMReX_IFData.cpp Src/GeometryShop/AMReX_IndexedMoments.H Src/GeometryShop/AMReX_MetaPrograms.H Src/GeometryShop/AMReX_MonomialPowers.H Src/GeometryShop/Make.package commit 83e29538b67b2b34a4635480d130a7d88c120045 Author: Weiqun Zhang Date: Thu Mar 15 10:24:57 2018 -0700 include ParallelContext in ParallelDescriptor header Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ccse-mpi.H commit ad852b511c7f3cb79021cc9ab1df2dbfcecaf29f Author: Weiqun Zhang Date: Thu Mar 15 09:00:46 2018 -0700 more to private of ForkJoin Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp commit 33983cf09a9ab572483babb2b6049d4b07849074 Merge: cdf96dcdd 3bedeeba6 Author: Andrew Myers Date: Wed Mar 14 23:15:12 2018 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit cdf96dcddf021e3d0c22eab06dcb8d0a8dfefa5d Author: Andrew Myers Date: Wed Mar 14 23:14:48 2018 -0700 some changes needed in the test suite for SedonaBox Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py commit 3ecede96d91f2ae836865eefd08b0e14c3fa46de Author: dtgraves Date: Wed Mar 14 15:58:42 2018 -0700 lots of progress made in the big slog. Src/GeometryShop/AMReX_IFSlicer.H Src/GeometryShop/AMReX_IndexedMoments.H Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_IrregNode.cpp Src/GeometryShop/AMReX_MinimalCCCMImplem.H Src/GeometryShop/AMReX_NormalDerivativeNew.H Src/GeometryShop/AMReX_WrappedGShop.cpp commit 816ad96ddc456520c28bb361c6fa94a1956be9f2 Author: Weiqun Zhang Date: Wed Mar 14 14:42:10 2018 -0700 move MFFork to private and other minor changes Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp commit 1cd1c7434b971b73cee077197bbf1d69fc8d7439 Author: Weiqun Zhang Date: Wed Mar 14 14:00:50 2018 -0700 make MultiColor_C compile again OldTutorials/MultiColor_C/GNUmakefile OldTutorials/MultiColor_C/inputs OldTutorials/MultiColor_C/main.cpp commit a817800907dbd3e0ad55a05d4ff43b2b7a56871e Author: Weiqun Zhang Date: Wed Mar 14 12:36:23 2018 -0700 remove Color Src/Base/AMReX.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_ForkJoin.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_ParallelContext.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_Utility.cpp Src/Base/AMReX_iMultiFab.cpp Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_FabSet.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 0e61fe483e9faa50baf00751e87b2d8589efbb2b Author: dtgraves Date: Wed Mar 14 11:53:24 2018 -0700 waist deep in the big muddy Src/GeometryShop/AMReX_EB_TYPEDEFS.H Src/GeometryShop/AMReX_IndexTM.H Src/GeometryShop/AMReX_IndexedMoments.H Src/GeometryShop/AMReX_IndexedMomentsImplem.H Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_MomentIterator.H Src/GeometryShop/AMReX_MomentIteratorImplem.H Src/GeometryShop/AMReX_MonomialPowers.H Src/GeometryShop/Make.package commit e83b15f04a2707fc765281ccfc48fb5e608606a5 Author: Weiqun Zhang Date: Wed Mar 14 09:42:51 2018 -0700 add ParallelContex::init and finalize to amrex::Initialize and Finalize OldTutorials/MultiColor_C/main.cpp Src/Base/AMReX.cpp commit 38e48529af1caf53fc6eaa630be1dfa3d12dda2d Author: Weiqun Zhang Date: Wed Mar 14 09:35:00 2018 -0700 move AMReX_ForkJoin and AMReX_ParallelContext to Base/ OldTutorials/MultiColor_C/GNUmakefile Src/Base/AMReX_ForkJoin.H Src/Base/AMReX_ForkJoin.cpp Src/Base/AMReX_ParallelContext.H Src/Base/AMReX_ParallelContext.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 3bedeeba6781f6b7d882850206fb95730589e029 Author: Michele Rosso Date: Tue Mar 13 16:27:56 2018 -0700 CMake:start setup for profiling improvements Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake commit b0abf0b1658bc85489674d0fc544f4344fdea696 Author: dtgraves Date: Tue Mar 13 15:34:16 2018 -0700 templates and namespaces are really not fond of one another Src/Base/AMReX_IntVect.H Src/GeometryShop/AMReX_ConstrainedLS.H Src/GeometryShop/AMReX_ConstrainedLS.cpp Src/GeometryShop/AMReX_CoordinateSystem.H Src/GeometryShop/AMReX_CoordinateSystemImplem.H Src/GeometryShop/AMReX_CutCellMoments.H Src/GeometryShop/AMReX_CutCellMoments.cpp Src/GeometryShop/AMReX_CutCellMomentsImplem.H Src/GeometryShop/AMReX_DivNormalRefinement.H Src/GeometryShop/AMReX_DivNormalRefinementImplem.H Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_EBGeomDebugDump.H Src/GeometryShop/AMReX_EBGeomDebugOut.H Src/GeometryShop/AMReX_EBGeomDebugOut.cpp Src/GeometryShop/AMReX_EB_TYPEDEFS.H Src/GeometryShop/AMReX_Factorial.H Src/GeometryShop/AMReX_GenericArithmetic.H Src/GeometryShop/AMReX_GenericArithmeticI.H Src/GeometryShop/AMReX_IFData.H Src/GeometryShop/AMReX_IFData.cpp Src/GeometryShop/AMReX_IFDataImplem.H Src/GeometryShop/AMReX_IFSlicer.H Src/GeometryShop/AMReX_IFSlicer.cpp Src/GeometryShop/AMReX_IFSlicerImplem.H Src/GeometryShop/AMReX_IndexTM.H Src/GeometryShop/AMReX_IndexTMI.H Src/GeometryShop/AMReX_IndexedMoments.H Src/GeometryShop/AMReX_IndexedMomentsImplem.H Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_LSProblem.H Src/GeometryShop/AMReX_LSProblem.cpp Src/GeometryShop/AMReX_LSProblemImplem.H Src/GeometryShop/AMReX_LSquares.H Src/GeometryShop/AMReX_LSquares.cpp Src/GeometryShop/AMReX_MinimalCCCM.H Src/GeometryShop/AMReX_MinimalCCCM.cpp Src/GeometryShop/AMReX_MinimalCCCMImplem.H Src/GeometryShop/AMReX_MomentIterator.H Src/GeometryShop/AMReX_MultiIndex.H Src/GeometryShop/AMReX_MultiIndexImplem.H Src/GeometryShop/AMReX_NoRefinement.H Src/GeometryShop/AMReX_NoRefinementImplem.H Src/GeometryShop/AMReX_NormalDerivative.H Src/GeometryShop/AMReX_NormalDerivative.cpp Src/GeometryShop/AMReX_NormalDerivativeImplem.H Src/GeometryShop/AMReX_NormalDerivativeNew.H Src/GeometryShop/AMReX_NormalDerivativeNewImplem.H Src/GeometryShop/AMReX_Notation.H Src/GeometryShop/AMReX_RefinementCriterion.H Src/GeometryShop/AMReX_SmoothAbsoluteValue.cpp Src/GeometryShop/AMReX_SmoothIntersection.cpp Src/GeometryShop/AMReX_WrappedGShop.H Src/GeometryShop/AMReX_WrappedGShop.cpp Src/GeometryShop/Make.package commit 208218a71e367934bdae9525ab62d5861284d727 Author: dtgraves Date: Mon Mar 12 16:34:47 2018 -0700 more slogging through the vast amount of code needed to get higher order geometric information. Src/GeometryShop/AMReX_ConstrainedLS.cpp Src/GeometryShop/AMReX_CutCellMoments.cpp Src/GeometryShop/AMReX_CutCellMomentsImplem.H Src/GeometryShop/AMReX_DivNormalRefinementImplem.H Src/GeometryShop/AMReX_EBGeomDebugOut.H Src/GeometryShop/AMReX_EBGeomDebugOut.cpp Src/GeometryShop/AMReX_EB_TYPEDEFS.H Src/GeometryShop/AMReX_IFDataImplem.H Src/GeometryShop/AMReX_IndexedMoments.H Src/GeometryShop/AMReX_IndexedMomentsImplem.H Src/GeometryShop/AMReX_LSProblemImplem.H Src/GeometryShop/AMReX_MinimalCCCM.cpp Src/GeometryShop/AMReX_MinimalCCCMImplem.H Src/GeometryShop/AMReX_MomentIterator.H Src/GeometryShop/AMReX_NormalDerivative.cpp Src/GeometryShop/AMReX_NormalDerivativeNew.H Src/GeometryShop/AMReX_RefinementCriterion.H Src/GeometryShop/AMReX_SmoothIntersection.cpp Src/GeometryShop/AMReX_WrappedGShop.H Src/GeometryShop/AMReX_WrappedGShop.cpp Src/GeometryShop/Make.package commit d7b6096010e8b10884c1696de268c894e5376f18 Author: dtgraves Date: Mon Mar 12 12:31:43 2018 -0700 the slog continues Src/Base/AMReX_IntVect.H Src/GeometryShop/AMReX_BaseIF.H Src/GeometryShop/AMReX_ConstrainedLS.cpp Src/GeometryShop/AMReX_CoordinateSystemImplem.H Src/GeometryShop/AMReX_CutCellMoments.cpp Src/GeometryShop/AMReX_Factorial.H Src/GeometryShop/AMReX_IFSlicer.H Src/GeometryShop/AMReX_IFSlicer.cpp Src/GeometryShop/AMReX_IndexTM.H Src/GeometryShop/AMReX_IndexTMI.H Src/GeometryShop/AMReX_IndexedMomentsImplem.H Src/GeometryShop/AMReX_LSProblem.cpp Src/GeometryShop/AMReX_NormalDerivative.H Src/GeometryShop/AMReX_NormalDerivative.cpp Src/GeometryShop/AMReX_SmoothAbsoluteValue.H Src/GeometryShop/AMReX_SmoothIntersection.H Src/GeometryShop/AMReX_SmoothUnion.H Src/GeometryShop/AMReX_SmoothUnion.cpp commit fa0b23106ffc05641823cab4aca9253ae977ee0a Author: Weiqun Zhang Date: Sun Mar 11 18:27:34 2018 -0700 move public apply from MLLinOp to MLMG Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit e7fd02204dec30a6e95d7ebed6832b9de872f3df Author: Weiqun Zhang Date: Sun Mar 11 16:18:28 2018 -0700 add public apply function to MLLinOp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit ab2724508068f0e7b6684779e4fc16d16b82ca37 Author: Weiqun Zhang Date: Sun Mar 11 14:07:09 2018 -0700 MLMG: option to set max coarsening level Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp commit 959aff2b96657a28aec5971d8c9e0d7783bd0e1a Author: Weiqun Zhang Date: Fri Mar 9 17:12:49 2018 -0800 add amrex_malloc and amrex_free to Fortran module amrex_fort_module Src/Base/AMReX_Utility.H Src/Base/AMReX_fort_mod.F90 commit 9c92d47e382ca25bb58915f703451379d890cf0c Author: dtgraves Date: Fri Mar 9 15:57:30 2018 -0800 slogging through the vast amount of code needed to get higher order geometric information. Src/GeometryShop/AMReX_CH_EBIS_ORDER.H Src/GeometryShop/AMReX_ConstrainedLS.H Src/GeometryShop/AMReX_ConstrainedLS.cpp Src/GeometryShop/AMReX_CoordinateSystem.H Src/GeometryShop/AMReX_CoordinateSystemImplem.H Src/GeometryShop/AMReX_CutCellMoments.H Src/GeometryShop/AMReX_CutCellMoments.cpp Src/GeometryShop/AMReX_CutCellMomentsImplem.H Src/GeometryShop/AMReX_DivNormalRefinement.H Src/GeometryShop/AMReX_DivNormalRefinementImplem.H Src/GeometryShop/AMReX_EBGeomDebugDump.H Src/GeometryShop/AMReX_EBGeomDebugOut.H Src/GeometryShop/AMReX_EBGeomDebugOut.cpp Src/GeometryShop/AMReX_EB_TYPEDEFS.H Src/GeometryShop/AMReX_Factorial.H Src/GeometryShop/AMReX_FixedRefinement.H Src/GeometryShop/AMReX_FixedRefinementImplem.H Src/GeometryShop/AMReX_GenericArithmetic.H Src/GeometryShop/AMReX_GenericArithmeticI.H Src/GeometryShop/AMReX_IFData.H Src/GeometryShop/AMReX_IFData.cpp Src/GeometryShop/AMReX_IFDataImplem.H Src/GeometryShop/AMReX_IFSlicer.H Src/GeometryShop/AMReX_IFSlicer.cpp Src/GeometryShop/AMReX_IFSlicerImplem.H Src/GeometryShop/AMReX_IndexTM.H Src/GeometryShop/AMReX_IndexTMI.H Src/GeometryShop/AMReX_IndexedMoments.H Src/GeometryShop/AMReX_IndexedMomentsImplem.H Src/GeometryShop/AMReX_LSProblem.H Src/GeometryShop/AMReX_LSProblem.cpp Src/GeometryShop/AMReX_LSProblemImplem.H Src/GeometryShop/AMReX_MetaPrograms.H Src/GeometryShop/AMReX_MinimalCCCM.H Src/GeometryShop/AMReX_MinimalCCCM.cpp Src/GeometryShop/AMReX_MinimalCCCMImplem.H Src/GeometryShop/AMReX_MomentIterator.H Src/GeometryShop/AMReX_MultiIndex.H Src/GeometryShop/AMReX_MultiIndexImplem.H Src/GeometryShop/AMReX_NoRefinement.H Src/GeometryShop/AMReX_NoRefinementImplem.H Src/GeometryShop/AMReX_NormalDerivative.H Src/GeometryShop/AMReX_NormalDerivative.cpp Src/GeometryShop/AMReX_NormalDerivativeImplem.H Src/GeometryShop/AMReX_NormalDerivativeNew.H Src/GeometryShop/AMReX_NormalDerivativeNewImplem.H Src/GeometryShop/AMReX_Notation.H Src/GeometryShop/AMReX_RefinementCriterion.H Src/GeometryShop/AMReX_SmoothAbsoluteValue.H Src/GeometryShop/AMReX_SmoothAbsoluteValue.cpp Src/GeometryShop/AMReX_SmoothIntersection.H Src/GeometryShop/AMReX_SmoothIntersection.cpp Src/GeometryShop/AMReX_SmoothUnion.H Src/GeometryShop/AMReX_SmoothUnion.cpp Src/GeometryShop/AMReX_WrappedGShop.H Src/GeometryShop/AMReX_WrappedGShop.cpp Src/GeometryShop/Make.package commit fed290126d8ce7d786a15c6ad4196f88f8e2ab40 Author: dtgraves Date: Fri Mar 9 15:56:28 2018 -0800 slogging through the vast amount of code needed to get higher order geometric information. Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp commit 3895ff8afb4ee799a30c6aa180f0e4bc54f5a9ed Author: Cy Chan Date: Thu Mar 8 20:35:20 2018 -0800 bunch of small updates to fork-join follow some of weiqun's suggestions trying to follow existing AMReX conventions put mpi_tag back as frame member so each frame has its own copy OldTutorials/MultiColor_C/AMReX_ForkJoin.H OldTutorials/MultiColor_C/AMReX_ForkJoin.cpp OldTutorials/MultiColor_C/AMReX_ParallelContext.H OldTutorials/MultiColor_C/AMReX_ParallelContext.cpp OldTutorials/MultiColor_C/main.cpp commit 970eec0eaf15a26085ac5275c6d499589c81271f Author: Weiqun Zhang Date: Thu Mar 8 16:04:00 2018 -0800 don't use MPI_COMM_WORLD directly Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp commit 1332dda393ea2eb65ce4d2e3415f1fac5ae27645 Author: Andrew Myers Date: Thu Mar 8 14:14:47 2018 -0800 improve profiling in Neighbor Particles. Src/Particle/AMReX_NeighborParticlesI.H commit 1dbdcc499932a4752d2067b47c4fc0816f512528 Author: Weiqun Zhang Date: Thu Mar 8 11:32:01 2018 -0800 a bunch of small changes OldTutorials/MultiColor_C/AMReX_ForkJoin.H OldTutorials/MultiColor_C/AMReX_ForkJoin.cpp OldTutorials/MultiColor_C/AMReX_ParallelContext.H OldTutorials/MultiColor_C/AMReX_ParallelContext.cpp OldTutorials/MultiColor_C/main.cpp commit b58875a0159cc0ad03a7a26772fff2182542db55 Merge: c2caa8ad2 78c40fccf Author: Weiqun Zhang Date: Thu Mar 8 08:56:09 2018 -0800 Merge branch 'development' into forkjoin commit cfa145c7fe6c977a2b84dcdbcf2931344de8376f Author: Weiqun Zhang Date: Wed Mar 7 17:13:03 2018 -0800 nodal projection: bug fix in restriction Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit c2caa8ad2aaafaaaebad7f3b7002c39c3df7a8dd Author: Cy Chan Date: Wed Mar 7 16:14:01 2018 -0800 moved ParallelContext and ForkJoin into separate files OldTutorials/MultiColor_C/AMReX_ForkJoin.H OldTutorials/MultiColor_C/AMReX_ForkJoin.cpp OldTutorials/MultiColor_C/AMReX_ParallelContext.H OldTutorials/MultiColor_C/AMReX_ParallelContext.cpp OldTutorials/MultiColor_C/GNUmakefile OldTutorials/MultiColor_C/main.cpp commit 9e6ee23cf4837c72505376100c5327444630b8fe Author: Cy Chan Date: Wed Mar 7 15:37:56 2018 -0800 fork join can be invoked multiple times using same ForkJoin object reuses forked multifabs and distribution maps across invocations added distribution map cache member added verbose debugging information OldTutorials/MultiColor_C/main.cpp commit 349d8e445f8060f06006ebb40b8a1cfaeb9edae7 Merge: ec308f9ac 78c40fccf Author: Weiqun Zhang Date: Wed Mar 7 14:47:16 2018 -0800 Merge branch 'development' into weiqun/mlmg commit 78c40fccf3aa177c6d80c893b4c0b049f6417246 Author: Weiqun Zhang Date: Wed Mar 7 14:44:09 2018 -0800 mlmg: print the correct residual for vebose>=4 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit ec308f9ac99ed64e163494bf6e83e826a1bd7deb Author: Weiqun Zhang Date: Wed Mar 7 13:52:57 2018 -0800 nodal projection: allow coarsening strategy be sigma for all regular eb Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H commit c81274a78d742d315b1ba185e89a0c59b7710272 Author: Weiqun Zhang Date: Wed Mar 7 13:34:16 2018 -0800 nodal projection: in restriction and interpolation, if both weights are zero, take average Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 921e97f6325b78babb0dc792e39389977e5cb3c9 Author: Weiqun Zhang Date: Wed Mar 7 12:58:44 2018 -0800 nodal projection: fix bug Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit ae7631683c28acf21728375b04e4df009da53dea Author: Weiqun Zhang Date: Wed Mar 7 12:52:30 2018 -0800 nodal projection: fix array bound and index bug Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 3045b4d3c3c6b7e1789e5b1229eda0e773e76eac Author: Weiqun Zhang Date: Wed Mar 7 12:50:55 2018 -0800 nodal projection: fix array bound Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit bab21f13549de27c696edf2fc97c02ced0a3e943 Author: Weiqun Zhang Date: Wed Mar 7 12:49:22 2018 -0800 nodal projection: fix divide by zero and change some parameters back to default Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 2d460ec83a0490f410be489ec65709fdfdf7983e Author: Weiqun Zhang Date: Wed Mar 7 09:57:03 2018 -0800 WIP: RAP stencil for testing constant sigma Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 3d815fa3fc92f4db0d3736bf9b6f3e97ce94fe0b Author: Weiqun Zhang Date: Wed Mar 7 09:50:44 2018 -0800 3d nodal projection: RAP version of restriction Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit edeaf205100bbb6b5e40e0f8d56b9138d6408df9 Author: Weiqun Zhang Date: Tue Mar 6 17:32:04 2018 -0800 remove _images/ from top directory because the only figure there has a copy already in Docs/ as it should be _images/ParaView_filegroup.png commit 642704cfabeabba269952f421338ab97da8c4a9e Author: Weiqun Zhang Date: Tue Mar 6 17:07:21 2018 -0800 WIP: RAP version of restriction Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 7ff28fb18c6bd4758c96e249aaf064aebfafc88c Author: Cy Chan Date: Tue Mar 6 16:26:46 2018 -0800 only create distribution mapping object once per (box array, task) pair multiple multifabs accessed by each task may share the same boxarray they need to have same distribution mapping OldTutorials/MultiColor_C/main.cpp commit 5f06351c043fac623f6913f971cb8822dd1bc256 Author: Weiqun Zhang Date: Tue Mar 6 14:33:44 2018 -0800 3d nodal projection: RAP version of interpolation Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit d1c7d748a40bc7ee3f502a76735abfac796ad14f Author: Cy Chan Date: Tue Mar 6 14:14:39 2018 -0800 more work on fork join and parallel context frames: updated local/global rank translation added mpi tag getter/incrementer with wrap-around init first frame to ParallelDescriptor::Communicator update asserts to AMREX_ style update enum to enum class OldTutorials/MultiColor_C/main.cpp Src/Base/AMReX_ParallelDescriptor.H commit c096c8f5ec56a7fe82e9bed2300e206df3db6d6a Merge: b31a41f25 231dc4856 Author: Weiqun Zhang Date: Tue Mar 6 13:14:52 2018 -0800 Merge branch 'development' into weiqun/mlmg commit b7de7cdd1fa8502be3a4f87ea2f885db089f992c Author: Brandon Runnels Date: Tue Mar 6 10:21:08 2018 -0700 added update for ghost corners (2D only) Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 commit 231dc485621cf47e5074feeda2693c2b93bd59e1 Author: Andrew Myers Date: Tue Mar 6 09:04:50 2018 -0800 put this preprocessor macro back. Src/GeometryShop/AMReX_EBFluxFAB.H commit feb7c1b58706c6b03dad7b4ba63d9c8cf91caffa Author: Ann Almgren Date: Mon Mar 5 16:29:42 2018 -0800 Update the multifab norms to use versions in Src/Base instead of local definitions. Tests/LinearSolvers/C_CellMG/macprojTest.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit b31a41f25e598b6e52ef4af7581bacc1b2db43df Merge: 5196ae8ab 45cb356e0 Author: Weiqun Zhang Date: Mon Mar 5 16:17:11 2018 -0800 Merge branch 'development' into weiqun/mlmg commit 45cb356e0cd1214f7aab9b7d0958416ceaec822b Merge: 729dc16bf 40b5df8fb Author: Weiqun Zhang Date: Mon Mar 5 16:16:15 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 729dc16bf7d19618bda09883d1bd10ae5801bd16 Author: Weiqun Zhang Date: Mon Mar 5 16:08:19 2018 -0800 update CHANGES CHANGES commit 170af22b45514e8ed226dba6f2d97085876e2f00 Author: Brandon Runnels Date: Mon Mar 5 17:00:10 2018 -0700 removed comment Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit fd87a795750892d36f56d6b78f6a268306e9c46e Author: Cy Chan Date: Mon Mar 5 12:13:21 2018 -0800 added single mode for MF access in fork-join added task bound split calculation misc. clean up OldTutorials/MultiColor_C/main.cpp commit 40b5df8fbe377a2a7a6647a3b052b0f2c5f37240 Author: Ann Almgren Date: Mon Mar 5 09:36:45 2018 -0800 Cleaning out more headings for consistency Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H Src/EBAMRElliptic/AMReX_BaseBCFuncEval.H Src/EBAMRElliptic/AMReX_BiCGStabSolver.H Src/EBAMRElliptic/AMReX_ConductivityBaseDomainBC.H Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.cpp Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRElliptic/AMReX_EBMultiGrid.H Src/EBAMRElliptic/AMReX_EBSimpleSolver.H Src/EBAMRElliptic/AMReX_EBSimpleSolver.cpp Src/EBAMRElliptic/AMReX_LinearSolver.H Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.H Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.cpp Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.H Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.cpp Src/EBAMRElliptic/AMReX_NoOpSolver.H Src/EBAMRElliptic/AMReX_VCAggStencil.H Src/EBAMRElliptic/AMReX_VCAggStencil.cpp Src/EBAMRTools/AMReX_EBCoarseAverage.cpp commit 3efbb0e76318b75a1ec3223ba46d682145573d2f Author: Ann Almgren Date: Mon Mar 5 09:30:43 2018 -0800 More consistency fixes. Src/GeometryShop/AMReX_ZCylinder.H Src/GeometryShop/AMReX_ZCylinder.cpp commit 4bc8a06fed3b226019300e34971c85b091494977 Author: Ann Almgren Date: Mon Mar 5 09:28:45 2018 -0800 For consistency, remove logo at top of files. If we decide on a common header later we can then add it to all files uniformly Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseIndex.H Src/Base/AMReX_BoxIterator.H Src/Base/AMReX_BoxIterator.cpp Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp Src/Base/AMReX_SPMD.H Src/Base/AMReX_SPMD.cpp Src/Base/AMReX_SPMDI.H Src/Base/AMReX_parstream.H Src/Base/AMReX_parstream.cpp Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Src/EBAMRTools/AMReX_DivergenceOp.H Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_EBCFInterp.H Src/EBAMRTools/AMReX_EBCFInterp.cpp Src/EBAMRTools/AMReX_EBCoarseAverage.H Src/EBAMRTools/AMReX_EBFastFR.H Src/EBAMRTools/AMReX_EBFastFR.cpp Src/EBAMRTools/AMReX_EBFineInterp.H Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/EBAMRTools/AMReX_GradientOp.H Src/EBAMRTools/AMReX_GradientOp.cpp Src/EBAMRTools/AMReX_MeshRefine.H Src/EBAMRTools/AMReX_MeshRefine.cpp Src/GeometryShop/AMReX_AggStencil.H Src/GeometryShop/AMReX_AggStencilI.H Src/GeometryShop/AMReX_AllRegularService.H Src/GeometryShop/AMReX_AllRegularService.cpp Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H Src/GeometryShop/AMReX_AnisotropicIF.H Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_BaseEBCellFactory.H Src/GeometryShop/AMReX_BaseEBFaceFAB.H Src/GeometryShop/AMReX_BaseEBFaceFABI.H Src/GeometryShop/AMReX_BaseIF.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_BaseIFFactory.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_CellEdge.H Src/GeometryShop/AMReX_CellEdge.cpp Src/GeometryShop/AMReX_ComplementIF.H Src/GeometryShop/AMReX_ComplementIF.cpp Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_EBCellFAB.H Src/GeometryShop/AMReX_EBCellFAB.cpp Src/GeometryShop/AMReX_EBCellFactory.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBDataFactory.H Src/GeometryShop/AMReX_EBDataVarMacros.H Src/GeometryShop/AMReX_EBDebugDump.H Src/GeometryShop/AMReX_EBDebugOut.H Src/GeometryShop/AMReX_EBDebugOut.cpp Src/GeometryShop/AMReX_EBFaceFAB.H Src/GeometryShop/AMReX_EBFaceFAB.cpp Src/GeometryShop/AMReX_EBFluxFAB.H Src/GeometryShop/AMReX_EBFluxFAB.cpp Src/GeometryShop/AMReX_EBFluxFactory.H Src/GeometryShop/AMReX_EBFluxFactory.cpp Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISBox.H Src/GeometryShop/AMReX_EBISBox.cpp Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_EBLevelGrid.H Src/GeometryShop/AMReX_EBLevelGrid.cpp Src/GeometryShop/AMReX_EBLevelRedist.H Src/GeometryShop/AMReX_EBLevelRedist.cpp Src/GeometryShop/AMReX_EBLoHiCenter.H Src/GeometryShop/AMReX_EBLoHiCenter.cpp Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.H Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp Src/GeometryShop/AMReX_Ellipsoid.cpp Src/GeometryShop/AMReX_EllipsoidIF.H Src/GeometryShop/AMReX_EllipsoidIF.cpp Src/GeometryShop/AMReX_ExtrudeIF.H Src/GeometryShop/AMReX_ExtrudeIF.cpp Src/GeometryShop/AMReX_FabArrayIO.H Src/GeometryShop/AMReX_FabArrayIO.cpp Src/GeometryShop/AMReX_FaceIndex.H Src/GeometryShop/AMReX_FaceIndex.cpp Src/GeometryShop/AMReX_FaceIterator.H Src/GeometryShop/AMReX_FaceIterator.cpp Src/GeometryShop/AMReX_FlatPlateGeom.H Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryService.cpp Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_GraphNode.H Src/GeometryShop/AMReX_GraphNode.cpp Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntVectSet.cpp Src/GeometryShop/AMReX_IntersectionIF.H Src/GeometryShop/AMReX_IntersectionIF.cpp Src/GeometryShop/AMReX_IrregFAB.H Src/GeometryShop/AMReX_IrregFAB.cpp Src/GeometryShop/AMReX_IrregFABFactory.H Src/GeometryShop/AMReX_IrregFABFactory.cpp Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_IrregNode.cpp Src/GeometryShop/AMReX_KDStruct.H Src/GeometryShop/AMReX_LSquares.H Src/GeometryShop/AMReX_LSquares.cpp Src/GeometryShop/AMReX_LatheIF.H Src/GeometryShop/AMReX_LatheIF.cpp Src/GeometryShop/AMReX_LoHiSide.H Src/GeometryShop/AMReX_LoHiSide.cpp Src/GeometryShop/AMReX_Moments.H Src/GeometryShop/AMReX_Moments.cpp Src/GeometryShop/AMReX_PXStuff.H Src/GeometryShop/AMReX_PXStuff.cpp Src/GeometryShop/AMReX_PlaneIF.H Src/GeometryShop/AMReX_PlaneIF.cpp Src/GeometryShop/AMReX_PolyGeom.H Src/GeometryShop/AMReX_PolyGeom.cpp Src/GeometryShop/AMReX_PolynomialIF.H Src/GeometryShop/AMReX_PolynomialIF.cpp Src/GeometryShop/AMReX_RedistStencil.H Src/GeometryShop/AMReX_RedistStencil.cpp Src/GeometryShop/AMReX_STLAsciiReader.H Src/GeometryShop/AMReX_STLAsciiReader.cpp Src/GeometryShop/AMReX_STLBox.H Src/GeometryShop/AMReX_STLBox.cpp Src/GeometryShop/AMReX_STLExplorer.H Src/GeometryShop/AMReX_STLExplorer.cpp Src/GeometryShop/AMReX_STLIF.H Src/GeometryShop/AMReX_STLIF.cpp Src/GeometryShop/AMReX_STLMesh.H Src/GeometryShop/AMReX_STLMesh.cpp Src/GeometryShop/AMReX_STLReader.H Src/GeometryShop/AMReX_STLUtil.H Src/GeometryShop/AMReX_STLUtil.cpp Src/GeometryShop/AMReX_SlabService.H Src/GeometryShop/AMReX_SlabService.cpp Src/GeometryShop/AMReX_SphereIF.H Src/GeometryShop/AMReX_SphereIF.cpp Src/GeometryShop/AMReX_Stencils.H Src/GeometryShop/AMReX_Stencils.cpp Src/GeometryShop/AMReX_TransformIF.H Src/GeometryShop/AMReX_TransformIF.cpp Src/GeometryShop/AMReX_UnionIF.H Src/GeometryShop/AMReX_UnionIF.cpp Src/GeometryShop/AMReX_VoFIterator.H Src/GeometryShop/AMReX_VoFIterator.cpp Src/GeometryShop/AMReX_VolIndex.H Src/GeometryShop/AMReX_VolIndex.cpp commit 4d1fcaea98880b2d05e0a5ea928320714bc660b7 Merge: d138fd9ab 696c3e7ed Author: dtgraves Date: Mon Mar 5 08:55:37 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d138fd9abf681b57a892a8842775d5f5783d7f56 Author: dtgraves Date: Mon Mar 5 08:55:21 2018 -0800 fixed a bug in ZCylinder Src/GeometryShop/AMReX_ZCylinder.cpp commit 696c3e7edaf561da4540fcb286d73d17fa8121b3 Merge: fe64e6e89 3d6516385 Author: Andrew Myers Date: Sat Mar 3 22:32:28 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit fe64e6e89077844fa34918edca9c7c4d4fb26fc8 Author: Andrew Myers Date: Sat Mar 3 22:30:23 2018 -0800 improving the scaling of particle redistribute when the changes are known to be local. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 3d6516385914c0282805b21f7afa6b6555a03428 Author: dtgraves Date: Fri Mar 2 16:13:53 2018 -0800 added simple cylinder geometry Src/GeometryShop/AMReX_ZCylinder.H Src/GeometryShop/AMReX_ZCylinder.cpp Src/GeometryShop/Make.package commit 65d7e63672cf2a91f6c027849daf210388656767 Author: Cy Chan Date: Fri Mar 2 15:41:42 2018 -0800 working on test implementation of fork-join OldTutorials/MultiColor_C/inputs OldTutorials/MultiColor_C/main.cpp commit 316cbbecaa88817519f1913f6980a694ae9a0672 Author: Weiqun Zhang Date: Fri Mar 2 10:48:16 2018 -0800 new BoxList constructor making n Boxes by chopping a given Box in a given direction Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit 65d0016f2d357dd71dc4165226672e6994c1bcd6 Author: Weiqun Zhang Date: Fri Mar 2 10:46:42 2018 -0800 add enum class Direction Src/Base/AMReX_Orientation.H commit de5b11344fe365154e8d656f7f2f9d45d90262fe Author: Weiqun Zhang Date: Fri Mar 2 10:04:19 2018 -0800 more flush fixed MiniApps/SMC/main.f90 MiniApps/SMC/smc.f90 OldTutorials/AMR_Adv_F/Source/main.f90 OldTutorials/Random_F/main.f90 commit 6389be19d59fc84d00f8b97a9de9af71aad13492 Merge: 44762fc9e 229948bd5 Author: WeiqunZhang Date: Fri Mar 2 09:56:12 2018 -0800 Merge pull request #219 from AMReX-Codes/flush Use Fortran intrinsic flush instead of call flush commit 44762fc9ef860b7b695ce80a96d01fa974de03ce Author: Weiqun Zhang Date: Fri Mar 2 09:53:08 2018 -0800 new BoxList constructor that makes n Boxes from a single Box where n is an argument to the constructor Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit 0c44e047247d43f18a110ab1a99e18702d632c33 Author: Ann Almgren Date: Thu Mar 1 19:10:31 2018 -0800 Add README for Tutorials/SWFFT Tutorials/SWFFT/README commit 3a41d13d1437a17f283f8c7ff085aa82ab674cae Author: Ann Almgren Date: Thu Mar 1 19:04:39 2018 -0800 Change in comment only. Src/Base/AMReX_parstream.H Src/Base/AMReX_parstream.cpp commit 5196ae8ab52524006c1016adde37346d3e9b0b17 Author: Weiqun Zhang Date: Thu Mar 1 17:17:33 2018 -0800 WIP nodal projection Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H commit abdb7dfba6f2043469f7fbd4e4e90e620c576848 Author: Brandon Runnels Date: Thu Mar 1 17:45:47 2018 -0700 Basic multicomponent MLMG solves working in 2D. Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_F.H commit 1b9ddcebe807ad7536e4709cac1b0fceb91a3afc Merge: 27f5943e5 17767d6f2 Author: Andrew Myers Date: Thu Mar 1 15:36:41 2018 -0800 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 27f5943e5adf60874b48cd11d6234a611f9cba0f Author: Andrew Myers Date: Thu Mar 1 15:36:30 2018 -0800 update AMReX_BCUtil.cpp to reflect recent API change to the wrapper around cudaMemcpyAsync. Src/Base/AMReX_BCUtil.cpp commit 5b1fabe297a9b71bac30b0019369028c0205f7ab Author: Andrew Myers Date: Thu Mar 1 15:34:50 2018 -0800 remove use of 'ParticleVector', which doesn't exist on the gpu branch anymore Src/Particle/AMReX_Particles.H commit ae454798e44ebebd68c0c16d421913b60e7542c2 Author: Ann Almgren Date: Thu Mar 1 13:18:22 2018 -0800 Remove unused MyProc and quiet some gnu compiler warnings. Src/Particle/AMReX_ParticleContainerI.H commit aff015988adc082f56489baa7c8a4a1e0b327e1b Author: Michael Zingale Date: Thu Mar 1 13:01:50 2018 -0500 add an option to specific the height (in 2-d) for a slice Tools/Postprocessing/F_Src/fextract.f90 commit 23deb1d54400d5cbf7160e4c8a8d60b0b0c6dc75 Author: Weiqun Zhang Date: Thu Mar 1 08:47:24 2018 -0800 update CHANGES CHANGES commit b50104b6c9e184129ddce1186266ba811da379b3 Author: Weiqun Zhang Date: Thu Mar 1 08:45:32 2018 -0800 update CHNAGES CHANGES commit d54de807307c48d33575e329ebbd43ffe209b2c3 Author: Brandon Runnels Date: Wed Feb 28 16:46:27 2018 -0700 Began update for MLMG, MLCG, MLLinop, MLCellLinop for multicomponent. Src/Base/AMReX_DistributionMapping.cpp Src/Boundary/AMReX_BndryData.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 91872c2515e670ed50a80cb9ef704b551a73845c Author: Weiqun Zhang Date: Wed Feb 28 15:12:25 2018 -0800 nodal projection: allow rhnd for rap if it's zero Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit fe3663383eb703c2b842be57a7f5243ab4957505 Author: Weiqun Zhang Date: Wed Feb 28 14:45:51 2018 -0800 nodal projection: clean up the simple rap Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 97227b188c4487621365b89076ee2f91ae684f27 Author: Weiqun Zhang Date: Wed Feb 28 14:36:25 2018 -0800 3d eb nodal projection: smoothers Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 2f067d85fcdcabb000e87b3c3e424a7795d855c5 Author: Weiqun Zhang Date: Wed Feb 28 14:08:46 2018 -0800 3d eb nodal projection: stencil verion of A dot x Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit c0c376258f8bd6c91193c6ba87957e809ff7f820 Author: Max Katz Date: Wed Feb 28 12:43:45 2018 -0800 Fix comments Tools/GNUMake/sites/Make.olcf commit e866df0609ad94a711cee19a69256766e0b188a8 Author: Ann Almgren Date: Wed Feb 28 11:54:23 2018 -0800 Add README and clean up GNUmakefile Tutorials/SWFFT/GNUmakefile Tutorials/SWFFT/inputs commit 3e6621e3d4fc2775f4540fb2db7f8d817f3fd61d Author: Ann Almgren Date: Wed Feb 28 11:35:24 2018 -0800 Slight tweaks Tutorials/SWFFT/SWFFT_Solver.cpp Tutorials/SWFFT/main.cpp commit 638f7b776df1c3e6d65360f393d4b4bf22280a69 Author: Ann Almgren Date: Wed Feb 28 11:18:51 2018 -0800 Add Tutorial demonstrating how to call the SWFFT wrapper for the fftw3 solver. Tutorials/SWFFT/GNUmakefile Tutorials/SWFFT/Make.package Tutorials/SWFFT/SWFFT_Solver.H Tutorials/SWFFT/SWFFT_Solver.cpp Tutorials/SWFFT/SWFFT_Solver_F.F90 Tutorials/SWFFT/SWFFT_Solver_F.H Tutorials/SWFFT/inputs Tutorials/SWFFT/main.cpp commit d9433cfaa8359e6c958a3c04b1682f13a7a4b7f5 Author: Michael Zingale Date: Wed Feb 28 09:07:01 2018 -0500 fix typo to make things compile Src/Amr/AMReX_extrapolater_2d.f90 commit bbb2f30bae8ad3266f6dabba5c2b4ff86f6ea9fd Author: Ann Almgren Date: Tue Feb 27 17:27:54 2018 -0800 BL_SPACEDIM --> AMREX_SPACEDIM Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AuxBoundaryData.cpp Src/Amr/AMReX_Derive.cpp Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.cpp Src/Amr/AMReX_extrapolater_2d.f90 commit 3cbfc624ac4fcb360387d170d564f5d3df332605 Author: Ann Almgren Date: Tue Feb 27 17:25:41 2018 -0800 BL_SPACEDIM --> AMREX_SPACEDIM Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_INTERPBNDRYDATA_F.H Src/Boundary/AMReX_InterpBndryData.cpp commit 20539f6c1d1f1c13d4927bfa2530ed0777668a80 Author: Ann Almgren Date: Tue Feb 27 17:23:08 2018 -0800 BL_SPACEDIM --> AMREX_SPACEDIM Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_EBDataVarMacros.H Src/GeometryShop/AMReX_EBFluxFAB.H Src/GeometryShop/AMReX_EBLoHiCenter.H Src/GeometryShop/AMReX_EBLoHiCenter.cpp Src/GeometryShop/AMReX_ExtrudeIF.cpp Src/GeometryShop/AMReX_GeometryService.cpp Src/GeometryShop/AMReX_LatheIF.cpp Src/GeometryShop/AMReX_PolyGeom.H Src/GeometryShop/AMReX_PolyGeom.cpp Src/GeometryShop/AMReX_STLExplorer.cpp Src/GeometryShop/AMReX_TransformIF.cpp Src/GeometryShop/AMReX_VolIndex.cpp commit 7100a1889529eeda751f62936debc14d18be0c12 Author: Ann Almgren Date: Tue Feb 27 17:17:24 2018 -0800 Change BL_SPACEDIM --> AMREX_SPACEDIM Src/Particle/AMReX_LoadBalanceKD.cpp Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_Particles_F.H Src/Particle/AMReX_TracerParticles.H Src/Particle/AMReX_TracerParticles.cpp commit 42f1de96916bb8d4dc43279fb2e612e89110e4aa Author: Weiqun Zhang Date: Tue Feb 27 17:02:24 2018 -0800 3d eb nodal projection: set integral and connection Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 996f423bcfc30067532d8fc39d88b51aaadd8c1e Author: Michael Zingale Date: Tue Feb 27 20:00:34 2018 -0500 fix spelling of AMREX_SPACEDIM Src/Base/AMReX_DistributionMapping.cpp commit d5e536378cec44ee172b23bc5eeeb2b6615fbb08 Author: Ann Almgren Date: Tue Feb 27 16:01:06 2018 -0800 Replace BL_SPACEDIM by AMREX_SPACEDIM Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FillPatchUtil_F.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_F.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_TagBox.cpp commit 31e0945a4b9793d3fdafd656081a58dd943c5b26 Author: Ann Almgren Date: Tue Feb 27 15:57:43 2018 -0800 Replace BL_SPACEDIM by AMREX_SPACEDIM. Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxIterator.H Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_Orientation.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_Periodicity.cpp Src/Base/AMReX_PhysBCFunct.cpp Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_RealVect.H Src/Base/AMReX_SPACE_F.H Src/Base/AMReX_Utility.cpp Src/Base/AMReX_filcc_mod.F90 Src/Base/AMReX_iMultiFab.cpp commit 6e23e6810c5cdc50ba3613ae399749408a15bb74 Author: Ann Almgren Date: Tue Feb 27 14:55:17 2018 -0800 Update with 3rd and 4th slide decks Docs/sphinx/source/Chapter12.rst commit 17767d6f234c9134546191f74f6c17cc3be953c9 Author: Max Katz Date: Mon Feb 26 13:11:05 2018 -0500 Hook in register capping to IBM compiler Tools/GNUMake/comps/ibm.mak commit 0125af4c5f04fe0b488b198d6de51a9d3afd7dae Author: Max Katz Date: Sat Feb 24 20:55:46 2018 -0500 Do cudaMemcpyAsync in C++, not Fortran Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_MFIter.cpp commit 9383f7de0388aa0f8009275cfc93defa47a1534c Author: Max Katz Date: Sat Feb 24 19:52:11 2018 -0500 Handle maximum register counts Tools/GNUMake/Make.defs Tools/GNUMake/comps/pgi.mak commit 059717041dc9160365c8c8d67f3a69a400f2b42c Author: Max Katz Date: Sat Feb 24 19:14:59 2018 -0500 Avoid unnecessary MPI linking for non-MPI code with IBM Tools/GNUMake/comps/ibm.mak commit 32b06d9377ed695bf7d963e627f9adb9a7571bd5 Author: Max Katz Date: Sat Feb 24 16:49:36 2018 -0500 Generalize CUDA version/compute capabilities Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_pgi.mak commit 099d6c6f85bacf6d95ea7a2281836794e1f0d7d6 Author: Max Katz Date: Sat Feb 24 16:33:06 2018 -0500 Fix preprocessing issues on summit Tools/F_mk/GMakedefs.mak commit de10637dfcfa9bf2fedaa07f58a110895e51cd05 Author: Max Katz Date: Fri Feb 23 20:45:45 2018 -0500 Specify a default maximum of 512 threads per CUDA threadblock This is because we usually need 8 threads to handle ghost zones in a FillPatch, and in a corner this could require 8x8x8 = 512 threads, so the default maximum should allowe for this case. Tools/GNUMake/Make.defs commit 5c8ad6a032fc9dedb0ad90f2df6525c0d930e87e Author: Max Katz Date: Fri Feb 23 20:45:36 2018 -0500 Specify CUDA/compute capabilities for summit/summitdev Tools/GNUMake/sites/Make.olcf commit a4af91448c10335d41dda2d2589930e6362371cc Author: Max Katz Date: Fri Feb 23 20:45:09 2018 -0500 Allow for a more general selection of CUDA version Tools/GNUMake/Make.defs Tools/GNUMake/comps/pgi.mak commit f5a296a9c71fb223e72d36adcfae708e31f465bd Author: Max Katz Date: Fri Feb 23 18:42:08 2018 -0500 Remove unnecessary CUDA specification Tools/GNUMake/comps/pgi.mak commit fdc0382eb39eebecb7b27939ce3d7ee3f93fa42f Author: Max Katz Date: Fri Feb 23 18:33:42 2018 -0500 Disable NVML on Summit since it's not working right now Tools/GNUMake/sites/Make.olcf commit 940e597833f6f6980e1a1a744915652516bcd07a Author: Max Katz Date: Fri Feb 23 18:32:50 2018 -0500 Only do immediate gcc_version expansion for CUDA Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/pgi.mak commit 08aa7ac7d4f4ed73ceaf2ff61abe3bfb65f70195 Author: Weiqun Zhang Date: Fri Feb 23 14:06:02 2018 -0800 mlmg: add assertions to some untested functions Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 6c4f45475ee1feccb384529f28787c28ff48d811 Author: Weiqun Zhang Date: Fri Feb 23 13:56:42 2018 -0800 mlmg: MLALaplacian Src/LinearSolvers/MLMG/AMReX_MLALap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLALap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLALap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLALap_F.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp commit 7755441e8676714d8a2a9caa8b0d2334975d5254 Author: Weiqun Zhang Date: Fri Feb 23 13:43:45 2018 -0800 mlmg: rescale 1d & 2d MLPoisson for bicgstab Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_F.H commit 4e4085af46831b61ce07108cfc9586b5f4046da8 Author: Weiqun Zhang Date: Fri Feb 23 13:03:25 2018 -0800 mlmg: rescale MLABecLaplacian for bicgstab Src/LinearSolvers/MLMG/AMReX_MLABecLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit ec38fcea03adbcf28ecc6f9a159301016b601774 Author: Michele Rosso Date: Fri Feb 23 10:24:19 2018 -0800 CMake: update source list for C_CellMG folder Src/LinearSolvers/CMakeLists.txt commit 12cbd6742f6270a69e147d6cf66ce178debd8178 Author: Brian Friesen Date: Thu Feb 22 22:52:27 2018 -0800 Update XL flags (#186) * Tools: move common XL Fortran compiler flags to GENERIC_IBM_FLAGS * Tools: add flag to enforce fixed form format in XL FORTRAN 77 compiler This compiler makes assumptions about the source code format based on file suffixes, which leads to errors when compiling some AMReX files. Fix this by explicitly stating the source code style with this flag. * Tools: change XL MPI compiler wrappers on summitdev to "mpifort" The OpenMPI man page for "mpif90" and "mpif77" notes that these wrappers are deprecated, and that one should instead use "mpifort" for all Fortran files, both free and fixed format. The observant user will note also that all three wrappers point to the same file ("opal_wrapper"). This change is currently in contradiction with the documentation on the OLCF summitdev website, which recommends continued use of "mpif77" and "mpif90". Tools/GNUMake/comps/ibm.mak Tools/GNUMake/sites/Make.olcf commit 9a3e56d83357db2f7213dc1150ffa59fa012d306 Merge: 0a337341c 63465ee35 Author: Andrew Myers Date: Thu Feb 22 17:12:15 2018 -0800 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 9d03a8ce22abc73cfd773ccc0840e38735ecc9b4 Author: Weiqun Zhang Date: Thu Feb 22 16:30:09 2018 -0800 nd mlmg: rescale the problem in bicgstab Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit e4f2dee9bb67757eec8012ea3c4a7061dc661227 Author: Weiqun Zhang Date: Thu Feb 22 14:01:45 2018 -0800 use local parameter Src/Base/AMReX_constants_mod.f90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 1603bbe7ac9f0132520463f0871875c9a294573e Merge: a389be8e6 680580da8 Author: Weiqun Zhang Date: Thu Feb 22 13:56:48 2018 -0800 Merge branch 'development' into weiqun/mlmg commit a389be8e65e236eab6fdb8f5b3a82ea00baf89f1 Author: Weiqun Zhang Date: Thu Feb 22 13:40:35 2018 -0800 rm centroid from EBTower Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp commit 20efe569b9127cc214ec8da59ad542c47280530c Author: Weiqun Zhang Date: Thu Feb 22 13:34:56 2018 -0800 nodal projection: stub for 1d and 3d Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit cd4f18f704892f71ba9fa8f148834277b1b2892d Author: Weiqun Zhang Date: Thu Feb 22 11:57:01 2018 -0800 nodal projection: clean up Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 63465ee35313a8bf1710245c4f9b66dc2cc4387b Author: Max Katz Date: Thu Feb 22 03:35:44 2018 -0500 Switch to C++ for UM hints Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit d53eaec802cb40c170a5e16167c33228be92cd9a Author: Donald E. Willcox Date: Thu Feb 22 01:12:30 2018 -0500 Change default CUDA_VERSION to 9.0 in Fortran build system. (#220) This changes the default CUDA version in the Fortran build system back to 9.0 instead of 8.0. CUDA 9.0 was formerly (cf. commit 23486c8) the default version of CUDA in the Fortran build system. Tools/F_mk/GMakedefs.mak commit cd4e69337de2d4f7fb54b0ae9207ff53d8782391 Merge: da3672c6c 680580da8 Author: Max Katz Date: Thu Feb 22 00:18:39 2018 -0500 Merge branch 'development' into gpu commit 680580da82753ec65113c90cce886edca4228b0d Author: Max Katz Date: Thu Feb 22 00:05:38 2018 -0500 Use the correct flag for enabling OpenMP in XL Tools/GNUMake/comps/ibm.mak commit 229948bd57fd426a4412ad9df1ef70149b696ecd Author: Max Katz Date: Wed Feb 21 23:30:51 2018 -0500 call flush -> flush Src/F_BaseLib/multifab_physbc_edgevel.f90 commit 5242c52b166446b03d201afb15bc1c9302cb16f9 Author: Max Katz Date: Wed Feb 21 23:29:57 2018 -0500 call flush -> flush Src/LinearSolvers/F_MG/cc_mg_cpp.f90 commit 7d0cde78c973ecc63ec03d662c9d16f5732225a2 Author: Max Katz Date: Wed Feb 21 23:24:31 2018 -0500 Move more F77 to F90 to please XL Src/Amr/AMReX_ARRAYLIM_1D.F Src/Amr/AMReX_ARRAYLIM_1D.F90 Src/Amr/AMReX_ARRAYLIM_2D.F Src/Amr/AMReX_ARRAYLIM_2D.F90 Src/Amr/AMReX_ARRAYLIM_3D.F Src/Amr/AMReX_ARRAYLIM_3D.F90 Src/Amr/CMakeLists.txt Src/Amr/Make.package Src/AmrCore/AMReX_FLUXREG_1D.F90 Src/AmrCore/AMReX_FLUXREG_2D.F90 Src/AmrCore/AMReX_FLUXREG_3D.F90 Src/AmrCore/AMReX_INTERP_1D.F90 Src/AmrCore/AMReX_INTERP_2D.F90 Src/AmrCore/AMReX_INTERP_3D.F90 Src/AmrCore/CMakeLists.txt Src/AmrCore/Make.package Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F90 Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F90 Src/Boundary/AMReX_LO_UTIL.F90 Src/Boundary/CMakeLists.txt Src/Boundary/Make.package Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_ABec_UTIL.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F90 Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F90 Src/LinearSolvers/C_CellMG/Make.package commit da3672c6ccc63de0857658ae3fbfb6ffa0ca31f8 Author: Andrew Myers Date: Wed Feb 21 18:45:38 2018 -0800 enforce max thread count in each direction (#218) Sometimes the current code create blocks that have too many threads in the z-direction. Src/Base/AMReX_CUDA.F90 commit 0a337341c6adb0cfce25b67417b70125aef141e4 Author: Andrew Myers Date: Wed Feb 21 17:01:01 2018 -0800 enforce max thread count in each direction Src/Base/AMReX_CUDA.F90 commit 481e48cd3d70c97bfe41df7453e6b301ba8cfd36 Author: Andrew Myers Date: Wed Feb 21 16:03:41 2018 -0800 re-add this figure. Docs/sphinx/source/Visualization/ParaView_filegroup.png commit c4c5a8e09b9c972a7f5393be479f68fd219ace0a Author: Utkarsh Ayachit Date: Wed Feb 21 15:22:19 2018 -0500 update docs for ParaView viz. Updated docs to reflect the new workflow for reading particles in ParaView 5.5. Docs/sphinx/source/Visualization.rst _images/ParaView_filegroup.png commit 385fe108bd3eb678aaa9bff8fc3cc268fab0d244 Author: Ann Almgren Date: Wed Feb 21 15:16:56 2018 -0800 Have the default be to build the optimized version Tests/GeometryShop/STLGeom/GNUmakefile commit 762896e79b2b9fbe9f4aa900de2ecae7fad72cd6 Merge: 0c1a90b95 0a21cba3f Author: Max Katz Date: Wed Feb 21 17:19:56 2018 -0500 Merge branch 'development' into gpu commit 0a21cba3f7072cb9434f5b9cdf51ce1330bf57b3 Author: Max Katz Date: Wed Feb 21 17:19:19 2018 -0500 Restore coalesced fabs option Src/Base/AMReX_BaseFab.cpp commit 0c1a90b955b26f71cfd0f6729581401a0af5c846 Merge: 83947cfef 974117720 Author: Max Katz Date: Wed Feb 21 15:42:33 2018 -0500 Merge branch 'development' into gpu commit 974117720df560da9540dc94d433a2066f75b3e0 Author: Max Katz Date: Wed Feb 21 14:55:22 2018 -0500 Make XLF compiler accept C-style comments Tools/GNUMake/comps/ibm.mak commit be25c21d310554a522f9402674dbdcde93fd22df Author: Max Katz Date: Wed Feb 21 14:32:20 2018 -0500 Convert some F77 files to F90 This is mainly done to make the IBM compiler happy Src/Base/AMReX_BLBoxLib_F.F90 Src/Base/AMReX_BLBoxLib_F.f Src/Base/AMReX_BLParmParse_F.F90 Src/Base/AMReX_BLParmParse_F.f Src/Base/AMReX_BLProfiler_F.F90 Src/Base/AMReX_BLProfiler_F.f Src/Base/AMReX_BLutil_F.F90 Src/Base/AMReX_BLutil_F.f Src/Base/AMReX_COORDSYS_1D.F Src/Base/AMReX_COORDSYS_1D.F90 Src/Base/AMReX_COORDSYS_2D.F Src/Base/AMReX_COORDSYS_2D.F90 Src/Base/AMReX_COORDSYS_3D.F Src/Base/AMReX_COORDSYS_3D.F90 Src/Base/CMakeLists.txt Src/Base/Make.package commit 8a28851c02d1efe08a5a370cc9bfab75b1250fda Author: Weiqun Zhang Date: Wed Feb 21 10:55:09 2018 -0800 nodal projection: flag to use simple interpolation Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit d9386203531c52556d18d88ee6d6c91cf6942435 Author: Weiqun Zhang Date: Tue Feb 20 16:58:27 2018 -0800 nodal projection: 2d rap for eb Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 9b8c46bf5f80d272bacb5578cc1c7d49f8e39c82 Merge: c6ae1650b dcf06e52a Author: WeiqunZhang Date: Tue Feb 20 14:57:02 2018 -0800 Merge pull request #215 from bcfriesen/update_CCE_flags Tools: update Cray compiler flags commit dcf06e52a4119eba582bf0d7cb149d997fa9f34f Author: Brian Friesen Date: Tue Feb 20 14:11:25 2018 -0800 Tools: make Cray compiler trap floating point exceptions when DEBUG=TRUE Tools/GNUMake/comps/cray.mak commit ffacfec217dd282468cd0ecff4f1bf20edb47e2c Author: Brian Friesen Date: Tue Feb 20 14:10:31 2018 -0800 Tools: make Cray compiler print opt report only if building optimized code There is no reason to save the opt report for debug (non-optimized) code. Tools/GNUMake/comps/cray.mak commit 6e1bd81a20d4622b713c86e963a5f41a3545e134 Author: Weiqun Zhang Date: Tue Feb 20 12:59:32 2018 -0800 nodal projection: rap works in 2d now Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 6beb36f33746911f84a67d3fdb4f10b98750b0e5 Author: Weiqun Zhang Date: Tue Feb 20 12:24:05 2018 -0800 comment out print in VisMF Src/Base/AMReX_VisMF.cpp commit 00363054c54e92d920342bc0c3e406c164551573 Author: Weiqun Zhang Date: Mon Feb 19 14:23:23 2018 -0800 nodal projection: remove scaling at Neumann boundary for RAP Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit c6ae1650b60c3f7ef5db2a5880130f58e0bb8483 Author: Ann Almgren Date: Mon Feb 19 12:18:08 2018 -0800 Add AMReX_KDStruct.H to Make.package and CMakeLists.txt Src/GeometryShop/CMakeLists.txt Src/GeometryShop/Make.package commit 935e0567f20a3019ed8d4690dcaa80fb5da4ee45 Author: Ann Almgren Date: Mon Feb 19 12:09:08 2018 -0800 Add the same files to CMakeLists.txt that we add to Make.package Src/GeometryShop/CMakeLists.txt commit b0c985eb5c83aa8f97071b932c199964ff323ac9 Author: Weiqun Zhang Date: Sun Feb 18 18:29:08 2018 -0800 nodal projection: first pass of RAP Fortran routines; still need work at boundaries Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 09cf7313debdb2a1bb5fc1f7798cb2529a1d60ff Author: Weiqun Zhang Date: Sun Feb 18 12:00:55 2018 -0800 nodal projection: R in RAP Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit b9fbbad0c5e6041a004055be36b886b5f5b636c1 Author: Weiqun Zhang Date: Sun Feb 18 08:22:19 2018 -0800 nodal projection: p in rap Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 5b6288c54696ff3e04d510f0b99a98386b33a942 Author: Weiqun Zhang Date: Sun Feb 18 07:45:39 2018 -0800 mlmg nodal: start RAP Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 22732a01187408630f22b2ec233b83e4b7ebd429 Merge: 9295178dc 292c1aa82 Author: Marc Day Date: Sat Feb 17 11:26:19 2018 -0800 Merge pull request #212 from JBlaschke/development Overlooked this in GNUMake. AMReX should build fine now... commit 292c1aa82ab9f456cd44e24ab88bfa5ad6283b8d Author: Johannes Blaschke Date: Sat Feb 17 11:16:51 2018 -0800 Overlooked this in GNUMake. AMReX should build fine now... Tools/GNUMake/Make.defs commit 9295178dcdff078d29e177ddab1138fc6b25acc2 Author: dtgraves Date: Fri Feb 16 15:07:00 2018 -0800 added some files that had been neglected. Tests/GeometryShop/STLGeom/GNUmakefile Tests/GeometryShop/STLGeom/stlgeom.cpp commit 8a3c2317de0ee7f3706df670aceba647f3d5dc1f Merge: dab4c6838 005a6acb0 Author: dtgraves Date: Fri Feb 16 13:26:04 2018 -0800 Merge pull request #211 from AMReX-Codes/dtg_branch merging STL capability into GeometryShop commit 005a6acb0de8c42d3a8e695c5ed8c6d27087943b Author: dtgraves Date: Fri Feb 16 13:21:14 2018 -0800 finished integrating STL geometry capability. Caveat emptor. If you can manage it, you are far better off using analytic geometric descriptions. Src/GeometryShop/AMReX_STLAsciiReader.cpp Src/GeometryShop/AMReX_STLExplorer.cpp Tests/GeometryShop/STLGeom/bad.cylinder.inputs Tests/GeometryShop/STLGeom/bad.reactor.inputs Tests/GeometryShop/STLGeom/good.cylinder.inputs Tests/GeometryShop/STLGeom/good.reactor.inputs Tests/GeometryShop/STLGeom/good.sphere.inputs Tests/GeometryShop/STLGeom/stl.inputs commit dab4c68385dfbbd85549b13f2bab3708d0d91c57 Merge: 5b00e582a 0639714c3 Author: WeiqunZhang Date: Fri Feb 16 09:02:34 2018 -0800 Merge pull request #210 from JBlaschke/development GNUMake respects Make.local's compile commands commit 0639714c3078157aa852b372c8ba9d8d17bf0575 Author: Johannes Blaschke Date: Fri Feb 16 08:52:01 2018 -0800 gnu.mak warns user if system's default gcc is outdated (<4.8), and reminds the user to specify a Make.local. Tools/GNUMake/comps/gnu.mak commit fc6e48dbd5cf062692cfe57a81da8c586237737d Merge: 872c6644c 5b00e582a Author: Johannes Blaschke Date: Thu Feb 15 22:28:14 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 872c6644cf15f14c700d6397bed6fee77a452c8b Author: Johannes Blaschke Date: Thu Feb 15 22:27:43 2018 -0800 WIP clean up documentation formatting Docs/sphinx/source/Chapter5.rst commit 6403c855fd6ce008093907728dd18f110104f7fc Author: Johannes Blaschke Date: Thu Feb 15 22:24:54 2018 -0800 WIP: clean up formatting (including table captions) Docs/sphinx/source/Basics.rst Docs/sphinx/source/Chapter4.rst commit 24696e43c68819a0a74b9c7578553e483bbe885a Author: Johannes Blaschke Date: Thu Feb 15 20:57:40 2018 -0800 WIP: clean up formatting of docs Docs/sphinx/source/BuildingAMReX.rst Docs/sphinx/source/Chapter2.rst Docs/sphinx/source/Chapter3.rst Docs/sphinx/source/GettingStarted.rst Docs/sphinx/source/Introduction.rst Docs/sphinx/source/index.rst commit 7dd0e9439f05e7593847e84f7a58b1657156bb8f Author: Johannes Blaschke Date: Thu Feb 15 20:38:14 2018 -0800 Document new Make.local behaviour Docs/sphinx/source/BuildingAMReX.rst commit 9d446e750409b674874c301dcaf21f92663013be Author: Johannes Blaschke Date: Thu Feb 15 20:10:40 2018 -0800 GNUMake compiler settings can be overwritten by Make.local (ie. introduce lazy evaluation to `comps/*.mak`). In order to work, compiler version checking for gnu had to be disabled (it makes little sense nowdays anyway). Tools/GNUMake/Make.defs Tools/GNUMake/comps/cray.mak Tools/GNUMake/comps/gnu-7.mak Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/ibm.mak Tools/GNUMake/comps/intel.mak Tools/GNUMake/comps/llvm.mak Tools/GNUMake/comps/nag.mak Tools/GNUMake/comps/pgi.mak commit d0c76e180e15ae99e5b901b74bb34277d867be35 Author: dtgraves Date: Thu Feb 15 16:20:32 2018 -0800 all the stl code is in geometryshop and it compiles. not tested yet. Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp commit 5b00e582ab38d4e852b831250a0fd5cca0e0e43e Author: Max Katz Date: Thu Feb 15 19:09:40 2018 -0500 Add Summit to machine list Tools/GNUMake/Make.machines Tools/GNUMake/comps/pgi.mak Tools/GNUMake/sites/Make.olcf commit 28d98da930dcce695edd5764099a3707a2b624e6 Merge: 875c1045a 8254b45ed Author: asalmgren Date: Thu Feb 15 15:57:29 2018 -0800 Merge pull request #209 from JBlaschke/development Forgot to add this file commit 8254b45ed638b03083c68df51911e4c367bff822 Author: Johannes Blaschke Date: Thu Feb 15 15:52:18 2018 -0800 Forgot to add this file Tools/GNUMake/comps/gnu-7.mak commit 875c1045a72546d6fe5270a67cccf62fb103aa5d Merge: c8f790df7 49254ba62 Author: asalmgren Date: Thu Feb 15 15:37:21 2018 -0800 Merge pull request #208 from JBlaschke/development Development, added gnu-7 compiler definition commit 49254ba626a40783fe610e57955c5e2976a8c85c Merge: 7d4c84159 c8f790df7 Author: Johannes Blaschke Date: Thu Feb 15 15:33:31 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 7d4c84159eaea8c98ad32f95ed6384857fa02d43 Author: Johannes Blaschke Date: Thu Feb 15 15:32:19 2018 -0800 added gnu-7 build target for gcc-7.x.x compilers. Needed, for example, for macOS where gcc links to gcc 4.2 Tools/GNUMake/Make.defs commit 04a2c7bbd57a97ededae6d52cc7c10987d4b5c56 Author: dtgraves Date: Thu Feb 15 15:04:09 2018 -0800 note to self: never volunteer to port code before looking it over first. Src/GeometryShop/#AMReX_STLExplorer.H# Src/GeometryShop/AMReX_CellEdge.cpp Src/GeometryShop/AMReX_KDStruct.H Src/GeometryShop/AMReX_KDTree.H Src/GeometryShop/AMReX_KDTree.cpp Src/GeometryShop/AMReX_PXStuff.H Src/GeometryShop/AMReX_PXStuff.cpp Src/GeometryShop/AMReX_STLAsciiReader.H Src/GeometryShop/AMReX_STLAsciiReader.cpp Src/GeometryShop/AMReX_STLBox.H Src/GeometryShop/AMReX_STLBox.cpp Src/GeometryShop/AMReX_STLExplorer.H Src/GeometryShop/AMReX_STLExplorer.cpp Src/GeometryShop/AMReX_STLIF.H Src/GeometryShop/AMReX_STLIF.cpp Src/GeometryShop/AMReX_STLMesh.H Src/GeometryShop/AMReX_STLMesh.cpp Src/GeometryShop/AMReX_STLReader.H Src/GeometryShop/AMReX_STLUtil.H Src/GeometryShop/AMReX_STLUtil.cpp Src/GeometryShop/Make.package Tests/GeometryShop/STLGeom/cylinder.stl Tests/GeometryShop/STLGeom/reactor.stl Tests/GeometryShop/STLGeom/sphere.stl commit c8f790df76793ea2002c9a595759a35bf85518d0 Author: Ann Almgren Date: Thu Feb 15 14:47:30 2018 -0800 Add additional print statements for the MultiGrid Vcycle when verbose > 1 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit cdd0ac9fbba5d3dee7fab0b2a0d4cd38d4d94c84 Author: dtgraves Date: Wed Feb 14 16:24:43 2018 -0800 slogging through Issac Asher's code to get STL files into EBIndexSpace. Src/GeometryShop/#AMReX_STLExplorer.H# Src/GeometryShop/AMReX_CellEdge.H Src/GeometryShop/AMReX_CellEdge.cpp Src/GeometryShop/AMReX_Ellipsoid.cpp Src/GeometryShop/AMReX_KDStruct.H Src/GeometryShop/AMReX_KDTree.H Src/GeometryShop/AMReX_KDTree.cpp Src/GeometryShop/AMReX_STLAsciiReader.H Src/GeometryShop/AMReX_STLAsciiReader.cpp Src/GeometryShop/AMReX_STLBox.H Src/GeometryShop/AMReX_STLBox.cpp Src/GeometryShop/AMReX_STLExplorer.H Src/GeometryShop/AMReX_STLExplorer.cpp Src/GeometryShop/AMReX_STLIF.H Src/GeometryShop/AMReX_STLIF.cpp Src/GeometryShop/AMReX_STLMesh.H Src/GeometryShop/AMReX_STLMesh.cpp Src/GeometryShop/AMReX_STLReader.H Src/GeometryShop/AMReX_STLUtil.H Src/GeometryShop/AMReX_STLUtil.cpp commit ea17de5024a8e01aeec548a455c1f47a569c4391 Merge: e022a28f2 f652fb60b Author: dtgraves Date: Wed Feb 14 12:58:56 2018 -0800 merging with dev branch commit 47b703f41c112e5773bec42cf02c09c0b535a243 Author: Weiqun Zhang Date: Tue Feb 13 17:09:25 2018 -0800 eb nodal projection: gauss seidel Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit a70fac42a6da56c685a8a80ca45e1a8f22589a93 Author: Weiqun Zhang Date: Tue Feb 13 16:37:57 2018 -0800 mlmg: harmonic average for jacobi Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 2e089f3a82eba3434a11fcbf369c86824ed167fc Author: Weiqun Zhang Date: Tue Feb 13 16:06:26 2018 -0800 mlmg: enable eb on coarse mg levels Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 63fc77345eca84154b4a0eff74036824745743cd Author: Weiqun Zhang Date: Tue Feb 13 15:58:14 2018 -0800 EBTower: add function testing if the domain is valid Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp commit 25d1efc8308122596546ea7952f671725c852439 Merge: 4c40e1524 f652fb60b Author: Weiqun Zhang Date: Tue Feb 13 15:18:56 2018 -0800 Merge branch 'development' into weiqun/mlmg commit 4c40e15245e556d1d59e547b7ce6aef6aaac0525 Author: Weiqun Zhang Date: Tue Feb 13 14:52:01 2018 -0800 mlmg: store factory as base class pointers Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit f652fb60bf7488a2c3153b35f703aaa9af485eb6 Author: Andy Nonaka Date: Tue Feb 13 12:53:42 2018 -0800 in the F_MG cell-centered solver, if the user tries to use the fancy bottom solver and the grid structure can't be re-arranged for further coarsening, use fancy_bottom_type in (if it was passed in) before resorting to the default BiCGStab Src/LinearSolvers/F_MG/mg.f90 commit f6dfa626cd4054c6ea9a3a2254018c08b5883251 Author: Weiqun Zhang Date: Tue Feb 13 09:58:27 2018 -0800 wip: eb nodal projection: fix rhs Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 8258baba86ab373c602e44a9444eeff038501743 Merge: 093fe4f33 68fed3c52 Author: Marc Day Date: Mon Feb 12 12:56:06 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 093fe4f33d56c85d19788fc3567fff340e1fb4ed Author: Marc Day Date: Mon Feb 12 12:55:14 2018 -0800 Fix code to predict data filename Tools/EBSurfaceTools/ConvertEBSurface.cpp commit e022a28f2dc45dbcf50e71b6b73ba3d3b4e4bb0c Merge: 025543c72 68fed3c52 Author: dtgraves Date: Mon Feb 12 09:32:34 2018 -0800 merging with dev branch commit 68fed3c52addf79574fedbab1f19fb4daa4092f0 Merge: 81869593d dc0e2bfdd Author: dtgraves Date: Mon Feb 12 09:31:28 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 81869593dd17b282a450433d7f9d2c44aefdd0a9 Author: dtgraves Date: Mon Feb 12 09:31:09 2018 -0800 added destructor fix that was found by Johannes Src/EB/AMReX_EBTower.cpp commit 025543c72c1048e6a73932154175a760addebf13 Author: dtgraves Date: Mon Feb 12 09:26:42 2018 -0800 tweaked inputs Tests/GeometryShop/regression/multicelllev.inputs commit dc0e2bfdd695c0a03049fbfee67289a3fc108dbe Merge: 3fb7d89d7 4c7ea3619 Author: Ann Almgren Date: Sun Feb 11 09:11:17 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 3fb7d89d78f141389b7e24f4908cb90450c8dc43 Author: Ann Almgren Date: Sun Feb 11 09:10:58 2018 -0800 Updated default DATA_Digits_Read from 4 to 5. Tools/Postprocessing/C_Src/particle_compare.cpp commit 31cda798338ea85a21a0f09af85275ed4c460a48 Author: Weiqun Zhang Date: Thu Feb 8 13:24:31 2018 -0800 wip: eb nodal projection: update velocity at centroids Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit fe01901bffb3ea25b34cc7328e69b93410139eec Author: Weiqun Zhang Date: Thu Feb 8 11:23:26 2018 -0800 wip: eb nodal projection jacobi smoother Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 0ba2e34e2e9ef0c270d45169ee3d5ace2bee94c1 Author: Weiqun Zhang Date: Thu Feb 8 09:46:47 2018 -0800 wip: eb node projection: a dot x Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit dd02b057d5062c35b69cbe2da0a167d251c41d8b Author: Johannes Blaschke Date: Thu Feb 8 10:24:09 2018 -0500 Updated build instructions for source (sphinx -> latex) Docs/Readme.sphinx commit 505bede66fd3fd19eae84d147c5f5aa34d52c782 Author: Weiqun Zhang Date: Wed Feb 7 17:00:41 2018 -0800 wip: compute the connections Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 48806c98af566909ce27be3f388201de05486e16 Author: Weiqun Zhang Date: Wed Feb 7 15:04:53 2018 -0800 wip: add stencil connection Src/Base/AMReX_constants_mod.f90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 413bf12250758251de4d0246ae9c3a43a8de0a02 Author: Weiqun Zhang Date: Tue Feb 6 15:24:37 2018 -0800 2d mlmg: another way of interpolation Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit a620fc93f6a8879d942b22a030ca59e324e9c111 Author: Weiqun Zhang Date: Tue Feb 6 15:08:18 2018 -0800 2d mlmg: interpolate velocity from cell centers to centroids Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 4c7ea3619e60730b8372754fb10858e716fd4c62 Author: Andy Nonaka Date: Tue Feb 6 14:39:52 2018 -0800 put IO in its own chapter Docs/sphinx/source/Basics.rst Docs/sphinx/source/Chapter6a.rst Docs/sphinx/source/IO.rst Docs/sphinx/source/index.rst commit 311f54b45dbb1426a7587bd3051268108928fe36 Author: Andy Nonaka Date: Tue Feb 6 14:33:28 2018 -0800 wrote documentation for how to do checkpoint/restart Docs/sphinx/source/Basics.rst Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit ae5e839d6add4bbbf700cfe6b9ef3da9e570bd12 Author: Andy Nonaka Date: Tue Feb 6 14:02:56 2018 -0800 implemented checkpoint-restart in Tutorials/Amr/Advection_AmrCore Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrCore/Source/main.cpp commit 97a8987aa9a99ba6b43fd784ccc30ffaf4f92cf8 Author: Weiqun Zhang Date: Tue Feb 6 13:31:03 2018 -0800 add centroid to EBTower Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp commit 8b7eebcd65cab4e30686b963947aa52c75fc6ff1 Author: Weiqun Zhang Date: Tue Feb 6 11:17:36 2018 -0800 mlmg: refactor Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 2f32da20adb7992b171e8fd25bc287dbb362f1dd Author: Weiqun Zhang Date: Tue Feb 6 09:52:32 2018 -0800 mlmg: using FactoryType Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 140bc721675ee820a57bf635787c8d9c9aac2b9c Merge: 731835f9f f180066cc Author: dtgraves Date: Mon Feb 5 15:39:43 2018 -0800 Merge pull request #207 from AMReX-Codes/dtg_branch ebindexspace now can tell you where multi-valued cells start commit f180066cca3bf56e8573349bbe43601f5597991d Author: dtgraves Date: Mon Feb 5 15:37:34 2018 -0800 added functionality to EBIndexSpace which allows the user to find out the finest level where the graph is multivalued in a cell. The test works in serial and in parallel. Also I added an ellipsoid implicit function. Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_EllipsoidIF.H Src/GeometryShop/AMReX_EllipsoidIF.cpp Src/GeometryShop/Make.package Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/fabfromif.cpp Tests/GeometryShop/regression/multicelllev.cpp Tests/GeometryShop/regression/multicelllev.inputs commit a2c658d787ca7a540583d1d645d59cbcf3aad528 Author: Weiqun Zhang Date: Mon Feb 5 15:31:55 2018 -0800 mlmg: turn off harmonic average for now because there seems to be a bug; set velocity in covered cells to zero before computing rhs Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 18c5031d1909e15960a1ee2e9492306bd49193f8 Author: Weiqun Zhang Date: Mon Feb 5 13:41:09 2018 -0800 mlmg: always use harmonic average for eb and make sure no divided-by-zero Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 7974031e5eacfdb0f742c6cc590bcbb0a997c528 Author: Weiqun Zhang Date: Mon Feb 5 12:29:02 2018 -0800 mlmg: make factory argument to be vector of ptrs Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit b6635de27ddd30b3190925e84a350056e3083f13 Author: Weiqun Zhang Date: Mon Feb 5 11:20:52 2018 -0800 rm EBNodalProjection tutorial Tutorials/LinearSolvers/EBNodalProjection/GNUmakefile Tutorials/LinearSolvers/EBNodalProjection/Make.package Tutorials/LinearSolvers/EBNodalProjection/MyTest.H Tutorials/LinearSolvers/EBNodalProjection/MyTest.cpp Tutorials/LinearSolvers/EBNodalProjection/initEB.cpp Tutorials/LinearSolvers/EBNodalProjection/main.cpp commit 95d086849a73171a3f57efb737d45fd2079115e0 Author: Weiqun Zhang Date: Mon Feb 5 11:18:43 2018 -0800 minor Tools/GNUMake/comps/gnu.mak commit 731835f9f472639881208fb92ac600a4163a8f27 Author: Ann Almgren Date: Sat Feb 3 11:19:16 2018 -0800 Remove unused variable Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit b093ad0016c07c8266062130b77054e8ac494a08 Author: Ann Almgren Date: Fri Feb 2 20:10:37 2018 -0800 Add line break between Lecture1 and Lecture2 Docs/sphinx/source/Chapter12.rst commit 6168e3ec65909bb7fbde4e57e78b9cc93a14b023 Author: Ann Almgren Date: Fri Feb 2 19:17:13 2018 -0800 Add link to 2nd week of profiling tutorial Docs/sphinx/source/Chapter12.rst commit e101256f8a7ba39c18b5287f04304a07c2abc614 Author: Ann Almgren Date: Fri Feb 2 16:09:07 2018 -0800 Add pointer to Amrvis/Docs/Amrvis.tex Docs/sphinx/source/Visualization.rst commit 47cc8addb7c26ecf4b6ef073a0426b34dee27464 Author: Ann Almgren Date: Fri Feb 2 15:48:43 2018 -0800 Update link to amrvis Docs/sphinx/source/Visualization.rst commit 0c770dc3e45a8a5b75047bd7229c71725c77756f Author: Minion Date: Fri Feb 2 15:48:40 2018 -0800 adding quadrature terms in sweeper Tutorials/Basic/SDCHeat_Equation_EX1_C/advance.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/main.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc.H commit 41c1e2b581d701aa5058e1f0c14f84293176cfe8 Merge: e52f15993 7b654d50f Author: dtgraves Date: Fri Feb 2 15:38:50 2018 -0800 Merge pull request #205 from AMReX-Codes/dtg_branch fixing a bunch of small stuff with EB commit 7b654d50fa431bfa1e18d6ec175a12e600c976d5 Author: dtgraves Date: Fri Feb 2 15:28:53 2018 -0800 fixed a bunch of tests that were broken because of interface changes. Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp Tests/GeometryShop/flatPlate/flatPlateTest.cpp Tests/GeometryShop/ramp/main.cpp Tests/GeometryShop/sparseDataSingleGrid/sparseDataSG.cpp Tests/GeometryShop/sphere/GNUmakefile Tests/GeometryShop/sphereEBISBox/GNUmakefile commit 1a0d5496911fe36b9eca0b32a74d4ed7a0d61ba2 Author: Minion Date: Thu Feb 1 17:42:40 2018 -0800 Using Vector correctly for SDC arrays and saxpy in C++ Tutorials/Basic/SDCHeat_Equation_EX1_C/advance.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/advance_2d.f90 Tutorials/Basic/SDCHeat_Equation_EX1_C/init_phi_2d.f90 Tutorials/Basic/SDCHeat_Equation_EX1_C/inputs_2d Tutorials/Basic/SDCHeat_Equation_EX1_C/main.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc.H commit 9fb3083b49e63817fcab730541a8917946f52cfa Author: Weiqun Zhang Date: Thu Feb 1 17:05:10 2018 -0800 MLMG: add factory as optional argument Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 27ee81e826c042d7942ef0dffc3e2f0ce49e5a7b Author: dtgraves Date: Thu Feb 1 16:52:44 2018 -0800 think I have the serialization issue beat but I need to test it more before I put it into dev branch. Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Tests/GeometryShop/regression/ebio.cpp Tests/GeometryShop/regression/ebio.inputs Tests/GeometryShop/regression/serialization.cpp commit b4ee205965ccce37bcc1464d4e45a5452051db4b Author: Weiqun Zhang Date: Thu Feb 1 15:09:21 2018 -0800 EBNodalProjection test: build factories Tutorials/LinearSolvers/EBNodalProjection/Make.package Tutorials/LinearSolvers/EBNodalProjection/MyTest.H Tutorials/LinearSolvers/EBNodalProjection/MyTest.cpp Tutorials/LinearSolvers/EBNodalProjection/initEB.cpp commit ea5f28f9098858938a102edbc7e254ee52140d14 Author: Weiqun Zhang Date: Thu Feb 1 13:33:19 2018 -0800 mlmg: make sure the corners do not trigger floating point exception and remove fillSolutionBC function because we always fill bc to compute residuals Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 41a4d2a130d833085abd74c4a9898558e1a3f6f0 Author: Weiqun Zhang Date: Thu Feb 1 10:32:10 2018 -0800 EBNodalProjection test: setup with eb is done Tutorials/LinearSolvers/EBNodalProjection/MyTest.H Tutorials/LinearSolvers/EBNodalProjection/MyTest.cpp commit e52f159939af967144d3335f51a72c106f9fe817 Merge: 26183c94e 578f76468 Author: WeiqunZhang Date: Thu Feb 1 10:15:28 2018 -0800 Merge pull request #203 from hsitaram/haribranch Extrude IF utility commit 1d4cf21e3a1ee65ffc246ddb6512bc895cfce4a3 Merge: 7a9ae4f0d 26183c94e Author: Weiqun Zhang Date: Thu Feb 1 08:52:20 2018 -0800 Merge branch 'development' into weiqun/dev commit a64f621da8f61d00c08c29441f5db8cb8e1346a6 Author: dtgraves Date: Wed Jan 31 16:24:50 2018 -0800 took out some directory thrashing. Src/GeometryShop/AMReX_EBISLevel.cpp Tests/GeometryShop/regression/ebio.cpp Tests/GeometryShop/regression/ebio.inputs commit 472634625e65113a545b2cdf9304c05b35493dd3 Author: dtgraves Date: Wed Jan 31 16:00:26 2018 -0800 made ebgraph serialization a bit more consistent. Src/GeometryShop/AMReX_EBGraph.cpp commit 4dbc2ed3ecddffef87b6581af2460ce5a728a9fe Author: dtgraves Date: Wed Jan 31 15:58:01 2018 -0800 some bugs had crept into EBIndexSpace linearization. this fixes some of them Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_FabArrayIO.H Tests/GeometryShop/regression/ebio.cpp commit 578f76468f80d5bcb04f34a49181af76dee69183 Author: hari Date: Wed Jan 31 14:58:27 2018 -0700 leaving 2D extruded surface as is Src/GeometryShop/AMReX_ExtrudeIF.H Src/GeometryShop/AMReX_ExtrudeIF.cpp Src/GeometryShop/CMakeLists.txt Src/GeometryShop/Make.package commit 26183c94ea697b546d8a30ecfc3c2dca56c75072 Merge: 86930319c 204692ac6 Author: dtgraves Date: Wed Jan 31 12:01:01 2018 -0800 Merge pull request #201 from AMReX-Codes/dtg_branch added ability to fill Node-centered FArrayBox from implicit function … commit 204692ac6ceeeab22d884cfd82da2a16b1c94c4c Author: dtgraves Date: Wed Jan 31 11:59:57 2018 -0800 added ability to fill Node-centered FArrayBox from implicit function values. Test lives in Tests/GeometryShop/regression Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryShop.H Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/fabfromif.cpp commit 7a9ae4f0dcfffc58b34f7f1609ebbf97ddb8cf83 Author: Weiqun Zhang Date: Wed Jan 31 10:45:06 2018 -0800 add a profiler to GeometryShop::fillGraph Src/GeometryShop/AMReX_GeometryShop.cpp commit 49e192a3649677b0cc0d6dd14531c7bb5d48ba07 Author: Weiqun Zhang Date: Wed Jan 31 10:02:34 2018 -0800 mlmg: if the solution multifab argument does not have exactly one ghost cell, make a local copy Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 86930319c4266ee9a4bef37b87b3c1f62c3e55d1 Author: Andy Nonaka Date: Tue Jan 30 17:37:40 2018 -0800 expanded on the Basics of the HeatEquation_EX1_C tutorial Docs/sphinx/source/Basics.rst Docs/sphinx/source/Basics/figs/flowchart.odg Docs/sphinx/source/Basics/figs/flowchart.pdf Docs/sphinx/source/Basics/figs/flowchart.png Docs/sphinx/source/GettingStarted.rst Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp commit 0014f11c07634b5dad3835b9684a7f6fe7e2c893 Author: Andy Nonaka Date: Tue Jan 30 17:01:23 2018 -0800 re-org tutorials Tutorials/Basic/HeatEquation_EX1_C/Exec/GNUmakefile Tutorials/Basic/HeatEquation_EX1_C/Exec/inputs_2d Tutorials/Basic/HeatEquation_EX1_C/Exec/inputs_3d Tutorials/Basic/HeatEquation_EX1_C/Source/Make.package Tutorials/Basic/HeatEquation_EX1_C/Source/advance.cpp Tutorials/Basic/HeatEquation_EX1_C/Source/advance_2d.f90 Tutorials/Basic/HeatEquation_EX1_C/Source/advance_3d.f90 Tutorials/Basic/HeatEquation_EX1_C/Source/init_phi_2d.f90 Tutorials/Basic/HeatEquation_EX1_C/Source/init_phi_3d.f90 Tutorials/Basic/HeatEquation_EX1_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc.H Tutorials/Basic/HeatEquation_EX1_C/Source/myfunc_F.H Tutorials/Basic/HeatEquation_EX2_C/Exec/GNUmakefile Tutorials/Basic/HeatEquation_EX2_C/Exec/inputs_2d Tutorials/Basic/HeatEquation_EX2_C/Exec/inputs_3d Tutorials/Basic/HeatEquation_EX2_C/Source/AMReX_FILCC_2D.F Tutorials/Basic/HeatEquation_EX2_C/Source/AMReX_FILCC_3D.F Tutorials/Basic/HeatEquation_EX2_C/Source/Make.package Tutorials/Basic/HeatEquation_EX2_C/Source/advance.cpp Tutorials/Basic/HeatEquation_EX2_C/Source/advance_2d.f90 Tutorials/Basic/HeatEquation_EX2_C/Source/advance_3d.f90 Tutorials/Basic/HeatEquation_EX2_C/Source/init_phi_2d.f90 Tutorials/Basic/HeatEquation_EX2_C/Source/init_phi_3d.f90 Tutorials/Basic/HeatEquation_EX2_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX2_C/Source/myfunc.H Tutorials/Basic/HeatEquation_EX2_C/Source/myfunc_F.H Tutorials/Basic/HeatEquation_EX3_C/Exec/GNUmakefile Tutorials/Basic/HeatEquation_EX3_C/Exec/inputs_2d Tutorials/Basic/HeatEquation_EX3_C/Source/Make.package Tutorials/Basic/HeatEquation_EX3_C/Source/advance.cpp Tutorials/Basic/HeatEquation_EX3_C/Source/init_phi_2d.f90 Tutorials/Basic/HeatEquation_EX3_C/Source/init_phi_3d.f90 Tutorials/Basic/HeatEquation_EX3_C/Source/inputs_3d Tutorials/Basic/HeatEquation_EX3_C/Source/main.cpp Tutorials/Basic/HeatEquation_EX3_C/Source/myfunc.H Tutorials/Basic/HeatEquation_EX3_C/Source/myfunc_F.H commit 0bae66b683d01dce49109104b85c8db2c6762a14 Author: Weiqun Zhang Date: Tue Jan 30 16:29:17 2018 -0800 added amrex_multifab_build_alias and amrex_imultifab_build_alias to Fortran interface CHANGES Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit dd8ae847d7b5990d4e017c45ed5a0e2f2b70a23e Author: Weiqun Zhang Date: Tue Jan 30 15:42:22 2018 -0800 WIP: nodal projection tutorial Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Tutorials/LinearSolvers/EBNodalProjection/MyTest.H Tutorials/LinearSolvers/EBNodalProjection/MyTest.cpp commit f10a0a855bcf9d13871417f339becd9fd795eddc Author: Weiqun Zhang Date: Tue Jan 30 15:08:32 2018 -0800 writeFabs function that writes out each individual fab Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 04c915ed16fda2178efe0a1e491e64893216b632 Author: Weiqun Zhang Date: Tue Jan 30 14:20:58 2018 -0800 add non-const version of BaseFab::ForEachIV Src/Base/AMReX_BaseFab.H commit 90d25fc062dc28ed951c2c0912a2d0fa992c5eaf Author: Weiqun Zhang Date: Tue Jan 30 14:20:22 2018 -0800 start eb nodal projection test Tutorials/LinearSolvers/EBNodalProjection/GNUmakefile Tutorials/LinearSolvers/EBNodalProjection/Make.package Tutorials/LinearSolvers/EBNodalProjection/MyTest.H Tutorials/LinearSolvers/EBNodalProjection/MyTest.cpp Tutorials/LinearSolvers/EBNodalProjection/main.cpp commit 9a308a3535bc7f65063f4c7afc18450bcf093531 Author: Andy Nonaka Date: Tue Jan 30 15:29:40 2018 -0800 pass in basic data types (int, real) into fortran using pointers, not pass-by-reference Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/Amr/Advection_AmrLevel/Source/Adv_F.H Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Basic/HeatEquation_EX1_C/advance.cpp Tutorials/Basic/HeatEquation_EX1_C/advance_2d.f90 Tutorials/Basic/HeatEquation_EX1_C/advance_3d.f90 Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H Tutorials/Basic/HeatEquation_EX2_C/advance.cpp Tutorials/Basic/HeatEquation_EX2_C/advance_2d.f90 Tutorials/Basic/HeatEquation_EX2_C/advance_3d.f90 Tutorials/Basic/HeatEquation_EX2_C/myfunc_F.H commit 92cf13e59f24ce645b767fb085da91f75783b7f6 Author: Lawrence Minion Date: Tue Jan 30 14:29:28 2018 -0800 adding quadrature routines and SDC arrays Tutorials/Basic/SDCHeat_Equation_EX1_C/Make.package Tutorials/Basic/SDCHeat_Equation_EX1_C/advance.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/advance_2d.f90 Tutorials/Basic/SDCHeat_Equation_EX1_C/advance_3d.f90 Tutorials/Basic/SDCHeat_Equation_EX1_C/main.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc.H Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc_F.H Tutorials/Basic/SDCHeat_Equation_EX1_C/pf_quadrature.f90 commit 6f3424051ba4a7b685329e63871ff6746f7d2456 Author: Weiqun Zhang Date: Tue Jan 30 10:12:51 2018 -0800 EB: make sure the BoxArray is cell-centered Src/EB/AMReX_EBDataCollection.cpp commit d843fe6138aab5eac38f151c5137a3acf105742f Merge: f0df7f71b e9223178a Author: Andrew Myers Date: Tue Jan 30 09:53:43 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f0df7f71b3fd38b1e84723ab0086ffdd37f4ccf2 Author: Andrew Myers Date: Tue Jan 30 09:53:33 2018 -0800 wrap these MPI helper functions in #ifdef BL_USE_MPI Src/Particle/AMReX_ParticleContainerI.H commit e9223178acff8e9ce4d451806754779eb7e34f43 Merge: 70d0240bf 815d6ccd8 Author: Andy Nonaka Date: Mon Jan 29 14:09:38 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 70d0240bf6623af528ac087f07376d28b1eb1e29 Author: Andy Nonaka Date: Mon Jan 29 14:09:18 2018 -0800 profiling lecture notes Docs/sphinx/source/Chapter12.rst commit 815d6ccd803958517fe3349aa123d19e214ceba6 Author: Andrew Myers Date: Mon Jan 29 12:14:04 2018 -0800 fix a couple of bugs in assert statements that broke compilation in DEBUG. Src/Particle/AMReX_ParticleContainerI.H commit 63deb83c7ffc859325f8e0e473b5c0287fc9fc0b Merge: 044b1bc7c b6a528bfe Author: Andrew Myers Date: Mon Jan 29 12:04:54 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 044b1bc7c23869a9f6ca4e4c07ef10454a93c8b3 Author: Andrew Myers Date: Mon Jan 29 12:04:10 2018 -0800 FabArray > -> iMultiFab Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 984bfa298b4f2de69ba65fa3fa447b132c096c70 Author: Andrew Myers Date: Mon Jan 29 11:59:49 2018 -0800 A version of Redistribute for particles that have only moved a certain amount (typically one cell) since the last Redistibute() call. This version does not need to do All-to-all communication. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit b6a528bfe2c966bc13bff29c9c0209cb6ad414fa Author: Kevin Gott Date: Mon Jan 29 11:18:53 2018 -0800 Docs update: BL_PROFILE_TINY_FLUSH Docs/sphinx/source/AMReX_Profiling_Tools.rst commit 7ab03b10403ec7ba912dea61092dab6af7b58bb5 Author: Andrew Myers Date: Mon Jan 29 10:42:21 2018 -0800 move Redistribute handshake stuff into helper function. Src/Particle/AMReX_ParticleContainerI.H commit 711de9897227a3b366aa2c62deaab2c88f59f0cd Author: Andrew Myers Date: Fri Jan 26 21:10:30 2018 -0800 remove now unused template parameter Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.H Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp commit eeb1fae5375901b78607bd7fe7743434aeee4a58 Author: Andrew Myers Date: Fri Jan 26 20:53:06 2018 -0800 Don't require users to call BuildLevelMask - just build it the first time it's needed. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 531f1310c641f396af01b5f37e7352c5bb353f0b Author: Weiqun Zhang Date: Fri Jan 26 19:45:09 2018 -0800 fix a bug recently introduced by me Src/Base/AMReX_BaseFab.H commit bcd8bc46c8dfdeb40298741e09da437ab5dc41c9 Author: Ann Almgren Date: Fri Jan 26 17:12:22 2018 -0800 Add link to sample output Docs/sphinx/source/AMReX_Profiling_Tools.rst commit 14c5e157bb8b33231a0a58dca21403baacb4fb45 Author: Ann Almgren Date: Fri Jan 26 17:05:40 2018 -0800 Update to include cmake flags as well as GNU make flags Docs/sphinx/source/AMReX_Profiling_Tools.rst commit 9f7d68bb90e236efb27509b9ee9a8dfd3bc511da Author: Ann Almgren Date: Fri Jan 26 16:59:01 2018 -0800 Update sample output Docs/sphinx/source/AMReX_Profiling_Tools.rst commit f4f9e73f1f0c1b8e1a8f57b97f61e3f33377c1f4 Author: Ann Almgren Date: Fri Jan 26 16:53:03 2018 -0800 This copy of Readme.profiling only contains information that has not been migrated to the online documentation. Docs/Readme.profiling commit 4c346d7f997a8e9abbbf6f62f347c5069337e556 Merge: c37d0194b 593bb93eb Author: Ann Almgren Date: Fri Jan 26 16:45:37 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit c37d0194bbafbabf95ea072fb55cf5eb8b8b4809 Author: Ann Almgren Date: Fri Jan 26 16:45:15 2018 -0800 Break profiling into two parts Docs/sphinx/source/AMReX_Profiling_Tools.rst Docs/sphinx/source/Chapter12.rst Docs/sphinx/source/Chapter13.rst Docs/sphinx/source/Chapter14.rst Docs/sphinx/source/External_Profiling_Tools.rst Docs/sphinx/source/index.rst commit 593bb93eb02e0c3ac7abbd853514faae161a7c1e Merge: 5332c15bc 8b0923717 Author: Andrew Myers Date: Fri Jan 26 16:25:10 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5332c15bcd3843abb0bb1fcc27e67b97abc19974 Author: Andrew Myers Date: Fri Jan 26 16:25:01 2018 -0800 use BL_PROFILE_VAR instead of BL_PROFILE here Src/Particle/AMReX_ParticleContainerI.H commit 8b0923717783c37df792ab678c54d4b2c3ca757c Author: kngott Date: Fri Jan 26 15:54:01 2018 -0800 Addition of BL_PROFILE_TINY_FLUSH() to allow the user to flush the TINYPROFILER results to stdout whenever they like. Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp commit 1bc2342e83ef7291c8480e9580290a7ae5cdf45f Merge: 719fbb386 dc5ba7621 Author: Weiqun Zhang Date: Fri Jan 26 12:42:34 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 719fbb38654dab71966828d1a4192c997bb60b05 Author: Weiqun Zhang Date: Fri Jan 26 12:41:24 2018 -0800 hypre add amrex_ prefix to some fortran functions Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H commit dc5ba76214fb71d0b140a3187de994e69dd17288 Merge: 4b56c9bce 82958167b Author: Andrew Myers Date: Fri Jan 26 11:16:07 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4b56c9bce85f728b487ef4d9961e6b9863b23748 Author: Andrew Myers Date: Fri Jan 26 11:15:57 2018 -0800 Real -> ParticleType::Real Src/Particle/AMReX_NeighborParticlesI.H commit 82958167b6e105a876f9a352348230f7295fde78 Author: Weiqun Zhang Date: Fri Jan 26 10:33:27 2018 -0800 hypre: rm duplicated calls to assemble vectors Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp commit cf314b572293df8701b1ff03d4c824681f016567 Merge: 6faa846b3 e49ebc66f Author: Weiqun Zhang Date: Fri Jan 26 09:01:40 2018 -0800 Merge branch 'hypre' into development commit 6faa846b3ecea367d685a56f46cd4a5911a0492b Merge: 60064d9d7 6f0a91df1 Author: Weiqun Zhang Date: Thu Jan 25 18:07:24 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 60064d9d7b686408d82af870a90ce2065302d6fa Merge: 2cc17a89b d7da52070 Author: Weiqun Zhang Date: Thu Jan 25 18:07:18 2018 -0800 Merge branch 'weiqun/looping' into development commit e49ebc66f13d1c2afabbe4f0c4d3574cc974aa7e Author: Weiqun Zhang Date: Thu Jan 25 16:08:08 2018 -0800 mlmg: set hypre verbosity Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit e7d2d40d107f516886360f63563bec8ac900b18f Author: Weiqun Zhang Date: Thu Jan 25 15:40:58 2018 -0800 MLMG: use hypre as bottom solver for cell-centered solve Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_InterpBndryData.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.H Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Tutorials/LinearSolvers/ABecLaplacian_C/GNUmakefile Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp commit 6f0a91df1687284dbad9b4304bb6837af35609d7 Merge: 12fbb4dbf 2cc17a89b Author: Ann Almgren Date: Thu Jan 25 13:05:46 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 12fbb4dbff217b525ab8c81683f193556552d54f Author: Ann Almgren Date: Thu Jan 25 12:10:25 2018 -0800 Change the default for probin_natonce from 32 to 512 since 32 reads at a time is way too few when running with many ranks. Src/Amr/AMReX_Amr.cpp commit d7da52070569839bf1bca86f768e03a545f496ed Author: Weiqun Zhang Date: Thu Jan 25 10:28:47 2018 -0800 add BaseFab::Transform Src/Base/AMReX_BaseFab.H commit 5e796c753a433fb1fadd2f2b5f112f2c3fd7b50b Author: Weiqun Zhang Date: Thu Jan 25 10:06:05 2018 -0800 make sure box passed to setVal is ok Src/Base/AMReX_BaseFab.H Src/Boundary/AMReX_MultiMask.cpp commit 2cc17a89bee22395146bb6195112606801de72df Author: Andy Nonaka Date: Thu Jan 25 09:17:52 2018 -0800 updates Docs/sphinx/source/Introduction.rst Docs/sphinx/source/index.rst commit 06924fb4bcc04487aeebc2ed807245f9e92c2a97 Author: Weiqun Zhang Date: Wed Jan 24 17:20:24 2018 -0800 bug fixes Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Boundary/AMReX_Mask.cpp commit 2eaaf6a9ce7f76e98b7dfb5724c5e765c58189c4 Author: Weiqun Zhang Date: Wed Jan 24 15:49:09 2018 -0800 rm AMReX_Looping.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseUmap.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_Looping.H Src/Base/CMakeLists.txt Src/Base/Make.package Src/Boundary/AMReX_Mask.cpp commit f7c72a62f1faa5b9cdfa67d298ccd1ff1db7ba32 Merge: a9830c214 d0ed19c38 Author: Lawrence Minion Date: Wed Jan 24 13:50:51 2018 -0800 Fixing double naming. Merge branch 'SDC' of https://github.com/AMReX-Codes/amrex into SDC commit a9830c214cb1d6328deba31e8c98fd92fedae767 Author: Andy Nonaka Date: Wed Jan 24 11:22:04 2018 -0800 User's Guide -> Documentation Docs/sphinx/source/Chapter9.rst Docs/sphinx/source/Introduction.rst Docs/sphinx/source/index.rst commit f2d47f8e0bb671e5111981d0b6a69a941f816f71 Author: Weiqun Zhang Date: Wed Jan 24 10:34:00 2018 -0800 rm ForAllThisBNNXC Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Looping.H Src/Boundary/AMReX_Mask.cpp commit 976f5059883873330b990204f785799ac3644a2e Author: Weiqun Zhang Date: Wed Jan 24 10:14:48 2018 -0800 rm ForAllThisBNNXCBN Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Looping.H Src/Boundary/AMReX_Mask.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit da0657fe1d5643ac7ca7ba2ef6f442e935e60b02 Merge: 906de24bc 86926a992 Author: Andy Nonaka Date: Tue Jan 23 19:00:37 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 906de24bccca65ab984c40d48a714d85a3ddcaf5 Author: Andy Nonaka Date: Tue Jan 23 19:00:24 2018 -0800 update intro Docs/sphinx/source/Introduction.rst commit 86926a9925812d03440f5e9513a693e102de0f14 Merge: 199c16e11 4d679e460 Author: Andrew Myers Date: Tue Jan 23 18:02:21 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 199c16e1165e4c476121723c88a801d2c0589ffb Author: Andrew Myers Date: Tue Jan 23 18:02:03 2018 -0800 add note about minimum version of yt needed for AMReX Datasets Docs/sphinx/source/Visualization.rst commit 8a17a5875c07775be6a37e15538fc59ffd947e77 Author: Weiqun Zhang Date: Tue Jan 23 17:15:16 2018 -0800 ForAllThisBNNXCBNYCBN is gone Src/Base/AMReX_Looping.H commit 4d679e460594b374c895bfec5eaa7990c81391e4 Author: Andy Nonaka Date: Tue Jan 23 17:13:35 2018 -0800 switch chapters Docs/sphinx/source/Chapter6.rst Docs/sphinx/source/Chapter7.rst commit 71c06479cdc66fb21a10dad6791e760ade4726a5 Author: Weiqun Zhang Date: Tue Jan 23 17:13:31 2018 -0800 rm linComb for non-Real type Src/Base/AMReX_BaseFab.H commit d35c0cb098892a3d88f2f74c5112ed3c41a7362e Author: Andy Nonaka Date: Tue Jan 23 17:11:13 2018 -0800 linear solver placeholder Docs/sphinx/source/Basics.rst Docs/sphinx/source/Chapter5.rst Docs/sphinx/source/Chapter6.rst Docs/sphinx/source/LinearSolvers.rst Docs/sphinx/source/index.rst commit 3c216fed5c405704cbd5f902cf3b7a49b9e9cae6 Author: Weiqun Zhang Date: Tue Jan 23 16:58:14 2018 -0800 use Accumulate; rm ForAllRevXBNYCBNNN and BaseFab::copyRev Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Looping.H commit 2ac6dec3456023fe7ce3b506653bccb194598bce Author: Weiqun Zhang Date: Tue Jan 23 16:47:53 2018 -0800 ForAllThisBNN is gone Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Looping.H commit 24eb0331c880c3a530861e2de99423c99e4ec8e0 Author: Weiqun Zhang Date: Tue Jan 23 16:31:55 2018 -0800 BaseFab: add ForEach and Accumulate Src/Base/AMReX_BaseFab.H commit 958a3561caa77fa9dbbf5b9c376c9c04d2180d30 Author: Andy Nonaka Date: Tue Jan 23 16:00:04 2018 -0800 teaching myself sphinx. cleaning up user's guide Docs/sphinx/source/AmrCore.rst Docs/sphinx/source/AmrLevel.rst Docs/sphinx/source/Basics.rst Docs/sphinx/source/Boundary.rst Docs/sphinx/source/GettingStarted.rst Docs/sphinx/source/index.rst commit d0ed19c383016c2145f198ae2b7d6bbd55e05aed Author: Minion Date: Tue Jan 23 15:37:21 2018 -0800 Framework for SDC Heat Example Tutorials/Basic/SDCHeat_Equation_EX1_C/GNUmakefile Tutorials/Basic/SDCHeat_Equation_EX1_C/Make.package Tutorials/Basic/SDCHeat_Equation_EX1_C/advance.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/advance_2d.f90 Tutorials/Basic/SDCHeat_Equation_EX1_C/advance_3d.f90 Tutorials/Basic/SDCHeat_Equation_EX1_C/init_phi_2d.f90 Tutorials/Basic/SDCHeat_Equation_EX1_C/init_phi_3d.f90 Tutorials/Basic/SDCHeat_Equation_EX1_C/inputs_2d Tutorials/Basic/SDCHeat_Equation_EX1_C/inputs_3d Tutorials/Basic/SDCHeat_Equation_EX1_C/main.cpp Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc.H Tutorials/Basic/SDCHeat_Equation_EX1_C/myfunc_F.H commit ff0ba17d28324a42d1f79b0841562eb5a6a282a7 Author: Weiqun Zhang Date: Tue Jan 23 14:41:11 2018 -0800 ForAllThisCPencil is gone Src/Base/AMReX_BaseFab.H Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_Looping.H commit dd32c33102195802d92132d4ea3f256c314efcd0 Author: Weiqun Zhang Date: Tue Jan 23 14:12:01 2018 -0800 add some functions to BaseFab in order to eliminate looping macros Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H commit 6155e3fb62cc2545ed8f72abbd179e5069de2964 Author: Weiqun Zhang Date: Tue Jan 23 12:29:29 2018 -0800 rm unused macros for looping over BaseFabs Src/Base/AMReX_Looping.H commit 67bf9244e13ae8dd964b974dae70e56494bf4ead Author: Weiqun Zhang Date: Tue Jan 23 12:04:53 2018 -0800 update CHANGES CHANGES commit 3e30884d2f5f9e8e0c746662e958e11a5e4db5e9 Author: Ann Almgren Date: Tue Jan 23 10:33:47 2018 -0800 Remove the latex source for the users guide -- we now use the .rst files in sphinx as the primary source for the documentation. Docs/AMReXUsersGuide/.gitignore Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/AmrCore/figs/Adv1.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv2.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv3.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv4.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv5.pdf Docs/AMReXUsersGuide/AmrCore/figs/flowchart.odg Docs/AMReXUsersGuide/AmrCore/figs/flowchart.pdf Docs/AMReXUsersGuide/AmrCore/figs/subcycling.pdf Docs/AMReXUsersGuide/AmrCore/figs/subcycling.tex Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex Docs/AMReXUsersGuide/AmrLevel/figs/flowchart.odg Docs/AMReXUsersGuide/AmrLevel/figs/flowchart.pdf Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/Basics/amrgrids.pdf Docs/AMReXUsersGuide/Basics/cc_growbox.pdf Docs/AMReXUsersGuide/Basics/cc_tilebox.pdf Docs/AMReXUsersGuide/Basics/cc_validbox.pdf Docs/AMReXUsersGuide/Basics/ec_growbox.pdf Docs/AMReXUsersGuide/Basics/ec_tilebox.pdf Docs/AMReXUsersGuide/Basics/ec_validbox.pdf Docs/AMReXUsersGuide/Basics/figs/flowchart.odg Docs/AMReXUsersGuide/Basics/figs/flowchart.pdf Docs/AMReXUsersGuide/Basics/indextypes.pdf Docs/AMReXUsersGuide/Boundary/Boundary.tex Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Docs/AMReXUsersGuide/CVODE/CVODE.tex Docs/AMReXUsersGuide/Debugging/Debugging.tex Docs/AMReXUsersGuide/EB/EB.tex Docs/AMReXUsersGuide/EB/EB_example.eps Docs/AMReXUsersGuide/EB/EB_example.fig Docs/AMReXUsersGuide/EB/EB_example.fig.bak Docs/AMReXUsersGuide/EB/EB_example.pdf Docs/AMReXUsersGuide/EB/areas_and_volumes.eps Docs/AMReXUsersGuide/EB/areas_and_volumes.fig Docs/AMReXUsersGuide/EB/areas_and_volumes.pdf Docs/AMReXUsersGuide/EB/eb_fluxes.eps Docs/AMReXUsersGuide/EB/eb_fluxes.fig Docs/AMReXUsersGuide/EB/eb_fluxes.fig.bak Docs/AMReXUsersGuide/EB/eb_fluxes.pdf Docs/AMReXUsersGuide/EB/graph.pdf Docs/AMReXUsersGuide/EB/multidivide.pdf Docs/AMReXUsersGuide/EB/parabsphere.pdf Docs/AMReXUsersGuide/EB/parabsphere.ps Docs/AMReXUsersGuide/EB/redist.eps Docs/AMReXUsersGuide/EB/redist.fig Docs/AMReXUsersGuide/EB/redist.pdf Docs/AMReXUsersGuide/EB/revolution.pdf Docs/AMReXUsersGuide/EB/revolution.ps Docs/AMReXUsersGuide/EB/volume.pdf Docs/AMReXUsersGuide/Fortran/Fortran.tex Docs/AMReXUsersGuide/GNUmakefile Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Docs/AMReXUsersGuide/Introduction/Introduction.tex Docs/AMReXUsersGuide/Particle/Particle.tex Docs/AMReXUsersGuide/Particle/neighbor_list.pdf Docs/AMReXUsersGuide/Particle/neighbor_list.tex Docs/AMReXUsersGuide/Particle/neighbor_particles.pdf Docs/AMReXUsersGuide/Particle/neighbor_particles.tex Docs/AMReXUsersGuide/Particle/particle_arrays.pdf Docs/AMReXUsersGuide/Particle/particle_arrays.tex Docs/AMReXUsersGuide/Preface/Preface.tex Docs/AMReXUsersGuide/Profiling/Profiling.tex Docs/AMReXUsersGuide/Profiling/figs/commtopo.png Docs/AMReXUsersGuide/Profiling/figs/mpi.png Docs/AMReXUsersGuide/Profiling/figs/msgsizes.png Docs/AMReXUsersGuide/Profiling/figs/papi.png Docs/AMReXUsersGuide/Profiling/figs/summary.png Docs/AMReXUsersGuide/Profiling/figs/timings.png Docs/AMReXUsersGuide/README.md Docs/AMReXUsersGuide/Visualization/Amrvis_2d.eps Docs/AMReXUsersGuide/Visualization/Amrvis_3d.eps Docs/AMReXUsersGuide/Visualization/ParaView.eps Docs/AMReXUsersGuide/Visualization/ParaView_particles.eps Docs/AMReXUsersGuide/Visualization/VisIt_2D.eps Docs/AMReXUsersGuide/Visualization/VisIt_3D.eps Docs/AMReXUsersGuide/Visualization/Visualization.tex Docs/AMReXUsersGuide/Visualization/yt_Nyx_density_slice.png Docs/AMReXUsersGuide/Visualization/yt_Nyx_density_vol_rend.png Docs/AMReXUsersGuide/amrexsymbols.tex commit 28e334f944d77f28fb63502987ffc7a9413584d3 Author: Weiqun Zhang Date: Tue Jan 23 09:25:43 2018 -0800 rm oboslete macros Src/Amr/AMReX_Amr.cpp Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/Base/AMReX_BLPgas.cpp Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_ccse-mpi.H Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F Src/Boundary/AMReX_LO_UTIL.F Src/LinearSolvers/F_MG/FParallelMG.mak commit c2ea96c7b2c32162cf69cf4e4e708d9506b08b1f Author: Ann Almgren Date: Tue Jan 23 09:54:32 2018 -0800 Fixed the centering commands. Docs/sphinx/source/CVODE.rst Docs/sphinx/source/EB.rst Docs/sphinx/source/Particle.rst Docs/sphinx/source/Visualization.rst commit 7fd8672702687c599d6e50c27f706eeeb1841a13 Author: Weiqun Zhang Date: Tue Jan 23 09:20:53 2018 -0800 finally fixed 1d node based bilinear interpolation Src/AmrCore/AMReX_INTERP_1D.F commit a8adbfcfcbd8a456f0a373a2209fde1d9563a610 Merge: 3260eec62 a49b2423d Author: Andrew Myers Date: Mon Jan 22 17:15:31 2018 -0800 merging. commit 3260eec62f3b4a77c4a18174ec23a323a9d9cd53 Author: Andrew Myers Date: Mon Jan 22 17:13:49 2018 -0800 clarify doc building instructions slightly Docs/Readme.sphinx commit a49b2423d6492df302644048343f35c7711e8bfb Author: Ann Almgren Date: Mon Jan 22 16:37:19 2018 -0800 Add details about "make latexpdf" Docs/Readme.sphinx commit 2c762a9a8fada91c5fd53ce8f1eba3058bd241d8 Merge: d704bdce5 39389a8b1 Author: Ann Almgren Date: Mon Jan 22 16:36:08 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d704bdce563cae6742bd5f8645c255d308a11e6e Author: Ann Almgren Date: Mon Jan 22 16:35:48 2018 -0800 Replace some centering commands so they work correctly for make latexpdf Docs/sphinx/source/AmrCore.rst Docs/sphinx/source/Basics.rst Docs/sphinx/source/Profiling.rst commit 39389a8b1a5fae266090fd9ae496d66d3bb48aea Author: Michele Rosso Date: Mon Jan 22 16:27:24 2018 -0800 CMake:do not retrieve git hash if git not installed or .git not present Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Utils.cmake commit 4943f1564468ef3be1971da7afa878b51b610f74 Author: Andrew Myers Date: Mon Jan 22 15:59:31 2018 -0800 fix the centering of the tables when building using latexpdf Docs/sphinx/source/BuildingAMReX.rst commit 2d27bc1f253626f9d703e43cf3c4393e08b11eea Merge: d4962a64a 7f0834490 Author: Ann Almgren Date: Mon Jan 22 15:23:54 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d4962a64a3beb6d2b56f5035203b06bff70225a5 Author: Ann Almgren Date: Mon Jan 22 15:23:47 2018 -0800 Update rst files Docs/sphinx/source/Basics.rst Docs/sphinx/source/BuildingAMReX.rst Docs/sphinx/source/Particle.rst Docs/sphinx/source/Visualization.rst commit 7f0834490eace9c932a07920450dcfe0806e76f5 Author: Andrew Myers Date: Mon Jan 22 15:03:22 2018 -0800 add a few comments. build_and_deploy.sh commit 2ca2a154e273bdc11b3775f81b8ad679f246f573 Author: Andrew Myers Date: Mon Jan 22 14:58:24 2018 -0800 minor Docs/sphinx/source/BuildingAMReX.rst commit e777b7caf4ace4a0995d39f9f97fa29dc02ca493 Author: Andrew Myers Date: Mon Jan 22 14:54:41 2018 -0800 update deploy script to compile libamrex before exiting early if not on development build_and_deploy.sh commit 1d85da3b256d49950e2e32acb77a1cdf6a6013b3 Author: Andrew Myers Date: Mon Jan 22 14:37:38 2018 -0800 override the default page width for the read the docs theme, which is optimized for mobile. Docs/sphinx/source/_static/theme_overrides.css Docs/sphinx/source/conf.py commit b9bd69cba4dc898efa501dc01540317fd4fc8c88 Author: Andrew Myers Date: Mon Jan 22 14:31:03 2018 -0800 update the AMReX version every time the docs are built. Docs/sphinx/source/conf.py commit bd308066ddee0f0e925f78ad06be9ab794527946 Merge: e5e52c10b a4a290e39 Author: Andrew Myers Date: Mon Jan 22 13:44:51 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e5e52c10b4987e8ad0d28be5e5b3c3a999904b59 Author: Andrew Myers Date: Mon Jan 22 13:44:41 2018 -0800 updates to the sphinx installation instructions. Docs/Readme.sphinx commit a4a290e39d21d468cecd95bf48605990cfc8ba8e Author: Weiqun Zhang Date: Mon Jan 22 13:28:27 2018 -0800 Array --> Vector Src/AmrTask/AMFIter/AMReX_AmrTask.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/Amr/AMReX_AmrLevelTask.H Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit c53c5cfae0df71d75fd11ef2e93b86ce8eaf66f4 Author: Ann Almgren Date: Mon Jan 22 13:00:15 2018 -0800 More path highlighting Docs/sphinx/source/AmrCore.rst Docs/sphinx/source/AmrLevel.rst Docs/sphinx/source/Basics.rst Docs/sphinx/source/Boundary.rst Docs/sphinx/source/Chapter4.rst Docs/sphinx/source/Chapter6.rst Docs/sphinx/source/Chapter7.rst Docs/sphinx/source/Fortran.rst Docs/sphinx/source/Particle.rst commit 563a74f08d73c4bb89dae103308dbcc3ba1e021b Author: Ann Almgren Date: Mon Jan 22 12:54:17 2018 -0800 More path names Docs/sphinx/source/BuildingAMReX.rst Docs/sphinx/source/CVODE.rst Docs/sphinx/source/Chapter4.rst Docs/sphinx/source/Chapter6.rst Docs/sphinx/source/Chapter7.rst Docs/sphinx/source/GettingStarted.rst Docs/sphinx/source/Particle.rst Docs/sphinx/source/Visualization.rst commit 267c8c67ed4ffc28bac71cbfb949e6cee255b39f Author: Ann Almgren Date: Mon Jan 22 12:49:50 2018 -0800 All path names should be highlighted Docs/sphinx/source/Boundary.rst Docs/sphinx/source/BuildingAMReX.rst Docs/sphinx/source/EB.rst Docs/sphinx/source/Fortran.rst commit 903910c819ffd03637e98d0c66b0270d2c9fc923 Author: Ann Almgren Date: Mon Jan 22 12:46:42 2018 -0800 formatting Docs/sphinx/source/Chapter6.rst commit dfa9df643eeaaac311d3f62997abfd761cff56b1 Author: Weiqun Zhang Date: Mon Jan 22 10:39:09 2018 -0800 MLMG N-Solve: refactor making grids Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp commit 3ef308ae2a11fff5ed2acfd3f199f76c6d8df799 Author: Weiqun Zhang Date: Mon Jan 22 09:23:36 2018 -0800 MLMG N-Solve: add paramter controlling grid size Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 1f73d6374412cb2d3edecefe2cd9e6bf1de64f3d Merge: d7b680cb3 ddfc4778a Author: Andrew Myers Date: Mon Jan 22 12:09:38 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d7b680cb33bce118a119e0b672b1dee86846a096 Author: Andrew Myers Date: Mon Jan 22 12:09:28 2018 -0800 update sphinx instructions. Docs/Readme.sphinx commit ddfc4778a390e67a27d6c984747a424a4ac8d097 Author: Ann Almgren Date: Mon Jan 22 12:07:48 2018 -0800 Update highlighting Docs/sphinx/source/AmrCore.rst commit d933f627966a95747d5281f56df150e0edb7d1e4 Author: Ann Almgren Date: Mon Jan 22 12:05:11 2018 -0800 Highlight path names Docs/sphinx/source/AmrCore.rst commit a0397ea9bbe2522342771dc35edf80f3fbbb37fd Merge: ff7d68889 e6718cdbb Author: Ann Almgren Date: Mon Jan 22 12:01:18 2018 -0800 Merge branch 'development' of https://www.github.com/AMReX-Codes/amrex into development commit e6718cdbb2dfe0e054fd39df984002d880081a8e Author: Andrew Myers Date: Mon Jan 22 11:56:27 2018 -0800 fix c++ syntax highlighting for this snippet. Docs/sphinx/source/Particle.rst commit ff7d68889bbc4fce4c61f1af2ce12b8a87f741d1 Merge: fe1dec75e 46e106b5b Author: Ann Almgren Date: Mon Jan 22 11:50:53 2018 -0800 Merge branch 'development' of https://www.github.com/AMReX-Codes/amrex into development commit fe1dec75e479d950347691ff327f79d14045c500 Author: Ann Almgren Date: Mon Jan 22 11:44:01 2018 -0800 1) updated BuildingAMReX.rst 2) Added notes for how to update AMReX documentation in Readme.sphinx Docs/Readme.sphinx Docs/sphinx/source/BuildingAMReX.rst commit 46e106b5b590cbea1e802604f99b1dfcc94e309f Author: Andrew Myers Date: Mon Jan 22 11:39:07 2018 -0800 minor docs typo fix Docs/sphinx/source/Particle.rst commit 4ace77e5476fd4cf695f9373bdbae850dbc1dd92 Merge: f299337a7 83fb4f4ec Author: Ann Almgren Date: Mon Jan 22 11:26:17 2018 -0800 Merge branch 'development' of https://www.github.com/AMReX-Codes/amrex into development commit 83fb4f4ecd1083424a6dbf3cf9b0cc7539901beb Author: Andrew Myers Date: Mon Jan 22 11:21:47 2018 -0800 remove reference to non-existent section. Docs/sphinx/source/EB.rst commit efb673a398c1fea3dd011d712edb5d55ae776eb5 Merge: 1211eb026 73f9b2653 Author: Andrew Myers Date: Mon Jan 22 11:16:28 2018 -0800 Merge pull request #199 from JBlaschke/development Fix figure in EB section commit 73f9b26536d0878052f3763160a870b30537df8c Merge: a14201047 1211eb026 Author: Johannes Blaschke Date: Mon Jan 22 11:10:09 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit a1420104709d64564a5b012e128e10a9aa11ff67 Author: Johannes Blaschke Date: Mon Jan 22 11:09:30 2018 -0800 fix .pdf->.png for figure Docs/sphinx/source/EB.rst Docs/sphinx/source/EB/areas_and_volumes.png Docs/sphinx/source/EB/eb_fluxes.png commit 1211eb0266bff58eeb8c32ec71310f5f85d82db9 Author: Weiqun Zhang Date: Mon Jan 22 10:37:40 2018 -0800 comparison operators for Box Src/Base/AMReX_Box.H Src/Base/AMReX_IndexType.H commit f299337a76ee791a8daa94b941a0df67654fb191 Author: Ann Almgren Date: Mon Jan 22 10:33:24 2018 -0800 Update several rst files Docs/sphinx/source/BuildingAMReX.rst Docs/sphinx/source/Chapter3.rst Docs/sphinx/source/GettingStarted.rst commit c6fc6fb4325b8d3b357111a5ab150cc26ed2286f Merge: 4abd11e07 3103dfc8b Author: asalmgren Date: Mon Jan 22 08:00:36 2018 -0800 Merge pull request #198 from JBlaschke/development Update Docs commit 3103dfc8bfa81ce1cb30e5cbba41c2c2ae225f35 Merge: 346490715 4abd11e07 Author: Johannes Blaschke Date: Sun Jan 21 22:52:45 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 34649071536cd61891300f56ad94d8d81422ec9f Author: Johannes Blaschke Date: Sun Jan 21 22:51:57 2018 -0800 fix label issue Docs/sphinx/source/Basics.rst commit be95285c79992396a7f48cc5d6bef0c6c99e5f5e Author: Johannes Blaschke Date: Sun Jan 21 22:47:39 2018 -0800 clean up some rst errors Docs/sphinx/source/Basics.rst Docs/sphinx/source/BuildingAMReX.rst Docs/sphinx/source/CVODE.rst Docs/sphinx/source/Chapter3.rst Docs/sphinx/source/GettingStarted.rst Docs/sphinx/source/Particle.rst Docs/sphinx/source/intro.rst commit 39f7742b8c47c9de4cbe67bf1441f69de2c4f131 Author: Johannes Blaschke Date: Sun Jan 21 22:32:15 2018 -0800 Finished formatting CVODE section Docs/sphinx/source/CVODE.rst Docs/sphinx/source/Chapter13.rst Docs/sphinx/source/index.rst commit c63663479cff4117f0290ebbcc84979b897be0e2 Author: Johannes Blaschke Date: Sun Jan 21 22:09:22 2018 -0800 Finished converting Profiling section Docs/sphinx/source/Profiling.rst commit 48baac6e88875b5f23e3cf05b8d4af1d9673ed0e Author: Johannes Blaschke Date: Sun Jan 21 21:37:16 2018 -0800 Begin converting section on profiling Docs/sphinx/source/Chapter12.rst Docs/sphinx/source/Profiling.rst Docs/sphinx/source/Profiling/figs/commtopo.png Docs/sphinx/source/Profiling/figs/mpi.png Docs/sphinx/source/Profiling/figs/msgsizes.png Docs/sphinx/source/Profiling/figs/papi.png Docs/sphinx/source/Profiling/figs/summary.png Docs/sphinx/source/Profiling/figs/timings.png commit a19b286dbd6fe9a73660221d920c4b55454d738a Author: Johannes Blaschke Date: Sun Jan 21 21:31:23 2018 -0800 finished reformatting visualization section Docs/sphinx/source/Chapter11.rst Docs/sphinx/source/Visualization.rst Docs/sphinx/source/Visualization/Amrvis_2d.png Docs/sphinx/source/Visualization/Amrvis_3d.png Docs/sphinx/source/Visualization/ParaView.png Docs/sphinx/source/Visualization/ParaView_particles.png Docs/sphinx/source/Visualization/VisIt_2D.png Docs/sphinx/source/Visualization/VisIt_3D.png Docs/sphinx/source/index.rst commit a3d576b84d13e7083b9e5e7e2e109febb08f6c3e Author: Johannes Blaschke Date: Sun Jan 21 20:05:29 2018 -0800 Finished converting EB chapter Docs/sphinx/source/Chapter10.rst Docs/sphinx/source/Chapter11.rst Docs/sphinx/source/EB.rst Docs/sphinx/source/EB/EB_example.eps Docs/sphinx/source/EB/EB_example.fig Docs/sphinx/source/EB/EB_example.fig.bak Docs/sphinx/source/EB/EB_example.pdf Docs/sphinx/source/EB/EB_example.png 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Docs/sphinx/source/Visualization/ParaView.pdf Docs/sphinx/source/Visualization/ParaView_particles.eps Docs/sphinx/source/Visualization/ParaView_particles.pdf Docs/sphinx/source/Visualization/VisIt_2D.eps Docs/sphinx/source/Visualization/VisIt_2D.pdf Docs/sphinx/source/Visualization/VisIt_3D.eps Docs/sphinx/source/Visualization/VisIt_3D.pdf Docs/sphinx/source/Visualization/yt_Nyx_density_slice.png Docs/sphinx/source/Visualization/yt_Nyx_density_vol_rend.png Docs/sphinx/source/index.rst commit 4abd11e07cea8a92d87cb7d5599b44ce124c3d68 Merge: e5544d422 ffc034594 Author: Ann Almgren Date: Sun Jan 21 11:41:27 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 5b8d0f099236ad0653b5131dc26f28f17db09564 Author: Johannes Blaschke Date: Sat Jan 20 23:49:16 2018 -0800 Finished converting the Fortran Interface Section Docs/sphinx/source/Chapter4.rst Docs/sphinx/source/Chapter9.rst Docs/sphinx/source/Fortran.rst Docs/sphinx/source/GettingStarted.rst Docs/sphinx/source/index.rst commit 4bfb5669cc07917bdfa0c9f9aae1c8751049e878 Author: Johannes Blaschke Date: Sat Jan 20 14:04:28 2018 -0800 Add particle figures to docs Docs/sphinx/source/Particle/neighbor_list.pdf Docs/sphinx/source/Particle/neighbor_list.png Docs/sphinx/source/Particle/neighbor_list.tex Docs/sphinx/source/Particle/neighbor_particles.pdf Docs/sphinx/source/Particle/neighbor_particles.png Docs/sphinx/source/Particle/neighbor_particles.tex Docs/sphinx/source/Particle/particle_arrays.pdf Docs/sphinx/source/Particle/particle_arrays.png Docs/sphinx/source/Particle/particle_arrays.tex commit b2eec895cfa9de3b6dceabac12142e84152e4d0d Merge: fe1d1ab6c ffc034594 Author: Johannes Blaschke Date: Sat Jan 20 14:00:36 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit fe1d1ab6c02699b2cb7e280f4ce4348851e6e019 Author: Johannes Blaschke Date: Sat Jan 20 13:59:47 2018 -0800 Finished fromatting particles section Docs/sphinx/source/Amr.rst Docs/sphinx/source/Particle.rst Docs/sphinx/source/Particles.rst Docs/sphinx/source/conf.py commit ffc0345944f67660b75912609c4a87793a6036e4 Author: Weiqun Zhang Date: Fri Jan 19 16:36:52 2018 -0800 less verbose Src/Amr/AMReX_Amr.cpp commit fde8be993257531debdbcf9b0d023669f6d78f3d Author: Weiqun Zhang Date: Fri Jan 19 16:33:31 2018 -0800 MLMG: clean up M-Solve because it has been replaced by nsolve Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 48379677a33411678bd23ff119a01be59a00d73d Author: kngott Date: Fri Jan 19 15:57:16 2018 -0800 Fix for SparseIO file number calculations. Src/Base/AMReX_VisMF.cpp commit 3ab4c9018240e1ec08767b1baffef28ee8cc678a Author: Weiqun Zhang Date: Fri Jan 19 13:30:39 2018 -0800 MLMG: use SFC in N-Solve Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 9a1289403848944347f37218eedbe507fd4abc55 Author: Weiqun Zhang Date: Fri Jan 19 13:15:29 2018 -0800 MLMG: N-Solve Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMGBndry.H Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit e5544d422fd17907738e7a8f81dac8238b5e4105 Author: Ann Almgren Date: Fri Jan 19 12:59:36 2018 -0800 Fix to formatting Docs/sphinx/source/GettingStarted.rst commit 21ef536401b60c6f9cc47233d3187fd34a8b829e Merge: eb48ac39d 587d9d86c Author: dtgraves Date: Fri Jan 19 09:09:45 2018 -0800 Merge pull request #195 from AMReX-Codes/dtg_branch bug fix push commit 587d9d86c3931d22702047c1ca23f3343fe7039f Author: dtgraves Date: Fri Jan 19 09:08:39 2018 -0800 fixed issue with regression test. The ghost routine was being called where there were no ghost cells. Src/EB/AMReX_EBTower.cpp commit eb48ac39d0684a7dc8f2199b317cda41bd96e7ff Merge: cfd7c6f07 49f4a67b5 Author: WeiqunZhang Date: Fri Jan 19 08:43:40 2018 -0800 Merge pull request #168 from bcfriesen/IOBenchmark_OpenMP IOBenchmark: make only master thread flush and close file in thread-shared IO commit 2b33b0e8fffaae7f1976f3c484397efbbd776145 Author: Johannes Blaschke Date: Fri Jan 19 00:21:07 2018 -0800 Fix some typos Docs/sphinx/source/AmrCore.rst Docs/sphinx/source/Basics.rst commit 4c3b9529f5f5eabb949058e993e847eb86d8222c Author: Johannes Blaschke Date: Fri Jan 19 00:13:36 2018 -0800 reformatted Amr Source Code section Docs/sphinx/source/AmrCore/figs/Adv1.pdf Docs/sphinx/source/AmrCore/figs/Adv1.png Docs/sphinx/source/AmrCore/figs/Adv2.pdf Docs/sphinx/source/AmrCore/figs/Adv2.png Docs/sphinx/source/AmrCore/figs/Adv3.pdf Docs/sphinx/source/AmrCore/figs/Adv3.png Docs/sphinx/source/AmrCore/figs/Adv4.pdf Docs/sphinx/source/AmrCore/figs/Adv4.png Docs/sphinx/source/AmrCore/figs/Adv5.pdf Docs/sphinx/source/AmrCore/figs/Adv5.png Docs/sphinx/source/AmrCore/figs/flowchart.odg Docs/sphinx/source/AmrCore/figs/flowchart.pdf Docs/sphinx/source/AmrCore/figs/flowchart.png Docs/sphinx/source/AmrCore/figs/subcycling.pdf Docs/sphinx/source/AmrCore/figs/subcycling.png Docs/sphinx/source/AmrCore/figs/subcycling.tex Docs/sphinx/source/AmrLevel.rst Docs/sphinx/source/AmrLevel/figs/flowchart.odg Docs/sphinx/source/AmrLevel/figs/flowchart.pdf Docs/sphinx/source/AmrLevel/figs/flowchart.png Docs/sphinx/source/Chapter7.rst Docs/sphinx/source/Chapter8.rst commit cfd7c6f07bd598f15d39d5a8975ef687b7895ee4 Merge: 49c2fb4ca 4f12d640c Author: asalmgren Date: Thu Jan 18 19:32:26 2018 -0800 Merge pull request #193 from JBlaschke/development Development commit 4f12d640c5f5452c2157145f6ef1f05ad7095ff0 Merge: ca475e4c6 49c2fb4ca Author: Johannes Blaschke Date: Thu Jan 18 18:10:57 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit ca475e4c61968ffc02f397b377e9adab5742eb91 Author: Johannes Blaschke Date: Thu Jan 18 18:05:37 2018 -0800 finished converting AmrCore Docs/sphinx/source/AmrCore.rst Docs/sphinx/source/Chapter6.rst commit 49c2fb4ca2e7bc2e9fdb732f34c5d579cc516ab9 Author: Weiqun Zhang Date: Thu Jan 18 14:59:27 2018 -0800 msolve: a different approach to make new BoxArray Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 6cfcb53ed063aa8e05282b5b9c2923704c4d232a Author: dtgraves Date: Thu Jan 18 14:48:38 2018 -0800 took print statements out of CNS.cpp Tutorials/EB/CNS/Source/CNS.cpp commit a7d629b47d8f41c29a18c980c5cbd41ed59f9779 Merge: e09a13dce acc1a936a Author: dtgraves Date: Thu Jan 18 13:48:02 2018 -0800 Merge pull request #192 from AMReX-Codes/dtg_branch bug fixes to the bug fixes to the ... commit acc1a936a5a509e3019d64c6c10acd1e40ef4a54 Author: dtgraves Date: Thu Jan 18 13:46:05 2018 -0800 more bug fixes for periodic stuff. now the corner cells seem to be correct Src/EB/AMReX_EBTower.cpp Tutorials/EB/CNS/Source/CNS.cpp commit e09a13dcefb00f718bbdc8ad98fad52380a1d459 Merge: bc55101b0 8166c49e7 Author: Andy Nonaka Date: Thu Jan 18 13:31:30 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit bc55101b082fe1dbe091739c94a9c54052f6e8be Author: Andy Nonaka Date: Thu Jan 18 13:31:20 2018 -0800 comments only Tutorials/Basic/HeatEquation_EX3_C/advance.cpp commit 8166c49e77840e09da5432393ceca16350ee9a47 Merge: 2f1d4e0dc 12088f0f3 Author: dtgraves Date: Thu Jan 18 11:48:14 2018 -0800 Merge pull request #191 from AMReX-Codes/dtg_branch bug fixes to periodic EBTower commit 12088f0f3ffab838b072d57dae9ccf8adba3c11a Author: dtgraves Date: Thu Jan 18 11:46:14 2018 -0800 bug fixes for periodic stuff. seems to do the right thing for Ann's case now. Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit f6baf4b03625f5f31f8c494857af137d2820de71 Author: Johannes Blaschke Date: Thu Jan 18 11:18:51 2018 -0800 finished formatting Boundary.rst Docs/sphinx/source/AmrLevel.rst Docs/sphinx/source/Basics/amrgrids.pdf Docs/sphinx/source/Basics/amrgrids.png Docs/sphinx/source/Basics/cc_growbox.pdf Docs/sphinx/source/Basics/cc_growbox.png Docs/sphinx/source/Basics/cc_tilebox.pdf Docs/sphinx/source/Basics/cc_tilebox.png Docs/sphinx/source/Basics/cc_validbox.pdf Docs/sphinx/source/Basics/cc_validbox.png Docs/sphinx/source/Basics/ec_growbox.pdf Docs/sphinx/source/Basics/ec_growbox.png Docs/sphinx/source/Basics/ec_tilebox.pdf Docs/sphinx/source/Basics/ec_tilebox.png Docs/sphinx/source/Basics/ec_validbox.pdf Docs/sphinx/source/Basics/ec_validbox.png Docs/sphinx/source/Basics/figs/flowchart.odg Docs/sphinx/source/Basics/figs/flowchart.pdf Docs/sphinx/source/Basics/figs/flowchart.png Docs/sphinx/source/Basics/indextypes.pdf Docs/sphinx/source/Basics/indextypes.png Docs/sphinx/source/Boundary.rst Docs/sphinx/source/Chapter6.rst Docs/sphinx/source/Chapter7.rst Docs/sphinx/source/Chapter8.rst Docs/sphinx/source/Particle.rst commit 2c45e12248577a11e51bb0df57acd2b535986686 Author: Johannes Blaschke Date: Thu Jan 18 11:03:21 2018 -0800 finished Basics.rst, added relevant links Docs/sphinx/source/AmrCore.rst Docs/sphinx/source/Basics.rst Docs/sphinx/source/Boundary.rst Docs/sphinx/source/GettingStarted.rst Docs/sphinx/source/Visualization.rst Docs/sphinx/source/index.rst commit 2f1d4e0dc5fc32547dc27cd6208c2fa117f45e9f Author: Weiqun Zhang Date: Thu Jan 18 10:50:22 2018 -0800 To placate gcc-7 Src/Base/AMReX_ParallelReduce.H Src/Base/AMReX_Vector.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit 83947cfefbb18a28622c52642326f352673a0999 Author: Max Katz Date: Thu Jan 18 13:27:20 2018 -0500 Update to CUDA 9.0 by default Tools/GNUMake/Make.defs commit 577c6232d6cb5b38458d0a9dbc024967a2d6636f Author: Weiqun Zhang Date: Thu Jan 18 10:00:12 2018 -0800 msolve: add parameter for grid size Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H commit 2798900b02a003c0a4dc983f3f0481e40f6c4a88 Author: Weiqun Zhang Date: Thu Jan 18 09:36:33 2018 -0800 msolve: minor optimization Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit e0248d4f6a175c6139314b697bd8672cc856cbfc Merge: 155175d77 46a2c0946 Author: dtgraves Date: Wed Jan 17 16:06:16 2018 -0800 Merge pull request #189 from AMReX-Codes/dtg_branch merging support for periodic EBTower into dev branch commit 46a2c09469a28f2f7d52e2a1839d220f96d66209 Author: dtgraves Date: Wed Jan 17 16:04:45 2018 -0800 added support for periodic to EBTower. For the tests that I ran, it does the right thing. I offer no guarantees for implicit functions which are not periodic. Src/EB/AMReX_EBTower.cpp Tutorials/EB/CNS/Exec/Pulse/GNUmakefile Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit 155175d774a3e8c05fea8e79a8330bc43de11ecf Author: Weiqun Zhang Date: Wed Jan 17 15:00:30 2018 -0800 remove mlcg Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 30693f1e6bc45ec98b6c8052791dc05ed3f006f9 Author: Weiqun Zhang Date: Wed Jan 17 10:42:39 2018 -0800 use MLALaplacian for M-Solve Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 4b5daa1911fcb38e45d5e8e26a91a856f77a0338 Author: Weiqun Zhang Date: Wed Jan 17 10:41:47 2018 -0800 mlmg: add MLALaplacian Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLALap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLALap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLALap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLALap_F.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.H Src/LinearSolvers/MLMG/AMReX_MLALaplacian.cpp Src/LinearSolvers/MLMG/Make.package commit 610fab9f298cfc4921a79f57ef27eb14c1ff1a18 Author: Weiqun Zhang Date: Wed Jan 17 09:35:31 2018 -0800 M-Solve: support for ref ratio of 4 Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 52814fbb21cfe27a325ab0c99e66044112869b65 Author: Johannes Blaschke Date: Tue Jan 16 23:20:53 2018 -0800 finished convering section on MFIter and Tiling Docs/sphinx/source/Basics.rst commit c97e235b2b501fd1b173881b19c50388cf7ae385 Author: Johannes Blaschke Date: Tue Jan 16 18:09:02 2018 -0800 finished FABs documentation Docs/sphinx/source/Basics.rst commit 96b71dde47fe0c35abb148615643e458b045f303 Author: Max Katz Date: Tue Jan 16 20:40:19 2018 -0500 Add Summit Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.olcf commit cf21f1065f26b6f6928ab13047115af92ba8a840 Author: Weiqun Zhang Date: Tue Jan 16 16:59:17 2018 -0800 msolve: clean up Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit df5a34f1e04b6d582bbf248733f13a7156f814e0 Author: Doreen Fan Date: Tue Jan 16 16:27:08 2018 -0800 Added implicit heat equation solver in Tutorials/Basic/HeatEquation_EX3_C/ Tutorials/Basic/HeatEquation_EX3_C/GNUmakefile Tutorials/Basic/HeatEquation_EX3_C/Make.package Tutorials/Basic/HeatEquation_EX3_C/advance.cpp Tutorials/Basic/HeatEquation_EX3_C/init_phi_2d.f90 Tutorials/Basic/HeatEquation_EX3_C/init_phi_3d.f90 Tutorials/Basic/HeatEquation_EX3_C/inputs_2d Tutorials/Basic/HeatEquation_EX3_C/inputs_3d Tutorials/Basic/HeatEquation_EX3_C/main.cpp Tutorials/Basic/HeatEquation_EX3_C/myfunc.H Tutorials/Basic/HeatEquation_EX3_C/myfunc_F.H commit 90132493868cd9deb024a349c2523f4579b7d5d4 Author: Weiqun Zhang Date: Tue Jan 16 16:00:57 2018 -0800 msolve works for at least one example Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 99b77e04b00a07e64d9cef4293eed9783501387a Author: Johannes Blaschke Date: Tue Jan 16 16:12:08 2018 -0800 work on basics Docs/sphinx/source/Basics.rst Docs/sphinx/source/BuildingAMReX.rst Docs/sphinx/source/Chapter4.rst Docs/sphinx/source/GettingStarted.rst commit 52b93d9409fee41f3e7e512a5ea1b5c5c3a0aa8b Author: Weiqun Zhang Date: Tue Jan 16 13:37:40 2018 -0800 firs pass of msolve Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit f664a23c1873f9caddf1dd382bed7d4be5b7b55a Author: Weiqun Zhang Date: Tue Jan 16 09:12:51 2018 -0800 make this regression test much smaller Tutorials/LinearSolvers/ABecLaplacian_F/inputs-rt-poisson-com commit ef84da7c9b80bd80d51c0f318cce31cb44631b09 Merge: bec03c6ae 197f26044 Author: Johannes Blaschke Date: Mon Jan 15 10:53:11 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit bec03c6ae98fc0a7915895749ce598ca4560da2e Author: Johannes Blaschke Date: Mon Jan 15 10:52:46 2018 -0800 completed the Building AMReX section Docs/sphinx/source/BuildingAMReX.rst Docs/sphinx/source/Chapter3.rst commit f9730fd405626b6958b20722b828979c3b4f40d0 Author: Johannes Blaschke Date: Sun Jan 14 12:54:56 2018 -0800 finished GettingStarted section Docs/sphinx/source/GettingStarted.rst Docs/sphinx/source/Visualization.rst commit 948b73603bcefe1ca89c74a4e09e9253a46276e5 Author: Johannes Blaschke Date: Sun Jan 14 12:45:00 2018 -0800 almost done with GettingStarted Docs/sphinx/source/Basics.rst Docs/sphinx/source/Chapter4.rst Docs/sphinx/source/GettingStarted.rst commit 926f5527ab149f98746e3f7fd4267699d7aaf982 Author: Johannes Blaschke Date: Sun Jan 14 12:21:15 2018 -0800 find a good comprimize solution for typesetting small fraction Docs/sphinx/source/GettingStarted.rst commit 8d7b8c59477b81fbe6975bb57b531dff48ddb37f Author: Johannes Blaschke Date: Sun Jan 14 11:53:39 2018 -0800 working on `GettingStarted` section of the sphinx docs. Note: changing LaTeX references to sphinx rst references for cross-referencing different sections Docs/sphinx/source/BuildingAMReX.rst Docs/sphinx/source/Chapter2.rst Docs/sphinx/source/Chapter3.rst Docs/sphinx/source/GettingStarted.rst commit 4d15e2ab0914dbbb80b3321048a2f54674b35942 Author: Johannes Blaschke Date: Sun Jan 14 11:12:32 2018 -0800 added preamble to doc index Docs/sphinx/source/index.rst commit 197f260443822bf8d767c01c1f20c5fe58ef687e Author: Ann Almgren Date: Sun Jan 14 09:52:55 2018 -0800 Replace FillBoundary by EnforcePeriodicity since the interior ghost cells are filled by the loop above Src/EB/AMReX_EBTower.cpp commit 1dd104b45dff38c40515df02d17e689e69a01811 Author: Ann Almgren Date: Sat Jan 13 18:17:58 2018 -0800 No longer have a FillBoundary call for MultiCutFabs Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit 9ac34d61f0f04677f85212b9fe129cbea2012ff0 Author: Johannes Blaschke Date: Sat Jan 13 17:27:07 2018 -0800 ingore sphinx build dir .gitignore commit 92b0151059531572e5b1e8adef7aa1c132464554 Author: Johannes Blaschke Date: Sat Jan 13 17:25:45 2018 -0800 LaTeX Introduction -> rst Docs/sphinx/source/Introduction.rst commit d6ee3882d3be0fda5afcf373a857b07e6f56b519 Merge: a29001481 b8bc70b78 Author: Johannes Blaschke Date: Sat Jan 13 16:49:44 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit a290014812009d568b8182c969c02f9579375d4c Author: Johannes Blaschke Date: Sat Jan 13 16:49:10 2018 -0800 tweak: avoid picking up on temporary files generated when making docs .gitignore commit b8bc70b78235058c7558491c5b3a207452c31ba9 Author: Ann Almgren Date: Sat Jan 13 15:23:46 2018 -0800 Add FillBoundary call when filling flag and other geometric info so that we can correctly fill periodic ghost cells. (Had to add interface for MultiCutFab) Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit 84d9aeae3d835c4a51c133a4f6683b34626acf44 Author: Ann Almgren Date: Sat Jan 13 10:14:27 2018 -0800 Modify parallel copy in the EBTower stuff to include the periodicity flag so it will fill periodic ghost cells correctly. Had to modify an interface for MultiCutFabs. Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit 42a27cde793af88caf2094bb286271cb83ec1203 Merge: 034975f81 08a8fdbf9 Author: WeiqunZhang Date: Fri Jan 12 12:47:40 2018 -0800 Merge pull request #188 from JBlaschke/development Documentation commit 034975f815c699e98fa95157576e5fe968eb74fc Merge: 137fa4748 b6f305f12 Author: Marc Day Date: Fri Jan 12 12:44:27 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 137fa474874fe24a3a7f2f05533f2ee1bca2f23d Author: Marc Day Date: Fri Jan 12 12:44:19 2018 -0800 Fix typ Docs/AMReXUsersGuide/Particle/Particle.tex commit 08a8fdbf911d9fd470b2af25378cfc824417ea3d Merge: b6f305f12 f10e3e5be Author: Johannes Blaschke Date: Fri Jan 12 12:39:31 2018 -0800 Merge branch 'jpb/ug/fix-typos' into development commit b6f305f120223f4a5084a88d5d5a6ca9304e61d3 Author: jbb Date: Fri Jan 12 12:24:07 2018 -0800 added more infomration Tools/Postprocessing/F_Src/faverplot.f90 commit 4707826fa0dac637caf85ca0907193e2b6ee1ece Author: jbb Date: Fri Jan 12 11:59:22 2018 -0800 cleanup Tools/Postprocessing/F_Src/faverplot.f90 commit 6e7ba6c4da6467104f8729db17bd08357361d98d Author: jbb Date: Fri Jan 12 11:54:59 2018 -0800 added build to makefile Tools/Postprocessing/F_Src/GNUmakefile commit 3259d4c62a358a9d13a72b7293de2dd3d7020591 Merge: 5dc222272 9b60bb15a Author: jbb Date: Fri Jan 12 11:52:23 2018 -0800 Merge branch 'development' of https://www.github.com/AMReX-Codes/amrex into development commit 5dc222272032b8a870a730ab6caee9d8a6a93041 Author: jbb Date: Fri Jan 12 11:51:42 2018 -0800 added code to average a collection of plotfiles Tools/Postprocessing/F_Src/faverplot.f90 commit 9b60bb15a0390c31bda3217c9c1d4f31cc4f163f Author: Weiqun Zhang Date: Fri Jan 12 09:28:07 2018 -0800 add some profilers Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 5bcc8136ff3225e67c1b7019981a02b4ea4417bb Author: Weiqun Zhang Date: Fri Jan 12 09:14:51 2018 -0800 nodal projection in 2d rz: turn on correction by default Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit d2e91018011119344171c73239066da6166d3428 Author: Weiqun Zhang Date: Thu Jan 11 17:34:06 2018 -0800 nodal projection: fix rz Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit b729366d7a732223997be249265f6acf6e4bb2db Author: Andrew Myers Date: Thu Jan 11 16:42:04 2018 -0800 Fix bug affecting the particle container when tiling is off but non-zero tile size is set. Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParticleContainerI.H commit b47acfe00a89f9d02098d53a2530c99227520e88 Author: Weiqun Zhang Date: Thu Jan 11 13:42:02 2018 -0800 nodal projection: some support for rz correction Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 288a12bbde859102a3781a39d46a81307e7f2619 Author: Weiqun Zhang Date: Thu Jan 11 12:56:11 2018 -0800 remove some const so that MPI 2 is happy Src/Base/AMReX_ParallelReduce.H commit 75d650a6b05dfb3fb17b81c2bebaa9283fd29080 Author: Weiqun Zhang Date: Thu Jan 11 10:19:54 2018 -0800 fix a bug in my last commit Src/F_Interfaces/Base/AMReX_FPhysBC.cpp commit 0b96d736066ba7015f09678d7b5cf263951749f8 Author: Weiqun Zhang Date: Thu Jan 11 09:02:30 2018 -0800 Fortran module AMReX_fillpatch_module takes a user provided callback function for filling physical boundary conditions. That function used to use 0-based index for component (i.e., the last index). For consistence with 1-based index for component in other Fortran modules, this has been changed to 1-based index for component. CHANGES Src/F_Interfaces/Base/AMReX_FPhysBC.cpp commit d29e7d61d2a51d5c010eb31b3982c627a8b369d8 Merge: 0ca13cead 57ca6eb65 Author: Weiqun Zhang Date: Wed Jan 10 17:37:56 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0ca13cead5cdbc1469f1206cef4d60b1a7b79c36 Author: Weiqun Zhang Date: Wed Jan 10 17:15:26 2018 -0800 nodal projection: no neumann bc doubling for fine sync residual because how SyncRegister works Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 57ca6eb65b6d174f2022797f33c2eb28ee2e7e3d Merge: 8a6b411b0 f1585c8b0 Author: vince Date: Wed Jan 10 16:03:05 2018 -0800 Merge branch 'profvis' into development commit 8a6b411b0892dce3b2bba8ff47d29da6b3d31ff8 Merge: 95686c107 f77b2a006 Author: vince Date: Wed Jan 10 16:02:57 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit f77b2a00677304f716e7ca894aab5b6ca7f15bc7 Author: Weiqun Zhang Date: Wed Jan 10 14:51:04 2018 -0800 nodal projection: add support for cc rhs Src/Base/AMReX_ArrayLim.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit f1585c8b0458509b972c407ef174217f8023188b Author: kngott Date: Wed Jan 10 12:44:12 2018 -0800 Addition of sends plotfile dispatch feature. Also includes filtering if using serial amrvis. Src/Extern/amrdata/AMReX_DataServices.cpp commit 2864f0a87fc11abd0e967688dabb64f6fd47b1b0 Merge: 66ea4b470 95686c107 Author: kngott Date: Wed Jan 10 12:40:59 2018 -0800 Merge branch 'profvis' of https://github.com/AMReX-Codes/amrex into profvis commit 66ea4b470cbd70336ae15d4ff7d5bcb4df967608 Author: kngott Date: Wed Jan 10 12:40:23 2018 -0800 Addition of a BroadcastBool class and appropriate test code. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Tests/C_BaseLib/BcastClasses/BcastClasses.cpp commit 95686c1072dd0a503c2a27350d3198753121bea8 Merge: 0aeeedeb7 384e66188 Author: vince Date: Wed Jan 10 11:57:46 2018 -0800 Merge branch 'development' into profvis commit 0aeeedeb78e0772afce1f96d72bb103a6bc7a97e Author: vince Date: Wed Jan 10 11:56:55 2018 -0800 add time range file for timelines. Src/Extern/amrdata/AMReX_DataServices.cpp commit 384e661882579ce12adb75a7e9c192e6bdcbc900 Author: Weiqun Zhang Date: Tue Jan 9 15:40:18 2018 -0800 fix a bug in 3d nodal projection Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 05c4ad9b8f371be8525a197ff9572fca5efee8ea Merge: 1c4c42d69 ac8541e5c Author: Andrew Myers Date: Tue Jan 9 12:45:37 2018 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1c4c42d698508def4b314248c3d80e77e60b4a2f Author: Andrew Myers Date: Tue Jan 9 12:45:18 2018 -0800 bugfix for neighbor particle container when tiling is turned off. Src/Particle/AMReX_NeighborParticlesI.H commit ac8541e5c8daa6db8c5917694e209afcc2dd3a3e Author: Weiqun Zhang Date: Tue Jan 9 10:03:18 2018 -0800 fix fmg for nodal solver Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit cc3f0cdd6fb20328beaa2923c9afbe8874c20dd3 Author: Weiqun Zhang Date: Tue Jan 9 09:43:54 2018 -0800 nodal projection: finish inflow Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit eea2f8ddfdc472a02d35ed2b417adcefa1c4cce6 Author: Weiqun Zhang Date: Mon Jan 8 15:50:57 2018 -0800 Fortran: add function for testing boxarray box intersection Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 commit cfec65ae9977c251e5f239cbb0d12fa5a79f9b8b Author: Weiqun Zhang Date: Mon Jan 8 11:10:53 2018 -0800 minor optimization Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 7085f5a5f8addd593e345724e018c6fdbf6ed89c Author: Weiqun Zhang Date: Mon Jan 8 11:06:32 2018 -0800 nodal projection: fix sync residual mask Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 1d4d96a7eb16c0d862106293ba6c06d1dc3d6ba3 Author: Weiqun Zhang Date: Mon Jan 8 10:17:30 2018 -0800 nodal projection: when fine boxes touch the symmetry axis Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit dbc7b6709d3ac4fea1d666db7b973052ad8943e2 Author: Weiqun Zhang Date: Mon Jan 8 09:14:55 2018 -0800 no need to apply metric term to coarse mg levels because they get coefficients from average down Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit 579f542416ca5bf9fb0108a97a148fdf9d8c22ec Author: Weiqun Zhang Date: Sat Jan 6 13:28:10 2018 -0800 fix crse/fine residual at Neumann boundary Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 990b47741ff5ee8c8b83f42d462ddc9c55ff8e7f Author: Weiqun Zhang Date: Fri Jan 5 17:46:44 2018 -0800 when fine boxes touch Neumann boundary Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit a26f306da4bc53aa26470ffededbbf6461d7c742 Author: Weiqun Zhang Date: Fri Jan 5 10:46:15 2018 -0800 nodal projection: be explicit on the number of components when calling FillBoundary on velocity because IAMR may pass a MulitFab with more components Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit cfbcf307e9ac6b0beaa49d08f853c0a139f9084f Merge: 77b439af7 cfdaa2b25 Author: vince Date: Thu Jan 4 14:34:34 2018 -0800 merge fix Merge branch 'development' into profvis commit cfdaa2b25919549b91db84c217fbca19bc54c7e2 Author: Weiqun Zhang Date: Wed Jan 3 13:40:30 2018 -0800 nodal projection: start support for inflow Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit bd8090d852d5290c5e66da8a428184e42cfae141 Author: Weiqun Zhang Date: Wed Jan 3 12:47:12 2018 -0800 nodal projection: clean up Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H commit 1dbfcbf052f00ba101231d812626291734f1850a Author: Weiqun Zhang Date: Wed Jan 3 12:44:15 2018 -0800 nodal projection: sync solutions after each iteration Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H commit 4d9f8aa435d96e9aa763661ed483ac44bb486a4a Author: Weiqun Zhang Date: Wed Jan 3 10:45:59 2018 -0800 fix mask in fine sync residual Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit d97a40ef57bf4cf43a72e11ab5ccfa6d7d5a1891 Author: Weiqun Zhang Date: Wed Jan 3 09:25:24 2018 -0800 3d nodal projection: fix a bug in crse/fine residual Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 8f33cda026caef49c8ce2db0d06cbbd1b55bb1e4 Author: Weiqun Zhang Date: Tue Jan 2 14:52:02 2018 -0800 fix cmake Src/LinearSolvers/CMakeLists.txt commit 24f85504ce4d7375f91530361f5240b249b2e939 Author: Weiqun Zhang Date: Tue Jan 2 13:29:13 2018 -0800 nodal projection: fix tiling bug Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 63827b87ba9cee0f27e444e2fe17092cd8072a56 Merge: c44049d7a 34b109d94 Author: Weiqun Zhang Date: Tue Jan 2 09:59:06 2018 -0800 Merge branch 'development' into weiqun/mlmg commit c44049d7ab08a1a5d314b5c585718d6d25e3c995 Author: Weiqun Zhang Date: Tue Jan 2 09:44:07 2018 -0800 nodal projection: fix solvability for bottom solver Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H commit 34b109d947c0795e7030d30cb59ae957b181cf7f Author: Weiqun Zhang Date: Tue Jan 2 08:30:37 2018 -0800 update CHANGES CHANGES commit cb164260feb181bf767a0baaf487b07d19427b3b Author: Weiqun Zhang Date: Sat Dec 30 21:11:59 2017 -0800 3d nodal projection: bug fixes Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 6e5ed1adbd336650686927e6b5c96d0aeae19533 Author: Weiqun Zhang Date: Sat Dec 30 13:29:39 2017 -0800 3d nodal projection: bug fix Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit c366ef70ae8b02ff4e35e69a19ee5093b0a011ea Author: Weiqun Zhang Date: Sat Dec 30 13:13:38 2017 -0800 3d nodal projection: bug fixes Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 746135dea78bd174f865add73b34b3300e93e4b6 Author: Weiqun Zhang Date: Sat Dec 30 12:32:07 2017 -0800 3d nodal projection: bug fix Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 2bf3c7e7a6507f1722871ebdef0d5cbbbb3ca667 Author: Weiqun Zhang Date: Sat Dec 30 12:26:44 2017 -0800 3d nodal projection: bug fix Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit ebbd594cc1d734634018f3366e7f34d60b5d5616 Author: Weiqun Zhang Date: Sat Dec 30 11:49:55 2017 -0800 3d nodal projection: bug fix Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 443609ac72ba8440348f8295ea20fc08c33b82ec Author: Weiqun Zhang Date: Sat Dec 30 11:14:32 2017 -0800 3d nodal projection: bug fixes Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 8e2b38650aba50508aac32fd9a169b70220e0f40 Author: Weiqun Zhang Date: Fri Dec 29 21:38:27 2017 -0800 3d nodal projection: first pass Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 1bb65d15a0181292fd32844a0901f94c1f35e78b Author: Weiqun Zhang Date: Fri Dec 29 18:01:58 2017 -0800 3d nodal projection: fine contribution of residual Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit c563b576e9ccff5a3f8185b3f1e965173c2b78da Author: Weiqun Zhang Date: Fri Dec 29 17:29:07 2017 -0800 nodal projection: refactor crse/fine residual Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 7e79dda389d052e5b1e4f7896921f4d1c8719039 Author: Weiqun Zhang Date: Fri Dec 29 15:44:45 2017 -0800 3d nodal projection: crse/fine divu Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit e77a329cfc3ea0e55da015d3bdc02963bc409642 Author: Weiqun Zhang Date: Fri Dec 29 15:28:15 2017 -0800 nodal projection: refactor fine contribution of divu Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 209b3977de6da219d3944edcf7a376353d26c9a7 Author: Weiqun Zhang Date: Thu Dec 28 19:20:29 2017 -0800 3d nodal projection: fine contribution of divu WIP Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 4f6a74b35ed634df1ccd1c0495e5db363408c472 Author: Weiqun Zhang Date: Tue Dec 26 16:20:28 2017 -0800 3d nodal projetion: add cell-centered rhs and make new u Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 251f05fd77c7c8fcf49f9301b91ff6528264a17e Author: Weiqun Zhang Date: Tue Dec 26 13:21:42 2017 -0800 3d nodal projection: divu Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit a2a408fe916eea98ad0581a68a93eefba8f40425 Author: Weiqun Zhang Date: Tue Dec 26 13:07:49 2017 -0800 3d nodal projection: arithmetic average version of interpolation Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 1dacb179852f34632e48418b876e1b931fb371a7 Author: Weiqun Zhang Date: Tue Dec 26 11:45:29 2017 -0800 3d nodal projection: harmonic average version of interpolation Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 8820cf298b3146005608358cd760f4e9325e90a0 Author: Weiqun Zhang Date: Tue Dec 26 10:20:17 2017 -0800 3d nodal projection: restriction Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 237a0506787633361b80199472979adc346fd9db Author: Weiqun Zhang Date: Mon Dec 25 17:18:37 2017 -0800 nodal projectoin: minor Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 402346397c5bef198226cd49f416b94bda8427eb Author: Weiqun Zhang Date: Mon Dec 25 17:16:15 2017 -0800 3d nodal projectoin: Gauss-Seidel smoother Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 453e517a57356dafd3869d6f53b871a446f3a051 Author: Weiqun Zhang Date: Mon Dec 25 16:49:53 2017 -0800 3d nodal projectoin: Jacobi smoother Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 328d25df9fd6330a903f4d8657fcf60ca9a08edf Author: Weiqun Zhang Date: Mon Dec 25 16:22:27 2017 -0800 3d nodal projectoin: arithmetic average version of A dot x Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 4e69a3debe0e6489581d1e267ba0b0d5751fd32d Author: Weiqun Zhang Date: Mon Dec 25 11:16:19 2017 -0800 3d nodal projection: refactor harmonic average version of A dot x Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit aa15ef8cb116cadd68787542274823667bc71263 Author: Weiqun Zhang Date: Sun Dec 24 16:48:53 2017 -0800 nodal projection: optimization of smoother Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 3f521589a830866942163c02952bf13c6dfa7a68 Author: Weiqun Zhang Date: Sun Dec 24 16:33:22 2017 -0800 nodal projection: optimization of A dot x Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 59ffd97c1c7797fa17e78a20d07d8362a1592066 Author: Weiqun Zhang Date: Sun Dec 24 14:22:01 2017 -0800 3d nodal projection: harmonic average version of A dot x Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit af129d50c8a87f907b0200661d8f5ebc6f44a5bc Author: Weiqun Zhang Date: Sun Dec 24 12:51:04 2017 -0800 3d nodal projection: bc Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit f10e3e5be0740985b5de3ea23947988d3e5382d3 Author: Johannes Blaschke Date: Sat Dec 23 09:50:10 2017 -0800 Typo in description of ghost cells (in MultiFab). This way makes more sense now Docs/AMReXUsersGuide/Basics/Basics.tex commit 1ae085b58172a75cc45595c230eb65be9b5560ed Author: Weiqun Zhang Date: Fri Dec 22 21:32:30 2017 -0800 3d nodal projection: average down coefficients Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 9bba765f433353af63c5b312efd31b1d2c6e891d Author: Weiqun Zhang Date: Fri Dec 22 21:20:40 2017 -0800 3d nodal projection: masks Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 00f9c35f4275e5412decd01814a63ff05964a59c Author: Weiqun Zhang Date: Fri Dec 22 21:00:11 2017 -0800 3d nodal projection: linear interpolation Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 commit 67d8beca72f53c0b6dc2a679b2c7b48133d90c74 Author: Weiqun Zhang Date: Fri Dec 22 18:05:49 2017 -0800 nodal projection: add stub functions so that 1d and 3d can compile Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 commit 0a2d35a8c6ced86a9dfcd85b7ec76453fbaec094 Author: Weiqun Zhang Date: Fri Dec 22 17:34:06 2017 -0800 nodal projection: organization Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H commit 8706ba48173719dfc5582f960dee90d3cc40eb15 Author: Weiqun Zhang Date: Fri Dec 22 17:03:54 2017 -0800 nodal projection: clean up Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit ec03816cb707643fcc0db0c83e2d58d297116e63 Author: Weiqun Zhang Date: Fri Dec 22 17:01:11 2017 -0800 nodal projection: cleanup Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 5dc1592c353270bee85b46d960dbb79710d25954 Author: Weiqun Zhang Date: Fri Dec 22 16:44:42 2017 -0800 nodal projection: add nodal mask in addition to cell mask Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit a4c11052ade24f7b5606b07327580213cf1657c1 Author: Weiqun Zhang Date: Fri Dec 22 16:17:07 2017 -0800 nodal projection: use parameter instead of hardwired number for dirichlet mask Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 24f40399d0869d18e58ba53afe76198401fcc22e Author: Weiqun Zhang Date: Fri Dec 22 15:40:16 2017 -0800 nodal projection: clean up overlap mask Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 912b8d18eabedddaca4c6ca3752ba62b9cf9cb7f Author: Weiqun Zhang Date: Fri Dec 22 15:36:59 2017 -0800 nodal projection: clean up weight Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 80bc4f44588a751e903b7c6ab5db35c144188620 Merge: 6fccf245d 23a04c4a6 Author: Tan Nguyen Date: Fri Dec 22 13:37:52 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6fccf245d458c85b6d4d499cdbf9993b0af1f0fc Author: Tan Nguyen Date: Fri Dec 22 13:37:39 2017 -0800 transform recursive timesteps into iterative tasks Src/AmrTask/AMFIter/AMReX_AmrTask.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/graph/AMReX_AbstractTask.H Src/Base/AMReX_FabArray.H commit 268c41942e5f2333795e5f58f1117d5aec73099b Author: Max Katz Date: Fri Dec 22 14:54:02 2017 -0500 Remove -lcudart for OpenACC Tools/GNUMake/comps/pgi.mak commit 40afb0966dc3e9cc63b93027b28eb4058a3da0fe Author: Max Katz Date: Fri Dec 22 14:45:51 2017 -0500 Add .ACC to exe name when USE_ACC=TRUE Tools/GNUMake/Make.defs commit d4910feb3c8c4f6062861ba32f24160cc0055a1c Author: Andrew Myers Date: Fri Dec 22 10:53:50 2017 -0800 Some fixes to the dot, sum, and norm routines of BaseFab. (#184) These routines were not correctly accessing device data on the return value, and were also inadvertently having each thread zero out the stored sum. Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_nd.F90 commit 7025414e3db9da566c1da8d06915fef0e4a4fdda Author: Weiqun Zhang Date: Thu Dec 21 16:21:36 2017 -0800 f90 nodal solver: the initial residual is now computed as composite residual Src/LinearSolvers/F_MG/ml_nd.f90 commit d7035b2ef5b536a8a3f6dc629bfed5ee579f5a5d Author: Weiqun Zhang Date: Thu Dec 21 15:55:32 2017 -0800 fix up residual mask Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 23a04c4a6aa70f2f818341d6adedc369726b66a6 Merge: e0c06c652 1c6826dbe Author: dtgraves Date: Thu Dec 21 15:21:42 2017 -0800 Merge pull request #185 from AMReX-Codes/dtg_branch moving document and bug fixes to dev branch. commit 1c6826dbe66e9710adbcbda46d6fe3ff831c0d12 Author: dtgraves Date: Thu Dec 21 15:20:21 2017 -0800 added section to tutorial document explaining derivation of time interpolation formulae Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs commit 4889fac9b1b83e46c6774ae7e6e97a7d3d190b16 Author: dtgraves Date: Thu Dec 21 15:19:52 2017 -0800 bug fix and took out unused functions Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 088769298e25ae910616502cd620fd8902d78ff7 Author: Weiqun Zhang Date: Thu Dec 21 15:19:13 2017 -0800 fix a bug Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 77b439af7fd12105e4abffafebb3527ff5be2afe Author: vince Date: Thu Dec 21 15:06:48 2017 -0800 precreate update for nyx support. Src/Amr/AMReX_Amr.cpp commit 55d8b641a6b5242c69b654c099689b64268e8e30 Merge: 51d2259a1 34c398009 Author: vince Date: Thu Dec 21 15:05:22 2017 -0800 merge fix. commit 51064aff8018bdd0d0c00a20b1e0e7b9cff76191 Author: Weiqun Zhang Date: Thu Dec 21 13:46:41 2017 -0800 use the restricted rhs for reflux Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 3d5953981db6ab00cc6b49ce6681f8710cc6a429 Author: Weiqun Zhang Date: Thu Dec 21 12:39:59 2017 -0800 nodal project: full weight restriction of rhs Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit e0c06c6520de863662d04c4297116ee73847d243 Author: Andrew Myers Date: Thu Dec 21 12:16:26 2017 -0800 patch fcompare to not choke on plotfiles that only have particle data. Tools/Postprocessing/F_Src/fcompare.f90 commit 978b6b142746ca3b3946087da8eb05a500d21e5c Author: Andrew Myers Date: Thu Dec 21 12:15:30 2017 -0800 initialize these pointers to Null() Src/F_BaseLib/plotfile.f90 commit bae3d32097517bf73f3eb56302d4e0610da36d71 Author: Max Katz Date: Wed Dec 20 23:32:40 2017 -0500 Do not compile in the old filcc when using CUDA Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_filcc_mod.F90 Src/Base/Make.package commit b28c056981e60cd99b5bb84d8a694a396dd0c558 Author: Andrew Myers Date: Wed Dec 20 17:55:50 2017 -0800 Removing the particle stuff from the GPU branch (will add again on a separate branch) (#158) Src/Particle/AMReX_CudaManagedAllocator.H Src/Particle/AMReX_Particles.H Src/Particle/Make.package Tests/Particles/CUDADeposition/GNUmakefile Tests/Particles/CUDADeposition/Make.package Tests/Particles/CUDADeposition/MyParticleContainer.H Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/cuda_deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_F.H Tests/Particles/CUDADeposition/inputs Tests/Particles/CUDADeposition/main.cpp Tests/Particles/CUDADeposition/solve_for_accel.cpp Tests/Particles/CUDADeposition/solve_with_f90.cpp Tests/Particles/ManagedCUDADeposition/GNUmakefile Tests/Particles/ManagedCUDADeposition/Make.package Tests/Particles/ManagedCUDADeposition/MyParticleContainer.H Tests/Particles/ManagedCUDADeposition/MyParticleContainer.cpp Tests/Particles/ManagedCUDADeposition/cuda_deposit_3d.f90 Tests/Particles/ManagedCUDADeposition/deposit_3d.f90 Tests/Particles/ManagedCUDADeposition/deposit_F.H Tests/Particles/ManagedCUDADeposition/inputs Tests/Particles/ManagedCUDADeposition/main.cpp Tests/Particles/ManagedCUDADeposition/solve_for_accel.cpp Tests/Particles/ManagedCUDADeposition/solve_with_f90.cpp commit 34c398009473552d2db84976fe89dc7e9029d464 Merge: 237275ec3 d1037c359 Author: WeiqunZhang Date: Wed Dec 20 17:07:53 2017 -0800 Merge pull request #183 from AMReX-Codes/marc/allow_strict_mode Marc/allow strict mode commit 0e4565098b029b4db6d92c1caf4d529602708f21 Author: Weiqun Zhang Date: Wed Dec 20 16:58:05 2017 -0800 fix weight Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 717a79e97fed3305a650c2812c75e70c6a15d065 Author: Max Katz Date: Wed Dec 20 19:10:19 2017 -0500 Make NVML support be opt-in Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Tools/GNUMake/Make.defs commit 2f8a657de7ba3799c3e5e296793bd2fca962989e Author: Weiqun Zhang Date: Wed Dec 20 15:38:46 2017 -0800 average down nodal rhs and solution Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 28a0f7eebf8b629aaf038b4e1f95267059d72920 Author: dtgraves Date: Wed Dec 20 15:14:57 2017 -0800 finished the parts ScalarAdvection Tutorial that anyone ought to care about. I will also add an appendix explaining where the formulae come from. Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex commit d1c55728c589bba1cff1d88dc01fa9cd35a5d9d3 Author: Weiqun Zhang Date: Wed Dec 20 14:42:53 2017 -0800 fix assertion Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 32d0103b3afb8b9cc99895faeaa545f545f02e38 Author: Weiqun Zhang Date: Wed Dec 20 14:36:56 2017 -0800 minor optimization Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit d1037c35972e8006922a655b775a0ccab3f07683 Author: Marc Day Date: Wed Dec 20 14:23:46 2017 -0800 Minor changes to satisfy compilation under AMREX_STRICT_MODE Src/Amr/AMReX_Amr.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_YAFluxRegister.cpp Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_MultiCutFab.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.cpp commit 4f5cf41f3d6727a50e3a8a03098dc469a053f990 Author: Weiqun Zhang Date: Wed Dec 20 14:09:13 2017 -0800 average down of solution is only needed for cell-centered solve Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit e57b82c0123bc385484c1cfbd1b52ec26cc95c24 Author: Weiqun Zhang Date: Wed Dec 20 14:03:19 2017 -0800 nodal interpolation of correction between amr levels Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_F.H commit 237275ec3bc3b943e1bec6f00fa315a1da575da2 Author: Andrew Myers Date: Wed Dec 20 13:54:52 2017 -0800 allow fcompare to work with plotfiles that only have particle data (for the regression testing suite) Src/F_BaseLib/plotfile.f90 commit 0abff787e6a0d1f53004a78140021436c0cd927e Author: Weiqun Zhang Date: Wed Dec 20 11:10:37 2017 -0800 use the correct rhs Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 881a2d3b70e6ec2ea8dc6c49e8b89e6f3417c713 Author: dtgraves Date: Tue Dec 19 18:29:05 2017 -0800 added a bunch to document for this tutorial Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 148452aa45902d1f0c646083dd4209793715bcf5 Author: Weiqun Zhang Date: Tue Dec 19 17:27:23 2017 -0800 restriction of residual Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 1812ba5d2d6fba6c5968187d09bdb5c9e9b4d94e Author: Weiqun Zhang Date: Tue Dec 19 12:44:21 2017 -0800 pass fine residual to reflux too Src/Base/AMReX_MultiFabUtil.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit d48c43aa3c29fdbb738131f0159f291344cdd7d8 Author: Weiqun Zhang Date: Tue Dec 19 12:03:03 2017 -0800 make average_down work for nodal too Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 66ec1882eb2d1e32cc34e2c2521c720e5da78486 Author: Weiqun Zhang Date: Tue Dec 19 12:01:22 2017 -0800 add MultiFab::is_cell_centered function Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 39709299a011e95fff6fa29446ef57f23ce60bb8 Author: Weiqun Zhang Date: Tue Dec 19 10:25:05 2017 -0800 fine contribution of A dot x Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 6501bdb17e6328fd6d647fde9780cb0fd0756fab Author: Weiqun Zhang Date: Mon Dec 18 17:41:28 2017 -0800 WIP: fine contribution of A dot x Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit cf7aeac42addf1ec328ae624104ad5f4df88a3ac Author: Andrew Myers Date: Mon Dec 18 17:18:05 2017 -0800 pass the pld by value instead of by reference. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 429d75269c7de698d591ef987db54ca62c73eec1 Author: Andrew Myers Date: Mon Dec 18 17:12:33 2017 -0800 allow caching of the particle location between calls to Reset() Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit c74e78a40a7821bae46e77a9eab7592610e90b3f Author: Weiqun Zhang Date: Mon Dec 18 15:24:02 2017 -0800 rework the weight Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit c7b320f766fb3656be65220a48ae929a0cdccbf2 Author: Andrew Myers Date: Mon Dec 18 12:39:36 2017 -0800 fix bad merge. Src/Particle/AMReX_ParticleContainerI.H commit e391b4ac11c890135b63cf12f288eeefd46b82c1 Merge: b8a52a719 693b96a1c Author: Andrew Myers Date: Mon Dec 18 12:36:58 2017 -0800 merging. commit b8a52a719d48d19bfaa9acb9e2519c7fc11e1d40 Author: Andrew Myers Date: Mon Dec 18 12:34:35 2017 -0800 don't profile this funtion - it gets called too many times and skews results. Src/Particle/AMReX_ParticleContainerI.H commit 54336b9aea3ab710c4139deda023cb350494c033 Author: Weiqun Zhang Date: Sat Dec 16 14:56:19 2017 -0800 nodal projection: fix fine contribution Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 11f679209e4152c5c7e37e2fdaffb53e9c6227b4 Author: Weiqun Zhang Date: Fri Dec 15 14:53:59 2017 -0800 add FabArray::ParallelAdd; coarse contribution in nodal projection Src/Base/AMReX_FabArray.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 51d2259a109e803bf5958323afd969812ec4679d Author: kngott Date: Fri Dec 15 17:35:30 2017 -0800 BroadcastString and BroadcastStringArray functions, plus corresponding test. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Tests/C_BaseLib/BcastClasses/BcastClasses.cpp commit 7e78747235652faa6efdf7c282a67406ce3bd294 Author: Weiqun Zhang Date: Fri Dec 15 13:10:23 2017 -0800 WIP: compute fine contribution Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit dd77972ddc09afcf37a199e0ac6481180b3231fc Author: kngott Date: Fri Dec 15 12:05:18 2017 -0800 Improved RemovePiece fix. Src/Extern/ProfParser/AMReX_BLProfStats.cpp commit 5f55dd0d909009c2d0fb71c99b900e815efa83d0 Author: kngott Date: Fri Dec 15 12:02:02 2017 -0800 BLProfStats::RemovePiece now successfully removes equal TimeRanges. Src/Extern/ProfParser/AMReX_BLProfStats.cpp commit 830698efa635c22e8ba33e849c5d11aef711dd32 Merge: 364618350 693b96a1c Author: Klaus Weide Date: Thu Dec 14 19:24:08 2017 -0600 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 693b96a1c88aed7a6c8f612737078ef0fe5b62e4 Author: kngott Date: Thu Dec 14 16:52:25 2017 -0800 Additional profiler flags. Src/Amr/AMReX_AmrLevel.cpp Src/GeometryShop/AMReX_EBISLevel.cpp commit e8d42df90bc39b64047f3b54a6481d9edf57ae8c Author: Weiqun Zhang Date: Thu Dec 14 14:47:32 2017 -0800 add rhcc Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 305c300f78beb88dd97b44bb28fa96adab4c6735 Merge: f1d9ec9b1 ae5fe2c0a Author: WeiqunZhang Date: Thu Dec 14 13:02:52 2017 -0800 Merge pull request #178 from bcfriesen/update_CVODE_build CVODE, Tools: use Cray version of SUNDIALS if module is loaded commit f1d9ec9b1061cdee9807ef8098f89010aab3cdb7 Merge: 8cb05991c 93599c8a8 Author: WeiqunZhang Date: Thu Dec 14 13:01:58 2017 -0800 Merge pull request #179 from AMReX-Codes/fextract Enable coarse and fine level selection in fextract commit 8cb05991c6ed9104b6a84e18f250ab7d8afc46b5 Author: Andy Nonaka Date: Thu Dec 14 12:43:03 2017 -0800 note about PhysBCFunct class Docs/AMReXUsersGuide/Boundary/Boundary.tex Src/Base/AMReX_PhysBCFunct.H commit 6263e9102d518055f7001b49ac65dd23b9f38786 Author: Weiqun Zhang Date: Wed Dec 13 21:23:48 2017 -0800 save the number of iterations Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit dcc515315f9d0fa257163e2b47c7e60e1f523ed4 Merge: 0e49c7a6f f378122a1 Author: vince Date: Wed Dec 13 18:13:46 2017 -0800 merge fixes. commit f378122a1315ca94b04fdde2fc25e7e153076439 Author: vince Date: Wed Dec 13 17:56:49 2017 -0800 added option to set size of DATA_nnnnn digits. Src/Particle/AMReX_ParticleContainerI.H commit 3ab04288ec6ceb0f21a5735186e448b7500e0649 Author: kngott Date: Wed Dec 13 17:40:42 2017 -0800 Timeline in GUI now runs in parallel. Src/Extern/amrdata/AMReX_DataServices.cpp commit 0e49c7a6fcd333f9a5862b6361f8ec68ce595672 Merge: 7b6fae42f 1a95fbee6 Author: vince Date: Wed Dec 13 16:29:14 2017 -0800 Merge branch 'development' into partio commit 1a95fbee644b661c44799e04771c69690bfc2435 Merge: 1b634f8a6 6645eaa04 Author: dtgraves Date: Wed Dec 13 14:52:46 2017 -0800 Merge pull request #180 from AMReX-Codes/dtg_branch merging in some small bug fixes and other sundries commit ae5fe2c0ab768147c2befe53f877ba4029841a08 Author: Brian Friesen Date: Wed Dec 13 14:10:38 2017 -0800 CVODE: Update user guide with instructions for linking SUNDIALS on Crays Docs/AMReXUsersGuide/CVODE/CVODE.tex commit 7335c588b53c81d80c79126fca98d567f3d9e062 Author: Weiqun Zhang Date: Wed Dec 13 14:05:10 2017 -0800 compute fine sync residual Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 6645eaa04589bc6406cea6bf1fa3e0d3448d4234 Author: dtgraves Date: Wed Dec 13 14:01:07 2017 -0800 scalar advection tests passing showing correct covergence 2d/3d, with and without limiting. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_mpi_driver.py commit 93599c8a8ce9e7b8e209062696dfc1131cef6ce3 Author: Max Katz Date: Wed Dec 13 16:44:06 2017 -0500 Enable coarse and fine level selection in fextract fextract previously would extract data on all levels by default. This adds options to select a different set of levels; for example, a use case might be to only see the data on the finest level so you can examine where the refined regions are. The new options are -c/--coarse_level and -f/--fine_level. Tools/Postprocessing/F_Src/fextract.f90 commit b2903a66401c59674581c08db35398a02ff00409 Author: Brian Friesen Date: Wed Dec 13 12:52:19 2017 -0800 CVODE, Tools: use Cray version of SUNDIALS if module is loaded Cray includes SUNDIALS in the "cray-tpsl" module. Use that if the module is loaded. If the module is not loaded, then look for the home-cooked version. Tools/GNUMake/packages/Make.cvode commit 7b6fae42f1f8ec545583ea53adbfe0dc6f8be28d Merge: ca6ffb031 1b634f8a6 Author: vince Date: Wed Dec 13 12:22:36 2017 -0800 Merge branch 'development' into partio commit 846da4a819f0c34db8c6d8b04f4d62c2b64452d7 Merge: de389f0d5 1b634f8a6 Author: vince Date: Wed Dec 13 12:20:29 2017 -0800 merge fixes. commit 4599726a50424caf3e2982be2e0492d3bdef1d9b Author: Weiqun Zhang Date: Wed Dec 13 12:12:51 2017 -0800 do not touch dirichlet boundary cells in applybc Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 189afedbb33419fcfdbadd987a270b6f8a0c5b51 Author: Weiqun Zhang Date: Wed Dec 13 10:55:48 2017 -0800 build dirichlet mask if it hasn't been built when compRHS is called Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 9ddfecf972c60114d22df706a7bed74daf31a64e Author: Weiqun Zhang Date: Tue Dec 12 17:12:47 2017 -0800 WIP: add nodal mask for inhomogeneous Dirichlet Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 01e15dc6e4398d92f37c638d013f1aada5a78a6a Author: dtgraves Date: Tue Dec 12 15:48:56 2017 -0800 added mpi-driven convergence utility Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_mpi_driver.py commit eef06337d78f4e2094f3c798fbeeca2606ea9c66 Author: dtgraves Date: Tue Dec 12 15:14:11 2017 -0800 found declaration bug that was causing code to act differently with chopped-up boxes Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 1b634f8a6496476af3a5a0499fd8d708a6286f6a Author: Weiqun Zhang Date: Tue Dec 12 15:10:57 2017 -0800 fix FillCoarsePatch as well Src/Amr/AMReX_AmrLevel.cpp commit 366045710fc69d0bba8aff4d23bf059a862d1cdb Merge: 92cc140fa 8ed5f4c7e Author: Weiqun Zhang Date: Tue Dec 12 15:07:12 2017 -0800 Merge branch 'development' into weiqun/mlmg commit 8ed5f4c7e2a9b8775ceafc9f9a10530915b384b8 Author: Weiqun Zhang Date: Tue Dec 12 15:02:44 2017 -0800 fix the old fillpath too Src/Amr/AMReX_AmrLevel.cpp commit bd835e997c15ba7ba507e87c20fe9a497ae244c6 Author: Weiqun Zhang Date: Tue Dec 12 14:53:57 2017 -0800 need to set ghost cells for temp mfs in FillPatch too Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArray.H commit 92cc140fa5bc2229d9ee15981f4f94455b2d44cc Merge: 9bdfb5137 266392d3c Author: Weiqun Zhang Date: Tue Dec 12 14:10:45 2017 -0800 Merge branch 'development' into weiqun/mlmg commit 266392d3c6aacfe1dc9b6a690f179c115098c9a1 Author: Weiqun Zhang Date: Tue Dec 12 13:20:19 2017 -0800 FillPatch: initialize the initial data outside physical domain to quiet nan otherwise in some corner cases floating point exception could happen Src/Amr/AMReX_AmrLevel.cpp commit e187cb0a48ae54a943c4953880788e68c2abbd64 Author: Marc Day Date: Tue Dec 12 12:44:16 2017 -0800 Quiet the compiler in DEBUG mode by avoiding shadowed and unused variables. Src/F_BaseLib/box_f.f90 Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp commit fcbed08bd56d94110427bf09edbd6c0d7825ba92 Merge: d06e8aa0b b73218d6c Author: Marc Day Date: Tue Dec 12 11:12:26 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b73218d6c302c381dce577e14505a530ccfc0c75 Merge: ea9c7dd50 e51bff66f Author: atmyers Date: Tue Dec 12 10:41:24 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ea9c7dd5098e6cf65fbc183717acc698d7f9b6e8 Author: atmyers Date: Tue Dec 12 10:41:07 2017 -0800 use the VectorIO stuff in particel checkpoint / restart (again) Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit e51bff66fa9f85ea015e7679dabf2ece81641713 Author: Michele Rosso Date: Tue Dec 12 10:25:06 2017 -0800 CMake: add new sources Src/GeometryShop/CMakeLists.txt commit 05d4d803e0e7df66119b0e776f6492fafc2efce6 Author: atmyers Date: Tue Dec 12 09:37:33 2017 -0800 add functions to write Vectors of float data when Real is double precision and vice versa. Src/Base/AMReX_FabConv.H Src/Base/AMReX_FabConv.cpp Src/Base/AMReX_VectorIO.H Src/Base/AMReX_VectorIO.cpp Tests/Particles/TypeDescriptor/main.cpp commit 9bdfb5137a9245a5bc2feb9710a8e468927106bb Author: Weiqun Zhang Date: Tue Dec 12 09:32:54 2017 -0800 nodal projection: make sync residual consistent with F90 solver Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit b76bbd419fdce8488cd1ff0c95d04de5d71ec7e6 Author: dtgraves Date: Mon Dec 11 16:17:45 2017 -0800 4th order with limiting has good convergence in the simplest case. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/debug.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 commit 41b53d0e6169d622f0afaf75e917fa5382d48a95 Author: Michele Rosso Date: Mon Dec 11 16:12:11 2017 -0800 Remove assertion from norm1() Src/Base/AMReX_MultiFab.cpp commit ca6ffb0318baacca60f73116b740ed932d11787c Author: vince Date: Mon Dec 11 13:52:20 2017 -0800 remove diagnostics. Src/Amr/AMReX_AmrLevel.cpp Src/Particle/AMReX_ParticleContainerI.H commit e4bc5e4128330f8292bc6ba287a508324b38dc99 Author: Weiqun Zhang Date: Mon Dec 11 13:34:56 2017 -0800 nodal projection: coarse sync residual Src/Base/AMReX_MultiFab.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 318ee2f5f18526b51de14a7dd186ed8f548a6310 Author: Weiqun Zhang Date: Mon Dec 11 09:04:26 2017 -0800 mlmg: assertions for periodic boundary Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 6d6e411032190c24b347186cd0eece6184b0dba0 Author: Weiqun Zhang Date: Sun Dec 10 21:06:47 2017 -0800 fix a compiler warning Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit ab6b9fded10ebf3abb342f4e083d9f219778d57f Author: Weiqun Zhang Date: Sun Dec 10 21:03:04 2017 -0800 nodal projection: use arithmetic average Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H commit d8f898ed3e0bc10890caf5c17cc8187f1fe280b4 Author: Weiqun Zhang Date: Sun Dec 10 20:48:24 2017 -0800 nodal projection: fix coefficent at periodic boundary Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 1f87c2702430b7cf1fc1ffb706fd58093e4f7e9e Author: Weiqun Zhang Date: Sun Dec 10 11:35:21 2017 -0800 add MLNodeLinOp::nodalSync function Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 1594d00a80b60726f4580b2884cbfe6e9a404a04 Author: Weiqun Zhang Date: Sat Dec 9 22:20:17 2017 -0800 nodal projection: add arithemic average in addition to harmonic average Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit c899b1a5a0382cb8285286312c68b75249f465af Author: Weiqun Zhang Date: Fri Dec 8 23:11:57 2017 -0800 nodal projection: fix periodici boundary Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 58c2528e556ecff269a77e1b72567ee9a132b207 Author: Weiqun Zhang Date: Fri Dec 8 17:52:05 2017 -0800 For Gauss Seidel, we need to sync Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H commit 27ed37053aef7a5282d02b5f112d1b6e029bf3a9 Author: Weiqun Zhang Date: Fri Dec 8 15:57:03 2017 -0800 mlmg: print more information Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 18b1707d8bbc4b3e44c9ef0a1cd2f59305f145e7 Author: Weiqun Zhang Date: Fri Dec 8 15:33:34 2017 -0800 nodal projection: make new u Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit a75442ecde356e763268d0d81804b3c84266a2b7 Merge: 72eab6ad9 18550f6f5 Author: atmyers Date: Fri Dec 8 14:10:16 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 72eab6ad959eee87ae2cef5b3bd90480afa2b13e Author: atmyers Date: Fri Dec 8 14:09:25 2017 -0800 have AmrMesh abort if it gets a problem domain with zero volume. Src/AmrCore/AMReX_AmrMesh.cpp commit fd52ecf8d108647e2813dd82badc7133ae7bbe5b Author: atmyers Date: Fri Dec 8 14:04:38 2017 -0800 add function returning the volume of the RealBox. Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit 679e801d07f9ba2f692782156fddbb86938f0bcc Author: atmyers Date: Fri Dec 8 14:00:22 2017 -0800 make the RealBox documentation consistent with its actual behavior. Src/Base/AMReX_RealBox.H commit 18550f6f55d9e208ab04c27043660da975515f5c Merge: a80f30792 18e5d9f26 Author: dtgraves Date: Fri Dec 8 12:45:19 2017 -0800 Merge pull request #177 from AMReX-Codes/dtg_branch merging in corrected rk time interpolators and geometry generation examples commit 18e5d9f268a38029a056abc3e0ed17a11b01cbda Author: dtgraves Date: Fri Dec 8 12:43:25 2017 -0800 fixed the same bugs in the pwm versions, even though they are not called. Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 2c3f3106823be3a75c9d2b876cb2e295f607be0e Author: vince Date: Fri Dec 8 12:40:56 2017 -0800 more precreate directory support. Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp commit 5daab1f75f0126c0a533071651c411e4c3bd68c2 Author: dtgraves Date: Fri Dec 8 12:35:49 2017 -0800 fixed bug in time interpolation (you have to be very careful which dt you use). both rk3 and rk4 get good convergence numbers. and there was much rejoicing. Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit de389f0d591f59a8e05f2341381c4f479bf7722f Author: kngott Date: Fri Dec 8 12:10:22 2017 -0800 RunTimeline error with va when using multiple procs in GUI. Src/Extern/ProfParser/AMReX_BLProfStats.H Src/Extern/ProfParser/AMReX_BLProfStats.cpp Src/Extern/ProfParser/AMReX_CommProfStats.H Src/Extern/ProfParser/AMReX_CommProfStats.cpp Src/Extern/ProfParser/AMReX_ProfParserBatch.cpp Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp commit 4cc636d9fc89bb4ee658fb36ce184ddb94a38808 Author: Weiqun Zhang Date: Fri Dec 8 11:08:41 2017 -0800 nodal projection: fixed jacobi and added gauss seidel Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit d06e8aa0ba7714181f9e1424403cbec57fb617bb Merge: a45cfe726 a80f30792 Author: Marc Day Date: Fri Dec 8 11:01:21 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a80f3079246718c24f14bd348c195f3d2ea33c4b Merge: 435aa15cf 22708ac12 Author: Marc Day Date: Fri Dec 8 10:26:55 2017 -0800 Merge branch 'marc/geom_surface' into development This commit adds a capability to write out the intersection points between the fine mesh and the embedded boundary geometry, and is triggered if the ParmParse option ebis.eb_surface_filename is set. By default it is not set. Since a surface is not a standard AMReX data structure (yet), a custom IO format was created for it. The surface is created and written in parallel, and written in a binary format. The amrex folder, Tools/EBSurfaceTools, contains some code to interact with this format. In particular, the files can be read and the surface merged to a single surface on a single processor, and written to a simple text file of node and element data (polylines in 2D, triangles in 3D). A Python script is provided there to convert the output to a VTK format that can be read natively in Paraview. The format of the surface files will be documented elsewhere, but can be used, e.g., to store isosurfaces/contours. It may also become useful for interacting with computed/fixed boundary data at the eb. commit 22708ac12ab85c42674a53f353f73af41576536b Author: Marc Day Date: Thu Dec 7 19:48:30 2017 -0800 Make compiler happier. Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeometryService.cpp Tools/EBSurfaceTools/ConvertEBSurface.cpp commit 7109568e2485909bf5499baf41120e7d9f5d88bc Author: Marc Day Date: Thu Dec 7 19:38:09 2017 -0800 Make 2D version of eb surface stuff compatible with the 3D approach. Src/GeometryShop/AMReX_EBISLevel.cpp Tools/EBSurfaceTools/ConvertEBSurface.cpp commit 29f61b95db24d02b8d5724a0d7a818066ec12dd8 Author: Marc Day Date: Thu Dec 7 18:11:49 2017 -0800 whoops! Gotta make the dir before writing to it. Src/GeometryShop/AMReX_EBISLevel.cpp commit f21564bd627c4b0ee8bcc2a782a8a1b700cff97b Author: Marc Day Date: Thu Dec 7 18:00:55 2017 -0800 Move some code around. Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeomIntersectUtils.H Src/GeometryShop/AMReX_GeomIntersectUtils.cpp commit b44b178b3625b53b1f52a84b5bde53fb6df0e387 Author: Marc Day Date: Thu Dec 7 17:40:20 2017 -0800 Make 3D output write to a folder+header and use binary IO. Add EBSurfaceTools folder with code to read surface out, and reduce the surface across boxes and write a simple ASCII text file. Include a python script to convert this to VTK-compatible format for viewing in Paraview. Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeomIntersectUtils.H Src/GeometryShop/AMReX_GeomIntersectUtils.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Tools/EBSurfaceTools/ConvertEBSurface.cpp Tools/EBSurfaceTools/GNUmakefile Tools/EBSurfaceTools/isoToVTK.py commit 5287a3451e837f653e27f8baed5bd8d6658a974c Merge: deba70e85 435aa15cf Author: vince Date: Thu Dec 7 17:12:55 2017 -0800 merge fix. commit 9af39fde1893f2b6f909523cb079cb922dc843b0 Author: Weiqun Zhang Date: Thu Dec 7 16:31:23 2017 -0800 nodal projection: clean up Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 796b449f7567bc75890ac4a26d57efe255ce9498 Author: Weiqun Zhang Date: Thu Dec 7 15:55:12 2017 -0800 nodal projection: zero out dirichlet boundary Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit deba70e855721ef8eb4a8b9fa63188483bb27ade Author: vince Date: Thu Dec 7 15:50:03 2017 -0800 fix warning. Src/Base/AMReX_FACopyDescriptor.H commit 7b01366fae63148b890b2b3da55ffe9d1364f885 Author: vince Date: Thu Dec 7 15:14:22 2017 -0800 prepost updates for plotfiles. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 141b8c85645d2836fc0ae39930b102115465aa0f Author: vince Date: Thu Dec 7 15:11:57 2017 -0800 prepost updates for plotfiles. Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp commit 81d2c3f310e83023bc10f80df94f3741ac3a3474 Author: Weiqun Zhang Date: Thu Dec 7 14:23:23 2017 -0800 nodal projection: fix a bug Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 commit 44db9344e8c7cc2d22126fabdccb5c9d4c85b874 Author: Weiqun Zhang Date: Thu Dec 7 13:41:13 2017 -0800 nodal projection: interpolation Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 537ff93d3a823beeeaccd8deaa0c23fdf73ab17f Author: dtgraves Date: Thu Dec 7 12:49:51 2017 -0800 more examples of geometries Tutorials/EB/GeometryGeneration/exec/GNUmakefile Tutorials/EB/GeometryGeneration/exec/parabolaWithSphere.cpp Tutorials/EB/GeometryGeneration/exec/parabolaWithSphere.inputs Tutorials/EB/GeometryGeneration/exec/surfaceOfRevolution.cpp Tutorials/EB/GeometryGeneration/exec/surfaceOfRevolution.inputs commit 1cedebd14bba8c8fb5247aada1e10e0a354464b5 Author: kngott Date: Thu Dec 7 12:22:29 2017 -0800 Addition of regions data checks to -check batch function. Src/Extern/ProfParser/AMReX_RegionsProfStats.H Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp Src/Extern/amrdata/AMReX_DataServices.cpp commit 65dcdb5465c7a68e45fe893e027b57a9b80d22c5 Author: Weiqun Zhang Date: Thu Dec 7 12:17:10 2017 -0800 add virtual MLLinOp::interpolation Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit d89c040692a6fa528f8b989f55f278a98864bcd4 Author: Weiqun Zhang Date: Thu Dec 7 11:20:17 2017 -0800 nodal projection: add nodal owner mask Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit c1079768bcc8fe7ea222134b0b01aaa4d2b47cb6 Merge: 25fdf08a2 435aa15cf Author: Marc Day Date: Thu Dec 7 11:17:25 2017 -0800 Merge remote-tracking branch 'origin/development' into marc/geom_surface commit 25fdf08a27baff443920153046a3d6cecc0a66bc Merge: 820a203a1 9b555da1c Author: Marc Day Date: Thu Dec 7 11:15:54 2017 -0800 Merge remote-tracking branch 'origin/development' into marc/geom_surface commit 748b57a3a71085da89b7f8eda96f51b2cb8e6335 Author: Weiqun Zhang Date: Thu Dec 7 11:15:41 2017 -0800 add MultiFab::Dot for nodal with mask Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 0f534749cc7c21d99268316f7ad19068c88718de Author: Weiqun Zhang Date: Thu Dec 7 10:17:54 2017 -0800 nodal projection: restriction Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit e0d1a4fc817e95bb1679484a506b59c34ffb876d Author: Weiqun Zhang Date: Thu Dec 7 10:16:34 2017 -0800 add free function coarsen for BoxArray Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit 435aa15cf5c1a311aeb5bba3f52e6cd68385d532 Author: Weiqun Zhang Date: Thu Dec 7 08:45:54 2017 -0800 update CHANGES CHANGES commit d6736bcebc83b8b74e3a4a87ded02a0e295fafcb Author: Andrew Myers Date: Thu Dec 7 06:33:17 2017 -0800 update LoadBalance tutorial Tutorials/Particles/LoadBalance/main.cpp commit fe5cc8b62bc5f3e90ba054275ac4d6b228d84c5f Author: Andrew Myers Date: Thu Dec 7 06:32:45 2017 -0800 add lo-dim versions of these functions too Src/Particle/AMReX_KDTree_1d.F90 Src/Particle/AMReX_KDTree_2d.F90 commit a9bab94350ef2675fbf1f6d30929319b9e3d067b Author: Andrew Myers Date: Thu Dec 7 06:24:23 2017 -0800 also add 1D and 2D versions of this function. Src/Particle/AMReX_KDTree_1d.F90 Src/Particle/AMReX_KDTree_2d.F90 commit ade1b78ff3a48c9275bbdd954363136f7f5d6878 Author: Andrew Myers Date: Wed Dec 6 20:01:08 2017 -0800 don't let the KD-tree create 0 cost boxes. Src/Particle/AMReX_KDTree_3d.F90 Src/Particle/AMReX_KDTree_F.H Src/Particle/AMReX_LoadBalanceKD.cpp commit c700579aadac2b10f15f3b64af84a9b1f94e7350 Author: Weiqun Zhang Date: Wed Dec 6 16:58:29 2017 -0800 nodal projection: add virtual restriction method Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 291c0b006490b392c868782827d52f5628e94f4f Author: Weiqun Zhang Date: Wed Dec 6 16:21:09 2017 -0800 nodal projection: applybc Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 6f50e0f47a5c5202ff577c4447d976629125072f Author: dtgraves Date: Wed Dec 6 16:00:25 2017 -0800 more examples of geometry generation Tutorials/EB/GeometryGeneration/exec/GNUmakefile Tutorials/EB/GeometryGeneration/exec/sphere.cpp Tutorials/EB/GeometryGeneration/exec/sphere.inputs Tutorials/EB/GeometryGeneration/src/CommonCode.cpp Tutorials/EB/GeometryGeneration/src/Make.package Tutorials/EB/GeometryGeneration/src/WriteEBPlotFile.H Tutorials/EB/GeometryGeneration/src/WriteEBPlotFile.cpp commit 5791765f321e04fb0975c56378135f9de70a789b Author: Weiqun Zhang Date: Wed Dec 6 15:32:47 2017 -0800 nodal projection: fillbc for sigma Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 820a203a17570c3de376215eed14916198ddf4ca Author: Marc Day Date: Wed Dec 6 13:04:05 2017 -0800 Separate out the IO of the eb surface file in order to better manage writes in parallel Src/GeometryShop/AMReX_EBISLevel.cpp commit 93e6d00476f96c7bd2742a2d0c02ce1bb88f385f Author: Weiqun Zhang Date: Wed Dec 6 10:43:48 2017 -0800 nodal projection: 2d Jacobi smoothing Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit e511988fe946939e33935b7812d068e619c3917b Author: Weiqun Zhang Date: Wed Dec 6 10:18:23 2017 -0800 fix a minor bug Src/LinearSolvers/MLMG/AMReX_MLLinOp.H commit 653186b21ee2ed078ac83a1e97f693e72ff5bb5c Author: Weiqun Zhang Date: Wed Dec 6 10:18:23 2017 -0800 fix a minor bug Src/LinearSolvers/MLMG/AMReX_MLLinOp.H commit 92197d947f64da7662a84c4000732202f43a04c1 Author: Weiqun Zhang Date: Wed Dec 6 09:45:28 2017 -0800 nodal projection: 2d A dot x Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 403d82b947851747c69605e6570f1ea1b3490373 Author: dtgraves Date: Tue Dec 5 16:38:10 2017 -0800 starting on tutorial where I show how to make a bunch of different geometries. Tools/C_util/Convergence/GNUmakefile Tutorials/EB/GeometryGeneration/exec/GNUmakefile Tutorials/EB/GeometryGeneration/exec/sphere.cpp Tutorials/EB/GeometryGeneration/exec/sphere.inputs Tutorials/EB/GeometryGeneration/src/CommonCode.H Tutorials/EB/GeometryGeneration/src/CommonCode.cpp Tutorials/EB/GeometryGeneration/src/Make.package Tutorials/EB/GeometryGeneration/src/WriteEBPlotFile.H Tutorials/EB/GeometryGeneration/src/WriteEBPlotFile.cpp commit 88a48a539c5ba26a953ebdb2efdc88d0ef2f0a7c Author: Tan Nguyen Date: Tue Dec 5 15:31:37 2017 -0800 build the body of an AMR task hierarchy Src/AmrTask/AMFIter/AMReX_AmrTask.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/main.cpp Src/Base/AMReX_FabArrayBase.H commit 13c348430e2010be3372dbb48dac3f2226b3dff4 Merge: 2877a7431 147324aad Author: dtgraves Date: Tue Dec 5 14:03:00 2017 -0800 merging with dev branch commit 147324aad5c29f5c9340c99f7a48e62fc290ef95 Author: Weiqun Zhang Date: Tue Dec 5 09:51:51 2017 -0800 stdint.h -> cstdint because this is C++ Src/Base/AMReX_IntConv.H commit b569c1cf83d477f0f6c49d7a1371def9cbf130a3 Author: Weiqun Zhang Date: Tue Dec 5 09:43:59 2017 -0800 fix template specialization Src/Base/AMReX_IntConv.cpp commit e7a491f3c7dc159e5f5a9aa22075c22e304c106b Author: Weiqun Zhang Date: Tue Dec 5 09:38:37 2017 -0800 Revert "use the new VectorIO routines in the particle checkpoint and restart routines." This reverts commit 2d1071f489a8467ebbeab68a7a8369465b160d3f. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit d3da503bda34319a334243459e4e8af1082a9fc9 Merge: e6353a7de 29355d17c Author: WeiqunZhang Date: Tue Dec 5 09:08:27 2017 -0800 Merge pull request #176 from AMReX-Codes/portable_particle_io Functions for writing Vectors of ints, longs, and Reals to disk in a portable manner. commit 29355d17c74d73f1ce65a90d8c7680e003b74302 Author: atmyers Date: Mon Dec 4 22:43:53 2017 -0800 clean up endianness macros Src/Base/AMReX_FPC.cpp commit 4dddfcb529ab97a0d8f22f5357204c23f5d73ad1 Author: kngott Date: Mon Dec 4 18:06:33 2017 -0800 ClickHistory and Send/Recv List Button. Src/Extern/ProfParser/AMReX_BLProfStats.H Src/Extern/ProfParser/AMReX_BLProfStats.cpp Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp Src/Extern/ProfParser/AMReX_CommProfStats.H Src/Extern/ProfParser/AMReX_ProfParserBatch.cpp Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp commit 2877a743177ef6a367311008f8fce1f6268d66b4 Author: dtgraves Date: Mon Dec 4 17:20:38 2017 -0800 redid the math for rk3 case---still not stable. Maybe I need to do something leastsquares-ish or add higher order terms. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 2d1071f489a8467ebbeab68a7a8369465b160d3f Author: atmyers Date: Mon Dec 4 16:49:35 2017 -0800 use the new VectorIO routines in the particle checkpoint and restart routines. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit e6353a7de7467171f2d777cb763196d55b4615c5 Merge: caad1573f 160c91566 Author: Andrew Myers Date: Mon Dec 4 16:45:47 2017 -0800 Merge pull request #175 from JBlaschke/development fix macros leading to incorrec endianness in fab io commit 160c91566e9d6e90430c743f73e9e2cd33f71980 Author: Johannes Blaschke Date: Mon Dec 4 16:28:08 2017 -0800 fix macros leading to incorrec endian-ness in fab io Src/F_BaseLib/fabio_c.c commit 9c253d821973af0d6e09b705b8f7a5c215e89b13 Author: atmyers Date: Mon Dec 4 13:25:07 2017 -0800 consolidate the vector IO functions into a file. Src/Base/AMReX_IntConv.H Src/Base/AMReX_IntConv.cpp Src/Base/AMReX_VectorIO.H Src/Base/AMReX_VectorIO.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Tests/Particles/TypeDescriptor/main.cpp commit 83d2afcf5f556cfeb695361d1c4e34cfa16550bc Author: atmyers Date: Mon Dec 4 13:12:22 2017 -0800 also testing real data. Tests/Particles/TypeDescriptor/main.cpp commit 6145a579dcb9e681850ca688899add92c17a4ab7 Author: atmyers Date: Mon Dec 4 12:37:29 2017 -0800 typo fix in comment. Src/Base/AMReX_FabConv.H commit 96925cca3e8c620f7bf1c26196e0036581d88f78 Author: atmyers Date: Mon Dec 4 12:32:14 2017 -0800 include negatives in test. Tests/Particles/TypeDescriptor/main.cpp commit 0487afe8c88da6d463f611ad9c3fea5df72e0881 Author: atmyers Date: Mon Dec 4 12:23:33 2017 -0800 also support long data; some reorganization. Src/Base/AMReX_IntConv.H Src/Base/CMakeLists.txt Src/Base/Make.package Tests/Particles/TypeDescriptor/main.cpp commit caad1573f07789821c4818141be5458115031115 Author: Weiqun Zhang Date: Mon Dec 4 10:30:23 2017 -0800 Fortran octree: add support for amr.max_grid_size_x, _y and _z Src/F_Interfaces/Octree/AMReX_octree_fi.cpp commit a76171bccaff831f667fe68e029d7388c754a2d3 Author: atmyers Date: Mon Dec 4 10:28:22 2017 -0800 also read/write the IntDescriptor to a header file. Tests/Particles/TypeDescriptor/main.cpp commit 8eee56354119f011ead59c7376459a236c37368c Author: Weiqun Zhang Date: Sat Dec 2 13:42:40 2017 -0800 WIP: nodal projection Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 075b3a95c1645a46a3b02b929ea39442670217c3 Author: atmyers Date: Sat Dec 2 12:55:45 2017 -0800 move the int conversion stuff to Base and install the header Src/Base/AMReX_IntConv.H Src/Base/CMakeLists.txt Src/Base/Make.package Tests/Particles/TypeDescriptor/Make.package Tests/Particles/TypeDescriptor/main.cpp commit 32828aef56b972841cb2ec4f59fcdc758412c481 Author: atmyers Date: Sat Dec 2 12:48:20 2017 -0800 swap bytes for unsigned as well. Tests/Particles/TypeDescriptor/Convert.H commit 5bab047df029f5ddf6d6cde33e22d3bf40f0d35c Author: atmyers Date: Sat Dec 2 12:42:08 2017 -0800 handle short Tests/Particles/TypeDescriptor/main.cpp commit 86207c8b7b8e7d14a4bf6dc3d3bc4807aec293a2 Author: atmyers Date: Sat Dec 2 12:39:02 2017 -0800 handle endianness Tests/Particles/TypeDescriptor/Convert.H Tests/Particles/TypeDescriptor/main.cpp commit f3a8d5301cdebe6ed38858bfb81d39510b5dcfe0 Author: atmyers Date: Sat Dec 2 12:28:36 2017 -0800 add a test for the more portable io stuff Tests/Particles/TypeDescriptor/Convert.H Tests/Particles/TypeDescriptor/GNUmakefile Tests/Particles/TypeDescriptor/Make.package Tests/Particles/TypeDescriptor/main.cpp commit 85bec3b8f06a9e9a775d882ad342120e8e42a554 Author: atmyers Date: Sat Dec 2 12:27:44 2017 -0800 some BoxLib -> AMReX Src/Base/AMReX_FabConv.H commit c5c4f25ec19d473da5661e024d6e3d71e26d51db Author: Andrew Myers Date: Sat Dec 2 10:07:55 2017 -0800 fix bug with rcv count caching in the neighbor particle code. Src/Particle/AMReX_NeighborParticlesI.H commit 4067a484f0261e727fce22e622d20f95b36c2b61 Author: Ann Almgren Date: Fri Dec 1 18:23:46 2017 -0800 Protect against negative grid ID in BuildLevelMask Src/Particle/AMReX_NeighborParticlesI.H commit c99f52f9f6dfd35850fc57564a6c6c9b9ba94d28 Author: atmyers Date: Fri Dec 1 13:50:35 2017 -0800 implement io operators for the IntDescriptor Src/Base/AMReX_FabConv.H Src/Base/AMReX_FabConv.cpp commit 4fa619701b5430ac6abfd8703af4d56da6990f25 Author: atmyers Date: Fri Dec 1 13:05:05 2017 -0800 adding a NativeIntDescriptor. Src/Base/AMReX_FPC.H Src/Base/AMReX_FPC.cpp Src/Base/AMReX_FabConv.H commit b386886327bc02b71d8e892fba69a0606ce72204 Author: Weiqun Zhang Date: Fri Dec 1 10:48:58 2017 -0800 average down edge coefficients Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H commit 2eaa2da915570d1cd3146bf02c30b79e483d0c9b Author: Marc Day Date: Fri Dec 1 09:09:36 2017 -0800 WIP: collect intersections from geo server into distributed data structure, connect up contour lines or triangulated surface patches, and write...if ebis.build_eb_surface=true Src/GeometryShop/AMReX_AllRegularService.H Src/GeometryShop/AMReX_AllRegularService.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_FlatPlateGeom.H Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_GeomIntersectUtils.H Src/GeometryShop/AMReX_GeomIntersectUtils.cpp Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryService.cpp Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/Make.package commit 0a2342274c43ba163ac6987245fd0781079f266a Merge: 207c75da3 dac8c433f Author: Weiqun Zhang Date: Fri Dec 1 08:40:29 2017 -0800 Merge branch 'development' commit dac8c433fe10b142d67fa4559a86bedbe13e1534 Author: Ann Almgren Date: Thu Nov 30 17:30:58 2017 -0800 Add more missing files to CMakeLists.txt Src/GeometryShop/CMakeLists.txt commit ac8ea924c813fdf62a43e95db918abcf78b5a57e Author: kngott Date: Thu Nov 30 17:18:45 2017 -0800 Comment distinguishing backtrace options. Src/Base/AMReX_BLBackTrace.H commit 338e3aafe9341951b125ae64307e59f5f2e94256 Author: Weiqun Zhang Date: Thu Nov 30 16:58:15 2017 -0800 add index type Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp commit 528d9762d1c60a5b37842b214dad0eb2771a218c Merge: 84eaea3cc e00b8a262 Author: Ann Almgren Date: Thu Nov 30 16:52:42 2017 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 84eaea3cc7e932974a6eda34badd856c865b8129 Author: Ann Almgren Date: Thu Nov 30 16:52:34 2017 -0800 Add missing .H file Src/GeometryShop/CMakeLists.txt commit 878ea0ed17ba59a7c2578e80fe02b65c039b9dfe Author: dtgraves Date: Thu Nov 30 16:30:04 2017 -0800 redid the calculations for rk4. still not showing the right convergence. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 4a3f1c4518f9c6c843a875d098ae7e19ad2487bb Author: Weiqun Zhang Date: Thu Nov 30 16:23:51 2017 -0800 move MLCellLinOp specific stuff from base class MLLinOp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H commit 009d918b47f10ade7094d64a059c1b1fd1e72c6e Author: Weiqun Zhang Date: Thu Nov 30 14:38:35 2017 -0800 nodal projection: compute divu Src/Boundary/AMReX_LO_BCTYPES.H Src/Boundary/AMReX_lo_bctypes_mod.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit e00b8a262cc78a171e6f48b7a37dcf32f8050fa2 Merge: ae47de3e8 853784401 Author: Andrew Myers Date: Thu Nov 30 13:44:43 2017 -0800 Merge pull request #174 from emotheau/master update commit 8537844019c08b8fca8f55110a77ab9e5a13f96a Author: Emmanuel Motheau Date: Thu Nov 30 13:41:59 2017 -0800 move file Tools/C_util/Convergence/AVGDOWN_1D.F commit 06cb21f94b11eb3865b54aae472f3fcd32972e2d Merge: 7e8d0237e 8f147ec4f Author: Emmanuel Motheau Date: Thu Nov 30 13:29:24 2017 -0800 Merge pull request #1 from emotheau/emotheau-patch-1 Add missing file for 1D convergence test commit 8f147ec4f2e94a585838900646b2f59483616148 Author: Emmanuel Motheau Date: Thu Nov 30 13:28:31 2017 -0800 Add missing file for 1D convergence test AVGDOWN_1D.F commit ae47de3e8d197c6eb5bf22807dc799864e3b994b Author: Ann Almgren Date: Thu Nov 30 12:57:18 2017 -0800 Add AMReX_AnisotropicIF.H to the CMakeLists.txt Src/GeometryShop/CMakeLists.txt commit b6de727f2da40baf698b861946f0138f4b85c3d1 Author: Weiqun Zhang Date: Thu Nov 30 10:01:43 2017 -0800 split MLLinOp into MLCellLinOp and MLNodeLinOp Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.H Src/LinearSolvers/MLMG/AMReX_MLCellLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/Make.package commit 23b5d04510b5557cd7ccbb6872370d4a7c4316c1 Author: Andrew Myers Date: Thu Nov 30 06:15:26 2017 -0800 fix assertion. Src/Particle/AMReX_NeighborParticlesI.H commit 17df40a77e1521ef6dbb3ce6a7e572b0e554aba9 Author: Weiqun Zhang Date: Wed Nov 29 17:15:27 2017 -0800 average nodal coefficients from cell centers to edges Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp commit 06bab81bbd826589cee624038cc020cd940a86db Author: Weiqun Zhang Date: Wed Nov 29 15:07:33 2017 -0800 start nodal projection Src/LinearSolvers/MLMG/AMReX_MLNodeLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLNodeLap_F.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLNodeLaplacian.cpp Src/LinearSolvers/MLMG/Make.package commit 9728f17d1c679b3ee94e8b1ecde81bebac89d9f0 Author: dtgraves Date: Wed Nov 29 09:56:59 2017 -0800 put back in abort message in CNS that disallows ansiotropic dx Tutorials/EB/CNS/Source/CNS.cpp commit 06da4f1a2b1521b1d80d42366236235663309361 Author: dtgraves Date: Wed Nov 29 09:55:54 2017 -0800 added general anisotropic dx implicit function (along with an example in CNS that calls it) Src/GeometryShop/AMReX_AnisotropicIF.H Tutorials/EB/CNS/Exec/ShockRef/aniso.inputs Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit 13ba38c349dcb09d46595a007eb981f8657b498c Merge: 641215042 93a87caa1 Author: dtgraves Date: Wed Nov 29 09:36:28 2017 -0800 Merge branch 'development' into dtg_branch commit 93a87caa16aacce235620f3efc09866d0950a4a9 Author: Weiqun Zhang Date: Wed Nov 29 09:25:37 2017 -0800 add amrex::second() that calls C++ clock. use it in TinyProfiler Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_TinyProfiler.cpp Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit cb04cb819184abf30c613ac637050beb70741bb7 Author: Ann Almgren Date: Tue Nov 28 16:15:10 2017 -0800 Don't need prob_domain in that routine Src/Particle/AMReX_NeighborParticlesI.H commit 64121504200f2cf5381d051121a342296a3062e7 Author: dtgraves Date: Tue Nov 28 12:30:52 2017 -0800 found a bug in jbb version of time interpolation. rk3 looks very good. have to check math for rk4 again. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 6024d5c03a7273f84e1918a8e23df24b00959fc6 Author: Weiqun Zhang Date: Tue Nov 28 09:04:32 2017 -0800 TinyProfiler: disable BL_PROFILE_REGION_START and STOP so that the output is smaller Src/Base/AMReX_BLProfiler.H commit 362c739b1573206b412a343c101719a5c53fe9fb Author: Marc Day Date: Mon Nov 27 18:59:01 2017 -0800 Add 3D code to dump triangulated surface. Src/GeometryShop/AMReX_GeometryShop.cpp commit 85d0ce25e874de32038cae69472d6d2e3925039c Author: Tan Nguyen Date: Mon Nov 27 18:03:11 2017 -0800 reuse some original Amr code Src/AmrTask/Amr/AMReX_AmrLevelTask.H Src/AmrTask/Amr/AMReX_AmrLevelTask.cpp Src/AmrTask/Amr/AMReX_AmrTask.cpp Src/AmrTask/Amr/Make.package Src/AmrTask/Amr/Makefile Src/AmrTask/AmrCore/AMReX_FillPatchUtil.H Src/AmrTask/AmrCore/AMReX_FillPatchUtil.cpp commit 64ea6ed3f7e6b8111bb864bb1ff5ebfc4e3fadc8 Merge: 2f42ddf97 257bafdab Author: Tan Nguyen Date: Mon Nov 27 17:56:16 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2f42ddf9750ee0c7a2f23d0b06a8eae1e2bc2ead Author: Tan Nguyen Date: Mon Nov 27 17:56:05 2017 -0800 writing a fully asynchronous version of the Advection code Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/CMakeLists.txt Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/Make.Adv Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/Make.package Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/Prob.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/inputs Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/inputs.tracers Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/SingleVortex/probin Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/Make.package Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_2d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_3d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/inputs Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/inputs.regt Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/probdata.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Exec/UniformVelocity/probin Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/README Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Adv_F.H Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.H Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/AmrLevelAdv.cpp Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/LevelBldAdv.cpp Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Make.package Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_2d/Make.package Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_2d/compute_flux_2d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_2d/slope_2d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_3d/Make.package Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_3d/compute_flux_3d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_3d/slope_3d.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_nd/Adv_nd.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_nd/Make.package Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_nd/Tagging_nd.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/Src_nd/tagging_params.f90 Src/AmrTask/tutorials/MiniApps/Advection_AmrLevel/Source/main.cpp commit 257bafdabd267c7dd7cd7c45bed1dd611830baa1 Author: Weiqun Zhang Date: Mon Nov 27 17:53:08 2017 -0800 add some regional profilers to MLMG Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tutorials/LinearSolvers/ABecLaplacian_C/main.cpp commit 364116a3ce7cfff44c79526cff9cbce0cc8d31d4 Merge: 4d4928a77 8eaca4fc4 Author: Tan Nguyen Date: Mon Nov 27 17:51:29 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4d4928a77acba89a1348fd606c5aba3455a96e90 Author: Tan Nguyen Date: Mon Nov 27 17:51:17 2017 -0800 add AmrTask support Src/Amr/AMReX_Amr.H Src/Amr/AMReX_AmrLevel.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/AMFIter/Makefile Src/AmrTask/Makefile Src/AmrTask/arch/arch.mpi.generic Src/AmrTask/graph/AMReX_AbstractTask.H commit 8eaca4fc4dc9cbf33c216a5ec1cb78d3800a1327 Merge: 79d1e0c02 518a64a0b Author: Weiqun Zhang Date: Mon Nov 27 17:39:43 2017 -0800 Merge branch 'tprof-region' into development commit 11a0b9b93ff775c310c5dbdb3bd7b764329c7278 Author: Marc Day Date: Mon Nov 27 16:35:55 2017 -0800 Fix scaling of intercept points. Src/GeometryShop/AMReX_GeometryShop.cpp commit 79d1e0c0257e85f89d9c55d5a109136a2d70ae08 Author: Michele Rosso Date: Mon Nov 27 15:49:23 2017 -0800 CMake: include MLMG in build Src/LinearSolvers/CMakeLists.txt commit a45cfe72635498b1251c8977b0428da60c60c3bc Merge: 9ad0b91e9 9b555da1c Author: Marc Day Date: Mon Nov 27 15:40:48 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 5a25c3e6b2c17d09f341896bf95ccf830fbd379d Author: dtgraves Date: Mon Nov 27 15:40:30 2017 -0800 coded yet another version of time interpolation. the simple polynomial version seems to work best. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 6a5f468576b166dbc0d1a1da8d54091e3af8fbb9 Author: Marc Day Date: Mon Nov 27 15:39:52 2017 -0800 WIP: Extracting intersections Src/GeometryShop/AMReX_GeometryShop.cpp Tests/GeometryShop/stencilTestbed/exec/GNUmakefile Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/sphere.inputs Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp commit 518a64a0b6d373b4f35617f9c62aae624efa7341 Author: Weiqun Zhang Date: Mon Nov 27 10:53:29 2017 -0800 add TinyProfileRegion class Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp commit 9b555da1c0f4586f881451703e9734749ea4b9b1 Author: Weiqun Zhang Date: Sun Nov 26 20:07:38 2017 -0800 put a global variable into anonymous namespace Src/Base/AMReX_Utility.cpp commit 11b7c2b5aa3a75f63a24683a6a0e450ae9197181 Author: Weiqun Zhang Date: Sun Nov 26 15:12:15 2017 -0800 Regional profiling support in TinyProfiler Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp Src/Particle/AMReX_ParticleContainerI.H commit 4abfa03a4e5b83bb301b92feb40461b3288e2ddf Author: Weiqun Zhang Date: Sun Nov 26 12:08:15 2017 -0800 TinyProfiler ctor optimization Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp commit a8646744758c6473d2411fb5c4a3db6db4d5a4bd Author: Max Katz Date: Sun Nov 26 13:45:16 2017 -0500 Add method to swap old/new data with another StateData Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp commit 8f0badd17f0383a4c24f3067507071f8695a8d76 Merge: 20bd46896 25d5ddfcf Author: Tan Nguyen Date: Fri Nov 24 17:04:11 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 20bd46896dfc4a9c18c6dded8628e78b628a7dbe Author: Tan Nguyen Date: Fri Nov 24 17:03:47 2017 -0800 remove an anonymous namespace Src/Amr/AMReX_Amr.cpp commit 25d5ddfcf619424a3bf2284d12868df905e66fe0 Author: Weiqun Zhang Date: Fri Nov 24 16:50:44 2017 -0800 make: if AMREX_HOME string contains ~, replace it because make won't like it and the error message cannot be easily understood. Tools/GNUMake/Make.defs commit 00540b1141b3d19959ecc6e704034c8b53de8b06 Author: Max Katz Date: Fri Nov 24 13:20:05 2017 -0500 Ensure uniform gcc version number reporting with -dumpfullversion Tools/F_mk/comps/gfortran.mak Tools/GNUMake/comps/gnu.mak commit 67b132e8f18d318250b01bbbcc6b7f104c9f22d1 Author: Max Katz Date: Fri Nov 24 13:14:23 2017 -0500 Throw error if gcc < 4.8 (F_mk) Tools/F_mk/comps/gfortran.mak commit 43259667d6190437bd85af83b20a0ab0d7e5bad0 Author: Weiqun Zhang Date: Fri Nov 24 08:40:25 2017 -0800 throw error if gcc < 4.8 Tools/GNUMake/comps/gnu.mak commit 9ad0b91e9257204b7d04b6029b7875962b58f624 Merge: 79665394a 4a9bb247b Author: Marc Day Date: Wed Nov 22 14:36:34 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit eeda38985c35977293c79496e34d67462fcefe9a Author: dtgraves Date: Wed Nov 22 13:48:32 2017 -0800 we now have three versions of time interpolation. for super smooth problems, the simply polynomial seems to work best. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 4a9bb247beb64f69b8968afb7d141271cb50efbe Author: Tan Nguyen Date: Wed Nov 22 13:04:33 2017 -0800 add a function that returns the number of data states Src/Amr/AMReX_AmrLevel.H commit f377be442d05cc486521d5b589ff1ac633a1d9e3 Merge: 2627d5a16 01abecf4d Author: Andrew Myers Date: Wed Nov 22 11:51:38 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2627d5a16e75f82664ad7298f69514ec1c3ca3b7 Author: Andrew Myers Date: Wed Nov 22 11:51:28 2017 -0800 functions for growing all the boxes in a BoxArray in a given direction on only the lo / hi side. Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit 01abecf4d3c66c4f8a9e438f20cc2879ad64573b Author: Weiqun Zhang Date: Wed Nov 22 11:30:07 2017 -0800 fix thread id Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.cpp commit 215a0677f4141be64c00d46a493407c16cbd537c Author: Weiqun Zhang Date: Wed Nov 22 11:20:14 2017 -0800 hopefully I fixed it this time. Shouldn't have done this before going out shopping Src/Base/AMReX_BoxArray.cpp commit 2ab1e37fdf417838874e93f6d175bf4213eda978 Author: Weiqun Zhang Date: Wed Nov 22 11:12:10 2017 -0800 fix a bug Src/Base/AMReX_BoxArray.cpp commit d3f41c270f4d53cc92dc171fd3302b7706e906b8 Author: Weiqun Zhang Date: Wed Nov 22 11:06:16 2017 -0800 fix a typo Src/Base/AMReX_BoxArray.cpp commit 9931113131df0b99fb65533fb17b1c8fadfabc84 Author: Weiqun Zhang Date: Wed Nov 22 11:02:27 2017 -0800 optimizatin of BoxList::complementIn Src/Base/AMReX_BoxList.cpp commit 58f02435a72f3361bae035f0e91e3d2c3a5764f2 Author: Weiqun Zhang Date: Wed Nov 22 11:02:00 2017 -0800 OMP BoxArray::minimalBox() Src/Base/AMReX_BoxArray.cpp commit 3736688dc741f84e378f250390e9b5bdf10b5a4b Author: Weiqun Zhang Date: Wed Nov 22 07:46:29 2017 -0800 added BoxList::swap and some minor changes Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit 34a87ff352800f1ef5bd86534b03729502177472 Author: Weiqun Zhang Date: Wed Nov 22 07:33:47 2017 -0800 OMP BoxList::complementIn Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit 5519a3354e51832ac60d4eec96f3f8c201811bb0 Author: Weiqun Zhang Date: Wed Nov 22 07:21:19 2017 -0800 A faster way of removing dupliates (which may break some regression tests). Added BoxList::reserve Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BoxList.H commit c7210bebb5f76aa47d16fdde3ba2795988b0f5ae Author: Weiqun Zhang Date: Wed Nov 22 07:06:00 2017 -0800 fix typos Tutorials/LinearSolvers/ABecLaplacian_C/initProb.cpp commit 4567d89d10c1f843d42687cbecbb3fc02493ff53 Author: dtgraves Date: Tue Nov 21 15:53:40 2017 -0800 redid the math and recoded time interpolation for rk3/4. I am still losing an order in solution error but it looks pretty good. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit b013b469402722152aa2aa2658672855726957fd Merge: 2b1832617 8e752e54b Author: Andrew Myers Date: Tue Nov 21 14:56:18 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2b1832617aa11da7d06c793b6ae08bec134402f5 Author: Andrew Myers Date: Tue Nov 21 14:56:06 2017 -0800 enable users to turn off the MPI communication of certain particle components when filling ghost particles. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 8e752e54b3e82b6463662763113bd4067fa187f1 Author: Weiqun Zhang Date: Tue Nov 21 14:54:10 2017 -0800 Tutorials/LinearSolvers/ABecLaplacian_C Tools/RegressionTesting/AMReX-tests.ini Tutorials/LinearSolvers/ABecLaplacian_C/GNUmakefile Tutorials/LinearSolvers/ABecLaplacian_C/Make.package Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.H Tutorials/LinearSolvers/ABecLaplacian_C/MyTest.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTestPlotfile.cpp Tutorials/LinearSolvers/ABecLaplacian_C/MyTest_F.H Tutorials/LinearSolvers/ABecLaplacian_C/initProb.cpp Tutorials/LinearSolvers/ABecLaplacian_C/init_prob.F90 Tutorials/LinearSolvers/ABecLaplacian_C/inputs Tutorials/LinearSolvers/ABecLaplacian_C/inputs-rt-abeclap-com Tutorials/LinearSolvers/ABecLaplacian_C/inputs-rt-poisson-lev Tutorials/LinearSolvers/ABecLaplacian_C/main.cpp commit ab1b0ec53b684b4408b0a20b51dee2a21fee9587 Merge: 574273550 deb4880de Author: kngott Date: Tue Nov 21 13:17:08 2017 -0800 Merge branch 'profvis' of https://github.com/AMReX-codes/amrex into profvis commit 6f1054e22a7582409e001d9918e9bc7c3b709b77 Author: Weiqun Zhang Date: Tue Nov 21 08:49:35 2017 -0800 add amrex:: Src/Base/AMReX_ParallelDescriptor.H commit 7d1c447ac2fda18ed353355f1c3ddc036002ee76 Author: dtgraves Date: Mon Nov 20 16:46:27 2017 -0800 more debugging hooks. new time interpolation not there yet. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 0181f8b8578966a9541276f3f74f5fd5c1278801 Author: vince Date: Mon Nov 20 13:14:08 2017 -0800 use 5 digits in DATA_ string. we need to sync thses sizes. Src/Particle/AMReX_ParticleContainerI.H commit 968cc0beeea86786bbe991b79bba83e0993bf951 Merge: a60747c15 9b8f68ea1 Author: WeiqunZhang Date: Fri Nov 17 20:44:59 2017 -0800 Merge pull request #165 from bcfriesen/EB_updates EB updates commit a60747c153a7d49722f94c708b2ad9089d4b6aeb Author: Weiqun Zhang Date: Fri Nov 17 20:42:35 2017 -0800 add README to the Fortran linear solver tutorial Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H Tutorials/LinearSolvers/ABecLaplacian_F/README commit 3fbffcf51fd9b6623f235d1720c43dd283cf37cb Author: vince Date: Fri Nov 17 18:16:46 2017 -0800 remove diagnostic. Src/Base/AMReX_NFiles.cpp commit 57d4820a10e1971c5f14f1111c01b17255f54df5 Author: Weiqun Zhang Date: Fri Nov 17 17:00:54 2017 -0800 update regression tests Tools/RegressionTesting/AMReX-tests.ini Tutorials/LinearSolvers/ABecLaplacian_F/inputs-rt-abeclap-lev Tutorials/LinearSolvers/ABecLaplacian_F/inputs-rt-poisson-com commit 5082186f0fe6852a32b9c4390483416e40051c74 Author: dtgraves Date: Fri Nov 17 15:57:13 2017 -0800 have rk3 and rk4 time interpolation coded in john's new way. Now I Have to figure out whether my algebra or my coding (or both) are incorrect Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs commit 28969cbff0a5db5bb3b509375f0ac09f546ecf27 Author: Weiqun Zhang Date: Fri Nov 17 15:48:01 2017 -0800 Fixed a bug that causes segfault when making alias FabArray of alias. The bug was introduced 3 days in fb2afb0891d9dc7 by me. Src/Base/AMReX_FabArray.H commit 0644bd18554a80f68103f8a76439b4e1a2252781 Author: Andrew Myers Date: Fri Nov 17 15:20:15 2017 -0800 don't need to do this intersection any more. Src/Particle/AMReX_NeighborParticlesI.H commit 52abbf6283c3bb8a4ce1adfafe2ddb96369c548d Author: Weiqun Zhang Date: Fri Nov 17 15:19:08 2017 -0800 finished Fortran linear solver tutorial Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit c95c6d83191fade9c0ef76710593985803fb4e77 Author: Weiqun Zhang Date: Fri Nov 17 13:04:41 2017 -0800 implement amrex_abeclaplacian_module Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_linear_solver_mod.F90 commit c50f4c8c3f7f07d9f66e6479003b3db4e2e47660 Author: Andrew Myers Date: Fri Nov 17 14:04:33 2017 -0800 this loop only needs to go over the real particles, not the real + neighbors. Src/Particle/AMReX_NeighborParticlesI.H commit 7022ebfe32293785816de956aacd941248e4cdf6 Merge: 4561a1d57 c77bd9087 Author: vince Date: Fri Nov 17 13:33:48 2017 -0800 merge fixes. commit 4561a1d57cde2e46b2be2701933a1b5d20e61a97 Author: vince Date: Fri Nov 17 13:21:47 2017 -0800 use dss from nfilesiter. Src/Base/AMReX_NFiles.H Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp commit fe99931ffea884de9417b11c84b66f7b05c7d824 Author: dtgraves Date: Fri Nov 17 12:55:08 2017 -0800 added in new style fourth-order limiting Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit c85f3c6441e34545d6fe1c6c4d7db49c9c761a90 Merge: 6d03135cb 6624f00e0 Author: vince Date: Fri Nov 17 12:35:42 2017 -0800 Merge branch 'partio' of https://github.com/AMReX-Codes/amrex into partio commit 6624f00e0511a66a30b04b3fa6874020ec99693c Author: vince Date: Fri Nov 17 12:35:20 2017 -0800 use long. Src/Extern/ProfParser/AMReX_CommProfStats.cpp commit 6d03135cb10a04532d0bfb548f3e94407947b549 Merge: 093a7b6cf b6ba71d22 Author: vince Date: Fri Nov 17 12:25:06 2017 -0800 merge fix. commit 093a7b6cf3c595536a4743140b93241d109eec36 Author: vince Date: Fri Nov 17 12:23:45 2017 -0800 init value. Src/Particle/AMReX_ParticleContainerI.H commit a09c2fbfe4770918348b6afa5471c82eb16a53e6 Author: vince Date: Fri Nov 17 12:23:14 2017 -0800 parser fixes. Src/Extern/ProfParser/AMReX_CommProfStats.H Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp commit 25df8b6496f68a31095764eb465fca302f977a13 Author: vince Date: Fri Nov 17 12:20:30 2017 -0800 fix comment. Src/Base/AMReX_NFiles.H Src/Base/AMReX_VisMF.cpp commit b6ba71d228e05efdd31f17c4b4c69ee8f8329021 Author: vince Date: Fri Nov 17 12:15:47 2017 -0800 use rank for sparse file number. Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_VisMF.cpp commit c77bd9087ccd44a8f2f28fd2cd4555499e439ced Merge: 3df61a944 42e505926 Author: Andrew Myers Date: Fri Nov 17 11:06:46 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3df61a944418e67d4732d97cd9bd658bb81831a0 Author: Andrew Myers Date: Fri Nov 17 10:57:04 2017 -0800 removing a couple of now un-needed functions. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 42e505926e48b8c7ecbd424a5ba5fa8ebf30a6fc Author: Weiqun Zhang Date: Fri Nov 17 10:56:04 2017 -0800 add amrex_average_cellcenter_to_face to amrex_multifabutil_module Src/F_Interfaces/Base/AMReX_multifabutil_fi.cpp Src/F_Interfaces/Base/AMReX_multifabutil_mod.F90 Tutorials/LinearSolvers/ABecLaplacian_F/init_prob.F90 Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit 314b3d17e4e8b8ff75c222291f9b9c9234b02db0 Merge: c9709d31f 9c7a54d63 Author: Andrew Myers Date: Fri Nov 17 10:39:52 2017 -0800 merging. commit c9709d31f96d77e46fb9de1b2921cbf54ad2f96e Author: Andrew Myers Date: Fri Nov 17 10:33:43 2017 -0800 reduce temporary copies in the neighbor particle code. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 48606764d0cf319e9090b68acd69990765a58a3e Author: Andrew Myers Date: Fri Nov 17 10:33:06 2017 -0800 more efficient to insert these at the end, rather than the beginning. Src/Particle/AMReX_ParticleContainerI.H commit 9c7a54d63e6a89d463de02741b0a86c2125e450e Author: Weiqun Zhang Date: Fri Nov 17 10:14:40 2017 -0800 port more features of MFIter from C++ to Fortran CHANGES Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit e63ddcad8f2a0b5b11f7f442fcdcfad2631b4692 Merge: f0156d281 ca3b0e389 Author: vince Date: Thu Nov 16 17:54:09 2017 -0800 Merge branch 'partio' of https://github.com/AMReX-Codes/amrex into partio commit ca3b0e389dd3a11ec85e975708bf3138d01296d0 Author: vince Date: Thu Nov 16 17:52:55 2017 -0800 header diagnostics for sparse fabarray writes. Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_NFiles.H Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp commit d1265d64283faacbf322871123b27b4c16948d0f Author: vince Date: Thu Nov 16 17:50:21 2017 -0800 temp flush fix. Src/Amr/AMReX_Amr.cpp commit a2af83a6fe2e1783ea2cae259ee082454cdb5aba Author: Weiqun Zhang Date: Thu Nov 16 17:11:43 2017 -0800 Fortran linear solver tutorial: init abeclapacian coefficients Tests/LinearSolvers/MLMG/fort_3d.F90 Tutorials/LinearSolvers/ABecLaplacian_F/init_prob.F90 Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit 2a8c901bc9d5b3727b7e80b12602b3d48204f874 Author: Weiqun Zhang Date: Thu Nov 16 16:45:11 2017 -0800 Fortran linear solver tutorial: level by level poisson solve works Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit 617b794ff190316576e2f0bf72edbeb71ec9d99b Author: Weiqun Zhang Date: Thu Nov 16 15:03:57 2017 -0800 rename setBCWithCoarseData to setCoarseFineBC Src/F_Interfaces/LinearSolvers/AMReX_linop_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_linop_mod.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit 8c38b2f82bb31fc48805e9db8ee2d5c49ee40887 Author: Weiqun Zhang Date: Thu Nov 16 14:31:51 2017 -0800 Fortran linear sovler tutorial works for compsite Poisson Tutorials/LinearSolvers/ABecLaplacian_F/init_prob.F90 Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit e4e9498286a42641e25edb694fccb14d589a855a Author: Weiqun Zhang Date: Thu Nov 16 14:25:23 2017 -0800 add more functions to Fortran amrex_multifab_module CHANGES Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 79665394a83783a3940ede4c4ab2a83ac6ac7880 Merge: 145c1a13f f8eaff1e4 Author: Marc Day Date: Thu Nov 16 14:20:49 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f8eaff1e409cc4d33965f7facb8d5b30d420bb6c Author: Weiqun Zhang Date: Thu Nov 16 13:10:03 2017 -0800 fix typo in amrex_multigrid_module Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90 commit e7077368ce17c2b6ce4c38918d278294a56a07e1 Author: Weiqun Zhang Date: Thu Nov 16 12:05:37 2017 -0800 fix omp bug in amrex_geometry_module; more on the linear solver tutorial Tutorials/LinearSolvers/ABecLaplacian_F/init_prob.F90 commit c6f38673687577fbed15b1bd234c2ac4c0b9a338 Author: Weiqun Zhang Date: Thu Nov 16 12:03:29 2017 -0800 fix omp bug in amrex_geometry_module; more on the linear solver tutorial Tutorials/LinearSolvers/ABecLaplacian_F/init_prob.F90 commit 217f53beccf631662c81c4b9ebefd1c4671087e1 Author: Weiqun Zhang Date: Thu Nov 16 12:02:21 2017 -0800 fix omp bug in amrex_geometry_module Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Tutorials/Basic/HeatEquation_EX1_F/init_phi.f90 Tutorials/LinearSolvers/ABecLaplacian_F/Make.package Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit fe7ab3856248ae216322d6953c96f1f31923d1b3 Author: Weiqun Zhang Date: Thu Nov 16 10:30:11 2017 -0800 amrex_box_module: add coarsen and refine Src/F_Interfaces/Base/AMReX_box_mod.F90 commit 2625346c5f7e29fd6cfc264f9e1b0b2a85ace97f Author: Weiqun Zhang Date: Thu Nov 16 09:34:31 2017 -0800 add some functions to amrex_geometry_module for setting coordinates, problem domain and periodicity through funcitons instead of inputs Src/F_Interfaces/Base/AMReX_geometry_mod.F90 commit 508b0bfb180113cc79c1fbc048fd9d0b86032aac Author: Weiqun Zhang Date: Thu Nov 16 08:55:06 2017 -0800 MLMG: test singularity on the bottom instead because it's cheaper Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit 1b7982f17956db593495317b475f51f049aa8de3 Author: dtgraves Date: Thu Nov 16 08:50:09 2017 -0800 bug fixes in 4th order limiting. Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 commit b99d48ec27f694dcf4817a3c91537bf8c526da8d Author: Weiqun Zhang Date: Wed Nov 15 18:09:11 2017 -0800 F_Interfaces/LinearSolvers: finished amrex_multigrid_module Src/F_Interfaces/LinearSolvers/AMReX_multigrid_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_poisson_mod.F90 commit 16f29d02686f648e29ad78df153415615c062f82 Author: dtgraves Date: Wed Nov 15 16:30:00 2017 -0800 slogged my way through writing the limiting code a la mccorquodale. The limiting versions still untested. Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 commit 49f4a67b5b39492cb8ae43d4a827bee9fef67756 Author: Brian Friesen Date: Wed Nov 15 14:56:40 2017 -0800 IOBenchmark: make only master thread flush and close file in thread-shared IO Tests/IOBenchmark/IOTestDriver.cpp commit 67f0f17a3df2f3e04e9f1e79d7797fb31d1950c5 Author: Weiqun Zhang Date: Wed Nov 15 14:28:31 2017 -0800 F_Interfaces/LinearSolvers: wip Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_linear_solver_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_linop_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_multigrid_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_poisson_mod.F90 Src/F_Interfaces/LinearSolvers/Make.package Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit b01636b4698ba47f5ee545a37d46b92fd61b16db Author: Weiqun Zhang Date: Wed Nov 15 13:14:25 2017 -0800 F_Interfaces/LinearSolvers: WIP Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_linop_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_linop_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_multigrid_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_multigrid_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_poisson_fi.cpp Src/F_Interfaces/LinearSolvers/AMReX_poisson_mod.F90 Src/F_Interfaces/LinearSolvers/Make.package Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit a2d4cc93903c619e72b197bb80d97227b2d8547a Author: Weiqun Zhang Date: Wed Nov 15 09:40:56 2017 -0800 start F_Interfaces/LinearSolvers Src/Base/AMReX_string_mod.F90 Src/Boundary/AMReX_LO_BCTYPES.H Src/Boundary/AMReX_lo_bctypes_mod.F90 Src/Boundary/CMakeLists.txt Src/Boundary/Make.package Src/F_Interfaces/LinearSolvers/AMReX_abeclaplacian_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_linear_solver_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_linop_mod.F90 Src/F_Interfaces/LinearSolvers/AMReX_poisson_mod.F90 Src/F_Interfaces/LinearSolvers/Make.package Tutorials/LinearSolvers/ABecLaplacian_F/GNUmakefile Tutorials/LinearSolvers/ABecLaplacian_F/Make.package Tutorials/LinearSolvers/ABecLaplacian_F/inputs Tutorials/LinearSolvers/ABecLaplacian_F/main.F90 Tutorials/LinearSolvers/ABecLaplacian_F/mytest.F90 commit 4764e4c113053da1f4ca49739128bc168b661dd4 Author: Michael Zingale Date: Wed Nov 15 13:57:03 2017 -0500 add the total time to the summary page Tools/RegressionTesting/regtest.py Tools/RegressionTesting/test_report.py commit b6885c18215660527ebfdb194cc857efb08b8f8c Merge: 4b509c780 661d4705e Author: Michael Zingale Date: Wed Nov 15 13:38:51 2017 -0500 Merge branch 'development' of ssh://github.com/AMReX-Codes/AMReX into development commit 4b509c7800736c93c5ac6c34b963618de80d0e85 Author: Michael Zingale Date: Wed Nov 15 13:38:41 2017 -0500 quote slack posts Tools/RegressionTesting/regtest.py commit 661d4705e863776cf932432d11a186e79b75c4b9 Merge: 723dd0ce3 35daefcf7 Author: WeiqunZhang Date: Wed Nov 15 08:09:03 2017 -0800 Merge pull request #167 from AMReX-Codes/fillpatchadd Add a FillPatch that adds, not copies commit 35daefcf7253882ed0a2137673c0a5eab64f7267 Author: Max Katz Date: Wed Nov 15 01:59:44 2017 -0500 Add a FillPatch that adds, not copies Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp commit 422c902ca3f76b009a8aec2c9356229c2ed94440 Author: dtgraves Date: Tue Nov 14 16:07:00 2017 -0800 put in hooks and started code for fourth order limiting. This stuff is complex. Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit 723dd0ce3a9df6129e780ffde4155244c8244565 Author: Weiqun Zhang Date: Tue Nov 14 15:49:10 2017 -0800 MLMG: make some changes so that Cy can put in his mapping Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit f0156d2818d3dead397ef04729089f52529600f9 Merge: 58bb9323c c692f2b43 Author: vince Date: Tue Nov 14 13:46:09 2017 -0800 Merge branch 'partio' of https://github.com/AMReX-Codes/amrex into partio commit fc4ff28f4de919a85bd82f21a2fbc85f069ccaf8 Author: Weiqun Zhang Date: Tue Nov 14 13:42:20 2017 -0800 update CHANGES CHANGES commit b22e68d05d27a901bd5aa824d5fd78c44207cbd2 Author: Weiqun Zhang Date: Tue Nov 14 13:21:51 2017 -0800 Tutorials/Amr/Advection_AmrCore: add memory log Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 14bd99c2513290972e4d3883b2ae1cf77544be35 Author: Weiqun Zhang Date: Tue Nov 14 13:20:26 2017 -0800 manually write MultiFab move ctor so that build can be logged Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit fb2afb0891d9dc736470b2605d2b9e335d67c379 Author: Weiqun Zhang Date: Tue Nov 14 12:48:05 2017 -0800 FabArray: clear before define; Tutorials/Amr/Advection_AmrCore: use Vector Src/Base/AMReX_FabArray.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 81ce8616e8cae3ca125c2b9f61908e4c800d2a6e Author: Weiqun Zhang Date: Tue Nov 14 11:45:10 2017 -0800 add clear() to FluxRegister Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp commit 493926033d868fee6ec31e6ffada42bae6509068 Author: Weiqun Zhang Date: Tue Nov 14 11:22:44 2017 -0800 implement move assignment operator for FabArray Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_iMultiFab.H commit 2d47723b4f36659c9e08219188bc2fc716f71a1c Merge: a5f28a791 8eeac0d44 Author: Weiqun Zhang Date: Tue Nov 14 09:14:04 2017 -0800 Merge branch 'development' into moveassign commit 8eeac0d44186a58f4fac37c6d110a3f0914ab75c Author: Weiqun Zhang Date: Tue Nov 14 09:13:22 2017 -0800 add GetVecOfPtrs again for FabArray types only Src/Base/AMReX_Vector.H commit ca793e1690f982d724f7035818da83e897e7ecf5 Author: Weiqun Zhang Date: Mon Nov 13 20:49:05 2017 -0800 revert Src/Base/AMReX_Vector.H commit a5f28a791582981ba55290209d6e8b7bb340ba25 Author: Weiqun Zhang Date: Mon Nov 13 17:35:31 2017 -0800 start writing move assignment for MultiFab and FabArray Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.H commit dab09741ac2f8d8e9a3bac88e9c34e30db3170a9 Author: Weiqun Zhang Date: Mon Nov 13 17:34:12 2017 -0800 add GetVecOfPtrs Src/Base/AMReX_Vector.H commit c692f2b434b7b2f52cf1ce17121cffada5e4959a Author: vince Date: Mon Nov 13 17:31:46 2017 -0800 remove flush. Src/Amr/AMReX_Amr.cpp commit 58bb9323c90ad18f3a91308aa4ba4d38eb4bd739 Merge: 84366119c 4136e3971 Author: vince Date: Mon Nov 13 16:28:29 2017 -0800 Merge branch 'partio' of https://github.com/AMReX-Codes/amrex into partio commit 4136e3971058ebab7038be542e076a0f36e9e3ed Author: vince Date: Mon Nov 13 16:19:13 2017 -0800 additions for pre and post checkpoint functions for i/o optimization. Src/Base/AMReX_NFiles.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 4b359904f75bea2f336084a44e4c79919843564d Merge: 74a70fa22 6898b2ded Author: dtgraves Date: Mon Nov 13 15:54:37 2017 -0800 merging with dev commit 74a70fa22188c4c3f2b73ea3de68718a92e78ad0 Author: dtgraves Date: Mon Nov 13 15:52:34 2017 -0800 added the hooks in the fortran to make limiting optional Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/slope_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/slope_3d.f90 commit 6898b2dedd5915213cb49b692bdd55c0b43ac1cd Merge: 594b5cd7c 916ad5728 Author: Andy Nonaka Date: Mon Nov 13 14:32:17 2017 -0800 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 594b5cd7c21ef502f57eb69a2f75c11d2d357717 Author: Andy Nonaka Date: Mon Nov 13 14:32:02 2017 -0800 add a CountCells function Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit ca337a5ab6623b92abc865f423f1ea9af11b4ced Author: dtgraves Date: Mon Nov 13 14:11:45 2017 -0800 cleaned up code--can now switch algorithm choice via the input file Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp commit 916ad5728df780720f9a69e5660802d32140a2af Author: Weiqun Zhang Date: Mon Nov 13 13:21:14 2017 -0800 add MLMG to libamrex GNUmakefile.in Tools/libamrex/configure.py commit aa71987abcce41ea089f9e7a588b37779d1b47a3 Merge: 58adc1d0c be4a1c208 Author: Andrew Myers Date: Mon Nov 13 13:23:28 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1b17ead7adfb3967b0e697351c772a6a1c353b35 Author: vince Date: Mon Nov 13 13:00:09 2017 -0800 additions for pre and post checkpoint functions for i/o optimization. Src/Particle/AMReX_Particles.H commit 2f78341957f238cb7be155a959fbc978942b9141 Author: vince Date: Mon Nov 13 12:59:13 2017 -0800 added particle nfiles. Docs/Readme.io commit f12381eb10ed15517fa9ef641b4beaf0b2099130 Author: vince Date: Mon Nov 13 12:52:00 2017 -0800 additions for pre and post checkpoint functions for i/o optimization. Src/Particle/AMReX_ParticleContainerI.H commit 0712b5c1af5b053daa3b405e2fc7aa0067894e7a Author: vince Date: Mon Nov 13 12:51:10 2017 -0800 increase default nfiles. Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_VisMF.cpp commit a7bd46d1b29dd24d5099887483a39c4e948ebd63 Author: vince Date: Mon Nov 13 12:49:27 2017 -0800 additions for pre and post checkpoint functions for i/o optimization. Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp commit eeb21798d95afd73d57d54755af161f3420529df Author: dtgraves Date: Mon Nov 13 12:01:09 2017 -0800 made progress on algorithm document Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex Tutorials/Amr/ScalarAdvectionDiffusion/Doc/references.bib commit be4a1c208663b123043ec786e5f84f76a855c79d Author: Weiqun Zhang Date: Mon Nov 13 11:00:18 2017 -0800 MLMG: some experimental approaches in consolidation Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 58adc1d0c763e3d08dcc227ea18779a573e8c96c Author: Andrew Myers Date: Mon Nov 13 10:38:23 2017 -0800 exit early from Redistribute if particle is invalidated. Src/Particle/AMReX_ParticleContainerI.H commit 913929fc0c4091d313f867c18a0c2b06bec829a2 Author: Weiqun Zhang Date: Sat Nov 11 20:39:39 2017 -0800 add some profilers Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 2cedd7752668e54dbcb3f66abe17bff6d5ebaf55 Author: Weiqun Zhang Date: Sat Nov 11 12:09:51 2017 -0800 fix a new bug in MLMGBndry Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp commit 1bf60c3ff06857e664a47a4e15a28fc443b52d86 Author: Weiqun Zhang Date: Sat Nov 11 10:48:04 2017 -0800 omp parallel Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp commit 1ac3ec5a394fe829f3f43d15ffc02e06d9412332 Author: Weiqun Zhang Date: Sat Nov 11 10:30:52 2017 -0800 add MLMGBndry Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_LO_BCTYPES.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMGBndry.H Src/LinearSolvers/MLMG/AMReX_MLMGBndry.cpp Src/LinearSolvers/MLMG/Make.package commit 4b156d381e59c8720fa0b5eeabbb6d4c5bde9314 Merge: 7b35779d8 8a3d5944b Author: Max Katz Date: Sat Nov 11 01:42:45 2017 -0500 Merge branch 'development' into gpu commit 8a3d5944b7b53699927c89a8f8178ff1907a8f40 Author: Weiqun Zhang Date: Fri Nov 10 17:52:14 2017 -0800 MLMG: add ReflectOdd and divide flux by beta Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H commit deb4880de11ad5a7a0b32db95fd207914feeecbd Author: kngott Date: Fri Nov 10 14:53:38 2017 -0800 Optimization tweaks. Src/Extern/amrdata/AMReX_DataServices.cpp commit 999fc1de082c58ecf1ef6df390f7b6b5a9049bd9 Merge: 040b79e60 0f53f804f Author: Andrew Myers Date: Fri Nov 10 14:20:10 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 040b79e60759c2fa115ef1fa07cadf751facd91b Author: Andrew Myers Date: Fri Nov 10 14:19:49 2017 -0800 some optimizations for neighbor particle finding and updating. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 0f53f804ff2d56fae862c03a9ab26c8550d7a479 Author: Weiqun Zhang Date: Fri Nov 10 12:00:15 2017 -0800 MLMG: fix 2d Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 23d9c7ff5acd727c66d2d41a94c13d9bec950b35 Author: Weiqun Zhang Date: Fri Nov 10 11:51:42 2017 -0800 MLMG: remove static memebers Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit f8391b16a834a8fcfeadca38e66af01d118e17a0 Author: Weiqun Zhang Date: Fri Nov 10 10:26:26 2017 -0800 MLMG: option to disable metric terms Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 574273550181ef513c4238a3f2731b05897e68f4 Merge: 54584dc74 f4611f4b1 Author: kngott Date: Thu Nov 9 18:09:04 2017 -0800 Merge branch 'partio' into profvis Conflicts: Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 54584dc741290cd6b12cfc1cda11223b2e2abcce Author: kngott Date: Thu Nov 9 17:31:45 2017 -0800 One more adjustment. Src/Extern/ProfParser/AMReX_CommProfStats.cpp commit fd4526b2ebd45b1463bc042f39a28b970fc5fd98 Author: kngott Date: Thu Nov 9 17:27:29 2017 -0800 OpenStreams adjustment. Src/Extern/ProfParser/AMReX_CommProfStats.cpp Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp commit add9692b146ab6f86719628b9707ee67a415d7cc Author: Weiqun Zhang Date: Thu Nov 9 16:44:15 2017 -0800 MLMG: option to fill final bc Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 6c143b780a8d0dbde690944a393531530d43b066 Author: kngott Date: Thu Nov 9 16:26:20 2017 -0800 bl_profprof Src/Extern/ProfParser/AMReX_ProfParserBatch.cpp commit 49d2a00b2030d7db8c502c0f4d8368d8f1623bf9 Author: dtgraves Date: Thu Nov 9 16:06:37 2017 -0800 working on more detailed document for this tutorial Tutorials/Amr/ScalarAdvectionDiffusion/Doc/paper.tex Tutorials/Amr/ScalarAdvectionDiffusion/Doc/references.bib Tutorials/Amr/ScalarAdvectionDiffusion/Doc/working_notes.tex commit 61c38d2b721a41af2a84a290ec419b40d10c5b97 Author: kngott Date: Thu Nov 9 15:41:36 2017 -0800 Additional/Corrected profiling flags in profiler. Src/Extern/ProfParser/AMReX_BLProfStats.cpp Src/Extern/ProfParser/AMReX_CommProfStats.cpp Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp Src/Extern/amrdata/AMReX_DataServices.cpp commit a60e8f63e61ce2a25f17ede7fad59722837a13ff Author: Weiqun Zhang Date: Thu Nov 9 14:50:40 2017 -0800 MLMG: fix periodic boundary Src/Base/AMReX_Geometry.H Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_FabSet.cpp Src/Boundary/AMReX_InterpBndryData.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit a37c4e53ff50fe65663e1d90b0bc6d246b0da172 Merge: 26748cd92 133236f5a Author: dtgraves Date: Thu Nov 9 13:50:36 2017 -0800 merging with dev branch commit 133236f5afa2c4df6cf390b97bf5a1d17e90d1c1 Author: kngott Date: Thu Nov 9 12:41:28 2017 -0800 Fixed incorrect bool. proxMap -> statsCollected Src/Extern/ProfParser/AMReX_ProfParserBatch.cpp Src/Extern/amrdata/AMReX_DataServices.cpp commit 26748cd92fe138adb73e120a835f8d7e0bd0792d Author: dtgraves Date: Thu Nov 9 12:39:54 2017 -0800 fixed time interpolation for TVD RK3 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp commit cf6ff64618daa1e2c387669a4c2b51d0aa089b70 Author: Weiqun Zhang Date: Thu Nov 9 11:15:42 2017 -0800 MLMG: fix the special case of alpha is zero Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit 84f3a7eaf378cff2af24e7472f5173c95be6c863 Author: Weiqun Zhang Date: Thu Nov 9 10:54:32 2017 -0800 MLMG: fix spherical Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 378404ac1a5750f009b986e9eea5cd64ac2d2bb5 Author: Weiqun Zhang Date: Thu Nov 9 10:49:22 2017 -0800 MLMG: skip applying metric terms in Cartesian Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit f4611f4b1f8b9632ab58122ab073032649de5abb Author: vince Date: Wed Nov 8 17:57:57 2017 -0800 add sparse vismf write for fabarrays with data on fewer mpi procs than nfiles. Src/Base/AMReX_NFiles.H Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_VisMF.cpp commit a8c6969accda6430b98894a510ef95252926bc73 Author: Weiqun Zhang Date: Wed Nov 8 17:39:18 2017 -0800 MLMG test: option to do fine level solve only Tests/LinearSolvers/MLMG/inputs.boxes Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit e58849fc539997c816f650dcf592b6117e415e80 Author: Weiqun Zhang Date: Wed Nov 8 17:29:27 2017 -0800 MLMG test: option to read grids Tests/LinearSolvers/MLMG/grids/gr.3_128cubed Tests/LinearSolvers/MLMG/grids/gr.3_256cubed Tests/LinearSolvers/MLMG/grids/gr.3_2boxes_a Tests/LinearSolvers/MLMG/grids/gr.3_2x3x4 Tests/LinearSolvers/MLMG/grids/gr.3_512cubed Tests/LinearSolvers/MLMG/grids/gr.3_big Tests/LinearSolvers/MLMG/grids/gr.3_disjoint_a Tests/LinearSolvers/MLMG/grids/gr.3_disjoint_b Tests/LinearSolvers/MLMG/grids/gr.3_disjoint_c Tests/LinearSolvers/MLMG/grids/gr.3_mac_tst Tests/LinearSolvers/MLMG/grids/gr.3_shiftedUp Tests/LinearSolvers/MLMG/grids/gr.3_small_a Tests/LinearSolvers/MLMG/grids/gr.3_stack_a Tests/LinearSolvers/MLMG/grids/grids.15456 Tests/LinearSolvers/MLMG/grids/grids.213 Tests/LinearSolvers/MLMG/grids/grids.25600 Tests/LinearSolvers/MLMG/grids/grids.5034 Tests/LinearSolvers/MLMG/inputs.boxes Tests/LinearSolvers/MLMG/main.cpp commit a56061c1351d9882a2f741f77afaad59ef639fb5 Author: dtgraves Date: Wed Nov 8 16:58:32 2017 -0800 fixed loop bound bug in 3d fortran Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Notes/notes.tex Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit b85f099fe30f67184a095ddbdb71213ee11ff4b2 Author: Weiqun Zhang Date: Wed Nov 8 16:24:15 2017 -0800 MLMG: if scalar a is zero, we can simply set coefficient to zero Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit 30bd8d6a3b069e87233be6bf9fcc9be72acdb861 Author: kngott Date: Wed Nov 8 14:09:38 2017 -0800 Testing and turning off of persistent streams for profparser when number of files is extremely large. Src/Extern/ProfParser/AMReX_CommProfStats.H Src/Extern/ProfParser/AMReX_CommProfStats.cpp Src/Extern/ProfParser/AMReX_RegionsProfStats.H Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp commit 121bb82763322fe3a3dc0ad83d2a37b693c6c1dd Author: kngott Date: Wed Nov 8 13:56:49 2017 -0800 Output cleanup for MoveAllFabs and MoveFabs. Src/Base/AMReX_FabArray.H commit aa4364b46729bd907a30efe3f70c990538a17410 Author: kngott Date: Wed Nov 8 13:45:26 2017 -0800 MoveAllFabs adjustment to allow testing at any number of procs. OldTutorials/MultiFabTests_C/MoveAllFabsTest.cpp commit 134de6997d04d484465ad3219733aab8286152fa Author: dtgraves Date: Wed Nov 8 13:37:17 2017 -0800 convergence results look pretty good Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs commit 6a5b7972f2b00f0f6e86d3defd9b7404b9a35054 Author: dtgraves Date: Wed Nov 8 13:20:41 2017 -0800 finished coding time interpolation for TVD rk3 scheme. Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit c7ffacc1cd721cecc281955753f6c1c0694635a2 Author: Weiqun Zhang Date: Wed Nov 8 09:36:53 2017 -0800 MLMG test: add option to do level by level solve Tests/LinearSolvers/MLMG/inputs Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 99d0b7abc2bbe2a39ac6206bd86494defd505106 Author: Weiqun Zhang Date: Wed Nov 8 09:36:21 2017 -0800 MLMG: agglomeration and consolidation flags need to be static because they are used by the constructor Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 559e79d7778f2c87a067e7165a0723a6ef21b0e9 Author: Weiqun Zhang Date: Tue Nov 7 16:55:12 2017 -0800 MLMG: 1d implemented but not tested Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 45e339a2c84c1d6d0ac5f5ad7dfde8206d65b599 Author: Weiqun Zhang Date: Tue Nov 7 16:39:59 2017 -0800 MLMG: 1d Src/LinearSolvers/MLMG/AMReX_MLABecLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_1d.F90 commit a07cb52fc81ac612a2f16d0850aba6fcf93f39a7 Author: Weiqun Zhang Date: Tue Nov 7 15:59:29 2017 -0800 MLMG: add getGradSolution function Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/Make.package commit e953bb0fc7ee87af19afe08b48b603897ed07090 Author: vince Date: Tue Nov 7 15:52:05 2017 -0800 more information for errors. Src/Extern/amrdata/AMReX_DataServices.cpp commit 16adbdb7c0e8ec5bd8103191c68eae149348773b Author: Weiqun Zhang Date: Tue Nov 7 15:22:42 2017 -0800 MLMG: metric terms for ABecLaplacian Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp commit 88de794b37cf5169c394dbc94b470e848206a282 Author: Weiqun Zhang Date: Tue Nov 7 13:56:44 2017 -0800 MLMG: 2d and cylindrical coordinates Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_F.H commit 9b8f68ea1bbee2355946ae4baad12e2f40dd733f Author: Brian Friesen Date: Tue Nov 7 14:16:08 2017 -0800 EB: change type of get_neighbor_cells_int_single() function from PURE to ELEMENTAL ELEMENTAL is a stronger statement about the function's behavior, and implies PURE anyway. Src/EB/AMReX_ebcellflag_mod.F90 commit c40d1aa92aea1c071460bd7aa37856ab99f3ba02 Author: dtgraves Date: Tue Nov 7 14:08:47 2017 -0800 now seeing third order solution error with AMR Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/face_velocity_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp commit 49383e700c6472eff805b19ca10c10f5557edd32 Author: Brian Friesen Date: Tue Nov 7 12:58:54 2017 -0800 EB, Combustor: add function get_neighbor_cells_int_single() This function behaves similarly to get_neighbor_cells_int(), except it returns a single value for the requested neighbor cell, rather than returning a 3x3x3 array containing values for all neighbors. This single-value approach is friendlier to function inlining and vectorization, and also yields better memory access patterns because a compiler attempting to vectorize a loop which calls this function need not generate private 3x3x3 arrays for each lane of a vector processing unit. Src/EB/AMReX_ebcellflag_mod.F90 Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90 commit 91f146b168acfcd0cd32678d62ffa84e8e94f2d2 Author: Andrew Myers Date: Tue Nov 7 12:40:41 2017 -0800 also cache the grown_gridbox in EnforcePeriodicWhere. Src/Particle/AMReX_ParticleContainerI.H commit 1ff88b844e5de4f8a1e7a82bbfd45dbb0f1e9b4c Author: dtgraves Date: Tue Nov 7 12:31:29 2017 -0800 now getting fourth order truncation error with AMR Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/fourthOrderCFInterpTest.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/test.inputs commit a0e1ef4390d1b60893a2a233bf9759bafc161b8d Merge: 0e110af47 2830155bd Author: Andrew Myers Date: Tue Nov 7 11:26:08 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0e110af470a663f975d3588a3d5816e973cbd58e Author: Andrew Myers Date: Tue Nov 7 11:25:57 2017 -0800 reset the pld cache after trying the grown particle locate (the next one might not have the same nGrow) Src/Particle/AMReX_ParticleContainerI.H commit 2830155bd1dd038ba79633d76cedd6660a92c6e5 Author: Weiqun Zhang Date: Tue Nov 7 10:16:29 2017 -0800 PlotFileUtil: option to pre-build extra directories in plotfile Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_PlotFileUtil.cpp commit 8895ad444953afd01d7a52de5ab0f28aecb62ac5 Author: Weiqun Zhang Date: Tue Nov 7 09:37:30 2017 -0800 PlotFileUtil: use default in VisMF Src/Base/AMReX_PlotFileUtil.cpp commit 7b35779d89162f9bb9d5207225be2d6ed1f2541b Author: Max Katz Date: Mon Nov 6 21:34:22 2017 -0500 Add C binding to get_loop_bounds Src/Base/AMReX_Device.H Src/Base/AMReX_fort_mod.F90 commit 145c1a13f0ebca0bd83043bf87f9cd1d613fd384 Author: Marc Day Date: Mon Nov 6 18:22:35 2017 -0800 Lower limit error mag for computing order Tools/C_util/Convergence/RichardsonConvergenceTest.cpp commit f09458efdb67b9f4e8e37371df80db70d2315028 Author: Andrew Myers Date: Mon Nov 6 17:43:26 2017 -0800 try four. build_and_deploy.sh commit d2f082fd647a730331055a86cc713385f6e24d51 Author: Andrew Myers Date: Mon Nov 6 17:37:56 2017 -0800 try two make jobs build_and_deploy.sh commit 39be9da1c811045e20ba5f0afb370f485c6c371b Author: Andrew Myers Date: Mon Nov 6 17:31:18 2017 -0800 do serial build. build_and_deploy.sh commit bba5ab3cdf86e8c1292e5401255eedd4d894275e Author: Andrew Myers Date: Mon Nov 6 17:25:23 2017 -0800 have travis build libamrex on each push. .travis.yml build_and_deploy.sh commit 361fa7cfd66f632c2c52fdf88054e34bf0ea6e05 Merge: bbf60e481 26d458ea3 Author: Max Katz Date: Mon Nov 6 20:23:55 2017 -0500 Merge branch 'development' into gpu commit 26d458ea360b898a09256424a6e3472d898a0f0d Author: Andrew Myers Date: Mon Nov 6 16:45:37 2017 -0800 another Redistribute optimization. Src/Particle/AMReX_ParticleContainerI.H commit e4159842aa65a6621ac6db07c3bb53785b9dc0c7 Author: dtgraves Date: Mon Nov 6 16:17:38 2017 -0800 added test for coarse-fine interpolation. FillPatchUtil with quartic_interp is indeed fourth order Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Tests/CFITest/fourthOrderCFInterpTest.cpp commit d8532319ae4b4ac7c9b43a0ee3795a21e23b64aa Author: Andrew Myers Date: Mon Nov 6 16:14:47 2017 -0800 an optmization for ParticleContainer::Redistribute Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit e2044b0862935263470c739fa99ecd6bee0b3d25 Merge: f4d64b821 a6f4ee4d8 Author: Andrew Myers Date: Mon Nov 6 12:10:43 2017 -0800 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a6f4ee4d89101d04bb27e244983a63f99fac4779 Author: Weiqun Zhang Date: Sun Nov 5 12:46:41 2017 -0800 MLMG make applybc work for any d Src/LinearSolvers/MLMG/AMReX_MLLinOp_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_nd.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/Make.package commit 973117ddb8d6ec85cfb4ab080d0d0cc1a3628452 Author: Weiqun Zhang Date: Sun Nov 5 12:23:50 2017 -0800 MLMG: implement 2D version of some funcitons Src/LinearSolvers/MLMG/AMReX_MLABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_3d.F90 commit d7b0d9ab619271aee0bdcf4e35582d54eb0207fe Author: Weiqun Zhang Date: Fri Nov 3 09:08:05 2017 -0700 fix for the most vexing parse in C++ Src/F_Interfaces/Base/AMReX_geometry_fi.cpp commit e17812c287b2ebf3311c91d9d09e9922daeb68d7 Author: Weiqun Zhang Date: Fri Nov 3 09:05:28 2017 -0700 fix particle module for 1d Src/Particle/AMReX_Particle_mod_1d.F90 commit 6d1941035a5a2b39299868a376a5716ba3e236da Author: Michael Zingale Date: Fri Nov 3 11:43:11 2017 -0400 warn if analysis failed and store analysis output Tools/RegressionTesting/regtest.py commit 9bd4e53ae73483a652c980f2f9dd12caac98631a Author: Michael Zingale Date: Thu Nov 2 20:03:16 2017 -0400 quote slack posts Tools/RegressionTesting/regtest.py commit 207c75da3ad51deb2da1ba20bf8ce0a86264332a Author: Neil Carlson Date: Thu Nov 2 12:55:13 2017 -0600 Use amrex_constants_module in amrex_filcc_2d Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 commit 236805b1144727cb6b2d939733cc9ad61a70e47b Author: Max Katz Date: Thu Nov 2 14:09:41 2017 -0400 Add protections against accessing invalid dimensions Src/Base/AMReX_filcc_mod.F90 commit f7295c25f59b558a992e867916299bd7c74131f4 Author: Neil Carlson Date: Thu Nov 2 10:41:13 2017 -0600 Use amrex_constants_module in amrex_filcc_3d; trivial nag fix Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_filcc_mod.F90 commit 306667ebd2024e27aa575a07de286702275b0870 Author: Weiqun Zhang Date: Wed Nov 1 17:23:50 2017 -0700 use amrex_constants_module in amrex_filcc_module Src/Base/AMReX_filcc_mod.F90 commit 3e242fd36154fea4c3e570d5993a5b47d572008c Author: Weiqun Zhang Date: Wed Nov 1 17:20:25 2017 -0700 add amrex_constants_module and make bl_constants_module use it Src/Base/AMReX_constants_mod.f90 Src/Base/CMakeLists.txt Src/Base/GPackage.mak Src/Base/Make.package Src/F_BaseLib/bl_constants.f90 commit f292c3634c4ca5d2fb9af475f433ac13f17c7a03 Merge: ff1606f3c bf1cba0db Author: Weiqun Zhang Date: Thu Nov 2 12:52:03 2017 -0700 Merge branch 'weiqun/mlmg' into development commit bf1cba0dbe95eb512bc68b4ef7b25d97f3edc0e8 Author: Weiqun Zhang Date: Thu Nov 2 12:51:22 2017 -0700 MLMG: must use the fine dx for bc location on coarse MG levels Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit ff1606f3c453a753e93aa6d29cb3ae1892832ef1 Merge: 45c301572 e2c995cac Author: WeiqunZhang Date: Thu Nov 2 11:59:51 2017 -0700 Merge pull request #163 from nncarlson/constants-fix Use amrex_constants_module in amrex_filcc_2d commit e2c995cacc324f26c99686abe745c066517fecf8 Author: Neil Carlson Date: Thu Nov 2 12:55:13 2017 -0600 Use amrex_constants_module in amrex_filcc_2d Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 commit 45c301572c9ca14da448f38167be1f4fbb2fb519 Author: Max Katz Date: Thu Nov 2 14:09:41 2017 -0400 Add protections against accessing invalid dimensions Src/Base/AMReX_filcc_mod.F90 commit f4d64b821d73a4213d6f42d7e4b2c4c750611dac Merge: f9a1cdc41 d053d7e2f Author: Andrew Myers Date: Thu Nov 2 10:05:04 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2a44019130a8fac1467b8cbd1cb47f98dcb7d614 Author: Weiqun Zhang Date: Thu Nov 2 10:02:44 2017 -0700 MLMG: simplify norm_inf calls Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit d053d7e2f4d6bca3be276e1e7db28cda271c2af0 Merge: 11335a50f 63b207c04 Author: WeiqunZhang Date: Thu Nov 2 09:47:49 2017 -0700 Merge pull request #161 from nncarlson/nag-fixes Use amrex_constants_module in amrex_filcc_3d; trivial nag fix commit 63b207c04d74601dd9628edd330b6346777527a2 Author: Neil Carlson Date: Thu Nov 2 10:41:13 2017 -0600 Use amrex_constants_module in amrex_filcc_3d; trivial nag fix Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_filcc_mod.F90 commit 149261548d0ce070843b7c6f1e3563bae61281b4 Merge: d7921da58 11335a50f Author: Weiqun Zhang Date: Thu Nov 2 08:48:00 2017 -0700 Merge branch 'development' into weiqun/mlmg commit d7921da58b26a4ebf20e03f7dbe49175b0c12c1b Author: Weiqun Zhang Date: Thu Nov 2 08:47:56 2017 -0700 minor Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 572f6ff4910409aa56d763dd47f877df3c39864c Author: Brian Friesen Date: Thu Nov 2 08:40:48 2017 -0700 EB: change INTENT of neighbor lists in get_neighbor_cells() to OUT Src/EB/AMReX_ebcellflag_mod.F90 commit 11335a50f0f2b2a0e7954e19b9285ff891112cdc Author: atmyers Date: Wed Nov 1 18:12:34 2017 -0700 revert testing stuff for now. .travis.yml build_and_deploy.sh commit b726bbb7f9898860f67602cb2ff7197a0ae01073 Author: atmyers Date: Wed Nov 1 18:02:39 2017 -0700 try openmpi and gfortran .travis.yml commit c63e556afdfe43dca4a5de56e26e29fb8d48000b Author: atmyers Date: Wed Nov 1 17:55:12 2017 -0700 add mpich to the packages to install .travis.yml commit 02af6e6a806d9cfffd83453c39a805650be78fc2 Author: atmyers Date: Wed Nov 1 17:36:24 2017 -0700 also test whether we can build libamrex in travis. build_and_deploy.sh commit 8f78681780f6a09d582bc64eed705605b4df9bdd Author: Weiqun Zhang Date: Wed Nov 1 17:23:50 2017 -0700 use amrex_constants_module in amrex_filcc_module Src/Base/AMReX_filcc_mod.F90 commit 5ffd46558f0fb9fafca769432b61238d01bfc503 Author: Weiqun Zhang Date: Wed Nov 1 17:20:25 2017 -0700 add amrex_constants_module and make bl_constants_module use it Src/Base/AMReX_constants_mod.f90 Src/Base/CMakeLists.txt Src/Base/GPackage.mak Src/Base/Make.package Src/F_BaseLib/bl_constants.f90 commit fc54c516d7c15488c2cc3225115a1b528cb7c2dd Author: atmyers Date: Wed Nov 1 17:03:27 2017 -0700 always return true from both git commit and git push. build_and_deploy.sh commit baf4f6cb3a7b4f6d343330b77c87f225e282afbe Author: dtgraves Date: Wed Nov 1 16:28:16 2017 -0700 bug fix in time interpolation Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp commit 39f7e39539042e60c830566a581bcfec14849d02 Author: atmyers Date: Wed Nov 1 16:26:06 2017 -0700 exit successfully if there are no changes. build_and_deploy.sh commit 09b6bf2eb086b6da1169527144fd43c2751cf53a Author: Weiqun Zhang Date: Wed Nov 1 16:08:01 2017 -0700 MLMG: fix bugs Src/Base/AMReX_ParallelDescriptor.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp commit 475819873c8b26edbe79975774c337b63dfdd1c1 Author: atmyers Date: Wed Nov 1 15:58:06 2017 -0700 always return true from git push build_and_deploy.sh commit 9966851a80cb2661e8a57212ac09f5d03077bd7a Merge: 4b0d13ca3 97d9c560c Author: WeiqunZhang Date: Wed Nov 1 15:47:11 2017 -0700 Merge pull request #160 from nncarlson/F2003-pure-fix Add argument intent for pure subroutine required by F2003 commit 97d9c560c07530d20cd3c28cd247d85e0d5c4c46 Author: Neil Carlson Date: Wed Nov 1 16:17:31 2017 -0600 Add argument intent for pure subroutine required by F2003 Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 commit 89eb733392dd6c382c477f7000c194252d69223f Author: Weiqun Zhang Date: Wed Nov 1 15:01:38 2017 -0700 MLMG: distribution map consolidation Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 57a8ae0e3b5ed5f4fafa954bb33e9a05050a202b Merge: 39ba5b957 4b0d13ca3 Author: dtgraves Date: Wed Nov 1 14:15:30 2017 -0700 keeping up with dev branch commit 39ba5b957ba37bc7156a2720328af9bc099e41f3 Author: dtgraves Date: Wed Nov 1 14:15:17 2017 -0700 added some small debugging hooks Tools/C_util/Convergence/DebugDump.H Tools/C_util/Convergence/DebugOut.H Tools/C_util/Convergence/DebugOut.cpp Tools/C_util/Convergence/Make.package Tools/C_util/Convergence/RichardsonConvergenceTest.cpp commit cc7e29abc5fa7cb1966e90dd9dc8df21a8772245 Author: dtgraves Date: Wed Nov 1 14:09:24 2017 -0700 now have fourth order interpolation running without NaN's---on to testing Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Tagging_nd.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit 1fd93d914b3c8fa7800e50533c399fdd998c8053 Author: dtgraves Date: Wed Nov 1 14:03:39 2017 -0700 added a hook to avoid dividing by zero in BaseFab::linInterp Src/Base/AMReX_BaseFab.H commit 0543fa21e0401d2a5715b13a141f8d9521347865 Author: Weiqun Zhang Date: Wed Nov 1 13:42:05 2017 -0700 MLMG: jump the sequence number before bottom solve and and then reset afterwards Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit fb787d8625c2f65bcad8a9c58344db8e9140f351 Author: Weiqun Zhang Date: Wed Nov 1 13:29:35 2017 -0700 MLMG: fix bug Src/Base/AMReX_ParallelReduce.H commit b9688193f10f389307d94ff9d0638a1dc77ecf34 Author: Weiqun Zhang Date: Wed Nov 1 11:34:58 2017 -0700 minor Src/LinearSolvers/MLMG/AMReX_MLLinOp.H commit 84c61854749032fa696bd2aad0eadbb1c4990dcf Author: Weiqun Zhang Date: Wed Nov 1 11:23:57 2017 -0700 MLMG::bottomSolve: use subcommunicator for allreaduce of sum Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 234609f8044f8bf4a16e2041343e1fee90b701eb Author: Weiqun Zhang Date: Wed Nov 1 11:16:39 2017 -0700 MLMG: build subcommunicator for bottom Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 06fd43b754c28ad334256e6706e366215fae231e Author: Weiqun Zhang Date: Wed Nov 1 09:27:14 2017 -0700 MLMG: only bottom needs a subcommunicator Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 4b0d13ca3ca27bcb4d9f068bc90b63f8d4d7d6e6 Author: Weiqun Zhang Date: Wed Nov 1 08:48:03 2017 -0700 add 17.11 to CHANGES CHANGES commit 2b5740ddb488c52933594998a8a67d672f1bdd76 Author: vince Date: Tue Oct 31 17:42:00 2017 -0700 fix for alternate bl_prof directory names. Src/Base/AMReX_BLProfiler.cpp commit 13ae296ee5d724e2d3870778d648379f34d6692b Author: Weiqun Zhang Date: Tue Oct 31 16:51:48 2017 -0700 MLMG: use sub communicator Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_ParallelReduce.H Src/Base/CMakeLists.txt Src/Base/Make.package Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H commit 1edfcffa1f7560dd2cb5142c01a97b0811e916cb Author: dtgraves Date: Tue Oct 31 16:53:41 2017 -0700 added rk4 time interpolation Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Source/timeinterpolate.f90 commit f9a1cdc41e94b82225eb2340678122a64dde99b4 Merge: c5c4f6be5 c63920657 Author: Andrew Myers Date: Tue Oct 31 16:09:30 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c63920657cb2742f88272173b3781836b3bd4e30 Author: atmyers Date: Tue Oct 31 15:41:37 2017 -0700 helps if you use the right format so Doxygen can parse it. Src/Particle/AMReX_Particles.H commit 0160244fdeeac5ea733a8e9d402abc2475102bd5 Author: Weiqun Zhang Date: Tue Oct 31 15:11:54 2017 -0700 MLMG: store communicators Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 484317651bc8a9915be30d68f89c7c742e00b7b6 Author: Weiqun Zhang Date: Tue Oct 31 14:40:02 2017 -0700 MLMG: build special distributionmapping Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H commit 18108cdbe20528424309161e27e9b349885f0428 Author: atmyers Date: Tue Oct 31 14:37:01 2017 -0700 don't need to remove this here. build_and_deploy.sh commit 52cc1c77528bcf18f5b7095c85a7f783eb280c1e Author: atmyers Date: Tue Oct 31 14:36:01 2017 -0700 only make new directories if they don't already exist. build_and_deploy.sh commit ba333d21cbaba29eb5f5e98d240ee7fe17741d3b Author: atmyers Date: Tue Oct 31 14:27:08 2017 -0700 add a doxygen-formated brief for ParticleContainer to test the Travis CI stuff. Src/Particle/AMReX_Particles.H commit 51185c10c5adbbb221472b203165f6168ff9546c Author: dtgraves Date: Tue Oct 31 14:13:05 2017 -0700 diffusion convergence rates are now correct, as well. On to time interpolation for AMR Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit 3d1e366187eb5effc4c70778527253ce0b2bb4c4 Author: atmyers Date: Tue Oct 31 14:09:59 2017 -0700 adding deploy script and configuration for Travis CI .travis.yml build_and_deploy.sh id_rsa_travis.enc commit 4175899b1711613e277490a610a5f771bda4c430 Author: atmyers Date: Tue Oct 31 14:01:25 2017 -0700 remove ystatic from html_static_path entry. Docs/sphinx/source/conf.py commit d0103d9aa3c702c43a9a15459bf6f0ffda42d9e8 Author: atmyers Date: Tue Oct 31 13:58:13 2017 -0700 update link location for the doxygen documentation. Docs/sphinx/source/intro.rst commit d4a7f1979c468201d9ba81dd3eeece66d1ea9ef6 Author: atmyers Date: Tue Oct 31 12:06:45 2017 -0700 turn off latex in the doxygen build. Docs/Doxygen/doxygen.conf commit 8bca9639d61cc15e5d6ede464f4067e84b5b1961 Author: dtgraves Date: Tue Oct 31 11:43:37 2017 -0700 bug fix Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit 0fb2c25daf6b6ea22c5e0e8ef6c58c65f3236105 Author: dtgraves Date: Tue Oct 31 11:31:31 2017 -0700 bug fix in diffusion flux stencil Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 commit bbf60e481ef1e878eb767c3e482f1be6b7302cca Author: Max Katz Date: Tue Oct 31 13:28:48 2017 -0400 Restore device copy of nvar Src/Base/AMReX_BaseFab.H commit 7c5b39e83e19dd2f2cd6f4843df6ddcdb958fbb3 Author: Max Katz Date: Tue Oct 31 13:00:15 2017 -0400 Update to use cellsize again Tutorials/GPU/HeatEquation_EX1_C/advance.cpp commit c7ed7d0ff2d01e8879d2b58fce30fa77602f2331 Author: Max Katz Date: Tue Oct 31 12:59:51 2017 -0400 Add device notation to dimensional filcc Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 commit 582538b999151ba251915f6d5db3f4f378db36ac Merge: cfdfed35b 4fbebf19b Author: Max Katz Date: Tue Oct 31 12:49:38 2017 -0400 Merge branch 'development' into gpu commit 4fbebf19bae0e3506b30ab2eeedb849967aee592 Merge: 31d1de11f 117956005 Author: WeiqunZhang Date: Tue Oct 31 09:38:40 2017 -0700 Merge pull request #154 from AMReX-Codes/filcc Have old filcc's call new filccn commit 31d1de11f1d13feb44e0d25091ad4b62f1d91f8a Author: Weiqun Zhang Date: Tue Oct 31 09:08:27 2017 -0700 F_Interfaces: add nodal_type function to multifab, imultifab and boxarray Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 2961366ffa5f9c4d6175dc4c59fe780138a76275 Merge: 6239438ed c5a0ceade Author: Weiqun Zhang Date: Mon Oct 30 17:54:35 2017 -0700 Merge branch 'development' into weiqun/mlmg commit 6239438edb46df244ce18a8048c25f78dd6327aa Author: Weiqun Zhang Date: Mon Oct 30 17:54:07 2017 -0700 MLMG: fix bugs in agglomeration Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 1696edea1b5f0efb42367eacff39bdf6ce1fd3dd Author: Weiqun Zhang Date: Mon Oct 30 17:37:02 2017 -0700 MLMG: build bc conditions and locations for each MG level Src/Base/AMReX_LayoutData.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit e10bfc7ae49085f8500a4f147b66a4b50304ff9c Author: dtgraves Date: Mon Oct 30 17:03:47 2017 -0700 Apparently, using pi=4.0d0*atan(1.0d0) is not an accurate enough representation of pi to avoid RK integrators producing bogus results at periodic boundaries (using this, I was getting sin(2.0d0*pi*1.0d0) = O(10^-7) instead of something near roundoff). Who knew? Now all looks correct in the convergence universe. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 commit 9840a79d68606da016cc608a143698ae31ae1487 Author: Weiqun Zhang Date: Mon Oct 30 15:24:12 2017 -0700 MLMG: use the new applybc Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 5b18b9da431931a7a683b02fb332c5730f409aca Author: dtgraves Date: Mon Oct 30 13:41:50 2017 -0700 bug fixes for rk4 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 commit c5c4f6be5bc4bae95293f99b39c100a7cdea698a Merge: 59aacf1d8 c5a0ceade Author: Andrew Myers Date: Mon Oct 30 10:43:29 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c5a0ceadeb4654d4055763260f69eaa01bd2fd21 Merge: b91488773 539147872 Author: Max Katz Date: Mon Oct 30 09:23:33 2017 -0700 Merge pull request #156 from zingale/development if we are doing `print-`, then don't do dependency checking commit 539147872e154f6d3119742038e5edb7c27edeb8 Author: Michael Zingale Date: Mon Oct 30 12:08:19 2017 -0400 if we are doing `print-`, then don't do dependency checking Tools/GNUMake/Make.rules commit 893191b3a0be48a9794e49ef6794f3feacb77e8c Author: Weiqun Zhang Date: Sun Oct 29 16:00:32 2017 -0700 WIP MLMG: more on applybc Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H commit 8767bb07e2cf2c18ecb10a842771a27b133ac449 Author: Weiqun Zhang Date: Sun Oct 29 11:32:32 2017 -0700 MLMG: wip Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 6fb97e8278ed4178911991d38d0188b055ca2e96 Author: Weiqun Zhang Date: Sun Oct 29 08:16:20 2017 -0700 MLMG: add some fortran files in preparation for rewriting applybc Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp_F.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/Make.package commit 52335a994a4f387993207142387c4018af0abc39 Author: Weiqun Zhang Date: Sat Oct 28 21:28:16 2017 -0700 MLMG: finish first pass of agglomeration without consolidation Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 39ecff9760d5b7cfbb8f7ce3f7e757bd5655545b Author: Weiqun Zhang Date: Sat Oct 28 15:42:17 2017 -0700 make averag_down_faces more general Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit f238f56330e3529bd537ad620ff48fccbc14ef59 Author: Weiqun Zhang Date: Sat Oct 28 14:09:53 2017 -0700 MLMG: agglomeration WIP Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit 324b844425db23f813a086c45b73a4b7325dc398 Author: Weiqun Zhang Date: Sat Oct 28 13:21:22 2017 -0700 min width argument for coarsenable function Src/Base/AMReX_Box.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit cfdfed35b8153b5e9935bc63557b8d0785dc702b Merge: 7b1c0aa32 b91488773 Author: Max Katz Date: Sat Oct 28 14:45:17 2017 -0400 Merge branch 'development' into gpu commit b9148877355ca3fbfe2c332644e497c2f2228026 Author: Weiqun Zhang Date: Fri Oct 27 19:37:42 2017 -0400 fix omp atomic form Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit f3f33730609b2bee4e7a6ef1aa48adf4b7bd3e70 Author: dtgraves Date: Fri Oct 27 16:06:18 2017 -0700 more hooks and options Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/face_velocity_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugDump.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugOut.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugOut.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 commit ca0fc488e6c62908132c1668dff257c5a7f02b1a Author: kngott Date: Fri Oct 27 15:53:45 2017 -0700 Making it run again. Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H commit 0a5ac547203e681989b63dfb904e87935d956c25 Author: kngott Date: Fri Oct 27 15:25:24 2017 -0700 Removal of proximity mapping options. Src/Amr/AMReX_Amr.cpp Src/Base/AMReX_DistributionMapping.H commit 88be98cdc01c7f4ac5b21837715213284a362e43 Author: kngott Date: Fri Oct 27 14:58:15 2017 -0700 Constant reference adjustment. Src/Base/AMReX_BLBackTrace.H Src/Base/AMReX_BLBackTrace.cpp commit 37c33a04bfa6261bb721219d60d3d49297680442 Author: kngott Date: Fri Oct 27 14:46:19 2017 -0700 Addition of BoxArray and DistributionMapping hashing functions for comparison across MPI. Also, adjustment of BroadcastDistributionMapping to include color. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit fd197561908f97182eb1024099cdb96db8a8f6ad Author: kngott Date: Fri Oct 27 14:43:52 2017 -0700 Function that outputs a backtrace but does not abort. Src/Base/AMReX_BLBackTrace.H Src/Base/AMReX_BLBackTrace.cpp commit 3097fde8f091eb7c045839446850d34510eedd86 Author: Ann Almgren Date: Fri Oct 27 12:48:37 2017 -0700 Need to reflect FILCC change in the CMakeLists.txt Src/Base/CMakeLists.txt commit 75e3a5f1dafe658e6e3e8377c74a0e3049cf4994 Merge: 55b199e11 459c01157 Author: Ann Almgren Date: Fri Oct 27 12:47:19 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 55b199e115152c9877c8c23517190771344e99cd Author: Ann Almgren Date: Fri Oct 27 12:47:14 2017 -0700 Fix typo Docs/AMReXUsersGuide/EB/EB.tex commit 84366119c3389ce0659b04f2c7a965ef10b4a73b Merge: adf2f689f 459c01157 Author: vince Date: Fri Oct 27 11:57:53 2017 -0700 Merge branch 'development' into partio commit 117956005c93a9c40c4af41dffb87d5453983e94 Author: Max Katz Date: Fri Oct 27 11:16:32 2017 -0400 Have old filcc's call new filccn Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 commit 459c011578aca83f883fc1fcffceece96d45f643 Author: Max Katz Date: Fri Oct 27 02:57:46 2017 -0400 Move the FILCC functions to F90 files Src/Base/AMReX_FILCC_1D.F Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F Src/Base/AMReX_FILCC_3D.F90 Src/Base/Make.package commit 7b1c0aa3249f68f97a473f6809aab08d10d3b37a Author: Max Katz Date: Fri Oct 27 02:05:19 2017 -0400 Wrap a CUDA-only parameter in an ifdef Src/Base/AMReX_FabArrayBase.cpp commit 3753a226a570dcad6f611fee704abb597694113c Author: Max Katz Date: Fri Oct 27 01:55:04 2017 -0400 Move .F90 FILCC files back to .F Src/Base/AMReX_FILCC_1D.F Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F Src/Base/AMReX_FILCC_3D.F90 Src/Base/Make.package commit 869a68f364ef7afb2a73ef830c1a8640b486a9d2 Author: Max Katz Date: Fri Oct 27 01:33:13 2017 -0400 Use a larger string size for bl_error/warning Src/Base/AMReX_BLBoxLib_F.f commit 763b20ea40417ca1194a56f57d559effb91c8141 Author: Max Katz Date: Fri Oct 27 01:28:00 2017 -0400 Sync up heat equation with development Tutorials/Basic/HeatEquation_EX1_C/main.cpp commit 0a067632d75e3069ecc4d911240127e6ef5361bc Author: Max Katz Date: Fri Oct 27 01:16:33 2017 -0400 Update sites for CORAL early access systems Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_pgi.mak Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.llnl Tools/GNUMake/sites/Make.olcf Tools/GNUMake/sites/Make.unknown commit e6e22b90d09a453dcf46fee462e50ed29c826bac Author: Max Katz Date: Fri Oct 27 01:24:37 2017 -0400 summit -> summitdev Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_pgi.mak commit e52915056c48d696a51a40cbc2abd932fb709fb2 Merge: 0dfa04879 033bbf7dd Author: Max Katz Date: Fri Oct 27 00:57:22 2017 -0400 Merge branch 'development' into gpu commit 033bbf7dd40bfe187d008c76e5f1a1aa340e8de0 Merge: cd67099aa 5dd86b0ac Author: WeiqunZhang Date: Thu Oct 26 16:18:35 2017 -0700 Merge pull request #152 from AMReX-Codes/filcc Create a dimension agnostic, multi-component filcc commit 5dd86b0acaea96f3d4cded219c5f5adbde1ea62b Merge: c7969cda8 bfbf7689a Author: Max Katz Date: Thu Oct 26 16:04:39 2017 -0700 Merge pull request #153 from AMReX-Codes/fillcc2 move some if tests out of nested i-j-k loops commit cd67099aa6fad681e9e3d6ee136360607b312c4e Merge: 974bdbd9b 750344500 Author: vince Date: Thu Oct 26 15:58:10 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 974bdbd9b1764f48e9c9feb886d0b34b0b2e3da2 Author: vince Date: Thu Oct 26 15:57:46 2017 -0700 added 1-e/i percent time to html output. Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp commit 75034450058d266089a63d58e8dec4e03112fbbc Author: Weiqun Zhang Date: Thu Oct 26 13:34:31 2017 -0700 MLMG: fix ref ratio of 4 Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 commit bfbf7689a1e3996a6c6f549ec9a440d4583921a8 Author: Weiqun Zhang Date: Thu Oct 26 13:19:04 2017 -0700 move some if tests out of nested i-j-k loops Src/Base/AMReX_filcc_mod.F90 commit 0dfa04879431ca50e106f7706c8e58ac3629d3d3 Author: Max Katz Date: Thu Oct 26 12:11:01 2017 -0400 Revert to CUDA 8 default Tools/F_mk/GMakedefs.mak Tools/GNUMake/Make.defs commit 8807a139a3babfb9305288d2f3e0e69bf8be0dcb Author: Max Katz Date: Thu Oct 26 12:10:22 2017 -0400 Specify CUDA_VERSION at compile time for the PGI compiler Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_pgi.mak Tools/GNUMake/Make.defs Tools/GNUMake/comps/pgi.mak commit 962ed31c22136ef6e97664a83777d148ef65ddc7 Author: Weiqun Zhang Date: Wed Oct 25 17:56:33 2017 -0700 make sure relative tolerance is not less than 1.e-13 Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit f08c0da2b3518e2127e195689678d36de52a1709 Author: Weiqun Zhang Date: Wed Oct 25 17:35:08 2017 -0700 MLMG: in case crse bc data is not provides, use zero Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit e5315f8621fff7489aa72d22c058f1dc9e6f2c60 Author: vince Date: Wed Oct 25 16:51:35 2017 -0700 work on the profiler flush interval. Src/Amr/AMReX_Amr.cpp Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp commit ea64bce4b2f7da3222c49b5115442cd76296f04a Author: Weiqun Zhang Date: Wed Oct 25 16:48:39 2017 -0700 fix assertion Src/Boundary/AMReX_YAFluxRegister.cpp Src/EB/AMReX_EBFluxRegister.cpp commit 60ee9f6d6c2f3b5eb58f25e9dfec6cea1a1005b8 Author: Weiqun Zhang Date: Wed Oct 25 16:47:05 2017 -0700 fix bug in YAFluxRegister Src/Boundary/AMReX_YAFluxRegister.cpp Src/Boundary/AMReX_YAFluxRegister_1d.F90 Src/Boundary/AMReX_YAFluxRegister_2d.F90 Src/Boundary/AMReX_YAFluxRegister_3d.F90 Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_2d.F90 Src/EB/AMReX_EBFluxRegister_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 205fb7a52b3fa1a7f72c47670a225180e629464b Author: dtgraves Date: Wed Oct 25 16:07:37 2017 -0700 fillboundary needs to know about periodicity Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 commit e22dca9863b104d99b2b68d5f953e0357aac1819 Author: dtgraves Date: Wed Oct 25 15:51:52 2017 -0700 ScalarAdvectionDiffusion now fourth order for non-AMR calcs. Now on the hard part. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit c7969cda8fa2a5bfb5a81facf5dee505795ee654 Author: Max Katz Date: Wed Oct 25 17:17:57 2017 -0400 Create a dimension agnostic, multi-component filcc This version of filcc is both dimension agnostic, and works over an arbitrary number of components. It gives the same results as the dimensionful versions of filcc. It will be necessary for performance reasons to use a version like this on the GPU. This also applies the new filcc to amrex_fab_filcc. Src/Base/AMReX_filcc_mod.F90 commit 59aacf1d87cdf1505a7103da7d9970fa531a0206 Author: Andrew Myers Date: Wed Oct 25 14:17:28 2017 -0700 remove unused variable. Src/Particle/AMReX_NeighborParticlesI.H commit ad55fb3f0c99a4b33e1b893e9591490ec356f814 Merge: 21de8a8ae d35997ea3 Author: Max Katz Date: Wed Oct 25 17:16:57 2017 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 21de8a8ae35df84bb2b47b8b0322365d49b30e73 Author: Max Katz Date: Wed Oct 25 16:54:10 2017 -0400 Bring over a few stub functions from gpu branch Src/Base/AMReX_BLFort.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_fort_mod.F90 Tools/GNUMake/Make.defs commit bb01cceb76589e2c5575e3224293ec1f9b92831f Author: Andrew Myers Date: Wed Oct 25 14:16:07 2017 -0700 add profiling to amrex::get_slice_data Src/Base/AMReX_MultiFabUtil.cpp commit d35997ea3bb7296d8d6695f3e90cf52c168cc06e Author: Weiqun Zhang Date: Wed Oct 25 13:53:25 2017 -0700 MLMG: add getFluxes and compResidual Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit de9d552ed3b3ac9fe32229d79fce4f51a6a16a16 Author: Max Katz Date: Wed Oct 25 16:44:57 2017 -0400 Compile fix for ppc64le Src/Base/AMReX_FPC.cpp commit e3c6104b228b96725408d7d7e6a93ccc5d023058 Author: Max Katz Date: Wed Oct 25 15:42:49 2017 -0400 Simplify logic for copying Box data Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_RealBox.H commit 03f4d2916e8d773f159a26db4d2dbe3ad2ad3a82 Author: Max Katz Date: Wed Oct 25 14:42:50 2017 -0400 CUDA-awareness in MPI is now a runtime option Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Tools/GNUMake/Make.defs commit 7c2ed9b03cfd9373344c123b07572c9468ad6ecd Author: Max Katz Date: Wed Oct 25 14:29:41 2017 -0400 Remove unnecessary device synchronizations Src/Base/AMReX_FabArray.H Src/Base/AMReX_Geometry.cpp commit fa1edb48466578c8f4faf71462cdac58d483a617 Author: Max Katz Date: Wed Oct 25 14:14:07 2017 -0400 Reduce more diffs with development Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H commit 223a14e7ded3ef6d59751fdd712793c267d25f86 Author: Weiqun Zhang Date: Wed Oct 25 11:02:46 2017 -0700 update Users Guide for Array -> Vector Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/EB/EB.tex Docs/AMReXUsersGuide/amrexsymbols.tex commit c3f65a2c8da1e9bff928546c6d6434d2efc72780 Author: Max Katz Date: Wed Oct 25 13:56:48 2017 -0400 Remove functionality to have device data in Fab's/MF's/StateData This may be introduced in a future GPU release, but is currently unnecessary. Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabFactory.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 8ca02f5f6f28e1580b152f9d81309be2ee9e114d Author: Weiqun Zhang Date: Wed Oct 25 10:46:39 2017 -0700 add macros AMREX_ASSERT_WITH_MESSAGE and AMREX_ALWAYS_ASSERT_WITH_MESSAGE CHANGES Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_BLassert.H commit f65974d27a335afe1409f576d3377bdf2108922a Author: dtgraves Date: Wed Oct 25 10:44:50 2017 -0700 put check for isotropic dx back into CNS Tutorials/EB/CNS/Source/CNS.cpp commit 1eb04b4a8ea52516772e9f374d71a8ed8af132a0 Author: Max Katz Date: Wed Oct 25 13:29:56 2017 -0400 Reduce some diffs with development Src/Amr/AMReX_StateData.cpp commit 582c0fbefcd15e3a951bd45531e857bc8514a883 Author: Weiqun Zhang Date: Wed Oct 25 09:57:59 2017 -0700 MLPoisson: fix bug Src/LinearSolvers/MLMG/AMReX_MLPoisson_3d.F90 commit e61e52bc0afa4ad07669363b4dd8dbe4e2cbceeb Author: Weiqun Zhang Date: Tue Oct 24 17:20:10 2017 -0700 minor typo Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 1a61b0d778e6510a3ce0b608ca390a98174a0f2a Author: Max Katz Date: Wed Oct 25 12:43:20 2017 -0400 No longer need a special gcc configuration for PGI on summitdev Tools/GNUMake/comps/pgi.mak commit 9d98fb3dc2903725221865e14d3faccd0fe72f23 Merge: 7c118fd86 19a9fbd24 Author: Ann Almgren Date: Wed Oct 25 09:17:52 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 7c118fd86e977fde8e786a0c46c5fa72db2c1bea Author: Ann Almgren Date: Wed Oct 25 09:17:07 2017 -0700 Update BuildingAMReX chapter of the sphinx docs Docs/sphinx/source/BuildingAMReX.rst commit 19a9fbd243bad7307716b95be914db8e1a870b5d Author: dtgraves Date: Wed Oct 25 09:09:18 2017 -0700 added new header to CMakeLists.txt Src/GeometryShop/CMakeLists.txt commit bcc307680e234ace323756ceeea1368bc31ff126 Merge: 2b39b1c51 3db61e53d Author: dtgraves Date: Wed Oct 25 09:06:37 2017 -0700 Merge branch 'dtg_branch' into development commit 3db61e53d1825568b415228b663ddb27161e935d Author: dtgraves Date: Wed Oct 25 09:05:52 2017 -0700 bug fix (needed to also add new factory function) Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H Src/GeometryShop/AMReX_PlaneIF.H commit 2b39b1c51cb293bedcc48c089842df63d51fd6be Merge: e52895d0f 9b0f9fcde Author: dtgraves Date: Wed Oct 25 08:50:20 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit e52895d0f46127a3ee7a0a0bfa6bf6778d5a5a49 Author: dtgraves Date: Wed Oct 25 08:49:24 2017 -0700 adding missing file Src/GeometryShop/AMReX_AnisotropicDxPlaneIF.H commit 9b0f9fcde5113ffd456c40581c76b168ecbf0a98 Author: Weiqun Zhang Date: Tue Oct 24 16:58:06 2017 -0700 MLPoisson: rm member m_Anorm Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit e94e68ff46cb78881ba8f9658920b0179729bdbd Author: Weiqun Zhang Date: Tue Oct 24 16:31:44 2017 -0700 add MLPoisson::Anorm Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp commit fbb0bd519ff7af3d9825c5f7c8e7f773dd3df5f4 Author: Weiqun Zhang Date: Tue Oct 24 16:21:59 2017 -0700 add amrex_mlpoisson_gsrb Src/LinearSolvers/MLMG/AMReX_MLABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_F.H commit 380f5927d7661c6f9b44f462fc400337b6287c13 Author: Max Katz Date: Tue Oct 24 19:14:09 2017 -0400 Remove remaining calls to get_host_pointer Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.H commit 6879e8281f98f50b16d9651f4c11a3794ca25fe1 Merge: a4bfea1f8 71e455855 Author: dtgraves Date: Tue Oct 24 16:11:39 2017 -0700 Merge pull request #151 from AMReX-Codes/dtg_branch merging with dev so Jordan can get implicit function for plane with anistropic dx. commit 71e4558559185b4b0db487b98dd955af75122f57 Merge: 248498c53 a4bfea1f8 Author: dtgraves Date: Tue Oct 24 16:09:32 2017 -0700 Merge branch 'development' into dtg_branch commit 248498c531d0f445574141e632bb32a987f7ba2e Author: dtgraves Date: Tue Oct 24 16:08:45 2017 -0700 added Plane geometry for anistropic dx. I tested it on CNS and it seems to give the right geometry Tools/C_util/TV_TempWrite.H Tutorials/EB/CNS/Exec/ShockRef/aniso.inputs Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit cd83c0069aba024b2274817fab95325e27c09be1 Author: Max Katz Date: Tue Oct 24 18:54:33 2017 -0400 Remove RealBox::loF/hiF Src/Amr/AMReX_AmrLevel.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit b736c43475a7283caca28455933c42805f13beb2 Author: dtgraves Date: Tue Oct 24 15:45:30 2017 -0700 more debugging hooks Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit 63cf39164acb4f28ad8c52c61775af423162ef24 Author: Max Katz Date: Tue Oct 24 18:40:33 2017 -0400 Remove Geometry::CellSizeF() Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_CoordSys.H commit b1ac0bb00acba4bce83249dd15b935669ffe7829 Author: Max Katz Date: Tue Oct 24 18:39:23 2017 -0400 Avoid using write-combined pinned memory This can in theory provide a performance benefit, but in practice it probably never will matter, and we want to switch to using a uniform pointer for pinned memory between the host and device, which means we need to avoid WC memory if we want to skip the use of cudaHostGetDevicePointer(). Src/Base/AMReX_CUDA.F90 commit a4bfea1f8d115b44d47c8d43cb3b463fab88980a Author: Weiqun Zhang Date: Tue Oct 24 15:31:22 2017 -0700 start MLPoisson Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.H Src/LinearSolvers/MLMG/AMReX_MLPoisson.cpp Src/LinearSolvers/MLMG/AMReX_MLPoisson_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLPoisson_F.H Src/LinearSolvers/MLMG/Make.package commit f09047932715d6ef2b9928eaf12081156bced298 Author: Weiqun Zhang Date: Tue Oct 24 13:41:27 2017 -0700 minor tweak of amrex_array_to_vector.sh Tools/Migration/amrex_array_to_vector.sh commit 99d576fbd236eace8152cd2562feeedbe8d5027e Author: dtgraves Date: Tue Oct 24 13:10:59 2017 -0700 added a pile of debugging hooks. fluxes are fourth order. Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_serial_driver.py commit 627d1aaf0c2485f80a1704dca435c276ddddfa6a Author: Weiqun Zhang Date: Tue Oct 24 13:03:05 2017 -0700 MLMG: use more restrictive convergence criteria for CG Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit dc82640155c70ecf63c1b670b9be3254ef078a6e Author: Weiqun Zhang Date: Tue Oct 24 11:12:31 2017 -0700 MLMG: need to apply bc before reflux Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit c87e504e45887d24493b034cf43537c421052144 Merge: 10c09d063 d1edcd64f Author: WeiqunZhang Date: Tue Oct 24 09:24:21 2017 -0700 Merge pull request #150 from bcfriesen/update_F_mk_for_intel F_mk: add support for compiling with Intel v17 and v18 commit d1edcd64f634821172361b41c3c82beb0b856bde Author: Brian Friesen Date: Tue Oct 24 09:01:42 2017 -0700 F_mk: add support for compiling with Intel v17 and v18 Tools/F_mk/comps/Linux_intel.mak commit 10c09d06301f93d5579facc596f00bd75d3c12fa Author: Weiqun Zhang Date: Tue Oct 24 08:58:53 2017 -0700 MLMG: isSingular virtual function Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 4a7339f49be191ff6c16ff7ad0b3b5c8b2a22696 Author: Weiqun Zhang Date: Mon Oct 23 17:04:11 2017 -0700 MLMG: solvability WIP Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit a077821c13486d1587c7f3ef402e953245713898 Author: Weiqun Zhang Date: Mon Oct 23 15:16:44 2017 -0700 MLMG: enforce solvability Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/init_prob.cpp Tests/LinearSolvers/MLMG/main.cpp commit 7462434be818e9c740f6e8dec388239b85ad4dc8 Author: Weiqun Zhang Date: Mon Oct 23 11:16:13 2017 -0700 MLMG: add m_singular vector Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 4a2154be02dc3e16f93f2c48baaec4ecfd120971 Author: Weiqun Zhang Date: Mon Oct 23 10:41:59 2017 -0700 MLMG test: set up periodic and Neumann Tests/LinearSolvers/MLMG/fort.H Tests/LinearSolvers/MLMG/fort_3d.F90 Tests/LinearSolvers/MLMG/init_prob.cpp Tests/LinearSolvers/MLMG/inputs Tests/LinearSolvers/MLMG/prob_par.H Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit d242704c949e97f682d5f1196e98558b61f9067f Merge: 19b642a6d fe2098e36 Author: Andrew Myers Date: Mon Oct 23 17:02:46 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 19b642a6daf496d6ef85f32190e0c6dd90b64a1d Author: Andrew Myers Date: Mon Oct 23 17:02:29 2017 -0700 add a version of MakeMFIter that overrides the default tiling setting. Src/Particle/AMReX_Particles.H commit fe2098e36ce38af9dd1a5c13c4de21d2da4fa6e1 Author: Ann Almgren Date: Mon Oct 23 16:45:39 2017 -0700 Default for ENABLE_EB should be off. Tools/CMake/AMReX_Options.cmake commit a3e18df4043c7fd7ebe526f9590262d6e0b53ef5 Author: Ann Almgren Date: Mon Oct 23 16:44:44 2017 -0700 Fix bug where there were 0 neighbors and we were trying to fill an array with zero values. Src/Particle/AMReX_NeighborParticlesI.H commit bbdb5eb16d39594df0d95f6997a1dff3275a8579 Author: dtgraves Date: Mon Oct 23 16:36:20 2017 -0700 added interior box option as an example Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit 23486c89f022a276af249514a91480b7663379a6 Author: Max Katz Date: Mon Oct 23 18:09:55 2017 -0400 Add CUDA suffix for F90 builds Tools/F_mk/GMakedefs.mak commit 82be028b29408bf17fb155dbf6e8f9143fc49d1d Author: dtgraves Date: Mon Oct 23 14:42:26 2017 -0700 some bug fixes. dphi/dt for MOL code still only second order. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_serial_driver.py commit ec2e62d01f0c2e514e17a2a1061bfb066b73a66d Author: Max Katz Date: Mon Oct 23 17:13:19 2017 -0400 Update to CUDA 9 in F90 build system Tools/F_mk/comps/Linux_pgi.mak commit 223fff8dfebfe687b21a0e5ed344f3a3aaefcf1b Author: Max Katz Date: Mon Oct 23 16:28:30 2017 -0400 Support CUDA module in F90 build Src/Base/AMReX_CUDA.F90 Tools/F_mk/GMakedefs.mak commit 1b3791988203de532857904557cc952b23f2f80e Author: Weiqun Zhang Date: Mon Oct 23 10:06:06 2017 -0700 MLMG: no longer requires AmrCore Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/GNUmakefile commit 60f8dadbf973d6f5a6cc997607d555467b3d30e7 Author: Weiqun Zhang Date: Mon Oct 23 10:03:54 2017 -0700 MLMG: cleanup Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit a4edaf38d5dbe4fe40f804ff03cbcf4c18a93d94 Author: Weiqun Zhang Date: Sun Oct 22 12:26:03 2017 -0700 MLMG: set bc interface Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_InterpBndryData.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 3434d27e57d888558b09704daab2e98a704295b3 Author: Ann Almgren Date: Sun Oct 22 17:08:27 2017 -0700 Update the EBParticles Tutorial with 1) 3d bounce routine , 2) replace 0.0005 by dt in bounce. Tutorials/Particles/EBParticles/EBParticleContainer.H Tutorials/Particles/EBParticles/EBParticleContainer.cpp Tutorials/Particles/EBParticles/GNUmakefile Tutorials/Particles/EBParticles/ebparticles_2d.f90 Tutorials/Particles/EBParticles/ebparticles_3d.f90 Tutorials/Particles/EBParticles/ebparticles_F.H Tutorials/Particles/EBParticles/main.cpp commit b9f9398271d2e514f1fa69d89bb8f4551f727cd3 Author: Ann Almgren Date: Sat Oct 21 18:12:01 2017 -0700 Fix some typos Docs/AMReXUsersGuide/EB/EB.tex commit a2768172a131774e0f310223e4bf115a0594fd5d Author: dtgraves Date: Sat Oct 21 14:47:25 2017 -0700 added fixed_dt option so I can do proper convergence tests Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit 779145baa985596e280d4759ecd8fb685622103d Author: dtgraves Date: Sat Oct 21 13:31:17 2017 -0700 added a python utility for convergence tests Tutorials/Amr/ScalarAdvectionDiffusion/util/convtest_serial_driver.py commit d2ce70d0d0717a557b0aeb487da367e0638e254f Author: Michele Rosso Date: Fri Oct 20 17:42:43 2017 -0700 CMake: fix few bugs Src/Boundary/CMakeLists.txt Src/GeometryShop/CMakeLists.txt commit 396a3fae0a2d3a0a2909de188fc76ba484c99b01 Author: Ann Almgren Date: Fri Oct 20 17:14:01 2017 -0700 Fix another typo Src/GeometryShop/CMakeLists.txt commit c2daaab1b025a06dda6a7bae6edcfc1243b4c4ae Author: Ann Almgren Date: Fri Oct 20 17:13:07 2017 -0700 Fix typo Src/GeometryShop/CMakeLists.txt commit a66d88f22641bc33cba30279902a2ee63bfae9e2 Author: Ann Almgren Date: Fri Oct 20 17:11:50 2017 -0700 Fix typos Src/EB/CMakeLists.txt commit c6421dfa046b8c8fbb9bf179848f83fa3be55965 Author: Ann Almgren Date: Fri Oct 20 16:58:48 2017 -0700 Adding more cmake support for using EB Src/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake commit c8201f1e6a7ec83bf9321839ca1b03815d0be823 Author: Ann Almgren Date: Fri Oct 20 16:50:49 2017 -0700 Adding CMakeLists.txt for EB and GeometryShop Src/EB/CMakeLists.txt Src/GeometryShop/CMakeLists.txt commit b39198f1e7281b1cfe7c2fdead3ce86f0e83de63 Author: Weiqun Zhang Date: Fri Oct 20 16:34:18 2017 -0700 improve amrex_array_to_vector.sh Tools/Migration/amrex_array_to_vector.sh commit adf2f689fdd0880beaeae806b58b825d906c0899 Author: vince Date: Fri Oct 20 15:55:18 2017 -0700 more support for precreate directories and particle io. Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/Base/AMReX.cpp Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp Src/Particle/AMReX_ParticleContainerI.H commit 2cf04a6493e6bd6c197a8e41cefce9736b6c014a Author: Weiqun Zhang Date: Fri Oct 20 15:07:51 2017 -0700 MLMG: use linear interp for amr level prolongation Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 7d1cd03d59e28e36b2e2e3c0b7b7d00a059896c8 Merge: 531150943 d482ebfc0 Author: Andrew Myers Date: Fri Oct 20 15:11:38 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 53115094322f8e25a334919f3c6e55bd4ea515f8 Author: Andrew Myers Date: Fri Oct 20 15:09:13 2017 -0700 add utility functions for filling slices of data from a Multifab. Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_MultiFabUtil_nd.F90 commit d482ebfc0e510504ccb7a1aac7817c321eb9c373 Author: Weiqun Zhang Date: Fri Oct 20 15:00:41 2017 -0700 MLMG: fix linear interp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/AMReX_MLMG_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLMG_F.H Src/LinearSolvers/MLMG/Make.package commit 7dacec00dd6ccf327647a7b074783d958015908e Author: Weiqun Zhang Date: Fri Oct 20 13:59:05 2017 -0700 move heap allocation out of mfiiter Src/AmrCore/AMReX_FillPatchUtil.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 89854a4ddb44b74cf2867623af913a7fb8993e68 Author: vince Date: Fri Oct 20 13:35:42 2017 -0700 more support for precreate directories. Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Particle/AMReX_Particles.H commit 5c92e18fa5de657138482858b1a94abd6bb4ea43 Author: dtgraves Date: Fri Oct 20 13:13:41 2017 -0700 some bug fixes Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/init.2d.convtest.sh Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/init.3d.convtest.sh Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs commit 7a70b0325b676451ee691ed274c80aefdd01c7c3 Author: dtgraves Date: Fri Oct 20 11:49:27 2017 -0700 added (exact) smooth initial condition, confirmed via convergence test Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/debug.inputs Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/face_velocity_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/face_velocity_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/init.2d.convtest.sh Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/init.3d.convtest.sh Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/probdata.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/probin Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Smooth/smooth.inputs commit 73a8be4663d06d5577a1c7d881dbc62fe117aec6 Author: vince Date: Fri Oct 20 11:36:26 2017 -0700 shorten profiling names. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H commit 49e1f16a8bfadc0e03fccb9dfd8fe331c192d9f1 Merge: 3a91a76bf 2a4364240 Author: vince Date: Fri Oct 20 10:32:51 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 2a4364240650f6c49b4451826a5facc3172c1960 Author: Weiqun Zhang Date: Fri Oct 20 10:31:22 2017 -0700 MLMG: remove nu0 and fix mini-cycle Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit a1cbc387715adc665e32b4c34c4104ff3c013a55 Merge: cc0ef88b4 360a1533c Author: Michele Rosso Date: Fri Oct 20 09:51:39 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit cc0ef88b416dc1ec1c1fefd5faed88c97471d634 Author: Michele Rosso Date: Fri Oct 20 09:51:24 2017 -0700 CMake: add header to cmake list Src/Base/CMakeLists.txt commit 360a1533c3792aabd35c0e275c9fc0f41424e959 Author: Weiqun Zhang Date: Fri Oct 20 09:41:55 2017 -0700 MLMG: fix a minor bug Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit f5a8be5e2db90f412a744e2f61fc63ae1137c042 Author: Weiqun Zhang Date: Fri Oct 20 09:32:48 2017 -0700 MLMG:: add profilers Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit d5c4d48ae2ec6117af7ea72592d7e2589e9371f3 Author: Weiqun Zhang Date: Fri Oct 20 09:07:05 2017 -0700 MLMG test: add inputs Tests/LinearSolvers/MLMG/init_prob.cpp Tests/LinearSolvers/MLMG/inputs Tests/LinearSolvers/MLMG/prob_par.H commit 364618350a8dff5f712b3d1f0ed638f8ba55ef1c Merge: 663f856d8 7997d72f1 Author: Klaus Weide Date: Fri Oct 20 10:36:58 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7997d72f16714e3782630f704e2edca2978c1f20 Author: Ann Almgren Date: Thu Oct 19 18:26:11 2017 -0700 Add rst files for the rest of the user guide chapters. Docs/sphinx/source/Amr.rst Docs/sphinx/source/AmrCore.rst Docs/sphinx/source/Basics.rst Docs/sphinx/source/Boundary.rst Docs/sphinx/source/BuildingAMReX.rst Docs/sphinx/source/CVODE.rst Docs/sphinx/source/Chapter2.rst Docs/sphinx/source/Chapter3.rst Docs/sphinx/source/Chapter4.rst Docs/sphinx/source/EB.rst Docs/sphinx/source/Fortran.rst Docs/sphinx/source/GettingStarted.rst Docs/sphinx/source/Particles.rst Docs/sphinx/source/Profiling.rst Docs/sphinx/source/Visualization.rst Docs/sphinx/source/index.rst Docs/sphinx/source/intro.rst commit 48118035fe12bfc6f2420d8b5108572f2417aa8f Merge: 2fd0df428 603f02252 Author: Max Katz Date: Thu Oct 19 20:52:42 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 2fd0df4281f5d930f1a633173d970bce0e00e4be Author: Max Katz Date: Thu Oct 19 19:55:14 2017 -0400 Correct the reporting of how many total GPUs are available Src/Base/AMReX_Device.cpp commit 0feca1d1b9ff6fc1030b0d41d757655895c34ccc Author: Max Katz Date: Thu Oct 19 19:22:19 2017 -0400 Use the same CPU-GPU matching algorithm without MPI Src/Base/AMReX_Device.cpp commit 1e9210b22d96e97244e47df23c3612a63949f5cc Author: Ann Almgren Date: Thu Oct 19 16:11:02 2017 -0700 Fix subsections Docs/sphinx/source/Basics.rst commit 8c98a259e606dafdf7e02527f1cf3e0ad6cae5b9 Author: Ann Almgren Date: Thu Oct 19 16:03:57 2017 -0700 Fix the index Docs/sphinx/source/index.rst commit 14ff339d05538eb5901f739ecfc375a0048155ff Author: Ann Almgren Date: Thu Oct 19 15:59:29 2017 -0700 Add Basics/Basics.tex Docs/sphinx/source/Basics.rst Docs/sphinx/source/index.rst commit e68a997b562db5499ca5d28547ff7ae7476e9d6e Merge: b388b0984 0da2433c8 Author: Ann Almgren Date: Thu Oct 19 15:55:03 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b388b09848b1bce3e947f08f9bb5141ae17090bb Author: Ann Almgren Date: Thu Oct 19 15:54:48 2017 -0700 Missing curly brackets in emph lines Docs/AMReXUsersGuide/Basics/Basics.tex commit 41ce1e4d4dfd439ab60c909c07e143a504028794 Author: dtgraves Date: Thu Oct 19 15:46:47 2017 -0700 added an algorithm description to the notes Tutorials/Amr/ScalarAdvectionDiffusion/Notes/notes.tex Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 commit 0da2433c82d186cd1c8b5a8ef79d14a8b5f9b1ac Author: Weiqun Zhang Date: Thu Oct 19 15:37:13 2017 -0700 MLMG: remove unnecessary fillboundary Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 5676477379ffcf47c8a718d3fd31891f81841887 Author: Ann Almgren Date: Thu Oct 19 15:17:28 2017 -0700 sphinx for github.io pages Docs/sphinx/Makefile Docs/sphinx/source/conf.py Docs/sphinx/source/index.rst Docs/sphinx/source/intro.rst commit c47efdff25eab83836304c5aad98763b79ee4827 Author: Weiqun Zhang Date: Thu Oct 19 14:36:58 2017 -0700 MLMG: fix bug Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit f23ff154ff8ac443ac65c4d11a5ab52543967d11 Author: Weiqun Zhang Date: Thu Oct 19 14:23:05 2017 -0700 MLMG: refactor and comments Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 457792d36f7f868461fd8152111fbdd0619368dc Author: dtgraves Date: Thu Oct 19 14:19:36 2017 -0700 added fourth order fortran routines. On to testing. Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit 603f02252da14461a53d9141e3413e5dee5b56c8 Author: dwillcox Date: Thu Oct 19 17:09:38 2017 -0400 Add BL_USE_F_BASELIB as a preprocessor variable for F90 build system. This fixes CUDA compilation for the Microphysics test_react unit test. Tools/F_mk/GMakedefs.mak commit bd14f34f5e5ec7747670d4fe436ff88f5a7aa30a Author: Weiqun Zhang Date: Thu Oct 19 10:52:21 2017 -0700 MLMG: avoid recursive function Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 3b3c4726c7c460a211a731012d3e832020666a64 Author: Weiqun Zhang Date: Thu Oct 19 10:40:31 2017 -0700 MLMG test: add max_fmg_iter parameter Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit b744f0ed2e96e31160827748728bf2c840bbad51 Author: Weiqun Zhang Date: Thu Oct 19 10:20:27 2017 -0700 MLMG: add linear interpolation Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 3252734ce3031d924b3630a9b22aff085a894218 Author: Max Katz Date: Thu Oct 19 06:17:10 2017 -0400 Make NVML mandatory Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Tools/GNUMake/Make.defs commit 43cb1fa2d7147c0b235cf681f0f099eef1771df2 Author: Max Katz Date: Thu Oct 19 06:05:09 2017 -0400 Clean up the code for assigning ranks to GPUs Src/Base/AMReX_Device.cpp commit 186dcf254462db65b334697f90a8c7246f98b9a7 Author: Max Katz Date: Thu Oct 19 06:04:33 2017 -0400 Add an NVML error check macro Src/Base/AMReX_Device.H commit 132eeb2a7865695d9d2c78b5208a074c88f6c037 Author: Max Katz Date: Thu Oct 19 05:14:33 2017 -0400 Do not divide up GPUs that are not visible to CUDA Src/Base/AMReX_Device.cpp commit 9da69489f3fef47f14c73555d655b35ebb97abbd Merge: e4a07f73f abddd622a Author: Max Katz Date: Thu Oct 19 05:13:45 2017 -0400 Merge branch 'development' into gpu commit e4a07f73f45a2fea9b91f5a26bbcee8aad43b5a2 Author: Max Katz Date: Thu Oct 19 02:07:35 2017 -0400 Allow disabling of CUDA-aware MPI at compile time Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Tools/GNUMake/Make.defs commit 034f330863d0434b5939a6bc1291c1baca62e4c3 Author: Weiqun Zhang Date: Wed Oct 18 21:57:42 2017 -0700 MLMG: use swap Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit db9b82ec51c766a9a83031a9026844b763eb038d Author: Weiqun Zhang Date: Wed Oct 18 21:51:02 2017 -0700 MLMG: remove a temp mf Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit f1d1f7cb742b9be0f617c791ba4f7dcf2fd47b04 Author: Max Katz Date: Wed Oct 18 23:19:46 2017 -0400 Only link in NVTX if profiling Tools/GNUMake/Make.defs commit 0491d399b450154602b1344605d7e0ccbb7138c8 Author: Max Katz Date: Wed Oct 18 23:06:58 2017 -0400 Update to CUDA 9 (requires PGI 17.9+) Tools/GNUMake/comps/pgi.mak Tools/GNUMake/sites/Make.olcf commit abddd622aa0d9daf9fe35dcd9a44fb1a9cac4bd4 Author: Weiqun Zhang Date: Wed Oct 18 17:39:14 2017 -0700 MLMG: better name Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 818306296007c5c3c0a1075b00ad5e07533b9bc2 Author: Weiqun Zhang Date: Wed Oct 18 17:35:23 2017 -0700 MLMG: implement FMG cycle Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit d4da549b58f174e49b4cfd68c7fe6785a60dd000 Author: Weiqun Zhang Date: Wed Oct 18 12:13:07 2017 -0700 MLMG: some timers Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 5207a40b86c604f0f09253d788a70e13658121a7 Author: Weiqun Zhang Date: Wed Oct 18 11:02:28 2017 -0700 MLMG: some cleanup Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/MLMG/GNUmakefile commit 6e1785bb535a2bf0ee723abef6e0d36ff45d1ed0 Merge: d356e989f e52a09a55 Author: Andrew Myers Date: Wed Oct 18 16:37:50 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit d356e989f20a5de4f0e1bacd4e9658225f8d59b8 Author: Andrew Myers Date: Wed Oct 18 16:28:43 2017 -0700 change the value of insideRegular to be consistent with the above example, which has the solution domain on the inside of the sphere. Docs/AMReXUsersGuide/EB/EB.tex commit f5e0efa66f6aedcd5feef1234a0ab604abcf96c0 Author: dtgraves Date: Wed Oct 18 15:19:24 2017 -0700 added in fortran framework Tutorials/Amr/ScalarAdvectionDiffusion/Notes/notes.tex Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit e52a09a55cac2465c1ab76a312a20284895cf354 Merge: 9ae1138e4 1760c4918 Author: Michele Rosso Date: Wed Oct 18 14:41:29 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 9ae1138e499519454811de34d90870a3760b1031 Author: Michele Rosso Date: Wed Oct 18 14:40:40 2017 -0700 CMake: add support for Cray compiler Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Config.cmake commit c3fa77328ab3148be0e553c422eb3cc3ac98374c Author: dtgraves Date: Wed Oct 18 14:05:55 2017 -0700 added some more notes and put in 4th order framework for advance Tutorials/Amr/ScalarAdvectionDiffusion/Notes/notes.tex Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp commit d4beaca03828e145db09cd6c00237336c490becd Author: Michele Rosso Date: Wed Oct 18 14:00:11 2017 -0700 CMake: remove cmake file copied by mistake in Tutorials/ScalarAdvectionDiffusion Tutorials/Amr/ScalarAdvectionDiffusion/CMakeLists.txt commit 1760c491828f1715c3513f65e35ab407fcf433a8 Merge: c882b8b38 0f3cfe4ca Author: Andrew Myers Date: Wed Oct 18 12:17:28 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c882b8b3885de5e24157a778c4ad71b47535232f Author: Andrew Myers Date: Wed Oct 18 12:17:15 2017 -0700 clean up main. Tutorials/Particles/EBParticles/main.cpp commit f1693e9eebc554ce6afa2b001c5e6652820324cf Author: Andrew Myers Date: Wed Oct 18 12:16:20 2017 -0700 clean up inputs file. Tutorials/Particles/EBParticles/inputs commit daca9aca757715bc13d6c8af915ad54a1ffb4678 Author: Andrew Myers Date: Wed Oct 18 12:09:41 2017 -0700 Tutorial for particles that interact with embedded boundaries. Tutorials/Particles/EBParticles/EBParticleContainer.H Tutorials/Particles/EBParticles/EBParticleContainer.cpp Tutorials/Particles/EBParticles/GNUmakefile Tutorials/Particles/EBParticles/Make.package Tutorials/Particles/EBParticles/ebparticles_2d.f90 Tutorials/Particles/EBParticles/ebparticles_3d.f90 Tutorials/Particles/EBParticles/ebparticles_F.H Tutorials/Particles/EBParticles/inputs Tutorials/Particles/EBParticles/main.cpp commit 0f3cfe4caa93cee4b92691e6e294468798adbf2a Merge: d74ed798f 9e7fb7c60 Author: dtgraves Date: Wed Oct 18 11:37:44 2017 -0700 Merge pull request #148 from AMReX-Codes/dtg_branch moving a couple of things to dev so Marc can get the convergence test utility commit 9e7fb7c6039b84df74307e44c5fd1aa48ff3812a Author: dtgraves Date: Wed Oct 18 11:36:20 2017 -0700 added full Richardson convergence test utility to save some of the manual labor of convergence tests Tools/C_util/Convergence/GNUmakefile Tools/C_util/Convergence/RichardsonConvergenceTest.cpp commit d74ed798f48cc3546c65aa3acda0160eb4e39513 Author: Weiqun Zhang Date: Wed Oct 18 08:54:41 2017 -0700 add inputs for regression only Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/inputs.regt commit 90ac26b57394d84eb06924fbb8c294dd63f2eae2 Author: Max Katz Date: Wed Oct 18 04:31:28 2017 -0700 Correctly handle the case with fully interior boxes Src/Amr/AMReX_StateData.cpp commit 8a5ea22b7e873254cf73477c709210a6521248ef Author: Max Katz Date: Wed Oct 18 04:31:10 2017 -0700 Insert sanity check: positive number of CUDA threads/blocks Src/Base/AMReX_CUDA.F90 commit c2471d59f1a88c465f60a7eb85c98446b3cab95b Author: Max Katz Date: Wed Oct 18 03:46:56 2017 -0700 Add CORAL EA systems at LLNL Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.llnl commit 94df7c9a179cbd7a8b13194b91152940823c02b9 Author: Weiqun Zhang Date: Tue Oct 17 18:08:39 2017 -0700 MLMG: fix mask for compute residual Src/Base/AMReX_BaseFab_nd.f90 Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit f719e7a594f02e938b68884e7129bcf911fd6bcc Author: Max Katz Date: Tue Oct 17 17:49:17 2017 -0700 Add a second sanity check on number of threads Src/Base/AMReX_CUDA.F90 commit 9227fd554667610c85dd297f55b67935599b3feb Author: Weiqun Zhang Date: Tue Oct 17 17:42:20 2017 -0700 add a new function to compute masked inf norm Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_Print.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit c7cb86294b3557590c5f04d18f39cd6d2e352fc2 Author: dtgraves Date: Tue Oct 17 16:33:58 2017 -0700 added some working notes Tutorials/Amr/ScalarAdvectionDiffusion/Notes/notes.tex Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp commit 40494249656bc0f01c4394033ac43e281d1e9665 Author: Max Katz Date: Tue Oct 17 15:48:18 2017 -0700 Use the C++ CUDA error checker Src/Base/AMReX_Device.cpp commit fe4434e55efeb31197b68e784ac550e7a647ed69 Merge: 88c51afd0 01793d818 Author: dtgraves Date: Tue Oct 17 15:47:35 2017 -0700 Merge pull request #146 from AMReX-Codes/dtg_branch bringing convergence tool fixes over to dev branch commit 01793d818e6572a728496778d0b35a8ac32de9d7 Author: dtgraves Date: Tue Oct 17 15:45:13 2017 -0700 all the tools except for ComputeAmrNorms compile. ComputeAmrNorms has no main. Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameDomainRefinedComposite.cpp Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/GNUmakefile Tools/C_util/Convergence/PltFileNormB.cpp commit 14bda1a87f94cdf3f985be0f19d85ce6ecdb21f2 Author: Max Katz Date: Tue Oct 17 15:44:42 2017 -0700 Error check routines do not need to be on a single line Src/Base/AMReX_Device.H commit c9648f9a917f5cd863152465c1fc34e481fdbaa9 Author: Max Katz Date: Tue Oct 17 15:44:24 2017 -0700 Add Spectrum MPI to list of known implementations Tools/GNUMake/sites/Make.unknown commit 88c51afd01cbb96664462803ee54d20ae6f4724c Author: Weiqun Zhang Date: Tue Oct 17 14:11:03 2017 -0700 MLMG: need to update coarse level solution bc Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit a8460f4365815519d7778c7b4895779253d4af6a Author: dtgraves Date: Tue Oct 17 13:44:51 2017 -0700 more progress toward getting these tools working again. On a bunch of them, the MultiFab declarations need to be reworked Tools/C_util/Convergence/Add.cpp Tools/C_util/Convergence/ComputeAmrDataNorms.H Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameDomainRefinedComposite.cpp Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp Tools/C_util/Convergence/GNUmakefile Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileNormB.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp commit 31a8c7ad865232b5c600fac86866eeca5d241f29 Author: Weiqun Zhang Date: Tue Oct 17 12:58:17 2017 -0700 take out wrong assertion Src/Boundary/AMReX_YAFluxRegister.cpp commit 79b46159ec5be6d4afeed222542d4377450de158 Author: Weiqun Zhang Date: Tue Oct 17 12:41:27 2017 -0700 Revert "tiling: make sure tile boxes are generally coarsenable" This reverts commit 7da501d5ae6c2a3d681fa52e0fd4b19048e50188. Src/Base/AMReX_FabArrayBase.cpp commit 271742a92522737298fe8a8d3769b22a73440b3b Author: Marc Day Date: Tue Oct 17 12:41:52 2017 -0700 Add dest_comp argument to YAFluxRegister::Reflux Src/Boundary/AMReX_YAFluxRegister.H Src/Boundary/AMReX_YAFluxRegister.cpp commit 8d8abbd59f17107ab1a8da253b09b82908a058e9 Merge: 0398a6bbe 72deaa851 Author: dtgraves Date: Tue Oct 17 11:13:43 2017 -0700 merging with dev to get convergence tools commit 72deaa851c5d55df2a89bf182cd4fcfbd1e78972 Merge: 7da501d5a ff2daf4a7 Author: Marc Day Date: Tue Oct 17 10:58:33 2017 -0700 Merge pull request #143 from AMReX-Codes/migrate_Convergence_util Migrate convergence util commit 7da501d5ae6c2a3d681fa52e0fd4b19048e50188 Author: Weiqun Zhang Date: Tue Oct 17 09:28:10 2017 -0700 tiling: make sure tile boxes are generally coarsenable Src/Base/AMReX_FabArrayBase.cpp commit 0398a6bbeb65662bd4f32519d703f49a3ca15c85 Author: dtgraves Date: Mon Oct 16 14:19:05 2017 -0700 MOL2nd order now seems to work even with AMR. YAFluxRegister makes more sense in this context than FluxRegister. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp commit f00eb38382f1e0eb5c9e0e159496353f662910e5 Author: dtgraves Date: Mon Oct 16 12:00:45 2017 -0700 added some debugging tools and I got MOL to work without AMR. Still something off with AMR, however. Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/inputs Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugDump.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugOut.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/DebugOut.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/main.cpp commit 21c0b862c13f7ace28d1301f1a359e4a42407e0a Author: dtgraves Date: Sun Oct 15 12:51:27 2017 -0700 godunov version works fine. MOL version needs work. Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Make.Adv Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/inputs Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/inputs Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp commit 217efb292230ab182aa413acdee1e7ac2c92e855 Author: dtgraves Date: Sat Oct 14 21:39:37 2017 -0700 couple of dimension-specific bug fixes Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 commit 08eb078ba1fb638be3a113642079966bca23a74d Author: dtgraves Date: Sat Oct 14 21:36:49 2017 -0700 bunch of bug fixes Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Make.Adv.Diff Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit 2d1d98da62d2a3e4f8c5ece223303e6b1a36056f Author: dtgraves Date: Fri Oct 13 20:54:47 2017 -0700 changed adv diff integrator to 2nd Order MOL. Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit 34b037716783fb0929906a7d1eb755e68adc4d90 Author: Weiqun Zhang Date: Fri Oct 13 18:05:29 2017 -0700 MLMG test: add more parameters Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 3e1ff02ed3309ce22e9eda5299c3d3b50e3b52e9 Author: Weiqun Zhang Date: Fri Oct 13 17:41:55 2017 -0700 MLMG: fix data type Src/LinearSolvers/MLMG/AMReX_MLMG.H commit 1befec1a5b7e05ae9b9fc8ea0e14f6a7b0a46993 Author: Weiqun Zhang Date: Fri Oct 13 17:36:04 2017 -0700 MLMG: set cg parameters Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit fc7d416df225ae5b7139281505de087b6d318069 Author: Weiqun Zhang Date: Fri Oct 13 17:32:58 2017 -0700 MLMG: fix cg tolerance Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 247c8618f7a2e3c464ab6bf38a6af9fa12cde731 Author: Weiqun Zhang Date: Fri Oct 13 17:19:02 2017 -0700 CG for MLMG Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLCGSolver.H Src/LinearSolvers/MLMG/AMReX_MLCGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/Make.package commit b1efb70d55f44487332a5b80693e0700a03dce2d Author: Weiqun Zhang Date: Fri Oct 13 14:14:34 2017 -0700 add anonymous namespace aroung some functions in CGSolver Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 7369fcb3c851ab433996479551a299ebe71fbbd8 Author: Weiqun Zhang Date: Fri Oct 13 12:16:40 2017 -0700 MLLinOp::setMaxOrder Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 69405421700fec06c7037fb17cceec21cb3d3eef Merge: 2f1abf1e6 9c96f9374 Author: Andrew Myers Date: Fri Oct 13 14:54:16 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2f1abf1e6884a2b541a72032cdc6beb0fd1111a3 Author: Andrew Myers Date: Fri Oct 13 14:54:04 2017 -0700 clarify comment. Docs/AMReXUsersGuide/EB/EB.tex commit 8158efa8b3778a2f15ee0e835ff687dddd1fbf43 Author: dtgraves Date: Fri Oct 13 14:29:00 2017 -0700 advection/diffusion (in Godunov mode) reproduces advection tutorial. Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/inputs Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/inputs Tutorials/Amr/ScalarAdvectionDiffusion/README Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 commit 9c96f9374182f606c81ae13d064831a2d40fe54f Author: Weiqun Zhang Date: Fri Oct 13 11:16:32 2017 -0700 MLMG: bottomSolve Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit f937e0e0f7f0a465d2fd67e75b789641a99a5294 Author: Andrew Myers Date: Fri Oct 13 11:19:33 2017 -0700 handle low dimensionality in the neighbor particle finding. Src/Particle/AMReX_NeighborParticlesI.H commit 8a84a4fbcc605cb2ae01591d9ea1a368a23a3eb5 Author: Andrew Myers Date: Fri Oct 13 10:59:21 2017 -0700 fix a couple more typos. Docs/AMReXUsersGuide/EB/EB.tex commit 4231cdfe15d9ee88bce26dedc72bf29cb2ac1280 Merge: 759e0e5a6 11445c018 Author: Max Katz Date: Fri Oct 13 13:36:12 2017 -0400 Merge branch 'development' into gpu commit 11445c018712627e9ce51bbe70ca1c8638cbdf64 Merge: 937aee81d e9c6b16a6 Author: Andrew Myers Date: Fri Oct 13 10:28:13 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 937aee81d5a5f66033e534948c627dc10729f11c Author: Andrew Myers Date: Fri Oct 13 10:27:57 2017 -0700 fix minor formatting issue. Docs/AMReXUsersGuide/EB/EB.tex commit e9c6b16a62907b85a3169e07d7793617926415e1 Author: Weiqun Zhang Date: Fri Oct 13 10:24:23 2017 -0700 MLMG: add more set methods Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 759e0e5a61ba5afe749c6242ccd5947623a3dd6a Author: Max Katz Date: Fri Oct 13 13:14:59 2017 -0400 Add sanity check on total number of CUDA threads Src/Base/AMReX_CUDA.F90 commit d118c176866d51a69912fe75056ed9307fdc4dcf Author: Andrew Myers Date: Fri Oct 13 10:14:11 2017 -0700 fix typo in EB docs. Docs/AMReXUsersGuide/EB/EB.tex commit be42d06c4656e2c1f94878a8b8306fb7d8572a13 Author: Max Katz Date: Fri Oct 13 13:06:40 2017 -0400 Deal appropriately with varying box sizes in FillBoundary Src/Amr/AMReX_StateData.cpp commit d35a45959c961d31371206bbcf92a972c917c1dc Author: Ann Almgren Date: Thu Oct 12 18:39:44 2017 -0700 Changes to be compatible with Sam's latest changes to HPGMG for Nyx. Src/Extern/hpgmg/BL_HPGMG.H Tools/GNUMake/packages/Make.hpgmg commit 24f42d85a2037eb74e4d1e6b30547246fa8ca9a9 Author: Weiqun Zhang Date: Thu Oct 12 17:10:53 2017 -0700 MLMG test: add some runtime parameters Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit bab717026056e0721d309886e4a920fa61542f22 Author: Weiqun Zhang Date: Thu Oct 12 16:37:13 2017 -0700 MLMG: mgCycle Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 8b059e202e4c9bdf298e8689a468ef2b121906fe Author: Weiqun Zhang Date: Thu Oct 12 15:09:16 2017 -0700 MLMG: up the amr v-cycle Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit f392e8febb2b5b9b8b4d6e2b554270f77cc1f271 Author: Weiqun Zhang Date: Thu Oct 12 13:35:32 2017 -0700 MLMG: save BndryRegister used in updating bc Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 63fa38d9eda17642fc3e658381d1540bc9dc1a84 Author: Max Katz Date: Thu Oct 12 19:41:58 2017 -0400 Set a minimum threadblock size for StateData::FillBoundary Src/Amr/AMReX_StateData.cpp commit 5a247b3669a6be66da6525535ffc81aca703ec62 Author: Max Katz Date: Thu Oct 12 19:12:19 2017 -0400 Sync threads in between BC fill dimensions Src/Base/AMReX_filcc_mod.F90 commit 5f741cd74d5eb88349b89c8199a68e3559c25156 Author: Max Katz Date: Thu Oct 12 19:11:55 2017 -0400 Add capability to set minimum number of CUDA threads Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 75900292e60bcd7899c44f3982174d817de04838 Author: dtgraves Date: Thu Oct 12 15:34:36 2017 -0700 added advection-(explicit)diffusion example. Just starting to get this organized. Tutorials/Amr/ScalarAdvectionDiffusion/CMakeLists.txt Tutorials/Amr/ScalarAdvectionDiffusion/Exec/Make.Adv Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/inputs Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/inputs.tracers Tutorials/Amr/ScalarAdvectionDiffusion/Exec/SingleVortex/probin Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/GNUmakefile Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/Prob.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/face_velocity_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/face_velocity_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/inputs Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/probdata.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Exec/UniformVelocity/probin Tutorials/Amr/ScalarAdvectionDiffusion/README Tutorials/Amr/ScalarAdvectionDiffusion/Source/Adv_F.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.H Tutorials/Amr/ScalarAdvectionDiffusion/Source/AmrLevelAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/LevelBldAdv.cpp Tutorials/Amr/ScalarAdvectionDiffusion/Source/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_2d/slope_2d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_3d/slope_3d.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Adv_nd.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Make.package Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/Tagging_nd.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/Src_nd/tagging_params.f90 Tutorials/Amr/ScalarAdvectionDiffusion/Source/main.cpp commit b4b899ef8a82eb80032313194753903e92ec53b6 Merge: 4dfeff51c 5a9cc63a1 Author: Andrew Myers Date: Thu Oct 12 15:26:45 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4dfeff51cb9d8d0d9328f02bca59aec0c125dee2 Author: Andrew Myers Date: Thu Oct 12 15:26:33 2017 -0700 avoid allocating memory for temporaries in threaded regions. Src/Particle/AMReX_NeighborParticlesI.H commit 5a9cc63a191bded70ea8bacf5aa933fffa2e2245 Author: Weiqun Zhang Date: Thu Oct 12 13:13:39 2017 -0700 MLMG: updateSolBC Src/Base/AMReX_IntVect.H Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_MacBndry.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit f5b3abcaaeee28b44f9df17e2581ef278ac8e367 Author: Andrew Myers Date: Thu Oct 12 12:42:43 2017 -0700 constructing a ParIter with an MFItInfo should not imply tiling=true. Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParIterI.H commit c1d09bff93d65e8c7fa4f45ab67c6384b2c61340 Author: Andrew Myers Date: Thu Oct 12 11:07:48 2017 -0700 use async MPI communication in the particle neighbor fill Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit d4cd363a42e2702b91ae7086ab94d5744dab51fb Author: Andrew Myers Date: Thu Oct 12 11:07:14 2017 -0700 move the duplicate helper function to AMReX_Vector.H so it can be used elsewhere as well. Src/Base/AMReX_Vector.H commit 1ccfe6ac6978b2b87095e0e4b2deb8a9b0834d65 Author: Andrew Myers Date: Thu Oct 12 09:59:03 2017 -0700 std::vector -> amrex::Vector Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit f99f5df793a32218ce6c4271725b56a2529d525f Author: Andrew Myers Date: Thu Oct 12 09:56:41 2017 -0700 encapsulate remove duplicates from a vector into a function. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit b7874894aff3fe9af1a5f0b86d65a3c30c1096f2 Author: Weiqun Zhang Date: Thu Oct 12 08:58:51 2017 -0700 MLMG: clean up the interface and fix dx in reflux Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 0b48beee0712697205b6d15f1b2a5497b3730c55 Author: Max Katz Date: Thu Oct 12 06:20:19 2017 -0400 Wrap CUDA launch in its own block Src/Base/AMReX_BLFort.H commit 642f73f16ba5e88c936fcc4d9b042d0b4080d74a Author: Max Katz Date: Thu Oct 12 04:31:30 2017 -0400 Unify on a single filccn Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_filcc_mod.F90 commit a0e380e4d0d86c6e1956fa03303c2501063f4aab Author: Max Katz Date: Thu Oct 12 03:58:44 2017 -0400 Decrease default number of max CUDA threads Src/Base/AMReX_CUDA.F90 Tools/GNUMake/Make.defs commit bb7b43ffe5e810b348471043ba6ae257c7446f98 Author: Max Katz Date: Thu Oct 12 03:46:43 2017 -0400 Update heat equation GPU test Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 commit 364132415baef446ac491c1c3aedfd2235d9601a Author: Max Katz Date: Thu Oct 12 03:38:56 2017 -0400 Remove SUBROUTINE from macro names Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_filcc_mod.F90 Src/Base/AMReX_fort_mod.F90 Tools/GNUMake/Make.defs commit b1f2f55365b8ae4e37536042391459f11991fd23 Author: Max Katz Date: Thu Oct 12 03:31:02 2017 -0400 Use device subroutine macro Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_fort_mod.F90 Tools/GNUMake/Make.defs commit 7364833f30c940ab852419cfb2156e0f2386fa7d Author: Max Katz Date: Thu Oct 12 03:22:39 2017 -0400 Call filcc directly from C++ Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_filcc_f.H Src/Base/AMReX_filcc_mod.F90 commit 70607a82eff2c08c6cca03d4215d816f7d4236ec Merge: 4e5cc9ed0 0a1e15551 Author: Tan Nguyen Date: Thu Oct 12 00:19:20 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4e5cc9ed0f35e39c9954fc450edec0a8e8773d89 Author: Tan Nguyen Date: Thu Oct 12 00:19:08 2017 -0700 add SMC code Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/GNUmakefile Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/LiDryer.c Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/Make.package Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/SMC.H Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/SMC.cpp Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/SMC_F.H Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/SMC_advance.cpp Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/SMC_init.cpp Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/SMC_io.cpp Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/chemistry_module.f90 Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/derivative_stencil.f90 Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/init_data.f90 Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/inputs_SMC Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/kernels.f90 Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/main.cpp Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/make_plot.f90 Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/transport_properties.f90 Src/AmrTask/tutorials/MiniApps/SMC_fixed_dt/variables.f90 commit 0a1e155513072a5698607ae835e81fb13a08ddaf Merge: 448311a3d 4a703375f Author: WeiqunZhang Date: Wed Oct 11 16:45:38 2017 -0700 Merge pull request #145 from bcfriesen/pmi_fixes PMI: change computation of unique groups/chassis/slots from unordered_set to vector commit 4a703375f233c692db06c2005c64b1e3040fa872 Author: Brian Friesen Date: Wed Oct 11 16:39:55 2017 -0700 PMI: change computation of unique groups/chassis/slots from unordered_set to vector This has better performance for large arrays. Src/Base/AMReX_ParallelDescriptor.cpp commit 448311a3d0a24c36fc20c3a3251511d1f8f50544 Author: Weiqun Zhang Date: Wed Oct 11 16:22:47 2017 -0700 MLMG: prolongation of correction from coarse to fine amr level Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/GNUmakefile commit 6e8930d82915d186e5dbaa5eb7fdee0c1f6c696f Author: Weiqun Zhang Date: Wed Oct 11 15:35:38 2017 -0700 MLMG: Reflux Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit d54fe54e6f27ec9e6c127dc457cd9be910393f43 Merge: f6c9fd5aa 610fbcbdd Author: Weiqun Zhang Date: Wed Oct 11 15:10:35 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f6c9fd5aa6486f4a39cee81d575c878e7bcdef0a Author: Weiqun Zhang Date: Wed Oct 11 15:09:10 2017 -0700 MLMG: coarse part of reflux Src/Boundary/AMReX_YAFluxRegister.H Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 610fbcbdde4ce43b30ce5f84f24db1490ad91328 Merge: c0c023ed8 01279c142 Author: WeiqunZhang Date: Wed Oct 11 13:59:55 2017 -0700 Merge pull request #144 from bcfriesen/add_pmi_support Base: add support for querying Process Management Interface (PMI) commit 01279c14254d8e49b8ef3227960b1180843c966a Author: Brian Friesen Date: Wed Oct 11 13:36:07 2017 -0700 Base: print simple header to STDOUT before PMI statistics Src/Base/AMReX_ParallelDescriptor.cpp commit 9c60d80fbef6d81b81ca657a0b74a62e3381e76b Author: Brian Friesen Date: Wed Oct 11 13:35:53 2017 -0700 Base: "PMI" -> "AMREX_PMI" Src/Base/AMReX.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Tools/GNUMake/Make.defs commit c0c023ed811e16680610bc7be90f7989e243912d Author: kngott Date: Wed Oct 11 13:19:38 2017 -0700 Adjustments to test output and general cleanup of MoveAllFabs. Src/Base/AMReX_FabArray.H commit faa61d850ded34b915233ecb78608df148d4f281 Author: kngott Date: Wed Oct 11 13:10:18 2017 -0700 Change AddCompsToProc in FabSet to properly allocate FluxRegister FabArrays Src/Boundary/AMReX_FabSet.H commit 6e5495433a94324813223c5e1a5ae4604f1cfe62 Author: kngott Date: Wed Oct 11 13:07:46 2017 -0700 Rewrite a comment from Array to Vector Src/Amr/AMReX_Amr.H commit e7948db22ca4c30946ec814f5c9e1e3df8c0c4e5 Author: Brian Friesen Date: Fri Oct 6 13:17:33 2017 -0700 Base: add support for querying Process Management Interface (PMI) PMI is available on Cray systems and provides information about the topology of the job on the network. One can use this information to apply optimizations at run time which exploit higher bandwidth, lower-latency connections between particular groups of processes on the network. PMI support is disabled by default, and can be activated by setting USE_PMI=TRUE in the makefile. Src/Base/AMReX.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Tools/GNUMake/Make.defs commit d97d1f54f1507ba0c7e7beece219b46a3017c55c Author: Weiqun Zhang Date: Wed Oct 11 12:25:29 2017 -0700 move YAFluxRegister to Boundary/ Src/AmrCore/Make.package Src/Boundary/AMReX_YAFluxRegister.H Src/Boundary/AMReX_YAFluxRegister.cpp Src/Boundary/AMReX_YAFluxRegister_1d.F90 Src/Boundary/AMReX_YAFluxRegister_2d.F90 Src/Boundary/AMReX_YAFluxRegister_3d.F90 Src/Boundary/AMReX_YAFluxRegister_F.H Src/Boundary/AMReX_YAFluxRegister_nd.F90 Src/Boundary/CMakeLists.txt Src/Boundary/Make.package Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/write_plotfile.cpp commit ccad545b5d13b97d6a38860d1b6a6aaf05796362 Author: Weiqun Zhang Date: Wed Oct 11 10:37:39 2017 -0700 MLMG: smooth Src/LinearSolvers/MLMG/AMReX_MLABecLap_1d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_2d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 3a91a76bf218dd0d6a66e23aa0286084ec7c85c8 Merge: 7dbb5cdf3 080a69035 Author: vince Date: Wed Oct 11 10:23:07 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 080a69035686d103b343078c449aeea1575d865d Author: Weiqun Zhang Date: Wed Oct 11 09:36:38 2017 -0700 MLMG: finish applyBC Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp commit 4883eb473f789ebffae347303dc1722fba1d0d9e Author: Weiqun Zhang Date: Wed Oct 11 07:46:24 2017 -0700 Array is used by Fortran BoxLib and in that case cannot include AMReX_SPACE.H Src/Base/AMReX_Array.H commit 9f0db7ea2a181db080bf1b4b136116584db637d8 Author: Weiqun Zhang Date: Tue Oct 10 16:55:52 2017 -0700 MLMG: applyBC WIP Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_LayoutData.H Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_MacBndry.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/GNUmakefile Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 7dbb5cdf3a2d30bf19660823abc84d7c7c439437 Merge: 20d71ff5a 026269f16 Author: vince Date: Tue Oct 10 15:03:46 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 061f663e906678ea313aa500218c21ba02ead185 Author: Weiqun Zhang Date: Tue Oct 10 13:31:17 2017 -0700 MLMG: wip Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 6e916152a45a208f1f22de283524cc47621c182d Author: Max Katz Date: Tue Oct 10 15:59:35 2017 -0400 Fix rank <-> GPU identification for MPS case Src/Base/AMReX_Device.cpp commit 026269f16575f657fa9020c3d6034e178bb1bbb5 Author: Weiqun Zhang Date: Tue Oct 10 12:41:26 2017 -0700 MLMG: add A dot x Src/LinearSolvers/MLMG/AMReX_MLABecLap_3d.F90 Src/LinearSolvers/MLMG/AMReX_MLABecLap_F.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/Make.package commit c6a45385de8f426d3e1b7502678108686e804faa Author: Weiqun Zhang Date: Tue Oct 10 11:06:45 2017 -0700 add a few virtual function stubs to MLLinOp Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit cdecd983b5480f2d2cb05beb1ddb23447a1ba646 Merge: e24d801ec 552a71091 Author: Weiqun Zhang Date: Tue Oct 10 10:31:15 2017 -0700 Merge branch 'weiqun/mlmg' into development commit 552a710913935945370997c96b53daacabfa7279 Author: Weiqun Zhang Date: Tue Oct 10 10:30:35 2017 -0700 MLMG: WIP Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp commit 955105aafec83599bf3853e5339853d6725dc9ac Author: Weiqun Zhang Date: Mon Oct 9 17:23:58 2017 -0700 WIP Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/main.cpp commit e24d801ec6447aaebdc6d4c2d18d70039ae05b70 Merge: 3cc11496a ef248e1a2 Author: Andrew Myers Date: Mon Oct 9 16:36:50 2017 -0700 fixing merge conflict commit f1bd3901f0a35926b32e6c18ccef982d64547463 Author: Weiqun Zhang Date: Sun Oct 8 12:06:21 2017 -0700 MLMG: notes Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit e2de854d10f60e52c7f86ca7ddc03ffeb497124e Author: Max Katz Date: Sun Oct 8 06:39:10 2017 -0400 Fix a compile fail without MPI Src/Base/AMReX_Device.cpp commit 04165addd12eb451417d381914a9d16d1260b1b8 Author: Max Katz Date: Sun Oct 8 01:51:32 2017 -0400 Use 512 threads per block Note that for Pascal, this means you need to limit the number of registers per function to 128. Src/Base/AMReX_CUDA.F90 commit c12a237719a4e9d33b652ebb648b53d28d40d8fd Author: Max Katz Date: Sun Oct 8 01:19:50 2017 -0400 Do not tile threadblock size; this hurts performance Src/Base/AMReX_CUDA.F90 commit 94e4b7fed40f7e08e23edef4ef9237b1613929f2 Author: Max Katz Date: Sat Oct 7 22:00:51 2017 -0400 Move the loop over components to the top level Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 commit a42364713e78586f0b6e6c50b330fa048216c941 Author: Max Katz Date: Sat Oct 7 21:02:32 2017 -0400 filccn loops over all n variables Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_filcc_mod.F90 commit b26928c7bbf0c6849f331ff118f89b7572960d79 Author: Weiqun Zhang Date: Sat Oct 7 15:48:43 2017 -0700 WIP: MLMG Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/main.cpp commit e76ad038726c8a6a7a819d709173bdf0fff9fdc0 Author: Weiqun Zhang Date: Sat Oct 7 13:30:40 2017 -0700 MLMG: prepare for solve Src/Base/AMReX_Array.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 0023c745d2899f412ab3f1355d0b2d6a2ca1da6a Author: Weiqun Zhang Date: Fri Oct 6 17:12:30 2017 -0700 MLMG::solve WIP Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 27f708f38c0f3bac827e58bb91adb45357dc3029 Author: Weiqun Zhang Date: Fri Oct 6 16:49:18 2017 -0700 MLMG constructor Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit aef9a5f7439b6e40f92354206e57c2617105649e Author: Weiqun Zhang Date: Fri Oct 6 16:36:51 2017 -0700 set ABecLaplacian coefficients Src/Base/AMReX_MultiFabUtil.cpp Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 10790ecfbf611206973767b587754e6bd6d70c99 Author: Weiqun Zhang Date: Fri Oct 6 15:08:44 2017 -0700 MLLinOp and MLABecLaplacian constructors Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit 20d71ff5ae0d31cf81d688d918b532db4a150afc Author: vince Date: Fri Oct 6 14:41:02 2017 -0700 remove debug diagnostic. Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp commit 465c0a91abd9c49e5d5cf248a7ef7c9975a92230 Author: Weiqun Zhang Date: Fri Oct 6 12:35:15 2017 -0700 Array --> Vector in mlmg test Tests/LinearSolvers/MLMG/init_prob.cpp Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp Tests/LinearSolvers/MLMG/write_plotfile.cpp commit b0fbd7bee053acd2af1b4f24ce330715b406ac33 Merge: eb1a0739e ef248e1a2 Author: Weiqun Zhang Date: Fri Oct 6 12:32:19 2017 -0700 Merge branch 'development' into weiqun/mlmg Conflicts: Src/Base/AMReX_Array.H commit ff2daf4a76ad8bac354712076f36798648998bcc Merge: 8e9b78555 ef248e1a2 Author: rgrout Date: Fri Oct 6 13:20:28 2017 -0600 Merge branch 'development' into migrate_Convergence_util commit 8e9b78555e8c2571926a4c464ef311c684791f43 Author: Ray Grout Date: Fri Oct 6 09:30:05 2017 -0700 Updates to track AMReX development Tools/C_util/Convergence/ComputeAmrDataNorms.H Tools/C_util/Convergence/ComputeAmrDataNorms.cpp Tools/C_util/Convergence/DiffSameGrid2.cpp Tools/C_util/Convergence/GNUmakefile Tools/C_util/Convergence/Make.package Tools/C_util/WritePlotFile.H Tools/C_util/WritePlotFile.cpp commit ef248e1a2172054eeb7615109030bc3a39096071 Author: Weiqun Zhang Date: Fri Oct 6 08:53:01 2017 -0700 Array --> Vector in Tools Tools/AMRProfParser/TestCodes/BLProfCallTimes.cpp Tools/AMRProfParser/TestCodes/Pieces.cpp Tools/AMRProfParser/TestCodes/SendTest0.cpp Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp Tools/C_util/Convergence/ComputeAmrDataNorms.H Tools/C_util/Convergence/ComputeAmrDataNorms.cpp Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameDomainRefinedComposite.cpp Tools/C_util/Convergence/DiffSameDomainRefinedFD.cpp Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGrid2.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileNormB.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/Statistics/ComputeAmrDataStat.H Tools/C_util/Statistics/ComputeAmrDataStat.cpp Tools/C_util/Statistics/PltFileFluxAve.H Tools/C_util/Statistics/PltFileFluxAve.cpp Tools/C_util/Statistics/PltFileList.cpp Tools/C_util/Statistics/PltFileStat.cpp Tools/C_util/Statistics/PltFileXAve.H Tools/C_util/Statistics/PltFileXAve.cpp Tools/C_util/ViewMF/mfMinMax.cpp Tools/C_util/WritePlotFile.H Tools/C_util/WritePlotFile.cpp Tools/C_util/dbgTools/crsGrids.cpp Tools/C_util/dbgTools/intersectGrids.cpp commit 20c0614a5f2e1e8e1ed76fae1611cd0dc69ab7dd Merge: 2a67307f0 152cf934c Author: Tan Nguyen Date: Fri Oct 6 01:15:39 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2a67307f04c6a10cbee01d631ab1a0edf40d95a9 Author: Tan Nguyen Date: Fri Oct 6 01:15:30 2017 -0700 fix a memory leak bug Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H commit 0e84d892d23277e4da76c95d453a86192500d577 Merge: c9d6a437f 152cf934c Author: Max Katz Date: Fri Oct 6 03:11:53 2017 -0400 Merge branch 'development' into gpu commit c9d6a437fea600b63b6aac44c803c13ef1ff18d5 Author: Max Katz Date: Fri Oct 6 02:07:33 2017 -0400 Give simplified initial output if device is not verbose Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 031c5eacf78bc346ebb8e2350140cf3e1edca565 Author: Max Katz Date: Thu Oct 5 22:01:58 2017 -0400 Add device.verbose output parameter Src/Base/AMReX.cpp Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 152cf934caf433478a5c29eeb895d7380493fef5 Author: Weiqun Zhang Date: Thu Oct 5 17:48:51 2017 -0700 update CHANGES CHANGES commit be7d6dedca0db97a5a0b5dd60e97c48d7c39a89c Merge: 4557fa735 cc05981bc Author: Tan Nguyen Date: Thu Oct 5 17:39:25 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 4557fa7357fbd428bc9cf507e6a08d6dbf120790 Author: Tan Nguyen Date: Thu Oct 5 17:39:04 2017 -0700 grant friend access to MFGraph and Action classes Src/Base/AMReX_FabArray.H commit 146ad104c5ea31b03502d4b218f3883bed98ffd6 Author: Tan Nguyen Date: Thu Oct 5 17:36:45 2017 -0700 runtime support for AMFIter Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.cpp Src/AmrTask/AMFIter/AMReX_Connections.H Src/AmrTask/AMFIter/Makefile Src/AmrTask/graph/AMReX_AbstractTask.H Src/AmrTask/graph/AMReX_TaskGraph.H Src/AmrTask/rts_impls/MPI_Generic/Makefile Src/AmrTask/rts_impls/MPI_Generic/rts.C Src/AmrTask/tutorials/MiniApps/HeatEquation/advance.cpp Src/AmrTask/tutorials/MiniApps/HeatEquation/inputs_3d commit cc05981bcfeefd25e676bc81c32a249e65c10c72 Author: Weiqun Zhang Date: Thu Oct 5 17:35:05 2017 -0700 Array --> Vector in Docs Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/Boundary/Boundary.tex Docs/AMReXUsersGuide/EB/EB.tex Docs/AMReXUsersGuide/Particle/Particle.tex Docs/Readme.sidecars Tools/Migration/amrex_array_to_vector.sh commit cc706b6d8d14bb2209110cf451ddb3cc66ef34f8 Author: Weiqun Zhang Date: Thu Oct 5 17:29:43 2017 -0700 a script for Array --> Vector Tools/Migration/amrex_array_to_vector.sh commit b3a87b1fbcf1f20c319da2b5da38c4c127b08553 Author: Weiqun Zhang Date: Thu Oct 5 17:27:21 2017 -0700 Array --> Vector in Tutorials Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.H Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/Basic/HeatEquation_EX1_C/main.cpp Tutorials/Basic/HeatEquation_EX2_C/advance.cpp Tutorials/Basic/HeatEquation_EX2_C/main.cpp Tutorials/Basic/HeatEquation_EX2_C/myfunc.H Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_init_eb.cpp Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/main.cpp Tutorials/Particles/LoadBalance/main.cpp commit 1247bae570bd288da6ef2edcd5c85954fed62442 Author: Weiqun Zhang Date: Thu Oct 5 17:26:31 2017 -0700 Array --> Vector in Tests Tests/BBIOBenchmark/BBIOTest.cpp Tests/C_BaseLib/BcastClasses/BcastClasses.cpp Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tMF.cpp Tests/C_BaseLib/tParmParse.cpp Tests/C_BaseLib/tProfiler.cpp Tests/C_BaseLib/tRABcast.cpp Tests/EBAMRTools/regression/aggpwlfpTest.cpp Tests/EBAMRTools/regression/divergenceOpTest.cpp Tests/EBAMRTools/regression/ebCoarseAveTest.cpp Tests/EBAMRTools/regression/ebCoarseAveTestFace.cpp Tests/EBAMRTools/regression/ebFineInterpTest.cpp Tests/EBAMRTools/regression/fluxRegTest.cpp Tests/EBAMRTools/regression/gradientOpTest.cpp Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp Tests/EBAMRTools/regression/simpleMeshRefine.cpp Tests/FillBoundaryComparison/main.cpp Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp Tests/GeometryShop/flatPlate/flatPlateTest.cpp Tests/GeometryShop/ramp/main.cpp Tests/GeometryShop/sparseDataSingleGrid/sparseDataSG.cpp Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp Tests/GeometryShop/vofStructures/umapTest.cpp Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.H Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.H Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp Tests/Particles/AssignMultiLevelDensity/main.cpp Tests/Particles/ParticleIterator/main.cpp Tests/Particles/main.cpp commit dd1b202c4e76f6e92bec47163307ad720f472615 Author: Weiqun Zhang Date: Thu Oct 5 17:25:01 2017 -0700 Array --> Vector in OldTutorials OldTutorials/DataServicesTest0/DataServicesTest0.cpp OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp OldTutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp OldTutorials/GettingStarted_C/main.cpp OldTutorials/HeatEquation_EX2_C/main.cpp OldTutorials/MeshRefinement/MyAmr.H OldTutorials/MeshRefinement/MyAmr.cpp OldTutorials/MeshRefinement/main.cpp OldTutorials/MultiColor_C/main.cpp OldTutorials/MultiFabTests_C/GridMoveTest.cpp OldTutorials/MultiFabTests_C/MoveAllFabsTest.cpp OldTutorials/MultiFabTests_C/MultiFabFillBoundary.cpp OldTutorials/MultiFabTests_C/MultiFabReadWrite.cpp OldTutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp OldTutorials/MultiGrid_C/main.cpp OldTutorials/PGAS_HEAT/main.cpp OldTutorials/PIC_C/single_level.cpp OldTutorials/PIC_C/solve_for_accel.cpp OldTutorials/PIC_C/solve_with_f90.cpp OldTutorials/PIC_C/two_level.cpp OldTutorials/Sidecar_EX1/DestMFTest.cpp OldTutorials/Sidecar_EX1/NSidecarsTest.cpp OldTutorials/Sidecar_EX1/SidecarResizeTest.cpp OldTutorials/Sidecar_EX1/TestRankSets.cpp OldTutorials/Tiling_Heat_C/main.cpp OldTutorials/TwoGrid_PIC_C/main.cpp OldTutorials/TwoGrid_PIC_C/solve_for_accel.cpp OldTutorials/TwoGrid_PIC_C/solve_with_f90.cpp OldTutorials/TwoGrid_PIC_C/split_boxes.cpp OldTutorials/libamrex_C/MyAmr.H OldTutorials/libamrex_C/MyAmr.cpp OldTutorials/libamrex_C/main.cpp commit 1716e555d51199df242cdc1336907d7298f6596a Author: Weiqun Zhang Date: Thu Oct 5 17:21:44 2017 -0700 Array --> Vector in MiniApps MiniApps/PGAS_SMC/SMC.H MiniApps/PGAS_SMC/SMC.cpp MiniApps/PGAS_SMC/SMC_init.cpp commit f4f15593337e2e90740b2247ddf858240b632738 Author: Weiqun Zhang Date: Thu Oct 5 16:20:21 2017 -0700 Array --> Vector in Src/ Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_Derive.H Src/Amr/AMReX_Derive.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_AmrParGDB.H Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/AmrCore/AMReX_YAFluxRegister.H Src/AmrCore/AMReX_YAFluxRegister.cpp Src/AmrTask/tutorials/MiniApps/HeatEquation/main.cpp Src/AmrTask/tutorials/MiniApps/HeatEquation/physbc.cpp Src/Base/AMReX_Array.H Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BCUtil.H Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxDomain.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabConv.H Src/Base/AMReX_FabConv.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_LayoutData.H Src/Base/AMReX_MFCopyDescriptor.H Src/Base/AMReX_MFCopyDescriptor.cpp Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_NFiles.H Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParmParse.H Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_TinyProfiler.cpp Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_iMultiFab.cpp Src/Base/AMReX_parmparse_fi.cpp Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_MacBndry.cpp Src/Boundary/AMReX_MultiMask.cpp Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBInterpolater.H Src/EB/AMReX_EBInterpolater.cpp Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_EBCFInterp.H Src/EBAMRTools/AMReX_EBCFInterp.cpp Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_EBFineInterp.H Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/EBAMRTools/AMReX_GradientOp.H Src/EBAMRTools/AMReX_GradientOp.cpp Src/EBAMRTools/AMReX_MeshRefine.H Src/EBAMRTools/AMReX_MeshRefine.cpp Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/ProfParser/AMReX_BLProfStats.H Src/Extern/ProfParser/AMReX_BLProfStats.cpp Src/Extern/ProfParser/AMReX_BLProfUtilities.H Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp Src/Extern/ProfParser/AMReX_BLWritePlotFile.H Src/Extern/ProfParser/AMReX_BLWritePlotFile.cpp Src/Extern/ProfParser/AMReX_CommProfStats.H Src/Extern/ProfParser/AMReX_CommProfStats.cpp Src/Extern/ProfParser/AMReX_ProfParserBatch.cpp Src/Extern/ProfParser/AMReX_RegionsProfStats.H Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp Src/Extern/amrdata/AMReX_AmrData.H Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp Src/Extern/amrdata/AMReX_XYPlotDataList.H Src/Extern/amrdata/AMReX_XYPlotDataList.cpp Src/F_BaseLib/MultiFab_C_F.cpp Src/F_Interfaces/AmrCore/AMReX_amrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/Base/AMReX_distromap_fi.cpp Src/F_Interfaces/Base/AMReX_init_fi.cpp Src/F_Interfaces/Base/AMReX_plotfile_fi.cpp Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Src/GeometryShop/AMReX_AggStencil.H Src/GeometryShop/AMReX_AggStencilI.H Src/GeometryShop/AMReX_AllRegularService.H Src/GeometryShop/AMReX_AllRegularService.cpp Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_BaseEBFaceFAB.H Src/GeometryShop/AMReX_BaseEBFaceFABI.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_EBCellFAB.cpp Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBDebugOut.H Src/GeometryShop/AMReX_EBDebugOut.cpp Src/GeometryShop/AMReX_EBFaceFAB.cpp Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISBox.H Src/GeometryShop/AMReX_EBISBox.cpp Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp Src/GeometryShop/AMReX_FabArrayIO.H Src/GeometryShop/AMReX_FaceIterator.H Src/GeometryShop/AMReX_FaceIterator.cpp Src/GeometryShop/AMReX_FlatPlateGeom.H Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_GraphNode.H Src/GeometryShop/AMReX_GraphNode.cpp Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntVectSet.cpp Src/GeometryShop/AMReX_IntersectionIF.H Src/GeometryShop/AMReX_IntersectionIF.cpp Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_IrregNode.cpp Src/GeometryShop/AMReX_LSquares.H Src/GeometryShop/AMReX_LSquares.cpp Src/GeometryShop/AMReX_Moments.H Src/GeometryShop/AMReX_Moments.cpp Src/GeometryShop/AMReX_PolyGeom.H Src/GeometryShop/AMReX_PolyGeom.cpp Src/GeometryShop/AMReX_PolynomialIF.H Src/GeometryShop/AMReX_PolynomialIF.cpp Src/GeometryShop/AMReX_RedistStencil.cpp Src/GeometryShop/AMReX_SlabService.H Src/GeometryShop/AMReX_SlabService.cpp Src/GeometryShop/AMReX_Stencils.H Src/GeometryShop/AMReX_UnionIF.H Src/GeometryShop/AMReX_UnionIF.cpp Src/GeometryShop/AMReX_VoFIterator.H Src/GeometryShop/AMReX_VoFIterator.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Src/Particle/AMReX_LoadBalanceKD.H Src/Particle/AMReX_LoadBalanceKD.cpp Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_ParGDB.H Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit 387d0597ae6a40789263974904c0b65ac4841f18 Author: Weiqun Zhang Date: Thu Oct 5 16:12:14 2017 -0700 include AMReX_Vector.H in addition to AMReX_Array.H Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateDescriptor.H Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_Cluster.H Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_TagBox.H Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxList.H Src/Base/AMReX_CArena.H Src/Base/AMReX_CoordSys.H Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabConv.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_RealBox.H Src/Base/AMReX_Utility.H Src/Base/AMReX_parmparse_fi.cpp Src/EB/AMReX_EBMultiFabUtil.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/Extern/ProfParser/AMReX_BLProfUtilities.H Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp Src/Extern/ProfParser/AMReX_CommProfStats.H Src/Extern/ProfParser/AMReX_RegionsProfStats.H Src/Extern/amrdata/AMReX_AmrData.H Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_XYPlotDataList.H Src/F_Interfaces/Base/AMReX_init_fi.cpp Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Src/GeometryShop/AMReX_IntersectionIF.H Src/GeometryShop/AMReX_LSquares.H Src/GeometryShop/AMReX_Moments.H Src/GeometryShop/AMReX_PolyGeom.H Src/GeometryShop/AMReX_SlabService.H Src/GeometryShop/AMReX_UnionIF.H Src/GeometryShop/AMReX_UnionIF.cpp Src/GeometryShop/AMReX_VoFIterator.H Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H Src/Particle/AMReX_ParGDB.H Src/Particle/AMReX_Particles.H commit eb1a0739eae4556808fd1fc6fbaed67b3e52de37 Merge: 31469f4f3 224be3276 Author: Weiqun Zhang Date: Thu Oct 5 15:57:43 2017 -0700 Merge branch 'development' into weiqun/mlmg commit 224be32764d94b99fabc795181d872741e7af9d0 Author: Weiqun Zhang Date: Thu Oct 5 15:57:14 2017 -0700 add amrex::Vector Src/Base/AMReX_Vector.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 31469f4f3dbd154b5f635c81f7f4494b92a618d7 Author: Weiqun Zhang Date: Thu Oct 5 15:47:48 2017 -0700 MLMG test: wip Tests/LinearSolvers/MLMG/Make.package Tests/LinearSolvers/MLMG/init_prob.cpp Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/prob_par.H Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp commit c31a23598dcb9e0031bd1acfe09a67570100690a Author: Weiqun Zhang Date: Thu Oct 5 14:42:03 2017 -0700 set up a test problem for MLMG Src/Base/AMReX_Array.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Tests/LinearSolvers/MLMG/GNUmakefile Tests/LinearSolvers/MLMG/Make.package Tests/LinearSolvers/MLMG/fort.H Tests/LinearSolvers/MLMG/fort_3d.F90 Tests/LinearSolvers/MLMG/init_prob.cpp Tests/LinearSolvers/MLMG/main.cpp Tests/LinearSolvers/MLMG/solve_with_mlmg.cpp Tests/LinearSolvers/MLMG/write_plotfile.cpp commit 9a7e2833c839baf20551017c5f0ab3c3dc27bb9c Merge: 1bcb3aa85 54f78b4a9 Author: Michele Rosso Date: Thu Oct 5 11:21:41 2017 -0700 Merge branch 'development' into mr-cmake commit 54f78b4a99614237c0bfc92c8218f1e618a52c2d Merge: e6c9acd7b 82de08f47 Author: WeiqunZhang Date: Thu Oct 5 10:44:24 2017 -0700 Merge pull request #142 from zingale/development sync up with fcompare commit e6c9acd7baba2fbab8a7e5a3c5bdf64747766ad4 Author: Andrew Myers Date: Thu Oct 5 10:22:50 2017 -0700 update changelog CHANGES commit d7b77e1227a5a48c5bad2182ff9062c98b817f2b Author: Weiqun Zhang Date: Thu Oct 5 10:20:33 2017 -0700 start MLMG Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.H Src/LinearSolvers/MLMG/AMReX_MLABecLaplacian.cpp Src/LinearSolvers/MLMG/AMReX_MLLinOp.H Src/LinearSolvers/MLMG/AMReX_MLLinOp.cpp Src/LinearSolvers/MLMG/AMReX_MLMG.H Src/LinearSolvers/MLMG/AMReX_MLMG.cpp Src/LinearSolvers/MLMG/Make.package Tests/LinearSolvers/MLMG/GNUmakefile Tests/LinearSolvers/MLMG/Make.package Tests/LinearSolvers/MLMG/main.cpp commit e7fd9bbd94e407c3f2099fe6c2916bb1c7ade3d8 Author: Max Katz Date: Thu Oct 5 05:01:55 2017 -0400 Fix an error testing against a possibly empty vector Src/Base/AMReX_MFIter.cpp commit fa993750e5365f438ac5d39eba5ffc53afdee11d Author: Max Katz Date: Thu Oct 5 05:01:33 2017 -0400 Allow for multi-node CPU<->GPU mappings Src/Base/AMReX_Device.cpp commit 663f856d8cfc81d33cf76fda17128bfddbe0c219 Merge: 25c67ffa2 a9574b52d Author: Klaus Weide Date: Thu Oct 5 01:38:33 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 75434016d8c3f7c5e46b5fd5c3e06755fdf5cc9b Author: Max Katz Date: Thu Oct 5 02:10:54 2017 -0400 Use a distinct (non-coalesced) memory arena for FabArray Src/Base/AMReX_Arena.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit a9574b52d1f73e451f70fa37722a3362023dcd94 Merge: d4aeb9288 f02c2ff4d Author: Andy Nonaka Date: Wed Oct 4 18:32:57 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d4aeb928852f61c8e5fdb9e37ec7b71b5c9f60af Author: Andy Nonaka Date: Wed Oct 4 18:31:48 2017 -0700 add sort=.false. to the boxarray constructor for the diff multifab it fixes problems with this utility when the input plotfile boxarray are not in the "sorted" order Tools/Postprocessing/F_Src/fcompare.f90 commit 82de08f47049a5503d2e59a5f96578eb0c91b123 Author: Michael Zingale Date: Wed Oct 4 20:43:08 2017 -0400 sync up with fcompare you now don't need to use --infile1 and --infile2, just list the plot files after the command the 2 features it doesn't do that fcompare does is compare ghost cells (not sure if it makes sense with different boxes) and output a plotfile with the difference between plotfiles Tools/Postprocessing/F_Src/plt_compare_diff_grids.f90 commit f02c2ff4d04ded67e020c9c70f528d2f70c8cf1f Merge: 8e5ffbce3 1c5c62c25 Author: WeiqunZhang Date: Wed Oct 4 17:34:27 2017 -0700 Merge pull request #141 from AMReX-Codes/parallel_print_to_file Parallel print to file commit 1c5c62c258cb5d134332ef16368f53dd909137b0 Author: Andrew Myers Date: Wed Oct 4 16:58:48 2017 -0700 trading some code duplication for some clarity. Src/Base/AMReX_Print.H Tests/Particles/ParticleIterator/main.cpp commit 9ebec02400610825c8a1089a04703f774ed65685 Author: Max Katz Date: Wed Oct 4 19:50:40 2017 -0400 Add C++ CUDA error checking Src/Base/AMReX_BLFort.H Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 664c03dfc1619712c4fd6a22ef217c2a787191d8 Author: Andrew Myers Date: Wed Oct 4 15:31:58 2017 -0700 update this test to demonstrate the new amrex::Print() capability Tests/Particles/ParticleIterator/GNUmakefile Tests/Particles/ParticleIterator/main.cpp commit 109d9348b1a02f8491ee398e011e533c73221191 Author: Andrew Myers Date: Wed Oct 4 15:31:21 2017 -0700 new versions of amrex::Print() that send the output to a different file for each proc (and for each thread if called inside a parallel region). Src/Base/AMReX_Print.H commit 1bcb3aa854bf84e9783b0b3e38c326dca28454da Author: Michele Rosso Date: Wed Oct 4 15:29:53 2017 -0700 Remove garbage Tutorials/Amr/Advection_octree_F/CMakeLists.txt commit 8e5ffbce390715f251caa85f54d10a8eac816a81 Merge: 6421785df 628878089 Author: vince Date: Wed Oct 4 15:12:02 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 50037868120f7388cfbc0221d38c3e2a178307aa Merge: db028fe30 628878089 Author: Michele Rosso Date: Wed Oct 4 13:55:04 2017 -0700 Merge branch 'development' into mr-cmake Conflicts: Src/AmrCore/CMakeLists.txt Tutorials/Amr/Advection_AmrCore/CMakeLists.txt commit 62887808932b94d8f99b442a4b88e81264f15848 Author: Weiqun Zhang Date: Wed Oct 4 08:50:41 2017 -0700 clean up old files Src/EB/AMReX_EBFaceFlag.H Src/EB/AMReX_EBFaceFlag.cpp Src/EB/AMReX_EBLevel.H Src/EB/AMReX_EBLevel.cpp Src/EB/Make.package commit 3caf471d8f3cd6a6fe9c270f83ee34c5bc0cd9c3 Author: Weiqun Zhang Date: Tue Oct 3 17:50:46 2017 -0700 EB/CNS: tagging on density gradient Tutorials/EB/CNS/Exec/ShockRef/inputs.amr Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/fortran/CNS_tagging.F90 Tutorials/EB/CNS/Source/fortran/Make.package commit 6421785df9db027dae62b9948011d87889238ecd Author: vince Date: Tue Oct 3 16:09:03 2017 -0700 fix comments. Src/Base/AMReX.H commit 8746e72767c8a490d8c7fb7fdd75b6cc5aef21f0 Merge: d6d2e667e 14796c694 Author: Michele Rosso Date: Tue Oct 3 15:53:47 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d6d2e667e91250f15c9f735a9aee63699d9d5536 Author: Michele Rosso Date: Tue Oct 3 15:53:27 2017 -0700 CMake: update CMakeLists.txt in Tutorials Tutorials/Amr/Advection_AmrCore/CMakeLists.txt commit 14796c6941556f2264810f0fb23dd5fbed5601bc Merge: ffc6863fe 3f0305b0b Author: Weiqun Zhang Date: Tue Oct 3 15:41:34 2017 -0700 Merge branch 'weiqun/eb' into development commit ffc6863fef4b46ceec38cc4f5f64791cdcffe486 Merge: 7b05e9982 638b61ae4 Author: dtgraves Date: Tue Oct 3 15:27:43 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 7b05e9982b72865446c3988282cb63ffcc98c19d Author: dtgraves Date: Tue Oct 3 15:26:50 2017 -0700 added some timers Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 commit 3e2b5ea77adfca49ce0026f374b9a985b3ecde8d Author: vince Date: Tue Oct 3 14:42:50 2017 -0700 move file into Extern/ProfParser. Src/Extern/ProfParser/AMReX_ProfParserBatch.cpp Src/Extern/ProfParser/Make.package Tools/AMRProfParser/GNUmakefile commit 096d5c17df5f482dabb8cf7b6d4410c2b8367616 Author: vince Date: Tue Oct 3 14:22:56 2017 -0700 move the amrprofparser into amrex tools. the parser functionality will be replaced by amrvis. Tools/AMRProfParser/AMReX_ProfParserBatch.cpp Tools/AMRProfParser/BLProfParser.cpp Tools/AMRProfParser/GNUmakefile Tools/AMRProfParser/TestCodes/AMRProfTest0.cpp Tools/AMRProfParser/TestCodes/BLProfCallTimes.cpp Tools/AMRProfParser/TestCodes/GNUmakefile Tools/AMRProfParser/TestCodes/Pieces.cpp Tools/AMRProfParser/TestCodes/SendTest0.cpp Tools/AMRProfParser/TestCodes/TokenizeTest.cpp commit 086f2a0a9b154e9c8af40d41be91d26299b2d875 Merge: 07d8f6b87 638b61ae4 Author: vince Date: Tue Oct 3 14:07:30 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 07d8f6b87dc1c2250fcc310a239ac09d5ab3d099 Merge: 066322306 ae1f47d72 Author: vince Date: Tue Oct 3 14:07:28 2017 -0700 merge fix. commit 638b61ae45a05f56847fc4af5ee2ba6d774cddbe Merge: c55485bd2 ae1f47d72 Author: Andrew Myers Date: Tue Oct 3 13:28:41 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c55485bd25488feefa849c59840b4a134819adfa Author: Andrew Myers Date: Tue Oct 3 13:28:25 2017 -0700 add ability to load balance based on the square of the particle count. Src/Particle/AMReX_KDTree_3d.F90 Src/Particle/AMReX_KDTree_F.H Src/Particle/AMReX_LoadBalanceKD.H Src/Particle/AMReX_LoadBalanceKD.cpp commit 3f0305b0bf993786c91ffd99ab039998bfcce3bf Merge: e5ea2bb08 ae1f47d72 Author: Weiqun Zhang Date: Tue Oct 3 12:50:06 2017 -0700 Merge branch 'development' into weiqun/eb commit e5ea2bb08e071df4c6a9ca12d08b3a1c9ef2dae5 Author: Weiqun Zhang Date: Tue Oct 3 12:48:43 2017 -0700 fine tune # of ghost cells Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArrayBase.cpp Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_EBTower.cpp Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/main.cpp commit 06632230665dc4265caa997fe2b8717678c904a0 Author: vince Date: Tue Oct 3 12:19:22 2017 -0700 update for amrex. OldTutorials/Sidecar_EX1/SidecarResizeTest.cpp commit db47fcfb7081b3411b62eadd94b8b28064e4b710 Author: vince Date: Tue Oct 3 12:17:22 2017 -0700 fix comment. Src/Base/AMReX_ParallelDescriptor.H commit ae1f47d7213091a80b598e2ec7f9cd45fba4bdc3 Author: Weiqun Zhang Date: Tue Oct 3 10:05:29 2017 -0700 Revert "simplify overloaded calls to InterpFromCoarseLevel and FillPatchTwoLevels" This reverts commit a43a8465eb84091348496cb276c5e9047863cba5. Src/AmrCore/AMReX_FillPatchUtil.cpp commit 4fcb4e2095ba46eb84d961a4d695b4c152cbbdf4 Merge: 5fe5dd711 f5ba98cfb Author: Weiqun Zhang Date: Tue Oct 3 09:43:38 2017 -0700 Merge branch 'development' into weiqun/eb commit 5fe5dd711327c532214ed15dfe387dd3fa5dd40c Author: Weiqun Zhang Date: Tue Oct 3 09:43:26 2017 -0700 more clean up of EBMultiFabUtil Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_F.H Src/EB/AMReX_EBMultiFabUtil_nd.F90 Tutorials/EB/CNS/Source/CNS.cpp commit bae3ddb3069214e3c64d8a07daffd3bbdac10378 Author: Weiqun Zhang Date: Tue Oct 3 09:30:54 2017 -0700 EBTower: bug fix Src/EB/AMReX_EBTower.cpp commit 3e16e3634419e9bb08cd1dce77c8628a5476ed98 Author: Weiqun Zhang Date: Tue Oct 3 09:18:32 2017 -0700 clean up Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp commit f5ba98cfb81a85b02823b09062c2bda6d7b9d320 Merge: 95dea8b0e a43a8465e Author: Andrew Myers Date: Mon Oct 2 23:31:39 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 95dea8b0e1e5fbe49514f7618f780c8e836359a1 Author: Andrew Myers Date: Mon Oct 2 23:31:15 2017 -0700 handle case where a level is lost on restart in Particle::Redistribute() Src/Particle/AMReX_ParticleContainerI.H commit a43a8465eb84091348496cb276c5e9047863cba5 Author: Andy Nonaka Date: Mon Oct 2 17:42:51 2017 -0700 simplify overloaded calls to InterpFromCoarseLevel and FillPatchTwoLevels Src/AmrCore/AMReX_FillPatchUtil.cpp commit cde02570089797692100aef7bc51d8d4c0512000 Author: Weiqun Zhang Date: Mon Oct 2 17:32:16 2017 -0700 fix no-mpi Src/Base/AMReX_Box.cpp commit c127c59d0eee0ea0b156a09a4004f3c3cbcdaccb Author: Weiqun Zhang Date: Mon Oct 2 17:10:06 2017 -0700 update EB average down and fix local copy of CutFab Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit 8ae94795a81d3ed634fd1627db9df1317332b2fd Author: Andy Nonaka Date: Mon Oct 2 17:00:40 2017 -0700 boundary condition documentation, example cleanup Docs/AMReXUsersGuide/Boundary/Boundary.tex Src/Base/AMReX_PhysBCFunct.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit b8a843010eccd8dd506cc1f35244444038f76a88 Merge: a0c06be3f 819b1a578 Author: Weiqun Zhang Date: Mon Oct 2 16:29:08 2017 -0700 Merge branch 'development' into weiqun/eb commit a0c06be3f89c1d55574402af7a39963677a25c19 Author: Weiqun Zhang Date: Mon Oct 2 16:28:54 2017 -0700 ParallelCopy for MultiCutFab Src/Amr/AMReX_AmrLevel.cpp Src/Base/AMReX_FabArray.H Src/EB/AMReX_EBFArrayBox.cpp Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit 85d539124ccc75aca6584a5e69493d7839f54ab9 Merge: d9ce3cccc 611eb17d2 Author: Andy Nonaka Date: Mon Oct 2 13:52:42 2017 -0700 removing this file Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development Conflicts: Tutorials/Amr/Advection_AmrCore_Boundary/CMakeLists.txt commit d9ce3ccccce187befe866843640cb065a9cfec3d Author: Andy Nonaka Date: Mon Oct 2 13:50:47 2017 -0700 greatly cleaned up the Advection_AmrCore example so now it includes physical boundary conditions removed the derived AmrAdvPhysBC.H class, it wasn't needed and now uses PhysBCFunct class in amrex/Src/Base so there are less local files/classes Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdvPhysBC.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/Amr/Advection_AmrCore/Source/Make.package Tutorials/Amr/Advection_AmrCore/Source/bc_fill_nd.F90 Tutorials/Amr/Advection_AmrCore_Boundary/CMakeLists.txt Tutorials/Amr/Advection_AmrCore_Boundary/Exec/Make.Adv Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/Prob.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrCore_Boundary/README Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv_F.H Tutorials/Amr/Advection_AmrCore_Boundary/Source/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/slope_3d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_nd/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_nd/Tagging_nd.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/main.cpp commit d606be2ee388727c6ab7430fc07982d847c79f20 Author: Andy Nonaka Date: Mon Oct 2 13:39:52 2017 -0700 further simplification of this tutorial to rely on amrex-native classes Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.H Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.cpp Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv_F.H Tutorials/Amr/Advection_AmrCore_Boundary/Source/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Source/bc_fill_nd.F90 commit f33934bf3d88329cb8a5dd263e6881e6a4607478 Author: Andy Nonaka Date: Mon Oct 2 13:38:49 2017 -0700 overloaded FillPatchTwoLevels and InterpFromCoarseLevel to allow const BCRec& bcs as an option for input instead of const Array& bcs Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp commit 4ea3fd365de2383a1a8bff248e83f544095c4f34 Author: Andy Nonaka Date: Mon Oct 2 13:16:15 2017 -0700 boundary condition work in progress Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.H Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.cpp commit 611eb17d25d59c3daecb6017d4c6c01f112be893 Author: Andrew Myers Date: Mon Oct 2 12:43:56 2017 -0700 give this executable a different name so the cmake install will work. Tutorials/Amr/Advection_AmrCore_Boundary/CMakeLists.txt commit e87bce6d014abd6653aa636a9933a7be523162c5 Author: Andy Nonaka Date: Mon Oct 2 12:35:54 2017 -0700 start of expanded documenation on domain boundary conditions Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/Boundary/Boundary.tex Docs/AMReXUsersGuide/GNUmakefile Tutorials/Basic/HeatEquation_EX2_C/advance.cpp commit 819b1a5789c78314317531d4e663debbb6b91126 Merge: 2674bd5a4 1458b3c98 Author: Weiqun Zhang Date: Mon Oct 2 08:29:44 2017 -0700 Merge branch 'development' commit 1458b3c98a72b80bbf5bd01bb6819636fdfe5dbe Author: kngott Date: Sun Oct 1 16:52:44 2017 -0700 Fix some OldTutorials/MultiFabTests_C and OldTutorials/Sidecar_EX1 to function again. OldTutorials/MultiFabTests_C/MultiFabReadWrite.cpp OldTutorials/Sidecar_EX1/DestMFTest.cpp OldTutorials/Sidecar_EX1/GNUmakefile OldTutorials/Sidecar_EX1/GridMoveTest.cpp OldTutorials/Sidecar_EX1/InTransitAnalysis.H OldTutorials/Sidecar_EX1/SidecarResizeTest.cpp commit 14a736008c9d345f300e210a1d68014a6b2661d2 Author: Weiqun Zhang Date: Sun Oct 1 16:09:31 2017 -0700 update EB/CNS to use cached geometry data Src/EB/AMReX_EBFabFactory.H Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp commit a050071db388e50dae6c0a8201630ef77356689c Author: Weiqun Zhang Date: Sun Oct 1 15:55:15 2017 -0700 fill bndrycent, areafrac and facecent Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit c62518f213300aa869e98bfa214cc09bdefec364 Author: Weiqun Zhang Date: Sun Oct 1 15:08:43 2017 -0700 MultiCutFab: remove regular and covered fabs Src/Base/AMReX_FabArray.H Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit 0eba9c53c695d09eea52fb04e1697c4cf5038d70 Author: Weiqun Zhang Date: Sun Oct 1 14:56:49 2017 -0700 EBDataCollection: define bndrycent, areafrac and facecent Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp commit 2d2495d286755e790869e2f845f4a8ff7e01c0d3 Author: Weiqun Zhang Date: Sun Oct 1 12:55:24 2017 -0700 EBTower: added bndrycent, areafrac and facecent Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB/AMReX_MultiCutFab.H Src/EB/AMReX_MultiCutFab.cpp Src/EB/Make.package commit def8028dd35360d8a237106c5d0d6ba251e32eb4 Author: Max Katz Date: Sat Sep 30 19:24:56 2017 -0400 Broadcast plot_and_continue to all processors Src/Amr/AMReX_Amr.cpp commit f5226d16a8100a3fc9bb8e926abc6ff891671817 Author: Max Katz Date: Sat Sep 30 18:38:44 2017 -0400 Add small_plot_and_continue file checker Src/Amr/AMReX_Amr.cpp commit 67850b45c7278b4bda254e2901b6592d037b526f Author: Max Katz Date: Sat Sep 30 18:38:21 2017 -0400 Add a level option to fdump Tools/Postprocessing/F_Src/fdump.f90 commit 12d85a05d4b8284383c489a24bb45e2dc8f16c00 Author: Weiqun Zhang Date: Sat Sep 30 13:23:45 2017 -0700 function to delete the EBIndexSpace singleton Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Tutorials/EB/CNS/Source/main.cpp commit da48806b5369810b5876429d3392b0813053c6b3 Author: Weiqun Zhang Date: Fri Sep 29 18:05:56 2017 -0700 WIP: get volume fraction Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp commit 6e801f335efa807954ae7705599106583a0a2ba7 Merge: 67cfd4de4 09fc2722b Author: Andy Nonaka Date: Fri Sep 29 19:21:37 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 67cfd4de4bcdc5618df375567a2d1dea3b856661 Author: Andy Nonaka Date: Fri Sep 29 19:21:26 2017 -0700 comments Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.cpp commit 09fc2722b8838ea052334bf0f266b79877e35aab Author: Weiqun Zhang Date: Fri Sep 29 18:05:19 2017 -0700 EB/CNS: fix RK2 Tutorials/EB/CNS/Source/CNS_advance.cpp commit b4bb73b940af1e5f1bbd04b1ddb0af1013617b47 Author: Andy Nonaka Date: Fri Sep 29 17:20:59 2017 -0700 new Tutorial showing how to do walls (homogeneous Neumann) scalar bc's in the AmrCore framework Tutorials/Amr/Advection_AmrCore_Boundary/CMakeLists.txt Tutorials/Amr/Advection_AmrCore_Boundary/Exec/Make.Adv Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/Prob.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrCore_Boundary/README Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.H Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdvPhysBC.cpp Tutorials/Amr/Advection_AmrCore_Boundary/Source/AmrCoreAdv_F.H Tutorials/Amr/Advection_AmrCore_Boundary/Source/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_3d/slope_3d.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_nd/Make.package Tutorials/Amr/Advection_AmrCore_Boundary/Source/Src_nd/Tagging_nd.f90 Tutorials/Amr/Advection_AmrCore_Boundary/Source/main.cpp commit c5aae2806b71bcf54a4a75710aef78f05626f350 Author: Weiqun Zhang Date: Fri Sep 29 16:50:01 2017 -0700 WIP: EBTower: volume fraction Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBSupport.H Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/main.cpp commit 5a69ba4f597735d457e9011c54dee7752892fdb5 Author: Weiqun Zhang Date: Fri Sep 29 14:26:12 2017 -0700 WIP: EBTower: fill cell flags for EBDataCollection Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabFactory.H Src/Base/AMReX_MultiFab.H Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFArrayBox.H Src/EB/AMReX_EBFArrayBox.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBSupport.H Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB/Make.package Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp commit d5f9b715ff93f3d69a5ad472bd617518eca939ed Merge: 2502a53cc edd4bcef3 Author: vince Date: Fri Sep 29 11:14:42 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit edd4bcef31f365f479524bd7ef9106100118d06e Author: Weiqun Zhang Date: Fri Sep 29 10:40:57 2017 -0700 add ostream& operator<< for BoxArray::RefID, DistributionMapping::RefID and FabArrayBase::BDKey Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 5e4cb4a01357facc606bfd8222fa7810edaeb71e Author: Ann Almgren Date: Thu Sep 28 19:09:41 2017 -0700 Fix Oops in AMReX_DistributionMapping.cpp Src/Base/AMReX_DistributionMapping.cpp commit 04a3f5a9afc0869f5c4d1ead56b6e4d254ccd3ee Merge: ab67bc88a 1e1069495 Author: Ann Almgren Date: Thu Sep 28 19:04:27 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development Conflicts: Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit ab67bc88a7bb3729251852181c3cd88b6ba91bcd Author: Ann Almgren Date: Thu Sep 28 19:02:00 2017 -0700 Add the ability to call makeKnapsack with a list of weights rather than the boxes themselves -- this is what we want to do within the KD Load Balancing algorithm Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Particle/AMReX_LoadBalanceKD.H commit 2502a53ccb0d06fca62ab6b8ed76103c2a0d4dbd Author: vince Date: Thu Sep 28 18:11:05 2017 -0700 make html headers consistent with output. Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp commit 1f84555104273c77a62e6768b72da077bd632acf Author: vince Date: Thu Sep 28 17:27:03 2017 -0700 some cleanup. Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp commit 14729c600b8405db7e168e5a118dff2cfa3469c3 Author: vince Date: Thu Sep 28 17:14:02 2017 -0700 fix compiler warnings. Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp Src/Extern/ProfParser/AMReX_BLWritePlotFile.cpp Src/Extern/ProfParser/AMReX_CommProfStats.cpp Src/Extern/amrdata/AMReX_DataServices.cpp commit 1e10694956d3e7b3d4525de1ac1a09c6550c2352 Merge: 27865f1b5 fbed6ab30 Author: vince Date: Thu Sep 28 14:50:36 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 27865f1b5746a77bcf613820b64ad2f62d04a002 Author: vince Date: Thu Sep 28 14:37:17 2017 -0700 fix compiler warnings. Src/Extern/amrdata/AMReX_AmrData.cpp commit 59dd68fc554328f38aee1fd47dd8b78d49fd7d3e Author: vince Date: Thu Sep 28 14:24:04 2017 -0700 fix compiler warning. Src/Extern/ProfParser/AMReX_CommProfStats.H commit fbed6ab304321965316e592be88d1229ac0e1a3f Author: Weiqun Zhang Date: Thu Sep 28 13:45:27 2017 -0700 parameter to limit the number of boxes can be assigned to a single process in load balance Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit 3ffd34e49379b9f74dfbc65edfddf5fd6b65944f Author: vince Date: Thu Sep 28 14:14:30 2017 -0700 fix compiler warning. Src/Base/AMReX_BLProfiler.H commit 2e461da8285bd2948fcebd922b799bfa4017c227 Merge: 3036dfcc6 201117395 Author: vince Date: Thu Sep 28 14:05:37 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 3036dfcc6e69213971e465fe2ab5c45992493faf Author: vince Date: Thu Sep 28 14:03:05 2017 -0700 added show body flag for eb. Src/Extern/amrdata/AMReX_AmrData.H Src/Extern/amrdata/AMReX_AmrData.cpp commit 201117395671acce29d741a8732de15acf22a556 Author: Andrew Myers Date: Thu Sep 28 13:09:28 2017 -0700 fix cmake install Src/AmrCore/CMakeLists.txt commit 917f0eca7079bc17b8e7094da15c7c3db82bee1f Author: Weiqun Zhang Date: Wed Sep 27 17:30:44 2017 -0700 added EBDataCollection Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArrayBase.cpp Src/EB/AMReX_EBDataCollection.H Src/EB/AMReX_EBDataCollection.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBTower.H Src/EB/Make.package commit 02c3c0973d8f7b2f557dc2ea5a681e2b9dc898d4 Author: Andy Nonaka Date: Wed Sep 27 16:55:18 2017 -0700 add Dirichlet boundary conditions Tutorials/Basic/HeatEquation_EX2_C/AMReX_FILCC_2D.F Tutorials/Basic/HeatEquation_EX2_C/AMReX_FILCC_3D.F commit 70b9d3c59d493a5a5fca22be878ba6a7ff60034d Author: Weiqun Zhang Date: Wed Sep 27 16:21:50 2017 -0700 cache EBCellFlags Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp commit db028fe30744404c2f2744ef6480c8594c6b72ff Merge: b85fc1f5d 408874f4d Author: Michele Rosso Date: Wed Sep 27 15:31:49 2017 -0700 Merge branch 'development' into mr-cmake Conflicts: Src/AmrCore/CMakeLists.txt Src/Base/CMakeLists.txt Src/Particle/CMakeLists.txt commit 58d2a49a1d7ad9b5294ab9d02b7c0ae07f497e82 Author: Weiqun Zhang Date: Wed Sep 27 15:25:24 2017 -0700 started EBTower Src/EB/AMReX_EBTower.H Src/EB/AMReX_EBTower.cpp Src/EB/Make.package Tutorials/EB/CNS/Source/main.cpp commit 886b8747f71b1403d9622888db0f6772732620a4 Author: Weiqun Zhang Date: Wed Sep 27 15:23:57 2017 -0700 access to some EB internal data Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBIndexSpace.H commit 57438c608d736bb38a06243489fbe074bd2c0df8 Author: Weiqun Zhang Date: Wed Sep 27 15:23:02 2017 -0700 added a new BoxList constructor that takes rvalue Array Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit 3a6e20580e3d47f56b920c365e99b5869fabb63a Author: Weiqun Zhang Date: Wed Sep 27 15:22:16 2017 -0700 added amrex::AllGatherBoxes Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit 408874f4d0198768a62823f30415d2c304b527df Author: Weiqun Zhang Date: Wed Sep 27 10:31:45 2017 -0700 EB/CNS: update plotfile Tutorials/EB/CNS/Source/CNS_io.cpp commit 714b85a4cb2cfe970b0455e96c2ef12095217b6f Author: Weiqun Zhang Date: Wed Sep 27 10:12:58 2017 -0700 add CartGrid-V2.0 to plotfile types Src/F_BaseLib/fabio.f90 Src/F_BaseLib/plotfile.f90 commit 7b6356246877639d6842dd1b03d89f237ae4db9c Merge: 8592c9e6a bbaf56bfe Author: WeiqunZhang Date: Wed Sep 27 09:00:45 2017 -0700 Merge pull request #140 from bcfriesen/cvode_docs_fix Docs: add note to CVODE compilation about the examples linking dynamically commit bbaf56bfe2a434884ff1bfafc74b82afb92db85a Author: Brian Friesen Date: Tue Sep 26 21:12:34 2017 -0700 Docs: add note to CVODE compilation about the examples linking dynamically Docs/AMReXUsersGuide/CVODE/CVODE.tex commit 8592c9e6abf97b38a2056b93962ffc2bb9bfa46c Author: Andrew Myers Date: Tue Sep 26 17:20:47 2017 -0700 don't profile this function - called too many times. Src/Particle/AMReX_ParticleContainerI.H commit e868e5d66125c05e69778db468783652cb3bc908 Author: Andrew Myers Date: Tue Sep 26 17:20:15 2017 -0700 fix some parameters shadowings. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H commit 6fe4bb4b29e6389b639886fc0e63d09681ef9ecf Author: Weiqun Zhang Date: Tue Sep 26 16:39:08 2017 -0700 EB/CNS: use Amr's load balance approach Tutorials/EB/CNS/Exec/Combustor/benchmark.inputs Tutorials/EB/CNS/Exec/Combustor/inputs Tutorials/EB/CNS/Exec/Combustor/inputs.regt Tutorials/EB/CNS/Exec/Combustor/inputs.testing Tutorials/EB/CNS/Exec/Combustor/inputs_combustor Tutorials/EB/CNS/Exec/Pulse/inputs Tutorials/EB/CNS/Exec/Pulse/inputs.regt Tutorials/EB/CNS/Exec/ShockRef/inputs Tutorials/EB/CNS/Exec/ShockRef/inputs.regt Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/EB/CNS/Source/main.cpp commit e65dc20ae058fe2d7da00b390eed085a1d3e6785 Author: Weiqun Zhang Date: Tue Sep 26 16:21:10 2017 -0700 update CHANGES CHANGES commit ee1ead8397c5c5c079df94b657f27355082ba781 Author: Weiqun Zhang Date: Tue Sep 26 16:14:41 2017 -0700 add amr.loadbalance_with_workestimates and amr.loadbalance_level0_int Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H commit a94b2f7213a04ba3139a6882bf5da3c3436aa001 Author: Ann Almgren Date: Tue Sep 26 15:33:23 2017 -0700 Tweaks to some of the text in the User Guide Docs/AMReXUsersGuide/EB/EB.tex commit 3cc11496aa4c516c142511aa0419792ed752c9eb Author: Andrew Myers Date: Tue Sep 26 13:12:45 2017 -0700 also turn it on for building the neighbor list. Src/Particle/AMReX_NeighborParticlesI.H commit b5ae85616c980ff2741d5d57caba0c2288d27678 Author: Weiqun Zhang Date: Tue Sep 26 12:20:50 2017 -0700 EB/CNS: update plotfile to CartGrid-V2.0 Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS_io.cpp commit 6d9baef4de49104876bf70bf6cf9498fa1cda5ba Author: Andy Nonaka Date: Mon Sep 25 17:24:44 2017 -0700 implemented periodic, zero-flux, and Dirichlet options Tutorials/Basic/HeatEquation_EX2_C/advance_2d.f90 Tutorials/Basic/HeatEquation_EX2_C/advance_3d.f90 Tutorials/Basic/HeatEquation_EX2_C/inputs_2d Tutorials/Basic/HeatEquation_EX2_C/inputs_3d Tutorials/Basic/HeatEquation_EX2_C/main.cpp commit 12872d4c7d77985f0ff6ffff81dca0e4baa617fb Merge: 476b4c77a 28cf8db26 Author: dtgraves Date: Mon Sep 25 15:27:29 2017 -0700 merging with dtg_branch to get documentation changes over commit 28cf8db266d70f916bd534d3c7285397c4d75714 Author: dtgraves Date: Mon Sep 25 15:25:46 2017 -0700 added more geometry examples Docs/AMReXUsersGuide/EB/EB.tex Docs/AMReXUsersGuide/EB/EB_example.fig.bak Docs/AMReXUsersGuide/EB/eb_fluxes.fig.bak Docs/AMReXUsersGuide/EB/parabsphere.pdf Docs/AMReXUsersGuide/EB/parabsphere.ps Docs/AMReXUsersGuide/EB/revolution.pdf Docs/AMReXUsersGuide/EB/revolution.ps commit 908ae73c6eada0f9267990d181e87eb0f3d561ad Author: dtgraves Date: Mon Sep 25 15:09:07 2017 -0700 added polynomial geometry Src/GeometryShop/AMReX_PolynomialIF.H Src/GeometryShop/AMReX_PolynomialIF.cpp Src/GeometryShop/Make.package commit 57cec33cc479f31290db0d92f4962abfe5f99aed Author: dtgraves Date: Mon Sep 25 15:08:48 2017 -0700 added a couple more geometry options Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit 476b4c77a105bd588211eb9a6bd5b45f772b0402 Merge: ff6745b30 078689afd Author: Andy Nonaka Date: Mon Sep 25 15:01:12 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit ff6745b302545e2a49f4dc70142ca02ba2050471 Author: Andy Nonaka Date: Mon Sep 25 15:00:02 2017 -0700 split the Basic/HeatEquation_EX1_C into EX1 and EX2. EX1 is periodic, EX2 will support Neumann and Dirichlet conditions eventually (WIP) Tutorials/Basic/HeatEquation_EX1_C/Make.package Tutorials/Basic/HeatEquation_EX1_C/advance.cpp Tutorials/Basic/HeatEquation_EX1_C/advance_2d.f90 Tutorials/Basic/HeatEquation_EX1_C/advance_3d.f90 Tutorials/Basic/HeatEquation_EX1_C/inputs_2d Tutorials/Basic/HeatEquation_EX1_C/inputs_3d Tutorials/Basic/HeatEquation_EX1_C/main.cpp Tutorials/Basic/HeatEquation_EX1_C/myfunc.H Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H Tutorials/Basic/HeatEquation_EX1_C/physbc.cpp Tutorials/Basic/HeatEquation_EX2_C/GNUmakefile Tutorials/Basic/HeatEquation_EX2_C/Make.package Tutorials/Basic/HeatEquation_EX2_C/advance.cpp Tutorials/Basic/HeatEquation_EX2_C/advance_2d.f90 Tutorials/Basic/HeatEquation_EX2_C/advance_3d.f90 Tutorials/Basic/HeatEquation_EX2_C/init_phi_2d.f90 Tutorials/Basic/HeatEquation_EX2_C/init_phi_3d.f90 Tutorials/Basic/HeatEquation_EX2_C/inputs_2d Tutorials/Basic/HeatEquation_EX2_C/inputs_3d Tutorials/Basic/HeatEquation_EX2_C/main.cpp Tutorials/Basic/HeatEquation_EX2_C/myfunc.H Tutorials/Basic/HeatEquation_EX2_C/myfunc_F.H commit 078689afd6b3db5505120b30b0daf52df1b8925c Merge: 0a3b8a7bd b248ae6c2 Author: WeiqunZhang Date: Mon Sep 25 13:16:05 2017 -0700 Merge pull request #139 from zingale/development add stub versions of the new broadcasts commit b248ae6c2af44ff8e5a64d346dcd1a4503dc0406 Author: Michael Zingale Date: Mon Sep 25 16:11:58 2017 -0400 add stub versions of the new broadcasts Src/F_BaseLib/parallel_stubs.f90 commit 3a7f2324843ee74918eefe96350d5a77a8d7bc69 Author: Andrew Myers Date: Mon Sep 25 13:05:42 2017 -0700 fix some dynamic scheduling bugs. Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit 0a3b8a7bdec3636606ca5fe07ac070f0acf2d3ab Author: Weiqun Zhang Date: Mon Sep 25 12:55:54 2017 -0700 VisMF::Exist(const std::string&) returns ture iff a MultiFab with such name exists Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp commit 69822b3d5407493ed81e094a83deba4adc8dc365 Author: Weiqun Zhang Date: Mon Sep 25 09:16:48 2017 -0700 update EB regression test to include amr Tutorials/EB/CNS/Exec/Pulse/inputs.regt commit b7a6349dac76a70a0a3ba973dc45eaf58593470b Merge: 1e9d755c3 9adf8165c Author: WeiqunZhang Date: Mon Sep 25 08:48:03 2017 -0700 Merge pull request #138 from AMReX-Codes/multid_bcast Add 2D, 3D, 4D parallel_bcast commit 1e9d755c34f0d9f2c6180039c95dd45e7fba7ed7 Author: Max Katz Date: Mon Sep 25 01:37:52 2017 -0400 Add index options to fdump Tools/Postprocessing/F_Src/fdump.f90 commit 58077e4e9476897060df97db37a4841ece55e9ee Author: Max Katz Date: Mon Sep 25 01:14:32 2017 -0400 Add minimum and maximum value options to fdump Tools/Postprocessing/F_Src/fdump.f90 commit 9adf8165cc913712e5358eaac8b20cc5c9fa5ada Author: Max Katz Date: Sun Sep 24 23:26:20 2017 -0400 Add 2D, 3D, 4D parallel_bcast Src/F_BaseLib/parallel.f90 commit aa07042e6acbced220f9c8d571ab9419ea5b97c7 Author: Max Katz Date: Sun Sep 24 20:00:28 2017 -0400 Default last_smallplotfile to -1 This allows for a quick test to see if the user has requested any small plot files at all; the number will end up >= 0 if so, and stay negative if not. Src/Amr/AMReX_Amr.cpp commit 1937d1098bdf333626bad6b995637d5fbec94bc7 Author: Max Katz Date: Sun Sep 24 07:48:41 2017 -0400 Add function to set level_count Src/Amr/AMReX_Amr.H commit 7d78bb8d3f4dfc018ecc40854485a84fd25e9ffd Author: Weiqun Zhang Date: Sat Sep 23 13:13:47 2017 -0700 EB/CNS: turn off various profiling Src/Base/AMReX_BoxArray.cpp Tutorials/EB/CNS/Exec/Combustor/GNUmakefile commit 1e1d2d57532dbeec86fe9bcf181999de207a984a Author: Weiqun Zhang Date: Sat Sep 23 12:17:28 2017 -0700 fix 2d Src/EB/AMReX_EBFluxRegister_2d.F90 commit a96d98667595634c5fe90f7a6072637d8039bc6b Merge: e2df23edb fe5addfc8 Author: Weiqun Zhang Date: Sat Sep 23 12:14:42 2017 -0700 Merge branch 'weiqun/eb' into development commit fe5addfc816176a4ccfaba5da59260402df0e1bb Author: Weiqun Zhang Date: Sat Sep 23 12:14:22 2017 -0700 Merge branch 'development' into weiqun/eb Docs/AMReXUsersGuide/EB/EB.tex commit d3d8147e99d36ed2e59f8f54d3ce982b82e6e2ae Author: Weiqun Zhang Date: Sat Sep 23 12:13:40 2017 -0700 refactor EBFluxRegister Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_2d.F90 Src/EB/AMReX_EBFluxRegister_3d.F90 Src/EB/AMReX_EBFluxRegister_F.H Tutorials/EB/CNS/Exec/Pulse/inputs.debug commit e2df23edbd23074a64ec9d349d0fafef1c15220a Author: Marc Day Date: Fri Sep 22 20:15:14 2017 -0700 Work the EB section of the doc a bit Docs/AMReXUsersGuide/EB/EB.tex commit 963e9fe6a878c0ab0e9f29f5e855509403b139f1 Author: Weiqun Zhang Date: Fri Sep 22 17:30:47 2017 -0700 re-re-redistribution Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_3d.F90 commit 59f7760dfdcd4af41fc59d4c09ce34cf42dc2782 Author: Weiqun Zhang Date: Fri Sep 22 17:06:55 2017 -0700 WIP: Re-reflux Src/AmrCore/AMReX_YAFluxRegister.H Src/AmrCore/AMReX_YAFluxRegister.cpp Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_3d.F90 Src/EB/AMReX_EBFluxRegister_F.H Tutorials/EB/CNS/Source/CNS.cpp commit a4707311b3de8637649e3a6fcac01d147a55817d Author: vince Date: Fri Sep 22 15:38:39 2017 -0700 fixed error messages. Src/Extern/amrdata/AMReX_DataServices.cpp commit 571cd482aa998b81df11eb70af111ef2b4152577 Merge: 8e640a5c4 d8edcfbdb Author: dtgraves Date: Fri Sep 22 09:46:37 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 8e640a5c46ef2c70e070bec03fb7929a88272d40 Author: dtgraves Date: Fri Sep 22 09:45:49 2017 -0700 bug fixes in EB.tex Docs/AMReXUsersGuide/EB/EB.tex commit d8edcfbdbc2e6448872c83b31dafbb0959bca617 Author: Weiqun Zhang Date: Fri Sep 22 09:41:29 2017 -0700 YAFluxRegister: update comment Src/AmrCore/AMReX_YAFluxRegister.cpp commit 3218273a46989c657c4d2b0727fa053f20999824 Merge: 18592d4f8 3304b0fa1 Author: dtgraves Date: Fri Sep 22 09:27:43 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 18592d4f893aceb755722d880c542c583c2f9e5b Author: dtgraves Date: Fri Sep 22 09:26:07 2017 -0700 added surface of revolution section Docs/AMReXUsersGuide/EB/EB.tex commit 3304b0fa16841829959548f2a9d2f4e5db78452b Author: Weiqun Zhang Date: Fri Sep 22 09:21:19 2017 -0700 EB/CNS: add cns.do_reflux Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_io.cpp commit aa8d197ff09921a18a488ac80129905359e3cc70 Author: Weiqun Zhang Date: Fri Sep 22 09:11:43 2017 -0700 option to disable reredistribution for testing Src/EB/AMReX_EBFluxRegister_nd.F90 Tutorials/EB/CNS/Source/fortran/CNS_f.F90 commit 501fd54e521928afc581c3c6a4a9d719d4fdc965 Author: Weiqun Zhang Date: Thu Sep 21 17:56:11 2017 -0700 inputs for John to hack Tutorials/EB/CNS/Exec/Pulse/inputs.debug commit 3d4e6923930ed053944d5d59f6adb44393ba2835 Author: Weiqun Zhang Date: Thu Sep 21 17:47:46 2017 -0700 yet another flux register Src/AmrCore/AMReX_FillPatchUtil_1d.F90 Src/AmrCore/AMReX_YAFluxRegister.H Src/AmrCore/AMReX_YAFluxRegister.cpp Src/AmrCore/AMReX_YAFluxRegister_1d.F90 Src/AmrCore/AMReX_YAFluxRegister_2d.F90 Src/AmrCore/AMReX_YAFluxRegister_3d.F90 Src/AmrCore/AMReX_YAFluxRegister_F.H Src/AmrCore/AMReX_YAFluxRegister_nd.F90 Src/AmrCore/CMakeLists.txt Src/AmrCore/Make.package Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_2d.F90 Src/EB/AMReX_EBFluxRegister_3d.F90 Src/EB/AMReX_EBFluxRegister_F.H Src/EB/AMReX_EBFluxRegister_nd.F90 commit 99d6c426a2ffc9fa78174235f7a8bec67904c302 Author: Weiqun Zhang Date: Thu Sep 21 13:12:33 2017 -0700 add re-redistribution threshold Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_2d.F90 Src/EB/AMReX_EBFluxRegister_3d.F90 Src/EB/AMReX_EBFluxRegister_nd.F90 Src/EB/Make.package Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 commit d5a54e3d790d08dad1597a392883ca8a2a64870d Author: Weiqun Zhang Date: Thu Sep 21 10:05:11 2017 -0700 EBFluxRegister: fix periodic boundary Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBFluxRegister.cpp commit f6affb5cdf3530d4406290b637c0e6045752c177 Author: Weiqun Zhang Date: Thu Sep 21 10:03:16 2017 -0700 add a free function converting iMultiFab to MultiFab Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_MultiFabUtil_nd.F90 Src/Base/CMakeLists.txt Src/Base/Make.package commit eddb0793d23e597a9b8ab317d155adc02607a582 Merge: d12ac0405 f50afec36 Author: dtgraves Date: Thu Sep 21 16:29:29 2017 -0700 merging documentation changes over to dev so others can see them commit f50afec36d03ec94f8adec58d04d8328c63b6e99 Author: dtgraves Date: Thu Sep 21 16:27:34 2017 -0700 some missing files Docs/AMReXUsersGuide/EB/redist.eps Docs/AMReXUsersGuide/EB/redist.fig Docs/AMReXUsersGuide/EB/redist.pdf commit 30f6eacad69cf24e7c9bfb83e9ec9f90bc51fc27 Author: dtgraves Date: Thu Sep 21 16:27:12 2017 -0700 started on documentation revisions of EB stuff per John and Marc's recommendations Docs/AMReXUsersGuide/EB/EB.tex Docs/AMReXUsersGuide/EB/EB_example.eps Docs/AMReXUsersGuide/EB/EB_example.fig Docs/AMReXUsersGuide/EB/EB_example.pdf Docs/AMReXUsersGuide/EB/areas_and_volumes.eps Docs/AMReXUsersGuide/EB/areas_and_volumes.fig Docs/AMReXUsersGuide/EB/areas_and_volumes.pdf Docs/AMReXUsersGuide/EB/eb_fluxes.eps Docs/AMReXUsersGuide/EB/eb_fluxes.fig Docs/AMReXUsersGuide/EB/eb_fluxes.pdf commit d12ac0405823a7172777904dc239cd28e9c309c5 Author: Ann Almgren Date: Thu Sep 21 14:26:12 2017 -0700 Fix the flags getting passed to HPGMG Tools/GNUMake/packages/Make.hpgmg commit eeb53fc7139ff8e8385763b1763247a79e20e40a Author: Andrew Myers Date: Thu Sep 21 14:19:44 2017 -0700 First stab at making the particle iterator able to use dynamic scheduling with OpenMP. Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborList/inputs Tutorials/Particles/NeighborList/main.cpp commit dfcf401c99243b21a0b3fde7adbf8cd22d0841b0 Author: Ann Almgren Date: Thu Sep 21 11:57:34 2017 -0700 John's which --> that corrections. Docs/AMReXUsersGuide/CVODE/CVODE.tex commit b33cd5662440e9c98b88fc4b9a93b4ae4e35d00b Merge: 704bd1cc3 1c0012407 Author: WeiqunZhang Date: Thu Sep 21 09:03:32 2017 -0700 Merge pull request #137 from bcfriesen/update_cvode_docs Docs: update CVODE docs commit a3474efff4b7eb3c0ab6b5e05d73d126bc8d82e3 Author: Max Katz Date: Thu Sep 21 03:57:02 2017 -0400 Move BaseFab kernels to FORT_LAUNCH Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit 272156c79b528e05c6f8f7834ddd235fe42da6af Author: Max Katz Date: Thu Sep 21 03:56:46 2017 -0400 Do not pass MFIter to FORT_LAUNCH Src/Base/AMReX_BLFort.H Tutorials/GPU/HeatEquation_EX1_C/advance.cpp commit 7ccfe8fe696320e6a4f45f581a6eeab96b958a89 Author: Max Katz Date: Thu Sep 21 03:56:19 2017 -0400 Add static current CUDA stream Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 490c2a2531dda6469a3b8a2335797fb9d6377c62 Author: Max Katz Date: Thu Sep 21 03:08:10 2017 -0400 Fix non-GPU compilation of heat equation Tutorials/GPU/HeatEquation_EX1_C/main.cpp commit ce926b31ab5346c23623362cbc3397958fa9819c Author: Max Katz Date: Thu Sep 21 03:04:18 2017 -0400 Use subroutine defines in heat equation example Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 commit a9c940b5e3a9194acff2ee264411ab821eed0dd4 Author: Max Katz Date: Thu Sep 21 03:04:01 2017 -0400 Rename CUDA defines to all caps Tools/GNUMake/Make.defs commit 4397b9f1795847e03f6c63636727deffe2078032 Author: Max Katz Date: Thu Sep 21 02:58:01 2017 -0400 Launch heat equation kernels from C++ Tutorials/GPU/HeatEquation_EX1_C/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H commit ee0892788dcfd33d8097d09c1add6ac15cfa6e18 Author: Max Katz Date: Thu Sep 21 02:52:07 2017 -0400 Add FORT_LAUNCH and FORT_LAUNCHABLE macros for CUDA kernels Src/Base/AMReX_BLFort.H commit 8c4de0e8b4c6b7ff5f4ac2e96e999f6620be24aa Author: Max Katz Date: Thu Sep 21 02:51:37 2017 -0400 Add helper routines for launching kernels from C++ Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 1c0012407d4a74505d719e50191a6cfd4b3517db Author: Brian Friesen Date: Wed Sep 20 22:30:18 2017 -0700 Docs: add a new section describing the CVODE Tutorials Docs/AMReXUsersGuide/CVODE/CVODE.tex commit aef8e94d9534080c12a2238436e9f435b9881bbd Author: Brian Friesen Date: Wed Sep 20 22:29:47 2017 -0700 Docs: revise the wording of the CVODE Fortran 2003 interface description Docs/AMReXUsersGuide/CVODE/CVODE.tex commit b921de3090702eda6d426fc8e5912641b821e9e5 Author: Brian Friesen Date: Wed Sep 20 22:28:54 2017 -0700 Docs: add note discouraging FCVODE in favor of the Fortran 2003 interface Docs/AMReXUsersGuide/CVODE/CVODE.tex commit 6224b11687b8bdb67ba54fc894581dbd478ad94f Author: Max Katz Date: Thu Sep 21 01:01:37 2017 -0400 Handle the bl_error difference between the C++ and F90 build systems Src/Base/AMReX_CUDA.F90 commit 3778915f220605e26d4111f060ecda49f3facb55 Merge: ca161599d 704bd1cc3 Author: Max Katz Date: Thu Sep 21 00:51:52 2017 -0400 Merge branch 'development' into gpu commit 704bd1cc351f2a4588341f29aae2b46b54be6c85 Merge: 0846c2475 aca4204df Author: Andrew Myers Date: Wed Sep 20 14:59:33 2017 -0700 Merge branch 'development' into threaded_neighbor_particles commit aca4204dfc61976753aef46386df55c7e48db8de Author: Andy Nonaka Date: Wed Sep 20 14:26:44 2017 -0700 fix errors in comments Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 2674bd5a4da071ce111a1cbf795cb919fcac4521 Author: Andy Nonaka Date: Wed Sep 20 14:18:51 2017 -0700 Revert "fix comments regarding regridding functions" This reverts commit fe81ad7773f2d1581138146022892611a67462b5. Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit fe81ad7773f2d1581138146022892611a67462b5 Author: Andy Nonaka Date: Wed Sep 20 14:11:38 2017 -0700 fix comments regarding regridding functions Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit aea1f107a9bb6a9de027f332a5ef79752d3802de Author: Weiqun Zhang Date: Wed Sep 20 13:13:19 2017 -0700 check signal_handling for F_BaseLib too CHANGES Src/F_BaseLib/backtrace_c.cpp commit 0846c24753e38b7ce0105646333b05a942235cfa Author: Andrew Myers Date: Wed Sep 20 13:12:50 2017 -0700 avoid rellocating this vector repeatedly in parallel region. Src/Particle/AMReX_NeighborParticlesI.H commit 614cc7e0a057dcf720bee3ef37cd6c3bd1db4436 Author: Weiqun Zhang Date: Wed Sep 20 13:05:15 2017 -0700 runtime parameter amrex.signal_handling for disabling signal handling Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_ParallelDescriptor.cpp commit a23e607a503614132cf1e361c8f18aed4f6970be Author: Andrew Myers Date: Wed Sep 20 12:25:01 2017 -0700 just use regular parallel for regions here. Src/Particle/AMReX_NeighborParticlesI.H commit 094dc08b71d0fdd3e30bb4f96281114e19976ff7 Merge: 4729149d0 2bbf25884 Author: dtgraves Date: Wed Sep 20 12:03:12 2017 -0700 Merge pull request #136 from AMReX-Codes/dtg_branch with these fixes, I was able to run Pele with threads commit 2bbf25884da84b8dcde2bfa3c0459a8b6b471289 Author: dtgraves Date: Wed Sep 20 11:59:40 2017 -0700 took out some debugging statements Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp commit 2f5a85eb16fc6be8bbf74b25109365c971d59d7f Author: dtgraves Date: Wed Sep 20 11:57:19 2017 -0700 I added some return values to AMReX_RegionsProfStats.cpp for cases where it is being called incorrectly just to shut up the compiler. I also fixed EBGraph::fillIntMask to make it thread safe Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp commit c6edf06ab95a35b04b068de9e17baabb95fe7c71 Author: Andrew Myers Date: Wed Sep 20 11:08:01 2017 -0700 the local temporaries need entries for the neighboring tiles, too. Src/Particle/AMReX_NeighborParticlesI.H commit f78b07deda176affb354a18b660ccc4127967d30 Author: Andrew Myers Date: Wed Sep 20 10:45:49 2017 -0700 correctly build map for remote particles in serial to allow for multithreaded processing. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 4729149d0876d994bc73b858b1887953130252b1 Merge: 62872369d cd05bc912 Author: dtgraves Date: Wed Sep 20 09:14:48 2017 -0700 Merge pull request #134 from AMReX-Codes/dtg_branch missed one commit cd05bc91289de7eb4e6843988373626c983e3a53 Author: dtgraves Date: Wed Sep 20 09:13:31 2017 -0700 translation amount in ebinit was wrong if maxlev > 0 Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit 62872369ddf19ef9699fa4e9f960004f5f20cc59 Merge: 44efa2c99 322dbe547 Author: dtgraves Date: Wed Sep 20 09:07:15 2017 -0700 Merge pull request #133 from AMReX-Codes/dtg_branch minor bug fix commit 322dbe547dc8d0f4bfcac3169ff92f2598a16729 Author: dtgraves Date: Wed Sep 20 09:05:44 2017 -0700 volume fraction variable has to be named vfrac in order for visit to work Tutorials/EB/CNS/Source/CNS_io.cpp commit 44efa2c99f1119085b731cf16ca1a71cce321c64 Author: Ann Almgren Date: Tue Sep 19 16:38:51 2017 -0700 We now pass in "cell_weight" as the initialization for the weight of each cell. To this we will add the number of particles in that cell. Src/Particle/AMReX_LoadBalanceKD.H commit 7864ca7fda36fc3b94b9defb42b35524fe766c62 Author: Ann Almgren Date: Tue Sep 19 16:38:28 2017 -0700 Remove write statement "actually rebuilding" Src/Particle/AMReX_NeighborParticlesI.H commit adcdcd558eaa77a691be1d0a4d33bff70c01c4ef Author: Andrew Myers Date: Tue Sep 19 16:22:31 2017 -0700 remove some more debugging crap Src/Particle/AMReX_NeighborParticlesI.H commit 52a11043e32a85f4e94f45c52a094904ccc61610 Author: Andrew Myers Date: Tue Sep 19 16:21:57 2017 -0700 handle update neighbors too. Src/Particle/AMReX_NeighborParticlesI.H commit 4ec63f135d7e6ce69526c1c732d6af231ede3946 Author: Andrew Myers Date: Tue Sep 19 16:13:41 2017 -0700 handle threading for the local neighbor particles in fillNeighbors. Src/Particle/AMReX_NeighborParticlesI.H commit d66ce60145df3e3ff207b18e984c6307a431bdbf Author: Weiqun Zhang Date: Tue Sep 19 15:48:17 2017 -0700 EB/CNS: inputs parameters for fine level grids placement Src/Base/AMReX_RealBox.H Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp commit 98c67c88225678509a36d8b3387798dce8234b68 Merge: 7ccda4bb3 07214d561 Author: WeiqunZhang Date: Tue Sep 19 15:41:50 2017 -0700 Merge pull request #132 from cmsquared/osx_fix add missing library to link line for gfortran in osx commit 07214d5612eae85683dca8a4c47798a2a20b0bbb Author: Chris Malone Date: Tue Sep 19 16:27:11 2017 -0600 add missing library to link line for gfortran in osx Tools/F_mk/comps/gfortran.mak commit 9816eda2bf9f613412bb2d207649a6ec32bf0564 Author: Andrew Myers Date: Tue Sep 19 15:21:38 2017 -0700 handle threading for the remote neighbor particles. Src/Particle/AMReX_NeighborParticlesI.H commit 7ccda4bb3b87882098728d069dead19206e4d181 Author: Weiqun Zhang Date: Tue Sep 19 14:54:41 2017 -0700 #if 0 some debug code Tutorials/EB/CNS/Source/CNS.cpp commit 8077e91fd8198d98d416000d240e956baa5184ab Author: Weiqun Zhang Date: Tue Sep 19 14:52:09 2017 -0700 EB/CNS: minor tweak Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 commit 7529ec763c83cd848b128c25ff2f31d2b8a30dd0 Author: dtgraves Date: Tue Sep 19 13:24:58 2017 -0700 added some timers Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.cpp commit 52fa4993aaeaf103242a3c19cb1ccd934751e672 Author: Andrew Myers Date: Tue Sep 19 12:41:36 2017 -0700 remove some debugging junk. Src/Particle/AMReX_NeighborParticlesI.H commit 509d8c822ecd407d507c068f1d92011255e72d1a Author: Andrew Myers Date: Tue Sep 19 12:40:32 2017 -0700 refactor the neighbor particle code to make it easier to thread. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 339eb3a7dc9958339f15463937f260802fee376f Merge: b61a3044a deb4b1602 Author: dtgraves Date: Tue Sep 19 10:32:26 2017 -0700 Merge pull request #131 from AMReX-Codes/dtg_branch merging with development to get EBCellFlagFab caching in place commit deb4b1602b62e4a1a28db8cf84460bdd6387f3ba Author: dtgraves Date: Tue Sep 19 10:31:07 2017 -0700 took out some debugging statements Src/EB/AMReX_EBLevel.cpp commit a71e5eefd1039d453019c95b87dff275da100f4a Author: dtgraves Date: Tue Sep 19 10:26:20 2017 -0700 added cache of EBCellFlagFab inside EBGraph. For the CNS benchmark problem, this appears to speed things up quite a lot. Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBLevel.cpp Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISBox.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.cpp commit b61a3044a53d6594f4e3f2841366adb1a5f88c77 Author: Weiqun Zhang Date: Tue Sep 19 10:16:51 2017 -0700 add CHANGES CHANGES commit b185d3bebf86f6a732539aeb91ad28150d4a8d86 Merge: c69ecf8d6 124af9656 Author: Weiqun Zhang Date: Tue Sep 19 10:08:59 2017 -0700 Merge branch 'development' into weiqun/eb Conflicts: Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 commit c69ecf8d6723b854c16eaa48457a171ab32315cb Author: Weiqun Zhang Date: Tue Sep 19 10:07:33 2017 -0700 EBFluxRegister: finish 2D Src/EB/AMReX_EBFluxRegister_2d.F90 commit 1cc42515d90420b1c284b9c7374266787ab17b59 Author: Weiqun Zhang Date: Tue Sep 19 09:44:56 2017 -0700 add some comments to EBFluxRegister Src/EB/AMReX_EBFluxRegister.H commit 124af9656c271e4a3f1324ed53dcd6383e29f8a0 Author: Max Katz Date: Tue Sep 19 04:29:17 2017 -0400 Allow small plotfile to have derived variables Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp commit 0b062888beee0a704d72d44f712ec3a6a6cee4b3 Author: Tan Nguyen Date: Mon Sep 18 17:41:44 2017 -0700 remove an app Src/AmrTask/tutorials/AMReXApps/3DJacobi/3DJacobi.C Src/AmrTask/tutorials/AMReXApps/3DJacobi/Makefile commit f06ccc3a934e865431ad5cc7dd987199e4870ed1 Author: Tan Nguyen Date: Mon Sep 18 17:37:57 2017 -0700 add heat solver Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/graph/AMReX_WorkerThread.H Src/AmrTask/graph/AMReX_WorkerThread.cpp Src/AmrTask/rts_impls/MPI_Generic/rts.C Src/AmrTask/tutorials/MiniApps/HeatEquation/.DS_Store Src/AmrTask/tutorials/MiniApps/HeatEquation/GNUmakefile Src/AmrTask/tutorials/MiniApps/HeatEquation/Make.package Src/AmrTask/tutorials/MiniApps/HeatEquation/advance.cpp Src/AmrTask/tutorials/MiniApps/HeatEquation/advance_2d.f90 Src/AmrTask/tutorials/MiniApps/HeatEquation/advance_3d.f90 Src/AmrTask/tutorials/MiniApps/HeatEquation/init_phi_2d.f90 Src/AmrTask/tutorials/MiniApps/HeatEquation/init_phi_3d.f90 Src/AmrTask/tutorials/MiniApps/HeatEquation/inputs_2d Src/AmrTask/tutorials/MiniApps/HeatEquation/inputs_3d Src/AmrTask/tutorials/MiniApps/HeatEquation/main.cpp Src/AmrTask/tutorials/MiniApps/HeatEquation/myfunc.H Src/AmrTask/tutorials/MiniApps/HeatEquation/myfunc_F.H Src/AmrTask/tutorials/MiniApps/HeatEquation/physbc.cpp commit 5ee5684d72644d32fa58f3426a5fda48988b2a91 Author: Tan Nguyen Date: Mon Sep 18 16:50:46 2017 -0700 relocate files Src/AmrTask/graph/AMReX_AsyncMFIter.H Src/AmrTask/graph/AMReX_AsyncMFIter.cpp commit aae72018998ae12197fc5b0d259fc441cbb9ed3b Author: Tan Nguyen Date: Mon Sep 18 16:47:26 2017 -0700 async MFIter interface Src/AmrTask/AMFIter/AMReX_AsyncMFIter.H Src/AmrTask/AMFIter/AMReX_AsyncMFIter.cpp Src/AmrTask/AMFIter/Makefile Src/AmrTask/Makefile Src/AmrTask/arch/arch.mpi.generic Src/AmrTask/graph/RTS.H Src/AmrTask/rts_impls/MPI_Generic/rts.C Src/AmrTask/rts_impls/Serial/rts.C Src/AmrTask/tutorials/UnitTests/001_TokenRing.C Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C commit ba0eda7be1eafbe569e9c8b05bf20261ac256b40 Merge: bc4008461 c7e5669a1 Author: Andy Nonaka Date: Mon Sep 18 16:36:16 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit bc40084613adc13e1f180dc90aba7236a15fa13a Author: Andy Nonaka Date: Mon Sep 18 16:36:01 2017 -0700 fix comment Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit d8b2ad3a387bb8b84801dc83c0d26a92c3655f5e Author: Weiqun Zhang Date: Mon Sep 18 16:01:42 2017 -0700 fix octree tutorial Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90 commit c7e5669a19597b7d3a1175241432737b9fad7a81 Author: Weiqun Zhang Date: Mon Sep 18 16:01:42 2017 -0700 fix octree tutorial Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90 commit f9b5dcfc146417b9dd0b62e5a42a08633ae24575 Author: Brian Friesen Date: Mon Sep 18 15:57:46 2017 -0700 CVODE: "CVODE" -> "\cvode" Docs/AMReXUsersGuide/CVODE/CVODE.tex commit b98c1764976f0a3db953660058ef8b32acb53c7d Author: Brian Friesen Date: Mon Sep 18 15:27:32 2017 -0700 CVODE: Move FCVODE doc cite from inline to a footnote Docs/AMReXUsersGuide/CVODE/CVODE.tex commit 309861db0153a242647aeed25395dc3e21f4b988 Author: Weiqun Zhang Date: Mon Sep 18 13:26:09 2017 -0700 fix more gcc shadow warnings Src/Amr/AMReX_Amr.cpp Src/EB/AMReX_EBFArrayBox.cpp Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBCellFAB.cpp Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_FaceIndex.cpp Src/GeometryShop/AMReX_Stencils.cpp Src/GeometryShop/AMReX_TransformIF.cpp Tutorials/EB/CNS/Source/CNS_io.cpp commit cae5a18b3f02b43f416d5ab3e91aa7d1d1321c9c Author: Weiqun Zhang Date: Mon Sep 18 13:03:15 2017 -0700 fixed some gcc -Wshadow warnings Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_Derive.cpp Src/Amr/AMReX_StateDescriptor.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_Utility.cpp Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_iMultiFab.cpp Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_MacBndry.cpp Src/Boundary/AMReX_Mask.cpp Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_PolyGeom.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp commit e79bbfb6abf1b93d42ded1af92783d9b4b56c61b Author: Weiqun Zhang Date: Mon Sep 18 12:40:22 2017 -0700 for gcc >= 6, add -Wnull-dereference in DEBUG mode Tools/GNUMake/comps/gnu.mak commit 083b18ff3110c2fe6d6123fca50819ccde052a27 Author: dtgraves Date: Mon Sep 18 11:46:50 2017 -0700 added volume mask to GeometryShop--on to testing it. Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.H commit 102ee366e0b5cd972484ee528cff96a3adb26d68 Merge: 6bf65bfa1 266f31c00 Author: Andrew Myers Date: Mon Sep 18 11:02:05 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6bf65bfa1777d1730df8e140cb7647740bf9c1c8 Author: Andrew Myers Date: Mon Sep 18 11:01:46 2017 -0700 Give the NeighborParticleContainer a regrid method and update the necessary internal data structures. Src/Particle/AMReX_LoadBalanceKD.H Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 266f31c00dfacb03b58a551006dce04ee6cc60a7 Author: Weiqun Zhang Date: Mon Sep 18 09:16:20 2017 -0700 add -Wshadow to gcc flags in DEBUG Tools/GNUMake/comps/gnu.mak commit c23281d10b98d38d5f9262ecd4550aec5e513bb8 Author: Weiqun Zhang Date: Mon Sep 18 09:01:40 2017 -0700 tidy Src/EB/AMReX_EBFluxRegister.cpp commit cb6a3eb15fc075ff33807a787efd544091f87930 Author: Weiqun Zhang Date: Sat Sep 16 21:36:59 2017 -0700 EBFluxRegister: omp atomic Src/EB/AMReX_EBFluxRegister_3d.F90 commit 71eae8508f35579e9ada961edecaa119e77108fd Author: Weiqun Zhang Date: Sat Sep 16 21:18:46 2017 -0700 EB/CNS: fix re-redistribution scaling and cleanup Src/EB/AMReX_EBFluxRegister.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 commit 4abc707ede1a60ce03312a0240b019be3d2f7cfb Author: Weiqun Zhang Date: Sat Sep 16 14:51:41 2017 -0700 EB/CNS: minor change for clarity Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 commit db9b11f69b283b5d3428bd95ef68df3a91c51fcc Merge: 8644b6308 db791a712 Author: dtgraves Date: Sat Sep 16 13:53:43 2017 -0700 moving minor optimiizations over to development commit db791a7129242a768fb79618464fb451914b3f0a Author: dtgraves Date: Sat Sep 16 13:41:24 2017 -0700 Some clean up and optimization of EBLevel::defineDoIt. It did not speed stuff up as much as I had hoped (amounted to 20 seconds off a 500 second run). Src/EB/AMReX_EBLevel.H Src/EB/AMReX_EBLevel.cpp commit 870654d955a69b1a710b972679bc5b6a7d2bf1bd Author: Weiqun Zhang Date: Sat Sep 16 12:51:31 2017 -0700 EB/CNS: rename some variables Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 commit 8644b6308df54d87c8ff376ffdc3c46123c8b0f0 Author: Max Katz Date: Fri Jul 7 01:28:08 2017 -0700 Fix Intel Fortran compiler preprocessing of AMReX_REAL.H Src/Base/AMReX_REAL.H commit f675e52542fc0ca1cf75ae23d63901fd9d94c5e8 Author: Weiqun Zhang Date: Fri Sep 15 17:19:02 2017 -0700 EB Re-redistribution: fix scaling Src/EB/AMReX_EBFluxRegister_3d.F90 Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 commit 0c497106b56c9de470787bd99a6b4b279ea293b2 Author: Ann Almgren Date: Fri Sep 15 18:02:10 2017 -0700 Fix oops in last commit Tools/Postprocessing/F_Src/GNUmakefile commit 282450f23520d2ce00b25b07c20a32a7ca1eb4f1 Author: Ann Almgren Date: Fri Sep 15 17:41:14 2017 -0700 Update plt_compare_diff_grids so that it measures the relative error the same as fcompare does -- instead of dividing error by value pointwise it sums the error and sums the values and divides the sums. Tools/Postprocessing/F_Src/plt_compare_diff_grids.f90 commit 5dd917466eb7f10b88f32a28ae481fd94387a928 Merge: 6189b1439 d3892ea5a Author: Ann Almgren Date: Fri Sep 15 17:20:00 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 6189b14394ef4d24e443edaf4591ecc14d35bdfa Author: Ann Almgren Date: Fri Sep 15 17:19:47 2017 -0700 File should be fcompare not fcompareFinest Tools/Postprocessing/F_Src/GNUmakefile commit d6f0badb0b77fd7ef697b918ebbe27243be844ef Author: Weiqun Zhang Date: Fri Sep 15 16:05:11 2017 -0700 EB/CNS: pass level to fortran just in case Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 commit d3892ea5a1b8d864af8ed5b81585224875cd71e7 Author: John Bell Date: Fri Sep 15 15:23:37 2017 -0700 added new options for eb redsitribution weighting Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/fortran/CNS_f.F90 commit 3fffa5f0d94c7b0d5998417194c1962f05be87f6 Author: Weiqun Zhang Date: Fri Sep 15 14:44:59 2017 -0700 EB/CNS: add level mask Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_3d.F90 Src/EB/AMReX_EBFluxRegister_F.H Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 Tutorials/EB/CNS/Source/fortran/CNS_f.F90 commit 879429d010e93a80cf4285084ac0a36c93251668 Author: Weiqun Zhang Date: Fri Sep 15 13:10:44 2017 -0700 EB/CNS: fix bug Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 commit 78412f5230c692293d12f8be647553558fbb4d18 Author: Weiqun Zhang Date: Fri Sep 15 13:10:44 2017 -0700 EB/CNS: fix bug Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 commit 83bbd0c5ce0e0722aa685a29b8e27cb2ae9213b2 Author: dtgraves Date: Fri Sep 15 13:02:31 2017 -0700 turned on all the profiling flags I could find and I added some refinements on the benchmark inputs Tutorials/EB/CNS/Exec/Combustor/GNUmakefile Tutorials/EB/CNS/Exec/Combustor/benchmark.inputs commit 5492dc70b4775b24d51a857a7a03da03569fe949 Merge: c4a237ed0 29801844e Author: jbb Date: Fri Sep 15 12:47:48 2017 -0700 Merge branch 'development' of https://www.github.com/AMReX-Codes/amrex into development commit c4a237ed0f319b2f9299f2d8cec4faadd01ce064 Author: jbb Date: Fri Sep 15 12:45:33 2017 -0700 added combustor inputs Tutorials/EB/CNS/Exec/Combustor/inputs_combustor commit f2dc99ec80b1671c23b8f29ca5c25ec55f6cf3ab Author: jbb Date: Fri Sep 15 12:44:52 2017 -0700 added other swirling combustor Tutorials/EB/CNS/Exec/Combustor/bc_fill_nd.F90_jbb Tutorials/EB/CNS/Exec/Combustor/cns_prob.F90_jbb commit 29801844e12d2cf95b4faf0c799140c4df146ca0 Merge: 0338ae57f 413193591 Author: vince Date: Fri Sep 15 11:57:34 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 0338ae57fe877fb91d5765be55bd06c6b3438387 Author: vince Date: Fri Sep 15 11:57:19 2017 -0700 return from ReadData if filetype is PROFDATA. Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp Src/Extern/amrdata/AMReX_AmrData.cpp commit 413193591ee6bef00b4f72ac2d5e39722ead7708 Merge: 617113f00 5489c2abe Author: dtgraves Date: Fri Sep 15 11:31:08 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 617113f004dd15ade77e2fb54903ba97fdb08838 Author: dtgraves Date: Fri Sep 15 11:30:43 2017 -0700 found some more macro usages that needed to be removed for intel Src/EBAMRTools/AMReX_EBFortND.F90 commit bcf58c0309121459eb47a1db3c3bf02161478d84 Author: Weiqun Zhang Date: Fri Sep 15 11:18:16 2017 -0700 WIP: Re-Redistribution Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_3d.F90 Src/EB/AMReX_EBFluxRegister_F.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 commit 5489c2abe3e91b94a1522eddbb58aa195abcf3e9 Merge: f5a63f590 44bcfa549 Author: Andrew Myers Date: Fri Sep 15 11:16:36 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f5a63f5900d6300691014873afdeb2f3128b6bdb Author: Andrew Myers Date: Fri Sep 15 11:10:58 2017 -0700 miscellaneous bug fixes for the new neighbor filling stuff. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 44bcfa54929f920a26406b9fd40eb245ab8e619d Merge: 8f55ac29e 919bc2fe2 Author: dtgraves Date: Fri Sep 15 11:05:37 2017 -0700 getting fortran fix for intel compilers over commit 919bc2fe24e27bba677d77235dbf367e3d8b99cd Author: dtgraves Date: Fri Sep 15 11:02:38 2017 -0700 took out CONSTANTS.H macro usage because it was breaking on intel compilers Src/EBAMRTools/AMReX_EBFortND.F90 commit 8f55ac29edfe69a7c481150a68cf6381dd1e9464 Merge: ba7d3b20b 1192abe53 Author: WeiqunZhang Date: Fri Sep 15 09:11:44 2017 -0700 Merge pull request #129 from bcfriesen/fcompare_openmp Postprocessing: add OpenMP to fcompare tool commit 1192abe53a44fac50163d96f98d46c79dd691e38 Author: Brian Friesen Date: Thu Sep 14 20:53:41 2017 -0700 Postprocessing: add COLLAPSE(2) to OpenMP PARALLEL DO in fcompare This will likely result in better load balance across threads where there are lots of threads. E.g., on Xeon Phi on Cori, 2 threads per core means 136 threads total, which is comparable to the trip count of the outermost loop. Tools/Postprocessing/F_Src/fcompare.f90 commit 6f5530683ce89c5cfdcfa675e16750b467a26b2e Author: Brian Friesen Date: Thu Sep 14 17:54:32 2017 -0700 Postprocessing: add OpenMP to fcompare tool Tools/Postprocessing/F_Src/fcompare.f90 commit ba7d3b20bbeb8651568fb840925da33313c078b8 Merge: f89c68f19 6398c0444 Author: Andrew Myers Date: Thu Sep 14 18:20:02 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f89c68f1919ec52496299c71d616f1f176f69dfa Author: Andrew Myers Date: Thu Sep 14 17:13:46 2017 -0700 Fix bug in fillNeighbors when KDTree is used. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit f81662d58290a13f9ce1299b1bc868fffe338701 Author: dtgraves Date: Thu Sep 14 16:55:10 2017 -0700 turned profiling on and added a benchmark inputs file Tutorials/EB/CNS/Exec/Combustor/GNUmakefile Tutorials/EB/CNS/Exec/Combustor/benchmark.inputs commit daae5eeb54b84652155b8730cd3e39c961105a79 Author: Weiqun Zhang Date: Thu Sep 14 14:45:05 2017 -0700 EBFluxRegister 2D Src/EB/AMReX_EBFluxRegister_2d.F90 Src/EB/AMReX_EBFluxRegister_3d.F90 commit 6398c04443782f8b1c38c7b2ae3bf137066a3a6e Merge: 04445d338 1cd16a487 Author: dtgraves Date: Thu Sep 14 14:41:27 2017 -0700 merging so people can see EB section of the User's guide commit 1cd16a4871733df490bd89f573a3d00d1e2bb9df Author: dtgraves Date: Thu Sep 14 14:40:04 2017 -0700 added EBFArrayBox fortran example section to user's guide Docs/AMReXUsersGuide/EB/EB.tex commit 77f7b33f04c698c4ee6258a92114af9dafbeda00 Author: Weiqun Zhang Date: Thu Sep 14 14:20:05 2017 -0700 EB Reflux works in 3D Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_3d.F90 Src/EB/AMReX_EBFluxRegister_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 commit 72dc7459d8a0e02fd41fc4f39b606d227f8cb41a Author: dtgraves Date: Thu Sep 14 14:16:06 2017 -0700 added EBFArrayBox section to user's guide Docs/AMReXUsersGuide/EB/EB.tex commit 04445d3381ce00add8db133692620408acb5b8fa Merge: 11161155f 7f796da4b Author: Weiqun Zhang Date: Wed Sep 13 17:22:56 2017 -0700 Merge branch 'development' into weiqun/eb Conflicts: Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeometryShop.cpp commit 7f796da4bd1992b69c79ea033fab1e4d4976843c Author: Weiqun Zhang Date: Wed Sep 13 17:03:12 2017 -0700 EB regression tests inputs Tools/RegressionTesting/AMReX-tests.ini Tutorials/EB/CNS/Exec/Combustor/inputs.regt Tutorials/EB/CNS/Exec/Pulse/inputs.regt Tutorials/EB/CNS/Exec/ShockRef/inputs.regt commit 053fd070ca1894ba4782a7747a44178cd88cea4d Author: Weiqun Zhang Date: Wed Sep 13 16:34:06 2017 -0700 EB/CNS: for regression test, zero out Cost_Type Tutorials/EB/CNS/Source/CNS_io.cpp commit 3082cc013597727cb4c89fbec4399b87c7a109e3 Author: Weiqun Zhang Date: Wed Sep 13 16:12:12 2017 -0700 BaseIFFABI: whenever copying from memory, avoid copying nan Src/GeometryShop/AMReX_BaseIFFABI.H commit f3e831ad699b9798b2a1352d85e61b8e1cc0131d Author: Weiqun Zhang Date: Wed Sep 13 15:42:08 2017 -0700 EBData: use qnan instead of snan because gcc 4.8.4 crahes on calling std::isnan with snan Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp commit 68fccc43eebde0a3cae7ccbbb2a2d5d410279061 Author: Weiqun Zhang Date: Wed Sep 13 15:19:55 2017 -0700 always initialize EBData to snan. we can then use std::isnan to detect whether a face has good data Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBData.cpp Tests/GeometryShop/ramp/main.cpp commit 4445addd8f09a2c02a07bb47eaff440a0a987b34 Merge: 88939980b 5070a6c64 Author: vince Date: Wed Sep 13 14:56:06 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 88939980b61ae70cfed3e450573bb4a25b601245 Author: vince Date: Wed Sep 13 14:56:02 2017 -0700 added dirname to inputs, updated readme. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/IOBenchmark/README Tests/IOBenchmark/inputs.dirname Tests/IOBenchmark/inputs.small commit 5070a6c64696347f74c06ba24341163a4e3bf539 Merge: eafa6059c cddb5c1ba Author: dtgraves Date: Wed Sep 13 14:52:37 2017 -0700 Merge branch 'development' into dtg_branch Conflicts: Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_GeometryShop.cpp commit cddb5c1baaf8e19bce8c45699697383b3ad6e7c2 Author: Weiqun Zhang Date: Wed Sep 13 14:44:20 2017 -0700 mod ramp test for debugging Tests/GeometryShop/ramp/GNUmakefile Tests/GeometryShop/ramp/main.cpp commit eafa6059c0afa6decf1446b157dabceb5a389cdc Author: dtgraves Date: Wed Sep 13 14:40:04 2017 -0700 took out debugging statements and fixed Weiqun's test so that it has some chance of passing Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Tests/EBAMRTools/regression/runalltests.serial.sh Tests/GeometryShop/regression/ebio.cpp commit 4a5e8df0bb578db99749866ea5832cf67887f040 Author: Weiqun Zhang Date: Wed Sep 13 14:26:23 2017 -0700 BaseIFFAB copy in FabArray copy is not thread safe Src/GeometryShop/AMReX_BaseIFFAB.H commit 0ac8afdaa862509390952be2bed2c5f8b009c386 Author: Weiqun Zhang Date: Wed Sep 13 14:24:25 2017 -0700 comment out some debug codes Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeometryShop.cpp commit 0c09c8d2251c0c8940b06c3bf5b54c9a3a972765 Author: Weiqun Zhang Date: Wed Sep 13 13:58:38 2017 -0700 add an assertion Src/GeometryShop/AMReX_BaseIFFAB.H commit 401f29eb21a4ea32981ae22c2f1ea06c20c50b08 Author: Weiqun Zhang Date: Wed Sep 13 13:55:24 2017 -0700 The FabArray constructor that takes array of pointers must define factory data member too Src/Base/AMReX_FabArray.H commit 5f8d2e764412dbf9b7eb07eb9df05d3e2b7c0425 Merge: 1942ebb73 ff96aa5f1 Author: dtgraves Date: Wed Sep 13 13:09:42 2017 -0700 Merge pull request #127 from AMReX-Codes/dtg_branch Ann wanted this merged over mostly because of EB user's guide commit ff96aa5f1d75bb87848b2989ab7cd8a57e8f5067 Author: dtgraves Date: Wed Sep 13 13:07:12 2017 -0700 fixed more regression tests that were broken by recent interface changes Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/aggpwlfpTest.cpp Tests/EBAMRTools/regression/divergenceOpTest.cpp Tests/EBAMRTools/regression/ebCoarseAveTest.cpp Tests/EBAMRTools/regression/ebCoarseAveTestFace.cpp Tests/EBAMRTools/regression/ebFineInterpTest.cpp Tests/EBAMRTools/regression/fluxRegTest.cpp Tests/EBAMRTools/regression/gradientOpTest.cpp Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp Tests/EBAMRTools/regression/runalltests.mpi.sh Tests/EBAMRTools/regression/simpleMeshRefine.cpp commit bdc3654e6f44a5d3fa07d74ba0440f96e7df22d7 Author: dtgraves Date: Wed Sep 13 12:44:24 2017 -0700 fixed regression tests that were broken by recent interface changes Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Tests/GeometryShop/ebgraphDistributed/GNUmakefile Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp Tests/GeometryShop/ebgraphSingleGrid/GNUmakefile Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp Tests/GeometryShop/flatPlate/GNUmakefile Tests/GeometryShop/flatPlate/flatPlateTest.cpp Tests/GeometryShop/ramp/main.cpp Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/runalltests.mpi.sh Tests/GeometryShop/runalltests.serial.sh Tests/GeometryShop/sparseDataSingleGrid/GNUmakefile Tests/GeometryShop/sparseDataSingleGrid/sparseDataSG.cpp commit da069a060214d1f9369a948b343373678b998ce2 Merge: 57dd62ce9 c68c36e28 Author: dtgraves Date: Wed Sep 13 09:33:44 2017 -0700 Merge branch 'development' into dtg_branch commit c68c36e283a1c698997c48c1c4e666a67dd726b8 Author: dtgraves Date: Wed Sep 13 09:33:35 2017 -0700 make default debug=true Tests/GeometryShop/ramp/GNUmakefile commit 1942ebb73e50261711bb784352c03c5fb9cb63cc Author: Weiqun Zhang Date: Wed Sep 13 09:01:17 2017 -0700 fix compilation Src/EB/AMReX_EBAmrUtil.cpp Src/EB/AMReX_EBMultiFabUtil.cpp Tests/GeometryShop/ramp/GNUmakefile commit 9143e1e85d9ab510c8af35ec5e561fce9a0db3cc Author: Weiqun Zhang Date: Wed Sep 13 08:53:29 2017 -0700 fix make Tests/GeometryShop/ramp/GNUmakefile commit 57dd62ce955848b033cdf75f74559ca795204ed3 Merge: 731e38a90 d31db94c0 Author: dtgraves Date: Wed Sep 13 08:48:46 2017 -0700 Merge branch 'development' into dtg_branch commit d31db94c0d923b4163405beba9bb067c160795c5 Author: Weiqun Zhang Date: Wed Sep 13 08:44:35 2017 -0700 modify test for debugging Tests/GeometryShop/ramp/inputs Tests/GeometryShop/ramp/main.cpp commit 11161155ffcd57e81f82a49f7b8beb394a0ddd5c Author: Weiqun Zhang Date: Tue Sep 12 20:32:02 2017 -0700 typo Src/GeometryShop/AMReX_EBData.cpp commit 731e38a90a1587fc67ec5d22b1a7319460a9e851 Author: dtgraves Date: Tue Sep 12 16:23:28 2017 -0700 more user's guide stuff. Docs/AMReXUsersGuide/EB/EB.tex commit 96fbcfa66c43cf39c64d217f19a06928781324e1 Author: Weiqun Zhang Date: Tue Sep 12 15:27:37 2017 -0700 more const& Src/GeometryShop/AMReX_EBData.cpp commit a795e391f048142182c5952f392cc26cfaea88cc Author: dtgraves Date: Tue Sep 12 15:13:45 2017 -0700 starting to flesh out EB user's guide Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/EB/EB.tex Docs/AMReXUsersGuide/EB/graph.pdf Docs/AMReXUsersGuide/EB/multidivide.pdf Docs/AMReXUsersGuide/EB/volume.pdf Docs/AMReXUsersGuide/GNUmakefile Docs/AMReXUsersGuide/Particle/Particle.tex commit 8c22394aa6561d5bd3fb304e4b7e14815ab723c0 Author: Weiqun Zhang Date: Tue Sep 12 14:48:23 2017 -0700 constexpr instead of macros Src/GeometryShop/AMReX_EBDataVarMacros.H commit 356929617ad510cece469a5a01c0b9175903d157 Author: Weiqun Zhang Date: Tue Sep 12 13:49:03 2017 -0700 prefer make_shared; tidy Src/GeometryShop/AMReX_EBData.H commit b3cb3df2a0ecf62e7d087abb0b3a59c67c94c37c Author: Weiqun Zhang Date: Tue Sep 12 13:15:59 2017 -0700 built-in array to std::array; pass shared_ptr by reference Src/GeometryShop/AMReX_EBDataFactory.H Src/GeometryShop/AMReX_GraphNode.H Src/GeometryShop/AMReX_GraphNode.cpp commit 25c67ffa2540daf1133029232a103d7c0ac7c67b Merge: f2cd301e5 8c6be43ce Author: Klaus Weide Date: Tue Sep 12 14:49:36 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1d30664c0156dc8bf342f22b56af9d4d9e6dc1c9 Author: Weiqun Zhang Date: Tue Sep 12 11:56:42 2017 -0700 small changes Src/GeometryShop/AMReX_EBGraph.cpp commit 46cd1ee353dec13b9de06a2fcc7368f7812d8cb0 Merge: bdc8372d4 8c6be43ce Author: Weiqun Zhang Date: Mon Sep 11 16:24:50 2017 -0700 Merge branch 'development' into weiqun/eb Conflicts: Src/GeometryShop/AMReX_EBGraph.cpp commit 8c6be43ced5f8266610ee162ec1bb07744c60485 Author: Weiqun Zhang Date: Mon Sep 11 16:23:38 2017 -0700 remove unused and wrong functions with Dan's approval Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp commit bdc8372d461e773c6dfcf23cd12f9e3573f9ffde Author: Weiqun Zhang Date: Mon Sep 11 16:10:34 2017 -0700 tidy Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp commit a38af9dc8b81f796885261b5247cba11d0ec8ccb Merge: e7d081223 147d01c13 Author: Weiqun Zhang Date: Mon Sep 11 13:15:19 2017 -0700 Merge branch 'development' into weiqun/eb commit 147d01c13efe64f639780b4810ba50aace635abc Author: Weiqun Zhang Date: Mon Sep 11 13:15:02 2017 -0700 move LayoutData class from GeometryShop to Base Src/Base/AMReX_LayoutData.H Src/Base/CMakeLists.txt Src/Base/Make.package Src/GeometryShop/Make.package commit f75b10e96f3bf29954add0631c2cac324e3336e2 Author: Weiqun Zhang Date: Mon Sep 11 12:24:47 2017 -0700 add assertion to LayoutData Src/GeometryShop/AMReX_LayoutData.H commit e7d08122316ebe776ca218a2e5e73b3aaf2a8a02 Merge: dc314e693 d3e1c94c7 Author: Weiqun Zhang Date: Mon Sep 11 12:40:43 2017 -0700 Merge branch 'development' into weiqun/eb commit d3e1c94c72f3e3ce6dc65bdb16be220bec000d86 Author: Weiqun Zhang Date: Mon Sep 11 12:40:11 2017 -0700 LayoutData: operator[] now takes global index Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_IrregFABFactory.cpp Src/GeometryShop/AMReX_LayoutData.H commit dc314e6935b628743e857a5fe2082278e165f6db Author: Weiqun Zhang Date: Mon Sep 11 12:24:47 2017 -0700 add assertion to LayoutData Src/GeometryShop/AMReX_LayoutData.H commit d5eb663590961355981ecdb6362e047726f0cf20 Author: Weiqun Zhang Date: Mon Sep 11 12:06:50 2017 -0700 EB/CNS: test domain boundary in CNS_eb_fixup_geom Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/fortran/CNS_nd.F90 commit 11b183c9725bda96ffda4d9920ab0fa0c03db825 Author: Weiqun Zhang Date: Mon Sep 11 11:18:17 2017 -0700 tidy Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp commit a5d723f8bd7a3988c30d0fa930f365abfb3a641b Merge: e3ab6f356 3c59656a5 Author: Weiqun Zhang Date: Mon Sep 11 09:49:50 2017 -0700 Merge branch 'development' into weiqun/eb commit e3ab6f356d9743c0db6b7347143fc17acf45a7ff Author: Weiqun Zhang Date: Mon Sep 11 09:28:37 2017 -0700 use instead of our own code Src/GeometryShop/AMReX_EBIndexSpace.cpp commit 3c59656a53a87a41729bca65f48aaad4c433bad9 Merge: ecf268f4c 58b2345aa Author: dtgraves Date: Mon Sep 11 09:25:39 2017 -0700 Merge pull request #125 from AMReX-Codes/dtg_branch merging some bug fixes back over to development commit 58b2345aa890b63e9513336734df22a17c18c6f5 Author: dtgraves Date: Mon Sep 11 09:24:18 2017 -0700 in GeometryShop::fixRegularNextToCovered, corner cells outside the domain were recognized as such, causing some faces to be incorrectly labelled as non-boundary Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_IrregNode.cpp commit 9716943eaa8adb197e3e35afbdba98750d83a30e Author: Weiqun Zhang Date: Mon Sep 11 09:11:35 2017 -0700 raw pointer -> unique_ptr Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp commit 864d06c8ecd1ad400a897b765191e0031d5050ba Author: dtgraves Date: Mon Sep 11 09:11:59 2017 -0700 bug fix identified by Weiqun Src/GeometryShop/AMReX_GeometryShop.cpp commit e43d8238c4ccf7ed7ad38571cd53263f81eb2a30 Author: Weiqun Zhang Date: Sun Sep 10 12:58:59 2017 -0700 minor Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_Moments.H commit 8dd44e6fee2a46a07ca9dbd9b7a2bf08821b536d Author: Weiqun Zhang Date: Sat Sep 9 22:27:19 2017 -0700 tidy Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_IrregNode.cpp commit 1b7fa1e496a9b065e12758dbb798701a2c522263 Author: Weiqun Zhang Date: Sat Sep 9 21:39:53 2017 -0700 tidy Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_GraphNode.cpp commit 5abd70e709991ef5fc856bb911ec081da6e264bd Author: Weiqun Zhang Date: Sat Sep 9 21:31:10 2017 -0700 built-in array -> std::array Src/GeometryShop/AMReX_IrregNode.H commit ecf268f4cc5a694ee9303e8ed7753869fc5f0fac Merge: e6b1be46c 985f76f77 Author: Andrew Myers Date: Sat Sep 9 17:50:54 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e6b1be46cb8e2539362a642d8c9a319ad41f4502 Author: Andrew Myers Date: Sat Sep 9 17:50:38 2017 -0700 Fix logic that enforces a minimum split size in the KD Tree load balancer. Src/Particle/AMReX_LoadBalanceKD.cpp commit f8c3b39fe596a5a4d7055c612a40d3f5b29afa2b Author: Weiqun Zhang Date: Sat Sep 9 15:48:20 2017 -0700 tidy Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp commit 70787efcd7588db88548a72ae0fa6601968a63d1 Author: Weiqun Zhang Date: Sat Sep 9 15:24:48 2017 -0700 builtin array to std::array Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp commit b2273e83b67d0b8d0994be98a2e9a7f00fd98900 Author: Weiqun Zhang Date: Sat Sep 9 14:59:43 2017 -0700 tidy Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryService.cpp commit 985f76f77064b0296c3e0fedcd7b36c7e090ca28 Author: Weiqun Zhang Date: Sat Sep 9 14:44:32 2017 -0700 add back ivsFine Src/EBAMRTools/AMReX_EBCoarseAverage.cpp commit 66e3f5622519b6e46dbefee6c0e83f645eee7495 Merge: a8f9de56a bda8f708d Author: Weiqun Zhang Date: Sat Sep 9 14:21:26 2017 -0700 Merge branch 'development' into weiqun/eb commit bda8f708d3e4c894ec04826588239622ea534c55 Merge: c273fbbbd 8bc10d542 Author: Weiqun Zhang Date: Sat Sep 9 13:09:50 2017 -0700 Merge branch 'weiqun/cu' into development commit c273fbbbdccfe2c3b27c9e715ab3094ecc8b60b4 Author: Weiqun Zhang Date: Sat Sep 9 13:06:37 2017 -0700 remove virtual from IrregFAB and IVFAB Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_EBDataFactory.H Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_IrregFAB.H Src/GeometryShop/AMReX_LoHiSide.cpp commit a8f9de56a7e9c65e3d11183e8d7b2074574cec0f Merge: 56d5144fc bf5d80052 Author: Weiqun Zhang Date: Sat Sep 9 13:01:23 2017 -0700 merge commit bf5d80052ddf12c05cb5c1b31d12bb6e5b418453 Author: Weiqun Zhang Date: Sat Sep 9 12:56:45 2017 -0700 vector -> Array Src/GeometryShop/AMReX_EBISLevel.cpp commit 647c769f6b7f12f0b4a93dd840040cfe3d888a05 Merge: 9aa6ffe08 156889bc1 Author: dtgraves Date: Sat Sep 9 12:06:34 2017 -0700 Merge pull request #124 from AMReX-Codes/dtg_branch Getting some important bug fixes into development commit 156889bc1145f798e1fd030c75972a21e304a8e9 Merge: c3b7f7f6e 9aa6ffe08 Author: dtgraves Date: Sat Sep 9 12:06:13 2017 -0700 Merge branch 'development' into dtg_branch commit c3b7f7f6e6a4b2f07363bfdef673f2df1874a78a Author: dtgraves Date: Sat Sep 9 12:00:24 2017 -0700 took out debugging statements Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLevel.cpp commit c799b33df4e2b5eaa07b3fcdb2444bd85e37b396 Author: dtgraves Date: Sat Sep 9 11:47:03 2017 -0700 after much wailing and gnashing of teeth (and quite a bit of software refactoring), I have fixed the nan bug that Weiqun identified. There are still a bunch of debugging statements in the code. I will remove them before merging with development Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp commit 9aa6ffe08d054ec2844b743b2ba87658a96c2b89 Author: Weiqun Zhang Date: Sat Sep 9 08:16:33 2017 -0700 vector -> Array Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_EBCFInterp.H Src/EBAMRTools/AMReX_EBCFInterp.cpp Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_EBFineInterp.H Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/EBAMRTools/AMReX_GradientOp.H Src/EBAMRTools/AMReX_GradientOp.cpp Src/EBAMRTools/AMReX_MeshRefine.H Src/EBAMRTools/AMReX_MeshRefine.cpp commit fd4fe9722c2907961cefe6a5d9ce0d2ab669b2ab Author: Weiqun Zhang Date: Sat Sep 9 08:03:18 2017 -0700 vector -> Array to get bound checking in debug mode Src/GeometryShop/AMReX_AggStencil.H Src/GeometryShop/AMReX_AggStencilI.H Src/GeometryShop/AMReX_AllRegularService.H Src/GeometryShop/AMReX_AllRegularService.cpp Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_BaseEBCellFactory.H Src/GeometryShop/AMReX_BaseEBFaceFAB.H Src/GeometryShop/AMReX_BaseEBFaceFABI.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_ComplementIF.H Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_EBCellFAB.cpp Src/GeometryShop/AMReX_EBCellFactory.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBDebugOut.H Src/GeometryShop/AMReX_EBDebugOut.cpp Src/GeometryShop/AMReX_EBFaceFAB.cpp Src/GeometryShop/AMReX_EBFluxFAB.H Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISBox.H Src/GeometryShop/AMReX_EBISBox.cpp Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp Src/GeometryShop/AMReX_FabArrayIO.H Src/GeometryShop/AMReX_FaceIterator.H Src/GeometryShop/AMReX_FaceIterator.cpp Src/GeometryShop/AMReX_FlatPlateGeom.H Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_GraphNode.H Src/GeometryShop/AMReX_GraphNode.cpp Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntVectSet.cpp Src/GeometryShop/AMReX_IntersectionIF.H Src/GeometryShop/AMReX_IntersectionIF.cpp Src/GeometryShop/AMReX_IrregFAB.H Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_LSquares.H Src/GeometryShop/AMReX_LSquares.cpp Src/GeometryShop/AMReX_LatheIF.H Src/GeometryShop/AMReX_LayoutData.H Src/GeometryShop/AMReX_Moments.H Src/GeometryShop/AMReX_Moments.cpp Src/GeometryShop/AMReX_PolyGeom.H Src/GeometryShop/AMReX_PolyGeom.cpp Src/GeometryShop/AMReX_RedistStencil.cpp Src/GeometryShop/AMReX_SlabService.H Src/GeometryShop/AMReX_SlabService.cpp Src/GeometryShop/AMReX_Stencils.H Src/GeometryShop/AMReX_TransformIF.H Src/GeometryShop/AMReX_TransformIF.cpp Src/GeometryShop/AMReX_UnionIF.H Src/GeometryShop/AMReX_UnionIF.cpp Src/GeometryShop/AMReX_VoFIterator.H Src/GeometryShop/AMReX_VoFIterator.cpp Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit 8bc10d542fba3366d0e31fe473ac90fe7246494a Author: Weiqun Zhang Date: Fri Sep 8 21:47:05 2017 -0700 add virtual override Src/GeometryShop/AMReX_GeometryShop.H commit 2339925a215cb8dacd3aeba096a87426028a1daa Author: Weiqun Zhang Date: Fri Sep 8 21:38:49 2017 -0700 removed virtual from BaseIVFAB and IrregFAB Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_EBDataFactory.H Src/GeometryShop/AMReX_IrregFAB.H Src/GeometryShop/AMReX_LoHiSide.cpp commit df1524385a53b986c01e360fb9500d88d9aa0b5c Merge: 04cba2dc4 a2c0ecd18 Author: WeiqunZhang Date: Fri Sep 8 17:28:19 2017 -0700 Merge pull request #123 from AMReX-Codes/threaded_redistribute Threaded redistribute commit 04cba2dc4dcf41da8d06116e185ca9915fa5cadc Author: Weiqun Zhang Date: Fri Sep 8 17:24:41 2017 -0700 override and minor cleanup Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryService.cpp Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_IntVectSet.cpp commit 16cd3847eb939f88e5fbc52ef7cb51bf8c9e0eaf Author: Weiqun Zhang Date: Fri Sep 8 17:17:19 2017 -0700 minor clean up Src/GeometryShop/AMReX_PlaneIF.H Src/GeometryShop/AMReX_PlaneIF.cpp commit 56d5144fc2231b2232999def307ec78eb22bfb46 Author: Weiqun Zhang Date: Fri Sep 8 16:20:36 2017 -0700 EB/CNS: new parameter cns.refine_cutcells=1 Src/Amr/AMReX_Amr.cpp Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp commit c8d7ebda64dda72e214fa9a3d63d2db0a4316cd9 Merge: 5f60696fe 5512885be Author: Andrew Myers Date: Fri Sep 8 16:13:20 2017 -0700 Merge branch 'development' into threaded_neighbor_list commit 76f7616cf4f951f0c9f543491f90b210b5db485d Author: Weiqun Zhang Date: Fri Sep 8 14:27:02 2017 -0700 move some scattered EB files into a new directory Src/EB Src/AmrCore/Make.package Src/Base/Make.package Src/EB/AMReX_EBAmrUtil.H Src/EB/AMReX_EBAmrUtil.cpp Src/EB/AMReX_EBAmrUtil_F.H Src/EB/AMReX_EBAmrUtil_nd.F90 Src/EB/AMReX_EBCellFlag.H Src/EB/AMReX_EBCellFlag.cpp Src/EB/AMReX_EBCellFlag_F.H Src/EB/AMReX_EBFArrayBox.H Src/EB/AMReX_EBFArrayBox.cpp Src/EB/AMReX_EBFabFactory.H Src/EB/AMReX_EBFabFactory.cpp Src/EB/AMReX_EBFaceFlag.H Src/EB/AMReX_EBFaceFlag.cpp Src/EB/AMReX_EBFluxRegister.H Src/EB/AMReX_EBFluxRegister.cpp Src/EB/AMReX_EBFluxRegister_1d.F90 Src/EB/AMReX_EBFluxRegister_2d.F90 Src/EB/AMReX_EBFluxRegister_3d.F90 Src/EB/AMReX_EBFluxRegister_F.H Src/EB/AMReX_EBInterp_F.H Src/EB/AMReX_EBInterpolater.H Src/EB/AMReX_EBInterpolater.cpp Src/EB/AMReX_EBLevel.H Src/EB/AMReX_EBLevel.cpp Src/EB/AMReX_EBMultiFabUtil.H Src/EB/AMReX_EBMultiFabUtil.cpp Src/EB/AMReX_EBMultiFabUtil_2d.F90 Src/EB/AMReX_EBMultiFabUtil_3d.F90 Src/EB/AMReX_EBMultiFabUtil_F.H Src/EB/AMReX_EBMultiFabUtil_nd.F90 Src/EB/AMReX_ebcellflag_mod.F90 Src/EB/AMReX_ebinterp_1d.F90 Src/EB/AMReX_ebinterp_2d.F90 Src/EB/AMReX_ebinterp_3d.F90 Src/EB/Make.package Tutorials/EB/CNS/Exec/Make.CNS commit a2c0ecd181574ef1ad9bb9f27a06df07ef4dfb7c Author: Andrew Myers Date: Fri Sep 8 14:13:09 2017 -0700 Pass in the explicit tile size to the dummy mfiter Src/Particle/AMReX_ParticleContainerI.H commit 5512885be31c7b2ad17d25766e027a6447451c15 Merge: 201c6478c e9220363c Author: WeiqunZhang Date: Fri Sep 8 13:48:15 2017 -0700 Merge pull request #122 from bcfriesen/fix_vtune_linking GNUMake: update the env var pointing to the VTune directory at NERSC commit 201c6478cef788816a7bf565889356a066d9468e Merge: f20781b43 6954f4db9 Author: WeiqunZhang Date: Fri Sep 8 13:45:02 2017 -0700 Merge pull request #121 from bcfriesen/fix_cvode_linking GNUMake: remove links to FCVODE, the old Fortran wrapper to CVODE commit f5a56e6a03b43b80e3ca5bddcd21af1f283f6629 Author: Andrew Myers Date: Fri Sep 8 13:31:58 2017 -0700 set default tiling back to false. Src/Particle/AMReX_ParticleContainerI.H commit 452a3d9961e8637edcedde4127d8aca38a380927 Author: Andrew Myers Date: Fri Sep 8 12:58:27 2017 -0700 fix dumb mistake Src/Particle/AMReX_ParticleContainerI.H commit f20781b4306edfa8d1854e34c4ab7f217dca6998 Author: Ann Almgren Date: Fri Sep 8 12:45:58 2017 -0700 Slight typo corrections Docs/Migration/Migration.md commit 0bf9945de9168bb5689d9f6e5ebe6e9710267558 Author: Andrew Myers Date: Fri Sep 8 12:45:45 2017 -0700 also handle the soa data in the threaded redistrbute. Src/Particle/AMReX_ParticleContainerI.H commit e9220363cfc41679b19f819b22aa0fafb582548d Author: Brian Friesen Date: Fri Sep 8 12:16:47 2017 -0700 GNUMake: update the env var pointing to the VTune directory at NERSC The default version at NERSC is now VTune 2017, so we need to update this environment variable or else compiling will fail. Tools/GNUMake/tools/Make.vtune commit 6954f4db96919a271d3d40e944b9a7927a4849a4 Author: Brian Friesen Date: Fri Sep 8 12:10:53 2017 -0700 GNUMake: remove links to FCVODE, the old Fortran wrapper to CVODE FCVODE comes with CVODE and provides a Fortran interface to the CVODE library, but is not thread-safe. Recently the SUNDIALS developers provided us with a Fortran 2003 interface to CVODE which uses iso_c_binding to most of the functions in the library. So remove the links to the old FCVODE library since we don't need it anymore. Tools/GNUMake/packages/Make.cvode commit ecc9feddbaed890125ce30b2bff131f5847daa37 Author: Andrew Myers Date: Fri Sep 8 11:29:19 2017 -0700 removed this by mistake. Src/Particle/AMReX_ParticleContainerI.H commit 05ae37a5217b6addaf0e8152f45f05a000ef2dd2 Author: Andrew Myers Date: Fri Sep 8 11:20:35 2017 -0700 fix bug affecting hydrid MPI / OpenMP redistribute. Src/Particle/AMReX_ParticleContainerI.H commit fede1770d4e4220f1c5d8daf4ad54c9a41767ca4 Author: Andrew Myers Date: Fri Sep 8 10:43:29 2017 -0700 also reset has_hashmap here. Src/Base/AMReX_BoxArray.cpp commit 0e4c68c70113b25b8fd760995f066d1e633dc6f4 Author: Andrew Myers Date: Fri Sep 8 10:38:27 2017 -0700 reset has_hashmap when the map is cleared. Src/Base/AMReX_BoxArray.cpp commit 47a2f2d218f6472648ce5240f79d2b34af586a2f Merge: ebd9c4771 f7c2c536f Author: Andrew Myers Date: Fri Sep 8 10:24:25 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ebd9c477164299c71dd43c8c4c6899c25b9c5eb1 Author: Andrew Myers Date: Fri Sep 8 10:24:14 2017 -0700 enforce a min box size in the KDTree load balancer. Src/Particle/AMReX_LoadBalanceKD.H Src/Particle/AMReX_LoadBalanceKD.cpp commit 0c691a09dfecf5bbc22944b0e9b34177b7290206 Author: Weiqun Zhang Date: Fri Sep 8 09:33:19 2017 -0700 2D EBFluxRegister Src/AmrCore/AMReX_EBFluxRegister_2d.F90 commit 07fdb7eb1ad7969836a1841b8d662a107d2793cd Author: Weiqun Zhang Date: Fri Sep 8 09:21:59 2017 -0700 minor Src/AmrCore/AMReX_EBFluxRegister_3d.F90 Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp commit 83160ea694343ba5798bee165bd4b97a090b2c6c Merge: 034f5f0b7 f7c2c536f Author: dtgraves Date: Fri Sep 8 08:22:39 2017 -0700 merging with development to get weiqun's test commit f2cd301e5d643f15f2a15746c4586f9696dccf5b Merge: ed1df4a23 f7c2c536f Author: Klaus Weide Date: Fri Sep 8 00:13:18 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 69f2736346f4e3130dfd0e1b1ac5d03c84626c81 Author: Weiqun Zhang Date: Thu Sep 7 17:31:36 2017 -0700 EB: fix init_snan Src/GeometryShop/AMReX_EBData.cpp commit f7c2c536fb9c3ab69410b8fae94596a10970d499 Author: Weiqun Zhang Date: Thu Sep 7 17:31:36 2017 -0700 EB: fix init_snan Src/GeometryShop/AMReX_EBData.cpp commit 6250cf26e9eaa4536609c32bcf1924a298e4e218 Author: Weiqun Zhang Date: Thu Sep 7 17:09:38 2017 -0700 initialize EB data to snan to help debug Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp commit b6ea48c336c2975aac0789720f9cdf185d7a7310 Author: Weiqun Zhang Date: Thu Sep 7 17:10:58 2017 -0700 EB/CNS: pass mpi rank to fortran to help debugging Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/EB/CNS/Source/fortran/CNS_f.F90 commit 5f5272621a8abd0b53171eb24e0d4d60e41f4c86 Author: Weiqun Zhang Date: Thu Sep 7 17:09:38 2017 -0700 initialize EB data to snan to help debug Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp commit c5d431503bdb96806bff01533bd2f41f3cb712de Author: Andrew Myers Date: Thu Sep 7 16:54:43 2017 -0700 need to create any missing map entries in serial here before the parallel reduction. Src/Particle/AMReX_ParticleContainerI.H commit ec2b8a607cc751850aa866b366106866f7cbfd9c Merge: 7854d8cd1 ce08adbbd Author: Weiqun Zhang Date: Thu Sep 7 16:13:16 2017 -0700 Merge branch 'development' into weiqun/eb commit 52383e09dad02c112624b007a6e3b38b3b8843e1 Author: Andrew Myers Date: Thu Sep 7 15:33:14 2017 -0700 Don't want to perform this check inside a critical region, since in particle code we call this a lot from threaded regions. Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit 034f5f0b7682d8304b3cb754362b24e7bb2f1a4b Merge: 446d1750c ce08adbbd Author: dtgraves Date: Thu Sep 7 15:17:24 2017 -0700 Merge branch 'development' into dtg_branch commit 446d1750cc8dcc0d57fe388579219d0c9ac9594f Author: dtgraves Date: Thu Sep 7 15:02:52 2017 -0700 more bugs found. need to pivot toward writing documents now. Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Tests/EBAMRElliptic/exec/conductivitySolve.cpp commit 7854d8cd1f2d2e873b060558ab9e6224728310aa Author: Weiqun Zhang Date: Thu Sep 7 14:57:50 2017 -0700 WIP: don't tag covered cells Src/AmrCore/AMReX_EBAmrUtil_nd.F90 commit d28817e07a4ade2e8a848f2460aff1fc33c38aff Author: Weiqun Zhang Date: Thu Sep 7 14:27:37 2017 -0700 WIP: EBFluxRegister: bug fix Src/AmrCore/AMReX_EBFluxRegister.cpp Src/AmrCore/AMReX_EBFluxRegister_3d.F90 commit 1bc81d6dc45e79be1d510026352b2df1f269891a Author: Weiqun Zhang Date: Thu Sep 7 13:22:24 2017 -0700 WIP: EBFluxRegister::Reflux Src/AmrCore/AMReX_EBFluxRegister.H Src/AmrCore/AMReX_EBFluxRegister.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp commit ce5e0632bf810887b5c2d7f9399845a8849eb175 Author: Weiqun Zhang Date: Thu Sep 7 12:41:06 2017 -0700 WIP: EBFluxRegister::FineAdd Src/AmrCore/AMReX_EBFluxRegister.H Src/AmrCore/AMReX_EBFluxRegister.cpp Src/AmrCore/AMReX_EBFluxRegister_3d.F90 Src/AmrCore/AMReX_EBFluxRegister_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 commit e6434e6a273354b8a99b799348d03b358dda7c40 Author: dtgraves Date: Thu Sep 7 12:05:47 2017 -0700 conductivity op seems to work now. God I hate fortran. Src/EBAMRElliptic/AMReX_EBEllipticFort.F90 Src/EBAMRElliptic/AMReX_VCAggStencil.cpp Tests/EBAMRElliptic/exec/cond.inputs commit a3ea4dbbc0816f3caf22854282cb7e1809d38c35 Author: Andrew Myers Date: Thu Sep 7 10:46:51 2017 -0700 accidently screwed up caching by moving this - fixing. Src/Particle/AMReX_ParticleContainerI.H commit 09e39c7bb08bddf815ae2983af81460f7fe1f127 Author: Andrew Myers Date: Thu Sep 7 10:07:20 2017 -0700 give the AoS insert and delete methods and use them. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit ce08adbbda8bcc63860c1d2769a4543d92a5455c Merge: 3fa30fa11 c7e94b25c Author: WeiqunZhang Date: Thu Sep 7 08:47:17 2017 -0700 Merge pull request #120 from kweide/development Expose MFIter's index() method to Fortran code as grid_index() commit c7e94b25c4b6da79e37816ae034c66f9b02b4b46 Author: Klaus Weide Date: Wed Sep 6 22:08:10 2017 -0500 Expose MFIter's index() method to Fortran code as grid_index() The Fortran multifab already has a dataPtr() method that takes an index, so there should also be a way to get such an index from an iterator over a multifab. analogous to the AMReX_octree iterator's grid_index(), whence the name Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit e6eea6c3356a60e678aae687324d89e102647702 Author: Weiqun Zhang Date: Wed Sep 6 17:38:03 2017 -0700 WIP: EBFluxRegister Src/AmrCore/AMReX_EBFluxRegister.H Src/AmrCore/AMReX_EBFluxRegister.cpp Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp commit df91f46f8be18c2b3e51a90ce5d4509c62df1669 Author: Andrew Myers Date: Wed Sep 6 16:58:34 2017 -0700 in the first pass, thread over tiles instead of threading over the particles on a tile. Src/Particle/AMReX_ParticleContainerI.H commit 027bd72e2a5577f41b343c977e9af78ff6fad5b7 Author: Weiqun Zhang Date: Wed Sep 6 16:18:19 2017 -0700 WIP: EBFluxRegister Src/AmrCore/AMReX_EBFluxRegister.H Src/AmrCore/AMReX_EBFluxRegister.cpp Src/AmrCore/AMReX_EBFluxRegister_1d.F90 Src/AmrCore/AMReX_EBFluxRegister_2d.F90 Src/AmrCore/AMReX_EBFluxRegister_3d.F90 Src/AmrCore/AMReX_EBFluxRegister_F.H Src/AmrCore/Make.package Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_io.cpp Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 commit 3d8112328afbdd5e069a7fde9c2746d64b4e8cd7 Author: Andrew Myers Date: Wed Sep 6 15:53:03 2017 -0700 OpenMP support in Redistribute compiles and gives the right answers. Src/Particle/AMReX_ParticleContainerI.H commit 3fa30fa11322032a32b7d386cd4e92a859502acf Merge: 3c18ec4ee 41c2f7dc2 Author: WeiqunZhang Date: Wed Sep 6 14:30:42 2017 -0700 Merge pull request #119 from bcfriesen/add_arch_suffix GNUMake: add arch suffix to exe name when building on a Cray commit 41c2f7dc2ea9445f07a0c3b0ed45f4efa34b0ddb Author: Brian Friesen Date: Wed Sep 6 14:21:07 2017 -0700 GNUMake: add arch suffix to exe name when building on a Cray Cross-compiling on Cray systems is common, so adding the target architecture to the exe suffix clarifies which instruction set the binary was compiled with. Tools/GNUMake/Make.defs commit 3c18ec4ee0780630c9a449d8c3005a0715628add Merge: 8a2716fab 34514b31a Author: WeiqunZhang Date: Wed Sep 6 13:16:17 2017 -0700 Merge pull request #118 from bcfriesen/print_build_target_on_cray Print build target on Cray commit 34514b31a9f7aa286d6e3ea2e1d2b30a305f7f8d Author: Brian Friesen Date: Wed Sep 6 12:56:38 2017 -0700 GNUMake: print the build target at link time if running on a Cray AMReX does not have separate compiler flags for different architectures on Cray systems, e.g., separate compile flags for AVX2 vs. AVX-512 instructions. The user is responsible for choosing the correct build target, via the "craype-" modules. To make clear which target the user is compiling for, print the target at link time. Tools/GNUMake/Make.rules commit d497a60721dbde559f8c9e93140b164f6e61b9d4 Author: Andrew Myers Date: Wed Sep 6 12:32:47 2017 -0700 do reduction over threads for the non-local buffer. Src/Particle/AMReX_ParticleContainerI.H commit 2296aed57a0797fb0ed0f19aec52d359c8937a19 Author: Andrew Myers Date: Wed Sep 6 11:23:52 2017 -0700 only add entries to the remote tmp map on demand Src/Particle/AMReX_ParticleContainerI.H commit ffeea9ea888e11c8b2c5ca23618e8a6ddf1cbed9 Author: Weiqun Zhang Date: Wed Sep 6 11:16:34 2017 -0700 EB/CNS: add tagging on cutcells Src/AmrCore/AMReX_EBAmrUtil.H Src/AmrCore/AMReX_EBAmrUtil.cpp Src/AmrCore/AMReX_EBAmrUtil_F.H Src/AmrCore/AMReX_EBAmrUtil_nd.F90 Src/AmrCore/AMReX_EBFluxRegister.H Src/AmrCore/AMReX_EBFluxRegister.cpp Src/AmrCore/Make.package Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_error.cpp Tutorials/EB/CNS/Source/CNS_io.cpp Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/EB/CNS/Source/Make.package commit e7485f2dbb3931be38481d8f520a7f5b294a8806 Author: Andrew Myers Date: Wed Sep 6 10:49:39 2017 -0700 threading the non-local tmp container. Src/Particle/AMReX_ParticleContainerI.H commit 19ee98fdf27ec161c9aff68d63d471dad47fe810 Author: Andrew Myers Date: Wed Sep 6 09:52:52 2017 -0700 about the start threading the redistribute method. Src/Particle/AMReX_ParticleContainerI.H commit 5db147d8a2cb679d59c580516eeeb9ecb0477696 Author: dtgraves Date: Tue Sep 5 15:54:16 2017 -0700 found some bugs and added some debugging tools Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/GeometryShop/AMReX_EBDebugDump.H Src/GeometryShop/AMReX_EBDebugOut.H Src/GeometryShop/AMReX_EBDebugOut.cpp Src/GeometryShop/AMReX_Stencils.H Src/GeometryShop/AMReX_Stencils.cpp Tests/EBAMRElliptic/exec/cond.inputs Tests/EBAMRElliptic/exec/conductivitySolve.cpp commit 8a2716fabc6de876fb5e3d292c0ad136e2c93895 Author: Weiqun Zhang Date: Tue Sep 5 15:09:57 2017 -0700 make GraphNode thread safe Src/Base/AMReX_EBLevel.cpp Src/Base/AMReX_EBMultiFabUtil.cpp Src/GeometryShop/AMReX_GraphNode.cpp commit fe515b73f208e0647c0800145e4eab9cd71bb8eb Merge: 7494dbdd0 a395ef53a Author: WeiqunZhang Date: Tue Sep 5 12:03:10 2017 -0700 Merge pull request #117 from nncarlson/dfloat-fix Eliminate use of non-standard Fortran dfloat intrinsic commit 7494dbdd0840dac7a54f89ce3d1e500a4f813499 Author: Weiqun Zhang Date: Tue Sep 5 10:26:30 2017 -0700 remove BL_USE_FORT_STAR_PRECISION Src/Base/AMReX_REAL.H Src/Boundary/AMReX_LO_UTIL.F commit 6e8df6ea20a61e1cd12b761a1cef29de15ff8e31 Author: Weiqun Zhang Date: Tue Sep 5 10:12:44 2017 -0700 add linear solvers to libamrex GNUmakefile.in Src/Base/Make.package Tools/libamrex/configure.py commit 8720e66acbe83262e13d8cc796cdf6eb23b28cf2 Merge: 245763539 9a0dbf3e4 Author: dtgraves Date: Tue Sep 5 09:18:25 2017 -0700 Merge pull request #116 from AMReX-Codes/weiqun/sort BaseIVFAB and BaseIFFAB commit a395ef53ac964bd4e3b4dd117f2e23de871239cc Author: Neil Carlson Date: Tue Sep 5 10:11:38 2017 -0600 Eliminate use of non-standard Fortran dfloat intrinsic (fixes #115) Src/AmrCore/AMReX_INTERP_3D.F commit 24576353993d21fdb957e795b99901f72327209c Merge: 3fad1f5d7 9848d52ed Author: WeiqunZhang Date: Tue Sep 5 08:54:14 2017 -0700 Merge pull request #114 from nncarlson/imultifab-additions Additions to the Fortran imultifab interface commit 3fad1f5d745d6035d80f5feaccd24a93ea9d09f0 Merge: 908e3c1a3 0de2c84cf Author: dtgraves Date: Tue Sep 5 08:50:39 2017 -0700 Merge pull request #111 from AMReX-Codes/weiqun/cfivs replace simple loop over grids with BoxArray's fast complement function commit 9848d52ed5536ff4d5d387b69ac461895cd037a8 Author: Neil Carlson Date: Mon Sep 4 21:53:12 2017 -0600 Additions to the Fortran imultifab interface This extends the Fortran imultifab interface to include the setval method, and adds the optional nodal argument to amrex_imultifab_build, as defined for amrex_multifab_build. Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 9a0dbf3e4560f73a4631e43398ab3729fde792d8 Merge: b33cba6ba 3ba05dc6d Author: Weiqun Zhang Date: Sun Sep 3 12:11:55 2017 -0700 merge commit b33cba6baf2d76c1c71e76142bf346d6bb7dd533 Author: Weiqun Zhang Date: Sun Sep 3 12:08:01 2017 -0700 optimize IFFAB Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H commit 4f5e7ca1d17d655b3aa407c32cd789f8131f7ff4 Author: Weiqun Zhang Date: Sun Sep 3 11:04:50 2017 -0700 refactor IVFAB to make getIndex faster Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H commit 3ba05dc6d6d8e46317c1692ed001a9c9561bedc7 Author: Weiqun Zhang Date: Sun Sep 3 11:04:50 2017 -0700 refactor IVFAB to make getIndex faster Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H commit 908e3c1a3bca9e1a030838c5fd48b3977191fcec Author: Weiqun Zhang Date: Sat Sep 2 12:48:17 2017 -0700 inline operator== for VolIndex and FaceIndex and switch the order of comparison by comparing int first Src/GeometryShop/AMReX_FaceIndex.H Src/GeometryShop/AMReX_FaceIndex.cpp Src/GeometryShop/AMReX_VolIndex.H Src/GeometryShop/AMReX_VolIndex.cpp commit d28e8a3c28922b7eb1b0101f01a44e99da71a48c Author: Weiqun Zhang Date: Sat Sep 2 12:48:17 2017 -0700 inline operator== for VolIndex and FaceIndex and switch the order of comparison by comparing int first Src/GeometryShop/AMReX_FaceIndex.H Src/GeometryShop/AMReX_FaceIndex.cpp Src/GeometryShop/AMReX_VolIndex.H Src/GeometryShop/AMReX_VolIndex.cpp commit 1879975e75d94b3109eabfa309b57327cbc6bc97 Merge: e459b1cf5 0de2c84cf Author: Weiqun Zhang Date: Fri Sep 1 22:01:27 2017 -0700 Merge branch 'weiqun/cfivs' into weiqun/eb commit e459b1cf500060c8885dc3b40a2714a79b08330b Merge: 8e7211e2f 43b1d3421 Author: dtgraves Date: Fri Sep 1 19:40:57 2017 -0700 Merge pull request #110 from AMReX-Codes/weiqun/iffabcopy optimization of IFFAB copy commit 0de2c84cf46fb77a7113d7cd5846d26f770bf4b6 Author: Weiqun Zhang Date: Fri Sep 1 17:58:19 2017 -0700 replace simple loop over grids with BoxArray's fast complement function Src/GeometryShop/AMReX_EBLevelGrid.cpp commit 43b1d34216f35a2092ffa82fee8bc26c8778f888 Author: Weiqun Zhang Date: Fri Sep 1 16:40:13 2017 -0700 optimization of IFFAB copy Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntVectSet.cpp commit 7b8d42eb2d149963cdd788ade5849198d79526be Author: dtgraves Date: Fri Sep 1 16:23:52 2017 -0700 some simplification and debugging of EB solvers Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRTools/AMReX_EBCoarseAverage.cpp commit 8e7211e2f7327e409a6aa4d545ba8472300cc53f Author: Weiqun Zhang Date: Fri Sep 1 15:14:57 2017 -0700 add some profilers Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBLevelGrid.cpp commit d6ecdf87f92f646a83b31cc09d82c013e7d71eb6 Merge: 2086d8f07 4b2c75d2e Author: dtgraves Date: Fri Sep 1 13:31:11 2017 -0700 Merge pull request #109 from AMReX-Codes/dtg_branch putting some tweaks to IntVectSet into development commit 4b2c75d2e3739357169dc2750c52c7416e77f379 Author: dtgraves Date: Fri Sep 1 13:29:14 2017 -0700 with Weiqun's advice, I was able to restore the move constructors to IntVectSet. Src/GeometryShop/AMReX_IntVectSet.H commit 2086d8f07de76c511080911f043b0f72378082a8 Author: Weiqun Zhang Date: Fri Sep 1 13:25:04 2017 -0700 have to remove noexcept because gcc 4 does support Src/GeometryShop/AMReX_IntVectSet.H commit b587a4047634464158a7a85529417ed820055031 Author: dtgraves Date: Fri Sep 1 12:59:56 2017 -0700 my compiler was not eating some of weiqun's more sophistocated c++11-isms so I made IntVectSet old school again. Src/GeometryShop/AMReX_IntVectSet.H commit 0530fe6e44e142f8b74ae4e14387c5fb755477ca Author: dtgraves Date: Fri Sep 1 12:52:18 2017 -0700 fixed compilation bug in IntVectSet Src/GeometryShop/AMReX_IntVectSet.H commit 934c659a701088d96adcd0b45e735e5cd7036b2f Merge: 113508e37 f585ebd27 Author: dtgraves Date: Fri Sep 1 12:49:17 2017 -0700 Merge branch 'development' into dtg_branch commit f585ebd277adcf23e43ffedce2d6e43fcb681196 Merge: 77680b1dc 225996625 Author: dtgraves Date: Fri Sep 1 12:47:33 2017 -0700 Merge pull request #108 from AMReX-Codes/weiqun/intvectset Internal container of IntVectSet commit 113508e37a7d1d4e4b2173b09e9dbf6c5f4b9543 Author: dtgraves Date: Fri Sep 1 11:30:48 2017 -0700 eb plotfile routines now work. Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Tests/EBAMRElliptic/exec/cond.inputs Tests/EBAMRElliptic/exec/conductivitySolve.cpp commit 22599662569b544564cc1f708d40c6f9cc0d5dca Merge: 949322089 77680b1dc Author: Weiqun Zhang Date: Fri Sep 1 11:25:11 2017 -0700 Merge branch 'development' into weiqun/intvectset commit 77680b1dc203915773c2b34c2ca50b2451ab2f32 Author: Weiqun Zhang Date: Fri Sep 1 11:24:20 2017 -0700 more BL_PROFILE Src/GeometryShop/AMReX_EBLevelGrid.cpp commit 949322089e8239673bd0571013054c00ad837d94 Merge: 35aedde62 92a6169e0 Author: Weiqun Zhang Date: Fri Sep 1 11:02:29 2017 -0700 Merge branch 'development' into weiqun/intvectset commit 92a6169e05c1be9218c43064bce28a8ff8d84b61 Author: Weiqun Zhang Date: Fri Sep 1 10:59:43 2017 -0700 add/rmove some BL_PROFILEs Src/Amr/AMReX_Amr.cpp Src/Base/AMReX_DistributionMapping.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Tutorials/EB/CNS/Source/CNS.cpp commit 35aedde622e16e83c8283ad4b9a2c871a05a90b7 Author: Weiqun Zhang Date: Fri Sep 1 10:56:59 2017 -0700 IntVectSet: reimplement it with unordered_set rather than set Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntVectSet.cpp commit 32d6fcae3382e0e265a5351a23ed46602a375a45 Author: Weiqun Zhang Date: Thu Aug 31 21:30:02 2017 -0700 EB/CNS: flooring Tutorials/EB/CNS/Source/fortran/CNS_f.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90 commit 6390843fd87421370bb393fc0e97a39ce2735897 Author: Weiqun Zhang Date: Thu Aug 31 16:08:51 2017 -0700 Disable MPI checking if NO_MPI_CHECKING=TRUE. Tools/GNUMake/Make.local.template Tools/GNUMake/sites/Make.unknown commit 8537f6c168c16c9497ac28ce9607f698d804688e Author: dtgraves Date: Thu Aug 31 15:43:50 2017 -0700 added utilities to output visit and amrvis-compliant plot files from EB data. I also added a debugging utility that allows data to be visualized from inside a debugger.. Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBDebugOut.cpp Tests/GeometryShop/ramp/GNUmakefile Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp commit 4fe3b705d65753c043d40a4f9ff0e82d35624702 Author: Weiqun Zhang Date: Thu Aug 31 14:59:18 2017 -0700 less verbose Src/Amr/AMReX_Amr.cpp commit eff4f9fda9aa7da9775a52030e82249d00da3489 Author: Weiqun Zhang Date: Thu Aug 31 14:56:55 2017 -0700 EB/CNS: override post_restart to fix up geometry Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp commit f769d5df1c8ad61d63301dc7e3a2ea1001ae4f09 Author: Weiqun Zhang Date: Thu Aug 31 13:58:08 2017 -0700 EB/CNS: add testing inputs Tutorials/EB/CNS/Exec/Combustor/inputs.testing commit 554a419cb4cda90394572b25eaa56b2913e74fb0 Author: Weiqun Zhang Date: Thu Aug 31 13:49:52 2017 -0700 fix restart for EB Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp commit 68ad6526739eef3871e77f7fa317bca73e5dbae8 Author: dtgraves Date: Thu Aug 31 11:05:00 2017 -0700 bug fix to conductivityopfactory Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp commit c10992f5a2f716a8905cf2afcfb5354e5fb2e8c7 Author: Weiqun Zhang Date: Thu Aug 31 09:22:40 2017 -0700 commented out FaceFlag stuff Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp commit 83bbdd253209546c92f15179a3dbb7a4be7683f5 Author: Weiqun Zhang Date: Thu Aug 31 09:17:55 2017 -0700 EB/CNS: pass amr.max_level into EBIndexSpace::define so that we don't have to build extra coarse levels Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit 7e9d8b4567650fb26df0f61691be09ca61163a23 Merge: 2ffa01778 a1e639ea0 Author: Weiqun Zhang Date: Thu Aug 31 09:13:33 2017 -0700 Merge branch 'development' into weiqun/eb commit 2ffa01778f90dcbd2d92113a4341c23460f8ab62 Author: Weiqun Zhang Date: Thu Aug 31 09:12:55 2017 -0700 EB/CNS: if interior plus one ghost are all regular, no need to call eb functions Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 commit a739b15bee6d556f5ba3effeed23bf38861daab2 Author: Weiqun Zhang Date: Wed Aug 30 16:02:31 2017 -0700 EB/CNS: vectorization of riemann solver Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90 Tutorials/EB/CNS/Source/hydro/analriem3d.F90 Tutorials/EB/CNS/Source/hydro/cns_eb_hyp_wall.F90 commit a1e639ea0f94ff26a0c194ca2e56bd5b2ba85a41 Merge: 51be12d26 8600e494c Author: Tan Nguyen Date: Wed Aug 30 18:12:00 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 51be12d26e34fd0c8825f7f0246b9e65d37cc938 Author: Tan Nguyen Date: Wed Aug 30 18:11:50 2017 -0700 add task association feature to support dynamic task parallelism Src/AmrTask/graph/AMReX_AbstractTask.H Src/AmrTask/graph/AMReX_AbstractTask.cpp Src/AmrTask/graph/AMReX_DataTypes.H Src/AmrTask/graph/AMReX_TaskGraph.H Src/AmrTask/rts_impls/MPI_Generic/mylock.h Src/AmrTask/rts_impls/MPI_Generic/rts.C Src/AmrTask/rts_impls/MPI_Generic/rts_graphimpl.H Src/AmrTask/rts_impls/MPI_Generic/rts_taskimpl.H Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C commit 8600e494ca520df688f477d8b96948cad1ffa4ee Merge: 7ded18490 77b810c60 Author: dtgraves Date: Wed Aug 30 15:56:00 2017 -0700 Merge pull request #106 from AMReX-Codes/dtg_branch merging over improved serialization of EBGraph and a bug fix to BaseIFFAB. commit 77b810c604ec472a5f0dff4517f432d99b08237d Author: dtgraves Date: Wed Aug 30 15:54:23 2017 -0700 I reworked EBGraph serialization so that it will preserve the sparse nature of the object if it can. I also fixed a subtle bug in BaseIFFAB that may have been causing our valgrind troubles. Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_EBLevelGrid.cpp Tests/GeometryShop/regression/ebio.cpp commit ed1df4a2392a441533c906189b7e46f015dbfbbe Merge: dcad3ac0f 7ded18490 Author: Klaus Weide Date: Wed Aug 30 14:51:36 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 84a55da5585b66b8cd80cb0d3169c1ee7e09e6ac Author: Weiqun Zhang Date: Wed Aug 30 10:41:15 2017 -0700 dynamic OpenMP scheduling in MFIter Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp commit b767dc8bc2602741b53300ba0d27000e8e4a4fac Author: dtgraves Date: Wed Aug 30 08:57:53 2017 -0700 bug found by weiqun Src/GeometryShop/AMReX_EBIndexSpace.cpp commit 7ded1849096a0b35facad047210a13846372ff5b Author: Weiqun Zhang Date: Wed Aug 30 08:49:22 2017 -0700 not thread safe Src/Base/AMReX_EBLevel.cpp commit 35b648ea2b10e4a4300c3722a0095706041994fa Author: kngott Date: Wed Aug 30 03:09:46 2017 -0700 Add functions to allow access and updating of cached DistributionMappings in StateData, AmrLevel and AmrMesh objects. Used to fix functionality with MoveAllFabs. Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.H commit 945873db52a5b7bf97db61041a5be17c15f50d2f Author: Weiqun Zhang Date: Tue Aug 29 21:04:34 2017 -0700 turn off openmp for some eb codes because they are not thread safe yet Src/Base/AMReX_EBMultiFabUtil.cpp commit 4aecdbb631aa67ec4be3249e62ec68a350de25f9 Author: Weiqun Zhang Date: Tue Aug 29 15:15:57 2017 -0700 add headers to makefile Src/GeometryShop/Make.package commit 833d13e86c20a9b64c5feda0931caf470d9719e7 Merge: b117bcbf6 4a1bd452e Author: Weiqun Zhang Date: Tue Aug 29 14:22:29 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b117bcbf645d6190b19050b322ae8f1b667eea3a Author: Weiqun Zhang Date: Tue Aug 29 14:22:20 2017 -0700 EB/CNS: tile size Tutorials/EB/CNS/Source/CNS_advance.cpp commit 4a1bd452e55a2ff348560546bef0498768c76153 Merge: 65151d1e5 0552b969d Author: vince Date: Tue Aug 29 13:25:17 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 65151d1e5eeb99403b452f8c3d45b43cff743f4e Author: vince Date: Tue Aug 29 13:25:08 2017 -0700 option to graph top pct in write summary, extra information in call trac, replace spaces in function names. Src/Extern/ProfParser/AMReX_BLProfStats.H Src/Extern/ProfParser/AMReX_BLProfStats.cpp Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp Src/Extern/ProfParser/AMReX_RegionsProfStats.H Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp commit 0552b969d37ecab98cb29a2f4cf7080279ff3d7d Author: Weiqun Zhang Date: Tue Aug 29 13:01:58 2017 -0700 EB/CNS: don't have to go through all the eb stuff if interior plus one ghost cell are all regular Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 commit dcad3ac0fc264400ff86a45c618ab18e019b505c Merge: 272394908 a566abd57 Author: Klaus Weide Date: Tue Aug 29 14:54:42 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a566abd57b7a119086a44ee070b92e26894ace9a Author: Weiqun Zhang Date: Tue Aug 29 12:20:04 2017 -0700 use fortran for cell type counting Src/Base/AMReX_EBCellFlag.cpp Src/Base/AMReX_EBCellFlag_F.H Src/Base/AMReX_ebcellflag_mod.F90 Src/Base/Make.package commit 1806870cc9ed09c1ff316ac89cae5b472443e9e8 Merge: 201495180 48ca627c6 Author: Weiqun Zhang Date: Tue Aug 29 11:14:15 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2014951804084911ca721c25f12bcecc588b1cff Author: Weiqun Zhang Date: Tue Aug 29 11:13:53 2017 -0700 EB/CNS: disable initial load balance Tutorials/EB/CNS/Source/CNS.cpp commit 48ca627c6d01bb1ce8cd10af5278f141963a2255 Merge: 192bdaff0 cceeaab27 Author: Andrew Myers Date: Tue Aug 29 10:10:23 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 192bdaff02b59e8a5648003237ea946a9b8b50ec Author: Andrew Myers Date: Tue Aug 29 10:10:06 2017 -0700 make sure the Geometry offset is consistent with the RealBox. Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp commit 741327368c3193841780abe1d3a20a28ed7e4d0a Author: Weiqun Zhang Date: Tue Aug 29 10:04:29 2017 -0700 EB/CNS: dynamic load balance Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/EB/CNS/Source/fortran/CNS_nd.F90 Tutorials/EB/CNS/Source/main.cpp commit 2723949084632dcbf566ef97ad14d35cfd31e314 Merge: fd9eb6f55 cceeaab27 Author: Klaus Weide Date: Tue Aug 29 12:01:28 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 01c67649ad98a1e8e774f7f9c9b24a3560d2de2f Author: Weiqun Zhang Date: Tue Aug 29 08:41:15 2017 -0700 EB utility function for setting single valued cells Src/Base/AMReX_EBMultiFabUtil.H Src/Base/AMReX_EBMultiFabUtil.cpp Src/Base/AMReX_EBMultiFabUtil_F.H Src/Base/AMReX_EBMultiFabUtil_nd.F90 commit cceeaab27bf16a1dd815e8f3cc6f882a9f3baffe Author: Tan Nguyen Date: Mon Aug 28 17:53:40 2017 -0700 support local load balancing Src/AmrTask/graph/RTS.H Src/AmrTask/rts_impls/MPI_Generic/README Src/AmrTask/rts_impls/MPI_Generic/rts.C Src/AmrTask/rts_impls/Serial/rts.C Src/AmrTask/tutorials/UnitTests/001_TokenRing.C Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C commit 1f66de569c4a614f77010120a09250b02d97139a Author: Weiqun Zhang Date: Mon Aug 28 16:45:51 2017 -0700 EB/CNS: load balance Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/main.cpp commit b42539a632c92ba6401c8e3dcac939854e5d04be Author: Weiqun Zhang Date: Mon Aug 28 16:45:14 2017 -0700 new EB_set_covered function Src/Base/AMReX_EBMultiFabUtil.H Src/Base/AMReX_EBMultiFabUtil.cpp commit b61cacfb204fae27761ffd82797953ea43d7666c Author: Weiqun Zhang Date: Mon Aug 28 16:44:46 2017 -0700 add a new function to Amr for load balance Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp commit 0f8bccb2ebced1a3cf1b7931e0d5a58fdae56df3 Author: Weiqun Zhang Date: Mon Aug 28 15:47:51 2017 -0700 EB/CNS: fix a bug Tutorials/EB/CNS/Source/CNS_advance.cpp commit f380960cf42970d5a2c95a527ce184b4611c0f14 Author: Weiqun Zhang Date: Mon Aug 28 15:04:36 2017 -0700 EB/CNS: set inflow velocity correctly Tutorials/EB/CNS/Exec/Combustor/bc_fill_nd.F90 Tutorials/EB/CNS/Exec/Combustor/cns_prob.F90 Tutorials/EB/CNS/Exec/Combustor/inputs commit ab6ece4079f27494fea41edbec3d515c1e2fa896 Author: Weiqun Zhang Date: Mon Aug 28 13:34:07 2017 -0700 EB/CNS: Combustor test Tutorials/EB/CNS/Exec/Combustor/GNUmakefile Tutorials/EB/CNS/Exec/Combustor/Make.package Tutorials/EB/CNS/Exec/Combustor/bc_fill_nd.F90 Tutorials/EB/CNS/Exec/Combustor/cns_prob.F90 Tutorials/EB/CNS/Exec/Combustor/inputs commit 409950f8a34423f254a277c13adeb4df3f9f9311 Author: Weiqun Zhang Date: Mon Aug 28 12:20:16 2017 -0700 fix up cells that have volume fraction and apertures be exactly one but with a covered neighbor cell touching the corner Src/Base/AMReX_ebcellflag_mod.F90 Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/fortran/CNS_nd.F90 commit fa27ffd619c7b13118975558dbaf9b7293e6a867 Author: Weiqun Zhang Date: Mon Aug 28 10:25:54 2017 -0700 EB/CNS: more debug info Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/hydro/cns_eb_hyp_wall.F90 commit 4eeba5d77bdff7c60795bcee30e58307017946d5 Author: Weiqun Zhang Date: Mon Aug 28 09:57:33 2017 -0700 EB/CNS: save volume fraction in plotfile Tutorials/EB/CNS/Source/CNS_io.cpp commit 9ff5b2607e817c73cce457c5c4e6841fcd1b9b7c Author: Weiqun Zhang Date: Sun Aug 27 21:13:44 2017 -0700 EBFluxFAB is alos thread safe Src/GeometryShop/AMReX_EBFluxFAB.H commit 05c28a91c7d545613d15010a80e52378ab505971 Author: Weiqun Zhang Date: Sun Aug 27 21:12:14 2017 -0700 update FillBoundary for thread safety too Src/Base/AMReX_FabArray.H commit 271b3016eab61abc727ba877ca4df6f933587b92 Author: Weiqun Zhang Date: Sun Aug 27 21:04:58 2017 -0700 some GeometryShop classes are thread safe Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBFaceFAB.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIVFAB.H commit fe1c54d09c98d861ca80413869bb38537cc4f468 Author: Weiqun Zhang Date: Sun Aug 27 20:50:18 2017 -0700 fix AmrLevel and StateData Restart Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp commit 27e6b9a6aa3869cfd6a3d019ae65104624bd2023 Author: Weiqun Zhang Date: Sun Aug 27 16:43:18 2017 -0700 add BaseFab::isCopyOMPSafe() function so that ParallelCopy can turn off omp for unsafe FABs; add this to all EB Fabs. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBFaceFAB.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBFluxFAB.H Src/GeometryShop/AMReX_EBGraph.H commit 10d19bc5346db2f2b6f835a56be234225ea4afec Author: Weiqun Zhang Date: Sun Aug 27 15:02:31 2017 -0700 EB/CNS: fix a bug Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90 commit 320bba8cd6e5499e1f6eea08e11d0a7549d55ac6 Merge: d45683f6a 3747d3863 Author: dtgraves Date: Sun Aug 27 14:00:49 2017 -0700 Merge pull request #103 from AMReX-Codes/dtg_branch merging some small bug fixes into devlopment for weiqun commit 3747d3863703b4abe4e7d8aacb0f19a56f15a000 Author: dtgraves Date: Sun Aug 27 13:58:46 2017 -0700 using the MFIter(FabArray) constructor was breaking in EBISLevel because it seems to magically invoke OMP stuff. I switched it to MFIter(BoxArray, DM) and now it seems to work Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Tests/GeometryShop/ramp/GNUmakefile commit 7a8661ee1d53fa8dbc5f172c9902a239773e6087 Merge: 48fafcacf d45683f6a Author: dtgraves Date: Sun Aug 27 13:39:38 2017 -0700 Merge branch 'development' into dtg_branch commit d45683f6a2b0e6ed0729964478dafcade4e35f2c Merge: 2b1b9781b f10391732 Author: Weiqun Zhang Date: Sun Aug 27 13:34:53 2017 -0700 Merge branch 'development' into weiqun/eb commit 48fafcacfbeffb9e711ff47055aeb77905603004 Author: dtgraves Date: Sun Aug 27 13:34:22 2017 -0700 fixed some logic in GeometryShop Src/GeometryShop/AMReX_GeometryShop.cpp commit 2b1b9781b6c76dde5f7669b774893c749d7c7447 Author: Weiqun Zhang Date: Sun Aug 27 13:08:52 2017 -0700 add -lubsan for llvm when FSANITIZER is TRUE Tools/GNUMake/comps/llvm.mak commit e031b980ce0f708fbc61bc26563cf68cb2ca8928 Author: Weiqun Zhang Date: Sun Aug 27 13:04:17 2017 -0700 remove an unnecessary move Src/Base/AMReX_BoxList.cpp commit 8f15822b431ec5bdb2bc40ec42778d5b5f496b39 Author: Weiqun Zhang Date: Sun Aug 27 12:36:06 2017 -0700 clear some warnings Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_StateData.cpp Src/AmrCore/AMReX_ebinterp_3d.F90 Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_EBLevel.H Src/Base/AMReX_iMultiFab.H Src/GeometryShop/AMReX_BaseEBCellFactory.H Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_EBCellFactory.H Src/GeometryShop/AMReX_EBDataFactory.H Src/GeometryShop/AMReX_EBFluxFactory.H Src/GeometryShop/AMReX_IrregFABFactory.H Tutorials/EB/CNS/Source/hydro/analriem3d.F90 commit 5905cf02d28b5412e1d75010dadba0ca2ec988aa Author: Weiqun Zhang Date: Sun Aug 27 12:18:02 2017 -0700 EB/CNS: add some override Tutorials/EB/CNS/Source/CNS.H commit 16cc03352d08fd3d025895deaea01c16ab722346 Author: Weiqun Zhang Date: Sun Aug 27 11:49:17 2017 -0700 remove unused variable Src/Base/AMReX_EBMultiFabUtil.cpp commit f10391732f56b1a616c8b2273bb046de7f61b299 Author: Michael Zingale Date: Sun Aug 27 14:43:35 2017 -0400 remove unused argument that Cray complains about Src/LinearSolvers/F_MG/mg.f90 commit 450917ce79853c45b70353ba51d1623df81f2678 Author: Weiqun Zhang Date: Sun Aug 27 11:27:45 2017 -0700 EB/CNS: LAZY := TRUE Tutorials/EB/CNS/Exec/Make.CNS Tutorials/EB/CNS/Source/CNS.cpp commit 46b7baeddd105bc023cdda769e37032160ffce5b Author: Weiqun Zhang Date: Sun Aug 27 11:17:09 2017 -0700 EB/CNS: omp Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp commit 09d3085537c132742e3cbdfbf91f3ac5802ffa82 Author: Weiqun Zhang Date: Sun Aug 27 11:01:58 2017 -0700 EB/CNS: add profiler Src/Base/AMReX_EBLevel.cpp Src/Base/AMReX_EBMultiFabUtil.cpp Tutorials/EB/CNS/Exec/Pulse/GNUmakefile Tutorials/EB/CNS/Exec/ShockRef/GNUmakefile Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_init_eb.cpp Tutorials/EB/CNS/Source/CNS_io.cpp Tutorials/EB/CNS/Source/main.cpp commit dc32ea4b54e84d3507c9f4dcd27ddfa7ac3a8ccb Merge: dc25884a8 d9a9768c6 Author: Andrew Myers Date: Sat Aug 26 20:07:43 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit dc25884a899af6d1cd61a329560cc5bbcd664408 Author: Andrew Myers Date: Sat Aug 26 20:07:23 2017 -0700 don't let the kdtree load balancer make empty boxes Src/Particle/AMReX_KDTree_3d.F90 Src/Particle/AMReX_LoadBalanceKD.cpp commit e36edcddf79b4feb3a9440b2877552d2b1dc187c Author: Weiqun Zhang Date: Sat Aug 26 15:20:10 2017 -0700 EB/CNS: minor Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90 commit 0d1388e692b0a2e5c8d326bda1adb71bdbf4ddbb Author: Weiqun Zhang Date: Sat Aug 26 14:45:07 2017 -0700 EB/CNS: fix bug Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90 commit 3822058802a1ee6b1b9231f355900ca14839d942 Author: Weiqun Zhang Date: Sat Aug 26 11:19:03 2017 -0700 EB/CNS: cleanup Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90 Tutorials/EB/CNS/Source/fortran/CNS_derive.F90 Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/fortran/CNS_f.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90 commit 4973d49ecf950b4d8cbc7bfaa8d177dc7ef0f5bd Author: Weiqun Zhang Date: Sat Aug 26 07:25:56 2017 -0700 EB/CNS: clean up Tutorials/EB/CNS/Exec/ShockRef/inputs Tutorials/EB/CNS/Source/diffusion/diff_coef_mod.F90 Tutorials/EB/CNS/Source/fortran/CNS_nd.F90 Tutorials/EB/CNS/Source/fortran/CNS_physics.F90 commit e257e88061f039fc871b79acfb2e4aac08974f8b Author: Weiqun Zhang Date: Sat Aug 26 07:08:37 2017 -0700 CNS/EB: file reorganization Tutorials/EB/CNS/Exec/Make.CNS Tutorials/EB/CNS/Source/Make.package Tutorials/EB/CNS/Source/fortran/CNS_derive.F90 Tutorials/EB/CNS/Source/fortran/CNS_divop.F90 Tutorials/EB/CNS/Source/fortran/CNS_dudt.F90 Tutorials/EB/CNS/Source/fortran/CNS_f.F90 Tutorials/EB/CNS/Source/fortran/CNS_nd.F90 Tutorials/EB/CNS/Source/fortran/CNS_physics.F90 Tutorials/EB/CNS/Source/fortran/Make.package Tutorials/EB/CNS/Source/fortran/bc_fill_nd.F90 commit 11aae6fe7416e97475dc2fb0cdb418cfb99d1293 Author: Weiqun Zhang Date: Sat Aug 26 07:02:27 2017 -0700 EB/CNS: fix a bug in parameter initialization for constant viscosity Tutorials/EB/CNS/Source/CNS_physics.F90 commit 099094be7fef5bb579e79aa7daca87a406597b32 Merge: 32ff77ebd d9a9768c6 Author: Weiqun Zhang Date: Sat Aug 26 07:01:11 2017 -0700 Merge branch 'development' into weiqun/eb commit 539bfe8b25ba6f6078606647267220b7195fb0e1 Author: dtgraves Date: Sat Aug 26 06:31:13 2017 -0700 commented out debugging statement Src/GeometryShop/AMReX_EBISLevel.cpp commit d9a9768c678a26e32ec369a949079bef5181e997 Merge: 36f91880f 89cd8eb91 Author: dtgraves Date: Sat Aug 26 06:14:36 2017 -0700 Merge pull request #102 from AMReX-Codes/dtg_branch fixed another bug Weiqun identified. EBGraph linearization needs a l… commit 89cd8eb9138a67d4d12bb737f399bb64feae7702 Author: dtgraves Date: Sat Aug 26 06:08:05 2017 -0700 fixed another bug Weiqun identified. EBGraph linearization needs a little work but I will commit this first because this version of linearization works. Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeometryShop.cpp commit 32ff77ebd210df0c420d014eb5f95b73c3cbd572 Author: Weiqun Zhang Date: Fri Aug 25 18:43:54 2017 -0700 EB/CNS: fix index bugs Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90 Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.F90 commit 64b3fd6442d5ade58bf81bf37e26b58fead0de30 Author: Weiqun Zhang Date: Fri Aug 25 17:09:41 2017 -0700 EB/CNS: add a parameter for using total energy for weighting Tutorials/EB/CNS/Exec/ShockRef/inputs Tutorials/EB/CNS/Source/CNS_divop.F90 Tutorials/EB/CNS/Source/CNS_f.F90 commit d9220b5d101d1aecde45ff6ff99753d01eb65c75 Author: Weiqun Zhang Date: Fri Aug 25 17:03:51 2017 -0700 EB/CNS: use noslipwall for shock reflection test Tutorials/EB/CNS/Exec/ShockRef/inputs commit 36f91880fa7c5d266abea4e0168cf763f0e53142 Merge: 1fa234adf 9d9e009a2 Author: Andrew Myers Date: Fri Aug 25 16:31:28 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1fa234adf196879a5b78a93f65bccbcf85d469cf Author: Andrew Myers Date: Fri Aug 25 16:31:04 2017 -0700 we want to compile these functions even without _OPENMP. Src/Particle/AMReX_OMPDepositionHelper_nd.F90 Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 9d9e009a22d896e517a35c3ac39360e8754d6511 Author: Weiqun Zhang Date: Fri Aug 25 16:02:55 2017 -0700 modify GeomtryShop test Tests/GeometryShop/ramp/main.cpp commit 2d339fcedec82212b7598b11954604364a16bfac Merge: 4b957cf91 74379ad2c Author: Weiqun Zhang Date: Fri Aug 25 15:48:25 2017 -0700 Merge branch 'eb_development' into weiqun/eb commit e00152581ba30dc71f706c188181e8b6d1690a02 Merge: f824ae495 da11c4e2b Author: WeiqunZhang Date: Fri Aug 25 15:40:37 2017 -0700 Merge pull request #100 from emotheau/convtools New Convergence tool to compute the composite error. Was made with Bo… commit da11c4e2b140fa80e6d6376d959eb760b1406704 Author: Emmanuel Motheau Date: Fri Aug 25 15:29:11 2017 -0700 New Convergence tool to compute the composite error. Was made with BoxLib, we have to convert it to amrex Tools/C_util/Convergence/DiffSameDomainRefinedComposite.cpp Tools/C_util/Convergence/GNUmakefile commit 74379ad2c0ab71a95b0e9a454c2a6d331dfc569c Merge: 18e496a83 f824ae495 Author: Weiqun Zhang Date: Fri Aug 25 15:23:52 2017 -0700 Merge branch 'development' into eb_development Conflicts: Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 4b957cf91c2186ee6239878db707322581149f0c Author: Weiqun Zhang Date: Fri Aug 25 15:03:31 2017 -0700 EB/CNS: minor Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit f824ae495fb383f1ac07f54a39300a206af7e296 Merge: 5cdd8453b f93d4e89a Author: dtgraves Date: Fri Aug 25 14:54:05 2017 -0700 Merge pull request #99 from AMReX-Codes/dtg_branch moving bug fixes to development commit f93d4e89a4b3933002d2fe3cdc056ea7751f73a2 Author: dtgraves Date: Fri Aug 25 14:52:33 2017 -0700 fixed parallel bug identified by Weiqun Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Tests/GeometryShop/ramp/main.cpp commit ee404098ca25a94a02bdc098736d0c64221c9472 Author: Weiqun Zhang Date: Fri Aug 25 14:30:31 2017 -0700 EB/CNS: add contiguous Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90 commit 491b7ca34fb5eb5a7b3a021014a6e2cceebd9425 Author: Weiqun Zhang Date: Fri Aug 25 13:56:32 2017 -0700 EB/CNS: print mementa and energy too Tutorials/EB/CNS/Source/CNS.cpp commit 8c153130e7fe7f96f80f21597fe0b765d01c2850 Author: Weiqun Zhang Date: Fri Aug 25 13:36:28 2017 -0700 EB/CNS: parameter to turn off diffusion Tutorials/EB/CNS/Source/CNS_physics.F90 commit 5cdd8453b626e3000bcea7a2e9d370a1e2f4d10e Merge: 52be61f95 423cb862c Author: WeiqunZhang Date: Fri Aug 25 13:26:46 2017 -0700 Merge pull request #97 from kweide/development give the octree iterator a clear() method commit 3c8d27ce87684e5572c2c30a9cbba8245e3032ab Author: Weiqun Zhang Date: Fri Aug 25 13:11:15 2017 -0700 EB/CNS: add const viscosity Tutorials/EB/CNS/Exec/ShockRef/inputs Tutorials/EB/CNS/Source/CNS_divop.F90 Tutorials/EB/CNS/Source/CNS_physics.F90 Tutorials/EB/CNS/Source/diffusion/diff_coef_mod.F90 commit 07140e403d079e26694e69e7b8e688065c175d6d Author: Weiqun Zhang Date: Fri Aug 25 12:14:48 2017 -0700 EB/CNS: need one more ghost cell Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90 commit 52be61f9588a785a670db7e70cf6c741180de08b Merge: 77d5b50ca e7a6243cf Author: Tan Nguyen Date: Fri Aug 25 11:46:17 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 77d5b50ca6277aded1f2ff30e67420e0c09df191 Author: Tan Nguyen Date: Fri Aug 25 11:45:43 2017 -0700 MPI runtime implementation Src/AmrTask/rts_impls/Utils/dl_malloc.c Src/AmrTask/rts_impls/Utils/dl_malloc.h Src/AmrTask/rts_impls/Utils/sysInfo.C Src/AmrTask/rts_impls/Utils/sysInfo.H commit a15e0044e48bb82b3e6771709f4869dd210501e8 Author: Tan Nguyen Date: Fri Aug 25 11:45:06 2017 -0700 MPI runtime implementation Src/AmrTask/rts_impls/MPI_Generic/Makefile Src/AmrTask/rts_impls/MPI_Generic/README Src/AmrTask/rts_impls/MPI_Generic/mylock.h Src/AmrTask/rts_impls/MPI_Generic/rts.C Src/AmrTask/rts_impls/MPI_Generic/rts_graphimpl.H Src/AmrTask/rts_impls/MPI_Generic/rts_taskimpl.H commit e7a6243cfb9778af932cdbd90f811b074026089d Merge: 44ba48ed7 76b0ece0f Author: Andrew Myers Date: Fri Aug 25 11:33:01 2017 -0700 Merge pull request #98 from MaxThevenet/compile_on_theta Add possibility to compile on Theta ALCF commit 76b0ece0f901b086071fb4b18529f48593b3f41a Author: Maxence Thevenet Date: Fri Aug 25 11:19:25 2017 -0700 Add possibility to compile on Theta ALCF Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.alcf commit 423cb862c5cf6cbce9d07d88ef00eda0093bbebe Author: Klaus Weide Date: Fri Aug 25 13:18:42 2017 -0500 give the mfiter (Fortran) iterator a fabbox() method (tested only compilation and linking so far) Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit c6d16e1686b72f3188f2235b33b8351f86b6afdb Author: Weiqun Zhang Date: Fri Aug 25 11:11:49 2017 -0700 EB/CNS: first pass of diffusion wall flux Tutorials/EB/CNS/Source/CNS_divop.F90 Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90 commit b8d02a6828418ff2d132dfba11ab5aaf4ad34ac9 Merge: 9e31aa0c9 44ba48ed7 Author: Klaus Weide Date: Fri Aug 25 13:02:25 2017 -0500 Merge branch 'development' into kw-development commit 9e31aa0c9a729af550c1114650ed759bdb91484e Author: Klaus Weide Date: Fri Aug 25 09:05:10 2017 -0500 give the octree iterator a clear() method Src/F_Interfaces/Octree/AMReX_octree_mod.F90 commit 44ba48ed7f06d70bdcbc6e48dc0461e13dfae0ce Author: Tan Nguyen Date: Fri Aug 25 04:24:05 2017 -0700 add a multithreaded runtime implementation Src/AmrTask/Makefile Src/AmrTask/arch.common Src/AmrTask/arch/arch.mpi.generic Src/AmrTask/arch/arch.serial Src/AmrTask/graph/AMReX_AbstractTask.H Src/AmrTask/graph/AMReX_AbstractTask.cpp Src/AmrTask/graph/RTS.H Src/AmrTask/rts_impls/Serial/Makefile Src/AmrTask/rts_impls/Serial/rts.C Src/AmrTask/todolist Src/AmrTask/tutorials/UnitTests/001_TokenRing.C Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C Src/AmrTask/tutorials/UnitTests/Makefile commit 0e625b47fc7f3fd9ed0e5bf738dcdaae384f0aa4 Author: Weiqun Zhang Date: Thu Aug 24 14:29:58 2017 -0700 EB/CNS: fake 2D Tutorials/EB/CNS/Exec/ShockRef/inputs Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/CNS_f.F90 commit 13356e4e4ece59aa0f3b43fd0fe231d9baccbc86 Author: Weiqun Zhang Date: Thu Aug 24 14:21:47 2017 -0700 EB/CNS: use current density for redistribution Tutorials/EB/CNS/Source/CNS_divop.F90 commit e5923dfd0d15b95c8e932022a7189e59da01738b Author: Weiqun Zhang Date: Thu Aug 24 13:47:55 2017 -0700 EB/CNS: add a parameter to PLM Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90 Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.F90 commit 4bff9b31e4c849e8334cc0b8476c6b2c1c9b9f09 Author: Weiqun Zhang Date: Thu Aug 24 13:26:26 2017 -0700 EB/CNS: pass bndry centrold into Fortran Src/Base/AMReX_EBMultiFabUtil.H Src/Base/AMReX_EBMultiFabUtil.cpp Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_divop.F90 Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/CNS_physics.F90 Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90 commit d142b485900acbe8440b0774556516404c11f70e Author: dtgraves Date: Thu Aug 24 13:16:40 2017 -0700 fixed the bug that was breaking MPI in this branch Src/Base/AMReX_FabArrayBase.cpp commit 18e496a83c90d8453d11fa5207fa2e2a2108d845 Author: dtgraves Date: Thu Aug 24 12:54:21 2017 -0700 removed constant declaration from argument Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 486afcf050c6f3eeef4f10352cc5aabdb3d2d57b Author: dtgraves Date: Thu Aug 24 12:49:40 2017 -0700 simplified geometry generation stuff somewhat Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp commit 392b060742a295851a587f54630f2fd5fc6182e0 Author: Andrew Myers Date: Thu Aug 24 10:57:45 2017 -0700 remove unused variable. Src/Base/AMReX_FabArray.H commit 322dadebfda0baad5863f671b0434ac5248bab7f Author: Andrew Myers Date: Thu Aug 24 10:12:59 2017 -0700 take care of unused variable warning in parallel copy Src/Base/AMReX_FabArray.H commit 2c0156c14fca2ded36331ee57b4880003f821619 Author: dtgraves Date: Thu Aug 24 09:41:11 2017 -0700 took out const declaration in FabArrayBase to fix USE_MPI=TRUE compile Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 546c4806394973ee4ef5bcfb31b602ef151a9a58 Author: dtgraves Date: Thu Aug 24 08:45:58 2017 -0700 merging with branch eb_development Tests/EBAMRTools/regression/GNUmakefile commit 2ff3469ac3ba1f070ee1e1283d73895411419cc6 Author: Weiqun Zhang Date: Wed Aug 23 18:00:37 2017 -0700 EB/CNS: minor memory leak Tutorials/EB/CNS/Source/CNS_init_eb.cpp commit 1ba40cecdbbbb24b3e2a4bcc5eff5185b68dd6ca Author: Weiqun Zhang Date: Wed Aug 23 17:33:41 2017 -0700 EB/CNS: prepare for diffusion wall flux Tutorials/EB/CNS/Source/CNS_divop.F90 Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/diffusion/cns_diff_mod.F90 Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90 Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90 commit 49e9ef4757bd83ae378c176ba1a030bcb095e4d9 Author: Weiqun Zhang Date: Wed Aug 23 17:01:38 2017 -0700 EB/CNS: start diffusion wall flux module Tutorials/EB/CNS/Source/CNS_divop.F90 Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/Make.package Tutorials/EB/CNS/Source/diffusion/Make.package Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_wall.F90 Tutorials/EB/CNS/Source/hydro/Make.package commit cc01ff8341caf1cd76941fce28d69688197fd041 Author: Weiqun Zhang Date: Wed Aug 23 16:40:49 2017 -0700 EB/CNS: fix EB diffusion flux Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90 commit 96601a9a2ab548adefac480337073e00525cccfd Author: Andrew Myers Date: Wed Aug 23 16:12:38 2017 -0700 need to check for the __powerpc__ macro as well Src/Base/AMReX_FPC.cpp commit 35c8cc7b8dea618f873a8bf2f274dd2106b7d083 Author: Andrew Myers Date: Wed Aug 23 13:00:58 2017 -0700 a few more signed/unsigned Src/Base/AMReX_TinyProfiler.cpp commit 392c2c5c00a99f5ba05d2e6162ec5b01eefebc1b Author: Andrew Myers Date: Wed Aug 23 12:58:26 2017 -0700 fix unused variable warning. Src/Particle/AMReX_ParticleContainerI.H commit 4d0ac52d4db3242a33cd13efbe33f5186b0f1ed4 Author: Andrew Myers Date: Wed Aug 23 12:53:38 2017 -0700 switch from C-style arrays to std::arrays to avoid zero-length array warning. Src/Particle/AMReX_Particles.H commit e768ab2bbbbc4f24e5647239353859d29520d61e Author: Andrew Myers Date: Wed Aug 23 10:21:42 2017 -0700 fix signed/unsigned comparison. Src/Base/AMReX_Array.H commit 4187a98ca3dc6745e0045c6756e324530122efbb Merge: 1abbbc075 2ba37a78e Author: kngott Date: Tue Aug 22 22:40:38 2017 -0700 Merge branch 'development' of https://github.com/AMReX-codes/amrex into development commit 1abbbc075d0a93163e7ceeb1a58630a59b6ed1a2 Author: kngott Date: Tue Aug 22 22:40:34 2017 -0700 MoveAllFabs fix and updated test OldTutorials/MultiFabTests_C/MoveAllFabsTest.cpp Src/Base/AMReX_FabArray.H commit 2ba37a78e4f68e15e1a802c1688b451f0c3a382a Author: Weiqun Zhang Date: Tue Aug 22 22:02:46 2017 -0700 refactor the new amrex_boxarray_build for FLASH Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 commit 63edec824c82acdda327b37b753214c2b4061bff Merge: eea6473ab 9aa8aff4f Author: WeiqunZhang Date: Tue Aug 22 21:37:50 2017 -0700 Merge pull request #93 from kweide/development Add specific build routines for constructing boxarrays and distromaps from user-provided lists in Fortran commit 0b50176552d725ee5e34b165b6f5a41041e30381 Author: Weiqun Zhang Date: Tue Aug 22 18:08:28 2017 -0700 EB/CNS: EB diffusion flux Src/Base/AMReX_ebcellflag_mod.F90 Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/diffusion/cns_diff_mod.F90 Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90 commit 410e4906d17199553fdcca328cc3cec2b5a6e39b Author: Weiqun Zhang Date: Tue Aug 22 16:49:13 2017 -0700 EB/CNS: split hydro and diffsion fluxes Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/diffusion/cns_diff_mod.F90 Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90 commit eea6473abd9d942a6723075971b44c851768e096 Merge: e6c34ec11 511778ebe Author: WeiqunZhang Date: Tue Aug 22 16:18:55 2017 -0700 Merge pull request #95 from AMReX-Codes/perf-docs update Documentation: added IPM section to Profiling.tex commit 511778ebe0481e023d9c9d1c8ab809ef9e2beb80 Merge: bd38c46fa 51f3005c2 Author: Cy Chan Date: Tue Aug 22 16:15:22 2017 -0700 Merge branch 'development' into perf-docs commit bd38c46fa2eadbe581d5bfc43758ea5cde0deee3 Author: Cy Chan Date: Tue Aug 22 16:07:27 2017 -0700 update Documentation added IPM section to Profiling.tex Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Profiling/Profiling.tex Docs/AMReXUsersGuide/Profiling/figs/commtopo.png Docs/AMReXUsersGuide/Profiling/figs/mpi.png Docs/AMReXUsersGuide/Profiling/figs/msgsizes.png Docs/AMReXUsersGuide/Profiling/figs/papi.png Docs/AMReXUsersGuide/Profiling/figs/summary.png Docs/AMReXUsersGuide/Profiling/figs/timings.png commit cbde657fbbb2e6938240a757e2bb0ba6e78bc94b Author: Weiqun Zhang Date: Tue Aug 22 15:18:08 2017 -0700 EB/CNS: regular diffusion terms Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/diffusion/cns_diff_mod.F90 Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90 commit fd9eb6f553fe028a68fe466b608150426650b8af Merge: b66a8f46e e6c34ec11 Author: Klaus Weide Date: Tue Aug 22 15:09:32 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e6c34ec116b273500556d7358b3b11db2aca85ce Author: vince Date: Tue Aug 22 11:37:48 2017 -0700 add move all fabs test. OldTutorials/MultiFabTests_C/MoveAllFabsTest.cpp commit 7dca88c7da09381fa16f655154f8a9ba0ea63cd6 Author: Weiqun Zhang Date: Tue Aug 22 11:26:44 2017 -0700 EB/CNS: use future mass for weighting Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 commit 8b87b1bfacd8b323fa6732ed31c611fe83656b01 Author: Weiqun Zhang Date: Tue Aug 22 10:58:16 2017 -0700 EB/CNS: reorganization Tutorials/EB/CNS/Exec/Make.CNS Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_dudt.F90 Tutorials/EB/CNS/Source/CNS_nd.F90 Tutorials/EB/CNS/Source/Make.package Tutorials/EB/CNS/Source/diffusion/Make.package Tutorials/EB/CNS/Source/diffusion/cns_diff_mod.F90 Tutorials/EB/CNS/Source/diffusion/cns_eb_diff_mod.F90 Tutorials/EB/CNS/Source/diffusion/diff_coef_mod.F90 Tutorials/EB/CNS/Source/hydro/Make.package commit 666b68187f3c95e2cde35a640bb1bbd5c5a82727 Author: Weiqun Zhang Date: Mon Aug 21 14:45:30 2017 -0700 EB/CNS: use air as initial condition Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90 Tutorials/EB/CNS/Exec/Pulse/inputs commit d74ba149d04c7cac24612b2f269ad8756ee5016a Author: Weiqun Zhang Date: Mon Aug 21 14:23:18 2017 -0700 EB/CNS: add a module computing viscosity and thermal conductivity Tutorials/EB/CNS/Source/CNS_physics.F90 Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90 Tutorials/EB/CNS/Source/hydro/Make.package Tutorials/EB/CNS/Source/hydro/cns_diff_mod.F90 Tutorials/EB/CNS/Source/hydro/cns_eb_diff_mod.F90 Tutorials/EB/CNS/Source/hydro/diff_coef_mod.F90 commit ef1be96a1ae9208c531e7550b4d09700d00ddb77 Merge: a23ed91a2 f845398b8 Author: Weiqun Zhang Date: Mon Aug 21 13:53:36 2017 -0700 Merge branch 'weiqun/eb' into eb_development commit 51f3005c27f1c6b29ceda1952596878375777384 Merge: 7a1693ed4 ab14cef42 Author: Andrew Myers Date: Mon Aug 21 13:47:44 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7a1693ed4be904b4ac5d70c573d4fefae484fc26 Author: Andrew Myers Date: Mon Aug 21 13:47:26 2017 -0700 remove some debugging junk I checked in by mistake. Src/Particle/AMReX_ParticleInit.H commit f845398b810064639f36a92b1f6018c51619bccd Author: Weiqun Zhang Date: Mon Aug 21 13:43:11 2017 -0700 EB/CNS: fix a bug Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 commit 6090472cf76bd843dddbccf49f2b99647f6dbecb Author: Weiqun Zhang Date: Mon Aug 21 10:34:09 2017 -0700 EB/CNS: make sure flux outside the domain is not used Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 commit b66a8f46e2b5d875e1d8b06cd5777ddfbbb42f36 Merge: b8e1e510b ab14cef42 Author: Klaus Weide Date: Mon Aug 21 08:07:02 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ab14cef42f5a8e7a01a9f89c1a3e29d773271366 Author: Weiqun Zhang Date: Sat Aug 19 13:05:59 2017 -0700 add assertion making sure BoxArray::set is not called on non-trivial objects Src/Base/AMReX_BoxArray.cpp commit 99feeb59d7f52562f23ffe760fc91944c8f02e2c Merge: b301eca40 2d39bd09d Author: WeiqunZhang Date: Fri Aug 18 16:04:19 2017 -0700 Merge pull request #91 from AMReX-Codes/compiler_warnings Compiler warnings commit 2d39bd09d260619df781fdb633da9958c507c9b1 Author: Andrew Myers Date: Fri Aug 18 16:00:42 2017 -0700 give this a more descriptive name Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_Utility.H commit a23ed91a22230b123307d18c21414e680d66fe8c Author: Weiqun Zhang Date: Fri Aug 18 15:05:20 2017 -0700 a GeometryShop test Tests/GeometryShop/ramp/GNUmakefile Tests/GeometryShop/ramp/Make.package Tests/GeometryShop/ramp/inputs Tests/GeometryShop/ramp/main.cpp commit 8d53fa454778ef5bb4736bf993d8d9621e6fd1be Author: Andrew Myers Date: Fri Aug 18 15:43:40 2017 -0700 remove some vlas Src/Amr/AMReX_Amr.cpp commit fdbd5acf612834303d477a55371017eef4478c30 Author: Andrew Myers Date: Fri Aug 18 15:28:15 2017 -0700 some more cleanup Src/Base/AMReX.cpp Src/Base/AMReX_BCUtil.H Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_BC_TYPES.H Src/Particle/AMReX_LoadBalanceKD.H Src/Particle/AMReX_Particles_F.H commit 74619f225c0a652e821ede25627bea9c01b1a31f Author: Andrew Myers Date: Fri Aug 18 15:13:00 2017 -0700 initialize this variable Src/Base/AMReX_BaseFab.cpp commit c674d596898e5e50ec9f6a00a046d453e0d3f43f Author: Andrew Myers Date: Fri Aug 18 15:08:25 2017 -0700 switch this back to no by default. Tools/GNUMake/comps/gnu.mak commit 9fb3bb4c9fe22e7ce4862f3d73db2e84792d535f Author: Andrew Myers Date: Fri Aug 18 15:06:40 2017 -0700 fix bug in llvm.mak Tools/GNUMake/comps/llvm.mak commit b6d7fbcb67d1c6427d7051534b8a730570a4335f Author: Andrew Myers Date: Fri Aug 18 14:52:56 2017 -0700 turn on -Wsign-compare in Debug mode. Tools/GNUMake/comps/gnu.mak commit 549ca59ccfc69a7a042d25920ae7a23f40c573be Author: Andrew Myers Date: Fri Aug 18 14:46:54 2017 -0700 yet another signed/unsigned Src/Amr/AMReX_StateDescriptor.cpp commit 7c1debb06e84ed653dd93f4635a8023c22ac85de Author: Andrew Myers Date: Fri Aug 18 14:38:26 2017 -0700 a few more signed / unsigned Src/Amr/AMReX_AmrLevel.cpp commit 9aa8aff4f11dcfa16d5511c357d44f72ae821de2 Author: Klaus Weide Date: Fri Aug 18 16:00:41 2017 -0500 Add specific build routines for constructing boxarrays and distromaps from explicit Fortran data Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_distromap_fi.cpp Src/F_Interfaces/Base/AMReX_distromap_mod.F90 commit f40f8c5f4db200688669efe86e5c913f19254d76 Author: Andrew Myers Date: Fri Aug 18 13:53:00 2017 -0700 another signed/unsigned Src/Base/AMReX_DistributionMapping.cpp commit df768fc4410b5889dd1e282ca477c9dc561002d0 Author: Andrew Myers Date: Fri Aug 18 13:51:21 2017 -0700 ignore this unused variable. Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_Utility.H commit 6004ec772a283a1cabcc3518c254928b86b4daef Author: Andrew Myers Date: Fri Aug 18 13:37:22 2017 -0700 fix some signed / unsigned comparisons. Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX_Array.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_Utility.cpp Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_parmparse_fi.cpp commit 52d68b892a9a76dbed31e0b41796c3d041e2a75e Merge: 2c3337516 efe2c42e9 Author: Weiqun Zhang Date: Fri Aug 18 13:18:33 2017 -0700 Merge branch 'dtg_branch' into weiqun/eb commit 2c33375160f9eae86201d202d450b7076cb8abdb Merge: f8e7f3793 b301eca40 Author: Weiqun Zhang Date: Fri Aug 18 13:18:19 2017 -0700 Merge branch 'development' into weiqun/eb commit f8e7f37931e7536635d20e84e9174220d5d10344 Author: Weiqun Zhang Date: Fri Aug 18 12:49:14 2017 -0700 we may not even have a probin file Src/Amr/AMReX_Amr.cpp commit b4a3b83bd7335e874373dd6eae91ce8478fac2fe Author: Weiqun Zhang Date: Fri Aug 18 12:36:59 2017 -0700 EB/CNS: mod inputs Tutorials/EB/CNS/Exec/ShockRef/cns_prob.F90 Tutorials/EB/CNS/Exec/ShockRef/inputs commit b85fc1f5d41bf2399960e3d6de44b43126c0322b Author: Michele Rosso Date: Fri Aug 18 11:58:29 2017 -0700 CMake: update config file Tools/CMake/AMReXConfig.cmake.in commit 47748ef5e74439b3f033a877d3a8e8552313071c Author: Weiqun Zhang Date: Fri Aug 18 10:51:20 2017 -0700 EB/CNS: using mass weighting instead of volume weighting Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 commit 435fa5b1b699e39e4215bd2a8effe9d88082cb42 Author: Weiqun Zhang Date: Fri Aug 18 10:49:17 2017 -0700 EB/CNS: some parmparse parameters for the shock reflection test Tutorials/EB/CNS/Exec/ShockRef/cns_prob.F90 commit b301eca406c08aaafddf6e8e494239f19cc664c4 Author: Andrew Myers Date: Fri Aug 18 10:07:18 2017 -0700 Fix offset bug when initializing particle integer data. Src/Particle/AMReX_ParticleInit.H commit 62b076b3a9603c96d0e70a664768e689a813eefb Author: Andrew Myers Date: Fri Aug 18 10:04:29 2017 -0700 Fix copy/paste issue in comment. Src/Particle/AMReX_ParticleInit.H commit c936f3dfc6bbc2a79756893ab098aa59476cc0e7 Author: Andrew Myers Date: Fri Aug 18 10:02:25 2017 -0700 Real -> amrex::Real Src/Particle/AMReX_LoadBalanceKD.H commit 5c73610f1c54367ec93bad61e45776bff306ad10 Author: Weiqun Zhang Date: Fri Aug 18 09:23:45 2017 -0700 EB/CNS: fix a bug in 2-shock riemann solver; add HLL; floor density and pressure Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_nd.F90 Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90 Tutorials/EB/CNS/Source/hydro/analriem3d.F90 commit b8e1e510b422f01e3f6d583233d24cbbeb2d74e6 Merge: f1b476a72 6c802b1f0 Author: Klaus Weide Date: Fri Aug 18 07:36:41 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ca161599df0b612f8e0aa9c4b518e052eba700e3 Author: Max Katz Date: Fri Aug 18 01:35:09 2017 -0700 Add a missing device ifdef Src/Base/AMReX_BaseFab.H commit 56f9fcf7dd9d7096ba946e993fbe47e994e7018f Author: Max Katz Date: Fri Aug 18 01:54:12 2017 -0400 Fix the summitdev library typo Tools/GNUMake/comps/pgi.mak commit 9dbcbbf6a76b2602a7011d61f17450ddc6871a9f Author: Michele Rosso Date: Thu Aug 17 17:29:05 2017 -0700 Doc: fix typo Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex commit c609612a48df6451e293f62a26f4326f9b50c9ad Author: Michele Rosso Date: Thu Aug 17 17:27:36 2017 -0700 CMake: update exports Tools/CMake/AMReXConfig.cmake.in commit 95b2784d5c642cde7dd1b709c8b6ba6550037164 Author: Michele Rosso Date: Thu Aug 17 17:17:28 2017 -0700 CMake: update doc Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Tools/CMake/AMReX_Defines.cmake commit 57c21a41d92e751a91d6ae4a3065ab4bde240561 Author: Michele Rosso Date: Thu Aug 17 16:57:20 2017 -0700 CMake: update * Add support for ProfParser * Re-factor souce files lists * Change some config args. Src/Amr/CMakeLists.txt Src/AmrCore/CMakeLists.txt Src/Base/CMakeLists.txt Src/Boundary/CMakeLists.txt Src/CMakeLists.txt Src/Extern/CMakeLists.txt Src/F_BaseLib/CMakeLists.txt Src/F_Interfaces/CMakeLists.txt Src/LinearSolvers/CMakeLists.txt Src/Particle/CMakeLists.txt Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt Tutorials/Amr/Advection_F/CMakeLists.txt Tutorials/Amr/Advection_octree_F/CMakeLists.txt commit efe2c42e95532839a5a76aebf7df05e67c6b4841 Author: dtgraves Date: Thu Aug 17 16:29:05 2017 -0700 yet another attempt to silence valgrind Src/GeometryShop/AMReX_EBISBox.cpp commit 6c802b1f096121ddb8fb6648ac46bf4014bf2a4b Merge: e51402535 7b59d17c1 Author: Andrew Myers Date: Thu Aug 17 16:26:57 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 544df12d251c8aca742c446637f4d7b2faa3317d Author: Weiqun Zhang Date: Thu Aug 17 15:56:12 2017 -0700 EB/CNS: minor Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90 commit 9d6dda633fabf365973e9655942356e670d6f645 Author: Weiqun Zhang Date: Thu Aug 17 15:21:30 2017 -0700 EB/CNS: make sure dx == dy == dz Tutorials/EB/CNS/Exec/ShockRef/inputs Tutorials/EB/CNS/Source/CNS.cpp commit 7b59d17c15fb58da2bc95b115b017e91a92181ab Merge: 597aa740f 0f4eed95f Author: vince Date: Thu Aug 17 15:19:07 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 597aa740f79f311c3d4c7f27e256291abf0de43d Author: vince Date: Thu Aug 17 15:18:29 2017 -0700 uniqify coarsened boxarray. Src/Extern/amrdata/AMReX_DataServices.cpp commit 0c057eb37658e1b74762fea8d48fbb4cc3ec9e96 Author: vince Date: Thu Aug 17 15:13:31 2017 -0700 make uniqify public. Src/Base/AMReX_BoxArray.H commit e4a339eded5e0a974b6bf0f29a41f41584d21fd9 Author: Weiqun Zhang Date: Thu Aug 17 14:25:01 2017 -0700 EB/CNS: add Shock Reflection problem Src/Amr/AMReX_Amr.cpp Tutorials/EB/CNS/Exec/Pulse/GNUmakefile Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90 Tutorials/EB/CNS/Exec/ShockRef/GNUmakefile Tutorials/EB/CNS/Exec/ShockRef/Make.package Tutorials/EB/CNS/Exec/ShockRef/cns_prob.F90 Tutorials/EB/CNS/Exec/ShockRef/inputs Tutorials/EB/CNS/Source/CNS_f.F90 Tutorials/EB/CNS/Source/CNS_physics.F90 commit e51402535b7258f531525d5d91a1242e4c3c447a Author: Andrew Myers Date: Thu Aug 17 12:41:06 2017 -0700 1D and 2D versions of the KDTree fortran helper routines. Src/Particle/AMReX_KDTree_1d.F90 Src/Particle/AMReX_KDTree_2d.F90 Src/Particle/AMReX_KDTree_3d.F90 commit b5f5bfbb2a44206969f78547f44593e7585f6773 Author: Andrew Myers Date: Thu Aug 17 12:34:03 2017 -0700 move the load balancing stuff to Src/Particle Src/Particle/AMReX_KDTree_3d.F90 Src/Particle/AMReX_KDTree_F.H Src/Particle/AMReX_LoadBalanceKD.H Src/Particle/AMReX_LoadBalanceKD.cpp Src/Particle/CMakeLists.txt Src/Particle/Make.package Tutorials/Particles/LoadBalance/Make.package Tutorials/Particles/LoadBalance/kdtree_F.H Tutorials/Particles/LoadBalance/main.cpp Tutorials/Particles/LoadBalance/visualize_output.ipynb commit 0f4eed95f5efd6c41389566abdbe977ac0973d17 Author: atmyers Date: Thu Aug 17 11:19:10 2017 -0700 This needs to be a 'C' header so it will be installed when building amrex as a library. Src/Particle/Make.package commit 48854d986ef1d92d7007595c3c7682e0182afc66 Author: Andrew Myers Date: Thu Aug 17 10:46:22 2017 -0700 some more reorganization. Tutorials/Particles/LoadBalance/main.cpp commit 43a4a233dca8bf519c622fbbda3391da61e4dfbe Author: Weiqun Zhang Date: Thu Aug 17 10:42:38 2017 -0700 EB/CNS: forgot to call mpi reduce Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90 commit ac7812c70fd9c6b76527035d5831d8ce5b4f84ce Author: Andrew Myers Date: Thu Aug 17 10:23:16 2017 -0700 some reorganization. Tutorials/Particles/LoadBalance/main.cpp commit 8ed1402764d3f03dd33ff2f5c38abec73017580c Author: Weiqun Zhang Date: Wed Aug 16 18:04:27 2017 -0700 EB/CNS: minor Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 commit fdd72580ab5e54212c569a8f716a8e9f99863fcf Merge: 300c46f3e f1b476a72 Author: Klaus Weide Date: Wed Aug 16 19:52:40 2017 -0500 Merge branch 'development' into kw-development commit f1b476a7257a91df5e1d5fb2616026bcbbca827f Merge: 78cf06377 f5389eb2c Author: Klaus Weide Date: Wed Aug 16 19:45:18 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 457e801930ecfedb278bb4bfddac34b687ea69f2 Author: Weiqun Zhang Date: Wed Aug 16 17:23:07 2017 -0700 EB/CNS: print out the total mass Tutorials/EB/CNS/Exec/Pulse/inputs Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp commit 093ef08b39f0dfdd87b2483f2a7dd5755feb8581 Author: Weiqun Zhang Date: Wed Aug 16 16:57:26 2017 -0700 EB/CNS: bug fix Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90 Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90 Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 commit f5389eb2c98701be96fcb42d9e191edc7d1bac72 Author: Andrew Myers Date: Wed Aug 16 16:51:24 2017 -0700 minor tweaks. Tutorials/Particles/LoadBalance/create_binary_particle_file.py Tutorials/Particles/LoadBalance/inputs Tutorials/Particles/LoadBalance/main.cpp Tutorials/Particles/LoadBalance/visualize_output.ipynb commit c0fa09b223b322772b81a6bbe0fa1b1566988b84 Author: Andrew Myers Date: Wed Aug 16 16:51:04 2017 -0700 checked this file in by mistake. Tutorials/Particles/LoadBalance/binary_particle_file.dat commit b900d793162fe39323af7a8e5b4f1d8144d5ef0c Merge: 12e42b0d2 9139ec688 Author: Andrew Myers Date: Wed Aug 16 16:29:28 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 12e42b0d2a9c9c17f429d9f7c86aa4db6c4e0259 Author: Andrew Myers Date: Wed Aug 16 16:29:13 2017 -0700 some works towards using a kdtree for load balancing particles Tutorials/Particles/LoadBalance/GNUmakefile Tutorials/Particles/LoadBalance/Make.package Tutorials/Particles/LoadBalance/binary_particle_file.dat Tutorials/Particles/LoadBalance/create_binary_particle_file.py Tutorials/Particles/LoadBalance/inputs Tutorials/Particles/LoadBalance/kdtree_3d.f90 Tutorials/Particles/LoadBalance/kdtree_F.H Tutorials/Particles/LoadBalance/main.cpp Tutorials/Particles/LoadBalance/visualize_output.ipynb commit 5de07177c3a231e193caffa5eba65178136c40bc Author: Weiqun Zhang Date: Wed Aug 16 15:22:22 2017 -0700 EB/CNS: clean up Tutorials/EB/CNS/Source/hydro/comp.F90 Tutorials/EB/CNS/Source/hydro/comp_2d.F90 Tutorials/EB/CNS/Source/hydro/comp_3d.F90 Tutorials/EB/CNS/Source/hydro/wall.F commit 4f81a3198aac891096c73285b05ff98c1920dfa4 Author: Weiqun Zhang Date: Wed Aug 16 15:20:20 2017 -0700 EB/CNS: add wall flux and the first simple test seems to work now Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90 Tutorials/EB/CNS/Source/hydro/Make.package Tutorials/EB/CNS/Source/hydro/analriem3d.F90 Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 Tutorials/EB/CNS/Source/hydro/cns_eb_hyp_wall.F90 commit 300c46f3e35447254e457861302067d453c73471 Merge: 852455548 9139ec688 Author: Klaus Weide Date: Wed Aug 16 17:19:10 2017 -0500 Merge branch 'development' into kw-development commit c7cf7e4e63e339f7530690ff12615c33d4a53bbf Merge: 05f1af803 9139ec688 Author: Michele Rosso Date: Wed Aug 16 14:46:04 2017 -0700 Merge branch 'development' into mr-cmake commit 05f1af8030ebb7bd54a85472be58359e56d04323 Author: Michele Rosso Date: Wed Aug 16 14:45:08 2017 -0700 CMake: modify implementation of user options Tools/CMake/AMReX_Options.cmake commit 3404fa7cc95d61548d0567cbcf07bb63df3dddea Author: Weiqun Zhang Date: Wed Aug 16 11:17:33 2017 -0700 EB/CNS: add parmparse to probin Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90 Tutorials/EB/CNS/Exec/Pulse/inputs commit 767a6d6074b01c07f43416f469409427c1a25981 Author: Weiqun Zhang Date: Wed Aug 16 10:54:53 2017 -0700 fix a number of index problems Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90 Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 commit 4699dc03671612500cfb58d93b036814e7e8a824 Author: Weiqun Zhang Date: Tue Aug 15 18:07:33 2017 -0700 EB/CNS: fix bug Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 commit 0d5a115c44c23eee8cb2a6d44e7264e7c8e4db16 Author: Weiqun Zhang Date: Tue Aug 15 17:52:06 2017 -0700 EB/CNS: compute eb diffop Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_nd.F90 Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90 Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 commit 9139ec688647a632bf633d1d129a2eaa8458a374 Merge: 010ceb0a2 fe66eb1b2 Author: kngott Date: Tue Aug 15 17:51:50 2017 -0700 Merge branch 'development' of https://github.com/AMReX-codes/amrex into development commit 010ceb0a23bf05e6f09a54ef9f3b526baba4dacf Author: kngott Date: Tue Aug 15 17:51:07 2017 -0700 Update to make system for profiling and new profparser setup. Uses separate PROFILE and USE_PROFPARSER variables in GNUmakefiles and eliminates depreciated NOLINEVALUES directive. OldTutorials/DataServicesTest0/GNUmakefile Src/Extern/ProfParser/Make.package Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp Src/Extern/amrdata/AMReX_XYPlotDataList.H Src/Extern/amrdata/AMReX_XYPlotDataList.cpp Src/Extern/amrdata/Make.package Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit fae3bacece12a75f84811fccb6a1996849da95cd Author: Michele Rosso Date: Tue Aug 15 17:43:14 2017 -0700 CMake: modify way of adding include dirs Src/Amr/CMakeLists.txt Src/AmrCore/CMakeLists.txt Src/Base/CMakeLists.txt Src/Boundary/CMakeLists.txt Src/CMakeLists.txt Src/Extern/CMakeLists.txt Src/F_BaseLib/CMakeLists.txt Src/F_Interfaces/CMakeLists.txt Src/LinearSolvers/CMakeLists.txt Src/Particle/CMakeLists.txt Tools/CMake/AMReX_Utils.cmake commit fe66eb1b20e5634064989c10f646912234ce31a6 Author: Andrew Myers Date: Tue Aug 15 17:31:45 2017 -0700 This approach to testing whether the grids cover the domain is much more memory efficient and should be equivalent if the grids are non-overlapping. Src/Particle/AMReX_ParticleContainerI.H commit e5344e99dce4d5d65a7740d54b9f665498cf6e7f Author: Weiqun Zhang Date: Tue Aug 15 16:41:22 2017 -0700 build area fraction and face centroid Src/Base/AMReX_EBMultiFabUtil.H Src/Base/AMReX_EBMultiFabUtil.cpp Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp commit 7b3919bfa00f60b336bf7f89ed568293442b62cb Author: Michele Rosso Date: Tue Aug 15 16:28:42 2017 -0700 CMake: remove unused functions. Tools/CMake/AMReX_Utils.cmake commit b3e579ced3abcd4602cfd48fb86a7e7578de5a2e Author: Michele Rosso Date: Tue Aug 15 16:20:46 2017 -0700 CMake: move config of macro definitions to separate file Src/Extern/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Defines.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_Utils.cmake commit 6a61f552a476b15d7778513fec97c3e0a00b2e3a Author: Weiqun Zhang Date: Tue Aug 15 15:19:21 2017 -0700 EB/CNS: first pass of eb flux module Tutorials/EB/CNS/Source/hydro/Make.package Tutorials/EB/CNS/Source/hydro/cns_eb_flux_mod.F90 commit 4f42012edf7e3cdafac17c241e593aa3c45ae02d Merge: 07e3af78e e852b92ff Author: Andrew Myers Date: Tue Aug 15 15:07:33 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 07e3af78e75b18da5fb32fe4aa279a97c5bbd16b Author: Andrew Myers Date: Tue Aug 15 15:07:16 2017 -0700 Restore some variable names that were changed by some over-aggresive find/replacing. Src/Particle/AMReX_ParticleInit.H commit 687dbdda9bed045c8d1e36f46199ba6fbc0a9435 Author: Weiqun Zhang Date: Tue Aug 15 12:30:31 2017 -0700 EB/CNS: get comp_3d compile Tutorials/EB/CNS/Source/hydro/Make.package Tutorials/EB/CNS/Source/hydro/comp_3d.F90 commit f126aa9bbbb6d9db416b65195c662e59f3033e68 Author: Weiqun Zhang Date: Tue Aug 15 10:44:07 2017 -0700 EB/CNS: add john's code Tutorials/EB/CNS/Source/hydro/comp_3d.F90 commit bf2dc32ee6cf02cda50f316d1867ba93f115df40 Author: Weiqun Zhang Date: Tue Aug 15 10:42:21 2017 -0700 EB/CNS: fix physical boundary without EB Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.F90 commit 603a3b13211e99407a8914a29fd58cc240029ccd Author: Weiqun Zhang Date: Mon Aug 14 17:49:05 2017 -0700 EB/CNS: fix some bugs Tutorials/EB/CNS/Exec/Pulse/inputs Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90 Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90 Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.F90 commit 31e75724065271ee0938a0e96386850390f947ef Author: Weiqun Zhang Date: Mon Aug 14 16:51:41 2017 -0700 EB/CNS: merge John's eb hyperbolic code Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90 Tutorials/EB/CNS/Source/hydro/Make.package Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90 Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.F90 commit effd848c60f8a8e2fa8bf16714b0d326e0994a34 Author: Weiqun Zhang Date: Mon Aug 14 15:43:35 2017 -0700 EB/CNS: second order hydro with regular geometry works Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90 commit e852b92ffca6d042309b8bbe3564102c96ddf58e Author: kngott Date: Mon Aug 14 15:26:24 2017 -0700 Added BLProfParser parser files to the realclean command. Used specific names to ensure there are not accidental deletions. Tools/GNUMake/Make.rules commit 7366dc4b39c45f8f223843cafb75dcd24950d763 Author: kngott Date: Mon Aug 14 15:21:43 2017 -0700 A simple 3D TRACE profiling fix. Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp commit 6da2982f16f8468ce64348c65811931ccb416584 Author: Weiqun Zhang Date: Mon Aug 14 15:09:50 2017 -0700 EB/CNS: first order hydro with regular geometry works Tutorials/EB/CNS/Exec/Make.CNS Tutorials/EB/CNS/Exec/Pulse/inputs Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_f.F90 Tutorials/EB/CNS/Source/CNS_nd.F90 Tutorials/EB/CNS/Source/hydro/CNS_hydro_mod.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 Tutorials/EB/CNS/Source/hydro/Make.package Tutorials/EB/CNS/Source/hydro/analriem3d.F90 Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90 commit a57d3cd1e6ae9cedda8f5891c3c6829a3677a4a9 Author: kngott Date: Mon Aug 14 14:30:31 2017 -0700 Addition of profile specific requirements to standard amrex make. Should only require PROFILE=TRUE. Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit e015aec0f8d528878cf2f565431e2471f54af1a4 Author: Weiqun Zhang Date: Mon Aug 14 11:04:58 2017 -0700 EB/CNS: rename to F90 Tutorials/EB/CNS/Source/hydro/analriem3d.F90 Tutorials/EB/CNS/Source/hydro/comp.F90 Tutorials/EB/CNS/Source/hydro/comp_2d.F90 Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.F90 Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.F90 Tutorials/EB/CNS/Source/hydro/wall.F commit ba3aec18785b1dcfdca66895e35d615f677bab62 Author: Weiqun Zhang Date: Mon Aug 14 11:01:29 2017 -0700 EB/CNS: more code from John Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL.F90 Tutorials/EB/CNS/Source/hydro/Hyp_gamma_MOL_EB.F90 Tutorials/EB/CNS/Source/hydro/analriem3d.f Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma.f90 Tutorials/EB/CNS/Source/hydro/slope_mol_3d_gamma_EB.f90 commit d1a8abdb111c2a367c0a2bbeb523af9e655c8b4a Author: Weiqun Zhang Date: Mon Aug 14 10:43:13 2017 -0700 EB/CNS: john's hydro code Tutorials/EB/CNS/Source/hydro/comp.f Tutorials/EB/CNS/Source/hydro/comp_2d.f Tutorials/EB/CNS/Source/hydro/wall.f commit 44f1728f9c6af8ce647d5537b156f5c3af52dffa Author: Weiqun Zhang Date: Mon Aug 14 10:39:37 2017 -0700 EB/CNS: set up RK2 and plotfile Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90 Tutorials/EB/CNS/Exec/Pulse/inputs Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_io.cpp commit 29a852a0ff0867d1c0497992717e0f09775d9ba0 Merge: af19c754b d8d6269c6 Author: Michele Rosso Date: Mon Aug 14 10:36:33 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit db6ad19417b4825e6badd03a3e217b37686dc476 Merge: db97af3ae d8d6269c6 Author: Max Katz Date: Mon Aug 14 01:44:02 2017 -0700 Merge branch 'development' into gpu Conflicts: Src/Base/AMReX.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_parmparse_mod.F90 Tools/GNUMake/Make.rules Tools/GNUMake/comps/pgi.mak commit e3c3071db9a4a15feb645f4060f6461a5d86e871 Author: Weiqun Zhang Date: Sun Aug 13 08:00:29 2017 -0700 EB/CNS: initialzie EB Tutorials/EB/CNS/Exec/Pulse/inputs Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_init_eb.cpp Tutorials/EB/CNS/Source/Make.package Tutorials/EB/CNS/Source/main.cpp commit d8d6269c6e786e17876e7275cdf35eb45d1836a0 Author: Ann Almgren Date: Sat Aug 12 16:25:13 2017 -0700 Remove unused variables Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Extern/amrdata/AMReX_AmrData.cpp commit 0d84024a195ef7eae423e73707a7b115cef1d15c Merge: ebeeeea91 2c559038b Author: Tan Nguyen Date: Sat Aug 12 15:49:23 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ebeeeea91f32d3cfba0fb0972ebc1d2c6221ec17 Author: Tan Nguyen Date: Sat Aug 12 15:49:19 2017 -0700 add Dynamic Task Parallelism support Src/AmrTask/graph/AMReX_AbstractTask.H Src/AmrTask/graph/AMReX_DataTypes.H Src/AmrTask/graph/AMReX_TaskGraph.H Src/AmrTask/graph/RTS.H Src/AmrTask/rts_impls/Serial/rts.C Src/AmrTask/rts_impls/Serial/rts_taskimpl.H Src/AmrTask/tutorials/UnitTests/001_TokenRing.C Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C Src/AmrTask/tutorials/UnitTests/Makefile commit 2c559038b2ccdb9eef18d9067f49f3c2eafaabbb Author: kngott Date: Sat Aug 12 14:57:14 2017 -0700 Preprocessing to protect profiler services from 3D simulations. Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp Src/Extern/amrdata/AMReX_DataServices.cpp commit d32e5146bad8558c50696657d8df5f4791e779a4 Author: Weiqun Zhang Date: Sat Aug 12 12:23:33 2017 -0700 EB/CNS: estimate dt Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_nd.F90 commit 0e758713fbeaf768349d83f4a78d187102f92788 Author: Weiqun Zhang Date: Sat Aug 12 12:03:51 2017 -0700 EB/CNS: compute temperature Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_nd.F90 Tutorials/EB/CNS/Source/Make.package commit 223a72761ba6401986fab28b491e132f374c1305 Author: Weiqun Zhang Date: Sat Aug 12 11:37:02 2017 -0700 EB/CNS: set up a simple test problem Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90 Tutorials/EB/CNS/Exec/Pulse/inputs Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_f.F90 Tutorials/EB/CNS/Source/CNS_physics.F90 commit 176e7474eb75e1fc2ffc6fac5e533ec548bfc456 Author: Weiqun Zhang Date: Fri Aug 11 21:48:24 2017 -0700 CNS/EB: derive Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_derive.F90 Tutorials/EB/CNS/Source/CNS_physics.F90 Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/EB/CNS/Source/Make.package commit 4594c4a793b248e931339cb01903fd7d1e3c57b7 Author: Weiqun Zhang Date: Fri Aug 11 21:16:31 2017 -0700 EB/CNS: add physics module Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_f.F90 Tutorials/EB/CNS/Source/CNS_physics.F90 Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/EB/CNS/Source/Make.package commit 00073ac0463c62c1362821d7244e7ebd9feeaef1 Author: Weiqun Zhang Date: Fri Aug 11 17:59:36 2017 -0700 set up statedata Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/EB/CNS/Source/Make.package Tutorials/EB/CNS/Source/bc_fill_nd.F90 commit 1e081cd94d9ed6fa4bded1ec780b479d0e49a1cf Author: Weiqun Zhang Date: Fri Aug 11 17:43:31 2017 -0700 EB/CNS: pass parameters to fortran Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_ParallelDescriptor.H Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNS_F.H Tutorials/EB/CNS/Source/CNS_f.F90 Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/EB/CNS/Source/Make.package commit 61e917f8f8e13fa8919bfe48fb8fb9104da33243 Author: Weiqun Zhang Date: Fri Aug 11 15:16:27 2017 -0700 skeleton for EB/CNS Tutorials/EB/CNS/Exec/Make.CNS Tutorials/EB/CNS/Exec/Pulse/GNUmakefile Tutorials/EB/CNS/Exec/Pulse/Make.package Tutorials/EB/CNS/Exec/Pulse/cns_prob.F90 Tutorials/EB/CNS/Source/CNS.H Tutorials/EB/CNS/Source/CNS.cpp Tutorials/EB/CNS/Source/CNSBld.cpp Tutorials/EB/CNS/Source/CNS_advance.cpp Tutorials/EB/CNS/Source/CNS_error.cpp Tutorials/EB/CNS/Source/CNS_io.cpp Tutorials/EB/CNS/Source/CNS_setup.cpp Tutorials/EB/CNS/Source/Make.package Tutorials/EB/CNS/Source/main.cpp commit 145a54f61eb3876e3ff4f5b944a7825b5d0f416d Author: Weiqun Zhang Date: Fri Aug 11 12:17:36 2017 -0700 remove old ones Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 commit 0c7584d9fdac8c2b8b9b1dd3a548910791dafd68 Author: Weiqun Zhang Date: Fri Aug 11 12:11:55 2017 -0700 move some eb fortran subrtoutines into new files Src/Base/AMReX_EBMultiFabUtil_2d.F90 Src/Base/AMReX_EBMultiFabUtil_3d.F90 Src/Base/Make.package commit b514f682dfe60f4d72d0767ad4b0dd05546bf6c7 Author: Weiqun Zhang Date: Fri Aug 11 09:55:46 2017 -0700 Face neighbors: this is known to be flawed, but check in before we have a better alternative Src/Base/AMReX_EBLevel.cpp commit a2587082ec6698ee37894fb8f9e6179efcfa2c25 Merge: 66d7d006d 3d673fd3b Author: Tan Nguyen Date: Thu Aug 10 22:30:13 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 66d7d006d4e2936c37c52a743d4a5e73e2aed338 Author: Tan Nguyen Date: Thu Aug 10 22:30:06 2017 -0700 add more routines to the runtime interface Src/AmrTask/arch.common Src/AmrTask/arch/arch.serial Src/AmrTask/graph/AMReX_AbstractTask.H Src/AmrTask/graph/AMReX_AbstractTask.cpp Src/AmrTask/graph/AMReX_DataTypes.H Src/AmrTask/graph/AMReX_TaskGraph.H Src/AmrTask/graph/Makefile Src/AmrTask/graph/RTS.H Src/AmrTask/rts_impls/Serial/Makefile Src/AmrTask/rts_impls/Serial/rts.C Src/AmrTask/rts_impls/Serial/rts_graphimpl.H Src/AmrTask/rts_impls/Serial/rts_taskimpl.H Src/AmrTask/tutorials/UnitTests/001_TokenRing.C Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C Src/AmrTask/tutorials/UnitTests/Makefile commit f3fc21dbdf16c233507c4685af5249ccb792b273 Author: Weiqun Zhang Date: Thu Aug 10 17:06:25 2017 -0700 wip: face neighbors Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp commit 05e0c4c0f42f15f76ffcfd646899cab4852ee04e Author: Weiqun Zhang Date: Wed Aug 9 15:54:21 2017 -0700 wip: add EBFaceFlagFab Src/Base/AMReX_EBCellFlag.H Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_EBFaceFlag.H Src/Base/AMReX_EBFaceFlag.cpp Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp Src/Base/Make.package commit 3d673fd3bbd92ed9d48b8ecef2c7b2cb0b349467 Author: kngott Date: Wed Aug 9 15:24:38 2017 -0700 Adding a count of MPI function calls to the timeline profiling option. Src/Extern/ProfParser/AMReX_CommProfStats.cpp Src/Extern/amrdata/AMReX_DataServices.cpp commit 8ac56811d87c1ffba6bb7583f1c0632118b725c4 Merge: 362e3e268 022b4f313 Author: WeiqunZhang Date: Wed Aug 9 09:49:43 2017 -0700 Merge pull request #89 from nncarlson/fix-char-kind Fix character kind declarations commit 022b4f31373872bf19d32fbbe4362702fa3ca8fd Author: Neil Carlson Date: Wed Aug 9 09:12:32 2017 -0600 Fix character kind declarations Src/Base/AMReX_error_mod.F90 Src/F_BaseLib/bl_random_f.f90 Src/F_BaseLib/multifab_c.f90 Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90 Src/F_Interfaces/Base/AMReX_init_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Src/F_Interfaces/Base/AMReX_plotfile_mod.F90 Tutorials/Amr/Advection_F/Source/my_amr_mod.F90 Tutorials/Amr/Advection_F/Source/tagging_mod.F90 Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90 Tutorials/Amr/Advection_octree_F/Source/tagging_mod.F90 commit 362e3e268584a655360f91622a9d749df7fbd28f Author: Tan Nguyen Date: Wed Aug 9 00:01:46 2017 -0700 update jacobi test code Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C commit c7274253918a8d355bce473399f7d34c90093c6d Merge: 43b82d086 8653fce9f Author: vince Date: Tue Aug 8 18:02:54 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 43b82d0865019d4de184fb3cc2fd2f727b460705 Author: vince Date: Tue Aug 8 18:02:48 2017 -0700 some fixes for profiling data. Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp commit 756f0ff92c69d1e3ada6212dd7a4b7f6c70df3da Author: Weiqun Zhang Date: Tue Aug 8 13:20:53 2017 -0700 renaming some functions Src/AmrCore/AMReX_ebinterp_1d.F90 Src/AmrCore/AMReX_ebinterp_2d.F90 Src/AmrCore/AMReX_ebinterp_3d.F90 Src/Base/AMReX_EBMultiFabUtil_nd.F90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_ebcellflag_mod.F90 commit 4d0ef81c16e5ee24d367f323f3538a65b056a85e Author: Weiqun Zhang Date: Tue Aug 8 13:05:02 2017 -0700 EBFlagFab --> EBCellFlagFab Src/AmrCore/AMReX_EBInterpolater.cpp Src/Base/AMReX_EBCellFlag.H Src/Base/AMReX_EBCellFlag.cpp Src/Base/AMReX_EBFArrayBox.H Src/Base/AMReX_EBFArrayBox.cpp Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp Src/Base/AMReX_EBMultiFabUtil.cpp commit 9223f61c6b6b426177ac694db3aa72053d0916ee Merge: 6f710fc98 4c0d08c5d Author: Weiqun Zhang Date: Tue Aug 8 12:37:29 2017 -0700 Merge branch 'eb_development' into weiqun/eb commit 4c0d08c5dde7d67c784ac4eb7d667cb87bdfaa8f Merge: a09138202 919e8122a Author: Weiqun Zhang Date: Tue Aug 8 12:37:10 2017 -0700 Merge branch 'dtg_branch' into eb_development commit 919e8122af719ba3d015ed02fb8e4149a42daa25 Author: dtgraves Date: Tue Aug 8 12:25:43 2017 -0700 bug fix in FlatPlate Src/GeometryShop/AMReX_FlatPlateGeom.cpp commit 6f710fc985bf05596a4c0a09ef5e332d69e04eae Author: Weiqun Zhang Date: Tue Aug 8 10:03:10 2017 -0700 some pure --> elemental Src/Base/AMReX_ebcellflag_mod.F90 commit 7fa92f068183a0b23237edef00ef3dd67efb097e Author: Weiqun Zhang Date: Tue Aug 8 10:00:59 2017 -0700 fillpatch now works for single-valued cells when eb is close to coarse/fine boundary Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_EBInterp_f.H Src/AmrCore/AMReX_EBInterpolater.cpp Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_ebinterp_1d.F90 Src/AmrCore/AMReX_ebinterp_2d.F90 Src/AmrCore/AMReX_ebinterp_3d.F90 Src/AmrCore/Make.package Src/Base/AMReX_EBMultiFabUtil.H Src/Base/AMReX_EBMultiFabUtil.cpp Src/Base/AMReX_ebcellflag_mod.F90 commit 8653fce9f3f2446cd6c2eb2a0204a053354c3ffe Merge: 6cb027c88 7fd4feb41 Author: dtgraves Date: Mon Aug 7 19:00:05 2017 -0700 Merge pull request #88 from AMReX-Codes/dtg_branch merging to development to get bug fix over commit 7fd4feb4107fd76070bf5fbacb879752d9fc94aa Author: dtgraves Date: Mon Aug 7 18:57:15 2017 -0700 tweak to Polygeom to try to satisfy valgrind Src/GeometryShop/AMReX_PolyGeom.cpp commit 2f5d8cf89a384713ee6ddc19dd231501bd980c45 Author: dtgraves Date: Mon Aug 7 18:55:35 2017 -0700 bug fix to divergence op Src/EBAMRTools/AMReX_DivergenceOp.cpp commit 6cb027c88c1e151e8532b485df8cc4dc9e3cd599 Author: Tan Nguyen Date: Mon Aug 7 15:22:21 2017 -0700 task graph prototype Src/AmrTask/Makefile Src/AmrTask/arch.common Src/AmrTask/arch/arch.serial Src/AmrTask/graph/AMReX_AbstractTask.H Src/AmrTask/graph/AMReX_AbstractTask.cpp Src/AmrTask/graph/AMReX_Affinity.H Src/AmrTask/graph/AMReX_Affinity.cpp Src/AmrTask/graph/AMReX_AsyncMFIter.H Src/AmrTask/graph/AMReX_AsyncMFIter.cpp Src/AmrTask/graph/AMReX_DataTypes.H Src/AmrTask/graph/AMReX_TaskGraph.H Src/AmrTask/graph/AMReX_TaskGraph.cpp Src/AmrTask/graph/AMReX_WorkerThread.H Src/AmrTask/graph/AMReX_WorkerThread.cpp Src/AmrTask/graph/Makefile Src/AmrTask/graph/RTS.H Src/AmrTask/make_defaults/Cori Src/AmrTask/make_defaults/Edison Src/AmrTask/make_defaults/Summit-dev Src/AmrTask/rts_impls/README Src/AmrTask/rts_impls/Serial/Makefile Src/AmrTask/rts_impls/Serial/rts.C Src/AmrTask/tutorials/AMReXApps/3DJacobi/3DJacobi.C Src/AmrTask/tutorials/AMReXApps/3DJacobi/Makefile Src/AmrTask/tutorials/UnitTests/001_TokenRing.C Src/AmrTask/tutorials/UnitTests/002_Jacobi_StaticGraph.C Src/AmrTask/tutorials/UnitTests/003_Jacobi_DynamicGraph.C Src/AmrTask/tutorials/UnitTests/Makefile commit d2600e475b7a63a092526d04aa3d3322ca47eba0 Author: Weiqun Zhang Date: Mon Aug 7 14:27:59 2017 -0700 add EBInterpolater stub Src/Amr/AMReX_AmrLevel.H Src/AmrCore/AMReX_EBInterpolater.H Src/AmrCore/AMReX_EBInterpolater.cpp Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/Make.package commit 20d2b33b09e8ace7d82292b4b3e214c1a9b500f9 Author: Weiqun Zhang Date: Mon Aug 7 13:41:09 2017 -0700 fix graph walking Src/Base/AMReX_EBLevel.cpp commit 9a4a65f6d8cd92f51a993daa5834f1532ae58334 Author: Weiqun Zhang Date: Mon Aug 7 13:14:29 2017 -0700 fix dangling pointer/reference due to return-by-value in some EB data structure Src/Base/AMReX_EBFArrayBox.H Src/Base/AMReX_EBFArrayBox.cpp Src/Base/AMReX_EBFabFactory.H Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp Src/Base/AMReX_EBMultiFabUtil.cpp commit 5aecc3a407189973bcbc2db3629f20475131fc27 Author: Weiqun Zhang Date: Mon Aug 7 12:35:23 2017 -0700 add more access functions Src/Base/AMReX_EBFArrayBox.H Src/Base/AMReX_EBFArrayBox.cpp Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp Src/Base/AMReX_EBMultiFabUtil.cpp Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_MultiFab.H commit d24d8c29a24984473d34a3c6687296ef1633ccc3 Merge: a2442addb a09138202 Author: Weiqun Zhang Date: Mon Aug 7 11:05:48 2017 -0700 Merge branch 'eb_development' into weiqun/eb commit a091382021f733e43dcf4bfe52102e1a9979e699 Merge: d48468624 c99c19733 Author: Weiqun Zhang Date: Mon Aug 7 11:04:49 2017 -0700 Merge branch 'development' into eb_development commit c99c19733a5fb0132301c23981c4d2d2c35f6b75 Merge: abf80ea38 fdea11e20 Author: WeiqunZhang Date: Mon Aug 7 11:03:09 2017 -0700 Merge pull request #87 from nncarlson/add-nag [WIP] Add GNUmakefile support for the NAG Fortran compiler commit abf80ea38af7107b903236e9f5d787068670ec70 Author: Weiqun Zhang Date: Mon Aug 7 10:47:36 2017 -0700 move Tests/LinearSovlver/F_MG to boxlib test list Tools/CompileTesting/compiletesting.py commit 1b159b00b25337f55255be63285551af2e457e03 Author: Weiqun Zhang Date: Mon Aug 7 10:38:33 2017 -0700 update compiletesting.py Tools/CompileTesting/compiletesting.py commit a879ae78c006927f09e5cdad0e87a8f4f4177b16 Merge: 72c57aa9d 26c5f67d7 Author: WeiqunZhang Date: Mon Aug 7 10:13:21 2017 -0700 Merge pull request #76 from akreienbuehl/clrdDiffuSolve clrdDiffuSolve commit 72c57aa9dd355ee98810e5223f60edc79e859739 Author: Weiqun Zhang Date: Mon Aug 7 10:12:47 2017 -0700 fix compilation of a test OldTutorials/MultiFabTests_C/GNUmakefile commit 8d186422b98469176008fc8427416f456973c21e Author: Weiqun Zhang Date: Mon Aug 7 09:58:10 2017 -0700 update compiletesting.py Tools/CompileTesting/compiletesting.py commit a2442addb45aa4ef8d38c69a141d0f50433a98da Author: Weiqun Zhang Date: Mon Aug 7 09:43:35 2017 -0700 save pointers to ebflag fab in EbFArrayBox Src/Base/AMReX_EBFArrayBox.H Src/Base/AMReX_EBFArrayBox.cpp commit fdea11e2051e42c3843fad1267a9057d172395bc Author: Neil Carlson Date: Sun Aug 6 08:45:04 2017 -0600 Add GNUmakefile support for the NAG Fortran compiler Tools/GNUMake/Make.defs Tools/GNUMake/comps/nag.mak Tools/libamrex/configure.py Tools/libamrex/mkconfig.py commit 26c5f67d71b0c4a44f4129cc830e30da61771b70 Merge: ab9d64d60 dfaae4abe Author: Andreas Kreienbuehl Date: Sun Aug 6 12:36:36 2017 -0700 Merge branch 'clrdDiffuSolve' of https://github.com/akreienbuehl/amrex into clrdDiffuSolve commit ab9d64d60d1e081801eb59e7eedfdbc86be08faf Author: Andreas Kreienbuehl Date: Sun Aug 6 12:35:54 2017 -0700 Introduced variable `m_clr_map` along the lines of `m_nCommColors` Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit 7edd25cf549471edf8cf2384518ec81ce11064e0 Merge: 48ea7d2e9 5d605df43 Author: Andreas Kreienbuehl Date: Sun Aug 6 09:36:40 2017 -0700 Merge branch 'development' into clrdDiffuSolve commit db97af3ae08c082a874f6f9b52d24916bd550e36 Author: Max Katz Date: Sat Aug 5 19:23:59 2017 -0400 Add a new wrapper around Device functions Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/Base/AMReX.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_BArena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabFactory.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_MFIter.cpp Src/Base/Make.package Tools/GNUMake/Make.defs commit 39a93a8abc70f32d004d2dfa9d52759687a2bd78 Merge: b018eeedd c4f6b5569 Author: Max Katz Date: Sat Aug 5 18:00:19 2017 -0400 Merge branch 'development' into gpu Conflicts: Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Tools/GNUMake/Make.defs commit b018eeedd0511119c4c60a866982cfa6419eecc5 Author: Max Katz Date: Sat Aug 5 17:48:49 2017 -0400 Replace CUDA macro with AMREX_USE_CUDA Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp Src/Base/AMReX_filcc_mod.F90 Src/Base/AMReX_fort_mod.F90 Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/ManagedCUDADeposition/MyParticleContainer.cpp Tools/GNUMake/Make.defs Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 commit 0227b62c2e876f1a355687dab74f1b7caa11acaf Author: dtgraves Date: Fri Aug 4 19:11:38 2017 -0700 my tweak to the make system that should never be pushed Tools/GNUMake/comps/gnu.mak commit 5d605df438b019a1e41bb75740021d0a9cc23d69 Merge: effc069c2 3732407d0 Author: Ann Almgren Date: Fri Aug 4 18:55:14 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 4c1f2fde1e6f40e1c5fef023214b826a401f32fc Author: Marc Day Date: Fri Aug 4 18:31:28 2017 -0700 Add back changes to EB fortran in divflux...lost in merge conflict resolution Src/EBAMRTools/AMReX_EBFortND.F90 commit b61f10671a9e6734ac3bffa8cee26ca23660e380 Merge: 7666536e0 d48468624 Author: Marc Day Date: Fri Aug 4 18:22:18 2017 -0700 Merge branch 'eb_development' into weiqun/eb commit d48468624bba28fc86431d4612a248bf3ed7c58e Author: Marc Day Date: Fri Aug 4 18:21:24 2017 -0700 Undo adding of declaration...sorting out multiple merges Src/EBAMRTools/AMReX_EBFortND.F90 commit f7bfd8ef74b9556f5d06a9fe04062681974e55f5 Merge: ae63c4b73 c68eb5882 Author: Marc Day Date: Fri Aug 4 18:14:43 2017 -0700 Conflict resolution with dtg_branch commit 7666536e0cca43c7bbcdac74ef76739d31179e90 Merge: 5fc982dc6 ae63c4b73 Author: Marc Day Date: Fri Aug 4 18:03:50 2017 -0700 Merge branch 'eb_development' into weiqun/eb commit ae63c4b73a9db144957aa46e4ce85ef794270552 Author: Marc Day Date: Fri Aug 4 18:02:30 2017 -0700 Add declaration for flag Src/EBAMRTools/AMReX_EBFortND.F90 commit 5fc982dc66edb15e1814a0b17c4217e3d93915a8 Merge: 2f463ba74 d709627fd Author: Weiqun Zhang Date: Fri Aug 4 17:45:03 2017 -0700 Merge branch 'eb_development' into weiqun/eb Conflicts: Src/EBAMRTools/AMReX_EBFortND.F90 commit d709627fda4a1cef7ae34e07f2950824937f5604 Author: Marc Day Date: Fri Aug 4 17:08:21 2017 -0700 resolve conflicts Src/EBAMRTools/AMReX_EBFortND.F90 commit 2f463ba74c71f4b4313592272d9055a03fdb0d75 Author: Weiqun Zhang Date: Fri Aug 4 17:12:43 2017 -0700 fix 3d avgdown Src/Base/AMReX_EBMultiFabUtil.cpp commit 0f4be437d1ca74afb6a3545b17c0ff8c2672f2b4 Author: Weiqun Zhang Date: Fri Aug 4 17:01:15 2017 -0700 missed an enddo Src/Base/AMReX_MultiFabUtil_3d.f90 commit 00e7b0634a5412b6d1ebf01360b9d07c09450294 Author: Weiqun Zhang Date: Fri Aug 4 16:59:59 2017 -0700 finish eb average down Src/Base/AMReX_EBMultiFabUtil.H Src/Base/AMReX_EBMultiFabUtil.cpp Src/Base/AMReX_EBMultiFabUtil_F.H Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 commit 97c52f4d7f3e9696ad635079dada6500597d58b5 Author: vince Date: Fri Aug 4 16:16:16 2017 -0700 fix comment. Src/Base/AMReX_Utility.H commit 363aaa698288ff38dcee6c3f979e5d6ce6223ee2 Author: vince Date: Fri Aug 4 16:00:10 2017 -0700 removed old files. Src/Extern/ProfParser/backup/AMReX_AVGDOWN_2D.F Src/Extern/ProfParser/backup/AMReX_AVGDOWN_3D.F Src/Extern/ProfParser/backup/AMReX_AVGDOWN_F.H Src/Extern/ProfParser/backup/AMReX_BLProfStats.H Src/Extern/ProfParser/backup/AMReX_BLProfStats.cpp Src/Extern/ProfParser/backup/AMReX_BLProfUtilities.cpp Src/Extern/ProfParser/backup/AMReX_BLWritePlotFile.H Src/Extern/ProfParser/backup/AMReX_BLWritePlotFile.cpp Src/Extern/ProfParser/backup/AMReX_CommProfStats.H Src/Extern/ProfParser/backup/AMReX_CommProfStats.cpp Src/Extern/ProfParser/backup/AMReX_RegionsProfStats.H Src/Extern/ProfParser/backup/AMReX_RegionsProfStats.cpp Src/Extern/ProfParser/backup/AMReX_XYPlotDataList.H Src/Extern/ProfParser/backup/AMReX_XYPlotDataList.cpp Src/Extern/ProfParser/backup/BLProfParser.l Src/Extern/ProfParser/backup/BLProfParser.y Src/Extern/ProfParser/backup/Make.package commit c848ed9eff948ab175969ad2f7da9c6ada4edffb Merge: 94ca2035b 3732407d0 Author: vince Date: Fri Aug 4 15:52:45 2017 -0700 Merge branch 'development' into profvisDS commit 94ca2035bd0854142f7067bfab148a302a8e7d2b Merge: 3fbf880df 75319b34b Author: vince Date: Fri Aug 4 15:44:19 2017 -0700 sync with original code. commit c68eb588202b2ae53193cd6edfc27f0faa7e7a50 Author: dtgraves Date: Fri Aug 4 15:08:57 2017 -0700 added sphere option to redistribution test Tests/GeometryShop/regression/levelRedistTest.cpp Tests/GeometryShop/regression/levelredist.inputs commit af19c754bbfa000f688c9daedae63a30cd4bc523 Author: Michele Rosso Date: Fri Aug 4 14:51:07 2017 -0700 CMake: update docs. Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Tools/CMake/AMReX_Options.cmake commit 18282ec6c70a34b44a5df6f2cf7b79cf75b5f1de Author: Weiqun Zhang Date: Fri Aug 4 14:13:03 2017 -0700 finish EB_set_volume_fraction Src/Base/AMReX_BaseFab.H Src/Base/AMReX_EBCellFlag.cpp Src/Base/AMReX_EBLevel.cpp Src/Base/AMReX_EBMultiFabUtil.cpp Src/Base/AMReX_FabFactory.H commit 2fb0ac97f3d699f3e8907ad6ea55b7fee98a9bce Author: Weiqun Zhang Date: Fri Aug 4 13:44:05 2017 -0700 fix regular average_down Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_MultiFabUtil.cpp commit ab0a69e7e8c8a15a89ab1ffe52ee751b85cdc3e7 Author: Weiqun Zhang Date: Fri Aug 4 13:26:23 2017 -0700 EBFArrayBox can now get type info from EBLevel Src/Base/AMReX_EBFArrayBox.H Src/Base/AMReX_EBFArrayBox.cpp Src/Base/AMReX_EBFabFactory.cpp commit ebe88e49d7b9da15bb3cef72fc4208bdb468c291 Author: Weiqun Zhang Date: Fri Aug 4 13:09:59 2017 -0700 EBLevel: add FabType Src/Base/AMReX_EBCellFlag.H Src/Base/AMReX_EBCellFlag.cpp Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FabFactory.H commit 86c530542f1df6ab747ad11bc2f6be12169a634c Merge: 34cbe97f3 5d1ea017f Author: Weiqun Zhang Date: Fri Aug 4 12:32:24 2017 -0700 Merge branch 'eb_development' into weiqun/eb Conflicts: Src/EBAMRTools/AMReX_DivergenceOp.cpp commit 5d1ea017fc8a450f493af94bbd6235de256b2085 Author: Marc Day Date: Fri Aug 4 12:17:28 2017 -0700 Fix a couple bugs resulting from me not correctly specifying Dans jobs...my bad. Conflicts: Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_DivergenceOp.cpp commit 2664269f6e1f3878a3e4aac085ac3c883e0ab09c Author: Michele Rosso Date: Fri Aug 4 12:16:49 2017 -0700 CMake: fix defines for comm-profiling Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake commit 34cbe97f3c0041ea30b5475e13949b5c73c02d3a Author: Weiqun Zhang Date: Fri Aug 4 11:27:19 2017 -0700 add armrex::EB_set_volume_fraction stub Src/Base/AMReX_EBMultiFabUtil.H Src/Base/AMReX_EBMultiFabUtil.cpp commit 7b39b854e354e6c08c8ac1db4b94ba6f5b94e9ae Merge: 9b22f0b80 3732407d0 Author: Michele Rosso Date: Fri Aug 4 11:13:08 2017 -0700 Merge branch 'development' into mr-cmake commit 3e1ffc3e92ce8844d951f73793c4631cd1b04e89 Author: Weiqun Zhang Date: Fri Aug 4 10:56:18 2017 -0700 fix BoxIterator for empty box Src/Base/AMReX_BoxIterator.cpp commit 3732407d02da8750a45dca8d5877319295897d77 Author: Weiqun Zhang Date: Fri Aug 4 10:17:58 2017 -0700 Fortran: boxarray%maxsize now has three versions: single integer size, three integers and an integer array of size 3 Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 commit 367216b2eb38380bd009f6d09b9042dce7c19a40 Author: Weiqun Zhang Date: Thu Aug 3 22:17:54 2017 -0700 fix include hell Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabFactory.H commit effc069c20dbe482fb53f18c30ee0dc505307102 Merge: 052367c3d 5d5544b09 Author: Ann Almgren Date: Thu Aug 3 18:31:48 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 5d5544b090a8999df0acfcffa62fc7d8370b8e1b Author: Michael Zingale Date: Thu Aug 3 20:47:06 2017 -0400 more git error control sometimes if the repo is dirty or a branch doesn't exist the checkout of the branch can silently fail Tools/RegressionTesting/repo.py commit 9b22f0b805cfd49ff93d53b1fd33d2230ba8dc96 Author: Michele Rosso Date: Thu Aug 3 17:34:11 2017 -0700 CMake: add support for trace and comm profiling Src/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit d0a38efaf681e667cf695d9224d311ebe10d33cb Author: Weiqun Zhang Date: Thu Aug 3 17:06:37 2017 -0700 use fortran to set covered cells to min vals Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp Src/Base/AMReX_EBMultiFabUtil.cpp Src/Base/AMReX_EBMultiFabUtil_F.H Src/Base/AMReX_EBMultiFabUtil_nd.F90 Src/Base/Make.package commit 6aa474521246c73ec01c15aaa90f7e7868d2a002 Author: Michele Rosso Date: Thu Aug 3 16:46:22 2017 -0700 CMake: fix typo Src/CMakeLists.txt commit 12f7d8679ddb3750510b9de27fa2eb41f86e2492 Author: Michele Rosso Date: Thu Aug 3 16:08:17 2017 -0700 CMake: enable user to turn on/off AMReX components Src/CMakeLists.txt Src/LinearSolvers/CMakeLists.txt Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit c50e086bd9616a716bcbaefad27ab810aa452d7a Author: Weiqun Zhang Date: Thu Aug 3 15:55:16 2017 -0700 need this for pgi compiler Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90 commit 494bd12310471c06b522ea4bff05b061362ea8f6 Author: Weiqun Zhang Date: Thu Aug 3 15:47:33 2017 -0700 save a copy of EBLevel in EBFabFactory, which is in turn stored in MultiFab Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_EBFabFactory.H Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp Src/Base/AMReX_EBMultiFabUtil.cpp Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_FabFactory.H Src/Base/AMReX_MultiFab.H Src/Base/Make.package Src/GeometryShop/AMReX_IrregFABFactory.H Src/GeometryShop/AMReX_IrregFABFactory.cpp Src/GeometryShop/AMReX_LayoutData.H commit ebb6a7fd7acedd9ed1390ffc147ab76f0732a3e9 Author: dtgraves Date: Thu Aug 3 15:08:34 2017 -0700 got the conductivity solver to run to completion. still wrong. back to writing documents. Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/GeometryShop/AMReX_EBArith.cpp Tests/EBAMRElliptic/exec/cond.inputs Tests/EBAMRElliptic/exec/conductivitySolve.cpp commit 1b5cf62be4245770ddddc53a15da598e026ba6d1 Author: Michele Rosso Date: Thu Aug 3 14:47:39 2017 -0700 CMake: fix minor bugs Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake commit 9a2888d84f96ad88eacc8961c66e7ad684287630 Author: Weiqun Zhang Date: Thu Aug 3 14:21:26 2017 -0700 fix c_real in mempool module Src/Base/AMReX_fort_mod.F90 Src/Base/AMReX_mempool_f.f90 Src/F_BaseLib/GPackage.mak Src/F_BaseLib/amrex_fort_mod.f90 commit cb9d60a3e517e3a5b399992de0414e4303784c7a Author: Ondřej Čertík Date: Thu Aug 3 13:43:40 2017 -0600 Compare real kinds directly In order to determine if the real kinds are equal, one can just compare them directly, they are just integers. This is simpler, and also allows these lines to be compiled with NAG. For some reason NAG does not seem to have `c_sizeof()` as part of the `iso_c_binding` module and so it fails on these lines. This commit fixes it. Src/F_Interfaces/Base/AMReX_parallel_mod.F90 commit 7e8d0237e998f7a2252ef4bee3fb548da38b7e46 Merge: c025a3f87 a6d9aeea7 Author: WeiqunZhang Date: Thu Aug 3 13:22:34 2017 -0700 Merge pull request #80 from certik/size_of_fix Compare real kinds directly commit a6d9aeea7d93a9b7253490e6ff2045281e79ac74 Author: Ondřej Čertík Date: Thu Aug 3 13:43:40 2017 -0600 Compare real kinds directly In order to determine if the real kinds are equal, one can just compare them directly, they are just integers. This is simpler, and also allows these lines to be compiled with NAG. For some reason NAG does not seem to have `c_sizeof()` as part of the `iso_c_binding` module and so it fails on these lines. This commit fixes it. Src/F_Interfaces/Base/AMReX_parallel_mod.F90 commit 8fa1902cddf2193161d29bbf36de2af1b0f4938c Author: Weiqun Zhang Date: Thu Aug 3 11:42:23 2017 -0700 have to intersect with the domain because there is no eb information outside the domain Src/Base/AMReX_EBLevel.cpp commit ad1b544d6532a37d0a55bffcf9318cb6eee008f9 Author: Weiqun Zhang Date: Thu Aug 3 11:28:37 2017 -0700 add Fortran module for ebcellflag Src/Base/AMReX_ebcellflag_mod.F90 Src/Base/Make.package commit 443cd53e9071b3fe9506367c91a86c15cc01827e Author: Weiqun Zhang Date: Thu Aug 3 10:43:56 2017 -0700 set and get number of VoFs Src/Base/AMReX_EBCellFlag.H Src/Base/AMReX_EBLevel.cpp commit e102f53a50b50d949750de9ee36fdf8333492138 Author: Weiqun Zhang Date: Thu Aug 3 09:46:04 2017 -0700 reserve 3 bits for number of multi-valued cells and clean up CellFlag Src/Base/AMReX_EBCellFlag.H Src/Base/AMReX_EBCellFlag.cpp commit dfaae4abe08b015e290514117fb552f320023a09 Merge: 48ea7d2e9 f99cf23f7 Author: Andreas Kreienbuehl Date: Thu Aug 3 08:35:23 2017 -0700 Merge branch 'development' into clrdDiffuSolve commit 31524e96619fc4ac981478e38a3042f9bd40b659 Merge: 2e92a6c52 f99cf23f7 Author: dtgraves Date: Wed Aug 2 20:35:46 2017 -0700 Merge pull request #78 from AMReX-Codes/development trying to get bug fixes for DivergenceOp into weiqun/eb branch commit f99cf23f7d50f887f8ea6b9edf27a1598fb2d583 Merge: f589449f1 ccfa1d80e Author: dtgraves Date: Wed Aug 2 20:31:42 2017 -0700 Merge pull request #77 from AMReX-Codes/dtg_branch getting some bug fixes over to development branch commit 2e92a6c52bd15ea82ac3364c2da5adb5ca887e6e Author: Weiqun Zhang Date: Wed Aug 2 17:36:23 2017 -0700 finish setting up EBCellFlag in C++ Src/Base/AMReX_EBCellFlag.H Src/Base/AMReX_EBCellFlag.cpp Src/Base/AMReX_EBLevel.cpp Src/Base/Make.package commit bff4b948a24444244483b92d08c8e9f85fa6f6b5 Author: Weiqun Zhang Date: Wed Aug 2 14:25:47 2017 -0700 wip because pge is cutting power Src/Base/AMReX_EBCellFlag.H Src/Base/AMReX_EBLevel.cpp commit f589449f1996e2f7c05c4a420fd922eaff7b71c3 Merge: 4b42fea04 75319b34b Author: Michael Zingale Date: Wed Aug 2 17:06:36 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/AMReX into development commit 4b42fea043552232e706657398f9ac1ce23d151a Author: Michael Zingale Date: Wed Aug 2 17:06:18 2017 -0400 fix compilation + add a DO_ALL macro Tools/Postprocessing/F_Src/GNUmakefile Tools/Postprocessing/F_Src/fdump.f90 commit 130bfc28fcc98fc54304a63e1a3dc8f5f9a30df7 Author: Weiqun Zhang Date: Wed Aug 2 10:20:18 2017 -0700 start EBLevel and EBCellFlag Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Base/AMReX_EBCellFlag.H Src/Base/AMReX_EBLevel.H Src/Base/AMReX_EBLevel.cpp Src/Base/Make.package commit 052367c3dded30e5a9b3502debbc26656a413689 Merge: ddab51fb3 75319b34b Author: Ann Almgren Date: Wed Aug 2 09:47:51 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 48ea7d2e9cad6aceda5049f7c78f03ee117606c8 Merge: 5c3202b3d 75319b34b Author: Andreas Kreienbuehl Date: Wed Aug 2 09:36:07 2017 -0700 Merge branch 'development' into clrdDiffuSolve commit 20590773752dbb0a2ab2e2ffb3080b5d921ff279 Merge: 4f6bf67f6 75319b34b Author: Weiqun Zhang Date: Wed Aug 2 09:24:53 2017 -0700 Merge branch 'development' into eb_development commit 75319b34b8179736028ce11442f7a047efb8e000 Author: Ann Almgren Date: Tue Aug 1 17:48:30 2017 -0700 Need an option for mvapich (cooley.alcf.anl.go) as well in Make.unknown Tools/GNUMake/sites/Make.unknown commit c025a3f87be89e727c2f7df12780fd85b65c32b8 Author: Ann Almgren Date: Tue Aug 1 17:48:30 2017 -0700 Need an option for mvapich (cooley.alcf.anl.go) as well in Make.unknown Tools/GNUMake/sites/Make.unknown commit ddab51fb3dd658b1cd129002733ac7a2c5269ca1 Merge: 3d3f9d0a0 d28bcc47f Author: Ann Almgren Date: Tue Aug 1 17:48:55 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 3d3f9d0a042f9643cea44761c9767e5bf98b0869 Author: Ann Almgren Date: Tue Aug 1 17:48:30 2017 -0700 Need an option for mvapich (cooley.alcf.anl.go) as well in Make.unknown Tools/GNUMake/sites/Make.unknown commit d28bcc47f45ec12e6471c4a6945fdf2fde0c1042 Merge: d94c33e96 6a102876a Author: Michele Rosso Date: Tue Aug 1 17:12:35 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d94c33e96eec637c25615466e035d54b05ce5bb8 Author: Michele Rosso Date: Tue Aug 1 17:12:24 2017 -0700 CMake: update exported info Tools/CMake/AMReXConfig.cmake.in commit 6a102876aa255739f3220d3dfd9071dea86f3ca1 Author: Ann Almgren Date: Tue Aug 1 16:54:56 2017 -0700 Fix AMReX_HOME -- one more directory down Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile commit e932a4a9805e7bb9b8aba5ee117494d275c57bf1 Author: Ann Almgren Date: Tue Aug 1 16:54:25 2017 -0700 Fix AMREX_HOME -- one more directory down Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/GNUmakefile commit 4f6bf67f61def5d5c8f8d43b1131125660354855 Author: Weiqun Zhang Date: Tue Aug 1 16:53:24 2017 -0700 update fillpatch for eb Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 63e3cdfafbef53a84c1bdf73544bc0dbbf4048f5 Author: Michele Rosso Date: Tue Aug 1 16:38:47 2017 -0700 CMake: make assertions opt-in Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit ccfa1d80e37f1ae8e59e523b5ab2ef2e9557274c Author: dtgraves Date: Tue Aug 1 16:20:56 2017 -0700 EBAMRElliptic's big redesign of Chombo's elliptic stuff now compiles Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.cpp Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRElliptic/AMReX_EBSimpleSolver.H Src/EBAMRElliptic/AMReX_EBSimpleSolver.cpp Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.H Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.cpp Src/EBAMRElliptic/AMReX_VCAggStencil.cpp Src/EBAMRElliptic/Make.package Tests/EBAMRElliptic/exec/cond.inputs Tests/EBAMRElliptic/exec/conductivitySolve.cpp commit 74992e8c940f96ed491e3025be4fe772fea6fbc1 Author: Michael Zingale Date: Tue Aug 1 18:51:09 2017 -0400 make this work with python3 Tools/Py_util/plotsinglevar.py commit 5f60696fe488f52c19fad6f28d0247be03d185ee Author: Andrew Myers Date: Tue Aug 1 14:41:53 2017 -0700 threading the buildNeighborList method. Src/Particle/AMReX_NeighborParticlesI.H commit 5c3202b3d090149c8ece6492e93320c715e6aac4 Merge: 9c42c5323 758def051 Author: Andreas Kreienbuehl Date: Tue Aug 1 13:27:54 2017 -0700 Merge branch 'clrdDiffuSolve' of https://github.com/akreienbuehl/amrex into clrdDiffuSolve commit 9c42c5323eea92b76292b43cc2963a063077e045 Merge: 020293e55 b7d2ce7cf Author: Andreas Kreienbuehl Date: Tue Aug 1 13:27:15 2017 -0700 Merge branch 'development' into clrdDiffuSolve commit 6ff0fd158c9aca47aba4d91def891c274d815c05 Merge: fc1bec417 ec561e2ee Author: Weiqun Zhang Date: Tue Aug 1 13:12:00 2017 -0700 Merge branch 'weiqun/eb' into eb_development commit ec561e2eec0c8c80143bd2ae10f126e77af3c467 Author: Weiqun Zhang Date: Tue Aug 1 13:00:06 2017 -0700 use factory member variable Src/Base/AMReX_FabArray.H commit 46982ba3cb7168c4b3e859e77bce8fae2815f49d Author: Weiqun Zhang Date: Tue Aug 1 12:17:32 2017 -0700 fix FabType for nodal EBFArrayBox Src/Base/AMReX_EBFArrayBox.cpp commit c6f68547201b2cedea3133ab1bef85b4a2e30ca1 Author: Weiqun Zhang Date: Tue Aug 1 12:14:09 2017 -0700 add a strict mode in which one must pass factory to FabArray constructor Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AuxBoundaryData.cpp Src/Amr/AMReX_Extrapolater.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp Src/Boundary/AMReX_FabSet.cpp Src/Boundary/AMReX_MultiMask.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_FabArrayIO.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Tools/GNUMake/Make.defs commit fc1bec4177cb47b23d699192362f97c0beb2ebcc Merge: 5e157280d 285575501 Author: Marc Day Date: Tue Aug 1 11:27:21 2017 -0700 Merge branch 'vof-work' into eb_development commit 285575501e836d722b2e26bc38d6941f799fa50d Author: Marc Day Date: Tue Aug 1 11:25:43 2017 -0700 Pass the stencil box to further clean fort code Tests/GeometryShop/vofStructures/nbrsTest.cpp Tests/GeometryShop/vofStructures/nbrsTest_nd.f90 commit 0f5071942771efd8f875547c4a09439ef1b63c9e Author: Marc Day Date: Tue Aug 1 11:16:03 2017 -0700 Use better macros, clean resulting code Tests/GeometryShop/vofStructures/nbrsTest.cpp Tests/GeometryShop/vofStructures/nbrsTest_nd.f90 commit 5e157280dc4d1f9a3754690593a13d8e19ffe103 Merge: fb0cae213 b7d2ce7cf Author: Weiqun Zhang Date: Tue Aug 1 10:00:28 2017 -0700 Merge branch 'development' into weiqun/eb commit b7d2ce7cf584c5739dd0ee515c799fd9a40a722d Merge: 3724a070a 978ebb925 Author: Weiqun Zhang Date: Tue Aug 1 09:52:12 2017 -0700 Merge branch 'development' Conflicts: Tools/CMake/AMReX_Config.cmake commit 19c65dd5233eb69b31c24598419323741c6e13bc Author: Marc Day Date: Mon Jul 31 19:42:40 2017 -0700 Add a test code to make a simple redistribution stencil and apply it. Needs more generalization, but it shows one method of passing such data to fortran. Tests/GeometryShop/vofStructures/AMReX_EBRedist.H Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/nbrsTest.cpp Tests/GeometryShop/vofStructures/nbrsTest_mod.F90 Tests/GeometryShop/vofStructures/nbrsTest_nd.f90 commit fb0cae213ad0ed4b60c5dece0cb4fa7440b40d2d Author: Weiqun Zhang Date: Mon Jul 31 17:57:22 2017 -0700 AmrLevel: new MultiFabs should be built with factory member Src/Amr/AMReX_AmrLevel.cpp commit 28140af6b87d62ee46f41744a877fec8083e50e9 Author: Weiqun Zhang Date: Mon Jul 31 17:46:28 2017 -0700 store a copy of eb factory in AmrLevel Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp commit a0acc552295643bca48305d5fa8bba210efa8241 Author: Weiqun Zhang Date: Mon Jul 31 17:00:55 2017 -0700 because we don't have geometry information outside domain Src/Base/AMReX_EBFArrayBox.cpp commit 9437a62cc649bd98adb74212fdc5cc526af5e779 Merge: 236b0f753 7cfc8859b Author: Marc Day Date: Mon Jul 31 16:46:38 2017 -0700 Merge branch 'dtg_branch' into vof-work commit 37808a93d6e7715244f41000f06d8fe4eb2c08fd Author: Weiqun Zhang Date: Mon Jul 31 16:37:18 2017 -0700 get EBISLayout from eb factory Src/Base/AMReX_FabFactory.H commit 220a0ac36db6a981245a00b89d8c1eae9f954513 Author: Weiqun Zhang Date: Mon Jul 31 16:36:45 2017 -0700 add a eb utility function to set all covered to the min val for the temporary purpose of visualization Src/Base/AMReX_EBMultiFabUtil.H Src/Base/AMReX_EBMultiFabUtil.cpp Src/Base/Make.package commit 04e5f2df480a4f80727ecbd1cc9990b950106dde Author: dtgraves Date: Mon Jul 31 16:29:18 2017 -0700 made EBGraph::fillIntMask more closely resemble what Marc wants. Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp commit 8c1973a5665181034c4650f69e80d620482e96a3 Author: dtgraves Date: Mon Jul 31 12:10:40 2017 -0700 made DivergenceOp able to support fluxes that have area multiplied in to support PeleC Src/EBAMRTools/AMReX_DivergenceOp.H Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/EBAMRTools/AMReX_EBFortND_F.H commit 978ebb92575137c7402e290d972952c5e40595c5 Merge: 79a8af419 5e010d0f1 Author: Michele Rosso Date: Mon Jul 31 12:08:00 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 79a8af4198d7c9cc3230f53d31fad3d8d2a223cf Author: Michele Rosso Date: Mon Jul 31 12:07:14 2017 -0700 CMake:manually force C++11 compliance for Intel compiler Tools/CMake/AMReX_CMakeVariables.cmake commit 5e010d0f18cb4d8d33d8382ca0d0c12d9abc3659 Author: Andrew Myers Date: Mon Jul 31 10:36:00 2017 -0700 make this test work in 2D and 3D. Tests/Particles/AssignMultiLevelDensity/main.cpp commit 3321b41629661a65086dc2e21de9090b27021539 Author: Andrew Myers Date: Mon Jul 31 10:35:41 2017 -0700 consolidate OMP Deposition helpers. Src/Particle/AMReX_OMPDepositionHelper_1d.F90 Src/Particle/AMReX_OMPDepositionHelper_2d.F90 Src/Particle/AMReX_OMPDepositionHelper_nd.F90 Src/Particle/AMReX_ParticleContainerI.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 5d173917738e1d43afdd6d92be41842b90ddf514 Author: Andrew Myers Date: Mon Jul 31 10:11:37 2017 -0700 use PCInterp in the multilevel density deposition. Src/Particle/AMReX_ParticleContainerI.H commit 327efc81bfa3fe322b5f3006be72aeb76d19f91f Author: dtgraves Date: Mon Jul 31 09:54:46 2017 -0700 bug fix in DivergenceOp Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp commit 236b0f75351d864a18c345e111aa0b3b401ee351 Author: Marc Day Date: Mon Jul 31 09:23:42 2017 -0700 Add back code to set fluid cells to unity so that amrvis2d smooth works correctly. Just for demo purposes, keep code more explicitly handling the different types of cells. Tests/GeometryShop/vofStructures/umapTest.cpp commit 265ca5bbcd9e1a2c5ebfcadd911796a3e07824ba Merge: bc29c14f4 995ae32c4 Author: Weiqun Zhang Date: Sat Jul 29 11:49:05 2017 -0700 merge branch 'development' into weiqun/eb commit bc29c14f4a9b97e987704cd93eaa9a0402f3f309 Author: Weiqun Zhang Date: Sat Jul 29 11:48:17 2017 -0700 update comments Src/Base/AMReX_FArrayBox.H commit 995ae32c441bcc68c77164234aad188d244386d4 Author: Weiqun Zhang Date: Sat Jul 29 11:45:31 2017 -0700 make FabArray friend of DistributionMapping for sidecar's moveallfabs Src/Base/AMReX_DistributionMapping.H commit 255ff11da089183978e0d53ed0289c48a697f266 Author: Weiqun Zhang Date: Fri Jul 28 23:51:15 2017 -0700 fix typo Src/Amr/AMReX_AmrLevel.cpp commit 459e4b2ce1c50b0e15986554a8f723cac2dc2bbb Author: Weiqun Zhang Date: Fri Jul 28 23:49:31 2017 -0700 add factory and eb to AmrLevel and StateData Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp commit 413414364d91fdf297970596efb0bbc632f8ca2b Author: Weiqun Zhang Date: Fri Jul 28 22:59:59 2017 -0700 change default factory of MultiFab Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_FabFactory.H commit 828ed8b02f4121a552bc9f1f53bb96210dfdbc31 Author: Weiqun Zhang Date: Fri Jul 28 22:36:53 2017 -0700 add clone function to FabFactory Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabFactory.H Src/GeometryShop/AMReX_BaseEBCellFactory.H Src/GeometryShop/AMReX_BaseIFFactory.H Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_EBCellFactory.H Src/GeometryShop/AMReX_EBDataFactory.H Src/GeometryShop/AMReX_EBFluxFactory.H Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_IrregFABFactory.H commit 4972cd1d4798f06982c7bc3d4d35742119abab6d Author: Weiqun Zhang Date: Fri Jul 28 17:41:53 2017 -0700 add FabType Src/Base/AMReX_EBFArrayBox.H Src/Base/AMReX_EBFArrayBox.cpp Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_FArrayBox.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBISBox.H commit 81073db22280887a5e41e9bbb9aadb6273b830c2 Author: Michele Rosso Date: Fri Jul 28 17:27:07 2017 -0700 CMake: update source file list Src/F_Interfaces/CMakeLists.txt commit 1e0adf862d1a6678965d43de2194aec38bd7a768 Merge: 9c4fc56f5 8b3a3d1ed Author: Michele Rosso Date: Fri Jul 28 17:21:41 2017 -0700 Merge branch 'mr-cmake' into development commit 8b3a3d1ed811155109d3cecc7451473099b3dd28 Author: Michele Rosso Date: Fri Jul 28 17:21:08 2017 -0700 CMake: update documentation Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex commit 998ae55af4b50cf126c8e680ab8e723fc92aeb7e Author: Michele Rosso Date: Fri Jul 28 17:07:53 2017 -0700 CMake: add AMReX version info Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake commit f70a7d491593130fb2f8e3f0e38f1f70f372be56 Author: Weiqun Zhang Date: Fri Jul 28 16:52:28 2017 -0700 add optional factory to MultiFab constructor Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 583eeb1ee957bafcdab8b9d9d5f01cb4a34443d0 Author: Michele Rosso Date: Fri Jul 28 16:37:17 2017 -0700 CMake: build Amr tutorials CMakeLists.txt Tools/CMake/AMReX_Utils.cmake Tutorials/Amr/Advection_AmrCore/CMakeLists.txt Tutorials/Amr/Advection_AmrLevel/CMakeLists.txt Tutorials/Amr/Advection_F/CMakeLists.txt Tutorials/Amr/Advection_octree_F/CMakeLists.txt Tutorials/CMakeLists.txt commit fb8fae806f1e9a56114517da2fbf9ecbf6d5c50a Author: Weiqun Zhang Date: Fri Jul 28 16:35:28 2017 -0700 FArrayBoxFactory Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_FabFactory.H Src/Base/AMReX_MultiFab.H Src/GeometryShop/AMReX_EBFluxFactory.H Src/GeometryShop/AMReX_EBISLayout.H commit 7f77944523775870612f4a987ffddd542dcf81de Author: Michele Rosso Date: Fri Jul 28 16:34:06 2017 -0700 CMake: remove FindCCSE Tools/CMake/FindCCSE.cmake commit f0659de65311c476bb0250099d231f2faa6b9db2 Author: Michele Rosso Date: Fri Jul 28 16:32:34 2017 -0700 CMake: build fortran interfaces by default Tools/CMake/AMReX_Config.cmake commit 7764b8dea80d9765adfe37641b592a1f9e9b03f0 Author: dtgraves Date: Fri Jul 28 15:55:57 2017 -0700 bit more progress toward eb elliptic solvers Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp commit 1111a9063bbe228d64bd2d7f2f41a0df5e356794 Author: Weiqun Zhang Date: Fri Jul 28 15:27:33 2017 -0700 add EBFArrayBox Src/Base/AMReX_EBFArrayBox.H Src/Base/AMReX_EBFArrayBox.cpp Src/Base/AMReX_EBFabFactory.cpp Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FabFactory.H Src/Base/Make.package commit bb7e7058d818aa32cc41dbe773747465d7894703 Merge: 26eab28ce 9c4fc56f5 Author: Weiqun Zhang Date: Fri Jul 28 14:42:10 2017 -0700 Merge branch 'development' into weiqun/eb commit 9c4fc56f51ebcb0f114c98f8aa7cb2ef59809f63 Author: Weiqun Zhang Date: Fri Jul 28 14:38:56 2017 -0700 use std::function instead of function pointer for flexibility Src/Base/AMReX.H Src/Base/AMReX.cpp Src/F_Interfaces/Base/AMReX_init_fi.cpp commit 1290a24b38ed1bbfe6a2641e0463941835ffd2ed Author: Weiqun Zhang Date: Fri Jul 28 14:23:09 2017 -0700 have to link with pgfortran if pgi is used and the main is in Fortran Src/F_Interfaces/Base/Make.package Tools/GNUMake/Make.rules Tools/GNUMake/comps/pgi.mak commit 2063c5ccc0f2703ebf53f299b8d3134f5e86c679 Merge: 195dbc06f f2585d1e4 Author: dtgraves Date: Fri Jul 28 11:28:02 2017 -0700 Merge pull request #73 from AMReX-Codes/dtg_branch syncing with dtg_branch so Ray can get the combustor geometry tools. commit f2585d1e498f255b0b646fee509dfb3327590c02 Author: dtgraves Date: Fri Jul 28 11:26:08 2017 -0700 to give Ray the combustion geometry, I added Terry's transformation functions for implicit functions (Lathe (surfaces of revolution), Complement, Union, Intersection, Transforms (scale, translate, rotate) Src/GeometryShop/AMReX_ComplementIF.H Src/GeometryShop/AMReX_ComplementIF.cpp Src/GeometryShop/AMReX_IntersectionIF.H Src/GeometryShop/AMReX_IntersectionIF.cpp Src/GeometryShop/AMReX_IrregFABFactory.cpp Src/GeometryShop/AMReX_LatheIF.H Src/GeometryShop/AMReX_LatheIF.cpp Src/GeometryShop/AMReX_TransformIF.H Src/GeometryShop/AMReX_TransformIF.cpp Src/GeometryShop/AMReX_UnionIF.H Src/GeometryShop/AMReX_UnionIF.cpp Src/GeometryShop/Make.package commit 195dbc06fbbddb1ae3e4fc6b7c71c8960bc54483 Author: Weiqun Zhang Date: Fri Jul 28 11:06:13 2017 -0700 have to do this for pgi Src/Base/AMReX_parmparse_mod.F90 Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_distromap_mod.F90 Src/F_Interfaces/Base/AMReX_fab_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 8edc00987a0ce879809712076d7792adcfc3e613 Author: Michele Rosso Date: Fri Jul 28 10:43:41 2017 -0700 CMake: add missing files Src/Base/CMakeLists.txt commit 758def051a6438117497c027319d9ac52207e543 Merge: 2acb24482 020293e55 Author: Andreas Kreienbuehl Date: Fri Jul 28 07:07:53 2017 -0700 Merge branch 'clrdDiffuSolve' of https://github.com/akreienbuehl/amrex into clrdDiffuSolve commit 2acb2448287efbd9082f94638d6048c77e0f7562 Merge: bf919b624 27b0f8b0e Author: Andreas Kreienbuehl Date: Fri Jul 28 07:07:34 2017 -0700 Merge remote-tracking branch 'upstream/development' into clrdDiffuSolve commit 020293e55957350b35bded395cc18383f2945017 Merge: bf919b624 27b0f8b0e Author: Andreas Kreienbuehl Date: Fri Jul 28 07:02:49 2017 -0700 Merge remote-tracking branch 'upstream/development' into clrdDiffuSolve commit 26eab28ce868303bcc39b9324869790966d0d548 Author: Weiqun Zhang Date: Thu Jul 27 17:10:35 2017 -0700 add USE_EB to make system Tools/GNUMake/Make.defs commit 8be6fc70673048079354e304d4829ba1c614158c Author: Michele Rosso Date: Thu Jul 27 16:46:14 2017 -0700 CMake: default to Release if no build type is specified Tools/CMake/AMReX_Options.cmake commit 27b0f8b0ef47b3b328bd1710d20c216f8eb1b3a1 Merge: 7c5031916 ae075f777 Author: Michael Zingale Date: Thu Jul 27 19:37:28 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 7c50319160ae340e8bc76a8f5655d3bafd73cd4b Author: Michael Zingale Date: Thu Jul 27 19:36:39 2017 -0400 add keyword support to tests each test can now give a comma-separated lists of keywords with the `--keyword key` option, we can run only those tests with a specific keyword (e.g. gravity). Tools/RegressionTesting/params.py Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_util.py commit 7cfc8859b10edce0430b7b55b9992956089b3926 Author: dtgraves Date: Thu Jul 27 16:10:29 2017 -0700 fixed parallel bug identified by Marc. Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_EBLevelRedist.H Src/GeometryShop/AMReX_EBLevelRedist.cpp Src/GeometryShop/AMReX_IrregFABFactory.cpp commit 274cba1e2c9c4d4dedd64f1bddd0bae5d4972c51 Author: Michele Rosso Date: Thu Jul 27 16:04:11 2017 -0700 CMake: remove old cmake files Src/CMakeLists.txt Src/Particle/CMakeLists.txt Tools/CMake/CCSEConfig-install.cmake.in Tools/CMake/CCSEConfigReport.cmake Tools/CMake/CCSEConfigVersion-install.cmake.in Tools/CMake/CCSELinkLine.cmake Tools/CMake/CCSEOptions.cmake Tools/CMake/CMakeParseArguments.cmake Tools/CMake/ExampleBoxLibConfig.cmake Tools/CMake/ExampleCMakeLists.txt_CCSEApp Tools/CMake/InstallManager.cmake Tools/CMake/ParseLibraryList.cmake commit ae075f777821f4cf53a521591bc1a63ca47e90f4 Merge: 69bc16fc4 84c1f12cb Author: vince Date: Thu Jul 27 15:50:07 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 69bc16fc4b9a7e492a8ca21ba280b608398c78e8 Author: vince Date: Thu Jul 27 15:49:52 2017 -0700 remove diagnostic. Src/Base/AMReX_DistributionMapping.cpp commit 4da51d7874eb75e82df5a926e45ad57ff917ca69 Author: Michele Rosso Date: Thu Jul 27 15:31:53 2017 -0700 CMake: modify install process CMakeLists.txt Src/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Config.cmake commit 84c1f12cbd49d9b349a4838325bd764fe51a96f5 Merge: 924dcca2f 91a5cd52d Author: dtgraves Date: Thu Jul 27 12:57:50 2017 -0700 Merge pull request #72 from AMReX-Codes/dtg_branch merging some bug fixes over commit 057fb348ee9fc1d8df3ee5fa3c964a5b3024fa90 Author: Michele Rosso Date: Thu Jul 27 11:37:51 2017 -0700 CMake:clean-up obsolete CMakeLists.txt Src/CMakeLists.txt Src/Extern/amrdata/CMakeLists.txt Src/LinearSolvers/C_CellMG/CMakeLists.txt Src/LinearSolvers/C_CellMG4/CMakeLists.txt Src/LinearSolvers/C_TensorMG/CMakeLists.txt Src/LinearSolvers/C_to_F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt Tools/CMake/AMReX_Utils.cmake commit 3b1bbdfa95e0ed7fd70df0dcf5a24e217ccc1247 Author: Michele Rosso Date: Thu Jul 27 11:31:44 2017 -0700 CMake: modify structure of the build CMakeLists.txt Src/Amr/CMakeLists.txt Src/AmrCore/CMakeLists.txt Src/Base/CMakeLists.txt Src/Boundary/CMakeLists.txt Src/CMakeLists.txt Src/Extern/CMakeLists.txt Src/F_BaseLib/CMakeLists.txt Src/F_Interfaces/CMakeLists.txt Src/LinearSolvers/CMakeLists.txt Src/LinearSolvers/F_MG/sparse_solve.f90 Src/Particle/CMakeLists.txt Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake commit 924dcca2f80e7cd87a3399afa2d746f10b7adfd5 Merge: a25439535 6a2035d24 Author: vince Date: Thu Jul 27 10:28:49 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 91a5cd52d536d5589d8ae80a5aaa13d0b8c49393 Author: dtgraves Date: Thu Jul 27 10:23:57 2017 -0700 Changed MultiGrid.H to EBMultiGrid.H and AMRMultiGrid.H to AMREBMultiGrid.H per Marc's request. Src/EBAMRElliptic/AMReX_AMREBMultiGrid.H Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRElliptic/AMReX_EBMultiGrid.H Tests/EBAMRElliptic/exec/conductivitySolve.cpp commit 6a2035d24a8a363472fe827fea448ec4b65f6389 Author: Weiqun Zhang Date: Thu Jul 27 10:19:00 2017 -0700 fix call to mpi_finalize Tutorials/Basic/main_F/main.F90 commit b75a6441fe87741c8d4bb2c541437ce9dcd8b300 Author: dtgraves Date: Thu Jul 27 10:11:49 2017 -0700 bug fixes and another argument to DivergenceOp to allow fortran bit to be bypassed Src/EBAMRTools/AMReX_DivergenceOp.H Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_EBFortND.F90 commit bf919b6244d910626fb1523d73b304ca96f41110 Author: Andreas Kreienbuehl Date: Thu Jul 27 07:13:45 2017 -0700 Simplified color-map selection Src/Base/AMReX_ParallelDescriptor.cpp commit 982162340f3245c074dc4ad0e5c9fa00237505e4 Author: Weiqun Zhang Date: Thu Jul 27 06:29:53 2017 -0700 fix datatype Src/F_Interfaces/Base/AMReX_parallel_mod.F90 Tutorials/Basic/main_F/main.F90 commit de061b7a4948881dcbbdeb404ed8024d8b4a4529 Author: Weiqun Zhang Date: Wed Jul 26 18:08:47 2017 -0700 new Tutorials/Basic/main_C Tutorials/Basic/main_C/GNUmakefile Tutorials/Basic/main_C/Make.package Tutorials/Basic/main_C/main.cpp commit 3fbf880df894cf2985d371b34469e7f63de4c0a0 Author: kngott Date: Wed Jul 26 17:50:55 2017 -0700 First attempt to transfer ProfDataServices to amrex::DataServices. OldTutorials/DataServicesTest0/GNUmakefile Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Extern/ProfParser/AMReX_AVGDOWN_2D.F Src/Extern/ProfParser/AMReX_AVGDOWN_3D.F Src/Extern/ProfParser/AMReX_AVGDOWN_F.H Src/Extern/ProfParser/AMReX_BLProfStats.H Src/Extern/ProfParser/AMReX_BLProfStats.cpp Src/Extern/ProfParser/AMReX_BLProfUtilities.H Src/Extern/ProfParser/AMReX_BLProfUtilities.cpp Src/Extern/ProfParser/AMReX_BLWritePlotFile.H Src/Extern/ProfParser/AMReX_BLWritePlotFile.cpp Src/Extern/ProfParser/AMReX_CommProfStats.H Src/Extern/ProfParser/AMReX_CommProfStats.cpp Src/Extern/ProfParser/AMReX_RegionsProfStats.H Src/Extern/ProfParser/AMReX_RegionsProfStats.cpp Src/Extern/ProfParser/AMReX_XYPlotDataList.H Src/Extern/ProfParser/AMReX_XYPlotDataList.cpp Src/Extern/ProfParser/BLProfParser.l Src/Extern/ProfParser/BLProfParser.y Src/Extern/ProfParser/Make.package Src/Extern/ProfParser/backup/AMReX_AVGDOWN_2D.F Src/Extern/ProfParser/backup/AMReX_AVGDOWN_3D.F Src/Extern/ProfParser/backup/AMReX_AVGDOWN_F.H Src/Extern/ProfParser/backup/AMReX_BLProfStats.H Src/Extern/ProfParser/backup/AMReX_BLProfStats.cpp Src/Extern/ProfParser/backup/AMReX_BLProfUtilities.cpp Src/Extern/ProfParser/backup/AMReX_BLWritePlotFile.H Src/Extern/ProfParser/backup/AMReX_BLWritePlotFile.cpp Src/Extern/ProfParser/backup/AMReX_CommProfStats.H Src/Extern/ProfParser/backup/AMReX_CommProfStats.cpp Src/Extern/ProfParser/backup/AMReX_RegionsProfStats.H Src/Extern/ProfParser/backup/AMReX_RegionsProfStats.cpp Src/Extern/ProfParser/backup/AMReX_XYPlotDataList.H Src/Extern/ProfParser/backup/AMReX_XYPlotDataList.cpp Src/Extern/ProfParser/backup/BLProfParser.l Src/Extern/ProfParser/backup/BLProfParser.y Src/Extern/ProfParser/backup/Make.package Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp commit d66066ac0f05104fe1dd79e62e4820c5c61df258 Author: Weiqun Zhang Date: Wed Jul 26 17:17:10 2017 -0700 We have to pass a function adding parameters to amrex::Initialize, otherwise it might be too late. Src/Base/AMReX.H Src/Base/AMReX.cpp Src/F_Interfaces/Base/AMReX_init_fi.cpp Src/F_Interfaces/Base/AMReX_init_mod.F90 Tutorials/Basic/main_F/main.F90 commit a254395357defeeeb0dafcbc2a91857b2e9d17cf Author: vince Date: Wed Jul 26 17:08:42 2017 -0700 merge fix. Docs/Notes.io_implementation Src/Amr/AMReX_Amr.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Boundary/AMReX_FabSet.H Src/Particle/AMReX_Particles.H Tests/IOBenchmark/IOTestDriver.cpp commit d0fb5504c6a78aac37fc9471fe1b6697ae1340bf Merge: fd0b23f49 874058ed6 Author: Andrew Myers Date: Wed Jul 26 16:31:44 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit fd0b23f4925dfa4236c4fb927c606ed70f437066 Author: Andrew Myers Date: Wed Jul 26 16:31:34 2017 -0700 Adding a thread-safe random normal distribution to amrex. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 874058ed646b05a4c99aea6ce43cb5be44584f9e Merge: 3778442eb 73d5ff034 Author: vince Date: Wed Jul 26 15:49:19 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 3778442ebab450400b4109ee18e2719a448be3db Merge: 384c3c178 e6e872c7b Author: vince Date: Wed Jul 26 15:49:03 2017 -0700 merge fix. commit 73d5ff0347cbcda4ae4a2b78c041d7dd40c86ffb Merge: 95ed2b041 e6e872c7b Author: Weiqun Zhang Date: Wed Jul 26 15:34:50 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 384c3c178bf7643e744124d40a110284457ed061 Author: vince Date: Wed Jul 26 15:22:54 2017 -0700 some profiler optimizations. Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit 8af3472b32e9de3264d7795e02f78afaab4ec5a7 Author: vince Date: Wed Jul 26 15:13:54 2017 -0700 minor tutorial changes. Tests/IOBenchmark/GNUmakefile commit d70fb786302afb46871d7180bb3d576725fb61e1 Author: vince Date: Wed Jul 26 15:11:42 2017 -0700 minor tutorial changes. OldTutorials/DataServicesTest0/GNUmakefile OldTutorials/MultiFabTests_C/GNUmakefile OldTutorials/MultiFabTests_C/Make.package OldTutorials/Sidecar_EX1/NSidecarsTest.cpp commit e6e872c7b7277bf837c62fd692d6221c7faf7b86 Author: vince Date: Wed Jul 26 15:01:18 2017 -0700 dont send or clean up unused messages. Src/Base/AMReX_NFiles.H Src/Base/AMReX_NFiles.cpp Tests/IOBenchmark/GNUmakefile Tests/IOBenchmark/IOTest.cpp commit 95ed2b041795d2ef0b638fb6ce99effba73ea3ae Author: Weiqun Zhang Date: Wed Jul 26 14:58:50 2017 -0700 Fortran: fix non MPI Src/F_Interfaces/Base/AMReX_parallel_mod.F90 commit e4bc3a9ae9895401e6f4b20aa912d528da4a2cfc Author: Weiqun Zhang Date: Wed Jul 26 14:52:30 2017 -0700 Fortran: allow users pass their own communicator and skip building parmparse database from command line arguments Src/Base/AMReX.cpp Src/Base/AMReX_ParmParse.cpp Src/F_Interfaces/Base/AMReX_init_fi.cpp Src/F_Interfaces/Base/AMReX_init_mod.F90 Src/F_Interfaces/Base/AMReX_parallel_mod.F90 Tutorials/Basic/main_F/main.F90 commit 23394f79218c799bfb6877ed3acd52a0a0f2492c Author: Andreas Kreienbuehl Date: Wed Jul 26 13:12:05 2017 -0700 Introduced input parameter for choice of color-map Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit ab81bea42c9d57be9d31ff4305bdc42a5319865e Author: Weiqun Zhang Date: Wed Jul 26 10:49:54 2017 -0700 Fortran parmparse: add optional return flag to query functions Src/Base/AMReX_parmparse_fi.cpp Src/Base/AMReX_parmparse_mod.F90 commit 4c8be832f4bd16c41ce6ee88333ab8ce21f7ff2f Author: Weiqun Zhang Date: Wed Jul 26 10:29:51 2017 -0700 update User's Guide Docs/AMReXUsersGuide/Fortran/Fortran.tex commit 2ec2cd6b54ec0d0cc266da87606fa98e099dee7c Author: Weiqun Zhang Date: Wed Jul 26 10:17:54 2017 -0700 remove old Fotran miniapp MiniApps/AMR_Adv_Diff_F90/GNUmakefile MiniApps/AMR_Adv_Diff_F90/GPackage.mak MiniApps/AMR_Adv_Diff_F90/advance.f90 MiniApps/AMR_Adv_Diff_F90/compute_flux.f90 MiniApps/AMR_Adv_Diff_F90/init_phi.f90 MiniApps/AMR_Adv_Diff_F90/inputs_2d MiniApps/AMR_Adv_Diff_F90/inputs_3d MiniApps/AMR_Adv_Diff_F90/main.f90 MiniApps/AMR_Adv_Diff_F90/prob.f90 MiniApps/AMR_Adv_Diff_F90/update_phi.f90 MiniApps/AMR_Adv_Diff_F90/write_plotfile.f90 commit fda3cb22cd746ee19f0b31e22921125c1ba242c5 Author: Weiqun Zhang Date: Wed Jul 26 10:16:14 2017 -0700 Fortran: removed C++ main GNUmakefile.in Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 Src/F_Interfaces/Base/AMReX_fi_main.cpp Src/F_Interfaces/Base/AMReX_init_mod.F90 Src/F_Interfaces/Base/Make.package Tutorials/Amr/Advection_F/Source/fmain.F90 Tutorials/Amr/Advection_F/Source/my_amr_mod.F90 Tutorials/Amr/Advection_octree_F/Source/fmain.F90 Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90 Tutorials/Basic/HeatEquation_EX1_F/GNUmakefile Tutorials/Basic/HeatEquation_EX1_F/fmain.f90 Tutorials/Basic/HelloWorld_F/fmain.f90 Tutorials/Basic/main_F/GNUmakefile commit d69ac93fabfd99ce8e9a581ee2bde9506bdbd4fe Author: Weiqun Zhang Date: Wed Jul 26 07:07:53 2017 -0700 Fortran ParamParse: disable some functions for gfortran 4 because of (I believe) compiler bug Src/Base/AMReX_parmparse_mod.F90 Tutorials/Basic/main_F/main.F90 commit d22386bb171189ed1c20c28a58990276c24b0f31 Author: Weiqun Zhang Date: Tue Jul 25 21:38:41 2017 -0700 Fortran parmparse: trim before adding string Src/Base/AMReX_parmparse_mod.F90 commit 81cd10c9b74e9fc6b9f31258d1b5df58cb66518a Author: Weiqun Zhang Date: Tue Jul 25 21:30:30 2017 -0700 Fortran ParmParse: implement add and refactor string Src/Base/AMReX_parmparse_fi.cpp Src/Base/AMReX_parmparse_mod.F90 Src/Base/AMReX_string_mod.F90 Src/F_Interfaces/Base/AMReX_init_fi.cpp Tutorials/Basic/main_F/main.F90 commit f9e5cbb659c097450383873e6df6bb63ca98d54e Author: Michele Rosso Date: Tue Jul 25 13:13:24 2017 -0700 Modify way of add include paths CMakeLists.txt Src/Amr/CMakeLists.txt Src/AmrCore/CMakeLists.txt Src/Base/CMakeLists.txt Src/Boundary/CMakeLists.txt Src/CMakeLists.txt Src/Extern/amrdata/CMakeLists.txt Src/F_BaseLib/CMakeLists.txt Src/F_Interfaces/CMakeLists.txt Src/LinearSolvers/C_CellMG/CMakeLists.txt Src/LinearSolvers/C_CellMG4/CMakeLists.txt Src/LinearSolvers/C_TensorMG/CMakeLists.txt Src/LinearSolvers/C_to_F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt Src/Particle/CMakeLists.txt commit b608862e1bfb76e968ea8c9e0866a7e8f463a2d6 Author: Michele Rosso Date: Tue Jul 25 11:44:11 2017 -0700 Add utility to find subdirectories Tools/CMake/AMReX_Utils.cmake commit 2f8c97cdeed69802388fdf086da5f583cb36e7f6 Author: Weiqun Zhang Date: Tue Jul 25 06:46:28 2017 -0700 forgot to check in new files Src/F_Interfaces/Base/AMReX_init_fi.cpp Src/F_Interfaces/Base/AMReX_init_mod.F90 commit 48664f676df10663de49647bfd6ee5ecbdedbfac Author: Weiqun Zhang Date: Tue Jul 25 06:45:43 2017 -0700 fix relative path Tutorials/Amr/Advection_F/Exec/Make.Adv Tutorials/Amr/Advection_octree_F/Exec/Make.Adv commit 49449030bc7498d4fede80ca971494ff386797a0 Author: Weiqun Zhang Date: Mon Jul 24 17:31:27 2017 -0700 Fortran: allow main in Fortran GNUmakefile.in Src/Base/AMReX_ParallelDescriptor.cpp Src/F_Interfaces/Base/AMReX_base_mod.F90 Src/F_Interfaces/Base/AMReX_fi_main.cpp Src/F_Interfaces/Base/Make.package Tutorials/Basic/main_F/GNUmakefile Tutorials/Basic/main_F/Make.package Tutorials/Basic/main_F/main.F90 commit ad7024cda04481f834adcd962197cc962028782c Author: Marc Day Date: Mon Jul 24 14:43:10 2017 -0700 wip Tests/GeometryShop/vofStructures/umapTest.H Tests/GeometryShop/vofStructures/umapTest.cpp Tests/GeometryShop/vofStructures/umapTest_mod.f90 Tests/GeometryShop/vofStructures/umapTest_nd.f90 commit 94887bec2825b1ae90a870cdc65f38cbcb08cd79 Author: Weiqun Zhang Date: Mon Jul 24 14:17:11 2017 -0700 Fortran: add sum_boundary and average_sync Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit e6bbf4570c8b44be06693c2cbd838a70d2fe250c Author: Weiqun Zhang Date: Mon Jul 24 12:57:06 2017 -0700 OwnerMask is now iMultiFab Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit a6202208b877f23d2b63355e5de7059e698e039f Author: Michael Zingale Date: Mon Jul 24 15:06:47 2017 -0400 util_module -> box_util_module Tools/Postprocessing/F_Src/fnan.f90 commit a0addfa44629fbdd9b12dbecf37bcfde908bd36b Author: Weiqun Zhang Date: Mon Jul 24 11:59:19 2017 -0700 add some specialized ifab functions Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 commit 5b2ca6129a7903efdcedab7ad8b5533336705d88 Author: Andrew Myers Date: Fri Jul 21 17:28:36 2017 -0700 reverting Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit d8897b17770224d4a8b1b2b6c309d18f186b001f Author: Andrew Myers Date: Fri Jul 21 16:00:19 2017 -0700 revert the periodic shift optimization for now Src/Particle/AMReX_NeighborParticlesI.H commit 1fca2487d894d0d4480c1c3746f70ba4ae4b249f Merge: ae5e7d331 c4f6b5569 Author: Andrew Myers Date: Fri Jul 21 15:22:49 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ae5e7d331fbe9c4850ee2678858129341de6f766 Author: Andrew Myers Date: Fri Jul 21 15:22:41 2017 -0700 some minor optimization /refactoring of the neighbor particle code. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 8cc4cd9da2f0ab6f180e30848667c1b83b6ac948 Author: Max Katz Date: Fri Jul 21 11:23:02 2017 -0400 Link against the IBM OpenMP library Tools/GNUMake/comps/ibm.mak commit c4f6b5569e4b0574b2543c32f4b49c8e95435762 Author: Andy Nonaka Date: Thu Jul 20 17:39:01 2017 -0700 added a makeSFC distribution mapping interface (similar to the knapsack and roundrobin cases) Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit 7684db1a56d304623fdb68e9111f02a073502edc Author: Weiqun Zhang Date: Thu Jul 20 15:34:54 2017 -0700 F_Interfaces: owner mask and override_sync Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 1780e92a32d693e7acdc62062794f9963a579751 Merge: aaa5fb226 71a783f21 Author: Andrew Myers Date: Thu Jul 20 14:54:46 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit aaa5fb2261e32248f38e0c4113bced81ae8e8d41 Author: Andrew Myers Date: Thu Jul 20 14:54:37 2017 -0700 Update these Tutorials to account for the recent changes to NeighborParticleContainer. Tutorials/Particles/NeighborList/GNUmakefile Tutorials/Particles/NeighborList/NeighborListParticleContainer.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborList/neighbor_list_2d.f90 Tutorials/Particles/NeighborList/neighbor_list_3d.f90 commit 71a783f2163e95bb50b0bd33d78c8b594651bf4d Author: Weiqun Zhang Date: Thu Jul 20 14:46:00 2017 -0700 fix comment Src/Base/AMReX_MultiFab.H commit 2d426aa20709c445ab59b289a805c09af1c5b4ad Merge: 07fcbe2ec 22f11b4d3 Author: dtgraves Date: Thu Jul 20 14:16:30 2017 -0700 Merge pull request #61 from AMReX-Codes/dtg_branch fixed some bugs and wrote gradient operator that Marc wanted. commit 22f11b4d36867aee84fdcab03b0622da1b04bab3 Author: dtgraves Date: Thu Jul 20 14:15:02 2017 -0700 a few random bug fixes along with a brand new EB gradient operator that passes its test. Src/EBAMRTools/AMReX_DivergenceOp.H Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/EBAMRTools/AMReX_EBFortND_F.H Src/EBAMRTools/AMReX_GradientOp.H Src/EBAMRTools/AMReX_GradientOp.cpp Src/EBAMRTools/Make.package Src/GeometryShop/AMReX_AggStencilI.H Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/aggpwlfp.inputs Tests/EBAMRTools/regression/aggpwlfpTest.cpp Tests/EBAMRTools/regression/divop.inputs Tests/EBAMRTools/regression/ebcoarave.inputs Tests/EBAMRTools/regression/gradientOpTest.cpp Tests/EBAMRTools/regression/gradop.inputs Tests/EBAMRTools/regression/nwoebquadcfi.inputs commit 07fcbe2ec79002c184a69af6982c6c2625bfeaee Author: Weiqun Zhang Date: Thu Jul 20 14:08:20 2017 -0700 add OwnerMask and OverrideSync functions that let owners override nonowners Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit 8d766ab4563b3cf4edc4415d7735b895594df1b6 Merge: b66995bb4 84c8cfd2e Author: Andrew Myers Date: Thu Jul 20 14:05:50 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b66995bb49a4060dea01b5ea777f876bf4ce6edf Author: Andrew Myers Date: Thu Jul 20 14:05:40 2017 -0700 remove openmp pragmas from neighbor list code for now. Src/Particle/AMReX_NeighborParticlesI.H commit 84c8cfd2ebcfcc710ecea6853e11c4e0cc5fd190 Author: Weiqun Zhang Date: Thu Jul 20 10:01:47 2017 -0700 add a function performing nodal data sync via averaging Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit a3afe4e1ea87aa0dfa89817a2f7acd64f2326af3 Author: Andrew Myers Date: Thu Jul 20 10:37:49 2017 -0700 left out a #ifdef for MPI. Src/Particle/AMReX_NeighborParticlesI.H commit 02d2498db14c2d4ed86c4e63cffbada4a980800c Merge: 00fd6297f 726765e8c Author: Andrew Myers Date: Thu Jul 20 10:25:54 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 00fd6297f7a00bc18e419d31a0397c56b39b232f Author: Andrew Myers Date: Thu Jul 20 10:25:42 2017 -0700 do not recompute the number of snds / rcvs unless it changes. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 726765e8c464e45f3423b288f28c9abf631075f4 Author: Weiqun Zhang Date: Thu Jul 20 09:34:47 2017 -0700 fix typo Docs/AMReXUsersGuide/Basics/Basics.tex commit 056be47e30a4a59de510e52d5dced30218f9b16b Merge: 5b5af5768 3816af2d4 Author: Weiqun Zhang Date: Thu Jul 20 09:35:08 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7264df50e5ae503ee8abc4261b21181152e72fdf Author: Marc Day Date: Wed Jul 19 17:53:42 2017 -0700 WIP for umap tests Tests/GeometryShop/vofStructures/AMReX_ebstruct_mod.F90 Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/umapTest.H Tests/GeometryShop/vofStructures/umapTest.cpp Tests/GeometryShop/vofStructures/umapTest_mod.f90 Tests/GeometryShop/vofStructures/umapTest_nd.f90 commit 3816af2d41e84f26bf5d447acb073f2273405f92 Author: Andrew Myers Date: Wed Jul 19 13:57:05 2017 -0700 don't hard-code this cutoff. Src/Particle/AMReX_Particle_mod_3d.F90 commit 3df6e2679bfb0a21ef058a80b535717ed5a15e12 Merge: 9cc8203e8 04c9e6327 Author: Andrew Myers Date: Wed Jul 19 13:21:39 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9cc8203e837bf417a2cf8fcd2e275d3a7fd7da3d Author: Andrew Myers Date: Wed Jul 19 13:21:22 2017 -0700 add method to update the neighbor buffers without refilling them. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 04c9e63275b547a8c2523f138f60af8d93340994 Merge: 7d0321310 3e0cf08f5 Author: WeiqunZhang Date: Wed Jul 19 12:30:09 2017 -0700 Merge pull request #59 from zingale/development rewrite some of the area and volume terms commit 3e0cf08f51b191eebd5c6c2d6781245504b315ce Author: Michael Zingale Date: Wed Jul 19 14:45:25 2017 -0400 rewrite some of the area and volume terms this reduces roundoff for large values of r also use Pi and other constants from the constants header this closes #29 Src/Base/AMReX_COORDSYS_1D.F Src/Base/AMReX_COORDSYS_2D.F commit 5b5af57680c21de5ddf20c2cf2d8e78278f7c1e4 Author: Weiqun Zhang Date: Wed Jul 19 10:22:38 2017 -0700 quiet compiler Src/Amr/AMReX_StateData.H commit 080544a339d9f3767d70d1af36d33f9af25a49ad Merge: 30360ffc5 7d0321310 Author: Weiqun Zhang Date: Wed Jul 19 10:01:17 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7d0321310fa0fb27a621a8f6aef06e9f789f35c5 Author: Weiqun Zhang Date: Wed Jul 19 10:00:50 2017 -0700 replace UINT32_MAX with std::mt19937::max() Src/F_BaseLib/bl_random_c.cpp commit 30360ffc55f476675531c4e277c90e3c81b37d09 Merge: d809d8985 c2bdef933 Author: Weiqun Zhang Date: Wed Jul 19 09:41:14 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c2bdef933b7148369136257bf9bad0504a1ab6ef Author: Andrew Myers Date: Tue Jul 18 17:41:19 2017 -0700 Fortran version of buildNeighborList Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Src/Particle/AMReX_Particle_mod_3d.F90 Src/Particle/AMReX_Particles_F.H commit c5d129088f26d97024576266ffadfc12a31c22ce Author: dtgraves Date: Tue Jul 18 15:10:44 2017 -0700 bug fix in divergenceop Src/EBAMRTools/AMReX_DivergenceOp.cpp commit b4d550904abff4bd269963681f39e5af7d12be32 Author: Michele Rosso Date: Tue Jul 18 13:42:51 2017 -0700 Update documentation Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex commit 670d734a9af28eb54069594a8664b511dad133f9 Author: Michele Rosso Date: Tue Jul 18 13:33:49 2017 -0700 Provide default install dir other than /usr/local Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Config.cmake commit a42ec6084da1cb559dfc14ce29f824ad4d19d05f Author: Michele Rosso Date: Tue Jul 18 12:44:39 2017 -0700 Add CMake options to turn on/off FPE compiler flags Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit b87450c3313541575c11f33fa8b4e9fd4c3dd5f6 Merge: a89ecb289 ce19b4903 Author: dtgraves Date: Tue Jul 18 11:15:52 2017 -0700 Merge pull request #58 from AMReX-Codes/dtg_branch some bug fixes and a new divergence operator commit ce19b490328fdccffd7ff75095bbaf2ca917dafe Author: dtgraves Date: Tue Jul 18 11:14:39 2017 -0700 DivergenceOp now passes its test. Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp Tests/EBAMRTools/regression/divergenceOpTest.cpp commit 5314247461a602a85f88657c6f1c10f5f1cb98fe Author: dtgraves Date: Mon Jul 17 16:54:47 2017 -0700 Per Marc's request, I added a standalone hybrid divergence operator. It compiles but testing is not complete Src/EBAMRTools/AMReX_DivergenceOp.H Src/EBAMRTools/AMReX_DivergenceOp.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/EBAMRTools/AMReX_EBFortND_F.H Src/EBAMRTools/Make.package Src/GeometryShop/AMReX_EBLevelRedist.H Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.H Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/divergenceOpTest.cpp Tests/EBAMRTools/regression/divop.inputs commit a89ecb289ba9a436900363d7159fc08508c166c1 Merge: 0f4ae78bc 4c6cf5822 Author: Andrew Myers Date: Mon Jul 17 14:48:19 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0f4ae78bc54fb626c26d45034fcfad29c086af6f Author: Andrew Myers Date: Mon Jul 17 14:48:09 2017 -0700 optimizing / simplifying the neighbor list code. Src/Particle/AMReX_NeighborParticlesI.H commit 4c6cf5822e0f77e00f758e5c5493d9aa04c84828 Author: Weiqun Zhang Date: Mon Jul 17 12:47:26 2017 -0700 assert that we are not using tag that's too large Src/Base/AMReX_NFiles.cpp commit a54eb88f2494c39092c0da3687d5a07a04401ede Author: Weiqun Zhang Date: Mon Jul 17 12:42:06 2017 -0700 Abort if MPI_Comm_get_attr failes to get MPI_TAG_UB. Add ParallelDescriptor::MaxTag() Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit f6d87795a77e776b470cfd4269c581e8515fb20f Author: Andrew Myers Date: Mon Jul 17 10:33:16 2017 -0700 check getcwd error code. Src/F_BaseLib/backtrace_c.cpp commit 1e6b5781abb01063f92b710e9c37912c9f831b21 Author: Andrew Myers Date: Mon Jul 17 10:20:08 2017 -0700 check return code of std::system in amrex::UtilCreateDirectoryDestructive Src/Base/AMReX_Utility.cpp commit 260e8daf5de48e4695f13dfdc4aecaf56c1fdc29 Merge: 0f2ebb6e1 94db4b140 Author: Andrew Myers Date: Mon Jul 17 09:59:06 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 0f2ebb6e17ed2b67c270c7ca9bac71cae60d13cd Author: Andrew Myers Date: Mon Jul 17 09:58:55 2017 -0700 add option to sort nl after constructing it (useful for exactly comparing against the N^2 calculation. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 94db4b140a3b896fd7f490e9344d482593680d21 Author: Weiqun Zhang Date: Sat Jul 15 16:42:43 2017 -0700 more reduce funcitons Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit b5176f778bb7624ce292986c9f4e11033624d39a Author: Weiqun Zhang Date: Sat Jul 15 16:17:15 2017 -0700 add more reduce functions that do multiple reductions without user packing and unpack into arrays Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit dde8d7f4651f6cb9b49942162ace6966fbd3d496 Author: Weiqun Zhang Date: Sat Jul 15 15:50:54 2017 -0700 reorganize reduce functions Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit 8bcda9cfd57d764e8de251c1c9256209513295f1 Author: Max Katz Date: Sat Jul 15 04:13:58 2017 -0400 Fix the offset in copytomem/copyfrommem again Src/Base/AMReX_BaseFab_nd.F90 commit e53f9b6093503ac80ac0cd86715ce605ae4b8bf2 Author: Max Katz Date: Sat Jul 15 03:51:01 2017 -0400 Add device syncs after copyToMem/copyFromMem Src/Base/AMReX_FabArray.H commit c60f0b43cc2aebf82e35d41ffef113b67eeb6360 Author: Max Katz Date: Sat Jul 15 02:02:31 2017 -0400 Only do reductions when CUDA is enabled Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 2b865b4a8e33fd940d1932e4254a299ff0c6a9a1 Author: Max Katz Date: Sat Jul 15 01:45:50 2017 -0400 Fix the offset in copytomem/copyfrommem Src/Base/AMReX_BaseFab_nd.F90 commit a6e5fa31e266c86932a2fdab9e94ecf8b7e51369 Author: Max Katz Date: Sat Jul 15 00:11:16 2017 -0400 Do not perform Device operations for non-CUDA code Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_Device.H Src/Base/AMReX_MFIter.H commit 71cb56c5a3c5374c9f83992e12d41e4fd10ea256 Merge: 2b155da7e 844ce0e2b Author: Andrew Myers Date: Fri Jul 14 17:21:18 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2b155da7ed341094912c64a2c77d5721586b8a4f Author: Andrew Myers Date: Fri Jul 14 17:19:55 2017 -0700 also creating neighbor lists for ghost particles. Src/Particle/AMReX_NeighborParticlesI.H commit 176706f6c69be13faef153449250551d0034fa01 Author: dtgraves Date: Fri Jul 14 16:45:27 2017 -0700 more progress on EBAMRElliptic. Parking this for now so I can write Pele operators. Src/EBAMRElliptic/AMReX_AMRMultiGrid.H Src/EBAMRElliptic/AMReX_BaseBCFuncEval.H Src/EBAMRElliptic/AMReX_ConductivityBaseDomainBC.H Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.cpp Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRElliptic/AMReX_EBEllipticFort.F90 Src/EBAMRElliptic/AMReX_EBEllipticFort_F.H Src/EBAMRElliptic/AMReX_MultiGrid.H Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.cpp Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.H Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.cpp Src/EBAMRElliptic/AMReX_NoOpSolver.H Src/EBAMRElliptic/AMReX_VCAggStencil.H Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp commit 844ce0e2b177ebb362082e21739db7ba158d2c92 Author: Weiqun Zhang Date: Fri Jul 14 16:09:28 2017 -0700 hypre: provide initial guess and add BoomerAMG to inputs Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Tutorials/HYPRE/ABecLaplacian/inputs commit de2dcd1cfea4522f6c3a9c51300ce0c4a76f7c1e Author: Weiqun Zhang Date: Fri Jul 14 15:56:14 2017 -0700 Hypre tutorial: print out error Tutorials/HYPRE/ABecLaplacian/ABL.H Tutorials/HYPRE/ABecLaplacian/ABL.cpp Tutorials/HYPRE/ABecLaplacian/ABL_F.F90 Tutorials/HYPRE/ABecLaplacian/ABL_F.H commit 7ee4c0380bda301532d0e947e2a904b200c996f3 Author: Weiqun Zhang Date: Fri Jul 14 14:28:53 2017 -0700 first pass of Hypre Boomer AMG Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.H Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H Tutorials/HYPRE/ABecLaplacian/ABL.cpp commit f26200e3bc4fc788554da08d02bd2777b4dc3c50 Author: Weiqun Zhang Date: Fri Jul 14 10:31:37 2017 -0700 remove the inclusion of Hypre's Make.package from Make.hypre Tools/GNUMake/packages/Make.hypre Tutorials/HYPRE/ABecLaplacian/GNUmakefile commit 4dadc9dea8fadbf9e32ee3f0ebf4be84dc8a16a0 Author: Andrew Myers Date: Fri Jul 14 15:12:29 2017 -0700 Offset the neighbor particle number by Np Src/Particle/AMReX_NeighborParticlesI.H commit d809d8985ee5d4b827b8ef5a887512e4686d7bec Author: Weiqun Zhang Date: Fri Jul 14 10:23:47 2017 -0700 Abort if message sizes in parallel copy and fillboundary do not match Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 29d11a76fa1fa587964646adb7a43e6ee65edae3 Author: Weiqun Zhang Date: Thu Jul 13 21:05:02 2017 -0700 flush AMReX::Print by default Src/Base/AMReX_Print.H commit c185b85d6f4dac68a5a12556c9f044e9e0f33680 Merge: dae5029fd 0ddbb5a81 Author: vince Date: Fri Jul 14 12:21:49 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit b60778d39dc264f2688a46e68b6ffec40b90289c Author: dtgraves Date: Fri Jul 14 12:19:39 2017 -0700 you know you have been staring at stuff too long when it pisses you off that Dirichlet and Neumann have different numbers of letters Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Tests/EBAMRElliptic/exec/conductivitySolve.cpp commit dae5029fddee74916b767b384b5734bc99a3d8a3 Author: vince Date: Fri Jul 14 12:19:07 2017 -0700 call CleanUpMessages for nfilesiter. Src/Base/AMReX_NFiles.cpp commit 0ddbb5a816c357431ccef7406afbd59f0760e58e Merge: ec5132a5d 9a58dc9cd Author: Andrew Myers Date: Fri Jul 14 10:54:41 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ec5132a5ddec440716e7c4ed05ea327114d47090 Author: Andrew Myers Date: Fri Jul 14 10:54:30 2017 -0700 update the short range force tutorials to reflect recent changes in NeighborParticleContainer. Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborList/main.cpp Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp Tutorials/Particles/ShortRangeParticles/main.cpp commit 9a58dc9cd61ed9f2dc8e6f3f7c7aeeb60ba25ee5 Author: Ann Almgren Date: Thu Jul 13 21:42:56 2017 -0700 Add the ability to pass weights into the knapsack and round robin strategies -- the algorithms then use the weights instead of numpts. Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit ca48733dad2fc46a6b7fad1c0969e4b4c6ff9f75 Author: Andrew Myers Date: Thu Jul 13 19:04:12 2017 -0700 fixing fill neighbors for the case of ng>1 Src/Particle/AMReX_NeighborParticlesI.H commit 9928383df744ad7e6f6d87df74af4c39b9ff1b14 Author: Andrew Myers Date: Thu Jul 13 18:59:27 2017 -0700 fixing another bug... Src/Particle/AMReX_NeighborParticlesI.H commit dcdd155f13aa2188089ea211897e1fa9938a638f Author: Andrew Myers Date: Thu Jul 13 18:56:59 2017 -0700 got a sign wrong here. Src/Particle/AMReX_NeighborParticlesI.H commit 61aa80e29bcaee5ea752d80140ac4d01a9e4e101 Author: Andrew Myers Date: Thu Jul 13 18:53:08 2017 -0700 make these protected instead of private. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit b7727add8c24836b3a2b065577efb76dc60be72d Merge: 8171585c3 fa8014618 Author: Andrew Myers Date: Thu Jul 13 18:21:32 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8171585c38ed2f340f16b5f80749a621bd720760 Author: Andrew Myers Date: Thu Jul 13 18:21:19 2017 -0700 use the input dmap and geom rather than getting it from the pc. Src/Particle/AMReX_NeighborParticlesI.H commit fa8014618767e2dec6c4cdfa492d080e1a745b0e Author: Weiqun Zhang Date: Thu Jul 13 18:12:31 2017 -0700 BoxArray intersection for a corner case in which the box array has a single nodal box with a single node in one of the directions Src/Base/AMReX_Box.H Src/Base/AMReX_BoxArray.cpp commit 7174d1f73e12063b59fd20526fa71faffc2d24a6 Author: Andrew Myers Date: Thu Jul 13 17:45:43 2017 -0700 make the applyPeriodic and packGhost functions take the lev Src/Particle/AMReX_NeighborParticlesI.H commit 42a1225b04bbbf260e144d73ecbd6271ddc1ce05 Author: Andrew Myers Date: Thu Jul 13 17:42:37 2017 -0700 fix another typo. Src/Particle/AMReX_NeighborParticlesI.H commit d5d11e1e5d8dcd5cb3a68ab055b329de98a62e55 Author: Andrew Myers Date: Thu Jul 13 17:40:59 2017 -0700 fix typo Src/Particle/AMReX_NeighborParticles.H commit d727d0107c96dc75ad15282d2676e6f672e0bf5c Author: Andrew Myers Date: Thu Jul 13 17:38:09 2017 -0700 Add some asserts for safety. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit 039fa807d08c5dc52d9312a6e46c123c59432450 Author: Andrew Myers Date: Thu Jul 13 17:02:32 2017 -0700 add a ParGDB constructor to the neighbor particle container. Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp commit 2f9fdc469eb01faa9566b804ead61c8c5b57d005 Author: dtgraves Date: Thu Jul 13 16:17:10 2017 -0700 EBAMRElliptic continues to slouch toward Bethlehem Src/EBAMRElliptic/AMReX_AMRMultiGrid.H Src/EBAMRElliptic/AMReX_ConductivityBaseDomainBC.H Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.H Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.cpp Src/EBAMRElliptic/Make.package Tests/EBAMRElliptic/exec/GNUmakefile Tests/EBAMRElliptic/exec/conductivitySolve.cpp commit 4003bc679e6c782a5122ec8a34de100443436110 Author: Weiqun Zhang Date: Thu Jul 13 11:08:21 2017 -0700 remove plt_compare_diff_grids Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py commit c4d85aa7ece266f99c387a7e968f759563ec04a5 Author: Weiqun Zhang Date: Tue Jul 11 18:28:24 2017 -0700 WIP: hypre BoomerAMG Src/Extern/HYPRE/AMReX_HABEC_3D.F90 Src/Extern/HYPRE/AMReX_Hypre.H Src/Extern/HYPRE/AMReX_Hypre.cpp Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABecLap2.H Src/Extern/HYPRE/AMReX_HypreABecLap2.cpp Src/Extern/HYPRE/AMReX_HypreABec_F.H Src/Extern/HYPRE/Make.package Tutorials/HYPRE/ABecLaplacian/ABL.H Tutorials/HYPRE/ABecLaplacian/ABL.cpp commit 4b9dda44b9c14df98c917957a6b684c715612120 Merge: 1662c7b0b 94142d20e Author: Max Katz Date: Thu Jul 13 12:05:47 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 94142d20e29d6695e2c735a538864380bd626001 Author: Michael Zingale Date: Wed Jul 12 19:24:30 2017 -0400 fix the case where no B params are specified Tools/F_scripts/write_probin.py commit 96baa1de8ccd239584623c740b9602530bef6af2 Author: Donald Willcox Date: Wed Jul 12 16:54:29 2017 -0400 In write_probin, use --managed flag to turn on CUDA managed probin vars (off by default). Tools/F_scripts/write_probin.py commit b3cde66b50f78554c57b159598cd2d50701a43eb Author: Donald Willcox Date: Wed Jul 12 16:33:42 2017 -0400 Modified write_probin to use argparse instead of getopt. Tools/F_scripts/write_probin.py commit 45b5f655c062fabce959e10955b6eafd6d3be3d0 Author: vince Date: Wed Jul 12 12:46:56 2017 -0700 fix for AddProcsToComp. Src/Amr/AMReX_Amr.cpp commit 68763cdae7ac515812fe1805bbe5125948111533 Author: Donald Willcox Date: Wed Jul 12 03:14:02 2017 -0400 Modified write_probin to use managed memory. Tools/F_scripts/write_probin.py commit 1c5988c7b3ef0603658a2cb58dc2a6cac07d9bf9 Merge: bd19d4eda 524537d83 Author: WeiqunZhang Date: Tue Jul 11 17:18:39 2017 -0700 Merge pull request #56 from zingale/development add a print_state (and print_state_n) method commit 524537d8375973eb701a483868ff3c280a8fe4cd Author: Michael Zingale Date: Tue Jul 11 20:17:05 2017 -0400 wrong one -- single component gets more precision Src/Base/AMReX_MultiFabUtil.cpp commit f871574c879165f8eaed898e67c0c131163975c3 Author: Michael Zingale Date: Tue Jul 11 20:15:00 2017 -0400 max precision Src/Base/AMReX_MultiFabUtil.cpp commit 9247cafa6356e5926c39ef02e9a3af53fa9cbc72 Author: Michael Zingale Date: Tue Jul 11 20:02:59 2017 -0400 much nicer C++ implementation of print_state (thanks to Weiqun for pointers) Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_F.H commit ae2bf1d3951947c00590923984a66885593b6276 Merge: f0eb508f2 bd19d4eda Author: Michael Zingale Date: Tue Jul 11 19:28:20 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit bd19d4edafd22c49201ba2fd19b54494d60e4ea5 Author: Andrew Myers Date: Tue Jul 11 16:18:35 2017 -0700 adding a new test for tracer particles Tools/RegressionTesting/AMReX-tests.ini commit c0f2b9ceaae7b0453b815e007a2bf366b7daeb07 Author: Andrew Myers Date: Tue Jul 11 16:17:23 2017 -0700 adding myself to the list of people who get emailed if the AMReX tests fail. Tools/RegressionTesting/AMReX-tests.ini commit 4cd10ecb08eb74324598b1ecda74fab6d135718b Author: Andrew Myers Date: Tue Jul 11 16:16:03 2017 -0700 set up one of the advection tutorials to use tracer particles. Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/inputs.tracers commit f0eb508f2f7eca4f08352ad1ba1b210b9ceef6be Merge: 6ac161097 5f1b1be4e Author: Michael Zingale Date: Tue Jul 11 19:00:18 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 5f1b1be4eab1310a2eb3ec4538976061d299693a Merge: 231aef9ff 6e7a662ad Author: Andy Nonaka Date: Tue Jul 11 15:02:37 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 231aef9ff0d611d1c07165b7f12bf0e6f4285e0b Author: Andy Nonaka Date: Tue Jul 11 15:01:47 2017 -0700 some extra documentation for the Base code Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/Basics/figs/flowchart.odg Docs/AMReXUsersGuide/Basics/figs/flowchart.pdf Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex commit 6ac1610978dc0bed2918f556ba5809fd061f61d6 Author: Michael Zingale Date: Tue Jul 11 17:33:34 2017 -0400 add a print_state (and print_state_n) method Useful for dumping out the state for a single zone, for debugging Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_F.H commit 6e7a662ad181fced6b8f40dd86c17e213cf71436 Author: Andrew Myers Date: Tue Jul 11 14:06:13 2017 -0700 1D and 2D versions of the deposit_particle_dx routines, while I'm at it. Src/Particle/AMReX_Particle_mod_1d.F90 Src/Particle/AMReX_Particle_mod_2d.F90 commit c5d2c7a4194094b661b851b46469a854700654cb Author: Andrew Myers Date: Tue Jul 11 13:17:15 2017 -0700 Fix a couple of bugs in the routine I just added. Src/Particle/AMReX_Particle_mod_3d.F90 commit 20286227d11f654dbc32802a0eeb35dc6514ee2d Merge: 287a569c9 e7da3eb5d Author: Andrew Myers Date: Tue Jul 11 12:47:10 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e7da3eb5de411f6eaaee511f1f53e854996209bc Merge: f9afac2a8 4e2cd4179 Author: Weiqun Zhang Date: Tue Jul 11 12:37:26 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f9afac2a88f730458a611337e73eda3f198e79fe Author: Weiqun Zhang Date: Tue Jul 11 12:37:15 2017 -0700 fix memory profiling for BoxArray Src/Base/AMReX_BoxArray.cpp commit 287a569c9b75827e1479da6c534b3cd8740c2f76 Author: Andrew Myers Date: Tue Jul 11 11:04:10 2017 -0700 Fix copy/paste error. Src/Particle/AMReX_Particle_mod_3d.F90 commit aea9f06f4e210db4cba1d57ab6a23cdd4b809c91 Author: Andrew Myers Date: Tue Jul 11 10:53:02 2017 -0700 Fortran routine for deposition when dx != particle_dx Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_Particle_mod_3d.F90 Src/Particle/AMReX_Particles_F.H commit 4e2cd4179d936aa2b03d7e20b5954157f1ad16f9 Merge: b2317115f 21ee77557 Author: Andrew Myers Date: Tue Jul 11 09:28:52 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit b2317115fdb91b0712a61b192c389352a905223a Author: Andrew Myers Date: Tue Jul 11 09:28:39 2017 -0700 can't assume one ghost cell here because of sub-cycling Src/Particle/AMReX_ParticleContainerI.H commit 21ee775573bd85c00400fdbae8c1a021d49749bd Author: atmyers Date: Tue Jul 11 00:17:16 2017 -0700 DistributionMapping() -> DistributionMap() - the Mapping() version actually constructs an empty dm instead of returning the one used by this mf. Src/Base/AMReX_MultiFab.cpp commit 89cf0d75b505eb9c473c307d4c60151f6012c342 Author: Ann Almgren Date: Mon Jul 10 18:30:59 2017 -0700 Remove unused pmap Src/Particle/AMReX_ParticleContainerI.H commit 671e0c0f7d120b1a9977f9ef6497805f48a52588 Merge: a2c20da4c 97c1d3f56 Author: Andrew Myers Date: Mon Jul 10 17:53:05 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a2c20da4c846f98c73b5600ccaf77552537127ee Author: Andrew Myers Date: Mon Jul 10 17:52:29 2017 -0700 add some stuff to the docs about neighbor lists. Docs/AMReXUsersGuide/Particle/Particle.tex Docs/AMReXUsersGuide/Particle/neighbor_list.pdf Docs/AMReXUsersGuide/Particle/neighbor_list.tex commit 97c1d3f56df864251b6554f46237dd673b29f4fb Author: Weiqun Zhang Date: Mon Jul 10 17:05:02 2017 -0700 hypre: no need to make a new distributionmapping Src/Extern/HYPRE/AMReX_HypreABecLap.cpp commit 0095944719845267751d1f14482c664ec698a935 Merge: eb4ceaa08 f33ca7ce0 Author: atmyers Date: Mon Jul 10 16:48:01 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit eb4ceaa080e2806fdbf4658c3c621f4ce38b87e4 Author: atmyers Date: Mon Jul 10 16:47:19 2017 -0700 Turn on OpenMP by default in the NeighborList Tutorial. Tutorials/Particles/NeighborList/GNUmakefile commit 7926b2e82f1f66b5359b4a92cc9a2ccfb558d3e4 Author: atmyers Date: Mon Jul 10 16:46:56 2017 -0700 turn on tiling and domain decomposition by default in the NeighborList Tutorial inputs file. Tutorials/Particles/NeighborList/inputs commit d03643c7f5832b9de3571539967e74991fc030f4 Author: atmyers Date: Mon Jul 10 16:37:38 2017 -0700 Much of the functionality of these tutorials is now implemented in AMReX. Tutorials/Particles/NeighborList/NeighborListParticleContainer.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborList/inputs Tutorials/Particles/ShortRangeParticles/GNUmakefile Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.H Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp Tutorials/Particles/ShortRangeParticles/inputs Tutorials/Particles/ShortRangeParticles/main.cpp commit c6e2b82d146015de3c3d40d1e3a788bc0f18404e Author: atmyers Date: Mon Jul 10 16:36:47 2017 -0700 move the neighbor list stuff to Src/Particle Src/Particle/AMReX_NeighborParticles.H Src/Particle/AMReX_NeighborParticlesI.H commit f33ca7ce0b6c579b4d09a0f986adb0d5d9959957 Author: Weiqun Zhang Date: Mon Jul 10 16:34:58 2017 -0700 add inputs Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Tutorials/HYPRE/ABecLaplacian/ABL.cpp Tutorials/HYPRE/ABecLaplacian/inputs commit 95eb283a10f9bf387d38d2cd369c8b4d9becebd0 Author: atmyers Date: Mon Jul 10 16:22:24 2017 -0700 slight change to the check_pair method. Tutorials/Particles/NeighborList/NeighborListParticleContainer.H commit 332333d7cc9aa9e3db5ec9697af92f584e60e6cc Author: Weiqun Zhang Date: Mon Jul 10 16:14:56 2017 -0700 hypreabeclap: add communicator Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp commit 12491d110ebf709c9cff4252251a6cdbed7dd481 Author: dtgraves Date: Mon Jul 10 16:10:51 2017 -0700 progress made in EBAMRElliptic. I am close to where I can start actually trying to run stuff. Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRElliptic/AMReX_EBSimpleSolver.H Src/EBAMRElliptic/AMReX_EBSimpleSolver.cpp Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp commit 50babdbf77b1c070833ddcac05f5112ee8b25632 Author: Weiqun Zhang Date: Mon Jul 10 16:02:08 2017 -0700 add hypre tutorial Tutorials/HYPRE/ABecLaplacian/ABL.H Tutorials/HYPRE/ABecLaplacian/ABL.cpp Tutorials/HYPRE/ABecLaplacian/ABL_F.F90 Tutorials/HYPRE/ABecLaplacian/ABL_F.H Tutorials/HYPRE/ABecLaplacian/GNUmakefile Tutorials/HYPRE/ABecLaplacian/Make.package Tutorials/HYPRE/ABecLaplacian/main.cpp commit 74085cb5336c5d01b86bf3106f41cc5fad5bef5e Author: Weiqun Zhang Date: Mon Jul 10 16:01:00 2017 -0700 more hypre Src/Boundary/AMReX_LO_BCTYPES.H Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp commit 32925c4da4ce0ca814bd6fc4cb57098c98f786f6 Author: atmyers Date: Mon Jul 10 15:49:32 2017 -0700 make the distance function a 'check_pair' function. Tutorials/Particles/NeighborList/NeighborListParticleContainer.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp commit 46b291aca16410bfb8a5822647cc56d60e6d8525 Author: atmyers Date: Mon Jul 10 15:38:56 2017 -0700 Moving the neighbor particle stuff into Src/Particle so it can be re-used elsewhere. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 5bdc4367b0e98797c9e0bb601c5956d7d3f6672f Author: atmyers Date: Mon Jul 10 15:37:05 2017 -0700 making these static constexpr seems to improve performance slightly. Tutorials/Particles/NeighborList/NeighborListParticleContainer.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp commit 48c59e44db12568a0747fc930b6fcd1878cd22fe Author: Weiqun Zhang Date: Mon Jul 10 11:16:13 2017 -0700 add some support for Hypre Src/Extern/HYPRE/AMReX_HypreABecLap.H Src/Extern/HYPRE/AMReX_HypreABecLap.cpp Src/Extern/HYPRE/AMReX_HypreABec_3D.F Src/Extern/HYPRE/AMReX_HypreABec_F.H Src/Extern/HYPRE/Make.package Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.hypre commit d97e3f9255e39f677c06bdc90989975549f7d624 Author: Weiqun Zhang Date: Mon Jul 10 10:19:20 2017 -0700 converting size to int instead of int to unsigned. this is what the compiler implicitly does for us. Src/Base/AMReX_FabArray.H commit d1d1401ba3d9a0c624481e73dded3c653687e1ba Author: Weiqun Zhang Date: Mon Jul 10 10:13:35 2017 -0700 move Make.local to the last Tools/GNUMake/Make.defs commit 64363fc42c91a5d8480d88119a64979ce62803b0 Author: atmyers Date: Mon Jul 10 10:08:28 2017 -0700 fix unsigned to signed integer comparison. Src/Base/AMReX_FabArray.H commit 45834b30facc29099aecdbcedfb7c9949ee53322 Merge: 67f27f50e d84be4756 Author: asalmgren Date: Sun Jul 9 16:32:48 2017 -0700 Merge pull request #55 from bcfriesen/add_craypat_docs_part1 Docs: add section describing simple profiling with CrayPat commit d84be47565389f90222b8808e0fbda2b915c9821 Author: Brian Friesen Date: Sun Jul 9 16:24:36 2017 -0700 Docs: add section describing simple profiling with CrayPat Info about advanced profiling techniques with CrayPat will come separately. Docs/AMReXUsersGuide/Profiling/Profiling.tex commit 67f27f50ed63c1ac87763a83f862172fd5db9360 Merge: 75b305207 cee900e7b Author: asalmgren Date: Sun Jul 9 14:53:55 2017 -0700 Merge pull request #51 from atmyers/development Have the test suite also send an email if it has to abort for… commit 75b305207fd16e2ff47f31e379bfa195b4888895 Merge: 012618fb8 752680ff3 Author: asalmgren Date: Sun Jul 9 14:53:31 2017 -0700 Merge pull request #54 from bcfriesen/add_craypat Add CrayPAT support commit 752680ff3cfc7db0a4f5e86e8828842a194aa284 Author: Brian Friesen Date: Fri Jul 7 09:24:48 2017 -0700 Tools: add support for tracing user-defined regions with CrayPAT Tools/GNUMake/Make.defs Tools/GNUMake/tools/Make.craypat commit a031e99e9fb57bf923621f975dbc048c59471a7d Author: dtgraves Date: Sat Jul 8 18:26:46 2017 -0700 needed some functions to get FabArray to compile Src/GeometryShop/AMReX_EBFluxFAB.H commit 1662c7b0b6699f4fce70b44cae0791055f5dda05 Author: Max Katz Date: Sat Jul 8 21:24:03 2017 -0400 Prefer L1 cache to shared memory when available Src/Base/AMReX_CUDA.F90 commit b6bc5383410b8c92fbcf10121fe3f35517f33523 Author: Max Katz Date: Sat Jul 8 20:20:25 2017 -0400 Fix the kernel bounds in AmrLevel::Derive Src/Amr/AMReX_AmrLevel.cpp commit d93ac88cf4cd7f7c707250d51c9e7d4db600360d Author: Max Katz Date: Sat Jul 8 20:11:30 2017 -0400 Turn off CUDA 8 support on Titan Src/Base/AMReX_CUDA.F90 Tools/GNUMake/Make.defs Tools/GNUMake/sites/Make.olcf commit e4c2cfb59cd3c1a8766c2672a285ddd26efd3b5d Author: Max Katz Date: Sat Jul 8 20:10:48 2017 -0400 Return value to suppress compiler warning Src/Base/AMReX_MFIter.H commit cd4bd7b61c90e3f4657909ba9f23af2ae9c238c4 Author: Max Katz Date: Sat Jul 8 17:10:11 2017 -0400 Use correct deleter on operator new[] data Src/Base/AMReX_Device.H commit a571ff614851357867d65c3210f555a1650fb686 Author: Max Katz Date: Sat Jul 8 16:14:43 2017 -0400 Use smaller hunk sizes for small data Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_Box.cpp Src/Base/AMReX_RealBox.cpp commit 18ed8f892c91d0d87e7b50577a6cacda57ab954b Author: Max Katz Date: Sat Jul 8 15:59:46 2017 -0400 Use the correct RealBox lo expression in derive Src/Amr/AMReX_AmrLevel.cpp commit 305136c40e0a6208cd8d3f476cd537ecc59f28df Author: Max Katz Date: Sat Jul 8 15:59:29 2017 -0400 Fix the nullification of RealBox data Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit e76e88f01578c902dd7b66777bbea0d143482151 Author: Max Katz Date: Sat Jul 8 01:37:46 2017 -0400 Clean up various parts of BaseFab Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit e032b7ce00cb0a833506d07e6877b36fda61becf Author: Max Katz Date: Sat Jul 8 01:31:05 2017 -0400 Port copyToMem and copyFromMem to GPU Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit 9bc95808b7dfa64520ab45d85831b29f5f9a66ef Author: Max Katz Date: Sat Jul 8 01:15:55 2017 -0400 Make copyToMem and copyFromMem void and thread-safe Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit 2406801191081accca48d6c1257a1003e316195c Author: Max Katz Date: Sat Jul 8 01:15:15 2017 -0400 Add missing return statement Src/Base/AMReX_Device.H commit f071b98cc7c513dbec441b320715b42c7c73de9a Author: Max Katz Date: Sat Jul 8 00:38:52 2017 -0400 Port BaseFab::norm, sum, dot product to GPU Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit e31305736a1702beb6c546f40095776de1c06122 Author: Max Katz Date: Sat Jul 8 00:38:34 2017 -0400 Add a function to create a device pointer Src/Base/AMReX_Device.H commit 012618fb853ad841533996e588d1486ba2da01a7 Author: atmyers Date: Fri Jul 7 19:07:03 2017 -0700 move building the neighbor list into the compute forces routine. Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp commit 2e2ec5e9f8fd74bd39270b063a394e47771373eb Merge: 66db51d57 742082c88 Author: atmyers Date: Fri Jul 7 16:14:10 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 66db51d57556389f36cd8d2cc55bf1fa3a2d1e12 Author: atmyers Date: Fri Jul 7 16:13:56 2017 -0700 A tutorial that shows how to do neighbor lists for particles the see short-range forces. Tutorials/Particles/NeighborList/GNUmakefile Tutorials/Particles/NeighborList/Make.package Tutorials/Particles/NeighborList/NeighborListParticleContainer.H Tutorials/Particles/NeighborList/NeighborListParticleContainer.cpp Tutorials/Particles/NeighborList/compare.py Tutorials/Particles/NeighborList/inputs Tutorials/Particles/NeighborList/main.cpp Tutorials/Particles/NeighborList/neighbor_list_2d.f90 Tutorials/Particles/NeighborList/neighbor_list_3d.f90 Tutorials/Particles/NeighborList/neighbor_list_F.H commit 742082c885109ea7000aab51af03cb6d2f2be793 Merge: 0d3efd9ce f4be1b0da Author: dtgraves Date: Fri Jul 7 15:16:58 2017 -0700 Merge pull request #53 from AMReX-Codes/dtg_branch Bug fix pull request. commit f4be1b0da001123cf0feaf28ec465acb114bd6c3 Author: dtgraves Date: Fri Jul 7 13:45:53 2017 -0700 got face averaging to work. found subtle bug in EBFaceFAB in the process Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/EBAMRTools/AMReX_EBFortND_F.H Src/GeometryShop/AMReX_BaseEBFaceFABI.H Tests/EBAMRTools/regression/ebCoarseAveTestFace.cpp Tests/EBAMRTools/regression/ebcoarave.inputs commit 5db2c8eaf7604cf29ee0155254a3f644371a91bd Author: Max Katz Date: Fri Jul 7 08:10:42 2017 -0400 Make cudaSetDevice be the first thing we do Src/Base/AMReX_CUDA.F90 commit 2233b1bc376d690efffdb077b0c42f69fe56f783 Author: Max Katz Date: Fri Jul 7 07:09:39 2017 -0400 Clean up the output about which GPU we're using Src/Base/AMReX_CUDA.F90 commit 4410985e29ad64b02ed1c7cff427c44bdd8b61f3 Author: Max Katz Date: Fri Jul 7 01:28:08 2017 -0700 Fix Intel Fortran compiler preprocessing of AMReX_REAL.H Src/Base/AMReX_REAL.H commit 7160ad79e0d6796fc9476d9b2a93589121d77fe9 Author: Max Katz Date: Fri Jul 7 03:15:16 2017 -0400 Add some math functions to amrex_fort_module Src/Base/AMReX_fort_mod.F90 commit 8193d1bb45bcbdec66627dca7c7f537e23c48d37 Author: dtgraves Date: Thu Jul 6 16:21:51 2017 -0700 added the ability to averaging face centered data with EB. Does not pass its test yet. Src/EBAMRElliptic/AMReX_EBEllipticFort.F90 Src/EBAMRTools/AMReX_EBCoarseAverage.H Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/EBAMRTools/AMReX_EBFortND_F.H Tests/EBAMRTools/README Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/ebCoarseAveTestFace.cpp commit 0d3efd9ce4e8f1eaff8f03ba78351fa6f01599ba Author: Weiqun Zhang Date: Thu Jul 6 15:43:23 2017 -0700 fix one-sided MPI Src/Base/AMReX_FabArray.H commit 3724a070adf93b46c4170eccb6d295e466abaed8 Author: Michele Rosso Date: Thu Jul 6 10:12:52 2017 -0700 Fix typo in Cmake files. Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit aa38d21611d32ee0937b3c4a2d8e67d3d89aaa9a Author: Michele Rosso Date: Thu Jul 6 10:12:52 2017 -0700 Fix typo in Cmake files. Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit d5eca97ee2b6b691539a14e68d03d41ba9238103 Author: Max Katz Date: Thu Jul 6 07:36:34 2017 -0400 Use an Arena to store device reducer data Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 1efd3268048a42e6c87117f852f9d8947f538116 Author: Max Katz Date: Thu Jul 6 06:36:07 2017 -0400 Add a MFIter reduction operation for Reals Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit e5f7b2566615419d57916a271f1973e13af04aa7 Author: Max Katz Date: Thu Jul 6 04:06:28 2017 -0400 Add a MFIter function to register a RealBox Src/Amr/AMReX_AmrLevel.cpp Src/Base/AMReX_MFIter.H commit 9d61de38c7e60d54751d7e22eb7b596abe7ea601 Author: dtgraves Date: Wed Jul 5 15:47:58 2017 -0700 Just to keep these messages different, I am looking for synonyms for 'slog'. Trudge? Schlep? Src/EBAMRElliptic/AMReX_AMRMultiGrid.H Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRElliptic/AMReX_EBEllipticFort.F90 Src/EBAMRElliptic/AMReX_EBEllipticFort_F.H Src/EBAMRElliptic/Make.package Tests/EBAMRElliptic/exec/GNUmakefile Tests/EBAMRElliptic/exec/cond.inputs Tests/EBAMRElliptic/exec/conductivitySolve.cpp commit af37f2ffefce8ca4b431508ccc82c5a6ffc8b8e8 Author: Max Katz Date: Wed Jul 5 01:13:17 2017 -0400 Make the CUDA device ID public Src/Base/AMReX_CUDA.F90 commit 75751d9cea176e04976c1d61eb0d60f59fd81ecd Author: Max Katz Date: Tue Jul 4 19:10:00 2017 -0400 Get F90 build with CUDA working again Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/GPackage.mak commit 822cc142014d3f285ce50b7c6a1c17dd76af831d Author: Max Katz Date: Tue Jul 4 18:36:15 2017 -0400 Do not compile dim3 without using nvcc Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 4e64d8bd6f952fbe5216755aa348a67340b310dd Author: Max Katz Date: Tue Jul 4 03:18:32 2017 -0400 Fix the synchronize strategy in ParallelCopy Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_FabArray.H commit f312046e076319bc39cfc78d628239c58ba99e6a Author: Max Katz Date: Tue Jul 4 01:53:24 2017 -0400 Make StateData::FillBoundary asynchronous Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp commit 99def5b23976e64aaec86d2488234a26b0cdd3f1 Author: dtgraves Date: Mon Jul 3 15:45:03 2017 -0700 Continued the EBAMRElliptic slog. There is a lot here. Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBEllipticFort.F90 Src/EBAMRElliptic/AMReX_EBEllipticFort_F.H Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp commit 86b5717e8e6c7eee5f374487be0a018127b53e6a Author: Max Katz Date: Mon Jul 3 18:34:01 2017 -0400 Disable FabArrayBase tiling when using CUDA Src/Base/AMReX_FabArrayBase.cpp commit 8cf71300a224a0559d55632bf7a59999674d8119 Author: Max Katz Date: Mon Jul 3 17:43:54 2017 -0400 Use MFIter pointer registration in AmrLevel::Derive Src/Amr/AMReX_AmrLevel.cpp commit fb8073ec40684b034a22df080c7ff37ea5f144aa Author: Max Katz Date: Mon Jul 3 17:18:25 2017 -0400 Add MFIter::get_fortran_pointer to assist with scalar values for device routines There are cases in the code where we pass scalar values like the current time to a Fortran kernel, and we pass it by reference. An example is AmrLevel::Derive. For backward compatibility we do not want to change the interface -- that would break a lot of codes. But we also want to pass a device pointer for the CUDA version, and to allow asynchrony across MFIter indices. The solution is to store a shared_ptr with a pinned host (or device, but I've gone with pinned host for now to avoid a cudaMemcpy call) copy of the data, so that the lifetime of the data is the lifetime of the MFIter. For the CPU version of the code, the function effectively does nothing. Src/Base/AMReX_MFIter.H commit 8ec8dac3f9e0831a07b67af461dd80f6689544d1 Author: Max Katz Date: Mon Jul 3 16:38:55 2017 -0400 Clean up temporary pointer creation Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_Device.H commit a00020d60b30a1707c8d57c34d13be796b38c54f Author: Ann Almgren Date: Sun Jul 2 17:07:19 2017 -0700 Fix the construction of the cost function in makeKnapSack Src/Base/AMReX_DistributionMapping.cpp commit d52c7de58913db31d5fe63352d129794692f7b4f Author: Max Katz Date: Mon Jul 3 05:28:07 2017 -0400 Add hook to start profiler Tutorials/GPU/HeatEquation_EX1_C/main.cpp commit ed21feaf630aeb7a069a98e2ee8d3d4aa9dd4ffc Author: Max Katz Date: Mon Jul 3 05:09:01 2017 -0400 Avoid use of parallel module in CUDA initialization Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit afeaa2ca94838bf6ad85df3741dda80c0976621d Author: Max Katz Date: Mon Jul 3 04:46:06 2017 -0400 Avoid calls to cudaFree/cudaFreeHost at end of program Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit b3dc97af053f93e13cb8cf4844c1b36791e38366 Author: Max Katz Date: Mon Jul 3 04:03:48 2017 -0400 Do not throw error for CUDA runtime unloading Src/Base/AMReX_CUDA.F90 commit 61e2f0bb374928a8c5c1b3abcdef7e394fe7167d Author: Max Katz Date: Mon Jul 3 03:37:35 2017 -0400 Delay initialization of the RealBox device memory Geometry contains a static RealBox object, and it was creating problems that a CUDA API call (to allocate memory) was being called before we got to the initialize_cuda step. By delaying allocation of the device memory until the first time we actually access the data, we still get the desired behavior from RealBox while not breaking the intended behavior that no CUDA API calls are done until we've mapped the MPI ranks to GPUs. Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit a766e131566e9f199a838378e0e2a6af1668abf2 Author: Max Katz Date: Mon Jul 3 01:59:38 2017 -0400 Enable round-robin assignment of MPI ranks to GPUs Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 275a1c6818ea8cc68a650cf14420080dfdd7cccd Author: Max Katz Date: Mon Jul 3 01:59:14 2017 -0400 Use nvcc as the MPI host compiler Tools/GNUMake/sites/Make.olcf commit e27d391e79c25dc948dec9ad38e62f5989b20544 Author: Max Katz Date: Mon Jul 3 01:58:43 2017 -0400 Define a host compiler variable Tools/GNUMake/comps/ibm.mak Tools/GNUMake/comps/pgi.mak commit 046582caaf41850033cf902f00f0c21d83e4ea22 Author: Max Katz Date: Sun Jul 2 21:14:14 2017 -0400 Add NVML build support Tools/GNUMake/Make.defs Tools/GNUMake/sites/Make.olcf commit 8aaab29289414865bbd9c31499d6a59adc4d942d Author: Ann Almgren Date: Sun Jul 2 17:07:19 2017 -0700 Fix the construction of the cost function in makeKnapSack Src/Base/AMReX_DistributionMapping.cpp commit 4a8c2f8d12ef14d08284b9a4d8d25ffa10d2a295 Author: Max Katz Date: Sun Jul 2 17:59:28 2017 -0400 Port more BaseFab routines to the GPU Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit 4aeaea56eab257fd0ad69cfa4e7975a485344277 Author: Max Katz Date: Sun Jul 2 16:36:17 2017 -0400 Add function to get threads and blocks in C++ Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 179cb095e6ad25d712703ddb54f1d628314db12d Author: Max Katz Date: Sun Jul 2 16:35:56 2017 -0400 Remove the CUDA compiler Tools/GNUMake/Make.defs Tools/GNUMake/comps/cuda.mak commit 960abe8a11f9deb12114b955568867b436f3b2bb Author: Max Katz Date: Sun Jul 2 16:33:33 2017 -0400 Use nvcc/g++ as C/C++ compiler when using CUDA with IBM Tools/GNUMake/comps/ibm.mak commit 46947670736b46cd649b65591517482a010ed468 Author: Max Katz Date: Sun Jul 2 13:56:15 2017 -0400 Use nvcc/g++ as C/C++ compiler when using CUDA with PGI Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/pgi.mak commit 579b9f1db3e39e8163ba86279b09326406c0b49e Author: Max Katz Date: Sun Jul 2 13:50:04 2017 -0400 Use the new dx call in advance Tutorials/GPU/HeatEquation_EX1_C/advance.cpp commit 797ab87e403d6523e9417d58959faa150d8c9443 Author: Weiqun Zhang Date: Sun Jul 2 08:47:47 2017 -0700 avoid self-move Src/Particle/AMReX_ParticleContainerI.H commit 49667d6aca6bf835df9605bec6d551b52334016d Author: Max Katz Date: Sun Jul 2 05:12:32 2017 -0400 Use pinned data for RealBox and CoordSys Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit 071dc9154dfcd1eb86ea7291176ab49771401005 Author: Max Katz Date: Sun Jul 2 05:11:48 2017 -0400 Make get_host_pointer a no-op for non-CUDA builds Src/Base/AMReX_Device.cpp commit 3246e2f71e6f71bf567812dcb6c6a697d0e96496 Author: Max Katz Date: Sun Jul 2 03:50:49 2017 -0400 Insert a device synchronize after MultiFab creation Src/Base/AMReX_FabArray.H commit dc1e3306479c8688ff4d14d34a77bdce2c024682 Author: Max Katz Date: Sat Jul 1 07:45:02 2017 -0400 Get FillDomainBoundary working on the GPU Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F90 Src/Base/AMReX_filcc_mod.F90 commit 260d5f7f7b729125caa206087091c0d999baa567 Author: Max Katz Date: Sat Jul 1 07:29:07 2017 -0400 Fix error in the BaseFab arenas Src/Base/AMReX_BaseFab.cpp commit 2a31ae6a12bb3e99fc9282ce5cb817828bf3a47b Author: Max Katz Date: Sat Jul 1 07:20:23 2017 -0400 Make some some arguments const Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit ece54523d70f1ae109b75d11220463e407364075 Author: Max Katz Date: Sat Jul 1 05:20:04 2017 -0400 Port the 1D and 2D filcc to GPU-friendly versions Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 commit 1f81189ac35883991e0370b0bfcc99fd9200127b Author: Max Katz Date: Sat Jul 1 04:09:40 2017 -0400 Complete GPU-friendly port of 3D filcc Src/Base/AMReX_FILCC_3D.F90 commit e5e5e82cec51bb1dbf44ac04de1a50ce5badb247 Merge: 2ebae0a52 7f5907b62 Author: Max Katz Date: Sat Jul 1 00:52:08 2017 -0400 Merge branch 'gpu' into gpu_lessmanaged commit 7f5907b62a807c027184cd6fd894234abca9c915 Author: Max Katz Date: Sat Jul 1 00:51:27 2017 -0400 Use a new thread block layout Src/Base/AMReX_CUDA.F90 commit 14841e85e74a1626a4d011260c717e3373c86d00 Author: dtgraves Date: Fri Jun 30 15:44:13 2017 -0700 the slog continues Src/EBAMRElliptic/AMReX_ConductivityBaseDomainBC.H Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBEllipticFort.F90 Src/EBAMRElliptic/AMReX_EBEllipticFort_F.H Src/EBAMRElliptic/AMReX_VCAggStencil.H Src/EBAMRElliptic/AMReX_VCAggStencil.cpp Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/aggpwlfpTest.cpp Tests/EBAMRTools/regression/simpleMeshRefine.cpp commit cee900e7b197facc6265f4e18c926d0fe4376720 Author: Andrew Myers Date: Fri Jun 30 15:35:49 2017 -0700 Have the test suite also send an email if it has to abort for whatever reason (if emails are turned on...) Tools/RegressionTesting/params.py Tools/RegressionTesting/test_util.py commit 3d87e1a4a3655429dcacb90c3cff15936f2f2396 Author: Weiqun Zhang Date: Fri Jun 30 15:03:01 2017 -0700 option to turn off checkInput() Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit 0b53d33a7e7d45d12fac718d49ecef0e6af8af1c Merge: b1f6154f3 c861721c4 Author: Weiqun Zhang Date: Fri Jun 30 12:23:07 2017 -0700 Merge branch 'master' into development Conflicts: Tools/CMake/PreprocessAMReXFortran90.cmake commit b1f6154f37d60f63188995842873f14e79bdc9fe Author: Ann Almgren Date: Fri Jun 30 09:44:23 2017 -0700 Fix the sizing and offset of mf_to_be_filled in AssignDensityFort. Src/Particle/AMReX_ParticleContainerI.H commit 5277d6962045881c3a76c737c234eb61df648ad0 Author: Andrew Myers Date: Thu Jun 29 23:00:29 2017 -0700 fix momentum deposition for Nyx. Src/Particle/AMReX_Particle_mod_3d.F90 commit ebf60c3a2cadd94d3c84f2647a1eb02e61315997 Author: Andrew Myers Date: Thu Jun 29 22:58:49 2017 -0700 don't need my own plot file routine for this test. Tests/Particles/AssignDensity/main.cpp commit 2ebae0a5214dd8d983aee92587268209e1086109 Merge: 503e8fa6e d2255f4f1 Author: Max Katz Date: Fri Jun 30 01:47:28 2017 -0400 Merge branch 'gpu' into gpu_lessmanaged commit 503e8fa6ed77b4b23e8e67fccfd7e96625168bd4 Author: Max Katz Date: Fri Jun 30 01:43:56 2017 -0400 Remove managed memory in Box class Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit d2255f4f157564e0b12daed872e24825498304e5 Author: Max Katz Date: Fri Jun 30 01:14:22 2017 -0400 Fix the obsolete macros Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 commit f4d22153d21a07d17bd523565e76c7b76e67ec4d Author: Max Katz Date: Fri Jun 30 01:09:54 2017 -0400 Add some forgotten files to the heat equation case Tutorials/GPU/HeatEquation_EX1_C/advance.cpp Tutorials/GPU/HeatEquation_EX1_C/myfunc.H Tutorials/GPU/HeatEquation_EX1_C/physbc.cpp commit be05a9ce34b3f6c8baa4b1ce24f02f170b9c0bbd Author: Max Katz Date: Fri Jun 30 01:00:52 2017 -0400 Set the null stream as the default stream Src/Base/AMReX_CUDA.F90 commit a5b51b07fd5f3e28924eba34fcb6ab25b1c99817 Merge: a523628e4 b9bd187e8 Author: Max Katz Date: Fri Jun 30 00:58:12 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit ed5f3950dba2b25383c974349a8d514ed615a49c Merge: d4f2bf517 d43bc9674 Author: vince Date: Thu Jun 29 17:27:16 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d4f2bf517c618ae2a7a5ccae4e2f53dcc9e6b5d2 Author: vince Date: Thu Jun 29 17:27:12 2017 -0700 fixes for 1d slicing. Src/Extern/amrdata/AMReX_DataServices.cpp commit d43bc9674e3a5e0a3135f8125cffcba6b814cc79 Merge: 87f7e041f 1e27208ca Author: Andrew Myers Date: Thu Jun 29 17:26:14 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 87f7e041fa7f40874b61846f9ff3b6f0de78a0ba Author: Andrew Myers Date: Thu Jun 29 17:25:57 2017 -0700 Make eps an optional argument instead of a static member of RealBox. Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit 1e27208ca06bca1c13c4d66085fc24772bfcfad0 Author: Ann Almgren Date: Thu Jun 29 16:39:02 2017 -0700 Add some checking of input parameters -- the tests here are a subset of the tests that Amr.cpp does. Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit d4a46130741353089adb99844cf675776e0a71f5 Author: Ann Almgren Date: Thu Jun 29 16:38:49 2017 -0700 Fix the error messages Src/Amr/AMReX_Amr.cpp commit b8fe4dfd4436de3d116b1732c56735505544e911 Merge: 7d33f6c63 255efdbbd Author: Ann Almgren Date: Thu Jun 29 12:52:42 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 7d33f6c6337f59908dbd4dd199fb8b7c674b06b9 Author: Ann Almgren Date: Thu Jun 29 12:50:05 2017 -0700 Update how grids are created (section 5.3.5) Docs/AMReXUsersGuide/AmrCore/AmrCore.tex commit 255efdbbd2324f490c0164d584a852383c0ebd2a Merge: dcbc11986 bb78b917d Author: Michele Rosso Date: Thu Jun 29 12:37:37 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit dcbc119863b7e799218bfbd998d5f9595b7f8a05 Author: Michele Rosso Date: Thu Jun 29 12:37:24 2017 -0700 Some Cmake clean-up CMakeLists.txt Tools/CMake/TransformVersion.cmake commit b9bd187e84067fdd047f2b1edc8bd86db8bf8ac6 Merge: 17dd945c4 bb78b917d Author: Michael Zingale Date: Thu Jun 29 04:44:04 2017 -0400 Merge branch 'development' into gpu commit bb78b917d547318bea14b32c2f70d99cc134cf77 Author: Weiqun Zhang Date: Wed Jun 28 17:31:57 2017 -0700 fix amrex_particle_real for typecheck Tools/GNUMake/Make.rules commit 7d56a2acbc42c7ccfc8f2ddb4b2a7ecca5206120 Merge: ebb13289d 1b2f01efe Author: vince Date: Wed Jun 28 17:11:57 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit ebb13289d5fe7b35bb3c906359afcdd71fc9a3d6 Author: vince Date: Wed Jun 28 17:11:42 2017 -0700 added to the profiling and visualization documentation. Docs/AMReXUsersGuide/Profiling/Profiling.tex Docs/AMReXUsersGuide/Visualization/Visualization.tex commit 1b2f01efe1945286552a5ca7058eca154b792efb Merge: e2cb446e9 770a6095d Author: Ann Almgren Date: Wed Jun 28 16:55:17 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit e2cb446e98a0e83de28926d45390a5ca2a33393b Author: Ann Almgren Date: Wed Jun 28 16:54:44 2017 -0700 Update the Grid Creation subsection. Docs/AMReXUsersGuide/AmrCore/AmrCore.tex commit 810e4b52c870f676f872868cc90d3a6a10ffdc1a Author: Ann Almgren Date: Wed Jun 28 16:54:33 2017 -0700 fix typo in comment Src/AmrCore/AMReX_AmrMesh.cpp commit 770a6095d69daa4e959f50cb993f14c3df1f6e68 Merge: 496eacd91 817b15a9d Author: Michele Rosso Date: Wed Jun 28 16:29:22 2017 -0700 Merge branch 'mr-cmake' into development commit 817b15a9d6e7b36850eb23c87f7f4e2124215c80 Author: Michele Rosso Date: Wed Jun 28 16:28:37 2017 -0700 Update documentation on cmake Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex commit 92b50c17588018e41e0e176da554c6bde810d351 Author: Michele Rosso Date: Wed Jun 28 15:52:00 2017 -0700 Add new pre-preprocessor flags to cmake implementation Tools/CMake/AMReX_Config.cmake commit 119c2aa3834c78e9cb254a62e0d8e9e669e1bc2e Merge: e3179dab8 c38add954 Author: Michele Rosso Date: Wed Jun 28 15:34:44 2017 -0700 Merge branch 'development' into mr-cmake commit 496eacd9186e25ec0d2f7e4680e5ce39d25c5f31 Author: Weiqun Zhang Date: Wed Jun 28 15:28:59 2017 -0700 User's Guide: wip Docs/AMReXUsersGuide/Debugging/Debugging.tex commit 1845647254111d63169a337ecfe75a614df73010 Author: Weiqun Zhang Date: Wed Jun 28 15:22:46 2017 -0700 update deprecated gfortran option Tools/GNUMake/comps/gnu.mak commit e3179dab881c6d79b82a99ef0fab4f559ba33d26 Author: Michele Rosso Date: Wed Jun 28 14:57:44 2017 -0700 Some clean-up Tools/CMake/InstallManager.cmake commit 6ec42ae05816ded9042db825aa989ba7d92a52cc Author: Michele Rosso Date: Wed Jun 28 13:29:04 2017 -0700 Fix typo CMakeLists.txt commit f3e78d9a4897fb12afef4d3e7e6e1a0de01afcac Author: Michele Rosso Date: Wed Jun 28 13:03:22 2017 -0700 More changes to cmake system CMakeLists.txt Src/Amr/CMakeLists.txt Src/AmrCore/CMakeLists.txt Src/Base/CMakeLists.txt Src/Boundary/CMakeLists.txt Src/Extern/amrdata/CMakeLists.txt Src/F_BaseLib/CMakeLists.txt Src/LinearSolvers/C_CellMG/CMakeLists.txt Src/LinearSolvers/C_CellMG4/CMakeLists.txt Src/LinearSolvers/C_TensorMG/CMakeLists.txt Src/LinearSolvers/C_to_F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt Src/Particle/CMakeLists.txt Tools/CMake/AMReXConfig.cmake.in Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_Utils.cmake Tools/CMake/InstallManager.cmake commit c38add954b1cc882257b1a0184d5952c34e2c52e Author: Andrew Myers Date: Wed Jun 28 10:02:29 2017 -0700 switch order of these loops. Src/Particle/AMReX_OMPDepositionHelper_1d.F90 Src/Particle/AMReX_OMPDepositionHelper_2d.F90 Src/Particle/AMReX_OMPDepositionHelper_3d.F90 commit 3506f5aea50d27237dda43df3ba4611fd4eda638 Author: Ann Almgren Date: Wed Jun 28 09:27:20 2017 -0700 Resolve amrex namespace problems. Src/Extern/hpgmg/BL_HPGMG.H Src/Extern/hpgmg/BL_HPGMG.cpp commit 7703a0266ae088d05df9a2eb445775516adddc9a Author: Ann Almgren Date: Tue Jun 27 18:10:42 2017 -0700 Make sure to resize the local fab to be tile_size*ncomp (to allow for ncomp > 1) Src/Particle/AMReX_ParticleContainerI.H commit 7b40e8638869cf52f7012db0f61f6fd53b085691 Merge: 6a44c16e3 b88b9bc86 Author: Andrew Myers Date: Tue Jun 27 17:44:37 2017 -0700 merging commit 6a44c16e3c41c8c587dba6fd98c8baf470b09651 Author: Andrew Myers Date: Tue Jun 27 17:43:35 2017 -0700 Forgot to turn off ncomp check here. Src/Particle/AMReX_ParticleContainerI.H commit b88b9bc86234a2202ce5b6e17a4c35db4dc9eb62 Author: Ann Almgren Date: Tue Jun 27 17:43:11 2017 -0700 1) Fix incorrect print statement 2) Remove assertion on (ncomp == 1) in AssignDensityFort since we now correctly take ncomp > 1 cases. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H commit 4fdff49897d3c0d814e326ed7e5d2793077abe51 Author: Ann Almgren Date: Tue Jun 27 16:57:27 2017 -0700 Fix initialization of nthreads -- move it into InitRandom Src/Base/AMReX_Utility.cpp commit e10b9773ad4d35d293a33bca85d8cdf0491b02bb Author: Andrew Myers Date: Tue Jun 27 16:41:15 2017 -0700 generalize fortran deposition routines to use ncomps. Src/Particle/AMReX_OMPDepositionHelper_1d.F90 Src/Particle/AMReX_OMPDepositionHelper_2d.F90 Src/Particle/AMReX_OMPDepositionHelper_3d.F90 Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particle_mod_1d.F90 Src/Particle/AMReX_Particle_mod_2d.F90 Src/Particle/AMReX_Particle_mod_3d.F90 Src/Particle/AMReX_Particles_F.H commit 49b1035b475169335bc4a568f2399731a6a0091b Merge: 6678d9470 438e3b7b9 Author: Ann Almgren Date: Tue Jun 27 16:00:16 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 6678d94705e2957b5308e4ac93971b6bd517c871 Author: Ann Almgren Date: Tue Jun 27 16:00:01 2017 -0700 Added run-time parameters and an explanation of how grids are created Docs/AMReXUsersGuide/AmrCore/AmrCore.tex commit 438e3b7b9ed62a0b462bcbaff7929b268e0b61cc Author: Andy Nonaka Date: Tue Jun 27 15:25:13 2017 -0700 updates to doc Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Docs/AMReXUsersGuide/Introduction/Introduction.tex commit 51875485fe51d25127274967cbaf4dc8f9d2fc7f Author: Weiqun Zhang Date: Tue Jun 27 10:14:16 2017 -0700 User's Guide: octree Docs/AMReXUsersGuide/Fortran/Fortran.tex commit 4e6ab426a631fcd77c0e27878e72394d4b7fe147 Author: Michele Rosso Date: Tue Jun 27 08:58:35 2017 -0700 Add source file for tiny profiling Src/Base/CMakeLists.txt commit 3d51ec7579a9ee4f3c7e305cf1b6e88f27ea3bcf Author: Weiqun Zhang Date: Tue Jun 27 06:33:29 2017 -0700 remove old license Src/Base/OpenSource.txt commit b9183980225ffaeab27433e2cd9df2e8f2ce4dcb Author: Weiqun Zhang Date: Tue Jun 27 06:28:08 2017 -0700 fix tutorials Tutorials/Amr/Advection_F/Source/my_amr_mod.F90 Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90 commit a523628e4f4c68c97631172b8419d400f6e7495d Author: Max Katz Date: Mon Jun 26 23:51:58 2017 -0400 Start the profiler at the end of Amr initialization Src/Amr/AMReX_Amr.cpp commit 5653d6de43828c4c3aa4c3bf53de281c8ff46197 Author: Max Katz Date: Mon Jun 26 23:46:11 2017 -0400 Add C++ hooks to start and stop the profiler Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit f7fc1d4834afe5fbb4beb70906563d2d1494b77f Author: Weiqun Zhang Date: Mon Jun 26 18:05:24 2017 -0700 User's Guide: AMR in Fortran interface Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/Fortran/Fortran.tex Docs/AMReXUsersGuide/GNUmakefile commit a697a7e099cee2bbc500613307d4e4619ea03ef6 Author: Michele Rosso Date: Mon Jun 26 17:40:13 2017 -0700 Add option for tiny profiling Tools/CMake/AMReX_Config.cmake commit 201eb40132307cb7db093961eaafe040358f1d89 Author: Weiqun Zhang Date: Mon Jun 26 16:46:53 2017 -0700 F_Interfaces: fix component index bug Docs/AMReXUsersGuide/Fortran/Fortran.tex Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 1d5e077474e37106afd6cdbd415d183d281ce70c Author: Weiqun Zhang Date: Mon Jun 26 14:18:58 2017 -0700 User's Guide: Fortran interface basics Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/Fortran/Fortran.tex Tutorials/Basic/HeatEquation_EX1_F/advance.f90 commit 78cf063775a4d94ae7bbdc890bde5625816549e6 Merge: 77f52a245 6ed367be6 Author: Klaus Weide Date: Mon Jun 26 15:14:10 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6ed367be6d0dd5fb2d50d6f78d1ee7a82126ecf7 Author: Weiqun Zhang Date: Mon Jun 26 12:40:26 2017 -0700 F_interfaces: fix bug in setval and parallelcopy; note that the component index starts with 1 in Fortran Src/Base/AMReX_fort_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 77f52a245b4a7974e72a560cfaa5266001d61860 Merge: 47ca57149 4b3c08000 Author: Klaus Weide Date: Mon Jun 26 11:26:44 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 17dd945c421994bae49f51694b3e15157ef7969a Author: Michael Zingale Date: Mon Jun 26 05:05:51 2017 -0400 fix linking with IBM XL and CUDA Tools/GNUMake/comps/ibm.mak Tools/GNUMake/sites/Make.olcf commit d8122d674927efb0e37158fe5e96d917772e84aa Author: Max Katz Date: Mon Jun 26 03:06:51 2017 -0400 Skip finalization routine if using XL Src/Base/AMReX_parmparse_mod.F90 commit 2c23ec392923146d2c4dc7c5843c1394d6d4aa67 Author: Max Katz Date: Mon Jun 26 02:52:34 2017 -0400 Remove CUF kernels; these should be replaced with real CUDA later Src/Base/AMReX_BaseFab_nd.F90 commit 0cb8e4ece866ac6d7f8e1b2e82924c2456785bb5 Author: Max Katz Date: Mon Jun 26 02:48:24 2017 -0400 Replace logical with integer to satisfy bind(c) property Src/Base/AMReX_CUDA.F90 commit 0d4606869a47bed795a225b463c80dada6acb73d Author: Max Katz Date: Mon Jun 26 02:41:19 2017 -0400 Create interface to cudaProfilerStart/cudaProfilerStop Src/Base/AMReX_CUDA.F90 commit 0c871b8ad32844eb23c7712df7e0031c18b6d33d Author: Max Katz Date: Mon Jun 26 02:30:09 2017 -0400 Use thread-safe XL compiler when using CUDA Tools/GNUMake/comps/ibm.mak commit 151594f64ea39e5dfa5af1648bbbc92567614d14 Author: Max Katz Date: Mon Jun 26 01:40:24 2017 -0400 Redefine the CUDA attributes(global/device) macros Tools/GNUMake/Make.defs commit 994f6c425b431d2dddd258e2762d18b0cfaa135e Author: Max Katz Date: Mon Jun 26 01:09:13 2017 -0400 Create device copies of data in AmrLevel::derive Src/Amr/AMReX_AmrLevel.cpp commit 066400613b42315671e7588b8678a398d98a1931 Author: Max Katz Date: Mon Jun 26 00:27:39 2017 -0400 Create device copies of data in FillBoundary Src/Amr/AMReX_StateData.cpp commit 6c811c1feb72d7937a9184f41968ead76e5c4a0e Author: Max Katz Date: Sun Jun 25 17:21:39 2017 -0400 Add Device hook for stream synchronize Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 4b3c08000b1402ea060ae871ce90995dc4a64737 Author: atmyers Date: Sun Jun 25 11:33:03 2017 -0700 don't need to define partMF in this test anymore. Tests/Particles/AssignMultiLevelDensity/main.cpp commit 3ced02f54bffa38b8e2106d6e12317919119a569 Author: atmyers Date: Sun Jun 25 11:30:46 2017 -0700 make behavior of AssignDensityFort consistent with AssignDensity in that the mfs don't need to be defined before being passed in. Src/Particle/AMReX_ParticleContainerI.H commit 28cb9408da28f5850c7364f3587bc00b776e84c4 Author: Max Katz Date: Sun Jun 25 06:01:40 2017 -0400 Have registerBox return the box Src/Base/AMReX_MFIter.H commit 350de886410ac4e3c4ffd642cb295edd667441c8 Author: Max Katz Date: Sun Jun 25 05:11:02 2017 -0400 Add Device hooks for malloc, free, memcpy Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit b6dc512f665ba354f2ea8248f72704911b55f68b Author: Weiqun Zhang Date: Sat Jun 24 22:09:06 2017 -0700 F_Interfaces: add amrex_multifab%parallel_copy Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 2562fc57c5cc6cd416c6ee9d55fd9c8b8af35136 Author: Max Katz Date: Sat Jun 24 21:19:08 2017 -0400 Use long x-blocks for coalesced memory access Src/Base/AMReX_CUDA.F90 commit ac691625190a6ca6768d0c681aad00f6c88cbddb Author: Ann Almgren Date: Sat Jun 24 16:57:16 2017 -0700 Remove all references to STATIONDATA, SLABSTAT or MAKESLICE in AMReX_Amr* or Make.package or CMakelists.txt Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/CMakeLists.txt Src/Amr/Make.package commit 6f2c2d163e13df2d6dbb97e613facdd427e54797 Author: Ann Almgren Date: Sat Jun 24 16:53:27 2017 -0700 None of the applications use MAKESLIDE_3D any more (and it can always be recovered from git history and/or the old BoxLib repo) Src/Amr/AMReX_MAKESLICE_3D.F Src/Amr/AMReX_MAKESLICE_F.H commit f944db74206442afd73755831afdb5c6e8fd6e0b Author: Ann Almgren Date: Sat Jun 24 16:52:17 2017 -0700 None of the applications use SlabStat any more (and it can always be recovered from git history and/or the old BoxLib repo) Src/Amr/AMReX_SLABSTAT_1D.F Src/Amr/AMReX_SLABSTAT_2D.F Src/Amr/AMReX_SLABSTAT_3D.F Src/Amr/AMReX_SLABSTAT_F.H Src/Amr/AMReX_SlabStat.H Src/Amr/AMReX_SlabStat.cpp commit b69a907f2af738a1f6ad76048bcd74a324270cc5 Author: Ann Almgren Date: Sat Jun 24 16:49:49 2017 -0700 None of the applications use StationData any more (and it can always be recovered from git history and/or the old BoxLib repo) Src/Amr/AMReX_StationData.H Src/Amr/AMReX_StationData.cpp commit 3ef3e8c1def18a008a147d3c088e965b738d1d1c Author: Ann Almgren Date: Sat Jun 24 16:47:52 2017 -0700 Update the Profiling section and spell-check the entire document. Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Docs/AMReXUsersGuide/Fortran/Fortran.tex Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Docs/AMReXUsersGuide/Particle/Particle.tex Docs/AMReXUsersGuide/Profiling/Profiling.tex Docs/AMReXUsersGuide/Visualization/Visualization.tex commit eac0308a1fd27232c62ccb694a97cc473f729a4f Author: Ann Almgren Date: Sat Jun 24 16:31:45 2017 -0700 Add material from Readme.profiling -- but this still needs Vince to make a pass. Docs/AMReXUsersGuide/Profiling/Profiling.tex commit 16d29be102c3efa03f5cbafc974f288b97375be0 Author: Max Katz Date: Sat Jun 24 18:07:12 2017 -0400 Sync up HeatEquation with development The filcc call had to be modified temporarily until we get the BCs working on the GPU. Src/Base/AMReX_BCUtil.cpp Tutorials/GPU/HeatEquation_EX1_C/Make.package Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/inputs_2d Tutorials/GPU/HeatEquation_EX1_C/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/main.cpp Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H commit 47846d54c23f2315db3050c7339a836089470c86 Author: Max Katz Date: Sat Jun 24 17:35:33 2017 -0400 Create a device pointer for a FAB's nvar Src/Base/AMReX_Arena.H Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp commit 852455548b0049af633114d2e60f5a3c833e772d Merge: 47ca57149 17c04cc7c Author: Klaus Weide Date: Sat Jun 24 16:15:19 2017 -0500 Merge branch 'development' into kw-development commit d511c446f8381cd8582470f82a069a2101c39020 Author: Max Katz Date: Sat Jun 24 17:04:05 2017 -0400 Set blocks and threads before entering Fortran Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_StateData.cpp Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 01e6ccb2e0a2592de70788e8dae5a76ba35b0961 Author: Max Katz Date: Sat Jun 24 16:24:51 2017 -0400 Create a current CUDA stream variable Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_CUDA.F90 commit 17c04cc7c600d5fff4336c64382518ecbe1427ba Merge: 389164b8d 95c88b10d Author: Andrew Myers Date: Sat Jun 24 12:56:46 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 389164b8ddb2c7a42bab4a442300d14d69364bab Author: Andrew Myers Date: Sat Jun 24 12:56:24 2017 -0700 A version of the electrostatic pic tutorial that works in 2D. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/GNUmakefile Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_2d.f90 Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H Tutorials/Particles/ElectrostaticPIC/inputs Tutorials/Particles/ElectrostaticPIC/main.cpp commit c1469e80701c23ac44c166b35897f68c2e8aec58 Author: Max Katz Date: Sat Jun 24 12:57:51 2017 -0400 Clarify intent of dm Src/F_BaseLib/knapsack.f90 commit 983586101a9ed25c7a87ad46885678d7303a3a0b Merge: 65b219f35 06bb82a17 Author: Max Katz Date: Sat Jun 24 09:55:55 2017 -0700 Merge pull request #47 from dwillcox/gpu Workaround for AMReX Issue 46 commit 65b219f353cc046deac2d554bcf6ab0a273a92b9 Author: Max Katz Date: Sat Jun 24 03:08:09 2017 -0400 Lower the optimization level when using CUDA Tools/GNUMake/comps/pgi.mak commit e90adc031b8985a7b680104d15809c357aaa303a Author: Max Katz Date: Sat Jun 24 01:43:39 2017 -0400 Do not set default stream, to avoid compiler bug Src/Base/AMReX_CUDA.F90 commit 06bb82a17cb0c15f2c7287a61158a2d84bd7e530 Merge: eba048b30 759925a5a Author: dwillcox Date: Sat Jun 24 00:54:07 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit eba048b30c335063780160c98573b67e6f1f3eed Author: dwillcox Date: Sat Jun 24 00:53:25 2017 -0400 Pass dm to function make_box_key as workaround for suspected PGI 17.4 bug. Src/F_BaseLib/knapsack.f90 commit 759925a5ac2528aef3282b99f837a41f2ab80e49 Author: Max Katz Date: Fri Jun 23 23:15:15 2017 -0400 Initialize with NULL value for non-CUDA Src/Base/AMReX_Device.cpp commit bdc949e7a057c506beca12b15734f8ba3f2c900c Author: Max Katz Date: Fri Jun 23 23:14:09 2017 -0400 Remove unnecessary CUDA ifdef Src/Base/AMReX_Device.cpp commit 4c0b94071860d281e36566d518883c550dd260a9 Merge: 63ffcba33 95c88b10d Author: Max Katz Date: Fri Jun 23 23:10:48 2017 -0400 Merge branch 'development' into gpu commit 95c88b10d6c760e5d1c34b26be5780060973f97a Author: Andy Nonaka Date: Fri Jun 23 18:48:22 2017 -0700 updates to Amr source doc Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex commit 84b1136be32c5caa6c01209984663edb804dbf4b Author: Michele Rosso Date: Fri Jun 23 18:04:14 2017 -0700 Downgrade cmake minimum required version to 3.3 CMakeLists.txt commit a208ecc54e07be900de90a205fba5bdb10a8cad1 Author: Andy Nonaka Date: Fri Jun 23 15:07:05 2017 -0700 note on running particles in Advection_AmrLevel Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex commit 41f48e7d18c3492f3f8a2fad19c2789f4272f841 Author: Andy Nonaka Date: Fri Jun 23 15:02:04 2017 -0700 particle stuff in Advection_AmrLevel Src/Amr/AMReX_AmrLevel.H Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/inputs commit e00ec4fcd0c02c0325fd34296a64a7182e074000 Author: dtgraves Date: Fri Jun 23 13:52:35 2017 -0700 fixed a broken test. now all the EBAMRTools tests also run in parallel Tests/EBAMRTools/regression/ebFineInterpTest.cpp Tests/EBAMRTools/regression/runalltests.mpi.sh commit b10ddd4c74dc807a2752c6fc0109330b74ea94fb Author: Michele Rosso Date: Fri Jun 23 13:16:36 2017 -0700 Fix bugs in new cmake implementation Src/AmrCore/CMakeLists.txt Src/Particle/CMakeLists.txt Tools/CMake/FindCCSE.cmake commit 47ca57149a03b6a4017fcb68db125dd409528c90 Merge: 19371f78a 3ca90c429 Author: Klaus Weide Date: Fri Jun 23 14:31:06 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 3ca90c429b29c96783fa129ee77a156a2b153eb5 Author: Andy Nonaka Date: Fri Jun 23 11:55:40 2017 -0700 various small cleanups to tutorial code Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/probin Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90 Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/Adv_nd.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/Tagging_nd.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/tagging_params.f90 commit d56b74eb03bc47730463cec14a2d580ff2aeffd2 Author: Michele Rosso Date: Fri Jun 23 11:19:36 2017 -0700 Comment out 'Find Perl' code Tools/CMake/FindCCSE.cmake commit a76430e441bbee7a8be4f6573cb12b4159ead137 Merge: 33242297e 86d9603c3 Author: dtgraves Date: Fri Jun 23 10:26:12 2017 -0700 Merge pull request #45 from AMReX-Codes/dtg_branch Push parallel fixes to development. commit 19371f78a0b404b371e5adf8a49569b14008c8bb Merge: fa3b1967e 33242297e Author: Klaus Weide Date: Fri Jun 23 11:56:14 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 86d9603c38832818414f2e1f0fdd497f897cf0de Author: dtgraves Date: Fri Jun 23 09:32:22 2017 -0700 All EB tests now work in parallel, including I/O. Src/Base/AMReX_SPMD.H Src/Base/AMReX_SPMDI.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Tests/GeometryShop/regression/ebio.2.inputs Tests/GeometryShop/regression/ebio.cpp Tests/GeometryShop/regression/runalltests.mpi.sh commit 33242297e4d21422d7059c2e589727a7255309d2 Author: Weiqun Zhang Date: Fri Jun 23 06:47:24 2017 -0700 remove ifdef USE_PARTICLES around function declarations Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles_F.H commit 6ed2c90b7f25af417cc98d8883f40d9fcd25c87a Author: Andy Nonaka Date: Thu Jun 22 18:19:56 2017 -0700 Remove old BoxLib docs. You can find the tex in the BoxLib repo if you need it (or in the git history here) Docs/BoxLibUsersGuide/C_AdvancedTopics/C_AdvancedTopics.tex Docs/BoxLibUsersGuide/F_AdvancedTopics/F_AdvancedTopics.tex Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example1.eps Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example1.fig Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example2.eps Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example2.fig Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example3.eps Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example3.fig Docs/BoxLibUsersGuide/F_AdvancedTopics/subcycling_algorithm.eps Docs/BoxLibUsersGuide/GNUmakefile Docs/BoxLibUsersGuide/GettingStarted/GettingStarted.tex Docs/BoxLibUsersGuide/GettingStarted/VisIt_2D.eps Docs/BoxLibUsersGuide/GettingStarted/VisIt_3D.eps Docs/BoxLibUsersGuide/GettingStarted/edison.run Docs/BoxLibUsersGuide/GettingStarted/edison_omp.run Docs/BoxLibUsersGuide/Introduction/AMR.eps Docs/BoxLibUsersGuide/Introduction/Introduction.tex Docs/BoxLibUsersGuide/Introduction/boxlib_directory_bw2.eps Docs/BoxLibUsersGuide/Introduction/castro_scaling.eps Docs/BoxLibUsersGuide/Introduction/data_loc.odg Docs/BoxLibUsersGuide/Introduction/data_loc2.eps Docs/BoxLibUsersGuide/Introduction/index_grid.odg Docs/BoxLibUsersGuide/Introduction/index_grid2.eps Docs/BoxLibUsersGuide/Introduction/lmc_scaling.eps Docs/BoxLibUsersGuide/Introduction/maestro_scaling.eps Docs/BoxLibUsersGuide/Introduction/varden1.eps Docs/BoxLibUsersGuide/Introduction/varden2.eps Docs/BoxLibUsersGuide/Introduction/varden3.eps Docs/BoxLibUsersGuide/Introduction/varden4.eps Docs/BoxLibUsersGuide/LinearSolvers/LinearSolvers.tex Docs/BoxLibUsersGuide/Preface/Preface.tex Docs/BoxLibUsersGuide/README Docs/BoxLibUsersGuide/Regression/test_suite.tex Docs/BoxLibUsersGuide/Regression/testsuite.eps Docs/BoxLibUsersGuide/UsersGuide.tex commit e64d8c2a722638410edd49c8d82b2861c5b8ce37 Author: Andy Nonaka Date: Thu Jun 22 18:04:39 2017 -0700 more doc work Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex commit 854fa84bede1968a660e4cf8f76b816079e0d844 Author: Andy Nonaka Date: Thu Jun 22 17:43:12 2017 -0700 docs update Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex Docs/AMReXUsersGuide/AmrLevel/figs/flowchart.odg Docs/AMReXUsersGuide/AmrLevel/figs/flowchart.pdf Tutorials/Amr/Advection_AmrCore/Exec/Make.Adv Tutorials/Amr/Advection_AmrLevel/Exec/Make.Adv commit 6cad10fb628603e7040fa64183aef52a2dd0cd20 Author: Marc Day Date: Thu Jun 22 16:40:23 2017 -0700 Start eb fortran work by copying the test code for inf norm. Also, build face aperatures and eb geom info in a form suitable for passing to fortran. Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/umapTest.cpp Tests/GeometryShop/vofStructures/umapTest_nd.f90 commit 9be747f6b9cf1f9d85180e05b97b039ff87dc8c8 Author: Andy Nonaka Date: Thu Jun 22 16:32:52 2017 -0700 make AmrLevel::thePlotFileType() and AmrLevel::okToContinue virtual (and not pure virtual) removed overriding functions from tutorial Src/Amr/AMReX_AmrLevel.H Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.H Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 3dab582f384bc94beef6c0e818d8a00c2d68201d Author: Michele Rosso Date: Thu Jun 22 16:26:14 2017 -0700 Disable c++11 gnu extensions CMakeLists.txt commit fedb542505eecbbb08e28b0378c18b3638fe1e2d Author: Michele Rosso Date: Thu Jun 22 16:14:13 2017 -0700 Fix some bugs with new cmake CMakeLists.txt Src/Base/CMakeLists.txt Src/CMakeLists.txt Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake commit 3fa9e1c7198c231ffcfca906a6b2f3efb84497f2 Author: Andy Nonaka Date: Thu Jun 22 16:13:04 2017 -0700 AmrLevel::writePlotFile is no longer pure virtual (it is simply virtual with a default implementation) change the Advection_AmrLevel tutorial to call the default implementation. Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 25a92dd8e594d83a29be26a8d63c2a5ee795e12a Author: Marc Day Date: Thu Jun 22 15:51:10 2017 -0700 Create eb data structrues in order to facilitate building lapl op, for example. Tests/GeometryShop/vofStructures/umapTest.cpp commit ed10d8e2a79653cdd25dd83a93122650f2118f9b Author: Marc Day Date: Thu Jun 22 15:50:21 2017 -0700 Comment out unused variables in BaseUmap.H Src/Base/AMReX_BaseUmap.H commit d2d65e732306a068bf801d5f2de5cde1c22f0e1a Author: Michele Rosso Date: Thu Jun 22 14:59:15 2017 -0700 Move some utility functions in AMReX_Utils.cmake Src/CMakeLists.txt Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Utils.cmake Tools/CMake/PreprocessAMReXFortran.cmake commit 7c222501fba4af5a3a2483d9712cc483dea17ee6 Merge: b0f660366 cda188b94 Author: Marc Day Date: Thu Jun 22 13:29:54 2017 -0700 Merge branch 'rgrout/sparse_fab' into vof-work commit b0f660366fe661ab882cdfc8b9464cfa95c94b4c Author: Marc Day Date: Thu Jun 22 13:28:45 2017 -0700 WIP: nothing interesting Tests/GeometryShop/vofStructures/umapTest.cpp commit a190998d54daa678d7b843d260d4923b4bcfc7e2 Author: Andrew Myers Date: Thu Jun 22 13:03:08 2017 -0700 do domain decomposition by default. Tutorials/Particles/ElectrostaticPIC/inputs Tutorials/Particles/ElectrostaticPIC/main.cpp commit 33487ea54eb0a63d50c04155a32544ad7e704d4e Author: Michele Rosso Date: Thu Jun 22 12:44:32 2017 -0700 Re-organize CMake structure CMakeLists.txt Src/CMakeLists.txt Tools/CMake/AMReX_CMakeVariables.cmake Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake Tools/CMake/AMReX_Utils.cmake commit cda188b94d468e9033bad5e22097509abc30c568 Merge: 2d83dd0a6 ec2420b54 Author: Grout Date: Thu Jun 22 11:18:18 2017 -0600 Merge branch 'rgrout/sparse_fab' of github.com:AMReX-Codes/amrex into rgrout/sparse_fab commit 2d83dd0a68f478919f17f11441590d582b37efd5 Author: Grout Date: Thu Jun 22 11:17:55 2017 -0600 Stripped allocation check that did not make sense with new object Src/Base/AMReX_BaseUmap.H commit a385f695481cbc888710950ba0edcf5a94b42ead Author: Andrew Myers Date: Thu Jun 22 10:01:24 2017 -0700 removing some more unused variables. Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90 Tutorials/Particles/ElectrostaticPIC/main.cpp commit 468fc2b0c5d354892d7a41e36315efbb5b8040df Merge: c80760503 357acab9d Author: Andrew Myers Date: Thu Jun 22 09:53:30 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c80760503e637903f5fe42276a68f5c42ae05fd0 Author: Andrew Myers Date: Thu Jun 22 09:52:54 2017 -0700 remove some more no-longer-needed temporaries. Tutorials/Particles/ElectrostaticPIC/main.cpp commit 2549d9aa335cf6e9b13a440a55c71d51645eb791 Author: Andrew Myers Date: Thu Jun 22 09:51:57 2017 -0700 remove tmp_phi, which is not actually used anymore. Tutorials/Particles/ElectrostaticPIC/main.cpp commit 7b852cf25eb88e4eafa9c2fddd750fb522bf4a95 Author: Andrew Myers Date: Thu Jun 22 09:50:51 2017 -0700 Change the setup of this test to match Vay et. al. 2012. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/inputs Tutorials/Particles/ElectrostaticPIC/main.cpp commit a6e4153b2cbc89deb7b808551b31fa9eb0d7d0e2 Merge: 4bb64a956 ec2420b54 Author: Marc Day Date: Thu Jun 22 09:49:03 2017 -0700 Merge branch 'rgrout/sparse_fab' into vof-work commit 357acab9d7e043b57b8e97e188b51282fcba1642 Author: Weiqun Zhang Date: Thu Jun 22 09:40:20 2017 -0700 The plot file type needs to be "HypreCLaw-V1.1", not "AMReX". Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit a10a40f11a67e1155e658c54306c480e6c2c90af Author: Weiqun Zhang Date: Thu Jun 22 09:35:50 2017 -0700 fix path to amrex home Tutorials/Amr/Advection_F/Exec/Make.Adv Tutorials/Amr/Advection_octree_F/Exec/Make.Adv commit 63ffcba33958d2681490f36e9020efd67e86882b Author: Max Katz Date: Thu Jun 22 06:02:16 2017 -0400 Fix a logic error in when to update the device copies Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_RealBox.H commit cc5aaf4717abcbda609ec9127b4d23a25142007f Author: Max Katz Date: Thu Jun 22 03:50:51 2017 -0400 Insert device synchronizes in DEBUG mode Src/Base/AMReX_MFIter.cpp commit 2849d91e0096c7b9d05c552c75e34621afb6bf1d Author: Max Katz Date: Thu Jun 22 02:37:03 2017 -0400 Refactor a little to hide CUDA in Device class Src/Base/AMReX.cpp Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_MultiFab.cpp commit 9178a17325adaf5125ce73daad50f48d5d34e422 Author: Max Katz Date: Thu Jun 22 02:00:35 2017 -0400 Do error checking in MFIter Src/Base/AMReX_MFIter.cpp commit 5491a54a48b656471745173777cc1664c6f31c91 Author: Max Katz Date: Thu Jun 22 02:00:21 2017 -0400 Add a test for any runtime/kernel launch errors Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit b40fd15613940e57df307fb0251d5001987a19b0 Author: Max Katz Date: Thu Jun 22 01:40:01 2017 -0400 Use loVectF/hiVectF in BL_TO_FORTRAN macros Src/Base/AMReX_ArrayLim.H commit 4bb64a95660b5bc4cbf008295edd0076f5f8aaba Author: Marc Day Date: Wed Jun 21 17:57:09 2017 -0700 WIP: Remove debugging info Tests/GeometryShop/vofStructures/umapTest.cpp commit ec2420b54489187ea7b5727afce29f064a56875e Author: Marc Day Date: Wed Jun 21 17:54:06 2017 -0700 Fix case on include file Tests/C_BaseLib/tUMap.cpp commit 271d2abc135ff7939ee400be1826710ff863c5ed Author: Marc Day Date: Wed Jun 21 17:34:43 2017 -0700 WIP: rework umap test to build CutCells and CutFaces with cell index of parent coarse object to allow that multi-level eb operations can be done in Fortran. Tests/GeometryShop/vofStructures/flatplate.inputs Tests/GeometryShop/vofStructures/sphere.inputs Tests/GeometryShop/vofStructures/umapTest.cpp commit 5bdf95d5999c33d80b2478cd2693dfd24c0895bb Author: Weiqun Zhang Date: Wed Jun 21 16:50:11 2017 -0700 User's Guide: start Fortran chapter Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Fortran/Fortran.tex Docs/AMReXUsersGuide/GNUmakefile Tutorials/Basic/HelloWorld_F/GNUmakefile Tutorials/Basic/HelloWorld_F/fmain.f90 commit 04c9a7b3455c6de6e4c19e151d050605c264001d Author: Andy Nonaka Date: Wed Jun 21 14:01:41 2017 -0700 tutorial cleanup Tutorials/Amr/Advection_AmrLevel/Source/main.cpp commit 3a3aa5d860de6b379da40c0638718054b8d3d3f9 Author: Grout Date: Wed Jun 21 14:32:15 2017 -0600 Add skeleton of how to access Umap from fortran; temporarily turn off failure for non-existant data; test to compute norm using fortran interface Src/Base/AMReX_BaseUmap.H Src/Base/AMReX_BaseUmap_f.H Src/Base/AMReX_BaseUmap_nd.f90 Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tUMap.cpp commit c140b8b1cd2295078330ef18b6862f5570cc29f4 Merge: 661398501 834f89d1e Author: WeiqunZhang Date: Wed Jun 21 12:46:50 2017 -0700 Merge pull request #43 from kweide/development some simple corrections to UsersGuide commit fa3b1967ef9b68f8de28990d539789ba697c9382 Merge: 834f89d1e 661398501 Author: Klaus Weide Date: Wed Jun 21 14:36:02 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 661398501b8af48f073a3af8b0e37dec9570c1a9 Author: Andy Nonaka Date: Wed Jun 21 11:22:24 2017 -0700 cout -> amrex::Print() Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/Amr/Advection_AmrLevel/Source/main.cpp commit c0c889d5dd423cd321bb81d685c057f35d11288a Merge: f088f5fcc 46e1db931 Author: Andy Nonaka Date: Wed Jun 21 11:05:30 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit f088f5fcc6c69ed3d8993d21c4f04e3dcc0b1c38 Author: Andy Nonaka Date: Wed Jun 21 11:05:07 2017 -0700 State_Type -> Phi_Type (to avoid confusion) more documentation Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.H Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp commit 828b5cb188d8ac386ad93f6e471a4a698cf2fb86 Author: Andy Nonaka Date: Wed Jun 21 11:03:38 2017 -0700 State_Type -> Phi_Type (avoid confusion) Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex commit 46e1db9313ee249de5451dcde749379a07e9b6af Author: Weiqun Zhang Date: Wed Jun 21 10:12:36 2017 -0700 move some new Fortran tutorials from OldTutorials to Tutorials Tutorials/Amr/Advection_F/Exec/Make.Adv Tutorials/Amr/Advection_F/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_F/Exec/SingleVortex/Make.package Tutorials/Amr/Advection_F/Exec/SingleVortex/Prob.f90 Tutorials/Amr/Advection_F/Exec/SingleVortex/face_velocity_2d.F90 Tutorials/Amr/Advection_F/Exec/SingleVortex/inputs Tutorials/Amr/Advection_F/Exec/SingleVortex/inputs.physbc Tutorials/Amr/Advection_F/Exec/SingleVortex/inputs.rt Tutorials/Amr/Advection_F/README Tutorials/Amr/Advection_F/Source/Make.package Tutorials/Amr/Advection_F/Source/Src_2d/Make.package Tutorials/Amr/Advection_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_F/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/Advection_F/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_F/Source/amr_data_mod.F90 Tutorials/Amr/Advection_F/Source/averagedown_mod.F90 Tutorials/Amr/Advection_F/Source/bc_mod.F90 Tutorials/Amr/Advection_F/Source/compute_dt_mod.F90 Tutorials/Amr/Advection_F/Source/evolve_mod.F90 Tutorials/Amr/Advection_F/Source/fillpatch_mod.F90 Tutorials/Amr/Advection_F/Source/fmain.F90 Tutorials/Amr/Advection_F/Source/initdata.F90 Tutorials/Amr/Advection_F/Source/my_amr_mod.F90 Tutorials/Amr/Advection_F/Source/plotfile_mod.F90 Tutorials/Amr/Advection_F/Source/tagging_mod.F90 Tutorials/Amr/Advection_octree_F/Exec/Make.Adv Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/Make.package Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/Prob.f90 Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/face_velocity_2d.F90 Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/inputs Tutorials/Amr/Advection_octree_F/Exec/SingleVortex/inputs.rt Tutorials/Amr/Advection_octree_F/README Tutorials/Amr/Advection_octree_F/Source/Make.package Tutorials/Amr/Advection_octree_F/Source/Src_2d/Make.package Tutorials/Amr/Advection_octree_F/Source/Src_2d/advect_2d_mod.F90 Tutorials/Amr/Advection_octree_F/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/Advection_octree_F/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_octree_F/Source/amr_data_mod.F90 Tutorials/Amr/Advection_octree_F/Source/averagedown_mod.F90 Tutorials/Amr/Advection_octree_F/Source/bc_mod.F90 Tutorials/Amr/Advection_octree_F/Source/compute_dt_mod.F90 Tutorials/Amr/Advection_octree_F/Source/evolve_mod.F90 Tutorials/Amr/Advection_octree_F/Source/fillpatch_mod.F90 Tutorials/Amr/Advection_octree_F/Source/fmain.F90 Tutorials/Amr/Advection_octree_F/Source/initdata.F90 Tutorials/Amr/Advection_octree_F/Source/my_amr_mod.F90 Tutorials/Amr/Advection_octree_F/Source/plotfile_mod.F90 Tutorials/Amr/Advection_octree_F/Source/tagging_mod.F90 commit d66985624a2686c136d9bc25e65b28b067c4c6da Author: Andy Nonaka Date: Wed Jun 21 09:59:08 2017 -0700 added back in check to make sure a fine level already hasn't been regridded from a coarser level regrid Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp commit 03fcfe24031006a2428b08296fc8d8339d7924a9 Author: Michele Rosso Date: Wed Jun 21 09:46:46 2017 -0700 Start re-writing of AMReX Cmake CMakeLists.txt Tools/CMake/AMReX_Config.cmake Tools/CMake/AMReX_Options.cmake commit 16b8d8963409fce3046076775787627ca7474a60 Author: Andy Nonaka Date: Wed Jun 21 09:29:50 2017 -0700 cleanup tutorial Tutorials/Amr/Advection_AmrLevel/Source/Adv.cpp Tutorials/Amr/Advection_AmrLevel/Source/Adv_advance.cpp Tutorials/Amr/Advection_AmrLevel/Source/Adv_dt.cpp Tutorials/Amr/Advection_AmrLevel/Source/Adv_io.cpp Tutorials/Amr/Advection_AmrLevel/Source/Adv_setup.cpp Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.H Tutorials/Amr/Advection_AmrLevel/Source/AmrLevelAdv.cpp Tutorials/Amr/Advection_AmrLevel/Source/LevelBldAdv.cpp Tutorials/Amr/Advection_AmrLevel/Source/Make.package commit 63e1d1113f5f6f53438419bf5f8c757ed6df821e Author: Andy Nonaka Date: Wed Jun 21 08:56:36 2017 -0700 move AMR_Adv_C example into Tutorials/Amr/Advection_AmrLevel and get it compiling/running again OldTutorials/AMR_Adv_C/README Tutorials/Amr/Advection_AmrLevel/Exec/Make.Adv Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/Make.package Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/Prob.f90 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrLevel/Exec/SingleVortex/probin Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/GNUmakefile Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/Make.package Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/Prob.f90 Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_2d.f90 Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/face_velocity_3d.f90 Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/inputs Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/probdata.f90 Tutorials/Amr/Advection_AmrLevel/Exec/UniformVelocity/probin Tutorials/Amr/Advection_AmrLevel/README Tutorials/Amr/Advection_AmrLevel/Source/Adv.H Tutorials/Amr/Advection_AmrLevel/Source/Adv.cpp Tutorials/Amr/Advection_AmrLevel/Source/AdvBld.cpp Tutorials/Amr/Advection_AmrLevel/Source/Adv_F.H Tutorials/Amr/Advection_AmrLevel/Source/Adv_advance.cpp Tutorials/Amr/Advection_AmrLevel/Source/Adv_dt.cpp Tutorials/Amr/Advection_AmrLevel/Source/Adv_io.cpp Tutorials/Amr/Advection_AmrLevel/Source/Adv_setup.cpp Tutorials/Amr/Advection_AmrLevel/Source/Make.package Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/Make.package Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_3d/Make.package Tutorials/Amr/Advection_AmrLevel/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_3d/slope_3d.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/Adv_nd.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/Make.package Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/Tagging_nd.f90 Tutorials/Amr/Advection_AmrLevel/Source/Src_nd/tagging_params.f90 Tutorials/Amr/Advection_AmrLevel/Source/main.cpp commit b66cb26cb417d0d74b3557104672be1e4e2ea50d Author: Andy Nonaka Date: Wed Jun 21 08:26:09 2017 -0700 cleanup of tutorial and associated documentation Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdvPhysBC.H Tutorials/Amr/Advection_AmrCore/Source/AmrCoreAdv_F.H Tutorials/Amr/Advection_AmrCore/Source/Make.package Tutorials/Amr/Advection_AmrCore/Source/main.cpp commit e974504b08e97b5af44171c6c699d8c69e406862 Author: Max Katz Date: Wed Jun 21 05:01:56 2017 -0400 Use default stream to simplify logic Src/Base/AMReX_CUDA.F90 commit 45938c3e5eff66f4267e4feb423baed5f7a45129 Author: Max Katz Date: Wed Jun 21 04:58:38 2017 -0400 Create a gpu_error function Src/Base/AMReX_CUDA.F90 commit 481c88b1fe1b09a760b50fb34347330e9b1e9344 Author: Max Katz Date: Wed Jun 21 04:43:10 2017 -0400 Add a hook to set the GPU stack limit Src/Base/AMReX_CUDA.F90 commit e833f10b88d38190c4593fc6ff7400f113f5ea6f Author: Max Katz Date: Wed Jun 21 04:15:47 2017 -0400 Avoid undefined non-CUDA behavior Src/Base/AMReX_Device.cpp commit 6b3e046c371da73a5fc066a0d2e605e27649bb84 Author: Max Katz Date: Wed Jun 21 04:12:57 2017 -0400 Add BaseFab hook to return pinned Box memory Src/Base/AMReX_BaseFab.H commit 1fe889bd7f9fd08bd570bf1520013971f8de601d Author: Max Katz Date: Wed Jun 21 03:31:37 2017 -0400 Add a pinned memory version of Box data Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit a805aba931c018fbd59e848ac68afadf491dcf81 Author: Max Katz Date: Wed Jun 21 03:14:38 2017 -0400 Use BL_TO_FORT macro in HeatEq again Tutorials/GPU/HeatEquation_EX1_C/main.cpp commit 253a7b54dc56c9b4ae6f1d49978f4a5d36d1fff7 Author: Max Katz Date: Wed Jun 21 02:53:39 2017 -0400 Add C++ hook to get host pointer for pinned memory Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit e9e006f1f766faf0375285982a759aca0afcdbd5 Author: Max Katz Date: Wed Jun 21 02:36:43 2017 -0400 Reset to the default stream on MFIter destruction Src/Base/AMReX_MFIter.cpp commit fdf87069da026bb5361f8538b8c171bfeda857b2 Author: Max Katz Date: Wed Jun 21 02:36:16 2017 -0400 Add cuda_streams(0) as the default stream Src/Base/AMReX_CUDA.F90 commit 1143d67aa3abf4e6e2840b7516ee94b92344280f Author: Max Katz Date: Wed Jun 21 02:17:10 2017 -0400 Add function to return current stream index Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 5a300545e3bb66521e07860313198d1a42f0eaa8 Author: Max Katz Date: Wed Jun 21 01:49:42 2017 -0400 Register a box for asynchronous execution Tutorials/GPU/HeatEquation_EX1_C/main.cpp commit 834f89d1e72fa3f5710c21be71dd1f7ddcef61d7 Author: Klaus Weide Date: Wed Jun 21 00:29:59 2017 -0500 triv Docs/AMReXUsersGuide/Basics/Basics.tex commit 050c381744700831784eabec8a98c8a437099ff0 Author: Max Katz Date: Wed Jun 21 01:04:35 2017 -0400 Update the RealBox device pointer in more cases Src/Base/AMReX_RealBox.H commit d06a7576a09a4e2ad60d88ab6381c192a313d5c1 Merge: 91cb0e154 991f058bb Author: Klaus Weide Date: Tue Jun 20 23:52:48 2017 -0500 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 91cb0e154af88fb0fa3b55b205d19372cbe8da76 Author: Klaus Weide Date: Tue Jun 20 23:52:30 2017 -0500 trivial edits Docs/AMReXUsersGuide/Basics/Basics.tex commit 991f058bbf095c3d3bfa40d1a7e26502de22e847 Merge: 743c65832 de6c335d4 Author: Weiqun Zhang Date: Tue Jun 20 21:27:14 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 743c65832c49d71985b46146b090312e011c8845 Author: Weiqun Zhang Date: Tue Jun 20 21:26:35 2017 -0700 make bl_random_f seeding thread safe Src/F_BaseLib/bl_random_c.cpp Src/F_BaseLib/bl_random_f.f90 commit de6c335d4573d3c034c87a7817a475d29ba4340a Merge: f05f50079 dc251b0c4 Author: Andy Nonaka Date: Tue Jun 20 21:00:01 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit f05f500799619602bcaebdb304d1655b54ccf866 Author: Andy Nonaka Date: Tue Jun 20 18:04:14 2017 -0700 more documentation Docs/AMReXUsersGuide/AmrCore/AmrCore.tex commit a8f8a1faeca99a012cb10e38bf6b375ac77fd704 Author: Andy Nonaka Date: Tue Jun 20 17:37:20 2017 -0700 comments Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.cpp commit 456021196db25ed16f437a67ff3f7da09ede7a9c Merge: 8a2831325 dc251b0c4 Author: Marc Day Date: Tue Jun 20 17:32:03 2017 -0700 Merge branch 'development' into vof-work commit dc251b0c42c26fd0efbf994dca4e99424b1f64a7 Author: Marc Day Date: Tue Jun 20 17:31:37 2017 -0700 Indexing bug in VolIndex output function Src/GeometryShop/AMReX_VolIndex.cpp commit ba965f18040fef7b5392f6738142d816a85847b2 Merge: 8c3ffcd69 8faedb6c8 Author: atmyers Date: Tue Jun 20 17:18:40 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8c3ffcd6929eac9bf2cbdf854e6efcf0600cd402 Author: atmyers Date: Tue Jun 20 17:18:29 2017 -0700 use enum instead of integer for specifying cartesian coordinates in the tutorials. Tests/Particles/AssignDensity/main.cpp Tests/Particles/AssignMultiLevelDensity/main.cpp Tests/Particles/ParticleIterator/GNUmakefile Tests/Particles/ParticleIterator/main.cpp Tests/Particles/main.cpp Tutorials/Basic/HeatEquation_EX1_C/main.cpp Tutorials/CVODE/EX1/main.cpp Tutorials/CVODE/EX2/main.cpp Tutorials/Particles/ElectrostaticPIC/main.cpp Tutorials/Particles/ShortRangeParticles/main.cpp commit 8faedb6c8f3acc573b822abe867c435b69ae6dad Merge: 491b39a18 dc8c06893 Author: Weiqun Zhang Date: Tue Jun 20 16:21:02 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 491b39a18c85c9988101247a574dc182744b1c6f Author: Weiqun Zhang Date: Tue Jun 20 16:20:56 2017 -0700 make max_grid_size and blocking_factor IntVect Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp commit dc8c06893a7f89e4a14f039d6a90266c66596109 Merge: 8be15ccae 2e73eabf6 Author: WeiqunZhang Date: Tue Jun 20 16:14:23 2017 -0700 Merge pull request #42 from AMReX-Codes/dtg_branch bunch of small parallel fixes commit 2e73eabf61459392cb1c86313debd466d4d22665 Author: dtgraves Date: Tue Jun 20 16:08:12 2017 -0700 put in the repo the working input file Tests/GeometryShop/regression/ebio.inputs commit 8be15ccae3ea538ff60db4e5b9837246c615b04a Merge: 66b418522 b59a203a6 Author: Andy Nonaka Date: Tue Jun 20 14:14:33 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 66b418522a6f968752dd74b5209092987d5e6e52 Author: Andy Nonaka Date: Tue Jun 20 14:14:19 2017 -0700 minor updates to doc Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.cpp commit b59a203a6892ad52b10f4f95a20ee955855bd470 Merge: 1e4ab6577 b5cb2a568 Author: Weiqun Zhang Date: Tue Jun 20 13:27:25 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1e4ab6577e3361b3711affcce06bd07134234c7b Author: Weiqun Zhang Date: Tue Jun 20 13:27:13 2017 -0700 add assertion to FabArray::operator[] making sure DistributionMapping is the same Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.H commit b5cb2a56867749261497ed12be52558f68fb0e9b Author: Andy Nonaka Date: Tue Jun 20 13:25:08 2017 -0700 more AmrCore doc and some code cleanup Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.cpp Tutorials/Amr/Advection_AmrCore/Source/main.cpp commit 673290d82c7f66b3a2c77ecc22f1da72deac1e23 Author: dtgraves Date: Tue Jun 20 12:00:43 2017 -0700 parallel I/O of FabArray objects is now correct Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_FabArrayIO.H Tests/GeometryShop/regression/fabio.cpp commit 23063f9e44a367efa94ca947603bd407e73dbcb9 Author: Michele Rosso Date: Mon Jun 12 17:20:04 2017 -0700 Modify main CMakeLists.txt CMakeLists.txt Tools/CMake/AMReX_Utils.cmake commit 9eb0af2d67d77f901d0b92d0915bd22843438f32 Author: Michele Rosso Date: Mon Jun 12 14:13:04 2017 -0700 Add missing file from source list Src/Base/CMakeLists.txt commit 0ae887f7a7cac73f7769e40e7949b0a84d6a82d3 Author: Michele Rosso Date: Fri Jun 9 15:30:21 2017 -0700 Modify previous fix to circular dependency problem Tools/CMake/FindCCSE.cmake commit e232221c21e1928e06e8e1bf95cb6be89594f146 Author: Michele Rosso Date: Fri Jun 9 10:06:39 2017 -0700 Force VERBOSE ON by default CMakeLists.txt commit 9492b1e16abcb386f90feed90ff17dd8f3fc41ec Author: Michele Rosso Date: Thu Jun 8 15:59:33 2017 -0700 Modify preprocessing for F77 files Tools/CMake/PreprocessAMReXFortran.cmake commit 9270c700b6ae8cc8a3602675cbc0e26192c8646c Author: Michele Rosso Date: Thu Jun 8 10:46:20 2017 -0700 Get rid of PreprocessAMReXFortran90 CMakeLists.txt Src/Base/CMakeLists.txt Src/CMakeLists.txt Tools/CMake/PreprocessAMReXFortran90.cmake commit 0f2c50895376be85eb676acdb6e8793bf477dfa9 Author: Max Katz Date: Tue Jun 20 00:05:03 2017 -0400 Further restrict the device synchronizes Src/Base/AMReX_FabArray.H Src/Base/AMReX_Geometry.cpp commit e1f4b32f81f7ad17d694788c55bd38f50ccecd87 Author: Max Katz Date: Mon Jun 19 23:53:21 2017 -0400 Suppress warning about driver shutting down Src/Base/AMReX_CUDA.F90 commit 12b55c8d1e5608ff4883234e5fa7690db3195853 Author: Max Katz Date: Mon Jun 19 23:28:53 2017 -0400 Use a less restrictive device sync policy Src/Base/AMReX_Device.H Src/Base/AMReX_FabArray.H commit 682483df2e3c9a4feb36aaa0fc783a9945354bd0 Author: Max Katz Date: Mon Jun 19 23:14:32 2017 -0400 Add a GPU synchronize on MFIter destruction Src/Base/AMReX_MFIter.cpp commit d0b5eb35465baf2d6a16fe8a3af67ae37bc7e57a Author: Max Katz Date: Mon Jun 19 23:13:17 2017 -0400 Add a stream synchronize hook Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H commit 96be11b832bceef9b5294ac4d4c4ecb602e192c0 Author: Max Katz Date: Mon Jun 19 22:42:31 2017 -0400 Handle device stream index automatically in MFIter Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.cpp Src/Base/AMReX_MultiFab.cpp commit 8a2831325fc01c129823c0c720cdea852d440976 Merge: 13fefcc42 84d5653dd Author: Marc Day Date: Mon Jun 19 19:14:33 2017 -0700 Merge branch 'development' into vof-work commit 1080c73eaa2a7ceb587b1aa74582d7d97f83a97b Author: Max Katz Date: Mon Jun 19 22:14:22 2017 -0400 Revert "Remove an unnecessary device synchronize" This reverts commit 88e2d30c6702d4eda05ac6e1e7b03b5944b13a69. Src/Base/AMReX_Device.H commit 84d5653dd8e6f4a7f9d90843edb20bffadf8f0c6 Merge: 1e96b02fc e3af48538 Author: Marc Day Date: Mon Jun 19 19:14:06 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 1e96b02fc26fc58283979abbfcafa4bb7e6f69fe Author: Marc Day Date: Mon Jun 19 19:13:53 2017 -0700 Rename dummy arguments in EBLevelGrid.H for refine function Src/GeometryShop/AMReX_EBLevelGrid.H commit 52702b0af82638e0173682f95a31339df3598850 Merge: f28a391e6 372ade123 Author: Max Katz Date: Mon Jun 19 21:25:51 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 372ade123b3b31b8c8a870283bac4593ad7a3071 Author: Michael Zingale Date: Mon Jun 19 21:22:59 2017 -0400 prevent ppc and little_endian from clashing on IBM power 8 Src/Base/AMReX_FPC.cpp commit f7ef24e07b0f9f2a0415bd02ae36056d738fa647 Author: Michael Zingale Date: Mon Jun 19 21:17:03 2017 -0400 wrap the comments in #if 0 ... #endif so we can compile with xlf Src/Base/AMReX_REAL.H commit 13fefcc424148c7a8e03693218b636453fb2f2e1 Author: Marc Day Date: Mon Jun 19 16:30:37 2017 -0700 Fix a problem associated with reference-counted semantics Tests/GeometryShop/vofStructures/umapTest.cpp commit f95f996eca5e344cb934e5fe4368cf6c95583017 Author: dtgraves Date: Mon Jun 19 15:52:11 2017 -0700 fixed nasty little parallel bug that was only happening when the EB ends near a box boundary. I/O is still broken in parallel but the other stuff seems to work. Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBLevelGrid.cpp Src/GeometryShop/AMReX_GraphNode.cpp Tests/GeometryShop/regression/fabio.cpp commit e3af48538baa9e9cf3fa70d6176ca66d7bf528c1 Author: Andrew Myers Date: Mon Jun 19 12:48:12 2017 -0700 Use PCInterp instead of CellConservativeLinear in multi-level assign density. Src/Particle/AMReX_ParticleContainerI.H commit cdc35cc117b1d0644f0ba5bcd444df1764ad488a Merge: 19de78df6 0fb29f2a0 Author: Marc Day Date: Mon Jun 19 12:39:35 2017 -0700 Merge branch 'development' into vof-work commit e4ca99086b5813eba0ce2e587f1958733f01f364 Author: atmyers Date: Mon Jun 19 12:26:21 2017 -0700 Add more detail about single precision particles in the docs. Docs/AMReXUsersGuide/Particle/Particle.tex commit 19de78df6332e44cd13e08eaedea3cdb9c01d9ef Author: Marc Day Date: Mon Jun 19 12:15:08 2017 -0700 Remove ebXXXID Tests/GeometryShop/vofStructures/AMReX_EBStruct.H Tests/GeometryShop/vofStructures/umapTest.cpp commit ddb566220b7ea11c1b1b08fcc6b0d95cf8c59ecf Author: Marc Day Date: Mon Jun 19 12:11:19 2017 -0700 WIP: Remove vofStructure sample code, choosing Umap structures over the original Node (IntVect-based) concept. Tests/GeometryShop/vofStructures/AMReX_EBStruct.H Tests/GeometryShop/vofStructures/AMReX_ebstruct_mod.F90 Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 Tests/GeometryShop/vofStructures/vofStructures_3d.F90 commit f9933ed00336d46aeeec965b8283ffbc22ad3473 Author: Andrew Myers Date: Mon Jun 19 11:14:06 2017 -0700 move amrex_particle_real to AMReX_fort_mod.F90 Src/Base/AMReX_fort_mod.F90 Src/Particle/AMReX_Particle_mod_1d.F90 Src/Particle/AMReX_Particle_mod_2d.F90 Src/Particle/AMReX_Particle_mod_3d.F90 Tutorials/Particles/ShortRangeParticles/short_range_2d.f90 Tutorials/Particles/ShortRangeParticles/short_range_3d.f90 commit 70e2eeba5cb10901ef7a72cb0aa425582e268b22 Author: Andrew Myers Date: Mon Jun 19 10:57:38 2017 -0700 Allow for single precision particles to be handled by Fortran routines. Src/Particle/AMReX_Particle_mod_1d.F90 Src/Particle/AMReX_Particle_mod_2d.F90 Src/Particle/AMReX_Particle_mod_3d.F90 Src/Particle/AMReX_Particles_F.H Tools/GNUMake/Make.defs Tutorials/Particles/ShortRangeParticles/main.cpp Tutorials/Particles/ShortRangeParticles/short_range_2d.f90 Tutorials/Particles/ShortRangeParticles/short_range_3d.f90 commit f28a391e6d68427c002a43196809adf6e2c98f19 Author: Max Katz Date: Mon Jun 19 05:09:13 2017 -0400 Handle stream indices more cleanly and consistently Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.cpp commit f9e02cad6afd03ab172a3b28f8dec9c53a957db4 Author: Max Katz Date: Mon Jun 19 04:43:42 2017 -0400 Prevent OpenMP when using CUDA Tools/GNUMake/Make.defs commit 41fcf09d9b1bd044366b15690549d29db059db72 Author: Max Katz Date: Mon Jun 19 03:10:09 2017 -0400 Make the device index thread safe Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit a66740408dfd660f0b949203d4c6863a6da4696c Author: Max Katz Date: Mon Jun 19 02:38:19 2017 -0400 Return to old MFIter style since boxes are now saved Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.cpp commit c5a99a99c59d4aaf818189466ce3266934093477 Author: Max Katz Date: Mon Jun 19 02:37:38 2017 -0400 Register boxes created by MFIter Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 76e703fca5804d07c5f79beb2be16266a3279c1e Author: Max Katz Date: Mon Jun 19 01:58:50 2017 -0400 Remove index from Fab interfaces Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit 5f0c67d7d6292e429339ee06562a561309795b13 Author: Max Katz Date: Mon Jun 19 01:50:07 2017 -0400 Make the MultiFab operations asynchrony-safe Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.cpp commit 88e2d30c6702d4eda05ac6e1e7b03b5944b13a69 Author: Max Katz Date: Mon Jun 19 01:33:22 2017 -0400 Remove an unnecessary device synchronize Src/Base/AMReX_Device.H commit df68d507bdc0d9e2858d984bfc0ba73d8b2b2d73 Author: Max Katz Date: Mon Jun 19 01:07:55 2017 -0400 Add a stream index variable Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H commit f38e887655c8d9e188504e2ed18500f96bc474cd Author: Max Katz Date: Sun Jun 18 23:12:03 2017 -0400 Add PGI compiler major and minor version definitions Tools/GNUMake/comps/pgi.mak commit b3416a3dc5fceee70c0f89344d0d58de36f585f1 Author: Michael Zingale Date: Sun Jun 18 20:55:29 2017 -0400 ifdef out some CUDA stuff Src/Base/AMReX_Device.cpp commit 82bc008ce3da95006d103e5abd720922689addf9 Author: Max Katz Date: Sun Jun 18 20:24:08 2017 -0400 Automatically pick up CUDA path on Titan and Summitdev Tools/GNUMake/Make.defs Tools/GNUMake/Make.machines Tools/GNUMake/comps/pgi.mak Tools/GNUMake/sites/Make.olcf commit 877ecfe4225bd2be4ffd5988a12cde45ac96d608 Author: Max Katz Date: Sun Jun 18 16:43:06 2017 -0400 Get the CUDA device ID from Fortran Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit 38ba15a069592767664c70eb9e5e830d9a396b7a Author: Max Katz Date: Sun Jun 18 16:30:49 2017 -0400 Drive CUDA initialization from C++ Src/Base/AMReX.cpp Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp commit e12b2e74cfaedf943301d33b5dc9853166dfc329 Author: Max Katz Date: Sun Jun 18 15:29:37 2017 -0400 Query GPU properties, use in avoiding unsupported calls Src/Base/AMReX_CUDA.F90 commit c87e1ce2c24d8e46c3216f941cc18a6b9b956b4b Author: Max Katz Date: Sun Jun 18 15:29:14 2017 -0400 Initialize CUDA before class initializations Src/Base/AMReX.cpp commit d712c2e7fb65cf6b939ea137af9feccab78503f1 Author: Max Katz Date: Sun Jun 18 01:17:12 2017 -0400 Create managed copy of RealBox data Src/Amr/AMReX_AmrLevel.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp commit 13ff92a8f6196099506db1caee9fcb3d125f395b Author: Max Katz Date: Sun Jun 18 00:48:40 2017 -0400 Add function to return number of MFIter indices Src/Base/AMReX_MFIter.H commit 2a2b7034155322480f9e69f4499692e2a4b7a7d6 Author: Max Katz Date: Sat Jun 17 23:14:26 2017 -0400 Fix the argument passing to cudaMemAdvise Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_Device.H commit 0ed145215ef3b62d6318bf117e1d154a964e4b14 Author: Max Katz Date: Sat Jun 17 22:00:19 2017 -0400 Insert CUDA finalization Src/Base/AMReX.cpp Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H commit d4c73be418a2d5c37565397afd46d20490260cc8 Author: Max Katz Date: Sat Jun 17 21:13:23 2017 -0400 Disable broken error checking for cudamemadvise Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CUDA.F90 commit 25335978427c91cf90b38e9784f43d8f76e9bdff Author: Max Katz Date: Sat Jun 17 20:32:45 2017 -0400 Add capability to use hostalloc'ed data Src/Base/AMReX_Arena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CArena.cpp commit 5df0c70f93ea8a4a781feabfc19ecfc028b67676 Author: Max Katz Date: Sat Jun 17 20:31:10 2017 -0400 Clean up CUDA functions, add error checking Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H commit 352635413626ef0963e9765c270ed0976e56de9a Author: Max Katz Date: Sat Jun 17 20:30:11 2017 -0400 Increase length of error string Src/Base/AMReX_BLBoxLib_F.f commit 7a862a772e790130f250860384c7b75802028b20 Author: dtgraves Date: Sat Jun 17 16:14:08 2017 -0700 took out unnecessary fillboundary calls Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBDebugOut.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBLevelGrid.cpp commit 0361c95f9d1878c4305c650e0cf3f33669d39e0a Merge: 5313c4ff8 c408b5644 Author: Max Katz Date: Sat Jun 17 06:31:37 2017 -0700 Merge pull request #40 from atmyers/gpu An approach to managed memory for particle data commit 5313c4ff8b1c4ca6a608307f4ec5529ba5423fed Author: Max Katz Date: Sat Jun 17 09:04:34 2017 -0400 Always use CArena in Box Src/Base/AMReX_Box.cpp commit 3a6de9321e0f24f78778d662c393a2894421e050 Author: Max Katz Date: Sat Jun 17 05:13:53 2017 -0400 Rely on data that is now managed Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 commit d89f396b93440a086d76d863b81a7fca07f00faf Author: Max Katz Date: Sat Jun 17 04:17:07 2017 -0400 Add an option to use cudaMalloc, not cudaMallocManaged Src/Base/AMReX_Arena.H Src/Base/AMReX_CArena.cpp commit a4894ef931d5fe3835e9da49800b345172b13336 Author: Max Katz Date: Sat Jun 17 04:13:21 2017 -0400 Use the default stream if passed an invalid index Src/Base/AMReX_CUDA.F90 commit 4ed4542794f4be4463ffba212fb1b7f0e86eb763 Author: Marc Day Date: Fri Jun 16 19:29:25 2017 -0700 Add faces to graph in Umap form. Src/Base/AMReX_BaseUmap.H Tests/GeometryShop/vofStructures/AMReX_EBStruct.H Tests/GeometryShop/vofStructures/flatplate.inputs Tests/GeometryShop/vofStructures/umapTest.cpp commit c408b5644343c2c0ce012a0dbfc0740fcb1bc8c1 Author: Andrew Myers Date: Fri Jun 16 17:28:36 2017 -0700 removing file checked in by mistake. Tests/Particles/ManagedCUDADeposition/make.out commit e3a4ccb1d2fff681b5e73aba771a09a78d48086a Author: Andrew Myers Date: Fri Jun 16 17:17:37 2017 -0700 check in test problem for Managed Cuda particle deposition. Tests/Particles/ManagedCUDADeposition/GNUmakefile Tests/Particles/ManagedCUDADeposition/Make.package Tests/Particles/ManagedCUDADeposition/MyParticleContainer.H Tests/Particles/ManagedCUDADeposition/MyParticleContainer.cpp Tests/Particles/ManagedCUDADeposition/cuda_deposit_3d.f90 Tests/Particles/ManagedCUDADeposition/deposit_3d.f90 Tests/Particles/ManagedCUDADeposition/deposit_F.H Tests/Particles/ManagedCUDADeposition/inputs Tests/Particles/ManagedCUDADeposition/main.cpp Tests/Particles/ManagedCUDADeposition/make.out Tests/Particles/ManagedCUDADeposition/solve_for_accel.cpp Tests/Particles/ManagedCUDADeposition/solve_with_f90.cpp commit f008b39feb1996861d9871f7857f0488d5d72b32 Author: Andrew Myers Date: Fri Jun 16 17:16:59 2017 -0700 remove old version of custom allocator from problem directory Tests/Particles/CUDADeposition/CUDAManagedAllocator.H commit 95528f9c19ba3df5f1c7a3de4187f4fa79bb7f05 Author: Andrew Myers Date: Fri Jun 16 17:16:18 2017 -0700 Add a custom allocator that uses Cuda managed memory and use it in the ParticleContainer when Cuda is enabled. Src/Particle/AMReX_CudaManagedAllocator.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Src/Particle/Make.package commit 3b0d562970942f436e80d192ea1fe6aedea9b7ef Author: Andrew Myers Date: Fri Jun 16 17:14:01 2017 -0700 modify AMReX_Array to optionally take a custom allocator (off by default) Src/Base/AMReX_Array.H commit efe6c6c756c1ae617d23fe731868f7be45039f6a Author: Andy Nonaka Date: Fri Jun 16 16:48:12 2017 -0700 more AmrCore documentation Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/AmrCore/figs/flowchart.odg Docs/AMReXUsersGuide/AmrCore/figs/flowchart.pdf commit 1e0285764b7f988f4883f0a0ef5bc9b87d0fd947 Author: Andrew Myers Date: Fri Jun 16 15:17:19 2017 -0700 Enabling OpenMP in the ShortRangeParticleContainer and adding timers. Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp commit 27d2b0b43af38d9c08f3ead0389fe822a54369bd Author: Weiqun Zhang Date: Fri Jun 16 14:47:39 2017 -0700 User's Guide: proofread Docs/AMReXUsersGuide/Basics/Basics.tex commit 1c47eebb2bc868c8f71de6a8605ba283f6ed7549 Merge: 3a92ab7e6 27608ae03 Author: vince Date: Fri Jun 16 12:46:37 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 3a92ab7e6f269236f92a2ecb374d84363de322ca Author: vince Date: Fri Jun 16 12:46:23 2017 -0700 fix uniform_int_distribution call to be consistent with header comments. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 27608ae031b77480e60b22aa9959fe9a8398f927 Author: atmyers Date: Fri Jun 16 11:25:22 2017 -0700 Clean up use of Fortran intent / const in the Particle tutorials. Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90 Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H Tutorials/Particles/ShortRangeParticles/short_range_F.H commit 0243da8e959d842c25c5f48fb8fc27b128c72a4c Author: Marc Day Date: Fri Jun 16 11:10:25 2017 -0700 For BaseUmap::const_iterator, add access to IntVect, L and n. Src/Base/AMReX_BaseUmap.H Tests/GeometryShop/vofStructures/umapTest.cpp commit e2b6deb45e9ae6945b8a2a04a4f1b085c47f0c23 Author: atmyers Date: Fri Jun 16 11:03:54 2017 -0700 Proofreading pass of particle documentation. Docs/AMReXUsersGuide/Particle/Particle.tex Docs/AMReXUsersGuide/Visualization/Visualization.tex commit 87a41b46349acc599c80d7a15b6bad08d39d6315 Author: Marc Day Date: Fri Jun 16 10:59:01 2017 -0700 Add an iterator to BaseUMap to allow iterating over all explicitly defined data....needs some work though Src/Base/AMReX_BaseUmap.H Tests/GeometryShop/vofStructures/umapTest.cpp commit 4399abd0a49eb96655fe46c4043459fcb2440ebf Author: Marc Day Date: Fri Jun 16 09:58:35 2017 -0700 Merge vof-work and sparse-fab stuff...wip Src/Base/AMReX_BaseUmap.H Src/Base/Make.package Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/umapTest.cpp Tests/GeometryShop/vofStructures/vofStructures.cpp commit f09c4ce521139f39a3e406131be54045e8b77e5f Merge: c3741f049 b1a932a78 Author: Michele Rosso Date: Fri Jun 16 10:00:09 2017 -0600 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit c3741f049430996878c1fd8c680e4145bf612eed Author: Michele Rosso Date: Fri Jun 16 10:00:02 2017 -0600 CMake: disable tiny_profiler for the time being Src/Base/CMakeLists.txt Tools/CMake/CCSEOptions.cmake commit b1a932a78202d4a59eafffd2dccf9dbe01bbd291 Author: Andrew Myers Date: Thu Jun 15 19:43:20 2017 -0700 use an explicit amrex:: namespace in the BL_PROFILE macro definitions. Src/Base/AMReX_BLProfiler.H commit 2632ca4667caf15239d29efa75a47fbba717e65e Merge: a148ffb6d 0ce485ff1 Author: Andrew Myers Date: Thu Jun 15 17:25:28 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a148ffb6daebabee994c672b5e970b6a23a07b6e Author: Andrew Myers Date: Thu Jun 15 17:23:04 2017 -0700 Same for the interpolation operation. Src/Particle/AMReX_ParticleContainerI.H commit b6b39e4d55c222ace2b490fc379b90f4ae1f4a6c Author: Andrew Myers Date: Thu Jun 15 17:10:02 2017 -0700 Make the deposition operation OpenMP-capable. Src/Particle/AMReX_ParticleContainerI.H commit 0ce485ff100a7065f99f20d22e198d9ffbb359eb Author: Weiqun Zhang Date: Thu Jun 15 17:01:39 2017 -0700 minor changes Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex commit 37c11511d02400e5796863930f1b6c18854a5ac4 Author: Andrew Myers Date: Thu Jun 15 16:49:48 2017 -0700 Functions to assist with particle deposition with OpenMP. Src/Particle/AMReX_OMPDepositionHelper_1d.F90 Src/Particle/AMReX_OMPDepositionHelper_2d.F90 Src/Particle/AMReX_OMPDepositionHelper_3d.F90 Src/Particle/AMReX_Particles_F.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit eae4c6689026a9bc482afa24c72c4fec4d35c901 Merge: fc0f4f263 2e76d4fdb Author: Marc Day Date: Thu Jun 15 16:48:40 2017 -0700 Merge branch 'rgrout/sparse_fab' into vof-merge commit 0fb29f2a0169c073713a3022d1d250e02ce47422 Author: Andy Nonaka Date: Thu Jun 15 16:44:49 2017 -0700 cleaned up tutorial code, added lots of comments Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrMesh.H Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvError.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvEvolve.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvIO.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvInit.cpp Tutorials/Amr/Advection_AmrCore/Source/Make.package Tutorials/Amr/Advection_AmrCore/Source/main.cpp commit 00212a70f82002d051fbaa6df3090cd194f65eb0 Author: dtgraves Date: Thu Jun 15 15:13:14 2017 -0700 another parallel bug found. More stuff works but not everything. Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBLevelGrid.cpp Src/GeometryShop/AMReX_IrregFABFactory.cpp Tests/GeometryShop/regression/fabio.cpp Tests/GeometryShop/regression/runalltests.mpi.sh Tests/GeometryShop/regression/serialization.cpp Tests/GeometryShop/regression/serialization.inputs commit 2274bf544f0bc5ad5674cc93dbe70a1eacaaf3bc Author: Weiqun Zhang Date: Thu Jun 15 14:59:42 2017 -0700 User's Guide: Boundary Docs/AMReXUsersGuide/Basics/Basics.tex commit eac9c3fa118625744f1b482f4a5d0629262741f5 Merge: 3e878bb15 e6aefc9d0 Author: Andy Nonaka Date: Thu Jun 15 14:35:50 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 3e878bb15f4b6d7d1327becc41eedb32d6dff862 Author: Andy Nonaka Date: Thu Jun 15 14:35:34 2017 -0700 small documentation adds Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Tutorials/Amr/Advection_AmrCore/Source/AmrAdvEvolve.cpp commit bf83a0e04bfd2ee7881dfa020821716e11d8bbcb Author: Andy Nonaka Date: Thu Jun 15 14:28:24 2017 -0700 tex version of subcycling fig Docs/AMReXUsersGuide/AmrCore/figs/subcycling.tex commit e6aefc9d0d3ddaae2d7e56168769467cdc4c14d1 Author: Andrew Myers Date: Thu Jun 15 14:27:06 2017 -0700 adding in the *.tex files for the new figures. Docs/AMReXUsersGuide/Particle/neighbor_particles.tex Docs/AMReXUsersGuide/Particle/particle_arrays.tex commit 660114ebb2ad19a6c01bd1a4829d4688d0e044a7 Merge: 114f3674c 87943e354 Author: Andrew Myers Date: Thu Jun 15 14:25:41 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 87943e354a7c17834f61eb1650f681734a5c7561 Merge: bcbd5a92d 5cdfa3e98 Author: atmyers Date: Thu Jun 15 14:20:50 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit bcbd5a92da4f87c66e5a14475e2ec7a54bf87c8f Author: atmyers Date: Thu Jun 15 14:20:35 2017 -0700 adding a couple of figures to the particle section of the user's guide. Docs/AMReXUsersGuide/Particle/Particle.tex Docs/AMReXUsersGuide/Particle/neighbor_particles.pdf Docs/AMReXUsersGuide/Particle/particle_arrays.pdf commit 5cdfa3e98591c52be2fb89c2bc9f2f1071608949 Author: Weiqun Zhang Date: Thu Jun 15 13:44:31 2017 -0700 update heat equation tutorial using the new amrex::FillDomainBoundary function Tutorials/Basic/HeatEquation_EX1_C/advance.cpp Tutorials/Basic/HeatEquation_EX1_C/myfunc.H Tutorials/Basic/HeatEquation_EX1_C/physbc.cpp commit b430b2b813709e477c76ad1021f12c0b9a61eb50 Author: Weiqun Zhang Date: Thu Jun 15 13:39:56 2017 -0700 add some helper functions for filling physical domain boundary conditions Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCUtil.H Src/Base/AMReX_BCUtil.cpp Src/Base/AMReX_BC_TYPES.H Src/Base/AMReX_BLassert.H Src/Base/AMReX_bc_types_mod.F90 Src/Base/AMReX_filcc_f.H Src/Base/AMReX_filcc_mod.F90 Src/Base/CMakeLists.txt Src/Base/Make.package Src/F_Interfaces/Base/Make.package Tutorials/Basic/HeatEquation_EX1_C/GNUmakefile Tutorials/Basic/HeatEquation_EX1_C/Make.package Tutorials/Basic/HeatEquation_EX1_C/inputs_2d Tutorials/Basic/HeatEquation_EX1_C/inputs_3d Tutorials/Basic/HeatEquation_EX1_C/main.cpp commit a19a861d5b571c4ae5005b4f68103086aa3004ad Merge: 98159eb82 4e863b1d3 Author: Michele Rosso Date: Thu Jun 15 14:00:40 2017 -0600 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 2e76d4fdb8b1df67552ac03599995d095a3e8f8e Merge: 16779ef65 4e863b1d3 Author: Grout Date: Thu Jun 15 13:59:20 2017 -0600 Merge branch 'development' of github.com:AMReX-Codes/amrex into rgrout/sparse_fab commit 98159eb827bf7e83d70b06ba1b78709e7048295e Author: Michele Rosso Date: Thu Jun 15 13:57:11 2017 -0600 Make TinyProfiler the deault profiling tool Src/Base/CMakeLists.txt Tools/CMake/CCSEOptions.cmake commit fc0f4f263b5e8d156bfbf58d13431672fd65e81c Author: Marc Day Date: Thu Jun 15 12:52:11 2017 -0700 WIP: Fixup test code for mv cells Tests/GeometryShop/vofStructures/flatplate.inputs Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 Tests/GeometryShop/vofStructures/vofStructures_3d.F90 commit b0914acdb043fb1d5a4b7ca0388e3f1e284fe03b Author: Michele Rosso Date: Thu Jun 15 13:43:13 2017 -0600 Update cmake with new source files Src/Base/CMakeLists.txt commit 16779ef65323ebff9b82dc3c43b75a1a4d721e26 Author: Grout Date: Thu Jun 15 13:40:15 2017 -0600 Start of sparse fab Src/Base/AMReX_BaseUmap.H Tests/C_BaseLib/tUMap.cpp commit e8c03ca063f75d52b3ec0760c7ab10495cdb30b1 Merge: bbc9109e7 4e863b1d3 Author: atmyers Date: Thu Jun 15 12:21:05 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit bb1da002ff864951c3103254e084765726599f5a Merge: e216f0708 4e863b1d3 Author: Marc Day Date: Thu Jun 15 11:52:17 2017 -0700 Merge branch 'development' into vof-work commit e216f07082c827d11c29226afa14b242d2f067a9 Merge: 36b637830 dd85172a0 Author: Marc Day Date: Thu Jun 15 11:52:12 2017 -0700 resolve merge conflicts commit 4e863b1d3b84f858b916fce23a636bc3f1271a9e Author: Marc Day Date: Thu Jun 15 11:49:31 2017 -0700 Add arguments to pltfile functions that enable passing versionName to writer so we can make CartGrid_V2.0 files Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_PlotFileUtil.cpp commit 36b63783028cba9457e40314a1568fb02a297e6d Author: Marc Day Date: Thu Jun 15 11:47:35 2017 -0700 WIP: Write plotfile with vfrac info Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/vofStructures.cpp commit c5ec0bbd17afea1a430271a6e69010bd3e8cd0dc Author: dtgraves Date: Thu Jun 15 10:51:01 2017 -0700 more bug fixes. EB I/O still broken for nproc > 1 Src/GeometryShop/AMReX_FabArrayIO.H Src/GeometryShop/AMReX_FabArrayIO.cpp Src/GeometryShop/AMReX_IrregFABFactory.cpp Tests/GeometryShop/regression/dataArith.cpp Tests/GeometryShop/regression/runalltests.mpi.sh commit 3ff5146ac4fa24b45e8ca87e45ded14585cb73d6 Author: Weiqun Zhang Date: Thu Jun 15 09:21:21 2017 -0700 move OldTutorials/HelloWorld_CF Tutorials/HelloWorld_F Tutorials/Basic/HelloWorld_F/GNUmakefile Tutorials/Basic/HelloWorld_F/Make.package Tutorials/Basic/HelloWorld_F/fmain.f90 commit f44535024d627ec3f9838a66c865b714f939fdda Author: Weiqun Zhang Date: Thu Jun 15 09:17:01 2017 -0700 User's Guide: add some discussion on const& and return by value Docs/AMReXUsersGuide/Basics/Basics.tex commit 9ded1de838e40b538e17fa2d172324aac7f9199d Author: Weiqun Zhang Date: Thu Jun 15 09:16:17 2017 -0700 move OldTutorials/HeatEquation_EX1_CF to Tutorials/HeatEquation_EX1_F Tutorials/Basic/HeatEquation_EX1_F/GNUmakefile Tutorials/Basic/HeatEquation_EX1_F/Make.package Tutorials/Basic/HeatEquation_EX1_F/advance.f90 Tutorials/Basic/HeatEquation_EX1_F/fmain.f90 Tutorials/Basic/HeatEquation_EX1_F/init_phi.f90 Tutorials/Basic/HeatEquation_EX1_F/inputs commit 5c9520666235a9b3a279ea80b5c8ddae722f8c1c Author: Max Katz Date: Thu Jun 15 10:23:45 2017 -0400 Always reset device memory when applying a Box transformation The original idea was to only reset the shared pointer containing the memory for routines that returned a new box by value rather than modifying the existing box by reference. Thus we could keep the CUDA managed memory without reallocating it if one did Box bx = mfi.validbox(), but create a new allocation if one did Box bx = surroundingNodes(mfi.validbox()). However, this is defeated by the use case where one first creates the box copy, and then applies the transformation operation in a second step. So the only safe approach is to always reset the allocation if the box is transformed. Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit 2cb20b7e710bb43c379ea62d3503dcc45c7dabc8 Author: Max Katz Date: Thu Jun 15 10:20:53 2017 -0400 Do nothing with BL_TO_FORTRAN_3D when CUDA is enabled Since we are using managed memory to hold a copy of the box bounds, we want to directly access the pointer containing that memory, rather than save a temporary copy. The CUDA version automatically enables the same functionality as the macro because the lo and hi vectors contain zeroes in unused spatial dimensions. Src/Base/AMReX_ArrayLim.H commit 1aff7256ea1bf19c879ceedcfcec7fa25b5e3b91 Author: Marc Day Date: Wed Jun 14 19:14:28 2017 -0700 WIP: prepare for multi-level work by making a couple of EBLevelGrid objects to start with. Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/flatplate.inputs Tests/GeometryShop/vofStructures/sphere.inputs Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 Tests/GeometryShop/vofStructures/vofStructures_3d.F90 commit b3de5375fb186e4fd3f3e196b93c140d7282da6c Author: Weiqun Zhang Date: Wed Jun 14 17:56:06 2017 -0700 User's Guide: bl_allocate, Abort and ASSERT Docs/AMReXUsersGuide/Basics/Basics.tex commit 52c520422012d01e0a9a18e01d1a28191df18561 Author: Weiqun Zhang Date: Wed Jun 14 17:44:09 2017 -0700 add AMREX_ASSERT and AMREX_ALWAYS_ASSERT Src/Base/AMReX_BLassert.H commit 9962fd9ea043f7a7af5ea06eb4a7e9ed5e69a49a Author: Weiqun Zhang Date: Wed Jun 14 16:31:43 2017 -0700 remove debug line Src/Base/AMReX_FabArray.H commit 6b127ea2fb6bdf5704af21f76482eeb4fc4244d2 Merge: 7e9f56436 be33b5bc7 Author: Weiqun Zhang Date: Wed Jun 14 16:30:46 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 7e9f564366690baef9e6f64c0fb13924a6e80323 Author: Weiqun Zhang Date: Wed Jun 14 16:30:41 2017 -0700 User's Guide: IO Docs/AMReXUsersGuide/Basics/Basics.tex commit 24a69c5046d069cf74c9b737affbbdbacbf9a6d1 Author: dtgraves Date: Wed Jun 14 15:56:17 2017 -0700 fixed IrregFABFactory parallel bug Src/GeometryShop/AMReX_EBCellFactory.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_IrregFABFactory.H Src/GeometryShop/AMReX_IrregFABFactory.cpp commit 114f3674c73d3c62014c85c98f1927950119d44c Author: Andrew Myers Date: Wed Jun 14 15:33:23 2017 -0700 remove some debugging junk from the ElectrostaticPIC example. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90 commit be33b5bc786d04d5a05295d02af4c6233389c423 Merge: 94061b074 1b9ff9592 Author: WeiqunZhang Date: Wed Jun 14 14:52:40 2017 -0700 Merge pull request #38 from AMReX-Codes/dtg_branch Peter M. wants some of the tools in dtg_branch and this should not break anything commit 1b9ff959206e940ca632dea09fece97aa0283925 Author: dtgraves Date: Wed Jun 14 14:47:29 2017 -0700 took out debugging statements Src/Base/AMReX_FabArray.H commit 9ddbcf4e983f164b4d212a72b702e8512afee988 Author: dtgraves Date: Wed Jun 14 14:10:38 2017 -0700 found subtle parallel bug. More of the EB regression tests now pass in parallel. Src/Base/AMReX_FabArray.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_GraphNode.H Src/GeometryShop/AMReX_GraphNode.cpp Tests/GeometryShop/regression/dataArith.cpp commit 94061b0741fc956fe856c402aa14a4fe1fcd88b7 Merge: 386746dc7 947b0d9d2 Author: Andy Nonaka Date: Wed Jun 14 14:01:50 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 386746dc7cb2c39e3c8b148a071bb59e98ae06e6 Author: Andy Nonaka Date: Wed Jun 14 14:01:29 2017 -0700 code comments, pseudocode of algorithm for AmrCore DesignDoc Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrAdvError.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvEvolve.cpp commit 617ac91aae66f9357c00e07db0b9df39a2b74229 Author: Andy Nonaka Date: Wed Jun 14 12:56:35 2017 -0700 cleaning up the code, no functional changes Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvIO.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvInit.cpp commit bbc9109e7c304a2de5d507a6094a52ce366c7e4c Author: atmyers Date: Wed Jun 14 12:35:16 2017 -0700 Adding more information about neighbor particles. Docs/AMReXUsersGuide/Particle/Particle.tex commit 74d46c099ac736a2a92107dac937a84aefe65b7c Merge: 49d386369 947b0d9d2 Author: atmyers Date: Wed Jun 14 12:12:26 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 49d38636965c58b2a9254860e3a38056d72b46b7 Author: atmyers Date: Wed Jun 14 12:12:17 2017 -0700 Adding some stuff about the ShortRangeTutorial. Docs/AMReXUsersGuide/Particle/Particle.tex commit 947b0d9d27424267c04dc96ac22933ed1f251f4e Author: Michael Zingale Date: Wed Jun 14 15:09:53 2017 -0400 fix build Docs/AMReXUsersGuide/Particle/Particle.tex commit 15604acf581214ae88aa7bef97bc35be6b23a12c Author: atmyers Date: Wed Jun 14 12:05:44 2017 -0700 Particle IO section in docs. Docs/AMReXUsersGuide/Particle/Particle.tex commit 048b2fa3047efaba1d55501206a79282392f3670 Author: Weiqun Zhang Date: Wed Jun 14 11:46:38 2017 -0700 User's Guide: boundary Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/Debugging/Debugging.tex commit e2bc9a59e4a08a600550a7ad2daeb0c7cc37e492 Merge: 138cae339 f2db746e9 Author: Weiqun Zhang Date: Wed Jun 14 09:27:32 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 138cae339fcb38f346bbec82c2115857ac94b6f0 Author: Weiqun Zhang Date: Wed Jun 14 09:26:20 2017 -0700 merge Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/AmrCore/figs/Adv1.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv1.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv2.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv2.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv3.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv3.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv4.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv4.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv5.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv5.pdf Docs/AMReXUsersGuide/AmrCore/figs/subcycling.eps Docs/AMReXUsersGuide/AmrCore/figs/subcycling.pdf commit 0996d4037c11f72856ee1f5039cfcd54d53a4634 Author: Andy Nonaka Date: Wed Jun 14 08:26:35 2017 -0700 fix cropping issue in figure Docs/AMReXUsersGuide/AmrCore/figs/subcycling.pdf commit 4ba0f2e63d29b5ca22cca307dcc33573793076f1 Merge: a3fe30b60 f2db746e9 Author: Max Katz Date: Wed Jun 14 01:19:35 2017 -0400 Merge branch 'development' into gpu commit a3fe30b60aa3eb54f5415f5aa607dd0b5dc13ad8 Merge: 2da2710fc 4ef2566fc Author: Max Katz Date: Tue Jun 13 21:34:40 2017 -0400 Merge branch 'gpu' into gpu_var2 commit 2da2710fcb2f942409a8d2ede36285036d4e4b89 Author: Max Katz Date: Tue Jun 13 21:34:16 2017 -0400 Define a CUDA attributes macro Tools/GNUMake/Make.defs Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 commit 7505b452f0797af8a38b3d707432274d42e32acf Author: Max Katz Date: Tue Jun 13 21:34:16 2017 -0400 Clean up the update_phi interface Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/main.cpp Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H commit af2b576e735acbde58529e942cb32d77e5eff8df Author: Max Katz Date: Tue Jun 13 21:34:16 2017 -0400 Allocate the flux box bounds in C++ driver Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/main.cpp commit 11faf097d73d94a035754a0ebf868f9e48e7b595 Author: Max Katz Date: Tue Jun 13 21:34:16 2017 -0400 Refactor to make directional splitting explicit Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/main.cpp Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H commit af4ed16619cc4371f2be9a27c8b8f407517afd0b Author: Max Katz Date: Tue Jun 13 21:34:16 2017 -0400 Set readonly for CoordSys dx Src/Base/AMReX_CoordSys.cpp commit ad0633c9cbc7d777bfb239d82b310100da7cfdcc Author: Max Katz Date: Tue Jun 13 21:34:16 2017 -0400 Set preferred on BaseFab arena Src/Base/AMReX_BaseFab.cpp commit 77e35125f9dea61a3e8918f5a7df1c95f169ce30 Author: Max Katz Date: Tue Jun 13 21:34:16 2017 -0400 Set read only to the Box arena Src/Base/AMReX_Box.cpp commit 00901e2b1eb482436cb2f5a8a78f0888f256c211 Author: Weiqun Zhang Date: Tue Jun 13 17:25:32 2017 -0700 let's use BL_TO_FORTRAN_BOX Src/AmrCore/AMReX_FillPatchUtil.cpp Tutorials/Basic/HeatEquation_EX1_C/main.cpp commit f2db746e95e646052ef8b0e0d8685ddb9da1fd79 Merge: 1470574a1 f778523df Author: Andy Nonaka Date: Tue Jun 13 17:18:04 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 1470574a15f7a18045891f7b260880ee4da78230 Author: Andy Nonaka Date: Tue Jun 13 17:17:48 2017 -0700 convert eps to pdf. some small updates to doc Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/AmrCore/figs/Adv1.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv1.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv2.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv2.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv3.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv3.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv4.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv4.pdf Docs/AMReXUsersGuide/AmrCore/figs/Adv5.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv5.pdf Docs/AMReXUsersGuide/AmrCore/figs/subcycling.eps Docs/AMReXUsersGuide/AmrCore/figs/subcycling.pdf commit 4ef2566fcfa649232cc596892dcd72402c86c93f Author: atmyers Date: Tue Jun 13 17:13:44 2017 -0700 An allocator that wraps cudaMallocManaged for use with std::vector Tests/Particles/CUDADeposition/CUDAManagedAllocator.H Tests/Particles/CUDADeposition/Make.package commit f778523df8d112159b95fb9f704a79468adc5b46 Author: Weiqun Zhang Date: Tue Jun 13 17:12:57 2017 -0700 User's Guide: calling Fortran Docs/AMReXUsersGuide/Basics/Basics.tex commit 5b8299a2044e6210d8993e7087f256239f232b63 Merge: 0617d4f45 640acc0c7 Author: Andy Nonaka Date: Tue Jun 13 16:25:41 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 0617d4f458059a783c0e161b6f1d964f15859944 Author: Andy Nonaka Date: Tue Jun 13 16:25:10 2017 -0700 added a short explanation of the AMR algorithm for explicit advection before going into code details Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/AmrCore/figs/Adv1.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv2.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv3.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv4.eps Docs/AMReXUsersGuide/AmrCore/figs/Adv5.eps Docs/AMReXUsersGuide/AmrCore/figs/subcycling.eps commit 640acc0c7b2ee6e9fbae21a591a5999e14eec42c Merge: 2b4db4d23 15f327186 Author: Andrew Myers Date: Tue Jun 13 16:11:46 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 2b4db4d23189f81e1a486cdc0ab555b6279d0dc2 Author: Andrew Myers Date: Tue Jun 13 16:11:31 2017 -0700 Use a mask to shift the interpolation to the coarse level for particles near boundary. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90 Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H Tutorials/Particles/ElectrostaticPIC/inputs Tutorials/Particles/ElectrostaticPIC/main.cpp commit 041f75ca0b7485488ea898dc80f7378819cbe3f6 Author: Andy Nonaka Date: Tue Jun 13 15:39:11 2017 -0700 get rid of references to boxlib Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/Adv_3d.f90 commit 1dcbf138d1bc7eed32f17c02978ee1eb3174c22a Author: Andy Nonaka Date: Tue Jun 13 15:05:02 2017 -0700 update problem description Tutorials/Amr/Advection_AmrCore/README commit c96a13d7a59794f34e6dd8fd652bd1d8366d9553 Author: Andy Nonaka Date: Tue Jun 13 14:46:20 2017 -0700 boxlib ref -> amrex Tutorials/Amr/Advection_AmrCore/README commit 15f327186f7562b9a24f7e3379abde64f622ddd7 Merge: c8b0cc3b8 1e73d393c Author: Weiqun Zhang Date: Tue Jun 13 14:27:34 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c8b0cc3b89641708cd48a0455fbe5e68ebfe0c9f Author: Weiqun Zhang Date: Tue Jun 13 14:27:26 2017 -0700 move AmrCore advection tutorial out of OldTutorials Tutorials/Amr/Advection_AmrCore/Exec/Make.Adv Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/GNUmakefile Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/Make.package Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/Prob.f90 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/Amr/Advection_AmrCore/Exec/SingleVortex/inputs Tutorials/Amr/Advection_AmrCore/README Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.H Tutorials/Amr/Advection_AmrCore/Source/AmrAdv.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvBC.H Tutorials/Amr/Advection_AmrCore/Source/AmrAdvError.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvEvolve.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvIO.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdvInit.cpp Tutorials/Amr/Advection_AmrCore/Source/AmrAdv_F.H Tutorials/Amr/Advection_AmrCore/Source/Make.package Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Adv_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_2d/Make.package Tutorials/Amr/Advection_AmrCore/Source/Src_2d/compute_flux_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_2d/slope_2d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/Adv_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/Make.package Tutorials/Amr/Advection_AmrCore/Source/Src_3d/compute_flux_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_3d/slope_3d.f90 Tutorials/Amr/Advection_AmrCore/Source/Src_nd/Make.package Tutorials/Amr/Advection_AmrCore/Source/Src_nd/Tagging_nd.f90 Tutorials/Amr/Advection_AmrCore/Source/main.cpp commit 1e73d393c2b93192ee1b7faa012cb1bb7600b64f Merge: d746e0fe3 e3e0da3aa Author: Andy Nonaka Date: Tue Jun 13 14:26:24 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit d746e0fe3c7b8026330ce5af5e690e941d681a2a Author: Andy Nonaka Date: Tue Jun 13 14:26:09 2017 -0700 start of doc for amrcore Docs/AMReXUsersGuide/AmrCore/AmrCore.tex commit e3e0da3aa453b5a62ef4f5870f39518e7c20bbcc Author: Weiqun Zhang Date: Tue Jun 13 14:14:15 2017 -0700 User's Guide: MFIter and tiling Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/Basics/cc_growbox.pdf Docs/AMReXUsersGuide/Basics/cc_tilebox.pdf Docs/AMReXUsersGuide/Basics/cc_validbox.pdf Docs/AMReXUsersGuide/Basics/ec_growbox.pdf Docs/AMReXUsersGuide/Basics/ec_tilebox.pdf Docs/AMReXUsersGuide/Basics/ec_validbox.pdf commit 3533bc160ff4cf93b8cdba5b94f31cc14450a8ad Merge: f340bcf33 41b623d10 Author: atmyers Date: Tue Jun 13 13:18:33 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit f340bcf3362b2daa1bdc3e377831943415aeba88 Author: atmyers Date: Tue Jun 13 13:18:22 2017 -0700 more work on the Particle docs. Docs/AMReXUsersGuide/Particle/Particle.tex commit dd85172a0e9288e138b50dad66ebc2256e6e96d6 Author: dtgraves Date: Tue Jun 13 13:00:55 2017 -0700 After much wailing and gnashing of teeth, I found the bug that was causing Marc's test to fail in initialization (it now fails in his code). Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBDebugDump.H Src/GeometryShop/AMReX_EBDebugOut.H Src/GeometryShop/AMReX_EBDebugOut.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_FaceIndex.H Src/GeometryShop/AMReX_FaceIndex.cpp Src/GeometryShop/AMReX_FaceIterator.cpp Src/GeometryShop/AMReX_VolIndex.H Src/GeometryShop/AMReX_VolIndex.cpp Tests/GeometryShop/vofStructures/vofStructures.cpp commit 2c5badad65be13e575a21f5a4b02c9bed34140bb Author: Marc Day Date: Tue Jun 13 12:09:05 2017 -0700 WIP: Rename Node.H Tests/GeometryShop/vofStructures/AMReX_EBStruct.H Tests/GeometryShop/vofStructures/AMReX_ebstruct_mod.F90 Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 Tests/GeometryShop/vofStructures/vofStructures_3d.F90 commit 41b623d10f5d91d07eedd74ada40184e4de659a4 Author: vince Date: Tue Jun 13 11:32:06 2017 -0700 fix sleep seconds. Src/Base/AMReX_Utility.cpp commit c6b55eae2a5737cf8689275f7d6ed48a32922577 Merge: 10843df22 0fe126516 Author: vince Date: Tue Jun 13 11:30:55 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit a63814193feac3b5b8bdb7bda533f2d6e92b78fc Author: Max Katz Date: Tue Jun 13 13:47:54 2017 -0400 Add Arena flags for cudaMemAdvise Src/Base/AMReX_Arena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H commit 0fe1265167363add72bcd1fca39516c2c7a2fe42 Merge: ba956385b e2de30bdc Author: WeiqunZhang Date: Tue Jun 13 10:38:38 2017 -0700 Merge pull request #36 from bcfriesen/misc_cvode Misc CVODE commit ba956385bc7e2a8ff039bf1242ce696376753561 Merge: f97d34edb 2bafbf745 Author: WeiqunZhang Date: Tue Jun 13 10:38:29 2017 -0700 Merge pull request #37 from bcfriesen/update_cray_flags Update Cray flags commit 2bafbf74569bb8a22ce79fa0364798c0c8544ba9 Author: Brian Friesen Date: Thu Jun 8 15:09:54 2017 -0700 GNUMake: if DEBUG=TRUE, add Cray compiler flag that inits Fortran reals/complexes to NaN Tools/GNUMake/comps/cray.mak commit 89db4aa9f010d92c58e70435791d71c1d123a2fd Author: Brian Friesen Date: Wed Jun 7 16:02:56 2017 -0700 Tools/GNUMake: add optimization report output to Cray compiler Tools/GNUMake/comps/cray.mak commit e2de30bdc409d85c5c33ab7af407e6d7c752a249 Author: Brian Friesen Date: Tue Jun 13 10:12:14 2017 -0700 VODE: add misc functions for querying integration statistics Src/Extern/CVODE/Make.package Src/Extern/CVODE/integrator_stats.f90 commit d3b78a661b41a8858099b2b804d4dbb0255d0ff6 Author: Max Katz Date: Tue Jun 13 12:57:28 2017 -0400 Use an arena for Box data Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit c5139581d3f2366ba12de212dc2aeb0e1e89c09b Author: Max Katz Date: Tue Jun 13 12:17:22 2017 -0400 Avoid a Box conversion call if unnecessary Src/Base/AMReX_BoxArray.cpp commit 97b3eaf32f4ff2a29ec5f17e805c4450552de8be Merge: 96cd30e06 a94e639b7 Author: dtgraves Date: Tue Jun 13 08:38:48 2017 -0700 merging with dtg_branch before fixing some bugs commit 71ea27dce63d9d738aabb033f9666f3228c56ce9 Author: Max Katz Date: Tue Jun 13 10:17:20 2017 -0400 Move GPU heat equation example to new directory Tutorials/Basic/HeatEquation_EX1_C/Make.package Tutorials/Basic/HeatEquation_EX1_C/advance_2d.f90 Tutorials/Basic/HeatEquation_EX1_C/advance_3d.f90 Tutorials/Basic/HeatEquation_EX1_C/main.cpp Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H Tutorials/GPU/HeatEquation_EX1_C/GNUmakefile Tutorials/GPU/HeatEquation_EX1_C/Make.package Tutorials/GPU/HeatEquation_EX1_C/advance_2d.F90 Tutorials/GPU/HeatEquation_EX1_C/advance_3d.F90 Tutorials/GPU/HeatEquation_EX1_C/init_phi_2d.f90 Tutorials/GPU/HeatEquation_EX1_C/init_phi_3d.f90 Tutorials/GPU/HeatEquation_EX1_C/inputs_2d Tutorials/GPU/HeatEquation_EX1_C/inputs_3d Tutorials/GPU/HeatEquation_EX1_C/main.cpp Tutorials/GPU/HeatEquation_EX1_C/myfunc_F.H commit 8dea5f74880dfe34b9dc3dc0d0f19fac3fbc4927 Author: Max Katz Date: Tue Jun 13 10:01:13 2017 -0400 Pass idir and dt by value Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90 commit 96cd30e06b26c47a315ffa635ced52e6038e0bc3 Author: Marc Day Date: Mon Jun 12 21:14:25 2017 -0700 WIP: enforce that faces between regular and cut cells are regular, and seen that way from within the cut cell Tests/GeometryShop/vofStructures/Node.H Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 Tests/GeometryShop/vofStructures/vofStructures_3d.F90 commit ec3c493e212d0ab7f863b722cd357b49fd0c3aaa Author: Max Katz Date: Mon Jun 12 23:14:13 2017 -0400 Rely on managed memory in heat equation Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90 Tutorials/Basic/HeatEquation_EX1_C/main.cpp commit 5453f242219a2eca97726d0583ffb3eafb971762 Merge: 1aacf1cb9 ebd921409 Author: Max Katz Date: Mon Jun 12 23:05:30 2017 -0400 Merge branch 'gpu' into gpu_var2 commit 1aacf1cb947abe6d64848e7d1edc6766877bdc23 Author: Max Katz Date: Mon Jun 12 22:48:52 2017 -0400 Use a managed memory approach for the Box lo and hi bounds A shared pointer is created that stores the managed memory versions of lo and hi (which mirror what smallend and bigend store). The shared pointer is reset when a transforming function like surroundingNodes is called. Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit d0c3126a9429b98a32eb8ae9d341291551961a58 Author: Marc Day Date: Mon Jun 12 19:44:19 2017 -0700 WIP: remove unused member data from local struct Tests/GeometryShop/vofStructures/vofStructures.cpp commit 2c2cd581962a4d3b537ea4479f0e7223066b7153 Author: Marc Day Date: Mon Jun 12 19:39:31 2017 -0700 WIP: move fort graph construction into function call Tests/GeometryShop/vofStructures/vofStructures.cpp commit ebd921409518614f57c9df8ca60d975fea685fc3 Merge: e1867ca1b b22bc588c Author: Max Katz Date: Mon Jun 12 19:30:20 2017 -0700 Merge pull request #35 from xinshengqin/gpu2 Add 3d cuda version of the heat equation tutorial commit f97d34edb1acc058aa4d9d0ed798ed3062e4e2f3 Merge: 090cd5c8a 58b65d9a3 Author: Andrew Myers Date: Mon Jun 12 17:51:10 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 090cd5c8adf285b2a52b0643ea4621256914cc32 Author: Andrew Myers Date: Mon Jun 12 17:33:12 2017 -0700 generalize build mask to take a number of buffer cells instead of assuming 1. Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90 Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H Tutorials/Particles/ElectrostaticPIC/main.cpp commit 6bcd95ff814da0912d3093dd9bfd603de8d7ed90 Author: Andrew Myers Date: Mon Jun 12 17:32:02 2017 -0700 Need to special case num_levels = 1 here. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp commit 58b65d9a3875135d673bc72f8700f3ffad9bc678 Merge: 716dcf535 b2a8548a6 Author: Andy Nonaka Date: Mon Jun 12 17:20:53 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 716dcf535c391378236f63a6129785aa7f6cf9ba Author: Andy Nonaka Date: Mon Jun 12 17:20:24 2017 -0700 added basic documentation for how to open 3d plotfiles and amrex particle data with paraview Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Docs/AMReXUsersGuide/Introduction/Introduction.tex Docs/AMReXUsersGuide/Visualization/ParaView.eps Docs/AMReXUsersGuide/Visualization/ParaView_particles.eps Docs/AMReXUsersGuide/Visualization/Visualization.tex Docs/AMReXUsersGuide/amrexsymbols.tex commit b2a8548a613443bb2fa448270e4ba98a8f3f1a5f Author: Weiqun Zhang Date: Mon Jun 12 16:56:22 2017 -0700 User's Guide: MFiter without tiling Docs/AMReXUsersGuide/Basics/Basics.tex commit d184dfc880e73efe2cbada1025ebae776821394c Merge: c7e82049b 94abad6f7 Author: atmyers Date: Mon Jun 12 16:44:34 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c7e82049b52a18bb4e9f92cf4c17d491708ffb4f Author: atmyers Date: Mon Jun 12 16:44:27 2017 -0700 fix comment. Tutorials/Particles/ShortRangeParticles/short_range_2d.f90 Tutorials/Particles/ShortRangeParticles/short_range_3d.f90 commit 6dd376dc00e37568586ff7186288fcceca6a4810 Author: atmyers Date: Mon Jun 12 16:43:34 2017 -0700 some more work on the Particle docs. Docs/AMReXUsersGuide/Particle/Particle.tex commit 94abad6f7055ca1fe4580203baf6675f2fdca1d4 Merge: 057ad96c8 72d7c9e32 Author: Andy Nonaka Date: Mon Jun 12 16:22:59 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 057ad96c8144d2f5726e75444048f66c8d97e7e9 Author: Andy Nonaka Date: Mon Jun 12 16:22:20 2017 -0700 for python script to convert amrex particle data to .vtp format, throw out extra four lines in header (after # of particles) Tools/Py_util/amrex_particles_to_vtp/amrex_particles_to_vtp.py commit 9e7b6722a7391ae34d39b9882d640213ef4a8f9f Author: dtgraves Date: Mon Jun 12 16:22:08 2017 -0700 bugs found in EBGraph, FaceIterator Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_FaceIterator.cpp commit 72d7c9e3221ed1ffb1c66c056beeb8d849f7ec36 Author: Weiqun Zhang Date: Mon Jun 12 15:32:41 2017 -0700 User's Guide: parallel copy Docs/AMReXUsersGuide/Basics/Basics.tex commit a94e639b759488375e4986b3db8ca7a6e184c5fa Author: dtgraves Date: Mon Jun 12 15:24:33 2017 -0700 added some parallel debugging tools Src/Base/AMReX_FabArray.H Src/Base/AMReX_SPMD.H Src/Base/AMReX_SPMD.cpp Src/Base/AMReX_SPMDI.H Src/Base/AMReX_parstream.H Src/Base/AMReX_parstream.cpp Src/Base/Make.package Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_GraphNode.cpp Src/GeometryShop/Make.package Tests/GeometryShop/ebgraphDistributed/GNUmakefile Tests/GeometryShop/ebgraphSingleGrid/GNUmakefile Tests/GeometryShop/flatPlate/GNUmakefile Tests/GeometryShop/regression/dataArith.cpp Tests/GeometryShop/regression/dataarith.inputs Tests/GeometryShop/regression/serialization.cpp Tests/GeometryShop/regression/serialization.inputs Tests/GeometryShop/runalltests.mpi.sh Tests/GeometryShop/runalltests.serial.sh Tests/GeometryShop/sparseDataSingleGrid/GNUmakefile Tests/GeometryShop/sphere/GNUmakefile Tests/GeometryShop/sphereEBISBox/GNUmakefile commit c462a18e864b5f4ebd6ed4995b5bf56ab153f7a0 Author: Marc Day Date: Mon Jun 12 15:20:12 2017 -0700 WIP: Try to add flat plate geom, but there are issues... Tests/GeometryShop/vofStructures/flatplate.inputs Tests/GeometryShop/vofStructures/sphere.inputs Tests/GeometryShop/vofStructures/vofStructures.cpp commit b77ed4a5ec731aa5781754eb53fd1e48d0ed30b0 Author: Andrew Myers Date: Mon Jun 12 12:44:57 2017 -0700 removing some commented-out code. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90 Tutorials/Particles/ElectrostaticPIC/inputs Tutorials/Particles/ElectrostaticPIC/main.cpp commit a56b8473e814c569125c59ca45858da835ff524f Author: Marc Day Date: Mon Jun 12 12:38:05 2017 -0700 WIP: fix bug in eb f90 struct, add some checking of faces in fortran. Tests/GeometryShop/vofStructures/AMReX_ebstruct_mod.F90 Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 Tests/GeometryShop/vofStructures/vofStructures_3d.F90 commit d9f20d733b6ca36715b63a47d882ebbc9e242fd2 Author: Weiqun Zhang Date: Mon Jun 12 11:19:46 2017 -0700 User's Guide: FillBoundary Docs/AMReXUsersGuide/Basics/Basics.tex commit 5b64b3a768b962a93025de3e5d7bcd92c8b5eeb4 Author: Marc Day Date: Mon Jun 12 11:18:01 2017 -0700 WIP: Pass face-based structs to fortran, add note in README Tests/GeometryShop/vofStructures/README.txt Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 Tests/GeometryShop/vofStructures/vofStructures_3d.F90 commit 4b51388cc94378286f8134356401579880345a0c Author: Weiqun Zhang Date: Mon Jun 12 11:17:00 2017 -0700 add ParallelCopy to FabArray to make the parallel part clearer Src/Base/AMReX_FabArray.H commit 1c42d3123144fc153fd788ce34e75df624368e5e Author: Marc Day Date: Mon Jun 12 10:52:33 2017 -0700 WIP: Move eb struct def into mod file Tests/GeometryShop/vofStructures/AMReX_ebstruct_mod.F90 Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/vofStructures_2d.F90 Tests/GeometryShop/vofStructures/vofStructures_3d.F90 commit 95fbb1725bfd94f4dc9ce710718e564d1b9d0c8f Author: Andrew Myers Date: Mon Jun 12 10:36:14 2017 -0700 check in working version of ES single particle test. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90 Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H Tutorials/Particles/ElectrostaticPIC/inputs Tutorials/Particles/ElectrostaticPIC/main.cpp commit b22bc588c1bd99be50e76af6a308d2e947949046 Author: Xinsheng (Shawn) Qin Date: Sun Jun 11 14:33:19 2017 -0700 change blo(2) and bhi(2) in advance_2d to blo(3) and bhi(3) to avoid warning Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 commit 4cfc8ffd7652bd12665fdb00dbfc3a12631f7f24 Merge: 444373eda e1867ca1b Author: Xinsheng (Shawn) Qin Date: Sun Jun 11 14:01:23 2017 -0700 Merge remote-tracking branch 'origin/gpu' into gpu2 commit e1867ca1be30b67c4755eeee1bb4341f3033fdb4 Author: Max Katz Date: Sun Jun 11 16:02:48 2017 -0400 Fix loop bounds in update_phi_doit Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 commit 41b4c2e1ae5ff63a14f5d0d5ed83acd895a7707c Author: Max Katz Date: Sun Jun 11 14:56:57 2017 -0400 Do not copy dx now that it is managed memory Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 commit 9986fcb3710b8b078ef07b843c071dca4d38e37a Author: Max Katz Date: Sun Jun 11 14:56:24 2017 -0400 Create managed dx object in Geometry, returned by CellSize() Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_Geometry.cpp commit 444373eda467242c88e29f594e17c122de9aed6e Author: Xinsheng (Shawn) Qin Date: Sat Jun 10 23:22:43 2017 -0700 finish CUDA 3D version. Result tested. Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90 commit 0b0c4b858c2315228727f1a22483212841000ec9 Merge: a22d6c92a 46cdb87a5 Author: Xinsheng (Shawn) Qin Date: Sat Jun 10 23:17:21 2017 -0700 Merge remote-tracking branch 'origin/gpu' into gpu2 commit 5b6f3142ce9a3ad18a7ee17c2527090e5eff67cb Merge: e6d754c21 25fa446e9 Author: Marc Day Date: Sat Jun 10 19:34:38 2017 -0700 Merge branch 'dtg_branch' into vof-work commit e6d754c216fb2fbac0a9947e51101cc909116c90 Author: Marc Day Date: Sat Jun 10 19:33:54 2017 -0700 WIP: Add 3d fort for vofstructures test Tests/GeometryShop/vofStructures/vofStructures_3d.F90 commit 46cdb87a59b1a294e3d7644b2344e0b0426064da Author: Max Katz Date: Sat Jun 10 19:58:20 2017 -0400 Move C interfaces into a module Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 commit 9ea34d41414490e781d7f5f2bf73c6fa26b1a954 Author: Max Katz Date: Sat Jun 10 19:56:14 2017 -0400 Launch kernels directly, avoiding CUDA wrappers Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 commit a22d6c92abab63798fb1bc768ce4b60dfc893c02 Author: Xinsheng (Shawn) Qin Date: Sat Jun 10 16:38:11 2017 -0700 CUDA 3D version results checked Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90 commit 580a1413f666ed666e8af28ad7d8bb37272532b6 Author: Xinsheng (Shawn) Qin Date: Sat Jun 10 15:51:36 2017 -0700 Fix some issues for CPU part. CPU results checked Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90 commit c10d0f1770c174ea3a9023a6b5fbb699715a12a4 Author: Max Katz Date: Sat Jun 10 14:19:23 2017 -0400 Fix some issues in the GPU heat equation Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90 Tutorials/Basic/HeatEquation_EX1_C/main.cpp Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H commit a1ac3676d6d8c273fb394c8b9feda668d1cd0a67 Merge: afa58948a 93dacd0de Author: Max Katz Date: Sat Jun 10 12:17:46 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit b96c6c17fb1d7b5c2965fcab3c4bcec492f016a0 Author: Marc Day Date: Sat Jun 10 00:44:12 2017 -0700 Add a comment while I remember what I did. Tests/GeometryShop/vofStructures/vofStructures.cpp commit ff38c6fd6c7eaf862f804df06f567004e9fedc23 Author: Marc Day Date: Sat Jun 10 00:41:41 2017 -0700 Add ebFaceID to CNode struct Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/Node.H Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 commit 25fa446e946c6776884eeee0418f06118bc27ef5 Author: dtgraves Date: Fri Jun 9 19:57:49 2017 -0700 fixed IntVectSet to accomodate the fact that std::set is weird Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_GraphNode.cpp Src/GeometryShop/AMReX_IntVectSet.cpp commit 93dacd0deb5f975656ad502a03bc8c8579254945 Merge: 9acd09527 f3751650a Author: Michael Zingale Date: Fri Jun 9 13:01:06 2017 -0400 Merge branch 'development' into gpu commit f3751650a131f88378bc138ca0f86d6e44eaa6cf Author: atmyers Date: Fri Jun 9 12:51:05 2017 -0400 CMakeLists.txt was missing this header file. Src/AmrCore/CMakeLists.txt commit 10843df2283f3d55e68574ac96ba28e6d3f903f5 Merge: 9303d664f 5047bf858 Author: vince Date: Fri Jun 9 09:37:36 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 5047bf85879ceea910989efda42c7a089b2dfb60 Author: Weiqun Zhang Date: Fri Jun 9 09:10:28 2017 -0700 make: strip leading and trailing whitespace from many make variables Tools/GNUMake/Make.defs Tools/GNUMake/Make.machines commit 9acd09527aa1e9f203fb107eafa754af390fda44 Merge: e001022da a02692be9 Author: Andrew Myers Date: Fri Jun 9 11:40:21 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit e001022da578d127e7282ce83826c115c0027553 Author: Andrew Myers Date: Fri Jun 9 11:40:15 2017 -0400 some renaming. Tests/Particles/CUDADeposition/MyParticleContainer.H Tests/Particles/CUDADeposition/main.cpp commit afa58948a878e56b37c1f7ed6441f27df34265f1 Author: Max Katz Date: Fri Jun 9 11:24:29 2017 -0400 Strip out unnecessary CUDA wrappers Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_fort_mod.F90 commit 9a89ab20204ec1c7bb9351781e78a24ce1bf1570 Author: Andrew Myers Date: Fri Jun 9 11:02:18 2017 -0400 reorganizing the CUDA-enabled particle container. Tests/Particles/CUDADeposition/MyParticleContainer.H Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/inputs Tests/Particles/CUDADeposition/main.cpp commit a02692be95c5825d81ee3ec40cf01e35dadc7e52 Author: Max Katz Date: Fri Jun 9 08:45:29 2017 -0400 Don't do threads_and_blocks without BL_SPACEDIM Src/Base/AMReX_CUDA.F90 commit 7aea5ac75547760fd6f2429a961993c6551791ca Author: Max Katz Date: Thu Jun 8 22:23:37 2017 -0400 Remove incorrect underscore Src/Base/GPackage.mak commit 7a30ab8bbcc53b1683af1a79f77a0b554f4b82b4 Merge: 8cb138820 387e613b3 Author: Andrew Myers Date: Thu Jun 8 21:20:07 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 8cb138820f76b9d691caea1b0fc41f2abca221a2 Author: Andrew Myers Date: Thu Jun 8 21:19:59 2017 -0400 implementing multiple streams for the Cuda PIC example/ Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/cuda_deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_F.H Tests/Particles/CUDADeposition/inputs Tests/Particles/CUDADeposition/main.cpp commit 1d1642592bcaa3e7161db273c4c7df1af8d7074e Author: Marc Day Date: Thu Jun 8 18:11:44 2017 -0700 WIP: More testing of vof stuff in fortran Tests/GeometryShop/vofStructures/Node.H Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 commit e4dc52858c878a5dbdf995136209751f6b969cd3 Author: Marc Day Date: Thu Jun 8 17:06:48 2017 -0700 WIP: Move defines for mask type into .H file Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/Node.H Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 commit b70ce3c659db94cf8cb9ce848cf257c4a2633c85 Author: Marc Day Date: Thu Jun 8 15:54:27 2017 -0700 WIP: fix fortran and grow cell issue Tests/GeometryShop/vofStructures/sphere.inputs Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 commit 387e613b32ad3c6e921021d9bb348d952a764fe0 Merge: 7eeeb653d dafe1f1b4 Author: Max Katz Date: Thu Jun 8 18:40:34 2017 -0400 Merge pull request #33 from xinshengqin/gpu2 change Tools/GNUMake/Make.rules to be shell-independent commit dafe1f1b4f7aea130e21607314af04f2955d8f5a Merge: fc2a1cef1 7eeeb653d Author: Xinsheng (Shawn) Qin Date: Thu Jun 8 15:16:28 2017 -0700 Merge remote-tracking branch 'origin/gpu' into gpu2 commit fc2a1cef16dab6bf4c8c68b1b7baea9f9e72476b Author: Xinsheng (Shawn) Qin Date: Thu Jun 8 15:15:59 2017 -0700 update Make.rules to use shell-independent if condition Tools/GNUMake/Make.rules commit 7eeeb653de8d0db5b82fad909e7d4b817ca8c97a Author: Max Katz Date: Thu Jun 8 17:50:42 2017 -0400 Add in CUDA C++ to F90 build Src/Base/GPackage.mak commit 9b4107f61f1c53be26064f714bdbe075c57deb01 Author: Max Katz Date: Thu Jun 8 17:03:37 2017 -0400 Add an alternate FOEXTRAP version of filcc Src/Base/AMReX_FILCC_3D.F90 commit a2bfa6f40dbd0172f600232b06f75a9d410b5eed Author: Marc Day Date: Thu Jun 8 13:19:58 2017 -0700 WIP: Try adding a grow cell...failure Tests/GeometryShop/vofStructures/vofStructures.cpp commit 0f7524afa9ae5d92f1e1d8f96c829d94dafcf024 Merge: 272d0f82b 478351689 Author: Max Katz Date: Thu Jun 8 16:12:59 2017 -0400 Merge pull request #32 from alancalder/gpu Gpu What should complete the cudaizing of the advance_3d.F90 routine for the Heat Equation Test. commit cd42a7a3a30c2e06299348b921a1b989cf6771de Merge: ccfcdd6cf 052ece9da Author: WeiqunZhang Date: Thu Jun 8 13:03:38 2017 -0700 Merge pull request #31 from bcfriesen/CVODE_tutorial_fixes Tutorials: fix pointer mistake in CVODE/EX1 and CVODE/EX2 commit 272d0f82bbe3a69be12a71cdf4caad88d2e218f2 Author: Andrew Myers Date: Thu Jun 8 16:01:41 2017 -0400 use cuda streams when running with multiple boxes. Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/cuda_deposit_3d.f90 commit 478351689e5ccbb4de746947308c0f98fc48dd25 Author: Alan Calder Date: Thu Jun 8 15:57:10 2017 -0400 Another pass at the advance_3d.F90 routine from the Heat Equation Test. Should be complete this time. Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90 commit 052ece9da7d0c5e1d6be711771191f8dcfea0b8f Author: Brian Friesen Date: Thu Jun 8 12:38:54 2017 -0700 Tutorials: fix pointer mistake in CVODE/EX1 and CVODE/EX2 I mistakenly thought that the CVODE function N_VMake_Serial() allocates a new C array and deep copies the data from the corresponding Fortran. But in fact it simply creates a C pointer that points to the Fortran data. Tutorials/CVODE/EX1/integrate_ode.f90 Tutorials/CVODE/EX2/integrate_ode_no_jac.f90 Tutorials/CVODE/EX2/integrate_ode_with_jac.f90 commit e280a39c8e72c951f25df7e7428d51110f989f57 Author: Marc Day Date: Thu Jun 8 12:38:12 2017 -0700 WIP: Rework eb structures a bit, add fortran to test Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/README.txt Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructuresA.cpp Tests/GeometryShop/vofStructures/vofStructures_2d.F90 commit ccfcdd6cfa3ea5364046a1c27efb1cbc49636414 Merge: 766041da9 af96a3e01 Author: WeiqunZhang Date: Thu Jun 8 12:36:31 2017 -0700 Merge pull request #30 from AMReX-Codes/dtg_branch initial indications are that two-stage communication seems to be working commit af96a3e01c862bdda0b6e5bd4705c17eec72d805 Merge: 7644ea9ef 766041da9 Author: dtgraves Date: Thu Jun 8 12:22:49 2017 -0700 merging with development branch commit 7644ea9ef054c8e9d91a6e2ffda12dffe274ff39 Author: dtgraves Date: Thu Jun 8 12:21:35 2017 -0700 took out some unused variables Src/GeometryShop/AMReX_EBGraph.cpp commit 229c46ea50e67b44e53966ddb77876dc7980b6c8 Author: dtgraves Date: Thu Jun 8 11:08:17 2017 -0700 made EBData holders (since they are templated) preallocatable = false without a ton of thought. We can revisit this for template specializations where we know it to be true. Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBFaceFAB.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBGraph.H commit 04c312fd29492b49fb8513131b9b622c280ea06b Author: dtgraves Date: Thu Jun 8 10:56:43 2017 -0700 fixed merge bug Src/EBAMRTools/AMReX_EBFortND_F.H commit 2c65cfac84197ed5eb6dd9b76ffd18ffe4d5bf01 Merge: 99e54a2a8 74905aaab Author: dtgraves Date: Thu Jun 8 10:53:16 2017 -0700 merging with weiqun/2passes commit 22cb5abdde32bc27ec21853e844759fcba864a6d Author: Andrew Myers Date: Thu Jun 8 13:46:32 2017 -0400 Adding another timer. Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/main.cpp commit 32cc6f4da3d0886d33cbcbaf2ec6eb5f43abab5d Author: Andrew Myers Date: Thu Jun 8 13:43:20 2017 -0400 Also doing the Poisson solve. Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/cuda_deposit_3d.f90 Tests/Particles/CUDADeposition/main.cpp Tests/Particles/CUDADeposition/solve_for_accel.cpp commit 99e54a2a88877b9e6f6a772a2b9595cd6525bc65 Author: dtgraves Date: Thu Jun 8 10:40:24 2017 -0700 EBIndexSpace read/write now works and is tested. Src/Base/AMReX_Utility.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Tests/GeometryShop/README Tests/GeometryShop/regression/ebio.cpp Tests/GeometryShop/regression/ebio.inputs Tests/GeometryShop/regression/fabio.cpp commit 7e0d3ee32192cd60430b5ef24f3a1ecbf7bcbc44 Merge: b265c6846 f54d4e21a Author: Andrew Myers Date: Thu Jun 8 12:03:21 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit f54d4e21adb0dca44b4b27154c5e088300d90888 Merge: ffa672d11 766041da9 Author: Max Katz Date: Thu Jun 8 11:58:43 2017 -0400 Merge branch 'development' into gpu commit 766041da9bae335c6b0acceb28a6867e5385edaa Author: Max Katz Date: Thu Jun 8 11:55:34 2017 -0400 Specify CUDA 8.0 for OpenACC Tools/F_mk/comps/Linux_pgi.mak commit b265c6846924d7bf64c91a226a59b7279f2cca23 Author: Andrew Myers Date: Thu Jun 8 11:49:21 2017 -0400 fix capitalization issue. Tests/Particles/CUDADeposition/Make.package commit b8c5216ba3c883da13a52e8a4bf734dc2443d7ab Author: Andrew Myers Date: Thu Jun 8 11:47:14 2017 -0400 This compiles and runs correctly both with and without CUDA. Tests/Particles/CUDADeposition/GNUmakefile Tests/Particles/CUDADeposition/Make.package Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/cuda_deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_F.H Tests/Particles/CUDADeposition/main.cpp commit ebb4e157c108223e7c72972c18ecf4f4b22535ef Author: Andrew Myers Date: Thu Jun 8 11:27:27 2017 -0400 making this thing compile both with and without CUDA. Tests/Particles/CUDADeposition/cuda_deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_3d.f90 commit 458d871c7ddf19f9f8479ea3720c7359e871443c Author: Andrew Myers Date: Thu Jun 8 11:13:45 2017 -0400 bringing over some stuff needed for the MG solves. Tests/Particles/CUDADeposition/solve_for_accel.cpp Tests/Particles/CUDADeposition/solve_with_f90.cpp commit ffa672d11c7e15395833c0fc37f9a14f7e53feeb Merge: ad2a864bb 3c52ab1b0 Author: Andrew Myers Date: Thu Jun 8 10:59:56 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit ad2a864bb58248f1e6ef9586fd6b543a764a2e64 Author: Andrew Myers Date: Thu Jun 8 10:57:17 2017 -0400 fixed double-counting issue. Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_F.H Tests/Particles/CUDADeposition/main.cpp commit 3c52ab1b0906363d0fa2ca9900331a4957a7522a Merge: 067a94ff1 c8745ba8f Author: Michael Zingale Date: Thu Jun 8 10:51:30 2017 -0400 Merge branch 'gpu' of ssh://github.com/AMReX-Codes/amrex into gpu commit 067a94ff1a0cefe6feb769a5542eaa3c13848529 Author: Michael Zingale Date: Thu Jun 8 10:51:14 2017 -0400 remove the rest of the arraylim stuff for clarity Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F90 commit c8745ba8f68754d0b5ef6e683a1366b12a47883c Author: Max Katz Date: Thu Jun 8 10:32:28 2017 -0400 More cleanup of filcc interfaces Src/Base/AMReX_FILCC_3D.F90 commit 4dbef2bc3ae751a39e459ccc5d20447419cfd135 Merge: e3509b868 0145cb406 Author: Michael Zingale Date: Thu Jun 8 10:25:20 2017 -0400 Merge branch 'gpu' of ssh://github.com/AMReX-Codes/amrex into gpu commit e3509b868349fb1dc9eac83b12a9635bade7f05f Author: Michael Zingale Date: Thu Jun 8 10:25:07 2017 -0400 remove dim macros for clarity Src/Base/AMReX_FILCC_3D.F90 commit 0145cb40697143c5d6e0abb20027bf589aa05494 Author: Max Katz Date: Thu Jun 8 10:18:54 2017 -0400 Add some FabArray/MultiFab profiling Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.cpp commit ba190be17422a80e37cc0f6d6995a2dc17c7e11d Merge: 0af7853c3 08905f630 Author: Michael Zingale Date: Thu Jun 8 09:58:30 2017 -0400 Merge branch 'gpu' of ssh://github.com/AMReX-Codes/amrex into gpu commit 0af7853c3792d46cef8239c74b8753bae9e623af Author: Michael Zingale Date: Thu Jun 8 09:58:11 2017 -0400 make these free-form Src/Base/AMReX_FILCC_1D.F Src/Base/AMReX_FILCC_1D.F90 Src/Base/AMReX_FILCC_2D.F Src/Base/AMReX_FILCC_2D.F90 Src/Base/AMReX_FILCC_3D.F Src/Base/AMReX_FILCC_3D.F90 Src/Base/Make.package commit 08905f630e5195343db38eabec7913a4f61816d1 Author: Max Katz Date: Thu Jun 8 08:31:19 2017 -0400 Fix CPU versions of saxpy and plus Src/Base/AMReX_BaseFab_nd.F90 commit 656fc461c6c9fa60006f789fdcb58ca0821fcf8c Author: Marc Day Date: Wed Jun 7 20:17:30 2017 -0700 WIP: Remove covered faces from data set Tests/GeometryShop/vofStructures/vofStructuresA.cpp commit 0a10f81be263797e6aa0d89a450633807c584a95 Author: Marc Day Date: Wed Jun 7 20:08:27 2017 -0700 WIP: Rename FLUID to REGULAR Tests/GeometryShop/vofStructures/vofStructuresA.cpp commit 68a3b1a51d6d946d72fdf0ce10ebb2e683edbe99 Author: Marc Day Date: Wed Jun 7 20:00:46 2017 -0700 WIP: An alternative set of structures to chase the graph in Fortran. Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/vofStructures.cpp Tests/GeometryShop/vofStructures/vofStructuresA.cpp commit 2b7ddc51d68e15687f87bf9178338a76c31a7ac9 Author: Andrew Myers Date: Wed Jun 7 21:55:59 2017 -0400 fix to domain decomposed version. Tests/Particles/CUDADeposition/deposit_3d.f90 commit 49be4625d6fbca65006b10fcdb5b599429d51ac2 Merge: 854f3e2ce 729ed5254 Author: Andrew Myers Date: Wed Jun 7 20:25:51 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 854f3e2ce262d7f766326fe38c78126fa484da6a Merge: 0f27a9dde bc336d824 Author: Andrew Myers Date: Wed Jun 7 20:25:25 2017 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into gpu commit 0f27a9ddef1486404e82c30e1f048922bc25576d Author: Andrew Myers Date: Wed Jun 7 20:25:08 2017 -0400 converting more pic kernels to cuda. Tests/Particles/CUDADeposition/MyParticleContainer.H Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_F.H Tests/Particles/CUDADeposition/main.cpp commit d04eb38ad764a8a6fef80e61a74449d5d1b056a9 Author: dtgraves Date: Wed Jun 7 16:24:10 2017 -0700 fixed an I/O bug. Added istream for RealVect. On to trying out two-phase communication Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_FabArrayIO.H Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/ebio.cpp Tests/GeometryShop/regression/ebio.inputs Tests/GeometryShop/regression/fabio.inputs commit 729ed52543143d7c41735a925c120de94cadb8ab Author: Michael Zingale Date: Wed Jun 7 19:14:27 2017 -0400 enable CUDA for IBM Tools/GNUMake/comps/ibm.mak commit 9c7cf976cb54bde0d3e5378db60e23f248ab0b71 Merge: d8d170e9a bc336d824 Author: Michael Zingale Date: Wed Jun 7 19:08:54 2017 -0400 Merge branch 'development' into gpu commit 74905aaab6478ae5446b31cdd1baf75bd31a4031 Author: Weiqun Zhang Date: Wed Jun 7 15:23:46 2017 -0700 fix deadlock in 2-pass communication Src/Base/AMReX_FabArray.H commit c861721c4fea0ce2da5ea12bd336bd649a1fee72 Merge: 836d3c763 47d5cabb4 Author: WeiqunZhang Date: Wed Jun 7 15:06:45 2017 -0700 Merge pull request #28 from AMReX-Codes/weiqun/tmp Add Intel to the list of compilers we test on to set the --traditiona… commit 47d5cabb49f5c5fd721d97e237dddea4ec3f9f9b Author: Ann Almgren Date: Wed Jun 7 14:59:49 2017 -0700 Add Intel to the list of compilers we test on to set the --traditional flag Tools/CMake/PreprocessAMReXFortran90.cmake commit bc336d8245746dd317ae554bd8a48f6b4a794439 Merge: fdec367ff 8fa0e0a52 Author: Ann Almgren Date: Wed Jun 7 15:00:07 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit fdec367ff911b0d997cfc64b9d7df6cacff7d654 Author: Ann Almgren Date: Wed Jun 7 14:59:49 2017 -0700 Add Intel to the list of compilers we test on to set the --traditional flag Tools/CMake/PreprocessAMReXFortran90.cmake commit d8d170e9ab09a46ffeb5e875c5bfa5932a8b06e2 Author: Max Katz Date: Wed Jun 7 17:45:39 2017 -0400 Write proper kernels for copy, saxpy, setval, and plus Src/Base/AMReX_BaseFab_nd.F90 commit 54dd727611c3778b8280169b3acd584f391cf4b5 Author: Andrew Myers Date: Wed Jun 7 17:18:10 2017 -0400 some more work on the domain decomp stuff. Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/inputs commit 639e098afe0fed8fb7b1b67a28610fe3f0b3d466 Merge: eafa51e26 89469038e Author: Xinsheng (Shawn) Qin Date: Wed Jun 7 13:49:17 2017 -0700 Merge remote-tracking branch 'origin/gpu' into gpu2 commit a358cea0a60d632bc55b91078672d45d573f8d3c Author: dtgraves Date: Wed Jun 7 13:37:19 2017 -0700 I/O for FabArray (for T = EBGraph, EBData and BaseEBCellFAB) seems to work fine. Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_EBData.H Tests/GeometryShop/regression/fabio.cpp Tests/GeometryShop/regression/serialization.cpp Tests/GeometryShop/regression/serialization.inputs commit 89469038efd50b63f2c655bfdf6383806c56b70e Merge: 62c397dd3 3e1cbe7c6 Author: Michael Zingale Date: Wed Jun 7 16:37:03 2017 -0400 Merge pull request #27 from alancalder/gpu Alan's pass at cudaizing the 3-d advance routine for the heat commit 3e1cbe7c622b511917479250e538138d0c225b77 Author: Alan Calder Date: Wed Jun 7 16:34:13 2017 -0400 Fixed two bugs in advance_3d.F0 of the heat equation test identified by Mike and Max. Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90 commit 25c44c4c3aa0a7762f332d209847f85bc4369d45 Author: Weiqun Zhang Date: Wed Jun 7 13:30:12 2017 -0700 have to sum up number of bytes for each communication tile because of metadata Src/Base/AMReX_FabArray.H commit a0b6b9fb3fced944e93a04c64bcd0a7e7e2c4c97 Author: Alan Calder Date: Wed Jun 7 15:59:24 2017 -0400 Alan's pass at cudaizing the 3-d advance routine for the heat equation test. Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90 commit 4964cf82333eeba193ca57128913e841ae4d935e Author: Weiqun Zhang Date: Wed Jun 7 12:42:21 2017 -0700 Perform 2-pass communication if the receiver cannot preallocate the receive buffer. FAB in FabArray needs to have a preAllocatable() function indicate this. Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H commit a6510000050bfa91cd13df1623c9a16de6fe3b4e Author: dtgraves Date: Wed Jun 7 11:45:14 2017 -0700 serialization for everything in sight (EBGraph, EBData, BaseIFFAB, BaseIVFAB) seems to work in the test. Src/GeometryShop/AMReX_BaseIFFABI.H Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/serialization.cpp commit 62c397dd30906658608fa390524b5398eca48b58 Merge: 39712bdc1 38e63261a Author: Michael Zingale Date: Wed Jun 7 14:25:38 2017 -0400 Merge branch 'gpu' of ssh://github.com/AMReX-Codes/AMReX into gpu commit 39712bdc14b4d601258b976677210fc586c13519 Author: Michael Zingale Date: Wed Jun 7 14:25:28 2017 -0400 add an INCLUDE_LOCATIONS for CUDA Tools/GNUMake/Make.defs commit 38e63261a128f45bd9daa3163269dc387c626743 Author: Max Katz Date: Wed Jun 7 14:20:52 2017 -0400 Use CArena for CUDA Src/Base/AMReX_CArena.cpp Tools/GNUMake/Make.defs commit aac116396840aaf10e120d0344715b0ebe995c2b Merge: 11120df25 20fd0b6a4 Author: Max Katz Date: Wed Jun 7 14:19:32 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit eafa51e263a491e4cc214c356f5a69c084c5e602 Merge: d3702f3a5 20fd0b6a4 Author: Xinsheng (Shawn) Qin Date: Wed Jun 7 11:08:31 2017 -0700 Merge remote-tracking branch 'origin/gpu' into gpu2 commit 20fd0b6a44f62ae089b3cce4fcee62b99d7cd36e Author: Michael Zingale Date: Wed Jun 7 13:09:54 2017 -0400 fix compilation on summit with PGI Tools/F_mk/GMakeMPI.mak Tools/F_mk/comps/Linux_pgi.mak commit a4cc7f577143487fde6acc588e135252573b1a20 Author: Andrew Myers Date: Wed Jun 7 13:07:30 2017 -0400 some work towards working with domain decomposition. Tests/Particles/CUDADeposition/MyParticleContainer.H Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_F.H Tests/Particles/CUDADeposition/inputs commit 1a96e722d5e7b01a39b684ad9358a33e55a91715 Merge: 084464c2b 8fa0e0a52 Author: Michael Zingale Date: Wed Jun 7 13:00:57 2017 -0400 Merge branch 'development' into gpu commit 084464c2b633b18a0796d686d16eb4f282957fe0 Merge: fafdb047d 2a8b74ae1 Author: Michael Zingale Date: Wed Jun 7 12:21:08 2017 -0400 Merge branch 'gpu' of ssh://github.com/AMReX-Codes/AMReX into gpu commit 8fa0e0a526a65d69c9cce18007f341a118b37b4e Author: Michael Zingale Date: Wed Jun 7 11:54:09 2017 -0400 some initial support for summit -- note, cpp doesn't work with -traditional there so we override Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak commit 11120df250ad3d635f688ca1b825bd83888ca5b3 Author: Max Katz Date: Wed Jun 7 10:57:23 2017 -0400 Use synchronize after phi update Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 Tutorials/Basic/HeatEquation_EX1_C/main.cpp commit 760914dc6b3d03086eb1822ba9b0b098b65f6eca Author: Max Katz Date: Wed Jun 7 10:23:47 2017 -0400 Get the thread block count working in 2D Src/Base/AMReX_CUDA.F90 commit 6ebb6662a8a84ec1a01492edb4ce95948a1ad537 Author: Max Katz Date: Wed Jun 7 10:23:24 2017 -0400 Get update_phi on the device Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 Tutorials/Basic/HeatEquation_EX1_C/main.cpp Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H commit 2a8b74ae1541138b587d2d9aa7ae02fa7a1b5f07 Merge: 2b3e6b141 7d5fad9a0 Author: Andrew Myers Date: Wed Jun 7 09:37:56 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 2b3e6b14182137103d90f763b4916f44577073f6 Author: Andrew Myers Date: Wed Jun 7 09:37:47 2017 -0400 Fixing a couple more bugs. Tests/Particles/CUDADeposition/GNUmakefile Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/deposit_3d.f90 commit 9a131599d0a69bf3803045c17db93297e3bf2ff6 Author: Max Katz Date: Wed Jun 7 09:35:19 2017 -0400 Use separate streams in HeatEquation Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 Tutorials/Basic/HeatEquation_EX1_C/advance_3d.F90 Tutorials/Basic/HeatEquation_EX1_C/main.cpp Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H commit fafdb047d795551fc99e8d8a54ab8f35ce914949 Merge: 7d5fad9a0 b79409891 Author: Michael Zingale Date: Wed Jun 7 09:19:39 2017 -0400 Merge branch 'development' into gpu commit 7d5fad9a0ad6b430cd38246f3f6de46427074aad Author: Max Katz Date: Wed Jun 7 09:06:27 2017 -0400 Fix errors in advance_2d Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 commit cd10dfece8ef7c3566a5ae3e04d4275087dcf28b Author: Andrew Myers Date: Tue Jun 6 23:43:35 2017 -0400 a few bug fixes. Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/deposit_3d.f90 commit e79eacbe0bb6448049340a9bc5ef106e94ecdc2b Author: Andrew Myers Date: Tue Jun 6 22:10:10 2017 -0400 Code that deposits a bunch of particles, with no domain decomposition for now. Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/main.cpp commit 0d23e5b0fcd478541cdfb711e468f0d2dc414f84 Merge: 5dd18d542 8f7abdbd4 Author: Andrew Myers Date: Tue Jun 6 20:51:53 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 5dd18d542a4a37b09b941c25e500590e23b995a9 Author: Andrew Myers Date: Tue Jun 6 20:51:03 2017 -0400 remove file added my mistake Tests/Particles/CUDADeposition/.bashrc commit f9892b37658a0c23eb04681a98446c9ec8d5358d Author: Marc Day Date: Tue Jun 6 17:48:56 2017 -0700 Make vof struct pod Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/Make.package Tests/GeometryShop/vofStructures/vofStructures.cpp commit d4930369d9b2b354b126dfef16962b89a125cfbb Author: Andrew Myers Date: Tue Jun 6 20:42:05 2017 -0400 successfully passing a chunk of particles to the GPU and processing them. Tests/Particles/CUDADeposition/.bashrc Tests/Particles/CUDADeposition/GNUmakefile Tests/Particles/CUDADeposition/MyParticleContainer.H Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_F.H Tests/Particles/CUDADeposition/main.cpp commit e330c26e9bc24139403d8c1c678432517bf9cf0d Author: dtgraves Date: Tue Jun 6 16:38:46 2017 -0700 The Good News: EBGraph serializaton is correct to the degree that I can test it. Bad news: Parallel EB still broken until I can get two-pass communication. Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Tests/GeometryShop/regression/serialization.cpp commit 8f7abdbd4f0ba6410f2f35dd53ac0900cf7950a4 Author: Max Katz Date: Tue Jun 6 16:42:36 2017 -0400 Disable tiling if CUDA is enabled Src/Base/AMReX_FabArrayBase.cpp Tools/GNUMake/Make.defs commit b79409891552c5ad1ebc33b888bad86afd342fba Author: Weiqun Zhang Date: Tue Jun 6 11:26:26 2017 -0700 add amrex:growLo and amrex::growHi for Box Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit ad64a934ed5fbd090392fd53f4169ddbef2c02bb Merge: 55bbff3cb 4436ec9a5 Author: Michael Zingale Date: Tue Jun 6 12:04:35 2017 -0400 Merge branch 'development' into gpu commit 55bbff3cb059ae1316e5a56590778a781360acce Author: Max Katz Date: Tue Jun 6 10:30:25 2017 -0400 Put compute_flux on the GPU Tutorials/Basic/HeatEquation_EX1_C/Make.package Tutorials/Basic/HeatEquation_EX1_C/advance_2d.F90 Tutorials/Basic/HeatEquation_EX1_C/advance_2d.f90 commit 311b62539c2faf366d5c10397d7d3cc15c3df68a Author: Andrew Myers Date: Tue Jun 6 10:01:09 2017 -0400 Makings of a CUDA Deposition example program. Tests/Particles/CUDADeposition/GNUmakefile Tests/Particles/CUDADeposition/Make.package Tests/Particles/CUDADeposition/MyParticleContainer.H Tests/Particles/CUDADeposition/MyParticleContainer.cpp Tests/Particles/CUDADeposition/deposit_3d.f90 Tests/Particles/CUDADeposition/deposit_F.H Tests/Particles/CUDADeposition/inputs Tests/Particles/CUDADeposition/main.cpp commit 4436ec9a588c49d36d3ab169c9fe59e097142cfd Author: Michael Zingale Date: Tue Jun 6 09:20:16 2017 -0400 fix spacing for global additions Tools/RegressionTesting/params.py Tools/RegressionTesting/regtest.py commit a911d2f7ca033ecd3c92c6a2d18665d47f5e3d9d Author: Michael Zingale Date: Mon Jun 5 23:14:00 2017 -0400 a .F90 version of the programs syntax Tools/F_mk/GMakerules.mak commit 7b21e79648592ab7b3b8357f83bc1871ba67277b Merge: 48e641a9e 5f91a9a2c Author: Michael Zingale Date: Mon Jun 5 21:27:37 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 5f91a9a2c67dfa85692a95628b8c43b9105db32b Author: Weiqun Zhang Date: Mon Jun 5 17:15:36 2017 -0700 User's Guide: more on MultiFab Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/Basics/indextypes.pdf Docs/BoxLibUsersGuide/GettingStarted/GettingStarted.tex commit 16a65182f5888154b4bb47c1c9750e6f3bf36bcd Author: dtgraves Date: Mon Jun 5 16:21:48 2017 -0700 fixed some bugs in serialization. There are more to find. Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_EBISBox.H Src/GeometryShop/AMReX_FabArrayIO.H Src/GeometryShop/AMReX_FabArrayIO.cpp Src/GeometryShop/AMReX_SPMD.H Tests/GeometryShop/README Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/serialization.cpp Tests/GeometryShop/regression/serialization.inputs commit 4089970c3d81bf0006ea96df65a0dd7f236310c1 Author: Weiqun Zhang Date: Mon Jun 5 15:28:20 2017 -0700 fix memory profiler Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_MultiFab.cpp commit d3702f3a525c13bcf4b63d1088d24ab622e99adf Merge: 85b23f186 46526280b Author: Weiqun Zhang Date: Mon Jun 5 13:42:37 2017 -0700 Merge branch 'development' into gpu2 commit 46526280bd6c1283bced2637e7d0d3a4a2092c90 Merge: 000163650 046dee6d5 Author: Weiqun Zhang Date: Mon Jun 5 12:11:20 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 000163650a9db76b3a24a04e32d6c38f4197cabb Author: Weiqun Zhang Date: Mon Jun 5 12:11:16 2017 -0700 User's Guide: FabArray Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/Basics/amrgrids.pdf commit 48e641a9e89e4d7bab45c620055e94b7a6b23b70 Merge: dd3e50b89 046dee6d5 Author: Michael Zingale Date: Mon Jun 5 14:47:20 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 046dee6d5490f3c867aba34ba26a4481d9aae942 Merge: ba7415b36 591c3f755 Author: atmyers Date: Mon Jun 5 13:40:25 2017 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ba7415b36c4e51dd478e048fda9449530d810c41 Author: atmyers Date: Mon Jun 5 13:40:10 2017 -0400 fix silly mistake in convert script. Tools/Py_util/amrex_particles_to_vtp/amrex_binary_particles_to_vtp.py commit 85b23f1865f58d438a12dcd972383c46250c4126 Author: Max Katz Date: Mon Jun 5 12:24:28 2017 -0400 Use CUDA 8.0 Tools/F_mk/comps/Linux_pgi.mak commit 455fb3b7337e51c4b18c57036ad7b9efef072703 Author: Weiqun Zhang Date: Mon Jun 5 08:50:05 2017 -0700 typechecker: print debug information Tools/typechecker/typechecker.py commit 591c3f755a5a511ba5b492b3645be198a5251510 Merge: 90bf64fe5 a617a4063 Author: WeiqunZhang Date: Mon Jun 5 08:43:54 2017 -0700 Merge pull request #25 from bcfriesen/update_cvode_docs Update CVODE docs commit 7ef6aafd3c422598fc193cba3a43666ec49617b0 Author: Max Katz Date: Mon Jun 5 10:31:28 2017 -0400 Use streams for MultiFab operations Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.cpp commit 2c9aa604959dffc51f3c31f48d271fddfc3e1ddb Author: Max Katz Date: Mon Jun 5 10:24:23 2017 -0400 Remove Castro-specific variable Src/Base/AMReX_CUDA.F90 commit dd3e50b896f7060f6a98d92d5d46b996ccdad5a6 Merge: 974d23304 90bf64fe5 Author: Michael Zingale Date: Mon Jun 5 10:20:04 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 90bf64fe592a77293bdf44eecda076eb0c055ee6 Merge: 7824fe5a5 27a3894cf Author: Brian Friesen Date: Sun Jun 4 22:37:46 2017 -0700 Merge branch 'cvode_fixes' into development commit 27a3894cfdfeedab6cbd9ed2e74c0686a13173c9 Author: Brian Friesen Date: Sun Jun 4 22:36:37 2017 -0700 CVODE, Tools/GNUmake: add -DUSE_CVODE preprocessor flag when USE_CVODE=TRUE Tools/GNUMake/packages/Make.cvode commit 7824fe5a56fd06a9ab295654163cc431dbb51d4c Author: atmyers Date: Mon Jun 5 01:20:47 2017 -0400 Adding a script to write from the particle binary format to vtp. Tools/Py_util/amrex_particles_to_vtp/README Tools/Py_util/amrex_particles_to_vtp/amrex_binary_particles_to_vtp.py Tools/Py_util/amrex_particles_to_vtp/amrex_particles_to_vtp.py commit a617a406360228a4dfae0b90e5cf0d7ca96b4bde Author: Brian Friesen Date: Sun Jun 4 20:55:04 2017 -0700 Docs: remove Readme.cvode The material in this Readme has been moved to the User Guide. Docs/Readme.cvode commit 512fbd3d9018f7cdf8844a62ee2c077657d50e5c Author: Brian Friesen Date: Sun Jun 4 20:54:13 2017 -0700 Docs: add chapter to user guide regarding CVODE with the new Fortran 2003 interface Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/CVODE/CVODE.tex Docs/AMReXUsersGuide/amrexsymbols.tex commit 8b0213ea698f847e6b3a04afce88562157233d82 Merge: 5e8d233ea c3903f5f1 Author: atmyers Date: Sun Jun 4 23:29:32 2017 -0400 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c3903f5f13d31a1b8ca98b9f5162d5302e9335b7 Merge: 5c5e5252c e507f5d7c Author: Brian Friesen Date: Sun Jun 4 19:44:53 2017 -0700 Merge branch 'use_f03_cvode' into development These commits add support for the new Fortran 2003 interface to CVODE. They also migrate the two CVODE tutorials ("EX1" and "EX2") to this new interface. commit e507f5d7cb4a69cc4c96e49715b35173e600657d Author: Brian Friesen Date: Sun Jun 4 19:41:41 2017 -0700 Tutorials/CVODE/EX2: switch to new Fortran 2003 interface to CVODE Tutorials/CVODE/EX2/Make.package Tutorials/CVODE/EX2/fcvdjac.f90 Tutorials/CVODE/EX2/fcvfun.f90 Tutorials/CVODE/EX2/integrate_ode_no_jac.f90 Tutorials/CVODE/EX2/integrate_ode_with_jac.f90 Tutorials/CVODE/EX2/ode_mod.f90 commit abd4aabe3a883e4c9e36514c13362f03a81e3bda Author: Brian Friesen Date: Sun Jun 4 17:05:07 2017 -0700 Tutorials/CVODE/EX1: switch to new Fortran 2003 interface to CVODE Tutorials/CVODE/EX1/Make.package Tutorials/CVODE/EX1/fcvfun.f90 Tutorials/CVODE/EX1/integrate_ode.f90 Tutorials/CVODE/EX1/ode_mod.f90 commit 254edda7064b4123048261647e68030b14b33da7 Author: Brian Friesen Date: Sun Jun 4 17:02:39 2017 -0700 CVODE: add Fortran 2003 interface to CVODE This interface uses iso_c_binding and enables one to call CVODE C functions directly from Fortran without using FCVODE. It also includes a few helper functions which ease programming by, e.g., converting C array pointers to Fortran array pointers. AMReX will compile these modules if the USE_CVODE variable is set to TRUE. This interface was contributed by the SUNDIALS team. Src/Extern/CVODE/Make.package Src/Extern/CVODE/cvode_interface.f90 Src/Extern/CVODE/fnvector_serial.f90 Src/Extern/CVODE/sundials_fdlsmat.f90 Tools/GNUMake/packages/Make.cvode commit 5e8d233ea91c81aa52fdaa38878902296ef66114 Author: atmyers Date: Sun Jun 4 17:16:06 2017 -0700 Some work on the Particle section of the Users Guide. Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Particle/Particle.tex commit 13eef24bdbf28533c37143bcd47f4304b15605e6 Author: Max Katz Date: Sun Jun 4 13:27:30 2017 -0400 Put the device synchronizes in a sane place Src/Base/AMReX_BaseFab_nd.F90 Src/Base/AMReX_MultiFab.cpp commit c8aa1df2b81d7b861d741716e986eca9184a5fe0 Author: Max Katz Date: Sun Jun 4 11:37:47 2017 -0400 Add CUDA to executable name Tools/GNUMake/Make.defs commit 17aaeec3e5ccfd9304e95ee818bf6506790e3d84 Author: Max Katz Date: Sun Jun 4 11:25:28 2017 -0400 Collapse the fab copy loop Src/Base/AMReX_BaseFab_nd.F90 commit 80b0394bdc8234371b01ec4636039620741b0530 Author: Max Katz Date: Sun Jun 4 04:28:34 2017 -0400 Port more FAB functions Src/Base/AMReX_BaseFab_nd.F90 commit bff5c35397ba018a7cee19d95cbac61202c70311 Author: Max Katz Date: Sun Jun 4 03:31:43 2017 -0400 Build in NVTX into TinyProfiler Src/Base/AMReX_Device.H Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp commit 60b6d30a475ddbbf2a871d08b0a25c2bc753dcbe Author: Max Katz Date: Sun Jun 4 03:05:23 2017 -0400 Add support for NVTX Src/Base/AMReX_Device.H Tools/GNUMake/Make.defs commit 2cfe5be2c2af4e8124b665611cc195abc188823d Author: Max Katz Date: Sun Jun 4 02:13:50 2017 -0400 Undo unintentionally committed comments Src/Base/AMReX_BaseFab.H commit fa2aa7700c997f8e291802aa1003e2e16d4222a5 Author: Max Katz Date: Sun Jun 4 02:11:58 2017 -0400 Start putting FAB functionality on device Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab_nd.F90 Src/Base/Make.package commit 30d842b9d9436ba15f7da7aba75afa1ee3ff1e4c Author: Max Katz Date: Sun Jun 4 02:11:35 2017 -0400 Set preferred location to device Src/Base/AMReX_BArena.cpp Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H commit 5c5e5252c1c9252eeca1684a6147cf865cdc3ccf Author: Weiqun Zhang Date: Sat Jun 3 16:30:54 2017 -0700 it makes more sense to have SetPosition function in ParIter instead of ParIterBase Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit bbc414a7802e3fadfdabc30dc7203846d06f073c Author: Weiqun Zhang Date: Sat Jun 3 14:30:02 2017 -0700 fix ParConstIter Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit e32a092e472030fd19038e7137e63a22c0dcb9ab Author: Weiqun Zhang Date: Sat Jun 3 13:18:50 2017 -0700 fix ParContIter's enable_if Src/Particle/AMReX_Particles.H commit 0b66bb3366ea0e1fd9e3f38ea03ccd6086914175 Author: Weiqun Zhang Date: Sat Jun 3 13:05:19 2017 -0700 add ParConstiter Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit 52790f41811b018c7af79589d25bdd061ee44b13 Author: Weiqun Zhang Date: Fri Jun 2 19:04:16 2017 -0700 option to turn off limiter Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FillPatchUtil_2d.F90 Src/AmrCore/AMReX_FillPatchUtil_3d.F90 Src/AmrCore/AMReX_FillPatchUtil_F.H commit d7a5e5477acefa52c3c83d4bea3f4daf47078c5a Author: Weiqun Zhang Date: Fri Jun 2 18:40:10 2017 -0700 fix a bug in the new interp function for warpx Src/AmrCore/AMReX_FillPatchUtil_2d.F90 commit f17e733edb3f3a9b5e3fe7dc1b360a39324f551f Author: Marc Day Date: Fri Jun 2 18:36:33 2017 -0700 Start some new data structure dev/test code Tests/GeometryShop/vofStructures/GNUmakefile Tests/GeometryShop/vofStructures/Make.package Tests/GeometryShop/vofStructures/sphere.inputs Tests/GeometryShop/vofStructures/vofStructures.cpp commit 2f6f99a239379176a8f1a71d98fe5c7b793c840b Author: Weiqun Zhang Date: Fri Jun 2 14:07:35 2017 -0700 added some 2D functions for interpolation of EM fields Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FillPatchUtil_2d.F90 Src/AmrCore/AMReX_FillPatchUtil_3d.F90 Src/AmrCore/AMReX_FillPatchUtil_F.H Src/Base/AMReX_fort_mod.F90 commit 0cfd8dcfec4f5cacba3ecbcc8291f91d08ddc696 Author: dtgraves Date: Thu Jun 1 16:25:49 2017 -0700 Burrowing further into serialization routines. The tea at this unbirthday party is terrible. Many more tests coming so I can work my way out of this stuff. Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntVectSet.cpp Src/GeometryShop/AMReX_IrregFAB.cpp commit 1d8cbc58b28ed280d2c4eeb37201fefeea856eea Author: dtgraves Date: Thu Jun 1 16:22:55 2017 -0700 added a test for more fabarray objects Tests/GeometryShop/regression/fabio.cpp commit 974d23304c226718609550ca27c230609a79af4f Merge: a644ebff3 836d3c763 Author: Michael Zingale Date: Thu Jun 1 11:44:53 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit ba61cf154edab172f83ea4aaf7a079204b27ea91 Author: Max Katz Date: Thu Jun 1 02:01:39 2017 -0400 Also add -DCUDA to FPPFLAGS Tools/F_mk/GMakedefs.mak commit 3534f7b1a64f71bc0ae321bcbbbe5cb5fbfceb13 Author: Max Katz Date: Thu Jun 1 01:49:07 2017 -0400 Add -DCUDA Tools/F_mk/GMakedefs.mak commit 836d3c7635ebadbb234c725af5848b536d487779 Author: Weiqun Zhang Date: Wed May 31 17:21:17 2017 -0700 User's Guide: BoxArray and DistributionMapping Docs/AMReXUsersGuide/Basics/Basics.tex Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_FabArrayBase.cpp commit 79060e97d2524b0904effd781f26c0a560bd21bc Author: dtgraves Date: Wed May 31 16:02:40 2017 -0700 This is an awfully deep rabbit hole. And what kind of rabbit carries a pocket watch? Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_FabArrayIO.H Tests/GeometryShop/regression/fabio.cpp Tests/GeometryShop/regression/fabio.inputs commit 8d4f2186ae04f9e070b5b161e4d040059233de09 Author: dtgraves Date: Wed May 31 16:01:47 2017 -0700 added a utility to create a directory but moving the old one, it destroys it. Will only work on Unix Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 3386b6c1bd1aed5dcc82259fdeb12b8fec21319e Author: Weiqun Zhang Date: Wed May 31 14:24:57 2017 -0700 User's Guide: BaseFab Docs/AMReXUsersGuide/Basics/Basics.tex commit dffbfcd3c36c740d2a930121734965c395189712 Author: hsitaram Date: Wed May 31 14:49:41 2017 -0600 python script added to convert ascii amrex particle files to vtp (#23) * python script added to convert ascii amrex particle files to vtp * deleted extra particle plotfiles Tools/Py_util/amrex_particles_to_vtp/README Tools/Py_util/amrex_particles_to_vtp/amrex_particles_to_vtp.py Tools/Py_util/amrex_particles_to_vtp/samplefiles/particles00000 Tools/Py_util/amrex_particles_to_vtp/samplefiles/particles00001 Tools/Py_util/amrex_particles_to_vtp/samplefiles/particles00002 Tools/Py_util/amrex_particles_to_vtp/write_pview_file.py commit 722361d3734f2ff739df53a47e6c1ea66d3e08ad Author: Ann Almgren Date: Wed May 31 12:24:23 2017 -0700 Add the functionality to pass the variable names into WritePlotFile as well as into CheckPoint. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 4f9ad4c8167c3f45716ff9e8e16c54d526b3b3fe Author: Weiqun Zhang Date: Wed May 31 11:18:07 2017 -0700 User's Guide: Geometry Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Tutorials/Basic/HeatEquation_EX1_C/main.cpp commit e0c4757ddaaa32a689aefb8819fb66bbe7b94dc4 Author: Max Katz Date: Wed May 31 01:22:48 2017 -0400 Add CUDA to PGI in F_mk Tools/F_mk/comps/Linux_pgi.mak commit 4fa685ba6d14755a9ccf643ac1e1a01115980957 Author: dtgraves Date: Tue May 30 16:40:53 2017 -0700 more progress on EB I/O. Serialization ain't fun. Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_FabArrayIO.H Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntVectSet.cpp commit 3034f56cfe2cf6085aa9705b0b4d745573f80fb5 Author: dtgraves Date: Tue May 30 16:39:55 2017 -0700 added a couple of funtions to Box and IntVect to make my life a bit easier Src/Base/AMReX_Box.H Src/Base/AMReX_IntVect.H commit a644ebff30de9d4716357858e71af2f057d02838 Merge: 701a70aae 475523e99 Author: Michael Zingale Date: Tue May 30 15:48:33 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit b0f8e4cbf3f4d84cf990f9e216633093ce40ed28 Author: dtgraves Date: Mon May 29 16:39:33 2017 -0700 More progress on I/O for EB. Marc will be glad to hear that I added a couple of classes. Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_BaseEBCellFactory.H Src/GeometryShop/AMReX_FabArrayIO.H Src/GeometryShop/AMReX_FabArrayIO.cpp Tests/GeometryShop/regression/fabio.cpp commit 475523e99548fc6825efe5f180bf61f8afff8c94 Author: Weiqun Zhang Date: Mon May 29 12:11:12 2017 -0700 removeOverlap: option not to simplify Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit 701a70aaef9f76ef81566e47567b9c47a5def12e Merge: a573f9cef 7e5e3cd37 Author: Michael Zingale Date: Mon May 29 12:07:16 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 7e5e3cd375bf0306a20d155db16a86e2fee0711b Author: Weiqun Zhang Date: Mon May 29 07:19:28 2017 -0700 move printGridSummary function from Amr to AmrCore Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp commit fad102bb1d5a52f95b62b9dd64223dd8a1a7d633 Author: dtgraves Date: Sun May 28 18:36:54 2017 -0700 more progress toward (less general) I/O for more general objects Src/GeometryShop/AMReX_FabArrayIO.H Src/GeometryShop/AMReX_FabArrayIO.cpp Src/GeometryShop/FabArrayIO.H Src/GeometryShop/Make.package Tests/GeometryShop/regression/fabio.cpp commit 581ae3fe73997d1d253886d724997058daa5190f Merge: e19b9c2ca db7ed71e6 Author: Max Katz Date: Sun May 28 12:04:06 2017 -0400 Merge branch 'development' into gpu commit a573f9ceff084905690c4acdf974b9d468fbcfad Merge: 97b9cc514 db7ed71e6 Author: Michael Zingale Date: Sun May 28 09:45:12 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit db7ed71e63f23a53675f39a09985dbff6bc32731 Author: Weiqun Zhang Date: Sat May 27 19:39:36 2017 -0700 fix a bug in removeOverlap Src/Base/AMReX_BoxArray.cpp commit 362faebd29163cb36fa1fb9a410679dff55b46cb Author: Max Katz Date: Sat May 27 18:02:36 2017 -0400 Provide null implementation for post_restart Src/Amr/AMReX_AmrLevel.H commit 81684f0b30e20578a6d03f47bd8e7e925f33011a Author: Max Katz Date: Sat May 27 17:45:36 2017 -0400 Make post_restart not be pure virtual Src/Amr/AMReX_AmrLevel.H commit 36723214152108a7cdf26225631a917b7f9d265c Author: dtgraves Date: Fri May 26 16:32:09 2017 -0700 started getting some EB elliptic stuff moved over Src/EBAMRElliptic/AMReX_AMRMultiGrid.H Src/EBAMRElliptic/AMReX_BaseBCFuncEval.H Src/EBAMRElliptic/AMReX_BiCGStabSolver.H Src/EBAMRElliptic/AMReX_ConductivityBaseDomainBC.H Src/EBAMRElliptic/AMReX_ConductivityBaseEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityDomainBC.cpp Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.H Src/EBAMRElliptic/AMReX_DirichletConductivityEBBC.cpp Src/EBAMRElliptic/AMReX_EBConductivityOp.H Src/EBAMRElliptic/AMReX_EBConductivityOp.cpp Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.H Src/EBAMRElliptic/AMReX_EBConductivityOpFactory.cpp Src/EBAMRElliptic/AMReX_EBEllipticFort.F90 Src/EBAMRElliptic/AMReX_EBEllipticFort_F.H Src/EBAMRElliptic/AMReX_LinearSolver.H Src/EBAMRElliptic/AMReX_MultiGrid.H Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.H Src/EBAMRElliptic/AMReX_NeumannConductivityDomainBC.cpp Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.H Src/EBAMRElliptic/AMReX_NeumannConductivityEBBC.cpp Src/EBAMRElliptic/Make.package commit 7be09f615e7fcc734bdef62217c310716afb99f5 Author: dtgraves Date: Fri May 26 16:31:35 2017 -0700 started the bare bones of more general I/O with lots of help from Vince Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/FabArrayIO.H Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/fabio.cpp Tests/GeometryShop/regression/fabio.inputs commit bfe1d816108b8680a7d458282c1406f7fa916223 Merge: 620a4244f a240a8f88 Author: Andrew Myers Date: Fri May 26 15:40:02 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 620a4244fa0ce748245967e6c4b3ebe9569d837c Author: Andrew Myers Date: Fri May 26 15:39:52 2017 -0700 1D and 2D version of the particle deposition / interpolation operations. Src/Particle/AMReX_Particle_mod_1d.F90 Src/Particle/AMReX_Particle_mod_2d.F90 commit a240a8f88b45d5b72853308d1ac79df641559071 Author: Weiqun Zhang Date: Fri May 26 14:20:17 2017 -0700 make FillBoundary work for overlapping BoxArray Src/Base/AMReX_FabArrayBase.cpp commit 9292483e60b7fe0cc883bb195cac262568228097 Author: Ann Almgren Date: Fri May 26 13:53:52 2017 -0700 Don't initialize integers with 0.d0 Tools/Postprocessing/F_Src/fextract.f90 commit 176068774e3fe4c61e904fedf9c9d0e1b42e04af Author: Michele Rosso Date: Fri May 26 13:37:17 2017 -0700 Fix bug in fextract Tools/Postprocessing/F_Src/fextract.f90 commit 97b9cc51491fd29968ac5637fb18ca913a61a3b1 Merge: ec0246516 3aaa13073 Author: Michael Zingale Date: Fri May 26 16:04:27 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 3aaa130738808a963f8093dd38ea40c04b10d853 Merge: ada49be37 b82b25a1b Author: Andrew Myers Date: Fri May 26 10:57:32 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit ada49be3731957b6f509556e138831b26a72b842 Author: Andrew Myers Date: Fri May 26 10:57:19 2017 -0700 rename ghosts to neighbors to have a different name from Nyx-style ghost particles. Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.H Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp Tutorials/Particles/ShortRangeParticles/main.cpp Tutorials/Particles/ShortRangeParticles/short_range_2d.f90 Tutorials/Particles/ShortRangeParticles/short_range_3d.f90 Tutorials/Particles/ShortRangeParticles/short_range_F.H commit b82b25a1b4d62624a163c8957f44367ea71118dc Merge: 795588589 b1327927b Author: WeiqunZhang Date: Fri May 26 10:55:34 2017 -0700 Merge pull request #21 from bcfriesen/cvode_tutorial_updates CVODE tutorial updates commit b1327927b808fa16da67be1c1586300fb6deb38b Author: Brian Friesen Date: Fri May 26 10:50:38 2017 -0700 Docs: added Readme.cvode with instructions for building CVODE/FCVODE Docs/Readme.cvode commit 75453b9ad04fb2a8cb3e90a5b30960d94fc9a9e8 Author: Brian Friesen Date: Fri May 26 10:48:49 2017 -0700 Tutorials/CVODE/EX1: replace custom writePlotFile() with amrex::WriteSingleLevelPlotfile() Tutorials/CVODE/EX1/Make.package Tutorials/CVODE/EX1/main.cpp Tutorials/CVODE/EX1/writePlotFile.H Tutorials/CVODE/EX1/writePlotFile.cpp commit 34cc1937cfee05a93e5b3333dcd44a0a0d97db56 Author: Brian Friesen Date: Fri May 26 10:43:02 2017 -0700 Tutorials/CVODE: added "EX2" tutorial This tutorial solves a set of 3 coupled ODEs in each cell. It is taken from the "fcvRoberts_dns.f" file in the CVODE examples. Tutorials/CVODE/EX2/GNUmakefile Tutorials/CVODE/EX2/Make.package Tutorials/CVODE/EX2/fcvdjac.f90 Tutorials/CVODE/EX2/fcvfun.f90 Tutorials/CVODE/EX2/inputs Tutorials/CVODE/EX2/integrate_ode_no_jac.f90 Tutorials/CVODE/EX2/integrate_ode_with_jac.f90 Tutorials/CVODE/EX2/main.cpp Tutorials/CVODE/EX2/myfunc_F.H commit 79558858980538b6a4b77d8c023f578e0e38a07e Merge: a4dce9f3d b31f0565e Author: Andrew Myers Date: Fri May 26 10:23:13 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit a4dce9f3d2f2bfd871a62683160a1674c50be463 Author: Andrew Myers Date: Fri May 26 10:23:00 2017 -0700 Handle periodic boundaries in the short range particle tutorial. Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.H Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp commit b31f0565ee00ee6d8784f44b4630e2a533c66fdb Merge: 9743b5436 e9d777be2 Author: WeiqunZhang Date: Fri May 26 09:29:40 2017 -0700 Merge pull request #20 from akreienbuehl/clrdDiffuSolve Fixed `Make.unknown` commit e9d777be2660215b74880f3fd3f456843efebb26 Author: Andreas Kreienbuehl Date: Fri May 26 09:23:19 2017 -0700 Made fix more readable Tools/GNUMake/sites/Make.unknown commit 41198c1d45ea381d7e417d967781d600e4c3a060 Author: Andreas Kreienbuehl Date: Fri May 26 08:49:25 2017 -0700 Fixed Makefile Tools/GNUMake/sites/Make.unknown commit 9743b543665fbbc290fb09a1ef72ca49abb1ccfb Merge: 892f71447 f6800c909 Author: WeiqunZhang Date: Fri May 26 08:45:17 2017 -0700 Merge pull request #19 from AMReX-Codes/ibm_make add the ability to specify a prefix to preprocessor variables commit f6800c909b5ef371a2c3fbd0fe48acfe0d54ad8c Author: Michael Zingale Date: Thu May 25 21:43:46 2017 -0400 use the flush() intrinsic of Fortran 2003 instead of call flush() to get link issues resolved. Also add more to the library lines Src/Base/AMReX_BLBoxLib_F.f Src/F_BaseLib/layout.f90 Src/F_BaseLib/parallel.f90 Tools/GNUMake/comps/ibm.mak commit 892f71447c4d1a4f9b7a37337675c37fe98d1687 Author: Weiqun Zhang Date: Thu May 25 16:54:58 2017 -0700 fix ParallelDescriptor for non MPI Src/Base/AMReX_ParallelDescriptor.cpp commit 484ba6a58d1a3cc85021b5b36a005afb84da040c Author: Michael Zingale Date: Thu May 25 18:56:39 2017 -0400 defer the initialization of prefixes to the CPP_FLAGS to allow for user-code defines to be caught Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 439387a5902c0c94baee7fb0e2cee053cee22f46 Merge: 035239327 f25114935 Author: WeiqunZhang Date: Thu May 25 15:55:24 2017 -0700 Merge pull request #18 from akreienbuehl/clrdDiffuSolve clrdDiffuSolve commit f25114935bba024450b9df9a528c84ef8ef54456 Author: Andreas Kreienbuehl Date: Thu May 25 15:38:10 2017 -0700 Fixed issue with `std::vector::resize' and the MPICH installation prefix can now contain `mpich' in upper case as well Src/Base/AMReX_ParallelDescriptor.cpp Tools/GNUMake/sites/Make.unknown commit ec0246516e380721611477153324024c6d49da1e Merge: 59415a424 035239327 Author: Michael Zingale Date: Thu May 25 18:33:30 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 035239327b9aebb9779b9f7dd19f58869f928134 Author: Weiqun Zhang Date: Thu May 25 13:10:30 2017 -0700 User's Guide: Box Docs/AMReXUsersGuide/Basics/Basics.tex commit 0cea5b6edd35c6e19bd1e3d59e8927fef78c9d3f Author: Brian Friesen Date: Thu May 25 12:30:38 2017 -0700 Tutorials: move CVODE_EX1 to CVODE/EX1 Tutorials/CVODE/EX1/GNUmakefile Tutorials/CVODE/EX1/Make.package Tutorials/CVODE/EX1/fcvfun.f90 Tutorials/CVODE/EX1/inputs Tutorials/CVODE/EX1/integrate_ode.f90 Tutorials/CVODE/EX1/main.cpp Tutorials/CVODE/EX1/myfunc_F.H Tutorials/CVODE/EX1/writePlotFile.H Tutorials/CVODE/EX1/writePlotFile.cpp commit 1a4738197b52c288651781fe7180b96cf99070d4 Author: Michael Zingale Date: Thu May 25 15:06:02 2017 -0400 this gets IBM to the link stage (if you hack the endianness stuff) Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/comps/ibm.mak commit f475d91d55d336753f3cb3a5379db3f3ce2bd2cf Author: Michael Zingale Date: Thu May 25 14:00:06 2017 -0400 use -gnu99 standard for C Tools/GNUMake/comps/ibm.mak commit 6ca1dee0ecbc365e429dec1d70ad24946f7e6818 Merge: 1cbb60833 268ba6bba Author: WeiqunZhang Date: Thu May 25 10:44:25 2017 -0700 Merge pull request #17 from akreienbuehl/clrdDiffuSolve clrdDiffuSolve commit 4c4101e6a81c5c88ea89df29d24bb6af2efd766b Author: Brian Friesen Date: Thu May 25 10:42:22 2017 -0700 Tutorials/CVODE_EX1: add comment clarifying what the tutorial does Tutorials/CVODE_EX1/main.cpp commit 268ba6bba72cd33bba6733db2473031a9aab204d Author: Andreas Kreienbuehl Date: Thu May 25 10:07:31 2017 -0700 Improved initialization and color-free case Src/Base/AMReX_ParallelDescriptor.cpp commit d41a89ec0b15cb9555986395d81a5bc705782917 Author: Andreas Kreienbuehl Date: Wed May 24 21:05:51 2017 -0700 Added new var. `m_first_procs_clr' to header as well Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit b63e5772511347c21eff593f47eaa6ae4c9596e3 Author: Andreas Kreienbuehl Date: Wed May 24 16:37:47 2017 -0700 Testing `nProcs%nClrs != 0' Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit 59415a4242a98158ff8aa9b2d6ae796a1926110d Merge: d6bf4e2f8 1cbb60833 Author: Michael Zingale Date: Wed May 24 19:17:14 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 1cbb60833253068d5a5a8e29d96cf1f9dd4ab9fb Author: Weiqun Zhang Date: Wed May 24 15:18:15 2017 -0700 fix bug in amrex_interp_div_free_bfield Src/AmrCore/AMReX_FillPatchUtil_3d.F90 commit 3bff67c540ffe030ffe9cd4d6f9ae18917312734 Author: Weiqun Zhang Date: Wed May 24 10:51:35 2017 -0700 add optional arguments Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 3add2c7286a61bfcdc0db8d0a3c365cc3c693c57 Author: dtgraves Date: Wed May 24 10:01:35 2017 -0700 added clarifying comment and made sure added EBGraph::fillIntMask does not reach outside domain Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp commit 080057f704d3caf9e9bf49a397393fa8570f38eb Merge: 22cd88a70 f88225f8e Author: WeiqunZhang Date: Wed May 24 09:58:27 2017 -0700 Merge pull request #16 from bcfriesen/yt_at_nersc Docs: add documentation for using yt commit 848b1f5ed6f919a552fb34e3dfa5f894c3e5f8d1 Author: dtgraves Date: Wed May 24 09:52:38 2017 -0700 added EBGraph::fillIntMask Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp commit f88225f8e529caf9fdd8a7213a247cb0cab719bb Author: Brian Friesen Date: Wed May 24 09:47:40 2017 -0700 Docs: added section about visualization with yt This includes instructions for running yt on both a local workstation and at NERSC. The NERSC part is somewhat of a moving target because the dust is still settling on the implementation of Jupyter and IPython; the docs should be updated if those things change in the future. Docs/AMReXUsersGuide/Visualization/Visualization.tex Docs/AMReXUsersGuide/Visualization/yt_Nyx_density_slice.png Docs/AMReXUsersGuide/Visualization/yt_Nyx_density_vol_rend.png commit 22cd88a70b1cf4106900b98cc2a0ad5e9e218aa4 Merge: e5004fb46 4aa7b6d1b Author: WeiqunZhang Date: Wed May 24 09:39:14 2017 -0700 Merge pull request #14 from zingale/development define __LITTLE_ENDIAN__ commit e5004fb46af1277cf72b8499d7ef27b18243403b Merge: 23f6ada32 1e3db6b64 Author: WeiqunZhang Date: Wed May 24 09:38:55 2017 -0700 Merge pull request #12 from bcfriesen/add_cvode Add CVODE commit 23f6ada32c82605ebcb49004bc5e4a6121bdbc8d Author: Weiqun Zhang Date: Wed May 24 09:22:13 2017 -0700 fix a bug in the new amrex_interp_efield Src/AmrCore/AMReX_FillPatchUtil_3d.F90 commit f3ddc92a86fcaed4e8ae5e720316627ef02de74a Author: Weiqun Zhang Date: Wed May 24 08:41:53 2017 -0700 User's Guide: more place holders Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/AmrCore/AmrCore.tex Docs/AMReXUsersGuide/AmrLevel/AmrLevel.tex Docs/AMReXUsersGuide/Debugging/Debugging.tex Docs/AMReXUsersGuide/GNUmakefile Docs/AMReXUsersGuide/Particle/Particle.tex Docs/AMReXUsersGuide/Profiling/Profiling.tex commit 106581a8666905e672cdf87f09083313afcbfd4f Author: Andreas Kreienbuehl Date: Wed May 24 07:01:51 2017 -0700 Toward `nProcs%nClrs != 0' Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp commit d64dc72ad904e853cc93c761cfef5a8443cd8e43 Author: Weiqun Zhang Date: Tue May 23 16:56:55 2017 -0700 more options to CFinfo Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit bbdea9540e763e17cacc0d2be1ff20e59d22879f Author: Weiqun Zhang Date: Tue May 23 12:17:49 2017 -0700 Print: use the precision of the ostream argument Src/Base/AMReX_Print.H commit 6a81fabcf4e5d59a9f16b81cca6c9cd423f3b6d7 Author: Weiqun Zhang Date: Tue May 23 11:26:49 2017 -0700 User's Guide: IntVect and IndexTyp Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex commit 9bef23f4c376b81c0405bb53a0ffa34b44676124 Author: Andy Nonaka Date: Tue May 23 11:23:55 2017 -0700 revert the precision modifiers until we figure out how to set the global precision to be persistent Src/Base/AMReX_Print.H commit ce6beb9e5b31cbe0e80fcdc0b5cdd635f9a8ad91 Author: Andy Nonaka Date: Tue May 23 10:49:09 2017 -0700 create amrex::Print().Precision functionality that replicates std::cout.precision() Src/Base/AMReX_Print.H commit 9d41fa43c641a4a827672150a7d97f63985ca263 Author: Andrew Myers Date: Mon May 22 17:47:57 2017 -0700 Simply call std::map's clear here. Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp commit 0ffbb8960e45bae2c6c9db3b9b4f39d0d9ab15b5 Author: Weiqun Zhang Date: Mon May 22 13:45:25 2017 -0700 make IntVect::operator[] (int) const return a const& instead of value to avoid potentially passing addresss of temporary return value Src/Base/AMReX_IntVect.H commit 9eeaf4c09e14d9faaee0ef224e0c83998624daa9 Author: Weiqun Zhang Date: Mon May 22 13:26:31 2017 -0700 User's Guide: ParmParse Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex Src/Base/AMReX_REAL.H commit 9f02a686ef294af6b9156867cb06171c61cc469f Author: Ann Almgren Date: Mon May 22 12:49:45 2017 -0700 Fix clearGhosts routine. Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp commit d6bf4e2f84e0a506d519767a4d991f8e400dd59f Merge: 370429a92 509994c52 Author: Michael Zingale Date: Mon May 22 13:58:36 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 509994c524a7242a365cf70a303710c4081851e3 Author: Weiqun Zhang Date: Mon May 22 10:56:36 2017 -0700 turn off ghost cells in amrex::WriteMultiLevelPlotfile Src/Base/AMReX_PlotFileUtil.cpp commit e2bb8b36bf5eb51668175ac4fad8c014ce3861a8 Author: Weiqun Zhang Date: Mon May 22 09:56:07 2017 -0700 add AMREX_SPACEDIM Src/Base/AMReX_SPACE.H Tools/GNUMake/Make.defs commit bebeb4039e2e7939bdb60db65ac2731ec1f476ac Author: Weiqun Zhang Date: Mon May 22 09:46:18 2017 -0700 Remove some old scripts. If you miss them, revert my commit. Tools/C_scripts/boxlib-build.sh Tools/C_scripts/compressor Tools/C_scripts/gen_release_tarball commit 8728a8c0de42926d950e1579e4bafbc64b6fb3ea Merge: 26f5fb5c8 8b34476ad Author: Andrew Myers Date: Sat May 20 20:16:28 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 26f5fb5c82c7930b28414fd22da3ead58b8bc21a Author: Andrew Myers Date: Sat May 20 20:16:09 2017 -0700 remove unused variable. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp commit 219b004d8c4d64111ec64e683117153f969e823c Author: Andrew Myers Date: Sat May 20 20:15:48 2017 -0700 properly fillpatch the ghost cells for phi. Tutorials/Particles/ElectrostaticPIC/main.cpp commit 4aa7b6d1b517138ddb250b8ec4d7af38f0b3ae40 Merge: 479de96f6 370429a92 Author: Michael Zingale Date: Sat May 20 20:13:08 2017 -0400 Merge branch 'development' of ssh://github.com/zingale/amrex into development commit 479de96f62d1b9fc95aa7e0133c43657b765a147 Merge: 6f6a6f1e9 8b34476ad Author: Michael Zingale Date: Sat May 20 20:11:29 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 8b34476ad217cb0a0e9430d6a47599fba9144334 Author: Weiqun Zhang Date: Sat May 20 16:24:32 2017 -0700 implement 3d amrex_interp_efield Src/AmrCore/AMReX_FillPatchUtil_3d.F90 commit 50cfd595b4d6bde55e0f2d21421c1ca50f0bd490 Author: Michael Zingale Date: Sat May 20 18:40:58 2017 -0400 a hack for summit to find libatomic. This assumes that you've pointed PGI/17.4 to the gcc/5.4.0 install using the makelocalrc in PGI Tools/GNUMake/comps/pgi.mak commit 6f6a6f1e9216a16e27428c1830550a006495870a Merge: 7083cbe90 3bd9a57b4 Author: Michael Zingale Date: Sat May 20 18:21:37 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 370429a924e3f087a867360734a43b402b0e8f7b Merge: 3bd9a57b4 fc934705e Author: Michael Zingale Date: Sat May 20 18:19:43 2017 -0400 Merge branch 'development' of ssh://github.com/zingale/amrex into development commit 3bd9a57b4ef37d3cb4ad65fa13e29c0e36d79065 Author: Max Katz Date: Sat May 20 17:44:51 2017 -0400 Move internal subroutine out to avoid a PGI 17.4 bug Src/F_BaseLib/multifab_c.f90 commit f809a5b5a2e2a4bf53591a0b596a8ec508f5bdd8 Author: Max Katz Date: Sat May 20 17:44:29 2017 -0400 Restrict a use statement to avoid a PGI 17.4 bug Src/F_BaseLib/knapsack.f90 commit f86178209d1a282cf7f9d24008d603eae5a52f5d Author: Weiqun Zhang Date: Sat May 20 11:23:26 2017 -0700 add amrex_intep_efield stub Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FillPatchUtil_1d.F90 Src/AmrCore/AMReX_FillPatchUtil_2d.F90 Src/AmrCore/AMReX_FillPatchUtil_3d.F90 Src/AmrCore/AMReX_FillPatchUtil_F.H commit 7083cbe902e54053fe989ae4a7a256bd02e54840 Merge: fc934705e 37cb73e3d Author: Michael Zingale Date: Sat May 20 13:34:11 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 37cb73e3d933e1775785c9dc26d1f3a01ff23e8c Author: Michael Zingale Date: Fri May 19 22:11:42 2017 -0400 fix compilation error Src/AmrCore/AMReX_FillPatchUtil_1d.F90 commit 08f2ed15025506d0dec2669c7f608339ab28cb15 Author: Andrew Myers Date: Fri May 19 17:12:19 2017 -0700 do the proper coarse/fine interpolation before computing the electric field. Tutorials/Particles/ElectrostaticPIC/main.cpp commit 53bdab5ed13a37ecbad24a5c1afc3a479b8114e1 Merge: c0a3af0b4 aab48ecbc Author: Andrew Myers Date: Fri May 19 16:58:39 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit c0a3af0b49fcd20f002cce6e359b707feee4c379 Author: Andrew Myers Date: Fri May 19 16:58:24 2017 -0700 change the default inputs parameters Tutorials/Particles/ElectrostaticPIC/inputs commit 6d6b409df96a55a016f7e0bca8bdca304ebc32b7 Author: Andrew Myers Date: Fri May 19 16:58:00 2017 -0700 Some tweaks to the nodal poisson solve. Tutorials/Particles/ElectrostaticPIC/main.cpp commit 3713e4e9bf8dfba73d0e210ddab714714f903027 Author: Andrew Myers Date: Fri May 19 16:57:46 2017 -0700 Only initialize the particles on one process. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp commit aab48ecbc55c83ad34514cf7d455b0b7251cfad6 Author: Weiqun Zhang Date: Fri May 19 10:58:14 2017 -0700 fix a bug in SumBoundary Src/AmrCore/AMReX_FillPatchUtil_3d.F90 Src/Base/AMReX_MultiFab.cpp commit 5067c559d91ecd00c4799b60aacdfa5eda955697 Merge: 29da411d7 20a62ca4b Author: Andrew Myers Date: Fri May 19 10:14:26 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 29da411d7be67fec885c2e6af29cee262f63032a Author: Andrew Myers Date: Fri May 19 10:14:13 2017 -0700 Adding some commentary. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90 Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H commit 20a62ca4b0e6b4b6906ff8343698fea47a16b0be Merge: 446dfc771 3c49d1e0f Author: Weiqun Zhang Date: Fri May 19 09:41:20 2017 -0700 Merge branch 'weiqun/bfield' into development commit e19b9c2ca93b37fbeec8afa9b9492cad56f1db22 Author: Max Katz Date: Fri May 19 03:55:20 2017 -0400 Place device updates in non-default streams Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 3e5ac8cda9de9aace5ffc7705d3362465e0b5bee Author: Max Katz Date: Fri May 19 03:23:59 2017 -0400 Enable CUDA in the PGI compiler Tools/GNUMake/comps/pgi.mak commit ef425fda06f428f2856c29285e004a5c660ba7af Author: Max Katz Date: Fri May 19 03:03:20 2017 -0400 Move CUDA calls to Fortran Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CUDA.F90 Src/Base/AMReX_Device.H commit 446dfc771b87ca5efe99172f720dc03b181a10a9 Merge: 779a96db9 a0c2eef6a Author: Andrew Myers Date: Thu May 18 17:10:59 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 779a96db9aac1a76a2123bc9e3042b7d253c041b Author: Andrew Myers Date: Thu May 18 17:10:37 2017 -0700 Some work on the ES PIC Tutorial Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90 Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H Tutorials/Particles/ElectrostaticPIC/inputs Tutorials/Particles/ElectrostaticPIC/main.cpp commit a0c2eef6a8b255b07f4c8891b9e88836b841d34e Author: Weiqun Zhang Date: Thu May 18 16:03:16 2017 -0700 make it typechecker friendly Src/EBAMRTools/AMReX_EBFortND_F.H Src/EBAMRTools/Make.package commit 168cb376bd731a0340921a0cc5c7d826b0181d4e Author: dtgraves Date: Thu May 18 15:21:15 2017 -0700 fixed some 3d bugs and I think finally have EBFineInterp working Src/EBAMRTools/AMReX_EBFortND.F90 Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_PolyGeom.H Src/GeometryShop/AMReX_PolyGeom.cpp Tests/EBAMRTools/regression/ebFineInterpTest.cpp Tests/EBAMRTools/regression/ebfineinterp.inputs commit 93d06ecf1977556e5acc79fce39afc27e8a4b7bb Author: dtgraves Date: Thu May 18 15:19:24 2017 -0700 took out unwanted function Src/Base/AMReX_BaseFab.H commit 50d9829e71bfbbc0610faf8c73bc6c87fb19a3a5 Author: Andrew Myers Date: Thu May 18 11:27:10 2017 -0700 Adding a nodal average down function. Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_F.H commit 32e08186daeec11a34280c5b3f0dbf219d2b4055 Merge: b698761a4 e5e83170a Author: Michele Rosso Date: Thu May 18 11:23:10 2017 -0700 Merge branch 'mr-cmake' into development commit b698761a4176ee5b1a360334a9b3727d709eeba3 Author: Max Katz Date: Thu May 18 12:47:30 2017 -0400 Revert "Create a unique MFIter index" This reverts commit bead2d682cc5af2cf04cea81b377dac449b29705. Src/Base/AMReX_MFIter.H commit 1e3db6b6432bd083c9ee00758c50e08dfd383d4e Merge: 020bb8422 17c9bb048 Author: Brian Friesen Date: Thu May 18 09:42:20 2017 -0700 Merge branch 'CVODE_EX1_cleanup' into add_cvode This cleans up a few misc problems with the CVODE_EX1 tutorial, and adds OpenMP tiling support (although currently FCVODE, the Fortran interface to CVODE, is not thread-safe). commit 17c9bb048c694ac5f36c80a5c241de96989f2c8a Author: Brian Friesen Date: Thu May 18 09:40:13 2017 -0700 Tutorials/CVODE_EX1: remove incorrect comment Tutorials/CVODE_EX1/main.cpp commit 8e31fffe60ea517c355e7408e3d95a44f0c9357c Author: Brian Friesen Date: Thu May 18 09:39:52 2017 -0700 Tutorials/CVODE_EX1: remove unused variable "dx[]" Tutorials/CVODE_EX1/main.cpp commit 3bc45e47e31b8f437ffe08f24b174468df1ad8a1 Author: Brian Friesen Date: Thu May 18 09:39:21 2017 -0700 Tutorials/CVODE_EX1: remove doubly declared variable "is_periodic[]" Tutorials/CVODE_EX1/main.cpp commit 69ccd774e7deededecb90267b6d88d8143491c12 Author: Brian Friesen Date: Thu May 18 09:38:33 2017 -0700 Tutorials/CVODE_EX1: add OpenMP tiling option Tutorials/CVODE_EX1/inputs Tutorials/CVODE_EX1/main.cpp commit 3523ea07c040ff565dbc11366c135fe99049ed0a Merge: d63d706e2 bead2d682 Author: dtgraves Date: Thu May 18 09:30:53 2017 -0700 Merge branch 'development' into dtg_branch commit d63d706e21d1f225137e7648299efc931fb0bf8a Merge: 4a9fddce9 cd744ec08 Author: dtgraves Date: Thu May 18 09:30:40 2017 -0700 Merge branch 'dtg_branch' of https://github.com/AMReX-Codes/amrex into dtg_branch commit 4a9fddce93efd77a373037cc626ea42ba3fbc67a Author: dtgraves Date: Thu May 18 09:28:44 2017 -0700 some progress toward higher order EBFineInterp Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/EBAMRTools/AMReX_EBFortND_F.H Tests/EBAMRTools/regression/ebFineInterpTest.cpp commit bead2d682cc5af2cf04cea81b377dac449b29705 Author: Max Katz Date: Sun May 14 20:38:34 2017 -0400 Create a unique MFIter index Src/Base/AMReX_MFIter.H commit fc934705e520578d73d4b7344aa6b1f4c4caf0a4 Author: Michael Zingale Date: Thu May 18 09:20:18 2017 -0400 fix little endian locations Src/Base/AMReX_FPC.cpp commit 26f481c9b93ded922a3ef2f5df95ca1101aefda3 Merge: 567ce1006 cd744ec08 Author: WeiqunZhang Date: Wed May 17 20:29:04 2017 -0700 Merge pull request #13 from AMReX-Codes/dtg_branch EB bug fixes for Marc commit cd744ec085cecb805b605193aeec007661c87163 Merge: c06f777d3 567ce1006 Author: dtgraves Date: Wed May 17 19:04:19 2017 -0700 Merge branch 'development' into dtg_branch commit 020bb8422b59415465749c112776c6e01a2d27cf Author: Brian Friesen Date: Wed May 17 18:57:55 2017 -0700 CVODE: move Make.cvode into Tools/GNUMake/packages Tools/GNUMake/Make.defs Tools/GNUMake/packages/Make.cvode commit 57c0db8e0255d545fd6349e11e0707e91b3c8b2f Author: Michael Zingale Date: Wed May 17 21:53:02 2017 -0400 define __LITTLE_ENDIAN__ Src/Base/AMReX_FPC.cpp commit 567ce1006f776924cab97bc647764ae67b8653f3 Author: Michael Zingale Date: Wed May 17 21:47:18 2017 -0400 revert the CPP_PREFIX stuff required for IBM, since it breaks GNU. THis means that IBM will not work until we find a better way to define preprocessor variables Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 55d27ff5ff92533434f5bd4813c552eb5b6037bc Author: Michael Zingale Date: Wed May 17 21:17:56 2017 -0400 some library fixes for GNU/summit Tools/GNUMake/sites/Make.olcf commit 39c97c7a5e7bd6ec4dd72b016919792c50f56a14 Merge: ea2683f50 dd6f1b6ee Author: Michael Zingale Date: Wed May 17 20:39:46 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit ea2683f5001f1f8596fabf4b52a4b0498fa9c9e8 Author: Michael Zingale Date: Wed May 17 20:39:35 2017 -0400 fix the dependency checking Tools/GNUMake/Make.rules commit dd6f1b6eecf83223ce4615aace8da1cce4c0478f Merge: 93caf5ecc 5c9a2bbe5 Author: Andrew Myers Date: Wed May 17 17:30:41 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 93caf5eccbff08822c159dd71a86f132a9641157 Author: Andrew Myers Date: Wed May 17 17:26:08 2017 -0700 Adding a tutorial for electrostatic pic calculations. Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.H Tutorials/Particles/ElectrostaticPIC/ElectrostaticParticleContainer.cpp Tutorials/Particles/ElectrostaticPIC/GNUmakefile Tutorials/Particles/ElectrostaticPIC/Make.package Tutorials/Particles/ElectrostaticPIC/PhysConst.H Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_3d.f90 Tutorials/Particles/ElectrostaticPIC/electrostatic_pic_F.H Tutorials/Particles/ElectrostaticPIC/inputs Tutorials/Particles/ElectrostaticPIC/main.cpp commit c99c36867d2e3f6c0f50b064fe65f89bc9d748dc Author: Andrew Myers Date: Wed May 17 17:25:41 2017 -0700 Move the short range particles tutorial to the new tutorials directory. Tutorials/Particles/ShortRangeParticles/GNUmakefile Tutorials/Particles/ShortRangeParticles/Make.package Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.H Tutorials/Particles/ShortRangeParticles/ShortRangeParticleContainer.cpp Tutorials/Particles/ShortRangeParticles/inputs Tutorials/Particles/ShortRangeParticles/main.cpp Tutorials/Particles/ShortRangeParticles/short_range_2d.f90 Tutorials/Particles/ShortRangeParticles/short_range_3d.f90 Tutorials/Particles/ShortRangeParticles/short_range_F.H commit 5c9a2bbe537842f3c7a48a3326f3c8cf0ec1b059 Author: Michael Zingale Date: Wed May 17 20:22:28 2017 -0400 more progress with IBM -- only the F90 needs the -WF,-D... stuff. Also, the .F has uses cpp directly, so no need for the prefix there Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/comps/ibm.mak commit 0f780d332f4cbd3bf395a763c89f2ca075e6c665 Author: Andrew Myers Date: Wed May 17 17:15:13 2017 -0700 use scientific notation in particle compare. Tools/Postprocessing/C_Src/particle_compare.cpp commit c2d98bea4bcffe863d3af1685c3328059141d67b Author: Michael Zingale Date: Wed May 17 20:01:46 2017 -0400 add a CPP_PREFIX option that should do nothing for all compilers except IBM XL, which wants the preprocessor directives in the form -WF,-DFOO=BAR Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/comps/ibm.mak commit ea1d24dd52e639c560fb065a7a7a4294f7383adc Author: Michael Zingale Date: Wed May 17 19:33:51 2017 -0400 initial support for the IBM xl-series compilers Tools/GNUMake/Make.defs Tools/GNUMake/Make.machines Tools/GNUMake/comps/ibm.mak commit 05161a5203d74ec4eeb648866da0d8261b197a7e Author: Michael Zingale Date: Wed May 17 19:16:48 2017 -0400 add summit -- hopefully this doesn't break titan :) Tools/GNUMake/sites/Make.olcf commit 3c49d1e0f9a0959968a288b5835fc86d17f2d399 Merge: ecb8f8739 4ad908bfc Author: Weiqun Zhang Date: Wed May 17 16:08:58 2017 -0700 Merge branch 'development' into weiqun/bfield commit c06f777d338c04f29787ac30d89ff737f9235430 Author: dtgraves Date: Wed May 17 15:32:46 2017 -0700 fixed a bug in graph coarsening that Marc found. Src/EBAMRTools/AMReX_EBFortND.F90 Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Tests/GeometryShop/sphereEBISBox/GNUmakefile commit ecb8f8739fe2497292c5258eea3076ac2ce7f5d7 Author: Weiqun Zhang Date: Wed May 17 15:03:35 2017 -0700 remove debug line Src/AmrCore/AMReX_FillPatchUtil.cpp commit ab2ec6c41383fa5b55754a38d4796b1577af41b7 Author: Weiqun Zhang Date: Wed May 17 14:58:35 2017 -0700 first pass of 3d amrex_interp_div_free_bfield Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FillPatchUtil_1d.F90 Src/AmrCore/AMReX_FillPatchUtil_2d.F90 Src/AmrCore/AMReX_FillPatchUtil_3d.F90 Src/AmrCore/AMReX_FillPatchUtil_F.H commit 2997083743b8cfe908d58176def5ca73dabf1a74 Author: Brian Friesen Date: Wed May 17 12:47:24 2017 -0700 CVODE: add link hooks, Readme, and tutorial for using CVODE Tools/GNUMake/Make.cvode Tools/GNUMake/Make.defs Tutorials/CVODE_EX1/GNUmakefile Tutorials/CVODE_EX1/Make.package Tutorials/CVODE_EX1/fcvfun.f90 Tutorials/CVODE_EX1/inputs Tutorials/CVODE_EX1/integrate_ode.f90 Tutorials/CVODE_EX1/main.cpp Tutorials/CVODE_EX1/myfunc_F.H Tutorials/CVODE_EX1/writePlotFile.H Tutorials/CVODE_EX1/writePlotFile.cpp commit de9bc7e01c8a0b810183bb6f0a539b8b0aee5529 Author: dtgraves Date: Wed May 17 11:54:15 2017 -0700 found a subtle bug in EBFineInterp. Convergence rates are now correct. Src/EBAMRTools/AMReX_EBCFInterp.H Src/EBAMRTools/AMReX_EBFineInterp.H Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Tests/EBAMRTools/regression/ebFineInterpTest.cpp Tests/EBAMRTools/regression/ebfineinterp.inputs commit 4ad908bfc180c885f81a16eb41f60be07e93f7a5 Author: Weiqun Zhang Date: Wed May 17 11:01:20 2017 -0700 remove BL_ALWAYS_FIX_DENORMALS Src/Extern/amrdata/AMReX_AmrData.cpp Tools/CMake/CCSEOptions.cmake commit 6299ed90b1af3773ef1dbb5a7a92c1f50d2d11a4 Author: Max Katz Date: Wed May 17 13:39:23 2017 -0400 Add AMReX_CUDA.F90 Src/Base/AMReX_CUDA.F90 commit 96cd8669832dd04711eca22c67749f9c2630acf4 Merge: 70a73a148 d755c3686 Author: Max Katz Date: Wed May 17 13:39:07 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit 7619dcbaef5a3f2724bf62986160a899daa5e568 Author: Weiqun Zhang Date: Wed May 17 10:30:47 2017 -0700 removed a number of old if names: BL_AIX, BL_CRAY, BL_CRAYX1, BL_HOPPER, BL_SIM_HOPPER, BL_SIM_HOPPER_MAKE_TCFAB, and BL_T3E. Src/AmrCore/AMReX_FLUXREG_3D.F Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_Utility.cpp Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F Src/Extern/amrdata/AMReX_AmrData.cpp commit d755c368653cb111f4019eaacb5ced7537713dbf Author: Michael Zingale Date: Wed May 17 13:13:38 2017 -0400 wrap a CUDA call Src/Base/AMReX_Device.H commit 9013d1c2a9ce1a8d4f4d6797a23101eeb0cbfc1d Merge: d6e6fd6cd 0405dc2a7 Author: Michael Zingale Date: Wed May 17 13:02:13 2017 -0400 Merge branch 'development' into gpu commit 0405dc2a729779e1225ce0ae1cee99613d8f44ec Author: Weiqun Zhang Date: Wed May 17 09:51:24 2017 -0700 some BL_ --> AMREX_ Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex OldTutorials/AMR_Adv_C/Source/Adv.cpp OldTutorials/AMR_Adv_C/Source/Adv_F.H OldTutorials/AMR_Adv_C/Source/Adv_advance.cpp OldTutorials/AMR_Adv_C/Source/Adv_dt.cpp OldTutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp OldTutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H OldTutorials/HeatEquation_EX2_C/main.cpp OldTutorials/MeshRefinement/main.cpp OldTutorials/MultiColor_C/main.cpp OldTutorials/MultiGrid_C/main.cpp OldTutorials/ShortRangeParticles/main.cpp OldTutorials/Tiling_C/main.cpp OldTutorials/TwoGrid_PIC_C/split_boxes.cpp OldTutorials/libamrex_C/main.cpp Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_StationData.cpp Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_ErrorList.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_INTERP_F.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_IndexType.H Src/Base/AMReX_IndexType.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_Periodicity.H Src/Base/AMReX_Periodicity.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp Src/Base/AMReX_SPACE.H Src/Base/AMReX_iMultiFab.cpp Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_InterpBndryData.cpp Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_EBFastFR.cpp Src/EBAMRTools/AMReX_MeshRefine.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp Src/F_Interfaces/Base/AMReX_geometry_fi.cpp Src/F_Interfaces/Base/AMReX_plotfile_fi.cpp Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISBox.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_Moments.cpp Src/GeometryShop/AMReX_PolyGeom.cpp Src/GeometryShop/AMReX_VolIndex.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_Particles_F.H Src/Particle/AMReX_TracerParticles.cpp Tests/C_BaseLib/tVisMF.cpp Tests/EBAMRTools/regression/regFluxRegTest.cpp Tests/GeometryShop/sphere/sphereTest.cpp Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tests/Particles/main.cpp Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp Tools/C_util/ViewMF/main.cpp Tools/C_util/ViewMF/viewMFdiffHardWire.cpp Tools/C_util/WritePlotFile.cpp Tools/C_util/dbgTools/intersectGrids.cpp Tutorials/Basic/HeatEquation_EX1_C/main.cpp commit 8350f10dc16061749821b171dde19630880b2a67 Author: Weiqun Zhang Date: Wed May 17 09:36:02 2017 -0700 D_EXPR --> BL_D_EXPR Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_IndexType.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp Src/Base/AMReX_SPACE.H commit 212263f9de16125caf0c519f1505bdb59d792a6c Author: Weiqun Zhang Date: Wed May 17 09:32:06 2017 -0700 D_TERM --> BL_D_TERM OldTutorials/TwoGrid_PIC_C/split_boxes.cpp Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_StationData.cpp Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_IndexType.H Src/Base/AMReX_IndexType.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_Periodicity.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp Src/Base/AMReX_SPACE.H Src/Boundary/AMReX_InterpBndryData.cpp Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_EBFastFR.cpp Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISBox.cpp Src/GeometryShop/AMReX_Moments.cpp Src/GeometryShop/AMReX_PolyGeom.cpp Src/GeometryShop/AMReX_VolIndex.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_TracerParticles.cpp Tests/EBAMRTools/regression/regFluxRegTest.cpp Tests/GeometryShop/sphere/sphereTest.cpp Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/Particles/main.cpp Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp commit b72e6f01440bb6f2618864953a6563eb253eff6a Author: Weiqun Zhang Date: Wed May 17 09:28:18 2017 -0700 D_PICK --> BL_D_PICK Src/Base/AMReX_SPACE.H Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp commit 74561a0b27c4b48cf446d49cc891c9d151a3c9f4 Author: Weiqun Zhang Date: Wed May 17 09:24:05 2017 -0700 D_DECL --> BL_D_DECL Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex OldTutorials/AMR_Adv_C/Source/Adv.cpp OldTutorials/AMR_Adv_C/Source/Adv_F.H OldTutorials/AMR_Adv_C/Source/Adv_advance.cpp OldTutorials/AMR_Adv_C/Source/Adv_dt.cpp OldTutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp OldTutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H OldTutorials/HeatEquation_EX2_C/main.cpp OldTutorials/MeshRefinement/main.cpp OldTutorials/MultiColor_C/main.cpp OldTutorials/MultiGrid_C/main.cpp OldTutorials/ShortRangeParticles/main.cpp OldTutorials/Tiling_C/main.cpp OldTutorials/libamrex_C/main.cpp Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/AMReX_ErrorList.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_INTERP_F.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_IndexType.H Src/Base/AMReX_IndexType.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_Periodicity.H Src/Base/AMReX_Periodicity.cpp Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp Src/Base/AMReX_SPACE.H Src/Base/AMReX_iMultiFab.cpp Src/Boundary/AMReX_BndryRegister.cpp Src/EBAMRTools/AMReX_MeshRefine.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp Src/F_Interfaces/Base/AMReX_geometry_fi.cpp Src/F_Interfaces/Base/AMReX_plotfile_fi.cpp Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_Moments.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_Particles_F.H Src/Particle/AMReX_TracerParticles.cpp Tests/C_BaseLib/tVisMF.cpp Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp Tools/C_util/ViewMF/main.cpp Tools/C_util/ViewMF/viewMFdiffHardWire.cpp Tools/C_util/WritePlotFile.cpp Tools/C_util/dbgTools/intersectGrids.cpp Tutorials/Basic/HeatEquation_EX1_C/main.cpp commit 17564b97a7183f1ba86fe847471804a7a99122ee Author: Weiqun Zhang Date: Wed May 17 09:36:49 2017 -0700 User's Guide add more place holders Docs/AMReXUsersGuide/Basics/Basics.tex commit d6e6fd6cddd06931cc2aa923747b6125c53bb660 Merge: 569c9953e e4e539c91 Author: Michael Zingale Date: Wed May 17 08:35:26 2017 -0400 Merge branch 'development' into gpu commit e4e539c91886d32ec2a6a5d085fc460e2f7b698e Author: Max Katz Date: Wed May 17 01:31:21 2017 -0400 Initialize post_step_regrid to 0 in constructor Src/Amr/AMReX_AmrLevel.cpp commit e5e83170a3a1164536b3a0ac0b47da3257f79396 Author: Michele Rosso Date: Tue May 16 17:16:56 2017 -0700 Add section on CMake in AMReX documentation Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex commit 28d2c2a2affa3f9f11a54f62bb1769987ebd2a59 Author: Weiqun Zhang Date: Tue May 16 16:53:09 2017 -0700 wip Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FillPatchUtil_1d.F90 Src/AmrCore/AMReX_FillPatchUtil_2d.F90 Src/AmrCore/AMReX_FillPatchUtil_3d.F90 Src/AmrCore/AMReX_FillPatchUtil_F.H Src/AmrCore/CMakeLists.txt Src/AmrCore/Make.package commit 9303d664f7570ab26e734eb7a22d6434fa182c17 Author: vince Date: Tue May 16 16:43:37 2017 -0700 fix warnings for serial. delete perstreams after read. Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp commit b001398f29c1312a2fe320c9fa9fda767c18e380 Author: vince Date: Tue May 16 16:23:21 2017 -0700 profdata filetype. Src/Extern/amrdata/AMReX_AmrvisConstants.H commit 9829b44679bbef39608739b3c615c9f61d224bb8 Author: Weiqun Zhang Date: Tue May 16 13:25:14 2017 -0700 add coarse fine boundary cache Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 94c6b26a5c90e48113e3dde38838955e3eb9f329 Merge: 8d9d99dca 93670a920 Author: Andrew Myers Date: Tue May 16 12:55:29 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 8d9d99dca1aeb44b5eaa54499f99497f7544c4ee Author: Andrew Myers Date: Tue May 16 12:55:10 2017 -0700 update the test suite to use the compiled particle compare utility. Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py commit 93670a9204e5922b4fbdabdc254ab6dc0340bea7 Author: Andrew Myers Date: Tue May 16 12:54:47 2017 -0700 a few more tweaks to the particle compare utility. Tools/Postprocessing/C_Src/particle_compare.cpp commit 2397581b0af1ce24045ea58878784a9aac50b522 Author: Weiqun Zhang Date: Tue May 16 11:29:13 2017 -0700 User's Guide Basics Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_ccse-mpi.H commit 0c19ea7f9ef0ab1edb37188a00315c938999fafe Merge: adab5945c e511a7240 Author: Ann Almgren Date: Tue May 16 11:13:08 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit adab5945cfd026f0e5b05c9b4b54aa26d88a2cd1 Author: Ann Almgren Date: Tue May 16 11:12:42 2017 -0700 We need to update the dummy_mf after the grids have changed even if we haven't added levels. Src/Particle/AMReX_ParticleContainerI.H commit c10e89e6d15de6be6ae0257a3b29780ece5b5670 Author: dtgraves Date: Tue May 16 09:13:15 2017 -0700 Fixed bug in graph coarsening. EBFineInterp still needs some work. Src/Base/AMReX_BaseFab.H Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/GeometryShop/AMReX_EBDebugDump.H Src/GeometryShop/AMReX_EBDebugOut.H Src/GeometryShop/AMReX_EBDebugOut.cpp Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Tests/EBAMRTools/regression/ebFineInterpTest.cpp Tests/EBAMRTools/regression/ebfineinterp.inputs commit e511a7240bc98083dda00e97ceb7b455c5c6d6e6 Author: Weiqun Zhang Date: Mon May 15 16:52:58 2017 -0700 User's Guide: a little on basics Docs/AMReXUsersGuide/Basics/Basics.tex commit 2cf1659529f1185fd472bde617fdceb71de68fc5 Author: Weiqun Zhang Date: Mon May 15 14:48:57 2017 -0700 User's Guide: make Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Tutorials/Basic/HeatEquation_EX1_C/GNUmakefile Tutorials/Basic/HelloWorld_C/GNUmakefile commit 1c1a27551a8f57feba29e0eb24d4ccbb75a991b3 Author: Weiqun Zhang Date: Mon May 15 10:56:19 2017 -0700 Force DIM to be set. Minor edits in User's Guide Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/Basics/Basics.tex Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Docs/AMReXUsersGuide/GNUmakefile Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Tools/GNUMake/Make.defs Tutorials/Basic/HeatEquation_EX1_C/GNUmakefile Tutorials/Basic/HelloWorld_C/GNUmakefile commit 0c8b7245f533c4a72ac3ed599eed11f53e12cb1c Author: Weiqun Zhang Date: Mon May 15 10:24:47 2017 -0700 fix path to OldTutorials OldTutorials/AMR_Adv_C/Exec/Make.Adv OldTutorials/AMR_Adv_CF/Exec/Make.Adv OldTutorials/AMR_Adv_CF_octree/Exec/Make.Adv OldTutorials/AMR_Adv_C_v2/Exec/Make.Adv OldTutorials/Sidecar_EX1/GNUmakefile commit 70a73a14851ed695f13b93cd8e9e59002636d9dc Author: Max Katz Date: Sun May 14 20:38:34 2017 -0400 Create a unique MFIter index Src/Base/AMReX_MFIter.H commit 569c9953e1be5ec32402059ddf911b979b6a4e83 Author: Max Katz Date: Sun May 14 20:14:22 2017 -0400 Create a CUDA fortran module Src/Base/AMReX.cpp Src/Base/AMReX_Device.H Src/Base/Make.package commit 94ff5e0578cb08582a679aee10b644b08bd4487b Author: Max Katz Date: Sun May 14 19:06:28 2017 -0400 Move CUDA device ID into device class Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_FabArray.H commit 6e0364adf842cb1f88e5361bcca2cefd22af439b Author: Max Katz Date: Sun May 14 18:51:32 2017 -0400 Make a variable private Src/Base/AMReX_Device.H commit cb420f35be1ab8ed1ae1ca3a18762cb7053a93a4 Author: Max Katz Date: Sun May 14 18:23:31 2017 -0400 Synchronize device at end of kernel region Src/Base/AMReX_Device.H commit 6fb0466b4921d51fab38e6b3b94fe386a34ed826 Author: Max Katz Date: Sun May 14 17:14:16 2017 -0400 Add return type to null registerFab Src/Base/AMReX_MFIter.H commit 6d647d5fbc69f9f29ca1db10e033b6efbc239457 Author: Max Katz Date: Sun May 14 16:34:30 2017 -0400 Use the result of registerFab Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.H commit f0dd0ac04fab9daac02f957db31c432abfce0396 Author: Max Katz Date: Sun May 14 16:16:39 2017 -0400 If in device launch region, return device pointer Src/Base/AMReX_BaseFab.H commit 16bcf069e285920b777307b3dfa9e78b1299c31a Author: Max Katz Date: Sun May 14 15:57:09 2017 -0400 Only do device transfer if a FAB is not registered Src/Base/AMReX_MFIter.H commit 991288ff084baaeb757078a9a75465ba192b7c2d Author: Max Katz Date: Sun May 14 14:18:42 2017 -0400 Move device code to a separate header Src/Base/AMReX_Device.H Src/Base/AMReX_Device.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/Make.package commit 93a9ade35add195b06e2b6c9a19dc02c313ea4a8 Author: Max Katz Date: Sun May 14 04:43:39 2017 -0400 Fix registerFab Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 1a137ac07b86ece499b8aaabe5580412759e9b4f Author: Max Katz Date: Sun May 14 03:02:33 2017 -0400 Add a device copy of data to BaseFab, with hooks up to StateData Using the MFInfo struct, a MultiFab can optionally allocate a device copy of its data. A hook has been added to StateData so that this can be done there as well. Right now the device implementation is for NVIDIA GPUs with CUDA, but in principle other devices that require offloading could be used. Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_BArena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabFactory.H commit 55c0fedcd01d9eb3a11eceacf2fc6e17bba06e4f Author: Max Katz Date: Sat May 13 23:22:43 2017 -0400 Merge CUDArena into BArena Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_CUDArena.H Src/Base/AMReX_CUDArena.cpp Src/Base/Make.package commit 0196f9d881c45b4bbbfca1debfbfa5862700ecd0 Author: Max Katz Date: Sat May 13 23:07:50 2017 -0400 USE_CUDA_UM switches between managed and normal allocations Src/Base/AMReX_BaseFab.H Src/Base/AMReX_CUDArena.cpp Tools/GNUMake/Make.defs commit cbd1756056dca9afdf7009d5df3b4db143d435e6 Merge: d6a6374e0 d47978d78 Author: Max Katz Date: Sat May 13 20:49:59 2017 -0400 Merge branch 'gpu' of github.com:AMReX-Codes/amrex into gpu commit d6a6374e084145646e539498d1d738ca87bff945 Author: Max Katz Date: Sat May 13 20:49:42 2017 -0400 Create toDevice and toHost in BaseFab Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.cpp commit 6e142865c240ae2ad8ddff56c594107e71202d81 Author: Max Katz Date: Sat May 13 20:14:48 2017 -0400 Store FAB pointers instead of FAB member pointers Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit d47978d78d8782a1159731d31d6c3f8f1f84e64c Merge: dcd4f57a1 4c8c5503b Author: Michael Zingale Date: Sat May 13 16:34:23 2017 -0400 Merge branch 'gpu' of ssh://github.com/AMReX-Codes/amrex into gpu commit dcd4f57a15f3fec4f1e481dbf53b280ac783c02e Author: Michael Zingale Date: Sat May 13 16:34:06 2017 -0400 add cudafor to the ignores Tools/F_scripts/dep.py commit c9673be8283257c72bf7fd77ceec20a35c1ec299 Author: Weiqun Zhang Date: Fri May 12 21:06:46 2017 -0700 Revert "add optional argument to FillPatchUtil indicating ghost cells data are valid" This reverts commit 272839b3317f2b239cc377e86cb15873a505a18f. Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp commit 27f17477104309cbef1d3dde720d5580d49949b0 Author: Weiqun Zhang Date: Fri May 12 21:05:59 2017 -0700 clean up comments Src/AmrCore/AMReX_Interpolater.H commit 2b1b8a761f5c4858fb5a4d5a6904adb86bce2e55 Merge: 6ae5029c7 d90736896 Author: Weiqun Zhang Date: Fri May 12 21:05:22 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 6ae5029c73b7a701e35721a7742ac5ce78cbeadc Author: Weiqun Zhang Date: Fri May 12 21:04:55 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Docs/AMReXUsersGuide/Visualization/Amrvis_2d.eps Docs/AMReXUsersGuide/Visualization/Amrvis_3d.eps Docs/AMReXUsersGuide/Visualization/VisIt_2D.eps Docs/AMReXUsersGuide/Visualization/VisIt_3D.eps Docs/AMReXUsersGuide/Visualization/Visualization.tex Tools/Postprocessing/C_Src/GNUmakefile Tools/Postprocessing/C_Src/particle_compare.cpp commit d90736896e88faa88bb329caf8d687ba228ead2f Author: Andrew Myers Date: Fri May 12 17:50:04 2017 -0700 Better error handling in the particle compare program. Tools/Postprocessing/C_Src/GNUmakefile Tools/Postprocessing/C_Src/particle_compare.cpp commit 6212d2ebd8fd323e82610a8d0166a587c4062065 Author: dtgraves Date: Fri May 12 17:02:13 2017 -0700 made some progress on more general interpolation but I have exposed a bug in EBIS coarsening. Not fixed yet. Src/EBAMRTools/AMReX_EBFineInterp.H Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/EBAMRTools/AMReX_EBFortND_F.H Src/GeometryShop/AMReX_EBLoHiCenter.H Src/GeometryShop/AMReX_EBLoHiCenter.cpp Tests/EBAMRTools/regression/ebFineInterpTest.cpp commit f1b2e35b38f5cf0c55e740c67ea1c36b3a58e274 Author: Andy Nonaka Date: Fri May 12 15:53:35 2017 -0700 more visualization stuff Docs/AMReXUsersGuide/Visualization/Visualization.tex commit 5af0926e973fe154d6ed0a27a5bd385484c6b268 Author: Andy Nonaka Date: Fri May 12 15:20:38 2017 -0700 added instructions for amrvis and visit Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Docs/AMReXUsersGuide/Visualization/Amrvis_2d.eps Docs/AMReXUsersGuide/Visualization/Amrvis_3d.eps Docs/AMReXUsersGuide/Visualization/VisIt_2D.eps Docs/AMReXUsersGuide/Visualization/VisIt_3D.eps Docs/AMReXUsersGuide/Visualization/Visualization.tex commit 272839b3317f2b239cc377e86cb15873a505a18f Author: Weiqun Zhang Date: Fri May 12 14:50:10 2017 -0700 add optional argument to FillPatchUtil indicating ghost cells data are valid Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp commit 8dba736bf5eda9517867fa20af67047bda5cdf0e Author: Weiqun Zhang Date: Fri May 12 14:00:58 2017 -0700 make default BCRec contain bogus bc instead of uninitialized values Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp commit 1c495b954c2897ae28bfc6ae0fd7a03ba6793117 Author: Andy Nonaka Date: Fri May 12 13:53:29 2017 -0700 start of a Vis section Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/GNUmakefile Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Docs/AMReXUsersGuide/Visualization/Visualization.tex commit ba76267f6b3b0c2e62cc11b369c7443b5d5270b7 Merge: 270614f6d dadf45dcf Author: WeiqunZhang Date: Fri May 12 12:12:42 2017 -0700 Merge pull request #9 from kweide/development support for Flash as a site, machine "asterix" commit 270614f6d8f4331b0e850a07b3d5ac63357de548 Author: Weiqun Zhang Date: Fri May 12 11:12:21 2017 -0700 a bit more on make Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex commit 43809ecfcea6fbf522a050b670ea89bb1eb5b628 Author: Weiqun Zhang Date: Fri May 12 11:06:05 2017 -0700 add BL_TO_FORTRAN_ANYD, update tutorial Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BLFort.H Tutorials/Basic/HeatEquation_EX1_C/advance_2d.f90 Tutorials/Basic/HeatEquation_EX1_C/advance_3d.f90 Tutorials/Basic/HeatEquation_EX1_C/init_phi_2d.f90 Tutorials/Basic/HeatEquation_EX1_C/init_phi_3d.f90 Tutorials/Basic/HeatEquation_EX1_C/main.cpp Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H commit 2a25725e6606aad6e20709475aebd52d2efe9c36 Author: Weiqun Zhang Date: Fri May 12 09:59:17 2017 -0700 update AMREX_HOME Tutorials/Basic/HeatEquation_EX1_C/GNUmakefile Tutorials/Basic/HelloWorld_C/GNUmakefile commit 983927d1b0021a7348eea307ef79cddb2fd368fc Author: Weiqun Zhang Date: Fri May 12 09:53:17 2017 -0700 move HelloWorld_C and HeatEquation_EX1_C Tutorials/Basic/HeatEquation_EX1_C/GNUmakefile Tutorials/Basic/HeatEquation_EX1_C/Make.package Tutorials/Basic/HeatEquation_EX1_C/advance_2d.f90 Tutorials/Basic/HeatEquation_EX1_C/advance_3d.f90 Tutorials/Basic/HeatEquation_EX1_C/init_phi_2d.f90 Tutorials/Basic/HeatEquation_EX1_C/init_phi_3d.f90 Tutorials/Basic/HeatEquation_EX1_C/inputs_2d Tutorials/Basic/HeatEquation_EX1_C/inputs_3d Tutorials/Basic/HeatEquation_EX1_C/main.cpp Tutorials/Basic/HeatEquation_EX1_C/myfunc_F.H Tutorials/Basic/HelloWorld_C/GNUmakefile Tutorials/Basic/HelloWorld_C/Make.package Tutorials/Basic/HelloWorld_C/main.cpp commit cd35b0a90ba09dc32775e6813d15a9a4314bfbec Author: Weiqun Zhang Date: Fri May 12 09:50:58 2017 -0700 rename Tutorials to OldTutorials OldTutorials/.gitignore OldTutorials/AMR_Adv_C/Exec/Make.Adv OldTutorials/AMR_Adv_C/Exec/SingleVortex/GNUmakefile OldTutorials/AMR_Adv_C/Exec/SingleVortex/Make.package OldTutorials/AMR_Adv_C/Exec/SingleVortex/Prob.f90 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OldTutorials/WaveEquation_F/advance.f90 OldTutorials/WaveEquation_F/init_data.f90 OldTutorials/WaveEquation_F/inputs_2d OldTutorials/WaveEquation_F/inputs_3d OldTutorials/WaveEquation_F/main.f90 OldTutorials/WaveEquation_F/write_plotfile.f90 OldTutorials/libamrex_C/GNUmakefile OldTutorials/libamrex_C/MyAmr.H OldTutorials/libamrex_C/MyAmr.cpp OldTutorials/libamrex_C/main.cpp OldTutorials/libamrex_C/myf.f90 commit dadf45dcf9574534eb0bce4aeb22dacddf00b792 Author: Klaus Weide Date: Fri May 12 09:55:52 2017 -0500 support for Flash as a site, machine "asterix" Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.flash commit 38e9fdcd71aa98cd6a5b1f6012e13b30e5e1b86c Author: Max Katz Date: Fri May 12 02:22:09 2017 -0400 Remove unnecessary device synchronize Src/Base/AMReX_CUDArena.cpp commit 4c8c5503b6554d0537f602d7a405b27c45a6c818 Author: Max Katz Date: Fri May 12 01:50:48 2017 -0400 Add capability to do UM prefetches to/from device By setting the new parameter do_device_transfers in MFIter, one can enable the ability to prefetch any FArrayBox accessed by that MFIter to the device. Then, when the MFIter index is incremented or the object is destroyed, all of the prefetches are reversed, bringing the data back to the host. For now, we default to moving everything to GPU 0. In the future, we should generalize this so that we can operate on multiple devices. Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 6cd0cfcebc21e121472ca7434c71ed94f8b7e166 Merge: febc9fc58 684003e00 Author: Michael Zingale Date: Thu May 11 20:52:27 2017 -0400 Merge branch 'development' into gpu commit 779fb7b443091f8f513ee688a1cebfced06d8d00 Author: Ann Almgren Date: Thu May 11 17:29:20 2017 -0700 Remove print statement that shouldn't have been committed. Src/Particle/AMReX_ParticleContainerI.H commit 737846edc0301b41be12a8360359238f8b426045 Author: Weiqun Zhang Date: Thu May 11 16:13:08 2017 -0700 add average_down_edges to MultiFabUtil Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_F.H Src/Base/Make.package commit 20b5d5b18f885ed6d1fd1806168e820cad73619f Merge: 9d0547fdd 0e0641583 Author: Andrew Myers Date: Thu May 11 16:00:13 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 9d0547fdd6a938c761b8b7766c92febb451ae016 Author: Andrew Myers Date: Thu May 11 15:59:47 2017 -0700 A tool for comparing particle data in plt files for Regression testing. Tools/Postprocessing/C_Src/GNUmakefile Tools/Postprocessing/C_Src/Make.package Tools/Postprocessing/C_Src/particle_compare.cpp commit c57c687ce4a0252cd513899aeda9d5215f3ad3cb Author: dtgraves Date: Thu May 11 15:50:05 2017 -0700 prolongation operator passes its first test Src/EBAMRTools/AMReX_EBFineInterp.cpp Tests/EBAMRTools/README Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/ebFineInterpTest.cpp Tests/EBAMRTools/regression/ebfineinterp.inputs commit 45cbdf6d772945d6aa0ba9d44c1548ba0e70f657 Author: dtgraves Date: Thu May 11 15:09:54 2017 -0700 EBCoarseAverage now does the right thing with the new fortran Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_EBFortND.F90 commit d3fef0ff1f847804f882b944f207e7719afd2143 Author: dtgraves Date: Thu May 11 15:08:48 2017 -0700 fixed the new macros to actually work Src/Base/AMReX_ArrayLim.H commit e83c074fc7806f887ed1f87ab276d0d73d539793 Author: dtgraves Date: Thu May 11 14:36:19 2017 -0700 I added a macro to ArrayLim and a function to BaseFab to make calling Fortran slightly less painful. Also I added some fortran source to EBAMRTools since the relevant MultiFab utilities did communication. Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BaseFab.H Src/EBAMRTools/AMReX_EBCFInterp.H Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_EBFineInterp.H Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/EBAMRTools/AMReX_EBFortND.F90 Src/EBAMRTools/AMReX_EBFortND_F.H Src/EBAMRTools/Make.package commit 0e064158353aaaa01bd06142229f78aa6602bf87 Merge: 760893e67 d1b6f7b2c Author: Ann Almgren Date: Thu May 11 14:17:16 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 760893e67146a5d16bcc4581df31213fd65b958a Author: Ann Almgren Date: Thu May 11 14:16:46 2017 -0700 Must resize the dummy_mf when we resize m_particles in AddParticlesAtLevel Src/Particle/AMReX_ParticleContainerI.H commit d1b6f7b2cfff64557cdd2e01fd94e435628aba9c Author: Weiqun Zhang Date: Thu May 11 13:36:53 2017 -0700 add back BoxList BoxList intersection because Amrvis uses it Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit ba1c73ebddbf2cafe96b76780227ed2958e9496b Author: Weiqun Zhang Date: Thu May 11 13:21:18 2017 -0700 clean up Tutorials/HeatEquation_EX1_C Tutorials/HeatEquation_EX1_C/Make.package Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX1_C/myfunc_F.H Tutorials/HeatEquation_EX1_C/writePlotFile.H Tutorials/HeatEquation_EX1_C/writePlotFile.cpp commit fef92ae2d5e785b79a95bdb804501cd2328d7f6e Author: Weiqun Zhang Date: Thu May 11 10:41:44 2017 -0700 User's Guide: add new file for Building AMReX Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/BuildingAMReX/BuildingAMReX.tex Docs/AMReXUsersGuide/GNUmakefile Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex commit 749d8fdfe6d87b7be55a2cb850e8d16126273aa2 Author: Weiqun Zhang Date: Thu May 11 10:32:45 2017 -0700 User's Guide: Getting Started Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Tutorials/HeatEquation_EX1_C/main.cpp commit 60f8e9360c3a69885219a839ec6aeab831e26099 Author: Weiqun Zhang Date: Thu May 11 09:33:57 2017 -0700 update typechecker for gcc 7 Tools/typechecker/typechecker.py commit 1dc9d27f88cf88590e6ead6ef16041192e73d247 Author: dtgraves Date: Wed May 10 16:26:34 2017 -0700 took out stray file Src/EBAMRTools/AMReX_EBPWLFineInterp.H commit e9e3a648eaedbef51c88e99e308494987afb1a65 Author: dtgraves Date: Wed May 10 16:25:28 2017 -0700 I am most of the way there to having (regridding, multigrid) interpolation/prolongation operator for EB. Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H Src/EBAMRTools/AMReX_EBCFInterp.H Src/EBAMRTools/AMReX_EBCFInterp.cpp Src/EBAMRTools/AMReX_EBFineInterp.H Src/EBAMRTools/AMReX_EBFineInterp.cpp Src/EBAMRTools/AMReX_EBPWLFineInterp.H Src/EBAMRTools/AMReX_EBPWLFineInterp.cpp Src/EBAMRTools/Make.package Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp commit 684003e000324c0890c948eaf98ffd3636117ff4 Author: Weiqun Zhang Date: Wed May 10 10:13:16 2017 -0700 If ref_ratio, n_error_buf, max_grid_size, or blocking_factor from inputs has fewer counts than the number of levels, fill the rest with the last value. The old behavior was to abort except in the single value case. Src/AmrCore/AMReX_AmrMesh.cpp commit 449e5f10e688adc16960cbe54102fb735fb70932 Merge: e7155cadd 241ae643e Author: WeiqunZhang Date: Wed May 10 12:14:33 2017 -0700 Merge pull request #8 from AMReX-Codes/dtg_branch stuff from dtg_branch requested by jrood commit 241ae643eb2778d763fd0a80ce1e1617033d2ad9 Author: dtgraves Date: Wed May 10 11:52:10 2017 -0700 ported over some functions as requested by jrood Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp Src/GeometryShop/AMReX_EBLoHiCenter.H Src/GeometryShop/AMReX_EBLoHiCenter.cpp Src/GeometryShop/Make.package Tests/EBAMRTools/regression/aggpwlfpTest.cpp commit febc9fc58e18a4f92fd8cdbfac17f522da1437e2 Merge: 96b84b354 e7155cadd Author: Michael Zingale Date: Wed May 10 14:45:10 2017 -0400 Merge branch 'development' into gpu commit d636f1de734e7a4993b0537d0f4f6e51f72e1bbe Author: Andrew Myers Date: Wed May 10 11:20:22 2017 -0700 Write out particle box array information to the plt / chk files. Src/Particle/AMReX_ParticleContainerI.H commit e7155cadd321c5ef8bafb7465eb09208b18e40f0 Author: Weiqun Zhang Date: Wed May 10 09:29:32 2017 -0700 clean up BoxArray::GetBndryCells Src/Base/AMReX_BoxArray.cpp commit 78ebeb56fd9307a60c82283f7f5703effbffdeec Author: Weiqun Zhang Date: Wed May 10 08:38:00 2017 -0700 consistent names Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_FabArrayBase.cpp commit b5b193fa8d3cf9d0190d9cd09c2f1aa132d4c474 Author: Weiqun Zhang Date: Wed May 10 08:28:26 2017 -0700 Revert "Remove unused variable." This reverts commit 60335511524dd4e2dfaa4ff0219743e342f4fc0e. Src/Base/AMReX_IntVect.H commit adf66bdebf124ad6f35013374579d0e79fee81d4 Author: dtgraves Date: Wed May 10 08:25:24 2017 -0700 High order CFInterp now works with as many ghost cells as you like (as long as the nesting radius supports it) Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.H Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.cpp Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp commit 96b84b35463d708f704be3a51a844ff8226755ce Author: Max Katz Date: Wed May 10 03:45:45 2017 -0400 Use pgfortran as the linker Tools/GNUMake/Make.rules Tools/GNUMake/comps/cuda.mak commit 033217dc7bc76407db0a61253e90480d2728c3c5 Author: Max Katz Date: Wed May 10 03:15:41 2017 -0400 Add in the cuda.mak file Tools/GNUMake/comps/cuda.mak commit 899e95f4ed7c8dd8290db51103df24d880ac283b Merge: 603355115 a864c21f7 Author: Ann Almgren Date: Tue May 9 20:36:22 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit 60335511524dd4e2dfaa4ff0219743e342f4fc0e Author: Ann Almgren Date: Tue May 9 20:35:32 2017 -0700 Remove unused variable. Src/Base/AMReX_IntVect.H commit 2833744f7487d26d9e01d11898ca23fc34758fd2 Merge: bd412c627 a864c21f7 Author: Max Katz Date: Tue May 9 21:13:18 2017 -0400 Merge branch 'development' into gpu commit a864c21f7286f1d47bafc6751111378f6dcd6d7f Merge: 14c150bac 4dd495d51 Author: Weiqun Zhang Date: Tue May 9 16:58:48 2017 -0700 Merge branch 'development' into boxlist commit 4dd495d5103191e1edcbe21b43e6aea1adf0eece Merge: bb25bddbb e5caeffeb Author: Ann Almgren Date: Tue May 9 16:50:35 2017 -0700 Merge branch 'development' of https://github.com/AMReX-Codes/amrex into development commit bb25bddbb7100cba263a8df5cde75d19d8f09c46 Author: Ann Almgren Date: Tue May 9 16:50:03 2017 -0700 Remove unused variables. Src/Particle/AMReX_ParticleInit.H commit e5caeffeb4e6464aa7d013185d6be7cc1ff99096 Merge: 56dd910a1 29167cff4 Author: Andrew Myers Date: Tue May 9 16:32:36 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 56dd910a1e291ae9463629d4624eff8653111813 Author: Andrew Myers Date: Tue May 9 16:32:28 2017 -0700 make num ghosts a property of the container. Tutorials/ShortRangeParticles/ShortRangeParticleContainer.H Tutorials/ShortRangeParticles/ShortRangeParticleContainer.cpp Tutorials/ShortRangeParticles/main.cpp commit af7c808ccdd3072ff35365a63fa84dd83dbe35aa Author: dtgraves Date: Tue May 9 16:29:54 2017 -0700 nwoEBQuadCFInterp has had many bug fixes Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.H Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.cpp Src/GeometryShop/AMReX_EBArith.cpp Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp commit 14c150baca07a261592dd9f483a1146c92b088ab Author: Weiqun Zhang Date: Tue May 9 16:17:48 2017 -0700 fix recursive call Src/Base/AMReX_BoxArray.cpp commit bdf5ec062e4068ae57848d30676ac4e8faac68f5 Merge: a7a1695b9 29167cff4 Author: Weiqun Zhang Date: Tue May 9 16:04:24 2017 -0700 Merge branch 'development' into boxlist commit 29167cff4e9a84f1060c3669c04b61710396b875 Author: Ann Almgren Date: Tue May 9 15:54:41 2017 -0700 Get rid of warning with DIM=1 about unused variable. Src/Base/AMReX_BaseFab.H commit a7a1695b99d8dad83d4256782f91f9cb17ee3bff Merge: f595479bc 05d485533 Author: Weiqun Zhang Date: Tue May 9 14:38:37 2017 -0700 Merge branch 'development' into boxlist Conflicts: Tools/F_scripts/f90cat.py commit f595479bc8d502f79b7826010e6ddc6425d88d3b Author: Weiqun Zhang Date: Tue May 9 14:08:31 2017 -0700 minor optimizations Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.cpp commit 05d4855334dde961b6105dc95c94a79d7814eab2 Author: Andrew Myers Date: Tue May 9 14:32:40 2017 -0700 Update advection tutorial to reflect changes in particle initialization routines. Tutorials/AMR_Adv_C/Source/Adv.cpp commit 439a51128ccafed45ca22ce580f783f62bd7119c Author: dtgraves Date: Tue May 9 14:00:52 2017 -0700 bug fix for NWOEBQuadCFInterp Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.cpp commit 83fb502ce73d90d1a4565b950b6c21c1925a8612 Author: Weiqun Zhang Date: Tue May 9 13:33:38 2017 -0700 minor optimization BoxDomain: need to remove empty boxes Src/Base/AMReX_BoxDomain.cpp commit afdc6d9dff068d7e97f6d33eb6df795de11e9fe3 Merge: 90c027519 a42e6138c Author: Andrew Myers Date: Tue May 9 13:38:24 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit 90c0275195220d96b5810bfc41c17373883ddeaa Author: Andrew Myers Date: Tue May 9 13:38:10 2017 -0700 fix copy / paste error in previous commit. Src/Particle/AMReX_ParticleInit.H commit a42e6138c9a8a072890d985806b40d98b4970b3c Merge: 66b40ed5d 2186e74d7 Author: WeiqunZhang Date: Tue May 9 13:22:58 2017 -0700 Merge pull request #7 from AMReX-Codes/dtg_branch bug fixes from Dtg branch commit 2186e74d733719783425eb519372bc7e21c840a9 Author: dtgraves Date: Tue May 9 13:11:33 2017 -0700 more aggstencil pointer tricks for better performance. Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.H Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.cpp commit 66b40ed5d4311a6d7996c67135a36f6c35ed99ec Merge: e4dc2a733 102f99ec1 Author: Andrew Myers Date: Tue May 9 12:43:59 2017 -0700 Merge branch 'development' of github.com:AMReX-Codes/amrex into development commit e4dc2a73305e9a70f4de6de51dbe19f7408210d1 Author: Andrew Myers Date: Tue May 9 12:43:45 2017 -0700 Make the particle initialization routines agnostic as to the names of the components or how they are laid out in memory. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Tests/Particles/AssignDensity/main.cpp Tests/Particles/AssignMultiLevelDensity/inputs Tests/Particles/AssignMultiLevelDensity/main.cpp commit a279cba4a5e6117e80c3a8e183a53cdf0abf0f07 Author: Weiqun Zhang Date: Tue May 9 12:40:15 2017 -0700 change plot_int Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs commit 9fa960619b801de2a718127053e9ac52bc54f8cb Author: dtgraves Date: Tue May 9 12:39:47 2017 -0700 fixed another regression failure that Marc found Src/GeometryShop/AMReX_IrregFABFactory.H commit 102f99ec13beefcfb5f729ce3ca6ab3450f5a66c Author: Michael Zingale Date: Tue May 9 15:28:36 2017 -0400 take a list of F90 files, determine their interdependencies and perform a topological sort. Then output a single .F90 file with all input files concatenated together Tools/F_scripts/f90cat.py commit a8af0f1e8080de932e868a5323ff44a90fd7156f Author: Weiqun Zhang Date: Tue May 9 12:02:34 2017 -0700 remove unused function Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit 68c86628a70acd96eac7955de70e6cc8a2a77a9c Author: Weiqun Zhang Date: Tue May 9 11:55:53 2017 -0700 minor Src/Base/AMReX_BoxList.cpp commit d009156e01c9bd862e0226459d4f69cb362448b2 Author: dtgraves Date: Tue May 9 11:42:24 2017 -0700 bit of trickery to get more performance when making AggStencils Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp commit bdf8df54eb317689eaab22f93b160b3b55024a0b Author: Weiqun Zhang Date: Tue May 9 11:01:02 2017 -0700 change BoxList complement algorithm Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.cpp commit 0301b4998da56eb7ea68f1fb5bdf06f23cc7d552 Author: Weiqun Zhang Date: Tue May 9 10:26:24 2017 -0700 wip: finished first pass Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxDomain.H Src/Base/AMReX_BoxDomain.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit 07e6679f33c384ab87ac4460004ce1505cf8f4ce Author: dtgraves Date: Tue May 9 09:11:00 2017 -0700 Marc noticed one of the regression tests was failing. This fixes that failure. Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_RedistStencil.cpp commit e912085e4ea199b80b6d7bb11c80a998501725ff Author: Michael Zingale Date: Mon May 8 22:58:37 2017 -0400 concatenate a bunch of fortran files, first sorting them by dependency Tools/F_scripts/f90cat.py commit 2995d5c83fea4db3062acd1dc0f87202c7e630ef Author: Weiqun Zhang Date: Mon May 8 18:10:28 2017 -0700 wip: remove some unused functions Src/Amr/AMReX_AuxBoundaryData.cpp Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit 6334221debd0e83ef370359b686242f804e90dc2 Author: dtgraves Date: Mon May 8 16:44:55 2017 -0700 Another day, another class. I added high order coarse-fine interpolation (with EB). The test does not show the proper convergence rate yet. Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.H Src/EBAMRTools/AMReX_NWOEBQuadCFInterp.cpp Src/EBAMRTools/Make.package Tests/EBAMRTools/README Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/nwoEBQuadCFITest.cpp Tests/EBAMRTools/regression/nwoebquadcfi.inputs commit 708c73a0463d121f2c88dfc4c12e6305fa5b7a10 Author: Weiqun Zhang Date: Mon May 8 12:07:03 2017 -0700 wip: use Array instead of std::list as the internal data structure for BoxList Src/Amr/AMReX_Amr.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxDomain.H Src/Base/AMReX_BoxDomain.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp commit 0973824cf8c5c979db034d750f3f9a87ff44abb3 Author: Michele Rosso Date: Mon May 8 15:19:39 2017 -0700 Add amrex_fabio_c.f90 and amrex_timer_c.f90 to cmake build. Src/F_BaseLib/CMakeLists.txt commit 292148e874455bb21706d9bf599feaf0a1b18981 Author: Weiqun Zhang Date: Sun May 7 16:55:27 2017 -0700 unit test for typechecker Tests/TypeCheck/GNUmakefile Tests/TypeCheck/Make.package Tests/TypeCheck/f.f90 Tests/TypeCheck/f_F.H commit f53a8d7475104a49a32adc83b024d37e439820d0 Author: Weiqun Zhang Date: Sun May 7 13:24:25 2017 -0700 typecheck: add readme Docs/Readme.typecheck commit 60b22bf68a6006fbed8bcc900718c2e8e985a20a Author: Weiqun Zhang Date: Sun May 7 13:03:49 2017 -0700 type check: takes only the first part of the name Tools/typechecker/typechecker.py commit d29d0f4ca260c2d6ba9b052f1d011c0a59fa9bd2 Merge: 0b917ff3f 93c01fbd6 Author: WeiqunZhang Date: Sun May 7 12:10:32 2017 -0700 Merge pull request #1 from AMReX-Codes/maxpkatz/post_timestep_regrid Add a hook so that an AmrLevel can force a post-timestep regrid commit 0b917ff3f24cec2787124a52bf9806f7b51f4d8d Author: Weiqun Zhang Date: Sun May 7 07:44:11 2017 -0700 fix print Tools/typechecker/typechecker.py commit 44234da55280c9709a26b08c4d132f10a204d371 Author: Weiqun Zhang Date: Sun May 7 07:12:22 2017 -0700 typechecker: get rid of global variables and print more info Tools/typechecker/typechecker.py commit 20f54fe0222139573a9a57270ad50cccfb99345b Author: Weiqun Zhang Date: Sat May 6 21:30:57 2017 -0700 typo Tests/C_BaseLib/TPROFILER_F.H commit d6bdd5bf078a45bacc68a3a1156169484c27e2d6 Author: Weiqun Zhang Date: Sat May 6 19:09:14 2017 -0700 fix conflict due to merge Tutorials/ShortRangeParticles/short_range_F.H commit 443543b50ef14879f3dba431d2836723521270ed Merge: d73fedf7f 4a4f323dd Author: Weiqun Zhang Date: Sat May 6 19:06:52 2017 -0700 merge commit 4a4f323ddc0f930ef0dabec7cbecb8c12ac59542 Author: Weiqun Zhang Date: Sat May 6 16:51:02 2017 -0700 type Tools/typechecker/typechecker.py commit fa7f046c5aa0a4fb34ca7d3d87c30b3bcba5fa87 Author: Weiqun Zhang Date: Sat May 6 15:37:59 2017 -0700 typecheck: optimization Tools/typechecker/typechecker.py commit f98bf285431fdbd2995f388016c1034dd2e002e9 Author: Weiqun Zhang Date: Sat May 6 11:58:58 2017 -0700 typecheck: remove whitespace lines because they mess up the block detection Tools/typechecker/typechecker.py commit 090efa7b93cef02f8d065af2dc8d9ee67f15ff0d Author: Weiqun Zhang Date: Sat May 6 11:21:17 2017 -0700 found missing argument thanks to typcheck Src/AmrCore/AMReX_INTERP_1D.F commit bf4c7ad89b2da12f3c0d666498aac13c956c010b Author: Weiqun Zhang Date: Sat May 6 11:20:48 2017 -0700 better error message Tools/typechecker/typechecker.py commit afd06d65cb1dbed235188ad2e9d7c3781e3270e9 Author: Weiqun Zhang Date: Sat May 6 10:53:04 2017 -0700 match void* with any fortran reference Tools/typechecker/typechecker.py commit c63252e8db2e9bb5f22567d86d18dde7c41f141f Author: Weiqun Zhang Date: Sat May 6 08:49:45 2017 -0700 fix sed Tools/GNUMake/Make.rules commit 05770a01cecba65b84bf2479e9ec1efe249293d5 Author: Weiqun Zhang Date: Sat May 6 08:42:59 2017 -0700 minor tweak Src/Base/AMReX_BLFort.H Tools/GNUMake/Make.rules commit 74dbe2c92b84a2e237153ddac2e87bb16ea4adae Author: Weiqun Zhang Date: Sat May 6 08:31:35 2017 -0700 started #ifdef __cplusplus in EB tests, but quickly gave up Tests/GeometryShop/stencilTestbed/src/lapl_nd_F.H commit f4cd580fcd3ceff2b31095ace7ac6ce5bf32267c Author: Weiqun Zhang Date: Sat May 6 08:22:47 2017 -0700 don't need to build executable to use typecheck, but we do still need to compile fortran codes Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit a48509c255d2abbf7d7ee5134b8771a9147fd4bd Author: Weiqun Zhang Date: Sat May 6 07:50:17 2017 -0700 #ifdef __cplusplus Tests/LinearSolvers/C_TensorMG/main_F.H commit 10b0e0e1d81540e898e6b7154f5402a409fb2ae8 Author: Weiqun Zhang Date: Sat May 6 07:43:27 2017 -0700 remove non-existing header Tests/LinearSolvers/C_CellMG/MACPROJ_2D.F Tests/LinearSolvers/C_CellMG/MACPROJ_3D.F commit b37161d40a05aa14d4a70ba21534bda50e5d6bef Author: Weiqun Zhang Date: Sat May 6 07:30:09 2017 -0700 fix type(c_ptr), value and character(c_char) Tools/typechecker/typechecker.py commit d32dd46398ef853de772ba9ac82642703ac4ee9b Author: Weiqun Zhang Date: Sat May 6 07:19:38 2017 -0700 fix node.args is NoneType Tools/typechecker/typechecker.py commit fcc721d1190bf5d43bbab1ee325e950a49f4408e Author: Weiqun Zhang Date: Sat May 6 07:09:37 2017 -0700 type errors in C_CellMG4 Src/LinearSolvers/C_CellMG4/AMReX_ABec2_3D.F commit 37dcb84fc015ea8c7405fc9b2e9febe93db13d54 Author: Weiqun Zhang Date: Sat May 6 07:07:44 2017 -0700 fix type errors in C_CellMG4 Src/LinearSolvers/C_CellMG4/AMReX_ABec2_2D.F Src/LinearSolvers/C_CellMG4/AMReX_ABec2_3D.F commit 34d308ea7c78bafce38d73fca0b7824989643a0d Author: Weiqun Zhang Date: Sat May 6 07:00:35 2017 -0700 add variable name Tools/typechecker/typechecker.py commit fc82afbbe57bb8d6cfa34d1bb41a9e52401da310 Author: Weiqun Zhang Date: Sat May 6 06:54:43 2017 -0700 add support for array such as int lo[] Tools/typechecker/typechecker.py commit a7a8200c9a72bb5001b6464b78747ff24b2eb1e4 Author: Weiqun Zhang Date: Sat May 6 06:36:27 2017 -0700 remove 2d FORT_SETVOLPT that didn't have correct function signature (thanks to typechecker) Src/Base/AMReX_COORDSYS_2D.F Tools/typechecker/typechecker.py commit 58fcb2808535812940a048d7308080e7ba75783a Author: Weiqun Zhang Date: Fri May 5 23:48:45 2017 -0700 typecheck .f and .F files too Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/typechecker/typechecker.py commit 7ac3fa9bc57db88c19182a9b0d339670e064f42a Author: Weiqun Zhang Date: Fri May 5 23:00:27 2017 -0700 tweak output of typecheck Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/typechecker/typechecker.py commit b2a1bf808d466b9281177f68e447de935a249d9b Author: Weiqun Zhang Date: Fri May 5 21:56:34 2017 -0700 fix amrex::Real, amrex_real and & Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 1ae79de0378a18770cbc2da145fc59689f005d45 Author: Weiqun Zhang Date: Fri May 5 18:00:21 2017 -0700 refactor typechecker to handle both module and non-moudle procedures. add missing headers Src/AmrCore/AMReX_INTERP_F.H Tools/typechecker/typechecker.py Tutorials/AMR_Adv_C/Source/Adv_F.H commit d73fedf7f2e3db195ffa23da189347ce68488085 Author: Andrew Myers Date: Fri May 5 17:57:36 2017 -0700 Make WriteAsciiFile include the template parameters in the output. Src/Particle/AMReX_ParticleContainerI.H commit 658b27996aaf279ef48e9ba9d2b09731e51e5d2d Merge: 19fe5291c c9314aadb Author: Andrew Myers Date: Fri May 5 16:49:25 2017 -0700 Merging. commit 3e0b607616d74311b0cfbe0ba4030c8c679141bb Author: Weiqun Zhang Date: Fri May 5 16:01:24 2017 -0700 add missing header Src/Particle/AMReX_Particles_F.H Tools/GNUMake/Make.rules commit cf41635573051a1eea6af0538d68ef1a18c3d021 Author: dtgraves Date: Fri May 5 15:35:56 2017 -0700 added EBCoarseAverage (with an improved interface from Chombo) which calls a nifty function from MultiFab_Util for the regular grid bits. It passes its convergence test. Src/EBAMRTools/AMReX_EBCoarseAverage.H Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/Make.package Tests/EBAMRTools/README Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/ebCoarseAveTest.cpp Tests/EBAMRTools/regression/ebcoarave.inputs commit 8734cf9038ea6c8f91dac1b7fca29beb6b57ce1f Author: Weiqun Zhang Date: Fri May 5 15:10:45 2017 -0700 first pass of typechecker.py Src/Base/AMReX_SPACE.H Tools/GNUMake/Make.rules Tools/typechecker/typechecker.py commit 7278ea6dba2cd93a22a3658278593b0d1fbe029e Author: Weiqun Zhang Date: Fri May 5 11:33:30 2017 -0700 rule for making CPP'd headers Tools/GNUMake/Make.rules commit a9d314a73b41efe7ef578f7190e1004535b72dff Author: Weiqun Zhang Date: Fri May 5 11:32:37 2017 -0700 rm pycparser Tools/typechecker/pycparser/LICENSE Tools/typechecker/pycparser/__init__.py Tools/typechecker/pycparser/_ast_gen.py Tools/typechecker/pycparser/_build_tables.py Tools/typechecker/pycparser/_c_ast.cfg Tools/typechecker/pycparser/ast_transforms.py Tools/typechecker/pycparser/c_ast.py Tools/typechecker/pycparser/c_generator.py Tools/typechecker/pycparser/c_lexer.py Tools/typechecker/pycparser/c_parser.py Tools/typechecker/pycparser/ply/LICENSE Tools/typechecker/pycparser/ply/__init__.py Tools/typechecker/pycparser/ply/cpp.py Tools/typechecker/pycparser/ply/ctokens.py Tools/typechecker/pycparser/ply/lex.py Tools/typechecker/pycparser/ply/yacc.py Tools/typechecker/pycparser/ply/ygen.py Tools/typechecker/pycparser/plyparser.py commit 8d6ebe52a44c23874dd7241676cf9773adc00bab Author: Weiqun Zhang Date: Fri May 5 10:45:52 2017 -0700 add a script for amrex::Real --> amrex_real Tools/Migration/amrex_real.sh commit 5fa50aae8928453347b742a036e9177f3c143bdd Author: Weiqun Zhang Date: Fri May 5 10:44:59 2017 -0700 amrex::Real --> amrex_real in *_F.H and *_f.H files so that c parser can parse them MiniApps/MultiGrid_C/COEF_F.H MiniApps/MultiGrid_C/RHS_F.H MiniApps/PGAS_SMC/SMC_F.H Src/Amr/AMReX_MAKESLICE_F.H Src/Amr/AMReX_PROB_AMR_F.H Src/Amr/AMReX_SLABSTAT_F.H Src/AmrCore/AMReX_FLUXREG_F.H Src/AmrCore/AMReX_INTERP_F.H Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_COORDSYS_F.H Src/Base/AMReX_MultiFabUtil_F.H Src/Boundary/AMReX_INTERPBNDRYDATA_F.H Src/F_BaseLib/MultiFab_C_F.H Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H Src/LinearSolvers/C_CellMG/AMReX_LO_F.H Src/LinearSolvers/C_CellMG/AMReX_LP_F.H Src/LinearSolvers/C_CellMG/AMReX_MG_F.H Src/LinearSolvers/C_CellMG4/AMReX_ABec2_F.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4_F.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCLO_F.H Src/Particle/AMReX_Particles_F.H Tests/LinearSolvers/C_CellMG/COEF_F.H Tests/LinearSolvers/C_CellMG/MACOPERATOR_F.H Tests/LinearSolvers/C_TensorMG/main_F.H Tests/LinearSolvers/ComparisonTest/COEF_F.H Tests/LinearSolvers/ComparisonTest/COMP_NORM_F.H Tools/C_util/Convergence/AVGDOWN_F.H Tools/C_util/Statistics/AVGDOWN_F.H Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H Tutorials/HeatEquation_EX1_C/myfunc_F.H Tutorials/HeatEquation_EX2_C/myfunc_F.H Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/RHS_F.H Tutorials/ShortRangeParticles/short_range_F.H commit 2ee69595480989abd4ba79ac82bfe1591d59a38e Author: Weiqun Zhang Date: Fri May 5 10:35:35 2017 -0700 more #ifdef __cplusplus MiniApps/MultiGrid_C/COEF_F.H MiniApps/MultiGrid_C/RHS_F.H MiniApps/PGAS_SMC/SMC_F.H Src/Base/AMReX_BLFort.H Tests/C_BaseLib/AMRPROFTEST_F.H Tests/C_BaseLib/TPROFILER_F.H Tests/LinearSolvers/C_CellMG/COEF_F.H Tests/LinearSolvers/C_CellMG/MACOPERATOR_F.H Tests/LinearSolvers/ComparisonTest/COEF_F.H Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_F.H Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H Tutorials/HeatEquation_EX1_C/myfunc_F.H Tutorials/HeatEquation_EX2_C/myfunc_F.H Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/HypreABecLap/HypreABec_F.H Tutorials/MultiGrid_C/RHS_F.H Tutorials/ShortRangeParticles/short_range_F.H commit 04daefb5f064c8c455d9b4683f25c75fb2568650 Author: Weiqun Zhang Date: Fri May 5 10:18:44 2017 -0700 wrap extern C around ifdef __cplusplu. this will allow the headers to be included in C codes and be parsed by a C parser Src/Amr/AMReX_MAKESLICE_F.H Src/Amr/AMReX_PROB_AMR_F.H Src/Amr/AMReX_SLABSTAT_F.H Src/AmrCore/AMReX_FLUXREG_F.H Src/AmrCore/AMReX_INTERP_F.H Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_COORDSYS_F.H Src/Base/AMReX_MultiFabUtil_F.H Src/Boundary/AMReX_INTERPBNDRYDATA_F.H Src/F_BaseLib/MultiFab_C_F.H Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H Src/LinearSolvers/C_CellMG/AMReX_LO_F.H Src/LinearSolvers/C_CellMG/AMReX_LP_F.H Src/LinearSolvers/C_CellMG/AMReX_MG_F.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4_F.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCLO_F.H Src/Particle/AMReX_Particles_F.H commit dc17ab5cd9eceb2bf97500ce6b6ec7104f656788 Author: Weiqun Zhang Date: Fri May 5 10:05:16 2017 -0700 restart typeChecker.py Tools/GNUMake/Make.defs Tools/typechecker/typeChecker.py Tools/typechecker/typechecker.py commit c9314aadbdeba807e15ff223721eaa965a8449e4 Author: Michael Zingale Date: Fri May 5 11:32:26 2017 -0400 comment out an OpenMP version assert because of a PGI bug Src/Base/AMReX.cpp commit f1f932f3fb8b079e6ba76a8878f8bc011c3039a7 Author: Michael Zingale Date: Fri May 5 08:43:40 2017 -0400 fix compilation with PROF=t Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_prof.f90 commit bd412c6273b7df65869d777538727425cf05b3a6 Merge: 0c9c4d766 69c68a815 Author: Max Katz Date: Fri May 5 02:47:08 2017 -0400 Merge branch 'development' into gpu commit 19fe5291cc8259e209382040b944e356e1b7c3ca Merge: aa4da3521 5beaa2703 Author: Andrew Myers Date: Thu May 4 17:34:40 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit aa4da3521d78ad60a7aa2cb25075af99c41954ee Author: Andrew Myers Date: Thu May 4 17:34:28 2017 -0700 have the fillGhosts routine take a number of ghost zones as an argument. Tutorials/ShortRangeParticles/ShortRangeParticleContainer.H Tutorials/ShortRangeParticles/ShortRangeParticleContainer.cpp Tutorials/ShortRangeParticles/main.cpp commit e8d4dde0ee6509c6c57b3ddf0484b991e904bba3 Author: Andrew Myers Date: Thu May 4 17:31:50 2017 -0700 update the ShortRangeParticle example to show the use of the particle derived type in fortran Tutorials/ShortRangeParticles/ShortRangeParticleContainer.H Tutorials/ShortRangeParticles/ShortRangeParticleContainer.cpp Tutorials/ShortRangeParticles/short_range_2d.f90 Tutorials/ShortRangeParticles/short_range_3d.f90 Tutorials/ShortRangeParticles/short_range_F.H commit 69c68a815fb9edef9ff8e8459d20588980f12d7b Author: Michael Zingale Date: Thu May 4 18:09:33 2017 -0400 fix AMReX testing Tools/RegressionTesting/suite.py commit 2dec19d9159541be99e9df4dcb435c50b0c60423 Author: Weiqun Zhang Date: Thu May 4 12:43:01 2017 -0700 add pycparse license Tools/typechecker/pycparser/LICENSE commit 17ad5fdac649d450074adef5c83eedc93f53e535 Author: dtgraves Date: Thu May 4 11:56:41 2017 -0700 fixed EBFastFR. amrex::FluxRegister could really use a memory scrub. Src/AmrCore/AMReX_FluxRegister.cpp Src/EBAMRTools/AMReX_EBFastFR.H Src/EBAMRTools/AMReX_EBFastFR.cpp Src/GeometryShop/AMReX_EBFaceFAB.cpp Tests/EBAMRTools/regression/fluxRegTest.cpp Tests/EBAMRTools/regression/fluxreg.inputs Tests/EBAMRTools/regression/regFluxRegTest.cpp commit 4df02eaab1306d9be2ccc4fbf3c9883c0987e9c9 Author: Weiqun Zhang Date: Thu May 4 11:18:28 2017 -0700 fix merge Src/Base/Make.package commit 9974ffff22775001f93ba3cb7817019b96e293d0 Merge: f69274fc1 4e641e4ca Author: Weiqun Zhang Date: Thu May 4 11:10:58 2017 -0700 Merge branch 'development' into fortran_check Conflicts: Src/Base/Make.package Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 4e641e4ca436ed5684bb76414c00492aabc6941a Author: Weiqun Zhang Date: Thu May 4 11:06:09 2017 -0700 minor changes in User's Guide Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Docs/AMReXUsersGuide/Introduction/Introduction.tex commit 5775aed933c4e6cb296c93a7066d357bf4390e2f Author: Weiqun Zhang Date: Thu May 4 10:22:52 2017 -0700 more in .gitignore Docs/AMReXUsersGuide/.gitignore commit c04fd8bf0dc248e7dd89beffd0cc563ec0592635 Author: Michael Zingale Date: Thu May 4 09:16:06 2017 -0400 need iso_c_binding to compile Src/F_BaseLib/fabio.f90 commit 0c9c4d766997f90cdb5212f137d528e694ebfed0 Author: Max Katz Date: Thu May 4 04:34:20 2017 -0400 Add a CUDA compiler option (using nvcc+pgfortran) Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 83b30ca8f74b081da97512c672aa7171a05cfff2 Merge: 772d43d43 ea6305c4e Author: Max Katz Date: Thu May 4 03:16:15 2017 -0400 Merge branch 'development' into gpu commit ea6305c4e0284dc615e56a8296bc9b2704d1198b Author: Max Katz Date: Thu May 4 02:16:56 2017 -0400 Use ISO C bindings for timer_c and fabio_c Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/GPackage.mak Src/F_BaseLib/amrex_fabio_c.f90 Src/F_BaseLib/amrex_timer_c.f90 Src/F_BaseLib/bl_timer.f90 Src/F_BaseLib/fab.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c Src/F_BaseLib/parallel_stubs.f90 Src/F_BaseLib/timer_c.c commit cdbdfe4aa349feffea64ff066b8d72f20959724e Author: dtgraves Date: Wed May 3 16:20:08 2017 -0700 added a couple of clarifying (to me) comments to FluxRegister.H. EBFastFR still does not work but I am on the case. Src/AmrCore/AMReX_FLUXREG_2D.F Src/AmrCore/AMReX_FluxRegister.H Src/EBAMRTools/AMReX_EBFastFR.H Src/EBAMRTools/AMReX_EBFastFR.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Tests/EBAMRTools/regression/fluxRegTest.cpp Tests/EBAMRTools/regression/fluxreg.inputs Tests/EBAMRTools/regression/regFluxRegTest.cpp commit 86408cfb1474b388d7afad8e0086eae47963d74f Author: dtgraves Date: Wed May 3 14:10:08 2017 -0700 added all-regular flux register test that also fails. Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/regFluxRegTest.cpp commit c0387082a9de5b3ae0eeaea9c872f9d55e2d531f Author: dtgraves Date: Wed May 3 11:43:59 2017 -0700 adding README files that list the tests and what they do Tests/EBAMRTools/README Tests/GeometryShop/README commit 772d43d43bb596740ae323c93ae4755bd20b8691 Merge: 7a875675c be7c35813 Author: Max Katz Date: Wed May 3 01:37:09 2017 -0400 Merge branch 'development' into gpu commit f9cbd4c87bd0936f190ca47806d5719fa74d6eb6 Author: dtgraves Date: Tue May 2 16:48:52 2017 -0700 we now have an EB flux register and a test (that fails for now) Src/EBAMRTools/AMReX_EBFastFR.H Src/EBAMRTools/AMReX_EBFastFR.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/EBAMRTools/Make.package Src/GeometryShop/AMReX_EBFaceFAB.H Src/GeometryShop/AMReX_EBFaceFAB.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/fluxRegTest.cpp Tests/EBAMRTools/regression/fluxreg.inputs commit be7c3581382d81ff09c366401b7c1dd78f1cbdd4 Merge: b26efdbe3 1b457d8ca Author: Michael Zingale Date: Tue May 2 15:23:32 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit b26efdbe3e5d3f1b928b25e73a3a7b2cb757219f Author: Michael Zingale Date: Tue May 2 15:23:21 2017 -0400 boxlib -> amrex Tools/F_scripts/makebuildinfo.py commit 1b457d8ca241b275fb23d94be3bb168c11f1e1d3 Merge: 39b111c00 e34b6bbdf Author: Michael Zingale Date: Tue May 2 15:05:07 2017 -0400 Merge branch 'development' of ssh://github.com/AMReX-Codes/amrex into development commit 39b111c00791777c0f0f3f02f2a2bc021b00fa94 Author: Michael Zingale Date: Tue May 2 15:04:36 2017 -0400 fix the summary table info to be at the start of a line close some files that were left openned Tools/RegressionTesting/regtest.py commit e34b6bbdf86e942efc86fd8f74cc41e8c796a2f7 Author: Weiqun Zhang Date: Tue May 2 12:01:03 2017 -0700 assertion Src/Base/AMReX_FabArrayBase.cpp commit d4c2dabbf965e7be4f74c829abaacc353ab2e900 Merge: d65a45818 5742ef9bc Author: WeiqunZhang Date: Tue May 2 10:21:02 2017 -0700 Merge pull request #3 from AMReX-Codes/dtg_branch Dtg branch commit 5742ef9bc93461005c84de8c387c92cfaa820427 Author: dtgraves Date: Tue May 2 10:12:31 2017 -0700 removing unwanted files Tests/GeometryShop/regression/Backtrace.rg_0_rl_0 Tests/GeometryShop/regression/bl_prof/bl_call_stats_D_00000 Tests/GeometryShop/regression/bl_prof/bl_call_stats_H Tests/GeometryShop/regression/bl_prof/bl_call_stats_H_00000 Tests/GeometryShop/regression/bl_prof/bl_comm_prof_D_00000 Tests/GeometryShop/regression/bl_prof/bl_comm_prof_H Tests/GeometryShop/regression/bl_prof/bl_comm_prof_H_00000 Tests/GeometryShop/regression/bl_prof/bl_prof_D_00000 Tests/GeometryShop/regression/bl_prof/bl_prof_H commit d65a45818efa8227fe08c6d614e25f3af2135605 Merge: 85c9f8f4f 737e54db6 Author: Michael Zingale Date: Tue May 2 13:00:17 2017 -0400 Merge pull request #4 from WeiqunZhang/weiqun/regtest fix suite.py commit 85c9f8f4f56879221e53577dd9c060d826d02690 Author: Weiqun Zhang Date: Tue May 2 09:18:29 2017 -0700 AMR_Adv_CF: should use contains not intersects Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 commit a83ccbf609e2a0af42fd14a615f3982d59608afb Author: Weiqun Zhang Date: Tue May 2 09:17:59 2017 -0700 amrex_box_module: add contains function Src/F_Interfaces/Base/AMReX_box_mod.F90 commit 737e54db6007caeb5cd029cc6857dfa9002cb654 Author: Weiqun Zhang Date: Tue May 2 08:59:22 2017 -0700 fix suite.py Tools/RegressionTesting/suite.py commit de74865ea7f1379820341b1a45ac085005fa9edd Author: Weiqun Zhang Date: Tue May 2 06:01:14 2017 -0700 forgot a new file Src/Base/AMReX_filcc_mod.F90 commit 7a875675c2cac1a053f29ad56cc2372c76f3a5e5 Merge: 184d46d4f 1e5d7bbf4 Author: Max Katz Date: Tue May 2 01:46:32 2017 -0400 Merge branch 'development' into gpu commit 1e5d7bbf42a011953ee26a3a28fd094eb020deb7 Author: Weiqun Zhang Date: Mon May 1 17:26:26 2017 -0700 add inputs.physbc Tutorials/AMR_Adv_CF/Exec/SingleVortex/inputs.physbc commit 74bcc387c8fae8be49433f7f524bfdb3704ed11a Author: Weiqun Zhang Date: Mon May 1 17:24:12 2017 -0700 amrex_box_module: implement intersects Src/F_Interfaces/Base/AMReX_box_mod.F90 commit 45bd6da5b296f59a1b946e9b90f39b4c852ecb9b Author: Weiqun Zhang Date: Mon May 1 16:18:52 2017 -0700 add amrex_filcc_module and add non-periodic boundaries to AMR_Adv_CF example Src/Base/AMReX_parmparse_fi.cpp Src/Base/AMReX_parmparse_mod.F90 Src/Base/CMakeLists.txt Src/Base/Make.package Src/F_Interfaces/Base/AMReX_base_mod.F90 Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Tutorials/AMR_Adv_CF/Source/bc_mod.F90 Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit ef6b46feaf522faa27f6de8d5f425e1ce50c3d13 Author: Weiqun Zhang Date: Mon May 1 13:40:14 2017 -0700 Physbc module: add geometry Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/Base/AMReX_FPhysBC.H Src/F_Interfaces/Base/AMReX_FPhysBC.cpp Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_physbc_fi.cpp Src/F_Interfaces/Base/AMReX_physbc_mod.F90 Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/fillpatch_mod.F90 commit 7e29a630013bc2f4e0bc4d4023da792e7fcda51a Author: Dan Graves Date: Mon May 1 16:27:57 2017 -0700 added EBNormalizeByVolumeFraction (catchy name, no?) so we can do the whole conservative and non-conservative divergence thing. Src/EBAMRTools/AMReX_EBFastFR.H Src/EBAMRTools/AMReX_EBFastFR.cpp Src/GeometryShop/AMReX_EBCellFAB.cpp Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.H Src/GeometryShop/AMReX_EBNormalizeByVolumeFraction.cpp Src/GeometryShop/Make.package Tests/GeometryShop/regression/Backtrace.rg_0_rl_0 Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/bl_prof/bl_call_stats_D_00000 Tests/GeometryShop/regression/bl_prof/bl_prof_D_00000 Tests/GeometryShop/regression/bl_prof/bl_prof_H Tests/GeometryShop/regression/ebnormalizeTest.cpp Tests/GeometryShop/regression/ebnormtest.inputs commit 5beaa27037e925cf021e70aa8bbb1a42518001ec Author: Andy Nonaka Date: Mon May 1 11:08:58 2017 -0700 update scripts used to compile VARDEN Tools/F_scripts/makebuildinfo.py commit 185e8817718b09f795262a1eae7d9da2ca1a5850 Author: Michael Zingale Date: Mon May 1 12:29:20 2017 -0400 allow "source" to also contribute to the compile_string Tools/RegressionTesting/params.py Tools/RegressionTesting/suite.py commit 4d7ee2ece9b70c4c8d3a47ada8d75aaca6948d25 Author: Weiqun Zhang Date: Mon May 1 09:25:07 2017 -0700 give omp critical a name Src/Particle/AMReX_ParticleI.H commit 93c01fbd655a8f9f00a8d09acd8f7cb76faa5376 Author: Max Katz Date: Mon May 1 02:31:08 2017 -0400 Add a hook so that an AmrLevel can force a post-timestep regrid The motivation for this change is that sometimes, during the course of a coarse timestep, the timestep will found to be unstable due to a lack of resolution. In this case the coarse level may want to signal that more resolution is required immediately (as opposed to waiting for a future regrid), because even a single unstable step may cause significant harm to the integrity of the simulation. An example is a spurious numerical detonation caused by insufficient resolution in a thermonuclear burning region. If this numerically-seeded detonation is detected at the end of a timestep, more levels can be added immediately so that the fine levels can improve the situation and quench the detonation (since they will overwrite the coarse data at the end of the timestep). Each AmrLevel now has a member variable post_step_regrid. To trigger a regrid at the end of a step, but before any fine timesteps would be taken, they only need to set this variable to one. At the beginning of every timestep, it will be reset to 0. Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H commit c250a3358c1069ad503a9217edae6b3e35db853e Author: Weiqun Zhang Date: Fri Apr 28 20:48:01 2017 -0700 add EB to doxygen and move doxygen stuff to its own directory Docs/Doxygen/doxygen.conf Docs/Doxygen/main.dox commit 9cc44cfd6ed2c5f18d90a8e9612c80c3a410a462 Author: Dan Graves Date: Fri Apr 28 16:43:53 2017 -0700 started work on hybrid flux register. this one should be interesting Src/EBAMRTools/AMReX_EBFastFR.H Src/EBAMRTools/AMReX_EBFastFR.cpp commit e6142ea1cbc872cdb624e27020c23e1a4b5f08cf Merge: 6265c1efa b7e187697 Author: Weiqun Zhang Date: Fri Apr 28 16:04:08 2017 -0700 Merge branch 'master' into development commit b7e187697a295beef80b820c882f49897ffd845e Author: Weiqun Zhang Date: Fri Apr 28 15:48:08 2017 -0700 add a main page Docs/doxygen.conf Docs/doxygenmain.dox commit 6265c1efaa57459fec21ad1ed115a8ff45cbe197 Author: Weiqun Zhang Date: Fri Apr 28 14:47:07 2017 -0700 update migration guide Docs/Migration/Migration.md commit 0816406bbdfc7fa6e5a8b019821fac8ebdd82281 Author: Weiqun Zhang Date: Fri Apr 28 14:47:07 2017 -0700 update migration guide Docs/Migration/Migration.md commit d00569720139f42641401aadd92e01aaa02b9e1c Author: Weiqun Zhang Date: Fri Apr 28 14:28:48 2017 -0700 simplify helloworld Tutorials/HelloWorld_C/Make.package Tutorials/HelloWorld_C/main.cpp Tutorials/HelloWorld_C/work.f90 commit f9ac3816ce7c77b47d47f2b76b274f9719c70d01 Author: Weiqun Zhang Date: Fri Apr 28 14:25:00 2017 -0700 start AMReX User's Guide Docs/AMReXUsersGuide/.gitignore Docs/AMReXUsersGuide/AMReXUsersGuide.tex Docs/AMReXUsersGuide/GNUmakefile Docs/AMReXUsersGuide/GettingStarted/GettingStarted.tex Docs/AMReXUsersGuide/Introduction/Introduction.tex Docs/AMReXUsersGuide/Preface/Preface.tex Docs/AMReXUsersGuide/README.md Docs/AMReXUsersGuide/amrexsymbols.tex commit 59094381eb715409503a43e30f1085bc07a23af7 Author: Weiqun Zhang Date: Fri Apr 28 13:53:20 2017 -0700 rename UsersGuide to BoxLibUsersGuide Docs/BoxLibUsersGuide/C_AdvancedTopics/C_AdvancedTopics.tex Docs/BoxLibUsersGuide/F_AdvancedTopics/F_AdvancedTopics.tex Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example1.eps Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example1.fig Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example2.eps Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example2.fig Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example3.eps Docs/BoxLibUsersGuide/F_AdvancedTopics/bc_example3.fig Docs/BoxLibUsersGuide/F_AdvancedTopics/subcycling_algorithm.eps Docs/BoxLibUsersGuide/GNUmakefile Docs/BoxLibUsersGuide/GettingStarted/GettingStarted.tex Docs/BoxLibUsersGuide/GettingStarted/VisIt_2D.eps Docs/BoxLibUsersGuide/GettingStarted/VisIt_3D.eps Docs/BoxLibUsersGuide/GettingStarted/edison.run Docs/BoxLibUsersGuide/GettingStarted/edison_omp.run Docs/BoxLibUsersGuide/Introduction/AMR.eps Docs/BoxLibUsersGuide/Introduction/Introduction.tex Docs/BoxLibUsersGuide/Introduction/boxlib_directory_bw2.eps Docs/BoxLibUsersGuide/Introduction/castro_scaling.eps Docs/BoxLibUsersGuide/Introduction/data_loc.odg Docs/BoxLibUsersGuide/Introduction/data_loc2.eps Docs/BoxLibUsersGuide/Introduction/index_grid.odg Docs/BoxLibUsersGuide/Introduction/index_grid2.eps Docs/BoxLibUsersGuide/Introduction/lmc_scaling.eps Docs/BoxLibUsersGuide/Introduction/maestro_scaling.eps Docs/BoxLibUsersGuide/Introduction/varden1.eps Docs/BoxLibUsersGuide/Introduction/varden2.eps Docs/BoxLibUsersGuide/Introduction/varden3.eps Docs/BoxLibUsersGuide/Introduction/varden4.eps Docs/BoxLibUsersGuide/LinearSolvers/LinearSolvers.tex Docs/BoxLibUsersGuide/Preface/Preface.tex Docs/BoxLibUsersGuide/README Docs/BoxLibUsersGuide/Regression/test_suite.tex Docs/BoxLibUsersGuide/Regression/testsuite.eps Docs/BoxLibUsersGuide/UsersGuide.tex commit 6d1046cf0af9711aa1acc4245ef891b16e932675 Merge: 3415e38c6 a5dfe0691 Author: Weiqun Zhang Date: Fri Apr 28 19:30:30 2017 +0000 Merged in development (pull request #28) Development commit a5dfe06913c1b6e4c39f48505633d3dd2ac9158c Merge: 3e01abfb2 0f94d9b32 Author: Weiqun Zhang Date: Fri Apr 28 12:28:30 2017 -0700 Merge branch 'master' into development commit 0f94d9b322541407f87d8ee41d113749f3faeb4f Author: Weiqun Zhang Date: Fri Apr 28 12:27:36 2017 -0700 update copyright notice and license agreement README.txt license.txt commit 3e01abfb29158a2e35fe1f1061107a433f8b1d0f Merge: a8ccab06f aef2323ca Author: Andrew Myers Date: Thu Apr 27 16:35:18 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit aef2323ca1e49dcfc2ecb0c98e474a30db64a74f Author: Weiqun Zhang Date: Thu Apr 27 16:21:35 2017 -0700 print origin and value in addition to the fully expanded value when `make print-%` is invoked Tools/GNUMake/Make.rules commit 250c69ddb90075acdffd150166c14a3ddd6fbf42 Merge: 9923def2e 0ad28c184 Author: Dan Graves Date: Thu Apr 27 14:56:58 2017 -0700 getting Weiqun's fixes to aliasing stuff commit 9923def2e8cbfd3f7d9f4948284102357eb1f4cd Author: Dan Graves Date: Thu Apr 27 14:55:43 2017 -0700 found the bug that was making PWLFP get the wrong convergence rates. Looks good now. On to trying to figure out how to integrate with MultiFab fillpatch Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Tests/EBAMRTools/regression/aggpwlfpTest.cpp commit a8ccab06f7a948395535eceba05d96a25319c316 Author: Andrew Myers Date: Thu Apr 27 14:55:31 2017 -0700 Make the C interface to the nodal multigrid solver a bit more general. Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 5e3210fed27b5376874401b2545a6ab32fd51190 Author: Dan Graves Date: Thu Apr 27 13:55:43 2017 -0700 another change of a MFIter declaration Src/GeometryShop/AMReX_EBLevelGrid.cpp commit 1c474d66d5a191503d8279fe79e25cf877c9a868 Author: Dan Graves Date: Thu Apr 27 13:54:27 2017 -0700 added fancier static initialization to IntVect::Zero and IntVect::Unit from Chombo Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp commit 0ad28c184151be2f9535a40f642e023b73dc0dc8 Author: Weiqun Zhang Date: Thu Apr 27 13:25:49 2017 -0700 support amrex::Print() << std::endl Src/Base/AMReX_Print.H commit 536a8e9182c04e1573bdfbd6b407841ee4573fc0 Author: Weiqun Zhang Date: Thu Apr 27 12:26:21 2017 -0700 add new FArrayBox constructor that takes a Real* Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp commit d0d60c7d645c1bae93165c734f934c80cbfd690b Author: Dan Graves Date: Thu Apr 27 12:00:27 2017 -0700 some bug fixes improve convergence rate but not quite enough Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp commit 74eb2f54d9c2dea1e9bade5267efe52b7501672c Author: Dan Graves Date: Thu Apr 27 11:54:52 2017 -0700 apparently using a LayoutData for defining a MFIter makes bad things happen Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp commit aecb6eca58773b68434304f9b4dd28de3ffd60f1 Author: Dan Graves Date: Thu Apr 27 11:53:55 2017 -0700 added bounds checking to BaseIVFAB Src/GeometryShop/AMReX_BaseIVFABI.H commit e84bab7fe781c00a5d8aa60cbbb0fdfe7062f744 Merge: c3c8ddfc6 0ea5baa32 Author: Weiqun Zhang Date: Thu Apr 27 11:16:29 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 0ea5baa32c9c5ebf89ff363de9462dfc1b5693a7 Merge: a0b707d36 34e94cc9d Author: Dan Graves Date: Thu Apr 27 18:16:09 2017 +0000 Merged in dtg_branch (pull request #27) Dtg branch--merge to get Ray the dataholders he wants commit c3c8ddfc6d697d1d79e49c4003e81515062c2199 Author: Weiqun Zhang Date: Thu Apr 27 10:20:10 2017 -0700 add new MultiFab/FabArray constructors that take non-owning pointers; clean up FabArray StatusType Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/Make.package commit a0b707d36d8038b7104831a720b1bd485191594d Author: Andy Nonaka Date: Wed Apr 26 17:17:13 2017 -0700 added random number engine copy Src/F_BaseLib/bl_random_c.cpp Src/F_BaseLib/bl_random_f.f90 commit 34e94cc9da3ac4b4b720eddb1485d7f61bb2f442 Author: Dan Graves Date: Wed Apr 26 15:58:31 2017 -0700 I added EBFluxFAB, IrregFAB and their associated factories. They pass their a simple test. Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_EBFluxFAB.H Src/GeometryShop/AMReX_EBFluxFAB.cpp Src/GeometryShop/AMReX_EBFluxFactory.H Src/GeometryShop/AMReX_EBFluxFactory.cpp Src/GeometryShop/AMReX_FaceIndex.H Src/GeometryShop/AMReX_FaceIndex.cpp Src/GeometryShop/AMReX_IrregFAB.H Src/GeometryShop/AMReX_IrregFAB.cpp Src/GeometryShop/AMReX_IrregFABFactory.H Src/GeometryShop/AMReX_IrregFABFactory.cpp Src/GeometryShop/AMReX_VolIndex.H Src/GeometryShop/AMReX_VolIndex.cpp Src/GeometryShop/Make.package Tests/EBAMRTools/regression/aggpwlfp.inputs Tests/EBAMRTools/regression/aggpwlfpTest.cpp Tests/GeometryShop/regression/Backtrace.rg_0_rl_0 Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/bl_prof/bl_call_stats_D_00000 Tests/GeometryShop/regression/bl_prof/bl_prof_D_00000 Tests/GeometryShop/regression/bl_prof/bl_prof_H Tests/GeometryShop/regression/dataArith.cpp Tests/GeometryShop/regression/dataarith.inputs commit 60cce68efdd3427e763715262b5420ac7c871201 Author: Weiqun Zhang Date: Wed Apr 26 08:49:46 2017 -0700 fix shebang configure commit 1f827a6bc683eba18ebfc91a31cca4286991ffa4 Author: Dan Graves Date: Tue Apr 25 16:26:45 2017 -0700 Good news: PWL fill patch test works. Bad news: convergence rate is wrong. Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/EBAMRTools/AMReX_MeshRefine.H Src/EBAMRTools/AMReX_MeshRefine.cpp Tests/EBAMRTools/regression/aggpwlfp.inputs Tests/EBAMRTools/regression/aggpwlfpTest.cpp Tests/EBAMRTools/regression/sphere.inputs commit b2894dc991eea58e0ad7bc1581c7eaa8eeab7183 Author: Dan Graves Date: Tue Apr 25 12:44:32 2017 -0700 EBAMRTools again compiles. I added a bunch of EBLevelDataOps functionality Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/EBAMRTools/AMReX_MeshRefine.H Src/EBAMRTools/AMReX_MeshRefine.cpp Src/GeometryShop/AMReX_EBCellFAB.cpp Tests/EBAMRTools/regression/aggpwlfpTest.cpp commit f4e4b43b3f8d57f012dee088ec1a2a8e9e0a1ff9 Author: Dan Graves Date: Tue Apr 25 12:25:59 2017 -0700 added IntVect::Zero and IntVect::Unit because TheZeroVector() was pissing me off Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp commit d0778129f56f3c723e7b583826e7670e4f5401be Author: Andrew Myers Date: Tue Apr 25 09:49:49 2017 -0700 fix the advection tutorial. Src/Particle/AMReX_ParticleInit.H commit 259742807f66a68131c47b98725ac85cebacb231 Author: Dan Graves Date: Mon Apr 24 16:11:25 2017 -0700 I ported over a bunch of tools I use to write tests Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/EBAMRTools/AMReX_MeshRefine.H Src/EBAMRTools/AMReX_MeshRefine.cpp Src/EBAMRTools/Make.package Src/GeometryShop/AMReX_EBCellFAB.H Src/GeometryShop/AMReX_EBCellFAB.cpp Tests/EBAMRTools/regression/aggpwlfpTest.cpp commit be5521eaf47d46fa67587765c15164a3c414a18d Author: Andrew Myers Date: Mon Apr 24 15:54:05 2017 -0700 Use the new syntax to get the Real data from the struct-of-arrays. Src/Particle/AMReX_ParticleContainerI.H commit e2389b1cf0bdb80055524e186f249e3ca520489c Author: Andrew Myers Date: Mon Apr 24 15:47:35 2017 -0700 give the AmrParticleContainer 4 components as well. Src/AmrCore/AMReX_AmrParticles.H commit d5db875a670fc76db5a340597c194108af0531f0 Author: Andrew Myers Date: Mon Apr 24 10:50:45 2017 -0700 add some additional accessor methods to StructOfArrays. Src/Particle/AMReX_Particles.H commit 34bac78aefd84c9dfb8b1d3ad14f92c74c637f36 Merge: e3cec11d1 110ab0ee3 Author: Andrew Myers Date: Mon Apr 24 09:43:08 2017 -0700 Merge branch 'integer_soa_data' into development commit e3cec11d1323a78979d8b61c58f03ce05aa02085 Author: Weiqun Zhang Date: Mon Apr 24 08:51:58 2017 -0700 move some rules out of Tools/GNUMake to avoid potential conflicts GNUmakefile.in Tools/GNUMake/Make.rules commit c6aa7cefb514e581853e1fe72a8c46220ac75954 Author: Weiqun Zhang Date: Sun Apr 23 12:42:37 2017 -0700 configure: enforce libamrex and application are consistent on the use of OpenMP Tools/GNUMake/Make.rules Tools/libamrex/mkconfig.py commit 5eaea034235166c4fb75a72d35b81ffcbea3775e Author: Weiqun Zhang Date: Sun Apr 23 12:19:43 2017 -0700 configure: by default enforce the same compiler is used to build application Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/libamrex/configure.py Tools/libamrex/mkconfig.py commit cfaab9410cb58b5e8a3a34f50ed0317a305f48a0 Author: Weiqun Zhang Date: Sun Apr 23 12:17:29 2017 -0700 minor tweak Tutorials/libamrex_C/GNUmakefile commit 1031d3b3fb25ddfc20b649959032409ca798e86b Author: Weiqun Zhang Date: Sat Apr 22 22:14:00 2017 -0700 minor tweak of make GNUmakefile.in Tools/GNUMake/Make.rules commit 239ae7d88a554f9cf6cc7e880a194f341f25ee0e Author: Weiqun Zhang Date: Sat Apr 22 21:56:13 2017 -0700 add a note for linking to C++11 and Fortran libraries INSTALL commit 94aae453204b1518331a3166c9a8d671004454d5 Merge: 78a0f8b14 6558cd633 Author: Weiqun Zhang Date: Sat Apr 22 21:41:14 2017 -0700 Merge branch 'libamrex' into development commit 6558cd633dda37a57f13a1e1bf02e9e7a38cef8d Author: Weiqun Zhang Date: Sat Apr 22 21:40:31 2017 -0700 add INSTALL INSTALL Tools/libamrex/configure.py commit ca2ce26eac41a6ce876c8e31985c273f81fa96b2 Author: Weiqun Zhang Date: Sat Apr 22 21:19:38 2017 -0700 add configure GNUmakefile.in Tools/libamrex/configure.py configure commit cc1ae96204163bd38ca21ce55d79f179ecf4af9b Author: Weiqun Zhang Date: Sat Apr 22 15:46:16 2017 -0700 create a directory for libarmex scripts Tools/GNUMake/Make.defs Tools/libamrex/mkconfig.py commit 3638fd90a9802913c9ac488d9e793576925dae05 Author: Weiqun Zhang Date: Sat Apr 22 09:07:31 2017 -0700 An example using libamrex Tutorials/libamrex_C/GNUmakefile Tutorials/libamrex_C/MyAmr.H Tutorials/libamrex_C/MyAmr.cpp Tutorials/libamrex_C/main.cpp Tutorials/libamrex_C/myf.f90 commit 75543fb589d130be2d59fc8443b12ab456f71464 Author: Weiqun Zhang Date: Sat Apr 22 08:24:46 2017 -0700 install headers and modules GNUmakefile Src/Base/Make.package Tools/C_scripts/mkconfig.py Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 554c3141bad05b725982faae60f70035b1d52c6a Author: Weiqun Zhang Date: Fri Apr 21 18:04:45 2017 -0700 add a top level GNUmakefile for building libamrex GNUmakefile Src/Amr/Make.package Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 110ab0ee3e77fdaa830c6b86231e454f505fb178 Merge: 397801364 78a0f8b14 Author: Andrew Myers Date: Fri Apr 21 17:33:29 2017 -0700 Merging development into integer_soa_data commit 78a0f8b143c2f5e28aa35d2808ec447666872906 Merge: 0e1670085 547e213b4 Author: Andrew Myers Date: Fri Apr 21 17:19:44 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 0e1670085c614a152698378dcf4cd7b210e15da6 Author: Andrew Myers Date: Fri Apr 21 17:19:29 2017 -0700 Make Reset() return the particle location data. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit fdf2aa7639d22f202d09e16de50104f44972c931 Author: Dan Graves Date: Fri Apr 21 16:02:08 2017 -0700 starting to wade into EBLevelDataOps. I managed to cut out everything I think is redundant and just keep what I think is useful. Src/EBAMRTools/AMReX_EBLevelDataOps.H Src/EBAMRTools/AMReX_EBLevelDataOps.cpp Src/GeometryShop/AMReX_EBCellFAB.H Src/GeometryShop/AMReX_EBCellFAB.cpp Src/GeometryShop/AMReX_EBLevelRedist.cpp commit 397801364b593de91ec2a032b1b4a36f3e203692 Author: Andrew Myers Date: Fri Apr 21 15:03:43 2017 -0700 fix dumb mistake. Src/Particle/AMReX_ParticleContainerI.H commit 4cc16e6279519b45694d61174011438aa975ae8a Merge: e79c1d0e5 24541b2d8 Author: Andrew Myers Date: Fri Apr 21 12:57:34 2017 -0700 Merge branch 'integer_soa_data' of bitbucket.org:berkeleylab/amrex into integer_soa_data commit e79c1d0e5d1de07ff0c6e43e231e053d4dd361ef Author: Andrew Myers Date: Fri Apr 21 12:57:13 2017 -0700 rename these variables. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 0e7fa93315c99f48c282b30b3db818a29c62b7bb Author: Andrew Myers Date: Fri Apr 21 12:52:40 2017 -0700 reset this to TRUE Tests/Particles/GNUmakefile commit 24541b2d8d2ac7cd84a87d8b4868b44add38dfc3 Merge: 186e04e85 547e213b4 Author: Andrew Myers Date: Fri Apr 21 12:38:01 2017 -0700 Merge branch 'development' into integer_soa_data commit 186e04e85bce070d8c02dbffeb78d0764c96c613 Author: Andrew Myers Date: Fri Apr 21 12:15:18 2017 -0700 change the struct-of-array interface to make it harder to make mistakes. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Tests/Particles/main.cpp commit 0eaba419d1d239643e2bc82acbffe00308c5bb2b Author: Andrew Myers Date: Fri Apr 21 10:51:33 2017 -0700 Fix bug in assert statements. Src/Particle/AMReX_ParticleContainerI.H commit 547e213b4070888c68c39df3ce754318ef9b450d Merge: 436323abd b61031cd7 Author: Dan Graves Date: Fri Apr 21 17:17:08 2017 +0000 Merged in dtg_branch (pull request #25) Dtg branch Approved-by: Weiqun Zhang commit b61031cd7f7cef54c8946a8b7107a8a5d97ffd69 Merge: 4224d320b 436323abd Author: Dan Graves Date: Fri Apr 21 09:50:42 2017 -0700 getting the latest from the development branch commit 436323abda6efe8b53c030e02140f5b5ab96c6ac Author: Weiqun Zhang Date: Fri Apr 21 08:58:30 2017 -0700 add default move constructor to MFIter Src/Base/AMReX_MFIter.H commit ab66f824b98ba6f0480a7b1292362b368810df83 Author: Andrew Myers Date: Thu Apr 20 17:23:14 2017 -0700 Update test of the particle struct-of-arrays to also test the integer components. Src/Particle/AMReX_ParticleContainerI.H Tests/Particles/GNUmakefile Tests/Particles/main.cpp commit 4a7a81b9fa96c662c233d23ef13f756e59f9c64c Author: Andrew Myers Date: Thu Apr 20 17:04:48 2017 -0700 Add support for integer particle stored in the struct-of-arrays style. Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H commit c0d4adafb6c5c3f680da1ea8391d3c209fa74608 Author: Weiqun Zhang Date: Thu Apr 20 16:19:58 2017 -0700 add new MFIter constructors that take BoxArray and DistributionMapping Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp commit 4224d320bc816e4725bf13cbe3b65e06670c724a Author: Dan Graves Date: Thu Apr 20 15:44:33 2017 -0700 after some bug fixes, we now have working, single-level redistribution. Src/EBAMRTools/AMReX_MeshRefine.cpp Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_EBLevelGrid.cpp Src/GeometryShop/AMReX_EBLevelRedist.cpp Tests/GeometryShop/regression/Backtrace.rg_0_rl_0 Tests/GeometryShop/regression/GNUmakefile Tests/GeometryShop/regression/Make.package Tests/GeometryShop/regression/bl_prof/bl_call_stats_D_00000 Tests/GeometryShop/regression/bl_prof/bl_call_stats_H Tests/GeometryShop/regression/bl_prof/bl_call_stats_H_00000 Tests/GeometryShop/regression/bl_prof/bl_comm_prof_D_00000 Tests/GeometryShop/regression/bl_prof/bl_comm_prof_H Tests/GeometryShop/regression/bl_prof/bl_comm_prof_H_00000 Tests/GeometryShop/regression/bl_prof/bl_prof_D_00000 Tests/GeometryShop/regression/bl_prof/bl_prof_H Tests/GeometryShop/regression/levelRedistTest.cpp Tests/GeometryShop/regression/levelredist.inputs commit 943d5288096c4db416391a2601c385a79df8e44b Author: Andrew Myers Date: Thu Apr 20 13:17:17 2017 -0700 rename the particle template parameters to be more expressive. Src/AmrCore/AMReX_AmrParticles.H Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H commit 5c97a154ec9d83ec2cc5d061d57b07d3c7262434 Author: Dan Graves Date: Thu Apr 20 11:31:44 2017 -0700 Porting over EBLevelRedist was trickier than I thought. It compiles now. On to testing Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBLevelRedist.H Src/GeometryShop/AMReX_EBLevelRedist.cpp Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntVectSet.cpp Src/GeometryShop/AMReX_LayoutData.H Src/GeometryShop/Make.package commit baa41a5f6f11c49ff45e0be89783d4d7a344c2a3 Author: Andrew Myers Date: Wed Apr 19 20:25:19 2017 -0700 If you restore the random state using more threads than you saved it with, give the RNG a sensible seed on the new threads. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 935398fca9568bf35729a60d1bcc1a04c2f8725e Merge: 24283734d d395cae19 Author: Andrew Myers Date: Wed Apr 19 18:05:23 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 24283734ddada5aed7b294ccf6691eb3e4a532b3 Author: Andrew Myers Date: Wed Apr 19 18:04:50 2017 -0700 A hopefully more portable way of saving the random state. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit b5473e3996c30703e181a1ad39485f854f88e957 Author: Andrew Myers Date: Wed Apr 19 17:23:50 2017 -0700 use critical here instead of atomic capture on older versions of gcc Src/Particle/AMReX_ParticleI.H commit c61bd4f70cc69b174adf7b44b32993b4d6c57600 Author: Andrew Myers Date: Wed Apr 19 17:16:18 2017 -0700 replace the the current implementation of the thread-safe RNG with an array-of-generators, since clang doesn't support thread_local. Src/Base/AMReX_Utility.cpp commit d395cae199d33c5b4f113c384f08355eec8f26e4 Merge: 0e1bf7ade 3103189b8 Author: Michael Zingale Date: Wed Apr 19 23:07:37 2017 +0000 Merged in mzingale/amrex/development (pull request #24) add more compilation info to the build info routines commit df5b238bc6fd09311af7f18275c3eb2f4fd9f2dd Author: Dan Graves Date: Wed Apr 19 15:58:39 2017 -0700 RedistStencil now compiles. Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBLevelGrid.H Src/GeometryShop/AMReX_EBLevelRedist.H Src/GeometryShop/AMReX_EBLevelRedist.cpp Src/GeometryShop/AMReX_RedistStencil.H Src/GeometryShop/AMReX_RedistStencil.cpp Src/GeometryShop/Make.package commit 1b39022e2ed63fc02b30335d3cbd0e30375c6fec Author: Dan Graves Date: Wed Apr 19 15:32:36 2017 -0700 ported over the most important bits of EBArith. I only kept the bits that did not involve communication. The full level stuff I will leave to EBLevelDataOps (previously they had a lot of redundant functionality) Src/GeometryShop/AMReX_EBArith.H Src/GeometryShop/AMReX_EBArith.cpp commit 3103189b8def123ce44feee5834b6bbe72c58eeb Author: Michael Zingale Date: Wed Apr 19 17:50:20 2017 -0400 clean things up considerably Tools/C_scripts/makebuildinfo_C.py commit 0e1bf7ade60093f179bc68f162f6dcbbbf294d0b Merge: 3df179252 60f59307e Author: Andrew Myers Date: Wed Apr 19 14:46:51 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 3df179252493d64f58abcb741aa47b3ac7d02344 Author: Andrew Myers Date: Wed Apr 19 14:46:38 2017 -0700 Break up the short-range particle container into multiple files. Tutorials/ShortRangeParticles/Make.package Tutorials/ShortRangeParticles/ShortRangeParticleContainer.H Tutorials/ShortRangeParticles/ShortRangeParticleContainer.cpp Tutorials/ShortRangeParticles/main.cpp commit 4f35daf7625cf57909383507f7d950ad25a63c22 Author: Michael Zingale Date: Wed Apr 19 17:29:44 2017 -0400 more compiler options Tools/C_scripts/AMReX_buildInfo.H Tools/C_scripts/makebuildinfo_C.py commit 60f59307e45461cfd4697163a438c4870688ca0c Author: Andy Nonaka Date: Wed Apr 19 13:48:10 2017 -0700 revert last commit - this affects things in codes I wasn't aware of which assumed specifically dimensioned strings Src/F_BaseLib/fabio.f90 commit db1485453123c23e7a3de92941436e009ada8c4f Merge: 7c96d10d4 e1b6ac383 Author: Andy Nonaka Date: Wed Apr 19 13:32:22 2017 -0700 Merge branch 'development' of https://bitbucket.org/berkeleylab/amrex into development commit 7c96d10d47b5d62ab4351ac56ef79b0a408aba52 Author: Andy Nonaka Date: Wed Apr 19 13:32:07 2017 -0700 FABIO_MAX_VAR_NAME = 64 Src/F_BaseLib/fabio.f90 commit e1b6ac3833edbb45f96bd6defbc973176c69ef54 Merge: 78f2b0074 da95f7301 Author: Andrew Myers Date: Wed Apr 19 11:05:59 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 78f2b0074b7086cee16b1d5347474aa1ddd2d0b8 Author: Andrew Myers Date: Wed Apr 19 11:05:45 2017 -0700 Save and restore the state of the random number generator using an Array of ulongs. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit da95f7301ce22f87c4c4925d23b8479ae4e6741a Author: Weiqun Zhang Date: Tue Apr 18 19:50:43 2017 -0700 must include BaseFab header in TypeTraits otherwise it may give wrong results if the type is incomplete Src/Base/AMReX_TypeTraits.H commit 7e7b2b5147e2c4c1c1b634c551dd5870d732c2dd Author: Weiqun Zhang Date: Tue Apr 18 17:40:47 2017 -0700 need to include otherwise gcc 6 won't compile Src/Particle/AMReX_Particles.H commit e5a59a3c2fadd85da4f8737c79ce99bd29006aa7 Author: Andrew Myers Date: Tue Apr 18 17:31:27 2017 -0700 update the dependencies of this particle test, now that additional packages are required. Tests/Particles/GNUmakefile commit b72c25902103ae48829e2a8d93805a99c0b4b22d Author: Andrew Myers Date: Tue Apr 18 17:30:31 2017 -0700 no need to do this now - the random number generator will get different seeds on different threads by default. Src/Particle/AMReX_ParticleContainerI.H commit a54a8b8f6de14fc1bae830662ce6450086d6d092 Author: Andrew Myers Date: Tue Apr 18 16:03:38 2017 -0700 fix MoveRandom after changes to RNG stuff. Src/Particle/AMReX_ParticleContainerI.H commit 96a120f1cc14c5daeb8e095e85539beaa7b955a5 Author: Weiqun Zhang Date: Tue Apr 18 12:40:33 2017 -0700 move the specialization of IsBaseFab into AMReX_TypeTraits Src/Base/AMReX_BaseFab.H Src/Base/AMReX_TypeTraits.H commit bfaf74e444febeaa040148e43d6b168e1b6df17b Author: Andrew Myers Date: Tue Apr 18 15:39:05 2017 -0700 remove AMReX's C++ implemention of the Mersenne twister in favor of the one in C++11. Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp commit 001ab243211a1add544575f9491a42d3a14d49d7 Author: Weiqun Zhang Date: Tue Apr 18 10:13:33 2017 -0700 update cmake Src/Base/CMakeLists.txt Src/Base/Make.package commit b4ee6bae82cef6f6bacbca79b13508994ec7ffeb Author: Weiqun Zhang Date: Tue Apr 18 10:05:24 2017 -0700 enable_if a number of FabArray functions that make senses only if FAB is really a BaseFab Src/Base/AMReX_FabArray.H commit db9287dd369e072d1cce19721d8d64dbd7777a0a Author: Weiqun Zhang Date: Tue Apr 18 09:28:23 2017 -0700 add AMReX_TypeTraits for SFINAE Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_TypeTraits.H commit be1bae59ee1685cd4b0a594196f68b3113923bf7 Author: Dan Graves Date: Mon Apr 17 16:08:53 2017 -0700 started porting over redistribution (on a single level) objects Src/GeometryShop/AMReX_RedistStencil.H Src/GeometryShop/AMReX_RedistStencil.cpp commit f6ee03cb4ebd0d49b3aa46a9292efaabadfdd380 Author: Dan Graves Date: Mon Apr 17 14:33:54 2017 -0700 fixed bug in MeshRefine test. Seems to work fine now. Src/GeometryShop/AMReX_EBFluxFAB.H Tests/EBAMRTools/regression/meshref.inputs Tests/EBAMRTools/regression/simpleMeshRefine.cpp commit 06524577379bcb5a60ad5d94c0229872c6414033 Author: Weiqun Zhang Date: Mon Apr 17 13:12:50 2017 -0700 move MakeType to a new header Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_MakeType.H Src/Base/CMakeLists.txt Src/Base/Make.package commit 6cf88c00ae58ee757e9a58fa677c09f7c664725d Merge: c889ed276 df05600dd Author: Andrew Myers Date: Mon Apr 17 13:01:23 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit c889ed276b108df25e4fe6ef37bb26be6a6a8c1c Author: Andrew Myers Date: Mon Apr 17 13:00:55 2017 -0700 Use the c++11 random number generator here. Src/Particle/AMReX_ParticleInit.H commit df05600dd95ee06e1c383271f70dc452ea746f39 Author: Weiqun Zhang Date: Mon Apr 17 11:15:16 2017 -0700 add new make_alias constructor for MultiFab and iMultiFab Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp commit 39648a9dc64a79b8d09bad014b0dfb210a6dfc15 Author: Weiqun Zhang Date: Mon Apr 17 10:54:49 2017 -0700 add a new FabArray constructor for making alias; I think it's very confusing to make a deep copy with constructor so make_deep_copy is not support for FabArray Src/Base/AMReX_FabArray.H commit 3afa9e6b92673ca4ced6516b071941fec221ee04 Author: Dan Graves Date: Mon Apr 17 10:41:22 2017 -0700 adding debugging tools so I can figure out what is wrong with AMReX_MeshRefine Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_EBDebugDump.H Src/GeometryShop/AMReX_EBDebugOut.H Src/GeometryShop/AMReX_EBDebugOut.cpp Src/GeometryShop/AMReX_EBFaceFAB.H Src/GeometryShop/AMReX_EBFaceFAB.cpp Src/GeometryShop/AMReX_EBFluxFAB.H Src/GeometryShop/Make.package commit 8395b4903de3b299d8ff8aa56360c954f068f8c8 Author: Dan Graves Date: Mon Apr 17 10:40:58 2017 -0700 added face-centered stuff Src/GeometryShop/AMReX_BaseEBFaceFAB.H Src/GeometryShop/AMReX_BaseEBFaceFABI.H commit 90be4f1e26ef9d752766e10177c7c20149aa6f9e Author: Weiqun Zhang Date: Mon Apr 17 09:45:35 2017 -0700 add StatusType to FabArray Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.cpp commit 4c618bed51612a090b86a7b9a390dab8da2181c9 Author: Marc Day Date: Sun Apr 16 22:15:48 2017 -0700 Partial fix of CMakeLists.txt files - still need to fix mpi CMakeLists.txt Tutorials/MultiGrid_C/CMakeLists.txt Tutorials/MultiGrid_C/main.cpp commit d48d96dbd3f1c882617d19e716a08529319107b7 Author: Weiqun Zhang Date: Sun Apr 16 18:49:47 2017 -0700 new IArrayBox constructor for making alias or deep copy Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp commit 6ffdfcd180de82befd00404e4433828c4ec18c36 Author: Weiqun Zhang Date: Sun Apr 16 18:36:27 2017 -0700 new FArrayBox constructor for make alias or deep copy Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp commit 4f564c4ab6ab2f67e64ef3e8029f2ee02d690baa Author: Andrew Myers Date: Sat Apr 15 20:38:26 2017 -0700 a couple of changes to the InitRandomPerBox routine. Src/Particle/AMReX_ParticleInit.H commit 997d3fa38684a763ab0d83201679a3625f44ecb0 Author: Ann Almgren Date: Sat Apr 15 19:25:25 2017 -0700 Clarify the comment and error message Src/Particle/AMReX_ParticleInit.H commit 83285a517b6630177b477a948d98036bdaae3adc Author: Ann Almgren Date: Sat Apr 15 18:59:20 2017 -0700 Add a new initialization routine for particles -- InitRandomPerBox -- which is used when we want the particle distribution to be random within a box but we want to be able to replicate the box exactly for a scaling study. Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H commit c0b87801dc49967ebf6dd925eb49bd2144e41821 Author: Weiqun Zhang Date: Sat Apr 15 07:56:57 2017 -0700 mod migration script for IAMR Fortran code Tools/Migration/step-7-bindc/bindc.sh commit 46e6ac1af25df8262945695b89ccb03a0bdabb2a Author: Andrew Myers Date: Fri Apr 14 15:50:08 2017 -0700 ParmParse inputs. Tutorials/ShortRangeParticles/main.cpp commit 890e4d2307d651a2701f93c193f3ca15c4b6fe4e Author: Andrew Myers Date: Fri Apr 14 14:30:05 2017 -0700 updating this thing to work in 3D as well. Tutorials/ShortRangeParticles/main.cpp commit 50687c4b5bb2ef5b72e6fb5eb82d58a7d7d6a808 Merge: 1393697ff 4b26e1a03 Author: Andrew Myers Date: Fri Apr 14 13:09:46 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 1393697ffcb3133aabcf62c5dd4da6e268d4dba9 Author: Andrew Myers Date: Fri Apr 14 13:09:22 2017 -0700 add 3d versions of fortran routines. Tutorials/ShortRangeParticles/main.cpp Tutorials/ShortRangeParticles/short_range_2d.f90 Tutorials/ShortRangeParticles/short_range_3d.f90 commit 15e95ae5635f6e7bf4e1475953324188b3ecf500 Author: Andrew Myers Date: Fri Apr 14 12:59:06 2017 -0700 renaming / reorganization. Tutorials/ShortRangeParticles/Make.package Tutorials/ShortRangeParticles/main.cpp Tutorials/ShortRangeParticles/short_range_2d.f90 Tutorials/ShortRangeParticles/short_range_F.H commit b691edfd772c3ee4f38d1a70025f3b5f203fc613 Author: Andrew Myers Date: Fri Apr 14 12:55:18 2017 -0700 removing some now un-needed code. Tutorials/ShortRangeParticles/main.cpp commit 70d596f33d147a1d7572e156afa5be50ca0ea23a Author: Andrew Myers Date: Fri Apr 14 12:48:24 2017 -0700 move the particle time integration to a fortran subroutine. Tutorials/ShortRangeParticles/compute_force_2d.f90 Tutorials/ShortRangeParticles/compute_force_F.H Tutorials/ShortRangeParticles/main.cpp commit 4b26e1a039bb501e1b47d9dbaa36519132d8df49 Author: Weiqun Zhang Date: Fri Apr 14 09:48:00 2017 -0700 new BaseFab constructor that makes either an alias or a deep copy Src/Base/AMReX_BaseFab.H commit 64fe93da0cd9d27dc0e7dbec006dde0e33950702 Author: Dan Graves Date: Fri Apr 14 11:04:34 2017 -0700 EBIS coarsening issues resolved for now. BoxArray's ostream operator does seem to have weird integer overflow issues, however. Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Tests/EBAMRTools/regression/meshref.inputs commit 3f939c41bdd1bd9dec7c25db3ed6f370304edcf1 Author: Dan Graves Date: Fri Apr 14 10:43:48 2017 -0700 made another destructor virtual to get the compiler to shut up. Src/Base/AMReX_BaseFab.H commit 1f0eb3a06109ed20fd780f6500718cb64a3a8952 Author: Andrew Myers Date: Fri Apr 14 09:52:21 2017 -0700 more comments. Tutorials/ShortRangeParticles/main.cpp commit e232c96bbebee3cc5c54bf10caf4b0e547da2e67 Merge: 84e54a63d 50a278a1e Author: Andrew Myers Date: Thu Apr 13 23:08:37 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 84e54a63da80b082a9d8a93751fa1f21cfd239c1 Author: Andrew Myers Date: Thu Apr 13 23:08:05 2017 -0700 MPI communication for ghost particles working now. Tutorials/ShortRangeParticles/main.cpp commit f1617e4f61f45e3e45e2f9ce1b8a01c7ce9e2cae Author: Dan Graves Date: Thu Apr 13 15:39:47 2017 -0700 did I forgot to add these? Src/EBAMRTools/AMReX_MeshRefine.H Src/EBAMRTools/AMReX_MeshRefine.cpp commit 790c8d65ca4795f8cab8ecbe48019c8c46865d8a Author: Dan Graves Date: Thu Apr 13 15:39:06 2017 -0700 made one base constructor virtual to shut the compiler up. I also coded up a standalone meshrefine and a test from Weiqun's example. EBIndexSpace coarsening is currently having some problems. Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/Base/AMReX_IArrayBox.H Src/EBAMRTools/Make.package Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_IntVectSet.cpp Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/Make.package Tests/EBAMRTools/regression/meshref.inputs Tests/EBAMRTools/regression/simpleMeshRefine.cpp commit 5d7e3e0f162bfb6574456645ac4b50a872918742 Author: Andrew Myers Date: Thu Apr 13 14:27:20 2017 -0700 first stab at getting the MPI comm stuff working. Tutorials/ShortRangeParticles/main.cpp commit 50a278a1e43cc886a789c6bfb55eee8320654af7 Author: Weiqun Zhang Date: Thu Apr 13 14:00:43 2017 -0700 add average_node_to_cellcenter Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_F.H commit 6aebb93d191a866af457ea7b11f27f1a53be7aa6 Merge: 4ee2ab0b1 cfea73f6a Author: Andrew Myers Date: Thu Apr 13 11:22:08 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 4ee2ab0b1b8d70ce44f3b8ecbc990333852b41b8 Author: Andrew Myers Date: Thu Apr 13 11:21:53 2017 -0700 more functionality for the particle neighbors tutorial. this works in serial now. Tutorials/ShortRangeParticles/Make.package Tutorials/ShortRangeParticles/compute_force_2d.f90 Tutorials/ShortRangeParticles/compute_force_F.H Tutorials/ShortRangeParticles/main.cpp commit fdedab9b59869a8de349f1613696ed14016971cd Merge: a550b7f8e cfea73f6a Author: Dan Graves Date: Thu Apr 13 10:23:23 2017 -0700 merging with dev branch commit cfea73f6ac9b37b554e564be7c88cd78a6fb597b Author: Weiqun Zhang Date: Thu Apr 13 10:20:11 2017 -0700 fix assertion Src/AmrCore/AMReX_AmrMesh.H commit 2c28ebb5de30c74b7afa2f98732163de72488bd1 Author: Andrew Myers Date: Wed Apr 12 23:20:13 2017 -0700 more work on the ghost particle stuff. Tutorials/ShortRangeParticles/main.cpp commit c5227f28bce49c5abfd7e23a5683cd234700fbbc Merge: 6b7de322b fb1bce420 Author: Andrew Myers Date: Wed Apr 12 17:01:16 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 6b7de322b00a2c66d1fed1b0e452b30896d1229f Author: Andrew Myers Date: Wed Apr 12 17:00:50 2017 -0700 Some work towards neighbor computation for particles that see short-range forces. Src/Particle/AMReX_ParticleContainerI.H Tutorials/ShortRangeParticles/GNUmakefile Tutorials/ShortRangeParticles/Make.package Tutorials/ShortRangeParticles/main.cpp commit fb1bce4201b4c7b897395731f8d6491c121374a6 Author: Weiqun Zhang Date: Wed Apr 12 16:07:42 2017 -0700 Box: remove the lengthy overflow check because I don't think it could happen on exascale machines unless they run Windows Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp commit a550b7f8edd3165f81f015ef169ee4c26bf6ba12 Merge: f3aca12c6 0a9ce5599 Author: Dan Graves Date: Wed Apr 12 15:56:15 2017 -0700 merging to get new fancier mesh generator commit 0a9ce5599a509c700e3c880aa7b69b66d3d81f87 Author: Weiqun Zhang Date: Wed Apr 12 15:41:02 2017 -0700 clean up the MeshRefinement example Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Tutorials/MeshRefinement/main.cpp commit f3aca12c65a8b0e21381e780b6fa0231c345ec65 Author: Dan Graves Date: Wed Apr 12 15:29:34 2017 -0700 EBAMRTools first tool now compiles. Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Src/GeometryShop/AMReX_AllRegularService.H Src/GeometryShop/AMReX_AllRegularService.cpp Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_EBCellFAB.H Src/GeometryShop/AMReX_EBCellFactory.H Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/Make.package Tests/EBAMRTools/regression/aggpwlfpTest.cpp commit 84d80a01c9cc27b2a34a602ab1204fa7431419e7 Author: Weiqun Zhang Date: Wed Apr 12 14:40:10 2017 -0700 Geometry: allow default coordinates and let passed in paramters take precedence over parmparse parameters Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp commit a795ac8ca68c4c504185f348d07f09805d8884aa Author: Weiqun Zhang Date: Wed Apr 12 14:20:31 2017 -0700 AmrMesh: add some set functions Src/AmrCore/AMReX_AmrMesh.H commit 38ceee3da8750ff4a9c18484b9bf1745cba0ab9f Author: Weiqun Zhang Date: Wed Apr 12 13:41:17 2017 -0700 add assertion Src/Base/AMReX_MFIter.cpp commit e3f1e105192b7f8e1fcf090b0c96182a434bf2dc Author: Weiqun Zhang Date: Wed Apr 12 13:12:37 2017 -0700 minor optimization Src/Base/AMReX_ParmParse.cpp commit 7d51f01bf96d19fbcb3ca2c8a3f87d9133d9f30f Author: Weiqun Zhang Date: Wed Apr 12 13:09:49 2017 -0700 move BoxIterator from GeometryShop to Base Src/Base/AMReX_BoxIterator.H Src/Base/AMReX_BoxIterator.cpp Src/Base/AMReX_RealVect.H Src/Base/CMakeLists.txt Src/Base/Make.package Src/GeometryShop/Make.package commit 22983df2250a62a18f89146f204c22dbe5621faf Author: Weiqun Zhang Date: Wed Apr 12 12:58:53 2017 -0700 move RealVect from GeometryShop to Base Src/Base/AMReX_RealVect.H Src/Base/AMReX_RealVect.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Src/GeometryShop/Make.package commit b8eb01ba9a8ab087b474ffb8415efc2f73e14732 Author: Dan Graves Date: Wed Apr 12 11:18:06 2017 -0700 more fixes to get all the geometryshop tests working again (now with hybrid EBCellFAB) Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseIndex.H Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp commit 93585e48920e6b2b0f765bffa2cf740c7c97284d Merge: fafa273ef 0c2393fe2 Author: Dan Graves Date: Wed Apr 12 11:02:13 2017 -0700 merging with deveopment branch because I have to add a function to BaseFab commit fafa273efd9d3b0dea4f9c6b7a2cc6bf5bcc8176 Author: Dan Graves Date: Wed Apr 12 11:00:35 2017 -0700 tweaking test to fit changing API (EBCellFAB is no longer just a wrapper) Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp commit 5ff340024817c6cf002010e10e9231650717503d Author: Dan Graves Date: Wed Apr 12 10:30:46 2017 -0700 changed argument names to make the API less of a lie Src/GeometryShop/AMReX_EBGraph.H commit 3280897897b74cb5cd4c4bf068738cb0226cd95d Author: Dan Graves Date: Wed Apr 12 10:29:56 2017 -0700 fixed this test to reflect API changes Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp commit 0c2393fe2aa41de306cc4ef5f9a539ab50d93939 Author: Weiqun Zhang Date: Tue Apr 11 16:55:02 2017 -0700 add clang-analyze and clang-tidy to make Tools/GNUMake/Make.rules commit 00266c435f87bcedd98094d31f44e062540dd2ae Author: Dan Graves Date: Tue Apr 11 16:07:40 2017 -0700 had to put in real EBCellFAB and associated stuff Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H Src/GeometryShop/AMReX_BaseEBCellFAB.H Src/GeometryShop/AMReX_BaseEBCellFABI.H Src/GeometryShop/AMReX_EBCellFAB.H Src/GeometryShop/AMReX_EBCellFAB.cpp Src/GeometryShop/AMReX_EBCellFactory.H Src/GeometryShop/AMReX_EBCellFactory.cpp commit ea00075d67c4c932970fbc9dd086dba6a228cfee Author: Weiqun Zhang Date: Tue Apr 11 13:00:38 2017 -0700 add llvm Tools/GNUMake/Make.defs Tools/GNUMake/comps/llvm.mak commit 1e97a545937cde2041b74a29728804ed0299aa74 Author: Weiqun Zhang Date: Tue Apr 11 12:31:57 2017 -0700 add some braces Src/Base/AMReX_ArrayLim.H commit 16322a2dcdeead5d4922ece56f7d373e5e5a6caf Author: Weiqun Zhang Date: Tue Apr 11 10:04:31 2017 -0700 add override Tutorials/AMR_Adv_C/Source/Adv.H commit 99a66ec7bea6fb852813935594d06143d5a5665e Author: Weiqun Zhang Date: Tue Apr 11 10:02:14 2017 -0700 reimplement a few macros so that Clang 4.0.0 is happy. Src/Base/AMReX_ArrayLim.H commit af2758c1551ee0dfb52a1b84c72eea28ba249ef3 Author: Weiqun Zhang Date: Fri Apr 7 12:59:10 2017 -0700 add a new AmrMesh constructor Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit 184d46d4f3d4f5c2ec75f2e8a19c4f26b0b6e08a Merge: bda6e93cd aa8d35cde Author: Max Katz Date: Mon Apr 10 00:53:27 2017 -0400 Merge branch 'development' into gpu commit aa8d35cde8ac01d76c56b4455adb4ab565e23a56 Merge: 247d17d67 d9710d2ae Author: Jon Rood Date: Fri Apr 7 21:05:48 2017 +0000 Merged in jrood-nrel/amrex/nrel_intel_make_fix (pull request #23) Fixing GCC in the make files for NREL machines. Approved-by: Jon Rood commit 247d17d67330b1044332703d1270c871328c0b84 Author: Weiqun Zhang Date: Fri Apr 7 12:53:38 2017 -0700 need to call some initialization functions in one of the AmrMesh constructor Src/AmrCore/AMReX_AmrMesh.cpp commit d9710d2aece3697682eca40be5d382c607586317 Author: Jon Rood Date: Fri Apr 7 10:39:30 2017 -0600 Fixing GCC in the make files for NREL machines. Tools/GNUMake/sites/Make.nrel commit e7a83ae4e0796c95d23c6e401f93b379fa8fa3c2 Author: Jon Rood Date: Fri Apr 7 10:10:57 2017 -0600 Fixing GCC in the make files for NREL machines. Tools/GNUMake/sites/Make.nrel commit adf7842663ed8469808bfc8376e1cb9225584ea6 Merge: bb9a80289 387693a8f Author: Dan Graves Date: Thu Apr 6 15:54:28 2017 -0700 Merge branch 'development' into dtg_branch commit bb9a80289ddfd5b457116c93939d9fbd82108d55 Author: Dan Graves Date: Thu Apr 6 15:53:31 2017 -0700 commit premerge with development branch Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Src/EBAMRTools/Make.package Src/GeometryShop/AMReX_EBLevelGrid.H Tests/EBAMRTools/regression/GNUmakefile Tests/EBAMRTools/regression/Make.package Tests/EBAMRTools/regression/aggpwlfpTest.cpp Tests/EBAMRTools/regression/sphere.inputs Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp commit 387693a8f4d81d270e31f0577ce4f1d9eb2362a8 Merge: af94b1e55 98d66fa81 Author: Jon Rood Date: Thu Apr 6 20:09:05 2017 +0000 Merged in jrood-nrel/amrex/nrel_intel_make_fix (pull request #21) Adding Intel compiler compatiblity into make system for NREL machines. Approved-by: Ray Grout commit 98d66fa8160a60dfa565ddbf488833a1a370a343 Author: Jon Rood Date: Thu Apr 6 13:59:38 2017 -0600 Adding Intel compiler compatiblity into make system for NREL machines. Tools/GNUMake/Make.machines Tools/GNUMake/sites/Make.nrel commit af94b1e55c25ca4a6d9b6fd0a282e45099cddc74 Author: Weiqun Zhang Date: Wed Apr 5 17:12:15 2017 -0700 MeshRefinement test: write a mf with value set to amr level Tutorials/MeshRefinement/main.cpp commit 2278ac01e85e9199bac7407243005580cebfb2e3 Author: Weiqun Zhang Date: Wed Apr 5 17:02:51 2017 -0700 Add an example showing how to generate Amr meshes for testing Tutorials/MeshRefinement/GNUmakefile Tutorials/MeshRefinement/Make.package Tutorials/MeshRefinement/MyAmr.H Tutorials/MeshRefinement/MyAmr.cpp Tutorials/MeshRefinement/main.cpp commit dcf416a658fb39e84fc4c339a357283be04b0e92 Author: Weiqun Zhang Date: Wed Apr 5 15:59:12 2017 -0700 add AmrMesh::SetFinestLevel Src/AmrCore/AMReX_AmrMesh.H commit 6e02eee13877b990eff688f8ea90a7ddbf70341a Author: Weiqun Zhang Date: Wed Apr 5 15:16:03 2017 -0700 add const Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/AmrCore/AMReX_AmrMesh.H commit 4515ea61b5bd04bb0ace3fa48d8f739ac38d9751 Author: Weiqun Zhang Date: Wed Apr 5 13:56:36 2017 -0700 add comments Src/AmrCore/AMReX_AmrMesh.H commit 423a68f9fd12a3477a6ed8897df11fa9895ad233 Author: Weiqun Zhang Date: Wed Apr 5 13:42:48 2017 -0700 make AmrMesh concrete Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp commit 5efe08026ec3096c6a07e8c6f4a73e9f4be22858 Author: Weiqun Zhang Date: Wed Apr 5 10:54:16 2017 -0700 Split AmrCore into two. The new AmrMesh class will allow for more flexible grids generation for testing. Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrMesh.H Src/AmrCore/AMReX_AmrMesh.cpp Src/AmrCore/CMakeLists.txt Src/AmrCore/Make.package commit 4a70ea8378c564f2d48f3a554ec0b304a0f29cbe Author: Weiqun Zhang Date: Tue Apr 4 12:45:21 2017 -0700 add kiryu to CCSE_MACHINES make Tools/GNUMake/Make.machines commit 506da3851402e2ce9849e69571ce16a0b1c031e5 Merge: 5e4c57975 4a4a085d1 Author: Michele Rosso Date: Tue Apr 4 03:38:29 2017 +0000 Merged in mrosso84/amrex/cmake_build_tools (pull request #20) Cmake build tools commit 4a4a085d11849f91cfc7ea875da8dda4e91ffd80 Author: Michele Rosso Date: Mon Apr 3 16:32:03 2017 -0700 Use plt_compare_diff_grids instead of fcompare for cmake-enabled projects Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py commit 30ce48251d06e20bcf01e35e2d04eb502c18e0a6 Author: Michele Rosso Date: Mon Apr 3 16:15:38 2017 -0700 Add plt_compare_diff_grids to cmake build Tools/Postprocessing/F_Src/CMakeLists.txt commit c4a65bcb897619c3af1a9faf333554cf28f0fbbc Author: Dan Graves Date: Mon Apr 3 15:45:57 2017 -0700 As Zhukov said to Eisenhower, If we come to a minefield, our infantry attacks exactly as if it were not there. Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp commit 3415e38c685618958a8ed9403468e0b6f0b86a59 Merge: cc970b1da 5e4c57975 Author: Weiqun Zhang Date: Mon Apr 3 17:18:51 2017 +0000 Merged in development (pull request #19) AMReX 17.04 commit 5e4c5797531b77182803a4664c38e86a0f770cd5 Merge: cc970b1da d86963511 Author: Weiqun Zhang Date: Mon Apr 3 10:12:29 2017 -0700 Merge branch 'development' commit d86963511d92d5c231e041a280b266e10929fea9 Author: Weiqun Zhang Date: Mon Apr 3 09:55:45 2017 -0700 Reimplement BoxArray::RefID, DistributionMapping::RefID and FabArrayBase::BDKey using std::less for pointer comparison. This fixes the undefined behavior in the old implementation. In C++11, std::less is guaranteed to work for pointers (even if operator < does not). Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit f0918844d70a7494bc4a1aa020960be7e726bd64 Author: Weiqun Zhang Date: Sat Apr 1 19:05:00 2017 -0700 have to include MultiFab.H because it's used as template paramter for Array Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 1028a577eeff41bdbcbde089faf28f6ff407d6d0 Author: Ann Almgren Date: Sat Apr 1 17:13:30 2017 -0700 Revert the latest revert. Src/Base/AMReX_MultiFabUtil.H commit 36f6645f03e1c100b7e30b0a628444737479446a Author: Weiqun Zhang Date: Sat Apr 1 15:31:52 2017 -0700 add include back to MulitFabUtil.H Src/Base/AMReX_MultiFabUtil.H commit 215dd0e74fb1c177a38efd8d85b0691c3a6fdce0 Author: Weiqun Zhang Date: Sat Apr 1 10:57:58 2017 -0700 add MultiFab::OverlapMask function that counts how many duplicates are at each point; add new versions of norm1 and norm2 that do not double count for nodal data Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp commit ca777cccdf6436ce87fea7baf7473a06d44c5df1 Author: Weiqun Zhang Date: Sat Apr 1 10:34:36 2017 -0700 add FabArrayBase::ixType() and other minor changes Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp commit 5b2592437eaf1b7ad39e42f49a99daea3f97eacd Author: Weiqun Zhang Date: Fri Mar 31 16:12:22 2017 -0700 fix a new bug in BoxArray::minimalBox Src/Base/AMReX_BoxArray.cpp commit 14e0b225a720f88bc98a9c3a0e721d1a3d50cd4e Author: Weiqun Zhang Date: Fri Mar 31 15:54:56 2017 -0700 use uint64_t instead of long long in initializing snan Src/Base/AMReX_MemPool.cpp commit 0b8afe33f7e597bdf1a0a761df6a468a2ce40ebb Author: Weiqun Zhang Date: Fri Mar 31 15:31:07 2017 -0700 fix some particle initialization functions for 1d and 2d Src/Particle/AMReX_ParticleInit.H commit c75e05c3c034543741d575bff1876f742a4dbdfe Merge: 7043f2a55 9c1442def Author: Weiqun Zhang Date: Fri Mar 31 14:55:03 2017 -0700 Merge branch 'development' into weiqun/cba commit 9c1442defcebf13e397d26feca323765a13adf14 Author: Weiqun Zhang Date: Fri Mar 31 14:53:09 2017 -0700 add a missing header Src/Base/AMReX_FabArrayBase.cpp commit 7043f2a55c5beec3af8734592c82795c761e0d77 Author: Weiqun Zhang Date: Fri Mar 31 14:08:12 2017 -0700 fix a new bug Src/Base/AMReX_BoxArray.cpp commit 3db1dcc246c0a749109ab4c2914d11e437dbbbb5 Author: Weiqun Zhang Date: Fri Mar 31 13:24:29 2017 -0700 minor Src/Amr/AMReX_Amr.cpp commit 6697a6240f6411412285552d004657acb36f2f71 Author: Dan Graves Date: Fri Mar 31 13:17:56 2017 -0700 EBLevelGrid and LayoutData now compile. On to porting the tools that use them Src/Base/AMReX_BoxArray.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArrayBase.H Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_EBLevelGrid.H Src/GeometryShop/AMReX_EBLevelGrid.cpp Src/GeometryShop/AMReX_LayoutData.H Src/GeometryShop/Make.package commit 11605d9bcccdde08b77bba742709838c57a4b6e0 Author: Weiqun Zhang Date: Fri Mar 31 13:09:53 2017 -0700 update FluxRegister for crse_ratio Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Boundary/AMReX_BndryRegister.cpp Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX1_C/writePlotFile.H Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/HeatEquation_EX2_C/writePlotFile.H Tutorials/PGAS_HEAT/main.cpp Tutorials/PGAS_HEAT/writePlotFile.H Tutorials/Tiling_Heat_C/main.cpp Tutorials/Tiling_Heat_C/writePlotFile.H Tutorials/WaveEquation_C/main.cpp Tutorials/WaveEquation_C/writePlotFile.H commit f3def00c19c6049921d9c89b0a698f6e5cc0d47f Author: Ann Almgren Date: Fri Mar 31 11:49:33 2017 -0700 Oops -- that was the wrong file for plt_compare_diff_grids.f90 -- this one should work. Tools/Postprocessing/F_Src/GNUmakefile Tools/Postprocessing/F_Src/plt_compare_diff_grids.f90 commit 237ebf1c136e1e49fca6c7f1ba345201dc8f3a34 Author: Ann Almgren Date: Fri Mar 31 11:41:59 2017 -0700 Build plt_compare_diff_grids.f90 instead of fcompare.f90 Tools/Postprocessing/F_Src/CMakeLists.txt commit 411a2667addb3141d33da9eb81f7bcc2aa5bc4f4 Author: Ann Almgren Date: Fri Mar 31 11:31:33 2017 -0700 Add a new file that can be used to compare plotfiles that have the same problem domain at each level but that have different grids covering that domain. This is particularly useful for comparing different domain decompositions of the same problem Tools/Postprocessing/F_Src/plt_compare_diff_grids.f90 commit 948a505a8bfb75d571c6e2ed0dc1ef1782544c92 Merge: dcd120b3c 23f69a29b Author: Weiqun Zhang Date: Fri Mar 31 11:26:46 2017 -0700 Merge branch 'development' into weiqun/cba commit dcd120b3c59f773e679fec7585b60a1193d26241 Author: Weiqun Zhang Date: Fri Mar 31 11:25:49 2017 -0700 update tiling for crse_ratio Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 94696e6379e59836b08e97651e706a96e20c8d45 Author: Weiqun Zhang Date: Fri Mar 31 10:29:09 2017 -0700 update FillBoundary for crse_ratio Src/Base/AMReX_BoxArray.H Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp commit 24bc848bb51f830c2101071c282c926aed12611d Author: Weiqun Zhang Date: Fri Mar 31 09:58:42 2017 -0700 more changes due to the addition of crse ratio to BoxArray Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit 23f69a29bcb4d87f8256b650ad1405a97d73576f Author: Weiqun Zhang Date: Fri Mar 31 08:35:03 2017 -0700 add a missing header Tutorials/MultiGrid_C/writePlotFile.cpp commit 3390a804ad6eea68d8032f230c1b0555ff6fa9db Author: Weiqun Zhang Date: Fri Mar 31 08:31:09 2017 -0700 fix a typo Src/F_Interfaces/Base/AMReX_multifab_fi.cpp commit 2dede58e208ef003daa547f88dc3d49a29a5a597 Author: Weiqun Zhang Date: Fri Mar 31 08:29:26 2017 -0700 remove a print Src/Base/AMReX_DistributionMapping.cpp commit bbc68bd7bfe62ab126fcc911cf838acf381b372b Merge: e4d242cf0 0d3f8f377 Author: Dan Graves Date: Fri Mar 31 15:25:46 2017 +0000 Merged in dtg_branch (pull request #16) eb sort of works so it should be merged commit e4d242cf0d03b001add79163c7b4b085c3babb52 Merge: 9604329d3 de92bf733 Author: Michele Rosso Date: Thu Mar 30 23:49:44 2017 +0000 Merged in mrosso84/amrex/cmake-mpi-build (pull request #18) Add fextract and fcompare as part of the install commit 961af63f34cc3b58f38781328e8b0fa6d9786b66 Author: Weiqun Zhang Date: Thu Mar 30 16:47:30 2017 -0700 changes due the addition of crse ratio to BoxArray Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit de92bf73359b3dc8075afb7665aab83add4aee45 Author: Michele Rosso Date: Thu Mar 30 16:04:29 2017 -0700 Add fextract and fcompare as part of the install CMakeLists.txt Tools/Postprocessing/F_Src/CMakeLists.txt commit 63575c0af94e0d5c1d97997a6cc7f1014124b96b Author: Weiqun Zhang Date: Thu Mar 30 14:12:08 2017 -0700 BoxArray: moved some functions from .H to .cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit a120d6dd7d48fa2267622284518e34d27f1a1302 Author: Weiqun Zhang Date: Thu Mar 30 13:48:32 2017 -0700 Coarsen the boxes in BoxArray::uniqify Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit 94cb2c6dabb7fde9fd4a60ed3a34f33efd848466 Author: Weiqun Zhang Date: Thu Mar 30 13:00:47 2017 -0700 rm BoxArray::shiftHalf Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit c50feb5ee63e672fd0275b07918c73991afa8f57 Author: Weiqun Zhang Date: Thu Mar 30 11:27:18 2017 -0700 add a special case to IntVect::coarsen Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp commit 24ee14fb28236907aa422a3ff625984228a363d2 Author: Weiqun Zhang Date: Thu Mar 30 10:55:22 2017 -0700 add crse ratio to BoxArray class Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit 0d3f8f37753e3d924b410bbe001f8564a1f416b4 Merge: 37bbd5326 9604329d3 Author: Dan Graves Date: Thu Mar 30 10:53:59 2017 -0700 Merge branch 'development' into dtg_branch commit 37bbd53268767eb7ddfd21e381e82f7181954d5a Author: Dan Graves Date: Thu Mar 30 10:53:48 2017 -0700 committing some temporary stuff so I can merge with development branch Src/GeometryShop/AMReX_EBLevelGrid.H Src/GeometryShop/AMReX_EBLevelGrid.cpp commit ec861b74b3239027acd34d913c643b4bd84c322d Author: Dan Graves Date: Thu Mar 30 10:52:30 2017 -0700 committing some temporary stuff so I can merge with development branch Tests/GeometryShop/sphereEBISBox/sphere.inputs commit 1dc4c5a784e22160405c3f5ca7e800f9b1cf30f5 Author: Dan Graves Date: Thu Mar 30 10:51:52 2017 -0700 committing some temporary stuff so I can merge with development branch Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H commit 68fcf5cf6c4848966c2017316b8df8c5927da7f6 Author: Dan Graves Date: Thu Mar 30 10:49:23 2017 -0700 starting adding multi-level EB objects into EBAMRTools layer Src/EBAMRTools/AMReX_AggEBPWLFillPatch.H Src/EBAMRTools/AMReX_AggEBPWLFillPatch.cpp Src/EBAMRTools/AMReX_EBCoarseAverage.H Src/EBAMRTools/AMReX_EBCoarseAverage.cpp Src/EBAMRTools/AMReX_EBPWLFineInterp.H Src/EBAMRTools/AMReX_EBPWLFineInterp.cpp Src/EBAMRTools/Make.package commit 9604329d3fc9001f96cab1d68b93eb233742ca1a Author: Weiqun Zhang Date: Wed Mar 29 13:12:05 2017 -0700 add FabArray::setDomainBndry Src/Base/AMReX_FabArray.H Src/Base/AMReX_Geometry.H commit f910c05283ea55a288f30981a5bad4ed42d6dc9f Author: Weiqun Zhang Date: Wed Mar 29 12:24:19 2017 -0700 To avoid confusion, remove nodal flag from FabArray constructor. Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_FabArray.H Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/Particle/AMReX_TracerParticles.cpp Tutorials/MultiColor_C/main.cpp commit bc6e7afe8a79ca7bc05b4177a0bc202943c6926e Merge: b7cdd9e7a 2f0f1757b Author: Michele Rosso Date: Thu Mar 30 13:27:31 2017 +0000 Merged in mrosso84/amrex/regtest_fix (pull request #17) Fix regtest bug for builds using cmake Approved-by: Michael Zingale commit b7cdd9e7a68d13b0be5319e930093d44fa228a89 Author: Weiqun Zhang Date: Wed Mar 29 21:05:12 2017 -0700 make clean: rm dSYM directory Tools/GNUMake/Make.rules commit 2f0f1757bcd963a4526ff989d0a70d9aed213a2e Author: Michele Rosso Date: Wed Mar 29 17:37:25 2017 -0700 Fix regtest bug for builds using cmake Tools/RegressionTesting/suite.py commit 46cb7d7fad94cdea835e2f18c90b70ee2a0a5e1d Author: Dan Graves Date: Wed Mar 29 14:27:28 2017 -0700 one more bug fix Src/GeometryShop/AMReX_EBISLevel.cpp commit 27ffe4bbf128408e49263719e0c58cb87fde6944 Merge: e365d87fe 95a3d796b Author: Michele Rosso Date: Wed Mar 29 18:22:36 2017 +0000 Merged in mrosso84/amrex/cmake-mpi-build (pull request #15) Cmake mpi build commit 7a985879da545406cb43f394485f24e1edebb92c Author: Dan Graves Date: Wed Mar 29 10:09:59 2017 -0700 needed to recompute normals and boundary areas after copies (otherwise they can be wrong at box boundaries) Src/GeometryShop/AMReX_EBData.cpp commit 305e60d4761a22175bff58497d6a93890a80d591 Author: Dan Graves Date: Tue Mar 28 15:46:30 2017 -0700 after many bug fixes, I got an actual test that uses EBISLayout and EBIndexSpace and everythign to run correctly. Src/Base/AMReX_Box.H Src/Base/AMReX_DistributionMapping.cpp Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp Tests/GeometryShop/sphereEBISBox/sphere.inputs commit eb6e2737d3516f337fbd1abf624f8c5dad986309 Author: Dan Graves Date: Tue Mar 28 11:41:12 2017 -0700 this unholy union is proceeding according to our fiendish plan Src/GeometryShop/AMReX_BaseIVFactory.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_FlatPlateGeom.H Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Tests/GeometryShop/sphereEBISBox/Make.package Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp commit 28aae44dd63fb5d487ed41c911505638db672b06 Author: Dan Graves Date: Mon Mar 27 15:56:08 2017 -0700 I added a first test for the new classes Tests/GeometryShop/sphereEBISBox/GNUmakefile Tests/GeometryShop/sphereEBISBox/Make.package Tests/GeometryShop/sphereEBISBox/sphere.inputs Tests/GeometryShop/sphereEBISBox/sphereConvTest.cpp commit 8d46deeb5bca2fb8587b1e616b549bcb7ceac0e1 Author: Dan Graves Date: Mon Mar 27 13:04:47 2017 -0700 everything compiles, off to testing the core stuff Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.cpp commit e365d87fe7ca1bd9e57dddb7423eaa8a511f97cc Author: Weiqun Zhang Date: Sat Mar 25 11:06:58 2017 -0700 put temp build directory d/ o/ f/ into tmp_build_dir/ .gitignore Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 38e3c3ab5320f70c5853e29e7e82b8bcc23a8a8e Author: Dan Graves Date: Fri Mar 24 15:56:48 2017 -0700 lots of progress but still many compilation errors. Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBDataFactory.H Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryService.cpp Src/GeometryShop/AMReX_SPMD.cpp Src/GeometryShop/AMReX_VoFIterator.H Src/GeometryShop/AMReX_VoFIterator.cpp Src/GeometryShop/Make.package commit ab0b852c02a2fa7b6c055b6d5f93f4f3a4ca766e Author: Weiqun Zhang Date: Fri Mar 24 13:06:45 2017 -0700 add num_multifabs back, but wrap them inside BL_MEM_PROFILING Src/Base/AMReX_MultiFab.cpp commit a65bd3bbdfae2bbcb2d7fbd2e9d8b50473f70fd5 Merge: 39f9cdaaa 4ea636f20 Author: Weiqun Zhang Date: Fri Mar 24 13:00:47 2017 -0700 Merge branch 'dtg_branch' into development commit 4ea636f20dfbf18d70fddcf14275400141fe85b3 Author: Dan Graves Date: Fri Mar 24 11:43:02 2017 -0700 But wait, there's more! Now EBISLevel has many fewer communication stages in coarsening! Now how much would you pay? Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp commit 39f9cdaaaacfbf8fd84ffce5e6ceaf3bdd04d26b Merge: 025bd1976 023c49017 Author: Weiqun Zhang Date: Fri Mar 24 11:00:07 2017 -0700 Merge branch 'development' into weiqun/split_fabarray commit 025bd1976ed330bafccbd28c90e507944351c69b Author: Weiqun Zhang Date: Fri Mar 24 10:58:12 2017 -0700 update AmrData Src/Extern/amrdata/AMReX_AmrData.cpp commit 36480dd0819e45dd27904caeafda57aa94ca4f88 Author: Weiqun Zhang Date: Fri Mar 24 10:01:09 2017 -0700 update cmake Src/Base/CMakeLists.txt commit 4b8177a4ac8c471961a3d3c2b63edc27dd793913 Author: Dan Graves Date: Thu Mar 23 18:51:15 2017 -0700 redesign of EBISLevel::coarsenVoFs. Now with fewer temporaries and communications. Not available in stores. Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.cpp commit 023c49017574c0a7721db3df59b831a0d75cd0ae Author: Weiqun Zhang Date: Thu Mar 23 17:12:36 2017 -0700 make mpi-2 happy by const_cast Src/Base/AMReX_ParallelDescriptor.H commit 37ef41e3322911474c86c293eda7990a71d67900 Author: Weiqun Zhang Date: Thu Mar 23 16:29:34 2017 -0700 more on splitting FabArray Src/Amr/AMReX_StateData.H Src/Base/AMReX_FACopyDescriptor.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFCopyDescriptor.H Src/Base/AMReX_MFCopyDescriptor.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/Make.package commit 113b72972e9e1daaf801769eaefdeaf2697ad501 Author: Weiqun Zhang Date: Thu Mar 23 13:05:19 2017 -0700 change how gfortran library is linked Tools/GNUMake/comps/gnu.mak commit 07bf61528eb22f75dff9658df264000f8a775e2f Author: Weiqun Zhang Date: Thu Mar 23 11:05:30 2017 -0700 split off MFIter Src/Base/AMReX_FabArray.H Src/Base/AMReX_MFIter.H Src/Base/AMReX_MFIter.cpp Src/Base/Make.package commit d26dee8991d91f1947527bd14ac131a312f1bbd6 Author: Weiqun Zhang Date: Thu Mar 23 10:55:42 2017 -0700 split off FabArrayBase Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp Src/Base/AMReX_FabArrayBase.H Src/Base/AMReX_FabArrayBase.cpp Src/Base/Make.package commit 6f2525f1ac5f96f3da1144a4fa4af085ae085d90 Merge: a7bb4d9c9 8d6e9bf33 Author: atmyers Date: Thu Mar 23 10:53:01 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit a7bb4d9c9de0c1e373fd232c8bf4df2425aa85b7 Author: atmyers Date: Thu Mar 23 10:52:44 2017 -0700 move the num local tiles function to ParticleContainer. Src/Particle/AMReX_Particles.H commit 8d6e9bf336dec1f1ef9081a18c69d1e6ea994329 Author: Weiqun Zhang Date: Thu Mar 23 09:08:16 2017 -0700 make: strip the whitespace around DIM to make the make system more robust Tools/GNUMake/Make.defs commit ebf95fcc4ef2f2b79173cb5240853e144ceb89f4 Author: atmyers Date: Wed Mar 22 16:55:43 2017 -0700 Add a function ParIter to return the total number of tiles. Src/Particle/AMReX_Particles.H commit 7eb4eebf8683e40264a65eb72c7617eeba6b9f66 Author: Dan Graves Date: Wed Mar 22 15:03:57 2017 -0700 still pretty deep in the weeds over here Src/Base/AMReX_Box.H Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_SPMD.cpp commit 95a3d796b771e7a757dac2f5b9efa0e80297ed98 Author: Michele Rosso Date: Wed Mar 22 13:50:55 2017 -0700 Fix cmake mpi-enabled build. Tools/CMake/FindCCSE.cmake commit 92e12d7bc9c8e1a16ded2d19db7221f21aee37eb Author: Dan Graves Date: Tue Mar 21 16:16:11 2017 -0700 slogged my way through EBIndexSpace and EBISLayout--some minor redesign (and some major cleanup) from the Chombo versions Src/GeometryShop/AMReX_EBDataFactory.H Src/GeometryShop/AMReX_EBISBox.H Src/GeometryShop/AMReX_EBISLayout.H Src/GeometryShop/AMReX_EBISLayout.cpp Src/GeometryShop/AMReX_EBISLevel.H Src/GeometryShop/AMReX_EBISLevel.cpp Src/GeometryShop/AMReX_EBIndexSpace.H Src/GeometryShop/AMReX_EBIndexSpace.cpp Src/GeometryShop/AMReX_GeometryService.H Src/GeometryShop/AMReX_GeometryService.cpp Src/GeometryShop/AMReX_SlabService.H Src/GeometryShop/AMReX_SlabService.cpp commit d70a572b1d37c8e5f61c3d41ac5302e31669a95a Author: Michele Rosso Date: Tue Mar 21 14:44:34 2017 -0700 Remove all references to PETSc and X11. Tools/CMake/FindCCSE.cmake commit d74601713d28abcf7ac4e4ef68bfe8ba72e4f4e9 Author: Michele Rosso Date: Tue Mar 21 13:31:51 2017 -0700 Replace "BOXLIB" with "AMREX" in CMake variables name. Src/Base/CMakeLists.txt Src/CMakeLists.txt Tools/CMake/CCSEOptions.cmake commit 9e97a63f0ae536e9af29327bed4959bffb18852e Merge: a2bb657b5 b67797bd4 Author: Weiqun Zhang Date: Tue Mar 21 13:16:08 2017 -0700 Merge branch 'fortran_interface' into development commit b67797bd4796e45d476cec4876505ba0464d3815 Author: Weiqun Zhang Date: Tue Mar 21 13:15:30 2017 -0700 fixe memory leaks Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/my_amr_mod.F90 commit 1b85ddbdf5b92133fc22dd0c82f36811117282fd Author: Weiqun Zhang Date: Tue Mar 21 12:47:45 2017 -0700 fix reflux due grids coveed by fine do not have fluxes computed Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/evolve_mod.F90 commit d3e4853d5bd17a1d297b24c290b0e37c37edf16b Author: Weiqun Zhang Date: Tue Mar 21 11:17:35 2017 -0700 tidy Tutorials/AMR_Adv_CF_octree/Source/evolve_mod.F90 commit 4d15a81cbe0b581da7d74c96cc5437e954d1017f Author: Weiqun Zhang Date: Tue Mar 21 11:03:55 2017 -0700 add octree iterator Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Src/F_Interfaces/Octree/AMReX_octree_mod.F90 Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs.rt Tutorials/AMR_Adv_CF_octree/Source/evolve_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/my_amr_mod.F90 commit 728332558d0987128d4e22a108dfe4f57fff5b95 Author: Weiqun Zhang Date: Tue Mar 21 08:35:43 2017 -0700 build octree leaf nodes Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Src/F_Interfaces/Octree/AMReX_octree_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/evolve_mod.F90 commit a2bb657b507a17b8a0c9ddcce30b012157e38d95 Author: Weiqun Zhang Date: Tue Mar 21 08:28:52 2017 -0700 add a new MFIter::tilebox takes nodal IntVect flag Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp commit 13563d41aa6ae064c84b8bc0fa1975004a7059ee Author: Weiqun Zhang Date: Mon Mar 20 12:48:12 2017 -0700 add F_Interfaces/Octree Src/AmrCore/AMReX_AmrCore.cpp Src/F_Interfaces/Octree/AMReX_octree_fi.cpp Src/F_Interfaces/Octree/AMReX_octree_mod.F90 Src/F_Interfaces/Octree/Make.package Tutorials/AMR_Adv_CF_octree/Exec/Make.Adv Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs.rt Tutorials/AMR_Adv_CF_octree/Source/fmain.F90 commit bfd0c6e33d402f1b44102f1ceb3016c70ca161f1 Author: Dan Graves Date: Mon Mar 20 11:00:07 2017 -0700 EBData, EBISBox, and PolyGeom all compile now. On to writing more tests. Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISBox.cpp Src/GeometryShop/AMReX_PolyGeom.cpp commit 42a5988527c15d9b7e2bdcab1c763977878173bd Author: Weiqun Zhang Date: Mon Mar 20 08:46:43 2017 -0700 AMR_Adv_CF_octree: no subcycling Tutorials/AMR_Adv_CF/Source/averagedown_mod.F90 Tutorials/AMR_Adv_CF_octree/Exec/Make.Adv Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs Tutorials/AMR_Adv_CF_octree/Source/averagedown_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/compute_dt_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/evolve_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/my_amr_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/plotfile_mod.F90 commit f941a90dc456d66026e14d6d3d84ad2f3b277c5a Merge: 93707ec00 1decdcd1d Author: Michael Zingale Date: Fri Mar 17 20:34:23 2017 -0400 Merge branch 'development' of ssh://bitbucket.org/berkeleylab/AMReX into development commit 93707ec00d6c340d6d1010f5090a699e2bd20aa8 Author: Michael Zingale Date: Fri Mar 17 20:34:14 2017 -0400 don't need FCOMP for C++ codes Tools/RegressionTesting/suite.py commit 1decdcd1d8de0e0269f6e307c40dc3b794fe6eeb Merge: 812ed974d e6dd77c09 Author: Michele Rosso Date: Fri Mar 17 23:59:58 2017 +0000 Merged in mrosso84/amrex/cmake-regtest (pull request #14) Enable AMReX regression testing tools to build using CMake. commit fc6e2ab9dbad2685d77fb809369ea13d2f8855b1 Author: Dan Graves Date: Fri Mar 17 16:02:49 2017 -0700 finished EBData/EBISBox/PolyGeom transition --- still working on getting it all to compile Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBISBox.H Src/GeometryShop/AMReX_EBISBox.cpp Src/GeometryShop/AMReX_PolyGeom.H Src/GeometryShop/AMReX_PolyGeom.cpp Src/GeometryShop/Make.package commit e6dd77c099e8cc05bdabcf91f10c4ad9be9c9bc4 Author: Michele Rosso Date: Wed Mar 15 13:52:59 2017 -0700 Enable AMReX regression testing tools to build using CMake. Tools/RegressionTesting/params.py Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_util.py commit ba0dd51248ff18679aa678ac483a078d425d588b Author: Weiqun Zhang Date: Fri Mar 17 12:35:40 2017 -0700 start Tutorials/AMR_Adv_CF_octree Tutorials/AMR_Adv_CF_octree/Exec/Make.Adv Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/Make.package Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/Prob.f90 Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/face_velocity_2d.F90 Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs Tutorials/AMR_Adv_CF_octree/Exec/SingleVortex/inputs.rt Tutorials/AMR_Adv_CF_octree/README Tutorials/AMR_Adv_CF_octree/Source/Make.package Tutorials/AMR_Adv_CF_octree/Source/Src_2d/Make.package Tutorials/AMR_Adv_CF_octree/Source/Src_2d/advect_2d_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/Src_2d/compute_flux_2d.f90 Tutorials/AMR_Adv_CF_octree/Source/Src_2d/slope_2d.f90 Tutorials/AMR_Adv_CF_octree/Source/amr_data_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/averagedown_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/bc_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/compute_dt_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/evolve_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/fillpatch_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/fmain.F90 Tutorials/AMR_Adv_CF_octree/Source/initdata.F90 Tutorials/AMR_Adv_CF_octree/Source/my_amr_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/plotfile_mod.F90 Tutorials/AMR_Adv_CF_octree/Source/tagging_mod.F90 commit 4c5202f716fd9f1cb703ab4d35b8f5d2928bb8b8 Author: Weiqun Zhang Date: Fri Mar 17 12:12:59 2017 -0700 allow blocking factor greater than max_grid_size Src/AmrCore/AMReX_AmrCore.cpp Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp commit 812ed974d647700b02f781203f379047aa383024 Merge: 68b203be8 351780396 Author: Weiqun Zhang Date: Thu Mar 16 14:56:48 2017 -0700 Merge branch 'fortran_interface' into development commit 351780396f3df2f6b3c14dbd9681170beab203a7 Author: Weiqun Zhang Date: Thu Mar 16 14:55:57 2017 -0700 add some assertions to fortran amrcore Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp commit a85e8bca48540eb504ff5203f0986725d6a5f5f3 Author: Weiqun Zhang Date: Thu Mar 16 14:55:31 2017 -0700 assert blocking factor is not too small relative to ref_ratio Src/AmrCore/AMReX_AmrCore.cpp commit f72c8963cdd74ef21029afb0218b856e3b9d2d35 Author: Weiqun Zhang Date: Thu Mar 16 13:59:14 2017 -0700 add string version of amrex::Abort, Warning and Error Src/Base/AMReX.H Src/Base/AMReX.cpp commit 68b203be857cc1ad95769a5b5c377f55735b99b9 Author: Andrew Myers Date: Thu Mar 16 09:45:06 2017 -0700 fixing the Nyx restart test. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H commit deafe834f73735e541277b1e205c8f02adde1a8a Merge: b37731852 3ac792028 Author: Weiqun Zhang Date: Thu Mar 16 08:27:34 2017 -0700 Merge branch 'fortran_interface' into development commit 201b3b0b4e146a004e0cca796100ecfe8e9a0416 Author: Dan Graves Date: Wed Mar 15 16:06:25 2017 -0700 progress made on EBData (and I took it out of the make.package in case people want to compile this branch) Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/Make.package commit 3ac792028efdeb938481a1af44f08d4666837f8b Author: Weiqun Zhang Date: Wed Mar 15 15:03:45 2017 -0700 cleanup Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 commit bde246a71b31d1cc7ec303b6d2077dced7bf52ba Author: Weiqun Zhang Date: Wed Mar 15 14:52:43 2017 -0700 make some variables in fortran geometry static Src/F_Interfaces/Base/AMReX_geometry_fi.cpp Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Tutorials/AMR_Adv_CF/Source/compute_dt_mod.F90 Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit c1de770bd0a8b5ae6ed61bb2c9424095e99a466a Author: Weiqun Zhang Date: Wed Mar 15 13:59:20 2017 -0700 simplify the regrid logic Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp commit 746626ef4fabd3e46140b554ca8f8f3ca7ae6738 Author: Weiqun Zhang Date: Wed Mar 15 12:22:26 2017 -0700 comments Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit b3773185261d64a8fb83a813e705d0c0610e8a70 Author: atmyers Date: Wed Mar 15 12:15:08 2017 -0700 increment particle version string. Src/Particle/AMReX_ParticleI.H commit 693b0e6355d0c1f0be80a4afc147fa444e10c504 Author: Dan Graves Date: Tue Mar 14 16:13:41 2017 -0700 starting the long slog of redesigning ebdata Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/AMReX_EBData.H Src/GeometryShop/AMReX_EBData.cpp Src/GeometryShop/AMReX_EBDataVarMacros.H Src/GeometryShop/Make.package commit 1e850dddf3e48bf3ff314c9ef57942f0b7533b37 Author: Weiqun Zhang Date: Tue Mar 14 16:02:27 2017 -0700 add Fortran fillcoarsepatch and tweak the test problem to test teh new functionality Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 Tutorials/AMR_Adv_CF/Source/tagging_mod.F90 Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp commit 37210f34a7aacf4b132c4c8fbaf9ec325c3c533e Author: Weiqun Zhang Date: Tue Mar 14 14:14:06 2017 -0700 add a new regression test inputs Tutorials/AMR_Adv_CF/Exec/SingleVortex/inputs.rt commit 5cce154cbff8591511de23a39be057868eca6e76 Author: Weiqun Zhang Date: Tue Mar 14 14:12:32 2017 -0700 fix a bug in fortran fillpatch Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 commit 8d487a3a58c01466164d6636b22fc5762beb2ff9 Merge: a54eb9db6 cc72019bc Author: Weiqun Zhang Date: Tue Mar 14 13:23:46 2017 -0700 Merge branch 'fortran_interface' into development commit cc72019bc9cc1d4785c8ad58091869c5fde3f298 Merge: 6021a92d8 8456be21e Author: Weiqun Zhang Date: Tue Mar 14 13:23:08 2017 -0700 Merge branch 'development' into fortran_interface commit a54eb9db69a0aa99472d02ef187a1f951f1d2e54 Merge: 76317eeef ff6e879aa Author: Michele Rosso Date: Tue Mar 14 20:16:28 2017 +0000 Merged in mrosso84/amrex/cmake-installation-fix (pull request #13) Fix issue with Tools not being copied to installation dir. commit ff6e879aa2e4e237b0b712dbbc20c405dd0e240d Author: Michele Rosso Date: Tue Mar 14 13:09:20 2017 -0700 Fix issue with Tools not being copied to installation dir. Src/CMakeLists.txt commit 26b6e179284dd402d2add3b59390bdead56f2926 Author: Dan Graves Date: Tue Mar 14 13:08:10 2017 -0700 sparse data tests pass now Src/GeometryShop/AMReX_BaseIVFABI.H commit 76317eeefae340b519a0f751d4dea6e2fceca600 Author: Michael Zingale Date: Tue Mar 14 15:27:42 2017 -0400 PGI explicitly needs libatomic to link Tools/GNUMake/comps/pgi.mak commit 0f74a7f598749cb97b1ec5eafb327a5edcdaea2b Merge: 8456be21e 32c79bbe9 Author: Michael Zingale Date: Tue Mar 14 16:04:28 2017 +0000 Merged in mzingale/amrex/development (pull request #8) some reporting fixes commit bb3e345d963f6f7c85686326beadc20609d1c17e Author: Dan Graves Date: Mon Mar 13 14:29:13 2017 -0700 got sparse, distributed data test to run to complettion but still failing one of the tests Src/Base/AMReX_BaseFab.H Src/Base/AMReX_MultiFab.cpp Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFactory.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFactory.H Tests/GeometryShop/sparseDataSingleGrid/sparseDataSG.cpp commit 8456be21eef1aed9057c4268846d184e7dc80990 Merge: f3983d56c 8f881ac1b Author: Michele Rosso Date: Mon Mar 13 16:44:58 2017 +0000 Merged in mrosso84/amrex/cmake-regtest (pull request #12) Fix CMake dependencies issue. commit 8f881ac1b66d5d20d1b042452ff8400bdb4e4913 Author: Michele Rosso Date: Fri Mar 10 16:44:35 2017 -0800 Fix CMake dependencies issue. Src/Amr/CMakeLists.txt Src/Boundary/CMakeLists.txt Src/Extern/amrdata/CMakeLists.txt Src/F_BaseLib/CMakeLists.txt Src/Particle/CMakeLists.txt commit f3983d56cc03a7785e3b699b85602b83c16bfbf8 Merge: a17c7a9d2 b81da5bc7 Author: Ray Grout Date: Sat Mar 11 21:40:35 2017 +0000 Merged in regtest_for_gitlabci (pull request #11) Adjust regtest script to allow empty branch and return number of failures as exit code commit b81da5bc7c4a522cba24729d9e4ea2f73c5ddb3d Merge: 9a0c4d3f5 a17c7a9d2 Author: Ray Grout Date: Sat Mar 11 12:01:30 2017 -0700 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into regtest_for_gitlabci commit 9a0c4d3f5cea44a8aa6c6ff33e0994980e2c2699 Author: Ray Grout Date: Sat Mar 11 12:01:07 2017 -0700 Adjust regtest script to allow empty branch and return number of failures as exit code Tools/RegressionTesting/regtest.py commit a17c7a9d20fdb84d234c5d3596792da2755eaf85 Author: atmyers Date: Sat Mar 11 09:33:24 2017 -0800 explicitly mark these methods as override. Src/AmrCore/AMReX_TagBox.H Src/Base/AMReX_MultiFab.H commit 39ab3e5e3b162e9b893344ce9a05c716c2f3a59c Author: atmyers Date: Sat Mar 11 08:20:27 2017 -0800 fix GetArrayData function. Src/Particle/AMReX_ParticleContainerI.H commit bda6e93cdc722e97070f89ae6083efdc140f6d66 Author: Max Katz Date: Sat Mar 11 01:19:57 2017 -0500 Add a CUDArena memory management system using CUDA UM CUDA Unified Memory (available for NVIDIA GPUs of the Kepler generation or newer) allows a single pointer to point to a region of memory that can live either on the CPU or the GPU, and switches back and forth on demand. This is done by declaring a managed memory allocation using cudaMallocManaged, a drop-in replacement for malloc. The CUDArena as currently written is a drop-in replacement for BArena. Credit for the name and original idea belong to Brian Friesen. Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_CUDArena.H Src/Base/AMReX_CUDArena.cpp Src/Base/Make.package commit 059d701ec6f899632a01b4a7085b3d466fe9d91d Author: Max Katz Date: Sat Mar 11 01:12:37 2017 -0500 Allow C/C++ builds with nvcc using USE_CUDA This replaces the CC/CXX executable with nvcc, and sets the nvcc host compiler to what was previously set there (based on COMP). Tools/GNUMake/Make.defs commit 46d250d3e9a993f3a63074069b33da3ae1c1d1fe Merge: 91b6476cd 91523616d Author: atmyers Date: Fri Mar 10 21:43:48 2017 -0800 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 91b6476cd159984c87eb423d6671730c81006f76 Author: atmyers Date: Fri Mar 10 21:43:37 2017 -0800 Adding methods for getting the SoA data Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 91523616d563fc79ddb9d8a0fd40880dabfd071d Merge: 1a6dccc53 bf5562e76 Author: Andrew Myers Date: Fri Mar 10 15:43:24 2017 -0800 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 1a6dccc534a94976450d015b87686025b1729f54 Author: Andrew Myers Date: Fri Mar 10 15:43:09 2017 -0800 Adding fortran CIC interpolation function. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particle_mod_3d.F90 Src/Particle/AMReX_Particles.H Src/Particle/AMReX_Particles_F.H Tests/Particles/AssignDensity/main.cpp Tests/Particles/AssignMultiLevelDensity/inputs Tests/Particles/AssignMultiLevelDensity/main.cpp commit bf5562e765661f02b13cb3b77c0902094c92f491 Author: Weiqun Zhang Date: Fri Mar 10 15:08:59 2017 -0800 have to initialize the data otherwise it may crash due to fpe Src/Boundary/AMReX_FabSet.cpp commit 6021a92d86ae2a6b69306c8dfa5cc6420f333dbc Author: Weiqun Zhang Date: Thu Mar 9 16:20:12 2017 -0800 AMR_Adv_v2: finished reflux Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 commit b8a49fb351c9f97c2a02913e9d26b3626aa0f949 Author: Weiqun Zhang Date: Thu Mar 9 14:17:48 2017 -0800 fix a bug I introduced when FillBoundary was modified a few days ago Src/Base/AMReX_FabArray.cpp commit e8bb5fd1fdf1d09483bae9298ec4715317a89abe Author: Weiqun Zhang Date: Thu Mar 9 14:00:20 2017 -0800 AMR_Adv_CF: start to add flux register Tutorials/AMR_Adv_CF/Source/amr_data_mod.F90 Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 3b56ba5629ba135a413f5c14ef78c74357b4f03b Author: Weiqun Zhang Date: Thu Mar 9 11:10:38 2017 -0800 add fluxregister module Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90 Src/F_Interfaces/AmrCore/AMReX_fluxregister_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fluxregister_mod.F90 Src/F_Interfaces/AmrCore/Make.package commit 67ef5a9c1b07d72936e791f8900cf08780484d73 Author: Weiqun Zhang Date: Thu Mar 9 10:25:17 2017 -0800 AMR_Adv_CF runs Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 58f23d0d10739faff14585ce63aa3a041d7a9abe Author: Weiqun Zhang Date: Thu Mar 9 10:20:33 2017 -0800 fix fortran index Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 commit 7344240d818dec093812f6f2fdcb40c02529febc Author: Weiqun Zhang Date: Thu Mar 9 10:11:43 2017 -0800 refactor fillpatch module Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/Make.package Tutorials/AMR_Adv_CF/Source/amr_data_mod.F90 Tutorials/AMR_Adv_CF/Source/bc_mod.F90 Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 2048bcb27c10c1fd8a909f068af23664eb39a28a Author: Weiqun Zhang Date: Wed Mar 8 18:10:45 2017 -0800 wip: need to fix circular dependency of fortran modules Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 commit e8a6435e6f443f8e2eaaa61ec1672f65ab316f1d Merge: 4b7956e8d 32c90ddc0 Author: Dan Graves Date: Wed Mar 8 15:33:31 2017 -0800 Merge branch 'development' into dtg_branch commit 1e0068a8869139caa396c79494e5d0bc4db500da Author: Weiqun Zhang Date: Wed Mar 8 14:44:39 2017 -0800 wip Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 4b7956e8dc98aaf65138490433c5f0642d53a515 Author: Dan Graves Date: Wed Mar 8 14:39:13 2017 -0800 sparse data holders pass single grid test Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H Src/GeometryShop/Make.package Tests/GeometryShop/sparseDataSingleGrid/GNUmakefile Tests/GeometryShop/sparseDataSingleGrid/Make.package Tests/GeometryShop/sparseDataSingleGrid/sparseDataSG.cpp Tests/GeometryShop/sparseDataSingleGrid/sphere.inputs commit 6237c479104bb861b34b70d7d6d182c9e0357237 Author: Weiqun Zhang Date: Wed Mar 8 11:53:32 2017 -0800 add more virtual functions Src/F_Interfaces/AmrCore/AMReX_amrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 32c90ddc0c56aec0734ee9bdff8c259a76901a65 Author: Weiqun Zhang Date: Wed Mar 8 10:38:21 2017 -0800 do a const_cast in make_aliase Src/Base/AMReX_BaseFab.H commit e01677665bcc5577ff0050e3a06593497927bc86 Merge: 76fd30278 08961bac5 Author: Weiqun Zhang Date: Wed Mar 8 09:59:49 2017 -0800 Merge branch 'development' into fortran_interface commit 08961bac5bafee45b072f3908cf7f9d9ef0b8945 Author: Andrew Myers Date: Tue Mar 7 16:39:50 2017 -0800 More fixes to the build system from Michele Rosso. Tools/CMake/FindCCSE.cmake commit a4108a49f066b5978d23def5ba55334a126da5fe Author: Dan Graves Date: Tue Mar 7 16:21:23 2017 -0800 added (as yet still untested) sparse data holders Src/GeometryShop/AMReX_BaseIFFAB.H Src/GeometryShop/AMReX_BaseIFFABI.H Src/GeometryShop/AMReX_BaseIVFAB.H Src/GeometryShop/AMReX_BaseIVFABI.H commit a59e78737633f177a4e76bf13135f9317c95a8a4 Author: Andrew Myers Date: Tue Mar 7 14:41:50 2017 -0800 Fix CMake build stuff for AMReX. CMakeLists.txt Src/Amr/CMakeLists.txt Src/Base/CMakeLists.txt Src/CMakeLists.txt commit cb011b97248f8b8a3bfda5c14a32eea4a8d3b585 Author: Dan Graves Date: Tue Mar 7 11:18:52 2017 -0800 after figuring out that FabArray and LevelData have somewhat different copy semantics, I was able to get FabArray to behave as advertised Src/GeometryShop/AMReX_EBGraph.cpp Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp commit 072e13bde9886366baf3780d0b6b8b2d3f47479c Merge: 8c0c443cd a48254c66 Author: Ann Almgren Date: Tue Mar 7 11:07:45 2017 -0800 Merge branch 'development' of https://bitbucket.org/berkeleylab/amrex into development commit 8c0c443cdfc692f5d49831af6e26dc0f02cad806 Author: Ann Almgren Date: Tue Mar 7 11:07:17 2017 -0800 Change instances of BoxLib/boxlib/BOXLIB to AMReX/amrex/AMREX. This occurs only in cmake stuff and README* CMakeLists.txt Src/CMakeLists.txt Tools/CMake/AMReX_Version.cmake Tools/CMake/PreprocessAMReXFortran.cmake Tools/CMake/PreprocessAMReXFortran90.cmake Tutorials/README_C Tutorials/README_F commit a48254c66d6eb611ae3ef1e4a5dac34a9371acbe Merge: ac91a939d 163037a1b Author: Andrew Myers Date: Mon Mar 6 17:17:18 2017 -0800 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit ac91a939d23f0d7daba68608a50c3a009f14b074 Author: Andrew Myers Date: Mon Mar 6 17:15:34 2017 -0800 Avoid redefined macro warning in AMReX_INTERP_1D.F Src/AmrCore/AMReX_INTERP_1D.F commit 173b04a76069c3b968c12065f9d680eee03764c3 Author: Dan Graves Date: Mon Mar 6 16:16:25 2017 -0800 working on distributed graph Src/Base/AMReX_BaseFab.H Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_SPMD.cpp Src/GeometryShop/AMReX_SPMDI.H Tests/GeometryShop/ebgraphDistributed/GNUmakefile Tests/GeometryShop/ebgraphDistributed/Make.package Tests/GeometryShop/ebgraphDistributed/ebgraphDist.cpp Tests/GeometryShop/ebgraphDistributed/sphere.inputs commit 163037a1bf7b09be82550e9ad216080e883c0650 Author: Andrew Myers Date: Fri Mar 3 21:47:07 2017 -0800 Capture the return code of the analysis scripts in the test suite. Tools/RegressionTesting/regtest.py commit ecc773a5f74fc52ba67f6e5bde978a7400e91ece Author: Andrew Myers Date: Mon Mar 6 13:54:22 2017 -0800 porting some changes to the CMake stuff from BoxLib to AMReX. CMakeLists.txt Tools/CMake/CCSEOptions.cmake commit cc970b1da64fb00226eb9f77fb67073d78746a09 Merge: 74b0a87e0 da72b07ca Author: Weiqun Zhang Date: Mon Mar 6 17:01:58 2017 +0000 Merged in development (pull request #9) Development commit da72b07ca20ce6fd3a58cc6a7441ebe74b08868d Merge: 23b4c6887 e1dc6e2f9 Author: Andrew Myers Date: Sun Mar 5 10:39:36 2017 -0800 Merge branch 'development' into particle_refactor commit 23b4c6887a525948fc766d220f856b6d9135280f Author: Weiqun Zhang Date: Sun Mar 5 07:35:05 2017 -0800 explicitly mark amrex_deposit_cic public Src/Particle/AMReX_Particle_mod_3d.F90 commit c2e6805d1f41a5330dce3859df839c3b8b19abab Author: Weiqun Zhang Date: Sun Mar 5 07:31:36 2017 -0800 merge SingleLevelWhere into Where Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt commit e1dc6e2f95b131b36640975cfdd434a34654a113 Author: Andrew Myers Date: Fri Mar 3 17:12:28 2017 -0800 Add my computer name to the list of CCSE machines. Tools/GNUMake/Make.machines commit 579a1979daf179eeaa34bc2c92b8c74b230dfe4a Merge: 8fb7da032 72ddd691f Author: Andrew Myers Date: Fri Mar 3 17:09:06 2017 -0800 Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor merging. commit 8fb7da03214ff8c3cc4cebda9f0324cd462c7c0d Author: Andrew Myers Date: Fri Mar 3 17:08:11 2017 -0800 Move the new deposition stuff to the fortran particle module. Src/Particle/AMReX_Deposition_F.F90 Src/Particle/AMReX_Deposition_F.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particle_mod_3d.F90 Src/Particle/AMReX_Particles.H Src/Particle/AMReX_Particles_F.H Src/Particle/Make.package commit 72ddd691f83dc0cfd8dfa8ba669e3d47554d51a3 Author: Weiqun Zhang Date: Fri Mar 3 16:28:16 2017 -0800 fix an assertion and a static constexpr Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H commit 9fc23198510774eeddd83e9e9bdd35e28d93edc5 Author: Dan Graves Date: Fri Mar 3 14:52:51 2017 -0800 added linearization routines to EBGraph. On to seeing if I can get this to work with FabArray Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp commit 1b8c54835604635293d9259c6b480ff0547d4b1c Author: Andrew Myers Date: Fri Mar 3 12:38:25 2017 -0800 fixing restart. Src/Particle/AMReX_ParticleContainerI.H commit 1c3b36f6353d2505454757b8db0d76b129f50048 Author: Andrew Myers Date: Fri Mar 3 11:10:51 2017 -0800 Making redistribute work when lev_min = lev_max (needed by virtual particles). Src/Particle/AMReX_ParticleContainerI.H commit 2a01b0753a93282c0b000a5b2d12a2cc80ae6897 Merge: 24c676c01 74259aa4e Author: Weiqun Zhang Date: Fri Mar 3 10:54:51 2017 -0800 Merge branch 'dtg_branch' into development Conflicts: Src/Base/AMReX_FabArray.H commit 24c676c01ae54988b4c013bb427ad9051171d6f0 Author: Weiqun Zhang Date: Fri Mar 3 10:36:20 2017 -0800 fix conflict Src/Base/AMReX_FabArray.H commit 572de45e7a862b83d3839d2377889d8efca9db82 Author: Weiqun Zhang Date: Fri Mar 3 09:53:13 2017 -0800 fix FillBoundary's cross option Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp commit 297f423b5cc75b0786f28f5e44b9b2ab9e220973 Author: Weiqun Zhang Date: Fri Mar 3 08:33:23 2017 -0800 fix a new bug Src/Base/AMReX_FabArray.H commit 51d9d88410ed3aedd84d3605a8bb83f6618aff1f Author: Weiqun Zhang Date: Thu Mar 2 20:49:06 2017 -0800 fix some issues copyInter Src/Base/AMReX_FabArray.H commit f5693af8469bc777e9221139baea9b7702e1600d Author: Weiqun Zhang Date: Thu Mar 2 17:17:59 2017 -0800 modified FabArray's communication for EB Conflicts: Src/Base/AMReX_FabArray.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp commit 614a6542d947bb990d01dc85705827fcf8ee2bf7 Author: Weiqun Zhang Date: Mon Feb 27 17:12:23 2017 -0800 forgot a new file in last commit Src/Base/AMReX_FabFactory.H commit 8c832ff6af4a3469e9bb10806a5f9de4ec606fc0 Author: Weiqun Zhang Date: Mon Feb 27 17:09:51 2017 -0800 add Fab factory; note that dynamic sidecar and FabArrayCopyDescriptor do not work with non-default factory Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 74259aa4e435262b643b75082ced80a78e7c9332 Merge: c2be9dc07 0cd92abf9 Author: Weiqun Zhang Date: Fri Mar 3 09:57:57 2017 -0800 Merge branch 'weiqun/mpibuffer' into dtg_branch commit 0cd92abf9b324ca974f7622dda3889d161e035b5 Author: Weiqun Zhang Date: Fri Mar 3 09:53:13 2017 -0800 fix FillBoundary's cross option Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp commit 33b4c0e6c234e041678097d96c3784c156591b3d Author: Weiqun Zhang Date: Fri Mar 3 08:33:23 2017 -0800 fix a new bug Src/Base/AMReX_FabArray.H commit b49332d907bc947353ee3ec0c00793ff3e6907a7 Author: Weiqun Zhang Date: Thu Mar 2 20:49:06 2017 -0800 fix some issues copyInter Src/Base/AMReX_FabArray.H commit 84a426143555b984a22003b8140e4e14df845e0f Author: Weiqun Zhang Date: Thu Mar 2 17:17:59 2017 -0800 modified FabArray's communication for EB Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp commit c2be9dc0798e5ac3fc6e73cae8e56e3b16346d27 Author: Dan Graves Date: Thu Mar 2 15:52:55 2017 -0800 ebgraph test now also tests coarsening Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp commit c78f1cefa83c5e08cdc3fe1dadd71ac0e28e6d37 Author: Dan Graves Date: Thu Mar 2 13:32:03 2017 -0800 EBGraph passes its first test Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp commit 4ed7aa3b785cff313a4104586ee560246a18e1e6 Author: Dan Graves Date: Wed Mar 1 16:12:20 2017 -0800 added a test for the graph Tests/GeometryShop/ebgraphSingleGrid/GNUmakefile Tests/GeometryShop/ebgraphSingleGrid/Make.package Tests/GeometryShop/ebgraphSingleGrid/ebgraphSG.cpp Tests/GeometryShop/ebgraphSingleGrid/sphere.inputs commit 59a1b555c78b1b85ea90d63388e4f3ea3b98ea04 Author: Andrew Myers Date: Wed Mar 1 14:49:49 2017 -0800 fix container resizing in redistribute Src/Particle/AMReX_ParticleContainerI.H commit 40a44eac4b12a76648858509935a1cc3acb64c5d Author: Andrew Myers Date: Wed Mar 1 13:42:51 2017 -0800 There is no need for a Where() call here. Src/Particle/AMReX_ParticleContainerI.H commit a21e6e01a3365c70dcb41336c211d5692a0e239b Author: Andrew Myers Date: Wed Mar 1 13:04:55 2017 -0800 Have AddParticlesAtLevel clear the input container, as before. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 9ad716e1368fc48217c14fcdb6f43acd4f9edb65 Author: Andrew Myers Date: Wed Mar 1 12:17:52 2017 -0800 Check whether we need to resize m_particles in AddParticlesAtLevel() Src/Particle/AMReX_ParticleContainerI.H commit 2518577ecadd7ce16c833d0835aa3dde7c49446d Author: Andrew Myers Date: Wed Mar 1 11:13:10 2017 -0800 Rename here also. Src/Particle/AMReX_ParticleContainerI.H commit be6e58a34d0024104696a5ac31795a78e2b44c4d Merge: afc6f81cb 9007f2cd1 Author: Andrew Myers Date: Wed Mar 1 11:11:59 2017 -0800 Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor merging. commit afc6f81cb63942ce257112d2bebe3ba2a568b146 Author: Andrew Myers Date: Wed Mar 1 11:11:47 2017 -0800 forgot to include this file. Src/Particle/AMReX_ParticleContainerI.H commit c68ca859569062ee61b12dabebb9d7ea35b050a4 Author: Andrew Myers Date: Wed Mar 1 11:11:17 2017 -0800 Give the AddParticlesAtLevel function an nGrow argument. Src/Particle/AMReX_Particles.H commit 9007f2cd151d982e00e66306c29f7c436a891699 Merge: a9a5394fa abdef39df Author: Andrew Myers Date: Wed Mar 1 11:10:01 2017 -0800 merging commit a9a5394faade33af707102ab7a455402f515f6d9 Author: Andrew Myers Date: Wed Mar 1 11:08:23 2017 -0800 rename SingleLevelWhere and give it a default of 0 grow cells. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 15f65ee0efc0481a1773f09987b8c2eee6db73f0 Author: Dan Graves Date: Wed Mar 1 10:15:08 2017 -0800 I managed to wedge EBGraph into AMReX. Only missing the parallel communication stuff now. I can now start testing it. Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_FaceIndex.H Src/GeometryShop/AMReX_FaceIndex.cpp Src/GeometryShop/AMReX_FaceIterator.H Src/GeometryShop/AMReX_FaceIterator.cpp Src/GeometryShop/AMReX_SPMD.H Src/GeometryShop/AMReX_VoFIterator.H Src/GeometryShop/AMReX_VoFIterator.cpp Src/GeometryShop/Make.package commit abdef39df00abc7d977de323ce5ec1a9e7a69e5b Merge: a3003421e 7a224b887 Author: Weiqun Zhang Date: Wed Mar 1 09:23:02 2017 -0800 Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor Conflicts: Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H commit a3003421ebebff5ef2564ca65795ea3dc9af6f1d Author: Weiqun Zhang Date: Wed Mar 1 09:18:25 2017 -0800 add functions to get/set particle positions Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particle_mod_1d.F90 Src/Particle/AMReX_Particle_mod_2d.F90 Src/Particle/AMReX_Particle_mod_3d.F90 Src/Particle/AMReX_Particles.H Src/Particle/AMReX_Particles_F.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 7a224b887c624c522c1d43cd3af45841143ad861 Author: Andrew Myers Date: Tue Feb 28 18:05:34 2017 -0800 remove unused variable. Src/Particle/AMReX_ParticleInit.H commit 7f5d41d3a8170aceb4a4f3915f7f756c18e2c553 Author: Andrew Myers Date: Tue Feb 28 18:05:08 2017 -0800 Fix an assertion. Src/Particle/AMReX_ParticleContainerI.H commit dfe8835cf46928f06bee78990376b4d36a4d2c81 Merge: 8babd9d43 1aacdd9cd Author: Andrew Myers Date: Tue Feb 28 17:46:28 2017 -0800 Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor merging. commit 8babd9d432812dad22d772d683e5dfe9516f4742 Author: Andrew Myers Date: Tue Feb 28 17:27:42 2017 -0800 update advection tutorial to use the new form of Redistribute() Tutorials/AMR_Adv_C/Source/Adv.cpp commit 196461407d398d27a39fe194ba7812b711de8661 Author: Andrew Myers Date: Tue Feb 28 17:25:34 2017 -0800 Making the new particle data structures work with Nyx. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit 464ed581d61fae6a55365b6e358828c230379fce Author: Andrew Myers Date: Tue Feb 28 17:23:54 2017 -0800 Fix a bug in an assert. Src/Base/AMReX_MultiFabUtil.cpp commit 67a1e7c02e15179f74ee9a76abf5017c446bc3c9 Author: Weiqun Zhang Date: Tue Feb 28 15:13:53 2017 -0800 renaming Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit db351ff63cf7a0bdbd4a268e8003abca6aac4331 Author: Dan Graves Date: Tue Feb 28 14:51:36 2017 -0800 added more of the components of EBGraph---I had forgotten how complicated this stuff is Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_GraphNode.H Src/GeometryShop/AMReX_GraphNode.cpp Src/GeometryShop/AMReX_SPMD.H Src/GeometryShop/AMReX_SPMD.cpp Src/GeometryShop/AMReX_SPMDI.H Src/GeometryShop/AMReX_VolIndex.H Src/GeometryShop/AMReX_VolIndex.cpp Src/GeometryShop/Make.package commit 1aacdd9cd4d9d1bdc618a3acea19dc565a5b0340 Author: Weiqun Zhang Date: Tue Feb 28 13:59:42 2017 -0800 fix an assertion Src/Base/AMReX_MultiFabUtil.cpp commit 764e481221ff6e9d5c8909b50c65630b864bb0bc Author: Weiqun Zhang Date: Tue Feb 28 13:57:16 2017 -0800 add some push_back and access functions Src/Particle/AMReX_Particles.H commit 32c79bbe9f37c718c63d663f8c6152ca1f97e306 Author: Michael Zingale Date: Tue Feb 28 10:27:39 2017 -0500 handle the reporting for when no benchmark is found. Also don't get confused by variable names that start with diff Tools/RegressionTesting/test_report.py commit 257a342b1b92a29744335c7af243fb4300605372 Author: Weiqun Zhang Date: Mon Feb 27 17:12:23 2017 -0800 forgot a new file in last commit Src/Base/AMReX_FabFactory.H commit 193992102d627a946b99eaa0faf6ad4990c78a6f Author: Weiqun Zhang Date: Mon Feb 27 17:09:51 2017 -0800 add Fab factory; note that dynamic sidecar and FabArrayCopyDescriptor do not work with non-default factory Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 04d234d759b09c2db23f7bd9a5d0d04410cf9823 Author: Andrew Myers Date: Mon Feb 27 14:12:40 2017 -0800 minor. Src/Particle/AMReX_ParticleContainerI.H commit 43f5ce96a69a54c180cda7fdf916a2b606552000 Author: Andrew Myers Date: Mon Feb 27 13:52:42 2017 -0800 Use fancy new helper functions to access the particle data pointer, instead of doing it manually. Src/Particle/AMReX_ParticleContainerI.H commit 6009988e463a72ca0b99a52280cc8d267ebafa9c Merge: 284a6cfbf 6b46e5b20 Author: Andrew Myers Date: Mon Feb 27 12:22:40 2017 -0800 merging. commit 284a6cfbf2a67a7fccf470b5dbc01eec351f7ce0 Author: Andrew Myers Date: Mon Feb 27 12:21:00 2017 -0800 Also call average_down at the end of AssignDensityFort Src/Particle/AMReX_ParticleContainerI.H commit 8d98be024a54232f753dd2879ad6724943a2a361 Author: Andrew Myers Date: Mon Feb 27 12:20:06 2017 -0800 An extra sanity check for the sum_fine_to_coarse function. Src/Base/AMReX_MultiFabUtil.cpp commit f9f38988040567379fc82a8b4d40c01678df1641 Author: Dan Graves Date: Mon Feb 27 11:38:33 2017 -0800 keeping up with the development branch--some fortran stuff had changed names. Also, fortran declarations need to be in amrex namespace. Also, moved some files from test directory to Src/GeometryShop. Stuff compiles again Src/GeometryShop/AMReX_AggStencil.H Src/GeometryShop/AMReX_AggStencilI.H Src/GeometryShop/AMReX_BaseIndex.H Src/GeometryShop/AMReX_EBCellFAB.H Src/GeometryShop/AMReX_EBCellFAB.cpp Src/GeometryShop/AMReX_EBGraph.H Src/GeometryShop/AMReX_EBGraph.cpp Src/GeometryShop/AMReX_FaceIndex.H Src/GeometryShop/AMReX_FaceIndex.cpp Src/GeometryShop/AMReX_Stencils.H Src/GeometryShop/AMReX_Stencils.cpp Src/GeometryShop/AMReX_VolIndex.H Src/GeometryShop/AMReX_VolIndex.cpp Src/GeometryShop/Make.package Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H Tests/GeometryShop/stencilTestbed/src/Make.package Tests/GeometryShop/stencilTestbed/src/lapl_nd.F90 Tests/GeometryShop/stencilTestbed/src/lapl_nd_F.H commit 7689b5a4b8590b1b8bd6df7de69a88b18109397a Author: Dan Graves Date: Mon Feb 27 10:37:03 2017 -0800 paring this down to the minimum number of files because I am about to add a bunch more Src/GeometryShop/AMReX_CellEdge.H Src/GeometryShop/AMReX_CellEdge.cpp Src/GeometryShop/AMReX_ComplementIF.H Src/GeometryShop/AMReX_ComplementIF.cpp Src/GeometryShop/AMReX_EllipsoidIF.H Src/GeometryShop/AMReX_EllipsoidIF.cpp Src/GeometryShop/AMReX_IntersectionIF.H Src/GeometryShop/AMReX_IntersectionIF.cpp Src/GeometryShop/AMReX_IrregNode.cpp Src/GeometryShop/AMReX_LatheIF.H Src/GeometryShop/AMReX_LatheIF.cpp Src/GeometryShop/AMReX_TransformIF.H Src/GeometryShop/AMReX_TransformIF.cpp Src/GeometryShop/AMReX_UnionIF.H Src/GeometryShop/AMReX_UnionIF.cpp commit 6b46e5b20d938e9bfde408c445fb8ba289fc6593 Author: Weiqun Zhang Date: Mon Feb 27 09:11:00 2017 -0800 add a new IntVect::operator== for comparing IntVect with int, and fix an out of bound problem Src/Base/AMReX_IntVect.H Src/Base/AMReX_MultiFabUtil.cpp commit 2999b7a330af89c049d6e35d5d4ed3698d73618b Author: Andrew Myers Date: Fri Feb 24 16:22:56 2017 -0800 quick bug fix to TotalNumberOfParticles in parallel. Src/Particle/AMReX_ParticleContainerI.H commit f1ed3ac9c445b9d6694cd87f5aaa4a4df21c6771 Author: Dan Graves Date: Fri Feb 24 15:55:02 2017 -0800 bug fix for flat plate Src/GeometryShop/AMReX_FlatPlateGeom.cpp commit 94b597dbeb7ef0f11b6c83028cfbcd71dabb3728 Author: Dan Graves Date: Fri Feb 24 15:10:54 2017 -0800 got flat plate geometry working as far as I have tested it Src/GeometryShop/AMReX_FlatPlateGeom.cpp Tests/GeometryShop/flatPlate/GNUmakefile Tests/GeometryShop/flatPlate/Make.package Tests/GeometryShop/flatPlate/flatPlateTest.cpp Tests/GeometryShop/flatPlate/flatplate.inputs commit c626eb5d6a2a0916e9764f1a69fb6e4e79f7dcbe Author: Andrew Myers Date: Fri Feb 24 13:46:24 2017 -0800 Also write out the extra integer components. Src/Particle/AMReX_ParticleContainerI.H commit e25a6fc0db422e96d2e350a2099e298abdbddd2f Author: Andrew Myers Date: Fri Feb 24 13:32:25 2017 -0800 Also write out whether this is a checkpoint format particle file or not. Src/Particle/AMReX_ParticleContainerI.H commit e07f237f8a63f277166ff4fd0ab538b4244d2e59 Author: Andrew Myers Date: Fri Feb 24 13:08:52 2017 -0800 Add ability to specify particle component names for IO. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Tests/Particles/AssignMultiLevelDensity/main.cpp commit 1aec76bb6d39b1d2ddfba78d65a7ec51f42a2113 Merge: 19ec1ef99 b7b600f7b Author: Andrew Myers Date: Fri Feb 24 10:57:35 2017 -0800 merging. commit 19ec1ef99d9817fb0a84ce803ebb4ffefd19cadf Author: Andrew Myers Date: Fri Feb 24 10:35:23 2017 -0800 rewrite the multi-level charge deposition code. Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Particle/AMReX_Deposition_F.F90 Src/Particle/AMReX_Deposition_F.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Tests/Particles/AssignDensity/GNUmakefile Tests/Particles/AssignDensity/Make.package Tests/Particles/AssignDensity/inputs Tests/Particles/AssignDensity/main.cpp Tests/Particles/AssignMultiLevelDensity/GNUmakefile Tests/Particles/AssignMultiLevelDensity/Make.package Tests/Particles/AssignMultiLevelDensity/inputs Tests/Particles/AssignMultiLevelDensity/main.cpp Tutorials/PIC_C/GNUmakefile commit f69274fc13b362ea916b16268e9d110a2ebba69d Author: Tan Nguyen Date: Thu Feb 23 23:10:02 2017 -0800 just used this version to test castro, and no bug was found Tools/typechecker/typeChecker.py commit 7e787ab7d749ed64d8f363fc59d2786b9f48134e Merge: 7ff4d964c fbcf31ec4 Author: atmyers Date: Thu Feb 23 17:35:15 2017 -0800 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development merging # the commit. commit 7ff4d964c5a92214e625a4daa3bcd060d7c532c1 Author: atmyers Date: Thu Feb 23 17:34:48 2017 -0800 Fixing a bug in the PIC_C tutorial pointed out by Matthias Frey. Tutorials/PIC_C/two_level.cpp commit dfed65883f9ccd1c701d83a2c54891d0d2731a9f Author: Andrew Myers Date: Thu Feb 23 17:30:25 2017 -0800 Fixing a bug in the PIC_C tutorial pointed out by Matthias Frey. Tutorials/PIC_C/two_level.cpp commit 147e894d97b25f903f7217405e9968eed312e1c4 Author: Dan Graves Date: Thu Feb 23 16:11:04 2017 -0800 made some progress on flat plate goem. trickier than I thought (story of my life) Src/GeometryShop/AMReX_FlatPlateGeom.H Src/GeometryShop/AMReX_FlatPlateGeom.cpp Src/GeometryShop/Make.package commit cf19eab8be0a56315af080156103ead1576a410d Merge: fabf9de00 fbcf31ec4 Author: Dan Graves Date: Thu Feb 23 09:08:06 2017 -0800 Merge branch 'development' into dtg_branch commit c49c7f5b9baf7944819be9a29ed111e6a91d2485 Author: Tan Nguyen Date: Wed Feb 22 18:42:01 2017 -0800 type checker can handler C++ input Tools/typechecker/typeChecker.py commit b7b600f7bc911b7de8f5b0a236d002d316dad6ff Author: Weiqun Zhang Date: Tue Feb 21 16:59:38 2017 -0800 Particle: merge two maps into one Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit 581b399723fd66ae3bd76a83e2bb45783534836d Author: Weiqun Zhang Date: Tue Feb 21 09:45:31 2017 -0800 no need to reset dummy mulitfab if the boxarray and distribution map do not change Src/Particle/AMReX_ParticleContainerI.H commit 48072b332088ae52ce8f91afb97686e105e534ba Author: Weiqun Zhang Date: Tue Feb 21 09:32:54 2017 -0800 remove the where_already_called flag from Redistribute Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Tutorials/AMR_Adv_C/Source/Adv.cpp commit 81a19375ecfca646b3e1f651c99ff93e27c722c6 Author: Weiqun Zhang Date: Mon Feb 20 10:49:49 2017 -0800 update AmrParticleContainer Src/AmrCore/AMReX_AmrParticles.H commit 763c812210515509c91c1b149e3294641b6bde28 Author: Weiqun Zhang Date: Mon Feb 20 10:26:29 2017 -0800 ParticleContainer::GetParticles --> GetAoSMap; add GetSoAMap Src/Particle/AMReX_Particles.H commit fb683a38c7911da06c2bba3c75e2d28d650ae552 Author: Weiqun Zhang Date: Mon Feb 20 10:17:26 2017 -0800 define dummy multifab in resizeData Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 53104a6ae5205e40f4403df6a54d293050546e0c Author: Weiqun Zhang Date: Mon Feb 20 07:52:16 2017 -0800 add ParticleContainer::MakeMFiter that returns a normal MFIter Src/Particle/AMReX_Particles.H commit 5c99b16657338f853e66c30fb9a57fd3d2ba298a Author: Weiqun Zhang Date: Mon Feb 20 07:43:57 2017 -0800 fix typo Src/Particle/AMReX_Particles.H commit 4043ad78a549ed2c5e377fb96ee832f50053dded Author: Weiqun Zhang Date: Mon Feb 20 07:26:59 2017 -0800 add a few functions to ParticleContainer for convenience Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 26327768b03f2b09e3343234f20b668b235c8a3c Author: Weiqun Zhang Date: Sun Feb 19 15:43:59 2017 -0800 ParIter: skip tiles that do not exist in maps Src/Particle/AMReX_ParIterI.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit a36764fa344f69b84b70d28d002c2b28bcd6f0b5 Author: Weiqun Zhang Date: Sun Feb 19 15:17:02 2017 -0800 Make sure [] will insert a new item to the map even when SoA has no data, otherwise erase may fail Src/Particle/AMReX_ParticleContainerI.H commit a25d50ca793eadbdd5ddb9a725eb69c19664bfc3 Author: Weiqun Zhang Date: Sun Feb 19 15:15:09 2017 -0800 add const to MFIte::isValid() Src/Base/AMReX_FabArray.H commit 18455e9345b2e772f0711c0cc00d58de66d6f950 Author: Weiqun Zhang Date: Sun Feb 19 12:07:56 2017 -0800 Particle Iterator: rename Src/Particle/AMReX_Particles.H commit 1533b8ee45416b69577b74f4eb284f5be5659aa4 Author: Weiqun Zhang Date: Sun Feb 19 10:16:47 2017 -0800 add class ArrayOfStructs Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit 72927dab5ccfca0d09a443d368c456a36d18872b Author: Weiqun Zhang Date: Sat Feb 18 16:34:37 2017 -0800 rm the iterator get functions for a single component to avoid being called repeatedly; one can always get the whole data and access each component. some other minor changes Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 483222545872d36b9ea802dfb3888c04c438f8f0 Author: Weiqun Zhang Date: Sat Feb 18 12:40:35 2017 -0800 add ParIter Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.H commit 596b03f356683898357c91769810047a63084377 Author: Weiqun Zhang Date: Sat Feb 18 11:32:48 2017 -0800 add static assertion the size of particle is a multiple of the size of real Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 64f5c17872ad1c183fb9990e4dea99a438ba81cb Author: Weiqun Zhang Date: Sat Feb 18 11:30:37 2017 -0800 typo Src/Particle/CMakeLists.txt commit 80b3ca8b778ae209029532899cb084c2d6970454 Merge: a76e34bd5 6d0026f2c Author: Andrew Myers Date: Fri Feb 17 16:48:40 2017 -0800 merging. commit a76e34bd5f05ecaabf93ad52ca77859cded6020e Author: Andrew Myers Date: Fri Feb 17 16:45:05 2017 -0800 Faster particle deposition routines. Src/Particle/AMReX_Deposition_F.F90 Src/Particle/AMReX_Deposition_F.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 6d0026f2cc6854629613ad6949e68d412fae6c21 Merge: 8f3656c39 fbcf31ec4 Author: Weiqun Zhang Date: Fri Feb 17 15:43:45 2017 -0800 Merge branch 'development' into particle_refactor commit fbcf31ec4023cb641d83dc4288e1ebcec12f165f Author: Weiqun Zhang Date: Fri Feb 17 15:42:55 2017 -0800 de-virtualize some BoxArray functions Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit 5a1ac955087a76f14f86b8f73a048a4cef7e3bf3 Author: Weiqun Zhang Date: Fri Feb 17 14:49:48 2017 -0800 add amrex::Print::SetPrecision Src/Base/AMReX_Print.H commit 8f3656c397548e1de478df8c70e9442fe84c228a Author: Weiqun Zhang Date: Fri Feb 17 14:51:24 2017 -0800 tweak locateParticle to handle particles right on domain boundary Src/Particle/AMReX_ParticleContainerI.H commit 97574b6a3cd10267cd1a9b4f5927ee3663303d05 Author: Weiqun Zhang Date: Fri Feb 17 14:49:48 2017 -0800 add amrex::Print::SetPrecision Src/Base/AMReX_Print.H commit 26849c00e726192e43cddffec370865bd77c7f88 Author: Weiqun Zhang Date: Fri Feb 17 13:33:42 2017 -0800 refactor OK() Src/Particle/AMReX_ParticleContainerI.H commit 76292465f77bdfeedc068b803fbab051b72f0797 Author: Weiqun Zhang Date: Fri Feb 17 13:28:22 2017 -0800 refactor OK and locateParticle Src/Particle/AMReX_ParticleContainerI.H commit fc6c677b4aa78b28db4e94defd37b5b7463d8482 Author: Weiqun Zhang Date: Fri Feb 17 12:15:18 2017 -0800 fix SingleLevelGrownWhere Src/Particle/AMReX_ParticleContainerI.H commit aeb7d8c15a9797a76421639ebba3e9c365a03bca Author: Weiqun Zhang Date: Fri Feb 17 10:50:30 2017 -0800 refactor Where and OK Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit aeee9fdd90db86588fe45352b0839c6d4e7fef94 Author: Weiqun Zhang Date: Fri Feb 17 09:53:21 2017 -0800 rm single level where Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit 53130a9f9cfdbd53227141c9e89efdecc92b07fa Author: Weiqun Zhang Date: Fri Feb 17 08:54:56 2017 -0800 minor optimization Src/Particle/AMReX_ParticleContainerI.H commit 06edb1a774b78fc7909eddc944cdc3cafd17c3a3 Merge: eb7827372 cce9c8492 Author: Andrew Myers Date: Thu Feb 16 13:14:22 2017 -0800 Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor merging. commit eb78273722c003f1cd762ccb6c12fe8a986c6144 Author: Andrew Myers Date: Thu Feb 16 13:13:59 2017 -0800 Implementing particle restart for the advection test. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv_io.cpp commit cce9c8492631735d1c4aa27a272df448d5b61fdf Merge: c1dccaf1e 39a19098b Author: Weiqun Zhang Date: Thu Feb 16 10:50:47 2017 -0800 Merge branch 'development' into particle_refactor commit c1dccaf1e9d7bac0727849bdaa20c0bb44ff0aec Author: Weiqun Zhang Date: Thu Feb 16 10:19:14 2017 -0800 make the particle tiling consistent with MFIter tiling Src/Base/AMReX_FabArray.cpp Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 0acf4cb3e72f86ad01fe93a595a7abfd9b315eb2 Author: Weiqun Zhang Date: Thu Feb 16 09:29:37 2017 -0800 optimization of Where Src/Particle/AMReX_ParticleContainerI.H commit 6e5bf080b8583f587fd7b7c38e0207d02caa73af Author: Andrew Myers Date: Thu Feb 16 09:34:58 2017 -0800 also read the extra int information from checkpoint files. Src/Particle/AMReX_ParticleContainerI.H commit e92eca953a079156c991317062c672c0814ae8ce Author: Andrew Myers Date: Wed Feb 15 20:14:38 2017 -0800 cleaning up the particle restart routines. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit fabf9de00b9bc86e7f2ce273d49fc984991a078f Author: Marc Day Date: Wed Feb 15 19:20:55 2017 -0800 Fix up MSD version of stencil test again. Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp commit 723a7dd18ca84b4b48bd6992fd397061938a1938 Merge: 9bca83b8c d9152203e Author: Andrew Myers Date: Wed Feb 15 17:46:53 2017 -0800 Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor merging commit 9bca83b8c92df11e99fbf5b2433a69175658cb54 Author: Andrew Myers Date: Wed Feb 15 17:46:25 2017 -0800 Remove duplicate versions of ReadParticles by using a template function. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit d9152203e0f20daa20ba8f9c168248e795490143 Author: Weiqun Zhang Date: Wed Feb 15 17:01:08 2017 -0800 need to test for nullptr Src/Particle/AMReX_ParticleContainerI.H commit 113e407aa6ae1dcb77b547709e9ca1f75661a1e4 Author: Weiqun Zhang Date: Wed Feb 15 16:55:57 2017 -0800 add dummy multifabs to particle container Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H commit f50606a6f4def747026774aef1c7049f736fdd42 Author: Weiqun Zhang Date: Wed Feb 15 15:47:37 2017 -0800 add tilebox and gridbox to particle location data Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit c418a39f0b024a58e5ea3db289cc1a1bead95038 Author: Weiqun Zhang Date: Wed Feb 15 15:24:46 2017 -0800 Where: optimization Src/Particle/AMReX_ParticleContainerI.H commit 81fda70d88c8bd14f8dc264f143331fec4224a31 Author: Andrew Myers Date: Wed Feb 15 16:16:00 2017 -0800 This reference can't be const, as this function updates the particles. Src/Particle/AMReX_ParticleContainerI.H commit 4a74850fbd9990dd7591037125924358552ac255 Author: Andrew Myers Date: Wed Feb 15 15:12:48 2017 -0800 Add the SoA data to the restart routines Src/Particle/AMReX_ParticleContainerI.H commit acf7426a93f029a567da81763cf5be22918e30c7 Author: Marc Day Date: Wed Feb 15 13:00:44 2017 -0800 Fix the mess I made in the stencilTest folder...still messy, but correct. Tests/GeometryShop/stencilTestbed/exec/GNUmakefile Tests/GeometryShop/stencilTestbed/exec/Make.package Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD_3d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD_F.H Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H commit 81c3ed026a17320c072e0ad868a750cfdebe2d55 Author: Weiqun Zhang Date: Wed Feb 15 11:06:41 2017 -0800 add a static Initialize function to ParticleContainer Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit ecd77a2e133f0ea9520f0bbd7550cf9ea2b2f4f4 Author: Weiqun Zhang Date: Wed Feb 15 10:53:44 2017 -0800 minor Src/Particle/AMReX_ParticleContainerI.H commit d3bae0435e9ccb26485b765eb7239c0922711ebf Author: Weiqun Zhang Date: Wed Feb 15 10:46:03 2017 -0800 fix assertion Src/Particle/AMReX_ParticleContainerI.H commit 309c17aafa6005a50a99e5b70c64c7380e0053ae Author: Weiqun Zhang Date: Wed Feb 15 10:43:13 2017 -0800 update tutorial because of the interface of Redistribute Tutorials/AMR_Adv_C/Source/Adv.cpp commit 5aead5ef6d07a74ff4faa7e65841264f1ee8e020 Author: Weiqun Zhang Date: Wed Feb 15 10:31:18 2017 -0800 refactor Redistribute Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit b2ea643c615c5a1876ade023d29fd1a7781ced41 Author: Marc Day Date: Tue Feb 14 18:43:09 2017 -0800 Add logic to shift bc interp stencil to avoid extrapolations and more smoothly continue with sign changes of the normal components. Not sure if this has a direct analogue in 3d yet. Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90 commit 5867cf8816b489c1d128ee939ba7cae7ad9c1333 Author: Weiqun Zhang Date: Tue Feb 14 17:29:43 2017 -0800 fix last commit Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit ea77b4f6ce851e942e5153fbb2aac504b0e115a8 Author: Weiqun Zhang Date: Tue Feb 14 17:02:10 2017 -0800 clean up and add a test for trivally copyable Src/Particle/AMReX_ParticleContainerI.H commit 65b6e42ab4132b2c72f3cb51d91624684a646ab7 Author: Weiqun Zhang Date: Tue Feb 14 16:56:19 2017 -0800 Assertion on pointers obtained with c type cast won't work. Src/Particle/AMReX_ParticleContainerI.H commit 159af4a57ab42270d7f49d4c9d2a384d1d2f9fc0 Author: Weiqun Zhang Date: Tue Feb 14 16:48:40 2017 -0800 minor Src/Particle/AMReX_ParticleContainerI.H commit de23748ab34d918cd0b8ac9ccf88b1dafd5f9d40 Author: Weiqun Zhang Date: Tue Feb 14 15:58:13 2017 -0800 add where_already_called option to Redistribution Src/Particle/AMReX_ParticleContainerI.H commit a0e668bbf5eac8f51716736471dbe576795a9b0e Author: Marc Day Date: Tue Feb 14 15:21:02 2017 -0800 Nearly trivial hack to stencil Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/dirichletTest_F.H commit b486b9fa2a2b815af8a2b8681da4b90320208271 Author: Weiqun Zhang Date: Tue Feb 14 15:06:13 2017 -0800 remove SoA data too Src/Particle/AMReX_ParticleContainerI.H commit c9b31cd288764c29471121a670ea431cd4ca5581 Author: Weiqun Zhang Date: Tue Feb 14 14:56:49 2017 -0800 remove some duplicated code Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 5961ef317de2beead4722d87c32ec0f937244365 Author: Weiqun Zhang Date: Tue Feb 14 14:28:27 2017 -0800 some cout --> Print() Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H commit ecf3f74b60bb7e5ce72bdc2ef0245b1945fba177 Author: Weiqun Zhang Date: Tue Feb 14 13:27:13 2017 -0800 add some optional argument for skipping mpi reduction Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 91b216a1c521f953cfc29bd42737f86e3e1a6140 Author: Weiqun Zhang Date: Tue Feb 14 13:05:35 2017 -0800 add some optional argument for skipping mpi reduction Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 18ebb7f07aea83ab86940d1b9119c500a86977a0 Author: Weiqun Zhang Date: Tue Feb 14 12:46:39 2017 -0800 add SoA to ByteSpread Src/Particle/AMReX_ParticleContainerI.H commit a50d900e2a84057493cf4d0a70820b70fdf7d98a Author: Weiqun Zhang Date: Tue Feb 14 12:41:08 2017 -0800 fix a bug: when tiling is on, we may visit a grid multiple times Src/Particle/AMReX_ParticleContainerI.H commit 41b13bc448607d2cb0a6fa48de960b030883c5bf Author: Weiqun Zhang Date: Tue Feb 14 12:25:45 2017 -0800 forgot #ifdef; use unique_ptr Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/Adv_setup.cpp commit 852fe3fd0ed8b6392f02b24b8389bfe94920561d Author: Weiqun Zhang Date: Tue Feb 14 12:19:13 2017 -0800 unroll a loop Src/Particle/AMReX_ParticleContainerI.H commit d77b36bedda3dff90bfc44a3bfdcb85f181ad781 Author: Marc Day Date: Tue Feb 14 09:49:19 2017 -0800 Minor mod to stencil test. Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90 commit acaa62499a016d15689c14192a0fd5a7620e4cf0 Author: Marc Day Date: Tue Feb 14 09:46:24 2017 -0800 Working on EB stencil stuff, pushing WIP Tests/GeometryShop/stencilTestbed/exec/GNUmakefile Tests/GeometryShop/stencilTestbed/exec/Make.package Tests/GeometryShop/stencilTestbed/exec/dirichletTest.cpp Tests/GeometryShop/stencilTestbed/exec/dirichletTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/dirichletTest_F.H Tests/GeometryShop/stencilTestbed/exec/sphere.inputs Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H commit dd389d75faf17a32e98147a2b107a0f4c4a37a71 Merge: abb1f86dd b251b54d0 Author: Andrew Myers Date: Mon Feb 13 16:29:48 2017 -0800 Merge branch 'particle_refactor' of bitbucket.org:berkeleylab/amrex into particle_refactor merging. commit abb1f86dd53680544607f2212b2d77a0ab217f23 Author: Andrew Myers Date: Mon Feb 13 16:29:25 2017 -0800 remove redundant Where() call Src/Particle/AMReX_ParticleContainerI.H commit b251b54d0545ab158c75e3e242e01bca08409e62 Author: Weiqun Zhang Date: Mon Feb 13 15:46:07 2017 -0800 take a shortcut in Where Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit 6ae0942d98506e2abc082d923bcedb5f518e71c7 Author: Andrew Myers Date: Mon Feb 13 14:33:28 2017 -0800 Initialize the communicate_comp member properly Src/Particle/AMReX_Particles.H commit 374bfceef8538918aa7c10f4129e6c03368270cc Merge: 2068dd4a9 76a7199c8 Author: Andrew Myers Date: Mon Feb 13 14:12:36 2017 -0800 Merging. commit 2068dd4a97e699caa32b29861fc785d76520d291 Author: Andrew Myers Date: Mon Feb 13 13:57:53 2017 -0800 Some renaming for clarity. Src/AmrCore/AMReX_AmrParticles.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H commit 76a7199c8a489b8e43df1dfb60439395e0d3e450 Author: Weiqun Zhang Date: Mon Feb 13 13:41:14 2017 -0800 rm using std::make_pair from headers Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H commit ffa05214ce759365032b1855e40958b00ecbf996 Author: Weiqun Zhang Date: Mon Feb 13 13:02:58 2017 -0800 use std::vector instead of built-in array because zero size built-in array is not allowed Src/Particle/AMReX_Particles.H commit 48e1605578e4e103ffc81286713ed209e4eb2193 Author: Weiqun Zhang Date: Mon Feb 13 12:45:33 2017 -0800 minor changes for consistence Src/Particle/AMReX_Particles.H commit bc3c4bfcbbae00c395ece55a2074a31573a7f154 Author: Weiqun Zhang Date: Mon Feb 13 12:43:21 2017 -0800 use amrex::Array instead of std::vector in some places Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit d01b78706f4ab3a0a722565559bf2fba73b54fb6 Author: Weiqun Zhang Date: Mon Feb 13 12:25:17 2017 -0800 fix omp race conditions Tutorials/AMR_Adv_C/Source/Adv_advance.cpp commit 2a80710a233d9e84806411fa5756c61d9397979e Author: Weiqun Zhang Date: Mon Feb 13 12:24:41 2017 -0800 delete particle container Tutorials/AMR_Adv_C/Source/Adv_setup.cpp commit e3efb60da4ef9b2d4fc6ae511d86bc2af1f37256 Author: Weiqun Zhang Date: Mon Feb 13 11:17:04 2017 -0800 rename to avoid confusion Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp commit c22c094e6e4c0755dd20c2c23abba6bab5cb5101 Author: Weiqun Zhang Date: Mon Feb 13 10:38:49 2017 -0800 CoordSys: bcast inv_dx and set default inv_dx to infinity Src/Base/AMReX_CoordSys.cpp commit 76fd302784b66eb980027109e8ebbfb6ea099fb8 Author: Weiqun Zhang Date: Thu Feb 9 21:52:42 2017 -0800 AMR_Adv_CF: multiple levels without regridding works Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 commit ac5f934246a19882b0fb427f376424c195f2f5c6 Author: Weiqun Zhang Date: Thu Feb 9 17:09:15 2017 -0800 add amrex_bc_types_module and fillpatch from two levels Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 Src/F_Interfaces/Base/AMReX_bc_types_mod.F90 Src/F_Interfaces/Base/Make.package commit 130c31849b307eead2ee96a1ff4b464b3c756df7 Merge: 290515a63 39a19098b Author: Tan Nguyen Date: Thu Feb 9 16:28:32 2017 -0800 resolve a confict when merging dev to check_fortran commit 6fb2db01d3039c3c8f80a7075d534b85d5895c85 Author: Weiqun Zhang Date: Thu Feb 9 15:35:28 2017 -0800 AMR_Adv_CF: add clear level function Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90 Src/F_Interfaces/AmrCore/AMReX_amrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/AmrCore/Make.package Src/F_Interfaces/Base/AMReX_base_mod.F90 Src/F_Interfaces/Base/Make.package Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 661faa835d73978eb25bc4d35d892667963da769 Author: Weiqun Zhang Date: Thu Feb 9 15:33:35 2017 -0800 add amrex_interpolater_module Src/F_Interfaces/AmrCore/AMReX_interpolater_mod.F90 commit db549b6430d504eb8a39304ffca7dd8dcd2be7ee Author: Andrew Myers Date: Thu Feb 9 13:34:56 2017 -0800 Also write out the SoA data to the plt files. Src/Particle/AMReX_ParticleContainerI.H commit a2b2c2d8213bb594c8c69412f78c853c40afca98 Author: Andrew Myers Date: Thu Feb 9 11:38:14 2017 -0800 Updating the AMR_Adv_C tutorial to optionally use tracer particles. Tutorials/AMR_Adv_C/Exec/Make.Adv Tutorials/AMR_Adv_C/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs Tutorials/AMR_Adv_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_io.cpp commit dbe13c30efb64f048dbfa512cb371815011923ef Author: Andrew Myers Date: Thu Feb 9 11:37:07 2017 -0800 Updating the tiled particles to use a pair-indexed map. Src/AmrCore/AMReX_AmrParticles.H Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp Tests/Particles/main.cpp commit 87e3b96fb5decb56e346a787d3349a9cb6bc47b7 Author: Weiqun Zhang Date: Thu Feb 9 10:53:55 2017 -0800 AMR_Adv_CF: works for single level now Src/F_Interfaces/Base/AMReX_box_mod.F90 Tutorials/AMR_Adv_CF/Exec/Make.Adv Tutorials/AMR_Adv_CF/Source/Src_2d/Make.package Tutorials/AMR_Adv_CF/Source/Src_2d/advect_2d_mod.F90 Tutorials/AMR_Adv_CF/Source/Src_2d/compute_flux_2d.f90 Tutorials/AMR_Adv_CF/Source/Src_2d/slope_2d.f90 Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 commit 55be81daf390cbb28bdc5d77147296a012e75e66 Author: Weiqun Zhang Date: Thu Feb 9 10:14:08 2017 -0800 fix box type for amrex_mfiter Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 027e117cbaeee16087a9c578f514ea815d7116cb Author: Weiqun Zhang Date: Thu Feb 9 09:52:48 2017 -0800 AMR_Adv_CF: get face velocity Tutorials/AMR_Adv_CF/Source/compute_dt_mod.F90 Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 commit 5bdc5430249bb7af7ce142f1592a5dfe7e1c71bc Author: Weiqun Zhang Date: Thu Feb 9 09:40:16 2017 -0800 simplify amrex_print Src/F_Interfaces/Base/AMReX_box_fi.cpp Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_distromap_fi.cpp Src/F_Interfaces/Base/AMReX_distromap_mod.F90 commit a59d07adaab57d4cee902f29b19ed290581f99eb Author: Weiqun Zhang Date: Thu Feb 9 09:30:33 2017 -0800 add nodal flag to amrex_box Src/F_Interfaces/Base/AMReX_box_mod.F90 commit 904a37a6158fb79f5547d2f01e906ea73d77ad04 Author: Weiqun Zhang Date: Thu Feb 9 08:56:56 2017 -0800 clean up by using fab%resize Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_fab_mod.F90 Tutorials/AMR_Adv_CF/Exec/SingleVortex/face_velocity_2d.F90 Tutorials/AMR_Adv_CF/Source/compute_dt_mod.F90 commit 21d6a03dc5705e79d4863e532d067835a1e34948 Author: Weiqun Zhang Date: Wed Feb 8 21:05:32 2017 -0800 more amrex fab procedures Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_fab_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 89da4fed282496731fa0a4759480a893975e06e6 Author: Weiqun Zhang Date: Wed Feb 8 17:04:34 2017 -0800 start amrex_fab_module Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 Src/F_Interfaces/Base/AMReX_base_mod.F90 Src/F_Interfaces/Base/AMReX_fab_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Src/F_Interfaces/Base/Make.package Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 commit 675bbe80e293aa30948a96018a4601b3c7efae93 Author: Weiqun Zhang Date: Wed Feb 8 16:50:52 2017 -0800 add amrex prefix to mempool functions Src/Base/AMReX.cpp Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_MemPool.H Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_mempool_f.f90 Src/F_BaseLib/boxlib_f.f90 Src/F_BaseLib/fab.f90 Src/F_Interfaces/Base/AMReX_fab_mod.F90 commit 9ff2febe70f4ed6be58f26b39913db46814785d6 Author: Weiqun Zhang Date: Wed Feb 8 15:38:29 2017 -0800 add generic assignment for tagboxarray Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 3baa8d9db64729bd95c1338ca820d2e59f3e633f Author: Weiqun Zhang Date: Wed Feb 8 15:32:27 2017 -0800 define some amrex function interfaces a user code must provide Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 Src/F_Interfaces/Base/AMReX_physbc_mod.F90 Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit afd65cd30d89d2cdf6f836ad3cf9149ded84d7ba Author: Weiqun Zhang Date: Wed Feb 8 14:44:06 2017 -0800 add amrex_fillpatch_single Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90 Src/F_Interfaces/AmrCore/AMReX_fillpatch_fi.cpp Src/F_Interfaces/AmrCore/AMReX_fillpatch_mod.F90 Src/F_Interfaces/AmrCore/Make.package Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 commit 0394db00d820b06ba8f361d1c8299e003ec1e6d9 Author: Weiqun Zhang Date: Wed Feb 8 14:12:35 2017 -0800 add physbc Src/F_Interfaces/Base/AMReX_FPhysBC.H Src/F_Interfaces/Base/AMReX_base_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_distromap_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Src/F_Interfaces/Base/AMReX_physbc_fi.cpp Src/F_Interfaces/Base/AMReX_physbc_mod.F90 Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit ff8b8fe25cf6e8886059712062345e605ec71113 Author: Weiqun Zhang Date: Wed Feb 8 12:49:25 2017 -0800 rename for consistence Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90 Src/F_Interfaces/AmrCore/AMReX_amrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_amrcore_mod.F90 Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp Src/F_Interfaces/AmrCore/Make.package Tutorials/AMR_Adv_CF/Source/fmain.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 521a804c1c103e583382a921a1314b67073a4009 Author: Weiqun Zhang Date: Wed Feb 8 12:40:04 2017 -0800 add AMReX_FPhysBC Src/F_Interfaces/Base/AMReX_FPhysBC.H Src/F_Interfaces/Base/AMReX_FPhysBC.cpp Src/F_Interfaces/Base/AMReX_physbc_fi.cpp Src/F_Interfaces/Base/AMReX_physbc_mod.F90 Src/F_Interfaces/Base/Make.package Tutorials/AMR_Adv_CF/Source/Make.package Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 Tutorials/AMR_Adv_CF/Source/fillpatch_mod.F90 commit 290515a63563bc3b4c84d33e53a1138e1cfb473a Author: Tan Nguyen Date: Wed Feb 8 11:56:25 2017 -0800 update type checker Tools/typechecker/typeChecker.py commit 25d93bf5bf3fd622ea75afdbcfeb46a5219948e7 Author: Tan Nguyen Date: Wed Feb 8 11:52:01 2017 -0800 fix a few fortran headers Src/AmrCore/AMReX_FLUXREG_F.H Src/AmrCore/AMReX_INTERP_F.H Src/Base/AMReX_COORDSYS_F.H Src/Boundary/AMReX_INTERPBNDRYDATA_F.H commit 42e7a3d07d892d1376c0325d477608ff1f4a7f68 Author: Weiqun Zhang Date: Wed Feb 8 10:21:31 2017 -0800 call regrid Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Tutorials/AMR_Adv_CF/Exec/SingleVortex/inputs Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 Tutorials/AMR_Adv_CF/Source/plotfile_mod.F90 commit f077ec590a9662dbddef7791e661d91e90c5c5bf Author: Weiqun Zhang Date: Wed Feb 8 08:54:28 2017 -0800 change how amrex_mpi_real is initialzied Src/F_Interfaces/Base/AMReX_parallel_mod.F90 commit 0d86a15bfcda17edfd2136d09df743853158635d Author: Weiqun Zhang Date: Tue Feb 7 20:40:55 2017 -0800 mpi_amrex_real --> amrex_mpi_real Src/F_Interfaces/Base/AMReX_parallel_mod.F90 commit d914aa135f37dc3f2643db081dcf614b74d4574b Author: Weiqun Zhang Date: Tue Feb 7 17:09:39 2017 -0800 add recursive timestep function Tutorials/AMR_Adv_CF/Source/compute_dt_mod.F90 Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 commit 18bf56bcb3221754bc076b6f0ab0a1b954634c43 Author: Weiqun Zhang Date: Tue Feb 7 17:01:18 2017 -0800 add some parallel reduce functions Src/F_Interfaces/Base/AMReX_parallel_mod.F90 commit 10624518bd05329b168ceb5e85270872a75cde78 Author: Weiqun Zhang Date: Tue Feb 7 16:17:38 2017 -0800 implement compute dt Src/F_Interfaces/Base/AMReX_base_mod.F90 Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Tutorials/AMR_Adv_CF/Exec/SingleVortex/Make.package Tutorials/AMR_Adv_CF/Exec/SingleVortex/face_velocity_2d.F90 Tutorials/AMR_Adv_CF/Source/Make.package Tutorials/AMR_Adv_CF/Source/compute_dt_mod.F90 Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 commit 86e9043708204c34ed46e5a385099cf6a88c2d44 Author: Weiqun Zhang Date: Tue Feb 7 14:33:23 2017 -0800 move geometry array into amrex_famrcore module Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Tutorials/AMR_Adv_CF/Source/averagedown_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 Tutorials/AMR_Adv_CF/Source/plotfile_mod.F90 commit 8e9a8741fe1813db14bd6a4cfc1f4eeb8d0fe000 Author: Weiqun Zhang Date: Tue Feb 7 14:26:59 2017 -0800 add evolve module Tutorials/AMR_Adv_CF/Source/Make.package Tutorials/AMR_Adv_CF/Source/averagedown_mod.F90 Tutorials/AMR_Adv_CF/Source/evolve_mod.F90 Tutorials/AMR_Adv_CF/Source/fmain.F90 commit 2e46859bd6fd7995e3a1e4ca76e20ce96a7beba9 Author: Weiqun Zhang Date: Tue Feb 7 14:23:36 2017 -0800 add missing use module Src/F_Interfaces/Base/AMReX_box_mod.F90 commit 88a44374e9b88b5085f0201b286aa136675cc831 Author: Weiqun Zhang Date: Tue Feb 7 14:22:48 2017 -0800 add implicit none to interface blocks Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90 Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_distromap_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 440b736a5cbc1d37a02bc2df44a0b49f13f8ff20 Author: Weiqun Zhang Date: Tue Feb 7 14:17:08 2017 -0800 add multifabutil module Src/F_Interfaces/Base/AMReX_base_mod.F90 Src/F_Interfaces/Base/AMReX_multifabutil_fi.cpp Src/F_Interfaces/Base/AMReX_multifabutil_mod.F90 Src/F_Interfaces/Base/Make.package Tutorials/AMR_Adv_CF/Source/Make.package Tutorials/AMR_Adv_CF/Source/initdata.F90 commit 5461d410bda8933efefda33a61c8aa5e870e4522 Author: Weiqun Zhang Date: Tue Feb 7 13:48:58 2017 -0800 write plotfile Src/Base/AMReX_string_mod.F90 Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Src/F_Interfaces/AmrCore/AMReX_tagbox_fi.cpp Src/F_Interfaces/Base/AMReX_base_mod.F90 Src/F_Interfaces/Base/AMReX_plotfile_fi.cpp Src/F_Interfaces/Base/AMReX_plotfile_mod.F90 Src/F_Interfaces/Base/Make.package Tutorials/AMR_Adv_CF/Source/Make.package Tutorials/AMR_Adv_CF/Source/error_estimate_mod.F90 Tutorials/AMR_Adv_CF/Source/initdata.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 Tutorials/AMR_Adv_CF/Source/plotfile_mod.F90 Tutorials/AMR_Adv_CF/Source/tagging_mod.F90 commit e9e1fb7aec6019f6962fe74c6131f47f01b01647 Author: Weiqun Zhang Date: Tue Feb 7 11:10:10 2017 -0800 finish error estimate module for the example Src/F_Interfaces/AmrCore/AMReX_FAmrCore.H Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Tutorials/AMR_Adv_CF/Source/error_estimate_mod.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 3c54af27e3d8c1ae10d8520bb310fdf7ed6c97f3 Author: Weiqun Zhang Date: Tue Feb 7 10:42:03 2017 -0800 add getarr and queryarr for int and real Src/Base/AMReX_parmparse_fi.cpp Src/Base/AMReX_parmparse_mod.F90 commit 39a19098b3904d7ec08ce47a6d933f320936601a Author: Weiqun Zhang Date: Tue Feb 7 09:08:13 2017 -0800 fix extra argument Src/Base/AMReX_BaseFab_nd.f90 commit 8bd648b3b1a385afb3b90799d0e0017b9a37aa70 Author: Weiqun Zhang Date: Tue Feb 7 09:04:43 2017 -0800 rename amrex_module to amrex_base_module Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90 Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90 Src/F_Interfaces/Base/AMReX_base_mod.F90 Src/F_Interfaces/Base/AMReX_fi_mod.F90 Src/F_Interfaces/Base/Make.package Tutorials/HeatEquation_EX1_CF/advance.f90 Tutorials/HeatEquation_EX1_CF/fmain.f90 Tutorials/HeatEquation_EX1_CF/init_phi.f90 Tutorials/HelloWorld_CF/fmain.f90 commit 93cb474425ac4c1698d38c6fa2edfcc96d2af790 Author: Weiqun Zhang Date: Tue Feb 7 08:56:48 2017 -0800 add amrex_tagbox_module Src/F_Interfaces/AmrCore/AMReX_amr_mod.F90 Src/F_Interfaces/AmrCore/AMReX_tagbox_mod.F90 Src/F_Interfaces/AmrCore/Make.package Tutorials/AMR_Adv_CF/Source/fmain.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 063d5ace8afd52f65398fc79f3a4761d40f1ffa7 Author: tannguyen Date: Tue Feb 7 03:39:25 2017 -0800 first version of the static type checker Tools/typechecker/pycparser/__init__.py Tools/typechecker/pycparser/_ast_gen.py Tools/typechecker/pycparser/_build_tables.py Tools/typechecker/pycparser/_c_ast.cfg Tools/typechecker/pycparser/ast_transforms.py Tools/typechecker/pycparser/c_ast.py Tools/typechecker/pycparser/c_generator.py Tools/typechecker/pycparser/c_lexer.py Tools/typechecker/pycparser/c_parser.py Tools/typechecker/pycparser/ply/LICENSE Tools/typechecker/pycparser/ply/__init__.py Tools/typechecker/pycparser/ply/cpp.py Tools/typechecker/pycparser/ply/ctokens.py Tools/typechecker/pycparser/ply/lex.py Tools/typechecker/pycparser/ply/yacc.py Tools/typechecker/pycparser/ply/ygen.py Tools/typechecker/pycparser/plyparser.py Tools/typechecker/typeChecker.py commit c865e9bc4c9c8d8382fe1365524334f41ae44b7f Author: Andrew Myers Date: Mon Feb 6 17:38:36 2017 -0800 Don't go through this if tiling is turned off. Src/Particle/AMReX_ParticleContainerI.H commit dff43c62c375c9dfcb4c5410aa720761949d91c1 Author: Weiqun Zhang Date: Mon Feb 6 16:42:07 2017 -0800 add imultifab and errorest Src/F_Interfaces/AmrCore/AMReX_FAmrCore.H Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Tutorials/AMR_Adv_CF/Source/Make.package Tutorials/AMR_Adv_CF/Source/error_estimate_mod.F90 Tutorials/AMR_Adv_CF/Source/initdata.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit b0b2d3887dc8af4b99e10050293e2e0e5f31ef21 Merge: f93763b9d f33cae74d Author: Andrew Myers Date: Mon Feb 6 15:11:22 2017 -0800 Merge branch 'development' of https://bitbucket.org/berkeleylab/amrex into particle_refactor merging with development. commit f33cae74dc2d38d19fba3fffb2a0cc72dc804692 Author: Weiqun Zhang Date: Mon Feb 6 15:01:02 2017 -0800 start to support virtual functions in F_Interface Src/AmrCore/AMReX_AmrCore.H Src/F_Interfaces/AmrCore/AMReX_FAmrCore.H Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Tutorials/AMR_Adv_CF/Source/initdata.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H commit f93763b9dc40feb7cbd657e4e22f63a5b36d6eb2 Author: Andrew Myers Date: Mon Feb 6 14:52:04 2017 -0800 Fixing a couple of tiling-related bugs. Src/Particle/AMReX_ParticleContainerI.H commit 3c9f6f3a7169785f0ce2d987e861f5f616c1c036 Author: Weiqun Zhang Date: Mon Feb 6 13:31:12 2017 -0800 fix typo Src/Amr/AMReX_Amr.H commit 0acee88807e68bdc54b92c9e4ba1d967470e953d Author: Weiqun Zhang Date: Mon Feb 6 13:20:20 2017 -0800 add a few virtual functions to AmrCore Src/Amr/AMReX_Amr.H Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp commit c63c72898583ef14a6927841d36a5680c4d978c9 Author: Andrew Myers Date: Mon Feb 6 12:41:56 2017 -0800 Adding tiling information to the particle location functions. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit d9db03a6f11467f9251ad6bc5dad74bd14c52628 Author: Andrew Myers Date: Mon Feb 6 11:27:39 2017 -0800 Moving many of the Particle static methods to the ParticleContainer class instead. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit 0aa445240365ad8c33767904d6a1b33ba9a6341a Author: Andrew Myers Date: Mon Feb 6 10:12:20 2017 -0800 Restructure unpacking the particle data so we don't have to call Where twice. Src/Particle/AMReX_ParticleContainerI.H Tests/Particles/test.py commit 4b64dfffeb776e9c6e28a85e2461d3f3b608ce0b Author: Andrew Myers Date: Sun Feb 5 19:15:10 2017 -0800 Communicate the particle data in one MPI burst instead of two. Src/Particle/AMReX_ParticleContainerI.H commit b7dd089a920ede5667ca2b34153b9cf7098e56ac Author: Weiqun Zhang Date: Fri Feb 3 21:25:31 2017 -0800 update amrex_multifab_build Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit ccd395899c1b507c6ebd801971c72085882bab94 Author: Weiqun Zhang Date: Fri Feb 3 17:14:50 2017 -0800 build fine levels Tutorials/AMR_Adv_CF/Source/initdata.F90 commit 014a1fd2748995e90034274a9a4ab9c2a20b6ecf Author: Weiqun Zhang Date: Fri Feb 3 16:33:06 2017 -0800 add amrex_multifab_write Src/F_Interfaces/Base/AMReX_fi_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Src/F_Interfaces/Base/AMReX_vismf_fi.cpp Src/F_Interfaces/Base/Make.package Tutorials/AMR_Adv_CF/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_CF/Exec/SingleVortex/Prob.f90 Tutorials/AMR_Adv_CF/Source/initdata.F90 commit 2b90c7118d6df5cb25e89f794e998c75cb97d672 Author: Andrew Myers Date: Fri Feb 3 16:08:59 2017 -0800 Have the particle iterator inherit as much as possible from MFITer Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp Tests/Particles/ParticleIterator/main.cpp commit bcdfbb75e7931b2b98828ace9d5eb68f0c7024fb Author: Andrew Myers Date: Fri Feb 3 15:57:20 2017 -0800 Allocating dummy multifabs in the particle container for helping with iteration. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H commit b5b9eee72bfa396cce0517e58374883a05b09f88 Author: Weiqun Zhang Date: Fri Feb 3 15:13:28 2017 -0800 Add amrex_fi_module. It doesn't do anything now. But in the future we might do some fortran specific init and finalize stuff Src/F_Interfaces/Base/AMReX_fi_main.cpp Src/F_Interfaces/Base/Make.package Tutorials/AMR_Adv_CF/Source/initdata.F90 commit afa11385021649a0e9e8879a0199c2348f996c68 Author: Andrew Myers Date: Fri Feb 3 15:06:28 2017 -0800 Adding a couple of useful tile-related methods to MFIter. Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp commit 67b6b4c31c2f1c0f994eaad916a34f31133485cb Author: Weiqun Zhang Date: Fri Feb 3 14:56:21 2017 -0800 make base level Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Tutorials/AMR_Adv_CF/Source/initdata.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 1b2c950ba7500c4255d8ba594db537cbb3dee49f Author: Weiqun Zhang Date: Fri Feb 3 13:36:13 2017 -0800 add some set functions Src/F_Interfaces/AmrCore/AMReX_FAmrCore.H Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 commit ef4e438ddbbadebb314040661b148176b74d0e04 Author: Andrew Myers Date: Fri Feb 3 11:47:13 2017 -0800 update main particle test. Tests/Particles/main.cpp commit 9e550736ccb3a1de12a3bddaa6e4d9f53aed8540 Merge: e552feef2 957c3760b Author: Andrew Myers Date: Fri Feb 3 11:46:15 2017 -0800 Merge branch 'particle_refactor' of https://bitbucket.org/berkeleylab/amrex into particle_refactor merging. commit e552feef21451ae56755a8d11f515476009e6f0f Author: Andrew Myers Date: Fri Feb 3 11:44:04 2017 -0800 Make the_next_id static member data of particle. Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_Particles.H commit 957c3760b82e0835cdefe28e9c5f54be08bd1dcb Author: Weiqun Zhang Date: Fri Feb 3 10:48:54 2017 -0800 minor Src/Particle/AMReX_Particles.H commit ed22b51bc76296d02216e5753661f05e0b901380 Author: Weiqun Zhang Date: Fri Feb 3 09:48:15 2017 -0800 fix cpu() and add const & version of some functions Src/Particle/AMReX_Particles.H commit 7e1b06f8828fc4e5e59d8e652fece7c79f5f383f Author: Weiqun Zhang Date: Fri Feb 3 09:28:52 2017 -0800 some constexpr Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_Particles.H commit 83ad54db4c93046bb28c6e9dfc9d2918b7bf7b14 Author: Weiqun Zhang Date: Fri Feb 3 08:49:35 2017 -0800 mark some finalization procedures as impure elemental Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_distromap_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 73cf606758792f9b70d6eefe861700539e03bc7d Author: Andrew Myers Date: Thu Feb 2 17:43:27 2017 -0800 Allocate the appropriate data structures for the tiling case. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 19399a4520aa90ffe456bfaa298031067160ebd4 Author: Weiqun Zhang Date: Thu Feb 2 17:04:20 2017 -0800 need to clear the old level and update finest_level variable Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Tutorials/AMR_Adv_CF/Source/initdata.F90 Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp commit 7677bec27815886def3b455492fb1cd5b2ff1c87 Author: Andrew Myers Date: Thu Feb 2 16:44:47 2017 -0800 Replacing the loops in the particle code with ones that use the tiling iterators. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp Tests/Particles/ParticleIterator/main.cpp commit 165a892e8cdb0fa61e0c57c33a93581e82f18d5e Author: Weiqun Zhang Date: Thu Feb 2 16:24:26 2017 -0800 add amrex_print to box, boxarray and distromap modules Src/Base/AMReX_Print.H Src/F_Interfaces/Base/AMReX_box_fi.cpp Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_distromap_fi.cpp Src/F_Interfaces/Base/AMReX_distromap_mod.F90 Src/F_Interfaces/Base/Make.package Tutorials/AMR_Adv_CF/Source/initdata.F90 commit 97fc16df9db593fe95cd8f959a128d5d8760e075 Author: Weiqun Zhang Date: Thu Feb 2 15:13:15 2017 -0800 add some get functions Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_fi.cpp Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Tutorials/AMR_Adv_CF/Source/Make.package Tutorials/AMR_Adv_CF/Source/fmain.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 4937ad326558ffe5c8b6d6dd3d7c0be88f2e999e Author: Andrew Myers Date: Thu Feb 2 14:01:44 2017 -0800 A tiling particle iterator that works in parallel. Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp Tests/Particles/ParticleIterator/main.cpp commit 4c7555911b3b2037be6ff8a8961558c4be642ffb Author: Weiqun Zhang Date: Thu Feb 2 12:28:47 2017 -0800 amrex_famr_core: add static data Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Tutorials/AMR_Adv_CF/Source/fmain.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit 7f713251f933680bffe159a234cc567f422062f1 Author: Andrew Myers Date: Thu Feb 2 11:36:48 2017 -0800 Some renaming for clarity. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit b3f60c51a1b406eac2b11c3ca9ddf3103bf3d02c Author: Andrew Myers Date: Thu Feb 2 11:21:51 2017 -0800 Some work towards implementing tiling for the Particle Container. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit 7e28790e68cbca53e3497e3d0de65da3a421a2e2 Author: Weiqun Zhang Date: Thu Feb 2 10:52:44 2017 -0800 add amrex_error_module and call amrex_abort if amrex_mfiter assignment is called Src/Base/AMReX_error_fi.cpp Src/Base/AMReX_error_mod.F90 Src/Base/CMakeLists.txt Src/Base/Make.package Src/F_Interfaces/Base/AMReX_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 25db6fc5ee26539c76f99cbdf29aaddeb5bd73c1 Author: Weiqun Zhang Date: Thu Feb 2 10:14:19 2017 -0800 define assignment operator for types containing c_ptr Src/Base/AMReX_parmparse_mod.F90 Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_distromap_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Tutorials/AMR_Adv_CF/Source/fmain.F90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 commit ba0fa92301a594f9ed52b1a7e0a1a028352a6e3f Author: Andrew Myers Date: Wed Feb 1 19:29:02 2017 -0800 Cleaning up the code a bit with some typedefs. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_Particles.H commit 2501a682b72ee3023575f9b77dbad032abeb6722 Author: Andrew Myers Date: Wed Feb 1 19:16:42 2017 -0800 an iterator for doing tiling with particles and a test. Tests/Particles/ParticleIterator/GNUmakefile Tests/Particles/ParticleIterator/Make.package Tests/Particles/ParticleIterator/main.cpp commit fec786482ff4c58d05f33d52aa20fe5796084940 Author: Andrew Myers Date: Wed Feb 1 17:13:42 2017 -0800 don't need this data structure to store pointers. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H commit 90ddd82a74fd73234254ea24084c53daba2c9c91 Merge: 2d762bd45 1a44fcc93 Author: Weiqun Zhang Date: Wed Feb 1 17:07:55 2017 -0800 Merge branch 'development' into fortran_interface commit 1a44fcc937e038d7b37784e0ee24b472966ae96c Author: Weiqun Zhang Date: Wed Feb 1 17:07:12 2017 -0800 fix BLBackTrace namespace issue Src/Base/AMReX_BLBackTrace.H commit 2d762bd45ba2aadef4337ebb6c98bf8bd144f7c3 Author: Weiqun Zhang Date: Wed Feb 1 17:07:12 2017 -0800 fix BLBackTrace namespace issue Src/Base/AMReX_BLBackTrace.H commit d9330cd13618f1503c55f33d6f149ac35f7b747a Author: Weiqun Zhang Date: Wed Feb 1 16:12:32 2017 -0800 WIP: F_Interfaces/AmrCore Src/F_Interfaces/AmrCore/AMReX_FAmrCore.H Src/F_Interfaces/AmrCore/AMReX_FAmrCore.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_fi.cpp Src/F_Interfaces/AmrCore/AMReX_famrcore_mod.F90 Src/F_Interfaces/AmrCore/Make.package Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_distromap_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Src/F_Interfaces/Base/AMReX_parallel_mod.F90 Tutorials/AMR_Adv_CF/Exec/Make.Adv Tutorials/AMR_Adv_CF/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_CF/Exec/SingleVortex/inputs Tutorials/AMR_Adv_CF/Source/Make.package Tutorials/AMR_Adv_CF/Source/fmain.F90 Tutorials/AMR_Adv_CF/Source/fmain.f90 Tutorials/AMR_Adv_CF/Source/my_amr_mod.F90 Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/GNUmakefile commit a75eec3969ad1a089e2655644ab6eebf5ca465b8 Author: Andrew Myers Date: Wed Feb 1 16:04:56 2017 -0800 No longer shift particles silently in add particle / initialization routines. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H commit 3a1caf52107ff028bd701b6727527e6e7aaec67c Author: Weiqun Zhang Date: Wed Feb 1 14:15:22 2017 -0800 fix HelloWorld_CF Tools/CompileTesting/compiletesting.py Tutorials/AMR_Adv_CF/README Tutorials/HeatEquation_EX1_CF/GNUmakefile Tutorials/HelloWorld_CF/GNUmakefile Tutorials/HelloWorld_CF/fmain.f90 commit b1be564ddff0b4e42341bc1d0f5b0dff7cf91a09 Author: Andrew Myers Date: Tue Jan 31 12:55:28 2017 -0800 Make communicating SOA data optional. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Tests/Particles/main.cpp commit 0bfc8c56372003b2be44a7f8689992d2aef9e200 Author: Andrew Myers Date: Tue Jan 31 12:31:06 2017 -0800 Fix bug in initialization. Src/Particle/AMReX_ParticleInit.H commit 39ad93df07d10a7c1de1dec598a444dc2f31e83d Author: Andrew Myers Date: Tue Jan 31 12:20:52 2017 -0800 Don't template on the particle container type. We always use std::vector. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.H commit 5e2352a4faedbf02fcd7cb1a42f421428b199b68 Author: Andrew Myers Date: Tue Jan 31 10:25:09 2017 -0800 Making the SOA particle test use two levels. Tests/Particles/main.cpp commit 996ec66e58a09f4efa59e082a5956cd7fbc98032 Author: Andrew Myers Date: Mon Jan 30 17:01:22 2017 -0800 Make this zero by default. Src/Particle/AMReX_Particles.H commit 067f470a2387710549e176ebcf6a0748a876fe0b Author: Andrew Myers Date: Mon Jan 30 16:45:54 2017 -0800 Use zero SoA attributes by default. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Tests/Particles/main.cpp Tests/Particles/test.py commit 9cfdde56747e7d6b7515beea2559fa07c4fb21c6 Author: Andrew Myers Date: Mon Jan 30 15:54:07 2017 -0800 Implementing MPI communication of struct-of-array style particle data and adding a test. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Tests/Particles/GNUmakefile Tests/Particles/Make.package Tests/Particles/main.cpp Tests/Particles/test.py commit f712c0e5eb86344646f1441fc0ba4c6729eb3406 Author: Weiqun Zhang Date: Mon Jan 30 14:54:28 2017 -0800 add --always to git describe as fallback. some codes may not have tags Tools/C_scripts/makebuildinfo_C.py commit 16787d31a4aaaf6aa33ab1864823976231db9805 Merge: 55dbe278c f84a50358 Author: Weiqun Zhang Date: Mon Jan 30 10:33:33 2017 -0800 Merge branch 'fortran_interface' into development commit f84a50358e7bd6b235162ccf1211c2620c91bb52 Author: Weiqun Zhang Date: Mon Jan 30 10:32:44 2017 -0800 set pointer to null after being deleted Src/F_Interfaces/Base/AMReX_geometry_mod.F90 commit e660ce58f472d9dc33f8013da75661e9fa561523 Author: Weiqun Zhang Date: Mon Jan 30 10:20:10 2017 -0800 fix gfortran macro Src/Base/AMReX_parmparse_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_distromap_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 55dbe278cdfce3ae12f089f88f20b65183821da9 Merge: e4c621fdd 93bd6c359 Author: Michael Zingale Date: Mon Jan 30 15:40:03 2017 +0000 Merged in mzingale/amrex/development (pull request #7) some updates to the Fortran commandline tools commit 93bd6c3591a6d6340d042e6b5dfe057c3fb203e7 Author: Michael Zingale Date: Sun Jan 29 12:01:36 2017 -0500 extend the `-v` option to take a string of space-separated variable to allow for outputing a specific set of variables. Previously it only allowed for a single variable. Tools/Postprocessing/F_Src/fextract.f90 commit 9d1676a23066898975c1199d4df8f257df30cbc0 Author: Michael Zingale Date: Sun Jan 29 12:01:25 2017 -0500 also output the % of domain covered Tools/Postprocessing/F_Src/fboxinfo.f90 commit ea9095daf9d154f3d344b4b0f5b984f7b1521418 Author: Weiqun Zhang Date: Sat Jan 28 15:37:59 2017 -0800 add contiguous to Fortran pointers Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit e4c621fdd8059e5acaa5698ada9c640a8d930881 Author: Weiqun Zhang Date: Sat Jan 28 12:54:55 2017 -0800 clean up Src/F_Interfaces/Base/AMReX_parallel_fi.cpp Src/F_Interfaces/Base/Make.package commit f7d5d1910fa0cf117b515475781f68404e3f16ab Author: Weiqun Zhang Date: Sat Jan 28 12:50:49 2017 -0800 add DistributionMapping fortran wrapper Src/F_Interfaces/Base/AMReX_distromap_fi.cpp Src/F_Interfaces/Base/AMReX_distromap_mod.F90 commit 368680a66c8fa03f003c9ade067f9b53919199e4 Author: Weiqun Zhang Date: Sat Jan 28 12:48:33 2017 -0800 forgot to check in a new file Src/Base/AMReX_omp_mod.F90 commit 327654ae2a067067d381abe24d839aa41f7bafb7 Author: Weiqun Zhang Date: Sat Jan 28 12:45:35 2017 -0800 remove deprecated threadbox.f90 Src/Base/AMReX_threadbox.f90 Src/Base/CMakeLists.txt Src/Base/Make.package commit c0701c0544ef1a56bea5a90e175b41c7f70d39df Author: Weiqun Zhang Date: Sat Jan 28 12:43:13 2017 -0800 change the way of passing a c null char array because pgi didn't like it Src/Base/AMReX_parmparse_mod.F90 Src/Base/AMReX_string_mod.F90 commit 7752373e496d97e2329e52dbff17edec557445db Author: Weiqun Zhang Date: Sat Jan 28 12:11:00 2017 -0800 fix macro around final and add destroy calls Src/Base/AMReX_parmparse_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Tutorials/HeatEquation_EX1_CF/advance.f90 Tutorials/HeatEquation_EX1_CF/fmain.f90 Tutorials/HeatEquation_EX1_CF/init_phi.f90 commit 200c000f13dc146b2f27b23c7dc025b1c99861ee Author: Weiqun Zhang Date: Sat Jan 28 10:41:16 2017 -0800 turn on finalize for gfortran > 4 Src/Base/AMReX_parmparse_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 commit 1d9de1affcffac1aeb723211a929a22bb26d3296 Author: Weiqun Zhang Date: Sat Jan 28 10:35:02 2017 -0800 make F_Interfaces compile again in AMReX Src/Base/AMReX.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_parmparse_mod.F90 Src/Base/CMakeLists.txt Src/Base/Make.package Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_geometry_fi.cpp Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Src/F_Interfaces/Base/AMReX_omp_mod.F90 Src/F_Interfaces/Base/AMReX_parallel_fi.cpp Src/F_Interfaces/Base/AMReX_parallel_mod.F90 Src/F_Interfaces/Base/Make.package Tutorials/HeatEquation_EX1_CF/GNUmakefile Tutorials/HeatEquation_EX1_CF/advance.f90 Tutorials/HeatEquation_EX1_CF/fmain.f90 Tutorials/HeatEquation_EX1_CF/init_phi.f90 commit 92fa2074acb6c724e622bd72f4b0499379cab0eb Author: Andrew Myers Date: Fri Jan 27 22:12:52 2017 -0800 Provide a more convenient API for working with the new particle class. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit 93341032fb90dbb299cbd7aecc54e16e10ca80da Author: Andrew Myers Date: Fri Jan 27 16:42:31 2017 -0800 Splitting the implementation of the particle and particle container classes into seperate files. Src/Particle/AMReX_ParticleContainerI.H Src/Particle/AMReX_ParticleI.H Src/Particle/AMReX_Particles.H Src/Particle/CMakeLists.txt Src/Particle/Make.package commit e7ffb211e745eb66c3c9698a15abbd74d88a5feb Author: Andrew Myers Date: Fri Jan 27 16:23:17 2017 -0800 Removing the full_where option - making this always true. Src/Particle/AMReX_Particles.H commit 89afe1a9aadd9a70ba3487298c59ab6602407129 Author: Andrew Myers Date: Fri Jan 27 16:06:40 2017 -0800 Remove where_already_called option, since the particles no longer store their cell / level / grid data. Src/Particle/AMReX_Particles.H commit 0ee8c7cef05610844b48fb90ece4a1236ddcd6b5 Author: Andrew Myers Date: Fri Jan 27 15:27:40 2017 -0800 This version gets the same test results as before the refactor, in parallel and on multiple levels. Src/Particle/AMReX_Particles.H commit 62ac78ec4c7ec5932ed04e502cee18390181999c Author: Andrew Myers Date: Fri Jan 27 15:15:24 2017 -0800 make sure to call Where in MoveKick Src/Particle/AMReX_Particles.H commit 8221b4c7d6e9e0cf5986a86729482b240ec55ade Author: Andrew Myers Date: Fri Jan 27 13:00:57 2017 -0800 Fix bug I just introduced into the MPI communication code. Src/Particle/AMReX_Particles.H commit 7053e70b7c3f6124484d1fe07567634cf6f52f3d Author: Andrew Myers Date: Fri Jan 27 12:40:48 2017 -0800 Getting rid of the extra arrays in the particle struct. Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit de9e12cb08a3426e8264bdca793e2da3a5f8b430 Merge: 9e5f84f8c a9ad31d28 Author: Weiqun Zhang Date: Fri Jan 27 12:32:45 2017 -0800 Merge branch 'development' into fortran_interface Conflicts: Src/Amr/AMReX_extrapolater_1d.f90 Src/Amr/AMReX_extrapolater_2d.f90 Src/Amr/AMReX_extrapolater_3d.f90 Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_fort_mod.F90 Src/Base/AMReX_mempool_f.f90 Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/Prob.f90 Tutorials/HeatEquation_EX2_C/bc_fill_nd.F90 commit a9ad31d289d39a239c447a527da915c1ae478fb2 Author: Weiqun Zhang Date: Fri Jan 27 10:34:05 2017 -0800 migration doc Docs/Migration/Migration.md commit 1e7be978b8b047628d088d6dc4d33314456098fb Author: Andrew Myers Date: Fri Jan 27 09:47:05 2017 -0800 Making Particle a POD type. Src/Particle/AMReX_Particles.H commit 6c59987244d108d66e5be5ed0ead76ff647f8b2f Merge: 65b9f54c0 d350fc6a3 Author: Andrew Myers Date: Thu Jan 26 20:41:31 2017 -0800 merging. commit 65b9f54c05d775c5d0b58275b25c9797a4dd89b5 Author: Andrew Myers Date: Thu Jan 26 20:33:17 2017 -0800 Removing the lev, grid, and cell attributes from the particle class - compute these on the fly instead. Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit e970737b619932ab328cb70d35639e9498e4860d Author: Marc Day Date: Thu Jan 26 18:02:36 2017 -0800 New version of stencil test, stenciTestMSD.cpp that takes a flag compute_geom to either compute or read EB info Tests/GeometryShop/stencilTestbed/exec/GNUmakefile Tests/GeometryShop/stencilTestbed/exec/sphere.inputs Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTestMSD.cpp commit 7f070328cc4a537d24e124902d47aae79db19d8b Author: Weiqun Zhang Date: Thu Jan 26 16:02:54 2017 -0800 Real --> amrex::Real MiniApps/MultiGrid_C/COEF_F.H MiniApps/MultiGrid_C/RHS_F.H MiniApps/PGAS_SMC/SMC.H MiniApps/PGAS_SMC/SMC_F.H Src/Amr/AMReX_Derive.H Src/Amr/AMReX_Extrapolater.cpp Src/Amr/AMReX_MAKESLICE_F.H Src/Amr/AMReX_PROB_AMR_F.H Src/Amr/AMReX_SLABSTAT_F.H Src/Amr/AMReX_SlabStat.H Src/Amr/AMReX_extrapolater_1d.f90 Src/Amr/AMReX_extrapolater_2d.f90 Src/Amr/AMReX_extrapolater_3d.f90 Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_FLUXREG_F.H Src/AmrCore/AMReX_INTERP_F.H Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BLFort.H Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_COORDSYS_F.H Src/Base/AMReX_MemPool.H Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_REAL.H Src/Base/AMReX_Utility.cpp Src/Base/AMReX_bl_fort_module.F90 Src/Base/AMReX_fort_mod.F90 Src/Base/AMReX_mempool_f.f90 Src/Base/AMReX_parmparse_fi.cpp Src/Base/AMReX_parmparse_mod.F90 Src/Base/AMReX_string_mod.F90 Src/Base/CMakeLists.txt Src/Base/Make.package Src/Boundary/AMReX_INTERPBNDRYDATA_F.H Src/Extern/amrdata/AMReX_AmrData.cpp Src/F_BaseLib/MultiFab_C_F.H Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H Src/LinearSolvers/C_CellMG/AMReX_LO_F.H Src/LinearSolvers/C_CellMG/AMReX_LP_F.H Src/LinearSolvers/C_CellMG/AMReX_MG_F.H Src/LinearSolvers/C_CellMG4/AMReX_ABec2_F.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4_F.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCLO_F.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp_f.h Src/Particle/AMReX_Particles_F.H Tests/LinearSolvers/C_CellMG/COEF_F.H Tests/LinearSolvers/C_CellMG/MACOPERATOR_F.H Tests/LinearSolvers/C_CellMG/MacOpMacDrivers.H Tests/LinearSolvers/C_CellMG/MacOperator.H Tests/LinearSolvers/C_TensorMG/main_F.H Tests/LinearSolvers/ComparisonTest/COEF_F.H Tests/LinearSolvers/ComparisonTest/COMP_NORM_F.H Tools/C_util/Convergence/AVGDOWN_F.H Tools/C_util/Statistics/AVGDOWN_F.H Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/Prob.f90 Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdvBC.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H Tutorials/HeatEquation_EX1_C/myfunc_F.H Tutorials/HeatEquation_EX1_C/writePlotFile.H Tutorials/HeatEquation_EX2_C/bc_fill_nd.F90 Tutorials/HeatEquation_EX2_C/myfunc_F.H Tutorials/HeatEquation_EX2_C/writePlotFile.H Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/RHS_F.H commit 9e5f84f8c9bd92199681ace4bed6c4ce1e499478 Author: Weiqun Zhang Date: Thu Jan 26 13:31:12 2017 -0800 more renaming Src/F_Interfaces/Base/AMReX_boxarray_mod.F90 Src/F_Interfaces/Base/AMReX_boxlib_mod.F90 Src/F_Interfaces/Base/AMReX_fi_main.cpp Src/F_Interfaces/Base/AMReX_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_mod.F90 Src/F_Interfaces/Base/Make.package commit d086eacafec6593c90d1ab48867b0fe8b24f1295 Author: Andrew Myers Date: Thu Jan 26 13:14:33 2017 -0800 Fix error in template instantiation. Src/Particle/AMReX_Particles.H commit 24fd81f0bb2ae3fd3815e921e84691c03a3f43df Author: Weiqun Zhang Date: Thu Jan 26 13:12:16 2017 -0800 F_Interfaces/BaseLib --> F_Interfaces/Base for consistence Src/F_Interfaces/Base/AMReX_box_mod.F90 Src/F_Interfaces/Base/AMReX_boxarray_fi.cpp Src/F_Interfaces/Base/AMReX_boxlib_mod.F90 Src/F_Interfaces/Base/AMReX_fi_main.cpp Src/F_Interfaces/Base/AMReX_geometry_fi.cpp Src/F_Interfaces/Base/AMReX_geometry_mod.F90 Src/F_Interfaces/Base/AMReX_multifab_fi.cpp Src/F_Interfaces/Base/AMReX_omp_mod.F90 Src/F_Interfaces/Base/AMReX_parallel_fi.cpp Src/F_Interfaces/Base/AMReX_parallel_mod.F90 Src/F_Interfaces/Base/Make.package commit fc5f7ea7363d4a1cc653f3afbca48b0e64b0527b Author: Weiqun Zhang Date: Thu Jan 26 13:11:09 2017 -0800 add AMReX prefix Src/F_Interfaces/BaseLib/AMReX_box_mod.F90 Src/F_Interfaces/BaseLib/AMReX_boxarray_fi.cpp Src/F_Interfaces/BaseLib/AMReX_boxlib_mod.F90 Src/F_Interfaces/BaseLib/AMReX_fi_main.cpp Src/F_Interfaces/BaseLib/AMReX_geometry_fi.cpp Src/F_Interfaces/BaseLib/AMReX_geometry_mod.F90 Src/F_Interfaces/BaseLib/AMReX_multifab_fi.cpp Src/F_Interfaces/BaseLib/AMReX_omp_mod.F90 Src/F_Interfaces/BaseLib/AMReX_parallel_fi.cpp Src/F_Interfaces/BaseLib/AMReX_parallel_mod.F90 Src/F_Interfaces/BaseLib/Make.package Src/F_Interfaces/BaseLib/boxarray_mod.f90 Src/F_Interfaces/BaseLib/multifab_mod.f90 commit aa1bbe50510598a9ae6ea8cd2aabd265dba98ada Author: Weiqun Zhang Date: Thu Jan 26 12:59:17 2017 -0800 no longer need bl_space_module Src/F_Interfaces/BaseLib/Make.package Src/F_Interfaces/BaseLib/bl_space_mod.F90 commit f5f35f5a9bdd6355fa5e1c501378a92931d6c4db Author: Weiqun Zhang Date: Thu Jan 26 12:58:13 2017 -0800 bl_fort_module --> amrex_fort_module Src/Amr/AMReX_extrapolater_1d.f90 Src/Amr/AMReX_extrapolater_2d.f90 Src/Amr/AMReX_extrapolater_3d.f90 Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_fort_mod.F90 Src/Base/AMReX_mempool_f.f90 Src/Base/CMakeLists.txt Src/Base/Make.package Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/Prob.f90 Tutorials/HeatEquation_EX2_C/bc_fill_nd.F90 commit ae4d0dcf4573994961e110dce00154916bbd2772 Author: Weiqun Zhang Date: Thu Jan 26 12:46:45 2017 -0800 rm parparse from F_Interfaces because they are now in Base Src/F_Interfaces/BaseLib/Make.package Src/F_Interfaces/BaseLib/parmparse_fi.cpp Src/F_Interfaces/BaseLib/parmparse_mod.f90 Src/F_Interfaces/BaseLib/string_mod.f90 commit 52c6ea3a6a153cf24f4290144e0f3e504c9cff0b Author: Weiqun Zhang Date: Thu Jan 26 12:39:04 2017 -0800 add parmparse to Fortran Src/Base/AMReX_parmparse_fi.cpp Src/Base/AMReX_parmparse_mod.F90 Src/Base/AMReX_string_mod.F90 Src/Base/CMakeLists.txt Src/Base/Make.package commit a6412f1b3eb0187d7a511cc7873d70b6dac1ae0f Author: Andrew Myers Date: Thu Jan 26 12:22:09 2017 -0800 Precompute the inverse cell spacing for particle binning. Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_Geometry.cpp Src/Particle/AMReX_Particles.H commit d350fc6a30cf2551e03580a96894160cf6f25b1e Author: Weiqun Zhang Date: Thu Jan 26 09:45:00 2017 -0800 reorder data layout Src/Particle/AMReX_Particles.H commit a347305ec71123b2cffdf981738b51480b523801 Author: Weiqun Zhang Date: Wed Jan 25 21:13:18 2017 -0800 fix some tests Tests/C_BaseLib/tVisMF.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp commit 7c1273664b89f8c77a918ba1eacf63339c29d0cb Author: Weiqun Zhang Date: Wed Jan 25 21:04:49 2017 -0800 replace the timer using gettimeofday with C++ timer Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Tutorials/HelloWorld_C/main.cpp commit ee0f0b50c8be52558cf136f339de8f817638dd13 Author: Weiqun Zhang Date: Wed Jan 25 16:19:40 2017 -0800 use constexpr and get rid of if in IntVect::shift_hasher Src/Base/AMReX_IntVect.H Src/Base/AMReX_Utility.H commit efaceac207440589de3eb136d7fa7448eefea7b8 Author: Andrew Myers Date: Wed Jan 25 14:54:45 2017 -0800 use a typedef to save typing Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H commit b6a9418aaf5bac6112d5ba142357572eb8b5c407 Author: Andrew Myers Date: Wed Jan 25 14:37:19 2017 -0800 Begin refactor of Particle classes. Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_Particles.cpp Src/Particle/AMReX_TracerParticles.cpp Src/Particle/CMakeLists.txt Src/Particle/Make.package commit c190f27d093484d7d85e12841a68ec5f3b691fac Author: Weiqun Zhang Date: Wed Jan 25 14:10:56 2017 -0800 remove WIN32 macro MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp Src/Base/AMReX.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FPC.cpp Src/Base/AMReX_ParallelDescriptor.cpp Src/Extern/amrdata/AMReX_AmrData.cpp Src/F_BaseLib/fabio_c.c Src/F_BaseLib/timer_c.c Tests/C_BaseLib/tCArena.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp Tools/CMake/CCSEConfigReport.cmake Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp Tools/C_util/ViewMF/MFNorm.cpp Tools/C_util/ViewMF/checkMFghostcells.cpp Tools/C_util/ViewMF/main.cpp Tools/C_util/ViewMF/mfMinMax.cpp Tools/C_util/ViewMF/viewMF.cpp Tools/C_util/ViewMF/viewMFcol.cpp Tools/C_util/ViewMF/viewMFdiffHardWire.cpp Tools/C_util/WritePlotFile.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/timer_c.c Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp commit b5911ab2267c18e976b9aae5529750349a88a972 Author: Weiqun Zhang Date: Wed Jan 25 13:49:27 2017 -0800 remove BL_USE_SETBUF macro MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp Src/Amr/AMReX_Amr.cpp Src/Base/AMReX_VisMF.cpp Src/Extern/amrdata/AMReX_AmrData.cpp Tools/CMake/CCSEOptions.cmake Tools/C_util/WritePlotFile.cpp Tools/C_util/dbgTools/crsGrids.cpp Tools/C_util/dbgTools/intersectGrids.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp commit 4f37d1da5b6d028a59630be3665277687ea742f0 Author: Weiqun Zhang Date: Wed Jan 25 12:26:57 2017 -0800 fix some util tools Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp commit d027942785f657519f88f8c42c2a4a49aafcdeed Author: Andrew Myers Date: Tue Jan 24 17:00:12 2017 -0800 Porting changes to regression test suite forward from BoxLib. Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py commit bd3d60d2a6c570a08c900fb17b6a42162cc095a1 Merge: a28a117e8 44ef0c41b Author: Weiqun Zhang Date: Mon Jan 23 12:12:17 2017 -0800 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 86402cc2dea5649afa0383bb1a8512dff147e32e Author: Marc Day Date: Mon Jan 23 11:54:47 2017 -0800 Add access to tileindex in MFIter and use that to cache EB data in stencil test code. Src/Base/AMReX_FabArray.H Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90 commit 44ef0c41b74c2ae0afdf062c5ba4c3e85c8e6b21 Author: tannguyen Date: Sat Jan 21 23:50:15 2017 -0800 add some more comments Src/Amr/AMReX_AuxBoundaryData.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BoxArray.H Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryRegister.H commit cdae7fb6072767ee3462e2e0a58a85e655e08389 Author: Tan Nguyen Date: Sat Jan 21 22:48:56 2017 -0800 fix doxygen comments Src/Amr/AMReX_AuxBoundaryData.H Src/Base/AMReX_BoxArray.H commit 0c40ff18ac2cba731dcbb3b148e54cda3bd5502b Author: Tan Nguyen Date: Sat Jan 21 22:40:52 2017 -0800 hide the description of some internal classes Src/Amr/AMReX_AuxBoundaryData.H Src/Base/AMReX_BoxArray.H commit 07826a192d9c81f1b0b7701b5708b619d163da94 Author: Marc Day Date: Fri Jan 20 18:45:03 2017 -0800 More minor cleaning of stencil testBench Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90 Tests/GeometryShop/stencilTestbed/src/AMReX_AggStencilI.H commit 871ec1ac18ad55cefdde51c382ed36a14fabd8ee Author: Marc Day Date: Fri Jan 20 14:27:06 2017 -0800 Make boundary treatment the same for all the different forms of the stencil operator in the stencelTests Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp commit aefd738e6deb50cd082a26d6ffa3076e205f5fba Merge: 8aa1b8235 5b5513989 Author: Marc Day Date: Fri Jan 20 13:55:03 2017 -0800 Merge branch 'dtg_branch' of bitbucket.org:berkeleylab/amrex into dtg_branch commit 8aa1b823587770934a0c148b01b685b8cbb9f349 Author: Marc Day Date: Fri Jan 20 13:54:50 2017 -0800 Fix a bug in the irregular stencils for the stencil tests Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90 commit 5b55139899997dfb05f51a489b3cf1b8d2c61eab Merge: db7db13cf 3dee0591b Author: Dan Graves Date: Fri Jan 20 12:35:14 2017 -0800 Merge branch 'development' into dtg_branch commit db7db13cfdb986557c97b883cb2ba41c036a8128 Author: Dan Graves Date: Fri Jan 20 12:34:16 2017 -0800 added counts Tests/GeometryShop/stencilTestbed/src/AMReX_AggStencilI.H commit 6001a73c5a4972db2548a1e696ee03935d83890d Author: Marc Day Date: Fri Jan 20 11:11:32 2017 -0800 Fix up fortran-only stencils in stencil testbed, add nontrivial initial data. Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H commit facd5c7f4c4a5172a33c6220aa8ce017b2e445c6 Author: Marc Day Date: Fri Jan 20 10:07:19 2017 -0800 Remove div by kappa in fortran-only Laplace stencil test. Minor reformatting. Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp commit 60e4d28be477bd7b91dda6cee101b2a6a264224a Merge: 5c40a752a 347668b7c Author: Marc Day Date: Thu Jan 19 20:24:54 2017 -0800 Merge branch 'dtg_branch' of bitbucket.org:berkeleylab/amrex into dtg_branch commit 5c40a752af7ea20da67ac987ec923c7ef8a75532 Author: Marc Day Date: Thu Jan 19 20:23:55 2017 -0800 Add Fortran-only version to stencilTest, add some timers... still need to confirm correctness Tests/GeometryShop/stencilTestbed/exec/GNUmakefile Tests/GeometryShop/stencilTestbed/exec/Make.package Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/exec/stencilTest_2d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_3d.f90 Tests/GeometryShop/stencilTestbed/exec/stencilTest_F.H Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp commit 3dee0591b08c3a3f8eb9395887afbdb01e1f20cf Author: Tan Nguyen Date: Thu Jan 19 19:17:29 2017 -0800 fix hash func Src/Base/AMReX_IntVect.H commit 347668b7cadca72a2e12e0e90a5373a347c544e3 Author: Dan Graves Date: Thu Jan 19 15:52:27 2017 -0800 ported the regular-kitty-corner-to-covered fix from Pele Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp commit a56bfe874fa4527438273ff1ee23eb3d5bbcc9d2 Author: Tan Nguyen Date: Thu Jan 19 12:32:43 2017 -0800 hash boxArray Src/Base/AMReX_BoxArray.H Src/Base/AMReX_IntVect.H commit f0903474f1b5dddb45d5214925faf4e772ed0e4a Author: Dan Graves Date: Thu Jan 19 09:53:08 2017 -0800 bug fix for bug found by Marc Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp commit a28a117e80a20bbff3d0fe7bc3c4602cf1383bcb Author: Weiqun Zhang Date: Wed Jan 18 10:48:39 2017 -0800 use some C++11 headers and remove some Windows stuff Src/Base/AMReX.H Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_AmrvisConstants.H Src/F_BaseLib/backtrace_c.cpp Src/F_BaseLib/f2kgetcl.c commit c8cf6ae9c9315f1b94407f560d7ca14ee8c3d49e Author: Weiqun Zhang Date: Wed Jan 18 08:57:40 2017 -0800 add -P to cpp Tools/GNUMake/Make.rules commit a73f9adfe44c641805804851a78aec4d25bb8b2f Author: Weiqun Zhang Date: Tue Jan 17 13:46:19 2017 -0800 save cpp'd headers containing C binding of Fortran function Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit c18aa051ddd734252e0cb365b72dc38146e95993 Author: Weiqun Zhang Date: Tue Jan 17 12:45:09 2017 -0800 typo Src/Base/Make.package commit 4532821436dbf034f5f6449ecd635e9ee5815c7f Author: Weiqun Zhang Date: Tue Jan 17 12:44:13 2017 -0800 start to tweak the make sytem for fortran call checking Src/Base/Make.package Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules commit 6b2c1d543df89d3cecbf94406568b91767ea158c Author: Weiqun Zhang Date: Fri Jan 13 16:03:38 2017 -0800 add a function AmrData to return Distribution Map Src/Extern/amrdata/AMReX_AmrData.H commit 190f2d9d568159bf7b71960d7c13ea511826be5b Merge: 29914f9c7 727f40e8b Author: Weiqun Zhang Date: Fri Jan 13 15:33:36 2017 -0800 Merged in mzingale/amrex/development (pull request #6) switch from a hash to describe --tags --dirty commit 727f40e8b77700062eb843c09b88818f5abd4e8c Author: Michael Zingale Date: Fri Jan 13 18:05:32 2017 -0500 switch from a hash to describe --tags --dirty to get a more complete picture of the state Tools/C_scripts/makebuildinfo_C.py commit 29914f9c72f7034040d054d83b93db10dd668b55 Author: Tan Nguyen Date: Fri Jan 13 14:08:39 2017 -0800 fix comments in AMReX_Print.H Src/Base/AMReX_Print.H commit f7c9bd4d81c757f529397316fee38fb92d6f62b6 Author: Tan Nguyen Date: Fri Jan 13 13:56:44 2017 -0800 add some more comments Src/Amr/AMReX_Amr.H Src/AmrCore/AMReX_AmrCore.H Src/Base/AMReX_Print.H commit b4c3015ca60acd8567673a2e4fda710b2552b628 Author: Tan Nguyen Date: Fri Jan 13 00:22:25 2017 -0800 add more comments in AMReX_FabArray.H Src/Base/AMReX_FabArray.H commit a9d806ce397dace26cd8b85b4013c9db45a93f33 Author: Tan Nguyen Date: Thu Jan 12 21:13:30 2017 -0800 fix a comment Src/Base/AMReX_FabArray.H commit 2edbc9fd7ec81945a743b4b1b579a4666f07eddf Author: Tan Nguyen Date: Thu Jan 12 19:03:53 2017 -0800 add comments to functions in AMReX_FabArray.H Src/Base/AMReX_FabArray.H commit 50c362f5cb90746a96934391948cc6a378441198 Author: Michael Zingale Date: Thu Jan 12 12:44:57 2017 -0500 switch to unicode by default, since some source files have unicode characters Tools/F_scripts/dep.py commit 1b677a507fe90043584263ea1fda210b6de7252e Author: Dan Graves Date: Wed Jan 11 16:51:06 2017 -0800 stencil test bed is complete and seems to work for the four cases I have programmed Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.H Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp Tests/GeometryShop/stencilTestbed/src/Make.package Tests/GeometryShop/stencilTestbed/src/lapl_nd.F90 Tests/GeometryShop/stencilTestbed/src/lapl_nd_F.H commit 273e01099beba5bc3f7a2d786f63f2f954119f42 Author: Weiqun Zhang Date: Wed Jan 11 13:28:50 2017 -0800 add amrex::AllPrint() to save some typing Src/Base/AMReX_Print.H Tutorials/HelloWorld_C/main.cpp commit 5e9695a9f1c854f6397737414866aabc7a4bbaa6 Author: Dan Graves Date: Wed Jan 11 11:27:08 2017 -0800 trying to keep up with the development branch Src/GeometryShop/AMReX_IntVectSet.H commit b3a310729b814c1fcb8424be03026e3f5d9c8679 Merge: cc24b4c4a 3a406ac9d Author: Dan Graves Date: Wed Jan 11 11:22:51 2017 -0800 Merge branch 'development' into dtg_branch commit cc24b4c4a92b632cb215b689090ec08c171cb150 Author: Dan Graves Date: Wed Jan 11 11:19:33 2017 -0800 added some files to make.package Src/GeometryShop/Make.package commit fd74d9837ba6e58c5dfb969cb317843b406891e4 Author: Dan Graves Date: Wed Jan 11 11:16:08 2017 -0800 The AggSten everywhere example works now. On to figuring out how to get AMReX to call fortran Tests/GeometryShop/stencilTestbed/exec/sphere.inputs Tests/GeometryShop/stencilTestbed/src/#AMReX_FaceIndex.H# Tests/GeometryShop/stencilTestbed/src/AMReX_AggStencil.H Tests/GeometryShop/stencilTestbed/src/AMReX_AggStencilI.H Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.H Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp commit 3a406ac9d5531fb676f702be226ad57098012772 Author: Weiqun Zhang Date: Tue Jan 10 16:17:06 2017 -0800 minor Src/Base/AMReX_mempool_f.f90 commit 97a473d45ecf5a4f38dd34cda5c4b1478f23a6fa Author: Weiqun Zhang Date: Tue Jan 10 16:16:00 2017 -0800 don't have bl_fort_module for Fortran build Src/Base/AMReX_mempool_f.f90 commit 73c2494ddd4db2a29dfb14438e170a8db22a5b1e Author: Weiqun Zhang Date: Tue Jan 10 16:03:25 2017 -0800 some double precision --> real(c_real) Src/Amr/AMReX_Extrapolater.cpp Src/Amr/AMReX_extrapolater_1d.f90 Src/Amr/AMReX_extrapolater_2d.f90 Src/Amr/AMReX_extrapolater_3d.f90 Src/Base/AMReX_MemPool.H Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_mempool_f.f90 Src/F_BaseLib/fab.f90 Src/Particle/AMReX_Particles.H commit 1c94d1bdd9a5a0ec9d490ae784dca676bce04874 Author: Dan Graves Date: Tue Jan 10 16:00:29 2017 -0800 put initialize and bl_profile_start/stop calls into test so we can get stats Tests/GeometryShop/stencilTestbed/exec/GNUmakefile Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp commit 3faed4747ff04b5d7c80edadbb5982e39b9055fe Author: Dan Graves Date: Tue Jan 10 15:16:08 2017 -0800 simplest version of the testbed now runs Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.H Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_Stencils.H Tests/GeometryShop/stencilTestbed/src/AMReX_Stencils.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp commit de874546f84d046183df4b503b1e6b1fa3d2cfd0 Author: Weiqun Zhang Date: Tue Jan 10 14:56:47 2017 -0800 std:iota can be used now. Src/Base/AMReX_FabArray.cpp commit a9bc19795a5f42a228d3ea29eb36cbebd6437b62 Author: Weiqun Zhang Date: Tue Jan 10 14:46:48 2017 -0800 removed hack for Cray compiler Src/Base/AMReX_FArrayBox.cpp commit d8eaf738f8c4bc047ea78e023bb344bb7cb06a91 Author: Weiqun Zhang Date: Tue Jan 10 14:35:12 2017 -0800 if AMREX_GIT_VERSION is not defined, reutrn Unknown Src/Base/AMReX.cpp commit 1f69c90104bddff2e189af91d3cdfe5ba13734a5 Author: Weiqun Zhang Date: Tue Jan 10 14:26:15 2017 -0800 add amrex::Version() Src/Base/AMReX.H Src/Base/AMReX.cpp Tools/GNUMake/Make.defs Tutorials/HelloWorld_C/main.cpp commit 683a230bcb33f656e5cfe186ecfbfb1bd86f66a1 Author: Weiqun Zhang Date: Tue Jan 10 13:41:35 2017 -0800 rm BL_USE_ARLIM Src/Base/AMReX_ArrayLim.H commit fed22e997c510be986856f2d9a36e60b6f227c20 Author: Weiqun Zhang Date: Tue Jan 10 12:59:38 2017 -0800 make_build_info_cpp no longer used Tools/C_scripts/make_build_info_cpp commit 66db4153d5f02d7bebaa3e2944efba34e2124678 Author: Weiqun Zhang Date: Tue Jan 10 12:58:04 2017 -0800 start to use Print in some places Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AuxBoundaryData.cpp Src/AmrCore/AMReX_AmrCore.cpp Src/Base/AMReX.cpp Src/Base/AMReX_BLPgas.cpp Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxDomain.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H commit 41ed1852300b0c86f4d092cbf71918488e8681c2 Author: Dan Graves Date: Tue Jan 10 11:22:32 2017 -0800 got the testbed to compile on this branch Tests/GeometryShop/stencilTestbed/exec/GNUmakefile Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.H Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_FaceIndex.H Tests/GeometryShop/stencilTestbed/src/AMReX_FaceIndex.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_Stencils.H Tests/GeometryShop/stencilTestbed/src/AMReX_Stencils.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.H Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_VolIndex.H commit 9e57b6da551fb6ef3d81760a9befdda9060ac734 Author: Weiqun Zhang Date: Tue Jan 10 11:02:14 2017 -0800 Revert "Print: change the default to print on all calling processes. To print on IO Process only, do Print(Print::IOProc) << ..." This reverts commit 08ec43c8d42b81275c16e43bb45728497648d1f9. Src/Base/AMReX_Print.H Tutorials/HelloWorld_C/main.cpp commit 08ec43c8d42b81275c16e43bb45728497648d1f9 Author: Weiqun Zhang Date: Tue Jan 10 10:16:05 2017 -0800 Print: change the default to print on all calling processes. To print on IO Process only, do Print(Print::IOProc) << ... Src/Base/AMReX_Print.H Tutorials/HelloWorld_C/main.cpp commit 9016a6e9a184b9ad19e229195a2bd52939a4da55 Author: Weiqun Zhang Date: Tue Jan 10 09:31:19 2017 -0800 minor Src/Particle/AMReX_Particles.H commit 524dd65555a0ac8d6f4f9b5c7fd4c5f4eb2c0127 Author: Weiqun Zhang Date: Tue Jan 10 09:26:13 2017 -0800 Add amrex::Print. One can use this to replace if (ParallelDescriptor::IOProcessor() { std::cout << ....; } with amrex::Print() << ....; To print on all processes, one can do amrex::Print(amrex::Print::AllProcs) << ...; To print on a particular process in a communicator, one can do amrex::Print(rank_for_print, communicator) << ...; By default Print uses std::cout. By it also takes an optional std::ostream argument. Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_Print.H Src/Base/CMakeLists.txt Src/Base/Make.package Tutorials/HelloWorld_C/main.cpp commit f6e2250fd3708a421a4cfee2bac9039d5fe30ecd Merge: 8f29b5386 a62c3de2d Author: Dan Graves Date: Mon Jan 9 20:55:44 2017 -0800 Merge branch 'dtg_branch' of https://bitbucket.org/berkeleylab/amrex into dtg_branch commit 8f29b53866622a3f929b8ba8404437c51d0437ea Author: Dan Graves Date: Mon Jan 9 20:55:14 2017 -0800 I had the variable names incorrect Tests/GeometryShop/stencilTestbed/src/Make.package commit 5a89ed30f29c272f73a5af73112b96bf73670c1f Author: Dan Graves Date: Mon Jan 9 20:49:43 2017 -0800 forgot to add the src directory into the makefile Tests/GeometryShop/stencilTestbed/exec/GNUmakefile commit a62c3de2d12a2e0235aae91538214170962f679e Author: Brian VS Date: Mon Jan 9 18:17:47 2017 -0800 needed right std::sqrt Src/GeometryShop/AMReX_RealVect.H commit fc0d0ac0cf3592cb479f962aaf1076d7dc7fc25e Author: Dan Graves Date: Mon Jan 9 16:43:06 2017 -0800 lots of progress on the testbed. should have it compiling soon. Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp Tests/GeometryShop/stencilTestbed/src/#AMReX_FaceIndex.H# Tests/GeometryShop/stencilTestbed/src/AMReX_BaseIndex.H Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.H Tests/GeometryShop/stencilTestbed/src/AMReX_EBCellFAB.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_FaceIndex.H Tests/GeometryShop/stencilTestbed/src/AMReX_FaceIndex.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_Stencils.H Tests/GeometryShop/stencilTestbed/src/AMReX_Stencils.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.H Tests/GeometryShop/stencilTestbed/src/AMReX_TestbedUtil.cpp Tests/GeometryShop/stencilTestbed/src/AMReX_VolIndex.H Tests/GeometryShop/stencilTestbed/src/AMReX_VolIndex.cpp Tests/GeometryShop/stencilTestbed/src/Make.package commit 136aaf5c381a2934b69e2f3bac282944a357cf87 Author: Weiqun Zhang Date: Mon Jan 9 10:45:19 2017 -0800 minor MiniApps/PGAS_SMC/SMC_io.cpp Src/Amr/AMReX_AmrLevel.cpp Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Tutorials/AMR_Adv_C/Source/main.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/two_level.cpp Tutorials/TwoGrid_PIC_C/main.cpp commit 4cd35c7bf423f783ceffe996cbc045ab327d873f Merge: e0afb3b73 600677eed Author: Weiqun Zhang Date: Sun Jan 8 12:31:43 2017 -0800 Merge branch 'development' into weiqun/development commit e0afb3b73bc2484efe7e2d601d626f1ce9d46169 Author: Weiqun Zhang Date: Sun Jan 8 12:31:29 2017 -0800 forward --> move in non-template function Src/Base/AMReX_MemProfiler.cpp commit 600677eed4a3861f63fef3b6bfff71cee065a0c2 Merge: b653b46bd a0e582ce2 Author: Tan Nguyen Date: Sun Jan 8 00:20:05 2017 -0800 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit b653b46bdc88843367e495d3c297a8f7523baa98 Author: Tan Nguyen Date: Sun Jan 8 00:19:31 2017 -0800 modify comments in BoxArray.H Src/AmrCore/AMReX_TagBox.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.H Src/F_BaseLib/MemProfiler_f.cpp Tools/GNUMake/Make.rules commit 9debcebfeaf7e5ae928eef3f91d2a9b71dadd891 Author: Tan Nguyen Date: Sun Jan 8 00:11:46 2017 -0800 modify comments in BoxArray.H Src/Base/AMReX_BoxArray.H commit d3f2a643662363df51f6a28547314d758d62d380 Author: Weiqun Zhang Date: Sat Jan 7 20:27:56 2017 -0800 removed some Array Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp commit db49394520a5a1a026110f68c953106d6834d9be Author: Weiqun Zhang Date: Sat Jan 7 13:04:44 2017 -0800 explicitly delete some constructors and operator= Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_MacBndry.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H commit 627f45228f9ebf8496f67385c5b1c72e2d1e1aff Author: Weiqun Zhang Date: Sat Jan 7 12:41:43 2017 -0800 make Tuple simply a template alias of std:array; add move constructors to FabSet, FluxRegister, BndryRegister, etc. Src/AmrCore/AMReX_FluxRegister.H Src/Base/AMReX_CoordSys.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_Tuple.H Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_FabSet.cpp Src/Boundary/AMReX_InterpBndryData.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp commit 6595e593159ea71e33eabd198a12a9eec80ca3fb Author: Weiqun Zhang Date: Sat Jan 7 10:39:13 2017 -0800 store MultiMasks in Array Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_MultiMask.H Src/Boundary/AMReX_MultiMask.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp commit 790528876089b4734fc84962e2dac4d01207ad58 Author: Weiqun Zhang Date: Sat Jan 7 08:01:30 2017 -0800 move constructor for Mask and MultiMask Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_Mask.cpp Src/Boundary/AMReX_MultiMask.H commit a0e582ce28cd624f1471ea742cdd3abf129fce41 Author: Weiqun Zhang Date: Fri Jan 6 21:31:42 2017 -0800 F_BaseLib: fix memory profiling by add using namespace amrex Src/F_BaseLib/MemProfiler_f.cpp commit d71952c66bf89d7a1f389954ab094cae06884b84 Author: Weiqun Zhang Date: Fri Jan 6 17:22:55 2017 -0800 minor Src/Base/AMReX_BaseFab.H commit f64341c3920f9125b58228e5d471e5c5a034dc72 Author: Weiqun Zhang Date: Fri Jan 6 17:13:45 2017 -0800 add noexcept Src/Base/AMReX_FabArray.H commit 392b82e07c4038de47114942b4bc691f9cc0e679 Author: Weiqun Zhang Date: Fri Jan 6 17:04:10 2017 -0800 add noexcept Src/AmrCore/AMReX_TagBox.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_IArrayBox.H commit 99697f933a760c5dece9439b4c01468fe789bef4 Author: Weiqun Zhang Date: Fri Jan 6 17:02:33 2017 -0800 add move constructor to MultiFab, iMultiFab, and TagBoxArray Src/AmrCore/AMReX_TagBox.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_iMultiFab.H commit a9e1a396f30cac934eea5f6c7a16b9f714dff2bc Author: Weiqun Zhang Date: Fri Jan 6 16:50:45 2017 -0800 move constructor for FabArray Src/Base/AMReX_FabArray.H commit a46d013543189e663934171ca811bd0508caa543 Author: Dan Graves Date: Fri Jan 6 16:31:07 2017 -0800 made some slow progress on the testbed Tests/GeometryShop/stencilTestbed/exec/GNUmakefile Tests/GeometryShop/stencilTestbed/exec/Make.package Tests/GeometryShop/stencilTestbed/exec/sphere.inputs Tests/GeometryShop/stencilTestbed/exec/stencilTest.cpp commit e80dfa87df4a5fb6b67299fa90f159159595d314 Author: Weiqun Zhang Date: Fri Jan 6 15:47:28 2017 -0800 move constructor for FArrayBox, IArrayBox, and TagBox Src/AmrCore/AMReX_TagBox.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp commit 089e2a553b8e08c7ac0463ac6b3fe5efca5ed572 Author: Weiqun Zhang Date: Fri Jan 6 15:30:22 2017 -0800 BaseFab: add move constructor Src/Base/AMReX_BaseFab.H commit 48f7824c415d89c67828fc322b0199ccf0019c33 Author: Weiqun Zhang Date: Fri Jan 6 15:23:14 2017 -0800 add a BARef constructor taking a single Box Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit d3c950921f95e56bea7b20521d7e98f053076d18 Author: Weiqun Zhang Date: Fri Jan 6 15:17:18 2017 -0800 add explicit to a BoxList ctor taking a single Box, and tidy Src/Base/AMReX_BoxList.H commit 8d1516bdd21ba64407c99b441cc0fbc9dae929f9 Author: Weiqun Zhang Date: Fri Jan 6 15:10:15 2017 -0800 remove Geometry's copy ctor and dtor to let compilers auto-generate copy and move constructors. Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp commit 5ffe8862a18fdc2a6c4146d1b43bfe74573cf92d Author: Weiqun Zhang Date: Fri Jan 6 15:08:56 2017 -0800 remove the do-nothing ~CoordSys so that compilers will auto-generate copy and move constructors. Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp commit 65969c4882f7e7cb33902555da785244853bbd26 Author: Weiqun Zhang Date: Fri Jan 6 14:59:16 2017 -0800 minor Tools/GNUMake/Make.rules commit 7c9bd8de0a2e1f2d3f95238f5e6e05fcd1b38d1a Author: Weiqun Zhang Date: Fri Jan 6 14:54:17 2017 -0800 comments on make Tools/GNUMake/Make.rules commit b746b7e56f7dbc3803e7e059c4adedbeb83b5d56 Author: Weiqun Zhang Date: Fri Jan 6 12:50:55 2017 -0800 change due to IntVect operator<= change Src/Base/AMReX_BoxArray.cpp commit 3f39513e39c210b999c789b11a05f6ce39e6c91c Merge: ab9a79eed f1a11e421 Author: Weiqun Zhang Date: Fri Jan 6 11:45:47 2017 -0800 Merge branch 'weiqun/development' of bitbucket.org:WeiqunZhang/amrex into weiqun/development Conflicts: Src/Base/AMReX_Box.cpp commit ab9a79eedfe074ee2cb91b3479cdb56adc4521e7 Author: Weiqun Zhang Date: Fri Jan 6 11:09:09 2017 -0800 Change the behavior of IntVect::operator< and >. They now do lexicographical comparisons that are suitable for STL. The per component comparison is now done by IntVec::allLT, allLE, allGT, and allGE. We have also removed IntVect::Compare, IntVect::lexLT, and IntVect::lexGT for simplicity. Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Particle/AMReX_Particles.H Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp commit f1a11e421b01cfe2cf8199637fbdd149dcf8798e Author: Weiqun Zhang Date: Fri Jan 6 11:09:09 2017 -0800 Change the behavior of IntVect::operator< and >. They now do lexicographical comparisons that are suitable for STL. The per component comparison is now done by IntVec::allLT, allLE, allGT, and allGE. We have also removed IntVect::Compare, IntVect::lexLT, and IntVect::lexGT for simplicity. Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Particle/AMReX_Particles.H Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp commit 5cf86cd5570e9c2695a826b4f3b6be4d6157de07 Author: Weiqun Zhang Date: Thu Jan 5 16:29:39 2017 -0800 migration doc Docs/Migration/Migration.md commit fc1c3530847620c4f97c91dff68859c31ba4c30f Merge: aa37db726 2f6ddcac4 Author: Weiqun Zhang Date: Thu Jan 5 15:25:49 2017 -0800 Merge branch 'development' into weiqun/development Conflicts: Src/Amr/AMReX_Amr.H Src/Amr/AMReX_AmrLevel.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_PList.H Src/Base/AMReX_Pointers.H Src/Base/AMReX_UseCount.H commit aa37db72631bd179f2d7e56cab8c504be8d821e6 Author: Weiqun Zhang Date: Thu Jan 5 13:48:21 2017 -0800 rm PList Src/Base/AMReX_PList.H Src/Base/CMakeLists.txt commit 201812859d6f5b7a6c46e874e00f36be750a7522 Author: Weiqun Zhang Date: Thu Jan 5 13:45:43 2017 -0800 rm UseCount Src/Base/AMReX_UseCount.H Src/Base/AMReX_UseCount.cpp Src/Base/CMakeLists.txt Src/Base/Make.package commit 71c3c63cb78add139b71d41f2458b087185e79bf Merge: 69297ffd9 2f6ddcac4 Author: Dan Graves Date: Thu Jan 5 10:16:59 2017 -0800 Merge branch 'development' into dtg_branch commit 2f6ddcac45ea25f5c0a3c502f620713b57c492b4 Author: Weiqun Zhang Date: Thu Jan 5 08:42:48 2017 -0800 CompileTesting: Change the default to running a small set of tests; add --full for running the full testing. Tools/CompileTesting/compiletesting.py commit a748e4a16208c09bab41b5ec978a229e5b41d189 Author: Weiqun Zhang Date: Wed Jan 4 22:12:23 2017 -0800 add a compile testing script Tools/CompileTesting/compiletesting.py commit 80db81998c3e4fc595bd0d7c2af7aa49b2e9b03e Author: Weiqun Zhang Date: Wed Jan 4 21:49:43 2017 -0800 fix comment line Src/Amr/AMReX_AmrLevel.H commit 926a41241763c90630335eb69fa60879280ade36 Author: Weiqun Zhang Date: Wed Jan 4 21:48:34 2017 -0800 revert AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.H commit 480d188f611ffb635a6ad0b5d917032cb5c49745 Author: Weiqun Zhang Date: Wed Jan 4 21:46:41 2017 -0800 remove a duplicated line Src/Base/AMReX_BaseFab.H commit 8514a01d90340d03c1a7ca0fd801fe732f4f154d Author: Weiqun Zhang Date: Wed Jan 4 21:43:52 2017 -0800 fix comment line Src/Base/AMReX_Pointers.H commit cfa306673642fcec5bbbaa4ead671dc29d1a1e2d Author: Weiqun Zhang Date: Wed Jan 4 21:40:54 2017 -0800 Too hard to fix. I am just going to revert to back to a working vesion. The lost works are comments Src/Base/AMReX_FabArray.H commit 0f75e2fb543342d41d924c1c21951d1fcb2186df Author: Weiqun Zhang Date: Wed Jan 4 21:32:41 2017 -0800 fix more merge problems Src/Base/AMReX_DistributionMapping.H commit db1d42d0a34b0fb4d32f488be94fd17d850afae8 Author: Weiqun Zhang Date: Wed Jan 4 21:07:46 2017 -0800 fix more merge problems Src/Base/AMReX_DistributionMapping.H commit 12336368e28568d013d33f1dacf9704fbad6c930 Author: Weiqun Zhang Date: Wed Jan 4 20:41:07 2017 -0800 fix conflicts from previous merge Src/Base/AMReX_Box.H Src/Base/AMReX_FPC.H Src/Base/AMReX_MultiFab.H commit e19e1248b69954c2139230b3ba9dad34221de6c0 Author: Weiqun Zhang Date: Wed Jan 4 20:28:36 2017 -0800 MultiFab.H no longer exists Src/Base/MultiFab.H commit e026620e0ea1dc34d2b2c0f80b4263a3731e12c8 Author: tannguyen Date: Wed Jan 4 18:51:43 2017 -0800 add comments to the amr and amrLevel files Src/Amr/AMReX_Amr.H Src/Amr/AMReX_AmrLevel.H commit e1d9d3f5a9ebed4357115d64602662ddcf0cb41f Merge: 3bcde2338 5ea14f827 Author: tannguyen Date: Wed Jan 4 16:44:17 2017 -0800 resolved conflit commit acc78edb2e1cc4e4bb670eb49213c9e770d680a2 Author: Weiqun Zhang Date: Wed Jan 4 16:32:16 2017 -0800 make Amr & AmrLevel::derive return std::unique_ptr instead of raw ptr Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp commit 3bcde2338dc0e7f5eb3e991a3129cd96be7035ad Author: tannguyen Date: Wed Jan 4 16:18:33 2017 -0800 update header files with comments Src/Base/AMReX_Arena.H Src/Base/AMReX_Array.H Src/Base/AMReX_BArena.H Src/Base/AMReX_BCRec.H Src/Base/AMReX_BLPgas.H Src/Base/AMReX_BLPgas.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxDomain.H Src/Base/AMReX_BoxLib.H Src/Base/AMReX_BoxList.H Src/Base/AMReX_CArena.H Src/Base/AMReX_CoordSys.H Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FPC.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabConv.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_Looping.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_Orientation.H Src/Base/AMReX_PList.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParmParse.H Src/Base/AMReX_Periodicity.H Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_Pointers.H Src/Base/AMReX_RealBox.H Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_Tuple.H Src/Base/AMReX_UseCount.H Src/Base/AMReX_Utility.H Src/Base/AMReX_VisMF.H Src/Base/AMReX_ccse-mpi.H Src/Base/AMReX_iMultiFab.H Src/Base/MultiFab.H commit 797b0fe48e55b76dc1d88e02966129241205e646 Author: Weiqun Zhang Date: Wed Jan 4 16:10:37 2017 -0800 turn on C++14 for Intel >= 17 Src/Base/AMReX_DistributionMapping.H Tools/GNUMake/comps/intel.mak commit f81553c7ab7dd2a71575439028902f47c8767b13 Author: Weiqun Zhang Date: Wed Jan 4 16:02:47 2017 -0800 For gcc >= 6, C++14 is on by default. Src/Base/AMReX_DistributionMapping.H Tools/GNUMake/comps/gnu.mak commit 86daefc3d5accdccfef77748440e8baa7baba78b Author: Weiqun Zhang Date: Wed Jan 4 15:52:06 2017 -0800 fix a bug in last commit Src/Base/AMReX_FabArray.cpp commit 101cdc0c92b8b2cb2068e8c0ddd84952a0032ca7 Author: Weiqun Zhang Date: Wed Jan 4 15:25:21 2017 -0800 get rid of the sentinel in DistributionMapping Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Base/AMReX_VisMF.cpp Src/Extern/amrdata/AMReX_AmrData.cpp Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.H Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp Tutorials/Sidecar_EX1/DestMFTest.cpp Tutorials/Sidecar_EX1/NSidecarsTest.cpp commit e7c8685fad52d1768c6f92ed0c0efad4febeed79 Author: Weiqun Zhang Date: Wed Jan 4 13:43:02 2017 -0800 remove AMReX_Pointers.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_Pointers.H Src/Base/CMakeLists.txt Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H commit 1022772f7af7fb0b8f09d7e2a2415c5bb1b506f8 Author: Weiqun Zhang Date: Wed Jan 4 13:39:12 2017 -0800 FArrayBox: use unique_ptr instead of CpClassPtr for RealDescriptor Src/Base/AMReX_FArrayBox.cpp commit 840026facc1920a413d1f26071813db486ce3c85 Author: Weiqun Zhang Date: Wed Jan 4 13:25:09 2017 -0800 remove the use of LnPtr and LnClassPtr Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp commit 74b44bc5e1ec3ce47f94949c6fce079eff2f3a4b Author: Weiqun Zhang Date: Wed Jan 4 13:07:17 2017 -0800 PhysBCFunct: use std::unique_ptr Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp commit 69297ffd901260777d2127bf030d8bd9d28ec049 Author: Dan Graves Date: Wed Jan 4 13:03:09 2017 -0800 AMReX_GeometryShop now does the right thing with its test once I realized IntVect::operator < is stupid Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_IntVectSet.H Src/GeometryShop/AMReX_IntVectSet.cpp Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/Make.package Tests/GeometryShop/sphere/GNUmakefile Tests/GeometryShop/sphere/sphere.inputs Tests/GeometryShop/sphere/sphereTest.cpp commit df75b1df631ab766706a975a1cdc39909dd45b7d Author: Weiqun Zhang Date: Wed Jan 4 12:51:26 2017 -0800 remove unsafe assertion Src/Base/AMReX_BoxArray.cpp commit 6f3712a5924344cf5e86dec42035ec9e986f10de Author: Weiqun Zhang Date: Wed Jan 4 12:21:43 2017 -0800 BoxArray::clear() should leave it at a valid state Src/Base/AMReX_BoxArray.cpp commit 74b219fd94716b66092bc17d1c7c9acf1d3a2c11 Author: Weiqun Zhang Date: Wed Jan 4 10:50:56 2017 -0800 BoxArray: move constructor Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp commit 449a02a0ec698f7300dc91cee66914981ff670c2 Author: Weiqun Zhang Date: Wed Jan 4 10:44:52 2017 -0800 BoxArray: use std::shared_ptr Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_DistributionMapping.H commit 5f52629e7c51e18fd82703e241a184dffc08be0c Author: Weiqun Zhang Date: Tue Jan 3 16:16:59 2017 -0800 DistributionMapping: use std::shared_ptr and add move constructor Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp commit 02ccdcd74fa709fb40ec3e39f744cf72df1cfe7f Merge: b334840c6 5ea14f827 Author: Dan Graves Date: Tue Jan 3 15:09:33 2017 -0800 Merge branch 'development' into dtg_branch commit b334840c6254fe93be6affcb69d5db8cfd19469d Author: Dan Graves Date: Tue Jan 3 15:08:33 2017 -0800 more paranoid commits Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_SphereIF.H commit e2c7579123fff5bdd64683809a91f5cda552a292 Author: Dan Graves Date: Tue Jan 3 15:07:35 2017 -0800 committing so that I can merge with development changes Tests/GeometryShop/sphere/sphere.inputs Tests/GeometryShop/sphere/sphereTest.cpp commit 5ea14f8272b52b0e1c669ebe04ea6f3938fea406 Merge: b0fc6e360 e088f183f Author: Weiqun Zhang Date: Tue Jan 3 14:52:17 2017 -0800 Merge branch 'weiqun/development' into development commit b0fc6e3601de9ac3400c82fcfde43a37b848276b Author: Weiqun Zhang Date: Tue Jan 3 13:30:38 2017 -0800 typo Docs/Migration/Migration.md commit e088f183fa186bcdab42d94ae58f62d37274245a Author: Weiqun Zhang Date: Tue Jan 3 12:59:43 2017 -0800 comments on dtor, copy-ctor, copy-op=, move-ctor, and move-op= Src/Base/AMReX_Box.H Src/Base/AMReX_IndexType.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_RealBox.H commit 72c3191922d3d00b42260eab1c8f9f2722d84bd6 Author: Dan Graves Date: Tue Jan 3 11:24:40 2017 -0800 geometryshop port now compiles. on to testing. Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Tests/GeometryShop/sphere/sphereTest.cpp commit a5ed4aa04f4a708c2cd4bfdbd56f065319e227f6 Author: Weiqun Zhang Date: Tue Jan 3 11:01:16 2017 -0800 add assertion for OpenMP >= 3.1 Src/Base/AMReX.cpp commit 8c271d4ebb9471b85dd864de5a77302f2725044d Author: Weiqun Zhang Date: Fri Dec 30 13:20:38 2016 -0800 add explicit to DistributionMapping constructors Src/Base/AMReX_DistributionMapping.H Tutorials/MultiFabTests_C/GridMoveTest.cpp commit 467ec1e34428c9524e611bee55fe2f48a696fafa Merge: 86f03a4f2 5fdd80794 Author: Weiqun Zhang Date: Fri Dec 30 12:58:11 2016 -0800 Merged in mzingale/amrex/development (pull request #5) this fixes an issue when using ⁠⁠-copy_benchmarks⁠⁠ on tests that crashed and did not output commit 5fdd807947d1e3225c8802b502ced3f2cf29c233 Author: Michael Zingale Date: Fri Dec 30 10:25:51 2016 -0500 this fixes an issue when using ⁠⁠-copy_benchmarks⁠⁠ on tests that crashed and did not output Tools/RegressionTesting/regtest.py commit 86f03a4f27a3e5ad99e5a06e90d3cb4a61239da0 Author: Weiqun Zhang Date: Thu Dec 29 21:47:01 2016 -0800 forgot to check in step 5 script Tools/Migration/step-5-amrex-namespace/amrex-namespace.sh commit d6148d66e027cf451be46dfa67dd6824d31badeb Author: Weiqun Zhang Date: Thu Dec 29 21:44:13 2016 -0800 update buildInfo Docs/Migration/Migration.md Tools/C_scripts/AMReX_buildInfo.H Tools/C_scripts/makebuildinfo_C.py Tools/Migration/step-8-deboxlib/deboxlib.sh commit d91ae3c082302f79084338e46f650f6be491d6de Author: Weiqun Zhang Date: Thu Dec 29 12:49:33 2016 -0800 Migration document Docs/Migration/Migration.md commit bfe733e8955e578824d749b44acb76edb8fe0a1b Author: Weiqun Zhang Date: Thu Dec 29 12:16:21 2016 -0800 more BoxLib --> AMReX MiniApps/MultiGrid_C/GNUmakefile Src/Amr/Make.package Src/Base/AMReX_BLPgas.cpp Src/Base/AMReX_BLassert.H Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_FPC.H Src/Base/AMReX_FPC.cpp Src/Base/AMReX_FabConv.H Src/Base/AMReX_MemProfiler.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_REAL.H Src/Base/AMReX_SPACE.H Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Base/Make.package Src/Boundary/Make.package Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/Particle/AMReX_Particles.H Src/Particle/Make.package commit afddb081805fe09b23ef8ed47f51545d7429e77a Author: Weiqun Zhang Date: Thu Dec 29 11:46:20 2016 -0800 rm BoxLib version and change ParmParse parameters starting with boxlib. to amrex. Src/Base/AMReX.cpp commit 1bb46d6551a124b8f27fbf5f6a2ee8bf77c113d7 Author: Weiqun Zhang Date: Thu Dec 29 11:36:35 2016 -0800 AMReX_BoxLib --> AMReX Docs/Readme.backtrace Docs/Readme.profiling Docs/Readme.sidecars Src/Base/AMReX.H Src/Base/AMReX.cpp Src/Base/AMReX_Arena.cpp Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BLassert.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabConv.cpp Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_MemProfiler.cpp Src/Base/AMReX_Orientation.cpp Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_Pointers.H Src/Base/AMReX_UseCount.H Src/Base/AMReX_Utility.cpp Src/Base/CMakeLists.txt Src/Base/Make.package Src/F_Interfaces/BaseLib/main.cpp Tools/C_util/ViewMF/checkMFghostcells.cpp Tools/Migration/step-8-deboxlib/deboxlib.sh Tutorials/AMR_Adv_C_v2/Source/main.cpp Tutorials/HelloWorld_C/main.cpp Tutorials/PIC_C/main.cpp Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/two_level.cpp Tutorials/Sidecar_EX1/DestMFTest.cpp Tutorials/Sidecar_EX1/GridMoveTest.cpp Tutorials/Sidecar_EX1/NSidecarsTest.cpp Tutorials/Sidecar_EX1/SidecarResizeTest.cpp Tutorials/Sidecar_EX1/TestRankSets.cpp Tutorials/Tiling_C/main.cpp Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp commit a26ee433a3bc8b15d06feae5c9361da23cddd224 Author: Weiqun Zhang Date: Thu Dec 29 09:04:46 2016 -0800 add migration step 8 script and rm #include MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AuxBoundaryData.cpp Src/Amr/AMReX_Derive.cpp Src/Amr/AMReX_SlabStat.cpp Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.cpp Src/Amr/AMReX_StationData.cpp Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BoxLib.cpp Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArray.cpp Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_Utility.H Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_ccse-mpi.H Src/Base/AMReX_iMultiFab.cpp Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_MacBndry.cpp Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_DataServices.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Tests/C_BaseLib/tFillFab.cpp Tests/C_BaseLib/tMF.cpp Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/MKDir/MKDir.cpp Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp Tools/C_util/WritePlotFile.cpp Tools/C_util/dbgTools/crsGrids.cpp Tools/C_util/dbgTools/intersectGrids.cpp Tools/Migration/step-8-deboxlib/deboxlib.sh Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp commit 9ae8396b148734cc5120e8327f50b7c5cfb8e679 Author: Weiqun Zhang Date: Thu Dec 29 08:40:40 2016 -0800 remove Base/GNUmakefile and winstd.H Src/Base/AMReX_winstd.H Src/Base/CMakeLists.txt Src/Base/GNUmakefile commit ab8d9604911f108adfdee3bea5a09c364f4e7a5e Author: Weiqun Zhang Date: Wed Dec 28 12:46:49 2016 -0800 migration document Docs/Migration/Migration.md commit 039cf6b8020504fd204332b946fc7664c09b8892 Author: Weiqun Zhang Date: Wed Dec 28 12:37:46 2016 -0800 fix typo in migration doc Docs/Migration/Migration.md commit 328277ad4dab53c00048de1743b0d3c054bc5c64 Author: Weiqun Zhang Date: Wed Dec 28 12:14:31 2016 -0800 migration script for bind(c) Tools/Migration/step-7-bindc/bindc.sh commit dab1fdbb0d2dc71e2bd064d9ee616806fe2c0507 Author: Weiqun Zhang Date: Wed Dec 28 12:13:29 2016 -0800 fix subroutine probinit Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90 commit f0b2034d36c0e1207079252388898adba8fdfb3a Author: Weiqun Zhang Date: Wed Dec 28 11:48:00 2016 -0800 FORT_PROBINIT --> amrex_probinit and remove unused BL_SYNC_RANTABLES Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_PROB_AMR_F.H commit eda09c3656198f59c2065cecb234df59bce495ff Author: Weiqun Zhang Date: Wed Dec 28 10:56:47 2016 -0800 remove unused AMReX_FLUSH_F.H Src/Amr/AMReX_FLUSH_F.H Src/Amr/CMakeLists.txt commit 3b7bd6f0c9957a0da12f2c2de2f222d9d405f810 Merge: f42629ee8 8b50be7f2 Author: Weiqun Zhang Date: Wed Dec 28 10:45:39 2016 -0800 Merge branch 'migration/6-distributionmap' into development commit 8b50be7f28c950d2c946cef53be7beb44f18ce99 Author: Weiqun Zhang Date: Wed Dec 28 10:45:22 2016 -0800 some bugs fixed: forgot to pass MFInfo to MultiFab constructor Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp commit f42629ee8b33dbddce2925f16834ae81672fd0a9 Merge: 0050eb052 10f7096ea Author: Weiqun Zhang Date: Wed Dec 28 08:16:54 2016 -0800 Merge branch 'migration/6-distributionmap' into development commit 10f7096eaea3796622a87f3dd15d75576b99f5ee Author: Weiqun Zhang Date: Wed Dec 28 08:16:11 2016 -0800 Set Amr's BoxArray and DistributionMapping in AmrLevel::restart. This is safer Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp commit 5fad52a6235f5ab00b90bb0a34a3466c4ac9c6c6 Author: Weiqun Zhang Date: Tue Dec 27 23:21:07 2016 -0800 make sure FluxRegister, BndryRegister and FabSet::read() functions only read data into predefined objects. Src/AmrCore/AMReX_FluxRegister.cpp Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_FabSet.cpp commit 0050eb0521829f8418e4fc697e0972493b8a6f62 Merge: 9b8f3073a 54f685bae Author: Weiqun Zhang Date: Tue Dec 27 16:39:46 2016 -0800 Merge branch 'migration/6-distributionmap' into development commit 54f685bae8a90c68f99ae110d4c3852398da8282 Author: Weiqun Zhang Date: Tue Dec 27 16:39:32 2016 -0800 typo Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp commit 9b8f3073af491799abfde0f49aab831b0ee4e9a7 Merge: 0384140b7 88a41e94d Author: Weiqun Zhang Date: Tue Dec 27 13:28:30 2016 -0800 Merge branch 'migration/6-distributionmap' into development commit 88a41e94d85933521cdeed57cf653927855ddd29 Author: Weiqun Zhang Date: Tue Dec 27 13:28:13 2016 -0800 minor update to migration document Docs/Migration/Migration.md commit 9444d5a71cefedda5c2d72fa52708411e3bb7935 Author: Weiqun Zhang Date: Tue Dec 27 13:18:45 2016 -0800 update migration document Docs/Migration/Migration.md commit 9e365a507fa373e8db0f16951c37e516bb81cc3b Author: Weiqun Zhang Date: Tue Dec 27 12:02:14 2016 -0800 update C_TensorMG Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.H Tests/LinearSolvers/C_TensorMG/testVI.cpp commit 4b44fc39f761dd92901e88ac7618e4684b0d1f02 Author: Weiqun Zhang Date: Tue Dec 27 08:33:40 2016 -0800 update more tests MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp MiniApps/MultiGrid_C/main.cpp MiniApps/PGAS_SMC/SMC_init.cpp MiniApps/PGAS_SMC/SMC_io.cpp Tests/C_BaseLib/tFAC.cpp Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tMFcopy.cpp Tests/C_BaseLib/tVisMF.cpp Tests/C_BaseLib/tVisMF2.cpp Tests/FillBoundaryComparison/main.cpp Tests/IOBenchmark/IOTest.cpp Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp commit ee0719e4637f40721d2b09d84a556bbd35e0e21d Author: Weiqun Zhang Date: Tue Dec 27 07:39:21 2016 -0800 update Particles Src/Particle/AMReX_Particles.H Src/Particle/AMReX_TracerParticles.cpp Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/two_level.cpp commit 120053968fb9d5ff731fe6a71b0cbbf2794d6a78 Author: Weiqun Zhang Date: Mon Dec 26 16:56:02 2016 -0800 update C_CellMG4 and C_to_F_MG Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Tutorials/MultiGrid_C/main.cpp commit 450fb1a938f9789192bb57f9b55e3b78cff88bd9 Author: Weiqun Zhang Date: Mon Dec 26 16:27:16 2016 -0800 update C_CellMG Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Tutorials/MultiColor_C/main.cpp commit 02d5bf730f3601e005fa85d7a2e8ab8d787744b7 Author: Weiqun Zhang Date: Mon Dec 26 15:38:17 2016 -0800 update Amr Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AuxBoundaryData.cpp Src/Amr/AMReX_Extrapolater.cpp Src/Amr/AMReX_LevelBld.H Src/Amr/AMReX_SlabStat.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StationData.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/Base/AMReX_DistributionMapping.H Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_FabSet.cpp Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/AdvBld.cpp Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_io.cpp Tutorials/AMR_Adv_C/Source/main.cpp commit 0384140b772be57507bf168443084e193775b080 Author: Weiqun Zhang Date: Sun Dec 25 11:47:43 2016 -0800 uncomment BaseFab::size Src/Base/AMReX_BaseFab.H commit 8a853f81dc909d47d47226c18f8c98c3fb1b0bcb Author: Weiqun Zhang Date: Sun Dec 25 20:49:39 2016 -0800 update Boundary and AmrCore Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_FabSet.cpp Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_MacBndry.H Src/Boundary/AMReX_MacBndry.cpp Src/Boundary/AMReX_MultiMask.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp commit 87924b105cca2801f5d844eaad273ce9e076e2c2 Author: Weiqun Zhang Date: Sun Dec 25 12:18:22 2016 -0800 modify VisMF::Read to allow predefined MF Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp commit 9d8c3bc6cc01f9d01eacf6a3a458dcd38860e36a Author: Weiqun Zhang Date: Sun Dec 25 11:54:30 2016 -0800 make FabArray::define virtual Src/Base/AMReX_FabArray.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_iMultiFab.H commit 81208a3c7ad04a4a108c2e8eedd2d26415a7e293 Author: Weiqun Zhang Date: Sun Dec 25 11:47:56 2016 -0800 fix a number of tutorials Tutorials/GettingStarted_C/main.cpp Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/MultiColor_C/main.cpp Tutorials/MultiFabTests_C/GNUmakefile Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp Tutorials/PGAS_HEAT/main.cpp Tutorials/Sidecar_EX1/DestMFTest.cpp Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Sidecar_EX1/GridMoveTest.cpp Tutorials/Sidecar_EX1/NSidecarsTest.cpp Tutorials/Tiling_C/main.cpp Tutorials/Tiling_Heat_C/main.cpp Tutorials/WaveEquation_C/main.cpp commit 917df37a9c09c0cfef266c13959f23ed6383fcd3 Author: Weiqun Zhang Date: Sun Dec 25 11:47:43 2016 -0800 uncomment BaseFab::size Src/Base/AMReX_BaseFab.H commit 31f2df7f4e401172aa706546b283d8a08b395163 Author: Weiqun Zhang Date: Sun Dec 25 08:33:08 2016 -0800 fix AmrData Src/Base/AMReX_FabArray.H Src/Extern/amrdata/AMReX_AmrData.cpp Tutorials/DataServicesTest0/DataServicesTest0.cpp commit 14505f27cf8e6a0e5204684a16cf19b667b9117e Author: Weiqun Zhang Date: Sun Dec 25 07:44:59 2016 -0800 removed DistributionMapping cache Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_Utility.cpp commit 62ec4b432a9783c4feddbae53f9ccb94e929198c Author: Weiqun Zhang Date: Sun Dec 25 07:26:41 2016 -0800 DistributionMapping is now a required argument of FabArray and hence MultiFab constructors. Docs/Migration/Migration.md Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_FabArray.H Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp Tutorials/HelloWorld_C/main.cpp commit 18aeb792ec77e6ca3805505ad6a46549d8c48427 Author: Dan Graves Date: Thu Dec 22 16:46:20 2016 -0800 these are too useful to go away Src/GeometryShop/AMReX_LoHiSide.H Src/GeometryShop/AMReX_LoHiSide.cpp commit 7516caae04b327240aa149babcb8f927a998caed Author: Dan Graves Date: Thu Dec 22 16:45:40 2016 -0800 more progress toward geometry port Src/GeometryShop/AMReX_BaseIF.H Src/GeometryShop/AMReX_BoxIterator.H Src/GeometryShop/AMReX_BoxIterator.cpp Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_IrregNode.cpp Src/GeometryShop/AMReX_LSquares.H Src/GeometryShop/AMReX_LSquares.cpp Src/GeometryShop/AMReX_Moments.H Src/GeometryShop/AMReX_Moments.cpp Src/GeometryShop/AMReX_PlaneIF.H Src/GeometryShop/AMReX_PlaneIF.cpp Src/GeometryShop/AMReX_RealVect.H Src/GeometryShop/AMReX_RealVect.cpp Src/GeometryShop/Make.package Tests/GeometryShop/sphere/GNUmakefile commit 535f4989b6b8de82d60f4ec9a23a08fe33a24a69 Author: Dan Graves Date: Thu Dec 22 16:08:34 2016 -0800 some casts to make stuff compile on our crappy mpi platform Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_ParallelDescriptor.cpp commit 6e56c72593d9c9066f906dec84b4700a78fd7ece Author: Dan Graves Date: Thu Dec 22 15:29:28 2016 -0800 adding some files Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_PlaneIF.H Src/GeometryShop/AMReX_PlaneIF.cpp Src/GeometryShop/AMReX_SphereIF.H Src/GeometryShop/AMReX_SphereIF.cpp Src/GeometryShop/Make.package Tests/GeometryShop/sphere/GNUmakefile Tests/GeometryShop/sphere/sphereTest.cpp commit ec14b80312642e1ae0311380d7155b3b689c7b5c Author: Dan Graves Date: Thu Dec 22 15:26:46 2016 -0800 making more progress on geometry Src/GeometryShop/AMReX_HyperPlaneIF.H Src/GeometryShop/AMReX_HyperPlaneIF.cpp Src/GeometryShop/AMReX_HyperSphereIF.H Src/GeometryShop/AMReX_HyperSphereIF.cpp Tests/GeometryShop/sphere/GNUmakefile Tests/GeometryShop/sphere/Make.package Tests/GeometryShop/sphere/sphere.inputs Tests/GeometryShop/sphere/sphereConvTest.cpp Tests/GeometryShop/sphere/sphereTest.cpp commit 303fb8939062c68367a67c8856e768e33524b531 Merge: 426ada953 14242dbf8 Author: Weiqun Zhang Date: Thu Dec 22 10:31:13 2016 -0800 Merged in mzingale/amrex/zingale/work (pull request #3) update regtest to AMReX commit 426ada953fe3216223e8f8e21c493b1989c3d72f Merge: 39bd01070 c92b95418 Author: tannguyen Date: Wed Dec 21 16:19:45 2016 -0800 Merge branch 'development' of bitbucket.org:berkeleylab/amrex into development commit 39bd0107096d8e6de47d66f84585076e23b1d502 Author: tannguyen Date: Wed Dec 21 16:18:48 2016 -0800 mark up a few dot H files Src/Base/AMReX_Arena.H Src/Base/AMReX_Array.H Src/Base/AMReX_BCRec.H Src/Base/AMReX_BaseFab.H commit 14242dbf809ea2a680d9656d01e6d3419ade1376 Merge: 77b6e51ae 5e5f16b30 Author: Michael Zingale Date: Wed Dec 21 14:29:43 2016 -0500 Merge branch 'development' into zingale/work commit c92b95418ff5da6cebdc7626a0a0707102176fef Merge: 98f6362cb 5e5f16b30 Author: Michael Zingale Date: Wed Dec 21 14:28:34 2016 -0500 Merged in mzingale/amrex/development (pull request #4) add --log_file option to the test suite commit 5e5f16b30fbee920876e6ca1274c72f5ce903911 Author: Michael Zingale Date: Wed Dec 21 14:22:10 2016 -0500 add a --log_file option to direct output to a log file (it still goes to stdout too) Tools/RegressionTesting/params.py Tools/RegressionTesting/test_util.py commit 7998fb4a971fef9211484d1128e570af6c073836 Merge: 2cdeb3e9d 98f6362cb Author: Michael Zingale Date: Wed Dec 21 11:26:58 2016 -0500 Merge branch 'development' of ssh://bitbucket.org/berkeleylab/AMReX into development commit 98f6362cbce0b2040c4a6b6b39f969fcdbeb91b8 Author: tannguyen Date: Tue Dec 20 19:47:38 2016 -0800 doxygen config file Docs/doxygen.conf commit 456aa1bcedeb9a01547fe0af502e0a18fee70748 Author: Dan Graves Date: Tue Dec 20 15:35:28 2016 -0800 lots of progress made here but not quite done Src/GeometryShop/AMReX_BaseIF.H Src/GeometryShop/AMReX_BoxIterator.H Src/GeometryShop/AMReX_BoxIterator.cpp Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_LSquares.H Src/GeometryShop/AMReX_LSquares.cpp Src/GeometryShop/AMReX_Moments.H Src/GeometryShop/AMReX_Moments.cpp Src/GeometryShop/AMReX_MultiSphereIF.H Src/GeometryShop/AMReX_MultiSphereIF.cpp Src/GeometryShop/AMReX_RealVect.H Src/GeometryShop/AMReX_RealVect.cpp Src/GeometryShop/Make.package commit b216bee0f47efa6b804d19a51323da35f053d463 Author: Dan Graves Date: Mon Dec 19 16:21:57 2016 -0800 starting the geometryshop port in this branch Src/GeometryShop/AMReX_BaseIF.H Src/GeometryShop/AMReX_BoxIterator.H Src/GeometryShop/AMReX_BoxIterator.cpp Src/GeometryShop/AMReX_CellEdge.H Src/GeometryShop/AMReX_CellEdge.cpp Src/GeometryShop/AMReX_ComplementIF.H Src/GeometryShop/AMReX_ComplementIF.cpp Src/GeometryShop/AMReX_EllipsoidIF.H Src/GeometryShop/AMReX_EllipsoidIF.cpp Src/GeometryShop/AMReX_GeometryShop.H Src/GeometryShop/AMReX_GeometryShop.cpp Src/GeometryShop/AMReX_HyperPlaneIF.H Src/GeometryShop/AMReX_HyperPlaneIF.cpp Src/GeometryShop/AMReX_HyperSphereIF.H Src/GeometryShop/AMReX_HyperSphereIF.cpp Src/GeometryShop/AMReX_IntersectionIF.H Src/GeometryShop/AMReX_IntersectionIF.cpp Src/GeometryShop/AMReX_IrregNode.H Src/GeometryShop/AMReX_IrregNode.cpp Src/GeometryShop/AMReX_LatheIF.H Src/GeometryShop/AMReX_LatheIF.cpp Src/GeometryShop/AMReX_MultiSphereIF.H Src/GeometryShop/AMReX_MultiSphereIF.cpp Src/GeometryShop/AMReX_PlaneIF.H Src/GeometryShop/AMReX_PlaneIF.cpp Src/GeometryShop/AMReX_RealVect.H Src/GeometryShop/AMReX_RealVect.cpp Src/GeometryShop/AMReX_SphereIF.H Src/GeometryShop/AMReX_SphereIF.cpp Src/GeometryShop/AMReX_TransformIF.H Src/GeometryShop/AMReX_TransformIF.cpp Src/GeometryShop/AMReX_UnionIF.H Src/GeometryShop/AMReX_UnionIF.cpp Src/GeometryShop/Make.package commit 77b6e51aecba0fbf823d83fd8e399e02d45a9a60 Author: Michael Zingale Date: Sun Dec 18 20:53:29 2016 -0500 update ini Tools/RegressionTesting/AMReX-tests.ini commit 28ad5205fc6e861bdce0cd4e307cc983509e6b63 Author: Michael Zingale Date: Sun Dec 18 20:51:56 2016 -0500 remove old inis Tools/RegressionTesting/Castro-tests.ini Tools/RegressionTesting/VARDEN-tests.ini Tools/RegressionTesting/radiation-tests.ini commit 6217ca31739512df701fe34b0d97b7b772f60553 Author: Michael Zingale Date: Sun Dec 18 20:51:21 2016 -0500 switch to AMReX Tools/RegressionTesting/README Tools/RegressionTesting/example-tests.ini Tools/RegressionTesting/params.py Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_util.py commit 2cdeb3e9d2aa6192564f56e9e3d05aa5ae2636cf Merge: 2e6e79fdf a7e456d0a Author: Michael Zingale Date: Sun Dec 18 20:14:35 2016 -0500 Merge /home/zingale/temp/AMReX into development commit 2e6e79fdf55a4838d514fd1814fdbdffc2637d31 Merge: dbda33c9b 74b0a87e0 Author: Michael Zingale Date: Sun Dec 18 20:10:48 2016 -0500 Merge ssh://bitbucket.org/berkeleylab/AMReX into development commit a7e456d0afcc27b9d331a926eccbb0676d376555 Author: Weiqun Zhang Date: Sun Dec 18 07:15:32 2016 -0800 fix tests MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp MiniApps/MultiGrid_C/main.cpp MiniApps/PGAS_SMC/SMC.H MiniApps/PGAS_SMC/SMC.cpp MiniApps/PGAS_SMC/SMC_advance.cpp MiniApps/PGAS_SMC/SMC_init.cpp MiniApps/PGAS_SMC/SMC_io.cpp MiniApps/PGAS_SMC/main.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp Tests/BBIOBenchmark/BBIOTest.cpp Tests/BBIOBenchmark/BBIOTestDriver.cpp Tests/C_BaseLib/AMRProfTestBL.cpp Tests/C_BaseLib/t8BIT.cpp Tests/C_BaseLib/tBA.cpp Tests/C_BaseLib/tCArena.cpp Tests/C_BaseLib/tDM.cpp Tests/C_BaseLib/tFAC.cpp Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tFillFab.cpp Tests/C_BaseLib/tMF.cpp Tests/C_BaseLib/tMFcopy.cpp Tests/C_BaseLib/tParmParse.cpp Tests/C_BaseLib/tProfiler.cpp Tests/C_BaseLib/tRABcast.cpp Tests/C_BaseLib/tRan.cpp Tests/C_BaseLib/tVisMF.cpp Tests/C_BaseLib/tVisMF2.cpp Tests/C_BaseLib/tread.cpp Tests/FillBoundaryComparison/main.cpp Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/LinearSolvers/C_CellMG/MacOpMacDrivers.H Tests/LinearSolvers/C_CellMG/MacOperator.H Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_CellMG/macprojTest.cpp Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.H Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.H Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp Tests/MKDir/MKDir.cpp commit 8db0c298629d79cb956d8f30446ac24eccfedb7b Author: Weiqun Zhang Date: Sun Dec 18 06:41:25 2016 -0800 put pgas into amrex namespace Src/Base/AMReX_BLPgas.H commit f226206e94c12df28bfe3196f978e84ba1f3731e Author: Weiqun Zhang Date: Sun Dec 18 06:36:26 2016 -0800 fix some name conflicts in amrdata Docs/Migration/Migration.md Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_DataServices.H Tutorials/DataServicesTest0/DataServicesTest0.cpp Tutorials/GettingStarted_C/main.cpp Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX1_C/writePlotFile.H Tutorials/HeatEquation_EX1_C/writePlotFile.cpp Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/HeatEquation_EX2_C/writePlotFile.H Tutorials/HeatEquation_EX2_C/writePlotFile.cpp Tutorials/MultiColor_C/main.cpp Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp Tutorials/PGAS_HEAT/main.cpp Tutorials/PGAS_HEAT/writePlotFile.H Tutorials/PGAS_HEAT/writePlotFile.cpp Tutorials/Sidecar_EX1/DestMFTest.cpp Tutorials/Sidecar_EX1/GridMoveTest.cpp Tutorials/Sidecar_EX1/InTransitAnalysis.H Tutorials/Sidecar_EX1/InTransitAnalysis.cpp Tutorials/Sidecar_EX1/NSidecarsTest.cpp Tutorials/Sidecar_EX1/SidecarResizeTest.cpp Tutorials/Sidecar_EX1/TestRankSets.cpp Tutorials/Tiling_C/main.cpp Tutorials/Tiling_Heat_C/main.cpp Tutorials/Tiling_Heat_C/writePlotFile.H Tutorials/Tiling_Heat_C/writePlotFile.cpp Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp Tutorials/TwoGrid_PIC_C/split_boxes.cpp Tutorials/WaveEquation_C/main.cpp Tutorials/WaveEquation_C/writePlotFile.H Tutorials/WaveEquation_C/writePlotFile.cpp commit af1ed48b3b2ccd6d7b6b720e719ec2c86501a3eb Author: Weiqun Zhang Date: Sat Dec 17 17:15:36 2016 -0800 add amrex namespace to particle Src/Particle/AMReX_ParGDB.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_Particles.cpp Src/Particle/AMReX_TracerParticles.H Src/Particle/AMReX_TracerParticles.cpp Tutorials/PIC_C/main.cpp Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/two_level.cpp commit 2bc0998eefaab84646e3fc6d4426dd62d6721c2c Author: Weiqun Zhang Date: Sat Dec 17 17:09:30 2016 -0800 add amrex namespace to linear solvers Docs/Migration/Migration.md Src/F_BaseLib/MultiFab_C_F.H Src/F_BaseLib/MultiFab_C_F.cpp Src/F_BaseLib/backtrace_c.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2.H Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Src/LinearSolvers/C_to_F_MG/AMReX_stencil_types.H Tutorials/MultiGrid_C/main.cpp Tutorials/MultiGrid_C/writePlotFile.H Tutorials/MultiGrid_C/writePlotFile.cpp commit 9439af2400d89018c89f2db627d9593fca7e0fa6 Author: Weiqun Zhang Date: Sat Dec 17 16:59:49 2016 -0800 move a few variables in amrex namespace into amrex::system namespace; one of the variables, verbose, was likely to cause conflict when using namespace amrex is used. Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BoxLib.H Src/Base/AMReX_BoxLib.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FabArray.cpp commit 4aaae4451d1eea339bf22751ba42cbdc219bcc39 Author: Weiqun Zhang Date: Sat Dec 17 15:56:19 2016 -0800 add namespace to Amr Docs/Migration/Migration.md Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AuxBoundaryData.H Src/Amr/AMReX_AuxBoundaryData.cpp Src/Amr/AMReX_Derive.H Src/Amr/AMReX_Derive.cpp Src/Amr/AMReX_Extrapolater.H Src/Amr/AMReX_Extrapolater.cpp Src/Amr/AMReX_LevelBld.H Src/Amr/AMReX_SlabStat.H Src/Amr/AMReX_SlabStat.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/Amr/AMReX_StationData.H Src/Amr/AMReX_StationData.cpp Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/AdvBld.cpp Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_dt.cpp Tutorials/AMR_Adv_C/Source/Adv_io.cpp Tutorials/AMR_Adv_C/Source/Adv_setup.cpp Tutorials/AMR_Adv_C/Source/main.cpp commit c83b8b3c5bb2d6adecfd1b6ad72af3e8851a29bb Author: Weiqun Zhang Date: Sat Dec 17 15:14:38 2016 -0800 add namespace to Boundary and AmrCore Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrParGDB.H Src/AmrCore/AMReX_AmrParticles.H Src/AmrCore/AMReX_Cluster.H Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_ErrorList.cpp Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_BoundCond.H Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_FabSet.cpp Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_MacBndry.H Src/Boundary/AMReX_MacBndry.cpp Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_Mask.cpp Src/Boundary/AMReX_MultiMask.H Src/Boundary/AMReX_MultiMask.cpp Src/Extern/amrdata/AMReX_AmrData.H Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_AmrvisConstants.H Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvBC.H Tutorials/AMR_Adv_C_v2/Source/AmrAdvError.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp Tutorials/AMR_Adv_C_v2/Source/main.cpp commit ae4fbbe76d3c42bfcc7fcb7914d839434e4c971a Author: Weiqun Zhang Date: Fri Dec 16 15:56:09 2016 -0800 add namespace to Base Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_Array.H Src/Base/AMReX_BArena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BLBackTrace.H Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BLPgas.cpp Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxDomain.H Src/Base/AMReX_BoxDomain.cpp Src/Base/AMReX_BoxLib.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FPC.H Src/Base/AMReX_FPC.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp Src/Base/AMReX_FabConv.H Src/Base/AMReX_FabConv.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_IndexType.H Src/Base/AMReX_IndexType.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_Lazy.H Src/Base/AMReX_Lazy.cpp Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_MemProfiler.H Src/Base/AMReX_MemProfiler.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_NFiles.H Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_Orientation.H Src/Base/AMReX_Orientation.cpp Src/Base/AMReX_PList.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParmParse.H Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_Periodicity.H Src/Base/AMReX_Periodicity.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_Pointers.H Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp Src/Base/AMReX_Tuple.H Src/Base/AMReX_UseCount.H Src/Base/AMReX_UseCount.cpp Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_ccse-mpi.H Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp Tutorials/HelloWorld_C/main.cpp commit 334001ff6e166485e4396df50399b16fa644d4c8 Author: Weiqun Zhang Date: Fri Dec 16 13:32:07 2016 -0800 namespace BoxLib --> namespace amrex Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/Base/AMReX_Arena.H Src/Base/AMReX_BCRec.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_Box.H Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxDomain.H Src/Base/AMReX_BoxLib.H Src/Base/AMReX_BoxLib.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_IntVect.H Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_SPACE.H Src/Base/AMReX_Utility.H commit 690c64a827ffa6efecc53ce4af3b9f0549446c8a Author: Weiqun Zhang Date: Fri Dec 16 12:58:01 2016 -0800 BoxLib:: --> amrex:: Docs/Migration/Migration.md Docs/Readme.profiling MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp MiniApps/MultiGrid_C/main.cpp MiniApps/PGAS_SMC/SMC_io.cpp MiniApps/PGAS_SMC/main.cpp Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AuxBoundaryData.cpp Src/Amr/AMReX_Derive.cpp Src/Amr/AMReX_SlabStat.cpp Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StationData.cpp Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_TagBox.cpp Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BLPgas.cpp Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_BLassert.H Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxDomain.cpp Src/Base/AMReX_BoxLib.H Src/Base/AMReX_BoxLib.cpp Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp Src/Base/AMReX_FabConv.cpp Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_IndexType.cpp Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_MemProfiler.cpp Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_NFiles.H Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_Orientation.cpp Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_PhysBCFunct.cpp Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_TinyProfiler.cpp Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_iMultiFab.cpp Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_FabSet.cpp Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_MacBndry.cpp Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_DataServices.cpp Src/Extern/hpgmg/BL_HPGMG.cpp Src/F_BaseLib/MultiFab_C_F.cpp Src/F_Interfaces/BaseLib/main.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_Particles.cpp Src/Particle/AMReX_TracerParticles.cpp Tests/BBIOBenchmark/BBIOTest.cpp Tests/BBIOBenchmark/BBIOTestDriver.cpp Tests/C_BaseLib/AMRProfTestBL.cpp Tests/C_BaseLib/BcastClasses/BcastClasses.cpp Tests/C_BaseLib/tBA.cpp Tests/C_BaseLib/tCArena.cpp Tests/C_BaseLib/tDM.cpp Tests/C_BaseLib/tDir.cpp Tests/C_BaseLib/tFAC.cpp Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tFillFab.cpp Tests/C_BaseLib/tMF.cpp Tests/C_BaseLib/tMFcopy.cpp Tests/C_BaseLib/tParmParse.cpp Tests/C_BaseLib/tProfiler.cpp Tests/C_BaseLib/tRABcast.cpp Tests/C_BaseLib/tRan.cpp Tests/C_BaseLib/tVisMF.cpp Tests/C_BaseLib/tVisMF2.cpp Tests/C_BaseLib/tread.cpp Tests/FillBoundaryComparison/main.cpp Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_CellMG/macprojTest.cpp Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp Tests/MKDir/MKDir.cpp Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp Tools/C_util/Convergence/Add.cpp Tools/C_util/Convergence/ComputeAmrDataNorms.cpp Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameDomainRefinedFD.cpp Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGrid2.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileNormB.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/Statistics/ComputeAmrDataStat.cpp Tools/C_util/Statistics/PltFileFluxAve.cpp Tools/C_util/Statistics/PltFileList.cpp Tools/C_util/Statistics/PltFileStat.cpp Tools/C_util/Statistics/PltFileXAve.cpp Tools/C_util/TV_TempWrite.H Tools/C_util/ViewMF/MFNorm.cpp Tools/C_util/ViewMF/checkMFghostcells.cpp Tools/C_util/ViewMF/main.cpp Tools/C_util/ViewMF/mfMinMax.cpp Tools/C_util/ViewMF/viewMF.cpp Tools/C_util/ViewMF/viewMFcol.cpp Tools/C_util/ViewMF/viewMFdiff.cpp Tools/C_util/ViewMF/viewMFdiffHardWire.cpp Tools/C_util/WritePlotFile.cpp Tools/C_util/dbgTools/crsGrids.cpp Tools/C_util/dbgTools/intersectGrids.cpp Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_io.cpp Tutorials/AMR_Adv_C/Source/main.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp Tutorials/AMR_Adv_C_v2/Source/main.cpp Tutorials/DataServicesTest0/DataServicesTest0.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp Tutorials/GettingStarted_C/main.cpp Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX1_C/writePlotFile.cpp Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/HeatEquation_EX2_C/writePlotFile.cpp Tutorials/HelloWorld_C/main.cpp Tutorials/MultiColor_C/main.cpp Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp Tutorials/MultiGrid_C/main.cpp Tutorials/MultiGrid_C/writePlotFile.cpp Tutorials/PGAS_HEAT/main.cpp Tutorials/PGAS_HEAT/writePlotFile.cpp Tutorials/PIC_C/main.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/two_level.cpp Tutorials/Sidecar_EX1/DestMFTest.cpp Tutorials/Sidecar_EX1/GridMoveTest.cpp Tutorials/Sidecar_EX1/NSidecarsTest.cpp Tutorials/Sidecar_EX1/SidecarResizeTest.cpp Tutorials/Sidecar_EX1/TestRankSets.cpp Tutorials/Tiling_C/main.cpp Tutorials/Tiling_Heat_C/main.cpp Tutorials/Tiling_Heat_C/writePlotFile.cpp Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp Tutorials/WaveEquation_C/main.cpp Tutorials/WaveEquation_C/writePlotFile.cpp commit ec88b492fffe02822d7a412257631a9f9032bb2e Author: Weiqun Zhang Date: Fri Dec 16 10:39:36 2016 -0800 AMReX:: --> amrex:: Docs/Migration/Migration.md Src/Base/AMReX_Array.H Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tutorials/MultiColor_C/main.cpp Tutorials/MultiGrid_C/main.cpp Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/two_level.cpp Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp commit 7eaad3e5c1be30edb8aeb574e9b0f9c33afb7ae1 Author: Weiqun Zhang Date: Fri Dec 16 09:43:57 2016 -0800 fix Fortran BoxLib tests too Src/F_BaseLib/GPackage.mak Tools/Migration/step-1-amrex_home/amrex_home.sh commit 15006cde5f4145a4f2bfb379ae2a6fb2fec8783a Author: Weiqun Zhang Date: Fri Dec 16 09:19:46 2016 -0800 update migration document and scripts Docs/Migration/Migration.md Tools/Migration/step-1-amrex_home/amrex_home.sh Tools/Migration/step-3-amrex-prefix/amrexprefix.sh Tools/Migration/step-4-dirname/dirname.sh commit 2020c5bc5d580fbd34cd343bed56956da956d5db Author: Weiqun Zhang Date: Fri Dec 16 09:00:16 2016 -0800 update make files for the directory name changes MiniApps/FillBoundary/GNUmakefile MiniApps/MultiGrid_C/GNUmakefile MiniApps/PGAS_SMC/GNUmakefile Src/Amr/Make.package Src/AmrCore/Make.package Src/Base/GNUmakefile Src/Base/Make.package Src/Boundary/Make.package Src/CMakeLists.txt Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/GPackage.mak Src/Particle/Make.package Tests/BBIOBenchmark/GNUmakefile Tests/C_BaseLib/BcastClasses/GNUmakefile Tests/C_BaseLib/GNUmakefile Tests/FillBoundaryComparison/GNUmakefile Tests/IOBenchmark/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile.dumpi Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/ComparisonTest/GNUmakefile Tests/MKDir/GNUmakefile Tools/C_util/AmrDeriveTecplot/GNUmakefile Tools/C_util/Convergence/GNUmakefile Tools/C_util/Statistics/GNUmakefile Tools/C_util/dbgTools/GNUmakefile Tools/GNUMake/Make.defs Tools/GNUMake/Make.rules Tools/GNUMake/README.md Tutorials/AMR_Adv_C/Exec/Make.Adv Tutorials/AMR_Adv_CF/Exec/Make.Adv Tutorials/AMR_Adv_CF/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_C_v2/Exec/Make.Adv Tutorials/DataServicesTest0/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile Tutorials/GettingStarted_C/GNUmakefile Tutorials/HeatEquation_EX1_C/GNUmakefile Tutorials/HeatEquation_EX1_CF/GNUmakefile Tutorials/HeatEquation_EX2_C/GNUmakefile Tutorials/HelloWorld_C/GNUmakefile Tutorials/HelloWorld_CF/GNUmakefile Tutorials/MultiColor_C/GNUmakefile Tutorials/MultiFabTests_C/GNUmakefile Tutorials/MultiGrid_C/GNUmakefile Tutorials/PGAS_HEAT/GNUmakefile Tutorials/PIC_C/GNUmakefile Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Tiling_C/GNUmakefile Tutorials/Tiling_Heat_C/GNUmakefile Tutorials/TwoGrid_PIC_C/GNUmakefile Tutorials/WaveEquation_C/GNUmakefile commit 39641fe47122ea373774ee900ef79901b72a26ee Author: Weiqun Zhang Date: Fri Dec 16 08:53:23 2016 -0800 shorten directory names Src/Amr/AMReX_ARRAYLIM_1D.F Src/Amr/AMReX_ARRAYLIM_2D.F Src/Amr/AMReX_ARRAYLIM_3D.F Src/Amr/AMReX_Amr.H Src/Amr/AMReX_Amr.cpp Src/Amr/AMReX_AmrLevel.H Src/Amr/AMReX_AmrLevel.cpp Src/Amr/AMReX_AuxBoundaryData.H Src/Amr/AMReX_AuxBoundaryData.cpp Src/Amr/AMReX_Derive.H Src/Amr/AMReX_Derive.cpp Src/Amr/AMReX_Extrapolater.H Src/Amr/AMReX_Extrapolater.cpp Src/Amr/AMReX_FLUSH_F.H Src/Amr/AMReX_LevelBld.H Src/Amr/AMReX_MAKESLICE_3D.F Src/Amr/AMReX_MAKESLICE_F.H Src/Amr/AMReX_PROB_AMR_F.H Src/Amr/AMReX_SLABSTAT_1D.F Src/Amr/AMReX_SLABSTAT_2D.F Src/Amr/AMReX_SLABSTAT_3D.F Src/Amr/AMReX_SLABSTAT_F.H Src/Amr/AMReX_SlabStat.H Src/Amr/AMReX_SlabStat.cpp Src/Amr/AMReX_StateData.H Src/Amr/AMReX_StateData.cpp Src/Amr/AMReX_StateDescriptor.H Src/Amr/AMReX_StateDescriptor.cpp Src/Amr/AMReX_StationData.H Src/Amr/AMReX_StationData.cpp Src/Amr/AMReX_extrapolater_1d.f90 Src/Amr/AMReX_extrapolater_2d.f90 Src/Amr/AMReX_extrapolater_3d.f90 Src/Amr/CMakeLists.txt Src/Amr/Make.package Src/AmrCore/AMReX_AmrCore.H Src/AmrCore/AMReX_AmrCore.cpp Src/AmrCore/AMReX_AmrParGDB.H Src/AmrCore/AMReX_AmrParticles.H Src/AmrCore/AMReX_Cluster.H Src/AmrCore/AMReX_Cluster.cpp Src/AmrCore/AMReX_ErrorList.H Src/AmrCore/AMReX_ErrorList.cpp Src/AmrCore/AMReX_FLUXREG_1D.F Src/AmrCore/AMReX_FLUXREG_2D.F Src/AmrCore/AMReX_FLUXREG_3D.F Src/AmrCore/AMReX_FLUXREG_F.H Src/AmrCore/AMReX_FillPatchUtil.H Src/AmrCore/AMReX_FillPatchUtil.cpp Src/AmrCore/AMReX_FluxRegister.H Src/AmrCore/AMReX_FluxRegister.cpp Src/AmrCore/AMReX_INTERP_1D.F Src/AmrCore/AMReX_INTERP_2D.F Src/AmrCore/AMReX_INTERP_3D.F Src/AmrCore/AMReX_INTERP_F.H Src/AmrCore/AMReX_Interpolater.H Src/AmrCore/AMReX_Interpolater.cpp Src/AmrCore/AMReX_TagBox.H Src/AmrCore/AMReX_TagBox.cpp Src/AmrCore/CMakeLists.txt Src/AmrCore/Make.package Src/Base/AMReX_Arena.H Src/Base/AMReX_Arena.cpp Src/Base/AMReX_Array.H Src/Base/AMReX_ArrayLim.H Src/Base/AMReX_BArena.H Src/Base/AMReX_BArena.cpp Src/Base/AMReX_BCRec.H Src/Base/AMReX_BCRec.cpp Src/Base/AMReX_BC_TYPES.H Src/Base/AMReX_BLBackTrace.H Src/Base/AMReX_BLBackTrace.cpp Src/Base/AMReX_BLBoxLib_F.f Src/Base/AMReX_BLFort.H Src/Base/AMReX_BLParmParse_F.f Src/Base/AMReX_BLPgas.H Src/Base/AMReX_BLPgas.cpp Src/Base/AMReX_BLProfiler.H Src/Base/AMReX_BLProfiler.cpp Src/Base/AMReX_BLProfiler_F.f Src/Base/AMReX_BLassert.H Src/Base/AMReX_BLutil_F.f Src/Base/AMReX_BaseFab.H Src/Base/AMReX_BaseFab.cpp Src/Base/AMReX_BaseFab_f.H Src/Base/AMReX_BaseFab_nd.f90 Src/Base/AMReX_Box.H Src/Base/AMReX_Box.cpp Src/Base/AMReX_BoxArray.H Src/Base/AMReX_BoxArray.cpp Src/Base/AMReX_BoxDomain.H Src/Base/AMReX_BoxDomain.cpp Src/Base/AMReX_BoxLib.H Src/Base/AMReX_BoxLib.cpp Src/Base/AMReX_BoxList.H Src/Base/AMReX_BoxList.cpp Src/Base/AMReX_CArena.H Src/Base/AMReX_CArena.cpp Src/Base/AMReX_CONSTANTS.H Src/Base/AMReX_COORDSYS_1D.F Src/Base/AMReX_COORDSYS_2D.F Src/Base/AMReX_COORDSYS_3D.F Src/Base/AMReX_COORDSYS_F.H Src/Base/AMReX_CoordSys.H Src/Base/AMReX_CoordSys.cpp Src/Base/AMReX_DistributionMapping.H Src/Base/AMReX_DistributionMapping.cpp Src/Base/AMReX_FArrayBox.H Src/Base/AMReX_FArrayBox.cpp Src/Base/AMReX_FILCC_1D.F Src/Base/AMReX_FILCC_2D.F Src/Base/AMReX_FILCC_3D.F Src/Base/AMReX_FPC.H Src/Base/AMReX_FPC.cpp Src/Base/AMReX_FabArray.H Src/Base/AMReX_FabArray.cpp Src/Base/AMReX_FabConv.H Src/Base/AMReX_FabConv.cpp Src/Base/AMReX_Geometry.H Src/Base/AMReX_Geometry.cpp Src/Base/AMReX_IArrayBox.H Src/Base/AMReX_IArrayBox.cpp Src/Base/AMReX_IndexType.H Src/Base/AMReX_IndexType.cpp Src/Base/AMReX_IntVect.H Src/Base/AMReX_IntVect.cpp Src/Base/AMReX_Lazy.H Src/Base/AMReX_Lazy.cpp Src/Base/AMReX_Looping.H Src/Base/AMReX_MemPool.H Src/Base/AMReX_MemPool.cpp Src/Base/AMReX_MemProfiler.H Src/Base/AMReX_MemProfiler.cpp Src/Base/AMReX_MultiFab.H Src/Base/AMReX_MultiFab.cpp Src/Base/AMReX_MultiFabUtil.H Src/Base/AMReX_MultiFabUtil.cpp Src/Base/AMReX_MultiFabUtil_1d.f90 Src/Base/AMReX_MultiFabUtil_2d.f90 Src/Base/AMReX_MultiFabUtil_3d.f90 Src/Base/AMReX_MultiFabUtil_F.H Src/Base/AMReX_NFiles.H Src/Base/AMReX_NFiles.cpp Src/Base/AMReX_Orientation.H Src/Base/AMReX_Orientation.cpp Src/Base/AMReX_PList.H Src/Base/AMReX_ParallelDescriptor.H Src/Base/AMReX_ParallelDescriptor.cpp Src/Base/AMReX_ParmParse.H Src/Base/AMReX_ParmParse.cpp Src/Base/AMReX_Periodicity.H Src/Base/AMReX_Periodicity.cpp Src/Base/AMReX_PhysBCFunct.H Src/Base/AMReX_PhysBCFunct.cpp Src/Base/AMReX_PlotFileUtil.H Src/Base/AMReX_PlotFileUtil.cpp Src/Base/AMReX_Pointers.H Src/Base/AMReX_REAL.H Src/Base/AMReX_RealBox.H Src/Base/AMReX_RealBox.cpp Src/Base/AMReX_SPACE.H Src/Base/AMReX_SPACE_F.H Src/Base/AMReX_TinyProfiler.H Src/Base/AMReX_TinyProfiler.cpp Src/Base/AMReX_Tuple.H Src/Base/AMReX_UseCount.H Src/Base/AMReX_UseCount.cpp Src/Base/AMReX_Utility.H Src/Base/AMReX_Utility.cpp Src/Base/AMReX_VisMF.H Src/Base/AMReX_VisMF.cpp Src/Base/AMReX_bc_types.fi Src/Base/AMReX_bl_flush.f Src/Base/AMReX_bl_fort_module.F90 Src/Base/AMReX_ccse-mpi.H Src/Base/AMReX_iMultiFab.H Src/Base/AMReX_iMultiFab.cpp Src/Base/AMReX_mempool_f.f90 Src/Base/AMReX_threadbox.f90 Src/Base/AMReX_winstd.H Src/Base/CMakeLists.txt Src/Base/GNUmakefile Src/Base/GPackage.mak Src/Base/Make.package Src/Base/OpenSource.txt Src/Boundary/AMReX_BndryData.H Src/Boundary/AMReX_BndryData.cpp Src/Boundary/AMReX_BndryRegister.H Src/Boundary/AMReX_BndryRegister.cpp Src/Boundary/AMReX_BoundCond.H Src/Boundary/AMReX_FabSet.H Src/Boundary/AMReX_FabSet.cpp Src/Boundary/AMReX_INTERPBNDRYDATA_1D.F Src/Boundary/AMReX_INTERPBNDRYDATA_2D.F Src/Boundary/AMReX_INTERPBNDRYDATA_3D.F Src/Boundary/AMReX_INTERPBNDRYDATA_F.H Src/Boundary/AMReX_InterpBndryData.H Src/Boundary/AMReX_InterpBndryData.cpp Src/Boundary/AMReX_LO_BCTYPES.H Src/Boundary/AMReX_LO_UTIL.F Src/Boundary/AMReX_MacBndry.H Src/Boundary/AMReX_MacBndry.cpp Src/Boundary/AMReX_Mask.H Src/Boundary/AMReX_Mask.cpp Src/Boundary/AMReX_MultiMask.H Src/Boundary/AMReX_MultiMask.cpp Src/Boundary/CMakeLists.txt Src/Boundary/Make.package Src/Boundary/OpenSource.txt Src/Particle/AMReX_ParGDB.H Src/Particle/AMReX_ParticleInit.H Src/Particle/AMReX_Particles.H Src/Particle/AMReX_Particles.cpp Src/Particle/AMReX_Particles_1D.F Src/Particle/AMReX_Particles_2D.F Src/Particle/AMReX_Particles_3D.F Src/Particle/AMReX_Particles_F.H Src/Particle/AMReX_TracerParticles.H Src/Particle/AMReX_TracerParticles.cpp Src/Particle/CMakeLists.txt Src/Particle/Make.package commit 7824e9c8f3f94dc69a30bb5f070a0211cc7a7343 Author: Weiqun Zhang Date: Fri Dec 16 08:48:28 2016 -0800 rename C_mk to GNUMake Tools/GNUMake/Make.defs Tools/GNUMake/Make.local.template Tools/GNUMake/Make.machines Tools/GNUMake/Make.rules Tools/GNUMake/Make.upcxx Tools/GNUMake/README.md Tools/GNUMake/comps/cray.mak Tools/GNUMake/comps/gnu.mak Tools/GNUMake/comps/intel.mak Tools/GNUMake/comps/pgi.mak Tools/GNUMake/packages/Make.hpgmg Tools/GNUMake/sites/Make.ccse Tools/GNUMake/sites/Make.nersc Tools/GNUMake/sites/Make.olcf Tools/GNUMake/sites/Make.unknown Tools/GNUMake/tools/Make.vtune commit 184bbec1f539deb896e4422dae56c6dbc41e0181 Author: Weiqun Zhang Date: Fri Dec 16 08:35:21 2016 -0800 migration script: limit the scope of search and replace for performace Tools/Migration/step-3-amrex-prefix/amrexprefix.sh commit 5453beecd30e2564f446ff381e7ca06586d496a5 Author: Weiqun Zhang Date: Thu Dec 15 17:11:34 2016 -0800 add migration step 3 script Tools/Migration/step-3-amrex-prefix/amrexprefix.sh commit 7ad6cef05c79d48b4bcfca807696a9aed4e4098c Author: Weiqun Zhang Date: Thu Dec 15 17:06:32 2016 -0800 missed a few names Src/LinearSolvers/C_CellMG4/AMReX_ABec2.H Src/LinearSolvers/C_CellMG4/AMReX_ABec2_F.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4.H Src/LinearSolvers/C_CellMG4/AMReX_ABec4_F.H commit 5be9f3e58e103d4bf2482e638bab541fc4d82360 Author: Weiqun Zhang Date: Thu Dec 15 16:39:37 2016 -0800 remove duplicated AMReX_ Src/C_AMRLib/AMReX_ARRAYLIM_1D.F Src/C_AMRLib/AMReX_ARRAYLIM_2D.F Src/C_AMRLib/AMReX_ARRAYLIM_3D.F Src/C_AMRLib/AMReX_Amr.H Src/C_AMRLib/AMReX_Amr.cpp Src/C_AMRLib/AMReX_AmrLevel.H Src/C_AMRLib/AMReX_AmrLevel.cpp Src/C_AMRLib/AMReX_AuxBoundaryData.H Src/C_AMRLib/AMReX_AuxBoundaryData.cpp Src/C_AMRLib/AMReX_Derive.H Src/C_AMRLib/AMReX_Derive.cpp Src/C_AMRLib/AMReX_Extrapolater.H Src/C_AMRLib/AMReX_Extrapolater.cpp Src/C_AMRLib/AMReX_FLUSH_F.H Src/C_AMRLib/AMReX_LevelBld.H Src/C_AMRLib/AMReX_MAKESLICE_3D.F Src/C_AMRLib/AMReX_MAKESLICE_F.H Src/C_AMRLib/AMReX_PROB_AMR_F.H Src/C_AMRLib/AMReX_SLABSTAT_1D.F Src/C_AMRLib/AMReX_SLABSTAT_2D.F Src/C_AMRLib/AMReX_SLABSTAT_3D.F Src/C_AMRLib/AMReX_SLABSTAT_F.H Src/C_AMRLib/AMReX_SlabStat.H Src/C_AMRLib/AMReX_SlabStat.cpp Src/C_AMRLib/AMReX_StateData.H Src/C_AMRLib/AMReX_StateData.cpp Src/C_AMRLib/AMReX_StateDescriptor.H Src/C_AMRLib/AMReX_StateDescriptor.cpp Src/C_AMRLib/AMReX_StationData.H Src/C_AMRLib/AMReX_StationData.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.cpp commit 2e600fd501475071031daf3d9353281483347def Author: Weiqun Zhang Date: Thu Dec 15 16:34:15 2016 -0800 update Migration document Docs/Migration/Migration.md commit f064e00df56fac04ddd7b658fa725b453d5b5a82 Author: Weiqun Zhang Date: Thu Dec 15 16:29:12 2016 -0800 add AMReX_ to include Docs/Readme.backtrace MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp MiniApps/MultiGrid_C/COEF_3D.F MiniApps/MultiGrid_C/COEF_F.H MiniApps/MultiGrid_C/RHS_3D.F MiniApps/MultiGrid_C/RHS_F.H MiniApps/MultiGrid_C/main.cpp MiniApps/PGAS_SMC/SMC.H MiniApps/PGAS_SMC/SMC.cpp MiniApps/PGAS_SMC/SMC_F.H MiniApps/PGAS_SMC/SMC_io.cpp MiniApps/PGAS_SMC/main.cpp Src/C_AMRLib/AMReX_AMReX_ARRAYLIM_1D.F Src/C_AMRLib/AMReX_AMReX_ARRAYLIM_2D.F Src/C_AMRLib/AMReX_AMReX_ARRAYLIM_3D.F Src/C_AMRLib/AMReX_AMReX_Amr.H Src/C_AMRLib/AMReX_AMReX_Amr.cpp Src/C_AMRLib/AMReX_AMReX_AmrLevel.H Src/C_AMRLib/AMReX_AMReX_AmrLevel.cpp Src/C_AMRLib/AMReX_AMReX_AuxBoundaryData.H Src/C_AMRLib/AMReX_AMReX_AuxBoundaryData.cpp Src/C_AMRLib/AMReX_AMReX_Derive.H Src/C_AMRLib/AMReX_AMReX_Derive.cpp Src/C_AMRLib/AMReX_AMReX_Extrapolater.H Src/C_AMRLib/AMReX_AMReX_Extrapolater.cpp Src/C_AMRLib/AMReX_AMReX_LevelBld.H Src/C_AMRLib/AMReX_AMReX_MAKESLICE_3D.F Src/C_AMRLib/AMReX_AMReX_SLABSTAT_1D.F Src/C_AMRLib/AMReX_AMReX_SLABSTAT_2D.F Src/C_AMRLib/AMReX_AMReX_SLABSTAT_3D.F Src/C_AMRLib/AMReX_AMReX_SlabStat.H Src/C_AMRLib/AMReX_AMReX_SlabStat.cpp Src/C_AMRLib/AMReX_AMReX_StateData.H Src/C_AMRLib/AMReX_AMReX_StateData.cpp Src/C_AMRLib/AMReX_AMReX_StateDescriptor.H Src/C_AMRLib/AMReX_AMReX_StateDescriptor.cpp Src/C_AMRLib/AMReX_AMReX_StationData.H Src/C_AMRLib/AMReX_AMReX_StationData.cpp Src/C_AmrCoreLib/AMReX_AmrCore.H Src/C_AmrCoreLib/AMReX_AmrCore.cpp Src/C_AmrCoreLib/AMReX_AmrParGDB.H Src/C_AmrCoreLib/AMReX_AmrParticles.H Src/C_AmrCoreLib/AMReX_Cluster.H Src/C_AmrCoreLib/AMReX_Cluster.cpp Src/C_AmrCoreLib/AMReX_ErrorList.H Src/C_AmrCoreLib/AMReX_ErrorList.cpp Src/C_AmrCoreLib/AMReX_FLUXREG_1D.F Src/C_AmrCoreLib/AMReX_FLUXREG_2D.F Src/C_AmrCoreLib/AMReX_FLUXREG_3D.F Src/C_AmrCoreLib/AMReX_FLUXREG_F.H Src/C_AmrCoreLib/AMReX_FillPatchUtil.H Src/C_AmrCoreLib/AMReX_FillPatchUtil.cpp Src/C_AmrCoreLib/AMReX_FluxRegister.H Src/C_AmrCoreLib/AMReX_FluxRegister.cpp Src/C_AmrCoreLib/AMReX_INTERP_1D.F Src/C_AmrCoreLib/AMReX_INTERP_2D.F Src/C_AmrCoreLib/AMReX_INTERP_3D.F Src/C_AmrCoreLib/AMReX_INTERP_F.H Src/C_AmrCoreLib/AMReX_Interpolater.H Src/C_AmrCoreLib/AMReX_Interpolater.cpp Src/C_AmrCoreLib/AMReX_TagBox.H Src/C_AmrCoreLib/AMReX_TagBox.cpp Src/C_BaseLib/AMReX_Arena.H Src/C_BaseLib/AMReX_Arena.cpp Src/C_BaseLib/AMReX_Array.H Src/C_BaseLib/AMReX_ArrayLim.H Src/C_BaseLib/AMReX_BArena.H Src/C_BaseLib/AMReX_BArena.cpp Src/C_BaseLib/AMReX_BCRec.H Src/C_BaseLib/AMReX_BCRec.cpp Src/C_BaseLib/AMReX_BLBackTrace.cpp Src/C_BaseLib/AMReX_BLFort.H Src/C_BaseLib/AMReX_BLPgas.H Src/C_BaseLib/AMReX_BLPgas.cpp Src/C_BaseLib/AMReX_BLProfiler.H Src/C_BaseLib/AMReX_BLProfiler.cpp Src/C_BaseLib/AMReX_BLassert.H Src/C_BaseLib/AMReX_BaseFab.H Src/C_BaseLib/AMReX_BaseFab.cpp Src/C_BaseLib/AMReX_BaseFab_f.H Src/C_BaseLib/AMReX_Box.H Src/C_BaseLib/AMReX_Box.cpp Src/C_BaseLib/AMReX_BoxArray.H Src/C_BaseLib/AMReX_BoxArray.cpp Src/C_BaseLib/AMReX_BoxDomain.H Src/C_BaseLib/AMReX_BoxDomain.cpp Src/C_BaseLib/AMReX_BoxLib.H Src/C_BaseLib/AMReX_BoxLib.cpp Src/C_BaseLib/AMReX_BoxList.H Src/C_BaseLib/AMReX_BoxList.cpp Src/C_BaseLib/AMReX_CArena.H Src/C_BaseLib/AMReX_CArena.cpp Src/C_BaseLib/AMReX_CONSTANTS.H Src/C_BaseLib/AMReX_COORDSYS_1D.F Src/C_BaseLib/AMReX_COORDSYS_2D.F Src/C_BaseLib/AMReX_COORDSYS_3D.F Src/C_BaseLib/AMReX_COORDSYS_F.H Src/C_BaseLib/AMReX_CoordSys.H Src/C_BaseLib/AMReX_CoordSys.cpp Src/C_BaseLib/AMReX_DistributionMapping.H Src/C_BaseLib/AMReX_DistributionMapping.cpp Src/C_BaseLib/AMReX_FArrayBox.H Src/C_BaseLib/AMReX_FArrayBox.cpp Src/C_BaseLib/AMReX_FILCC_1D.F Src/C_BaseLib/AMReX_FILCC_2D.F Src/C_BaseLib/AMReX_FILCC_3D.F Src/C_BaseLib/AMReX_FPC.H Src/C_BaseLib/AMReX_FPC.cpp Src/C_BaseLib/AMReX_FabArray.H Src/C_BaseLib/AMReX_FabArray.cpp Src/C_BaseLib/AMReX_FabConv.H Src/C_BaseLib/AMReX_FabConv.cpp Src/C_BaseLib/AMReX_Geometry.H Src/C_BaseLib/AMReX_Geometry.cpp Src/C_BaseLib/AMReX_IArrayBox.H Src/C_BaseLib/AMReX_IArrayBox.cpp Src/C_BaseLib/AMReX_IndexType.H Src/C_BaseLib/AMReX_IndexType.cpp Src/C_BaseLib/AMReX_IntVect.H Src/C_BaseLib/AMReX_IntVect.cpp Src/C_BaseLib/AMReX_Lazy.cpp Src/C_BaseLib/AMReX_MemPool.cpp Src/C_BaseLib/AMReX_MemProfiler.cpp Src/C_BaseLib/AMReX_MultiFab.H Src/C_BaseLib/AMReX_MultiFab.cpp Src/C_BaseLib/AMReX_MultiFabUtil.H Src/C_BaseLib/AMReX_MultiFabUtil.cpp Src/C_BaseLib/AMReX_MultiFabUtil_F.H Src/C_BaseLib/AMReX_NFiles.H Src/C_BaseLib/AMReX_NFiles.cpp Src/C_BaseLib/AMReX_Orientation.H Src/C_BaseLib/AMReX_Orientation.cpp Src/C_BaseLib/AMReX_ParallelDescriptor.H Src/C_BaseLib/AMReX_ParallelDescriptor.cpp Src/C_BaseLib/AMReX_ParmParse.cpp Src/C_BaseLib/AMReX_Periodicity.H Src/C_BaseLib/AMReX_Periodicity.cpp Src/C_BaseLib/AMReX_PhysBCFunct.H Src/C_BaseLib/AMReX_PhysBCFunct.cpp Src/C_BaseLib/AMReX_PlotFileUtil.H Src/C_BaseLib/AMReX_PlotFileUtil.cpp Src/C_BaseLib/AMReX_Pointers.H Src/C_BaseLib/AMReX_RealBox.H Src/C_BaseLib/AMReX_RealBox.cpp Src/C_BaseLib/AMReX_SPACE_F.H Src/C_BaseLib/AMReX_TinyProfiler.H Src/C_BaseLib/AMReX_TinyProfiler.cpp Src/C_BaseLib/AMReX_Tuple.H Src/C_BaseLib/AMReX_UseCount.H Src/C_BaseLib/AMReX_UseCount.cpp Src/C_BaseLib/AMReX_Utility.H Src/C_BaseLib/AMReX_Utility.cpp Src/C_BaseLib/AMReX_VisMF.H Src/C_BaseLib/AMReX_VisMF.cpp Src/C_BaseLib/AMReX_ccse-mpi.H Src/C_BaseLib/AMReX_iMultiFab.H Src/C_BaseLib/AMReX_iMultiFab.cpp Src/C_BoundaryLib/AMReX_BndryData.H Src/C_BoundaryLib/AMReX_BndryData.cpp Src/C_BoundaryLib/AMReX_BndryRegister.H Src/C_BoundaryLib/AMReX_BndryRegister.cpp Src/C_BoundaryLib/AMReX_BoundCond.H Src/C_BoundaryLib/AMReX_FabSet.H Src/C_BoundaryLib/AMReX_FabSet.cpp Src/C_BoundaryLib/AMReX_INTERPBNDRYDATA_1D.F Src/C_BoundaryLib/AMReX_INTERPBNDRYDATA_2D.F Src/C_BoundaryLib/AMReX_INTERPBNDRYDATA_3D.F Src/C_BoundaryLib/AMReX_INTERPBNDRYDATA_F.H Src/C_BoundaryLib/AMReX_InterpBndryData.H Src/C_BoundaryLib/AMReX_InterpBndryData.cpp Src/C_BoundaryLib/AMReX_LO_UTIL.F Src/C_BoundaryLib/AMReX_MacBndry.H Src/C_BoundaryLib/AMReX_MacBndry.cpp Src/C_BoundaryLib/AMReX_Mask.H Src/C_BoundaryLib/AMReX_Mask.cpp Src/C_BoundaryLib/AMReX_MultiMask.H Src/C_BoundaryLib/AMReX_MultiMask.cpp Src/C_ParticleLib/AMReX_ParGDB.H Src/C_ParticleLib/AMReX_Particles.H Src/C_ParticleLib/AMReX_Particles.cpp Src/C_ParticleLib/AMReX_Particles_F.H Src/C_ParticleLib/AMReX_TracerParticles.H Src/C_ParticleLib/AMReX_TracerParticles.cpp Src/Extern/amrdata/AMReX_AmrData.H Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_AmrvisConstants.H Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp Src/Extern/amrdata/AMReX_FABUTIL_1D.F Src/Extern/amrdata/AMReX_FABUTIL_2D.F Src/Extern/amrdata/AMReX_FABUTIL_3D.F Src/Extern/hpgmg/BL_HPGMG.H Src/F_BaseLib/MemProfiler_f.cpp Src/F_BaseLib/MultiFab_C_F.H Src/F_BaseLib/backtrace_c.cpp Src/F_Interfaces/BaseLib/boxarray_fi.cpp Src/F_Interfaces/BaseLib/geometry_fi.cpp Src/F_Interfaces/BaseLib/main.cpp Src/F_Interfaces/BaseLib/multifab_fi.cpp Src/F_Interfaces/BaseLib/parallel_fi.cpp Src/F_Interfaces/BaseLib/parmparse_fi.cpp Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F Src/LinearSolvers/C_CellMG/AMReX_ABec_F.H Src/LinearSolvers/C_CellMG/AMReX_ABec_UTIL.F Src/LinearSolvers/C_CellMG/AMReX_AMReX_ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_AMReX_CGSolver.cpp Src/LinearSolvers/C_CellMG/AMReX_AMReX_Laplacian.cpp Src/LinearSolvers/C_CellMG/AMReX_AMReX_LinOp.cpp Src/LinearSolvers/C_CellMG/AMReX_AMReX_MultiGrid.cpp Src/LinearSolvers/C_CellMG/AMReX_CGSolver.H Src/LinearSolvers/C_CellMG/AMReX_LO_1D.F Src/LinearSolvers/C_CellMG/AMReX_LO_2D.F Src/LinearSolvers/C_CellMG/AMReX_LO_3D.F Src/LinearSolvers/C_CellMG/AMReX_LO_F.H Src/LinearSolvers/C_CellMG/AMReX_LP_1D.F Src/LinearSolvers/C_CellMG/AMReX_LP_2D.F Src/LinearSolvers/C_CellMG/AMReX_LP_3D.F Src/LinearSolvers/C_CellMG/AMReX_LP_F.H Src/LinearSolvers/C_CellMG/AMReX_Laplacian.H Src/LinearSolvers/C_CellMG/AMReX_LinOp.H Src/LinearSolvers/C_CellMG/AMReX_MG_1D.F Src/LinearSolvers/C_CellMG/AMReX_MG_2D.F Src/LinearSolvers/C_CellMG/AMReX_MG_3D.F Src/LinearSolvers/C_CellMG/AMReX_MG_F.H Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_CellMG4/ABec2.H Src/LinearSolvers/C_CellMG4/ABec2_F.H Src/LinearSolvers/C_CellMG4/ABec4.H Src/LinearSolvers/C_CellMG4/ABec4_F.H Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2_2D.F Src/LinearSolvers/C_CellMG4/AMReX_ABec2_3D.F Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4_2D.F Src/LinearSolvers/C_CellMG4/AMReX_ABec4_3D.F Src/LinearSolvers/C_TensorMG/AMReX_DV_2D.F Src/LinearSolvers/C_TensorMG/AMReX_DV_3D1.F Src/LinearSolvers/C_TensorMG/AMReX_DV_3D2.F Src/LinearSolvers/C_TensorMG/AMReX_DV_3D3.F Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_2D.F Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_3D.F Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/AMReX_MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCLO_2D.F Src/LinearSolvers/C_TensorMG/AMReX_MCLO_3D.F Src/LinearSolvers/C_TensorMG/AMReX_MCLO_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.H Src/LinearSolvers/C_TensorMG/AMReX_MCLinOp.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.H Src/LinearSolvers/C_TensorMG/AMReX_MCMultiGrid.cpp Src/LinearSolvers/C_TensorMG/DV_2D.mF Src/LinearSolvers/C_TensorMG/DV_3D1.mF Src/LinearSolvers/C_TensorMG/DV_3D2.mF Src/LinearSolvers/C_TensorMG/DV_3D3.mF Src/LinearSolvers/C_TensorMG/DV_3D4.mF Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.H Src/LinearSolvers/C_to_F_MG/AMReX_FMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.H Src/LinearSolvers/C_to_F_MG/AMReX_MGT_Solver.cpp Tests/BBIOBenchmark/BBIOTest.cpp Tests/BBIOBenchmark/BBIOTestDriver.cpp Tests/C_BaseLib/AMRProfTestBL.cpp Tests/C_BaseLib/BcastClasses/BcastClasses.cpp Tests/C_BaseLib/t8BIT.cpp Tests/C_BaseLib/tBA.cpp Tests/C_BaseLib/tCArena.cpp Tests/C_BaseLib/tDM.cpp Tests/C_BaseLib/tDir.cpp Tests/C_BaseLib/tFAC.cpp Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tFillFab.cpp Tests/C_BaseLib/tMF.cpp Tests/C_BaseLib/tMFcopy.cpp Tests/C_BaseLib/tParmParse.cpp Tests/C_BaseLib/tProfiler.cpp Tests/C_BaseLib/tRABcast.cpp Tests/C_BaseLib/tRan.cpp Tests/C_BaseLib/tVisMF.cpp Tests/C_BaseLib/tVisMF2.cpp Tests/C_BaseLib/tread.cpp Tests/FillBoundaryComparison/main.cpp Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/LinearSolvers/C_CellMG/COEF_2D.F Tests/LinearSolvers/C_CellMG/COEF_3D.F Tests/LinearSolvers/C_CellMG/COEF_F.H Tests/LinearSolvers/C_CellMG/MACOPERATOR_2D.F Tests/LinearSolvers/C_CellMG/MACOPERATOR_3D.F Tests/LinearSolvers/C_CellMG/MACOPERATOR_F.H Tests/LinearSolvers/C_CellMG/MACPROJ_2D.F Tests/LinearSolvers/C_CellMG/MACPROJ_3D.F Tests/LinearSolvers/C_CellMG/MacOperator.H Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_CellMG/macprojTest.cpp Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.H Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp Tests/LinearSolvers/C_TensorMG/main_2D.F Tests/LinearSolvers/C_TensorMG/main_3D.F Tests/LinearSolvers/C_TensorMG/main_F.H Tests/LinearSolvers/C_TensorMG/testVI.cpp Tests/LinearSolvers/ComparisonTest/COEF_1D.F Tests/LinearSolvers/ComparisonTest/COEF_3D.F Tests/LinearSolvers/ComparisonTest/COEF_F.H Tests/LinearSolvers/ComparisonTest/COMP_NORM_F.H Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.H Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_3D.F Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_F.H Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.H Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp Tests/MKDir/MKDir.cpp Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp Tools/C_util/Convergence/AVGDOWN_2D.F Tools/C_util/Convergence/AVGDOWN_3D.F Tools/C_util/Convergence/AVGDOWN_F.H Tools/C_util/Convergence/Add.cpp Tools/C_util/Convergence/ComputeAmrDataNorms.H Tools/C_util/Convergence/ComputeAmrDataNorms.cpp Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameDomainRefinedFD.cpp Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGrid2.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileNormB.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/Statistics/AVGDOWN_2D.F Tools/C_util/Statistics/AVGDOWN_3D.F Tools/C_util/Statistics/AVGDOWN_F.H Tools/C_util/Statistics/ComputeAmrDataStat.H Tools/C_util/Statistics/ComputeAmrDataStat.cpp Tools/C_util/Statistics/PltFileFluxAve.H Tools/C_util/Statistics/PltFileFluxAve.cpp Tools/C_util/Statistics/PltFileList.cpp Tools/C_util/Statistics/PltFileStat.cpp Tools/C_util/Statistics/PltFileXAve.H Tools/C_util/Statistics/PltFileXAve.cpp Tools/C_util/TV_TempWrite.H Tools/C_util/ViewMF/MFNorm.cpp Tools/C_util/ViewMF/checkMFghostcells.cpp Tools/C_util/ViewMF/main.cpp Tools/C_util/ViewMF/mfMinMax.cpp Tools/C_util/ViewMF/viewMF.cpp Tools/C_util/ViewMF/viewMFcol.cpp Tools/C_util/ViewMF/viewMFdiff.cpp Tools/C_util/ViewMF/viewMFdiffHardWire.cpp Tools/C_util/WritePlotFile.H Tools/C_util/WritePlotFile.cpp Tools/C_util/dbgTools/crsGrids.cpp Tools/C_util/dbgTools/intersectGrids.cpp Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/AdvBld.cpp Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C/Source/Adv_io.cpp Tutorials/AMR_Adv_C/Source/Adv_setup.cpp Tutorials/AMR_Adv_C/Source/main.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvBC.H Tutorials/AMR_Adv_C_v2/Source/AmrAdvError.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H Tutorials/AMR_Adv_C_v2/Source/main.cpp Tutorials/DataServicesTest0/DataServicesTest0.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp Tutorials/GettingStarted_C/main.cpp Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX1_C/myfunc_F.H Tutorials/HeatEquation_EX1_C/writePlotFile.H Tutorials/HeatEquation_EX2_C/FILCC_2D.F Tutorials/HeatEquation_EX2_C/FILCC_3D.F Tutorials/HeatEquation_EX2_C/advance_2d.f90 Tutorials/HeatEquation_EX2_C/advance_3d.f90 Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/HeatEquation_EX2_C/myfunc_F.H Tutorials/HeatEquation_EX2_C/writePlotFile.H Tutorials/HelloWorld_C/main.cpp Tutorials/MultiColor_C/main.cpp Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp Tutorials/MultiGrid_C/COEF_2D.F90 Tutorials/MultiGrid_C/COEF_3D.F90 Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H Tutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F Tutorials/MultiGrid_C/HypreABecLap/HypreABec_F.H Tutorials/MultiGrid_C/RHS_2D.F90 Tutorials/MultiGrid_C/RHS_3D.F90 Tutorials/MultiGrid_C/RHS_F.H Tutorials/MultiGrid_C/main.cpp Tutorials/MultiGrid_C/writePlotFile.H Tutorials/MultiGrid_C/writePlotFile.cpp Tutorials/PGAS_HEAT/main.cpp Tutorials/PGAS_HEAT/writePlotFile.H Tutorials/PGAS_HEAT/writePlotFile.cpp Tutorials/PIC_C/main.cpp Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/two_level.cpp Tutorials/Sidecar_EX1/DestMFTest.cpp Tutorials/Sidecar_EX1/GridMoveTest.cpp Tutorials/Sidecar_EX1/InTransitAnalysis.cpp Tutorials/Sidecar_EX1/NSidecarsTest.cpp Tutorials/Sidecar_EX1/SidecarResizeTest.cpp Tutorials/Sidecar_EX1/TestRankSets.cpp Tutorials/Tiling_C/main.cpp Tutorials/Tiling_Heat_C/main.cpp Tutorials/Tiling_Heat_C/writePlotFile.H Tutorials/Tiling_Heat_C/writePlotFile.cpp Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp Tutorials/TwoGrid_PIC_C/split_boxes.cpp Tutorials/WaveEquation_C/main.cpp Tutorials/WaveEquation_C/writePlotFile.H Tutorials/WaveEquation_C/writePlotFile.cpp commit 3e78f45c421b1114ebf5f07202415f4d4eaf34d1 Author: Weiqun Zhang Date: Thu Dec 15 15:34:10 2016 -0800 rm Tests/F_BaseLib Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/ball_def.14656 Tests/F_BaseLib/conn_defs Tests/F_BaseLib/def_knapsack.out Tests/F_BaseLib/fornberg_weights.f90 Tests/F_BaseLib/inputs.domain Tests/F_BaseLib/main.f90 Tests/F_BaseLib/makefile Tests/F_BaseLib/mt19937ar.f90 Tests/F_BaseLib/t_bl_prof.f90 Tests/F_BaseLib/t_bx.f90 Tests/F_BaseLib/t_bxasc.f90 Tests/F_BaseLib/t_cls.f90 Tests/F_BaseLib/t_knapsack.f90 Tests/F_BaseLib/t_main.f90 Tests/F_BaseLib/t_particles.f90 commit 3e0ab6b198ce301db8f4b0db6de916a001ac5239 Author: Weiqun Zhang Date: Thu Dec 15 15:33:28 2016 -0800 rm Src/Python Src/Python/.gitignore Src/Python/F90/Makefile Src/Python/F90/README Src/Python/F90/fboxlib/__init__.py Src/Python/F90/fboxlib/boxarray.py Src/Python/F90/fboxlib/fab.py Src/Python/F90/fboxlib/layout.py Src/Python/F90/fboxlib/multifab.py Src/Python/F90/fboxlib/regrid.py Src/Python/F90/setup.py Src/Python/F90/src/blobjects.f90 Src/Python/F90/src/blobjects.py Src/Python/F90/src/boxlib_numpy_c.c Src/Python/F90/src/boxlib_numpy_f.f90 Src/Python/F90/src/fboxlib.f90 Src/Python/F90/src/fboxlib_c.c Src/Python/F90/src/make_new_grids.f90 Src/Python/F90/src/regrid.f90 Src/Python/F90/src/tag_boxes.f90 Src/Python/F90/tests/regrid.py Src/Python/GMakerules.mak Src/Python/GNUmakefile Src/Python/GNUmakefile_CXX.mak Src/Python/GPackage.mak Src/Python/README Src/Python/boxlib/__init__.py Src/Python/boxlib/bl1.py Src/Python/boxlib/bl2.py Src/Python/boxlib/bl3.py Src/Python/contrib/chemSupport.H Src/Python/contrib/chemSupport.cpp Src/Python/contrib/support.H Src/Python/contrib/support.cpp Src/Python/setup.py Src/Python/src/boxlib_wrap_1.cpp Src/Python/src/boxlib_wrap_2.cpp Src/Python/src/boxlib_wrap_3.cpp Src/Python/swig/boxlib.i Src/Python/swig/numpy.i Src/Python/tests/test-multifab.py commit 8a54e0b49e906e4537e73b250c7092354dba2250 Author: Weiqun Zhang Date: Thu Dec 15 15:32:50 2016 -0800 add AMReX prefix to file names Src/C_AMRLib/AMReX_AMReX_ARRAYLIM_1D.F Src/C_AMRLib/AMReX_AMReX_ARRAYLIM_2D.F Src/C_AMRLib/AMReX_AMReX_ARRAYLIM_3D.F Src/C_AMRLib/AMReX_AMReX_Amr.H Src/C_AMRLib/AMReX_AMReX_Amr.cpp Src/C_AMRLib/AMReX_AMReX_AmrLevel.H Src/C_AMRLib/AMReX_AMReX_AmrLevel.cpp Src/C_AMRLib/AMReX_AMReX_AuxBoundaryData.H Src/C_AMRLib/AMReX_AMReX_AuxBoundaryData.cpp Src/C_AMRLib/AMReX_AMReX_Derive.H Src/C_AMRLib/AMReX_AMReX_Derive.cpp Src/C_AMRLib/AMReX_AMReX_Extrapolater.H Src/C_AMRLib/AMReX_AMReX_Extrapolater.cpp Src/C_AMRLib/AMReX_AMReX_FLUSH_F.H Src/C_AMRLib/AMReX_AMReX_LevelBld.H Src/C_AMRLib/AMReX_AMReX_MAKESLICE_3D.F Src/C_AMRLib/AMReX_AMReX_MAKESLICE_F.H Src/C_AMRLib/AMReX_AMReX_PROB_AMR_F.H Src/C_AMRLib/AMReX_AMReX_SLABSTAT_1D.F Src/C_AMRLib/AMReX_AMReX_SLABSTAT_2D.F Src/C_AMRLib/AMReX_AMReX_SLABSTAT_3D.F Src/C_AMRLib/AMReX_AMReX_SLABSTAT_F.H Src/C_AMRLib/AMReX_AMReX_SlabStat.H Src/C_AMRLib/AMReX_AMReX_SlabStat.cpp Src/C_AMRLib/AMReX_AMReX_StateData.H Src/C_AMRLib/AMReX_AMReX_StateData.cpp Src/C_AMRLib/AMReX_AMReX_StateDescriptor.H Src/C_AMRLib/AMReX_AMReX_StateDescriptor.cpp Src/C_AMRLib/AMReX_AMReX_StationData.H Src/C_AMRLib/AMReX_AMReX_StationData.cpp Src/C_AMRLib/AMReX_extrapolater_1d.f90 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Src/C_BaseLib/AMReX_Periodicity.H Src/C_BaseLib/AMReX_Periodicity.cpp Src/C_BaseLib/AMReX_PhysBCFunct.H Src/C_BaseLib/AMReX_PhysBCFunct.cpp Src/C_BaseLib/AMReX_PlotFileUtil.H Src/C_BaseLib/AMReX_PlotFileUtil.cpp Src/C_BaseLib/AMReX_Pointers.H Src/C_BaseLib/AMReX_REAL.H Src/C_BaseLib/AMReX_RealBox.H Src/C_BaseLib/AMReX_RealBox.cpp Src/C_BaseLib/AMReX_SPACE.H Src/C_BaseLib/AMReX_SPACE_F.H Src/C_BaseLib/AMReX_TinyProfiler.H Src/C_BaseLib/AMReX_TinyProfiler.cpp Src/C_BaseLib/AMReX_Tuple.H Src/C_BaseLib/AMReX_UseCount.H Src/C_BaseLib/AMReX_UseCount.cpp Src/C_BaseLib/AMReX_Utility.H Src/C_BaseLib/AMReX_Utility.cpp Src/C_BaseLib/AMReX_VisMF.H Src/C_BaseLib/AMReX_VisMF.cpp Src/C_BaseLib/AMReX_bc_types.fi Src/C_BaseLib/AMReX_bl_flush.f Src/C_BaseLib/AMReX_bl_fort_module.F90 Src/C_BaseLib/AMReX_ccse-mpi.H Src/C_BaseLib/AMReX_iMultiFab.H Src/C_BaseLib/AMReX_iMultiFab.cpp Src/C_BaseLib/AMReX_mempool_f.f90 Src/C_BaseLib/AMReX_threadbox.f90 Src/C_BaseLib/AMReX_winstd.H Src/C_BaseLib/CMakeLists.txt 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Src/C_ParticleLib/AMReX_ParticleInit.H Src/C_ParticleLib/AMReX_Particles.H Src/C_ParticleLib/AMReX_Particles.cpp Src/C_ParticleLib/AMReX_Particles_1D.F Src/C_ParticleLib/AMReX_Particles_2D.F Src/C_ParticleLib/AMReX_Particles_3D.F Src/C_ParticleLib/AMReX_Particles_F.H Src/C_ParticleLib/AMReX_TracerParticles.H Src/C_ParticleLib/AMReX_TracerParticles.cpp Src/C_ParticleLib/CMakeLists.txt Src/C_ParticleLib/Make.package Src/Extern/amrdata/AMReX_AmrData.H Src/Extern/amrdata/AMReX_AmrData.cpp Src/Extern/amrdata/AMReX_AmrvisConstants.H Src/Extern/amrdata/AMReX_DataServices.H Src/Extern/amrdata/AMReX_DataServices.cpp Src/Extern/amrdata/AMReX_FABUTIL_1D.F Src/Extern/amrdata/AMReX_FABUTIL_2D.F Src/Extern/amrdata/AMReX_FABUTIL_3D.F Src/Extern/amrdata/CMakeLists.txt Src/Extern/amrdata/Make.package Src/LinearSolvers/C_CellMG/AMReX_ABecLaplacian.H Src/LinearSolvers/C_CellMG/AMReX_ABec_1D.F Src/LinearSolvers/C_CellMG/AMReX_ABec_2D.F Src/LinearSolvers/C_CellMG/AMReX_ABec_3D.F 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Src/LinearSolvers/C_CellMG/AMReX_MultiGrid.H Src/LinearSolvers/C_CellMG/AMReX_lo_bctypes.fi Src/LinearSolvers/C_CellMG/CMakeLists.txt Src/LinearSolvers/C_CellMG/Make.package Src/LinearSolvers/C_CellMG4/AMReX_ABec2.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec2_2D.F Src/LinearSolvers/C_CellMG4/AMReX_ABec2_3D.F Src/LinearSolvers/C_CellMG4/AMReX_ABec4.cpp Src/LinearSolvers/C_CellMG4/AMReX_ABec4_2D.F Src/LinearSolvers/C_CellMG4/AMReX_ABec4_3D.F Src/LinearSolvers/C_CellMG4/CMakeLists.txt Src/LinearSolvers/C_CellMG4/Make.package Src/LinearSolvers/C_TensorMG/AMReX_DV_2D.F Src/LinearSolvers/C_TensorMG/AMReX_DV_3D1.F Src/LinearSolvers/C_TensorMG/AMReX_DV_3D2.F Src/LinearSolvers/C_TensorMG/AMReX_DV_3D3.F Src/LinearSolvers/C_TensorMG/AMReX_DivVis.H Src/LinearSolvers/C_TensorMG/AMReX_DivVis.cpp Src/LinearSolvers/C_TensorMG/AMReX_DivVis_F.H Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.H Src/LinearSolvers/C_TensorMG/AMReX_MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/AMReX_MCINTERPBNDRYDATA_2D.F 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1afd0353a44ac6ef5e39f9e63825f22710f77805 Author: Weiqun Zhang Date: Thu Dec 15 14:52:55 2016 -0800 fix Tensor MG test Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp Tests/LinearSolvers/C_TensorMG/main_2D.F Tests/LinearSolvers/C_TensorMG/main_3D.F Tests/LinearSolvers/C_TensorMG/main_F.H commit 63465bb70618dd81079be33488a5a4799d746da2 Author: Weiqun Zhang Date: Thu Dec 15 14:52:40 2016 -0800 rm duplicated source file Tests/LinearSolvers/C_CellMG/Make.package commit 8aae64c8819e3c186e4d1bee42e7478ed96927ee Author: Weiqun Zhang Date: Sun Dec 11 16:00:58 2016 -0800 rm Tests/StencilOrder Tests/StencilOrder/README Tests/StencilOrder/program.f90 commit 487259cbad84f6886c3200ee83e158499f29f0d4 Author: Weiqun Zhang Date: Sun Dec 11 15:58:57 2016 -0800 rm LinearSolvers/F_MG_Old_Nodal_Stencil Conflicts: Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/GNUmakefile Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/GNUmakefile 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Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/mg.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/ml_nd.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/ml_solve.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_interface_stencil.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_mg_cpp.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_mg_tower_smoother.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_multi.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_rhs.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_smoothers.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_stencil.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_stencil_apply.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_stencil_fill.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_sync_resid.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/regression Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/t_smoother.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/t_stencil.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/wrapper.f90 commit 630d48d5bc9208f566edd0283832061825d72899 Author: Weiqun Zhang Date: Sun Dec 11 08:16:23 2016 -0800 rm Tutorials/MultiFab_C_F Conflicts: Tutorials/MultiFab_C_F/GNUmakefile Tutorials/MultiFab_C_F/main.cpp Tutorials/MultiFab_C_F/GNUmakefile Tutorials/MultiFab_C_F/Make.package Tutorials/MultiFab_C_F/ff.f90 Tutorials/MultiFab_C_F/main.cpp commit 83f1da4ee6c24c3b189362c0d188e60707ab0d4e Author: Weiqun Zhang Date: Sat Dec 10 11:43:48 2016 -0800 rm AMR_Trilinos_C Conflicts: Tutorials/AMR_Trilinos_C/GNUmakefile Tutorials/AMR_Trilinos_C/Solver.H Tutorials/AMR_Trilinos_C/Solver.cpp Tutorials/AMR_Trilinos_C/driver.cpp Tutorials/AMR_Trilinos_C/writePlotFile.H Tutorials/AMR_Trilinos_C/writePlotFile.cpp Tutorials/AMR_Trilinos_C/GNUmakefile Tutorials/AMR_Trilinos_C/Make.package Tutorials/AMR_Trilinos_C/README Tutorials/AMR_Trilinos_C/Solver.H Tutorials/AMR_Trilinos_C/Solver.cpp Tutorials/AMR_Trilinos_C/SolverBoundary.cpp Tutorials/AMR_Trilinos_C/driver.cpp Tutorials/AMR_Trilinos_C/inputs Tutorials/AMR_Trilinos_C/writePlotFile.H Tutorials/AMR_Trilinos_C/writePlotFile.cpp commit 8f327fc55988571b55bf0c55595616f960a4faab Author: Weiqun Zhang Date: Thu Dec 15 14:28:52 2016 -0800 rm boxlib release notes ReleaseNotes/release-notes-16.12.1 commit cd20ef75a037fec1d27cce2e3475a8e39f0a0f20 Author: Weiqun Zhang Date: Sat Dec 10 10:59:17 2016 -0800 rm BoxLib ReleaseNotes Conflicts: ReleaseNotes/release-notes-16.11 ReleaseNotes/release-notes-16.04 ReleaseNotes/release-notes-16.05 ReleaseNotes/release-notes-16.06 ReleaseNotes/release-notes-16.07 ReleaseNotes/release-notes-16.08 ReleaseNotes/release-notes-16.09 ReleaseNotes/release-notes-16.10 ReleaseNotes/release-notes-16.11 ReleaseNotes/release-notes-16.12 commit a773d63ccd6408231692d9c97570c33d9f597635 Author: Weiqun Zhang Date: Fri Dec 9 13:18:25 2016 -0800 rm Extern/gslib Src/Extern/gslib/CMakeLists.txt Src/Extern/gslib/acorni.f Src/Extern/gslib/backtr.f Src/Extern/gslib/beyond.f Src/Extern/gslib/blue.f Src/Extern/gslib/chknam.f Src/Extern/gslib/chktitle.f Src/Extern/gslib/cova3.f Src/Extern/gslib/dlocate.f Src/Extern/gslib/dpowint.f Src/Extern/gslib/dsortem.f Src/Extern/gslib/gauinv.f Src/Extern/gslib/gcum.f Src/Extern/gslib/getindx.f Src/Extern/gslib/getz.f Src/Extern/gslib/green.f Src/Extern/gslib/hexa.f Src/Extern/gslib/ksol.f Src/Extern/gslib/ktsol.f Src/Extern/gslib/locate.f Src/Extern/gslib/nscore.f Src/Extern/gslib/numtext.f Src/Extern/gslib/ordrel.f Src/Extern/gslib/picksupr.f Src/Extern/gslib/powint.f Src/Extern/gslib/psfill.f Src/Extern/gslib/psline.f Src/Extern/gslib/pstext.f Src/Extern/gslib/rand.f Src/Extern/gslib/red.f Src/Extern/gslib/resc.f Src/Extern/gslib/scal.f Src/Extern/gslib/setrot.f Src/Extern/gslib/setsupr.f Src/Extern/gslib/sortem.f Src/Extern/gslib/sqdist.f Src/Extern/gslib/srchsupr.f Src/Extern/gslib/strlen.f commit c6f7efcfaa4b6843cdd5844761d2ddc9f1e11640 Author: Weiqun Zhang Date: Fri Dec 9 13:17:43 2016 -0800 rm Tutorials/Chemotaxis_F Conflicts: Tutorials/Chemotaxis_F/GNUmakefile Tutorials/Chemotaxis_F/GNUmakefile Tutorials/Chemotaxis_F/GPackage.mak Tutorials/Chemotaxis_F/README Tutorials/Chemotaxis_F/advance.f90 Tutorials/Chemotaxis_F/chemotaxis.f90 Tutorials/Chemotaxis_F/dtypes.f90 Tutorials/Chemotaxis_F/inputs.mwe Tutorials/Chemotaxis_F/kernels.f90 Tutorials/Chemotaxis_F/main.f90 Tutorials/Chemotaxis_F/sdcquad.f90 Tutorials/Chemotaxis_F/write_plotfile.f90 Tutorials/README_F commit 40ac28820b60f53571740c04ea0f5b7cf4672941 Author: Weiqun Zhang Date: Thu Dec 15 14:25:15 2016 -0800 add a readme for migration tools Tools/Migration/README.md commit a3fd91f367f6c7c8b694af4006bca2b18f41aecf Author: Weiqun Zhang Date: Thu Dec 15 14:14:30 2016 -0800 update migration document for step 2 Docs/Migration/Migration.md commit e8c7e2a9729ffcb2af68802d63bf683e61629692 Author: Weiqun Zhang Date: Thu Dec 15 13:59:14 2016 -0800 start to use AMReX namespace for new functions Src/C_BaseLib/Array.H Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tutorials/MultiColor_C/main.cpp Tutorials/MultiGrid_C/main.cpp Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/two_level.cpp Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp commit e29fcd91ac27810be2d05d9eb1cf1796f969da5b Author: Weiqun Zhang Date: Thu Dec 15 09:24:14 2016 -0800 add the equivalent of PArray::clear() Src/C_BaseLib/Array.H commit 74b0a87e006caedf3f1344fe2916440d9e18c386 Merge: 40dd135ce 41be670cc Author: John Bell Date: Wed Dec 14 15:49:18 2016 -0800 Merged in license (pull request #2) fixed copyright commit 41be670ccb17abbce281d7b3cdbc35bf0be067f5 Author: jbb Date: Wed Dec 14 15:48:00 2016 -0800 fixed copyright README.txt license.txt commit 8abddcd5f6f3a5c4bc53bd28b94e40ab63fd8b8a Merge: dbda33c9b e22717895 Author: Weiqun Zhang Date: Wed Dec 14 12:48:56 2016 -0800 Merge branch 'weiqun/tmp' into migration/2-parray Conflicts: Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Make.package commit dbda33c9bbc9800e11e63be43294c8df1b8db9bd Author: Weiqun Zhang Date: Wed Dec 14 12:24:12 2016 -0800 start migration document Docs/Migration/Migration.md Tools/Migration/step-1-amrex_home/amrex_home.sh commit bdfd45faef2f97276581b0c5b98ae371903d1bc8 Author: Weiqun Zhang Date: Wed Dec 14 10:47:59 2016 -0800 fix compilation of some tests Tests/FillBoundaryComparison/GNUmakefile Tutorials/MultiFabTests_C/GNUmakefile Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/Tiling_Heat_C/GNUmakefile commit 77476238794137ce8485fceba7a890f08a948d38 Author: Weiqun Zhang Date: Wed Dec 14 10:11:09 2016 -0800 some Fortran BoxLib update Tools/C_mk/README.md Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak Tools/Migration/step-1-amrex_home/amrex_home.sh commit 39fc5d6b91c32979f084ff3205522f03a56ee763 Author: Weiqun Zhang Date: Wed Dec 14 09:42:19 2016 -0800 Migration step 1: replace BOXLIB_HOME with AMREX_HOME MiniApps/AMR_Adv_Diff_F90/GNUmakefile MiniApps/FillBoundary/GNUmakefile MiniApps/MultiGrid_C/GNUmakefile MiniApps/PGAS_SMC/GNUmakefile MiniApps/SMC/GNUmakefile Src/C_AMRLib/Make.package Src/C_AmrCoreLib/Make.package Src/C_BaseLib/GNUmakefile Src/C_BaseLib/Make.package Src/C_BoundaryLib/Make.package Src/C_ParticleLib/Make.package Src/Extern/amrdata/Make.package Src/Extern/hpgmg/Make.package Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/unittests/GNUmakefile Src/LinearSolvers/C_CellMG/Make.package Src/LinearSolvers/C_CellMG4/Make.package Src/LinearSolvers/C_TensorMG/Make.package Src/LinearSolvers/C_to_F_MG/Make.package Src/LinearSolvers/F_MG/FParallelMG.mak Tests/BBIOBenchmark/GNUmakefile Tests/C_BaseLib/BcastClasses/GNUmakefile Tests/C_BaseLib/GNUmakefile Tests/F_BaseLib/GNUmakefile Tests/FillBoundaryComparison/GNUmakefile Tests/IOBenchmark/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/ComparisonTest/GNUmakefile Tests/LinearSolvers/F_MG/GNUmakefile Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/GNUmakefile Tests/MKDir/GNUmakefile Tools/C_mk/Make.defs Tools/C_mk/Make.rules Tools/C_mk/packages/Make.hpgmg Tools/C_util/AmrDeriveTecplot/GNUmakefile Tools/C_util/Convergence/GNUmakefile Tools/C_util/Statistics/GNUmakefile Tools/C_util/ViewMF/GNUmakefile Tools/C_util/dbgTools/GNUmakefile Tools/Migration/step-1-amrex_home/amrex_home.sh Tools/Postprocessing/F_Src/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_xrb/GNUmakefile Tools/Postprocessing/F_Src/tutorial/GNUmakefile Tools/Py_util/GNUmakefile Tutorials/AMR_Adv_C/Exec/Make.Adv Tutorials/AMR_Adv_C/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Adv_CF/Exec/Make.Adv Tutorials/AMR_Adv_C_v2/Exec/Make.Adv Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_F/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_F/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Trilinos_C/GNUmakefile Tutorials/Chemotaxis_F/GNUmakefile Tutorials/DataServicesTest0/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile Tutorials/GettingStarted_C/GNUmakefile Tutorials/GettingStarted_F/GNUmakefile Tutorials/HeatEquation_EX1_C/GNUmakefile Tutorials/HeatEquation_EX1_CF/GNUmakefile Tutorials/HeatEquation_EX1_F/GNUmakefile Tutorials/HeatEquation_EX2_C/GNUmakefile Tutorials/HeatEquation_EX2_F/GNUmakefile Tutorials/HeatEquation_EX3_F/GNUmakefile Tutorials/HeatEquation_EX4_F/GNUmakefile Tutorials/HeatEquation_EX5_F/GNUmakefile Tutorials/HelloWorld_C/GNUmakefile Tutorials/HelloWorld_CF/GNUmakefile Tutorials/MultiColor_C/GNUmakefile Tutorials/MultiFabTests_C/GNUmakefile Tutorials/MultiFab_C_F/GNUmakefile Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_F/GNUmakefile Tutorials/PGAS_HEAT/GNUmakefile Tutorials/PIC_C/GNUmakefile Tutorials/Random_F/GNUmakefile Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Tiling_C/GNUmakefile Tutorials/Tiling_Heat_C/GNUmakefile Tutorials/Tiling_Heat_F/GNUmakefile Tutorials/TwoGrid_PIC_C/GNUmakefile Tutorials/WaveEquation_C/GNUmakefile Tutorials/WaveEquation_F/GNUmakefile commit 40dd135ce62e8b3559ac383903652385696c4b92 Merge: c46162a47 08086379a Author: Weiqun Zhang Date: Wed Dec 14 09:01:26 2016 -0800 Merged in development (pull request #1) fix 2d addNParticles commit 08086379adb0edf72434227581b0001e2c45a83d Merge: c46162a47 12fe9c19a Author: Weiqun Zhang Date: Wed Dec 14 08:56:45 2016 -0800 Merge branch 'github-development' into development commit 12fe9c19a66d0a7b68466f2a8915f3f689ea9f51 Author: Weiqun Zhang Date: Wed Dec 14 08:54:56 2016 -0800 fix 2d addNParticles Src/C_ParticleLib/Particles.H commit c46162a47e0a5888a539a0923c8e6bff2f5260c1 Merge: 16b2cf07c 52a33992c Author: Weiqun Zhang Date: Tue Dec 13 14:46:28 2016 -0800 Merge branch 'github' commit 16b2cf07c9e640256322b04aab41f97cf665d269 Merge: 117cf7a69 61a226686 Author: Weiqun Zhang Date: Tue Dec 13 14:46:01 2016 -0800 Merge branch 'master' into development commit 52a33992c9bef954590395ea76f52f98589a591c Author: Weiqun Zhang Date: Tue Dec 13 14:24:13 2016 -0800 Release 16.12.1 ReleaseNotes/release-notes-16.12.1 commit 022f93c6e6cb42b28180116b9adbf7cc4c0835be Merge: 0edba1491 f48a5ebda Author: Weiqun Zhang Date: Tue Dec 13 13:56:06 2016 -0800 Merge branch 'master' into development commit 0edba1491d75581366639a96e1b0059ca85c825b Author: Weiqun Zhang Date: Tue Dec 13 13:27:09 2016 -0800 fix generic plotfile writer Src/C_BaseLib/PlotFileUtil.cpp commit 8254951f730f3b0a2114c39d41f3a826e1258329 Author: vince Date: Tue Dec 13 11:40:41 2016 -0800 fix comment, format. Src/C_BaseLib/PlotFileUtil.H commit 59ee7fddd494088e6eacc362fe53ceb4bd28da80 Author: vince Date: Tue Dec 13 11:34:57 2016 -0800 clarify comment. Src/C_BaseLib/PlotFileUtil.H commit 563bb08e36c82876120a89912676277f03650859 Merge: c0f427ffd 999ee83cb Author: vince 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 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 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 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 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 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 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 Date: Fri Dec 9 12:04:16 2016 -0800 remove static. Src/C_BaseLib/PlotFileUtil.H commit c29776a65a824fd5a8fe5b00c580fe70aa4539b4 Author: Weiqun Zhang Date: Fri Dec 9 10:13:40 2016 -0800 better way to detect Open MPI Tools/C_mk/sites/Make.unknown commit 06deceff62a48ef8906941742f225020cbcbfb18 Author: vince Date: Thu Dec 8 16:11:07 2016 -0800 support for new cartgrid format. Src/Extern/amrdata/AmrData.H Src/Extern/amrdata/AmrData.cpp commit f3840d8c41d5cabd35d1e632f0c77d630e3b3498 Author: vince Date: Thu Dec 8 16:01:24 2016 -0800 functions for generic plotfiles. Src/C_BaseLib/PlotFileUtil.H Src/C_BaseLib/PlotFileUtil.cpp commit 61a2266868d29ae17642b91d59a13a7db3a54b7c Author: vince Date: Thu Dec 8 15:13:08 2016 -0800 bitbucketpushtest. Docs/Notes.io_implementation commit 117cf7a69eb342bfff17c93ae110d3c59c76497c Merge: 38bdc6fd3 d21ce8f87 Author: Michael Zingale Date: Sat Dec 3 16:41:25 2016 -0500 Merge pull request #16 from nbren12/development raise error in dep.py if fortran preprocessor fails commit 38bdc6fd32c9585e112c3f8751027acd989aefa3 Author: Weiqun Zhang Date: Fri Dec 2 15:43:46 2016 -0800 add support for trapping ABRT. this allows for backtracing interger overflow with gcc. Src/C_BaseLib/BLBackTrace.H Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Utility.cpp commit 96ed1879934d12d92a0d0c21863e379035fed7c8 Author: Weiqun Zhang Date: Fri Dec 2 13:48:26 2016 -0800 gfortran: in debug mode use 2^31 - 1 as the initial value for integers Tools/C_mk/comps/gnu.mak commit 09ce7a93494b2a9df8c5ed24400024b20fbc1c75 Author: Weiqun Zhang Date: Fri Dec 2 13:07:59 2016 -0800 make missing f90.depends an error so that error messages become more helpful Tools/C_mk/Make.rules Tutorials/HelloWorld_C/Make.package commit e4a0174d08abcf45071cad32fa6512c364434906 Author: Weiqun Zhang Date: Fri Dec 2 10:35:33 2016 -0800 because of pgi compiler issue, have to remove -traceback Tools/C_mk/comps/pgi.mak commit e227178958ab1d9efa112537dd8b72a58d5a952e Merge: 8f2473c54 f8db96233 Author: Weiqun Zhang Date: Fri Dec 2 09:04:37 2016 -0800 Merge branch 'development' into experimental commit f8db962333edf1c70b9f90fbba2005acc841b257 Author: Weiqun Zhang Date: Fri Dec 2 09:02:56 2016 -0800 Release Notes for BoxLib 16.12 ReleaseNotes/release-notes-16.12 commit a292fe30405e92d2d519ca20fbf36ca9377f5c72 Merge: 68cd920ad 598124051 Author: Weiqun Zhang Date: Fri Dec 2 08:35:31 2016 -0800 Merge branch 'master' into development commit 68cd920ad003ff87259abd2b47dff0f66665d3d8 Merge: 67b3f9c93 bf891ba50 Author: Michael Zingale Date: Fri Dec 2 01:12:57 2016 -0500 Merge pull request #18 from BoxLib-Codes/preprocessing continue if we encounter a module that is not provided commit bf891ba505df61ea901262486206cbc6a9b1f7c5 Author: Michael Zingale Date: Fri Dec 2 01:11:32 2016 -0500 use a GNU make $(warning...) to report unfound module dependencies. We retain the print to stderr too, so we can easily see these by simply redirecting stdout if desired Tools/F_scripts/dep.py commit d4a3af4ec49472f546bc917f1cd5029cdf0288fe Author: Michael Zingale Date: Thu Dec 1 20:12:21 2016 -0500 if we file requests a module that nothing provides then continue on to the next. This was the intended behavior originally, but we missed a `continue` statement. This allows for system-provided modules to work without them in the `IGNORES` list. This fixes a bug that Brian ran into Tools/F_scripts/dep.py commit 67b3f9c93eaa1f49983a07078518b89429a4e143 Merge: 374357f56 f430d84cb Author: Michael Zingale Date: Thu Dec 1 20:03:18 2016 -0500 Merge pull request #17 from BoxLib-Codes/preprocessing catch dep.py errors and have make abort with an error message commit f430d84cb18e4ee61bbe41ff787bb41f6ca6a74b Author: Michael Zingale Date: Thu Dec 1 19:22:12 2016 -0500 address Weiqun's PR comments Tools/F_scripts/dep.py commit f28293e1d4fa2de063e6ce6881cf74979615adfa Author: Michael Zingale Date: Thu Dec 1 19:14:43 2016 -0500 catch dep.py errors and have make abort with an error message explaining how to enable debug info in the dependency checking Tools/C_mk/Make.rules Tools/F_scripts/dep.py commit 374357f5664efdc4bb5aa1decf6437b76abbf520 Author: vince Date: Thu Dec 1 14:09:42 2016 -0800 make extra stream flushes the default for now. Src/C_BaseLib/VisMF.cpp commit 188d63c8b6629fd418fdc7cc2dced2353ee030ad Merge: 26b290a33 918e06dfc Author: vince 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 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 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 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 Date: Wed Nov 30 22:45:55 2016 -0500 remove bash stuff Tools/F_scripts/dep.py commit ee5e5de582f2100207aeb94abb25b937847b0c60 Author: Noah D. Brenowitz Date: Wed Nov 30 22:37:59 2016 -0500 raise error if fortran preprocessor fails Fixes https://github.com/BoxLib-Codes/BoxLib/issues/15 Tools/F_scripts/dep.py commit 52550d6756a28f31ba5b76e8c0281942a1d0bf72 Author: vince Date: Wed Nov 30 17:39:38 2016 -0800 added flush options to try to fix titan. Src/C_BaseLib/VisMF.cpp commit 9ffecde6469adf3432ac963db3120db49b795115 Author: Weiqun Zhang Date: Wed Nov 30 16:10:02 2016 -0800 more compiler flag tweaks Tools/C_mk/comps/intel.mak Tools/C_mk/comps/pgi.mak commit 26b290a33e9229a16259761374302784a9de6551 Merge: bef6d663b 90ea36bf9 Author: vince 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 Date: Wed Nov 30 14:27:32 2016 -0800 gcc: trap integer overflow Tools/C_mk/comps/gnu.mak commit 90ea36bf9b5d5ba90e4aaeab0c023c5ee8dff803 Author: Weiqun Zhang Date: Wed Nov 30 10:14:24 2016 -0800 fix due to recently deleted functions Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 3daeda968ed2ec8e66259ff30a91750dae20b6eb Author: Weiqun Zhang Date: Wed Nov 30 10:13:30 2016 -0800 we can now safely inline validbox and fabbox Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 6668abfda83e5a9fc6b479aa47e3d2200956d6d8 Author: Weiqun Zhang Date: Wed Nov 30 09:17:17 2016 -0800 fix make for a test Tests/C_BaseLib/GNUmakefile commit a2136c184c7306153163efdb2c4e207e304e7b7b Author: Weiqun Zhang Date: Wed Nov 30 08:55:47 2016 -0800 fix a dangling pointer Src/C_BaseLib/FabArray.H commit 9f1393eac9ad1f47114024e054f8086b0847f650 Author: Weiqun Zhang Date: Wed Nov 30 08:51:00 2016 -0800 delete functions that return a pointer to internal data of rvalue objects Src/C_BaseLib/BCRec.H Src/C_BaseLib/Box.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/RealBox.H commit bef6d663b803c1da68f717fa1f999436a190b337 Merge: 5959d808b 22b914115 Author: vince 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 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 Date: Mon Nov 28 14:15:10 2016 -0800 fix memory leak Src/C_BaseLib/VisMF.cpp commit 732162a6ac435972dcf1b9f13229524d2e1bef71 Author: Ann Almgren Date: Mon Nov 28 13:01:32 2016 -0800 Don't want to get compile error because of call to 3d routine with lo,hi hardwired to lo(2),hi(2) Tutorials/GettingStarted_F/work_on_data.f90 commit 5981240513fcdf4bca3a1db816d484db53560aab Author: Ann Almgren Date: Mon Nov 28 13:00:05 2016 -0800 Don't want to get warning about calling 3d routine with lo,hi hardwired to lo(2),hi(2) Tutorials/GettingStarted_F/work_on_data.f90 commit c31024e152461fa66d2f6c5e3ceaef867f268f70 Merge: 70985bbe7 3f88aba66 Author: WeiqunZhang Date: Mon Nov 28 10:25:40 2016 -0800 Merge pull request #12 from zingale/development add USE_GPROF to enable profiling with gprof commit 3f88aba6671c34a0f0fb426ffc0c3b55c237038a Author: Michael Zingale Date: Mon Nov 28 13:19:15 2016 -0500 add USE_GPROF to enable profiling with gprof Tools/C_mk/comps/gnu.mak commit 70985bbe7fd405313ab47425e7a64f31439eef6a Author: Michael Zingale Date: Sun Nov 27 18:46:11 2016 -0500 remove tcsort -- this is not used by anything Tools/F_mk/GMakedefs.mak Tools/F_scripts/tcsort.pl commit 365a4e9233cc461781e275dc9be612840e13d216 Author: Weiqun Zhang Date: Sat Nov 26 22:42:53 2016 -0500 isinf --> std::isinf Src/LinearSolvers/C_CellMG/CGSolver.cpp commit f536a28bdd25f675f2fe333a921a9f9f70fe1b92 Author: Weiqun Zhang Date: Sat Nov 26 17:03:53 2016 -0800 Intel: -openmp --> -qopenmp for Intel >= 16 because -openmp is deprecated. Tools/C_mk/comps/intel.mak commit 7ec47c8cdf55aab36714c12491f6f1fd213a5ad4 Author: Weiqun Zhang Date: Sat Nov 26 12:32:47 2016 -0800 Intel: add more checks Tools/C_mk/comps/intel.mak commit b5c10a6ea052a760d55261af05f92032e8315726 Author: Weiqun Zhang Date: Sat Nov 26 12:06:57 2016 -0800 PGI: add fpe trap and force implicit none on f90 files Tools/C_mk/comps/pgi.mak commit 73d19d20d5718792e6e437fb40ca67a4fd310764 Author: Weiqun Zhang Date: Sat Nov 26 12:06:04 2016 -0800 GNU: initialize fortran integers to a large bogus number in debug mode Tools/C_mk/comps/gnu.mak commit 2be838c5a6fd4ed332004c082ccfb839f0af77ca Author: Weiqun Zhang Date: Sat Nov 26 11:26:39 2016 -0800 force implicit none for f90 files with gnu Tools/C_mk/comps/gnu.mak commit 8f2473c54ae7aa3bf77a2549778f53883399931e Author: Weiqun Zhang Date: Sat Nov 26 10:57:22 2016 -0800 typo Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp commit 5959d808b01b4cdc98c155cb4e1409b5fe0d7f40 Author: vince 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 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 0e901df8a7aabaec09f798be87ab7f8bb0c7ad17 Author: Weiqun Zhang Date: Tue Nov 22 15:03:47 2016 -0800 amr_level is a unique_ptr Src/C_AMRLib/Amr.cpp commit 82c68c2969b7e2f275de7c910bb31e94ce5b1018 Merge: 613ea2794 9b4c4dfc4 Author: Weiqun Zhang Date: Tue Nov 22 14:53:10 2016 -0800 Merge branch 'development' into experimental Conflicts: Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Array.H Src/C_BaseLib/CMakeLists.txt Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp commit 9b4c4dfc4e19b5cc12b2209820b9f9796c491266 Author: Weiqun Zhang Date: Tue Nov 22 13:34:22 2016 -0800 add python version check and force make to exit if requirement is not met Tools/C_mk/Make.defs commit 12c4332b02c88c2b30f3fa913859010018329567 Author: Weiqun Zhang Date: Tue Nov 22 11:11:25 2016 -0800 fix Tutorials/AMR_Adv_C_v2 Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp commit 1adbcda6d278b10239764f7772bf61f72d2592a8 Author: Weiqun Zhang Date: Tue Nov 22 11:11:03 2016 -0800 std::min -> std::min because Array::size() returns size_t now Src/C_BaseLib/VisMF.cpp commit 67752f677165e4a42060428fdf6ca9724a86436e Author: Weiqun Zhang Date: Thu Nov 17 10:45:54 2016 -0800 more helpful message Tools/C_mk/Make.rules commit 2b28b7be21cf35590d0bd9177a6fdf1ebe63d3bd Author: Weiqun Zhang Date: Tue Nov 15 17:01:10 2016 -0800 mpif90 --> Tools/C_mk/sites/Make.unknown commit 21fce1be4c8122fde085a096ffcbdb08bc41a501 Author: Weiqun Zhang Date: Tue Nov 15 16:14:53 2016 -0800 more intelligent way of adding link flags Tools/C_mk/sites/Make.unknown commit 17a22481484c83ea936ff2bbcfb93b70d0508bc1 Author: Weiqun Zhang Date: Sat Nov 12 12:47:43 2016 -0800 turn on C++11 in F_mk Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_cray.mak Tools/F_mk/comps/Linux_intel.mak Tools/F_mk/comps/Linux_pgi.mak Tools/F_mk/comps/gfortran.mak commit f59972f22b15b2d2d6e07d66e29f46e31def3e63 Author: Weiqun Zhang Date: Fri Nov 11 13:23:05 2016 -0800 rm Rose Tests/RoseTests/CPP/NullTransTest/GNUmakefile Tests/RoseTests/CPP/NullTransTest/PROB_3D.F Tests/RoseTests/CPP/NullTransTest/PROB_F.H Tests/RoseTests/CPP/NullTransTest/README Tests/RoseTests/CPP/NullTransTest/RoseNullTest.cpp Tests/RoseTests/F90/Readme Tests/RoseTests/F90/test1/GNUmakefile Tests/RoseTests/F90/test1/main.f90 Tests/RoseTests/F90/test2/GNUmakefile Tests/RoseTests/F90/test2/main.f90 Tests/RoseTests/F90/test3/GNUmakefile Tests/RoseTests/F90/test3/bc.f90 Tests/RoseTests/F90/test4/GNUmakefile Tests/RoseTests/F90/test4/main.f90 Tests/RoseTests/F90/test5/GNUmakefile Tests/RoseTests/F90/test5/main.f90 Tests/RoseTests/F90/test6/GNUmakefile Tests/RoseTests/F90/test6/main.f90 Tests/RoseTests/F90/test6/omp.f90 Tests/RoseTests/F90/test7/GNUmakefile Tests/RoseTests/F90/test7/main.f90 Tests/RoseTests/F90/test7/probin.f90 Tests/RoseTests/F90/test7/runtime.f90 Tests/RoseTests/F90/test8/GNUmakefile Tests/RoseTests/F90/test8/init_data.f90 Tests/RoseTests/F90/test8/main.f90 commit fc381bbca5cc26694d73c02e55781cdfd69cdef9 Author: Weiqun Zhang Date: Fri Nov 11 12:59:41 2016 -0800 rm C_TowerLib with Marc's permission Src/C_TowerLib/Layout.H Src/C_TowerLib/Layout.cpp Src/C_TowerLib/MFTower.H Src/C_TowerLib/MFTower.cpp Src/C_TowerLib/MFTower_2D.F Src/C_TowerLib/MFTower_3D.F Src/C_TowerLib/MFTower_F.H Src/C_TowerLib/Make.package Tutorials/AMR_PETSc_C/Exec/Make.PETSc Tutorials/AMR_PETSc_C/Exec/UniformVelocity/.gdbinit Tutorials/AMR_PETSc_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_PETSc_C/Exec/UniformVelocity/Make.package Tutorials/AMR_PETSc_C/Exec/UniformVelocity/Prob_2d.f90 Tutorials/AMR_PETSc_C/Exec/UniformVelocity/grid_file_2d_2lev.dat Tutorials/AMR_PETSc_C/Exec/UniformVelocity/grid_file_2d_3lev.dat Tutorials/AMR_PETSc_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_PETSc_C/Exec/UniformVelocity/petsc_options_file Tutorials/AMR_PETSc_C/Exec/UniformVelocity/probdata.f90 Tutorials/AMR_PETSc_C/Exec/UniformVelocity/probin.2d Tutorials/AMR_PETSc_C/README Tutorials/AMR_PETSc_C/Source/Darcy.H Tutorials/AMR_PETSc_C/Source/Darcy.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES.H Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES_2D.F Tutorials/AMR_PETSc_C/Source/DarcySNES_F.H Tutorials/AMR_PETSc_C/Source/Darcy_2D.f90 Tutorials/AMR_PETSc_C/Source/Darcy_F.H Tutorials/AMR_PETSc_C/Source/MLBoundary.H Tutorials/AMR_PETSc_C/Source/MLBoundary.cpp Tutorials/AMR_PETSc_C/Source/Make.package Tutorials/AMR_PETSc_C/Source/extern_probin.template Tutorials/AMR_PETSc_C/Source/interpolate.f90 Tutorials/AMR_PETSc_C/Source/main.cpp Tutorials/README_C commit b94c1654e8d24bf62d4092e29591d7d643bd80e4 Author: Weiqun Zhang Date: Fri Nov 11 12:34:56 2016 -0800 add a few functions for converting array of (unique) pointers to array of (const) pointers Src/C_BaseLib/Array.H commit 92ffa41ce280312df69f22c4e3d3af7f194beba7 Author: Weiqun Zhang Date: Fri Nov 11 12:29:20 2016 -0800 fix in make Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit b2ff35199f5726c47619d7103fe92c4ab6d5c816 Merge: a4f3ea913 3c55e33b7 Author: Weiqun Zhang Date: Tue Nov 22 10:48:07 2016 -0800 Merge branch 'before-parray' into dev-exp-make-array Conflicts: Src/C_BaseLib/CMakeLists.txt commit a4f3ea913289dec8fa61a0cbf4dc0e1a735982c5 Author: vince Date: Mon Nov 21 13:24:13 2016 -0800 fix for ieee_32 rd. Src/C_BaseLib/VisMF.cpp commit cd5d9ef48b08e1134487fe27edac67262d7187ae Author: vince Date: Fri Nov 18 14:54:22 2016 -0800 clean up debugging diagnostics. Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.cpp commit 611d5e3a5eaa3d618bdf297a293b2873daab50bb Merge: 799526165 19d60984b Author: vince Date: Fri Nov 18 13:00:50 2016 -0800 merge fix. commit 799526165e97d110d836d4be5a40e6ba1fe475f1 Author: vince Date: Fri Nov 18 12:57:26 2016 -0800 output cleanup. Src/C_BaseLib/VisMF.cpp commit 5a333bb429fae9b5c697b5f48f01ec99c45bd41f Author: vince Date: Fri Nov 18 12:56:33 2016 -0800 additions to i/o documentation. Docs/Notes.io_implementation Docs/Readme.io commit 29d9f74ea67557c99a3d458ebe6d65e47e4ace86 Merge: 87e0c4639 901757962 Author: vince 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 Date: Thu Nov 17 16:19:15 2016 -0800 combine nfiles dependent iterators. Src/C_BaseLib/BLProfiler.H Src/C_BaseLib/BLProfiler.cpp commit 613ea279457edcef505ff608439f2b66940dc448 Author: Weiqun Zhang Date: Thu Nov 17 10:45:54 2016 -0800 more helpful message Tools/C_mk/Make.rules commit 3f12bad9a62a7b9b6f9a48a681e699d3ebc06c9c Author: Weiqun Zhang Date: Thu Nov 17 10:34:00 2016 -0800 rm MLSDCAmr Src/C_AMRLib/MLSDCAmr.H Src/C_AMRLib/MLSDCAmr.cpp Src/C_AMRLib/MLSDCAmrEncap.cpp Src/C_AMRLib/Make.package commit 19d60984bdb3ca8413e39f285585ae61d260ccc8 Author: Weiqun Zhang Date: Wed Nov 16 16:56:53 2016 -0800 bl_avg_eg_to_cc for 2 and 1D Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_1d.f90 Src/C_BaseLib/MultiFabUtil_2d.f90 Src/C_BaseLib/MultiFabUtil_F.H commit 87e0c463923c71fe46275de803946937ab592ce6 Author: vince Date: Wed Nov 16 15:33:02 2016 -0800 fix comment. Src/C_BaseLib/NFiles.H commit 7c7850c798aed5c29a6070636ad0596c4713f77f Author: Marc Day Date: Wed Nov 16 15:16:56 2016 -0800 Fixup README to use the example-tests.py example file instead of one that no longer exists. Tools/RegressionTesting/README commit 1dd1af6e5d25e34f6ec2864a42593fc85abe2806 Merge: 63671d634 e5ac3aac3 Author: Michael Zingale Date: Wed Nov 16 16:16:52 2016 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 63671d634c2e150c7c4ac5b480c954321191c58d Author: Michael Zingale Date: Wed Nov 16 16:16:37 2016 -0500 add a heavily commented example inputs file Tools/RegressionTesting/example-tests.ini commit e5ac3aac39ceeeb7ce595c4546c4bbc6084be7e9 Merge: 80404fc3c 0b132625a Author: Weiqun Zhang Date: Wed Nov 16 09:18:11 2016 -0800 Merge branch 'fnodalfillpatch' into development commit 80404fc3c50deebcc9ff689ae89cbcbf4bfcb9b7 Author: Max Katz Date: Wed Nov 16 01:25:59 2016 -0500 Fix error message Src/C_AMRLib/Amr.cpp commit 624c49fd48653029553dd65fb1045b36ede25611 Author: Michael Zingale Date: Tue Nov 15 22:27:14 2016 -0500 fix the --no_update functionality to work when a repo is specified Tools/RegressionTesting/regtest.py commit d027dadba614dd486dd48c201d772b8810e9dc67 Author: Weiqun Zhang Date: Tue Nov 15 17:01:10 2016 -0800 mpif90 --> Tools/C_mk/sites/Make.unknown commit 84cb8f317d3d62324b62e108609aed85873e00e2 Author: Weiqun Zhang Date: Tue Nov 15 16:14:53 2016 -0800 more intelligent way of adding link flags Tools/C_mk/sites/Make.unknown commit 3a7213d120d12d52f73fc82db10b379370137fd9 Merge: 943f03036 6deb8e517 Author: Michael Zingale Date: Tue Nov 15 18:03:32 2016 -0500 Merge pull request #11 from jrood-nrel/development Adding exception handling to a particular shutil.rmtree(). commit 6deb8e5178a93f7a085b544a71012c9ce59b59e1 Author: Jon Rood Date: Tue Nov 15 15:59:44 2016 -0700 Reducing exception to only OSError. Tools/RegressionTesting/regtest.py commit 7c886bdab2a19617c87b8b6bd59486804e614d6b Author: Jon Rood Date: Tue Nov 15 15:12:43 2016 -0700 Adding exception handling to a particular shutil.rmtree(). Otherwise, this command can cause errors on certain filesystems and the test suite can completely fail before finishing. Tools/RegressionTesting/regtest.py commit b27820873f784c15e914703a1c4747f958023440 Author: Weiqun Zhang Date: Tue Nov 15 13:20:21 2016 -0800 fix more int and unsigned comparisons for OPAL because it uses -Werror=sign-compare. Src/C_ParticleLib/Particles.H commit 79af55aef7edeebc06c6d6568f607ce067c16b12 Author: Weiqun Zhang Date: Tue Nov 15 12:12:45 2016 -0800 typo Src/C_ParticleLib/Particles.H commit 010566fb1d18919736e9860c3cb12cef5861a782 Author: Weiqun Zhang Date: Tue Nov 15 12:12:01 2016 -0800 fix more int and unsigned comparisons for OPAL because it uses -Werror=sign-compare. Src/C_ParticleLib/Particles.H commit bb51bff19ca1fc46c1542e420e9a3c90c2ceeff8 Author: Weiqun Zhang Date: Tue Nov 15 10:33:05 2016 -0800 fix more int and unsigned comparisons for OPAL because it uses -Werror=sign-compare. Src/C_ParticleLib/Particles.H commit fe3e4cb77e93ff481525e3801c04cdd1c9b7f5cc Author: Weiqun Zhang Date: Tue Nov 15 09:07:48 2016 -0800 fix a number of typos; fix a number of int and unsigned comparison for OPAL Src/C_AMRLib/SlabStat.cpp Src/C_AMRLib/StationData.H Src/C_AMRLib/StationData.cpp Src/C_BaseLib/FabArray.H Src/C_ParticleLib/Particles.H Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H commit 9b916e36d34ab8d32379a2ade362f2d538b9e127 Author: vince Date: Mon Nov 14 16:17:43 2016 -0800 more code for nfiles and blprof. Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit f1bcf8faaee96e99628205382fc43aa9cecf8641 Author: Weiqun Zhang Date: Sun Nov 13 17:29:57 2016 -0800 fix signature of function average_down_faces Src/C_BaseLib/MultiFabUtil.cpp commit 70f881126e7d31e8927e8abee11b5fdfff321a25 Author: Weiqun Zhang Date: Sun Nov 13 10:17:31 2016 -0800 fix new bug in last commit Src/C_BaseLib/Array.H commit 01b008d43ea0ab2ca13fd436358960aab60091c5 Author: Weiqun Zhang Date: Sun Nov 13 08:27:18 2016 -0800 more consistent style Src/C_BaseLib/Array.H Src/C_ParticleLib/Particles.H Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.H Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp Tutorials/MultiColor_C/main.cpp Tutorials/MultiGrid_C/main.cpp Tutorials/PIC_C/Make.package Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/solve_with_hpgmg.cpp Tutorials/PIC_C/two_level.cpp Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp commit 1a37a90fc15bd218877f5154df986c20fbde65da Author: Weiqun Zhang Date: Sat Nov 12 12:47:43 2016 -0800 turn on C++11 in F_mk Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_cray.mak Tools/F_mk/comps/Linux_intel.mak Tools/F_mk/comps/Linux_pgi.mak Tools/F_mk/comps/gfortran.mak commit 6c605dced8af61e821e14f8194f917ab0ac37439 Author: Weiqun Zhang Date: Sat Nov 12 12:28:49 2016 -0800 fix tutorials Tutorials/GettingStarted_C/GNUmakefile Tutorials/GettingStarted_C/main.cpp Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/MultiColor_C/main.cpp Tutorials/MultiFabTests_C/GridMoveTest.cpp Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp Tutorials/MultiGrid_C/main.cpp Tutorials/PGAS_HEAT/main.cpp Tutorials/PIC_C/solve_with_hpgmg.cpp Tutorials/README_C Tutorials/Tiling_Heat_C/main.cpp Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp commit 94edfe3d6faad2bc9c8422a084d849b207341a3b Author: vince Date: Fri Nov 11 17:17:14 2016 -0800 use NFilesIter for profiling output. Src/C_BaseLib/BLProfiler.H Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/NFiles.H commit adb48ce1180e77f436abb4e4a1cd8b757ca0fe36 Author: Weiqun Zhang Date: Fri Nov 11 15:14:19 2016 -0800 fix compilation of a number of tests Tests/C_BaseLib/GNUmakefile Tests/FillBoundaryComparison/main.cpp Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.H Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp commit c62adc90568bdd6d6a72eebb605f3560063ab219 Author: vince Date: Fri Nov 11 14:46:04 2016 -0800 add support for appending nfiles set. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit 850a637780eb440405018a20b5c6406f2690dd00 Author: Weiqun Zhang Date: Fri Nov 11 14:30:00 2016 -0800 add const Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 7f1c62a40fcf933bd7c544a417a047afa8668f45 Author: vince 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 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 a0f9950d78ed06098e8e6786963e01fe80e54dd9 Author: Weiqun Zhang Date: Fri Nov 11 13:23:05 2016 -0800 rm Rose Tests/RoseTests/CPP/NullTransTest/GNUmakefile Tests/RoseTests/CPP/NullTransTest/PROB_3D.F Tests/RoseTests/CPP/NullTransTest/PROB_F.H Tests/RoseTests/CPP/NullTransTest/README Tests/RoseTests/CPP/NullTransTest/RoseNullTest.cpp Tests/RoseTests/F90/Readme Tests/RoseTests/F90/test1/GNUmakefile Tests/RoseTests/F90/test1/main.f90 Tests/RoseTests/F90/test2/GNUmakefile Tests/RoseTests/F90/test2/main.f90 Tests/RoseTests/F90/test3/GNUmakefile Tests/RoseTests/F90/test3/bc.f90 Tests/RoseTests/F90/test4/GNUmakefile Tests/RoseTests/F90/test4/main.f90 Tests/RoseTests/F90/test5/GNUmakefile Tests/RoseTests/F90/test5/main.f90 Tests/RoseTests/F90/test6/GNUmakefile Tests/RoseTests/F90/test6/main.f90 Tests/RoseTests/F90/test6/omp.f90 Tests/RoseTests/F90/test7/GNUmakefile Tests/RoseTests/F90/test7/main.f90 Tests/RoseTests/F90/test7/probin.f90 Tests/RoseTests/F90/test7/runtime.f90 Tests/RoseTests/F90/test8/GNUmakefile Tests/RoseTests/F90/test8/init_data.f90 Tests/RoseTests/F90/test8/main.f90 commit a39467e45951282be87c3f255db6c2b31df2856c Author: Weiqun Zhang Date: Fri Nov 11 12:59:41 2016 -0800 rm C_TowerLib with Marc's permission Src/C_TowerLib/Layout.H Src/C_TowerLib/Layout.cpp Src/C_TowerLib/MFTower.H Src/C_TowerLib/MFTower.cpp Src/C_TowerLib/MFTower_2D.F Src/C_TowerLib/MFTower_3D.F Src/C_TowerLib/MFTower_F.H Src/C_TowerLib/Make.package Tutorials/AMR_PETSc_C/Exec/Make.PETSc Tutorials/AMR_PETSc_C/Exec/UniformVelocity/.gdbinit Tutorials/AMR_PETSc_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_PETSc_C/Exec/UniformVelocity/Make.package Tutorials/AMR_PETSc_C/Exec/UniformVelocity/Prob_2d.f90 Tutorials/AMR_PETSc_C/Exec/UniformVelocity/grid_file_2d_2lev.dat Tutorials/AMR_PETSc_C/Exec/UniformVelocity/grid_file_2d_3lev.dat Tutorials/AMR_PETSc_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_PETSc_C/Exec/UniformVelocity/petsc_options_file Tutorials/AMR_PETSc_C/Exec/UniformVelocity/probdata.f90 Tutorials/AMR_PETSc_C/Exec/UniformVelocity/probin.2d Tutorials/AMR_PETSc_C/README Tutorials/AMR_PETSc_C/Source/Darcy.H Tutorials/AMR_PETSc_C/Source/Darcy.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES.H Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES_2D.F Tutorials/AMR_PETSc_C/Source/DarcySNES_F.H Tutorials/AMR_PETSc_C/Source/Darcy_2D.f90 Tutorials/AMR_PETSc_C/Source/Darcy_F.H Tutorials/AMR_PETSc_C/Source/MLBoundary.H Tutorials/AMR_PETSc_C/Source/MLBoundary.cpp Tutorials/AMR_PETSc_C/Source/Make.package Tutorials/AMR_PETSc_C/Source/extern_probin.template Tutorials/AMR_PETSc_C/Source/interpolate.f90 Tutorials/AMR_PETSc_C/Source/main.cpp Tutorials/README_C commit 65ea5fb4b545bcff2207443d9d833367a63b41a1 Author: Weiqun Zhang Date: Fri Nov 11 12:55:04 2016 -0800 add const to MultiFabUtil functions Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_F.H Tutorials/PIC_C/solve_for_accel.cpp commit f3a0ad47b90972e95e9c5ffef2cf5b56dd6b6e90 Author: Weiqun Zhang Date: Fri Nov 11 12:34:56 2016 -0800 add a few functions for converting array of (unique) pointers to array of (const) pointers Src/C_BaseLib/Array.H commit c81a9def247b51213c3308340c77f0d7eee81bdc Author: vince Date: Fri Nov 11 12:45:40 2016 -0800 change function name. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit eccd73c4001e765436d784d70f55762c0b653bee Author: Weiqun Zhang Date: Fri Nov 11 12:29:20 2016 -0800 fix in make Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit e257ed7d85a03105a5e16a1f2ca19cce976c9f39 Author: Weiqun Zhang Date: Fri Nov 11 11:33:41 2016 -0800 rm PArray from ParticleLib and LinearSolver Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp Src/C_ParticleLib/Particles.H Src/C_ParticleLib/TracerParticles.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG4/ABec2.cpp Src/LinearSolvers/C_CellMG4/ABec4.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Tutorials/MultiGrid_C/main.cpp Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/two_level.cpp commit 7ed5b2efb021786df49ba59a3e65d36f5f862cee Author: Weiqun Zhang Date: Thu Nov 10 13:46:02 2016 -0800 remove PArray Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/SlabStat.H Src/C_AMRLib/SlabStat.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp Src/C_AMRLib/StationData.H Src/C_AMRLib/StationData.cpp Src/C_AmrCoreLib/AmrCore.cpp Src/C_AmrCoreLib/ErrorList.H Src/C_AmrCoreLib/ErrorList.cpp Src/C_AmrCoreLib/FillPatchUtil.H Src/C_AmrCoreLib/FillPatchUtil.cpp Src/C_AmrCoreLib/TagBox.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/C_BaseLib/MemPool.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_F.H Src/C_BaseLib/PArray.H Src/C_BaseLib/iMultiFab.cpp Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/InterpBndryData.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp commit 943f030366fbf85556f9c59765c632ee7ccabbc9 Author: Michael Zingale Date: Wed Nov 9 19:54:49 2016 -0500 report for each variable in a plotfile if there is a NaN Tools/Postprocessing/F_Src/fnan.f90 commit 5288c043fecd3f9af838b68425b44cd7f10e3997 Merge: 903392928 5ec341bc4 Author: Michael Zingale Date: Wed Nov 9 19:37:30 2016 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 903392928617c740619e8d1d563e1c2d72c1b29e Author: Michael Zingale Date: Wed Nov 9 19:37:13 2016 -0500 add a simple tool to dump data to the screen Tools/Postprocessing/F_Src/fdump.f90 commit 3c55e33b7ea46c7818e535b4960917735e56b1a8 Merge: 855d3ab8e 5ec341bc4 Author: Weiqun Zhang Date: Wed Nov 9 10:27:46 2016 -0800 Merge branch 'development' into experimental commit 5ec341bc4945c8a5eb3dccb3bf6e27c8dad1cf4c Author: Weiqun Zhang Date: Wed Nov 9 10:27:16 2016 -0800 use size_t instead of int as loop index in a few places so that OPAL can compile Src/C_ParticleLib/Particles.H commit 855d3ab8e7442e2d4e08d695051e4ee904c59d5b Author: Weiqun Zhang Date: Wed Nov 9 09:37:30 2016 -0800 use Array instead of vector for consistence and bound checking Src/C_BaseLib/PlotFileUtil.H Src/C_BaseLib/PlotFileUtil.cpp commit a0fdcb1e4e5a71358d1e0ba13e4a3a53c7fcdc27 Author: Weiqun Zhang Date: Tue Nov 8 14:43:06 2016 -0800 rework on the Array class Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Array.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/FabConv.cpp Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp Tools/C_mk/Make.defs commit 116a3c82f2a5cbd7518b0317d05a617eb010f950 Author: Weiqun Zhang Date: Tue Nov 8 14:41:21 2016 -0800 rm BL_CXX11.H because C++11 is now require; replace BL_OVERRIDE with override MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp Src/C_AMRLib/Amr.H Src/C_AMRLib/MLSDCAmr.H Src/C_AMRLib/StateDescriptor.H Src/C_AmrCoreLib/Interpolater.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BLPgas.cpp Src/C_BaseLib/BL_CXX11.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/CArena.H Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/MemPool.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/PhysBCFunct.H Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/MacBndry.H Src/C_ParticleLib/Particles.H Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_TensorMG/DivVis.H Tests/C_BaseLib/BcastClasses/GNUmakefile Tests/C_BaseLib/GNUmakefile Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/AdvBld.cpp Tutorials/AMR_Adv_C_v2/Exec/Make.Adv Tutorials/MultiFabTests_C/GNUmakefile commit 91139e84109bbdece29329815c9d52e865b7f639 Author: vince Date: Tue Nov 8 14:38:23 2016 -0800 change Array to vector to run with the intel compiler. Src/C_BaseLib/VisMF.cpp commit 763d40de7089057e0c4e9efb5b23f10a0ca90b51 Author: Weiqun Zhang Date: Tue Nov 8 14:21:30 2016 -0800 no longer need to specify FCOMP Tutorials/AMR_Adv_C/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/GNUmakefile Tutorials/AMR_PETSc_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Trilinos_C/GNUmakefile Tutorials/HeatEquation_EX1_C/GNUmakefile Tutorials/HeatEquation_EX2_C/GNUmakefile Tutorials/HelloWorld_C/GNUmakefile Tutorials/MultiColor_C/GNUmakefile Tutorials/MultiFabTests_C/GNUmakefile Tutorials/MultiGrid_C/GNUmakefile Tutorials/PGAS_HEAT/GNUmakefile Tutorials/PIC_C/GNUmakefile Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Tiling_C/GNUmakefile Tutorials/Tiling_Heat_C/GNUmakefile Tutorials/TwoGrid_PIC_C/GNUmakefile commit 6db7238fcbbc09649b178ea5864671d839c843c5 Author: Weiqun Zhang Date: Tue Nov 8 14:12:28 2016 -0800 Src/C_AMRLib/Make.package doe not include C_AmrCoreLib anymore MiniApps/FillBoundary/GNUmakefile MiniApps/MultiGrid_C/GNUmakefile Src/C_AMRLib/Make.package Tests/C_BaseLib/BcastClasses/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/MacOpMacDrivers.H Tests/LinearSolvers/C_CellMG/MacOperator.H Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/ComparisonTest/GNUmakefile Tests/MKDir/GNUmakefile Tutorials/AMR_Adv_C/Exec/Make.Adv Tutorials/AMR_PETSc_C/Exec/Make.PETSc Tutorials/Tiling_Heat_C/GNUmakefile Tutorials/WaveEquation_C/GNUmakefile commit 0a4289e158faa52745188736907920f36fa457b7 Author: Weiqun Zhang Date: Tue Nov 8 13:34:44 2016 -0800 need to pass fincludes into MODDEP Tools/C_mk/Make.rules commit f9fdf39b0b7007925e10fef36d68b7d38845c29d Merge: a94a542be 870356bbb Author: Weiqun Zhang Date: Tue Nov 8 12:24:12 2016 -0800 Merge branch 'development' into experimental Ray will have to add his make setup back to maybe Tools/C_mk/sites/Make.nrel. Conflicts: Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit a94a542bec013763ef53429fd814d8e0a411a19b Author: Weiqun Zhang Date: Mon Nov 7 17:06:03 2016 -0800 try to detect mpich or openmpi Tools/C_mk/sites/Make.unknown commit 8601f2e6f1dc7159344b50562a1a003425c40739 Author: Weiqun Zhang Date: Mon Nov 7 16:37:48 2016 -0800 more on README.md Tools/C_mk/README.md commit 4a9abfd9ecd2fba6b03df9746d5fe7ed9d7c1678 Author: Weiqun Zhang Date: Mon Nov 7 16:25:45 2016 -0800 minor Tools/C_mk/README.md commit 2a953fdca757e1a423f9c9db2785cebd6cfe9d0d Author: Weiqun Zhang Date: Mon Nov 7 16:22:08 2016 -0800 fix format Tools/C_mk/README.md commit cba55c7d8626206345f157265299c36c9dca34da Author: Weiqun Zhang Date: Mon Nov 7 16:17:57 2016 -0800 more on README.md for make Tools/C_mk/Make.defs Tools/C_mk/README.md commit 870356bbba96593354337350bd8017ae4ce604dd Author: Brian Friesen Date: Sun Nov 6 18:45:02 2016 -0800 C_mk: add workaround for compiling C++11 features using Intel compilers at NERSC This is a known but unfixed Cray bug. The workaround is to force Intel compilers to use compatible header files from GCC, specifically from GCC 4.9.3. The user can do this by loading the 'gcc/4.9.3' module. Tools/C_mk/Make.defs commit 618b12bc587ef1435d3c0493cc616e31edce1504 Author: Brian Friesen Date: Mon Nov 7 08:16:54 2016 -0800 C_mk, F_mk: remove Babbage compiler hooks (it has been retired) Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 5110c59f062ca157a301a808fbcc21a7974bd923 Author: Weiqun Zhang Date: Mon Nov 7 09:14:31 2016 -0800 MLSDCAmr: restrict --> Restrict to avoid name conflict. Although restrict is not a C++ keyword and it was used as a member function of class MLSDCAmrLevel, cray compiler is unhappy about it being used because it is a C keyword. Src/C_AMRLib/MLSDCAmr.H Src/C_AMRLib/MLSDCAmr.cpp commit 22c03f20e3e5ea488e17145bf22d802fc88938e3 Author: Weiqun Zhang Date: Sun Nov 6 12:08:51 2016 -0800 add python to build requirement Tools/C_mk/README.md commit 6b1063aa7ba23bcd0e54c3038aff93e38674995d Merge: 4ebc314cc 0d1366e05 Author: Michael Zingale Date: Sat Nov 5 21:40:01 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 4ebc314cc8d077b664092ff15534c8fc0eed0d3c Author: Michael Zingale Date: Sat Nov 5 21:39:38 2016 -0400 need to actually pass FPP_DEFINES to the dependency script Tools/F_mk/GMakerules.mak commit 728bf0607159971efe38f2ae0886f24630a0f12d Author: Weiqun Zhang Date: Fri Nov 4 20:12:54 2016 -0400 do not exit due to compiler mismatch for goals like clean, realclean, etc. Tools/C_mk/Make.rules Tools/C_mk/sites/Make.nersc Tools/C_mk/sites/Make.olcf commit 960544637190137e7c7c63e68336a26c604abf0d Author: Weiqun Zhang Date: Fri Nov 4 16:39:21 2016 -0700 removed -fimplicit-none flag because we have some really old Fortran code Tools/C_mk/comps/gnu.mak commit 2ffa34a88f41baccc13e9238e13ac71f0aba57b8 Author: Weiqun Zhang Date: Fri Nov 4 14:45:25 2016 -0700 Make.nersc: add -lmpichf90 Tools/C_mk/sites/Make.nersc Tools/C_mk/sites/Make.olcf commit a8526ded7b7187367808b7042506bd3936f20d4c Author: Weiqun Zhang Date: Fri Nov 4 12:58:20 2016 -0700 add intel.mak and Make.vtune Tools/C_mk/Make.defs Tools/C_mk/comps/cray.mak Tools/C_mk/comps/gnu.mak Tools/C_mk/comps/intel.mak Tools/C_mk/comps/pgi.mak Tools/C_mk/tools/Make.vtune commit 17a83d162275f8bc58830c873b4d0c8724a2747e Author: Weiqun Zhang Date: Fri Nov 4 11:21:58 2016 -0700 add Make.nersc and cray.mak Tools/C_mk/comps/cray.mak Tools/C_mk/comps/pgi.mak Tools/C_mk/sites/Make.nersc commit f37391551d24bf6f3d42fc7704568ee6b364cc53 Author: Weiqun Zhang 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 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 Date: Fri Nov 4 13:11:30 2016 -0400 rename gcc.mak to gnu.mak to match Cray's convention for naming PrgEnv; add sites/Make.olcf Tools/C_mk/Make.defs Tools/C_mk/Make.local.template Tools/C_mk/comps/gnu.mak Tools/C_mk/sites/Make.olcf Tools/C_mk/sites/Make.unknown commit ef3c38233f8e604ae5162fda05015c8acbe51a3c Author: Weiqun Zhang Date: Thu Nov 3 19:19:27 2016 -0400 add an example of filter-out in Make.local.template Tools/C_mk/Make.local.template commit 51bfe1b1be1f3d46f469c4c4c9a51820cc3728d6 Author: Weiqun Zhang Date: Thu Nov 3 18:33:50 2016 -0400 In C++11, isnan and isinf are in std namespace Src/C_BaseLib/FArrayBox.cpp commit 3f6775fafe199b1ecc66e03d989b9637ef15b29a Author: Weiqun Zhang Date: Thu Nov 3 18:33:22 2016 -0400 add pgi.mak Tools/C_mk/Make.defs Tools/C_mk/comps/gcc.mak Tools/C_mk/comps/pgi.mak commit f8e624553b6c81d64b709f3c09e8ab2ab0151965 Author: Weiqun Zhang Date: Thu Nov 3 17:21:47 2016 -0400 add Make.unknown Tools/C_mk/Make.defs Tools/C_mk/Make.local.template Tools/C_mk/sites/Make.ccse Tools/C_mk/sites/Make.unknown commit c33e6005f6d93039041f08c5c006f17942ad1849 Author: Weiqun Zhang Date: Thu Nov 3 13:37:30 2016 -0700 another typo in README Tools/C_mk/README.md commit 315c35f12aee4ea2af48be37a2b232b3265d1c44 Author: Weiqun Zhang Date: Thu Nov 3 13:34:43 2016 -0700 typo in README Tools/C_mk/README.md commit 6e81196ef418b06a7662643e1df4f00e422d482a Author: Weiqun Zhang Date: Thu Nov 3 13:27:43 2016 -0700 new Make system work in progress: gcc and CCSE are done Tools/C_mk/Make.AIX Tools/C_mk/Make.CYGWIN_NT Tools/C_mk/Make.Darwin Tools/C_mk/Make.FreeBSD Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.local.template Tools/C_mk/Make.machines Tools/C_mk/Make.mpi Tools/C_mk/Make.rules Tools/C_mk/Make.upcxx Tools/C_mk/README.md Tools/C_mk/comps/gcc.mak Tools/C_mk/packages/Make.hpgmg Tools/C_mk/sites/Make.ccse commit 0d1366e054df9e2bdef2031b6249cdddc2dbe484 Author: Grout Date: Thu Nov 3 09:22:38 2016 -0600 Revised Peregrine (NREL) configuration to use intel or gcc toolchains Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 5ae09d854e18984117afeef427b873df667c2c9d Author: vince Date: Wed Nov 2 15:34:12 2016 -0700 set default header formats. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/VisMF.cpp commit 960953503702f956e35557a8e47830d08aacf4a6 Merge: b0f22fc18 a5f35cd25 Author: vince Date: Wed Nov 2 13:36:45 2016 -0700 fix merge conflicts. commit 46e8ce25b57a8d2aa08ee08dea0095ab0dd47426 Author: Grout Date: Wed Nov 2 13:11:20 2016 -0600 Add makefile defs for Peregrine (NREL cluster) Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit b0f22fc1806df57fc89326b1338996a39943e137 Author: vince 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 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 Date: Tue Nov 1 16:37:18 2016 -0700 simplify file order reads. Src/C_BaseLib/VisMF.cpp commit a1c492a30c8d6529e655fe2a664a03a8c242b38e Author: vince Date: Tue Nov 1 16:35:41 2016 -0700 function for items per bin. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 3929b37f98c3c0aedf5eaa93ab972a76ccdc06c1 Merge: 2fa75f1ac ee93a0dce Author: Michael Zingale Date: Tue Nov 1 12:31:57 2016 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 2fa75f1acd09a9979d8ab044a7e0878c235be2f3 Author: Michael Zingale Date: Tue Nov 1 12:28:26 2016 -0700 Intel doesn't seem to define __STDC__ for its Fortran preprocessor, so force it to take a particular branch for macro expansion Src/C_BaseLib/ArrayLim.H commit ee93a0dce616a01658e642a891c8777e142e59eb Merge: a86a9544e 7f461b4cc Author: Weiqun Zhang Date: Tue Nov 1 09:17:51 2016 -0700 Merge branch 'development' commit a86a9544ebd0c8454935818037088372ba9218b3 Author: Weiqun Zhang Date: Tue Nov 1 09:17:28 2016 -0700 Release Notes 16.11 ReleaseNotes/release-notes-16.11 commit 7f461b4cc2cba860a1bff90ee1561c653e61b0a9 Merge: e0abafc57 7ae9f9e85 Author: Weiqun Zhang Date: Tue Nov 1 09:16:50 2016 -0700 Merge branch 'master' into development commit 0b132625a9c94f3c9882b8cfcb1a9c8edd647429 Author: Weiqun Zhang Date: Mon Oct 31 20:46:15 2016 -0700 fix a new bug in Fortran fillpatch for face data Src/F_BaseLib/fillpatch.f90 commit e0abafc574b98a2f1abdd0b6fbeb4620ede988c0 Author: Michael Zingale Date: Mon Oct 31 13:59:36 2016 -0400 don't require probin -- this will be on the user to ensure it exists Tools/RegressionTesting/params.py Tools/RegressionTesting/regtest.py Tools/RegressionTesting/test_report.py commit 3daa965c6f0b777d5306a4f2aee8c4ba43a0afa4 Author: Weiqun Zhang Date: Mon Oct 31 09:11:34 2016 -0700 fix some new bugs in Fortran fillpatch for face data Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/interp.f90 commit 9ea233a077380fe7a9608805b121accd19030dda Author: Weiqun Zhang Date: Fri Oct 28 14:56:59 2016 -0700 minor Src/C_BaseLib/Box.cpp commit 986c5ef7cf561922f090e061adbefc053f402707 Author: vince Date: Fri Oct 28 14:48:44 2016 -0700 optimize sync reads. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit af5db3ea9fdcd93a60d14998a0113738e98573e7 Author: Weiqun Zhang Date: Fri Oct 28 10:37:02 2016 -0700 fillpatch for face data Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/interp.f90 commit c8f268411d9cc96d5e321f3cccb70794ae535ddf Author: Weiqun Zhang Date: Fri Oct 28 10:35:35 2016 -0700 add some functions for nodal box coarsening Src/F_BaseLib/box_f.f90 Src/F_BaseLib/boxarray_f.f90 commit 79bb66193ecfa5ef2e32e4e76b36621755b9a0b7 Author: Ann Almgren Date: Thu Oct 27 16:21:43 2016 -0700 Last one ... Tools/RegressionTesting/IAMR-tests.ini commit 04554663f918deb8bf80e8e2ceacfdc6ac8db82d Author: Ann Almgren Date: Thu Oct 27 15:58:22 2016 -0700 Remove more app specific regression test files. Tools/RegressionTesting/LMC-tests.ini Tools/RegressionTesting/RNS-tests.ini Tools/RegressionTesting/SMC-tests.ini commit d0bf9427540600afc1059698a8004c34d880ac4c Author: vince Date: Thu Oct 27 15:43:39 2016 -0700 support for non-native format conversions. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 2b3c39a2a32834443ced697e8951d911b933d05a Author: vince 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 Date: Thu Oct 27 15:38:54 2016 -0700 correct comments. Src/C_BaseLib/FArrayBox.H commit 4e137b69ee4dd84e083d2720ea329c9aaccd3935 Author: Michael Zingale Date: Thu Oct 27 18:37:48 2016 -0400 move these to the application codes Tools/RegressionTesting/Castro-SBU-tests.ini Tools/RegressionTesting/Maestro-tests.ini Tools/RegressionTesting/Microphysics-tests-pgi.ini Tools/RegressionTesting/Microphysics-tests.ini commit f0a23f738403bafe6022b117a66016ae68c1dfc4 Author: Ann Almgren Date: Thu Oct 27 15:26:05 2016 -0700 Removed Nyx-tests.ini from the regression testing directory. Tools/RegressionTesting/Nyx-tests.ini commit 44a3642d2b90b202459fc466488826eb3c5a56ef Author: vince Date: Wed Oct 26 12:26:21 2016 -0700 change to a more searchable name. Src/C_BaseLib/FArrayBox.cpp commit 8ff36f474ccc768e0a700060e4a902becf1c1bf0 Author: Grout 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 Date: Mon Oct 24 15:33:45 2016 -0700 make sure grid id is valid Src/C_ParticleLib/Particles.cpp commit df65a1e9b7600e49c9628f7bc16539ec72242f26 Merge: f187776d0 a5f4e52bd Author: vince 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 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 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 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 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 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 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 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 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: 339ebc947 50fd0c773 Author: Weiqun Zhang Date: Thu Oct 20 16:43:52 2016 -0700 Merge branch 'development' into amrcore commit 339ebc94761ea312dd484da8c474c1cac04ee036 Author: Weiqun Zhang Date: Thu Oct 20 16:43:45 2016 -0700 minor Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp commit 7ae9f9e85ae7a6c09296fbac413aff8849b6131b Author: Weiqun Zhang Date: Thu Oct 20 16:07:36 2016 -0700 add missing template parameter Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/MultiFab.cpp commit 50fd0c77302e9dddf82768a35a92c3a5eff57e7c Author: Weiqun Zhang Date: Thu Oct 20 16:07:36 2016 -0700 add missing template parameter Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/MultiFab.cpp commit 5859154ed48c7d46750a798de6a2235836546bcf Merge: ae0e39483 6dd04a593 Author: Weiqun Zhang 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 Date: Thu Oct 20 15:06:59 2016 -0700 Getting the cmake stuff to work ... Src/CMakeLists.txt commit 4bd890b701a8eaec1cca4e168073a2543a809937 Author: Ann Almgren Date: Thu Oct 20 15:05:50 2016 -0700 Rename box_camr --> box_camrcore for C_AmrCoreLib. Src/C_AmrCoreLib/CMakeLists.txt commit 6f07d1dc6ab4d331e28250df20f716bdc54247b2 Author: Ann Almgren Date: Thu Oct 20 15:00:46 2016 -0700 We want AmrParticles to depend on AmrCore not Amr Src/C_AmrCoreLib/AmrParticles.H commit 88b3a24fbf41dbc457cf384d5a9df23ea1e8ca7c Author: Ann Almgren Date: Thu Oct 20 14:58:30 2016 -0700 Add new CMakeLists.txt for C_AmrCoreLIb and modify the ones in C_AMRLib and Source. Src/CMakeLists.txt Src/C_AMRLib/CMakeLists.txt Src/C_AmrCoreLib/CMakeLists.txt commit ae0e39483fde5cf3d49430f9f36287110783915a Author: Weiqun Zhang Date: Wed Oct 19 20:48:33 2016 -0700 minor Src/C_BaseLib/PlotFileUtil.cpp commit 7b81d83a97977208142114e242e4d6cc3639662b Author: Weiqun Zhang Date: Wed Oct 19 16:58:10 2016 -0700 AmrAdv/AmrCore tutorial: write the last plotfile Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp commit e42d4f6aac796560a1d09c53475ac99c882c85fe Author: Weiqun Zhang Date: Wed Oct 19 16:43:13 2016 -0700 pass explicit distributionmap Src/C_AMRLib/FillPatchUtil.cpp commit 1ff582f2f16834f0c66e50e1a96e359c685cbc55 Author: Weiqun Zhang Date: Wed Oct 19 16:41:46 2016 -0700 minor Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp commit 2e7a8785fb459a82bd82a9135e147b2ad710c5a1 Author: Weiqun Zhang Date: Wed Oct 19 16:34:50 2016 -0700 AmrAdv/AmrCore tutorial: flush distributionmap cache Src/C_AmrCoreLib/FillPatchUtil.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp commit 13284b2ff42dc4ecb3ce68d40d4cc17daee8ea15 Author: Weiqun Zhang Date: Wed Oct 19 16:15:46 2016 -0700 AmrAdv/AmrCore tutorial: add regrid Src/C_AmrCoreLib/AmrCore.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp commit 71e1618772de65d9cc75ec7f1e11f4d52d07e6b5 Merge: a2b39dcfd 36ba7c1e9 Author: Michael Zingale Date: Wed Oct 19 17:16:29 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit a2b39dcfd29190de72e8f218f1929962e2891618 Author: Michael Zingale Date: Wed Oct 19 17:15:47 2016 -0400 since there can be many more system-provided modules, don't abort if a module is not found, but instead print a warning to STDERR Tools/F_scripts/dep.py commit 36ba7c1e93f824e715a7d2d88bb6e28a921a897b Author: Weiqun Zhang Date: Wed Oct 19 10:28:55 2016 -0700 fix a typo Tools/Release/ppCleanup.py commit cb7e2b4ce415f7416b5de560059c00675d378510 Author: Weiqun Zhang Date: Wed Oct 19 10:28:06 2016 -0700 wip Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp commit d57496744b12ba7cca056dbbf0d9e2fa4d84ab44 Author: Weiqun Zhang Date: Wed Oct 19 09:47:18 2016 -0700 AmrAdv/AmrCore tutorial: add reflux Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/inputs Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp commit 82dca060736d9d15494a2a45effb57c63cd7d22a Author: Weiqun Zhang Date: Wed Oct 19 09:01:16 2016 -0700 AmrAdv/AmrCore tutorial: average down in post timestep Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvError.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp commit 450c8c2ce46c559361cc50b9741d2a511d5635ad Author: Weiqun Zhang Date: Wed Oct 19 11:37:45 2016 -0400 fix isinf and isnan for PGI; it looks like PGI pretends to be __GNUC__ Src/C_BaseLib/FArrayBox.cpp commit 1de7f66285b0970fbb9911daad6d244b8620b62f Author: Weiqun Zhang Date: Tue Oct 18 17:06:10 2016 -0700 AmrAdv/AmrCore tutorial: write plotfiles Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp commit 2d1f11ea1a0a58106b87bfa17b6690011a5fa1ba Author: Weiqun Zhang Date: Tue Oct 18 16:50:39 2016 -0700 AmrAdv/AmrCore tutorial: add advect Fortran routines Tutorials/AMR_Adv_C_v2/Exec/Make.Adv Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H Tutorials/AMR_Adv_C_v2/Source/Src_2d/Adv_2d.f90 Tutorials/AMR_Adv_C_v2/Source/Src_2d/Make.package Tutorials/AMR_Adv_C_v2/Source/Src_2d/compute_flux_2d.f90 Tutorials/AMR_Adv_C_v2/Source/Src_2d/slope_2d.f90 Tutorials/AMR_Adv_C_v2/Source/Src_3d/Adv_3d.f90 Tutorials/AMR_Adv_C_v2/Source/Src_3d/Make.package Tutorials/AMR_Adv_C_v2/Source/Src_3d/compute_flux_3d.f90 Tutorials/AMR_Adv_C_v2/Source/Src_3d/slope_3d.f90 commit e1f2f80607ba3eee58711d88ec9f84d985170575 Author: Weiqun Zhang Date: Tue Oct 18 16:12:55 2016 -0700 AmrAdv/AmrCore tutorial: FillPatch Src/C_BaseLib/PhysBCFunct.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvBC.H Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp Tutorials/AMR_Adv_C_v2/Source/Make.package commit e990765c5c27ff8dbc193576103ee5d93d8e1884 Author: Weiqun Zhang Date: Tue Oct 18 16:12:32 2016 -0700 new BaseFab::make_alias function Src/C_BaseLib/BaseFab.H commit 7f962893dfdba8ce2272cbfd5cd9983089dd4616 Author: Weiqun Zhang Date: Tue Oct 18 16:12:32 2016 -0700 new BaseFab::make_alias function Src/C_BaseLib/BaseFab.H commit 8b7606532a7c0f4db1b4b336d72b46e6db91dce9 Author: Weiqun Zhang Date: Tue Oct 18 13:29:34 2016 -0700 AmrAdv/AmrCore tutorial: compute dt; set up time stepping Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/inputs Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp Tutorials/AMR_Adv_C_v2/Source/main.cpp commit 5fe3a97d2b21f0bb464bac48b28f4e05748eee15 Author: Weiqun Zhang Date: Tue Oct 18 10:46:43 2016 -0700 AmrAdv/AmrCore tutorial: put tagging parameters in inputs Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/inputs Tutorials/AMR_Adv_C_v2/Source/AmrAdvError.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H Tutorials/AMR_Adv_C_v2/Source/Src_nd/Make.package Tutorials/AMR_Adv_C_v2/Source/Src_nd/Tagging_nd.f90 Tutorials/AMR_Adv_C_v2/Source/Src_nd/tagging_params.f90 commit 9050383ea90f974da451516db70bcff8db9bae05 Author: Weiqun Zhang Date: Tue Oct 18 10:29:12 2016 -0700 AmrAdv/AmrCore tutorial: write plotfile Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp commit 59e2c1b4472302e400afed55a112d997b679ef01 Author: Weiqun Zhang Date: Tue Oct 18 10:28:36 2016 -0700 remove unused variables Tutorials/AMR_Adv_C_v2/Source/Src_nd/Tagging_nd.f90 commit d3aa0bc6769301d4263919da3d0d885693c2e3e3 Author: Weiqun Zhang Date: Tue Oct 18 10:27:40 2016 -0700 PlotFileUtil: write multi-level plotfile Src/C_BaseLib/PlotFileUtil.H Src/C_BaseLib/PlotFileUtil.cpp commit d9de3d8c163f4aa5f939dfb1ef03ccbfb67bc350 Author: Michael Zingale Date: Mon Oct 17 19:26:43 2016 -0400 copy the string routines over from Castro Src/F_Interfaces/BaseLib/parmparse_fi.cpp Src/F_Interfaces/BaseLib/parmparse_mod.f90 commit 3e5e27631afa36b23444ad54742452a8695f2c2e Author: Weiqun Zhang Date: Sat Oct 15 22:07:39 2016 -0700 AmrAdv/AmrCore tutorial: implement ErrorEst Tutorials/AMR_Adv_C_v2/Exec/Make.Adv Tutorials/AMR_Adv_C_v2/Source/AmrAdvError.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H Tutorials/AMR_Adv_C_v2/Source/Src_nd/Make.package Tutorials/AMR_Adv_C_v2/Source/Src_nd/Tagging_nd.f90 Tutorials/AMR_Adv_C_v2/Source/Src_nd/tagging_params.f90 commit 19445c76e190b9498aa9baaff4eae6b449fec57a Author: Weiqun Zhang Date: Sat Oct 15 16:58:50 2016 -0700 AmrAdv/AmrCore tutorial: build fine grids and init data on fine levels; ErrorEst to be implemented Src/C_AmrCoreLib/AmrCore.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp commit 773ac23ecca15476bf45c055e0f061055a129688 Author: Weiqun Zhang Date: Sat Oct 15 11:59:18 2016 -0700 AmrAdv/AmrCore tutorial: init data on base level Src/C_AmrCoreLib/AmrCore.H Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/Prob.f90 Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/inputs Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvIO.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdv_F.H Tutorials/AMR_Adv_C_v2/Source/Make.package commit 05abd40e9bb03373d399d5429094c6e3665be604 Author: Michael Zingale Date: Sat Oct 15 13:16:31 2016 -0400 change how we record COMP_VERSION and FCOMP_VERSION to be safer for Ubuntu Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit beb75b32a6c383cb792be0ffbaf84eabf448fefb Merge: 8075a327e 9a8abe7d2 Author: Weiqun Zhang Date: Fri Oct 14 15:55:58 2016 -0700 Merge branch 'development' into amrcore commit 8075a327e86c2a5bd78db4fb31d3f64e24714711 Author: Weiqun Zhang Date: Fri Oct 14 13:36:40 2016 -0700 start AMR_Adv tutorial based on AmrCoreLib Src/C_AmrCoreLib/AmrCore.H Tutorials/AMR_Adv_C_v2/Exec/Make.Adv Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/Make.package Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/Prob.f90 Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/AMR_Adv_C_v2/Exec/SingleVortex/inputs Tutorials/AMR_Adv_C_v2/README Tutorials/AMR_Adv_C_v2/Source/AmrAdv.H Tutorials/AMR_Adv_C_v2/Source/AmrAdv.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvError.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvEvolve.cpp Tutorials/AMR_Adv_C_v2/Source/AmrAdvInit.cpp Tutorials/AMR_Adv_C_v2/Source/Make.package Tutorials/AMR_Adv_C_v2/Source/main.cpp Tutorials/README_C commit 428e613719e373de266f6129bede28f57d5fb2c4 Merge: 9c41ffd16 db02f7e48 Author: Weiqun Zhang Date: Fri Oct 14 12:47:04 2016 -0700 Merge branch 'amrcore' of github.com:BoxLib-Codes/BoxLib into amrcore Conflicts: Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AmrCoreLib/AmrCore.H Src/C_AmrCoreLib/AmrCore.cpp commit 9c41ffd16d669ba09950ff6dfda4913d26d95102 Author: Weiqun Zhang Date: Wed Oct 12 14:22:29 2016 -0700 move part of the regrid function into AmrCore Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AmrCoreLib/AmrCore.H Src/C_AmrCoreLib/AmrCore.cpp commit 9a8abe7d2960e3c44d865c3794f5047870525981 Author: Weiqun Zhang Date: Thu Oct 13 16:00:06 2016 -0700 using std::isinf & std::isnan for GCC >= 5 Src/C_BaseLib/FArrayBox.cpp commit 86d93d88b8130281b0a55434c328e6aeb977fc6a Author: Weiqun Zhang Date: Thu Oct 13 10:42:42 2016 -0700 Add PlotFileUtil for writing plotfiles; some functions in MultiFabUtil for averaging from face and edge to cell center Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_3d.f90 Src/C_BaseLib/PlotFileUtil.H Src/C_BaseLib/PlotFileUtil.cpp commit f45fb5a6d12f73099bc3c720b4d6990b0c5927c6 Author: Michael Zingale 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 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 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: 3c1a07afe 131eca701 Author: Marc Day Date: Wed Oct 12 17:58:53 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 3c1a07afedfda2468716f77febe35d3852e706e0 Author: Marc Day Date: Wed Oct 12 17:58:24 2016 -0700 Add more info in the RegTest README Tools/RegressionTesting/README commit 131eca70163b71a58aebab7ce14653bc82d18cab Author: Weiqun Zhang Date: Wed Oct 12 15:14:55 2016 -0700 cmake update CMakeLists.txt Src/C_AMRLib/CMakeLists.txt Src/C_BaseLib/CMakeLists.txt Src/C_ParticleLib/CMakeLists.txt Tools/CMake/CCSEOptions.cmake commit ceb1e1241ed8e71ab355388dab116652fdbb9099 Merge: 29987274f 599057cee Author: vince 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 Date: Wed Oct 12 15:11:33 2016 -0700 fix typo in profiling call. Src/C_BaseLib/ParallelDescriptor.H commit a5f4e52bd92a11ca5a1fc2f533d9fbbaf7de26fd Author: vince Date: Wed Oct 12 15:09:43 2016 -0700 fix typo in profiling call. Src/C_BaseLib/ParallelDescriptor.H commit e3995e0a8fb944a1a1a1cd87da9218af67a0520e Merge: 6821c17f7 599057cee Author: Weiqun Zhang Date: Wed Oct 12 12:44:38 2016 -0700 Merge branch 'development' into amrcore commit 6821c17f7fd4d8d502d36e4369c24eaaf58dcac4 Author: Weiqun Zhang Date: Wed Oct 12 12:37:21 2016 -0700 fix particle grids and dmap; move the two grids stuff from AmrLevel to AmrParGDB Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AmrCoreLib/AmrCore.H Src/C_AmrCoreLib/AmrCore.cpp Src/C_AmrCoreLib/AmrParGDB.H commit f8edfc208ce60e4c47e6094194292b7feed89759 Author: Weiqun Zhang Date: Wed Oct 12 11:02:03 2016 -0700 remove a number of unused and do-nothing functions Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H commit 599057ceef6d7191a887385dafe038ce349f7ef2 Author: Michael Zingale Date: Wed Oct 12 11:16:54 2016 -0400 hook in preprocessing of the .F90 files -- some code bases need this Tools/F_mk/GMakerules.mak commit e154eb2f0a51f8415318d44bc8b3b180078a89ee Author: Michael Zingale Date: Wed Oct 12 11:16:43 2016 -0400 make the use of the f90_preprocessor optional Tools/F_scripts/dep.py commit 2389ad3fbfacba6d8a311321a36ce6bcb934acec Author: Michael Zingale Date: Wed Oct 12 10:33:20 2016 -0400 module matching needs to be case-insensitive Tools/F_scripts/dep.py commit 95e4493c575a12296eb6225c8b97b438adef5db7 Author: Weiqun Zhang Date: Tue Oct 11 15:57:03 2016 -0700 AmrCore: finish particles Src/C_AmrCoreLib/AmrCore.H Src/C_AmrCoreLib/AmrCore.cpp Src/C_AmrCoreLib/AmrParGDB.H Src/C_BaseLib/DistributionMapping.H Src/C_ParticleLib/ParGDB.H Src/C_ParticleLib/Particles.H Tutorials/PIC_C/two_level.cpp Tutorials/TwoGrid_PIC_C/main.cpp commit 067597517a762c7c4d9e353122be5733e5d262e8 Author: vince 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 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 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 Date: Tue Oct 11 13:05:29 2016 -0700 fix for faminmax header. Src/C_BaseLib/VisMF.cpp commit 9f8d37ddafc3f2c657f7a892664527f8bfd7ceac Author: Weiqun Zhang Date: Tue Oct 11 11:19:10 2016 -0700 particle: minor Src/C_ParticleLib/ParticleInit.H Src/C_ParticleLib/Particles.H commit 7f3b1d48760a9bbc66a128d49edaeb65c81ff71b Author: Michael Zingale Date: Tue Oct 11 13:38:00 2016 -0400 fix dupe Tools/F_mk/GMakerules.mak commit 97ff7e99f17b0f3f41665d9c12d1340b859a9c1c Author: Michael Zingale Date: Tue Oct 11 11:12:02 2016 -0400 capture the return code from dep.py and abort if it was not happy Tools/F_mk/GMakerules.mak commit 38213faf3004b58ae451ddea80d4839b54903f64 Author: Michael Zingale Date: Tue Oct 11 09:48:56 2016 -0400 clarify where EXT_DIR data lives Src/C_BaseLib/BC_TYPES.H commit 8281f3c8e13035ec93001eeec2027fcee7eb9892 Author: Michael Zingale Date: Tue Oct 11 09:44:58 2016 -0400 move the F90 BoxLib dependency checking over to the same dep.py that we use for C++ builds. Remove the old perl script. Note, for F90 BoxLib, we do not preprocess the files before the dependency checking. This is easy to add in, if necessary. Also remove the old deppairs target -- that does not seem to be used anywhere. Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak Tools/F_scripts/moddep.pl commit c83e139cb281cfa7aad0fcd5487bea46db00cbcf Author: Weiqun Zhang Date: Mon Oct 10 13:37:39 2016 -0700 move more files from C_AMRLib into C_AmrCoreLib Src/C_AMRLib/Make.package Src/C_AmrCoreLib/ErrorList.H Src/C_AmrCoreLib/ErrorList.cpp Src/C_AmrCoreLib/FLUXREG_1D.F Src/C_AmrCoreLib/FLUXREG_2D.F Src/C_AmrCoreLib/FLUXREG_3D.F Src/C_AmrCoreLib/FLUXREG_F.H Src/C_AmrCoreLib/FillPatchUtil.H Src/C_AmrCoreLib/FillPatchUtil.cpp Src/C_AmrCoreLib/FluxRegister.H Src/C_AmrCoreLib/FluxRegister.cpp Src/C_AmrCoreLib/INTERP_1D.F Src/C_AmrCoreLib/INTERP_2D.F Src/C_AmrCoreLib/INTERP_3D.F Src/C_AmrCoreLib/INTERP_F.H Src/C_AmrCoreLib/Interpolater.H Src/C_AmrCoreLib/Interpolater.cpp Src/C_AmrCoreLib/Make.package Src/C_AmrCoreLib/TagBox.H Src/C_AmrCoreLib/TagBox.cpp commit 05c950c1a4efb66110904764998c92ebd15380e6 Author: Weiqun Zhang Date: Mon Oct 10 13:13:54 2016 -0700 start C_AmrCoreLib Src/C_AMRLib/Make.package Src/C_AmrCoreLib/AmrParGDB.H Src/C_AmrCoreLib/AmrParticles.H Src/C_AmrCoreLib/Cluster.H Src/C_AmrCoreLib/Cluster.cpp Src/C_AmrCoreLib/Make.package commit 659660db1b4400952e80219290da6b14d1bd43b0 Merge: 8009fd204 bc191e4d0 Author: Michael Zingale Date: Mon Oct 10 15:58:13 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 8009fd2049ad972c2f98c5c89b8200b5eb841fbc Author: Michael Zingale Date: Mon Oct 10 15:58:00 2016 -0400 allow for no preprocessing if --cpp is not supplied Tools/F_scripts/dep.py commit bc191e4d05ab2ca76dba78b05062116729b4314b Author: Weiqun Zhang Date: Mon Oct 10 10:44:01 2016 -0700 Particle: template on container type, vector or deque Src/C_ParticleLib/AmrParticles.H Src/C_ParticleLib/ParticleInit.H Src/C_ParticleLib/Particles.H Src/C_ParticleLib/TracerParticles.H commit d10d39bcda674f3d9e4421fd30e6e6a3f93c1b57 Author: Weiqun Zhang Date: Mon Oct 10 10:12:01 2016 -0700 Particle: reimplement removing particles so that we can use either deque or vector Src/C_ParticleLib/Particles.H commit bfaf8b873eea4a5b486435ffe9878cd48f8e03df Author: Weiqun Zhang 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 Date: Sun Oct 9 20:29:21 2016 -0700 Particle: loop fusion Src/C_ParticleLib/Particles.H commit 8010a033958143b228c73c69b5cb1dd09e3fb136 Author: Weiqun Zhang Date: Sun Oct 9 13:19:23 2016 -0700 Particle: fix my recent bug Src/C_ParticleLib/Particles.H commit 1de010788e9c857827bf77a6caba75a48fced773 Author: Weiqun Zhang Date: Sun Oct 9 13:09:22 2016 -0700 particle: a comment Src/C_ParticleLib/Particles.H commit 44bcdaddf1b24daa7be762e21b227f4ff3541582 Author: Weiqun Zhang 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 Date: Sat Oct 8 22:57:56 2016 -0700 Particles: range for and auto Src/C_ParticleLib/Particles.H commit 28ec6ef3c8b7943f26261811297486db96ea34de Author: Michael Zingale Date: Sun Oct 9 16:21:45 2016 -0400 skip dependency if a file provides the modules it needs on its own Tools/F_scripts/dep.py commit c6143eb19189f86700ab5bd1ea5b9c7cb053b62b Merge: 4ce583e17 909045fd3 Author: Michael Zingale Date: Sat Oct 8 19:37:53 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 4ce583e17d655d39ebf846e7226f45d16c82a0f5 Author: Michael Zingale Date: Sat Oct 8 19:37:13 2016 -0400 we don't use Solaris anywhere in the make stuff Tools/C_mk/Make.defs Tools/C_mk/README.md commit 909045fd33bcfc2e9aacc0f5380db6534717ad1c Author: Weiqun Zhang 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 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 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 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 Date: Sat Oct 8 15:07:23 2016 -0400 fix endit Tools/C_mk/Make.Linux commit 47ee436eed5a7e78dae8d5534ff05819d4fd5472 Author: Michael Zingale Date: Sat Oct 8 15:06:53 2016 -0400 some machine clean-ups Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit d84c63d19e1e83117f27b3b7003fe9076ddd4c16 Author: Michael Zingale Date: Sat Oct 8 11:19:58 2016 -0400 ppCleanup is obsoleted by Release Tools/ppCleanup/README Tools/ppCleanup/cleanWords.txt Tools/ppCleanup/ppCleanup.py commit 850db1f51c2a83b532abcd92708433cb3aa9a636 Author: Michael Zingale Date: Sat Oct 8 11:18:26 2016 -0400 darter, lens, alphacluster, and pccluster are no more Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit f92c74a66bf102a9774f9c255e63840d01443aa1 Author: Weiqun Zhang Date: Fri Oct 7 21:43:54 2016 -0700 Add a new script that does macro cleanup on a directory Tools/Release/ppCleanupDir.py Tools/Release/release.py commit c88891c7950f714c5e8f1644cb5e60624399f8a5 Merge: 287553c3d 5b0ca8f28 Author: Michael Zingale Date: Fri Oct 7 21:36:51 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 5b0ca8f2868cd52593c0a8afb233eeada3dfd4a5 Author: Weiqun Zhang Date: Fri Oct 7 13:39:43 2016 -0700 MultiFabUtil average_edge_to_cellcenter Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_3d.f90 Src/C_BaseLib/MultiFabUtil_F.H commit 660183d11ce0d419c629e99e16e345962d50aa05 Author: Weiqun Zhang Date: Fri Oct 7 12:31:11 2016 -0700 add particlecontainer default constructor Src/C_ParticleLib/Particles.H commit 0ddb7040c21ac96230f85f95f652cc65c7bc2331 Author: vince 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 Date: Fri Oct 7 10:36:25 2016 -0700 fix for serial. Src/C_BaseLib/NFiles.cpp commit 287553c3df1fe1c119f2e22803b5069f3427d181 Author: Michael Zingale Date: Fri Oct 7 12:41:59 2016 -0400 we don't use the library building features for C++ BoxLib, so remove them to make the make stuff clearer and easier to read Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 36f1d3d2a3ca7497fba987e404376ae2c9eda7b3 Author: Michael Zingale Date: Fri Oct 7 12:31:41 2016 -0400 compressor is a job management script -- it doesn't belong here Tools/F_scripts/compressor commit e317783dd4c95d0ada02ecc2f2e1358698d06c4f Author: Michael Zingale Date: Fri Oct 7 12:31:28 2016 -0400 remove coco -- this is not used Tools/F_scripts/coco/coco.pl Tools/F_scripts/coco/coco_e.FF Tools/F_scripts/coco/e1.FF Tools/F_scripts/coco/e1.II commit 6b3971a8f877f006b81370a70beab691262a1e45 Author: Michael Zingale 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 Date: Fri Oct 7 09:35:07 2016 -0400 add a few comments Tools/F_scripts/dep.py commit 29edebce25f956743c7200ed19afdc3b0028c8b1 Author: Michael Zingale Date: Fri Oct 7 08:58:54 2016 -0400 add some system modules to IGNORES, make things case insensitive Tools/F_scripts/dep.py commit d3b3495911479b677871c92b4f0e4991fa4fa039 Merge: 49b8bb8a8 6b403b3e3 Author: Michael Zingale Date: Thu Oct 6 20:57:23 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 49b8bb8a8513be22204d447a81e12b25732056f4 Author: Michael Zingale Date: Thu Oct 6 20:56:57 2016 -0400 add a readme, remove a very old submission script Tools/F_scripts/README.md Tools/F_scripts/dep.py Tools/F_scripts/ibm_sp_batch.poe commit 6b403b3e39620207c013766b340b26611d1290d3 Author: Weiqun Zhang 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: 720699835 56f0fb697 Author: Michael Zingale Date: Thu Oct 6 19:58:20 2016 -0400 Merge branch 'development' into preprocessing commit 720699835f8b90c6ae25a2d0a145046e2aebdae9 Author: Michael Zingale Date: Thu Oct 6 19:40:32 2016 -0400 add debugging option, make the "use module" be matched at the start of a line (perhaps with some whitespace) and test for key errors Tools/F_scripts/dep.py commit 56f0fb697b1012c5e16b8580f77a72bbf2cd29e7 Author: Weiqun Zhang Date: Thu Oct 6 16:33:01 2016 -0700 FabArray: always respect the wish of nodal flag Src/C_BaseLib/FabArray.H commit 1b58ab0808122c1a9e12be84e036395f7fc433f2 Author: Michael Zingale Date: Thu Oct 6 15:16:52 2016 -0400 pylint + python 3 changes Tools/F_scripts/dep.py commit a659acf61d52ed16fe90814b251b6f29e8449fa8 Author: Michael Zingale Date: Thu Oct 6 15:00:04 2016 -0400 a little cleaning Tools/C_mk/Make.rules commit 254f4181b537af0700fc39c85076002edaf17b73 Author: Michael Zingale Date: Thu Oct 6 14:40:57 2016 -0400 this seems to work -- .F90 files are now preprocessed for dependency checking only (using the new dep.py script to find module dependencies) and then these preprocessed files are ignored and the Fortran compiler is invoked on the .F90 file itself, doing the preprocessing internally. Tools/C_mk/Make.rules Tools/F_scripts/dep.py commit f0d36ba124c9f23db71bc38ac6a545c49c0e56e2 Author: Michael Zingale Date: Thu Oct 6 13:35:17 2016 -0400 a little cleaning Tools/F_scripts/dep.py commit 9d3fe1dc0ce5084109e404bb4cdd03e95c074222 Author: Michael Zingale Date: Thu Oct 6 10:27:30 2016 -0400 prep for preprocessing Tools/F_scripts/dep.py commit b70153e9a45497cb6588d54eb4dfcd01e1e108dd Author: Michael Zingale Date: Thu Oct 6 10:05:11 2016 -0400 make it classy Tools/F_scripts/dep.py commit bff0d1558abf41f659dd7c4843f68380f81407c5 Author: Michael Zingale Date: Wed Oct 5 23:04:29 2016 -0400 add runtime hooks for preprocessing Tools/F_scripts/dep.py commit 54a78d8020fb3d117a3db584b2588fb166bbce54 Author: Michael Zingale Date: Wed Oct 5 22:46:21 2016 -0400 remove dupes Tools/F_scripts/dep.py commit 5e771f165c213968f3d65bd528f4e473964c4dbc Author: Michael Zingale Date: Wed Oct 5 22:15:48 2016 -0400 switch in a python F90 dependency checker this works for Castro in the current way of doing things. Needs more testing and cleaning, and then needs an option for doing preprocessing Tools/C_mk/Make.defs Tools/C_mk/Make.rules Tools/F_scripts/dep.py commit 7ba91529813c08d9cbc7ff9695ab91c41e51eb42 Author: vince Date: Wed Oct 5 17:34:40 2016 -0700 multiple deciders for chained fabarray reads, clean up ignored messages. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp Tests/IOBenchmark/IOTest.cpp commit b9dd897251827ec219fcd35ac3a820ba826b8939 Author: Weiqun Zhang Date: Wed Oct 5 16:34:13 2016 -0700 allow BaseFab change box type without changing size Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H commit b4b8ee8ddba3a710d3f534e5b20047d8d43e3eff Author: Michael Zingale Date: Wed Oct 5 19:17:30 2016 -0400 add support for OpenACC tests Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py Tools/RegressionTesting/test_util.py commit fceb58b1f8a1221363a1dc2ba43bf4321440a55e Author: Weiqun Zhang Date: Wed Oct 5 15:30:30 2016 -0700 NodalDepositionSingleLevel: the new MultiFab must have the same index type as the MultiFab to be filled Src/C_ParticleLib/Particles.H commit 51818f93bf1bafe48cdb3f85244a5bcf5a0610a7 Merge: a894e900d d373d2984 Author: Weiqun Zhang 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 Date: Tue Oct 4 17:07:03 2016 -0700 cmake Src/C_AMRLib/CMakeLists.txt commit a894e900d21da15a9a81783dd8dfa863b6045edf Author: Weiqun Zhang Date: Tue Oct 4 17:01:55 2016 -0700 cmake Src/CMakeLists.txt Src/C_AMRLib/CMakeLists.txt Src/C_ParticleLib/CMakeLists.txt commit 4abbc7a9158262616ca41dfe1f68746c908cbbc0 Author: Weiqun Zhang Date: Tue Oct 4 16:49:13 2016 -0700 include(PreprocessBoxLibFortran90) Src/CMakeLists.txt commit e3902af3778a37493bd8e94fac80d839a01ed5fd Merge: 3508d11e5 f60c93463 Author: Weiqun Zhang Date: Tue Oct 4 16:30:38 2016 -0700 Merge branch 'master' into development commit f60c93463dfe2797e4959286ca179a2bf1a55dd5 Author: Weiqun Zhang Date: Tue Oct 4 16:30:25 2016 -0700 typo Src/C_BaseLib/CMakeLists.txt commit 3508d11e5fbef2343822e1dfb4efb1aa184fdcd9 Merge: 004bfa5bc ff09063e5 Author: Weiqun Zhang Date: Tue Oct 4 16:29:17 2016 -0700 Merge branch 'master' into development commit ff09063e57d0ade988e898bfa751c6016ea6fc17 Author: Weiqun Zhang Date: Tue Oct 4 16:28:42 2016 -0700 trying to fix cmake; not tested because I don't know how to run cmake CMakeLists.txt Src/C_BaseLib/CMakeLists.txt Tools/CMake/PreprocessBoxLibFortran90.cmake commit 72c6b91b54cac59ec9527abb8dc2502251c64a0b Author: Ann Almgren Date: Tue Oct 4 07:07:33 2016 -0700 FILCC* now live in C_BaseLib so remove them from C_AMRLib/CMakeLists.txt Src/C_AMRLib/CMakeLists.txt commit 004bfa5bc16e568e9e75d6a1456657b20f56fdce Author: Weiqun Zhang Date: Tue Oct 4 15:50:19 2016 -0700 clean up Tutorials/HelloWorld_C/GNUmakefile commit 64b4fe89a1e19e4c752e049d7d69110eb28adf3c Author: Weiqun Zhang Date: Tue Oct 4 13:23:55 2016 -0700 move Timestamp function into TracerParticleContainer class Src/C_ParticleLib/Particles.H Src/C_ParticleLib/TracerParticles.H Src/C_ParticleLib/TracerParticles.cpp commit 4bc357fcb4f036258befafd30b55ffaac2055cf5 Author: Weiqun Zhang Date: Tue Oct 4 12:26:55 2016 -0700 move Particle stuff into C_ParticleLib; add TracerParticleContainer; note that cmake needs to be fixed Src/C_AMRLib/Make.package Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/C_ParticleLib/AmrParGDB.H Src/C_ParticleLib/AmrParticles.H Src/C_ParticleLib/Make.package Src/C_ParticleLib/ParGDB.H Src/C_ParticleLib/ParticleInit.H Src/C_ParticleLib/Particles.H Src/C_ParticleLib/Particles.cpp Src/C_ParticleLib/Particles_1D.F Src/C_ParticleLib/Particles_2D.F Src/C_ParticleLib/Particles_3D.F Src/C_ParticleLib/Particles_F.H Src/C_ParticleLib/TracerParticles.H Src/C_ParticleLib/TracerParticles.cpp Tutorials/PIC_C/GNUmakefile Tutorials/TwoGrid_PIC_C/GNUmakefile commit 95a37040793ff1d4946c570cfe69f081dc004e94 Author: Ann Almgren Date: Tue Oct 4 12:57:43 2016 -0700 Make 1d and 2d versions of NodalDeposition Src/C_BaseLib/Particles.H commit 9d1c45d64695d4ba80670106872e94a4d7097f21 Author: Weiqun Zhang Date: Tue Oct 4 08:39:31 2016 -0700 NodalDepositionSingleLevel only works in 3d Src/C_BaseLib/Particles.H commit e0420052a7abec2330e66b6822bd324b764e3cde Author: Ann Almgren Date: Tue Oct 4 07:07:33 2016 -0700 FILCC* now live in C_BaseLib so remove them from C_AMRLib/CMakeLists.txt Src/C_AMRLib/CMakeLists.txt commit 8d20a658166e21f17d2284468cc24912f1fbf695 Author: vince Date: Mon Oct 3 17:30:18 2016 -0700 name barriers for profiling. Src/C_BaseLib/VisMF.cpp Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit 5745df4a4f0d6e66f4f7c08f4b3bb45c8d899b67 Author: Weiqun Zhang Date: Mon Oct 3 17:13:05 2016 -0700 some minor changes Src/C_BaseLib/Particles.H commit b732db1929e400685ba2ab61467aada02af32c4f Merge: 47b975a13 42c99e11f Author: Ann Almgren Date: Mon Oct 3 16:34:12 2016 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 47b975a13159bd92f58923553113206cbed80bf8 Author: Ann Almgren Date: Mon Oct 3 16:34:01 2016 -0700 Add the single level nodal deposition routine here. Src/C_BaseLib/Particles.H commit 42c99e11fe8928745b0c5e7b554c8160f3c7b86f Author: Weiqun Zhang Date: Mon Oct 3 16:30:24 2016 -0700 elide some mpi reduce Src/C_BaseLib/Particles.H commit 8ece093706ea996b73d8f9220d6ddf81365cfbe9 Author: Weiqun Zhang Date: Mon Oct 3 15:04:12 2016 -0700 Particle: use std::array for Real m_data Src/C_BaseLib/Particles.H commit a5df41f42f56636b9638becdac78addc7a0ddc59 Merge: 497a57e33 382bea219 Author: Ann Almgren Date: Mon Oct 3 14:51:22 2016 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 497a57e33cbeebf101c552ec9f1aa7ffb4fddc87 Author: Ann Almgren Date: Mon Oct 3 14:50:58 2016 -0700 Get rid of everything to do with neutrinos / relativistic mass -- that all now lives in the Nyx repo. Src/C_BaseLib/Particles.H commit 1ef6cef37a5a414e35b798a1bb9a84b090c9fa60 Author: vince Date: Mon Oct 3 14:21:03 2016 -0700 added option to provide coordinator processor number to VisMF::Read for chained fabarray reads. Src/C_BaseLib/NFiles.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 382bea2191b66e5912e636fa9d9e316c42f482ec Author: Weiqun Zhang Date: Mon Oct 3 14:07:13 2016 -0700 update function parameter names Src/C_BaseLib/Particles.H commit 7b458502716b13f7011fd26eaf17f473733bb79a Merge: 389825f8e 9de54a6af Author: Weiqun Zhang Date: Mon Oct 3 13:58:24 2016 -0700 Merge branch 'development' into devel-particle Conflicts: Src/C_BaseLib/Particles.H commit 9de54a6afedf40aa58c26db900818f8410c283a7 Author: Ann Almgren Date: Mon Oct 3 13:50:23 2016 -0700 1) Remove the versions of moveKick and moveKickDrift that took normal acceleration vectors on faces (keep the versions that use cell-centered accelerations) 2) Remove movePredict and moveCorrect -- no one is using those. 3) Remove AssignDensityAndVels -- that now lives in the Nyx repo. 4) Replace references to "gravity" by references to "acceleration" Src/C_BaseLib/Particles.H commit 389825f8edfe51268e221901676ce32a631bf3d0 Author: Weiqun Zhang Date: Mon Oct 3 13:48:03 2016 -0700 white space Src/C_BaseLib/Particles.H commit ae589c43b2026502bf5a4327dcdf788719344c41 Author: Weiqun Zhang Date: Mon Oct 3 12:49:51 2016 -0700 Add number of intergers to Particle template Src/C_AMRLib/AmrParticles.H Src/C_BaseLib/Make.package Src/C_BaseLib/ParticleInit.H Src/C_BaseLib/Particles.H Tools/C_mk/Make.defs commit 1af09f5b86a399f87462c9d3aa448ef39db108fb Merge: b493084d5 a15e0ee6b Author: Andy Nonaka Date: Mon Oct 3 09:08:45 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit b493084d55f4adcf61866fd7dfb9047097ad479f Author: Andy Nonaka Date: Mon Oct 3 09:08:27 2016 -0700 update readme_'s Tutorials/GettingStarted_F/main.f90 Tutorials/README_C Tutorials/README_F commit a15e0ee6b043cb87dc99c8fe902b10217eb4fe94 Author: Weiqun Zhang Date: Mon Oct 3 08:56:32 2016 -0700 comment Src/C_BaseLib/FabArray.cpp commit 6d2298177821a37a81d36708b98e99a3af69289c Author: Weiqun Zhang Date: Mon Oct 3 08:54:09 2016 -0700 Release Notes 16.10 ReleaseNotes/release-notes-16.10 commit 135c4b0f1c48ebf7a9b750b329fc4925316a3b2d Merge: 1af3979e0 e45a5499e Author: Weiqun Zhang Date: Mon Oct 3 08:53:20 2016 -0700 Merge branch 'development' commit 1af3979e0a06900a89ca95091df4e676b56bd040 Author: Weiqun Zhang Date: Mon Oct 3 08:53:16 2016 -0700 fix a typo ReleaseNotes/release-notes-16.09 commit e45a5499ed7ffcbdc39852fe1a8127683d932499 Author: Ann Almgren Date: Sun Oct 2 16:13:26 2016 -0700 Move all of the ParticleContainer::InitCosmo... routines out of BoxLib and into Nyx because they are specific to cosmological applications Src/C_BaseLib/ParticleInit.H Src/C_BaseLib/Particles.H commit b224804c67097af7dbd4767c6064fa55f93880db Author: vince Date: Thu Sep 29 16:43:34 2016 -0700 more preread headers. Tests/IOBenchmark/IOTest.cpp commit a57f79e844b60e77e97bfb0c0c133dea7607bb63 Author: vince Date: Thu Sep 29 16:31:21 2016 -0700 workaround for intel compiler, preread mf headers. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit 9347616c69478427f5efb97e53bcce19e0558202 Author: Andy Nonaka Date: Wed Sep 28 19:26:54 2016 -0700 cleanup of C++ tutorials. start bc documentation Docs/UsersGuide/C_AdvancedTopics/C_AdvancedTopics.tex Docs/UsersGuide/F_AdvancedTopics/F_AdvancedTopics.tex Docs/UsersGuide/GettingStarted/GettingStarted.tex Docs/UsersGuide/UsersGuide.tex Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX1_C/writePlotFile.H Tutorials/HeatEquation_EX1_C/writePlotFile.cpp Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/HeatEquation_EX2_C/writePlotFile.H Tutorials/HeatEquation_EX2_C/writePlotFile.cpp commit 898e9535b01c38590b4d7ec39e9b1695baca20ac Author: Andy Nonaka Date: Wed Sep 28 18:49:03 2016 -0700 setup.cpp not needed Tutorials/HeatEquation_EX2_C/setup.cpp commit 6c38b29b2be3c4df63ba8dbf8260933acab579fa Author: Andy Nonaka Date: Wed Sep 28 16:08:29 2016 -0700 implemented dirichlet and neumann conditions in HeatEquation_EX2_C. Results match HeatEquation_EX2_F Tutorials/HeatEquation_EX2_C/advance_2d.f90 Tutorials/HeatEquation_EX2_C/advance_3d.f90 Tutorials/HeatEquation_EX2_C/bc_fill_nd.F90 Tutorials/HeatEquation_EX2_C/inputs_2d Tutorials/HeatEquation_EX2_C/inputs_3d Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/HeatEquation_EX2_C/writePlotFile.cpp Tutorials/HeatEquation_EX2_F/inputs_2d Tutorials/HeatEquation_EX2_F/inputs_3d commit 697ce623b732ebd9ab8befbdd656e5f4de5a10b1 Author: Andy Nonaka Date: Wed Sep 28 15:47:49 2016 -0700 index bugfix in bcs Tutorials/HeatEquation_EX2_F/advance.f90 Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX4_F/advance.f90 Tutorials/HeatEquation_EX5_F/advance.f90 commit 264efc7690f1f6514f76bc32fd51c553d11533ed Author: vince Date: Wed Sep 28 15:06:17 2016 -0700 remove init, more options. Docs/Readme.io Src/C_BaseLib/NFiles.cpp Src/C_BaseLib/VisMF.cpp commit a1a4e0a29422bd5cc11a31806aed382dc6eb71c4 Author: vince Date: Wed Sep 28 14:52:13 2016 -0700 tests to read and write multiple multifabs. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/IOBenchmark/inputs.dssmf commit 5e81c7f2ce8cc0ccefe8ca7a76d25a8759d3d014 Author: vince 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 Date: Tue Sep 27 16:14:55 2016 -0700 fix comment Src/C_BaseLib/Box.H commit 3b227094fcfdd476390a1f324ef0dedbdab8a188 Author: Weiqun Zhang Date: Tue Sep 27 16:02:28 2016 -0700 comment Src/C_BaseLib/Box.H commit 1dc4b2fdf8b43a9d7a27691bb3328ca47bac1494 Author: Weiqun Zhang Date: Tue Sep 27 16:02:19 2016 -0700 minor Src/C_BaseLib/BoxArray.cpp commit 2398bf92c336f0ec991473eecd569d70817278e9 Author: vince Date: Tue Sep 27 15:42:11 2016 -0700 fix for combined transfer. Src/C_BaseLib/VisMF.cpp commit 27195c7d8c32f39337d7848f76e8953ad4b63be9 Author: vince Date: Tue Sep 27 15:41:15 2016 -0700 separate options for plot and checkpoint formats. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 3f5f0407f3908f58dbba1210463590c79c542afd Author: Weiqun Zhang Date: Tue Sep 27 08:15:17 2016 -0700 nodal SumBoundary: forgot to zero out the destination Src/C_BaseLib/MultiFab.cpp commit e2597f80c558e2f3208802a644709a21becfb4e1 Author: Weiqun Zhang Date: Mon Sep 26 22:22:57 2016 -0700 nodal SumBoundary: fix new bug Src/C_BaseLib/IntVect.H Src/C_BaseLib/MultiFab.cpp commit 8bdd7f55a6a533d9d4c5c6c3efc8b22402957d5d Author: Andy Nonaka Date: Mon Sep 26 13:44:30 2016 -0700 pass in bc(:,:) and domlo/hi into compute_flux Tutorials/HeatEquation_EX2_C/advance_2d.f90 Tutorials/HeatEquation_EX2_C/advance_3d.f90 Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/HeatEquation_EX2_C/myfunc_F.H commit 5b44f9e2deadc533c772e6e242e368bddfd83fc4 Merge: 55f38b145 1e86e03c5 Author: Andy Nonaka Date: Mon Sep 26 13:08:33 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 55f38b14539998b80bfa947f15f427e1d7452bad Author: Andy Nonaka Date: Mon Sep 26 13:06:41 2016 -0700 starting to put Dirichlet BC's in. This doesn't work quite right yet, as compute_flux() in advance_xd.f90 needs to know to alter the stencil at the boundary for the EXT_DIR case, where the ghost cell stores the value on the boundary. Tutorials/HeatEquation_EX2_C/FILCC_2D.F Tutorials/HeatEquation_EX2_C/FILCC_3D.F Tutorials/HeatEquation_EX2_C/inputs_2d Tutorials/HeatEquation_EX2_C/inputs_3d commit 1e86e03c59cd4be4acf7be85df644a8779801758 Merge: 621888807 e28d9d3d6 Author: Weiqun Zhang Date: Mon Sep 26 12:06:25 2016 -0700 Merge branch 'weiqun/SumBoundary' into development commit e28d9d3d664461491b3167bc9162ad853bb3de18 Author: Weiqun Zhang Date: Mon Sep 26 11:29:01 2016 -0700 SumBoundary: fix new bug Src/C_BaseLib/FabArray.H commit 1a8c1d0fff390f31aaba4a151208f0964ed931d1 Author: Weiqun Zhang Date: Mon Sep 26 10:08:43 2016 -0700 make MultiFab::SumBoundary work for nodal Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp commit 6218888079cbce611f5b74c8165e262b6ec571e4 Author: Andy Nonaka Date: Mon Sep 26 09:53:43 2016 -0700 C++ plotfiles now report the time and variable name properly Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX1_C/writePlotFile.H Tutorials/HeatEquation_EX1_C/writePlotFile.cpp Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/HeatEquation_EX2_C/writePlotFile.H Tutorials/HeatEquation_EX2_C/writePlotFile.cpp commit 70c8d6b0d3f29abb33294ac190983c043a8a14ba Author: Weiqun Zhang Date: Mon Sep 26 09:10:38 2016 -0700 MultiFab::AddProduct that computes dst += src1*src2 Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 291aa8c68a6a6a768504b11b24ce9e2886b37151 Author: Weiqun Zhang Date: Mon Sep 26 08:37:50 2016 -0700 typos Src/C_BaseLib/IntVect.H commit beeaeac1c6765c90734de91fad2ff9216517c728 Author: Michael Zingale Date: Sun Sep 25 18:16:49 2016 -0400 add -Mbounds for PGI in debug mode Tools/C_mk/Make.Linux commit 8078ce585b55b263b2b4e53fd101aba55fc0caa2 Author: Ann Almgren Date: Sat Sep 24 15:19:34 2016 -0700 Add two more initialization routines for particles to ParticleInit.H Src/C_BaseLib/ParticleInit.H Src/C_BaseLib/Particles.H commit 3938fd4ea859ecc3fb2c727e3af1f9ad6fb62675 Author: Ann Almgren Date: Sat Sep 24 14:48:43 2016 -0700 Moved the ParticleContainer::Init... routines into their own file. Src/C_BaseLib/Make.package Src/C_BaseLib/ParticleInit.H Src/C_BaseLib/Particles.H commit 153adb24468cd047c27f805a3915a6292db4ace1 Author: Andy Nonaka Date: Fri Sep 23 17:37:21 2016 -0700 added explicit array shaping to the C++ version and a note in the user's guide Docs/UsersGuide/GettingStarted/GettingStarted.tex Tutorials/GettingStarted_C/work_on_data_2d.f90 Tutorials/GettingStarted_C/work_on_data_3d.f90 Tutorials/GettingStarted_F/main.f90 commit 43ede216114719f0a04c26c50117d85fade8c94f Author: Andy Nonaka Date: Fri Sep 23 17:15:34 2016 -0700 finish updating chapter 2. looking pretty good now. next on the list is documenting the first 'advanced' C++ feature: boundary conditions Docs/UsersGuide/GettingStarted/GettingStarted.tex commit 1bca1789ee917f89515575d817fe0f40d0c626f4 Author: Andy Nonaka Date: Fri Sep 23 16:51:34 2016 -0700 created a fortran version of the GettingStarted tutorial, and the User's Guide links directly to the source code for a first example Docs/UsersGuide/GettingStarted/GettingStarted.tex Tutorials/GettingStarted_F/GNUmakefile Tutorials/GettingStarted_F/GPackage.mak Tutorials/GettingStarted_F/main.f90 Tutorials/GettingStarted_F/work_on_data.f90 commit 215c3e9861d5b7c05c7c7453ef99964cf4cd4a12 Author: Andy Nonaka Date: Fri Sep 23 16:07:01 2016 -0700 created a new C++ tutorial, "GettingStarted_C", which is basically a 'hello-world' type program that builds multifabs, accesses the multifab data in an f90 routine, and fills interior/periodic boundaries. Bonus points is that the user's guide now directly links to the source code! I hope to do the same for fortran90 shortly. Docs/UsersGuide/GettingStarted/GettingStarted.tex Docs/UsersGuide/UsersGuide.tex Tutorials/GettingStarted_C/GNUmakefile Tutorials/GettingStarted_C/Make.package Tutorials/GettingStarted_C/main.cpp Tutorials/GettingStarted_C/work_on_data_2d.f90 Tutorials/GettingStarted_C/work_on_data_3d.f90 commit 5b5ae8cd578ac5ce04c5d6402bf640e792f681d1 Author: vince Date: Fri Sep 23 15:18:24 2016 -0700 added support for precreating plot file level directories. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H commit b724d19864b0390055ebee0dbedaee6baa771d6d Author: vince Date: Fri Sep 23 15:15:12 2016 -0700 added io parameters. Docs/Readme.io commit 4693c8bc87918d7853b8b1e4542e602e83d19b6a Author: vince Date: Fri Sep 23 14:09:21 2016 -0700 sync vismf vars for dsc. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_BaseLib/VisMF.H commit defe644d85833fb68019d605501815dcba64385a Author: Andy Nonaka Date: Fri Sep 23 13:11:28 2016 -0700 remove the bl_abort statements when using the default EXT_DIR option. Some codes with mixed inflow + extrapolation (on different faces) boundary conditions rely on EXT_DIR being a null-op Src/C_BaseLib/FILCC_1D.F Src/C_BaseLib/FILCC_2D.F Src/C_BaseLib/FILCC_3D.F Src/F_BaseLib/multifab_physbc.f90 commit aa3c10f9929510a7cb52c95ea7707c6c9bc4be1f Author: Andy Nonaka Date: Fri Sep 23 12:57:54 2016 -0700 now FILLCC has EXT_DIR options built in for C++, just like multifab_physbc.f90 for F90 however, both C++ and F90 will now abort if you use EXT_DIR as given - we are forcing users to supply their own Dirichlet values Src/C_BaseLib/FILCC_1D.F Src/C_BaseLib/FILCC_2D.F Src/C_BaseLib/FILCC_3D.F Src/F_BaseLib/multifab_physbc.f90 commit b6075e912cbcbc9bfbb364492acb2e18365e6e4c Author: vince Date: Fri Sep 23 12:15:24 2016 -0700 parmparse inputs, change defaults. Src/C_BaseLib/VisMF.cpp commit 2459c7dca86cb59b724c4a01275ad7c67c1b6099 Author: vince 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 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 Date: Thu Sep 22 18:12:55 2016 -0700 Cleaned up Tutorials/PIC_C/GNUmakefile. Tutorials/PIC_C/GNUmakefile commit 47834f6a3464d5b6d0d966d99323c2f5f37b639d Author: Weiqun Zhang Date: Thu Sep 22 16:06:42 2016 -0700 add PArray copy assignment operator so that we can assert that the sizes are zero Src/C_BaseLib/PArray.H commit 5461e2270a766f51a7cfc3670e26721bacc322db Author: vince Date: Thu Sep 22 11:51:57 2016 -0700 added setting for synchronous reads. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit aeb3dc5157dbaba8cb453e0afd5f78650c43096a Author: Andy Nonaka Date: Wed Sep 21 15:21:14 2016 -0700 minor name changes to user's guide matches tutorial Docs/UsersGuide/GettingStarted/GettingStarted.tex Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX2_C/main.cpp commit d05a83891536b8b17a57538eeaebb93b7e24209a Author: Andy Nonaka Date: Wed Sep 21 14:47:07 2016 -0700 periodic and outflow working in 2d and 3d Tutorials/HeatEquation_EX2_C/inputs_2d Tutorials/HeatEquation_EX2_C/inputs_3d commit 3e5624a4fcb69342d295a3f11d3f8338512cf8ac Author: Andy Nonaka Date: Wed Sep 21 14:43:08 2016 -0700 outflow bcs working for HeatEquation_EX2_C Tutorials/HeatEquation_EX2_C/inputs_2d Tutorials/HeatEquation_EX2_C/main.cpp commit 102df475d42883d9e2b78ea062b491c4c6d911ff Merge: d071ee705 9fadf6768 Author: vince Date: Wed Sep 21 13:24:01 2016 -0700 merge fixes. commit 769c01c3e23205408c368079da556977460a01cd Merge: 562ed986b 807c70bad Author: Andy Nonaka Date: Wed Sep 21 13:17:07 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 562ed986b53f4549411be1ada8013399c58fce2f Author: Andy Nonaka Date: Wed Sep 21 13:16:18 2016 -0700 HeatEquation_EX1_C to uses PArray now for the state and fluxes Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX2_C/main.cpp commit 2b4b2c716fb611cfdf95a31a5eaabd1dfdcbc87a Author: Andy Nonaka Date: Wed Sep 21 12:57:44 2016 -0700 updating HeatEquation_EX1_C to more closely match EX2_C. WIP Tutorials/HeatEquation_EX1_C/GNUmakefile Tutorials/HeatEquation_EX1_C/Make.package Tutorials/HeatEquation_EX1_C/advance_3d.f90 Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX1_C/myfunc_F.H Tutorials/HeatEquation_EX2_C/Make.package Tutorials/HeatEquation_EX2_C/main.cpp commit 807c70badaae8964d12ea3f945dda2c173f32b23 Author: Weiqun Zhang Date: Wed Sep 21 09:06:28 2016 -0700 move User's Guide from Docs/ to Docs/UsersGuide/ Docs/UsersGuide/C_AdvancedTopics/C_AdvancedTopics.tex Docs/UsersGuide/F_AdvancedTopics/F_AdvancedTopics.tex Docs/UsersGuide/F_AdvancedTopics/bc_example1.eps Docs/UsersGuide/F_AdvancedTopics/bc_example1.fig Docs/UsersGuide/F_AdvancedTopics/bc_example2.eps Docs/UsersGuide/F_AdvancedTopics/bc_example2.fig Docs/UsersGuide/F_AdvancedTopics/bc_example3.eps Docs/UsersGuide/F_AdvancedTopics/bc_example3.fig Docs/UsersGuide/F_AdvancedTopics/subcycling_algorithm.eps Docs/UsersGuide/GNUmakefile Docs/UsersGuide/GettingStarted/GettingStarted.tex Docs/UsersGuide/GettingStarted/VisIt_2D.eps Docs/UsersGuide/GettingStarted/VisIt_3D.eps Docs/UsersGuide/GettingStarted/edison.run Docs/UsersGuide/GettingStarted/edison_omp.run Docs/UsersGuide/Introduction/AMR.eps Docs/UsersGuide/Introduction/Introduction.tex Docs/UsersGuide/Introduction/boxlib_directory_bw2.eps Docs/UsersGuide/Introduction/castro_scaling.eps Docs/UsersGuide/Introduction/data_loc.odg Docs/UsersGuide/Introduction/data_loc2.eps Docs/UsersGuide/Introduction/index_grid.odg Docs/UsersGuide/Introduction/index_grid2.eps Docs/UsersGuide/Introduction/lmc_scaling.eps Docs/UsersGuide/Introduction/maestro_scaling.eps Docs/UsersGuide/Introduction/varden1.eps 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 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 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 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 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 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 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 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 Date: Tue Sep 20 15:53:13 2016 -0700 just use sends for now. Src/C_BaseLib/NFiles.cpp commit fa3d491edbb8313053cbb6a0ad02d29f285e5387 Author: vince Date: Tue Sep 20 15:49:21 2016 -0700 make stream pointer so intel will compile. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 9fadf6768dd63c4b30a9d3bf1cca313569344060 Author: Weiqun Zhang Date: Tue Sep 20 15:38:40 2016 -0700 make PhysBCFunct concrete so that we can use it without StateData; move FILCC to C_BaseLib Src/C_AMRLib/CMakeLists.txt Src/C_AMRLib/Make.package Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/FILCC_1D.F Src/C_BaseLib/FILCC_2D.F Src/C_BaseLib/FILCC_3D.F Src/C_BaseLib/Make.package Src/C_BaseLib/PhysBCFunct.H Src/C_BaseLib/PhysBCFunct.cpp Src/C_BaseLib/bc_types.fi commit 6862211293ed9882e8026e285b44f9031e330a8f Author: vince Date: Tue Sep 20 15:34:22 2016 -0700 remove check from timed block, cleanup. Tests/IOBenchmark/IOTest.cpp commit 951bd837c673743fe77a161490da3db1d0083bcc Author: Weiqun Zhang Date: Tue Sep 20 12:37:22 2016 -0700 PhysBCFunct --> PhysBCFunctBase and doit --> FillBoundary Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FillPatchUtil.H Src/C_AMRLib/FillPatchUtil.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_BaseLib/PhysBCFunct.H commit 35b74d54465e2611a8e867e41d391ef82e6d8ab5 Author: Ann Almgren Date: Tue Sep 20 12:12:45 2016 -0700 We don't actually need C_BndryLib for this example. Tutorials/HeatEquation_EX1_C/GNUmakefile commit 70fdfcd53c9ab4079389e22cf797cc179f5e6fa9 Author: Weiqun Zhang Date: Tue Sep 20 11:09:30 2016 -0700 make it compile Tutorials/HeatEquation_EX2_C/main.cpp commit 7eb4d971e46696b69b2029fa67b9d6642a1118f3 Author: Weiqun Zhang Date: Tue Sep 20 08:54:14 2016 -0700 minor Tutorials/HeatEquation_EX1_C/GNUmakefile commit 1e56dfe1a338b52b835130da54a56e7a31f007fe Author: Weiqun Zhang Date: Tue Sep 20 08:53:45 2016 -0700 add default EBASE Tools/C_mk/Make.defs commit 58640777a059c4995e694f9bfe1637a2fd668729 Author: Weiqun Zhang Date: Tue Sep 20 08:37:47 2016 -0700 simplify GNUmakefile Tutorials/HeatEquation_EX1_C/GNUmakefile commit ecce81e41ccb4e2f8c62f2d6158d002d6ea42ca6 Author: Weiqun Zhang Date: Tue Sep 20 08:37:33 2016 -0700 move the rule for building executable to the top Tools/C_mk/Make.rules commit aa5f86c948591999736d0da0a4abb4c2b8059d1e Author: Ann Almgren Date: Mon Sep 19 21:05:25 2016 -0700 Making progress but this still doesn't quite work yet ... Tutorials/HeatEquation_EX2_C/Make.package Tutorials/HeatEquation_EX2_C/bc_F.H Tutorials/HeatEquation_EX2_C/bc_fill_2d.F90 Tutorials/HeatEquation_EX2_C/bc_fill_3d.F90 Tutorials/HeatEquation_EX2_C/bcfill_nd.f90 Tutorials/HeatEquation_EX2_C/main.cpp commit 45bf6b4da70a50e48099cdbba3e102650294bda2 Author: Ann Almgren Date: Mon Sep 19 20:20:44 2016 -0700 Move the source file names from GNUmakefile to Make.package Tutorials/HeatEquation_EX2_C/GNUmakefile Tutorials/HeatEquation_EX2_C/Make.package commit d5315b51e93dd09b0a5fac80c577289cecf98c5a Author: Michael Zingale Date: Mon Sep 19 22:18:24 2016 -0400 use bind(C) Tutorials/MultiGrid_C/COEF_2D.F Tutorials/MultiGrid_C/COEF_2D.F90 Tutorials/MultiGrid_C/COEF_3D.F Tutorials/MultiGrid_C/COEF_3D.F90 Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/Make.package Tutorials/MultiGrid_C/RHS_2D.F Tutorials/MultiGrid_C/RHS_2D.F90 Tutorials/MultiGrid_C/RHS_3D.F Tutorials/MultiGrid_C/RHS_3D.F90 Tutorials/MultiGrid_C/RHS_F.H Tutorials/MultiGrid_C/main.cpp commit 3082fef8cbcf764949f2374ece24729ff4b6626f Author: Michael Zingale Date: Mon Sep 19 21:31:42 2016 -0400 use bind(C) Tutorials/HeatEquation_EX2_C/advance_2d.f90 Tutorials/HeatEquation_EX2_C/advance_3d.f90 Tutorials/HeatEquation_EX2_C/bcfill_nd.f90 Tutorials/HeatEquation_EX2_C/init_phi_2d.f90 Tutorials/HeatEquation_EX2_C/init_phi_3d.f90 Tutorials/HeatEquation_EX2_C/main.cpp commit 517528be279b807fa23bbe4bff2808046cc4fc20 Author: Michael Zingale Date: Mon Sep 19 21:16:05 2016 -0400 add new example Tutorials/README_C commit 6e2b82016dc12a69d7691273a2d84329fb8d9259 Author: Michael Zingale Date: Mon Sep 19 21:14:13 2016 -0400 get this compiling Tutorials/HeatEquation_EX2_C/GNUmakefile commit 2ec86d8f18b510bed0bd32c3fe6fb20632c797b3 Merge: db82c041c 24d4f9bad Author: Michael Zingale Date: Mon Sep 19 20:58:59 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit db82c041c58ccaa4c69c2bab804dce3a1719955f Author: Michael Zingale Date: Mon Sep 19 20:58:47 2016 -0400 use bind(C) for Fortran interfaces Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/face_velocity_2d.f90 Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_dt.cpp Tutorials/AMR_Adv_C/Source/Adv_setup.cpp Tutorials/AMR_Adv_C/Source/Src_2d/Adv_2d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/Adv_3d.f90 Tutorials/AMR_Adv_C/Source/Src_nd/Adv_nd.f90 Tutorials/AMR_Adv_C/Source/Src_nd/Tagging_nd.f90 Tutorials/Tiling_Heat_C/advance_3d.f90 Tutorials/Tiling_Heat_C/init_phi_3d.f90 Tutorials/Tiling_Heat_C/main.cpp Tutorials/WaveEquation_C/advance_2d.f90 Tutorials/WaveEquation_C/advance_3d.f90 Tutorials/WaveEquation_C/init_data_2d.f90 Tutorials/WaveEquation_C/init_data_3d.f90 Tutorials/WaveEquation_C/main.cpp commit 24d4f9bad5d2354d6de217fb93501065121bfd86 Merge: b118d0a03 94d13f221 Author: Ann Almgren Date: Mon Sep 19 17:49:51 2016 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit b118d0a03cdfaaed0660e56b66f0a5705e65eb1b Author: Ann Almgren Date: Mon Sep 19 17:49:18 2016 -0700 Add a new Tutorial example that demonstrates how to use StateData without Amr or AmrLevel -- this allows us to introduce boundary conditions in the C++ stuff without being multilevel. Tutorials/HeatEquation_EX2_C/GNUmakefile Tutorials/HeatEquation_EX2_C/Make.package Tutorials/HeatEquation_EX2_C/advance_2d.f90 Tutorials/HeatEquation_EX2_C/advance_3d.f90 Tutorials/HeatEquation_EX2_C/bc_F.H Tutorials/HeatEquation_EX2_C/bcfill_nd.f90 Tutorials/HeatEquation_EX2_C/init_phi_2d.f90 Tutorials/HeatEquation_EX2_C/init_phi_3d.f90 Tutorials/HeatEquation_EX2_C/inputs_2d Tutorials/HeatEquation_EX2_C/inputs_3d Tutorials/HeatEquation_EX2_C/main.cpp Tutorials/HeatEquation_EX2_C/setup.cpp Tutorials/HeatEquation_EX2_C/writePlotFile.H Tutorials/HeatEquation_EX2_C/writePlotFile.cpp commit 94d13f221a7986750a515ee57cf7ed783c5edd32 Author: Michael Zingale Date: Mon Sep 19 20:30:12 2016 -0400 use bind(C) to make the Fortran interfaces cleaner Tutorials/HeatEquation_EX1_C/advance_2d.f90 Tutorials/HeatEquation_EX1_C/advance_3d.f90 Tutorials/HeatEquation_EX1_C/init_phi_2d.f90 Tutorials/HeatEquation_EX1_C/init_phi_3d.f90 Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HelloWorld_C/main.cpp Tutorials/HelloWorld_C/work.f90 Tutorials/README_C Tutorials/Tiling_C/main.cpp Tutorials/Tiling_C/work.f90 commit f799329c5de18a3a4dd0ef70ffff1ddbd2990639 Author: Ann Almgren Date: Mon Sep 19 17:25:48 2016 -0700 We don't need C_AMRLib to compile this example. Tutorials/HeatEquation_EX1_C/GNUmakefile commit 7941c772ece5f5c533db815ae3b47809190f4b87 Author: Weiqun Zhang Date: Mon Sep 19 14:44:41 2016 -0700 add FluxRegister::ClearInternalBorders Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 6285e8f8eaa6957fef0c60283f812ca509963430 Merge: c646bffb2 13cdd5231 Author: Andy Nonaka Date: Mon Sep 19 12:59:47 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit c646bffb266e086bc1d0c867fe0e156f498ea9cb Author: Andy Nonaka Date: Mon Sep 19 12:59:30 2016 -0700 update info for running on NERSC Docs/F_AdvancedTopics/hopper_omp.run Docs/GettingStarted/GettingStarted.tex Docs/GettingStarted/edison.run Docs/GettingStarted/edison_omp.run Docs/GettingStarted/hopper.run Docs/UsersGuide.tex commit ae20e7de5d32047eded9616a6a3bdc21771e2062 Author: vince Date: Mon Sep 19 12:48:17 2016 -0700 fix for special case. Src/C_BaseLib/NFiles.cpp commit 13cdd523167eb13899cfd59d05f31a31d7dc03ab Author: Weiqun Zhang Date: Mon Sep 19 12:36:20 2016 -0700 FabSet::plusTo (a MultiFab) Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 7e1160ce3ec4c575470084e8b17443ff5527bfc5 Author: vince Date: Mon Sep 19 11:49:06 2016 -0700 another test inputs file. Tests/IOBenchmark/inputs.dssmf commit bafc22d746e03db9ed17617757e863a90aac912b Author: vince Date: Mon Sep 19 11:42:31 2016 -0700 remove implied order. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 38c55fde144f2c43138224d4d88d7810f0e717ec Author: vince 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 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 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 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 Date: Mon Sep 19 11:30:24 2016 -0400 start documenting tutorials Tutorials/README_C commit faaaa5d8c258379109f3dfae68c0e914d244cd5d Author: vince Date: Thu Sep 15 17:39:00 2016 -0700 new test flag. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit 0eda9c50ecef6502af3d993d3b85013c93a00eab Author: vince Date: Thu Sep 15 17:38:24 2016 -0700 fixes for dss offsets. Src/C_BaseLib/NFiles.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 3c0e404e131d8edae6156893836a40faea65ef71 Author: vince Date: Thu Sep 15 14:59:22 2016 -0700 ifdef for serial. Src/C_BaseLib/NFiles.cpp commit 583adec092f41a5f9d81007c578e7107f90489d3 Author: vince Date: Wed Sep 14 17:23:54 2016 -0700 add option for writing with dynamic set selection. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit aaca2036ead9a0cc785b5719d9165241a8d5f0ec Author: vince Date: Wed Sep 14 17:22:11 2016 -0700 update test check for nonzero decider. Tests/IOBenchmark/IOTest.cpp commit a5d1c04f3a8edaee838e508aaa544db07e4f25ad Author: vince Date: Wed Sep 14 17:20:36 2016 -0700 make sure the decider is not in set zero. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit 8c3930ad12c53e493924a696cfc6e7c9e7390a93 Author: vince Date: Wed Sep 14 14:26:37 2016 -0700 SetDynamic function instead of constructor. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp Tests/IOBenchmark/IOTest.cpp commit 07060ff938508cd6f70654991f8b7890db49f4b5 Author: vince Date: Wed Sep 14 14:11:01 2016 -0700 change names to be more correct. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp Tests/IOBenchmark/IOTest.cpp commit e1aaf0e8e6ddcf6cac214d94806917b174ae2d0c Author: Weiqun Zhang 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 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 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 Date: Tue Sep 13 17:36:20 2016 -0700 clean up comments Src/LinearSolvers/C_CellMG/MG_3D.F commit 8cfba06dff661eb202244916ced1305738f05b74 Author: vince Date: Tue Sep 13 17:26:37 2016 -0700 more dss support. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 1dcbfd685f07dc6e66e052a6f5dd444ed80332ac Author: Weiqun Zhang Date: Tue Sep 13 16:29:37 2016 -0700 more omp and tiling in linear solvers Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit 02998ec6e870aae89d64afe1597b777a5214185c Author: Weiqun Zhang Date: Tue Sep 13 16:15:10 2016 -0700 C_TensorMG: tiling Src/LinearSolvers/C_TensorMG/MCLO_2D.F Src/LinearSolvers/C_TensorMG/MCLO_3D.F Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 2ced6d48b01bce76023de397af7bf442f4e4388a Author: Weiqun Zhang Date: Tue Sep 13 16:07:09 2016 -0700 C_TensorMG: cleanup Src/LinearSolvers/C_TensorMG/DivVis_F.H commit 4ec71cabdab36b47ce1d2fa0019dbd046c2355ae Author: vince Date: Tue Sep 13 16:01:46 2016 -0700 fix the special case. Src/C_BaseLib/NFiles.cpp commit 1db87e4d134d5cc7c9ac8c2955c3b68c7004c9cb Author: Weiqun Zhang Date: Tue Sep 13 15:57:36 2016 -0700 remove FArrayBox::norm functions Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/MultiFab.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 77ca7a8b7064038ba3c01c5a432e836c311260e2 Author: vince Date: Tue Sep 13 15:51:42 2016 -0700 new iterator tests. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit 5f0323af8337b6f3c027eb939feb1bf63ceff4d5 Author: vince Date: Tue Sep 13 15:51:19 2016 -0700 make the test code into an iterator for dynamic set selection. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit 37400d928cc002f4911ce5123e1cd229852830c1 Author: Weiqun Zhang Date: Tue Sep 13 15:30:33 2016 -0700 C_TensorMG: remove omp from Fortran subroutines Src/LinearSolvers/C_TensorMG/DV_3D1.F Src/LinearSolvers/C_TensorMG/DV_3D2.F Src/LinearSolvers/C_TensorMG/DV_3D3.F Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F Src/LinearSolvers/C_TensorMG/MCLO_3D.F commit 6082ae6b2fe8ed80951ea61ff30f6bf829e1af2d Author: Weiqun Zhang Date: Tue Sep 13 15:17:18 2016 -0700 use MulitFab::Xpay in linear solvers Src/LinearSolvers/C_CellMG/LO_1D.F Src/LinearSolvers/C_CellMG/LO_2D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LO_F.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG4/ABec4.cpp Src/LinearSolvers/C_TensorMG/DivVis_F.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLO_2D.F Src/LinearSolvers/C_TensorMG/MCLO_3D.F Src/LinearSolvers/C_TensorMG/MCLO_F.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 7ff2fabf1e29cf35742307f08eb48469c9c78d3c Author: Weiqun Zhang Date: Tue Sep 13 15:01:43 2016 -0700 MultiFab::Xpay and BaseFab::xpay that do y = x + a*y Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 9d988826ca3858ced89cebcd1232da142c86f79f Author: Weiqun Zhang Date: Tue Sep 13 14:40:15 2016 -0700 omp in C_Tensor Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp commit e2971deb5b8e07e6dcfb98b4926c64b51cdec8a1 Author: Weiqun Zhang Date: Tue Sep 13 14:34:56 2016 -0700 omp in MCCGSolver Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp commit 9779ef992d5ede03ebd9f1f67220abc0d31d5750 Author: Weiqun Zhang Date: Tue Sep 13 14:31:47 2016 -0700 remove CG_?D.F and use BaseFab and MulitFab functions instead Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/CG_1D.F Src/LinearSolvers/C_CellMG/CG_2D.F Src/LinearSolvers/C_CellMG/CG_3D.F Src/LinearSolvers/C_CellMG/CG_F.H Src/LinearSolvers/C_CellMG/CMakeLists.txt Src/LinearSolvers/C_CellMG/Make.package Src/LinearSolvers/C_CellMG4/CMakeLists.txt Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp commit 1f9a1e5e0428131079217699b52ec736ca5e6973 Author: Weiqun Zhang Date: Tue Sep 13 14:16:03 2016 -0700 CGSolver and MCCgSolver: use BaseFab::dot and MultiFab::Dot Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp commit fcb941e4e11c6c03862bc761d68567ad7a4a1ada Author: Weiqun Zhang Date: Tue Sep 13 14:03:55 2016 -0700 add MultiFab::Dot and use it in CGSolver Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 82acf67443dacb2355eb62bcf62b8f86118e4138 Author: Weiqun Zhang Date: Tue Sep 13 13:22:41 2016 -0700 CGSolver: use MultiFab::linComb Src/LinearSolvers/C_CellMG/CGSolver.cpp commit ff4ce5e573862bc673b42eafec7df05cc27c1097 Author: Weiqun Zhang Date: Tue Sep 13 13:22:16 2016 -0700 add MultiFab::LinComb Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 65f4fc450ee29346672ff62745468c466c7dcf80 Author: Weiqun Zhang Date: Tue Sep 13 13:10:38 2016 -0700 BaseFab: make linInterp call linComb Src/C_BaseLib/BaseFab.H commit 4677a543d507612f335a5078c5b6ff2f70564e68 Author: Weiqun Zhang Date: Tue Sep 13 13:06:48 2016 -0700 BaseFab: specialize linComb Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 commit ac7900445f36cbc141b72895871e6a7f44797646 Author: Weiqun Zhang Date: Tue Sep 13 10:30:47 2016 -0700 BaseFab: fix new bug Src/C_BaseLib/BaseFab_nd.f90 commit 212608799a59a7ef3fbc2f3bdcd92d019eef3b9c Author: Weiqun Zhang Date: Tue Sep 13 10:11:38 2016 -0700 BaseFab: remove SPECIALIZE_?D.F Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/C_BaseLib/SPECIALIZE_1D.F Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit 2f002e1fd0567c3c0d7edce8ca6b74d05ba543ad Author: Weiqun Zhang Date: Tue Sep 13 10:08:32 2016 -0700 BaseFab: dimension agnostic minus, mult, divide, and invert Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 commit fe3f65c640cff8e25867a7b010002077270e7492 Author: Weiqun Zhang Date: Tue Sep 13 09:53:22 2016 -0700 BaseFab: dimension agnostic plus Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 commit d247ef8080b477ed9ff426f3c5b0daa740bafc56 Author: Weiqun Zhang Date: Tue Sep 13 09:40:40 2016 -0700 BaseFab: dimension agnostic norm Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 commit e59c5b210d79a23d65131eab737ebe286572d3d9 Author: Weiqun Zhang Date: Tue Sep 13 09:25:13 2016 -0700 BaseFab: dimension agnostic setval Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 commit 89bcb3d6fe30a820a9423e8bbd44aa52bbc64a81 Author: Weiqun Zhang Date: Tue Sep 13 09:05:41 2016 -0700 BaseFab: dimension agnostic copyfrommem Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 commit 8f86cfd2af8370bf31b04f5ca63169c6d5d2b871 Author: Weiqun Zhang Date: Tue Sep 13 08:51:40 2016 -0700 BaseFab: dimension agnostic copy Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 commit 73bf0e7c584bdeeff879b4e6b8651e6e4fc3e17a Author: Weiqun Zhang Date: Mon Sep 12 13:44:20 2016 -0700 move fortran saxpy routine to dimension agnostic BaseFab_nd.f90 Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BaseFab_f.H Src/C_BaseLib/BaseFab_nd.f90 Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package commit e5db468e3630f867320961df786731adfd782a7d Author: vince Date: Mon Sep 12 13:21:24 2016 -0700 test implementation of nfiles dynamic set selection. Src/C_BaseLib/VisMF.cpp Tests/IOBenchmark/GNUmakefile Tests/IOBenchmark/IOTest.cpp commit b0326d182fb86c1b02d7a1166435fc8ccf65cde9 Author: Weiqun Zhang Date: Mon Sep 12 12:30:43 2016 -0700 add bl_fort_module.F90 Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/C_BaseLib/bl_fort_module.F90 commit a4a3997267100128b15e877e85eb2be84a2298ee Author: Weiqun Zhang Date: Mon Sep 12 12:14:12 2016 -0700 clean up some GNUmakefile MiniApps/PGAS_SMC/GNUmakefile Tools/C_mk/Make.defs Tutorials/AMR_Adv_C/Exec/Make.Adv commit 69b6d74afeaf4148bb123bc0086acf55e1be3072 Author: Weiqun Zhang Date: Mon Sep 12 11:19:27 2016 -0700 add vpath %.fi Tools/C_mk/Make.rules commit 94178a0787f23f8f5656bff4aed028c6f6f64744 Author: Weiqun Zhang Date: Mon Sep 12 11:10:43 2016 -0700 set up VPATH_LOCATIONS and INCLUDE_LOCATIONS in various Make.package and add vpath ... to Make.rules so that the user does not need to do it Src/C_AMRLib/Make.package Src/C_BaseLib/Make.package Src/C_BoundaryLib/Make.package Src/C_TowerLib/Make.package Src/Extern/amrdata/Make.package Src/Extern/hpgmg/Make.package Src/F_BaseLib/FParallelMG.mak Src/LinearSolvers/C_CellMG/Make.package Src/LinearSolvers/C_CellMG4/Make.package Src/LinearSolvers/C_TensorMG/Make.package Src/LinearSolvers/C_to_F_MG/Make.package Src/LinearSolvers/F_MG/FParallelMG.mak Tools/C_mk/Make.rules commit 519e8ee1d5de71bce8f0f39f9d2d53495ca18a76 Merge: 2d31b05fd 2ea1f8acc Author: Michael Zingale Date: Sun Sep 11 10:02:50 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 2d31b05fd80b37cfef087fb266afa773a3b6a842 Author: Michael Zingale Date: Sun Sep 11 10:02:37 2016 -0400 new inputs for the merged castro + radiation Tools/RegressionTesting/Castro-SBU-tests.ini commit 2ea1f8acc0ec1ababa04f6ab5dbbed9230c255f1 Author: Weiqun Zhang Date: Fri Sep 9 14:52:51 2016 -0700 omp in TensorMG Src/LinearSolvers/C_TensorMG/DivVis.cpp commit ef975d342b79974fec903b4294480ee4667736c7 Author: Weiqun Zhang Date: Fri Sep 9 14:19:32 2016 -0700 omp in CellMG4 Src/LinearSolvers/C_CellMG4/ABec4.cpp commit 665580da15f6a50354ea39020307b0f8fccfb971 Author: Weiqun Zhang Date: Fri Sep 9 13:57:02 2016 -0700 omp in cg and remove XBLAS stuff Src/LinearSolvers/C_CellMG/CGSolver.cpp commit f9c50dedd4b2e9f553ea2fbd092c2b71ea567de5 Author: Weiqun Zhang Date: Fri Sep 9 13:56:40 2016 -0700 remove nested omp parallel Src/LinearSolvers/F_MG/itsol.f90 commit d6b582803fa4bd0e9c3579704efb206ba3f771e4 Author: Weiqun Zhang Date: Fri Sep 9 13:43:42 2016 -0700 fix assertion Src/C_BaseLib/BoxArray.cpp commit 70322ab9034b0a6a77704702b9e20087ab30fd46 Author: Weiqun Zhang Date: Fri Sep 9 09:45:40 2016 -0700 use BL_ASSERT for calls to contains_nan Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 455170e92a6c0f2bec362ce66e292c65406f0860 Author: Weiqun Zhang Date: Fri Sep 9 09:21:01 2016 -0700 remove the fast version of contains function from Cluster.cpp and incorporate it into BoxArray class Src/C_AMRLib/Cluster.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit ed6fc46764fffd9e5f7d947f48d78a0a5ea7df9c Author: vince Date: Thu Sep 8 17:57:51 2016 -0700 test implementation of nfiles dynamic set selection. not complete. Tests/IOBenchmark/IOTest.cpp commit 871455cab87a10e36c3c0a463170018ee2d46928 Author: vince Date: Thu Sep 8 17:39:58 2016 -0700 more io notes. Docs/Readme.io commit 8ec8008f2d76a1f7add87e84b86b10bcff015601 Author: vince Date: Thu Sep 8 17:39:27 2016 -0700 test inputs. Tests/IOBenchmark/inputs Tests/IOBenchmark/inputs.dss Tests/IOBenchmark/inputs.nft commit e3a879e1b4144001d1875d4f804165d85a373bf8 Author: vince Date: Thu Sep 8 17:38:28 2016 -0700 test for nfiles dynamic set selection. Tests/IOBenchmark/IOTestDriver.cpp commit 80dd25c11867536405f813ddfb47feb8bb5248dd Author: Weiqun Zhang 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 Date: Thu Sep 8 17:11:43 2016 -0700 comment Src/C_BoundaryLib/BndryData.cpp commit 94330293631b9b0841439b376fff08748ea321d4 Author: Weiqun Zhang Date: Thu Sep 8 17:01:01 2016 -0700 tiling in FabArray::BuildMask Src/C_BaseLib/FabArray.H commit 921326919c1ef7ad80bc13cea710948daac081c5 Author: Weiqun Zhang 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 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 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 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 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 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 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 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 Date: Wed Sep 7 11:55:06 2016 -0700 use buffer size function. Src/C_BaseLib/Particles.H commit 81128c082a995cdbb380c97a192818f5caf708d5 Merge: 391256842 89acb8e00 Author: Weiqun Zhang Date: Wed Sep 7 10:02:22 2016 -0700 Merge branch 'development' into weiqun/multimask commit 89acb8e008f1e833efb7fb4638972fae238afd91 Author: Weiqun Zhang Date: Wed Sep 7 09:53:14 2016 -0700 minor Src/C_BaseLib/BoxArray.cpp commit e99605ff30550686ef2264c9b374071458c6df2c Author: Weiqun Zhang Date: Wed Sep 7 09:10:33 2016 -0700 Cluster: if there is a tie, z-direction has the highest precedence whereas x-direction the lowest. This is more likely to generate boxes with the longest dimension in x. Src/C_AMRLib/Cluster.cpp commit 860c18c75f9a7a0c8d55f38022e86cf429cb55ff Author: Weiqun Zhang Date: Wed Sep 7 08:36:52 2016 -0700 clean up fpb Src/C_BaseLib/BLPgas.H Src/C_BaseLib/BLPgas.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 5aaf35a3f184f7246d75b116f53f03799df523b4 Author: vince Date: Tue Sep 6 15:30:59 2016 -0700 long seeks and separate tags for reads and signals. Src/C_BaseLib/VisMF.cpp commit fc66fe206b2b1b27ab57548b2b77d9f9861bf771 Author: vince Date: Tue Sep 6 15:28:41 2016 -0700 updated comment. Src/C_BaseLib/ParallelDescriptor.H commit cdca79623bd27b6e90e6ec407d5afb842c7b7d32 Author: Weiqun Zhang Date: Tue Sep 6 13:30:30 2016 -0700 fix the new FabSet::Copy: cannot use MultiFab::Copy Src/C_BoundaryLib/FabSet.cpp commit 9eb9faef59aed6e2888805becd4c64562ff51dc2 Author: Weiqun Zhang Date: Tue Sep 6 11:24:52 2016 -0700 add static local Copy function for FabSet and BndryRegister Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 6b3de59aec4088b2d3a7277273745bc40bf7f35d Author: Weiqun Zhang Date: Tue Sep 6 11:09:48 2016 -0700 BoxLib::match: shortcut when BoxArrays are equal (i.e., ==) Src/C_BaseLib/BoxArray.cpp commit 91a1aa1c203b4c9723e6669f13197ea999672f9d Author: Weiqun Zhang Date: Tue Sep 6 10:17:17 2016 -0700 When provided with BoxArray, StateData::restart will use the provided one and make sure it matches the one in the istream. This helps reduce duplicated BoxArrays. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit a6d4c69cc4cb5a0d8cff091359b693c9d834fe73 Author: Weiqun Zhang Date: Tue Sep 6 09:51:53 2016 -0700 add BoxLib::match that returns ture if the boxes returned by operator[] in two BoxArrys match. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 19da91cdad8ef14af6702402b3d1f33a435fa924 Merge: b46583396 05926f7ac Author: Michael Zingale Date: Mon Sep 5 22:58:04 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit b465833965d0f103119e909551a94d16cfc7eb13 Author: Michael Zingale Date: Mon Sep 5 22:57:23 2016 -0400 add the ability to put the point we slice through at the lower left instead of the center of the domain. Tools/Postprocessing/F_Src/fextract.f90 commit 05926f7ac7ea3e1defac6d8828870eb1b1ceeeae Author: Weiqun Zhang Date: Fri Sep 2 14:56:34 2016 -0700 FillCoarsePatch: call bc function to fill physical boundaries instead of interploating Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.cpp commit 1b847063e0e5c9446b1f198bc40d31a1e9373c27 Author: Weiqun Zhang Date: Fri Sep 2 11:09:15 2016 -0700 minor clean up Src/C_BaseLib/Geometry.cpp commit c957058221c8d12607cdf064518af5ccf6355c18 Author: Weiqun Zhang Date: Fri Sep 2 11:06:16 2016 -0700 assertion Geometry::Setup is not called inside omp parallel Src/C_BaseLib/Geometry.cpp commit 102872089e7d570d3740999cb9e761b46c4ee522 Author: Weiqun Zhang Date: Fri Sep 2 10:50:09 2016 -0700 rm deprecated Geometry::FillPeriodicBoundary and Geometry::PeriodicCopy Src/C_AMRLib/Amr.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit af3b040bf410bbcc4cd3df6b9d73848726fcd1f5 Author: Weiqun Zhang Date: Thu Sep 1 10:16:49 2016 -0700 call various Initialize() in BoxLib::Initialize() to ensure thread safety Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/IArrayBox.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/iMultiFab.cpp commit 3c29d664ae1b9d23d2d570c18428b3e16b54a136 Author: Weiqun Zhang Date: Thu Sep 1 08:30:29 2016 -0700 Release Notes 16.09 ReleaseNotes/release-notes-16.09 commit 2ed19502810c534428cf6d68abc14afca948a240 Merge: 1398a3ff8 4aa17a383 Author: Weiqun Zhang Date: Thu Sep 1 08:29:30 2016 -0700 Merge branch 'master' into development Conflicts: Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/FabArray.H commit f8704739908324cd4015bee58491694c2a223804 Author: vince Date: Wed Aug 31 15:44:44 2016 -0700 close persistent streams before each test. Tests/IOBenchmark/IOTest.cpp commit 8bc4cd560afc718f4f1291743c00ea9981eb254d Author: vince Date: Wed Aug 31 14:57:50 2016 -0700 added more test options. Tests/IOBenchmark/IOTestDriver.cpp Tests/IOBenchmark/inputs commit 44b970156bc22f212c5d61a172f2fa5b0d7a63ac Author: vince Date: Wed Aug 31 14:56:25 2016 -0700 implemented persistent streams for reading. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 839e42139dfc25a08377c9c78b70f80f39552cac Author: vince Date: Wed Aug 31 14:54:54 2016 -0700 changed default buffer size. Src/C_BaseLib/ParallelDescriptor.cpp commit db95bff08514b9f9c712858187bf0fe1354c9b96 Author: vince Date: Wed Aug 31 10:54:26 2016 -0700 changed default buffer size. Src/C_BaseLib/FabConv.cpp commit 1398a3ff80ffd58eb35b75c7a6992e51b4f89761 Merge: b9ccda63f 6266695a0 Author: Michael Zingale Date: Wed Aug 31 13:12:21 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit b9ccda63f33fb5fa018a771aa62ff50d81acba19 Author: Michael Zingale Date: Wed Aug 31 13:11:59 2016 -0400 print out zone info for the biggest error zone to make Dr. Katz happy :) Tools/Postprocessing/F_Src/fcompare.f90 commit 6266695a0875133324d03fc44d70fc3544bb4d5c Author: Weiqun Zhang Date: Tue Aug 30 20:31:58 2016 -0700 BoxLib::InterpFromCoarseLevel(): fix box type Src/C_AMRLib/FillPatchUtil.cpp commit 046cfca3da94c0fd2627955c194088bf2fd4d8e1 Author: Weiqun Zhang Date: Tue Aug 30 20:23:32 2016 -0700 fix BoxLib::InterpFromCoarseLevel() Src/C_AMRLib/FillPatchUtil.cpp commit 1495f9cc268700f33bace73ee96d3b28dfc5ff95 Author: Weiqun Zhang Date: Tue Aug 30 16:47:05 2016 -0700 add BoxLib::InterpFromCoarseLevel() Src/C_AMRLib/FillPatchUtil.H Src/C_AMRLib/FillPatchUtil.cpp commit efe65a4051078bd048abb0001d032af5e6a13dad Author: Weiqun Zhang Date: Tue Aug 30 18:06:20 2016 -0400 Revert "protect FArrayBox::Initialize with omp single because it is not thread safe" This reverts commit 2f44eda2d24eaa5063650ba714bb886359b87d9f. Src/C_BaseLib/FArrayBox.cpp commit b201405c356509182a5fee86ccdfb924a824670a Author: Weiqun Zhang Date: Tue Aug 30 17:37:22 2016 -0400 fix the fix (but I think it's compiler's fault): In MultiFab::Iniitialize, construct a FArrayBox so that the FArrayBox class will be properly initialized. Src/C_BaseLib/MultiFab.cpp commit 2f44eda2d24eaa5063650ba714bb886359b87d9f Author: Weiqun Zhang Date: Tue Aug 30 16:42:37 2016 -0400 protect FArrayBox::Initialize with omp single because it is not thread safe Src/C_BaseLib/FArrayBox.cpp commit 1513952fb063846c7f1f7f5b9d4e0462f27574a0 Author: Weiqun Zhang Date: Tue Aug 30 13:14:03 2016 -0400 Insert flush() between writing header and data to get around a bug (?) on Titan. Src/C_BaseLib/FArrayBox.cpp commit 029754cbb749279ebd33e7e1d70b64aeea82b0f3 Author: Weiqun Zhang Date: Mon Aug 29 15:18:46 2016 -0700 given a MultiFab filled with weights, make a KnapSack DistributionMapping Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 2127bbb4639a41806bdac6ab42c113492b49ace0 Author: vince Date: Thu Aug 25 18:35:18 2016 -0700 more support for persistent streams. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 64411fb997327396c9f15ee0ff8cc7da64ab6f86 Author: vince Date: Thu Aug 25 18:34:23 2016 -0700 level directory creation setting. Src/C_AMRLib/AmrLevel.H commit 72f3433e0920ea315fb07755011bdbb80117ef1f Author: vince Date: Thu Aug 25 18:33:25 2016 -0700 add more parmparse options. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit d6cff30fb8ff97915f350546692a8312c3fbf27b Author: Weiqun Zhang Date: Thu Aug 25 17:41:17 2016 -0700 because the do_async_sends flag is ignored by FillBoundary now, we should not test that flag in WaitForAsyncSends Src/C_BaseLib/FabArray.H commit f979d9bdc1b53b3c724ce22dfe1d702f4a3dc65e Author: Weiqun Zhang Date: Thu Aug 25 17:21:59 2016 -0700 remove calls to BoxLib::fill_boundary because it is deprecated Tutorials/MultiFab_C_F/main.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp commit df4eedff0822d71ae9ed61596fe5fed3cb6eb679 Author: vince Date: Thu Aug 25 15:53:53 2016 -0700 more io tasks. Docs/Readme.io commit 72a4900c43ca27c9058ee4082c0802342ed22bac Author: vince Date: Thu Aug 25 12:24:07 2016 -0700 check for sufficient memory for single reads and writes. Src/C_BaseLib/VisMF.cpp commit 2f6a34d8ea45fe6b29d763dd597efbaab2d1665b Author: vince Date: Thu Aug 25 11:45:35 2016 -0700 format, set version for plot files. Src/C_AMRLib/Amr.cpp commit ebae10cefc6aa9aa07b253ac214cb391b327a40e Author: vince Date: Wed Aug 24 18:20:01 2016 -0700 added use single read and write code. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 4aa3624f029bc63e127f0d8b4586681d4489b991 Author: Weiqun Zhang Date: Wed Aug 24 17:32:35 2016 -0700 remove Geometry::SumPeriodicBoundary Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 204c107c619e1ef606f210d37898244ab8fa0edd Author: vince Date: Wed Aug 24 17:18:28 2016 -0700 add use single read and write parmparse variables. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 37271db05377b25ab92d28a2dd37e5bb73b7b514 Author: Weiqun Zhang Date: Wed Aug 24 16:57:09 2016 -0700 use MulitFab::SumBoundary for periodic boundaries too. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/Particles.H commit 7e3a41b68846bb270ed669599c46be2df5653763 Author: vince Date: Wed Aug 24 16:11:37 2016 -0700 statedata support for prereading fabarray headers. Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 022d26f337d3aacf7c8d7a54e78281847f9eae78 Author: vince Date: Wed Aug 24 14:46:09 2016 -0700 fix for in file order. Src/C_BaseLib/VisMF.cpp commit 226fb95ab85821ab519d547a50d753fb9df402df Author: Weiqun Zhang Date: Wed Aug 24 14:43:36 2016 -0700 fix MemProfiler by casting lambda functions into std::function with the correct type. Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MemPool.cpp Src/C_BaseLib/MultiFab.cpp Src/F_BaseLib/MemProfiler_f.cpp commit 2e8c9482249db67f109e40dbbcfd130464f46c02 Author: Weiqun Zhang Date: Wed Aug 24 13:18:26 2016 -0700 remove const from return type Tools/C_scripts/buildInfo.H Tools/C_scripts/makebuildinfo_C.py commit b2db3d6fe23fb89c7173a931b5d539715eb6cade Author: Weiqun Zhang Date: Wed Aug 24 13:11:38 2016 -0700 Add template argument to BATBase otherwise some compilers are not happy. Src/C_BaseLib/BoxArray.H Src/C_BoundaryLib/BndryRegister.cpp commit 4f17b8fa951304eccdcfc7d03818b457cb05b500 Merge: 9db9e2af7 3f38888e2 Author: Weiqun Zhang Date: Wed Aug 24 12:21:27 2016 -0700 Merge branch 'development' into weiqun/work Conflicts: Src/C_BaseLib/CMakeLists.txt commit 4aa17a3831426bb3929f8257072601df9f09eb7d Author: Ann Almgren Date: Wed Aug 24 09:55:48 2016 -0700 We need to add the line include_directories(${CBOXLIB_INCLUDE_DIRS}) to the CMakeLists.txt so that backtrace_c.cpp can find BLBackTrace.H (which is in C_BaseLib). Src/F_BaseLib/CMakeLists.txt commit 3f38888e230da72cd89142105c294fd1b01cc91e Author: Ann Almgren Date: Wed Aug 24 09:55:48 2016 -0700 We need to add the line include_directories(${CBOXLIB_INCLUDE_DIRS}) to the CMakeLists.txt so that backtrace_c.cpp can find BLBackTrace.H (which is in C_BaseLib). Src/F_BaseLib/CMakeLists.txt commit 5987a781bd81329b6ec6c5d162975e7a4b1e7d8f Author: Weiqun Zhang Date: Wed Aug 24 06:27:05 2016 -0700 fix assertion: the recvcount and disp vections are insignificant on non-root processes. Src/C_BaseLib/ParallelDescriptor.H commit 3337f6b321cbd9e59ad2c787fe95f85e3c192db1 Author: Weiqun Zhang Date: Tue Aug 23 21:57:57 2016 -0700 TagBoxArray::collate: use the long version of ParallelDescriptor::gatherv to avoid interger overflow. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 338020123665fa43cee52efc5746a4b18dd4ed3e Author: Weiqun Zhang Date: Tue Aug 23 21:16:45 2016 -0700 add two version of ParallelDescriptor::gatherv: one takes int as offset and the other takes long. The int version calls MPI_gatherv. The long version uses MPI_Irecv and MPI_Send because MPI does not support using long as offset in MPI_gatherv. Src/C_BaseLib/ParallelDescriptor.H commit 771a7133f3afe420fb8ca726d9fa1ce7929ca12e Author: Weiqun Zhang Date: Tue Aug 23 20:56:43 2016 -0700 add a non-const version of IntVect::getVect Src/C_BaseLib/IntVect.H commit 42bbff243804e2153ff5c7f14a1aae27d9be95a6 Author: vince Date: Tue Aug 23 15:11:27 2016 -0700 added option to preread and broadcast all multifab headers to avoid synchronization during restart. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 9db9e2af752f361300195dc2516aa071f9396596 Author: Weiqun Zhang Date: Tue Aug 23 12:42:28 2016 -0700 Extrapolater: should still use masks even after setting all crse cells to zero first because these cells get updated. Src/C_AMRLib/extrapolater_2d.f90 Src/C_AMRLib/extrapolater_3d.f90 commit 16eb9f192ade0a4e96b83cd54467a09546a3a538 Author: Weiqun Zhang Date: Mon Aug 22 17:32:14 2016 -0700 tidy Src/C_AMRLib/extrapolater_3d.f90 commit 709c59024afa8c6b0a29c31bd21270e6209ac917 Author: Weiqun Zhang 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 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 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 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 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 Date: Mon Aug 22 12:08:03 2016 -0700 remove old code. Src/C_AMRLib/Amr.cpp commit 98a784a097208d7247f408225c4aadadb38617bf Author: vince Date: Mon Aug 22 11:59:58 2016 -0700 formatting. Src/C_AMRLib/StateData.cpp commit 3922379dcdabdc3de293e0ab5f07e43b3b74315a Author: vince Date: Mon Aug 22 11:06:34 2016 -0700 formatting. Src/C_AMRLib/Amr.cpp commit 80f631d56f4574d2045f98e850426753bd7d5728 Author: Weiqun Zhang Date: Sun Aug 21 16:41:16 2016 -0700 FillBoundary: return immediately if there are no ghost cells Src/C_BaseLib/FabArray.H commit 27e9961bb27077e131a3447c7d09a24c18197f28 Author: Weiqun Zhang Date: Sun Aug 21 16:32:51 2016 -0700 EnforcePeriodicity: return immediately if there is no periodic boundaries Src/C_BaseLib/FabArray.H commit 6a06f33f6961032e8399d9250126fc20df514787 Author: Weiqun Zhang Date: Sun Aug 21 16:20:36 2016 -0700 FabArray::BuildMask: treat ghost cells outside periodic boundaries as normal ghost cells not physical boundary cells Src/C_BaseLib/FabArray.H commit 23a65ae20f87dbe4994ea6be36ef6af97daf83fd Author: Weiqun Zhang Date: Sun Aug 21 16:01:41 2016 -0700 minor name changes Src/C_BaseLib/FabArray.H commit 6bb1526420b4b134daf9650c85a7c4bc23fe9036 Author: Weiqun Zhang Date: Sun Aug 21 15:36:27 2016 -0700 move iMultiFab::buildMask to FabArray::BuildMask so that it becomes a template Src/C_AMRLib/Extrapolater.H Src/C_AMRLib/Extrapolater.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/iMultiFab.H Src/C_BaseLib/iMultiFab.cpp commit 1c34b28b631a82f13a0acb619de73b7164ea18b8 Author: Weiqun Zhang Date: Sat Aug 20 12:46:11 2016 -0700 EnforcePeriodicity: allow ghost cells to be source Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 994a90e816241dc5f4f81450ac0cc71d73619324 Author: Weiqun Zhang Date: Sat Aug 20 12:14:52 2016 -0700 Extrapolater: set coarse cells to zero first to ensure there are no NaNs Src/C_AMRLib/extrapolater_2d.f90 Src/C_AMRLib/extrapolater_3d.f90 commit 3063f0ded5d77fc834f1dc6b9c355f016531cf26 Author: vince Date: Fri Aug 19 15:52:28 2016 -0700 set relative path. Src/C_BaseLib/VisMF.cpp commit cb353640091c8bab3f82405e3340f1b6fb9a2dea Author: vince Date: Fri Aug 19 15:51:57 2016 -0700 option to precreate checkpoint directories to avoid a barrier at each level. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 683fdd229750afd8af15e9b3bc834c3067089e8f Author: vince Date: Fri Aug 19 15:50:18 2016 -0700 more io notes. Docs/Readme.io commit 8bb1537fab6f37fe121be1e5bdfcff1c2b38b75d Author: vince Date: Thu Aug 18 17:56:10 2016 -0700 add nstreams readers. Src/C_BaseLib/VisMF.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/IOBenchmark/inputs commit c7b76169354bde2bcf2cf33814342d231533b944 Author: Weiqun Zhang Date: Thu Aug 18 15:42:48 2016 -0700 Extrapolater: fix bugs Src/C_AMRLib/extrapolater_3d.f90 commit eadafe0c8c8cc41f50e20cf435820b57fac4e321 Author: Weiqun Zhang Date: Thu Aug 18 15:35:50 2016 -0700 Extrapolater: fix a bug Src/C_AMRLib/extrapolater_3d.f90 commit 2f6e243b3eead7b494b721d9d8ead6732692bc74 Author: Weiqun Zhang Date: Thu Aug 18 15:07:08 2016 -0700 Extrapolater: fix index bug Src/C_AMRLib/extrapolater_2d.f90 commit aff43705290e1003bd114cb7847d5ac6af6466d4 Author: Weiqun Zhang Date: Thu Aug 18 14:54:43 2016 -0700 let Extrapolater build the mask Src/C_AMRLib/Extrapolater.H Src/C_AMRLib/Extrapolater.cpp commit c5ced5d457fbc4a8d52c48373d7e1ed5e4c9190b Author: Weiqun Zhang Date: Thu Aug 18 12:21:59 2016 -0700 Add Extrapolater to replace IAMR functions for extraploating viscout terms. Src/C_AMRLib/CMakeLists.txt Src/C_AMRLib/Extrapolater.H Src/C_AMRLib/Extrapolater.cpp Src/C_AMRLib/Make.package Src/C_AMRLib/extrapolater_1d.f90 Src/C_AMRLib/extrapolater_2d.f90 Src/C_AMRLib/extrapolater_3d.f90 Src/C_BaseLib/iMultiFab.H Src/C_BaseLib/iMultiFab.cpp commit 7ae16f6351bebe9149edc0b5cad06b40204c7e6d Author: vince Date: Thu Aug 18 13:55:23 2016 -0700 removed diagnostics, added timer. Src/C_BaseLib/VisMF.cpp commit 1fdcde08b4ace67239ff75660017de65867a2d1c Author: vince Date: Thu Aug 18 13:32:41 2016 -0700 file order fabarray reads. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 20e04134ff9c812709f1a62f5dbe695a231f73d1 Author: Ann Almgren Date: Thu Aug 18 11:54:05 2016 -0700 Update CMakeLists.txt to reflect the fact that Particles* have moved from C_AMRLib to C_BaseLib and also to include PhysBCFunct.H and ParGDB.H in C_BaseLib/CMakeLists.txt Src/C_AMRLib/CMakeLists.txt Src/C_BaseLib/CMakeLists.txt commit b88556c16f24d7446e7b55aa667766b27b77a71c Author: Ann Almgren Date: Thu Aug 18 11:54:05 2016 -0700 Update CMakeLists.txt to reflect the fact that Particles* have moved from C_AMRLib to C_BaseLib and also to include PhysBCFunct.H and ParGDB.H in C_BaseLib/CMakeLists.txt Src/C_AMRLib/CMakeLists.txt Src/C_BaseLib/CMakeLists.txt commit 4fbf9009479bc2f21c081f865e734645f7c052e6 Author: Weiqun Zhang Date: Wed Aug 17 16:35:42 2016 -0700 new function iMultiFab::buildMask Src/C_BaseLib/iMultiFab.H Src/C_BaseLib/iMultiFab.cpp commit 98b37b9ea69eaca81a9b740fcc97d5cc28520380 Author: vince Date: Wed Aug 17 14:35:35 2016 -0700 changed mf name. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 9e4d7b89737af6d76cd811e750fef0b11c8ff4f1 Author: Weiqun Zhang Date: Wed Aug 17 14:31:09 2016 -0700 tweak FabArrayBase::TheFB interface Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp commit 8c332365a9566920273dc7d22ff12033ad6e3fbd Author: vince Date: Wed Aug 17 14:15:41 2016 -0700 calculate header offsets. Src/C_BaseLib/VisMF.cpp commit efe5713d0b69d8b6e9ac4bcb700986e5f6e699a4 Author: Weiqun Zhang Date: Wed Aug 17 13:58:59 2016 -0700 clean up iMultiFab Src/C_BaseLib/iMultiFab.H Src/C_BaseLib/iMultiFab.cpp commit 08b812a83d613fc13bceb9140b435749c44e0054 Author: Weiqun Zhang Date: Wed Aug 17 13:50:24 2016 -0700 FillPeriodicBoundary --> EnforcePeriodicity Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp commit 1afc15b3cee93b8d28c1b74e6dfb2b964553a7aa Author: Weiqun Zhang Date: Wed Aug 17 13:42:47 2016 -0700 clean up outdated stuff Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 05284ad6fac4ab3b499c8ce750720d0a53773d55 Author: Weiqun Zhang Date: Wed Aug 17 13:38:03 2016 -0700 simplify the way of filling boundary corners Src/LinearSolvers/C_CellMG4/ABec4.cpp commit 3770ed59cd72b4ccf5e04c6873f04de80f9eead5 Author: Weiqun Zhang Date: Wed Aug 17 13:09:36 2016 -0700 a number of small changes related to FillBoundary interface Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Tests/C_BaseLib/tFB.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/PGAS_HEAT/main.cpp Tutorials/PIC_C/solve_with_hpgmg.cpp Tutorials/Tiling_Heat_C/main.cpp commit 1f87a4376542c2a5664f5aa452440708049140ec Author: Weiqun Zhang Date: Wed Aug 17 12:31:23 2016 -0700 assertion that FillBoundary's (cell-centered verions) BoxArray is non-overlapping Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 0f9460c0ba818ae4cefedc8bf37307f95223eec4 Author: Weiqun Zhang Date: Wed Aug 17 12:28:15 2016 -0700 add BoxLib::convert for BoxArray Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 19e13f8a363362f0ce637e4a919ed788ae0051ba Author: Weiqun Zhang Date: Wed Aug 17 12:14:32 2016 -0700 add assertion and comments Src/C_AMRLib/FillPatchUtil.cpp Src/C_BaseLib/FabArray.cpp commit 4e5f268695bb43f4a1a7858a435bf918f30bc8dd Author: Weiqun Zhang Date: Wed Aug 17 11:20:36 2016 -0700 use FillBoundary for periodic boundaries MiniApps/PGAS_SMC/SMC_advance.cpp Src/F_Interfaces/BaseLib/multifab_fi.cpp commit a59257d276bcc2b265bc381e6153f60612fde888 Author: Weiqun Zhang Date: Wed Aug 17 10:56:43 2016 -0700 fix thread safety for FabArray::EnforcePeriodicity Src/C_BaseLib/FabArray.cpp commit 7fb3e909dc30e8689dbfbcd59e94a905e72eb0c8 Author: vince Date: Tue Aug 16 16:59:17 2016 -0700 removed old test function. Tests/IOBenchmark/IOTest.cpp commit 6324f562ca8bb53083ce69319d64c9a89bcb8f87 Author: Weiqun Zhang Date: Tue Aug 16 16:52:34 2016 -0700 fix bind c name for PGI MiniApps/PGAS_SMC/chemistry_module.f90 MiniApps/PGAS_SMC/derivative_stencil.f90 MiniApps/PGAS_SMC/init_data.f90 MiniApps/PGAS_SMC/kernels.f90 MiniApps/PGAS_SMC/make_plot.f90 MiniApps/PGAS_SMC/transport_properties.f90 MiniApps/PGAS_SMC/variables.f90 commit 9a9cd4734ed571756a519e104fa5f8242a6d433a Author: vince Date: Tue Aug 16 16:48:43 2016 -0700 removed debugging diagnostics. Src/C_BaseLib/VisMF.cpp commit 00963b39a0aee866e18b7a495fc37bcc40c7fc33 Author: vince Date: Tue Aug 16 16:45:25 2016 -0700 added NFiles. Src/C_BaseLib/CMakeLists.txt commit c9f95701957190fdaf5e65400b5b69b697ee42f6 Author: vince Date: Tue Aug 16 16:27:01 2016 -0700 removed test functions. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 85f4e608db5c05975f94915d8a8853ec2e3daa7d Author: vince Date: Tue Aug 16 16:26:28 2016 -0700 more notes. Docs/Readme.io commit b48bd055bf966b1ef57a26c79d53a6c57b0f8958 Author: vince Date: Tue Aug 16 16:21:51 2016 -0700 consolidate write functions for all formats. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit eb3a3fa29a81fe470a14bd8380072eb905a97df8 Author: vince Date: Tue Aug 16 16:20:40 2016 -0700 consolidate nfiles write tests for the new formats. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/IOBenchmark/inputs commit 5579ba6b3a7751b8182a6d81fe3aebc5ad95241e Author: vince Date: Tue Aug 16 15:06:42 2016 -0700 calculate offsets for old version without communication. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit fa6d37a287d82e39a29eef2f8213c933601818fb Author: vince Date: Tue Aug 16 11:20:20 2016 -0700 change names to be more general. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/IOBenchmark/inputs commit 5e055d0d0a42e9b23189ed9206d89ed170ac8d2a Author: Weiqun Zhang Date: Tue Aug 16 07:42:31 2016 -0700 FabArray::EnforcePeriodicity: use a bool flag instead of a domain box Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/Periodicity.H Src/C_BaseLib/Periodicity.cpp commit 4e3bff7cd0811de3b9ce1eb26d3534d6c4e86795 Author: Weiqun Zhang Date: Mon Aug 15 23:23:12 2016 -0700 fix EnforcePeriodicity function Src/C_BaseLib/FabArray.H commit 9c4546cfbefdadae32191bbd42bcb4787d0f2958 Author: Weiqun Zhang Date: Mon Aug 15 23:14:43 2016 -0700 FabArray::EnforcePeriodicity() Src/C_BaseLib/Box.H Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp commit b9def673244f6e3383acc322fc36c92e97c823ff Author: vince Date: Mon Aug 15 19:01:44 2016 -0700 combine write functions. Tests/IOBenchmark/IOTest.cpp commit 14edacb60a601562938d68836037e55102302802 Author: vince Date: Mon Aug 15 19:01:09 2016 -0700 combine write functions. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 6d81218c8155a61ddf02c53ea9b34231074eaff4 Author: Weiqun Zhang Date: Mon Aug 15 16:11:27 2016 -0700 remove FabArrayBase::SetSendTag and SetRecvTag because IAMR SyncRegister no longer needs them Src/C_BaseLib/FabArray.H commit 3712af23880eedc967ff68d61c6b36da2127524d Author: Ann Almgren Date: Fri Aug 12 16:01:12 2016 -0700 Add an option for setting constant coefficients for a nodal solve. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 85eda5859c490d179034de8fb4394ebd16c000e0 Author: Weiqun Zhang Date: Fri Aug 12 13:13:33 2016 -0700 remove nested omp parallel. they seem to cause some problems. Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/INTERP_3D.F commit e8551deb8c7bdbfe7a15d01f8993a7ddf2ebca3c Author: Brian Friesen Date: Thu Aug 11 21:45:56 2016 -0700 Remove last bits of old sidecar implementation. The new stuff doesn't need it. Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.cpp Src/F_BaseLib/parallel.f90 commit 6d0f19d37b5929f35360b220d7ebdb9caa351362 Author: Brian Friesen Date: Tue Aug 9 12:57:01 2016 -0700 C_mk: add SDE ifdef for using Intel SDE for FLOP counting Tools/C_mk/Make.defs commit 9c63724f8cbe07970e61d2f6bd5c2a8d996cdd5d Author: Weiqun Zhang Date: Thu Aug 11 21:53:48 2016 -0700 remove unused variable Src/C_BaseLib/CArena.cpp commit 6e699ac172bc6d76830b153de5aeee7e1c39a264 Author: vince Date: Thu Aug 11 17:22:57 2016 -0700 native reads, fixes for vis with no min max values in the header. Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit a0b782ef7a9c266caee5ba0d055396bf0bfc773d Author: Weiqun Zhang Date: Thu Aug 11 12:40:02 2016 -0700 Fabset::plusFrom takes Periodicity argument Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 504fc67c5a0a65de47d3d9074d0e827240b79ed8 Author: vince Date: Wed Aug 10 18:26:54 2016 -0700 implemented new vismf reads for file order reads. not finished yet. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit d424b89a163736a96b1f99aa0f18941270535292 Author: vince Date: Wed Aug 10 18:24:30 2016 -0700 added consts. Tests/IOBenchmark/IOTest.cpp commit e232c3b8b7137eaf0e1ee89cf5b6b35fe3d988d8 Author: vince Date: Wed Aug 10 16:49:48 2016 -0700 added functions for reading. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit 9ef0c90eadd4bdcec22a3e97d5ed304d2656d2a0 Author: vince Date: Wed Aug 10 16:46:23 2016 -0700 added more inputs. Tests/IOBenchmark/inputs commit 8ec0a697d7a05faadd94139fd4c3d1c449bf5d69 Author: Andy Nonaka Date: Wed Aug 10 15:45:47 2016 -0700 you can pass in an optional argument to ml_cc_solve, ok_to_fix_singular=.false. (default true). If false, the multigrid solver will not subtract off the average of the RHS for singular matrices. Useful for debugging singular problems if you want to see, e.g., if S integrates to zero for low mach codes, or if total charge integrates to zero for electrostatic potential solves. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit 335a2f365a0f07960bd936a146a92ad5de58e042 Merge: 17abee428 7c646acd6 Author: Weiqun Zhang Date: Wed Aug 10 14:23:38 2016 -0700 Merge branch 'development' into weiqun/work commit 17abee428f7c1f659ddb1cfe1255c49c2e19721a Author: Weiqun Zhang Date: Wed Aug 10 13:22:53 2016 -0700 minor Src/C_AMRLib/FillPatchUtil.cpp commit f2b8718bd13a074f48c0779e8d3e095af48faab6 Author: Weiqun Zhang Date: Wed Aug 10 13:06:08 2016 -0700 add static function Periodicity::NonPeriodic() for clarity Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/Periodicity.H Src/C_BaseLib/Periodicity.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit d0dc3b9cd4a3392044c43cba68d2bb6a03066a9f Author: Weiqun Zhang Date: Wed Aug 10 12:55:56 2016 -0700 use FabArray::copy for periodic copy Src/C_AMRLib/FillPatchUtil.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 7c646acd65b2ce53700b8d04d96a9eb61ad590bf Author: Andy Nonaka Date: Wed Aug 10 12:51:08 2016 -0700 call parallel reduce only on elements in an array which are initialized. Otherwise code would crash Src/LinearSolvers/F_MG/ml_cc.f90 commit 71bca54d650e47d61d5180f9573975a209c54eea Author: Weiqun Zhang Date: Wed Aug 10 12:45:27 2016 -0700 FabArray::copy does periodic copy too Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 9d59112c89ff5d25ca6cd3e3db8e9ccf6ea1fe5b Author: vince Date: Wed Aug 10 12:31:33 2016 -0700 more io tests. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/IOBenchmark/inputs commit b82877c83361cad10916ac4f300f80da06f9c8a9 Author: Weiqun Zhang Date: Wed Aug 10 11:11:50 2016 -0700 FabArray::copy: add a new Periodicity argument Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BoundaryLib/FabSet.cpp commit 9fa0b1d9c6ac43f94a983175913ccce8faac2007 Merge: 2f9dba79d c47bc1a3b Author: Weiqun Zhang Date: Wed Aug 10 10:53:40 2016 -0700 Merge branch 'development' into weiqun/work Conflicts: Src/C_BaseLib/FabArray.H commit 2f9dba79d58cc4851b182686eb7f40eed94069e6 Author: Weiqun Zhang Date: Tue Aug 9 21:16:33 2016 -0700 minor optimization Src/C_BaseLib/FabArray.cpp commit 2efd0bce04647018f13e8af29680895e5af18e4d Author: Weiqun Zhang Date: Tue Aug 9 18:13:39 2016 -0700 fix new bug Src/C_BaseLib/FabArray.cpp commit c290274efa30c47e89aa709a72ee1e0db6108491 Author: Ann Almgren Date: Tue Aug 9 17:55:17 2016 -0700 Needed to move the computation of coeff_sum and coeff_max ahead of the singular test on rh -- this meant separating back out the parallel reductions. Src/LinearSolvers/F_MG/ml_cc.f90 commit 19f8c921547a7cb99b270d523dba8988a8c7883d Merge: 5817fa28d c47bc1a3b Author: Ann Almgren Date: Tue Aug 9 17:42:52 2016 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 5817fa28d24c39d00e700421ec2647c43e01bd97 Author: Ann Almgren Date: Tue Aug 9 17:42:24 2016 -0700 Impose solvability on rh not res at the start of ml_cc -- we need to do this because res is recomputed as rh - L(full_soln) after each cycle. Src/LinearSolvers/F_MG/ml_cc.f90 commit df9064d3b5008a8498729c482df9a9824ce0fc8d Author: vince Date: Tue Aug 9 17:29:50 2016 -0700 started implementing new FabArray reads. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Tests/IOBenchmark/GNUmakefile commit 9cafc7ff4ef6f618823c494fabd50441a1957003 Author: vince Date: Tue Aug 9 17:22:50 2016 -0700 more io notes. Docs/Readme.io commit c47bc1a3b517480a9abd696e75b050fc030487a9 Author: Weiqun Zhang Date: Tue Aug 9 16:13:19 2016 -0700 update the regtest clean script Tools/RegressionTesting/reg_test_gc.py commit b2ab1a535420a92e4b56666565ccf0dcb7138f06 Author: vince 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 Date: Tue Aug 9 15:45:28 2016 -0700 more notes. Docs/Readme.io commit f60dc304fd66510a68d2b895eca8ed72b9024faa Author: Weiqun Zhang Date: Tue Aug 9 14:37:14 2016 -0700 fix new bugs Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Periodicity.cpp commit 61b9fb3f3406fe46116edf705e7a2f26e059f14b Author: Weiqun Zhang Date: Tue Aug 9 14:30:46 2016 -0700 remove MultiFab::FillBoundary because it blocks FabArray::FillBoundary Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/MultiFabUtil.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG4/ABec4.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit f7bc27e1864e384b8c6e7db4ea41274c0921c096 Author: Weiqun Zhang Date: Tue Aug 9 13:18:42 2016 -0700 start to use FillBoundary for periodic boundaries Src/C_AMRLib/FillPatchUtil.cpp Src/C_BaseLib/MultiFabUtil.cpp Src/C_TowerLib/Layout.cpp Src/C_TowerLib/MFTower.cpp commit 4b66811950d86874d0d62f14e8eb78c7119c8c30 Author: Weiqun Zhang Date: Tue Aug 9 13:03:57 2016 -0700 add Geometry::periodicity Src/C_BaseLib/Geometry.H commit eb1bef34732b3a442bd13eecb8dfac3704b4fdf6 Author: Weiqun Zhang Date: Tue Aug 9 12:58:31 2016 -0700 tweak FillBoundary interface Src/C_BaseLib/FabArray.H commit ccb1da39a108c59e02307dc8a107150ae313233b Author: Weiqun Zhang Date: Tue Aug 9 12:47:07 2016 -0700 make FabArray::FillBoundary fill periodic boundaries too Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/Periodicity.H Src/C_BaseLib/Periodicity.cpp commit e7b2ad9da5049c6a52a69bf980f4747c424e92b6 Merge: 4f30d354e f0f79c622 Author: Brian Friesen Date: Tue Aug 9 11:19:27 2016 -0700 Merge branch 'VTune_fixes' into development commit f0f79c622e7ed05bd60c975593c40a14f7cac5ec Author: Brian Friesen Date: Tue Aug 9 11:16:45 2016 -0700 C_mk: add -DVTUNE and -DITTNOTIFY defines for USE_VTUNE and USE_ITTNOTIFY Tools/C_mk/Make.defs commit d0d0bb985adc085f3443fb98ecd3a47a4cf76b99 Author: Brian Friesen Date: Tue Aug 9 11:13:11 2016 -0700 C_mk: move Intel compiler flag "-parallel-source-info=2" into USE_VTUNE Tools/C_mk/Make.defs commit e0963ce801e97a6407a73fd4a1e038ab45cce664 Author: vince Date: Mon Aug 8 16:30:30 2016 -0700 read tests for raw native format. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit af537ec921a2fc2c0299de1d0eca0ac775814cd7 Author: vince Date: Mon Aug 8 16:28:44 2016 -0700 add read functions for raw native format. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 0bf8a381e9f5b75b1a5dccaf5811bf7ec586c7a0 Author: vince Date: Mon Aug 8 14:48:21 2016 -0700 remove BL_VISMF_MSGCHECK code. Src/C_BaseLib/VisMF.cpp commit 0aacc4ffcb787bca982ebf474894e793cfc2bb27 Author: vince Date: Mon Aug 8 14:45:31 2016 -0700 combine write code. Src/C_BaseLib/VisMF.cpp commit 9e4485417ea2b2445d07db022c40276d62cc67d4 Author: vince Date: Mon Aug 8 11:57:00 2016 -0700 change path Tests/IOBenchmark/GNUmakefile commit ad81c9ad25447032f98d9846fda684404af5b0c8 Author: vince Date: Mon Aug 8 11:14:30 2016 -0700 some cleanup. Src/C_BaseLib/VisMF.cpp commit 4f30d354e6c93ab01ed4c6f7042d0e9d0ddd048e Author: Weiqun Zhang Date: Mon Aug 8 07:45:59 2016 -0700 promote FabArrayBase::CpOp to public Src/C_BaseLib/FabArray.H commit 96d02406d0ae2624152b4d40ddbb06917a44a3f2 Author: Weiqun Zhang Date: Mon Aug 8 07:29:59 2016 -0700 Add optional argument Periodicity to FillBoundary Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/Periodicity.H commit 0ca53a9419d847cf18602dbcea996d1d458894a9 Author: Weiqun Zhang 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 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 Date: Fri Aug 5 17:51:51 2016 -0700 some cleanup. Src/C_BaseLib/VisMF.cpp commit 551176e7128c73649d55a6b7b7558720eb4d1ee6 Author: vince Date: Fri Aug 5 17:13:19 2016 -0700 more io notes. Docs/Readme.io commit e7a3edeac293cbe20548d618f6a4890cceb2d838 Author: vince Date: Fri Aug 5 17:12:18 2016 -0700 update tests for new vismf versions. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit 0a446f8c4f3b07a5246619d068600ddba7f708bd Author: vince Date: Fri Aug 5 17:11:10 2016 -0700 new header versions, calc famin famax values. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 1f296878d1d24d0a78c14f603cd545b406806e51 Author: Weiqun Zhang Date: Fri Aug 5 15:14:58 2016 -0700 add ngrow to FabSet::copyTo Src/C_AMRLib/FluxRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit f3bf0fa45dddc1c84f2d1bf41809c4bb8bd04c0a Author: Weiqun Zhang Date: Fri Aug 5 14:48:31 2016 -0700 FabSet: new version of plusFrom that add two FabSets together Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit b3b155f7c5c8e2480217a3f24e72824d810f32b3 Merge: 95d4ed321 e4cd60b91 Author: Weiqun Zhang Date: Fri Aug 5 14:03:53 2016 -0700 Merge branch 'development' into weiqun/boxarrayconverter Conflicts: Src/C_BaseLib/FabArray.H commit 95d4ed321cd7eff7a17a77b21e7f96a36cff81a8 Author: Weiqun Zhang 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 Date: Fri Aug 5 13:20:37 2016 -0700 indexMap --> indexArray Src/C_BaseLib/FabArray.cpp commit f1ef4361516a9725dc357f498fb4bc0dcd74c140 Merge: 690d59cd4 e4cd60b91 Author: Michael Zingale Date: Thu Aug 4 21:09:46 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 690d59cd4ebbfa6d9e2682b949b1eea55c85a335 Author: Michael Zingale Date: Thu Aug 4 21:08:46 2016 -0400 add another color to the summary pages black = test crashed (as determined by backtrace files) the compile and crash failures now also show on the summary page for the entire run Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py commit 7e4cff1b06ae297a119cdc69abf58902ebaf977b Author: vince Date: Thu Aug 4 17:27:53 2016 -0700 filename fix for ungrouped sets for VisMF::Write. Src/C_BaseLib/VisMF.cpp commit 235db4f93707ed611d3b548b6ca8ab6613a7add6 Author: vince 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 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 Date: Thu Aug 4 16:58:08 2016 -0700 FabSet: remove aliasing in linComb Src/C_BoundaryLib/FabSet.cpp commit bebafa5cd1d2748d7714948f87bcbae35a4ddc67 Author: Weiqun Zhang Date: Thu Aug 4 16:35:38 2016 -0700 FabSet: reimplement linComb Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit d14fe5d1ac5e625c0c977efed9442797e7ef65ea Author: Weiqun Zhang Date: Thu Aug 4 16:17:44 2016 -0700 fix linComb that was temporarily disabled because only castro radiation uses it Src/C_BoundaryLib/FabSet.cpp commit 59876f89bfb392da7f91d1a04dbd126af2fa8f9e Author: vince Date: Thu Aug 4 16:10:35 2016 -0700 use NFilesIter. Src/C_BaseLib/VisMF.cpp commit 0d92f380e42a5a5c4448adb9b9f3536996ea44b8 Merge: ed58889d9 bfbcb5893 Author: vince Date: Thu Aug 4 15:37:41 2016 -0700 change mf to FabArray. commit 37fa9dd8047ff8b8373f714f56354ba44e62f1da Author: Weiqun Zhang Date: Thu Aug 4 15:01:48 2016 -0700 BoxArray: clear hash bin whenever the boxes change Src/C_BaseLib/BoxArray.cpp commit af7e58b9c270fac11b77fe2cd2db056c05645781 Author: Weiqun Zhang Date: Thu Aug 4 14:33:59 2016 -0700 remove calls to clear_hash_bin() Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/FabArray.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 172db44b074fc12dcf8c2498d6dcc5b672c68dcd Author: Weiqun Zhang Date: Thu Aug 4 14:17:41 2016 -0700 clean up BoxArray::intersections functions Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/Particles.H Src/C_BaseLib/Particles.cpp Src/C_BoundaryLib/FabSet.cpp commit 7a69fffa8abbe1b5cc32fe46eeb504f9c5a86fcc Author: Weiqun Zhang Date: Thu Aug 4 13:47:29 2016 -0700 minor tweak of TINY_PROFILE in make Tools/C_mk/Make.defs commit bfbcb589334600629b5d58d64fedf269eaf92cc7 Author: vince Date: Thu Aug 4 13:09:07 2016 -0700 fixec calls to bl_fortran_set_nprocs_sidecar Src/C_BaseLib/ParallelDescriptor.cpp commit 0bce0a16eff0fd595f5da6ff0dc2e4a7764264e5 Author: vince Date: Thu Aug 4 13:07:53 2016 -0700 allocate arrays for set_nprocs_sidecar. needs some error checking. Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit 022b4ea7807a63e4d659acf394a5f8fbc7dfdd4c Author: Weiqun Zhang Date: Tue Aug 2 15:00:02 2016 -0700 add optional no_assertion argument to a number of functions in FabArray because they might get called in situations the assertion for BDKey fails Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit ed58889d99b531013a5eb3302824063ddf6f32be Author: vince Date: Wed Aug 3 15:52:49 2016 -0700 more notes. Docs/Readme.io commit 7eedfe01e2566225f0a379ca6f59e416a8aa2709 Author: vince Date: Wed Aug 3 15:52:03 2016 -0700 move remove out of timed block. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit 0e4b6ccd426380abd079437a5a498e13c2d05aba Author: Brian Friesen Date: Wed Aug 3 17:46:40 2016 -0400 Tutorials: write correct number of component names in plotfile header in writePlotFile() The plotfile header file should list the same number of component names as there are components. This was already done correctly in a few versions of writePlotFile() in other tutorials, but not in these. Tutorials/HeatEquation_EX1_C/writePlotFile.cpp Tutorials/PGAS_HEAT/writePlotFile.cpp Tutorials/Tiling_Heat_C/writePlotFile.cpp commit 9e2a42713856befcce3c84fca68b991dc75f0160 Author: Ann Almgren Date: Wed Aug 3 14:06:37 2016 -0700 Also want to change the comments in HeatEquation_EX*F/main.f90 Tutorials/HeatEquation_EX2_F/main.f90 Tutorials/HeatEquation_EX3_F/main.f90 Tutorials/HeatEquation_EX4_F/main.f90 commit 09daa5baf11f5558eb3d347dd5ebed3b0a20fad4 Author: Ann Almgren Date: Wed Aug 3 14:05:22 2016 -0700 Analogous changes to those just made in the other HeatEquation_EX*F Tutorials/HeatEquation_EX5_F/define_bc_tower.f90 Tutorials/HeatEquation_EX5_F/inputs-rt Tutorials/HeatEquation_EX5_F/inputs-rt-expl Tutorials/HeatEquation_EX5_F/inputs-rt-impl Tutorials/HeatEquation_EX5_F/inputs_2d Tutorials/HeatEquation_EX5_F/inputs_3d Tutorials/HeatEquation_EX5_F/main.f90 Tutorials/HeatEquation_EX5_F/multifab_physbc.f90 commit 5045e2da6969915e1b0fa96e74cfee3ce9f0ada1 Author: Ann Almgren Date: Wed Aug 3 13:54:31 2016 -0700 Analogous changes in HeatEquation_EX4_F to the most recent changes in HE*2_F and HE*3_F Tutorials/HeatEquation_EX4_F/define_bc_tower.f90 Tutorials/HeatEquation_EX4_F/inputs_2d Tutorials/HeatEquation_EX4_F/inputs_3d Tutorials/HeatEquation_EX4_F/multifab_physbc.f90 commit bf286044245a6a3fa8d99c68492b5bf329ae0efa Author: Ann Almgren Date: Wed Aug 3 13:51:17 2016 -0700 Update HeatEquation_EX2_F and HeatEquation_EX3_F so that we include local versions of define_bc_tower.f90 and multifab_physbc.f90 so that we can allow for a larger range of bc types in the inputs files and so that it more clear where to set the Dirichlet values of phi if we are using INLET. Tutorials/HeatEquation_EX2_F/define_bc_tower.f90 Tutorials/HeatEquation_EX2_F/inputs_2d Tutorials/HeatEquation_EX2_F/inputs_3d Tutorials/HeatEquation_EX2_F/multifab_physbc.f90 Tutorials/HeatEquation_EX3_F/define_bc_tower.f90 Tutorials/HeatEquation_EX3_F/inputs_2d Tutorials/HeatEquation_EX3_F/inputs_3d Tutorials/HeatEquation_EX3_F/multifab_physbc.f90 commit be704c847f5a27ed79d9538e077da786c93e0707 Author: Weiqun Zhang Date: Tue Aug 2 23:28:08 2016 -0700 fix bounding box bug in the new BoxArray intersection function Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp commit 2c31579821f925e4729b207392cf9935801a267b Author: Weiqun Zhang Date: Tue Aug 2 15:00:02 2016 -0700 add optional no_assertion argument to a number of functions in FabArray because they might get called in situations the assertion for BDKey fails Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 4665185f92432bf2a2be625ea5140f9f57a703fa Author: Weiqun Zhang Date: Tue Aug 2 15:00:02 2016 -0700 add optional no_assertion argument to a number of functions in FabArray because they might get called in situations the assertion for BDKey fails Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit e3a06ac8a683a9aaa3e1dd44ba6ee9f002e5f2cf Author: Weiqun Zhang Date: Tue Aug 2 14:38:57 2016 -0700 assertion and minor cleanup Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/FabArray.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit ef7f2ef47eaa28e1553cfe59707650e5f38d3875 Author: Michael Zingale Date: Tue Aug 2 10:13:27 2016 -0400 fix benchmade link Tools/RegressionTesting/test_report.py commit 80963113ad23fbf10a2145dec75f8bebf34318b5 Author: vince Date: Mon Aug 1 16:18:49 2016 -0700 forgot the header. Src/C_BaseLib/VisMF.H commit f81b7d29f7988a87d531fc726197b31ec01552ab Author: vince Date: Mon Aug 1 16:14:59 2016 -0700 test remove nfiles. Tests/IOBenchmark/IOTest.cpp commit 910eb4ad6d54774d1dda8deab41dd3ac8a088cd0 Author: vince Date: Mon Aug 1 16:14:33 2016 -0700 tweak set groups. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit f869d1fc31d24fb865c2264e2592a7f3822af67b Author: vince Date: Mon Aug 1 16:13:42 2016 -0700 added function to remove nfiles. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit bbb73ed6607dcc1cc58484ee5a785558585816a2 Author: vince 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 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 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 Date: Mon Aug 1 07:26:59 2016 -0700 Release Notes 16.08 ReleaseNotes/release-notes-16.08 commit 66e00d3159a4d4624eb4b4009917cc7b2838c996 Merge: d57e2f068 328afc50b Author: Weiqun Zhang Date: Sun Jul 31 15:07:46 2016 -0700 Merge branch 'development' Conflicts: Src/C_BaseLib/FabArray.H commit d5aed8ce0b2cc272b901f43f59127691f04a73d2 Author: Weiqun Zhang Date: Sun Jul 31 07:15:24 2016 -0700 BoxArray: In some special cases, the internal reference counted cell-center boxes may look empty. Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.cpp commit 62424b60f3e3f45c9c98c20b385f2faf8bc40262 Author: Weiqun Zhang Date: Sat Jul 30 22:12:32 2016 -0700 FabSet::periodicCopyTo Src/C_AMRLib/FluxRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 2a3ab71877423622fe5a408643bf570c1acabb7d Author: Weiqun Zhang Date: Sat Jul 30 16:49:29 2016 -0700 use doi (domain of influence) in BoxArray intersection Src/C_BaseLib/Box.H Src/C_BaseLib/BoxArray.cpp commit 4ee59a3efecaac1018308ae055689148eb544387 Author: Weiqun Zhang Date: Sat Jul 30 13:47:53 2016 -0700 BoxArray Transformer: add doi (domain of influence) Src/C_BaseLib/BoxArray.H Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit 9b0d0d5548a322b9d8068deee0efde0453169636 Author: Weiqun Zhang 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 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 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 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 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 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 Date: Fri Jul 29 16:48:15 2016 -0700 updated readme. Tests/IOBenchmark/README commit 7a3ad28390271622aca18809cc9a1b280b6df4cf Author: vince Date: Fri Jul 29 16:42:35 2016 -0700 command line option for writeminmax. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit 9e3860dbf8ff4230c2dc4fa69ba71b6fd7fc73ec Author: vince Date: Fri Jul 29 16:27:35 2016 -0700 calc offsets without communication, option to write minmax. Src/C_BaseLib/VisMF.cpp commit 04c7a7dfcc9fb46b7f7a550bcc4353d940b318a2 Author: vince Date: Fri Jul 29 16:26:29 2016 -0700 util function, enforce proc range. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit 355f1c117a9d62b364e122c825c03c30739cd6ee Author: Weiqun Zhang Date: Fri Jul 29 16:10:34 2016 -0700 add a new version of FabSet::setVal Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 706471c6ad0127b04d02d7009a47400af26efe91 Author: vince Date: Fri Jul 29 14:22:35 2016 -0700 added stream buffer option. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit deac159078fa90ad3a40181bc08a616734a89b01 Author: Weiqun Zhang Date: Fri Jul 29 11:24:45 2016 -0700 WIP: get it to compile be commenting out a lot of codes in FabSet Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 328afc50bb07d82c2ffe47649bbd3d4449324f3a Author: Michael Zingale Date: Fri Jul 29 10:16:46 2016 -0400 testnew.py -> regtest.py Docs/Regression/test_suite.tex commit f5a5253c29b8b146b5226e222edb3d9a45bbb187 Merge: 052845cde f848e1d70 Author: Michael Zingale Date: Fri Jul 29 10:11:34 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 052845cdef3ca8ddc2631aa42fbc66cc202718e3 Author: Michael Zingale Date: Fri Jul 29 10:11:18 2016 -0400 remove the older suite -- use regtest.py now Tools/RegressionTesting/testnew.py commit f848e1d70619e6dddb641bf35dac25f6a66b7db7 Merge: 9a7643e0c 9974bfc07 Author: Michael Zingale Date: Fri Jul 29 09:44:42 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 9a7643e0c7ef8729836d87a22fd87e2c83379bf5 Author: Michael Zingale Date: Fri Jul 29 09:44:30 2016 -0400 update to point to regtest.py Tools/RegressionTesting/README commit 3d9b95b831a9f809ef6ea1359dfc5090948d991a Author: Weiqun Zhang Date: Thu Jul 28 22:11:33 2016 -0700 WIP: reimplement FabSet with MultiFab as member instead of base class; this allows more control over hiding MulitFab methods from FabSet Src/C_AMRLib/FluxRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 57e261630717fcfbadf94fc8417c964952f7e3c9 Author: Weiqun Zhang Date: Thu Jul 28 21:04:09 2016 -0700 define BndryRegister with BoxArray with special transformer Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit 401f2f6059ab33ebd688f8ef4eedafd2a24accc1 Author: vince Date: Thu Jul 28 17:22:21 2016 -0700 continue write raw native wirtes. Src/C_BaseLib/VisMF.cpp Tests/IOBenchmark/GNUmakefile commit 0c16b277c1c4a699c294120735118e6f81ea13b8 Author: vince Date: Thu Jul 28 16:54:13 2016 -0700 test write minmax to raw native mf. Tests/IOBenchmark/IOTest.cpp commit feb10d1cd554a3be6bb261960e4edae1fbdb8a18 Author: vince Date: Thu Jul 28 16:24:51 2016 -0700 add option to write fab minmax to the data. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 04c6cbb4c624eb33fc2d4a97dddd18e377c172cf Author: vince Date: Thu Jul 28 16:04:52 2016 -0700 added comments and an example. Src/C_BaseLib/NFiles.H commit 9b0c570d1bd0dd13c3917ceac6fb34fb565ca553 Author: Weiqun Zhang Date: Thu Jul 28 15:02:15 2016 -0700 BoxArray: add transformer that transforms internally stored and possibly shared boxes into boxes of the public interface Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 8e1e394e12b31f237c4ca46431ab8a274da36c13 Author: vince Date: Thu Jul 28 14:04:14 2016 -0700 change defaults. Src/C_AMRLib/AmrLevel.H commit 9974bfc07d18cf109a153f2c4466f71d4c6879ea Author: Michael Zingale Date: Thu Jul 28 13:00:54 2016 -0400 a little cleaning Tools/RegressionTesting/test_report.py Tools/RegressionTesting/test_util.py commit 7ef6ca80d8961607fe26085e6be2744b70f92337 Author: Michael Zingale Date: Thu Jul 28 12:39:19 2016 -0400 highlight a compilation failure in a different color (purple) than regular failure (comparison) Tools/RegressionTesting/test_report.py commit 1228b99e603be1ede13a5cdf6cb2975cb80b5b94 Author: Michael Zingale Date: Thu Jul 28 11:31:57 2016 -0400 fix stderr output when we aren't sending it to its own file Tools/RegressionTesting/test_util.py commit d57e2f068be95dfcefb6201e60b6118f0ea7fa7c Author: Weiqun Zhang Date: Wed Jul 27 22:43:53 2016 -0700 add libquadmath Tools/C_mk/Make.defs commit c4a888687905ae953842c2d141d83b0d07ddaf77 Author: Weiqun Zhang Date: Wed Jul 27 22:43:53 2016 -0700 add libquadmath Tools/C_mk/Make.defs commit 1acd4e1721ec734bd3b179d9388613689b3ff0c8 Author: vince Date: Wed Jul 27 17:19:15 2016 -0700 test functions for VisMF::WriteRawNative. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit 3f7cc0b4ef8518cdfb1c42a419901670aefba355 Author: vince Date: Wed Jul 27 17:18:33 2016 -0700 added WriteRawNative function. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 96127b63d0da230bd0aab323bcd828eeee20b5ba Author: vince Date: Wed Jul 27 17:17:32 2016 -0700 added file name functions. Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp commit 1e1c279ba41b75d6670520c73eed09708145760e Author: Brian Friesen Date: Wed Jul 27 13:30:10 2016 -0700 C_mk: add some extra compiler flags when using VTune This adds support for the GNUmakefile options USE_VTUNE and USE_ITTNOTIFY when using the Intel compilers. USE_VTUNE adds some extra debugging output during compilation which allows VTune to resolve more information about the code during profilng, while USE_ITTNOTIFY provides support for manual code instrumentation with VTune to profile only certain regions instead of the entire thing. Tools/C_mk/Make.defs commit 01ccfb5f6e122862e84b7ae3b895b792244b9720 Author: Brian Friesen Date: Thu Jul 7 13:15:31 2016 -0700 C_mk, HPGMG: rename DUNLIMIT_FMG_VCYCLES -> DUNLIMIT_FMG_ITERATIONS Sam renamed this in HPGMG so we need to follow suit in our compilation scripts. Tools/C_mk/Make.defs commit d2dee333bfca5fb305da934b21414c4958b4f056 Author: vince Date: Wed Jul 27 12:12:27 2016 -0700 change how default, some cleanup. Src/C_AMRLib/Amr.cpp commit cec928c163f4068dbd5d97d90095efb0356e69a1 Author: Weiqun Zhang Date: Wed Jul 27 07:07:49 2016 -0700 fix assertion Src/C_BaseLib/Geometry.cpp commit b9fe517c01b7d3ac1b505bf277f4bf32a7c33dce Author: Weiqun Zhang Date: Tue Jul 26 22:28:52 2016 -0700 explicit Src/C_BaseLib/BoxArray.H commit 410671d6548f59a3416f387f00cd9625181bb280 Author: Weiqun Zhang Date: Tue Jul 26 21:02:46 2016 -0700 reimplement fillperiodicboundary cache using boxarray-distributionmap key Src/C_AMRLib/Amr.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 81174da4ee4ebd157191935e702ea686313cfb9a Author: Weiqun Zhang Date: Tue Jul 26 16:12:45 2016 -0700 clean up FB Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit d8fe990e75cc477cab54544fea8b3da35211c3b0 Author: Weiqun Zhang Date: Tue Jul 26 15:06:33 2016 -0700 reimplement parallel copy cache using boxarray-distributionmap key Src/C_AMRLib/Amr.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 7faa29464abcf83f7eb3888cd5ec08c8932c242b Author: Weiqun Zhang Date: Tue Jul 26 10:55:13 2016 -0700 MemPool: static_assert Src/C_BaseLib/MemPool.cpp commit 7194d443830c0ebd30bc247412aa4e9efc6e0b08 Author: Weiqun Zhang Date: Tue Jul 26 07:51:00 2016 -0700 reimplement fillboundary cache using boxarray-distributionmap key Src/C_AMRLib/Amr.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp commit 70b965cc94f9d34d3ca63b5aff89b701ee7a994e Author: vince Date: Tue Jul 26 17:55:19 2016 -0700 packaged nfiles writing. Src/C_BaseLib/Make.package Src/C_BaseLib/NFiles.H Src/C_BaseLib/NFiles.cpp Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit 8f0452ded238f97bbc8290e1bd823ea5df20bfc4 Author: Ann Almgren Date: Tue Jul 26 14:57:44 2016 -0700 Enable us to call fourth_order interpolation without having to define the stencil_width to 2 independently -- affects multifab_fill_ghost_cells and fillpatch. Also fix the fourth_order_interp routine so that it can fill some but not all fine cells in a coarse cell. Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit da0c58fd96e46323f018924bee9d26d9596698a0 Author: vince Date: Tue Jul 26 14:44:12 2016 -0700 limit buffer size. Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabConv.cpp commit 00ae1cea8ef0e8da63b50a0b10a006ea2bf0ae3a Author: vince 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 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 Date: Mon Jul 25 15:53:54 2016 -0700 fix tilearray memory profiling counter Src/F_BaseLib/layout.f90 commit cfa7a5df6990e62117b60abf3039041602bf9103 Author: Weiqun Zhang Date: Mon Jul 25 15:48:56 2016 -0700 nullify fortran pointer in bl_deallocate Src/C_BaseLib/mempool_f.f90 commit c6df358858f100f9e326291e10fa51673e49a0b1 Author: Weiqun Zhang Date: Mon Jul 25 15:10:33 2016 -0700 use constexpr Src/C_BaseLib/MemProfiler.cpp commit abeddd4f0bba1a1cc845807bec61115cda15d4d4 Merge: 535fe779e dd6181a91 Author: Weiqun Zhang Date: Mon Jul 25 14:50:33 2016 -0700 Merge branch 'development' into weiqun/coarsenboxarray Conflicts: Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit dd6181a91059fa84da1981aa906264e157289982 Author: Weiqun Zhang Date: Mon Jul 25 14:41:49 2016 -0700 MEM_PROFILE: keep track of the number of BoxArrays and MultiFabs Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/MemProfiler.H Src/C_BaseLib/MemProfiler.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 535fe779ed3b7999c86272587df7791d086aee41 Author: Weiqun Zhang Date: Sun Jul 24 18:57:48 2016 -0700 update because BoxArray::define(const BoxArray&) is gone Tests/LinearSolvers/ComparisonTest/main.cpp commit 5cc6462d4d3de78a6b43da1e844fddf420415b7d Author: Weiqun Zhang Date: Sun Jul 24 17:35:17 2016 -0700 cache coarse BoxArrays Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/Pointers.H commit 87451a8c4bbcc37a30a3d2afb5129348b11e1c65 Author: Michael Zingale Date: Sun Jul 24 17:33:22 2016 -0400 'make file_locations' will printout where in the VPATH each source file is found as well as indicate which files are not found Tools/C_mk/Make.rules commit 9dee60b57f9aa99a1a75728a666dd8f3b2a4e1da Author: Michael Zingale Date: Sun Jul 24 17:26:58 2016 -0400 'make file_locations' will output where each source file is found by make this will also indicate which files make cannot find Tools/F_mk/GMakerules.mak commit 68e6ac5ee5d4a4f29b6664bd4c019802a920b9ef Author: Michael Zingale Date: Sun Jul 24 17:23:39 2016 -0400 a useful tool for makefile debugging -- this script will print out where files are found in the vpath and which files are not in the vpath Tools/F_scripts/find_files_vpath.py commit 3f209bffcde7a79c76ee2d24b4340800fd7d0000 Author: Weiqun Zhang Date: Sat Jul 23 12:55:15 2016 -0700 remove BoxArray::define(const BoxArray& bs) because it is equivalent to the assignmeent operator Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 06f36ed02bd163b661710520125efb480e90a787 Author: Weiqun Zhang Date: Sat Jul 23 11:14:17 2016 -0700 use BoxArray assignment operator instead of define function because I plan to remove the define fucntion Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/StateData.cpp Src/C_BaseLib/FabArray.H Src/C_BoundaryLib/BndryRegister.cpp commit a1b55f1ca9863c6a06cdc9d072231599627a4d83 Author: Weiqun Zhang Date: Sat Jul 23 07:33:28 2016 -0700 make ~FabArrayBase just in case Src/C_BaseLib/FabArray.H commit 2b81914948429444d7dc1fc0cddd70bbec03aac6 Author: Weiqun Zhang Date: Fri Jul 22 17:03:04 2016 -0700 virtualize a few functions in FabArray and make VisMF a class for FabArray instead of MultiFab Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit f93c7c5b6adff62736728fadda3f0ea80f9b8e65 Author: vince Date: Fri Jul 22 14:29:40 2016 -0700 added dir tests. Tests/MKDir/MKDir.cpp commit 19a5b243b529a7e00787e307015090aeac2f0eeb Author: vince Date: Thu Jul 21 16:30:16 2016 -0700 code cleanup. Src/C_BaseLib/VisMF.cpp commit 391256842d2e983c6093a99ebb9410296308917d Author: Weiqun Zhang Date: Thu Jul 21 14:45:00 2016 -0700 wip Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/MultiMask.H Src/C_BoundaryLib/MultiMask.cpp commit b2073cee431dfc5365c52eb2c501de2a0b2fc3f0 Author: vince Date: Thu Jul 21 14:33:22 2016 -0700 some code cleanup. Src/C_BaseLib/FArrayBox.cpp commit f079dd7a9510632b6ac1979c1928a1741a2cdbd6 Author: Weiqun Zhang Date: Thu Jul 21 12:58:12 2016 -0700 start MultiMask class Src/C_BoundaryLib/CMakeLists.txt Src/C_BoundaryLib/Make.package Src/C_BoundaryLib/MultiMask.H Src/C_BoundaryLib/MultiMask.cpp commit 38d19b60d981dc71bcbe996b2db4ba3d048369eb Author: Weiqun Zhang Date: Thu Jul 21 12:48:04 2016 -0700 add alloc and shared as optional arguments to Mask class in preparation for new MultiMask class Src/C_BoundaryLib/Mask.H Src/C_BoundaryLib/Mask.cpp commit 791407d71c5244673cd4a36662507c3ee560b55e Author: vince Date: Thu Jul 21 12:38:27 2016 -0700 added functions to set buffer sizes. Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp commit 754d3805f8339bd60e2470dfbd122b468b6a8aa4 Author: Weiqun Zhang Date: Thu Jul 21 11:14:30 2016 -0700 remove edge_restriction.f90 because all its functions are already duplicated in cc_restrition_module and the edge restriction functions are called by functions in ml_cc_restriction_module (since there is no ml_edge_restriction_module Src/F_BaseLib/CMakeLists.txt Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/GPackage.mak Src/F_BaseLib/edge_restriction.f90 Src/F_BaseLib/ml_cc_restriction.f90 Src/LinearSolvers/F_MG/FParallelMG.mak commit 872ef6bab747636c0f4086022edbf5bf57eb101c Author: vince Date: Thu Jul 21 11:14:01 2016 -0700 added test files and io doc. Docs/Readme.io Tests/C_BaseLib/AMRPROFTEST_F.H Tests/C_BaseLib/AMRProfTestBL.cpp Tests/C_BaseLib/tRABcast.cpp Tutorials/MultiFabTests_C/MultiFabFillBoundary.cpp commit c29b8c337c5d6498874693b8a0783403591df07b Merge: 147638bd6 1ddb9538b Author: Michael Zingale Date: Thu Jul 21 12:28:13 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 147638bd64e704f7849da91504bb5d8994cf974e Author: Michael Zingale Date: Thu Jul 21 12:27:53 2016 -0400 move the return code logic to _after_ we do zone info Tools/Postprocessing/F_Src/fcompare.f90 commit 1ddb9538b27bf8cfea3d503ed8edb9ec02eaaa64 Author: vince Date: Wed Jul 20 16:46:53 2016 -0700 remove the word grok. Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit 3641b641c7196011f3ab87d1a7c990f00d53667d Merge: ad071144c 70304c16a Author: Michael Zingale Date: Wed Jul 20 19:33:46 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 70304c16a3981a9e591a5ccf4f0576b3f7358008 Merge: cb41d52ce 19e17f344 Author: vince 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 Date: Wed Jul 20 12:39:15 2016 -0700 remove profile call. Src/C_BaseLib/ParallelDescriptor.cpp commit 19e17f344373af3e8240b2a6c899793262fd43d4 Author: Michael Zingale Date: Sun Jul 17 14:13:04 2016 -0400 the microphysics suite inputs Tools/RegressionTesting/Microphysics-tests-pgi.ini Tools/RegressionTesting/Microphysics-tests.ini commit 5fd051b36d3a54a5b0a8510a9799572f75a9f243 Author: Michael Zingale Date: Sun Jul 17 13:07:59 2016 -0400 detect variable mismatch in comparison Tools/RegressionTesting/test_report.py commit 5dd647bca3a37fc4ef84cc07e3435060dd085d1e Author: Michael Zingale Date: Sun Jul 17 12:28:40 2016 -0400 return error code if there are different / missing variables in the plotfiles Tools/Postprocessing/F_Src/fcompare.f90 commit ad071144c91a3ee41319bede942d8af1822db857 Merge: bb8f42f81 ade08f76f Author: Michael Zingale Date: Thu Jul 14 10:03:17 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit ade08f76f051954e2b5d760b82e3402c4d722b00 Author: Weiqun Zhang Date: Wed Jul 13 13:42:15 2016 -0700 tweak Fortran make system to support codes relying on the programs variable Tools/F_mk/GMakerules.mak Tools/Postprocessing/F_Src/GNUmakefile commit 9219d56700097259118a92f83fb8747f3adc63b1 Author: Weiqun Zhang Date: Wed Jul 13 12:51:32 2016 -0700 Fortran random: add more static_assert Src/F_BaseLib/bl_random_c.cpp commit c848f609182ee19c2d1f349e281acf413075aed9 Author: Weiqun Zhang Date: Tue Jul 12 18:30:01 2016 -0700 Fortran random: add single precision Src/F_BaseLib/bl_random_c.cpp commit e2e6e7a8acad6fb311b80fa45c00f65ec0c0c11b Merge: bf3cb03a8 12e9925c8 Author: vince Date: Tue Jul 12 16:33:44 2016 -0700 refix name change. commit 40fb363bfacf7cb09230c1baab6e4e8069033af2 Author: Weiqun Zhang Date: Tue Jul 12 16:10:48 2016 -0700 promote IndexMap() and localindex() to public so that some codes can use Src/C_BaseLib/FabArray.H commit 12e9925c8fda1b8dacab99630ea80ce6536faf88 Author: Weiqun Zhang Date: Tue Jul 12 16:10:48 2016 -0700 promote IndexMap() and localindex() to public so that some codes can use Src/C_BaseLib/FabArray.H commit bf3cb03a84c133e8218824b51f7cfab15e8a69f0 Merge: f9c6762d5 527bf4339 Author: vince 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 Date: Tue Jul 12 15:59:38 2016 -0700 add a default real function. Src/C_AMRLib/LevelBld.H commit b03e71d823234e57f74342c831e49e4411f58f85 Author: vince Date: Tue Jul 12 15:41:32 2016 -0700 dont free the comm from fortran for intransit. Src/C_BaseLib/BoxLib.cpp commit be07a5fce321209ff37b33c9f860e201c04de596 Author: vince Date: Tue Jul 12 14:32:32 2016 -0700 flush another cache for MoveFabs. Src/C_BaseLib/FabArray.H commit 690f5e7de6606ecaf5d4026e4c5d28dda06e0c19 Author: vince Date: Tue Jul 12 14:28:03 2016 -0700 flush another cache for MoveFabs. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit f2c69c59d503e873a116df5e454cff6af1b5fcfd Author: vince Date: Tue Jul 12 14:26:08 2016 -0700 remove unused vars. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/FillPatchUtil.cpp commit bb8f42f814920dfbf67b924c17d99b9118ae0f82 Merge: dfae56617 527bf4339 Author: Michael Zingale Date: Tue Jul 12 14:55:37 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit e4f61530162450c2bf33bac8a071fe4cca176438 Author: vince Date: Mon Jul 11 14:07:46 2016 -0700 merge fix. Src/C_AMRLib/Amr.cpp commit 527bf4339b1ec1adbf4405d4d47e54299ee74962 Author: Weiqun Zhang Date: Mon Jul 11 14:02:55 2016 -0700 Fortran random: allow using FluctHydro/HydroGrid distribution Src/F_BaseLib/bl_random_c.cpp Src/F_BaseLib/bl_random_f.f90 commit 09001e549f231bd3e386ab1a3df736fed146f7b0 Author: vince Date: Mon Jul 11 13:33:32 2016 -0700 fix for serial. Src/C_BaseLib/ParallelDescriptor.cpp commit fd1cf86046460719aa25d9903f0c68046cf497ad Merge: 27cc3ce0b a9b1a1fd4 Author: vince Date: Mon Jul 11 12:19:05 2016 -0700 merge fix. commit dfae56617be1d861a7ba05ac891de042ff0e9bb9 Author: Michael Zingale Date: Mon Jul 11 09:55:21 2016 -0400 minor formatting Tools/RegressionTesting/test_report.py Tools/RegressionTesting/test_util.py commit 129705b267628c9d4c29fa1ce9aa908d5f750dec Author: Michael Zingale Date: Mon Jul 11 09:48:46 2016 -0400 replace redefined name Tools/RegressionTesting/regtest.py commit 27cc3ce0bb544d3206cd28c0248327017f502e0e Merge: 3c6085da5 418e329ec Author: Michael Zingale Date: Sun Jul 10 16:59:48 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 3c6085da5c23154672923836aef2c08e1e29029a Author: Michael Zingale Date: Sun Jul 10 16:59:21 2016 -0400 a little cleaning Tools/RegressionTesting/test_report.py Tools/RegressionTesting/test_util.py commit 418e329ec6dd2be328d3508a768b8f6626316170 Author: Michael Zingale Date: Sun Jul 10 12:01:08 2016 -0400 a little more PEP-8 Tools/RegressionTesting/params.py Tools/RegressionTesting/regtest.py Tools/RegressionTesting/repo.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py Tools/RegressionTesting/test_util.py commit 217cfbb157ae2ff6685483ee0a06b9d91f34f2dd Merge: c6abf0818 409be0af2 Author: Michael Zingale Date: Sun Jul 10 11:55:47 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit c6abf0818e877886a13dac2866913778aee9ceed Author: Michael Zingale Date: Sun Jul 10 11:55:32 2016 -0400 use is to compare to None Tools/RegressionTesting/regtest.py commit 409be0af20ed4ec6a055fc318384ad37c364df0a Author: Michael Zingale Date: Sun Jul 10 11:51:20 2016 -0400 actually check whether the user-specified compareFile exists Tools/RegressionTesting/regtest.py commit b035c2d88edee2c40b843e27c831de010bf6c08e Author: Michael Zingale Date: Sat Jul 9 19:53:01 2016 -0400 rely on the return code from fcompare to determine if the comparison was successful Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py commit 4fd292bad34bb200a4dcd1619d46d5f4c422af39 Author: Michael Zingale Date: Sat Jul 9 15:08:17 2016 -0400 explicitly send return codes of success or failure Tools/Postprocessing/F_Src/fcompare.f90 commit b4faf15d4b5ef4791b40aef334db5281d96a213b Merge: 91dad08b6 8176a2f82 Author: Michael Zingale Date: Sat Jul 9 14:55:58 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 91dad08b67c58639f470bc50891107b615d1d16f Author: Michael Zingale Date: Sat Jul 9 14:55:41 2016 -0400 two new functions for sending return codes from Fortran Src/F_BaseLib/system_util_c.c commit 8176a2f8273f6258872319e88ee45567dff85dd0 Author: Max Katz Date: Sat Jul 9 14:49:44 2016 -0400 Write a plotfile on demand with plot_and_continue Src/C_AMRLib/Amr.cpp commit e2b8c0d14449bbb4895e0e1afff0e2c4fa118163 Author: Michael Zingale Date: Sat Jul 9 13:27:41 2016 -0400 use the return code to determine if compilation was successful consolodate the main copying code Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py commit c04e630b991edb129fc2a3a3054f8c642d60fadf Author: Michael Zingale Date: Sat Jul 9 12:55:31 2016 -0400 no really, .pyc .gitignore commit 60eb0eb4e05bc0cb0f8ab33392b2b19fe5d137e1 Author: Michael Zingale Date: Sat Jul 9 12:55:04 2016 -0400 add .pyc .gitignore commit 19d2d2d6be8205060c5be0e8f2295f04d7768785 Author: Michael Zingale Date: Sat Jul 9 12:27:47 2016 -0400 use the return code from make to determine if the tools built Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py commit a9b1a1fd429ba1b682749808cf20dd2d025bcb2a Author: vince 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 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 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 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: f8434f0ce b4e253d7c Author: Michael Zingale Date: Fri Jul 8 18:37:18 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 5a79389385ead2442e8aabe0f58bfe5de756cc9a Author: vince Date: Fri Jul 8 15:23:54 2016 -0700 some changes for sidecars and teams. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/ParallelDescriptor.cpp commit 741f04332fa9ef6fd2b72de0a01f9a4a874a8b4b Author: vince Date: Fri Jul 8 15:21:12 2016 -0700 remove test output. Tutorials/Sidecar_EX1/NSidecarsTest.cpp commit 6b8be66cf6639046197d9c01d71d43f15c5ede04 Author: vince Date: Fri Jul 8 15:20:28 2016 -0700 option to print unique set. Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit b4e253d7c73055dc84dd55d75a9d46a217057bda Author: vince Date: Fri Jul 8 13:31:12 2016 -0700 added serial initializations. Src/C_BaseLib/ParallelDescriptor.cpp commit a6e43ded7fdb40082eece730394ab574277f542a Merge: cb130b48f 2549a2a99 Author: Michael Zingale Date: Fri Jul 8 10:40:13 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit cb130b48fd0794a3e4eab9bccada7c2ea9c30b2e Author: Michael Zingale Date: Fri Jul 8 10:38:45 2016 -0400 don't process _parameters until we ask for a net or eos Tools/Postprocessing/F_Src/GNUmakefile commit 2549a2a99a82cd85f4b0cdf66bca04b65d984d76 Author: Weiqun Zhang Date: Fri Jul 8 07:35:08 2016 -0700 fix make Tools/Postprocessing/F_Src/GNUmakefile commit 02b573211db641d57a71ec25393ed954d49e6567 Author: Weiqun Zhang Date: Fri Jul 8 07:22:24 2016 -0700 fixed a typo Tools/F_mk/GMakedefs.mak commit d2628c19e51a77bdedd5ea8e7ec3fdf31477ae07 Author: Weiqun Zhang Date: Thu Jul 7 16:13:41 2016 -0700 add F_mk/Readme and some minor tweaks Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak Tools/F_mk/Readme commit c9f77d4837c0d2723348c7e7752615e16d2499d2 Author: Weiqun Zhang Date: Thu Jul 7 12:13:56 2016 -0700 Make: -include Make.local allowing users to reset variables; add ccache and f90cache to speed up compilation Tools/C_mk/Make.defs Tools/C_mk/Make.rules Tools/F_mk/GMakedefs.mak commit 4e366d0f957bc425a8988af3e02c2e47412afb30 Merge: 9cf3ab851 df98653b2 Author: Michael Zingale Date: Wed Jul 6 22:09:35 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 9cf3ab8516b38daf57af32e0e7180b5d30baf471 Author: Michael Zingale Date: Wed Jul 6 22:09:11 2016 -0400 split stdout/err and save stderr from the run, if present Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py Tools/RegressionTesting/test_util.py commit f8434f0ce949fc48321c97e946d9131c9073ffc5 Merge: 79b7bb674 df98653b2 Author: Michael Zingale Date: Wed Jul 6 18:45:49 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit df98653b2943c35c0cc8c66e1bdb909aac4b2dcd Author: Michael Zingale Date: Wed Jul 6 16:45:56 2016 -0400 copy -> move for executable Tools/RegressionTesting/regtest.py commit a5d6cbaaf9a78fd954eef54074beb7daf10419be Author: Michael Zingale Date: Wed Jul 6 09:57:45 2016 -0400 clean-up memory to quiet memory sanitizer Tools/Postprocessing/F_Src/fcompare.f90 commit 79b7bb674d761ee98309c53c06672af72677417c Merge: 9149bcb0e f97b7e114 Author: Michael Zingale Date: Tue Jul 5 18:48:33 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 9149bcb0efb2aec3a2a906f6ee81121bb5ae3755 Author: Michael Zingale Date: Tue Jul 5 18:48:24 2016 -0400 remove trailing blanks Tools/RegressionTesting/suite.py commit f97b7e1144cd6fba5b3b9b1d189c22eb665a5e13 Author: Michael Zingale Date: Tue Jul 5 13:52:26 2016 -0400 add a warning if we are running on a non-default branch Tools/RegressionTesting/regtest.py commit 7ecc8c44b63ece879c9161cda6b7bffc6be6947c Author: Weiqun Zhang Date: Tue Jul 5 07:00:43 2016 -0700 Release Notes 16.07 ReleaseNotes/release-notes-16.07 commit 4514924e2d1b8608fb45ad625db04017a1b0470c Merge: 8ee5a13d8 f4abc0a00 Author: Weiqun Zhang Date: Tue Jul 5 06:59:44 2016 -0700 Merge branch 'development' commit f4abc0a00e2015ee1fcd9d1de4f16510cc0078b6 Author: Michael Zingale Date: Mon Jul 4 21:56:37 2016 -0400 add an indicator if we are running on a non-default branch + bug fix now we add an '*' next to the date on the master page if any of the git repos are not on "suite.default_branch". This helps delineate the normal tests from those we run occassionally on feature branches. Also fix a crash if we ran with only self-tests (no output file is ever defined) Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py commit cc7c213016993c67976db929a38383896e3ad9c1 Author: Michael Zingale Date: Mon Jul 4 13:05:02 2016 -0400 remove legacy comma warning Tools/Postprocessing/F_Src/fcompare.f90 commit 9cc12191d766e23e389c424bd649e936cc788dc5 Author: Michael Zingale Date: Mon Jul 4 12:51:25 2016 -0400 fcompare no longer needs --infile1/2 Tools/RegressionTesting/regtest.py commit 403f634031529482e97210e718958173187fa3b5 Author: Weiqun Zhang Date: Tue Jun 28 21:44:56 2016 -0700 Only test skewed for the current level Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90 commit eb8c9f9548b03c720477bf0abceda13b1a5b7bc1 Author: Weiqun Zhang Date: Tue Jun 28 14:09:09 2016 -0700 Turn off tiling for skewed stencil Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/cc_smoothers.f90 commit 0d3acb0760942281cd2abe04db8f1a9f28459176 Author: Weiqun Zhang Date: Tue Jun 28 11:04:42 2016 -0700 function to turn on fpe trapping in Fortran BoxLib Src/F_BaseLib/backtrace_c.cpp Src/F_BaseLib/backtrace_f.f90 commit 9f09e8ab700bab0b246c4d6d7a3a3f7dc1fbff55 Author: Weiqun Zhang Date: Tue Jun 28 10:51:07 2016 -0700 indentation Tutorials/Tiling_Heat_F/advance.f90 commit fb3870861ea7bb02e09c4fa724e2179e7b25b5f2 Merge: fefa60f3e 7dcfaab44 Author: Michael Zingale Date: Tue Jun 28 14:02:53 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit fefa60f3e246b0b0ca30df220c83ec9f5466ca4a Author: Michael Zingale Date: Tue Jun 28 14:02:40 2016 -0400 latest version Tools/RegressionTesting/Maestro-tests.ini commit 7dcfaab445353c778db672e6f492c2a15fc6327f Author: Michael Zingale Date: Tue Jun 28 14:00:45 2016 -0400 latest version Tools/RegressionTesting/Castro-SBU-tests.ini commit 84d86d626c7d3da5427c6d0f11c4204230edb44e Author: Weiqun Zhang 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 Date: Mon Jun 27 19:28:10 2016 -0400 fix typo Tools/RegressionTesting/suite.py commit 97b1f3486f48d444221387ebd04fb328a3df128c Author: Weiqun Zhang Date: Mon Jun 27 19:13:53 2016 -0400 use subroutine instead of function to get around a gcc 6.1.1 bug Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 Tools/C_mk/Make.mpi commit bcf032e2558f055b0511b96ab041df151bd3c627 Author: Michael Zingale Date: Mon Jun 27 15:46:09 2016 -0400 remove some debug prints Tools/F_scripts/write_probin.py commit 5f15a56f2761cfd0db4235ff001e92ea72372962 Author: Michael Zingale Date: Mon Jun 27 15:40:48 2016 -0400 sanitize apostrophes in the slack Tools/RegressionTesting/suite.py commit 120bec97339b97c33eec3d8c257dd11ece0951db Merge: eaa7492b1 c197e45dc Author: Michael Zingale Date: Mon Jun 27 15:39:04 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit eaa7492b15dbfc75173371ca339ddfd4a837d945 Author: Michael Zingale Date: Mon Jun 27 15:38:54 2016 -0400 add future Tools/RegressionTesting/suite.py commit c197e45dca24c2bbcfd8a7205447a000e473b04f Author: Weiqun Zhang Date: Mon Jun 27 11:24:06 2016 -0700 missed omp end parallel Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90 commit b2374063cce8bae9bc7125b7e3f706defc512ff0 Author: Weiqun Zhang Date: Mon Jun 27 11:18:50 2016 -0700 turn off tiling for 1d and 2d because they are not ready; fix MS_SMOOTHER_EFF_RB Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90 commit e6c44ece8580f1c1ceb2455ba4ac3852742394c5 Author: Weiqun Zhang Date: Mon Jun 27 11:10:26 2016 -0700 turn off tiling for 1d, 2d and nodal because they are not ready Src/LinearSolvers/F_MG/mg.f90 commit dc9cdec74c6444626188d7724096e1aa99b73bd3 Author: Michael Zingale Date: Mon Jun 27 10:01:26 2016 -0400 using std::isinf for __GNUC__ >= 6 Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 5873450c1470c09a0045fd61f1fd7d6fa3fb2ea2 Merge: 49d418217 8a8a88e41 Author: Brian Friesen Date: Sun Jun 26 17:10:15 2016 -0700 Merge branch 'fix_tiled_CC_F_MG_2D' into development commit 49d4182171d378f31c24b9a91651685eb2d41164 Author: Brian Friesen Date: Sun Jun 26 11:56:32 2016 -0700 C_BaseLib: make Box::isSquare() always return false in 1-D Src/C_BaseLib/Box.cpp commit 8a8a88e41b44779ca9716025d088e36ed289daad Author: Brian Friesen Date: Sun Jun 26 12:01:24 2016 -0700 F_MG: set dim of tile box indicies "tlo" and "thi" to mgt%dim In commit 59ab377 ("F_MG: tile the cell-centered restriction") I hard-coded the dimension of tlo and thi to 3, anticipating that tiling will only benefit 3-D problems and not so much 2-D. However this breaks 2-D problems which need to use Fortran multigrid, so instead we set the dim of tlo and thi to whatever dim is set to in the mgt object. Src/LinearSolvers/F_MG/mg.f90 commit b68c8867e8dbf3649b36b494440b90e9cd684d60 Author: Michael Zingale Date: Sun Jun 26 10:12:40 2016 -0400 got g++ 6.1, we need use std::isnan and std::isinf Src/C_BaseLib/FArrayBox.cpp commit b245a13653d607dbb669c772b36e46ccf3007575 Merge: 32d456897 1f6d4ed59 Author: Andy Nonaka Date: Fri Jun 24 16:47:38 2016 -0700 Merge branch 'weiqun/random' into development commit 1f6d4ed5976d2afecf964ca41b7596cdab0d9b9e Author: Weiqun Zhang 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 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 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 Date: Fri Jun 24 13:39:38 2016 -0700 add initialization flag to IArrayBox.cpp Src/C_BaseLib/IArrayBox.cpp commit 18cc38b8b8cecde81e6a792a810d91265d3b8513 Merge: b31035be1 926fb7bc9 Author: Brian Friesen Date: Fri Jun 24 10:55:47 2016 -0700 Merge branch 'tile_MultiGrid_C_tutorial' into development These commits add tiling to setup_rhs() and setup_coeffs() in the MultiGrid_C tutorial. These are just initialization routines specific to this tutorial and thus the speedup from these commits does not benefit any other BoxLib code. commit b31035be1da1f629df7fcf08e16c8677edb7598a Merge: 4374e3640 59ab37788 Author: Brian Friesen Date: Fri Jun 24 10:52:01 2016 -0700 Merge branch 'tile_CC_F_MG' into development These commits add OpenMP tiling to the cell-centered GSRB smooths and restrictions in F_MG. The prolongation is not as simple as replacing the nfabs() loop with a next_tile() loop so that will be done in a different series of commits. Using the MultiGrid_C tutorial with a 512^3 grid decomposed into 8 256^3 boxes, these changes yield a roughly 8% speedup on both Ivy Bridge (using 2 MPI x 12 OpenMP) and pre-production Knights Landing (using 1 MPI x 64 OpenMP). commit 59ab3778866da96f4d7405b894055d7223c174fe Author: Brian Friesen Date: Thu Jun 23 22:34:47 2016 -0700 F_MG: tile the cell-centered restriction Src/F_BaseLib/cc_restriction.f90 Src/F_BaseLib/ml_cc_restriction.f90 Src/LinearSolvers/F_MG/mg.f90 commit 846b02fefbe7290a316558ea381e2b636ca75af0 Author: Brian Friesen Date: Thu Jun 23 22:32:32 2016 -0700 F_MG: tile the cell-centered GSRB smoothers Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/cc_smoothers.f90 commit 4374e364017adb87f2af9604e5980d897130ba39 Author: Max Katz Date: Thu Jun 23 21:50:15 2016 -0400 Add dimension agnostic version of BL_FORT_IFAB_ARG Src/C_BaseLib/BLFort.H commit 926fb7bc990bcd4ae10d09fc8a90416e25c5c4f8 Author: Brian Friesen Date: Wed Jun 22 17:23:46 2016 -0700 Tutorials: tile setup_rhs() in MultiGrid_C Tutorials/MultiGrid_C/main.cpp commit d36acfda5a603b163ca35b9c2c93e93433d8cdfc Author: Brian Friesen Date: Wed Jun 22 17:22:40 2016 -0700 Tutorials: tile setup_coeffs() in MultiGrid_C Tutorials/MultiGrid_C/main.cpp commit b23d9e59f6d322f0afe7b2629ad42c2592cde9e4 Author: vince Date: Wed Jun 22 14:34:51 2016 -0700 fixes for merge. Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp commit a488a98d68924aab2a0a5ee30e05ac051e7a8a57 Merge: f5dd5900f 37e95a29d Author: vince Date: Wed Jun 22 14:15:09 2016 -0700 fixed merge conflicts. commit fa3d8baea31cf0d26498deb7ef1451c96b6e39c4 Author: Weiqun Zhang Date: Wed Jun 22 13:24:18 2016 -0700 Fortran random: consistent names Src/F_BaseLib/bl_random_f.f90 Tutorials/Random_F/main.f90 commit c6465e222e2d92952f173d1e3b42f2ccdd010560 Author: Weiqun Zhang 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 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 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 Date: Wed Jun 22 06:55:19 2016 -0700 Fortran random: minor Src/F_BaseLib/bl_random_c.H commit 37e95a29d6eeb1d4665e45eaafc833a454e6f96b Author: Michael Zingale Date: Tue Jun 21 22:46:54 2016 -0400 fix the zone_info functionality we were not resetting the current zone error Tools/Postprocessing/F_Src/fcompare.f90 commit a435fe3fca6d4e35a3d0cf35770f9543c00ec8d1 Author: Michael Zingale Date: Tue Jun 21 22:25:54 2016 -0400 remove "use f2kcli" -- our compilers support the F2003 command line stuff that module was a compatibilty-layer module for codes before Fortran 2003 was commonplace Tools/Postprocessing/F_Src/CASTRO_radiation/fgaussianpulse.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/flgt_frnt1d.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradshock.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradsource.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradsphere.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/frhdshocktube.f90 Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/fsubchandra_mod.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/fgaussianpulse.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/fmlcompare.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/fmlconverge.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/fnorm.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/feint.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fthermo.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fwdconvect.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fad_excess.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fconv_slopes.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/frates.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fspec_total_mass.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fspeciesmass.f90 Tools/Postprocessing/F_Src/faverage.f90 Tools/Postprocessing/F_Src/fboxinfo.f90 Tools/Postprocessing/F_Src/fcoarsen.f90 Tools/Postprocessing/F_Src/fcompare.f90 Tools/Postprocessing/F_Src/fdumpdata2d.f90 Tools/Postprocessing/F_Src/fextract.f90 Tools/Postprocessing/F_Src/fextrema.f90 Tools/Postprocessing/F_Src/ffdcompare.f90 Tools/Postprocessing/F_Src/fintgvar2d.f90 Tools/Postprocessing/F_Src/fsnapshot2d.f90 Tools/Postprocessing/F_Src/fsnapshot3d.f90 Tools/Postprocessing/F_Src/ftime.f90 Tools/Postprocessing/F_Src/fvarnames.f90 Tools/Postprocessing/F_Src/old_flame/fbubble_position.f90 Tools/Postprocessing/F_Src/old_flame/fbubble_position_3d.f90 Tools/Postprocessing/F_Src/old_flame/fcusp.f90 Tools/Postprocessing/F_Src/old_flame/fcylflame.f90 Tools/Postprocessing/F_Src/old_flame/fflamelength.f90 Tools/Postprocessing/F_Src/old_flame/finteg.f90 Tools/Postprocessing/F_Src/old_flame/fturbkin.f90 Tools/Postprocessing/F_Src/old_flame/fwidth.f90 Tools/Postprocessing/F_Src/tutorial/fspeciesmass2d.f90 Tools/Postprocessing/F_Src/tutorial/fwrite2d.f90 commit da9e48deb9ed3ed7c980ceb9b138753b69149418 Author: Weiqun Zhang Date: Tue Jun 21 15:53:46 2016 -0700 Fortran random: clean up Src/F_BaseLib/bl_random_c.H Src/F_BaseLib/bl_random_c.cpp commit 37b182fc8930810792d223836723575bd5c22353 Author: Weiqun Zhang Date: Tue Jun 21 15:41:58 2016 -0700 Fortran random: update tutorial Tutorials/Random_F/main.f90 commit d16b04eb00aa26dfcd96e29b5b01068193472422 Author: Weiqun Zhang Date: Tue Jun 21 15:40:05 2016 -0700 Fortran random: remove change_distribution Src/F_BaseLib/bl_random_f.f90 commit 7c7de12fbdcb56552d45bd50dd595dae3075fb66 Author: Weiqun Zhang Date: Tue Jun 21 15:32:21 2016 -0700 Fortran random: separate engine from distribution just like C++ standard Src/F_BaseLib/bl_random_c.H Src/F_BaseLib/bl_random_c.cpp Src/F_BaseLib/bl_random_f.f90 Tutorials/Random_F/main.f90 commit f5dd5900f3ef7df357acde3866f4d75866ef79a3 Author: vince Date: Tue Jun 21 13:57:18 2016 -0700 add new test to makefile. Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Sidecar_EX1/Make.package commit 2191b221be40a3ef37bd790e6e4a1c88322c8203 Author: Michael Zingale Date: Tue Jun 21 16:41:39 2016 -0400 remove debug print Tools/F_scripts/write_probin.py commit 4e398a10efc55cfb9d152c35afa767b1094125c4 Author: Michael Zingale Date: Tue Jun 21 16:40:32 2016 -0400 fix priorities Tools/F_scripts/write_probin.py commit 9443bee4516b96b4922112b0300fa74167c5d873 Author: Michael Zingale Date: Tue Jun 21 12:58:44 2016 -0400 add some help Tools/F_scripts/findparams.py commit 17b54f07b401cae511795832f523018d2d982e4c Author: Michael Zingale Date: Mon Jun 20 21:38:46 2016 -0400 some cleaning -- no change in functionality Tools/F_scripts/write_probin.py commit 48fb87de44a91d22a04c0da1c3a10634c1267c3e Author: Weiqun Zhang 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 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: d201f6e55 689256eb6 Author: Michael Zingale Date: Mon Jun 20 18:58:41 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit d201f6e559526858758fb754258c21fff0e60f58 Author: Michael Zingale Date: Mon Jun 20 18:57:47 2016 -0400 add the ability to inspect the zone where the largest error (for a given variable) is set Tools/Postprocessing/F_Src/fcompare.f90 commit 7190908b3efafb87b7705efc66a2c8e8852dee72 Author: vince Date: Mon Jun 20 15:30:10 2016 -0700 add check for ranks moving both from and to comp during sidecar resize. this is currently disallowed. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tutorials/Sidecar_EX1/TestRankSets.cpp commit 8ee5a13d86237b958a1d628f2cb0929584caaff9 Author: Weiqun Zhang Date: Mon Jun 20 14:35:44 2016 -0700 remove extra MultiFabUtil.H and .cpp. Src/C_BaseLib/Make.package commit 689256eb6c29e334e61c7b3573ffd3b6a1ecba94 Merge: b4cbaf0d5 9eda5ccb9 Author: Michael Zingale Date: Sat Jun 18 16:20:19 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit b4cbaf0d50fb897c90cbc575322cb92a9bd80eaa Author: Michael Zingale Date: Sat Jun 18 16:20:02 2016 -0400 only consider the base name of the aux files when copying Tools/RegressionTesting/regtest.py commit 9eda5ccb971bb93bb4e20aaab13d22c1008af54c Author: Weiqun Zhang Date: Thu Jun 16 15:15:45 2016 -0700 GCC option for fsantizer Tools/F_mk/comps/gfortran.mak commit abade70376cb162d786bf1c0acf05841c53d47c1 Author: Weiqun Zhang Date: Thu Jun 16 15:15:12 2016 -0700 Fortran BoxLib: respect do_init_fabs parameter Src/F_BaseLib/fab.f90 commit cfb9bf2c9b7a06efbb7dfe19e262f5d1c20ccbee Author: vince Date: Thu Jun 16 14:12:15 2016 -0700 added file to test resizing sidecars with disallowed rank sets. Tutorials/Sidecar_EX1/TestRankSets.cpp commit 19b8225790254794bac7c664e37186b533c47d40 Author: vince Date: Thu Jun 16 12:29:19 2016 -0700 random sidecar ranks test. Tutorials/Sidecar_EX1/NSidecarsTest.cpp commit 8fa4fa123c6dbebe5747188a7605f440f03802a4 Author: vince Date: Thu Jun 16 12:26:56 2016 -0700 clarified comments. Src/C_BaseLib/Utility.H commit 98edfa89a1b6f12b8257379de0b7483939a83941 Author: Michael Zingale Date: Wed Jun 15 19:52:16 2016 -0400 this scripts are obsolete things should be switched over to to the python version, makebuildinfo.py See Maestro's GMakestro.mak and the rule for build_info.py for an example of using that. Tools/F_scripts/make_build_info Tools/F_scripts/make_build_info2 commit d80c690f213f7c4132d2efa113dbd3727b003340 Author: Michael Zingale Date: Wed Jun 15 19:51:46 2016 -0400 clean this up and switch to argparse this now requires python 2.7 or later Tools/F_scripts/makebuildinfo.py commit 59e5ba24226f20284320c2f68120e7ee537c3530 Author: Michael Zingale Date: Wed Jun 15 10:58:51 2016 -0400 port the job_info_field3 stuff over from this point forward, new features will only go into regtest.py and co, testnew.py will not be updated with new features Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py commit 559a50951cc1129ca1c0beb87bed1c11b195c8f0 Merge: f6c347a0f 4e6ea8d7c Author: Michael Zingale Date: Wed Jun 15 10:37:30 2016 -0400 Merge branch 'master' into development commit f6c347a0f900633d4c0dadae3a4f6e5f4d950ddb Author: Andy Nonaka Date: Mon Jun 13 16:36:14 2016 -0700 if generating a random seed, print out the seed Src/F_BaseLib/bl_random_f.f90 commit a452aa09ec9c6dff7fba87e08ea6182f0316e9bf Author: Andy Nonaka Date: Mon Jun 13 15:18:00 2016 -0700 seed verbosity Src/F_BaseLib/bl_random_f.f90 commit 83cc3c8d5274c2ab2143a6d1b5582178bba0549c Merge: 41b03612d 37969e197 Author: Andy Nonaka Date: Mon Jun 13 14:04:49 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 41b03612d7a1f800892df31482bd44937f1be0aa Author: Andy Nonaka Date: Mon Jun 13 14:04:32 2016 -0700 print out the random seed info Src/F_BaseLib/bl_random_f.f90 commit 37969e1976e377cd685379975d61ee130955792e Author: Ann Almgren 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 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 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: 0f537fc9e 34c1b2dcf Author: Andy Nonaka Date: Mon Jun 13 10:37:16 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 0f537fc9e060692b758dce629bf88dbea4d455f0 Author: Andy Nonaka Date: Mon Jun 13 10:35:56 2016 -0700 mpi settings for laptop Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 34c1b2dcf5faaf40c18059b0504cab383d1438b5 Author: Michael Zingale Date: Mon Jun 13 13:31:09 2016 -0400 saner default -- for 1 plotfile, give each var its own line Tools/Postprocessing/F_Src/fextrema.f90 commit 5e15da676569bfda06e0c052772b234163662b16 Author: Michael Zingale Date: Mon Jun 13 09:13:30 2016 -0400 add integrator Tools/F_scripts/makebuildinfo.py commit 3bcd8d17a93873b020f1f49670c03f99377d80e7 Author: Max Katz Date: Sat Jun 11 23:35:19 2016 -0400 Add Cray compiler version variables to C_mk Tools/C_mk/Make.Linux commit 560db9f4dfacff7684a2d864a8d353d187ad3690 Author: Michael Zingale Date: Sat Jun 11 16:45:43 2016 -0400 the stub version of parallel_tag needs reset Src/F_BaseLib/parallel_stubs.f90 commit e4a2bd665a5fe05c58741611af56e829e3511875 Author: Max Katz Date: Sat Jun 11 11:38:33 2016 -0400 Permit disabling of forced plotfile on checkpoint Presently the code writes a plotfile when we force a checkpoint with the dump_and_stop or dump_and_continue capability. We can now disable this behavior by setting amr.write_plotfile_with_checkpoint = 0. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit ded4c690c693239dde5bcc6e38da1979aa457ca8 Author: Weiqun Zhang Date: Fri Jun 10 16:45:02 2016 -0700 Fortran BoxLib: reset mpi tag after fancy bottom solve Src/F_BaseLib/parallel.f90 Src/LinearSolvers/F_MG/mg.f90 commit 6f301a06f6c8265ca16b6a0b605879722159f4d8 Author: vince Date: Fri Jun 10 12:21:13 2016 -0700 new mpi location for naphta. Tools/C_mk/Make.mpi commit 50b868ce8d63643144061a481d064dff787cda49 Author: vince Date: Fri Jun 10 12:19:07 2016 -0700 more testing of multiple sidecars. Tutorials/Sidecar_EX1/NSidecarsTest.cpp commit 0b6f697443c3d294b85fcf14454a648a8fb5babe Author: vince Date: Fri Jun 10 12:18:20 2016 -0700 added commBoth, removed default whichSidecar. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 6a9475b8799c2fe67a64799b3d1cc33fc617ff49 Author: vince Date: Fri Jun 10 12:11:46 2016 -0700 more documentation. Docs/Readme.sidecars commit fe38fa861a7704aac4bf427cc1e43ceebda8572b Author: vince Date: Fri Jun 10 11:39:25 2016 -0700 add copyInter support for multiple sidecars. Src/C_BaseLib/FabArray.H commit f68f1c1fbd5700d574556dd7437f7aacac5ea66f Merge: 8eee587a5 7cd7f838b Author: Brian Friesen Date: Fri Jun 10 09:26:59 2016 -0700 Merge branch 'particle_threading' into development These commits slightly change the way OpenMP parallelizes over particles to improve thread scaling when using a small number of boxes with a large number of threads per MPI process. commit 7cd7f838b9847b761a30b6221ab873954635c78d Author: Brian Friesen Date: Fri Jun 10 09:12:52 2016 -0700 ParticleContainer: add TODO about tiling over grid loop in AssignCellDensitySingleLevel() Src/C_BaseLib/Particles.H commit 35abc24efabf2dd6080b65aad1d7064fffff915c Author: Brian Friesen Date: Fri Jun 10 09:11:36 2016 -0700 ParticleContainer: add comment suffix to #endif for NEUTRINO_PARTICLES for clarity Src/C_BaseLib/Particles.H commit 663544fe49b12de18edf6cbd3e315b87f74e4134 Author: Brian Friesen Date: Thu Jun 9 18:37:21 2016 -0700 ParticleContainer: move OpenMP parallel region from grid loop to PBox loop in AssignCellDensitySingleLevel() If the OpenMP region parallelizes over grids, and if we have a small number of large grids and a large number of OpenMP threads (which is the typical Nyx use case), then this routine scales extremely poorly. So instead we parallelize threads over PBoxes within each grid, which leads to much better thread scaling. Src/C_BaseLib/Particles.H commit 985ebc21f4439ddef113f7b1cba8259dc1485e0a Author: vince Date: Thu Jun 9 16:34:01 2016 -0700 update for multiple sidecars. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 98b178191b4315352484c9c1a020c462c99f6fba Author: vince Date: Thu Jun 9 16:33:34 2016 -0700 update for multiple sidecars. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit b6346fab1ddbf2c9898388dceb99bf7c6cdd8d0d Author: vince Date: Thu Jun 9 16:03:29 2016 -0700 remove send to sidecar function. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 7289dd1872d386074890786ba42408c0069cc896 Author: vince Date: Thu Jun 9 15:56:34 2016 -0700 remove SendMultiFabToSidecars function, use FabArray::copyInter instead. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 8eee587a5572803c1d7e75815b92e2f8ed56003c Merge: fe60abf9c 58a032346 Author: Adam M. Jacobs Date: Thu Jun 9 18:13:14 2016 -0400 Merge upsteam 'development' into Adam's local 'development' commit fe60abf9c1ca2086411d4d7d17486d4041ad4d91 Author: Adam M. Jacobs Date: Thu Jun 9 18:09:00 2016 -0400 Add a comment to particle_where noting it sets particle properties. I found this to be quite unexpected, so I wanted to document in the code that particle_where doesn't just indicate a particle's position is valid within the grid heirarchy but also sets a found particle's level, grid, and cell properties. Src/F_BaseLib/particles_f.f90 commit 2f3e12605ef05b4cc5aa00d6fa24401674c4d0fa Author: vince Date: Wed Jun 8 13:44:37 2016 -0700 include both local and global ranks in filename. Src/C_BaseLib/BLBackTrace.cpp commit 4b917b687afe85e7db80c193337f6efeaa758c74 Author: vince Date: Tue Jun 7 16:47:54 2016 -0700 started documenting the sidecars. Docs/Readme.sidecars commit 58a032346fb39b2b3050d7a71e937b92b21384f6 Author: Ann Almgren Date: Tue Jun 7 16:30:29 2016 -0700 Put in error statement if we try to call create_umac_grown with factor 4 refinement since we don't currently support that Src/F_BaseLib/create_umac_grown.f90 commit 96947fba4f8af4cccd14371cd5b5ebc0791cc73b Merge: b751105de be8d7f090 Author: Ann Almgren Date: Tue Jun 7 15:08:43 2016 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit b751105debdca92cf0970946aeeb79ef3b2694f0 Author: Ann Almgren Date: Tue Jun 7 15:08:27 2016 -0700 Oops -- was printing the wrong times in my print statement! Tutorials/PIC_C/single_level.cpp commit be8d7f09056dbf34b5a097194340098d151bcb3e Merge: bb64b23f6 b2d24ed12 Author: Michael Zingale Date: Tue Jun 7 14:24:29 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit bb64b23f6dc318ec6801502f7db20482bf387547 Author: Michael Zingale Date: Tue Jun 7 14:23:23 2016 -0400 add a module flexibilty way of specifying build components now you can use --module to send in key=value for the different components, e.g., as: "EOS=helmeos NETWORK=triple_alpha" and get them through the module name and value functions Tools/C_scripts/buildInfo.H Tools/C_scripts/makebuildinfo_C.py commit b2d24ed1234b253650f0d0787457e8d8b705d920 Author: Weiqun Zhang Date: Mon Jun 6 21:24:40 2016 -0700 make sure mpi tags in Fortran and C++ do not overlap Src/F_BaseLib/parallel.f90 commit 3a71ba4e02e474fbb24eb54e21c96e7b4ad60cc3 Author: Weiqun Zhang Date: Mon Jun 6 17:06:04 2016 -0700 Fortran BoxLib: add a function that returns mpi tag just like C++ BoxLib; don't call mpi_wait unless the size mpi statuses is greater than 0 Src/F_BaseLib/multifab_f.f90 Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit d8f7b826be6ac749db8b96c01641b91b398685b5 Author: vince Date: Mon Jun 6 17:04:24 2016 -0700 write proc number to abort message. Src/C_BaseLib/BoxLib.cpp commit 644491f3906157e9c4c670e9498f97aabd4e3e7d Author: vince 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 Date: Sat Jun 4 13:34:06 2016 -0700 Release Notes 16.06 ReleaseNotes/release-notes-16.06 commit 16d972d92ab93c47c1f99f7080f5e73cfaf867f8 Merge: 9eae5b88c 792ac5a74 Author: Weiqun Zhang Date: Sat Jun 4 12:54:54 2016 -0700 Merge branch 'development' Conflicts: Tools/C_mk/Make.defs commit 792ac5a743d56ef1bde43f986fd02bd71ff783d7 Author: Michael Zingale Date: Fri Jun 3 21:00:31 2016 -0400 remove ALCF intrepid and all bits of Intel < 13 Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 47807e4362f5278cf6e74963a5187bfa31b5f646 Author: Michael Zingale Date: Fri Jun 3 20:24:37 2016 -0400 remove OSF1 and Intel 11,12 support -- they're old Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_intel.mak Tools/F_mk/comps/osf1.mak commit f0c49d9ed238f1f4bee145238225ffd4dbb683ad Author: Michael Zingale Date: Fri Jun 3 16:26:37 2016 -0700 define intel versions so they appear in job_info Tools/C_mk/Make.defs commit 6071394e5c38010ebbd84f6ae2f6a804e645dfb8 Author: Weiqun Zhang Date: Thu Jun 2 22:17:50 2016 -0700 PIC_C: fix memory leak Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/two_level.cpp commit bb89a7db6e511af645abf839767508668946c1aa Author: Ann Almgren Date: Thu Jun 2 18:31:07 2016 -0700 This verison of PIC_C is designed for doing timing studies. There is also now an inputs file rather than hard-wiring the size of the problem into main.cpp Tutorials/PIC_C/GNUmakefile Tutorials/PIC_C/Make.package Tutorials/PIC_C/README Tutorials/PIC_C/inputs Tutorials/PIC_C/main.cpp Tutorials/PIC_C/single_level.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/two_level.cpp commit 6c1a2affcdf5b833986bdd274a46b78193fa0169 Author: Weiqun Zhang Date: Thu Jun 2 09:50:58 2016 -0700 Make: option to use fsanitizer for debug build too Tools/C_mk/Make.defs commit 6c3e0ae1a4499690236dce7d8d1d9c20555577f1 Author: Michael Zingale Date: Wed Jun 1 22:39:35 2016 -0400 some cleaning Tools/RegressionTesting/test_report.py commit 6c85d0328509dd60a1eb7583b5edf055d15d4983 Author: Michael Zingale Date: Wed Jun 1 22:39:27 2016 -0400 simplify run() Tools/RegressionTesting/test_util.py commit 636cfc416a7783a3d7d3a6d7196c6b2d390ad663 Author: Michael Zingale Date: Wed Jun 1 21:09:53 2016 -0400 clean up the warnings Tools/RegressionTesting/params.py Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_util.py commit 9814217b870627372f947134c8fa2e2205325360 Author: Michael Zingale Date: Wed Jun 1 20:33:31 2016 -0400 a little more clean-up Tools/RegressionTesting/regtest.py commit e2de7dc31e58da8bc2a85088770de85e7793e729 Author: Michael Zingale Date: Wed Jun 1 19:47:31 2016 -0400 more refactoring Tools/RegressionTesting/regtest.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_util.py commit 01c69f1c4e10b92ca742f631fa938965078c6dd4 Author: Michael Zingale Date: Wed Jun 1 15:19:11 2016 -0400 start of some refactoring split up the main test suite into separate files to make it easier to maintain. regtest.py is now the entrypoint. Tools/RegressionTesting/params.py Tools/RegressionTesting/regtest.py Tools/RegressionTesting/repo.py Tools/RegressionTesting/suite.py Tools/RegressionTesting/test_report.py Tools/RegressionTesting/test_util.py commit 3592a09826ca6eb4ae6b3121eb303fa0bf71e4d3 Author: Weiqun Zhang Date: Tue May 31 10:55:16 2016 -0700 Fortran bl_random: use 0 as a special flag for using random device to generate a seed Src/F_BaseLib/bl_random_c.cpp Src/F_BaseLib/bl_random_f.f90 commit 39a617f655407d50222068a48a42215ba3b7b4ac Author: Michael Zingale Date: Tue May 31 12:34:43 2016 -0400 need to rename job_info when copying to the web dir this prevents job_info from being overwritten by the next test Tools/RegressionTesting/testnew.py commit ece381eee676e2ec6d7101f1d8323af388eb69d6 Merge: 553d30a6d 193faaa57 Author: Michael Zingale Date: Tue May 31 12:29:41 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 193faaa5718e34544314af476031b02e604ed3d5 Author: Weiqun Zhang Date: Mon May 30 20:44:45 2016 -0700 MultiColor_C: minor Tutorials/MultiColor_C/main.cpp commit e89d789f12d1bb95d361d4ed07d13601cca50d07 Author: Weiqun Zhang Date: Mon May 30 18:10:12 2016 -0700 MultiColor_C test: add a ne fortran file Tutorials/MultiColor_C/ff.f90 commit 8fffa7cc39596d202b168429b8c96ad8656654ba Author: Weiqun Zhang Date: Mon May 30 18:09:24 2016 -0700 Color C_CellMG Src/C_BoundaryLib/BndryRegister.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp Tutorials/MultiColor_C/Make.package Tutorials/MultiColor_C/inputs Tutorials/MultiColor_C/main.cpp commit eb26240969ef7faa20ec11cbc96a0605961eb7a6 Author: Weiqun Zhang Date: Mon May 30 16:29:26 2016 -0700 color InterpBndry and MacBndry Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp Src/C_BoundaryLib/MacBndry.H Src/C_BoundaryLib/MacBndry.cpp commit 31d37bf289996d2b060dce121b06a26ca57a35e7 Author: Weiqun Zhang Date: Mon May 30 13:38:31 2016 -0700 color BndryData Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp commit 49cae39bed3e512eb6dd0d276c279812863a2b06 Author: Weiqun Zhang Date: Mon May 30 13:28:44 2016 -0700 color BndryRegister Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit 7af662492946bdabfe7983e64664817b015e07c0 Author: Michael Zingale Date: Mon May 30 11:27:16 2016 -0400 if a restart test produces backtraces -- abort previously we didn't look for backtraces on the first run of a restart test. Now we do and abort if they are produced. Tools/RegressionTesting/testnew.py commit 553d30a6d46533ed43192dfaa3598e5e3f4b93a3 Merge: 78729fc72 151f8a688 Author: Michael Zingale Date: Sun May 29 22:28:59 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 151f8a688e5a1734c9f058e97ffff05cf7c98113 Author: Max Katz Date: Sun May 29 22:17:06 2016 -0400 Turn off PGI Fortran debug symbols if using OpenACC Tools/C_mk/Make.Linux commit 75376b97bcf9de8d08d1956b7fc4b7d5ab0cd396 Author: Weiqun Zhang Date: Sun May 29 17:30:02 2016 -0700 Color FabSet Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit ebbae08e1b6672699dcd94b22153cbe59dd0c7cd Author: Weiqun Zhang Date: Sun May 29 09:59:13 2016 -0700 Fortran bl_random: more assertion and make sure no duplicates in parallel seeds Src/F_BaseLib/bl_random_c.cpp commit f761d17d5f1926e6d98f3c5459d75ebc76977e19 Author: Weiqun Zhang Date: Sun May 29 09:47:45 2016 -0700 Fortran bl_random: assert seed >0 Src/F_BaseLib/bl_random_f.f90 commit f10c67208fee9457298f72227d1e8b5e0c0f7df1 Author: Weiqun Zhang Date: Sat May 28 23:20:38 2016 -0700 Fortran bl_random: Use random numbers instead of seed_seq as parallel seed. The latter has a high chance of collision. Src/F_BaseLib/bl_random_c.cpp commit 5a4e91df3809c121a0ffd3a7d5bd0b7fe9fc050b Author: Michael Zingale Date: Sat May 28 21:58:06 2016 -0400 fix formatting of the job_info summary fields Tools/RegressionTesting/testnew.py commit a6a1d7faae3ec8c60d7fbf856d95deb124d77793 Author: Michael Zingale Date: Sat May 28 21:11:07 2016 -0400 if we produce backtraces, we fail Tools/RegressionTesting/testnew.py commit 78729fc72a6f3f08b1af65181d5c1112118cae3a Author: Michael Zingale Date: Sat May 28 20:32:17 2016 -0400 shorten some headings Tools/RegressionTesting/testnew.py commit 074e2aa8f98e2ab9b72b98a0c38e49f3816731a8 Author: Michael Zingale Date: Sat May 28 18:58:19 2016 -0400 initialize the job_info fields Tools/RegressionTesting/testnew.py commit da05ade716a65033f06865749b11b7a48424c6b6 Merge: c14401dae 8f24082ee Author: Michael Zingale Date: Sat May 28 16:02:43 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit c14401dae0457a6a08c6b21eeec9847402011dbd Author: Michael Zingale 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 Date: Sat May 28 14:56:34 2016 -0400 update prototypes Tools/C_scripts/buildInfo.H commit 0ff28f2d3e1cf18e164043e986f4d5f53353b636 Author: Michael Zingale Date: Sat May 28 14:41:42 2016 -0400 hook in the compiler versions Note: we cannot quote the shell output because we quote it when passing to the makebuildinfo_C.py routine, and trouble ensues. Also make the names consistent Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_scripts/makebuildinfo_C.py commit 3d7c62be7b05ef563c1ff95b7019a736720d5a9c Merge: 872630aa9 913764148 Author: Michael Zingale Date: Sat May 28 14:27:26 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 872630aa97c010d1bb3486cca03591f2d08af8e9 Author: Michael Zingale Date: Sat May 28 14:27:01 2016 -0400 add FCOMP_VERSION and CCOMP_VERSION for gfortran and PGI THis mirrors the F_mk stuff Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit 913764148efc5397428375159959629f4d70be27 Author: Michael Zingale Date: Sat May 28 13:43:59 2016 -0400 robustify the summary table Tools/RegressionTesting/Maestro-tests.ini Tools/RegressionTesting/testnew.py commit 88194d2adddf64b9ca5e29b428fd999b11a80783 Author: Weiqun Zhang Date: Fri May 27 21:46:51 2016 -0700 Fortran bl_random: minor tweak Src/F_BaseLib/bl_random_c.cpp commit 85e68cc646a38590013a8748622b6d206c880b26 Author: Michael Zingale Date: Fri May 27 21:41:27 2016 -0400 updated test file Tools/RegressionTesting/Castro-SBU-tests.ini commit b180eb1b00169bfcafacc09ad67a27586345fa12 Author: Michael Zingale Date: Fri May 27 21:36:01 2016 -0400 add custom fields to the summary table Now we can define special fields to appear in the suite summary table. These fields should appear in the job_info file, and we split on a ":", and store the result in the table (we also remove anything before the last "/" to handle paths) Tools/RegressionTesting/testnew.py commit caf0f1e09c5eae47627f6c5b3cdb9ce574052d73 Merge: 23e3ef166 ad40f8dd4 Author: Michael Zingale Date: Fri May 27 20:03:20 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 23e3ef1669f08e8138a30eb7bb7de0e3ddd5aed7 Author: Michael Zingale Date: Fri May 27 20:02:44 2016 -0400 add network, EOS, and conductivity for easy parsing in the test suite Tools/F_scripts/makebuildinfo.py commit ad40f8dd422f62de74e37e35893162edabd8e5b9 Author: Weiqun Zhang Date: Fri May 27 17:01:06 2016 -0700 Fortran bl_random: add bl_rng_change_distribution for poisson and binomial Src/F_BaseLib/bl_random_c.H Src/F_BaseLib/bl_random_c.cpp Src/F_BaseLib/bl_random_f.f90 Tutorials/Random_F/main.f90 commit d3401ebb590540d3988a6ac6efffc049a41228f0 Author: Weiqun Zhang Date: Fri May 27 16:17:48 2016 -0700 Fortran bl_random: add binomial Src/F_BaseLib/bl_random_c.H Src/F_BaseLib/bl_random_c.cpp Src/F_BaseLib/bl_random_f.f90 Tutorials/Random_F/main.f90 commit be9419da58987b7648572d9753a74f62bb61cff8 Author: Weiqun Zhang Date: Fri May 27 15:55:15 2016 -0700 Fortran bl_random: add poisson Src/F_BaseLib/bl_random_c.cpp Src/F_BaseLib/bl_random_f.f90 Tutorials/Random_F/main.f90 commit 0d9af67e5e1d59810cbba312ccdc60ff5134a845 Author: Weiqun Zhang Date: Fri May 27 15:40:52 2016 -0700 forgot to add a file Src/F_BaseLib/bl_random_c.H commit fe6de64532abd4fc6511efbf35e1e15401e5b90c Author: Weiqun Zhang Date: Fri May 27 15:19:02 2016 -0700 Fortran: use C++11's random number generators Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_random_c.cpp Src/F_BaseLib/bl_random_f.f90 Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/Linux_cray.mak Tools/F_mk/comps/Linux_intel.mak Tools/F_mk/comps/Linux_pgi.mak Tools/F_mk/comps/gfortran.mak Tutorials/Random_F/GNUmakefile Tutorials/Random_F/GPackage.mak Tutorials/Random_F/main.f90 commit ab0efd2d68af799350e3c922ed99a888dffd615a Author: vince Date: Thu May 26 17:34:43 2016 -0700 working test code with three sidecars. Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Sidecar_EX1/NSidecarsTest.cpp commit e5e1ad5453a640b6eae2435c890b809404b6989b Author: vince Date: Thu May 26 17:30:15 2016 -0700 fix for multiple sidecars. Src/C_BaseLib/ParallelDescriptor.cpp commit 8ac9b2a4d3b1177cda20a21a4affc25443f33be9 Author: vince Date: Thu May 26 17:29:17 2016 -0700 added more error checking. Src/C_BaseLib/ParallelDescriptor.H commit 17384985b9ab5b6709ec57516337a4f8d78446e0 Author: vince Date: Thu May 26 14:48:05 2016 -0700 added function for which sidecar. Src/C_BaseLib/ParallelDescriptor.H commit db3841078cd371b02ed296d1f475e154a3b66a50 Merge: efc17f1dd c4d2b9f5b Author: Michael Zingale Date: Thu May 26 12:07:07 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit efc17f1dd8fff0d68005cd2e50cbee0ff7c4e4f0 Author: Michael Zingale 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 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 Date: Wed May 25 13:20:16 2016 -0700 free extra groups. Src/C_BaseLib/ParallelDescriptor.cpp commit c5f1b27b6f70f8802e2ee2bb53014974e56b61dc Author: Michael Zingale Date: Wed May 25 13:27:08 2016 -0400 add FPP_DEFINES for .F90 preprocessing Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak commit bd44b0de658e9a5df55a6d8c454a12fac548b16d Author: Michael Zingale Date: Wed May 25 13:01:49 2016 -0400 no need to have 2 copies of moddep.pl The C++ build now uses the version in the F_scripts Tools/C_mk/Make.defs Tools/C_scripts/moddep.pl commit 2fe5efbe48f60d7dc032cb1fdbca9f7693770cf1 Author: Michael Zingale Date: Wed May 25 12:45:36 2016 -0400 sync up with the version in C_scripts Tools/F_scripts/moddep.pl commit 9df4fb965d4101e0b9bb2f9cb779fd573a4e203e Author: Max Katz Date: Wed May 25 11:49:42 2016 -0400 Conditionally disable -g on PGI when using OpenACC Tools/F_mk/comps/Linux_pgi.mak commit da74b7ea04080600471540bdb5a4363ecfe52e97 Merge: 919cba8e4 f964d7f3c Author: Max Katz Date: Wed May 25 11:42:37 2016 -0400 Merge branch 'development' into openacc commit f964d7f3c91e2978971438f501568d6e66c17309 Author: Michael Zingale Date: Wed May 25 11:16:41 2016 -0400 add support for .F90 files -- these will be preprocessed. We adopt the convention that the Fortran compiler is smart enough to handle the preprocessing, recognizing the .F90 (caps) means preprocess Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak commit 40ad46de290097bdfff17711b15c39a87deb6188 Author: Michael Zingale Date: Wed May 25 11:15:28 2016 -0400 make the Fortran dependency script recognize .F90 too Tools/F_scripts/moddep.pl commit 9a40a1c8e8708f05328ad1a61c4ae03acaac8cf9 Merge: 34997c400 e49345048 Author: Michael Zingale Date: Wed May 25 10:40:59 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 34997c4000a1ab3de36e233ed1f5da7f83d2ce1f Author: Michael Zingale Date: Wed May 25 10:40:37 2016 -0400 fix the permissions so this is executable so 'make doc' works Tools/F_scripts/f90doc/f90doc commit e49345048292994ff938401202c16aee2b86262e Merge: 318ca6c4f bb9f3d64a Author: Ann Almgren Date: Wed May 25 07:04:45 2016 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development Conflicts: Src/F_BaseLib/ml_nd_restriction.f90 commit 318ca6c4f0d4c1dbfbb0086bab55554990ee4da7 Author: Ann Almgren Date: Wed May 25 07:03:25 2016 -0700 Oops -- should have removed mp_crse, mp_fine Src/F_BaseLib/ml_nd_restriction.f90 commit bb9f3d64ae442584bbbf40f228a36e5b1e6cc343 Author: Michael Zingale Date: Wed May 25 08:40:46 2016 -0400 fix the OMP here Src/F_BaseLib/ml_nd_restriction.f90 commit 0a24a157b0cdb6cc3aba8429692e0cda79abbc5c Merge: fa8895e98 a4fe94c7f Author: Michael Zingale Date: Tue May 24 20:42:45 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit fa8895e98e6e4286f22af501e2439f9333eb84e1 Author: Michael Zingale Date: Tue May 24 20:42:22 2016 -0400 cause why not ... define FIVE12TH and FIVE32ND Src/F_BaseLib/bl_constants.f90 commit 92fa8c51ca3dd45594715976ac214e114e3b6531 Author: vince Date: Tue May 24 16:13:07 2016 -0700 added a new test. Tutorials/Sidecar_EX1/NSidecarsTest.cpp commit 039bf2ddde3564ae6ee04c7254823e70fcb3aa42 Author: vince Date: Tue May 24 16:12:47 2016 -0700 added a new test. Tutorials/Sidecar_EX1/Make.package commit 65dd12525c634880287bd4b8f139a971de0cde7d Author: vince Date: Tue May 24 16:12:23 2016 -0700 update test for latest boxlib dsc. Tutorials/Sidecar_EX1/DestMFTest.cpp commit c7617c38143d74241edf1d1d0939e344ef61347d Author: vince Date: Tue May 24 16:11:37 2016 -0700 fix group free for zero sidecars. Src/C_BaseLib/ParallelDescriptor.cpp commit a4fe94c7f9c04b07fbec3837676059a0ec97e56e Merge: 2fa5f517d e12b35845 Author: Ann Almgren Date: Tue May 24 15:26:30 2016 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 2fa5f517d2fb45fc3adb17d03b103f57a7e2057c Author: Ann Almgren Date: Tue May 24 15:26:11 2016 -0700 Add nodal injection (in addition to nodal restriction) Src/F_BaseLib/ml_nd_restriction.f90 Src/F_BaseLib/nodal_restriction.f90 commit 351b0af891d32df3e1666435b8b0f7c4dd9b8f20 Author: vince Date: Tue May 24 14:21:35 2016 -0700 fix for serial. Src/C_BaseLib/ParallelDescriptor.cpp commit a0b0e7e102b99ae1e3a685e6f3a9f0a5a5476a19 Author: vince Date: Tue May 24 14:11:18 2016 -0700 default arg. Src/C_BaseLib/ParallelDescriptor.H commit d2da9753995d23ac87c6d09d6bd008ba3d1d979e Author: vince Date: Tue May 24 13:58:30 2016 -0700 fix for zero sidecars. Src/C_BaseLib/ParallelDescriptor.H commit 4613779b2300a28813af60384f40bcec1f7418d1 Author: vince Date: Tue May 24 13:45:15 2016 -0700 additions for multiple sidecars. fortran interface needs testing. Src/F_BaseLib/parallel.f90 commit 9ac403a22f6620e1a1a4e47cb127ffb57e3e53ce Author: vince Date: Tue May 24 13:44:17 2016 -0700 additions for multiple sidecars. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit e12b35845ccae8564da3cc339bb5625169325d04 Author: Michael Zingale Date: Tue May 24 14:35:45 2016 -0400 fix convert_type wrapper for None Tools/RegressionTesting/testnew.py commit 54ab7e3579d64638e2db229abbc30eb3ec7de8ea Merge: e830c381a 37ee0b85c Author: Michael Zingale Date: Tue May 24 14:32:10 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit e830c381ac737800afa745c4134799ca93027905 Author: Michael Zingale Date: Tue May 24 14:31:58 2016 -0400 a little clean-up Tools/RegressionTesting/testnew.py commit 37ee0b85cde6dc58f61cc6be19eb09e32a85a2e4 Author: Michael Zingale Date: Tue May 24 11:01:42 2016 -0400 gracefully handle the "grids don't match" error from fcompare Tools/RegressionTesting/testnew.py commit 9ad353b5872e5d549b02ccad02a65023464b548a Merge: da9ad0a75 1d756884e Author: Michael Zingale Date: Sun May 22 16:39:23 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 1d756884e0779f0f0a89816adf1086415fb66cfd Author: Weiqun Zhang Date: Fri May 20 22:56:01 2016 -0700 a multi-color test Tutorials/MultiColor_C/GNUmakefile Tutorials/MultiColor_C/Make.package Tutorials/MultiColor_C/inputs Tutorials/MultiColor_C/main.cpp commit 7b52641ab4b1aa8e5cb1bb8e3216d277e4134bc1 Author: Weiqun Zhang Date: Fri May 20 17:14:55 2016 -0700 fix non-parallel build Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ccse-mpi.H commit 83822b4885744c493fa818940caebcd2885263cc Author: Weiqun Zhang Date: Fri May 20 16:51:34 2016 -0700 make reduce work with color Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/iMultiFab.cpp commit c9d4a74c7e45109f61670519deaecf734f17e59a Author: Weiqun Zhang Date: Fri May 20 13:49:13 2016 -0700 update SeqNum functions for multi-color Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 107ac44f0b6b4e24bea6ee2f1d5871a37c3aca87 Author: Weiqun Zhang Date: Thu May 19 21:52:18 2016 -0700 operator<< for ParallelDescriptor::Color Src/C_BaseLib/ParallelDescriptor.H commit a76aec166d7fe1b143e757312be9b68a1dc83f24 Author: Weiqun Zhang Date: Thu May 19 21:15:33 2016 -0700 DistributionMapping: finished coloring Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 71ee01ddcf0e928d6b7a7bdfc361145ad3a1daf1 Author: Weiqun Zhang Date: Thu May 19 10:56:41 2016 -0700 DistributionMapping: use color as part of the key Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 055648c85867b3207ba9f5fdae0d23b55d8b1d0c Author: Weiqun Zhang Date: Thu May 19 10:34:59 2016 -0700 replace int type color with ParallelDescriptor::Color class for type safety Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit b1e80e20024d2e776eedb55a177aabe5a2f6018b Author: Weiqun Zhang Date: Thu May 19 07:13:36 2016 -0700 remove useless 'explicit' Src/C_BaseLib/BLBackTrace.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 71b8711fe3b5364c7e2d77aba463cf7d9f566281 Author: Weiqun Zhang Date: Wed May 18 22:30:44 2016 -0700 start sub-communicators controlled by boxlib.ncolors Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tutorials/MultiGrid_C/GNUmakefile commit b3706b953b927f05c1cba96ff72c40963092738b Author: Weiqun Zhang Date: Fri May 20 17:01:19 2016 -0700 clean up an unused template for parallel reduce Src/C_BaseLib/ParallelDescriptor.H commit 9eae5b88c2cf97d8c8ea250c36710d6ced7afd58 Author: Weiqun Zhang Date: Fri May 20 11:21:42 2016 -0700 update make for CCSE machines because of new MPI installation Tools/C_mk/Make.defs Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 136b6392c23d41a256662424af2291840c8a75e9 Author: Weiqun Zhang Date: Fri May 20 10:38:15 2016 -0700 update make for battra and baragon Tools/C_mk/Make.defs Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 4e0234d8cf2fd8b1488aef527a5dbb97a299284b Author: Weiqun Zhang Date: Fri May 20 11:21:42 2016 -0700 update make for CCSE machines because of new MPI installation Tools/C_mk/Make.defs Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 63b78366a82eb9d88d406c24fb3076aa75c257f7 Author: Weiqun Zhang Date: Fri May 20 10:38:15 2016 -0700 update make for battra and baragon Tools/C_mk/Make.defs Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 20d3b1c2ac184406d1bee40686459dca7f2eac58 Author: Max Katz Date: Thu May 19 19:51:30 2016 -0400 Permit disabling of PGI OpenACC Tools/C_mk/Make.Linux commit 54a361ccf5f1947ff565053321bc26a519435c61 Author: vince Date: Thu May 19 14:58:13 2016 -0700 additions for multiple sidecars, check bl_fortran_set_nprocs_sidecar. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 77f06c16733d282d30f63de4fe994cb39039bb87 Author: vince Date: Thu May 19 14:56:56 2016 -0700 fixes for multiple sidecars. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 1c2bb06731cfde122545e4f54985ad5d2389b968 Author: Weiqun Zhang Date: Thu May 19 08:24:11 2016 -0700 fix bug in my last commit Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 4738dbd8059c31ed823e97e63cc1fe0ed0d9f5d5 Author: vince Date: Wed May 18 18:00:04 2016 -0700 dont need arrays for sidecar groups or comm. made simple interface function for one sidecar case. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit d6016415ffc8b1edc181b9019a354a60f3f4bd62 Author: vince Date: Wed May 18 16:03:46 2016 -0700 update NProcsSidecar for multiple sidecars. Src/C_BaseLib/ParallelDescriptor.H commit 0919756abd7aeb173be7f89750a04ae430c213d5 Author: vince Date: Wed May 18 15:43:36 2016 -0700 update SetNProcsSidecars to support multiple sidecars. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 66abf3925b6f321dca66721ff0053386b3235422 Author: Weiqun Zhang Date: Wed May 18 13:36:55 2016 -0700 MultiFab::norm0 add nghost optional argument Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/iMultiFab.H Src/C_BaseLib/iMultiFab.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 31152ff89df765c6aa37da6a400ac5bb61e0b4d2 Author: Weiqun Zhang Date: Tue May 17 12:25:10 2016 -0700 typo Src/C_BaseLib/ParallelDescriptor.H commit 9b928b6f129a8b38b192d9add29fd4ae21e6c6c2 Author: Weiqun Zhang Date: Tue May 17 12:19:02 2016 -0700 runtime parameter team.reduce Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 9e48c86442eeab6b16d6e3925e1be1241d5b334e Author: Weiqun Zhang Date: Tue May 17 12:05:39 2016 -0700 keep track of UPC++ and MPI mode Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 51769c0228b3b80b73b386fb9b79d9de38190000 Author: Weiqun Zhang Date: Mon May 16 17:01:45 2016 -0700 Reduce: do team reduce first, then team lead reduce, and finally team bcast Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 3e42ba77dd2bb585d879789f18563c4cbd3becd8 Author: Weiqun Zhang Date: Mon May 16 15:06:38 2016 -0700 Team: create team lead communicator Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit c751987811c6e6c764ad155f2025037c0dac68bf Author: vince Date: Mon May 16 14:04:43 2016 -0700 updated error string and comments. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit ac427b36f9dbc3df641d581f0e9d4e7e0792c8ad Author: Weiqun Zhang Date: Mon May 16 12:24:13 2016 -0700 FMultiGrid: add const Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp commit ecfc8baaaef7af3cbf9d01c9b860c11d4d0bc546 Author: vince Date: Thu May 12 12:19:21 2016 -0700 only print error messages if abortOnError. these may not be errors during transient states. Src/C_BaseLib/FabArray.H commit c9261e6de550bea45105c07389ba41f48552f549 Author: vince Date: Thu May 12 12:14:32 2016 -0700 removed cout. Src/C_AMRLib/Amr.cpp commit da9ad0a75d1fb9c3adcd1f131af8e198c5490c92 Merge: 31acd25d3 5d7efcc2e Author: Michael Zingale Date: Wed May 11 22:24:33 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 5d7efcc2e7f127301836e6545d800aa74b050a4d Author: Weiqun Zhang Date: Wed May 11 12:42:15 2016 -0700 Array: removed the disallowed copy assignment so that C++11 compilers could auto-generate move constructor and move assignment Src/C_BaseLib/Array.H commit e18e3d925fe707af27ece62ca4b8ae9edf9accf6 Author: Weiqun Zhang Date: Wed May 11 12:18:46 2016 -0700 tweak IntVect comparison functions to make it consistent with Fortran convention. Src/C_BaseLib/IntVect.cpp commit e32e8b18e077979a698598529d9165cfcff272a1 Author: Weiqun Zhang Date: Tue May 10 20:50:30 2016 -0700 FillPatch: turn off omp for nodal. This is actually a benign race. Src/C_AMRLib/FillPatchUtil.cpp commit 241026e928590ff7b125b5d6aae51568f1e18d6a Author: Weiqun Zhang Date: Tue May 10 20:35:05 2016 -0700 FillBoundary: avoid writing to valid region Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H commit e18c71de2c95e555d40da181a0eb6f4fcb17ba5c Author: Weiqun Zhang 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 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 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: aaec6519a 58152be5a Author: Adam Jacobs Date: Mon May 9 18:35:11 2016 -0400 Merge branch 'development' into openacc commit 1a2f8ec82893f5e828be07af6307f3b9649be37b Author: Weiqun Zhang Date: Mon May 9 14:07:19 2016 -0700 baragon makefile Tools/C_mk/Make.defs commit 58152be5a2829bb12d46df1db9ed82a91702a427 Author: Michael Zingale Date: Sun May 8 18:55:09 2016 -0400 some more OpenACC PGI flags Tools/C_mk/Make.Linux commit e59fd253b98ecdac88183cce335159119c1a1810 Author: Weiqun Zhang Date: Sat May 7 17:33:24 2016 -0700 update make for baragon Tools/C_mk/Make.defs commit 3424a54597b6c631a378c266cff2f30852852cfc Author: Weiqun Zhang Date: Sat May 7 07:15:33 2016 -0700 fix some minor data race Src/C_BaseLib/MemPool.cpp commit 35085648eeb2974356664680b3c4c3d311b3da03 Author: Weiqun Zhang Date: Sat May 7 07:06:00 2016 -0700 add MultiFab::Saxpy Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 5becf0db126f163652088f85036c443e4808b7a2 Author: vince Date: Fri May 6 15:29:09 2016 -0700 dont abort on CheckFAPointers. Src/C_AMRLib/Amr.cpp commit 4da0c7dee0b06e65529cad2bb86be445f111065f Author: vince Date: Fri May 6 15:17:28 2016 -0700 added option to not abort on errors in CheckFAPointers. Src/C_BaseLib/FabArray.H commit 734537a203be2d7b147265594bf842aebfdb03a3 Author: vince Date: Fri May 6 13:36:17 2016 -0700 cleanup diagnostics. Src/C_BaseLib/FabArray.H commit 85662263af5fb7dec8ec69c593f12eb569d38798 Author: vince 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 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 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 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 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 Date: Thu May 5 17:07:26 2016 -0700 fix logic in new BoxArray::complement Src/C_BaseLib/BoxArray.cpp commit 7deed4faeccfcce72f78410e78517b7af0e959c8 Merge: dfa74ae94 a40ef15f4 Author: Weiqun Zhang Date: Thu May 5 14:38:37 2016 -0700 Merge branch 'development' into weiqun/complement commit a40ef15f4ea61aa253ab2e1a04d91f12a99dff8c Merge: 17bb255f7 4cc1c906d Author: Weiqun Zhang Date: Thu May 5 14:01:39 2016 -0700 Merge branch 'new_reflux' into development commit 4cc1c906d492973ad680689e069c65de7beecae8 Author: Weiqun Zhang Date: Thu May 5 13:23:54 2016 -0700 clean up Src/C_AMRLib/FluxRegister.cpp commit 17bb255f7a1d409000ba7e3db14db57515925dab Author: Michael Zingale Date: Thu May 5 15:35:58 2016 -0400 output more usage defails Tools/Postprocessing/F_Src/fcompare.f90 Tools/Postprocessing/F_Src/ffdcompare.f90 commit e8f6f98304a02caa24ad49c5223e6d4080baa3f4 Author: vince Date: Thu May 5 12:35:30 2016 -0700 another check for data integrity. Src/C_BaseLib/FabArray.H commit dfa74ae94a3515c3b398da0b94c86d92910c2333 Author: Weiqun Zhang Date: Thu May 5 11:18:48 2016 -0700 new complement list Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FabArray.cpp commit d1d520efc3439d0cae7ecebb201e0d76149bd552 Author: Max Katz Date: Thu May 5 01:57:54 2016 -0400 Update the probin script to handle OpenACC declarations Tools/F_scripts/write_probin.py commit e5c66c35d8d327daebba9c57fbe0f4cb06b3d815 Author: Weiqun Zhang Date: Wed May 4 18:12:50 2016 -0700 fix some errors in last commit Src/C_AMRLib/FLUXREG_3D.F commit 6b7813ccf8a2c03495371f391a26e26603be46f6 Author: Weiqun Zhang Date: Wed May 4 18:10:29 2016 -0700 FluxRegister: no longer use CollectData Src/C_AMRLib/FLUXREG_1D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp Src/C_BoundaryLib/FabSet.H commit a5763f202f2a3d4088fa472a353afb10a0e5b46b Author: Weiqun Zhang Date: Wed May 4 15:15:42 2016 -0700 omp in FluxRegister Src/C_AMRLib/FluxRegister.cpp commit f589cf83ee151635ef633940fb261f4905627166 Author: Weiqun Zhang Date: Wed May 4 13:53:26 2016 -0700 omp in BndryRegister Src/C_BoundaryLib/BndryRegister.cpp commit 4f6e12c26d469d7f0a9338e8bda3f5fc63768f88 Author: Weiqun Zhang Date: Wed May 4 12:46:34 2016 -0700 comment Src/C_BoundaryLib/FabSet.cpp commit 181dea331ebd02b02c941e51edf3a973717a9fe2 Author: Weiqun Zhang Date: Wed May 4 12:19:44 2016 -0700 Switch FillCoarsePatch to using the new FillPatch Src/C_AMRLib/AmrLevel.cpp commit 3741ecda0b1f71df81121145d2fbb248ed89afa9 Author: Weiqun Zhang Date: Wed May 4 11:24:08 2016 -0700 fix the new FillCoarsePatch Src/C_AMRLib/AmrLevel.cpp commit 193226ca3f2bc9e6cfe783cd9b4f926a4b0f2b8f Author: Weiqun Zhang Date: Wed May 4 10:40:14 2016 -0700 If the boxarray for a level does not change during regrid, assign the previous boxarray to the current to avoid making a duplicate with the same boxes but different reference id. This will help preserve caches associated with the previous boxarray. Src/C_AMRLib/Amr.cpp commit 5b250a5cba99b30e752ac47cd1f256ad2bc699cf Author: Max Katz Date: Wed May 4 12:50:44 2016 -0400 Use pgcc for compiling C code with PGI Tools/C_mk/Make.Linux commit b304b4fabb15b01b962343288df9c37a835c9628 Author: Weiqun Zhang Date: Tue May 3 17:54:48 2016 -0700 FillPatchIterator: switch to the point-to-point version. This may break some regression tests with nodal data and periodic boundaries. Src/C_AMRLib/AmrLevel.cpp commit 69b535d83127905d0ffa9197d8284fb12a4401c2 Author: Weiqun Zhang Date: Tue May 3 14:58:36 2016 -0700 FillCoarsePatch: optimization Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FillPatchUtil.H Src/C_AMRLib/FillPatchUtil.cpp commit ddf04fdcc155046cdeb1e4c9b79d81576972c08c Author: vince Date: Tue May 3 12:20:56 2016 -0700 mpi_require. Src/C_BaseLib/FabArray.H commit 4a9c25f9ce82bab611411ee81b589162414695cb Author: Weiqun Zhang Date: Tue May 3 12:06:22 2016 -0700 FillPatchCache: fix a bug Src/C_BaseLib/FabArray.cpp commit 0145b2eec0492bbae46b983b4ae8a0ca8f13f482 Author: Weiqun Zhang Date: Tue May 3 09:19:39 2016 -0700 FillPatch: optimization Src/C_AMRLib/FillPatchUtil.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 9e36dbf507db4f14c3bbd5b5b23e8c6d6aed02b2 Author: Weiqun Zhang Date: Tue May 3 08:29:36 2016 -0700 FillPatchCache: fix some bugs Src/C_AMRLib/FillPatchUtil.cpp Src/C_BaseLib/FabArray.cpp commit 7a3d673793f1315acc6a9a3112142e1a0900d75e Author: Weiqun Zhang Date: Mon May 2 16:53:22 2016 -0700 FillPatch cache stats Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 31acd25d37b21d589af0c05a070f4ec779972048 Merge: 596058ab7 a84a67892 Author: Michael Zingale Date: Mon May 2 19:15:30 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 610e92f3aab83731b86cc2d7b0164823d4591841 Author: Weiqun Zhang Date: Mon May 2 15:36:45 2016 -0700 FillPatch cache Src/C_AMRLib/FillPatchUtil.cpp Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/StateData.H Src/C_BaseLib/Box.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit a84a67892b840672df50948a16b3b7c71c7c6264 Author: Weiqun Zhang Date: Mon May 2 10:40:50 2016 -0700 Release Notes 16.05 ReleaseNotes/release-notes-16.05 commit def3694b8a604baf871fae548c93a95da2032a6e Merge: 3465a64aa 4b6f47113 Author: Weiqun Zhang Date: Mon May 2 10:13:10 2016 -0700 Merge branch 'master' into development commit 3465a64aaacf3402334c13d52c5498ccc9d56388 Author: Weiqun Zhang Date: Sat Apr 30 13:37:45 2016 -0700 add ghost cell option to PeriodicCopy Src/C_AMRLib/FillPatchUtil.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 3f6fb05661d46fcc8b9dc7bf6f5b62b1d16bdae0 Author: Weiqun Zhang Date: Fri Apr 29 18:34:44 2016 -0700 fix leastuseteam forUSE_MPI=FALSE Src/C_BaseLib/DistributionMapping.cpp commit 47ac1a30c7750d3b7721465a1a302039d39d9026 Author: Weiqun Zhang Date: Fri Apr 29 17:48:24 2016 -0700 clean up unused CPC constructor Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit e972938c3b825e2fd96c353e50492f4a0b045884 Author: Weiqun Zhang Date: Fri Apr 29 17:21:34 2016 -0700 fix a bug in paralle copy to ghost cells Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 9634cb9540e37a3fb0c059c14a528b53c8cb8af2 Author: Weiqun Zhang Date: Fri Apr 29 15:23:22 2016 -0700 new runtime parameter DistributionMapping.node_size that allows knapsack within a node and SFC at the node level Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 277643662200ac6a4f03db5035a1293a1cc3dec8 Author: vince 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 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 Date: Fri Apr 29 15:08:07 2016 -0700 const refs. Src/C_BaseLib/FabArray.H commit 2ec45eba50cc82d7eb990867955c31b53b251237 Author: vince Date: Fri Apr 29 15:07:17 2016 -0700 delete dm cache. Src/C_AMRLib/Amr.cpp commit de76c103ebd3879ff8091588c86c76795cf2ed72 Merge: 847fb4b99 21bb8079a Author: Weiqun Zhang 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 Date: Fri Apr 29 10:05:30 2016 -0700 Profiling reduce Src/C_BaseLib/ParallelDescriptor.cpp commit 2b30c77674c09f9c1801d100f9456a8dc7582788 Author: Weiqun Zhang Date: Fri Apr 29 10:03:50 2016 -0700 TinyProfiler: setfill Src/C_BaseLib/TinyProfiler.cpp commit 9ca1f8c5c02a33738bdcdb591236f3f8a8221cbf Author: Brian Friesen Date: Thu Apr 28 12:42:45 2016 -0700 Tutorials: revert changes to inputs file in MultiGrid_C Commit 49f3551 ("4th order in progress...") changed some default values of the "inputs" file. This changes them back. Tutorials/MultiGrid_C/inputs commit aaec6519aaa247d186b1d950944ef7f38188eba6 Merge: 47b0f0db0 227919378 Author: Adam M. Jacobs Date: Tue Apr 26 15:26:44 2016 -0400 Merge branch 'development' into openacc commit 47b0f0db049bd4351c380a6e4f2164672fc2f059 Merge: 2dda63c49 d2c6007d0 Author: Adam M. Jacobs Date: Tue Apr 26 15:26:32 2016 -0400 Merge branch 'openacc' of ssh://github.com/BoxLib-Codes/BoxLib into openacc commit 596058ab707270b200f923ed8c185304374c8a7f Merge: 14253514a 227919378 Author: Michael Zingale Date: Mon Apr 25 18:05:08 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 54911462d36fe813928c3f59bda4ad43d337e9e9 Author: vince Date: Mon Apr 25 12:59:25 2016 -0700 delete distmap cache function. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 847fb4b99f393e32ee2d469296a03dc946bfda23 Author: Weiqun Zhang Date: Mon Apr 25 12:32:18 2016 -0700 Start Tutorials/AMR_Adv_CF Tutorials/AMR_Adv_C/README Tutorials/AMR_Adv_CF/Exec/Make.Adv Tutorials/AMR_Adv_CF/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_CF/Exec/SingleVortex/Make.package Tutorials/AMR_Adv_CF/Exec/SingleVortex/Prob.f90 Tutorials/AMR_Adv_CF/README Tutorials/AMR_Adv_CF/Source/Make.package Tutorials/AMR_Adv_CF/Source/fmain.f90 commit 22791937872a4f118880ae6860e0922204474700 Author: Weiqun Zhang Date: Mon Apr 25 11:18:46 2016 -0700 runtime parameter boxlib.use_collectdata=1; to use the new fillpatch, set it to 0. Src/C_AMRLib/AmrLevel.cpp commit 0d5938db13cf3ce99f170b1197c1887e83d8f52a Author: Weiqun Zhang Date: Mon Apr 25 11:09:56 2016 -0700 move FillPatchUtil to C_AMRLib Src/C_AMRLib/CMakeLists.txt Src/C_AMRLib/FillPatchUtil.H Src/C_AMRLib/FillPatchUtil.cpp Src/C_AMRLib/Make.package Src/C_BaseLib/Make.package commit adb9772bd706610cada9cfdbb3e151b4c88f5978 Author: Weiqun Zhang 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/CMakeLists.txt Src/C_BaseLib/Make.package commit c022149e9e0a76cbc03c95537cd6f27a37df70f8 Merge: 4da1a83af 28607cb97 Author: Weiqun Zhang 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 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 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 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 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 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 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 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 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 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 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 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: e6a31c16f be1769b17 Author: Michael Zingale Date: Sat Apr 23 17:47:54 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 1a22a81235423f5e3b17b738845f084644a1541b Author: Weiqun Zhang Date: Sat Apr 23 14:05:36 2016 -0700 FI: more works Src/F_Interfaces/BaseLib/boxarray_fi.cpp Src/F_Interfaces/BaseLib/boxarray_mod.f90 Src/F_Interfaces/BaseLib/multifab_fi.cpp Src/F_Interfaces/BaseLib/multifab_mod.f90 Tutorials/HelloWorld_CF/GNUmakefile Tutorials/HelloWorld_CF/fmain.f90 commit a89de2352662910e09e354e62a0b17e945b5e5de Author: Weiqun Zhang Date: Sat Apr 23 07:13:35 2016 -0700 FI: remove fab because Fortran pointer is kind of like fab Src/F_Interfaces/BaseLib/Make.package Src/F_Interfaces/BaseLib/baselib_mod.f90 Src/F_Interfaces/BaseLib/fab_mod.f90 Src/F_Interfaces/BaseLib/multifab_mod.f90 Tutorials/HelloWorld_CF/fmain.f90 commit be1769b175620e1ef866fac5f58a85f5e713e0e8 Author: Weiqun Zhang Date: Sat Apr 23 00:12:26 2016 -0700 Start F_Interfaces/BaseLib that provides Fortran interfaces to C++ BoxLib Src/F_Interfaces/BaseLib/Make.package Src/F_Interfaces/BaseLib/baselib_mod.f90 Src/F_Interfaces/BaseLib/bl_space_mod.F90 Src/F_Interfaces/BaseLib/box_mod.f90 Src/F_Interfaces/BaseLib/boxarray_fi.cpp Src/F_Interfaces/BaseLib/boxarray_mod.f90 Src/F_Interfaces/BaseLib/fab_mod.f90 Src/F_Interfaces/BaseLib/main.cpp Src/F_Interfaces/BaseLib/multifab_fi.cpp Src/F_Interfaces/BaseLib/multifab_mod.f90 Tutorials/HelloWorld_CF/GNUmakefile Tutorials/HelloWorld_CF/Make.package Tutorials/HelloWorld_CF/fmain.f90 commit 4da1a83af75cc5037f0fbf76e4f566171d30ef63 Author: Weiqun Zhang Date: Fri Apr 22 14:44:33 2016 -0700 minor changes in profiling Src/C_AMRLib/AmrLevel.cpp commit 9c03cdf0a9ecd83c34b1367b2b845dfabc96368d Author: Weiqun Zhang Date: Fri Apr 22 14:40:26 2016 -0700 make echo-x will print out the value of x Tools/C_mk/Make.rules commit d59190e4def29bce9d3c8f44f4c912dc0a6d4afc Author: Weiqun Zhang Date: Fri Apr 22 12:32:00 2016 -0700 fix periodiccopy when the periodic length is very very short (say <= 4 cells) Src/C_BaseLib/Geometry.H commit 5b14f09350a5efc97fa6ce5a6d1c420ae967c2cc Author: Michael Zingale Date: Fri Apr 22 10:01:37 2016 -0400 add navigation links to the top of the test result page Tools/RegressionTesting/testnew.py commit a8727c270ce8f36532d7f283f648d11fbf12bea5 Author: Weiqun Zhang Date: Thu Apr 21 22:29:38 2016 -0700 more general periodic copy Src/C_BaseLib/Box.H Src/C_BaseLib/Geometry.H commit a58ea375de7e45038ad4bc8cf64b10b98ee28156 Author: Weiqun Zhang Date: Thu Apr 21 17:57:36 2016 -0700 BoxArray: need to update type after constructing from boxlist Src/C_BaseLib/BoxArray.cpp commit 4e1a640b10a6dbeb431615b4029fa5cf14aa7c4a Author: Weiqun Zhang Date: Thu Apr 21 21:41:31 2016 -0700 fillpatch: clean up Src/C_BaseLib/FillPatchUtil.cpp commit df2bc7abf2624dc15400a44c9dd5c7801f145042 Author: Weiqun Zhang Date: Thu Apr 21 21:36:45 2016 -0700 periodic copy: bug fix Src/C_BaseLib/Geometry.H commit feaa017604dced8f5f3ef9e89c11b60815deb490 Author: Weiqun Zhang Date: Thu Apr 21 17:57:36 2016 -0700 BoxArray: need to update type after constructing from boxlist Src/C_BaseLib/BoxArray.cpp commit 73e74ba26fc10c37fcfa058f034cce62a937b07b Author: Weiqun Zhang Date: Thu Apr 21 16:45:05 2016 -0700 new periodic copy: remove empty boxes from list Src/C_BaseLib/Geometry.H commit d7312a10d447dc88248191510ffe3e81dde7f3d9 Author: Weiqun Zhang Date: Thu Apr 21 16:39:44 2016 -0700 profiling two levels fillpatch Src/C_BaseLib/FillPatchUtil.cpp commit 75a38e96ae6d7696a0744572e6fdb3a642ca1a44 Author: Weiqun Zhang Date: Thu Apr 21 16:39:07 2016 -0700 fix the new periodic copy Src/C_BaseLib/Geometry.H commit f0eb04de19238a8594bcc0926a194624cb272e55 Author: Weiqun Zhang Date: Thu Apr 21 13:36:29 2016 -0700 change default blocking factor from 2 to 8 Src/C_AMRLib/Amr.cpp commit 3980d2c765ec0daa36420830becac7daaabd7b64 Author: Weiqun Zhang Date: Thu Apr 21 13:33:14 2016 -0700 new two levels fillpatch Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/Box.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FillPatchUtil.H Src/C_BaseLib/FillPatchUtil.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Interpolater.cpp commit fde3ced840c905f2ace2626e8568c5a43f2e1c49 Author: vince Date: Wed Apr 20 18:11:04 2016 -0700 cleanup. Src/C_BaseLib/ParallelDescriptor.cpp commit af1d1fbe784dfcfd4c954e3fd26f7c67f6789617 Author: vince Date: Wed Apr 20 18:08:35 2016 -0700 redistribute particles when resizing sidecars. Src/C_AMRLib/Amr.cpp commit 031aad31c9c044c75dbd3ad3388661970d7a0f27 Author: vince Date: Wed Apr 20 18:07:44 2016 -0700 syncronize sequence numbers across groups. Src/C_BaseLib/FabArray.H commit 9509a39a1528ee2eab21f9e589991620fed6df5a Author: Weiqun Zhang Date: Wed Apr 20 14:17:21 2016 -0700 move Interpolator from AMRLib to BaseLib Src/C_AMRLib/CMakeLists.txt Src/C_AMRLib/Make.package Src/C_BaseLib/ARRAYLIM_1D.F Src/C_BaseLib/ARRAYLIM_2D.F Src/C_BaseLib/ARRAYLIM_3D.F Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/INTERP_1D.F Src/C_BaseLib/INTERP_2D.F Src/C_BaseLib/INTERP_3D.F Src/C_BaseLib/INTERP_F.H Src/C_BaseLib/Interpolater.H Src/C_BaseLib/Interpolater.cpp Src/C_BaseLib/Make.package commit 85f11ff41dab48e1522db742581db585989ccdeb Author: Weiqun Zhang Date: Wed Apr 20 11:14:33 2016 -0700 single level fillpatch: parallel copy ghost cells too Src/C_BaseLib/FillPatchUtil.cpp commit 9bcc951219df1c29f6c04366befd529d8ee795d1 Author: Weiqun Zhang Date: Wed Apr 20 11:07:04 2016 -0700 single level fillpatch: support the case source and destination have different BoxArrays Src/C_BaseLib/FillPatchUtil.cpp commit 7db82ca58ba6d495478f3bc30eaab8c6db444011 Author: Weiqun Zhang 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 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 Date: Tue Apr 19 15:38:29 2016 -0700 new fillpatch: omp Src/C_AMRLib/StateData.cpp commit a4020dea4b70989622d6b76ace5185a3bdf0fee1 Author: Weiqun Zhang Date: Tue Apr 19 15:37:46 2016 -0700 new fillpatch: linear interp in time for level 0 Src/C_BaseLib/FillPatchUtil.cpp commit 424a49b77bcec30711a0a3bf6831ab8f2f59df1e Author: Weiqun Zhang Date: Tue Apr 19 14:41:33 2016 -0700 new fillpatch: add profiler and rm debug statements Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/FillPatchUtil.cpp commit 2bdab79ac39a08487fa9d754a1d2218872e2648c Author: Weiqun Zhang Date: Tue Apr 19 14:06:50 2016 -0700 new fillpatch: use it on level 0 Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_BaseLib/FillPatchUtil.H Src/C_BaseLib/FillPatchUtil.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/PhysBCFunct.H commit 77b8e8e87494334b1fb354beebb159ad30b4d443 Author: Weiqun Zhang Date: Mon Apr 18 14:56:50 2016 -0700 TinyProfiler: avg % --> max % Src/C_BaseLib/TinyProfiler.cpp commit 0adfdcc50bed5a29133a2e81a4a56dd36ff5b5f3 Author: Weiqun Zhang Date: Mon Apr 18 14:53:35 2016 -0700 TinyProfiler: avoid finalizing twice Src/C_BaseLib/TinyProfiler.cpp commit f593822bcc066185ad848049c3e20cca9e50f3f6 Author: vince Date: Mon Apr 18 11:12:30 2016 -0700 remove diagnostic. Src/C_BaseLib/FabArray.H commit e6a31c16f1242f246ff43e2b2cc07e0ef4f8eefd Author: Michael Zingale Date: Sat Apr 16 21:35:30 2016 -0400 make this python3-aware Tools/F_scripts/findparams.py commit 4b800f1fbe6e95d47ddd7ce4f462d1d1a41f165f Author: vince Date: Fri Apr 15 18:11:59 2016 -0700 resolve Fab_noallocate fabarrays for MoveAllFabs. Src/C_BaseLib/FabArray.H commit ac38ccb212451e1f74b4bf6ec8bf336929f2045d Author: vince Date: Fri Apr 15 12:08:12 2016 -0700 removed reduction. Src/C_BaseLib/FabArray.H commit 8ea1e562a26e6d1cba328d2b2c43bbc81ee03a82 Author: vince Date: Thu Apr 14 16:04:26 2016 -0700 fix for nyx. Src/C_AMRLib/Amr.cpp commit e202a26214deba76a6a4dd4415312ae110c4bbac Author: vince Date: Thu Apr 14 15:07:06 2016 -0700 remove temporary diagnostics. Src/C_BaseLib/FabArray.H commit cc619f8fde66cf72450789a066e04ad560e7c008 Author: vince Date: Thu Apr 14 14:25:24 2016 -0700 implemented BroadcastBoundaryPointList. Src/C_AMRLib/Amr.cpp commit a144b72e9a90c5b6f9e0c3fc7a3d9dd659aa5567 Author: vince 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 Date: Wed Apr 13 17:38:33 2016 -0700 TinyProfiler: fixed pop Src/C_BaseLib/TinyProfiler.cpp commit fabbacd9af508dbdffa7e2b36ea14beca1055b05 Author: Weiqun Zhang Date: Wed Apr 13 17:15:57 2016 -0700 TinyProfiler: fix OMP Src/C_BaseLib/TinyProfiler.cpp commit 586507c985cc30a5282590fe899888088ebda43e Author: Weiqun Zhang Date: Wed Apr 13 16:45:29 2016 -0700 TinyProfiler: warning about improperly nested timers Src/C_BaseLib/TinyProfiler.H Src/C_BaseLib/TinyProfiler.cpp commit 8dda631ef552f17247d41107be04905191bb078c Author: Weiqun Zhang Date: Wed Apr 13 14:54:55 2016 -0700 TinyProfiler: fix inclusive time by keeping track of the depth of the call tree Src/C_BaseLib/TinyProfiler.H Src/C_BaseLib/TinyProfiler.cpp commit 54eed4580da28e0ad4c2fb448a0217c3a29f19c7 Author: Weiqun Zhang Date: Wed Apr 13 13:59:18 2016 -0700 TinyProfiler: a tiny profiler that only supports a tiny fraction of what BLProfiler can offer. It does not need postprocessing. It shows inclusive and exclusive times. Src/C_BaseLib/BLProfiler.H Src/C_BaseLib/Make.package Src/C_BaseLib/TinyProfiler.H Src/C_BaseLib/TinyProfiler.cpp Tools/C_mk/Make.defs commit 2be16aa1ee8ed785d158459c8991e457773f0be7 Author: vince Date: Wed Apr 13 12:57:25 2016 -0700 remove diagnostic. Src/C_BaseLib/Geometry.cpp commit e9d6e11b7b27fe3e4210fce4ca5e9c73f835c3ff Author: Brian Friesen Date: Wed Apr 13 12:12:32 2016 -0700 C_scripts: squash warning about "hdf5" module Tools/C_scripts/moddep.pl commit dc3c7afd3fa50269678d2af21720482361b32297 Author: Brian Friesen Date: Wed Apr 13 10:37:00 2016 -0700 C_scripts: squash warning about "iso_fortran_env" module Tools/C_scripts/moddep.pl commit 546196aba38fe93e324977783afb0762cf8dbfe0 Author: Weiqun Zhang Date: Tue Apr 12 14:37:52 2016 -0700 update comments Src/C_AMRLib/Interpolater.cpp commit 87fbe270999a7e4c8395e1eb5d70cffa613e333f Author: Weiqun Zhang Date: Mon Apr 11 17:56:45 2016 -0700 remove unused variable Src/C_AMRLib/AmrLevel.cpp commit 01864cdec38a8261beaa25f8e7a9331f2e957130 Author: Weiqun Zhang Date: Mon Apr 11 17:55:23 2016 -0700 FillBoundary: timer Src/C_BaseLib/FabArray.H commit f2fe6298fa3f3d78738744592e321e030a1333b8 Author: Weiqun Zhang Date: Mon Apr 11 17:53:15 2016 -0700 add fixediter option to MultiGrid_C tutorial Tutorials/MultiGrid_C/main.cpp commit cff95a5132ed5602e6738edfeefcc22f1e8da11b Author: Weiqun Zhang Date: Mon Apr 11 17:46:50 2016 -0700 comment out the mpi-3 fix recommended by NERSC Tools/C_mk/Make.Linux commit b8e64b9bd4d4d31b912d6feb88c07f3cbc44d6c5 Merge: 8f158ad1f 75789d19e Author: Weiqun Zhang 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 Date: Mon Apr 11 15:42:12 2016 -0700 release-notes-16.04 ReleaseNotes/release-notes-16.04 commit 75243ee1e44764ecae14b701be0d3fc78ff7e8d4 Author: vince Date: Mon Apr 11 15:33:26 2016 -0700 fixes for nyx. Src/C_AMRLib/Amr.cpp commit 75789d19e9f3e429f9d2a9f89de7d0f0fe8a78d3 Merge: 41aa4bca9 9cb379a59 Author: Weiqun Zhang Date: Mon Apr 11 14:38:33 2016 -0700 Merge branch 'master' into development commit 1b6b13b8a1af6e56f070d88d5031d097708ef3e0 Author: vince Date: Fri Apr 8 13:49:50 2016 -0700 clean up proximity maps. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 1dab77ec3e0959794a844680f2eb24f58e3c3c50 Author: vince Date: Wed Apr 6 16:59:27 2016 -0700 additions for nyx dynamic sidecars. Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/F_BaseLib/parallel.f90 commit 89b907eae1e10c17de8e8eb039147f0844c3d02a Author: vince Date: Wed Apr 6 16:45:39 2016 -0700 stubs for dynamic sidecars support. Src/F_BaseLib/parallel_stubs.f90 commit 522c333b6eebdab67c9362dc2195eafe7fc9853c Author: vince Date: Wed Apr 6 16:06:57 2016 -0700 fix for non-mpi. Src/C_BaseLib/BoxArray.cpp commit ef06aae08aa11ac7e2d70dae46df2c33dbeb111f Author: vince Date: Wed Apr 6 16:04:27 2016 -0700 fix for non-mpi. Src/C_BaseLib/FabArray.H commit a4cc93dab0b82c8d84c8b9c75b49c33e53a01649 Author: vince Date: Wed Apr 6 14:38:54 2016 -0700 remove old SidecarProcess. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 41aa4bca90fe3a85bfdad602bdb1af441409eb90 Author: Andy Nonaka Date: Wed Apr 6 10:56:37 2016 -0700 utility from Aleks that writes the contents of a 2d plotfile into a text file, one line per data point Tools/Postprocessing/F_Src/GNUmakefile Tools/Postprocessing/F_Src/fwritecontents2d.f90 commit dbbb7c7a3e0e1d2e602e0c5f8933c998dd6132ab Author: Andy Nonaka Date: Wed Apr 6 10:49:18 2016 -0700 works for all ref ratios now as long as the cells you are averaging down are on the same grid Tools/Postprocessing/F_Src/fcoarsen.f90 commit fbf65dd6143a1cf148babb973c67ff3ed3c1b597 Author: Weiqun Zhang Date: Wed Apr 6 09:41:24 2016 -0700 fine_flx now starts at level 1, not level 2. Tutorials/HeatEquation_EX5_F/advance.f90 commit ac820f7ffb98205f945dcdf7da5b474a1f138dcf Author: Andy Nonaka Date: Tue Apr 5 14:45:51 2016 -0700 get dx for plotfile write correct Tools/Postprocessing/F_Src/fcoarsen.f90 commit 55c9e5dbd20445924fe6a275791a4069de44d430 Author: Andy Nonaka Date: Tue Apr 5 14:08:27 2016 -0700 updates from Aleks - add coarsening factor input Tools/Postprocessing/F_Src/fcoarsen.f90 commit 8db0b5ddbc85da0dbdd482f0bf21fad6960c2c44 Author: Andy Nonaka Date: Tue Apr 5 13:22:24 2016 -0700 turn back on 3d coarsening of plotfiles Tools/Postprocessing/F_Src/fcoarsen.f90 commit 71773f92f2a9012c8e280fc9202a7f2d148e6734 Author: Weiqun Zhang Date: Tue Apr 5 13:19:18 2016 -0700 add fcompiler option to f2py Tools/Py_util/GNUmakefile commit 7abae19a66e06ce80ddf26f01f416f2b8dbe5be5 Author: Andy Nonaka Date: Tue Apr 5 12:58:33 2016 -0700 revert accidental commit Tools/C_util/Convergence/GNUmakefile commit 99050b8885aae6e49e3cff64d30ed5c4656d8737 Merge: 2da885699 905452e97 Author: Andy Nonaka Date: Tue Apr 5 12:57:14 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 2da885699ca5934a8c2230eea9f3ab673397a5a1 Author: Andy Nonaka Date: Tue Apr 5 12:57:00 2016 -0700 forgot to add file Tools/Postprocessing/F_Src/fcoarsen.f90 commit 905452e97c9163b76414c75707d585ddb56fad42 Merge: 652dc2b99 023b6a5bb Author: Ann Almgren Date: Tue Apr 5 12:39:25 2016 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 652dc2b991dc7d1c3175681ff9f9a228524943c1 Author: Ann Almgren Date: Tue Apr 5 12:38:42 2016 -0700 The flux we pass into the F90 interface (in ml_solve.f90) for cell-centered solves now starts at the base level of the solve, not one level higher. Src/LinearSolvers/F_MG/ml_solve.f90 commit 023b6a5bb7bb272cec811b14998014085145f0c3 Merge: 94d7869a2 685bef8b2 Author: Andy Nonaka Date: Tue Apr 5 12:23:21 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 94d7869a2aedf59f598e727db955f04c755bc64f Author: Andy Nonaka Date: Tue Apr 5 12:22:44 2016 -0700 utility that reads in a single level plotfile and writes out a coarsened plotfile (rr=2) Tools/C_util/Convergence/GNUmakefile Tools/Postprocessing/F_Src/GNUmakefile commit fc2437922a5fb4ca37368c105242c051db2be52c Author: vince Date: Mon Apr 4 17:21:51 2016 -0700 check return of getcwd. Src/C_BaseLib/BoxLib.cpp commit 685bef8b2224ef64da30a18e4c2129bd203f3397 Author: Ann Almgren Date: Mon Apr 4 16:35:49 2016 -0700 Add the option in the F90 interfaces to the cell-centered solver to have the base level have Dirichletboundary conditions at a distance away from the boundary, not just at the boundary. You make this happen by passing in base_level > 1 and crse_ratio = the ratio of dx between the coarsest level of the solve to the coarser AMR level outside the solve. Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit 8535890dfda0dc51545e602385f5a93ca6a3538d Author: vince Date: Mon Apr 4 12:05:19 2016 -0700 fix for particles. Src/C_AMRLib/AmrLevel.cpp commit d3f5141be3a8768bbf1d540f4172bdbd716970b1 Author: Marc Day Date: Fri Apr 1 23:00:33 2016 -0700 Use gnu99 instead of c99 if using GNU compilers Tools/C_mk/Make.defs commit c6391d28c4adc8c6ef2831bdd80f4a90d7e17f91 Author: Marc Day Date: Fri Apr 1 16:37:58 2016 -0700 Add USERSuffix to optionsSuffix to allow generalized suffix creation in app build. Should probably move app-specific suffix defs out of BoxLib....someday Tools/C_mk/Make.defs commit d2c6007d04b0c5bdd9ccb790d6d748174b579e5d Author: Adam Jacobs Date: Fri Apr 1 18:18:41 2016 -0400 Get PGI compilation working for OpenACC on titan Tools/F_mk/comps/Linux_pgi.mak commit 7001c76b206c5f1852d8df3ae0805749593f880e Author: vince Date: Thu Mar 31 17:35:27 2016 -0700 fix for copyInter sidecar tutorial. Src/C_BaseLib/FabArray.H commit 24fef5b614f1458fbbec0a4c58ff91fb4dfe0adf Merge: 93c1f550d 530071426 Author: vince Date: Thu Mar 31 17:06:29 2016 -0700 merge with master. commit 17d1d78cd395ca5747ce4bff8a986fe160b93d78 Author: Ann Almgren Date: Thu Mar 31 15:29:15 2016 -0700 Fix another typo in the latest changes to create_umac_grown. Src/F_BaseLib/create_umac_grown.f90 commit d5cb69fb1c508d2ff658aa7d99e31f23060c0eab Author: Ann Almgren Date: Thu Mar 31 14:45:01 2016 -0700 Fix some oops from previous commit. Src/F_BaseLib/create_umac_grown.f90 commit a736625a3f3d91b8dd042238d22dd78ec12252e9 Author: Ann Almgren Date: Thu Mar 31 14:07:19 2016 -0700 Allow for factor 4 as well as factor 2 interpolation in create_umac_grown. Src/F_BaseLib/create_umac_grown.f90 commit 9cb379a599ffde00f31b72159443e3da050e3268 Author: Weiqun Zhang Date: Wed Mar 30 16:02:34 2016 -0700 try to fix CMake for F_BaseLib; not tested because I don't even know how to use CMake Src/F_BaseLib/CMakeLists.txt commit b9931eeacb93d6fe0c356704e53b106344998a01 Author: Weiqun Zhang Date: Wed Mar 30 16:02:34 2016 -0700 try to fix CMake for F_BaseLib; not tested because I don't even know how to use CMake Src/F_BaseLib/CMakeLists.txt commit 7b250e7b4b21d3c679f2eb29058ce75a2c9e00c3 Author: Adam Jacobs Date: Wed Mar 30 16:02:19 2016 -0400 Use Cray compiler wrappers, even for PGI, on Titan Tools/F_mk/comps/Linux_pgi.mak commit 9c5cb6d5a8cc57143c33176c7372b901db2fd860 Author: Adam Jacobs Date: Wed Mar 30 15:32:40 2016 -0400 For now, GPUs can't handle PGI's -gopt. Debug symbols break it with internal compiler errors. Tools/F_mk/comps/Linux_pgi.mak commit 7e0805f15ffc6ed249b3be7cd54a1c70810f0951 Merge: d73333662 913dbca1e Author: Adam Jacobs Date: Wed Mar 30 15:31:00 2016 -0400 Merge branch 'development' into openacc commit d7333366289d9f0d5bb30ae2acc9acfaae36220f Merge: 68553674d 8a7146780 Author: Adam Jacobs Date: Wed Mar 30 15:30:04 2016 -0400 Merge branch 'openacc' of ssh://github.com/BoxLib-Codes/BoxLib into openacc commit 68553674d47538bc1ee6b9364e1f79f353f05996 Author: Adam Jacobs Date: Wed Mar 30 15:29:52 2016 -0400 fix indent Tools/F_mk/comps/Linux_cray.mak commit 8f158ad1f15d843fde3c09952863268099f96196 Merge: 7e8fbefbd bfceb352f Author: Weiqun Zhang Date: Wed Mar 30 09:12:45 2016 -0700 Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas commit bfceb352f3d255d031996eb4d81f368360b2f543 Merge: 1ef0b9c0d 913dbca1e Author: Weiqun Zhang Date: Tue Mar 29 12:56:00 2016 -0700 Merge branch 'development' into pgas commit 1ef0b9c0d1811d3381691add34cf8e2744197309 Merge: 2df7cd5df 530071426 Author: Weiqun Zhang Date: Tue Mar 29 12:55:29 2016 -0700 Merge branch 'development' into pgas commit 913dbca1eb564e4df03c3e3a4e749c82a90157fc Author: Regression Tester Date: Tue Mar 29 11:02:48 2016 -0700 regression test: option to use valgrind, --with_valgrind Tools/RegressionTesting/testnew.py commit 0fcfe104fbc498329ea62652203a053c26792b3e Author: Weiqun Zhang Date: Tue Mar 29 10:56:24 2016 -0700 battra F_mk Tools/F_mk/GMakeMPI.mak commit 176c6944269951a8d7d72e174a42713269251124 Author: Weiqun Zhang Date: Tue Mar 29 10:30:22 2016 -0700 battra: use rpath so that we do not need to bother with LD_LIBRARY_PATH Tools/C_mk/Make.mpi commit 580ab8eaab1ddc6e470b467d1b06b7ac30c045f5 Author: Weiqun Zhang Date: Tue Mar 29 10:25:21 2016 -0700 battra: option to use valgrind friendly build of mpich at /usr/local Tools/C_mk/Make.mpi commit b8c7cb04d2d0cabf156b0483986a5935f92edb5b Author: Marc Day Date: Mon Mar 28 15:38:47 2016 -0700 Remove ifdefd code to set space-varying bcs. Was a remnant of debugging, and was incorrect anyway. Tutorials/MultiGrid_C/main.cpp commit 4de76c131324fd13112caf70b284b6aae2eb668d Merge: b8781e487 8bae1b5c8 Author: Adam M. Jacobs Date: Mon Mar 28 14:06:18 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit b8781e487220f4afc8670459710392aa2dced48a Author: Adam M. Jacobs Date: Mon Mar 28 14:06:12 2016 -0400 Add 5/6 to bl_constants Src/F_BaseLib/bl_constants.f90 commit 8bae1b5c81a41668622cc5d82b4641949c0ab2bd Author: Weiqun Zhang Date: Fri Mar 25 17:21:34 2016 -0700 bndry_reg: fix a bug when the fine level has a single box and covers the entire non-periodic domain Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 commit 7e8fbefbd65cb978fec1e85b8577458f5df9e52b Merge: 2df7cd5df 530071426 Author: Weiqun Zhang Date: Fri Mar 25 14:48:08 2016 -0700 Merge branch 'development' into pgas commit 93c1f550d9fc1e6e2ed75a576e599559571e04d6 Merge: bf6c4bf12 af19914ba Author: vince Date: Fri Mar 25 12:46:05 2016 -0700 Merge branch 'master' into dynamicsidecars commit bf6c4bf1275f67dd8aad89b465400598a6faa0db Author: vince Date: Fri Mar 25 12:40:27 2016 -0700 premerge cleanup. Src/C_BaseLib/FabArray.cpp commit e2e16eee1a52feba2270d0c6dff2e8a07fed92c2 Author: vince Date: Fri Mar 25 12:38:23 2016 -0700 added more profiling. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit e29f781d02d968726c3777105b428fed8549d6e7 Author: vince Date: Fri Mar 25 12:37:53 2016 -0700 premerge cleanup. Src/C_AMRLib/Amr.cpp commit 2df7cd5df0ad3e19cd291aadfa9e4386a9f7b929 Author: Weiqun Zhang 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 Date: Thu Mar 24 15:52:24 2016 -0700 PGAS_SMC: change defaults MiniApps/PGAS_SMC/SMC.cpp commit 9371b9858b2bc02f108c386e6c96424b37c0bf66 Author: Weiqun Zhang Date: Thu Mar 24 15:47:01 2016 -0700 PGAS_SMC: chop box into small pieces so that each process has at least one box MiniApps/PGAS_SMC/SMC_init.cpp commit be2917755b3d89beda1920d91ef760698799bf05 Author: vince Date: Tue Mar 22 11:56:38 2016 -0700 add periodic to output. Src/C_BaseLib/Geometry.cpp commit 5300714260c2cf994feb69e9b84bf4180cb64794 Author: Michael Zingale Date: Tue Mar 22 07:48:26 2016 -0400 fix typo Tools/RegressionTesting/testnew.py commit 2a36ac4e0c77278a0e523557b1efcae0b0b34c9c Author: Brian Friesen Date: Mon Mar 21 12:34:13 2016 -0700 C_mk, F_mk: add optimization reports for Cray compilers Tools/C_mk/Make.Linux Tools/F_mk/comps/Linux_cray.mak commit db6e18e2616e7e2cce01126497352686ed75fd1d Author: Weiqun Zhang Date: Mon Mar 21 13:14:35 2016 -0700 update make for baragon Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit d1211141f4b3dd8f99a9dd8f3c814666b8d0f809 Author: Weiqun Zhang Date: Mon Mar 21 13:14:08 2016 -0700 free MPI_group Src/C_BaseLib/ParallelDescriptor.cpp commit 783b35f6eef435236595d304f651156460ed02cf Merge: 32a0bfa63 a461a3ade Author: Michael Zingale Date: Mon Mar 21 10:54:13 2016 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 32a0bfa63658b9ccef1d31f22c5a5248f1827f3d Author: Michael Zingale Date: Mon Mar 21 10:53:58 2016 -0400 some slack cleaning Tools/RegressionTesting/testnew.py commit 18a216b48e01436f486b42c8aedb924ea0dc656e Merge: d745ca521 a461a3ade Author: Weiqun Zhang Date: Fri Mar 18 14:23:51 2016 -0700 Merge branch 'development' into pgas commit d745ca5215dc221d745c9166780766b0a5305b11 Author: Weiqun Zhang Date: Fri Mar 18 14:22:11 2016 -0700 add upcxx::barrier() before MPI reduce Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tests/FillBoundaryComparison/main.cpp Tutorials/PGAS_HEAT/main.cpp commit 02ee7a655fe9e7534fcb987f2a1fa6faf0126771 Author: vince Date: Fri Mar 18 13:10:51 2016 -0700 code cleanup. Src/C_AMRLib/Particles.H commit a461a3adea2d321a7d94d315efcbdd76335526c0 Author: Weiqun Zhang Date: Fri Mar 18 12:26:43 2016 -0700 add 'class' because extended friend syntax is a C++11 feature Src/C_BaseLib/Box.H commit 77867387f094f87c1a8c07a87e559108cbf2178d Author: vince Date: Thu Mar 17 16:52:52 2016 -0700 added profiling, cleanup. Src/C_AMRLib/Particles.H commit 8224e6160a7a889126414532de49861d2576e84b Author: Emmanuel Motheau Date: Thu Mar 17 16:51:57 2016 -0700 Bug fix restricted_build Src/F_BaseLib/ml_boxarray.f90 Src/F_BaseLib/ml_layout.f90 commit a74852e808c85425c21d6712cdb4c49eb967c52d Author: Emmanuel Motheau Date: Thu Mar 17 16:50:21 2016 -0700 Add varan machine Tools/F_mk/GMakeMPI.mak commit 91a37c09f022c462322b25432414f13b21e89f41 Author: vince Date: Thu Mar 17 16:48:09 2016 -0700 added profiling, cleanup. Src/C_AMRLib/Particles.H commit 62b2b697043416e5b58f91f98351b40f039daf33 Author: vince Date: Thu Mar 17 16:47:17 2016 -0700 added profiling, cleanup. Src/C_AMRLib/Particles.H commit f8271bd0c6aad1e72992e8901ebc8cd83151bb48 Author: Weiqun Zhang Date: Thu Mar 17 16:24:55 2016 -0700 new functions for doing shallow copies of ml_layout and ml_boxarray Src/F_BaseLib/ml_boxarray.f90 Src/F_BaseLib/ml_layout.f90 commit 31fdae155b05786c40584df889b70e62890eefc1 Merge: f911ccf9e ce604a709 Author: Weiqun Zhang Date: Thu Mar 17 14:19:10 2016 -0700 Merge branch 'development' into pgas Conflicts: Src/C_BaseLib/Make.package Tools/C_mk/Make.defs commit 1075b6babb32227ca5bbb3fabc0ab5688926f7f4 Author: Weiqun Zhang Date: Thu Mar 17 12:36:25 2016 -0700 fix a memory leak: must call MPI_Wait to free resources even when we know for sure the messages have been sucessfully sent. Src/C_BaseLib/FabArray.H commit ce604a709b0e22e8c5ba6d4332ecee9b44191892 Author: Weiqun Zhang Date: Thu Mar 17 12:36:25 2016 -0700 fix a memory leak: must call MPI_Wait to free resources even when we know for sure the messages have been sucessfully sent. Src/C_BaseLib/FabArray.H commit 1a2493eae27511b7cef5d3cc9e6741de53f2f5f7 Merge: d4e3fd68a 313036acf Author: Marc Day Date: Thu Mar 17 10:22:44 2016 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 313036acf21ab10ab7a97a2abd6a744a44cb516d Author: Weiqun Zhang Date: Thu Mar 17 08:41:01 2016 -0700 box_f: avoid using Huge(1) because it can cause integer overflow Src/F_BaseLib/box_f.f90 commit a73971e26f5a6d1569de679bab1eeb0bcfa133e3 Author: Marc Day Date: Wed Mar 16 21:34:14 2016 -0700 Add def for BL_PROFILE_VAR_NS when PROFILE=FALSE Src/C_BaseLib/BLProfiler.H commit d4e3fd68a6af1ce4789b0ce0a3e7d7c723ec2a17 Author: Marc Day Date: Wed Mar 16 21:34:14 2016 -0700 Add def for BL_PROFILE_VAR_NS when PROFILE=FALSE Src/C_BaseLib/BLProfiler.H commit 14d8aaeeb6ee0438adf246cc69ebfff4c52d7873 Author: vince Date: Wed Mar 16 13:08:17 2016 -0700 add section for start/stop. Docs/Readme.profiling commit 7619216e724b2f67f89b1125142feab54ed39f4f Author: vince Date: Wed Mar 16 12:23:36 2016 -0700 fort profiling fixes. Src/LinearSolvers/F_MG/mg.f90 commit 8a47149ddfac3ef3d0d5419ee1166a529cae484f Author: Weiqun Zhang Date: Wed Mar 16 10:37:26 2016 -0700 make: rm *.mod that could be left over because of wrong PrgEnv Tools/C_mk/Make.rules commit 71cad31f93a1d13e213dcddb28143526f3d4b868 Author: Weiqun Zhang Date: Wed Mar 16 10:35:15 2016 -0700 MemProfiler: add VmSize Src/C_BaseLib/MemProfiler.cpp commit f911ccf9ebf60da75ea3fed043436a8816021274 Author: yzheng Date: Wed Mar 16 09:24:42 2016 -0700 Add UPC++ version of CollectData, which needs the latest version of UPC++ Src/C_BaseLib/BLPgas.H Src/C_BaseLib/BLPgas.cpp Src/C_BaseLib/FabArray.H commit e96f52f897e4b7c3696dbf3becbc030f5ce48972 Author: Weiqun Zhang 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 Date: Tue Mar 15 22:01:21 2016 -0700 MemProfiler: fix an index Src/C_BaseLib/MemProfiler.cpp commit 4e2918fb89549126ddb59fbb6cb1a247bbff7d2c Author: Weiqun Zhang Date: Tue Mar 15 21:13:00 2016 -0700 decrement copyassoc_cnt Src/F_BaseLib/layout.f90 commit 893acb4acebd04f9c79b1e8a107bd23d62b831fa Author: Weiqun Zhang Date: Tue Mar 15 20:40:15 2016 -0700 cleanup Src/F_BaseLib/memprof.f90 commit 38b6b4aa9ee0e1e7f28d887e7aca78249d84d5a9 Author: Weiqun Zhang Date: Tue Mar 15 18:13:12 2016 -0700 MemProfiler: add data form /proc/pid/status Src/C_BaseLib/MemProfiler.cpp commit 047914c771885a87e50373ea7ee4bfaf380423e1 Author: Weiqun Zhang Date: Tue Mar 15 17:07:22 2016 -0700 add a header that Intel complains about missing Src/C_BaseLib/MemProfiler.cpp commit 2e4ee9ee69766ec9fd4e4cf63d6e6d55b813c25e Author: Weiqun Zhang Date: Tue Mar 15 16:31:34 2016 -0700 flush fortran copyassoc after regrid Src/C_AMRLib/Amr.cpp Src/LinearSolvers/F_MG/FParallelMG.mak commit 66bcb57f7897a82d2ec669d5634e60e4e9ceb2dd Author: Weiqun Zhang Date: Tue Mar 15 16:18:39 2016 -0700 add the new counters to MemProfiler Src/F_BaseLib/MemProfiler_f.cpp Src/F_BaseLib/memprof.f90 commit 8fdca51d2262cd2d5a80ebe23cf45745883db0b4 Author: Weiqun Zhang Date: Tue Mar 15 16:05:47 2016 -0700 layout: add more memory counters Src/F_BaseLib/layout.f90 commit c6b8354033d518b183535ebe64901bd7dcf26a39 Author: Weiqun Zhang Date: Tue Mar 15 15:18:39 2016 -0700 better estimates of memory cost of fortran data structures Src/F_BaseLib/box_f.f90 Src/F_BaseLib/layout.f90 commit e12c41b2803916854cbd647c34ee012b8812fdcb Author: vince Date: Tue Mar 15 14:26:00 2016 -0700 use max_level for size. Src/C_AMRLib/Amr.cpp commit 60929a9297033250471c1da292d739e11a03d25a Author: Weiqun Zhang Date: Tue Mar 15 13:28:44 2016 -0700 remove gcc-2 Tools/C_mk/Make.defs commit 35eed5356f710a3556633b8b941396e227437cb2 Author: vince Date: Tue Mar 15 12:25:05 2016 -0700 some cleanup. Tutorials/Sidecar_EX1/DestMFTest.cpp commit e890d91072e50518935cd0699fd77fb4aecb99ac Author: Weiqun Zhang Date: Tue Mar 15 12:23:44 2016 -0700 fix an uninitialized value that affects the memory usage counter Src/F_BaseLib/layout.f90 commit 4a47765b8791438a39eb3a3242bb9c746d1e1b8a Author: Weiqun Zhang Date: Tue Mar 15 12:17:06 2016 -0700 cleanup Src/F_BaseLib/layout.f90 commit 52d8f8b10e358fd33acd4ba18da20addb5ecf0c8 Author: Weiqun Zhang Date: Tue Mar 15 10:13:35 2016 -0700 Fortran copyassoc: change the max # allowed Src/F_BaseLib/layout.f90 commit 2a9dc240fb824ffd6f4c0b26547e89b324a2c274 Author: vince Date: Mon Mar 14 18:36:56 2016 -0700 added test to copy from sidecars to comp. Tutorials/Sidecar_EX1/DestMFTest.cpp commit e844e235cafb920d2a5812f168f50f12082a95b1 Author: vince 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 Date: Mon Mar 14 18:32:18 2016 -0700 MemProfiler: minor mistake Src/F_BaseLib/layout.f90 commit ff53ab84eefc3d3a3feb07bd40411f4374148718 Author: Weiqun Zhang Date: Mon Mar 14 18:26:01 2016 -0700 MemProfiler: add fortran copyassoc and boxassoc Src/F_BaseLib/MemProfiler_f.cpp Src/F_BaseLib/layout.f90 Src/F_BaseLib/memprof.f90 commit e5dacdec3608462a016982056a66ab1d37286e3b Author: Weiqun Zhang Date: Mon Mar 14 17:50:00 2016 -0700 MemProfiler: skip print if high water mark is zero Src/C_BaseLib/MemProfiler.cpp commit e4ffb3bf6059e09547600bebf02239ddf9e74225 Author: Weiqun Zhang Date: Mon Mar 14 17:47:03 2016 -0700 MemProfiler: fortran boxarray Src/F_BaseLib/MemProfiler_f.cpp Src/F_BaseLib/boxarray_f.f90 Src/F_BaseLib/memprof.f90 commit f5b0c967438768cb4132073e728bef745a4a4866 Author: Weiqun Zhang Date: Mon Mar 14 17:29:15 2016 -0700 MemProfiler: add fortran fab Src/C_BaseLib/BoxLib.cpp Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/MemProfiler_f.H Src/F_BaseLib/MemProfiler_f.cpp Src/F_BaseLib/memprof.f90 Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 6f8d93fde4bee5cffadc8dd757086dfb6f446289 Author: Weiqun Zhang Date: Mon Mar 14 17:27:38 2016 -0700 MemProfiler: sort the output Src/C_BaseLib/MemProfiler.cpp commit 0dc72ceb66ca3ffbe7918d7cb9c3938ab0f829ee Author: Weiqun Zhang Date: Mon Mar 14 15:59:23 2016 -0700 MemProfile: add cached memory Src/C_BaseLib/MemProfiler.cpp commit 8a2aec44fe014a0360d59fc168828b8e4c105a1e Author: Weiqun Zhang Date: Mon Mar 14 15:25:00 2016 -0700 MemProfiler: use sysinfo instead of sysconf so that we can get memory used by buffers; we still don't have know about cached memory unless we are going to read /proc/meminfo directly. Src/C_BaseLib/MemProfiler.cpp commit df5142b258e4367fb19d495e44e38d2dbf102c84 Author: Weiqun Zhang Date: Mon Mar 14 11:24:57 2016 -0700 BoxArray: do nothing if size does not change in maxSize(); cleanup Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit fcdc25b5cbdc44041ab11d7b82f9c03a379bb066 Author: Weiqun Zhang Date: Mon Mar 14 10:36:19 2016 -0700 fix a new bug in BoxArray I introduced yesterday Src/C_BaseLib/BoxArray.cpp commit 64b01d991e85f9140cabb269f560d2154fa3f969 Author: Brian Friesen Date: Mon Mar 14 09:44:31 2016 -0700 C_mk: remove explicit "-lmpich" flag from link line on Edison/Cori The Cray wrappers resolve MPICH for us automatically, so we don't need to link this by hand. Also, Chris Daley discovered that using this link flag overwrites Darshan's MPI_Init() call with the native MPICH MPI_Init(), which means Darshan can't collect I/O profiling data for any BoxLib code. Tools/C_mk/Make.mpi commit b1a7068bea831064597046885bf67b4bae6257f0 Author: Weiqun Zhang Date: Sun Mar 13 20:55:18 2016 -0700 MemProfiler: fix BoxArray::removeOverlap Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 1752b8cab8d21126e354edbccc498a563e3465e8 Author: Weiqun Zhang Date: Sun Mar 13 16:58:51 2016 -0700 MemProfiler: optimization Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit 9a8a9f8f4b4e071012be6b82a1c7b891cf917c46 Author: Weiqun Zhang Date: Sun Mar 13 16:13:49 2016 -0700 MemProfiler: save the log in a file Src/C_BaseLib/MemProfiler.H Src/C_BaseLib/MemProfiler.cpp commit b004dfde7a38c86f6fc38f624da058e181b57a51 Author: Weiqun Zhang Date: Sun Mar 13 12:58:45 2016 -0700 MemProfiler: pretty Src/C_BaseLib/MemProfiler.cpp commit 0973e69e20b854a3c5a12920f7d6aa169a922e1f Author: Weiqun Zhang Date: Sun Mar 13 09:08:21 2016 -0700 BoxArray MemProfiler: split box and cache data Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit c345b66ec823ecdf3f0336f46919dabc120ef83e Author: Weiqun Zhang Date: Sun Mar 13 09:03:21 2016 -0700 MemProfiler: Copy and FillBoundary Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit 3153ab32a9825ccbcbef7dac751c7b56515fc815 Author: Weiqun Zhang Date: Sat Mar 12 22:52:58 2016 -0800 MemProfile: TileArrayCache Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit b8f6ea6a7bfe68c2dd70b3a8c4d8527e732ba92d Author: Weiqun Zhang Date: Sat Mar 12 21:37:13 2016 -0800 MemProfiler: Geometry Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit f44bd45ceae4b6035dc6d66c79f9cc2af4f80e36 Author: Weiqun Zhang Date: Sat Mar 12 18:47:28 2016 -0800 Geometry & FabArray: use the new memory counting function. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit f8db73be4dda0bac795fae24afef17ece2d0ca8f Author: Weiqun Zhang Date: Sat Mar 12 17:56:48 2016 -0800 move memory counting functions into Utility.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/MemProfiler.H Src/C_BaseLib/MemProfiler.cpp Src/C_BaseLib/Utility.H commit 5572286aae77aa6b66a65209cf32ecc65b5e17bd Author: Weiqun Zhang Date: Sat Mar 12 17:21:58 2016 -0800 MemProfiler: replace templates with specialized codes Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/MemProfiler.H Src/C_BaseLib/MemProfiler.cpp commit 7d2889c8f45fb414aaac642e41617a18f455af16 Author: Weiqun Zhang Date: Sat Mar 12 16:24:04 2016 -0800 MemProfiler: BoxArray and bytesOf for map Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/MemProfiler.H Src/C_BaseLib/MemProfiler.cpp commit 9f0f3e51590661aa5509c3ede436cc1cd27a23fa Author: Weiqun Zhang Date: Sat Mar 12 11:09:28 2016 -0800 MemProfiler: minor Src/C_BaseLib/MemProfiler.cpp commit 75e19745dbdc7a81c4a6ad58983ac0f54782b64e Author: Weiqun Zhang Date: Sat Mar 12 11:08:52 2016 -0800 MemProfiler: bytesOf function for std::vector and Array Src/C_BaseLib/MemProfiler.H commit a26cad180aedc8f506839cabb3955733a602f144 Author: yzheng Date: Fri Mar 11 22:49:07 2016 -0800 Use map instead of unordered_map in BLPgas because unordered_map would cause some linking errors when using the Intel compilers with a recent version of GCC (4.8 or newer) on Cray XC systems Src/C_BaseLib/BLPgas.cpp commit 7ddaf82cae99ba7bcbce1351352a445e1c9c87a5 Author: Weiqun Zhang Date: Fri Mar 11 21:28:45 2016 -0800 MemProfiler: cleanup Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/MemProfiler.H Src/C_BaseLib/MemProfiler.cpp commit 3b84aa58d2caa381da2ab31b66d11582fc8fe1b6 Author: Weiqun Zhang Date: Fri Mar 11 17:15:31 2016 -0800 MemProfiler: when adding, make sure the name does not exist Src/C_BaseLib/MemProfiler.H Src/C_BaseLib/MemProfiler.cpp commit 0a36db7bb64aeb98a0dcf6aae293f04c64f36554 Author: Weiqun Zhang Date: Fri Mar 11 17:02:24 2016 -0800 Memory Profiler: first pass Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/MemPool.cpp Src/C_BaseLib/MemProfiler.H Src/C_BaseLib/MemProfiler.cpp Tools/C_mk/Make.defs commit 4de2b2dfe6aaa5b87886e3585972c8ea9b331896 Author: Michael Zingale Date: Fri Mar 11 19:44:40 2016 -0500 latest inputs file -- this has the slack integration Tools/RegressionTesting/Maestro-tests.ini commit 47140662befa1af1765e7ef62b817c8bd2a22339 Author: vince Date: Fri Mar 11 15:55:05 2016 -0800 changed inputs. Tutorials/Sidecar_EX1/inputs_sc commit d3c5ec0651ceeb2d90d750d8f9b4b471425c84b6 Author: vince Date: Fri Mar 11 15:54:16 2016 -0800 added several tests for shifted and grown multifab copies. Tutorials/Sidecar_EX1/DestMFTest.cpp commit edf8e108ef4ab0d37ebc9df5b95c9d2efcc31be1 Author: Michael Zingale Date: Fri Mar 11 18:00:00 2016 -0500 add slack integration using webhooks. Now, if you define the slack parameters it will post to the slack channel when the suite starts and post again when the suite ends, reporting the number of failures Tools/RegressionTesting/testnew.py commit 671a69ddcdf7cf932d768d89ddd7ad50e68c28b7 Author: vince Date: Fri Mar 11 14:34:56 2016 -0800 reenable assertions, add more error checking. Src/C_BaseLib/FabArray.H commit ec8dc20978445ed08a3b52b4445e7ffc71f06786 Author: vince Date: Fri Mar 11 13:57:42 2016 -0800 remove unused variables. Src/C_BaseLib/Geometry.cpp commit 7b0540e75ca5f3d0bcf623eefb719393f8bdc09d Author: vince Date: Fri Mar 11 13:57:25 2016 -0800 FabArray::copyInter seems to work. needs more testing. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit f1087aba21727100f94ac101943a0c0e18629242 Author: Michael Zingale Date: Thu Mar 10 22:04:18 2016 -0500 fix formatting when variables are not present Tools/RegressionTesting/testnew.py commit 1359de9bdd811a99997066dced5cbf71586dcf6b Author: vince Date: Thu Mar 10 18:37:33 2016 -0800 testing the new FabArray::copyInter. Tutorials/Sidecar_EX1/DestMFTest.cpp commit 229ea80abce03805ecb7a12a44064bed7d0e07e9 Author: vince Date: Thu Mar 10 18:33:46 2016 -0800 copyInter function, TheCPC that takes IndexMaps, not yet complete. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit b8e8b003ffbdcd4c4f03f21ed7696d864dceca26 Merge: 5f14ba27d a98d77beb Author: Andy Nonaka Date: Thu Mar 10 18:13:09 2016 -0800 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 5f14ba27d00e966cf28534353e91372eedd03a35 Author: Andy Nonaka Date: Thu Mar 10 18:12:32 2016 -0800 added a routine to do a nodal sum and nodal volume, weighting faces, edges, and corners appropriately Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/nodal_sum.f90 commit 6f1f7f7d8accb797d59406fa1da57909b30c3e1c Author: Weiqun Zhang Date: Thu Mar 10 14:05:46 2016 -0800 buildTileArray: fix reordering Src/C_BaseLib/FabArray.cpp commit e7cc029885a4b42f353dc3d4d83b7d1e3ae0512c Merge: 25a9fd763 a98d77beb Author: Weiqun Zhang Date: Thu Mar 10 10:58:32 2016 -0800 Merge branch 'development' into pgas commit a98d77bebc49cc784c9e5a98163b1bb54772c0a0 Author: Weiqun Zhang Date: Thu Mar 10 10:58:12 2016 -0800 FillBoundary: remove empty messages in case of cross=true Src/C_BaseLib/FabArray.cpp commit d708778fc449eb0218a17dcf0d1d39d93eb9b5ff Author: vince 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 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 Date: Wed Mar 9 16:15:04 2016 -0800 add headers Src/C_BaseLib/FabArray.cpp commit 2d8380cd43a88e32b1f8cd0e4499d00eb9e75fd1 Merge: d5f0a66e8 2b9c3040d Author: Ann Almgren Date: Wed Mar 9 16:06:31 2016 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit d5f0a66e876c06dbc00b24993fbc569b3d3815bf Author: Ann Almgren Date: Wed Mar 9 16:06:03 2016 -0800 Need to define nlevs based on the mgt, not on the array of multifabs. Src/LinearSolvers/F_MG/nodal_enforce_dirichlet_rhs.f90 commit de63f0bc54f3d9b4296e799ba3e54154ed3b7572 Merge: 8ac8ab422 4e60f2cd6 Author: vince Date: Wed Mar 9 15:44:49 2016 -0800 resolve confilicts. commit 63d1797aa5367bf2b5fdb296a22e7f837dd84f87 Author: Weiqun Zhang Date: Wed Mar 9 15:43:37 2016 -0800 make sure that each team worker is more likely to work on its own fabs Src/C_BaseLib/FabArray.cpp commit 8ac8ab42292d4e8429cc6362aba3357d9f67f506 Author: vince Date: Wed Mar 9 15:17:13 2016 -0800 copy setup test. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Particles.H Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/Utility.H Tools/C_mk/Make.defs Tutorials/Sidecar_EX1/DestMFTest.cpp Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Sidecar_EX1/GridMoveTest.cpp Tutorials/Sidecar_EX1/inputs_sc commit 4e60f2cd6d8fa547a5c945d29d1d835eac7b4fa1 Author: Brian Friesen Date: Wed Mar 9 15:07:57 2016 -0800 DestMFTest: add extra code showing how to translate DistributionMappings between groups Tutorials/Sidecar_EX1/DestMFTest.cpp commit c63c9d844f4179c862352ab625533ff27a00f393 Author: Brian Friesen Date: Wed Mar 9 15:05:46 2016 -0800 DistributionMapping: add static function TranslateProcMap() This function translates the processor map from a DistributionMapping on one MPI group into a map on another group. It currently does not set the sentinel rank, so this must be done manually after the call to this function. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 50204f23178719ca7c2efe8e40381426ab948616 Author: Brian Friesen Date: Wed Mar 9 15:05:07 2016 -0800 DestMFTest: add buzzard wings around cases to prevent variable cross-initialization Tutorials/Sidecar_EX1/DestMFTest.cpp commit aac2f6866fddd78bee9493f55d9bbcd2ba4acab4 Merge: 960302433 2b9c3040d Author: Weiqun Zhang Date: Wed Mar 9 14:05:38 2016 -0800 Merge branch 'development' into pgas commit 2b9c3040df93f9a85f032c6a779d4700a93360c7 Author: Weiqun Zhang Date: Wed Mar 9 14:02:42 2016 -0800 Renaming. C++ standard says, "Each name that contains a double underscore (__) or begins with an underscore followed by an uppercase letter (2.11) is reserved to the implementation for any use." Src/C_BaseLib/BaseFab.H Src/C_BaseLib/FabConv.cpp Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit f3d1c7015c09763d17b188389fde464e6d073581 Author: Brian Friesen Date: Wed Mar 9 13:11:13 2016 -0800 BoxArray: use new BoxArray serialization functions to reduce # of Bcasts() Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Tutorials/Sidecar_EX1/DestMFTest.cpp commit 6b1730f98a8ddc25bb789c97871cf156e7fe3839 Author: Brian Friesen Date: Wed Mar 9 12:59:00 2016 -0800 BoxArray: split SendBoxArrayToSidecars() into SendBoxArray() and RecvBoxArray() Originally SendBoxArrayToSidecars() had separate logic for senders and receivers internally, but this was confusing because receiving processes would still call "SendBoxArrayToSidecars()" so it looked like they were actually sending something. Splitting this into two functions brings it more in line with point-to-point MPI function names. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Tutorials/Sidecar_EX1/DestMFTest.cpp commit 54cd30ce51af9803a9c6479d0988c2c45ce4f621 Author: Ann Almgren Date: Wed Mar 9 12:42:21 2016 -0800 Oops -- in ml_layout restricted build, only define ref ratio up to max_levs-1, not max_levs. Src/F_BaseLib/ml_layout.f90 commit 960302433aea00bedc31f9956a0044ae820f7ccf Merge: 78ccbe529 8430ae8c8 Author: Weiqun Zhang Date: Wed Mar 9 11:29:10 2016 -0800 Merge branch 'development' into pgas commit fe7c1d7e449e8c07341de89941e73ef2aa605d30 Author: Brian Friesen Date: Wed Mar 9 11:24:43 2016 -0800 Sidecars_EX1: add Marc's new test code for moving MultiFabs Tutorials/Sidecar_EX1/DestMFTest.cpp Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Sidecar_EX1/Make.package commit 8430ae8c80cc6476faaa047cccbea4338e7a7562 Merge: 519a283a2 13f77ede1 Author: Ann Almgren Date: Wed Mar 9 11:21:19 2016 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 13f77ede1bc81451fb811a2e96e20d620b849c77 Author: Weiqun Zhang Date: Wed Mar 9 11:06:32 2016 -0800 Remove BLMap because (1) C++11 enhanced the thread safety of std::map (2) BLMap does not play well with FabArray in shared memory. Src/C_BaseLib/BLMap.H Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG4/ABec2.cpp Src/LinearSolvers/C_CellMG4/ABec4.cpp commit 519a283a255c09faba126fe8e803117c11d34891 Author: Ann Almgren Date: Wed Mar 9 10:33:40 2016 -0800 Fix typo in comment in Tutorials/Tiling_C/main.cpp Tutorials/Tiling_C/main.cpp commit b71c650cca5e9f1fbd2fd69b598321163e8556ad Author: Ann Almgren Date: Wed Mar 9 10:25:10 2016 -0800 Add a new version restricted build to ml_layout that takes a minimum and maximum level rather than just a new nlevs. Src/F_BaseLib/ml_layout.f90 commit 78ccbe5292b0f78b3a0b1470f6d4dc2658958649 Author: Weiqun Zhang 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 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 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 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 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 Date: Mon Mar 7 18:11:28 2016 -0800 0 --> nullptr Src/C_BaseLib/FabArray.H commit 4cecaa4d8da25d38b3665fe87a72cbf0ce4e1b29 Author: Weiqun Zhang Date: Mon Mar 7 17:06:09 2016 -0800 FabArray::AllocFabs: for upc++, allocate one big chunk of memory for the whole mulitfab just like what we do now in mpi Src/C_BaseLib/FabArray.H commit 6e2a235fa3195194eb2a2b8215a5c78d05ea474c Author: Weiqun Zhang Date: Mon Mar 7 16:13:07 2016 -0800 FabArray: move shared memory stuff into a struct Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp commit dc0432184d7834bcbdcf1678407c2ce10e8caf05 Author: Weiqun Zhang Date: Mon Mar 7 15:18:04 2016 -0800 MPI-3 shared memory: rewrite AllocFabs to reduce the number of shared memory allocation. There is a limit of 1024 sysv segments on Cori and Edison. Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit a1d3177f552be7487d2ac58cd11afc36ea0acd40 Author: Weiqun Zhang Date: Mon Mar 7 10:36:48 2016 -0800 BaseFab: remove swap function because it is used and it could be unsafe in shared memory model Src/C_BaseLib/BaseFab.H commit 699e2254e53cc7040147ee5da19f4aff28f32dda Author: Max Katz Date: Sat Mar 5 01:52:23 2016 -0500 Print out a more informative message if we crash because the user's Python is too old to support the print() command used in write_probin.py. Tools/F_scripts/write_probin.py commit 8a0e4e43be7b7b94517982ead6e713173076f5b5 Author: Weiqun Zhang Date: Fri Mar 4 21:30:55 2016 -0800 Set MPI_Info for MPI_Win_allocate_shared to alloc_shared_noncontig Src/C_BaseLib/BaseFab.H commit ee3aae76d25aa1f51daf09b1525170335d6de8a0 Author: Weiqun Zhang Date: Fri Mar 4 17:20:53 2016 -0800 Cray supports C++11 now. Tools/C_mk/Make.Linux commit 9ca1ec93c3f73cc6c4cba94a9fab48ab68d82419 Author: Weiqun Zhang Date: Fri Mar 4 17:20:53 2016 -0800 Cray supports C++11 now. Tools/C_mk/Make.Linux commit 8665b3d86b156e0cf351a199bb1ae1468449ecb4 Merge: bdab9d515 9e9a20d36 Author: Weiqun Zhang Date: Fri Mar 4 17:09:05 2016 -0800 Merge branch 'development' into pgas commit 9e9a20d364be88efc55ab681e38e09569da44b0b Author: Brian Friesen Date: Fri Mar 4 16:28:46 2016 -0800 C_mk: turn off debug symbols for optimized code with Cray compilers Using "-g" or "-G2" significantly reduces code performance, even with "-O2". So disable all debug symbols to get the fastest code. Tools/C_mk/Make.Linux commit 873e2a81aa90e0571f1262d0ffc98259adf8c3db Author: vince Date: Fri Mar 4 16:16:38 2016 -0800 use new broadcast functions. Src/C_AMRLib/Amr.cpp commit bdab9d515a97750c74b4b2ee4bb691bdce23b741 Author: Weiqun Zhang Date: Fri Mar 4 16:09:00 2016 -0800 fix LAZY for team Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit fe85b570c5f6fa6af52a97e7cf7f5fce64039ee6 Author: vince Date: Fri Mar 4 16:03:09 2016 -0800 move some code. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 16bbb18c3f9f517c97f942637ddae03f5214751d Author: Brian Friesen Date: Fri Mar 4 15:20:05 2016 -0800 C_mk: remove "-debug all" from Intel compiler flags on Edison and Cori This flag emits the same debug information as "-g", which we already use, so it's unnecessary. This partially reverts commit 4c2d110. Tools/C_mk/Make.defs commit 5f781a82026f041fdc8e46b621217d1909d5635c Merge: 3bccd760d ad5b4c3c0 Author: Brian Friesen Date: Fri Mar 4 14:51:54 2016 -0800 Merge branch 'compiler_flag_fixes' into development This merge fixes a few logic bugs in Make.defs related to selecting Intel compiler flags on Edison, Cori, and Babbage at NERSC. commit ad5b4c3c0f47184bf6c14fba9caa3baa6e982384 Author: Brian Friesen Date: Fri Mar 4 14:34:49 2016 -0800 C_mk: add back "-fp-model source" to Intel compiler flags on Edison, Intel, and Cori Tools/C_mk/Make.defs commit cd6cf78e44706deb821bc4b61570237d68a12a08 Author: Brian Friesen Date: Fri Mar 4 14:33:05 2016 -0800 C_mk: removed another "else" from "if Edison then" clause when selecting Intel compiler flags Tools/C_mk/Make.defs commit 4c2d1102ec3f9aa4ca7a3c4c3dff274168d24ca0 Author: Brian Friesen Date: Thu Mar 3 13:27:11 2016 -0800 C_mk: add "-parallel-source-info=2" and "-debug all" to Intel compiler flags on Edison and Cori These emit more complete debug information than is emitted by default, which is useful when running VTune and other profiling tools on optimized code. Tools/C_mk/Make.defs commit c14c39f5a14a22ceda014d4dec1a8df829f2fbc5 Author: Brian Friesen Date: Fri Mar 4 14:22:58 2016 -0800 C_mk: remove "else" from "if Edison then ..." clause when setting Intel compiler flags Tools/C_mk/Make.defs commit 217fe6c35de2cea8af382485dfcba80b2e2ea285 Author: Brian Friesen Date: Fri Mar 4 13:44:35 2016 -0800 C_mk: remove "-xHost" flag from Intel compiler flags on Edison and Cori The Cray compiler wrappers for the Intel compilers already contain the correct instruction set flags for both architectures ("-xCORE-AVX-I" on Edison and "-xCORE-AVX2" on Cori). Furthermore, "-xHost" uses the optimal instruction set on the architecture which hosts the compiler, which may be different than that of the compute nodes. This commit partially reverts commit 0088bae. Tools/C_mk/Make.defs commit 359296db185f3dadc5f649eb815cf47c2247d3dc Merge: c8d24409a 3bccd760d Author: Weiqun Zhang Date: Thu Mar 3 17:31:49 2016 -0800 Merge branch 'development' into pgas commit 3bccd760d7c027b9ce7533d08fd8c549dc314c9a Author: Weiqun Zhang Date: Thu Mar 3 17:31:33 2016 -0800 disable SIGFPE trapping by default because vectorized codes with if statement may have invalid floating point operations whose results are eventually masked out. Src/C_BaseLib/BoxLib.cpp Src/F_BaseLib/backtrace_c.cpp commit d0feb307cdc4f65353a8eaf3f025821579ba14bf Author: vince 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 Date: Wed Mar 2 17:20:57 2016 -0800 allow nSidecarProcs == 0 Src/C_BaseLib/ParallelDescriptor.cpp commit f3e28b9d9c05bd20a6b890940ee0b02e35ba917a Author: vince Date: Wed Mar 2 16:58:43 2016 -0800 allow nSidecarProcs == 0 Src/C_AMRLib/Amr.cpp commit 6838257d9b2cdcbad872670dd9aa6f0c6b3cdad1 Author: vince Date: Wed Mar 2 14:27:09 2016 -0800 some cleanup. Src/C_AMRLib/Amr.cpp commit 04966105735e6f097023ddcb7e3df3d9787e74bc Author: vince Date: Wed Mar 2 14:21:53 2016 -0800 first fully working version of dynamic sidecars. Src/C_AMRLib/LevelBld.H Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp commit 0deca343416e7d8fc255778ff7ef0d5f85082323 Author: vince Date: Wed Mar 2 14:10:55 2016 -0800 some cleanup. Src/C_AMRLib/AmrLevel.cpp commit c8d24409a4a1c82fe4ebb504ec515cb5fcdae5ad Merge: 3f4f6d0d9 56ee22a75 Author: Weiqun Zhang Date: Wed Mar 2 13:40:29 2016 -0800 Merge branch 'development' into pgas commit 56ee22a75f6ebdd4831c1a4595138f931341c9a6 Author: Weiqun Zhang 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 Date: Wed Mar 2 13:39:49 2016 -0800 explicitly add noinline attribute for gcc Src/C_BaseLib/FabArray.cpp commit 07ac173a75e86a8570f465c94e581b592032ce97 Author: vince Date: Wed Mar 2 13:39:18 2016 -0800 reinitialize fortran data for new procs. Src/C_AMRLib/Amr.cpp commit 95ea9ecc4c1834b9302048780b4779a1bee90126 Merge: d57c8e32b 41ab627d2 Author: Weiqun Zhang Date: Wed Mar 2 13:32:14 2016 -0800 Merge branch 'development' into pgas Conflicts: Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit d57c8e32b5b5c5c59c58c25909ab94e33be461ef Author: Weiqun Zhang Date: Wed Mar 2 13:19:45 2016 -0800 minor Src/C_BaseLib/FabArray.H commit 41ab627d23b3c741cb93a41443759a20e34a83dd Author: Weiqun Zhang Date: Wed Mar 2 16:13:31 2016 -0500 For whatever reason, gcc sometimes doesn't like some functions live in FabArray.H, unless '-fno-inline' is used. Moving them to .cpp file seems to solve the problem. And we can maybe remove the -fno-line from makefile. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Tools/C_mk/Make.defs commit e9c2fdb787909e5147400fd75940d9bbcd7d05a5 Author: Weiqun Zhang Date: Tue Mar 1 14:15:34 2016 -0800 read into MultiFab directly so that it works with shared memory Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit bb9023cd6bd434cdf1b8b73602448c099152e548 Author: Weiqun Zhang Date: Tue Mar 1 12:58:35 2016 -0800 define ownership even if fabs are not allocated so that mfite could work on empty multifabs Src/C_BaseLib/FabArray.H commit de4bbcd99ed889f0b30ff3e2581a0c9fe77c5f99 Author: Weiqun Zhang Date: Tue Mar 1 12:15:40 2016 -0800 avoid setFab because it does not work with the new MFIter Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/Geometry.cpp commit 4ec6f85a52321953ee44e0f1899755c4501383dc Author: Weiqun Zhang Date: Mon Feb 29 18:02:27 2016 -0800 MemoryBarrier: add omp barrier before upcxx and mpi barrier; only master thread calls upcxx or mpi barrier Src/C_BaseLib/ParallelDescriptor.H commit cebbb25028a4830a57371299c3aea9d21c66ad57 Author: Weiqun Zhang 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 Date: Mon Feb 29 17:06:49 2016 -0800 minor Src/C_BaseLib/ParallelDescriptor.H commit 4304604b6ead17dbad9247d19fa9bd6864d36b82 Author: Weiqun Zhang Date: Mon Feb 29 17:05:10 2016 -0800 team_for: rework on support for OMP Src/C_BaseLib/ParallelDescriptor.H commit 3fcc8aab027a3b181830ed5567d29672dfc38388 Author: Weiqun Zhang 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 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 Date: Mon Feb 29 15:21:34 2016 -0800 Don't call free if not allocated Src/C_BaseLib/Geometry.H commit d36e2ec260c4efad1818abc130f553d59ce9304e Merge: 740f9776f 32a46208f Author: Weiqun Zhang Date: Mon Feb 29 15:01:58 2016 -0800 Merge branch 'development' into pgas Conflicts: Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.cpp commit 32a46208f7b784b51f4dcfb24d86efb99a63842a Author: Weiqun Zhang Date: Mon Feb 29 14:39:19 2016 -0800 fix BL_AMRPROF Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.cpp commit 740f9776f83bf039c4e596164a4d0f15bbcbfc53 Author: Weiqun Zhang Date: Mon Feb 29 14:20:04 2016 -0800 make mpi onesided a runtime parameter mpi.onesided Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tests/FillBoundaryComparison/main.cpp Tools/C_mk/Make.defs Tutorials/PGAS_HEAT/GNUmakefile Tutorials/PGAS_HEAT/inputs_3d commit b7e4e6520a60eb842a1d6c7c4a99ba4d877d13d3 Author: vince Date: Mon Feb 29 13:27:39 2016 -0800 setVect function for broadcasts. Src/C_AMRLib/BCRec.H commit 51005fc56ca1f559cb5116be302c9ec4c560ef76 Author: vince Date: Mon Feb 29 13:15:07 2016 -0800 broadcast bcrec. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit f9e8edde96b1e93d9a18e3729909a73ec5afa6f0 Merge: 83967fb24 4f499c879 Author: Weiqun Zhang Date: Mon Feb 29 10:52:13 2016 -0800 Merge branch 'development' into pgas commit 4f499c8797cb5219222f50818ae0e2eac185478b Author: Weiqun Zhang Date: Mon Feb 29 10:51:03 2016 -0800 removed an unsafe omp parallel I recently added Src/C_AMRLib/TagBox.cpp commit 83967fb244b97a04568590119b652036d0f14894 Merge: 42791018b c12345dd7 Author: Weiqun Zhang 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 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 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: 1aaf53885 bc665e99e Author: Weiqun Zhang Date: Fri Feb 26 18:14:39 2016 -0800 Merge branch 'development' into pgas Conflicts: Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/FabArray.H commit bc665e99e3aca3a248413aa66bbb6f01e83df548 Author: Weiqun Zhang Date: Fri Feb 26 18:04:50 2016 -0800 protect IndexMap() function and thus preventing raw loops Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/FabArray.H Src/C_BoundaryLib/FabSet.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG4/ABec2.cpp Src/LinearSolvers/C_CellMG4/ABec4.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 1aaf5388553558e9dc501b86e3fb812e1e6629d3 Merge: 34c837916 6509c7664 Author: Weiqun Zhang Date: Fri Feb 26 16:50:39 2016 -0800 Merge branch 'development' into pgas commit 6509c76640b9c65f80521ec88d87fe1048f0dba6 Author: Weiqun Zhang Date: Fri Feb 26 16:50:27 2016 -0800 remove deprecated functions Src/C_AMRLib/FluxRegister.cpp commit 34c837916c9eba771629b0ddc2daf3b5593d904b Author: Weiqun Zhang Date: Fri Feb 26 16:16:06 2016 -0800 remove the owneronly flag and make owneronly the default when tiling is off Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/VisMF.cpp Src/C_BoundaryLib/FabSet.cpp commit 80cc7121c5ca14a3e2aecc943a10259a4e5be6fe Merge: f5268e5f7 9679fa2b7 Author: Weiqun Zhang Date: Fri Feb 26 13:07:45 2016 -0800 Merge branch 'development' into pgas Conflicts: Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 9679fa2b7e128da138f8d300e63dcea2a1551f2f Author: Weiqun Zhang Date: Fri Feb 26 13:04:44 2016 -0800 FillPatchIteratorHelper does not need to derive from MFIter Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 8f63142bae57878e14f738c7c0bec51d5707ff0f Author: Weiqun Zhang Date: Fri Feb 26 12:57:37 2016 -0800 TagBox: sync up with pgas branch Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit f5268e5f7c028b180e0299e93707f8edadc84e8e Author: Weiqun Zhang Date: Fri Feb 26 12:43:35 2016 -0800 Fix TagBox for team Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit b762a609df275f93ecfbb1066a5588fa2fc74dde Author: Weiqun Zhang Date: Fri Feb 26 09:50:02 2016 -0800 minor Src/C_BaseLib/BaseFab.H Src/C_BaseLib/FabArray.H commit 0dca9c894b0afc40e0c2dfcc4873c2f854427ad2 Merge: 9ac273406 171766adc Author: Weiqun Zhang Date: Thu Feb 25 16:27:18 2016 -0800 Merge branch 'development' into pgas commit 171766adcefde5f577e8ee94851cd256bdda386e Author: Weiqun Zhang Date: Thu Feb 25 16:22:45 2016 -0800 rename the fabarray to fab copy function to copyTo and optimize it a bit Src/C_BaseLib/FabArray.H commit 485b70f91f3b2f470c9ba0b907ac991ea2da3cd2 Author: Weiqun Zhang Date: Thu Feb 25 16:21:06 2016 -0800 add BoxCommHelper that helps communicating boxes Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit df2d7a540223dd970c774c29ac8e6914cada808a Author: Weiqun Zhang Date: Thu Feb 25 10:45:11 2016 -0800 remove some unused and potentially unsafe and inefficient functions Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 8936ff44472588d12b325f950ced07804dd1505c Author: Weiqun Zhang Date: Wed Feb 24 18:25:41 2016 -0800 remove some deprecated functions Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 9ac273406e76ad65d5f116cc3629683936312ba4 Author: Weiqun Zhang Date: Wed Feb 24 18:17:29 2016 -0800 Owner only in the parallel linComb Src/C_BoundaryLib/FabSet.cpp commit 54eaff74aa659a628c7856828f6eb5019dd09bc9 Author: vince Date: Wed Feb 24 18:14:06 2016 -0800 added min rank to random range map. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit ff9697f827ea1ab8ddad9000d891e0bbd3790542 Author: Weiqun Zhang Date: Wed Feb 24 17:47:40 2016 -0800 update FabSetIter constructor interface Src/C_BoundaryLib/FabSet.H commit b290c0e1912d22f69da25c914f068176637946c5 Author: vince Date: Wed Feb 24 17:07:51 2016 -0800 added grid redistribution. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 58d81ef7da7d22fc1184a07d818e2e9ff39fa74d Author: vince Date: Wed Feb 24 17:06:20 2016 -0800 more broadcast variables. Src/C_BaseLib/MultiFab.cpp commit 2c66269a68e28a57f0926bd5124d7be24c853e29 Author: vince Date: Wed Feb 24 17:05:52 2016 -0800 more broadcast variables. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 4ca44e43ea12e4e5eb6e384ce2495e202aff2d6b Merge: 552a00724 654abe8ed Author: Weiqun Zhang Date: Wed Feb 24 15:24:13 2016 -0800 Merge branch 'development' into pgas commit 654abe8edb2b08f875e02c03507730b360114535 Author: Weiqun Zhang Date: Wed Feb 24 15:23:54 2016 -0800 use quiet nans as initial values of some fabs Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/BndryRegister.cpp commit 552a00724a27e19bbc8a6118337933f20ccb9c65 Merge: fe348a149 4644c7852 Author: Weiqun Zhang Date: Wed Feb 24 15:15:05 2016 -0800 Merge branch 'development' into pgas commit 4644c785276e6cbe1e1aa17302ec68a20610ff5e Author: Weiqun Zhang Date: Wed Feb 24 15:14:41 2016 -0800 No need to use bogus values since in debug and test modes farraybox is filled with snan Src/C_BaseLib/MultiFab.cpp commit fe348a1494c8ba031854f8f9b4730556b909b91a Author: Weiqun Zhang Date: Wed Feb 24 15:10:12 2016 -0800 comment Src/C_BaseLib/FabArray.H commit 0b21218bd627e3c8f84863df3fe8e77038dba381 Author: Weiqun Zhang Date: Wed Feb 24 14:57:13 2016 -0800 Insert a memory barrier at the end of FillPatchIterator. Switch to MFIter in FillCoarsePatch Src/C_AMRLib/AmrLevel.cpp commit e7b87701910294c6f408a3dc4e32ac60a970defa Author: Brian Friesen Date: Wed Feb 24 14:25:07 2016 -0800 C_AMRLib: change "include 'omp_lib.h'" to "use omp_lib" The IBM XL Fortran compiler does not support omp_lib.h. Also that header often includes non-standard OpenMP functions. Using the "omp_lib" module is standard and is supported by all compilers. Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/INTERP_3D.F commit e500f43cd23f65e6f5fc6df98a2f61d951947ab2 Author: Brian Friesen 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 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 Date: Wed Feb 24 14:00:37 2016 -0800 added more vars to broadcast. Src/C_AMRLib/Amr.cpp commit ac1dbfb39b7df442af65648c289a4695ad6cb5e1 Author: Brian Friesen Date: Wed Feb 24 10:00:19 2016 -0800 MultiFab::SendMultiFabToSidecars: remove redundant check for Box indices in a procmap This check always returns true, so remove it. Src/C_BaseLib/MultiFab.cpp commit 582aac1081ad238e5428724b01698319877e7a03 Author: Brian Friesen Date: Mon Dec 21 10:45:32 2015 -0800 C_mk: update library locations for new custom-built versions of GCC and MPICH on orga Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi commit 76a51aabd884560f7407fe69b4f30c72aa76c4a5 Author: Weiqun Zhang Date: Tue Feb 23 22:32:56 2016 -0800 first pass of new fillpatch that avoid a mpi_alltoallv Src/C_BaseLib/FabArray.H commit 3605d734715ab911086415eefc73c4eeb1bcbdde Author: Weiqun Zhang Date: Wed Feb 24 12:22:06 2016 -0800 BaseFab::swap: swap those new meta data too Src/C_BaseLib/BaseFab.H commit f9953e3f12b1584ee5094b0bce3495557305524f Author: Weiqun Zhang Date: Wed Feb 24 12:20:06 2016 -0800 TagBox: should use local index instead of global index Src/C_AMRLib/TagBox.cpp commit 7e02e7d6fa07f56ee63ef3ca0d602751eb8d4b66 Author: vince 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 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 Date: Wed Feb 24 10:35:37 2016 -0800 handle zero size intvects. Src/C_AMRLib/Amr.cpp commit 069c5338bd2fae288f58af6e5a54be7e51f3829c Merge: 4f2228466 323f1d52b Author: Weiqun Zhang Date: Wed Feb 24 09:52:20 2016 -0800 Merge branch 'new_fillpatch' into pgas commit 323f1d52bccc1f58bbb49d164965256c4ecd815d Author: Weiqun Zhang Date: Tue Feb 23 22:32:56 2016 -0800 first pass of new fillpatch that avoid a mpi_alltoallv Src/C_BaseLib/FabArray.H commit 8d51a3d51dbe629f25926d1082880e87b1563c2f Author: Michael Zingale Date: Tue Feb 23 10:46:17 2016 -0500 now that xrb_simple has a different default network, explicitly compile in rprox Tools/RegressionTesting/Maestro-tests.ini commit 9c6922ddeec9a8c488e87e5bb953859ef47ba38f Author: vince Date: Mon Feb 22 15:32:42 2016 -0800 pass flag to add distmap to cache on broadcast. Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 0695fb9076e5e79abda3992e540f6e9ad5594f44 Author: vince Date: Mon Feb 22 15:15:10 2016 -0800 whichProc option for CacheStats. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit ac5e56d4269b23205e5356f1ccd581d7da3ff90f Author: vince Date: Mon Feb 22 15:09:01 2016 -0800 option to add map to cache when defining with Array. Src/C_AMRLib/ErrorList.H Src/C_BaseLib/FabArray.H commit 5d418d70127e0d35c04d1efb89fa7e4bd1614736 Author: vince Date: Mon Feb 22 15:07:07 2016 -0800 option to add map to cache when defining with Array. Src/C_BaseLib/Utility.cpp commit 1e60eacb069159be9f25e70d839c48819c3320e3 Author: vince Date: Mon Feb 22 15:05:30 2016 -0800 option to add map to cache when defining with Array. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 5d37f8088fdcc9ed63c48660ac44339546502628 Author: vince 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 Date: Mon Feb 22 12:24:51 2016 -0800 comments Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/FabArray.H commit 2cf03e656a3ee6dc9b32ee9a6248d1f5435242b0 Merge: 9aff1133c 227c307e7 Author: Weiqun Zhang Date: Mon Feb 22 12:20:33 2016 -0800 Merge branch 'development' into pgas commit 227c307e7e4df57343b9b008af58f639a52ba90d Author: Weiqun Zhang Date: Fri Feb 19 18:02:14 2016 -0800 use quiet nan as safe bogus value Src/C_BoundaryLib/BndryRegister.cpp commit f23802497c7f500c7b675535bdc50497e8b8f4f5 Author: Weiqun Zhang Date: Fri Feb 19 17:51:42 2016 -0800 no longer need to set special bogus values in DEBUG because it is done in constructor of fab now Src/C_AMRLib/AmrLevel.cpp commit 281de0835e9d0db3b1162981231ce65ebe148ef2 Author: Weiqun Zhang Date: Fri Feb 19 17:23:17 2016 -0800 tidy Src/C_AMRLib/AmrLevel.cpp commit 9aff1133c605bf66611b5f59aed6563fb9a1e0c7 Author: Weiqun Zhang Date: Fri Feb 19 16:04:07 2016 -0800 DistributionMapping: Support for team in KnapSack Src/C_BaseLib/DistributionMapping.cpp commit 27208bf299f76a83501f39e10d3e1b5bc10a0043 Author: vince Date: Fri Feb 19 15:31:32 2016 -0800 set dmid for new procs. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/Utility.cpp commit c3dab281ac8d94b8b7e9d57c146d4983ac03e88b Author: Weiqun Zhang Date: Fri Feb 19 15:07:59 2016 -0800 DistributionMapping: Support for team in RoundRobin Src/C_BaseLib/DistributionMapping.cpp commit 880cafc49b8a6c382adcb6062187e69c7c84ac57 Author: vince Date: Fri Feb 19 13:56:02 2016 -0800 print allocatedFAPtrs, remove unused maps. Src/C_BaseLib/FabArray.H commit 4ffde430c2ac3ce874a222e901caa51ac719fc86 Author: Weiqun Zhang Date: Fri Feb 19 13:38:41 2016 -0800 MPI one-sided FabArray::copy Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit ed7904779e0d3b151dab548cf6b8c4e3849aada9 Author: Marc Day Date: Thu Feb 18 18:15:45 2016 -0800 Uptick tag Tools/CMake/BoxLib_Version.cmake commit a78901fa1ecf5e8bfa2324871f8ac2f0c0bc7d17 Author: Weiqun Zhang Date: Tue Feb 16 16:42:38 2016 -0800 add Team support in CPC Src/C_BaseLib/FabArray.cpp commit e38c2419eb4a6f1b8b26af148ed738c3f237ea20 Author: Weiqun Zhang Date: Tue Feb 16 15:43:05 2016 -0800 UPC++ in FabArray::copy Src/C_BaseLib/BLPgas.H Src/C_BaseLib/BLPgas.cpp Src/C_BaseLib/FabArray.H commit c88514af6d23ad51add2ebecbe9916a0a5b94f82 Author: Marc Day Date: Wed Feb 17 10:26:08 2016 +1100 Initial changes for building on Australian machines Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit edf51e04af7138210ff97a0ea67cc79e4e5ef652 Merge: 1863c3eb5 325681b68 Author: Marc Day Date: Wed Feb 17 08:40:30 2016 +1100 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 1863c3eb5c833d45c3e3dc0fd79836d3cbab57a0 Author: Marcus Day 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 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: e66b96731 325681b68 Author: Weiqun Zhang Date: Tue Feb 16 12:40:09 2016 -0800 Merge branch 'development' into pgas Conflicts: Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FArrayBox.cpp commit 325681b687d75446274c1e5d2f1b46a17bdfd47f Author: Weiqun Zhang Date: Tue Feb 16 07:10:19 2016 -0800 Following up on parent commit, Fortran also likes to print 1.d99 as 0.1+100, so change the upper bound to 1.d98 Src/F_BaseLib/multifab_physbc_edgevel.f90 Tools/Postprocessing/F_Src/fcompare.f90 commit 6ce4758ce2ac9c0d822734e52491807652b9b902 Author: Michael Zingale Date: Tue Feb 16 09:56:25 2016 -0500 protect the prints at the high-end too -- if the error is larger than 1.d99, make it 1.d99, this avoids Fortran's habit of dropping the 'E' in the asci representation of numbers with 3-digit exponents. Tools/Postprocessing/F_Src/fcompare.f90 commit eaca6d91abd090f99faf1956223199be5395f3cd Author: Weiqun Zhang Date: Mon Feb 15 16:02:47 2016 -0500 Turn on floating point exception trapping for PGI 16 and later Src/C_BaseLib/BoxLib.cpp Src/F_BaseLib/backtrace_c.cpp commit a5554903a4a566d96a1f7477b216a71514bdb90d Author: Weiqun Zhang Date: Mon Feb 15 11:40:57 2016 -0800 Fortran fab build: skip memory allocation if box is empty. Src/F_BaseLib/fab.f90 commit e0f0c82b3fe7074358c904d568cc7a06a6eade78 Author: Max Katz Date: Mon Feb 15 13:09:50 2016 -0500 Only print warnings if we're on I/O processor Src/C_AMRLib/Amr.cpp commit d3763b7354ad07a4db675a1b4b40e51c4700defb Author: Michael Zingale Date: Sun Feb 14 20:59:46 2016 -0500 some png tweaks Tools/RegressionTesting/testnew.py commit a878bf842517b9370260335c6c0e52324f2629d3 Author: Max Katz Date: Sat Feb 13 20:16:42 2016 -0500 Add two new member functions to StateData: copyOld and copyNew. These copy the old_data and new_data from a source StateData to a destination StateData, and set the time levels correspondingly. Additionally, add a static function StateData::Initialize. Given a StateData generated using the default constructor, set it up with the same characteristics as a source StateData object and do a deep copy of the data. Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 8edf1357e3c10e9e7654d803d82cd2823ce979cd Author: Michael Zingale Date: Sat Feb 13 18:55:06 2016 -0500 fix a few uninitialized vars Tools/RegressionTesting/testnew.py commit 1cfc9152db462394609790da027d40a0f97e6477 Author: Michael Zingale Date: Sat Feb 13 18:17:14 2016 -0500 remove report_test_failure -- we can get that functionality from report_single_test now, with a failure_msg Tools/RegressionTesting/testnew.py commit 7d1d4dc934c2bfc582663b57797cf1e2c0505f85 Author: Michael Zingale Date: Sat Feb 13 15:53:22 2016 -0500 store the backtrace when we have failures during the benchmark creation Tools/RegressionTesting/testnew.py commit c8e8bb73fa9a7e98cfc829a709151bca7c364388 Author: Michael Zingale Date: Sat Feb 13 15:21:52 2016 -0500 more error reporting Tools/RegressionTesting/testnew.py commit 8116f7fb9e5c8359ade543a1c72be6aded6b8357 Merge: 03a0a2d3f 0e2731e0f Author: Michael Zingale Date: Sat Feb 13 15:16:36 2016 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 03a0a2d3f640c688eb8b1ae8da2a7211c070b764 Author: Michael Zingale Date: Sat Feb 13 15:16:29 2016 -0500 some failure reporting Tools/RegressionTesting/testnew.py commit 0e2731e0f480271dfd821962ef16ef648ea8ca69 Author: Michael Zingale Date: Sat Feb 13 14:52:19 2016 -0500 clean up some error messages Tools/RegressionTesting/testnew.py commit 2db9aff4d88116641b8514fc432ab976667ccc7a Author: Michael Zingale Date: Sat Feb 13 11:46:18 2016 -0500 fix the early abort test report for restart tests, and also fix the wallclock time. Tools/RegressionTesting/testnew.py commit 02787bb80fed324e8dc05fcdb4a7a3cb41ea7417 Author: Michael Zingale Date: Sat Feb 13 09:54:36 2016 -0500 remove some print debugs Tools/F_scripts/write_probin.py commit 2f554c3338be422ea556ca6184803ef90a273283 Author: Weiqun Zhang Date: Fri Feb 12 21:50:01 2016 -0800 Cray: use -G2 instead of -g for ndebug build Tools/C_mk/Make.Linux Tools/F_mk/comps/Linux_cray.mak commit 3d32a22ca896e665673710a964fe74aebb61c931 Author: Weiqun Zhang Date: Sat Feb 13 00:31:43 2016 -0500 PGI: use -gopt instead of -g for ndebug build Tools/C_mk/Make.Linux Tools/F_mk/comps/Linux_pgi.mak commit d0171c969d240326e469c917c414a9e952abf901 Author: Michael Zingale Date: Fri Feb 12 18:35:31 2016 -0500 this isn't used anywhere Tools/C_mk/Make.bgl commit 4c0daae6431889b145ab94edb46511d8d720e57b Author: Michael Zingale Date: Fri Feb 12 18:17:43 2016 -0500 remove carver Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi commit ec3453fa499719229ebe6d37a95c1a8e1505c6e4 Author: Weiqun Zhang Date: Fri Feb 12 12:48:12 2016 -0800 no longer define BL_TESTING when DEBUG=TRUE to avoid confusion Src/F_BaseLib/backtrace_c.cpp Tools/C_mk/Make.defs Tools/F_mk/GMakedefs.mak commit b7416c7e2dc3a381cb1918ddf68fe4e2eda42ae0 Author: Weiqun Zhang Date: Fri Feb 12 12:38:23 2016 -0800 Linear Solver: set full_soln corner cells to quiet nans Src/F_BaseLib/backtrace_c.cpp Src/F_BaseLib/backtrace_f.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 2214b1738749c416f7a0490ddfe76a54d62b34af Author: Michael Zingale Date: Fri Feb 12 15:10:19 2016 -0500 for the PGI compilers, we need to compile the C++ source with -O1 instead of -O. This eliminates some global optimizations. There is a compiler error that manifests itself at link time when we compile ParmParse.cpp with -O. Tools/C_mk/Make.Linux commit 0177f40fe01f1ce872f160566b46c7c6bbed4e9b Author: Michael Zingale Date: Fri Feb 12 14:07:02 2016 -0500 Carver is no more Tools/F_mk/GMakeMPI.mak commit 8a841a0eec5ea4c3e0330beb771a4c9fce9e0bb1 Author: Michael Zingale Date: Fri Feb 12 12:44:18 2016 -0500 update for PGI 16.1+ -- pgCC no longer exists. We now use pgc++. Also, we can use just -pgf90libs to get the F90 stuff linked Tools/C_mk/Make.Linux commit 4e81065d14eb29a9d298923d73eb7388a73c73e1 Author: Weiqun Zhang Date: Thu Feb 11 23:01:01 2016 -0800 do not need to avoid PGI in getting exception flags Src/F_BaseLib/backtrace_c.cpp commit 22930fff0ee70ed4406053d60f9cd7cabf3c49c6 Author: Weiqun Zhang Date: Thu Feb 11 22:52:49 2016 -0800 minor tweak of get_fpe_trap() Src/F_BaseLib/backtrace_c.cpp commit 4176dcdca8f6e70549b29f5304aff34ae203506e Author: Weiqun Zhang 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 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 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 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 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 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 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 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 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 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 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 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 Date: Wed Feb 10 15:23:18 2016 -0500 fix boxlib-only runs Tools/RegressionTesting/testnew.py commit 5c8f75874059644e782b65f60c48db97ac524c53 Author: Weiqun Zhang Date: Wed Feb 10 10:32:23 2016 -0800 latest regression test inputs files Tools/RegressionTesting/BoxLib-tests.ini Tools/RegressionTesting/Castro-tests.ini Tools/RegressionTesting/IAMR-tests.ini Tools/RegressionTesting/LMC-tests.ini Tools/RegressionTesting/Nyx-tests.ini Tools/RegressionTesting/RNS-tests.ini Tools/RegressionTesting/SMC-tests.ini Tools/RegressionTesting/VARDEN-tests.ini commit 6188817c2fe6f95634875344630b4a86655b4b09 Author: Weiqun Zhang Date: Wed Feb 10 09:58:14 2016 -0800 fix a bug in my last commit: accidentally deleted a line Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F commit 1adca55a4e04c97d01b6728b7bec376a96289155 Author: Weiqun Zhang Date: Tue Feb 9 15:25:54 2016 -0800 avoid nans Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F commit 196323f684226a391110075abb47e58f72584d1f Merge: 7a0b1b8a3 b529f4ae7 Author: Marc Day Date: Tue Feb 9 13:56:38 2016 -0800 Merge branch 'development' into 4thOrderMG commit 7a0b1b8a3a4c9830ee101dfa5aa4f7f8d5e21047 Author: Marc Day Date: Tue Feb 9 13:56:08 2016 -0800 Change default Tutorials/MultiGrid_C/GNUmakefile commit 2601815504334801f3d8d7a3511d3dcecbf7822a Author: Marc Day Date: Tue Feb 9 13:51:37 2016 -0800 Final junk Tutorials/MultiGrid_C/main.cpp commit b529f4ae7def727e56a14f4c8edb39342bb22e25 Author: Weiqun Zhang 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 Date: Tue Feb 9 11:56:30 2016 -0500 fix the backtrace links Tools/RegressionTesting/testnew.py commit c6f451a52ae9064e8d7a1af6ae4f4247337faf02 Author: Michael Zingale 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 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: 6b010a4c3 5f934031a Author: Michael Zingale Date: Mon Feb 8 21:08:33 2016 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 6b010a4c37bd7d354790716b34e1e8cc94249f09 Author: Michael Zingale Date: Mon Feb 8 21:08:21 2016 -0500 add support for copying and posting the Backtrace files Tools/RegressionTesting/testnew.py commit 5f934031a10d1639032e95f61d9f591cc9a123ab Author: Michael Zingale Date: Mon Feb 8 20:17:53 2016 -0500 enable TEST=TRUE in the tests Tools/RegressionTesting/Castro-SBU-tests.ini commit 4dfbb89382de6a4c77936db83358675322d18656 Author: Michael Zingale Date: Mon Feb 8 19:58:39 2016 -0500 split C and F add stuff. Now we have: add_to_f_make_line add_to_c_make_line update the Maestro suite to run with TEST=t Tools/RegressionTesting/Maestro-tests.ini Tools/RegressionTesting/testnew.py commit 49f3551e2cdf90fd99bcff9c37449e5436a4671c Author: Marc Day Date: Mon Feb 8 16:56:02 2016 -0800 4th order in progress... Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG4/ABec2.H Src/LinearSolvers/C_CellMG4/ABec2.cpp Src/LinearSolvers/C_CellMG4/ABec2_3D.F Src/LinearSolvers/C_CellMG4/ABec2_F.H Src/LinearSolvers/C_CellMG4/ABec4.H Src/LinearSolvers/C_CellMG4/ABec4.cpp Src/LinearSolvers/C_CellMG4/ABec4_2D.F Src/LinearSolvers/C_CellMG4/ABec4_3D.F Src/LinearSolvers/C_CellMG4/ABec4_F.H Tutorials/MultiGrid_C/COEF_3D.F Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/inputs Tutorials/MultiGrid_C/main.cpp commit 3588512b7eebf0c4edcc8d91e4747f5a7d54cec1 Author: Michael Zingale Date: Mon Feb 8 19:50:12 2016 -0500 add support for a global line to add to the make command Tools/RegressionTesting/testnew.py commit 08dfb7a7748f8aad777cd092f3282829b73e0dad Author: Weiqun Zhang Date: Mon Feb 8 14:28:54 2016 -0800 put abort_fortranboxlib back to module and add a c name for it Src/F_BaseLib/backtrace_f.f90 commit 15e974d91ffbc44cf79bb612f08bd6720cbfd836 Author: Weiqun Zhang Date: Mon Feb 8 14:14:40 2016 -0800 disable SIGFPE trapping for PGI Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/BoxLib.cpp Src/F_BaseLib/backtrace_c.cpp commit 9c6515e8ed6a89d96039f320f38324bdb3701285 Author: Weiqun Zhang Date: Mon Feb 8 13:40:47 2016 -0800 To make PGI happy, define _GNU_SOURCE for PGI on Linux Src/C_BaseLib/BLBackTrace.cpp commit 710ae0342614140bfe0c63da47e21689b9c9a7c6 Author: Weiqun Zhang Date: Mon Feb 8 13:22:19 2016 -0800 To make PGI happy, define _GNU_SOURCE for PGI on Linux and move subroutine abort_fortranboxlib out of module. Src/F_BaseLib/backtrace_c.cpp Src/F_BaseLib/backtrace_f.f90 commit 5d6637d94e55a20292f25c4beac0c2418278c623 Author: Weiqun Zhang Date: Sun Feb 7 16:24:16 2016 -0800 Backtrace: fix calling handler from Linear Solver in C++ BoxLib codes Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/backtrace_c.cpp commit fd61d6ee07ed5a534046c421904640de9ae8b62c Author: Weiqun Zhang Date: Sun Feb 7 13:16:59 2016 -0800 add write_to_stderr_without_buffering to BoxLib namespace Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp commit b8b9d6e1e344aa8887998c947c60c3378a8d90b3 Author: Weiqun Zhang Date: Sun Feb 7 12:17:02 2016 -0800 update Readme.backtrace Docs/Readme.backtrace commit 920bcd76b9275dd9e8422d6029b09b66de5c25de Author: Weiqun Zhang Date: Sun Feb 7 10:46:50 2016 -0800 Backtrace: remove SIGTERM because MPI_Abort might use it; cleanup Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/BoxLib.cpp Src/F_BaseLib/backtrace_c.cpp Src/F_BaseLib/bl_error.f90 commit 974b799cbda66eaf782ad75ab003cd6c7781fd85 Author: Weiqun Zhang Date: Sun Feb 7 00:41:57 2016 -0800 Fortran BoxLib: define BL_TESTING in DEBUG mode Tools/F_mk/GMakedefs.mak commit c75463e66358cd748b644d77be4c462b91a995b3 Author: Weiqun Zhang Date: Sun Feb 7 00:36:29 2016 -0800 Backtrace: remove SIGABRT from backtrace because that's abort sends Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/BoxLib.cpp Src/F_BaseLib/backtrace_c.cpp commit 65fd7d9747aeaf29f36bb96d612090d4776278fb Author: Weiqun Zhang Date: Sun Feb 7 00:13:43 2016 -0800 Fortran BoxLib: remove the old backtrace Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_error_backtrace.f90 Src/F_BaseLib/bl_prof_backtrace.f90 commit b5ba06701659e89c28a2811fc1d1d30745eadcfe Author: Weiqun Zhang Date: Sun Feb 7 00:10:02 2016 -0800 Fortran BoxLib bl_error: call backtrace before abort Src/F_BaseLib/backtrace_c.cpp Src/F_BaseLib/bl_error.f90 commit a912ac1ea2d07d7991a3076abb5247dcf1ec3939 Author: Weiqun Zhang Date: Sat Feb 6 23:51:09 2016 -0800 Fortran fab: if DEBUG or TEST, initialize fab to snan. Src/F_BaseLib/fab.f90 commit 6371b62da50777e8bba8238e3b333831cb1a6f9f Author: Weiqun Zhang 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 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 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 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 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 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 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 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 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: d9e0ece56 0de168128 Author: vince Date: Thu Feb 4 17:51:42 2016 -0800 Merge branch 'master' into development commit 0de1681280d937af895733ee52847c1154edefca Author: vince Date: Thu Feb 4 16:46:19 2016 -0800 i/o tests for the burst buffer. the read part needs to be finished. Tests/BBIOBenchmark/BBIOTest.cpp Tests/BBIOBenchmark/BBIOTestDriver.cpp Tests/BBIOBenchmark/GNUmakefile Tests/BBIOBenchmark/README commit d9e0ece560c51ae038319a80b06b7d3b25dcf037 Author: Michael Zingale Date: Wed Feb 3 15:53:04 2016 -0500 add priority to runtime parameters. When two parameters are encountered with the same name, the value corresponding to the highest priority one will be kept. Also, a lot of source code cleaning a la PEP-8 Tools/F_scripts/write_probin.py commit e66b96731e9f7c633bb78e80d9fce6f6f8278c8c Author: Weiqun Zhang Date: Tue Feb 2 17:47:56 2016 -0800 In simple test codes, MultiFabs are still alive after MPI_Finalize() has been called. The dtor of BaseFab calls MPI functions when MPI shared memory is used. To avoid MPI complaining, we explicitly destroy these MultiFabs before BoxLib::Finalize(). Tests/FillBoundaryComparison/main.cpp Tutorials/PGAS_HEAT/main.cpp commit f0551107b49ece3f0dd373ad5996356b0c76d235 Merge: aeb94a6a8 c8aeb9055 Author: Weiqun Zhang Date: Tue Feb 2 17:22:31 2016 -0800 Merge branch 'development' into pgas commit aeb94a6a825ef9a520782be044dae0f07bd64a9c Author: Weiqun Zhang Date: Tue Feb 2 17:22:04 2016 -0800 clean up FillPeriodicBoundary Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit ed1278d533e357fb8377c6d651d6584d0cc876d9 Author: Weiqun Zhang Date: Tue Feb 2 16:18:14 2016 -0800 clean up FillBoundary Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 834e3f962d4b6a6c1a02bc0dd6c51a987942ef81 Author: Weiqun Zhang Date: Tue Feb 2 14:27:21 2016 -0800 call MPI_Group_free to free the groups Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit c8684005ecb43fa207eee976ed662a46dcd4d9d1 Author: Weiqun Zhang Date: Tue Feb 2 14:11:37 2016 -0800 clean up Src/C_BaseLib/FabArray.H commit 6640fcbcb6b46d02ebde53cfb17e51f4481717e9 Author: Weiqun Zhang Date: Tue Feb 2 13:26:27 2016 -0800 test-mpi3: write and read Tutorials/PGAS_HEAT/test-mpi3/main.cpp commit 9bc80ea2a4804e349293bd73e5e9a5c9d4d555af Author: Weiqun Zhang Date: Tue Feb 2 13:25:43 2016 -0800 fix a typo Src/C_BaseLib/BaseFab.H commit 2256051dd9a7490a553bab9594317198293a9ba7 Author: Weiqun Zhang Date: Tue Feb 2 12:20:23 2016 -0800 fix typo Src/C_BaseLib/FabArray.H commit c3f590ae62c2a25dfba92858d33f8c36e6f0d632 Author: Weiqun Zhang Date: Tue Feb 2 12:19:04 2016 -0800 minor change for consistence Src/C_BaseLib/Geometry.H commit 432ee30e8a1cdc383c1cef5212a594b42bc49fe9 Author: Weiqun Zhang Date: Tue Feb 2 12:18:50 2016 -0800 another BL_USE_UPCXX --> BL_USE_TEAM Src/C_BaseLib/FabArray.cpp commit 336115c997dd0003db8e578892f39cc509754c0d Author: Weiqun Zhang Date: Tue Feb 2 11:23:13 2016 -0800 MFIter: BL_USE_UPCXX --> BL_USE_TEAM because of MPI3 team Src/C_BaseLib/FabArray.cpp commit 470ef6a20fa61121ae3ad9c560ea23eaa9c280e5 Author: Weiqun Zhang Date: Tue Feb 2 11:22:22 2016 -0800 add more Memory Barriers Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit f9ff1cab3c624418e2d6658991618f0d5a0c9f0b Merge: bd65fd65a c8aeb9055 Author: Marc Day Date: Tue Feb 2 10:45:59 2016 -0800 Merge in process, mg tutorial does not yet build commit bd65fd65a2d455b15cc5a81e6dbbd8af670f8d85 Author: Marc Day Date: Tue Feb 2 10:23:49 2016 -0800 Finish up 4th order implementation Src/LinearSolvers/C_CellMG4/ABec2.cpp Src/LinearSolvers/C_CellMG4/ABec2_2D.F Src/LinearSolvers/C_CellMG4/ABec2_3D.F Src/LinearSolvers/C_CellMG4/ABec2_F.H Src/LinearSolvers/C_CellMG4/ABec4.cpp Src/LinearSolvers/C_CellMG4/ABec4_2D.F Src/LinearSolvers/C_CellMG4/ABec4_F.H Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/main.cpp commit dc31be63864bd2299fa5e83848b0c3fcce3e2f71 Author: Yili Zheng Date: Mon Feb 1 20:44:14 2016 -0800 Minor fix of test-mpi3 Tutorials/PGAS_HEAT/test-mpi3/main.cpp commit 0be7b7d7162eb00245b233ccea44c6348596e996 Author: Weiqun Zhang Date: Mon Feb 1 20:07:49 2016 -0800 no need to allocate a MPI_Win in the initialization of team; remove MPI calls in the dtor of team Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit f0460b90d97e061e317e9c5d9436d595e5d5b2b8 Author: Weiqun Zhang Date: Mon Feb 1 19:57:23 2016 -0800 need to pass T** to MPI_Qin_allocate_shared Src/C_BaseLib/BaseFab.H commit 474d67af817b22b8638998c34f67cf9ae65be18a Author: Weiqun Zhang Date: Mon Feb 1 19:56:33 2016 -0800 update ifdef Src/C_BaseLib/Geometry.H commit 82cdf87adc7cc3bc2b4ae65f415a0e442370b42b Author: Weiqun Zhang 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 Date: Mon Feb 1 16:09:52 2016 -0800 fix ifdef Src/C_BaseLib/DistributionMapping.cpp commit 39c1d4e4bb88e19f182773d450ffc23993dbc26c Author: Weiqun Zhang Date: Mon Feb 1 15:49:48 2016 -0800 rename the memory barrier Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/ParallelDescriptor.H commit fcd1f4c2c2884d2f6533378591b04cbe560e0c79 Author: vince Date: Mon Feb 1 15:38:42 2016 -0800 sync sequence number. Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.cpp commit a6000dfedaf7d941f1090f65c5720db64c8ce73d Author: vince Date: Mon Feb 1 15:04:45 2016 -0800 braces. Src/C_BaseLib/VisMF.cpp commit e00190c13e7bd51acbaf958150db9963fd571da7 Author: vince Date: Mon Feb 1 15:02:37 2016 -0800 reset noutfiles. Src/C_AMRLib/Amr.cpp commit 0092622761e866bed1aa8c71c00c868a29bc06ff Author: Weiqun Zhang Date: Mon Feb 1 14:45:47 2016 -0800 fix MFIter::OwnerOnly and NoSharing Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit 3f58371f946f860f82086191f12d14e58720983b Author: Weiqun Zhang Date: Mon Feb 1 12:44:14 2016 -0800 add MPI3 team Src/C_BaseLib/BLPgas.H Src/C_BaseLib/BLPgas.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/IArrayBox.H Src/C_BaseLib/IArrayBox.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/UArena.H Src/C_BaseLib/UArena.cpp Tools/C_mk/Make.defs commit 62016c9a10d1e14fdd2bb2b40944a6688f97aad8 Merge: dc3358a82 9c6f04201 Author: Weiqun Zhang Date: Mon Feb 1 12:41:09 2016 -0800 Merge branch 'mpi-onesided' into pgas commit 9c6f042010c19e40625e364129e74901b710a190 Author: Weiqun Zhang Date: Mon Feb 1 09:07:39 2016 -0800 should be MPI_Group instead of MPI_Comm Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit c8aeb9055c6cabf09bfbae4872b2decc14631e3b Author: Weiqun Zhang Date: Mon Feb 1 09:02:03 2016 -0800 fix assertion when DEBUG=FALSE Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 23f5b06313b2466bfc81cb77aaa9e99d435eae54 Merge: 57289e35d 24d7dd15f Author: Michael Zingale Date: Sun Jan 31 20:36:28 2016 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 94f82bc2d0ed96f3a170b4e35162cc9481b2619a Author: vince Date: Fri Jan 29 19:05:03 2016 -0800 sync sequence numbers. Src/C_AMRLib/Amr.cpp commit 7afc06c45fc22a5dcde88886c5968e417e1c692b Author: vince Date: Fri Jan 29 19:04:52 2016 -0800 sync sequence numbers. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 9b13e4face283edf2740a22d61e18dd4dca44509 Author: vince Date: Fri Jan 29 16:56:53 2016 -0800 more code for the dynamic sidecars. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/Utility.cpp commit 24d7dd15fa2a5866e2af0cd8be0f8efb24e315d0 Author: Ann Almgren Date: Fri Jan 29 12:16:53 2016 -0800 Remove unused variables. Src/C_BaseLib/Particles.H commit 27ff264a3eb527d0822ec26e707a2c9127a9433f Author: vince Date: Fri Jan 29 11:36:02 2016 -0800 some name changes. Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H commit 9510a09703add2dce17c062831ca5a7373b20212 Author: vince Date: Fri Jan 29 11:35:08 2016 -0800 also bcast coordsys. Src/C_BaseLib/Geometry.cpp commit c43a79b3d5e7b593a70ef112fcca0c21533d6f77 Author: vince Date: Fri Jan 29 11:33:34 2016 -0800 some name changes. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 12318172c133b4e049117fc2b290909d7fa2fa4d Author: vince Date: Fri Jan 29 11:30:54 2016 -0800 sync distributionmap caches. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 8a5a9444e640f07302dc8620b368c636d05a8ce0 Author: vince Date: Fri Jan 29 11:29:59 2016 -0800 some name changes. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit dc3358a82943bd0698d53cee29b65877d85fbc5d Merge: b17f3d83e 4c8f3f780 Author: Weiqun Zhang Date: Thu Jan 28 14:49:46 2016 -0800 Merge branch 'development' into pgas commit 0b1e42611ca90e2e1d686514cefd6588047167fa Merge: 0dfc5ab89 4c8f3f780 Author: Weiqun Zhang Date: Thu Jan 28 14:49:15 2016 -0800 Merge branch 'development' into mpi-onesided commit 4c8f3f780d5f926bed876c0b306898f874e31f15 Author: Weiqun Zhang Date: Thu Jan 28 14:02:31 2016 -0800 Particles: fix array index Src/C_BaseLib/Particles.H commit cd5951d3a64f9d42e8447f9c1847b8f7539191d2 Author: Weiqun Zhang Date: Thu Jan 28 13:52:15 2016 -0800 TwoGridPIC: add min_grid_size, the smallest box size we can have Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/split_boxes.cpp commit d9ce2cab94c59e1b9abaf7386e54883763097d86 Author: Weiqun Zhang Date: Thu Jan 28 13:44:18 2016 -0800 Particles: add ParticleBoxArray() and ParticleDistributionMap() to container class Src/C_BaseLib/Particles.H commit 51cdf303869219150e8af9fc1170ca802b1e8774 Author: vince Date: Thu Jan 28 11:54:34 2016 -0800 func name changes. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 6fae764918f4a7f9ae6114995cb0c5470da831c9 Author: vince Date: Thu Jan 28 11:54:13 2016 -0800 func name changes. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit a7a1a8fdd62a86f97c6e957d81df13890dd94c95 Author: vince Date: Thu Jan 28 11:50:39 2016 -0800 func name changes. Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit f3acf2018d95912f1c88cb264cf79eb4265d3577 Author: vince Date: Thu Jan 28 11:16:51 2016 -0800 some cleanup. Src/C_AMRLib/TagBox.cpp commit 5afadbd2b912f92395d9e8e4dae4a8568793309e Author: vince Date: Thu Jan 28 11:15:51 2016 -0800 some cleanup. Src/C_AMRLib/StateData.cpp commit a85fb028c48d5937238cce60b5edf3cdd7244273 Author: Weiqun Zhang Date: Thu Jan 28 11:11:57 2016 -0800 MemPool: minor clean up Src/C_BaseLib/MemPool.cpp commit 64adc50a0a6b6c7065a8e68a8644602b66c025da Author: Weiqun Zhang Date: Thu Jan 28 10:57:03 2016 -0800 turn off printing various cache statistics by default; to turn it on, use boxlib.v=1 Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit f786b5bb5d814a90625ba6eef5bf4969a2422c99 Merge: 44dcf0261 dde9a7117 Author: Ann Almgren Date: Wed Jan 27 16:48:47 2016 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 44dcf0261a754cb94ff3838bd64f016c0cb14864 Author: Ann Almgren Date: Wed Jan 27 16:46:08 2016 -0800 This version checks the actual new efficiency instead of just the approximate efficiency and re-distributes the grid if need be. Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp Tutorials/TwoGrid_PIC_C/split_boxes.cpp commit 5288cb4598d167421ec35398a2768db335f9e29b Author: vince Date: Wed Jan 27 16:02:58 2016 -0800 tests for broadcasting and (un)serializing classes. Tests/C_BaseLib/BcastClasses/BcastClasses.cpp commit e09f798238a57516a28fc2940f69a6c7753014c5 Author: vince Date: Wed Jan 27 16:02:01 2016 -0800 (un)serializeboxarray. Src/C_BaseLib/BoxArray.cpp Tests/C_BaseLib/BcastClasses/GNUmakefile commit b17f3d83e521eaa32f085af3c4a8da0372d123ec Merge: 0dfc5ab89 dde9a7117 Author: Weiqun Zhang Date: Wed Jan 27 13:19:22 2016 -0800 Merge branch 'development' into pgas commit 0dfc5ab89b98014d83e506bd90294a3ce12e9253 Author: Weiqun Zhang Date: Wed Jan 27 13:03:15 2016 -0800 not possible to have zero size message in the communication tags Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit dde9a7117c4760baf04cec1240bb1ccd647d0fca Author: Weiqun Zhang Date: Wed Jan 27 12:35:16 2016 -0800 Particles: replace ParticlesOnSameGrids with OnSameGrids that always does the comparison. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/AmrParGDB.H Src/C_BaseLib/ParGDB.H Src/C_BaseLib/Particles.H commit 0201aeb11d37c41a8cbc5827b1abc93252352dd6 Author: Weiqun Zhang Date: Wed Jan 27 11:11:43 2016 -0800 BoxArray: new CellEqual function that returns true if the two BoxArrays are equal in enclosed cells. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 710988befacefae14ae57ed0d49de093fafd42c3 Author: Weiqun Zhang Date: Wed Jan 27 06:20:03 2016 -0800 fix omp problem due to recent renaming Src/C_BaseLib/Particles.H commit 893049c2882147fe645d2bb8e33006d12928796f Merge: 2e1617c07 74e389a49 Author: hongzhang shan Date: Wed Jan 27 00:17:55 2016 -0800 one more timer commit 2e1617c07ed783cc0437a0ed938c4be9bf64d376 Author: hongzhang shan Date: Tue Jan 26 22:33:31 2016 -0800 add profiling info Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tests/FillBoundaryComparison/main.cpp commit 9512e0cdf3bbb7038e0a2ea057f83d38d973c341 Author: Weiqun Zhang Date: Tue Jan 26 21:24:33 2016 -0800 fix AdvectWithUmac: (1) since umac is not cell-centered, we should not compare its boxarray with particle boxarray; (2) when we need to build new umac, we should build face-centered mf, not cell-centered Src/C_BaseLib/Particles.H commit c814cf42f16f862ee495bc495a8d36be4e1fb7f9 Author: Weiqun Zhang Date: Tue Jan 26 21:15:53 2016 -0800 TwoGrid PIC: leave the original ba untouched and fix a memory leak Tutorials/TwoGrid_PIC_C/main.cpp commit a23b2e0a8dfbe3d5e549494cce50d09c67cce452 Author: Weiqun Zhang Date: Tue Jan 26 21:14:21 2016 -0800 new MultiFab using Particle BoxArray should also use Particle DistributionMap Src/C_BaseLib/Particles.H commit bfa7647c31aa598f963246b97252b1c92f3a10e7 Author: Weiqun Zhang Date: Tue Jan 26 20:33:43 2016 -0800 store a copy of Geometry, DistributionMapping & BoxArray in non-Amr particle containers Src/C_BaseLib/ParGDB.H commit 74e389a497f7562e17a6d3f431db8c96134a970c Author: Weiqun Zhang Date: Tue Jan 26 16:24:39 2016 -0800 remove a barrier Src/C_BaseLib/FabArray.H commit 5d7d2b69f5847b7e27d82626244b3e8fff90f7b3 Author: Weiqun Zhang Date: Tue Jan 26 16:23:41 2016 -0800 fix typo Src/C_BaseLib/FabArray.H commit f06cefb1721745660c956501af8cad75f4342755 Author: Weiqun Zhang Date: Tue Jan 26 16:22:30 2016 -0800 fix a new bug; forgot that the address of vector element can be invalidate by push_back Src/C_BaseLib/FabArray.H commit eae5cf3abfd165e4a3eda156e62b7b6048efadc6 Author: Weiqun Zhang Date: Tue Jan 26 15:37:27 2016 -0800 Add recv_disp as a member of FabArray so that it is still alive when we exit from FillBoundary_nowai_MPI_Onesided, because it is possible that the sender has not received (or even posted recv for) the address stored in recv_disp yet. Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 0e1706c79f61ec6b984f0bcc726230c1837fb5b8 Author: Ann Almgren Date: Tue Jan 26 14:22:13 2016 -0800 Add a new Tutorial which uses a different boxArray for the particles than for the multigrid solve. This uses functions stolen from SedonaBox that split up boxes if they have a disproportionate share of the cost. Tutorials/TwoGrid_PIC_C/GNUmakefile Tutorials/TwoGrid_PIC_C/Make.package Tutorials/TwoGrid_PIC_C/main.cpp Tutorials/TwoGrid_PIC_C/solve_for_accel.cpp Tutorials/TwoGrid_PIC_C/solve_with_f90.cpp Tutorials/TwoGrid_PIC_C/split_boxes.cpp commit df2acc76e803fadbd86ae590bbe439e07d727a52 Merge: 345e30211 bf15ebcd7 Author: Ann Almgren Date: Tue Jan 26 14:15:16 2016 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 345e30211e027b1f85e5ac7e7173bce450ebaff8 Author: Ann Almgren Date: Tue Jan 26 14:13:05 2016 -0800 1) Put in placeholder for AssignDensity for nodal multifabs -- not fully implemented yet. 2) Enforce that mf in AssignDensitySingleLevel must have at least one ghost cell or we will lost part of the contribution of a particle near a fine-fine boundary! 3) Replace the "ParticlesOnSameGrids" flag by the actual test since that flag may not be set correctly when we are not calling it with an AMR. 4) Add NumberOfParticlesOnGrid so that we can count and return the number of particles per grid to use as a work estimate for load balancing. Src/C_BaseLib/Particles.H commit bf15ebcd753beaa055ebc28c52c4adc6347f672e Author: Marc Day Date: Tue Jan 26 13:10:46 2016 -0800 Add NumGrow as function to LinOp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit 3a1001538f7918751b7f9f4d51152bc87640a26a Author: Ann Almgren Date: Mon Jan 25 17:11:56 2016 -0800 Let us use the "set" command to reassign a pointer within a PArray if PArrayManage is not true (i.e. PArrayNoManage is true) Src/C_BaseLib/PArray.H commit 265b866e05035850f9dde1ed2a5f7e5fe9bebd19 Author: vince 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 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 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 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: 3d3ce9161 523548db6 Author: Michael Zingale Date: Fri Jan 22 19:39:13 2016 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit f33fadb9dd0acfd2f91cd101386e13f78241dbc0 Author: vince 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 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 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 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 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: f9d2c72a6 8c61951f0 Author: Ann Almgren Date: Thu Jan 21 14:28:19 2016 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 0f90451119af33ced46416acc462f3bc4396a293 Author: hongzhang shan Date: Wed Jan 20 18:36:14 2016 -0800 with finish function Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 8c61951f091afc37388f363506480f760e0ea6c3 Author: vince Date: Wed Jan 20 17:32:44 2016 -0800 the makefile. Tutorials/DataServicesTest0/GNUmakefile commit d424f67e486cdfac39459ed5d19a6d4b022e3aa6 Author: Hongzhang Shan Date: Wed Jan 20 17:19:57 2016 -0800 add finish functions Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit f9836086648329ac542257cdffa754aaae0e400b Merge: 13b328413 cf6ea9667 Author: vince 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 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 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: 7ab87975c 34598efcb Author: Ann Almgren Date: Wed Jan 20 10:59:42 2016 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 34598efcb6f44eb9ae9065a7310e121938f1e7c4 Author: Michael Zingale 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 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 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 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 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: 77aa394cf 3b7ef3ed2 Author: Ann Almgren Date: Tue Jan 19 12:06:31 2016 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 3b7ef3ed285136779dd385d7221ec7ed796d3e14 Author: Michael Zingale Date: Tue Jan 19 12:17:55 2016 -0500 use the Agg backend so that we can do plots when backgrounded Tools/RegressionTesting/testnew.py commit 7f628f149d114a39f791491291d394aeefea66cd Author: Hongzhang Shan Date: Tue Jan 19 01:59:40 2016 -0800 add onesided BL_USE_MPI_ONESIDED Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 3d3ce916105b3f48d08cdf44b552c03e6298014c Merge: 0df95b53d c2fb987f8 Author: Michael Zingale Date: Mon Jan 18 13:27:17 2016 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit c2fb987f8785fe7b1e30c617a9ebb8c851d1c80e Author: Michael Zingale Date: Sun Jan 17 16:47:51 2016 -0500 use font-awesome Tools/RegressionTesting/testnew.py commit b6abbf56fd1d23d55cf9e066bea8b81c4e56ae84 Author: Michael Zingale Date: Sun Jan 17 14:45:54 2016 -0500 add timing plots Tools/RegressionTesting/testnew.py commit ddc6c587eecf23476ec3180cda538d577b17d79d Author: Michael Zingale Date: Sun Jan 17 13:09:24 2016 -0500 fix complete_report_from_crash and isolate the code that parses all completed runs and tests to be a method of Suite Tools/RegressionTesting/testnew.py commit 0df95b53dadba8645d807b1743f36603544ceaa4 Merge: ff6af7e09 30aceeaa9 Author: Michael Zingale Date: Sun Jan 17 12:04:58 2016 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 30aceeaa9e98725b9ce47fd5199689fabcc5059f Author: Weiqun Zhang Date: Sat Jan 16 15:16:09 2016 -0800 more interfaces to bl_allocate Src/C_BaseLib/mempool_f.f90 commit ff6af7e09cb4f98785638b3b99f745412a63e012 Merge: df5374332 a79903bfe Author: Michael Zingale Date: Fri Jan 15 09:37:48 2016 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit fe075152b75230aa84a44806e17c10e7e748f287 Author: Weiqun Zhang Date: Wed Jan 13 09:07:16 2016 -0800 Just like PostRcvs, no need to pass in RcvTags in PostRcvs_PGAS Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit e667b3b4cf0b35fc34def231248faa136468cb2d Author: Weiqun Zhang Date: Wed Jan 13 08:59:09 2016 -0800 fix the merge Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit af09e176368ee5fe917c3bc0d7b16693cc2c1302 Merge: da6c33083 a79903bfe Author: Weiqun Zhang Date: Wed Jan 13 08:47:12 2016 -0800 merge commit a79903bfee85feff10e68c6b7b8c39906615135d Author: Weiqun Zhang Date: Wed Jan 13 08:31:39 2016 -0800 PostRcvs: no need to pass in RcvTags Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit 1afd18526f7616f95fc685a5e8e1640d46d173fb Author: Weiqun Zhang Date: Tue Jan 12 16:50:11 2016 -0800 add FabArrayBase::empty() Src/C_BaseLib/FabArray.H commit 12d04b363b76dadff7b5dbb8ec35922fe87e467e Author: Weiqun Zhang Date: Tue Jan 12 12:29:10 2016 -0800 add AdvectWithUcc that advects particles with cell-centered velocity Src/C_BaseLib/Particles.H commit 858fedf3c42fb2c668a4ceb8c806d74b70eb119a Author: Weiqun Zhang Date: Tue Jan 12 11:30:14 2016 -0800 AdvectWithUmac: fix boundary Src/C_BaseLib/Particles.H commit 827d0c747821c921a2bb4e816500a858ade9bb1f Author: Weiqun Zhang Date: Mon Jan 11 18:12:48 2016 -0800 remove an assertion Src/C_BaseLib/Particles.H commit 729dcd13ed18491407478ab25474cd37a0be3b0b Merge: b529ad933 3dc0793ec Author: Michael Zingale Date: Sun Jan 10 15:31:24 2016 -0500 Merge branch 'development' into preprocessing commit 3dc0793ecb1b2ad33356cfbe85e6e1a2837ff844 Author: Weiqun Zhang Date: Fri Jan 8 10:11:19 2016 -0800 Revert this for now because IAMR's SyncRegister actually needs these functions. Will need to fix SyncRegister. This reverts commit 7e4785917a4cf07e0e40a912efc6d5f43da9cc9e. Src/C_BaseLib/FabArray.H commit af42e2ec1240f7676763bec0d287142927614d55 Author: Weiqun Zhang Date: Fri Jan 8 10:07:14 2016 -0800 fix bug in my recent change to SumPeriodicBoundary Src/C_BaseLib/Geometry.cpp commit 0c37513b6084010f56ad8a8d101e17b7338ce360 Author: Weiqun Zhang Date: Fri Jan 8 10:05:36 2016 -0800 fix bug in my recent change to SumPeriodicBoundary Src/C_BaseLib/Geometry.cpp commit b1659eb5429665c7e935b11914ec04737a5be116 Author: Weiqun Zhang Date: Thu Jan 7 21:10:46 2016 -0800 add comments and tweak Geometry::FPB::Operator< Src/C_BaseLib/Geometry.H commit 3ffecba0d07364a294071e396cb9b99df0930b96 Author: Weiqun Zhang Date: Thu Jan 7 20:54:09 2016 -0800 comments Src/C_BaseLib/FabArray.H commit 7e4785917a4cf07e0e40a912efc6d5f43da9cc9e Author: Weiqun Zhang Date: Thu Jan 7 17:29:11 2016 -0800 no longer needed Src/C_BaseLib/FabArray.H commit 419c1dcd99d67dff72e37203f3144869f65e5509 Author: Weiqun Zhang Date: Thu Jan 7 17:28:11 2016 -0800 Optimization of SumPeriodicBoundary by reusing the FillPeriodicBoundary cache Src/C_BaseLib/Geometry.cpp commit 532d1102d579872e14b13adba08bce49c86e8e03 Author: Weiqun Zhang Date: Thu Jan 7 15:57:47 2016 -0800 readablity Src/C_BaseLib/MultiFab.cpp commit da6c330834da9e17a080743d66c5761c08cc8ce5 Author: Weiqun Zhang Date: Thu Jan 7 12:34:37 2016 -0800 minor clean up Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 2abd16a3ffb09e767993a780d58e7cc6c47642b5 Merge: 8865c069e e0fcd3e45 Author: Weiqun Zhang Date: Thu Jan 7 11:16:19 2016 -0800 Merge branch 'development' into pgas commit 8865c069e6f9918dd572b88cae809ed21a1749da Author: Weiqun Zhang Date: Thu Jan 7 11:16:03 2016 -0800 remove the option to break messages into smaller pieces Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H commit 4d40b0a37a0ca6d7835f44de0ab4b0212f69c764 Author: Weiqun Zhang Date: Wed Jan 6 18:08:16 2016 -0800 remove team sender and receiver because it does not perform Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit d107a037a0b2ebbc054bda6014968324307b9624 Author: Weiqun Zhang Date: Wed Jan 6 17:01:52 2016 -0800 started MPI-3 team Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tools/C_mk/Make.defs commit e0fcd3e45d6d9c1c9ab97a8f201427a9300cf4ce Author: Changho Kim Date: Wed Jan 6 14:44:49 2016 -0800 f90 codes do now work on cori. Tools/F_mk/GMakeMPI.mak commit fd0c441fbbe0448466375f6ecb6a3c8f5647f815 Author: Weiqun Zhang Date: Wed Jan 6 13:46:44 2016 -0800 TagBox: add optional alloc argument because of its base class BaseFab Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 8608bb6fdb5960b810967281bad94b7dd95932ae Merge: 622c874ba 31b5414d3 Author: Weiqun Zhang Date: Wed Jan 6 12:58:13 2016 -0800 Merge branch 'development' into pgas Conflicts: Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit 31b5414d3d0a0411238c62d73e93a53ce6475bbd Author: Weiqun Zhang Date: Wed Jan 6 12:19:59 2016 -0800 new way of thread safety check in FillBoundary, FillPeriodicBoundary and parallel copy Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit d7b19f0e9c922c6683daeaff689964ab1147ce81 Merge: f8eba750d 9f5b879a4 Author: Andy Nonaka Date: Tue Jan 5 18:59:38 2016 -0800 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit f8eba750d827bebc787507831a067d76de9ca619 Author: Andy Nonaka Date: Tue Jan 5 18:58:58 2016 -0800 plug memory leak in multifab_sum_boundary_c Src/F_BaseLib/multifab_f.f90 commit 9f5b879a42cb6240f888eeb32b311b6647ffe631 Author: Weiqun Zhang Date: Tue Jan 5 16:39:35 2016 -0800 FabArray::shift: need to update BoxArray-DistributionMap key. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 88f5540c59e861997c1445ef2f92f6ccaf0bc7b9 Author: Michael Zingale Date: Tue Jan 5 19:25:53 2016 -0500 update usage Tools/Postprocessing/F_Src/fextrema.f90 commit 9bae1d1a79c78c43c79374ed285b02376eb0f0e9 Author: Weiqun Zhang Date: Tue Jan 5 15:37:09 2016 -0800 clean up Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 622c874ba237972db135387e1f841e4fd32f869c Merge: 2b7e5ab74 5c7de19df Author: Weiqun Zhang Date: Tue Jan 5 15:08:12 2016 -0800 Merge branch 'development' into pgas Conflicts: Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 5c7de19dfed3ba57070052fcce99f5541085ccda Author: Weiqun Zhang Date: Tue Jan 5 13:22:01 2016 -0800 new functions that copy from periodically shifted MultiFab to another MultiFab. This is useful for restriction of nodal/edge/face MultiFabs Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 759ac5ef540fdfc6eed5c9f7236613bc278885c7 Author: vince Date: Tue Jan 5 13:21:11 2016 -0800 call bndryreg function. Src/C_AMRLib/FluxRegister.cpp commit df537433279438ba6ff61a1a41425e1b978cfab4 Merge: b529ad933 d8f0efc7b Author: Michael Zingale Date: Tue Jan 5 10:45:14 2016 -0500 Merge branch 'development' into preprocessing commit b529ad933ed95f93e077554e02bf832d1220093f Author: Weiqun Zhang Date: Mon Jan 4 21:17:04 2016 -0800 comment out rules for F90 and add VPATH for preprocessed F90 Tools/C_mk/Make.rules commit d8f0efc7be1b9ceb613a6547720834c1cbd6376b Merge: 29769b940 322d94c8c Author: Michael Zingale Date: Mon Jan 4 19:12:50 2016 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 29769b940e9fe7d00503af80273bd60d9e0a4c93 Author: Michael Zingale Date: Mon Jan 4 19:12:40 2016 -0500 new source format Tools/RegressionTesting/Maestro-tests.ini commit 322d94c8c78efa5de46557938e7503e0b049f684 Author: Michael Zingale Date: Mon Jan 4 19:11:23 2016 -0500 add the Detonation test Tools/RegressionTesting/Castro-SBU-tests.ini commit 77aa394cfb5ae273769af9b07fc9227be7b51a44 Author: Ann Almgren Date: Mon Jan 4 15:33:33 2016 -0800 Replace FillPeriodicBoundary by fill_boundary so we fill grad_phi on all ghost cells, not just periodic boundaries. Tutorials/PIC_C/solve_for_accel.cpp commit fc0cf7a3a455c62be794faa957992b84144a1bca Author: Michael Zingale Date: Mon Jan 4 14:15:51 2016 -0500 remove Intel compilers version 5 to 9.1 -- they are all more than 10 years old Tools/C_mk/Make.defs commit bf48920ba89657776545555b5f8cac3ecb469f43 Author: Michael Zingale Date: Mon Jan 4 11:30:35 2016 -0500 remove unneeded clause -- this now seems to work. The F90 files are preprocessed before the dependency checking is done. This eliminates spurrious warnings from the moddep script about modules that are ifdef-ed out not being found. Note: in your code's makefile, you need to add: $(f77TempDir) to the vpath %.f90 line Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 62df90774772030699457d2c424494b0d52b7c28 Author: Michael Zingale Date: Mon Jan 4 09:59:58 2016 -0500 some work to get F90 preprocessed before the dependency checking Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit e207f77fd02221483bfae6848787a8c7050a8995 Author: Michael Zingale Date: Sun Jan 3 22:08:03 2016 -0500 remove homer Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi commit 035b871990d8d0981aff472dd0bef9cb0694660b Author: Weiqun Zhang Date: Sun Jan 3 16:39:26 2016 -0800 PArray: add a new function to make it easy for PArray to be used in the 'resource acquisition is initialization' idiom. Src/C_BaseLib/PArray.H commit 4a305a3c07b2bccc3e5163a244d60a919aab93ee Author: Weiqun Zhang Date: Sat Jan 2 20:51:36 2016 -0800 Remove the SumPeriodicBoundary that takes two mfs. I don't think it is used in any codes now. This will allows further optimization of the remaining version of SumPeriodicBoundary. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 5ed5a54454186a96f0093262fe96c60fa2519f6b Author: Weiqun Zhang Date: Sat Jan 2 13:52:46 2016 -0800 optimize box-box intersection for FillPeriodicBoundary Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit a9745113adaecbcd36a136800c17f9988679ef43 Author: Weiqun Zhang Date: Sat Jan 2 13:52:00 2016 -0800 keep boxarray hash Src/C_BaseLib/FabArray.cpp commit 39bf0ba6670d99d08f06bdd60b37a29ce921f2e1 Author: Weiqun Zhang Date: Sat Jan 2 08:19:15 2016 -0800 comments on filling periodic boundary Src/C_BaseLib/Geometry.H commit 2a53a33a6b1610b277191842bed63032e0a61987 Author: Weiqun Zhang Date: Sat Dec 26 20:28:40 2015 -0800 minor optimization Src/C_BaseLib/FabArray.cpp commit 6738eb2b1dc9b293c76d8bffda6a5439cad19f99 Author: Weiqun Zhang Date: Sat Dec 26 20:28:09 2015 -0800 make it more readable Src/F_BaseLib/layout.f90 commit 1c4a907ab1e8f6026f2c552a3536f8f3bfebb99b Author: Michael Zingale Date: Sat Jan 2 16:34:07 2016 -0500 fix the make_realclean -- we need to be careful about whehter any build strings are None Tools/RegressionTesting/testnew.py commit 6c31a7b36a2ee0b590e002bbf7078625d17015cb Author: Michael Zingale Date: Sat Jan 2 12:53:46 2016 -0500 update to the new format + rad and wdmerger tests Tools/RegressionTesting/Castro-SBU-tests.ini commit 73075be8c85bf8388c7d49953baea8c1bacaf2ba Author: Michael Zingale Date: Sat Jan 2 12:51:57 2016 -0500 change the way source repos are defined -- they now all have their own block in the inputs file. See ./testnew.py -h for a description. This change makes it a lot easier to support multiple sources and define the desired branch for each. Tools/RegressionTesting/testnew.py commit 7b1153d6d5ab14eee38ce5025099847672576455 Author: Weiqun Zhang Date: Sat Dec 26 13:46:52 2015 -0800 tiling in local copy Src/C_BaseLib/FabArray.cpp commit 8856b3f051899bc9328a589837b3cf8c5be82b64 Author: Weiqun Zhang Date: Sat Dec 26 12:40:34 2015 -0800 optimize box-box intersection for parallel copy Src/C_BaseLib/FabArray.cpp commit bc0c75cdee8eb1b1634bc65a97042a98c27ec248 Author: Weiqun Zhang Date: Sat Dec 26 11:59:59 2015 -0800 fix thread safety in FillPeriodicboundary Src/C_BaseLib/Geometry.cpp commit a9d29ece4c151ca2d8656e128099502b9cc35c3f Author: Weiqun Zhang Date: Fri Dec 25 21:18:16 2015 -0800 have to make sure the intersection box is not empty Src/C_BaseLib/FabArray.cpp commit 738e15570f93a3cf8ee5e4df29bebd3d332af032 Author: Weiqun Zhang Date: Fri Dec 25 20:57:32 2015 -0800 revert some changes in the last commit because of IAMR Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit 9d53e95bd726632d465a2b477320b6e673b045cc Author: Weiqun Zhang Date: Fri Dec 25 17:33:04 2015 -0800 optimize box-box intersection for Fillboundary Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit 6e5299540757c6f91bd3a436f798f8bf705e8236 Author: Max Katz Date: Wed Dec 23 02:37:22 2015 -0500 Change the logic for amr.check_per so that it is analogous to amr.plot_per: we write a checkpoint at the first timestep *after* the interval has passed, whereas before we wrote a checkpoint at the timestep *before* we got to the interval. Src/C_AMRLib/Amr.cpp commit 3f2dd5099d73f5eeb532944491965f52bd964497 Author: Weiqun Zhang Date: Mon Dec 21 20:30:54 2015 -0800 Fortran layout: clean box hash to save memory Src/F_BaseLib/layout.f90 Src/F_BaseLib/ml_nd_restriction.f90 commit 1136ab8b98ee17bfa9c84457ccc4d650b402d5b9 Author: Weiqun Zhang Date: Mon Dec 21 17:09:46 2015 -0800 tidy Src/F_BaseLib/layout.f90 Src/F_BaseLib/ml_nd_restriction.f90 commit f7374e26c6ead1e5cbd704ce5d49fc068380c964 Author: Weiqun Zhang 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 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 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 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 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 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 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 Date: Thu Dec 17 17:19:19 2015 -0800 make the output more readable Src/C_BaseLib/BoxLib.cpp commit 54b884744ab37fad92cfc3063f8d49ae63e3ba88 Author: Ann Almgren Date: Thu Dec 17 15:50:03 2015 -0800 Add is_nodal() test for MultiFab so we can easily test if a MultiFab is fully nodal or not. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/MultiFabUtil.cpp commit 804aef575506abd9a5720b73a7bd272bcacefee5 Author: Weiqun Zhang Date: Wed Dec 16 12:14:34 2015 -0800 Particle: change the minimal number of ghost cells of mac velocity from 2 to 1 in assertion Src/C_BaseLib/Particles.H commit 7b7cccef911eac5323022954dd5d2db35e6c169b Author: Weiqun Zhang Date: Wed Dec 16 09:13:48 2015 -0800 tidy backtrace Src/C_BaseLib/BoxLib.cpp commit 64eecac545c0d01ccd052c849ab40a0c36bb2607 Author: Weiqun Zhang 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 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 Date: Tue Dec 15 16:07:51 2015 -0800 clean up Src/C_BaseLib/BoxLib.cpp commit 6150e6519bfd27ee2158c85497141209f11bea2d Author: Weiqun Zhang Date: Tue Dec 15 16:04:47 2015 -0800 For backtracing, use addr2line, if available, to print out function names and line numbers Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Tools/C_mk/Make.defs commit 848478ea2d3a4719da101a8d21769c427f78987c Author: Weiqun Zhang Date: Tue Dec 15 14:03:51 2015 -0800 mfiter: allow growntilebox to have negative ng Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 8785d94c6dc07619ed7d55d1fbd40d5b4f33e80b Author: vince 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 Date: Mon Dec 14 17:08:05 2015 -0800 promote MultiFab::MakeSidecarsSmaller Src/C_BoundaryLib/FabSet.H commit 0043e97c33c3925bbef8ac2d2a84970400ed0c24 Author: vince 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 Date: Mon Dec 14 17:04:19 2015 -0800 lock allocated fabarray pointers. Src/C_BaseLib/FabArray.H commit ad4da36b25bc462787ac429353facf8494f24cf9 Author: vince 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 Date: Mon Dec 14 17:02:39 2015 -0800 multifab movement. Src/C_AMRLib/StateData.cpp commit 6dca658885dae1280941be00acd1fb98dfe26d8d Author: vince Date: Mon Dec 14 17:01:29 2015 -0800 lock allocated fabarray pointers. Src/C_AMRLib/Amr.cpp commit e131e661dd3f6e781d5327f67c23af98d9b730e2 Author: Michael Zingale Date: Mon Dec 14 19:04:54 2015 -0500 no more hopper Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 2b7e5ab74329e92b8599ad2883d07035482680b5 Merge: 6b24b1bb6 63216b518 Author: Weiqun Zhang Date: Mon Dec 14 11:24:19 2015 -0800 Merge branch 'development' into pgas commit 63216b5185958fea11b57045edafd625130e37e3 Author: Weiqun Zhang Date: Mon Dec 14 11:23:11 2015 -0800 cleanup Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 6b24b1bb65db6f17a2e7d9231df70f36b2309ccc Merge: 5c02753b0 64323b528 Author: Weiqun Zhang Date: Mon Dec 14 11:06:58 2015 -0800 Merge branch 'development' into pgas Conflicts: Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H commit 64323b528fef5e4a51447916f3dfd58711e4f2bc Merge: c0ecbb794 f1f1c1fc2 Author: Michael Zingale Date: Mon Dec 14 11:45:53 2015 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit c0ecbb794e62f10cc150ee86d85d69dd7947a506 Author: Michael Zingale Date: Mon Dec 14 11:45:44 2015 -0500 goodbye hopper Tools/F_mk/GMakeMPI.mak commit f1f1c1fc265e2ae84af55ee96a87c77ffd8ee004 Author: Weiqun Zhang Date: Sun Dec 13 16:14:00 2015 -0800 clean up Src/C_BaseLib/FabArray.H commit 5802874e8d95f181e440dafc5cf3e04ee13edebb Author: Andy Nonaka Date: Fri Dec 11 08:21:10 2015 -0800 add gojira and kumonga to DEFAULT_MACHINES Tools/F_mk/GMakeMPI.mak commit 9d85114750b4d4627d913c7b35545d647271c350 Author: Michael Zingale Date: Thu Dec 10 20:58:43 2015 -0500 simplify a lot of entries in GMakeMPI.mak -- all these machines were doing the same thing, so we use a GNU make findstring() to simplify them. Tools/F_mk/GMakeMPI.mak commit 9f2371a1ceee34cac93015675bd01d3eb376a625 Merge: 39d7eab5c 728856b5d Author: Michael Zingale Date: Thu Dec 10 17:18:12 2015 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 39d7eab5c1e4e75218fd39a85336d52a181f6457 Author: Michael Zingale Date: Thu Dec 10 17:17:58 2015 -0500 update the build_info.f90 to allow for no modules Tools/F_scripts/makebuildinfo.py commit 728856b5d5fa97b950bfdae246ccd574f6cd5b56 Author: Weiqun Zhang Date: Thu Dec 10 12:35:24 2015 -0800 use the new BoxArray intersect functions Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/Particles.H Src/C_BoundaryLib/FabSet.cpp commit 88101551401c7dea70ed93d2efdadb4d4e1a2350 Author: Weiqun Zhang Date: Thu Dec 10 12:29:48 2015 -0800 fillpatch: remove the ngrow hack Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/AuxBoundaryData.H Src/C_AMRLib/AuxBoundaryData.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 9322fdee92d7b3ac706e4bb2d8574dd559fcc2d3 Author: Weiqun Zhang Date: Thu Dec 10 11:20:59 2015 -0800 Parallel copy: using the new BoxArray intersect function Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 040a0fa670bc3eab171516c8267a261abcc40dc5 Author: Weiqun Zhang Date: Thu Dec 10 11:07:01 2015 -0800 BoxArray: add ng argument to intersect functions. using it, we don't need to create temporary boxarrays in parallel copy Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit b5ed68e848eb3143eee59f4c79679016a4e4f03c Author: Michael Zingale Date: Thu Dec 10 12:40:16 2015 -0500 shut-up the iso_c_binding warning Tools/C_scripts/moddep.pl commit 45843b9f0bf70a0cc0708aa489f305a06420e5b3 Merge: d673db246 1a7943baa Author: Michael Zingale Date: Thu Dec 10 12:26:26 2015 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit d673db246034ebe8e8246737cc1007d37d0f596d Author: Michael Zingale Date: Thu Dec 10 12:26:13 2015 -0500 homer no longer exists Tools/C_mk/Make.defs commit 1a7943baa020860fd4f0e698fc2d1a5c80f20d3e Author: Michael Zingale Date: Thu Dec 10 12:17:45 2015 -0500 inlining of C++ doesn't work with GCC 5 and the recent BoxArray stuff. Disable it for now until gcc is fixe.d Tools/C_mk/Make.defs commit cf0767f8bc275cf605d72ed5e0ad9e8d1df2561e Author: Weiqun Zhang Date: Wed Dec 9 20:44:32 2015 -0800 fix typo Src/C_BaseLib/BoxArray.cpp commit 95c1040ad0340ddaf12554a00f677c5f05376e42 Author: Weiqun Zhang Date: Wed Dec 9 18:04:22 2015 -0800 Since BoxArray has index type now, we can use it insetead of the type of Box 0 in the array Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_TowerLib/MFTower.cpp Src/Extern/amrdata/AmrData.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Tools/C_util/WritePlotFile.cpp Tutorials/AMR_PETSc_C/Source/Darcy.cpp commit 8866f9e308eca8aa634f622a30ea2214d4baea4d Author: vince Date: Wed Dec 9 16:27:27 2015 -0800 broadcast array function. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 09bbf02861bb6b022d957b411c3a0642f12a3dc8 Author: Weiqun Zhang Date: Wed Dec 9 14:00:12 2015 -0800 BoxArray: Add index type to BoxArray. This allows nodal and cell-centers BoxArrays share the same reference, which is now always stored as cell-centered boxes. Because of the change, the operator[] now returns Box on demand instead of const Box&. MFIter: Because of the changes in BoxArray, the tile arrays now always store cell-centered boxes. This will construct a nodal box on-demand. A number of other changes have to be made due to that BoxArray no longer provides a const_iterator and the change in return type of operator[]. Src/C_AMRLib/AmrLevel.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 2fb17af1cbc970a588988f0fb7012ba01c6a8780 Author: Weiqun Zhang Date: Wed Dec 9 10:10:35 2015 -0800 IndexType: functions testing cell or node given a direction Src/C_BaseLib/IndexType.H commit 25e96522aeb44f90c2720321f084af90b9cc4b0d Author: Weiqun Zhang Date: Wed Dec 9 09:54:40 2015 -0800 Box: add convert more functions and remove a const Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit cd001c09c1271824d8ef27cfcbd651e657559f3f Author: Weiqun Zhang Date: Thu Dec 3 15:47:12 2015 -0800 add distributin mapping to cache even if it's a single process run so that the reference id could work Src/C_BaseLib/DistributionMapping.cpp commit 5c02753b0ddcfe322174c0808fe3a356d9d3bbc3 Merge: 1e4fc765f 8fcf8b361 Author: Weiqun Zhang Date: Wed Dec 9 09:39:14 2015 -0800 Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas commit 2dda63c49e313263f9d0a5ef525590f0cc2b1ed3 Merge: 8a7146780 4c52b6f4a Author: Adam M. Jacobs Date: Tue Dec 8 21:17:26 2015 -0500 Merge branch 'development' into openacc commit f4e684db535db211905da9ae8e0c4322cee6d1dd Author: vince Date: Tue Dec 8 18:03:45 2015 -0800 more broadcast functions. Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit fb73def4ce217b7b1731837cc00b079ffebd0dd8 Author: vince Date: Tue Dec 8 16:27:37 2015 -0800 added virtual destructor. Src/C_BaseLib/MultiFab.H commit 7dba73ecd2e43d9b2ab7603062c67c85d17e8763 Author: vince Date: Tue Dec 8 16:26:49 2015 -0800 replaced code with broadcast functions. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.cpp commit 74e1dc6c0f004435ab04a58e00282d894445738e Author: vince Date: Tue Dec 8 16:05:16 2015 -0800 functions to broadcast boxes and boxarrays. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 0003ac35cc9c4ae22f5eb84b3cb422f2687c7599 Author: Max Katz Date: Tue Dec 8 16:01:32 2015 -0500 Add a small plotfile functionality to C++ BoxLib. The small plotfile is very similar to a normal plotfile, but it can be output at a different rate using amr.small_plot_int and amr.small_plot_per. The major difference is that it only accepts state variables, and you have to manually specify each one using amr.small_plot_vars. This is designed for output of a small number of variables at a high rate, for purposes like making movies of your simulations. Unlike the plotfile functionality, this is not implemented as a pure virtual function, so it is not required for derived classes of AmrLevels to implement this functionality. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 4c52b6f4a15fffe87da98c9dc2be098156714d23 Merge: b76e7c418 fed05e06d Author: Michael Zingale Date: Tue Dec 8 12:55:40 2015 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit b76e7c418f3d350c99bf9dc3e5604bc1c1171192 Author: Michael Zingale Date: Tue Dec 8 12:55:23 2015 -0500 fix the flags for .F90 preprocessing with Linux Tools/C_mk/Make.Linux commit 443270eb6544adf406802f1f15c72ae5b728c4aa Author: vince Date: Mon Dec 7 18:28:52 2015 -0800 added undefined strategy. Src/C_BaseLib/DistributionMapping.H commit 8ebb6e8b0ba6a8ea9d8e6f28bde546f5182792b6 Author: vince Date: Mon Dec 7 17:56:04 2015 -0800 functions for making the sidecars smaller. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit d7b62bd70f821b1aa278e3ed77e6390959aa0e90 Author: vince Date: Mon Dec 7 16:35:46 2015 -0800 FabArray pointer locks, mpi only sections. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit fed05e06d02634ac5c7f83d398c9a1a09a89172b Merge: 88d419ae1 dfbe90517 Author: vince 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 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 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 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 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 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 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 Date: Wed Dec 2 14:15:09 2015 -0800 tidy Src/C_BaseLib/FabArray.H commit 92fafe604c2624223bbdf5720c89efb52feb8ebd Author: Weiqun Zhang Date: Wed Dec 2 14:04:06 2015 -0800 Fill Boundary Cache stats Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 8bc7c1c75dd2a96a862327aeedba653cf9f26452 Author: Weiqun Zhang Date: Wed Dec 2 13:08:28 2015 -0800 rework on cache stats Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 4b581880e4f48336ca0653d863aa6bfa0c0b2154 Author: Marc Day Date: Wed Dec 2 14:11:22 2015 -0800 Fixup CMakeLists.txt to reflect that BCRec and BC_TYPES.H moved from C_AMRLib to C_BaseLib Src/C_AMRLib/CMakeLists.txt Src/C_BaseLib/CMakeLists.txt commit fc393a9720d98767451af84014488cf20f122737 Author: Michael Zingale Date: Wed Dec 2 13:19:51 2015 -0500 hack in support for branches for the extra build directories Tools/RegressionTesting/testnew.py commit 8fcf8b3614051c403887e8d804e6a80e272f7ff8 Merge: 37489ef6b 1479ff053 Author: Weiqun Zhang Date: Tue Dec 1 21:31:30 2015 -0800 Merge branch 'development' into pgas commit 1479ff053addfd80ef0865a51dc7129621301beb Author: Weiqun Zhang Date: Tue Dec 1 21:28:55 2015 -0800 TileArrayCache: improve print() Src/C_BaseLib/FabArray.H commit 37489ef6ba330953264d2236cef50efcd3cd6cd8 Author: Weiqun Zhang Date: Tue Dec 1 21:28:55 2015 -0800 TileArrayCache: improve print() Src/C_BaseLib/FabArray.H commit d7aaeb83fdc52e1a7a95745d05c75c2a104c6e78 Author: Weiqun Zhang Date: Tue Dec 1 21:27:38 2015 -0800 PGAS_SMC: limit the scope of SMC for more accurate stats MiniApps/PGAS_SMC/main.cpp commit 9cdd3ca476471059d6226e39f0cde65e255d950d Author: Weiqun Zhang Date: Tue Dec 1 20:50:11 2015 -0800 MFGhostIter: need to set various indices Src/C_BaseLib/FabArray.cpp commit 9bea9bc719dbd394a079a8cdb65d834e639764d1 Merge: 29bc631cd 115dd3ce4 Author: Weiqun Zhang Date: Tue Dec 1 20:45:47 2015 -0800 Merge branch 'development' into pgas commit 115dd3ce46c33d2c40d2bd560e96e3fb983db883 Author: Weiqun Zhang Date: Tue Dec 1 20:45:07 2015 -0800 TileArrayCache: tidy Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 4d6ae524ec25c66f06510338a9074584a28dfd0f Merge: a8da7a130 c97e7dad4 Author: Weiqun Zhang Date: Tue Dec 1 17:56:06 2015 -0800 Merge branch 'tilearraycache' into development commit 1e4fc765f932ecd7393ea711aa5a9be9119cefb5 Author: Weiqun Zhang Date: Tue Dec 1 17:18:20 2015 -0800 PGAS_SMC: change defaults MiniApps/PGAS_SMC/SMC.cpp commit 29bc631cdcc73038de529e1f093d4ec51cc5d609 Merge: 894ec8477 c97e7dad4 Author: Weiqun Zhang Date: Tue Dec 1 17:06:40 2015 -0800 Merge branch 'tilearraycache' into pgas commit c97e7dad46f94747db894cc9718b5e90859c9199 Author: Weiqun Zhang Date: Tue Dec 1 17:06:33 2015 -0800 FabArray stats: don't need to use long long because long is 8 bytes on 64-bit Unix systems. Src/C_BaseLib/FabArray.H commit 894ec84773f16c6cbf1621abc4c4e5b9dc0e4616 Author: Weiqun Zhang Date: Tue Dec 1 17:03:24 2015 -0800 fixed MFGhostIter Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 03976e1ff583c8d01ab2fd8ae41f205886bb826d Merge: 033b7c71c b8c7b5466 Author: Weiqun Zhang Date: Tue Dec 1 16:34:39 2015 -0800 Merge branch 'tilearraycache' into pgas Conflicts: Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit b8c7b54660a837dd19bfbb08bc32de548f359f1c Author: Weiqun Zhang Date: Tue Dec 1 16:21:54 2015 -0800 tidy Src/C_BaseLib/FabArray.H commit 3aed4595fc82baaa9eba906e6237351a4fabecd4 Author: Weiqun Zhang Date: Tue Dec 1 15:09:28 2015 -0800 FabArray: stats Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit ed2b3865e25aaa7b775986e972cdc9aa307f8912 Author: Weiqun Zhang Date: Tue Dec 1 14:40:54 2015 -0800 TileArray: add stats Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 61e671722dcef20142ebc6a34ec352ac839850e2 Author: Weiqun Zhang Date: Tue Dec 1 10:54:18 2015 -0800 new MFIter ctor taking TileArray ptr Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 7d41c0305330497e913c746c7fed6ad6ed81dd57 Author: Weiqun Zhang Date: Tue Dec 1 10:42:51 2015 -0800 add MFIter dtor Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit c2bff24c65d89cf536c45073d1185d972276208a Author: Weiqun Zhang Date: Tue Dec 1 10:40:53 2015 -0800 cleanup Src/C_BaseLib/FabArray.cpp commit 6ed7000adf0a5926ff29d106c54aa471ef40182f Author: Weiqun Zhang Date: Tue Dec 1 10:30:29 2015 -0800 TileArray: use pointer instead of reference in MFIter so that we can pass null ptr; use omp critical instead of single. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit cb148f55963a5c5b6a4dca86bdef2cb581b2a58f Author: Weiqun Zhang Date: Mon Nov 30 16:33:42 2015 -0800 FabArray: if it is never defined, do not need erase tile array Src/C_BaseLib/FabArray.H commit a8da7a1303206af09d002b6c3c763321658c1ea9 Author: Weiqun Zhang Date: Mon Nov 30 16:10:04 2015 -0800 more regression tests inputs Tutorials/MultiGrid_C/inputs-rt-c-neu Tutorials/MultiGrid_C/inputs-rt-c-ord2 Tutorials/MultiGrid_C/inputs-rt-c-ord3 Tutorials/MultiGrid_C/inputs-rt-f-neu Tutorials/MultiGrid_C/inputs-rt-f-ord2 Tutorials/MultiGrid_C/inputs-rt-f-ord3 commit 2f828fb6139d7feefb1093efaa188ad01b112196 Author: Brian Friesen Date: Mon Nov 30 15:49:10 2015 -0800 Tutorials/MultiGrid_C: fix contradictory comments about Dirichlet boundary order in HPGMG Tutorials/MultiGrid_C/inputs commit 666a52fb5d506775cfe03acd4dfd8b65cd800111 Author: Weiqun Zhang Date: Mon Nov 30 15:45:56 2015 -0800 Linear Solvers Comparison Test: add maxorder parameter and new inputs for regression tests Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir-ord2 Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir-ord3 Tests/LinearSolvers/ComparisonTest/inputs.3d Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp commit 1424ba4c583ff0fcd84019459b22f96776f83bc3 Author: Brian Friesen Date: Mon Nov 30 15:39:56 2015 -0800 MultiFab: remove my inexplicable const_cast<> for getVect() pointers in MPI buffers in SendMultiFabToSidecars() I don't know what I was thinking here. Using const_cast<> sometimes sends nonsense data to the sidecars. Src/C_BaseLib/MultiFab.cpp commit 06ec6a3b1125a94a890ddc6d73bbe970a512430a Author: Weiqun Zhang Date: Mon Nov 30 15:37:17 2015 -0800 MultiGrid_C Tutorial: add inputs for new regression tests Tutorials/MultiGrid_C/inputs-rt-c-ord2 Tutorials/MultiGrid_C/inputs-rt-c-ord3 Tutorials/MultiGrid_C/inputs-rt-f-ord2 Tutorials/MultiGrid_C/inputs-rt-f-ord3 commit 92c64a6a751007a34f9c979b9c4159df707322c3 Author: Weiqun Zhang Date: Mon Nov 30 15:32:10 2015 -0800 MultiGrid_C Tutorial: rename mg.stencil_order to mg.maxorder Tutorials/MultiGrid_C/inputs Tutorials/MultiGrid_C/main.cpp commit 033b7c71c9c4f3fbf3ed36a52d2a00a11efebedb Merge: 32b6c95fe d82e900c1 Author: Weiqun Zhang Date: Mon Nov 30 14:56:53 2015 -0800 Merge branch 'tilearraycache' into pgas Haven't fixed all conflicts yet! Conflicts: Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit da0053a9100b71ab5425d620f55bfe8611014e7b Author: Brian Friesen Date: Mon Nov 30 13:58:27 2015 -0800 Tutorials/MultiGrid_C: set default Dirichlet boundary condition order to 2 in inputs file HPGMG uses 2nd-order Dirichlet boundary conditions, so use that by default in the BoxLib solvers so that all 3 solutions match. Tutorials/MultiGrid_C/inputs commit f1fcd4098ee923afd2f6aab813e548102fe5f70c Author: Brian Friesen Date: Mon Nov 30 13:57:13 2015 -0800 Tutorials/MultiGrid_C: enable writing numerical solution plotfiles by default in inputs file Tutorials/MultiGrid_C/inputs commit 1b8df2f9ef94af811f01b8d288abcb8f3974bd55 Author: Brian Friesen Date: Mon Nov 30 13:56:27 2015 -0800 Tutorials/MultiGrid_C: disable calculation of norms by default in inputs file Tutorials/MultiGrid_C/inputs commit 89a51fd3987c93e6e7b5e5fde7e4c7b3ed6d0e0b Author: Ann Almgren Date: Mon Nov 30 13:30:43 2015 -0800 We can now pass mg.stencil_order in through the inputs file to be used to set the max_order for the F90 solver through a set_maxorder call. Note that the "orders" must match (2 and 2, or 3 and 3) for the F90 and C++ solvers to give the same solution with Dirichlet boundaries. Tutorials/MultiGrid_C/inputs Tutorials/MultiGrid_C/main.cpp commit cd89721d766d0b35d667536555356df72f3d6374 Author: Ann Almgren Date: Mon Nov 30 13:29:55 2015 -0800 Typo in comment. Tutorials/MultiGrid_C/RHS_3D.F commit ae5c016c949d61ba367e6694b998b8759950a88b Author: Ann Almgren Date: Mon Nov 30 13:29:38 2015 -0800 Formatting changes so these are easier to read. Tutorials/MultiGrid_C/COEF_2D.F Tutorials/MultiGrid_C/RHS_3D.F commit 99f3ad5c6c81545c458968e2b03638c439a82010 Merge: a390f99f1 a7f095e84 Author: Ann Almgren Date: Mon Nov 30 13:29:13 2015 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit a390f99f187e50e9b1158f5a4250f2a3edd19b19 Author: Ann Almgren Date: Mon Nov 30 13:28:26 2015 -0800 We previously had the same RHS and the same exact solution in 2D and 3D. However, this is not analytically correct. We have modified the RHS in 2D so that it gives the 2D solution with the same magnitude as the 3D solution. Tutorials/MultiGrid_C/RHS_2D.F commit d82e900c1a5e224ce78b7a174afc0f19a965d124 Author: Weiqun Zhang Date: Mon Nov 30 13:26:49 2015 -0800 TileArray: fix typo Src/C_BaseLib/FabArray.cpp commit a7f095e84481d1d8dbb864dae19aa13d4f5c1184 Author: Michael Zingale Date: Mon Nov 30 16:23:02 2015 -0500 also fix fab_bind for 2-d w/ ghost-cells Src/F_BaseLib/plotfile.f90 commit 6d8fb99a0b7b1366f6982f549492dd58f54b9618 Merge: 253f58520 28225239d Author: Ann Almgren Date: Mon Nov 30 13:07:38 2015 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 253f5852086b05b3714431bbc0f76c14bc0dbd45 Author: Ann Almgren Date: Mon Nov 30 13:07:10 2015 -0800 Test on whether lo(3) = hi(3) -- if that is true then the data is really 2D so doesn't have ghost cells in the third direction. Src/F_BaseLib/plotfile.f90 commit 28225239dc461e8ae014cd7d809505e6d9b167fb Author: Weiqun Zhang Date: Mon Nov 30 12:40:12 2015 -0800 AMR_Adv: add some comments Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs Tutorials/AMR_Adv_F/Exec/SingleVortex/inputs_2d commit 45ad1bf97c3b9e323e3c6d727b169b58ca1da09d Author: Andy Nonaka Date: Mon Nov 30 12:33:10 2015 -0800 for each level advance, make sure we are not violating cfl since the time step is based on the velocity at t^n Tutorials/AMR_Adv_F/Source/advance.f90 commit f124691cbd68fd01613fa68889adf84122ec18c4 Merge: 818e5af56 45046f4a4 Author: Weiqun Zhang Date: Mon Nov 30 11:24:10 2015 -0800 Merge branch 'development' into tilearraycache commit 45046f4a48ca0dbacc3647c98991598ebbfd0aee Author: Weiqun Zhang Date: Mon Nov 30 11:22:10 2015 -0800 AMR_Adv: change cfl to 0.7 for the single vortext problem Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs Tutorials/AMR_Adv_F/Exec/SingleVortex/inputs_2d Tutorials/AMR_Adv_F/Exec/SingleVortex/inputs_3d commit 818e5af569dce274473dc17fa63217822ad3474b Author: Weiqun Zhang Date: Mon Nov 30 10:34:01 2015 -0800 FabArray: add some assertion making sure BoxArray and DistributionMapping do not change Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit b94f324ef97a96efe176559e0d8c1d29951af31e Author: Weiqun Zhang Date: Sun Nov 29 17:51:59 2015 -0800 FabArray & MFIter: cache tile array and use cached tile array in MFIter Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit e0e06ebce42a1e42a96790f3233056f812599b23 Merge: 279f67df3 e5d0548bb Author: Ann Almgren Date: Sun Nov 29 17:26:07 2015 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 279f67df3398320bd5ee2c7aa8b7852692f89c83 Author: Ann Almgren Date: Sun Nov 29 17:25:49 2015 -0800 See previous comments. Tutorials/MultiGrid_C/inputs commit d691c36713601e292efcf18eb03c4c3a3bf6ac7d Author: Ann Almgren Date: Sun Nov 29 17:24:28 2015 -0800 1) We only need a single inputs file for 2d and 3d. 2) Change the tolerance from 1e-6 to 1e-10 3) Set the maxorder for the BoxLib_C solver to be 3 in the inputs file. The default is 2, but if we set maxorder = 3 then the Cpp results match the F90 results. Tutorials/MultiGrid_C/inputs Tutorials/MultiGrid_C/inputs.f90.3d commit 03535ca0caf9f213928d8a2ff33274cfc2fd65be Author: Ann Almgren Date: Sun Nov 29 17:23:53 2015 -0800 Have the default be not to test HPGMG. Tutorials/MultiGrid_C/GNUmakefile commit 813e6b47a275975fe9f3def3b25b8bc269a06593 Author: Ann Almgren Date: Sun Nov 29 17:23:32 2015 -0800 Fix typo in comment. Tutorials/MultiGrid_C/COEF_2D.F Tutorials/MultiGrid_C/COEF_3D.F commit b73528734f2d58131dda416b2bf5606dbd7b8c75 Author: Weiqun Zhang Date: Sun Nov 29 07:57:42 2015 -0800 DistributionMapping: ID Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 9c36beab1b755fd1cf01015418dd48f53df7e65c Author: Weiqun Zhang Date: Sun Nov 29 07:50:40 2015 -0800 BoxArray: ID Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 32b6c95fe49dc109c50cbcf0d433af696314c2b6 Author: Weiqun Zhang Date: Fri Nov 27 20:12:00 2015 -0800 PGAS_SMC: tiling MiniApps/PGAS_SMC/SMC_advance.cpp commit 82050fb9928f399392d6dbf4a30ab8183df5553b Author: Weiqun Zhang Date: Fri Nov 27 20:11:43 2015 -0800 MFGhostIter: update for UPC++ Src/C_BaseLib/FabArray.cpp commit 1d4ea36ebaa33e59ec2993302958feb339b973b6 Author: Weiqun Zhang Date: Fri Nov 27 15:14:05 2015 -0800 PGAS_SMC: change default MiniApps/PGAS_SMC/SMC.cpp commit de001b87338894996a2e4096e0337e156574cccb Author: Weiqun Zhang Date: Fri Nov 27 12:15:16 2015 -0800 PGAS_SMC: replication for weak scaling MiniApps/PGAS_SMC/SMC.cpp MiniApps/PGAS_SMC/init_data.f90 commit b1a65db7013e0108719c4ee6d6a0b80a9844ed2e Author: Weiqun Zhang Date: Fri Nov 27 07:40:53 2015 -0800 PGAS_SMC: make max_grid_size a vector MiniApps/PGAS_SMC/SMC.H MiniApps/PGAS_SMC/SMC.cpp MiniApps/PGAS_SMC/SMC_init.cpp commit 77765edebbf098fb50295cf6f3f880d70dc14c4d Author: Weiqun Zhang Date: Thu Nov 26 15:53:39 2015 -0800 fix a bug and tidy Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/ParallelDescriptor.H commit e5d0548bbdfdca1aabd729f786b154f9c6340ce8 Author: Max Katz Date: Thu Nov 26 09:37:50 2015 -0500 Only print out a warning on the I/O processor. Src/C_AMRLib/Amr.cpp commit 34b8a5fcce04987c2fb91ace022f234cfb5184ba Author: Weiqun Zhang Date: Tue Nov 24 18:13:15 2015 -0800 add Team Free consisting of processes not involved in remote communication and use it for local copy in Fill Boundary Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/ParallelDescriptor.H commit 7f63169c1bacec4d8eb2851c2830361ed613164f Author: Weiqun Zhang Date: Tue Nov 24 16:35:28 2015 -0800 finished team message aggregation for periodic boundary Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit cb4276ad3f6b7fff3e1a82c2e6f8908044b7fc4e Author: Weiqun Zhang Date: Tue Nov 24 16:15:23 2015 -0800 fixed bug Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/ParallelDescriptor.H commit 377931fea7f9efbe4bf8f0fecb06c023631a0721 Author: Weiqun Zhang Date: Tue Nov 24 16:15:14 2015 -0800 added override Src/C_BaseLib/UArena.H commit 30ccf766f3f4604b715b6ed9aae23eaa4be5f41d Author: Weiqun Zhang Date: Tue Nov 24 15:28:34 2015 -0800 various message aggregation methods Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 96655578c9712f64c9e90dbfc61d5f6e35a2383c Merge: e53692594 62d03f5ac Author: Weiqun Zhang Date: Tue Nov 24 13:47:31 2015 -0800 Merge branch 'development' into pgas Conflicts: Src/C_BaseLib/Make.package commit e53692594c77a3090ba0586aa23087805068eba2 Merge: 017ec5969 5e57dfb4e Author: Weiqun Zhang 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 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 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: b51193da1 5f927d922 Author: Brian Friesen Date: Tue Nov 24 13:19:08 2015 -0800 Merge branch 'hpgmg_updates' into development This merge adds recent changes Sam made to the HPGMG code base, as well as significant reorganization of the HPGMG hooks in BoxLib. Specifically, the hooks (both headers and source files) have moved from MultiFab.{H,cpp} to Src/Extern/hpgmg/BL_HPGMG.{H,cpp}. commit 5f927d922ae32834f0804429e5de621a88b1ef4a Author: Brian Friesen Date: Tue Nov 24 13:12:26 2015 -0800 Tutorials, C_mk: move all HPGMG compile hooks from GNUmakefile into Make.defs This way we don't have to define the compile hooks in every GNUmakefile separately. Tools/C_mk/Make.defs Tutorials/MultiGrid_C/GNUmakefile commit 17b9e0d5bc05af4c54a6ca64d477e5bdee16c5d4 Author: Brian Friesen Date: Tue Nov 24 12:20:59 2015 -0800 MultiFab, HPGMG, Extern: move hooks for HPGMG from MultiFab to Extern Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/Extern/hpgmg/BL_HPGMG.H Src/Extern/hpgmg/BL_HPGMG.cpp Src/Extern/hpgmg/Make.package Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/main.cpp commit 5f46cbc97555347df8021a5dde2ab70918022699 Author: Brian Friesen Date: Thu Nov 19 09:21:03 2015 -0800 MultiFab, HPGMG: fix weird comment text alignment Src/C_BaseLib/MultiFab.cpp commit 24a7aa8b1a36616f44f25870baf1a4a6a346baa5 Author: Brian Friesen Date: Thu Nov 19 09:20:09 2015 -0800 MultiFab, HPGMG: misc. fixes which mirror Sam's most recent changes in HPGMG Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 59a6c55a2c198765084bd6ed9bd5f652ed936cba Author: Brian Friesen Date: Wed Nov 18 16:25:11 2015 -0800 MultiFab, HPGMG: minor fixes to boundary condition logic in MultiFab::CreateHPGMGLevel() Src/C_BaseLib/MultiFab.cpp commit 12f366dafedd38069b64766aea27c3aeeee87028 Author: Brian Friesen Date: Wed Nov 18 16:14:43 2015 -0800 MultiFab, HPGMG: in MultiFab::CreateHPGMGLevel(), iterate the MFIter until we find one that's valid Src/C_BaseLib/MultiFab.cpp commit b51193da11e2ab16fee9b49e8fb1effd6de0bf3e Author: Brian Friesen Date: Mon Nov 23 15:38:52 2015 -0800 Geometry: split retrieval of Box index int array into 2 steps in SendGeometryToSidecars() Doing Box.type().getVect() yields nonsense numbers. So instead we save the IntVect from type() as a temporary variable and then get the int array from it as a separate step. Src/C_BaseLib/Geometry.cpp commit c206e5f5d403847e7c8844b106c6efb55dc5cd88 Author: Weiqun Zhang Date: Mon Nov 23 16:13:36 2015 -0800 AMR_Adv_C: added override Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/AdvBld.cpp commit 5a1878a789fdb19fa310b2242880c9cd6f1c0e5d Author: Weiqun Zhang Date: Mon Nov 23 15:52:17 2015 -0800 omp clean up Src/F_BaseLib/multifab_f.f90 commit 1efe8d4a840d007409dc676873c70c14c40b33ea Author: Weiqun Zhang Date: Mon Nov 23 14:15:17 2015 -0800 added a new header file for C++ 11 stuff and added BL_OVERRIDE (which is preprocessed to override or space depending on BL_USE_CXX11) to overriding virtual functions. This can help virtual function sugnature mismatch bugs at compile time Src/C_AMRLib/AmrParGDB.H Src/C_AMRLib/Interpolater.H Src/C_AMRLib/MLSDCAmr.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BL_CXX11.H Src/C_BaseLib/CArena.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/Particles.H Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/MacBndry.H Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_TensorMG/DivVis.H commit 32ea7b39f4d011848834956aca2f212d02c736c1 Author: Weiqun Zhang Date: Mon Nov 23 11:18:02 2015 -0800 replaced omp critical with reduction Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/iMultiFab.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp commit 12f609ca4691ad9cd331c5ba866f2158f3a4c94a Author: Weiqun Zhang Date: Mon Nov 23 11:12:15 2015 -0800 replaced omp critical with omp atomic Src/F_BaseLib/bl_mem_stat.f90 commit c975328162185b393fd8cb8081de85de00457dfa Author: Weiqun Zhang Date: Mon Nov 23 10:49:25 2015 -0800 replaced an omp critical with omp atomic Src/C_BaseLib/Particles.cpp commit 2efd228e9c6460b45acfa527b5fbb1e23bb4bcb9 Author: Weiqun Zhang Date: Fri Nov 20 06:01:48 2015 -0800 Revert "bndry_reg: save have_periodic_bloxes when doing rr_build" This reverts commit 61cc7595c058eb9d843342ab54d0746ea727cecc. Src/F_BaseLib/bndry_reg.f90 commit 61cc7595c058eb9d843342ab54d0746ea727cecc Author: Weiqun Zhang Date: Thu Nov 19 12:57:59 2015 -0800 bndry_reg: save have_periodic_bloxes when doing rr_build Src/F_BaseLib/bndry_reg.f90 commit eef0431bb956a6b8f6e01be08643d6ea8a150c26 Author: vince Date: Wed Nov 18 18:28:53 2015 -0800 better names for allocated fabarray pointers. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 3e1d4d261787b93e9b589f2ce083bcb4e2079549 Author: vince Date: Wed Nov 18 18:28:11 2015 -0800 more support for dynamic sidecars. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.cpp commit d99c6fb6c25dd7f0fe0f12051916a434062ae6ba Author: vince Date: Wed Nov 18 18:26:43 2015 -0800 vectSize function. Src/C_AMRLib/BCRec.H commit e05c8a48961f402d4c42312ce78778ab52278128 Author: Weiqun Zhang Date: Wed Nov 18 14:45:51 2015 -0800 RegressionTesting: rm reg_test_blame because it does work well and updated reg_test_gc Tools/RegressionTesting/reg_test_blame.py Tools/RegressionTesting/reg_test_gc.py commit 6c81d31623800dd3bd0691794e6aea6ff4f3eb99 Author: vince Date: Wed Nov 18 14:31:38 2015 -0800 added virtual. Src/C_AMRLib/AmrLevel.H commit 23eed125dada541d6bad7f0b8f98f11454132ee7 Author: vince Date: Wed Nov 18 14:31:12 2015 -0800 duplicate the initial comm in case it is world. Src/C_BaseLib/ParallelDescriptor.cpp commit f053b8c603acb2b09f361e3dccd0c15479015ed1 Author: Weiqun Zhang Date: Wed Nov 18 13:32:01 2015 -0800 Fixed a bug in bndry_reg_copy. The mf source usually has only one ghost cell, whereas the bndry_reg can have two cell beyond periodic boundary. Thank Ashish Pathak for pointing this out to us. Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit bee502dc569fab9a865aa4feedb281f907dc8301 Author: Michael Zingale Date: Wed Nov 18 08:37:51 2015 -0500 allow test_suite to take a string of arguments to parse -- this allows it to be callable by other routines more easily Tools/RegressionTesting/testnew.py commit 54c67e68fc700a04c3fd0ca6c859ccef73a46601 Merge: 65f1a6766 606c15b27 Author: Michael Zingale Date: Tue Nov 17 20:54:10 2015 -0500 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit ba7def0ca5a3bfa3315786d012da73c0574e3c3c Author: vince Date: Tue Nov 17 17:52:01 2015 -0800 more sidecar copies on resize. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 65f1a6766a259e9f7e01725554de2a53cd3446f3 Author: Michael Zingale Date: Tue Nov 17 20:28:45 2015 -0500 clean up the parsing Tools/RegressionTesting/testnew.py commit 606c15b271f7f8005efe3d743b5fbc104764d12b Author: Weiqun Zhang Date: Tue Nov 17 15:56:34 2015 -0800 AMR_Adv_C: check CFL violation Tutorials/AMR_Adv_C/Source/Src_2d/Adv_2d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/Adv_3d.f90 commit de6ff6e3e94b9c226cbfd91a612cc473716b8bcc Author: Weiqun Zhang Date: Tue Nov 17 15:34:47 2015 -0800 AMR_Adv_F: fixed omp Tutorials/AMR_Adv_F/Exec/SingleVortex/init_phi.f90 commit 706676a683c1a0abf4a9d6be5d5119c92d6a8e62 Author: Weiqun Zhang Date: Tue Nov 17 15:22:17 2015 -0800 AMR_Adv_C: added change_max for dt Tutorials/AMR_Adv_C/Source/Adv_dt.cpp commit c1299ddb61118b3376ef9f02a438e1497d7a4ddb Author: Weiqun Zhang Date: Tue Nov 17 14:40:33 2015 -0800 AMR_Adv_C: updated SingleVortex Tutorials/AMR_Adv_C/Exec/SingleVortex/ACT_advection_2d.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/Make.package Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob_2d.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob_3d.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/amrvis.defaults Tutorials/AMR_Adv_C/Exec/SingleVortex/face_velocity_2d.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/face_velocity_3d.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.2d Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.3d Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.rt Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.rt.3d Tutorials/AMR_Adv_C/Exec/SingleVortex/probdata.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/probin Tutorials/AMR_Adv_C/Exec/SingleVortex/probin.2d Tutorials/AMR_Adv_C/Exec/SingleVortex/probin.3d Tutorials/AMR_Adv_F/Exec/SingleVortex/init_phi.f90 commit a9b927bea25d4cf4d21bce1e70a0179cf7d77068 Author: Weiqun Zhang Date: Tue Nov 17 13:52:45 2015 -0800 AMR_Adv_C: fixed 3d bug in scaling the flux Tutorials/AMR_Adv_C/Source/Src_3d/Adv_3d.f90 commit 3651b11aa31e86d51e4ddb69f6d687884bc7d1e3 Author: Weiqun Zhang Date: Tue Nov 17 13:47:53 2015 -0800 AMR_Adv_C: fixed tagging Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/Src_nd/Tagging_nd.f90 Tutorials/AMR_Adv_C/Source/Src_nd/tagging_params.f90 commit 777b9169a16e9dd5fbd829d3515aef4bcf0bb0ae Author: Weiqun Zhang Date: Tue Nov 17 13:11:44 2015 -0800 AMR_Adv_C: made the 2d consistent with AMR_Adv_F Tutorials/AMR_Adv_C/Source/Src_2d/Adv_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/Make.package Tutorials/AMR_Adv_C/Source/Src_2d/adv_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/compute_flux_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/trace_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/trans_2d.f90 commit 9e6f62995ecdfa62ce481c76d7447e600a63670a Author: Andy Nonaka 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 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 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 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 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: eee1a59f3 b5cdce2ea Author: Ann Almgren Date: Tue Nov 17 10:15:12 2015 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit b5cdce2eaf072b98ad0502734b3963ed35499f35 Author: Andy Nonaka Date: Tue Nov 17 08:11:25 2015 -0800 fixed crash issue when nlevs .ne. max_levs based on refinement criteria. the compute_dt routine was looping over max_levs, not nlevs Tutorials/AMR_Adv_F/Source/main.f90 commit 96a4ee7c702c733d2c2b7a3cf6579e3ccdaa0ba7 Author: Andy Nonaka Date: Tue Nov 17 08:06:36 2015 -0800 move bubble to center of domain in 3d Tutorials/AMR_Adv_F/Exec/SingleVortex/init_phi.f90 commit eee1a59f3eef65aa214863efe7efe63c90d932e2 Author: Ann Almgren Date: Mon Nov 16 18:45:23 2015 -0800 Fix this GNUmakefile Tutorials/AMR_Adv_C/Exec/SingleVortex/GNUmakefile commit fc45de027649e21cde40b81072617d2edee0fef8 Author: Ann Almgren Date: Mon Nov 16 18:44:25 2015 -0800 1) Renamed KotheRiderExample --> SingleVortex in AMR_Adv_C. 2) Copied tag_boxes.f90 into AMR_Adv_F/Source directory so it is easy to see how to set the refinement criteria. Tutorials/AMR_Adv_C/Exec/SingleVortex/ACT_advection_2d.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_C/Exec/SingleVortex/Make.package Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob_2d.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/Prob_3d.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/amrvis.defaults Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.2d Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.3d Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.rt Tutorials/AMR_Adv_C/Exec/SingleVortex/inputs.rt.3d Tutorials/AMR_Adv_C/Exec/SingleVortex/probdata.f90 Tutorials/AMR_Adv_C/Exec/SingleVortex/probin.2d Tutorials/AMR_Adv_C/Exec/SingleVortex/probin.3d Tutorials/AMR_Adv_F/Source/GPackage.mak Tutorials/AMR_Adv_F/Source/tag_boxes.f90 commit cf10ce5d2caa1f200d1c29897d4bf0fccd830c8c Merge: ae0e2bb5c 8ca4cb74a Author: Ann Almgren Date: Mon Nov 16 18:10:23 2015 -0800 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit ae0e2bb5cb8d33e4b5722b6c7c7ded98876f4ca7 Author: Ann Almgren Date: Mon Nov 16 18:09:21 2015 -0800 1) Add computation of dt based on time-n velocity at every coarse timestep. 2) Move the routines to set the velocity and initialize phi into the Exec/problem directories. 3) Set do_subcycling = T in the inputs files. Tutorials/AMR_Adv_F/Exec/SingleVortex/GNUmakefile Tutorials/AMR_Adv_F/Exec/SingleVortex/GPackage.mak Tutorials/AMR_Adv_F/Exec/SingleVortex/init_phi.f90 Tutorials/AMR_Adv_F/Exec/SingleVortex/inputs_2d Tutorials/AMR_Adv_F/Exec/SingleVortex/inputs_3d Tutorials/AMR_Adv_F/Exec/SingleVortex/set_velocity.f90 Tutorials/AMR_Adv_F/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Adv_F/Exec/UniformVelocity/GPackage.mak Tutorials/AMR_Adv_F/Exec/UniformVelocity/init_phi.f90 Tutorials/AMR_Adv_F/Exec/UniformVelocity/inputs_2d Tutorials/AMR_Adv_F/Exec/UniformVelocity/inputs_3d Tutorials/AMR_Adv_F/Exec/UniformVelocity/set_velocity.f90 Tutorials/AMR_Adv_F/Source/GPackage.mak Tutorials/AMR_Adv_F/Source/advance.f90 Tutorials/AMR_Adv_F/Source/main.f90 Tutorials/AMR_Adv_F/Source/slope.f90 commit 803a5d21d934962147b7090f831dfce593c4ade5 Author: vince Date: Mon Nov 16 17:42:18 2015 -0800 consolidate geometry broadcast functions. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp commit a2b0a281763a7ecb99747eac100426a6b3436481 Author: vince Date: Mon Nov 16 17:41:14 2015 -0800 consolidate geometry broadcast functions. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 8ca4cb74ade9a3e467dff2c4a52ceb897bfec4e5 Author: Weiqun Zhang Date: Mon Nov 16 16:45:12 2015 -0800 AMR_Adv_C: fixed a bug in 2d slope. The 2D C++ version works now. Tutorials/AMR_Adv_C/Source/Src_2d/slope_2d.f90 commit 89289210310deffd77dfce5d75657b5283c78fb4 Author: Weiqun Zhang Date: Mon Nov 16 16:44:25 2015 -0800 AMR_Adv: make the initial model consistent Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90 Tutorials/AMR_Adv_F/Source/init_phi.f90 commit d23af632bc6a6a9bebada61699bbd615234fefb3 Merge: c6c211111 e9790dfe0 Author: Weiqun Zhang 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 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 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 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: 2493e9f6d b525768a0 Author: Weiqun Zhang 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 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 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 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 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 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 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 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 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 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 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 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 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 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: 3ff9fef09 3a3b55d1f Author: Andy Nonaka Date: Mon Nov 16 07:35:04 2015 -0800 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 3a3b55d1fc7d21fc2a8d722c24f99b0ab0ee2be0 Author: Weiqun Zhang Date: Sun Nov 15 15:49:07 2015 -0800 AMR_Adv_C: write final checkpoint and plotfile Tutorials/AMR_Adv_C/Source/main.cpp commit ff88ca83fdc0db93d1d7a0962b759118860bfe36 Author: Weiqun Zhang 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 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 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 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 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 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 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 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 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 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 Date: Sat Nov 14 20:10:49 2015 -0800 AMR_Adv_C: edge --> face Tutorials/AMR_Adv_C/Exec/UniformVelocity/Make.package Tutorials/AMR_Adv_C/Exec/UniformVelocity/face_velocity_2d.f90 Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_dt.cpp commit 7a7c22dddcb4953ddf7b8c8aae90d18f882df630 Author: Weiqun Zhang Date: Sat Nov 14 20:05:21 2015 -0800 AMR_Adv_C: 2d finished not checked Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Src_2d/Make.package Tutorials/AMR_Adv_C/Source/Src_2d/adv_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/advection_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/flux_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/slope_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/trace_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/trans_2d.f90 commit ab7fe7d23a571e8a92cdbde12853bfae21fca01d Author: Weiqun Zhang Date: Fri Nov 13 22:04:31 2015 -0800 AMR_Adv_C: WIP Tutorials/AMR_Adv_C/Source/Src_2d/Make.package Tutorials/AMR_Adv_C/Source/Src_2d/adv_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/advection_2d.f90 commit 5473a3cc399a1ea54daf9c09daf1d2070570f4e4 Author: Weiqun Zhang Date: Fri Nov 13 21:11:54 2015 -0800 AMR_Adv_C: rm some files Tutorials/AMR_Adv_C/Exec/Make.Adv Tutorials/AMR_Adv_C/Source/Src_2d/Derive_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/EstDt_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/Make.package Tutorials/AMR_Adv_C/Source/Src_2d/Tagging_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/advection_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/bc_fill_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/ext_src_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/fill_diff_coeff_2d.f90 commit 8b0058d58962b4da7b7a26c74454df7d3e5aa9ff Author: Weiqun Zhang Date: Fri Nov 13 21:06:13 2015 -0800 AMR_Adv_C: compute dt Tutorials/AMR_Adv_C/Exec/UniformVelocity/Make.package Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/edge_velocity_2d.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/probdata.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_dt.cpp Tutorials/AMR_Adv_C/Source/Adv_setup.cpp Tutorials/AMR_Adv_C/Source/Make.package Tutorials/AMR_Adv_C/Source/Src_nd/Adv_nd.f90 Tutorials/AMR_Adv_C/Source/Src_nd/Make.package Tutorials/AMR_Adv_C/Source/Src_nd/Tagging_nd.f90 Tutorials/AMR_Adv_C/Source/Src_nd/tagging_params.f90 commit 8da06a9533e91e435e3dfe9c971051037099678b Author: Weiqun Zhang Date: Fri Nov 13 18:07:22 2015 -0800 AMR_Adv_C: remvoed prob_hi from initdata Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90 Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/Adv_F.H commit 3ac90bec61e4f36feaf31e9d03d59346d10e98fd Author: Weiqun Zhang Date: Fri Nov 13 17:56:22 2015 -0800 AMR_Adv_C: fixed boundary function Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C/Source/Adv_setup.cpp commit 3ff9fef0999c53abb85cee371368ba9b98aba6ed Author: Andy Nonaka Date: Fri Nov 13 17:52:46 2015 -0800 now computing velocity and half-time for both subcycling and non-subcycling cases Tutorials/AMR_Adv_F/Exec/GNUmakefile Tutorials/AMR_Adv_F/Source/advance.f90 Tutorials/AMR_Adv_F/Source/compute_velocity.f90 Tutorials/AMR_Adv_F/Source/main.f90 commit 8100d3ab7cab4b9ec5fb00755feb3e94bc119791 Author: Weiqun Zhang Date: Fri Nov 13 17:38:54 2015 -0800 AMR_Adv_C: clean up headers Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/AdvBld.cpp Tutorials/AMR_Adv_C/Source/main.cpp commit 52b54252b24f1d9065e50543fb3902213adb8289 Author: Weiqun Zhang Date: Fri Nov 13 17:32:18 2015 -0800 AMR_Adv_C: removed area and volume Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_io.cpp commit 672c81e4ae0b8e5afd444938b407c13bf79c9d7c Author: Weiqun Zhang Date: Fri Nov 13 17:24:22 2015 -0800 AMR_Adv_C: clean up Adv::advance Tutorials/AMR_Adv_C/Source/Adv_advance.cpp commit 3a78af91b50146af35e9a6e69f075b6185e109b6 Author: Weiqun Zhang Date: Fri Nov 13 16:44:23 2015 -0800 AMR_Adv_C: fixed 2d initdata Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90 commit 9b5e9072f860985471c7151e255eded9d04bab03 Author: Weiqun Zhang Date: Fri Nov 13 16:39:40 2015 -0800 AMR_Adv_C: fixed initdata Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90 Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_F/Source/init_phi.f90 commit 77e9042d7bfaf585341cd29767ccc1bba0d43e6b Author: Weiqun Zhang Date: Fri Nov 13 16:24:01 2015 -0800 AMR_Adv_C: WIP Tutorials/AMR_Adv_C/Exec/Make.Adv Tutorials/AMR_Adv_C/Exec/UniformVelocity/Make.package Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob_2d.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob_3d.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/amrvis.defaults Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.3d Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.rt Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.rt.3d Tutorials/AMR_Adv_C/Exec/UniformVelocity/probdata.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin.2d Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin.3d Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/AdvBld.cpp Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_error.cpp Tutorials/AMR_Adv_C/Source/Adv_io.cpp Tutorials/AMR_Adv_C/Source/Adv_nd.f90 Tutorials/AMR_Adv_C/Source/Adv_setup.cpp Tutorials/AMR_Adv_C/Source/Derive_F.H Tutorials/AMR_Adv_C/Source/Make.package Tutorials/AMR_Adv_C/Source/Src_2d/MGutils_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/Make.package Tutorials/AMR_Adv_C/Source/extern_probin.template Tutorials/AMR_Adv_C/Source/main.cpp Tutorials/AMR_Adv_C/Source/meth_params.f90 Tutorials/AMR_Adv_C/Source/prob_params.f90 commit ba538e111bea66fa260eef8a8ab545f5243ff19b Author: Weiqun Zhang Date: Fri Nov 13 11:25:13 2015 -0800 AMR_Adv_C: rm diffusion Tutorials/AMR_Adv_C/Source/ADR_diffusion.cpp Tutorials/AMR_Adv_C/Source/Diffusion.H Tutorials/AMR_Adv_C/Source/Diffusion.cpp Tutorials/AMR_Adv_C/Source/Make.package commit 552e562ac048f5810a3464a3669d878eb6ac18f2 Author: Weiqun Zhang Date: Fri Nov 13 11:24:12 2015 -0800 AMR_Adv_C: ADR --> Adv Tutorials/AMR_Adv_C/Source/Adv.H Tutorials/AMR_Adv_C/Source/Adv.cpp Tutorials/AMR_Adv_C/Source/AdvBld.cpp Tutorials/AMR_Adv_C/Source/Adv_F.H Tutorials/AMR_Adv_C/Source/Adv_advance.cpp Tutorials/AMR_Adv_C/Source/Adv_error.cpp Tutorials/AMR_Adv_C/Source/Adv_nd.f90 Tutorials/AMR_Adv_C/Source/Adv_setup.cpp Tutorials/AMR_Adv_C/Source/Make.package commit 09375d61de6cf8bfb4b5a1154f8da90761cd8083 Author: Weiqun Zhang Date: Fri Nov 13 11:21:06 2015 -0800 AMR_Adv_C: updated make Tutorials/AMR_Adv_C/Exec/Make.Adv Tutorials/AMR_Adv_C/Exec/UniformVelocity/GNUmakefile commit 04d47bd18c3103e957344bdb9f9b69db14fd091a Author: Weiqun Zhang Date: Fri Nov 13 11:09:46 2015 -0800 AMR_Adv_C: updated README Tutorials/AMR_Adv_C/README commit 2d55fb0dde98b0972a3564b44ca557dcd328aa5a Author: Weiqun Zhang Date: Fri Nov 13 11:09:30 2015 -0800 AMR_Adv_C: renamed file Tutorials/AMR_Adv_C/Exec/Make.Adv commit baf73ae135e851680c9108207235102b1520b5c4 Author: Andy Nonaka Date: Fri Nov 13 15:57:32 2015 -0800 more progress on test problem Tutorials/AMR_Adv_F/Exec/GNUmakefile Tutorials/AMR_Adv_F/Exec/inputs_2d Tutorials/AMR_Adv_F/Source/advance.f90 Tutorials/AMR_Adv_F/Source/compute_flux.f90 Tutorials/AMR_Adv_F/Source/compute_velocity.f90 Tutorials/AMR_Adv_F/Source/init_phi.f90 Tutorials/AMR_Adv_F/Source/main.f90 Tutorials/AMR_Adv_F/Source/update_phi.f90 commit d439d15412333bb7d882614dd6519f8229b27246 Author: Andy Nonaka Date: Fri Nov 13 14:47:36 2015 -0800 compute_velocity routine... need to fold it into subcycling case properly (so it uses most current time) Tutorials/AMR_Adv_F/Source/GPackage.mak Tutorials/AMR_Adv_F/Source/advance.f90 Tutorials/AMR_Adv_F/Source/compute_velocity.f90 Tutorials/AMR_Adv_F/Source/main.f90 commit dcb3828f88966566a1c4c321d3e8f5a0d6a7eef1 Author: Andy Nonaka Date: Fri Nov 13 12:53:46 2015 -0800 comments, initialize fluxes to zero now that the diffusive fluxes are gone Tutorials/AMR_Adv_F/Source/compute_flux.f90 Tutorials/AMR_Adv_F/Source/main.f90 commit e8ab7030074a39ca2c5802c3de61c17ee1ce6fc8 Author: Andy Nonaka Date: Fri Nov 13 12:27:56 2015 -0800 clean up namelist and inputs file Tutorials/AMR_Adv_F/Exec/inputs_2d Tutorials/AMR_Adv_F/Exec/inputs_3d Tutorials/AMR_Adv_F/Source/init_phi.f90 Tutorials/AMR_Adv_F/Source/main.f90 commit d38920a6491860feaa7c07488e7172de45a87a77 Author: Andy Nonaka 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 Date: Fri Nov 13 11:07:48 2015 -0800 remove some diffusion stuff re-org directories to make it look like the C version Tutorials/AMR_Adv_F/Exec/GNUmakefile Tutorials/AMR_Adv_F/Exec/inputs-rt Tutorials/AMR_Adv_F/Exec/inputs_2d Tutorials/AMR_Adv_F/Exec/inputs_3d Tutorials/AMR_Adv_F/Source/GPackage.mak Tutorials/AMR_Adv_F/Source/advance.f90 Tutorials/AMR_Adv_F/Source/compute_flux.f90 Tutorials/AMR_Adv_F/Source/init_phi.f90 Tutorials/AMR_Adv_F/Source/main.f90 Tutorials/AMR_Adv_F/Source/prob.f90 Tutorials/AMR_Adv_F/Source/slope.f90 Tutorials/AMR_Adv_F/Source/update_phi.f90 Tutorials/AMR_Adv_F/Source/write_plotfile.f90 commit c037514f59a4414da560f7ad3d3d033e0518f37c Author: Andy Nonaka Date: Fri Nov 13 11:01:55 2015 -0800 new amr advection examples from Ann's latest commit Tutorials/AMR_Adv_C/Exec/KotheRiderExample/ACT_advection_2d.f90 Tutorials/AMR_Adv_C/Exec/KotheRiderExample/GNUmakefile Tutorials/AMR_Adv_C/Exec/KotheRiderExample/Make.package Tutorials/AMR_Adv_C/Exec/KotheRiderExample/Prob_2d.f90 Tutorials/AMR_Adv_C/Exec/KotheRiderExample/Prob_3d.f90 Tutorials/AMR_Adv_C/Exec/KotheRiderExample/amrvis.defaults Tutorials/AMR_Adv_C/Exec/KotheRiderExample/inputs.2d Tutorials/AMR_Adv_C/Exec/KotheRiderExample/inputs.3d Tutorials/AMR_Adv_C/Exec/KotheRiderExample/inputs.rt Tutorials/AMR_Adv_C/Exec/KotheRiderExample/inputs.rt.3d Tutorials/AMR_Adv_C/Exec/KotheRiderExample/probdata.f90 Tutorials/AMR_Adv_C/Exec/KotheRiderExample/probin.2d Tutorials/AMR_Adv_C/Exec/KotheRiderExample/probin.3d Tutorials/AMR_Adv_C/Exec/Make.ADR Tutorials/AMR_Adv_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Adv_C/Exec/UniformVelocity/Make.package Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob_2d.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/Prob_3d.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/amrvis.defaults Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.3d Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.rt Tutorials/AMR_Adv_C/Exec/UniformVelocity/inputs.rt.3d Tutorials/AMR_Adv_C/Exec/UniformVelocity/probdata.f90 Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin.2d Tutorials/AMR_Adv_C/Exec/UniformVelocity/probin.3d Tutorials/AMR_Adv_C/README Tutorials/AMR_Adv_C/Source/ADR.H Tutorials/AMR_Adv_C/Source/ADR.cpp Tutorials/AMR_Adv_C/Source/ADRBld.cpp Tutorials/AMR_Adv_C/Source/ADR_F.H Tutorials/AMR_Adv_C/Source/ADR_advance.cpp Tutorials/AMR_Adv_C/Source/ADR_diffusion.cpp Tutorials/AMR_Adv_C/Source/ADR_error.cpp Tutorials/AMR_Adv_C/Source/ADR_nd.f90 Tutorials/AMR_Adv_C/Source/ADR_setup.cpp Tutorials/AMR_Adv_C/Source/Derive_F.H Tutorials/AMR_Adv_C/Source/Diffusion.H Tutorials/AMR_Adv_C/Source/Diffusion.cpp Tutorials/AMR_Adv_C/Source/Make.package Tutorials/AMR_Adv_C/Source/Src_2d/ACT_advection_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/Derive_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/EstDt_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/MGutils_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/Make.package Tutorials/AMR_Adv_C/Source/Src_2d/Tagging_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/bc_fill_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/ext_src_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/fill_diff_coeff_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/slope_2d.f90 Tutorials/AMR_Adv_C/Source/Src_2d/trace_2d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/ACT_advection_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/Derive_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/EstDt_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/Make.package Tutorials/AMR_Adv_C/Source/Src_3d/React_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/Tagging_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/bc_fill_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/ext_src_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/fill_diff_coeff_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/slope_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/trace_3d.f90 Tutorials/AMR_Adv_C/Source/Src_3d/trans_3d.f90 Tutorials/AMR_Adv_C/Source/extern_probin.template Tutorials/AMR_Adv_C/Source/main.cpp Tutorials/AMR_Adv_C/Source/meth_params.f90 Tutorials/AMR_Adv_C/Source/prob_params.f90 Tutorials/AMR_Adv_F/GNUmakefile Tutorials/AMR_Adv_F/GPackage.mak Tutorials/AMR_Adv_F/advance.f90 Tutorials/AMR_Adv_F/compute_flux.f90 Tutorials/AMR_Adv_F/init_phi.f90 Tutorials/AMR_Adv_F/inputs-rt Tutorials/AMR_Adv_F/inputs_2d Tutorials/AMR_Adv_F/inputs_3d Tutorials/AMR_Adv_F/main.f90 Tutorials/AMR_Adv_F/prob.f90 Tutorials/AMR_Adv_F/slope.f90 Tutorials/AMR_Adv_F/update_phi.f90 Tutorials/AMR_Adv_F/write_plotfile.f90 Tutorials/AMR_Advection_C/Exec/Make.ADR Tutorials/AMR_Advection_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Advection_C/Exec/UniformVelocity/Make.package Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_2d.f90 Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_3d.f90 Tutorials/AMR_Advection_C/Exec/UniformVelocity/amrvis.defaults Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.3d Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt.3d Tutorials/AMR_Advection_C/Exec/UniformVelocity/probdata.f90 Tutorials/AMR_Advection_C/Exec/UniformVelocity/probin.2d Tutorials/AMR_Advection_C/Exec/UniformVelocity/probin.3d Tutorials/AMR_Advection_C/README Tutorials/AMR_Advection_C/Source/ADR.H Tutorials/AMR_Advection_C/Source/ADR.cpp Tutorials/AMR_Advection_C/Source/ADRBld.cpp Tutorials/AMR_Advection_C/Source/ADR_F.H Tutorials/AMR_Advection_C/Source/ADR_advance.cpp Tutorials/AMR_Advection_C/Source/ADR_diffusion.cpp Tutorials/AMR_Advection_C/Source/ADR_error.cpp Tutorials/AMR_Advection_C/Source/ADR_nd.f90 Tutorials/AMR_Advection_C/Source/ADR_react.cpp Tutorials/AMR_Advection_C/Source/ADR_setup.cpp Tutorials/AMR_Advection_C/Source/Derive_F.H Tutorials/AMR_Advection_C/Source/Diffusion.H Tutorials/AMR_Advection_C/Source/Diffusion.cpp Tutorials/AMR_Advection_C/Source/Make.package Tutorials/AMR_Advection_C/Source/Src_2d/ACT_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/ACT_advection_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/ACT_sums_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/Derive_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/EstDt_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/MGutils_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/Make.package Tutorials/AMR_Advection_C/Source/Src_2d/React_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/Tagging_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/bc_fill_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/ext_src_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/fill_diff_coeff_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/trans_2d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/ACT_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/ACT_advection_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/ACT_sums_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/Derive_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/EstDt_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/Make.package Tutorials/AMR_Advection_C/Source/Src_3d/React_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/Tagging_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/bc_fill_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/ext_src_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/fill_diff_coeff_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/slope_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/trace_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/trans_3d.f90 Tutorials/AMR_Advection_C/Source/burner.f90 Tutorials/AMR_Advection_C/Source/extern_probin.template Tutorials/AMR_Advection_C/Source/main.cpp Tutorials/AMR_Advection_C/Source/meth_params.f90 Tutorials/AMR_Advection_C/Source/network.f90 Tutorials/AMR_Advection_C/Source/prob_params.f90 Tutorials/AMR_Advection_C/Source/sum_integrated_quantities.cpp commit 717c9c8c79235586d4f4290859dffa81a98a3102 Author: Ann Almgren Date: Fri Nov 13 10:17:13 2015 -0800 Add new Tutorial example -- AMR_Adv_Diff_C Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/ACT_advection_2d.f90 Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/GNUmakefile Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/Make.package Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/Prob_2d.f90 Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/Prob_3d.f90 Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/amrvis.defaults Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/inputs.2d Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/inputs.3d Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/inputs.rt Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/inputs.rt.3d Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/probdata.f90 Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/probin.2d Tutorials/AMR_Adv_Diff_C/Exec/KotheRiderExample/probin.3d Tutorials/AMR_Adv_Diff_C/Exec/Make.ADR Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/Make.package Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/Prob_2d.f90 Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/Prob_3d.f90 Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/amrvis.defaults Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/inputs.3d Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/inputs.rt Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/inputs.rt.3d Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/probdata.f90 Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/probin.2d Tutorials/AMR_Adv_Diff_C/Exec/UniformVelocity/probin.3d Tutorials/AMR_Adv_Diff_C/README Tutorials/AMR_Adv_Diff_C/Source/ADR.H Tutorials/AMR_Adv_Diff_C/Source/ADR.cpp Tutorials/AMR_Adv_Diff_C/Source/ADRBld.cpp Tutorials/AMR_Adv_Diff_C/Source/ADR_F.H Tutorials/AMR_Adv_Diff_C/Source/ADR_advance.cpp Tutorials/AMR_Adv_Diff_C/Source/ADR_diffusion.cpp Tutorials/AMR_Adv_Diff_C/Source/ADR_error.cpp Tutorials/AMR_Adv_Diff_C/Source/ADR_nd.f90 Tutorials/AMR_Adv_Diff_C/Source/ADR_setup.cpp Tutorials/AMR_Adv_Diff_C/Source/Derive_F.H Tutorials/AMR_Adv_Diff_C/Source/Diffusion.H Tutorials/AMR_Adv_Diff_C/Source/Diffusion.cpp Tutorials/AMR_Adv_Diff_C/Source/Make.package Tutorials/AMR_Adv_Diff_C/Source/Src_2d/ACT_advection_2d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_2d/Derive_2d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_2d/EstDt_2d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_2d/MGutils_2d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_2d/Make.package Tutorials/AMR_Adv_Diff_C/Source/Src_2d/Tagging_2d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_2d/bc_fill_2d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_2d/ext_src_2d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_2d/fill_diff_coeff_2d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_2d/slope_2d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_2d/trace_2d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/ACT_advection_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/Derive_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/EstDt_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/Make.package Tutorials/AMR_Adv_Diff_C/Source/Src_3d/React_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/Tagging_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/bc_fill_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/ext_src_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/fill_diff_coeff_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/slope_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/trace_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/Src_3d/trans_3d.f90 Tutorials/AMR_Adv_Diff_C/Source/extern_probin.template Tutorials/AMR_Adv_Diff_C/Source/main.cpp Tutorials/AMR_Adv_Diff_C/Source/meth_params.f90 Tutorials/AMR_Adv_Diff_C/Source/prob_params.f90 commit 353751f5973ad155fa65072385ea38d420d0ae99 Author: vince Date: Thu Nov 12 17:55:25 2015 -0800 added function to broadcast a geometry. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 47d26e5160c67c4e8f202c3d53a4b813387ff2d7 Author: vince Date: Thu Nov 12 17:54:05 2015 -0800 added function for serialized box size. Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit d442bace971fee8a131aa3fb998e184fab6d3493 Author: vince Date: Thu Nov 12 17:52:40 2015 -0800 added function to send data to procs moved from the sidecars into comp. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 95f776191aaf7d7ba40492975f3058f9f9400da2 Author: vince Date: Thu Nov 12 17:52:05 2015 -0800 added function to send data to procs moved from the sidecars into comp. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 5e57dfb4e8f72824ce348dd6ef90312d363f1923 Author: Weiqun Zhang Date: Thu Nov 12 16:04:58 2015 -0800 added a barrier after we finish advance Tutorials/PGAS_HEAT/main.cpp commit 0e701c1891b5ff88e2afea60cb22dd851092a121 Author: vince Date: Thu Nov 12 11:16:44 2015 -0800 added switch default. Src/C_BaseLib/CoordSys.cpp commit 68c4c23a45e3f3fdc2cabdc286de22547001e3d6 Author: Weiqun Zhang Date: Thu Nov 12 11:16:20 2015 -0800 added more barriers when we switch between MPI and UPC++ Tests/FillBoundaryComparison/main.cpp commit 0d15d9e26648f472b43c21e90f36b36864057579 Merge: 4b1193413 84b9edc82 Author: yzheng Date: Thu Nov 12 07:58:44 2015 -0800 Add a barrier before switching from UPC++ to MPI commit 017ec5969d95594d4943d06d90dc83cbe8941be8 Author: Weiqun Zhang Date: Wed Nov 11 16:24:18 2015 -0800 renamed parameter upcxx_team_size to team.size and added new parameter team.aggregate_message to control how to aggregate team messages Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 07598fefc221b1a8bdbe135ad5bcb027b938ab6b Author: Weiqun Zhang Date: Wed Nov 11 14:28:32 2015 -0800 change the default of comm_num_pieces to 1; it does not seem to help on cori Src/C_BaseLib/FabArray.cpp commit 0a3506f30fd7327cf60155e10386daf9052f0779 Author: Andy Nonaka Date: Wed Nov 11 11:08:22 2015 -0800 a separate version of fabio_ml_multifab_write_d that works when the input multifab is a single-level, non-array Src/F_BaseLib/fabio.f90 commit 84b9edc82ee21799f368536c3aae09bee6dba77b Author: Weiqun Zhang 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 Date: Tue Nov 10 14:42:27 2015 -0800 auto: fixed Intel complaints Src/C_BaseLib/FabArray.H commit ca4ecf8b09924de6a632d3adb43ff884cca0c6b0 Merge: 0cf8cc0d7 2e819baee Author: Weiqun Zhang 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 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 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 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 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 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 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 Date: Tue Nov 10 11:08:51 2015 -0800 DistributionMapping: use team_for Src/C_BaseLib/DistributionMapping.cpp commit c3d72fceac8b4eb33ff1e6a6f1bcbbb52dfe43fe Author: Weiqun Zhang 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 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 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 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 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 Date: Mon Nov 9 15:05:58 2015 -0800 added UPC++ team barrier. Src/C_BaseLib/ParallelDescriptor.H commit 8eb28b7e4b4ce83f370a4d4ef98182b39dabe47e Author: Weiqun Zhang 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 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 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 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 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: ea4ff7fff 4c7f76583 Author: Weiqun Zhang Date: Sat Nov 7 10:05:35 2015 -0800 Merge branch 'development' into pgas commit 4c7f765839cdc5ecd464a84b6c026cc272cdb801 Author: Weiqun Zhang Date: Sat Nov 7 10:05:15 2015 -0800 MFIter: use bitfield flags Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit ea4ff7fff123476732ba3acd19691a85bf493fbc Author: Weiqun Zhang Date: Fri Nov 6 20:24:10 2015 -0800 added fab ownership Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H commit 27f7a8720ffb5fbe36fcb2cb26594cd795437d2d Author: Weiqun Zhang Date: Fri Nov 6 19:58:40 2015 -0800 Added an Arena for UPC++ Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Make.package Src/C_BaseLib/UArena.H Src/C_BaseLib/UArena.cpp commit 713463616c77ca9c05b7d0739679ad240f44c7e8 Author: Weiqun Zhang Date: Fri Nov 6 17:14:00 2015 -0800 first pass of UPC++ team Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/IArrayBox.H Src/C_BaseLib/IArrayBox.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tutorials/PGAS_HEAT/GNUmakefile commit dd1103ba90ae8fac8b754e91ab0028946d4164f2 Author: vince Date: Fri Nov 6 16:26:36 2015 -0800 return coord type as an int (esp. for mpi) Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp commit 32db1dea91771506083576522cf58bfd4e3ad820 Author: vince Date: Fri Nov 6 16:01:53 2015 -0800 check for correct array size. Src/C_BaseLib/Box.cpp commit 4358286bfae8da31dedf7fa652e75e800a81aa21 Author: vince Date: Fri Nov 6 16:01:12 2015 -0800 fixed comment. Src/C_BaseLib/FabArray.H commit 62d0e51bb15519758c700e15e64c269fde7a4236 Author: vince Date: Fri Nov 6 16:00:49 2015 -0800 (un)serialize functions for boxarray. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 16730ccf6eb417023c826ba45b0c0403cd8118e8 Author: Ann Almgren Date: Fri Nov 6 11:56:16 2015 -0800 BoxLib/Tutorials/AMR_Adv_Diff_F: Put higher order slopes into algorithm -- now there is a separate slope routine which is called from compute_fluxes. There are still no transverse derivatives though. Tutorials/AMR_Adv_Diff_F/GPackage.mak Tutorials/AMR_Adv_Diff_F/compute_flux.f90 Tutorials/AMR_Adv_Diff_F/slope.f90 commit 4b1193413e03149942e9afd1dcacdbd504544722 Merge: 637f78d7b c30391f34 Author: yzheng 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 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 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 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 Date: Thu Nov 5 16:03:51 2015 -0800 parmparse setting for particles.particles_nfiles. Src/C_BaseLib/Particles.H commit c30391f34d25446297c8b38efc9079f75ec58ad0 Merge: a25f53e2d 67b3e4018 Author: Weiqun Zhang Date: Thu Nov 5 10:52:36 2015 -0800 Merge branch 'development' into pgas Conflicts: Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Make.package commit 67b3e4018e4726e752171a48216efe3355364710 Author: Weiqun Zhang Date: Thu Nov 5 10:02:49 2015 -0800 PIC tutorial: update to the FMultiGrid function name Tutorials/PIC_C/solve_with_f90.cpp commit d14dce0f027582711668041aeb40f214fd29c5cd Merge: 25c02d3f5 60ddc9634 Author: Weiqun Zhang Date: Thu Nov 5 09:51:16 2015 -0800 Merge branch 'development' into new_particle commit 25c02d3f5c406dd0d9bce2e87a7351372430b2c7 Author: Ann Almgren Date: Thu Nov 5 03:11:09 2015 -0800 Add versions of BoxLib::average_down that take an int rather than an IntVect for the refinement ratio. Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp commit e76280996f6f4496ee55129ee23554d31137eef4 Author: Ann Almgren Date: Thu Nov 5 03:09:41 2015 -0800 This version does a level-0-then-level-1 solve as well as a multilevel 0-1 solve. It compiles and runs with the latest versions of BoxLib::new_particle branch. Tutorials/PIC_C/main.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/solve_with_hpgmg.cpp commit a4842f6123e69a1817cef2e3d397d2c4abf68700 Author: vince Date: Wed Nov 4 16:13:49 2015 -0800 added functions to (un)serialize arrays of strings. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit b14be1b43c2d33e7ef5324d9154c7da43d2f2c92 Author: vince Date: Wed Nov 4 14:53:36 2015 -0800 proc numbers for all. Src/C_BaseLib/ParallelDescriptor.H commit 1393ed6b06df5e9d59a70f1922919028979644f6 Author: vince Date: Wed Nov 4 14:52:42 2015 -0800 (un)serialize box functions for communicating boxes. Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit 0e5d34d491e09332371bd9b2b94f8c8a9cb4648a Author: vince Date: Tue Nov 3 15:37:01 2015 -0800 random multilevel distribution map for testing the sidecars. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 6afa709c4b6886ba739b6ed2c92bf46f387eb3d5 Author: vince Date: Tue Nov 3 15:35:36 2015 -0800 added function to increase the number of processes in a sidecar. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 45a8717e4168bc14959fb469bacb15765432286a Author: vince Date: Tue Nov 3 15:34:02 2015 -0800 added a few diagnostics for dynamic sidecar development. Src/C_BaseLib/FabArray.H commit 60ddc9634c6e46d306fe71ed53b461a462e5acaf Merge: c88bdc114 d93465e6e Author: Regression Tester Date: Tue Nov 3 12:21:16 2015 -0800 Merge branch 'master' into development commit c88bdc1142bbae8dba20e2f48da50fb37bd6f45a Author: Weiqun Zhang Date: Mon Nov 2 16:27:42 2015 -0800 FMultiGrid: renamed get_grad_phi back to get_fluxes because the latter is more accurate. Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp Tutorials/MultiGrid_C/main.cpp commit 1d2f04f10e661ee4608f1aa72c01d606ffdc9bad Author: Weiqun Zhang Date: Mon Nov 2 16:03:08 2015 -0800 fixed comments thanks to Ashish Pathak of Umass Dartmouth Tutorials/HeatEquation_EX5_F/advance.f90 commit 3f418c12d625963f593301d9d10cdd25d9abfb7e Author: Brian Friesen Date: Mon Nov 2 15:27:46 2015 -0800 Revert "IntVect: move static variables returned by TheDimensionVector() to anonymous namespace" This reverts commit 77fdfa30c71e47db82c9e951e5fac1ee290beb28. Src/C_BaseLib/IntVect.cpp commit 249f3794da74f8fd289131a5dc1d96f50172be62 Author: Brian Friesen Date: Mon Nov 2 15:27:45 2015 -0800 Revert "IntVect: move all remaining static variable declarations to anonymous namespace" This reverts commit 90526ea2379029f87e03ec15a5410711be296878. Src/C_BaseLib/IntVect.cpp commit 7d0f0d3ddbdc297cf22799f02ba2d915c4aafef2 Author: Brian Friesen Date: Mon Nov 2 15:27:44 2015 -0800 Revert "Box: move static variable "Unit" (returned by TheUnitBox()) to anonymous namespace" This reverts commit 22722204fe5ec61e5a9a7b884eec3e098c8309f6. Src/C_BaseLib/Box.cpp commit 27821bce94cc9e2099f2d06cf3417ccdac9c5867 Author: Brian Friesen Date: Mon Nov 2 15:27:41 2015 -0800 Revert "IndexType: move static variables "Cell" and "Node" to anonymous namespace" This reverts commit b46bb53e161a418d6f14d5b6ab00a6224798a939. Src/C_BaseLib/IndexType.cpp commit b46bb53e161a418d6f14d5b6ab00a6224798a939 Author: Brian Friesen Date: Mon Nov 2 15:04:19 2015 -0800 IndexType: move static variables "Cell" and "Node" to anonymous namespace Src/C_BaseLib/IndexType.cpp commit 22722204fe5ec61e5a9a7b884eec3e098c8309f6 Author: Brian Friesen Date: Mon Nov 2 15:02:47 2015 -0800 Box: move static variable "Unit" (returned by TheUnitBox()) to anonymous namespace Src/C_BaseLib/Box.cpp commit 90526ea2379029f87e03ec15a5410711be296878 Author: Brian Friesen Date: Mon Nov 2 15:01:03 2015 -0800 IntVect: move all remaining static variable declarations to anonymous namespace Src/C_BaseLib/IntVect.cpp commit 77fdfa30c71e47db82c9e951e5fac1ee290beb28 Author: Brian Friesen Date: Mon Nov 2 14:33:51 2015 -0800 IntVect: move static variables returned by TheDimensionVector() to anonymous namespace This renders unnecessary (and partially reverts) the changes made in commit 3f16894 ("IntVect: added braces around cases of TheDimensionVector"). In C++11 the "static" qualifier is no longer necessary because variable declarations in anonymous namespaces are guaranteed to have internal linkage. However, in C++03, without the "static" qualifier they have external linkage. Src/C_BaseLib/IntVect.cpp commit 341767153c9bbaf3fc17510086700ff29fdf956c Author: Weiqun Zhang Date: Mon Nov 2 14:41:21 2015 -0800 MultiFabUtil: fixed bug in my last commit Src/C_BaseLib/MultiFabUtil.cpp commit 49cb0ad04d137c5c69a1f9e2e1ca6e4f535ce3d5 Author: Weiqun Zhang Date: Mon Nov 2 13:50:08 2015 -0800 FMultiFab: use crse mf to construct MFIter Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_1d.f90 Src/C_BaseLib/MultiFabUtil_2d.f90 Src/C_BaseLib/MultiFabUtil_3d.f90 Src/C_BaseLib/MultiFabUtil_F.H commit ff9b0150d5f81b4103122d93e15a0666c562128c Author: Weiqun Zhang Date: Mon Nov 2 11:27:26 2015 -0800 MultiFabUtil: thread safety Src/C_BaseLib/MultiFabUtil.cpp commit 405234dc1aa3a74c5a327437d53dd3da6d04fff6 Merge: 42813c734 d28433c25 Author: Ann Almgren Date: Mon Nov 2 11:25:43 2015 -0800 Merge branch 'development' into new_particle commit d52abac80e5e1eb8ee8238a444a3ea982796a382 Merge: 8ccf41e12 d28433c25 Author: Michael Zingale Date: Mon Nov 2 14:25:35 2015 -0500 Merge branch 'development' into plotfile_ghost commit 8ccf41e12c309cca100c7b668c104c89267ff8bd Merge: e36f0df5f 4a062adc3 Author: Michael Zingale Date: Mon Nov 2 14:25:05 2015 -0500 Merge branch 'development' into plotfile_ghost commit e36f0df5fb7ede7443691aa9aa459fa28cb0789c Author: Ann Almgren Date: Mon Nov 2 11:10:43 2015 -0800 Revert to writing the plotfiles with ghost cells -- the fcompare routine in Tools/PostProcessing/F_src is now able to handle plotfiles with ghost cells. Tutorials/MultiGrid_C/writePlotFile.cpp commit d28433c25f0ec2c5eab73debb44050610cc0c960 Author: Weiqun Zhang Date: Mon Nov 2 09:56:05 2015 -0800 MultiFabUtil: Removed bl_constants_module because it is in F_BaseLib, not C_BaseLib. Some codes may not include F_BaseLib. Src/C_BaseLib/MultiFabUtil_1d.f90 Src/C_BaseLib/MultiFabUtil_2d.f90 Src/C_BaseLib/MultiFabUtil_3d.f90 commit d93465e6e0324f52ed87a3c4ec052685f241e2db Author: Weiqun Zhang Date: Sun Nov 1 19:36:27 2015 -0800 fixed a bug in regrid.f90 thanks to Ashish Pathak of Umass Dartmouth Src/F_BaseLib/regrid.f90 Src/Python/F90/src/regrid.f90 commit 4a062adc31d335ba104beb7c01a465faf46dfc7e Author: Weiqun Zhang Date: Sun Nov 1 19:43:14 2015 -0800 Make: flags for using fsanitizer with gcc Tools/C_mk/Make.defs commit 3bd23d536cae2c99b599a570658ee17e037cb870 Author: Weiqun Zhang Date: Sun Nov 1 19:41:36 2015 -0800 C_CellMG: return immediately if the initial residual is already zero. this could happen for species diffusion when certain species is initially zero everywhere. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 603f0d835b33d2a0976df772c834b82ffc7c7c1a Author: Weiqun Zhang Date: Sun Nov 1 19:36:27 2015 -0800 fixed a bug in regrid.f90 thanks to Ashish Pathak of Umass Dartmouth Src/F_BaseLib/regrid.f90 Src/Python/F90/src/regrid.f90 commit 1bfebf668afef8c789518695e9f6a1c61d2d24be Author: Michael Zingale Date: Sun Nov 1 17:46:02 2015 -0500 copy the diffDir if we do copy_benchmarks Tools/RegressionTesting/testnew.py commit 8cedc1dc3a2159545fb05f8ae56bb577de566e1e Author: Ann Almgren Date: Sun Nov 1 12:49:08 2015 -0800 Have two separate versions of BoxLib::average_down -- one which uses volume weighting and one which does not. Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_1d.f90 Src/C_BaseLib/MultiFabUtil_2d.f90 Src/C_BaseLib/MultiFabUtil_F.H commit 6021957a58bae89efab7acb679601da0d28f8957 Author: Ann Almgren Date: Sun Nov 1 11:17:47 2015 -0800 Use tileboxes in BoxLib::average_down, and fix an indexing error in MultiFabUtil_*d.f90 Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_1d.f90 Src/C_BaseLib/MultiFabUtil_2d.f90 Src/C_BaseLib/MultiFabUtil_3d.f90 commit 28438156b80e8693397855ce9e29ec270d5fc880 Author: Michael Zingale Date: Sat Oct 31 18:39:09 2015 -0400 lots of compilation fixes Src/C_BaseLib/MultiFabUtil_1d.f90 commit 66da880452afb80f2c34c0d69eaa7e252f7746cc Author: Ann Almgren Date: Fri Oct 30 15:44:21 2015 -0700 Add the average down routines to 1d and 2d. Src/C_BaseLib/MultiFabUtil_1d.f90 Src/C_BaseLib/MultiFabUtil_2d.f90 commit 4934a856c6cd85d5f118f5cd85d39f2271e20830 Author: Weiqun Zhang Date: Fri Oct 30 15:16:15 2015 -0700 MultiFabUtil: fixed function arguments Src/C_BaseLib/MultiFabUtil.cpp commit 3fa7c97ede3676eb554292247e98b8b0a8dbe705 Merge: 72f390608 8425b25fd Author: Ann Almgren Date: Fri Oct 30 15:02:21 2015 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 72f39060861444aab887fc41f36bac03fafa441b Author: Ann Almgren Date: Fri Oct 30 15:01:48 2015 -0700 Put in first pass at generic routine in BoxLib namespace that averages a fine MultiFab onto a coarse MultiFab without having to be owned by an AmrLevel. Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_3d.f90 Src/C_BaseLib/MultiFabUtil_F.H commit 8425b25fdce2a8d4ae79be679a780fd3025deb7d Author: Marc Day Date: Fri Oct 30 13:13:16 2015 -0700 Update system for OSX 10.11.1 Tools/C_mk/Make.Darwin Tools/C_mk/Make.mpi commit c133a60dca215bbc0e7dbde45883942da3e78aad Merge: 147850eb9 520ce78a8 Author: Marc Day Date: Fri Oct 30 13:08:06 2015 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 147850eb97403cec73295015c1a8dac54babd0e1 Author: Marc Day Date: Fri Oct 30 13:04:50 2015 -0700 Remove question make from define of CC and CXX if USE_GNU in Make.defs because make defaults CC=cc before anything else. On Linux machines, CC then gets redefined explicitly. On Darwin it does not, and the USE_GNU bit fails to set CC and CXX as it should. Tools/C_mk/Make.defs commit 520ce78a872fe1fc072669a6ab774f39df90eaed Author: Weiqun Zhang Date: Fri Oct 30 12:50:51 2015 -0700 FMultiGrid: added mac projection Src/C_BoundaryLib/MacBndry.H Src/C_BoundaryLib/MacBndry.cpp Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp commit 42813c734cede4c9ab8a96225615346c2d1e3efa Merge: 114c6318c 99fa8b527 Author: Ann Almgren Date: Fri Oct 30 10:19:11 2015 -0700 Merge branch 'development' into new_particle commit 114c6318cc8df9b8c1fdc11f36f75cc4dc105edf Author: Ann Almgren Date: Fri Oct 30 10:18:28 2015 -0700 Latest versions ... still not soup yet. Tutorials/PIC_C/main.cpp Tutorials/PIC_C/solve_for_accel.cpp commit b28ac19101f0b760887502f09b3104cfc160f547 Author: Ann Almgren Date: Thu Oct 29 17:26:14 2015 -0700 This verison of Particles.H actually compiles after the latest change. Src/C_BaseLib/Particles.H commit 965a43dce9ebe4b3a4fb6a80ed12cfef24056ff8 Author: Ann Almgren Date: Thu Oct 29 17:24:03 2015 -0700 Modify ParticleContainer::InitRandom so that it can take an optional RealBox argument which allows you to constrain the particles to lie within a rectangular region. Src/C_BaseLib/Particles.H commit 7b04c5c3eb536b54a4bcfa9e748e2065e18504dd Merge: 0509a29ff bbe84d091 Author: Ann Almgren Date: Thu Oct 29 16:52:29 2015 -0700 Merge branch 'new_particle' of ssh://github.com/BoxLib-Codes/BoxLib into new_particle commit 99fa8b5277f77edfa4313488a8f7f98280ede50e Merge: 45f00af07 9fb393e0a Author: Changho Kim Date: Thu Oct 29 13:24:32 2015 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 45f00af07f5f88e35d65d98f9be602049ed28b64 Author: Changho Kim Date: Thu Oct 29 13:14:50 2015 -0700 new utility added !! fdumpdata2d generates plain-text-formatted data files from plotfiles. !! !! usage: fdumpdata2d --pf (pfs) [--var (vars)] [--lev (levs)] [--separate] !! where (pfs) = list of plotfiles, !! (vars) = list of variables, !! (levs) = list of levels, !! --var, --lev, --seprate are optional. Tools/Postprocessing/F_Src/GNUmakefile Tools/Postprocessing/F_Src/fdumpdata2d.f90 commit 9fb393e0ae6217851fef104793685b166fdbb101 Author: Michael Zingale Date: Thu Oct 29 16:12:08 2015 -0400 missing contiue Tools/RegressionTesting/testnew.py commit 12e81f889115769169a56997668d87506eadf930 Merge: 26b18fc7c c5231a2cc Author: Michael Zingale Date: Thu Oct 29 15:59:15 2015 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 26b18fc7c559860e3d4afd949b7bdeb6e459b736 Author: Michael Zingale Date: Thu Oct 29 15:59:07 2015 -0400 fix the output of the diff Tools/RegressionTesting/testnew.py commit bbe84d09135f7a724b218ff553848cd8714bca26 Author: Weiqun Zhang Date: Thu Oct 29 12:58:17 2015 -0700 PIC tutorial: use FMultiGrid Tutorials/PIC_C/solve_with_f90.cpp commit 1094e40892a7b36d9fd0684ad67435406503b157 Merge: af036f387 c5231a2cc Author: Weiqun Zhang Date: Thu Oct 29 12:57:25 2015 -0700 Merge branch 'development' into new_particle commit c5231a2cc8f391246508419fbccd561f877ec8d3 Author: Weiqun Zhang Date: Thu Oct 29 12:57:05 2015 -0700 FMultiGrid: minor tweak Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp commit af036f387a5262ff7bddad89c36374843faffed8 Merge: 3ccf73145 039bb0a6a Author: Weiqun Zhang Date: Thu Oct 29 10:48:32 2015 -0700 Merge branch 'development' into new_particle Conflicts: Tutorials/MultiGrid_C/main.cpp commit e798d71486615f6f4bc4a78731304c8222b87d41 Author: Michael Zingale Date: Wed Oct 28 20:06:39 2015 -0400 replace lbound() and ubound() with lo and hi, since these are safer in the presence of ghost cells Tools/Postprocessing/F_Src/CASTRO_radiation/fgaussianpulse.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/flgt_frnt1d.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradshock.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradsphere.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/feint.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fwdconvect.f90 commit 304b007051262d19ef87155dfd1146e0efe3a87b Merge: edcdac7ea b3e2fa6fa Author: Michael Zingale Date: Wed Oct 28 19:23:07 2015 -0400 Merge branch 'development' into plotfile_ghost commit edcdac7eadc5c9562dc8e2c9304d9e56121ad09b Author: Michael Zingale Date: Wed Oct 28 19:00:36 2015 -0400 get ghost cell support in here -- the size now refers to the size on disk, including ghost cells. There should be no difference at all for plotfiles without ghost cells Src/F_BaseLib/plotfile.f90 commit 3910470c035cd7a37b8fd4a18fa8e2af42b9d009 Author: Michael Zingale Date: Wed Oct 28 19:00:13 2015 -0400 this works with ghost cells now Tools/Postprocessing/F_Src/fcompare.f90 commit 039bb0a6aaa112f9d5fcee44ad41115f3833c433 Merge: 4e433a909 b3e2fa6fa Author: Weiqun Zhang Date: Wed Oct 28 14:19:23 2015 -0700 Merge branch 'development' into ctof commit 4e433a909738736b5fc3b1f9948d630d3803802e Author: Weiqun Zhang Date: Wed Oct 28 14:17:54 2015 -0700 capability of sharing a multifab from C++ to Fortran without copying the data Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/MultiFab_C_F.H Src/F_BaseLib/MultiFab_C_F.cpp Src/F_BaseLib/fab.f90 Src/F_BaseLib/multifab_c.f90 Tutorials/MultiFab_C_F/GNUmakefile Tutorials/MultiFab_C_F/Make.package Tutorials/MultiFab_C_F/ff.f90 Tutorials/MultiFab_C_F/main.cpp commit 83a25bb7f8b2261488207452e2c5ec28ebb9f795 Author: Weiqun Zhang Date: Wed Oct 28 13:07:55 2015 -0700 moved the stuff that starts mpi for fortran form mgt_solver to c++ boxlib init function Src/C_BaseLib/BoxLib.cpp Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/parallel.f90 Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit b3e2fa6fa569efe9eebb803a7c6ffd754068f1ed Author: Brian Friesen Date: Tue Oct 27 10:51:08 2015 -0700 Tutorials: add "beta" to argument list of solve_with_HPGMG() in MultiGrid_C HPGMG internally calculates beta at cell faces from the cell-centered beta MultiFab because BoxLib and HPGMG store cell face data in very different ways. It's much easier to do the averaging by hand than it is to translate array indices. However, in order to be consistent with the sign conventions of the other solvers, we want to calculate grad(Phi) in the same way that they do. So we use an AbecLaplacian to calculate the gradients. But AbecLaplacian needs the beta at cell faces, not cell centers. So we add beta to the arguments list. This also fixes a compile-time error if running this tutorial with HPGMG: the variable "abec_operator" was never declared. Tutorials/MultiGrid_C/main.cpp commit e65269c478c2724d5e46d766095d91661acf19fd Author: Brian Friesen Date: Mon Oct 26 23:00:43 2015 +0000 C_BaseLib: remove "__LP64__" preprocessor macro from list of macros describing long pointers This macro does not uniquely describe long pointers. It leads to compile-time errors on Mira (BG/Q) because many variables in FPC.cpp are duplicately declared, since both "__ppc__" and "__LP64__" are defined. This removal should (hopefully) not affect any architectures we run on, since at least one of the other macros should be defined. Src/C_BaseLib/FPC.cpp commit de7807387a77eaddb87cff06bf963aca774ec293 Author: Brian Friesen Date: Tue Oct 20 23:21:34 2015 +0000 F_MG: include "get_dim()" explicitly from multifab_module in ml_prolongation.f90 The XL Fortran compiler on Mira complains about being unable to find this function. Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 322f57749668b6cf84dba2003e78a45872845548 Author: Brian Friesen Date: Tue Oct 20 23:20:19 2015 +0000 C_BaseLib: add FORT_FASTSAXPY definition to SPECIALIZE_F.H for BL_FORT_USE_LOWERCASE Found this bug when trying to compile the MultiGrid_C tutorial with the XL compilers on Mira. Src/C_BaseLib/SPECIALIZE_F.H commit 3f16894617e0b3e011cc38d922ecebfaeea24f5c Author: Brian Friesen Date: Thu Oct 15 22:07:14 2015 +0000 IntVect: added braces around cases of TheDimensionVector Cases share scope, so without braces the variables declared in the different cases percolate down through the entire switch statement. This can lead to uninitialized variables if a particular case is skipped. Adding braces around each case creates a unique scope for each of these variables, which protects against this possibility. The IBM XL compiler caught this error. Src/C_BaseLib/IntVect.cpp commit 6730f829ef19b9d8182a798529da6d7e835b8f65 Author: Brian Friesen Date: Thu Oct 15 21:56:55 2015 +0000 C_mk, F_mk: add support for IBM XL compilers on Mira, the BlueGene/Q at ALCF Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/bgq.mak commit 998884b5727fe57abb0318522c34f0013fe50c64 Author: Weiqun Zhang Date: Tue Oct 27 10:14:34 2015 -0700 AMR_Advection_C Tutorial: consolidate diffusion code Tutorials/AMR_Advection_C/Source/ADR_diffusion.cpp Tutorials/AMR_Advection_C/Source/Diffusion.H Tutorials/AMR_Advection_C/Source/Diffusion.cpp commit a75c719d1eb17d3ba9254c543dda84711023840e Author: Weiqun Zhang Date: Tue Oct 27 10:14:01 2015 -0700 FMultiGRid: added functions for diffusion operator Src/LinearSolvers/C_to_F_MG/FMultiGrid.H commit 0509a29ffbf7dd59ee578657871e24cabb845a1d Merge: ced6c50c9 2b14f975f Author: Ann Almgren Date: Tue Oct 27 10:09:40 2015 -0700 Merge branch 'development' into new_particle commit 2b14f975f1b6fc4a1941183cd92a0e3dcaab093f Merge: 26ec4a967 8ccd90faa Author: vince 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 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 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 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 Date: Mon Oct 26 17:01:06 2015 -0700 dont use the word signal. Src/C_BaseLib/ParallelDescriptor.cpp commit 3822a65a1df6f8ca3b105f82479fad58285149fd Author: Weiqun Zhang Date: Mon Oct 26 16:25:18 2015 -0700 update Linear Solver Comparison Test to use FMultiGrid Tests/LinearSolvers/ComparisonTest/COEF_1D.F Tests/LinearSolvers/ComparisonTest/COEF_3D.F Tests/LinearSolvers/ComparisonTest/COEF_F.H Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp commit 28ded501cb40d0c11210180ed223865e688857fe Author: vince Date: Mon Oct 26 16:00:10 2015 -0700 make safer data broadcasts. Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit f73c2dd7cadec0447333f8d89fb5fb886e5c174c Author: Weiqun Zhang Date: Mon Oct 26 15:32:31 2015 -0700 minor cleanup Src/C_BaseLib/MultiFabUtil.cpp commit b9c2a185607f2d4f52c43a2b22ecf1ebdaea0138 Author: Weiqun Zhang Date: Mon Oct 26 14:09:59 2015 -0700 MultiGrid Tutorial: use FMultiGrid instead of MGT_Solver directly Tutorials/MultiGrid_C/main.cpp commit fe9c19967a416e85b82c78a3e8f9958a5e4ceb89 Author: Weiqun Zhang Date: Mon Oct 26 14:01:02 2015 -0700 FMultiGrid: make the interface consistent with C++ ABecLaplacian class Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp commit f8aea0c47d757c3acfa5ded8b44c6812cdb7524b Author: Weiqun Zhang Date: Mon Oct 26 13:50:59 2015 -0700 MultiGrid Tutorial: use the new BoxLib::average_face_to_cell_center function and use PArray for bcoeffs Tutorials/MultiGrid_C/COEF_2D.F Tutorials/MultiGrid_C/COEF_3D.F Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp Tutorials/MultiGrid_C/main.cpp commit 4abd17a413a984b9a1c600d5a26a57baaf3b2982 Author: Weiqun Zhang Date: Mon Oct 26 13:45:09 2015 -0700 C_CellMG: added a new function that takes PArray as b coeffs Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp commit 1ad11e7486af9f6f5aec8c7d60bc6b339875f663 Author: Weiqun Zhang Date: Mon Oct 26 13:43:52 2015 -0700 added a new function that averages from cell-centered to face MultiFabs Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_1d.f90 Src/C_BaseLib/MultiFabUtil_2d.f90 Src/C_BaseLib/MultiFabUtil_3d.f90 Src/C_BaseLib/MultiFabUtil_F.H commit e86986663d575dcc4221c8fdf537764840ef2828 Author: Weiqun Zhang 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 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 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 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 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 Date: Sun Oct 25 16:06:22 2015 -0700 FMultiGrid: bug fix Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp commit 26bc569df18ce3c948516bd937851149c9736bab Merge: d98a940e2 3ee6d99ef Author: Weiqun Zhang Date: Sat Oct 24 22:12:38 2015 -0700 Merge branch 'development' into mlcc commit d98a940e2c3075eca9ac367d48425c5e9c9d6a79 Merge: 1179ab8f6 c37a43d93 Author: Weiqun Zhang Date: Sat Oct 24 22:11:52 2015 -0700 Merge branch 'development' into mlcc commit 1179ab8f6117043315327c27017ad2732097e5de Author: Weiqun Zhang Date: Sat Oct 24 22:10:41 2015 -0700 minor Src/C_AMRLib/Amr.cpp commit 2c8cee1528b283856f0e7180a4e503cae4f2b8b1 Author: Weiqun Zhang Date: Sat Oct 24 20:42:05 2015 -0700 fixed comments Src/LinearSolvers/C_to_F_MG/FMultiGrid.H commit ff34bb6c78c35e38ef48cb4cd28f3d4bef53346c Author: Weiqun Zhang Date: Sat Oct 24 20:10:46 2015 -0700 FMultiFab: comments and minor tweak Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp commit 4afc30e719e77b61788ca100cfbdf349fbf5d74b Author: Weiqun Zhang Date: Fri Oct 23 17:35:49 2015 -0700 FMultiGrid: refactor Src/LinearSolvers/C_to_F_MG/FMultiGrid.H Src/LinearSolvers/C_to_F_MG/FMultiGrid.cpp commit ced6c50c95572b0fd127802bd19ada90f9d40d46 Merge: 3ccf73145 3ee6d99ef Author: Ann Almgren Date: Fri Oct 23 17:15:53 2015 -0700 Merge branch 'development' into new_particle commit 3ee6d99efe7becb16a58488f0ca44a835b760bf1 Author: Ann Almgren Date: Fri Oct 23 17:14:47 2015 -0700 In Tutorials/MultiGrid_C, I hard-wired the new grad_phi stuff for BL_SPACEDIM = 3. This generalizes it to work for BL_SPACEDIM = 2 or 3. Tutorials/MultiGrid_C/main.cpp commit 3ccf73145aa0c37d21b9230ce94b416904aafb6b Author: Ann Almgren Date: Fri Oct 23 17:14:47 2015 -0700 In Tutorials/MultiGrid_C, I hard-wired the new grad_phi stuff for BL_SPACEDIM = 3. This generalizes it to work for BL_SPACEDIM = 2 or 3. Tutorials/MultiGrid_C/main.cpp commit 092934fcadb1eb0bb5e615acffb37bdea3f55a7a Author: Ann Almgren Date: Fri Oct 23 17:12:17 2015 -0700 Since the C++ MultiGrid solver uses only V-cycles, we want to hard-wire piecewise constant, not piecewise linear interpolation -- the PC interpolation works better for V-cycles while the piecewise linear works better for F-cycles. Src/LinearSolvers/C_CellMG/MG_2D.F Src/LinearSolvers/C_CellMG/MG_3D.F commit 6b4cbeec4496ceb81c8bbd5a863655eaf8eae0d0 Author: Ann Almgren Date: Fri Oct 23 17:12:17 2015 -0700 Since the C++ MultiGrid solver uses only V-cycles, we want to hard-wire piecewise constant, not piecewise linear interpolation -- the PC interpolation works better for V-cycles while the piecewise linear works better for F-cycles. Src/LinearSolvers/C_CellMG/MG_2D.F Src/LinearSolvers/C_CellMG/MG_3D.F commit ec0c394836eae13840018bce3ecb0ddab8382ca7 Author: Michael Zingale Date: Fri Oct 23 16:42:53 2015 -0400 more safely get the box indicies Tools/Postprocessing/F_Src/tutorial/fspeciesmass2d.f90 commit 4979330b0a40e684640f8b9a19864e87bb000749 Author: Michael Zingale Date: Fri Oct 23 16:33:56 2015 -0400 eliminate lbound/ubound Tools/Postprocessing/F_Src/fsnapshot3d.f90 commit 5f44fd5458a40517b3735781ea56800679a75624 Author: Michael Zingale Date: Fri Oct 23 16:28:26 2015 -0400 remove lbound/ubound Tools/Postprocessing/F_Src/fextract.f90 commit c1339209db580cb6a0e5969dfaf167b7bea0e146 Author: Michael Zingale Date: Fri Oct 23 16:21:16 2015 -0400 add get_pbox Src/F_BaseLib/plotfile.f90 commit 9e479ad2a7a446fb413a320a9c661a9e852d624a Author: Ann Almgren Date: Thu Oct 22 22:13:57 2015 -0700 Remove excess print statements from Particles.H Src/C_BaseLib/Particles.H commit a5fff7240c8d622d4f491805cc42ebe145a37536 Merge: 3d2b66545 c37a43d93 Author: Ann Almgren Date: Thu Oct 22 22:13:36 2015 -0700 Merge branch 'development' into new_particle commit 864f35e2a1e008c0a19d6489c9ab4368ad8266f5 Author: Weiqun Zhang Date: Thu Oct 22 21:52:32 2015 -0700 PArray: removed isConstPointer Src/C_BaseLib/PArray.H commit c37a43d937df2fe368f42c5963623f1c48fc8a12 Author: Ann Almgren Date: Thu Oct 22 17:11:53 2015 -0700 After we compute the solution, use the operator to return the face-based fluxes, then average those onto cell centers using BoxLib::average_face_to_cellcenter and write the cell-centered gphi out into a plotfile just like we write out the solution. This allows us to test the gradient routines as well as the solver itself. Tutorials/MultiGrid_C/main.cpp commit 3d2b665451bd2f72daa2f5369d900b3ddeed0ffd Author: Ann Almgren Date: Thu Oct 22 17:11:53 2015 -0700 After we compute the solution, use the operator to return the face-based fluxes, then average those onto cell centers using BoxLib::average_face_to_cellcenter and write the cell-centered gphi out into a plotfile just like we write out the solution. This allows us to test the gradient routines as well as the solver itself. Tutorials/MultiGrid_C/main.cpp commit 50e8315c7e83a90c7990da17c0794cf6fc54292d Merge: 915a91c95 a62e608c4 Author: Chris Malone 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Wed Oct 21 17:23:51 2015 -0700 resize to zero at the end. Tutorials/Sidecar_EX1/SidecarResizeTest.cpp commit cafe58c6310dec78287ea45d96388d890ad7487e Author: vince Date: Wed Oct 21 17:21:05 2015 -0700 test with two sizes. Tutorials/Sidecar_EX1/SidecarResizeTest.cpp commit 68fe925d79c2b5e2bf826520bea7bc8a069b884a Author: vince Date: Wed Oct 21 16:39:59 2015 -0700 sidecar resize test. Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Sidecar_EX1/Make.package Tutorials/Sidecar_EX1/SidecarResizeTest.cpp Tutorials/Sidecar_EX1/inputs_sc commit fd6d17379041bfd5c75162c095f3efcf0d31c141 Merge: a9812a493 6d12365c7 Author: Ann Almgren Date: Wed Oct 21 15:00:18 2015 -0700 Merge branch 'development' into new_particle commit 6d12365c7fd86457d0aaee3c6a6c98cc8fe566a2 Merge: 2b0e48f95 57ed9f974 Author: Ann Almgren Date: Wed Oct 21 14:58:39 2015 -0700 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 2b0e48f955964e52d13e7715e042fffa8bf9dec8 Author: Ann Almgren Date: Wed Oct 21 14:57:38 2015 -0700 Write the plotfile with 0 ghost cells, otherwise fcompare will misinterpret the arrays. Tutorials/MultiGrid_C/writePlotFile.cpp commit a9812a49355a59d1629d1e701e3cc79ad2e0a969 Author: Ann Almgren Date: Wed Oct 21 14:57:38 2015 -0700 Write the plotfile with 0 ghost cells, otherwise fcompare will misinterpret the arrays. Tutorials/MultiGrid_C/writePlotFile.cpp commit 915a91c95e360424234a6f4019b13673c0653e16 Merge: 00aae4f64 57ed9f974 Author: Chris Malone 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 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: a3012f487 38a1fff6d Author: Chris Malone Date: Wed Oct 21 16:05:52 2015 -0400 Merge branch 'master' into development commit 11351d0cc0c06b3b3257d2ca46a3d3e59cc0307c Merge: 9400b5497 a3012f487 Author: Ann Almgren Date: Wed Oct 21 13:03:50 2015 -0700 Merge branch 'development' into new_particle commit a3012f48794238e9a0ae19a13788eaa97bfe93fc Author: Ann Almgren Date: Wed Oct 21 12:44:58 2015 -0700 Modify the C++ solver in MultiGrid.{H,cpp} in order to correctly compute and use the initial residual. There was an issue before when a non-zero initial guess was passed in. This is now closer to the decision-making in the F90 solver. Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 38a1fff6df105c5b0161bacf2a4e12495ac34fd1 Author: Chris Malone Date: Wed Oct 21 16:01:34 2015 -0400 add support for my mac Tools/F_mk/GMakeMPI.mak commit 8caf7d247062306b3dee32c1949a2e8b1ff8ba7a Author: Michael Zingale Date: Wed Oct 21 15:55:31 2015 -0400 when we do the first --make_benchmarks, the test on get_last_run() fails, but it isn't needed there (it is only needed for copy_benchmarks). Now we return None in this case. Tools/RegressionTesting/testnew.py commit 9400b54972512f389cb76308e0d7ddd454192d40 Merge: d6f49e3d9 b625fe80b Author: Ann Almgren Date: Wed Oct 21 12:55:10 2015 -0700 Merge branch 'new_particle' of ssh://github.com/BoxLib-Codes/BoxLib into new_particle commit d6f49e3d9af107730153d2277ab38d48cf5ae946 Author: Ann Almgren Date: Wed Oct 21 12:44:58 2015 -0700 Modify the C++ solver in MultiGrid.{H,cpp} in order to correctly compute and use the initial residual. There was an issue before when a non-zero initial guess was passed in. This is now closer to the decision-making in the F90 solver. Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit b625fe80bc7a6e1e0d6dab9b5b6473a06dfd37f7 Author: Weiqun Zhang Date: Wed Oct 21 11:10:10 2015 -0700 use Array instead of PArray in constructing ParGDB Src/C_BaseLib/ParGDB.H Src/C_BaseLib/Particles.H Tutorials/PIC_C/main.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp commit 094380191ec2e48da65f5e268d8385337ae8ca95 Merge: 184411870 c50314788 Author: Ann Almgren Date: Wed Oct 21 10:40:15 2015 -0700 Merge branch 'new_particle' of ssh://github.com/BoxLib-Codes/BoxLib into new_particle commit 184411870398b3491afab6cf90a7cea527c90e87 Author: Ann Almgren Date: Wed Oct 21 10:39:52 2015 -0700 Get rid of all the extra print statements in Particles.cpp Src/C_BaseLib/Particles.cpp commit 553a31940291f58f283d21bc46287c1efb1d0382 Author: vince Date: Mon Oct 19 11:10:37 2015 -0700 code cleanup. Src/C_BaseLib/ParallelDescriptor.cpp commit 4d9ce1c588841e9c2733522e3193464b6db33b82 Author: vince Date: Fri Oct 16 17:00:33 2015 -0700 moved group and comm initialization to SetNProcsSidecar function. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit ae87803b55ce54c70433b37d24538235cad2fa57 Author: vince Date: Fri Oct 16 15:28:52 2015 -0700 fixed comment. Src/C_BaseLib/Utility.H commit a87888a48a2fb064663542058203f145a60fe26f Author: vince Date: Tue Oct 13 13:51:25 2015 -0700 comments. Src/C_BaseLib/ParallelDescriptor.cpp commit 2b5532dbbd8a2421772af318b738fcb1e0699a84 Author: vince Date: Tue Oct 13 13:47:55 2015 -0700 comments. Src/C_BaseLib/ParallelDescriptor.H commit cf5c3586cf3ec3b189f0e328b62c75dc74448f4b Author: vince Date: Tue Oct 13 13:35:37 2015 -0700 comments. Src/C_BaseLib/ParallelDescriptor.cpp commit c50314788b13c9caef25670b675c003b376acc59 Merge: ae85828cf 7af747b0d Author: Weiqun Zhang Date: Wed Oct 21 10:27:42 2015 -0700 Merge branch 'development' into new_particle Conflicts: Src/C_BaseLib/Make.package commit 7af747b0d67791ba435623db8165c11ea391af65 Author: Weiqun Zhang Date: Wed Oct 21 10:25:07 2015 -0700 BoxArray: added a new define function Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit ae85828cf579692c6114b910f40a5cfe990ae9ab Author: Weiqun Zhang Date: Tue Oct 20 16:53:02 2015 -0700 only the I/O processor needs to do I/O Tutorials/PIC_C/solve_for_accel.cpp commit 9ffb2bf3e9a7c3403ce26d4d194625872508708f Author: Weiqun Zhang Date: Tue Oct 20 16:41:52 2015 -0700 bug fixes in PIC tutorial Tutorials/PIC_C/main.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp commit f2562316a806507d2759c5f595ed8b01f3551f7c Author: Weiqun Zhang Date: Tue Oct 20 16:40:13 2015 -0700 Particles: tweak constructors Src/C_BaseLib/PArray.H Src/C_BaseLib/ParGDB.H Src/C_BaseLib/Particles.H commit c7c7e27b23bd3bd67a637fb2d439921964c7a6a8 Author: Weiqun Zhang Date: Tue Oct 20 16:38:59 2015 -0700 BACKTRACE: don't have to sleep if there is only on processor Src/C_BaseLib/BLBackTrace.cpp commit 081b9cae3d63e73519fadb4b84aea0cce8c3870e Author: Ann Almgren Date: Tue Oct 20 13:01:48 2015 -0700 This is my latest version of the PIC_C tutorial code and the changes in the Particle stuff needed to accomodate a multilevel box array coming into ParGDB. Src/C_BaseLib/ParGDB.H Src/C_BaseLib/Particles.H Src/C_BaseLib/Particles.cpp Tutorials/PIC_C/main.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/work.f90 commit 9ab6db5a0a41712a5373965c834fd9ab3f1721b1 Author: Changho Kim Date: Tue Oct 20 09:49:55 2015 -0700 new utility to integrate a variable Tools/Postprocessing/F_Src/GNUmakefile Tools/Postprocessing/F_Src/fintgvar2d.f90 commit ce0800878614b2650fcdd8657e42d05701096f4b Author: Adam Jacobs Date: Tue Oct 20 11:02:35 2015 -0400 At the moment on OLCF machines, pgclibs does not work, so use libstdc++ Tools/F_mk/comps/Linux_pgi.mak commit 1d510d5c6894c0b2aa89485255ea85db4c875e3f Merge: e3a7e50bd 844e49f69 Author: Chris Malone 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 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 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 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 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: a25f53e2d 4a94cce60 Author: Weiqun Zhang Date: Thu Oct 15 11:15:03 2015 -0700 Merge branch 'development' into pgas commit 4a94cce60d09031e3108a78287e724ef5f101fc9 Author: Weiqun Zhang 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 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 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 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 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: e3843053c 7d4dadf0f Author: Ann Almgren Date: Tue Oct 13 13:04:43 2015 -0700 Merge branch 'new_particle' of https://github.com/BoxLib-Codes/BoxLib into new_particle commit 7d4dadf0f7db36f445e2888daae1d2f405439eec Author: Ann Almgren Date: Tue Oct 13 12:57:37 2015 -0700 Updated files for Tutorials/PIC_C. Tutorials/PIC_C/Make.package Tutorials/PIC_C/main.cpp Tutorials/PIC_C/solve_for_accel.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/solve_with_hpgmg.cpp commit e3843053cc30b4205ee11ea303029b822726d13c Author: Ann Almgren Date: Tue Oct 13 11:37:22 2015 -0700 Starting to add the option for HPGMG to Tutorials/PIC_C. Tutorials/PIC_C/GNUmakefile Tutorials/PIC_C/Make.package Tutorials/PIC_C/main.cpp Tutorials/PIC_C/solve_with_f90.cpp Tutorials/PIC_C/solve_with_hpgmg.cpp commit af19914ba6545779f5b429cbb7e67920801e26db Merge: 8b8e213ab 7b48024bc Author: vince Date: Tue Oct 13 10:41:37 2015 -0700 Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib commit a3357bb5912b85cd69cd7d53ce0bb8ad0ac3ecd7 Author: Ann Almgren Date: Tue Oct 13 10:33:15 2015 -0700 More changes to make the Particle stuff not require anything in C_AMRLib. * move BCRec* and BC_TYPES.H from C_AMRLib to C_BaseLib * add a "sum" function to MultiFab that sums up the values over all the valid region (analogous to the FArrayBox sum) * update the PIC_C Tutorial code so it actually computes the acceleration of each particle Src/C_AMRLib/Make.package Src/C_BaseLib/BCRec.H Src/C_BaseLib/BCRec.cpp Src/C_BaseLib/BC_TYPES.H Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Tutorials/PIC_C/GNUmakefile Tutorials/PIC_C/main.cpp commit 211f414c6ae4859f3d6d8a6ab3e4db7baa4359b4 Merge: 15a51cbd5 1408ae178 Author: Weiqun Zhang Date: Sun Oct 11 22:16:40 2015 -0700 Merge branch 'new_particle' of github.com:BoxLib-Codes/BoxLib into new_particle Conflicts: Tutorials/PIC_C/GNUmakefile Tutorials/PIC_C/Make.package Tutorials/PIC_C/main.cpp commit 15a51cbd5031e427106d2274d1648ca720851778 Merge: 9dd6cbd19 c49ce1084 Author: Weiqun Zhang Date: Sun Oct 11 22:08:58 2015 -0700 Merge branch 'PIC_Tutorial' into new_particle commit 1408ae17889d47c51fe3b78011c8b90b8fabf2ea Author: Ann Almgren Date: Sun Oct 11 22:06:02 2015 -0700 Add AssignDensity Tutorials/PIC_C/main.cpp commit 9dd6cbd1985d0693843ee8aaef048232e2ad5f4d Merge: 84aeeaeac 7b48024bc Author: Weiqun Zhang Date: Sun Oct 11 22:05:14 2015 -0700 Merge branch 'development' into new_particle Conflicts: Src/C_BaseLib/Particles.H Src/C_BaseLib/Particles.cpp commit fd82b7d4eed7da4aeb32aa5af1d6e8fc452ec97f Author: Ann Almgren Date: Sun Oct 11 22:01:20 2015 -0700 Make this work without creating an AMR object. Tutorials/PIC_C/GNUmakefile Tutorials/PIC_C/Make.package Tutorials/PIC_C/main.cpp commit 6842f7320e360c94687555e562ef772f7ea89dc5 Author: Ann Almgren Date: Sun Oct 11 22:00:48 2015 -0700 Fix for new gdb stuff. Src/C_BaseLib/Particles.H commit 84aeeaeac4b66b37bb78b01acacb44bf46db9e15 Author: Weiqun Zhang Date: Sun Oct 11 20:59:55 2015 -0700 Particle: forgot a new file Src/C_BaseLib/ParGDB.H commit 838e2e7168795cabb58619cb8d52fa5409666ee1 Author: Weiqun Zhang Date: Sun Oct 11 20:55:37 2015 -0700 moved Amr independent particle files to C_BaseLib Src/C_AMRLib/Make.package Src/C_AMRLib/ParGDB.H Src/C_BaseLib/Make.package Src/C_BaseLib/Particles.H Src/C_BaseLib/Particles.cpp Src/C_BaseLib/Particles_1D.F Src/C_BaseLib/Particles_2D.F Src/C_BaseLib/Particles_3D.F Src/C_BaseLib/Particles_F.H commit bb0f68db1759fde590b031833f722265946314a7 Author: Weiqun Zhang Date: Sun Oct 11 20:49:38 2015 -0700 Particle: created AmrParticleContainer and some other minor tweak Src/C_AMRLib/AmrParticles.H Src/C_AMRLib/Make.package Src/C_AMRLib/ParGDB.H Src/C_AMRLib/Particles.H commit 693e835377985473f3dda99ed04fc63d764c5b55 Author: Weiqun Zhang Date: Sun Oct 11 20:02:09 2015 -0700 Particle: forgot to wrap particle stuff inside ifdef USE_PARTICLES Src/C_AMRLib/Amr.cpp commit afb0ad4bcface9c61fbfc07fd021cfdbd08884a8 Author: Weiqun Zhang 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 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 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 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 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 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: d2c99ac7f 761bce39b Author: Ann Almgren Date: Sun Oct 11 15:44:46 2015 -0700 Merge branch 'development' into PIC_Tutorial commit 761bce39b21cb0d59619f3186c9fb768f118ca9d Merge: d0e3b804c 92bf9c96c Author: Ann Almgren 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 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 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 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 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: 6d02a726c 4563183b5 Author: Ann Almgren 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 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 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 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 Date: Fri Oct 9 16:18:16 2015 -0700 BACKTRACE: update Readme Docs/Readme.backtrace commit d56377f5c6631b06723cdb0e7ad0c008b5e958a4 Author: Weiqun Zhang Date: Fri Oct 9 15:48:02 2015 -0700 BACKTRACE: output to files instead stdout and stderr Src/C_BaseLib/BLBackTrace.cpp commit dba469396b672a1b141a4d0a6c40a22af9f98e9e Author: Weiqun Zhang Date: Fri Oct 9 14:08:31 2015 -0700 some minor cleanups in F_MG Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 commit 479282f0f3b6f1ae6d41aeec3af8839e72a7d9c9 Author: Weiqun Zhang Date: Fri Oct 9 14:07:21 2015 -0700 BACKTRACE: capture user interrupt too Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/BoxLib.cpp commit 6013d36fb609b6c6a07d96a6acb28909cca81c88 Author: Weiqun Zhang Date: Fri Oct 9 14:06:00 2015 -0700 MGT_Solver: avoid omp critical if we can Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit e27bd8e62a616a324818dc644dddd3eb252153f5 Author: Weiqun Zhang Date: Fri Oct 9 14:02:41 2015 -0700 add verbose to MGT_Solver Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit f88ef33a8ce83eaa0b6e9cdf29557540a011db69 Author: Weiqun Zhang Date: Fri Oct 9 13:44:10 2015 -0700 fixed a bug Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit d2c99ac7febe76774822a099964059c224ecbe25 Author: Ann Almgren Date: Fri Oct 9 09:25:05 2015 -0700 Latest... Tutorials/PIC_C/GNUmakefile Tutorials/PIC_C/Make.package Tutorials/PIC_C/main.cpp commit 1ad6e0879542b92fa4c6b7de7342a2edbefb1629 Merge: 81079ea9d f277d5849 Author: Michael Zingale Date: Fri Oct 9 11:32:59 2015 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 81079ea9df828f503441fb2a92feb1740a583e8e Author: Michael Zingale Date: Fri Oct 9 11:31:21 2015 -0400 this now works with python3 Tools/F_scripts/makebuildinfo.py commit f277d58494dbb95d871673c3946a07ae93adf0b5 Author: Michael Zingale Date: Thu Oct 8 22:33:49 2015 -0400 more python3 fixes (__cmp__ is replaced by __lt__ for comparing) Tools/RegressionTesting/testnew.py commit 38a6da182fbd2c25a431b3f9cb041f4dd8966f4b Merge: 29d3ffedb c94bcffb6 Author: Michael Zingale Date: Thu Oct 8 22:22:29 2015 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 29d3ffedb4c9bf126f837809d92b4b8b21e34c7f Author: Michael Zingale Date: Thu Oct 8 22:22:01 2015 -0400 .keys() is an iterator in python3, so convert it to a list Tools/RegressionTesting/testnew.py commit c94bcffb66fabf320af93808deb85c31c9333f21 Author: Michael Zingale Date: Thu Oct 8 22:07:54 2015 -0400 start of a port to python 3 -- this handles the prints now. We also have a new Log() object to make it easier to capture and format the output. Finally, fix a bug in the copy_benchmarks option when we are dealing with problems that define specific benchmark files instead of the last plotfile Tools/RegressionTesting/testnew.py commit 2f4584817b89173278321fbca00e1087ca75f8ce Author: vince Date: Thu Oct 8 13:45:39 2015 -0700 fix for 1d amrvis. Src/Extern/amrdata/AmrData.cpp commit 2835cc433b812c263fb4dfb6d96b71223189de48 Merge: 53fc7e7cb ce9c0e66c Author: Michael Zingale Date: Thu Oct 8 12:25:05 2015 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 53fc7e7cb0494bcb997c1331277ed3813ec00601 Author: Michael Zingale Date: Thu Oct 8 12:22:48 2015 -0400 start of restructing the log into a class so we can control its output Tools/RegressionTesting/testnew.py commit ce9c0e66c94fdbc5312d2710ec5f563af1c5b52b Merge: 96078bd75 1ef2d568a Author: vince 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 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 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: 76f504ef7 f54d01f55 Author: Weiqun Zhang Date: Tue Oct 6 14:51:08 2015 -0700 Merge branch 'development' into pgas commit 96078bd75b77361deaae57e85c72cb1fdb35dc45 Author: vince Date: Mon Oct 5 13:33:16 2015 -0700 define constant for 1d. Src/Extern/amrdata/AmrvisConstants.H commit f54d01f55ede0f5cfd566899a30ed15fa8e50441 Author: Michael Zingale Date: Mon Oct 5 12:01:32 2015 -0400 we were appending to the changelog, not writing a new one. This caused it to get big, and not be very useful. Now run() takes an outfile_mode Tools/RegressionTesting/testnew.py commit 9a8ca200a4ee5d4187ccedd929fa4ef9f0d2df86 Merge: bca88084f 80e1f612f Author: Weiqun Zhang Date: Mon Oct 5 08:58:58 2015 -0700 Merge branch 'poisson' into development commit bca88084f5e0285b4b1b22d108723da217399f43 Author: Weiqun Zhang Date: Sat Oct 3 11:45:33 2015 -0700 make BoxArray::boxList possible for return value optimization (RVO) Src/C_BaseLib/BoxArray.cpp commit 25c945158e12e37ab6ff93ee5a163237f6893c61 Author: Weiqun Zhang Date: Sat Oct 3 11:26:48 2015 -0700 removed a number of const's so that the compiler can do 'copy elision' Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/Orientation.H commit d1a6539fc485436cd4d3c10c5544d05f6ae83c2d Author: vince Date: Fri Oct 2 16:50:37 2015 -0700 quiet compiler warnings. Src/Extern/amrdata/DataServices.cpp commit 2d390ce4094770bc297d99bf52c05dd174ca8b13 Author: vince Date: Fri Oct 2 16:48:14 2015 -0700 only print for special debug. Src/C_BaseLib/FabArray.H commit c50577d1a8ea2c5a97c5cf0a248889867754a96e Author: vince Date: Fri Oct 2 16:47:39 2015 -0700 quiet compiler warnings. Src/Extern/amrdata/DataServices.cpp commit 80e1f612f078c1a9d51bf7592ec6436ef8933369 Author: Weiqun Zhang Date: Fri Oct 2 15:34:47 2015 -0700 bottom solver: use the simple stencil for interior boxes in the case of constant coefficients Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/stencil_util.f90 commit b08bef8f7c4405b39ec94a522bcf72bba01767bf Author: Weiqun Zhang Date: Thu Oct 1 20:30:34 2015 -0700 F_MG: fixed a new bug in my last commit optimizing box intersection Src/LinearSolvers/F_MG/cc_stencil.f90 commit 4d365d3bc1b0032b73b3bdaaacb7229d9532eb42 Author: Weiqun Zhang Date: Thu Oct 1 18:19:47 2015 -0700 optimization in stencil_set_bc Src/LinearSolvers/F_MG/cc_stencil.f90 commit 7a53e757bc3d65da260c360234c766bb11195f86 Author: Weiqun Zhang Date: Thu Oct 1 18:08:15 2015 -0700 fixed bug in stencil_norm and stencil_set_bc in periodic case Src/LinearSolvers/F_MG/cc_stencil.f90 commit 160e24dbb0e67e57b9afa196f6a298729361131e Author: vince Date: Wed Sep 30 15:12:38 2015 -0700 cxx11 setting. Tutorials/MultiFabTests_C/GNUmakefile commit 96e0c60866ba895f4b92330d70e8cb8909151eb3 Author: vince Date: Wed Sep 30 15:10:41 2015 -0700 added profiling to tFB. Tests/C_BaseLib/tFB.cpp commit 80b5c7c20e64cb4f937e9f7d841efe32a2ccc5e5 Author: vince Date: Wed Sep 30 15:09:55 2015 -0700 cxx11 setting. Tests/C_BaseLib/GNUmakefile commit 6c8ab1d6f3765c60361f74c7c66f9711acbfcc94 Author: vince Date: Wed Sep 30 15:08:17 2015 -0700 more tests for the profiler. Tests/C_BaseLib/tProfiler.cpp commit 89de500025f2ee39d8cb0cf6f2885a2f5b9abf8c Author: vince Date: Wed Sep 30 14:57:01 2015 -0700 set n files for profiler, add comm names if not already called. Src/C_BaseLib/BLProfiler.H Src/C_BaseLib/BLProfiler.cpp commit 7e5a62f9f253d8943c219a9ac23e67b67cfc8b1f Author: Michael Zingale Date: Wed Sep 30 08:41:51 2015 -0400 fix NDEBUG -- it is the opposite of what people expect it should be Tools/RegressionTesting/testnew.py commit 7a447683d24137aeca9c759d233d7ac1bd2abdea Author: Michael Zingale Date: Sun Sep 27 09:58:53 2015 -0400 some more cleaning Tools/RegressionTesting/testnew.py commit 3dcd5a28035c70b64c04b649c06b3278d6f57089 Author: Weiqun Zhang Date: Fri Sep 25 13:27:49 2015 -0700 changed makefile for babbage Tools/C_mk/Make.Linux Tools/F_mk/comps/Linux_intel.mak commit a4c261757a60cf85750bf7389f79818429a31c37 Author: Weiqun Zhang Date: Fri Sep 25 12:39:52 2015 -0700 use relative path for BOXLIB_HOME since these tutorials are inside BOXLIB_HOME already MiniApps/AMR_Adv_Diff_F90/GNUmakefile Tutorials/AMR_Adv_Diff_F/GNUmakefile Tutorials/HeatEquation_EX1_C/GNUmakefile Tutorials/HeatEquation_EX1_F/GNUmakefile Tutorials/HeatEquation_EX2_F/GNUmakefile Tutorials/HeatEquation_EX3_F/GNUmakefile Tutorials/HeatEquation_EX4_F/GNUmakefile Tutorials/HeatEquation_EX5_F/GNUmakefile Tutorials/MultiGrid_F/GNUmakefile Tutorials/Tiling_Heat_C/GNUmakefile Tutorials/Tiling_Heat_F/GNUmakefile Tutorials/WaveEquation_C/GNUmakefile Tutorials/WaveEquation_F/GNUmakefile commit 26d92a2afb7e7e360631490689e19ab57d90c827 Author: Michael Zingale Date: Fri Sep 25 15:34:27 2015 -0400 a little more reorg Tools/RegressionTesting/testnew.py commit 519c16188b622cc35b4dee42e76879297ef0bcb0 Author: Weiqun Zhang Date: Fri Sep 25 12:31:31 2015 -0700 F_MG: fixed name conflicts Src/LinearSolvers/F_MG/cc_stencil.f90 commit 76f504ef7a5d21e04368ca4651844738027bd970 Author: Weiqun Zhang Date: Fri Sep 25 11:10:56 2015 -0700 added a new fill boundary test Tests/FillBoundaryComparison/GNUmakefile Tests/FillBoundaryComparison/Make.package Tests/FillBoundaryComparison/ba.max Tests/FillBoundaryComparison/main.cpp commit 5ab90cdee345703008794c88c1a7dd0ad993a5a0 Merge: 635796c46 ea5129b47 Author: Weiqun Zhang 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 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 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 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 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 Date: Thu Sep 24 17:58:53 2015 -0700 More typos in CMakeLists.txt Src/C_BaseLib/CMakeLists.txt commit d29646e510263e407ef3bb9add9508f054bde21c Merge: 40062836e 35167eb1c Author: Marc Day Date: Thu Sep 24 17:01:31 2015 -0700 Merge branch 'development' of https://github.com/BoxLib-Codes/BoxLib into development commit 40062836e9b4136a330ddeb72cfba78000f10a66 Author: Marc Day Date: Thu Sep 24 17:01:25 2015 -0700 Fix typo in CMakeLists.txt and uptick release number Src/C_BaseLib/CMakeLists.txt Tools/CMake/BoxLib_Version.cmake commit 35167eb1c079a24e99cbcdc8b5a8f7c061b07dfe Author: Michael Zingale Date: Thu Sep 24 19:49:31 2015 -0400 remove quotes from the branch name when creating the suite status file Tools/RegressionTesting/testnew.py commit c5d886735e5eb967fa3c4e785cd524199d1fe7fe Merge: 850bd7122 d458491af Author: Michael Zingale Date: Thu Sep 24 16:57:29 2015 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 850bd7122e13305b20072b4158d653fede029114 Author: Michael Zingale Date: Thu Sep 24 16:57:06 2015 -0400 fix the deletion of TEST_RUN if it doesn't already exist Tools/RegressionTesting/testnew.py commit d458491af4ceecb864180c868da591b3addce04d Author: Michael Zingale Date: Thu Sep 24 16:51:01 2015 -0400 clean up the compiling of the various tools -- no longer copy them to the run directory either Tools/RegressionTesting/testnew.py commit 10ae5250b693a25c421c4c7994c33c75915cbac4 Author: Michael Zingale Date: Thu Sep 24 14:53:08 2015 -0400 fix an unclosed file. Add the branch name to the test run status file Tools/RegressionTesting/testnew.py commit 60a93b29b557e83a831b9f1066785d993634c1b2 Author: Michael Zingale Date: Wed Sep 23 21:25:31 2015 -0400 fix the web output directory Tools/RegressionTesting/testnew.py commit 4bbca85d7062a6183c4660c29aaacded32303a2f Author: Michael Zingale Date: Wed Sep 23 20:38:14 2015 -0400 first cut at an easily parsable status for a run Tools/RegressionTesting/testnew.py commit 1727e668628702b632d72169085c3de3cc75287c Author: Michael Zingale Date: Wed Sep 23 15:39:29 2015 -0400 restructure all of the git logic. Now there is a Repo class that has the methods for updates, change log, etc., and knows where the repo is, what the current hash is, etc. This allows us to simply loop over all the repos in the suite.repos dictionary and greatly simplify code. Tools/RegressionTesting/testnew.py commit 42f20c9c0682b8c60a10f203aa542a65d528fa1d Author: Michael Zingale Date: Wed Sep 23 10:42:28 2015 -0400 bold heading in list of git info Tools/RegressionTesting/testnew.py commit 05e985f65348aad6556e9fa0b7ccb61664ca597a Merge: 89e40944d 575f636ac Author: Michael Zingale Date: Tue Sep 22 20:24:51 2015 -0400 Merge branch 'development' of ssh://github.com/BoxLib-Codes/BoxLib into development commit 89e40944d914ba58d5acd864ea4cba0340534961 Author: Michael Zingale Date: Tue Sep 22 20:24:15 2015 -0400 add libstdc++ to get around an import error -- not sure why this is pulling in the C++ boxlib though... Tools/Py_util/GNUmakefile commit 575f636ac4b4e701296e2ca27944f2781113c67f Author: Michael Zingale Date: Tue Sep 22 19:14:02 2015 -0400 updated version of our test suite inputs Tools/RegressionTesting/Maestro-tests.ini commit 9e07cb3d2ef9cd58ca0a637c84501609038e7545 Author: Michael Zingale Date: Tue Sep 22 19:10:45 2015 -0400 default to the development branch Tools/RegressionTesting/testnew.py commit 8b8e213abf3ec1a83649ef59a8b4c125f8f93815 Merge: 3c7d8a7f8 c2c99fc0b Author: vince Date: Tue Sep 22 15:46:15 2015 -0700 Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib commit c2c99fc0bc36035dfa6c60f32dc43c046f325f25 Merge: 70a33610d 40aa273e7 Author: Max Katz Date: Tue Sep 22 11:41:52 2015 -0400 Merge branch 'master' of github.com:BoxLib-Codes/BoxLib commit 70a33610df2e32551034c3628340942be67a98b4 Author: Max Katz Date: Tue Sep 22 11:37:25 2015 -0400 Add a dimension-agnostic version of the error function. Src/C_AMRLib/ErrorList.H Src/C_AMRLib/ErrorList.cpp commit 40aa273e7d9dc2a9099001b2f606bbff68466758 Author: Weiqun Zhang 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 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: bf8fcce72 c0fec89ea Author: Weiqun Zhang Date: Mon Sep 21 12:08:41 2015 -0700 Merge branch 'master' of github.com:BoxLib-Codes/BoxLib commit c0fec89ea01c117cc814de628c6ffc7ce52d733a Author: Michael Zingale Date: Mon Sep 21 14:27:41 2015 -0400 simplify convert_type Tools/RegressionTesting/testnew.py commit bf8fcce72f0ed61b56e52873136db822cdb963c7 Author: Weiqun Zhang Date: Mon Sep 21 11:27:29 2015 -0700 save a multifab build and copy Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 428ecae8bff186c4cf91e06f53dbcd868084e026 Author: Weiqun Zhang Date: Mon Sep 21 11:23:37 2015 -0700 MGT_Solver: rewrote the cell-centered coeffs stuff in a hopefully less confusing way that is also consistent with the approach in nodal solver Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit eae53d801410ba52ed3a62acb027b8ecc6527739 Author: Michael Zingale 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 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 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 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 Date: Sat Sep 19 23:02:07 2015 -0400 store the diff command Tools/RegressionTesting/testnew.py commit 42745e3337516991502b2a83d36703e06ec806d2 Author: Michael Zingale Date: Sat Sep 19 22:32:43 2015 -0400 switch the diff over to run() Tools/RegressionTesting/testnew.py commit 83466c8d48f1b5fc43f41177a69a3fdeab0e1f34 Author: Michael Zingale Date: Sat Sep 19 22:14:54 2015 -0400 switch to using subprocess.Popen() to run the tests instead of os.system(). THis is safer, and allows us to capture the stdout/err and return code. Note: for OMP, we need to pass a dictoionary of environment variables. Tools/RegressionTesting/testnew.py commit d594b43abc040203b52a4726a696249cee705eff Author: Weiqun Zhang Date: Thu Sep 17 17:03:03 2015 -0700 tiling in nodal MGT_Solver Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 3c7d8a7f87431fee557b0e57acef8f7475e24d1e Author: vince Date: Thu Sep 17 15:11:24 2015 -0700 added profiling. Tests/C_BaseLib/tFB.cpp commit da884a3dcca46362c58e826549ae0138d78c989a Author: Weiqun Zhang Date: Thu Sep 17 15:06:39 2015 -0700 added assertion Src/C_BaseLib/PArray.H commit b28d8375eab17dc5e4311251ad56fc89c8404fc1 Author: Weiqun Zhang Date: Thu Sep 17 13:49:44 2015 -0700 fixed assertion Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tutorials/MultiGrid_C/main.cpp commit cc29abc83582eaf1355747248125c5a27587fa1d Merge: 3c890f336 cca942219 Author: vince Date: Thu Sep 17 11:35:47 2015 -0700 Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib commit 3c890f33637d576bd01c2797be013a66b5a5cb22 Author: vince Date: Thu Sep 17 11:31:14 2015 -0700 unique set. Tutorials/MultiFabTests_C/GridMoveTest.cpp commit cca9422197a9ebb28eb3056e169d684e429a6aea Author: Weiqun Zhang Date: Wed Sep 16 17:31:38 2015 -0700 fixed a typo Src/C_BaseLib/IntVect.cpp commit bf1777b4fec8f931ee176ab5e5986ac95dd341e6 Author: Weiqun Zhang Date: Wed Sep 16 16:56:42 2015 -0700 clean up MGT_Solver Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Tests/LinearSolvers/C_CellMG/MacOperator.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tutorials/AMR_Advection_C/Source/Diffusion.cpp Tutorials/MultiGrid_C/main.cpp commit 6ace9a195b172595ac0a7275eefd5eb30f2758dc Author: Weiqun Zhang Date: Wed Sep 16 16:14:36 2015 -0700 Added a member function that takes a const * and removes the const. use it with care. Src/C_BaseLib/PArray.H commit 9029f08edf3818f537d0c882a96cdc7c8bc726b9 Author: Weiqun Zhang Date: Wed Sep 16 14:06:27 2015 -0700 added IntVect::TheDimensionVector for convenience Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp commit 7e05805531eb30c7ae25e6f193e5e1e85c558fca Author: Weiqun Zhang Date: Wed Sep 16 13:40:08 2015 -0700 optional nodal argument for MultiFab and FabArray constructors Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 59ab06a0f774b0e5b01bb52b17776b3f461295ed Author: Weiqun Zhang Date: Tue Sep 15 18:23:44 2015 -0700 tiling in cc MGT_Solver Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 1b02ba0ea9f3b6ea3d5242765b069c58a12e263a Author: Weiqun Zhang Date: Mon Sep 14 12:52:45 2015 -0700 In tiled tab_boxes, only the current tile should be touched. Src/F_BaseLib/tag_boxes.f90 commit d78fb47e50b2b76df9cf204b3a6ea4fe8640ad0b Merge: 41d173a6c 5e3be4424 Author: Max Katz Date: Mon Sep 14 15:38:45 2015 -0400 Merge branch 'master' of github.com:BoxLib-Codes/BoxLib commit 41d173a6c9919def40e6dae1073b3f3b5a88f10d Author: Max Katz Date: Mon Sep 14 15:38:41 2015 -0400 Add a function to StateData that accepts a pointer to a new MultiFab and replaces the old_data or new_data with it, then deletes the old copy of old_data or new_data. Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 5e3be44245db7d4194a0661adcc64faee059ab2a Author: Weiqun Zhang Date: Mon Sep 14 11:10:31 2015 -0700 fixed a new bug in tag_boxes Src/F_BaseLib/tag_boxes.f90 commit c156c849c5a121d8fadda539e69d0d7756865775 Author: Michael Zingale Date: Mon Sep 14 12:10:46 2015 -0400 need to define last_run earlier Tools/RegressionTesting/testnew.py commit 21ef91afe99f4ab7cbc7dead0f7db65ef52f58cd Author: Weiqun Zhang Date: Sat Sep 12 12:14:01 2015 -0700 modified Cray C++ compiler option to make it work with a C99 feature we use. Tools/C_mk/Make.Linux commit df0c0fd8cfb3c87cde16187b48745dd2456ca016 Author: Weiqun Zhang Date: Sat Sep 12 11:25:03 2015 -0700 tweak flags for .F90 files Tools/C_mk/Make.rules commit a1ef045490b30fab7d64bf74b0e5425ee06ce86e Author: Max Katz Date: Sat Sep 12 02:45:14 2015 -0400 Don't actually need a separate FILCC_ND.F file to do dimension agnostic boundary filling Src/C_AMRLib/FILCC_ND.F Src/C_AMRLib/Make.package Src/C_AMRLib/StateDescriptor.cpp commit 0ad8689a58997ee0ab902d217a83c6fe247f63fb Merge: 485626b2c fdb0b07c7 Author: Max Katz Date: Fri Sep 11 23:53:13 2015 -0400 Merge branch 'master' of github.com:BoxLib-Codes/BoxLib commit 485626b2cd47786c56f7bd77f37ef44d77324324 Author: Max Katz Date: Fri Sep 11 23:53:09 2015 -0400 Dimension agnostic boundary fill routine Src/C_AMRLib/FILCC_ND.F Src/C_AMRLib/Make.package Src/C_AMRLib/StateDescriptor.cpp commit fdb0b07c70365340062958d0d4c0c5af503ce83a Author: Brian Friesen Date: Fri Sep 11 13:43:04 2015 -0700 MultiFab: use local communicator with HPGMG instead of MPI_COMM_WORLD This lets us use the HPGMG solver in runs where we have multiple MPI groups/communicators. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 317f40b898a76166a04dc49c1759e173204cd3db Author: Brian Friesen Date: Thu Sep 10 13:05:52 2015 -0700 MultiFab: remove commented-out debugging print statement during HPGMG run Src/C_BaseLib/MultiFab.cpp commit 22dca70a7ea4283a597241d1fb80ccc41a0a3f94 Author: Brian Friesen Date: Thu Sep 10 13:05:17 2015 -0700 MultiFab: minor clean up of status output during HPGMG runs Src/C_BaseLib/MultiFab.cpp commit 3f33379d932a12d8daab8139428fdc1773af6cbf Author: Brian Friesen Date: Tue Sep 8 15:40:47 2015 -0700 C_mk: added compile-time options for smoothing behavior of HPGMG Tools/C_mk/Make.defs commit c073c3220de39e3f49df8151044afb524d284538 Author: Weiqun Zhang Date: Fri Sep 11 10:33:10 2015 -0700 tiling in tag_boxes Src/F_BaseLib/tag_boxes.f90 commit 13448ab43b758fcffec5a870babba239524df837 Author: Weiqun Zhang 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 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 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 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 Date: Thu Sep 10 16:21:32 2015 -0400 fix a few bugs Tools/RegressionTesting/testnew.py commit a5bf611f48be45d0992151331028e39588eedd68 Author: Michael Zingale Date: Thu Sep 10 15:58:34 2015 -0400 a little more cleaning Tools/RegressionTesting/testnew.py commit 913fe593d74e3b61636eebf3c41bbf595cf0ee09 Author: Michael Zingale Date: Thu Sep 10 12:34:02 2015 -0400 centralize the logic of how we select the tests to run into a method of the suite object. Tools/RegressionTesting/testnew.py commit f642017c59593c30d7d14aa3dcbc76cea255bba9 Author: Michael Zingale Date: Thu Sep 10 11:59:34 2015 -0400 let the HTMLTable take a list of div elements Tools/RegressionTesting/testnew.py commit ae36ba9b4a6a1c28a440261e408a8a12ac812b7e Author: Michael Zingale Date: Thu Sep 10 11:03:31 2015 -0400 fix missing ] Tools/RegressionTesting/testnew.py commit e820bb91a994903b18fd27a3cce9fd0cb0c05d01 Author: Michael Zingale Date: Thu Sep 10 10:20:43 2015 -0400 fix the handling of NaNs present in the compare table Tools/RegressionTesting/testnew.py commit bab2d57332da8dbe7d728ca44f44b4148e0aff47 Merge: e657004b8 e4b549018 Author: Weiqun Zhang Date: Wed Sep 9 21:03:30 2015 -0700 Merge branch 'master' of github.com:BoxLib-Codes/BoxLib commit e657004b80b8b85b35d390b9f496f2929e7b0da4 Author: Weiqun Zhang Date: Wed Sep 9 16:55:09 2015 -0700 tiling in nodal restriction Src/F_BaseLib/ml_nd_restriction.f90 Src/F_BaseLib/nodal_restriction.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/mg.f90 commit e4b5490188233f38d34dff069194037d6e0e5600 Author: Michael Zingale Date: Wed Sep 9 20:39:34 2015 -0400 be careful -- if a test did not produce any output and we used --copy_benchmarks, then there it can erase the entire benchmark directory (d'oh). This is fixed now by checking that the last plotfile found is not "" Tools/RegressionTesting/testnew.py commit 242f1b742a40b463922bbd7cc7c977d21f1b9e56 Author: Weiqun Zhang Date: Wed Sep 9 10:59:16 2015 -0700 reduced number of parallel reduce Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/multifab_f.f90 commit 7abac98be677ccb45bea53dc43560b84ffb12cb3 Author: Michael Zingale Date: Wed Sep 9 10:47:56 2015 -0400 add a copy_benchmarks functionality -- this does what make_benchmarks + redo_failed does, without rerunning any tests -- it simply copies all the benchmarks from the last runs that failed. Tools/RegressionTesting/testnew.py commit 635796c462765b19e0e70dd7e22e041bcc8b67a4 Author: Weiqun Zhang Date: Tue Sep 8 16:34:07 2015 -0700 Split MPI calls in FillBoundary and FillPeriodicBoundary into multiple pieces. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H commit 277a773c13f9c61543384f5d36e2023a9652e39d Author: Michael Zingale Date: Tue Sep 8 13:12:03 2015 -0400 some css tweaks Tools/RegressionTesting/testnew.py commit 694b18635a5c2c2eab915084f38ee260a26e9f8e Merge: f981ba351 3df0177ce Author: Weiqun Zhang 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 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 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 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 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 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 Date: Sat Sep 5 14:23:07 2015 -0700 always include sstream Src/C_BaseLib/BLBackTrace.H commit 92b478bd53475d666742aee71d6714834fc5fdb5 Author: Ann Almgren Date: Fri Sep 4 17:23:22 2015 -0700 Don't include bl_constants_module since that lives on F90 side. Src/C_BaseLib/MultiFabUtil_2d.f90 Src/C_BaseLib/MultiFabUtil_3d.f90 commit 21f4fc7a0c083df75208efa3ea3aae1d463b9dfe Author: Ann Almgren Date: Fri Sep 4 17:02:26 2015 -0700 Add the functionality to average down face-based MultiFabs as long as the crse BoxArray is a coarsened version of the fine BoxArray. Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_1d.f90 Src/C_BaseLib/MultiFabUtil_2d.f90 Src/C_BaseLib/MultiFabUtil_3d.f90 Src/C_BaseLib/MultiFabUtil_F.H commit 07e7083491dd89c38ec8de7e930117c043471570 Author: Weiqun Zhang Date: Fri Sep 4 13:45:23 2015 -0700 command line option for sending no email when regression tests fail Tools/RegressionTesting/testnew.py commit 08a44f63460c56ed6257dfdbe92aa24c33b8e8c7 Author: Weiqun Zhang Date: Fri Sep 4 13:19:19 2015 -0700 a bit of hack to get consistent answer with OMP Src/F_BaseLib/multifab_f.f90 commit 8a6052e4cc8aa42ad2b83feb3bffb26ca682b76b Author: Weiqun Zhang Date: Fri Sep 4 11:57:56 2015 -0700 minor changes that can cause roundoff errors Src/F_BaseLib/multifab_f.f90 commit 637f78d7b0410eafee8b5b7de7a021996c80aaa9 Author: yzheng Date: Fri Sep 4 11:08:23 2015 -0700 Make async slightly more efficient without the need of reply Src/C_BaseLib/BLPgas.cpp commit 6986349a9623f6bd12dedf166473fbe6666abc5b Merge: 1d3dc73c9 f981ba351 Author: yzheng 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 Date: Fri Sep 4 11:03:41 2015 -0400 fix a link + pretty up some CSS Tools/RegressionTesting/testnew.py commit 4dc415c1a2e35f3135a8e775dc59c8e01dba6c38 Merge: afda0e5a6 7bd027bac Author: Michael Zingale Date: Fri Sep 4 10:01:36 2015 -0400 Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib commit afda0e5a6a8d22419c2fe9cb6f5784b5ad5f7447 Author: Michael Zingale Date: Fri Sep 4 10:01:16 2015 -0400 switch the test run overview talbe to HTMLTable Tools/RegressionTesting/testnew.py commit 7bd027bac11ff47dc3bd8b1ba9ac6ce59e176d53 Author: Michael Zingale Date: Fri Sep 4 09:28:36 2015 -0400 wrong indentation in the MPI call Tools/RegressionTesting/testnew.py commit 63b472b1803dba0c71c697a374184c1060674fc6 Author: Michael Zingale Date: Fri Sep 4 08:27:55 2015 -0400 catch when boxes don't match in fcompare Tools/RegressionTesting/testnew.py commit e6440c7db5cda8f052f72fc23019d36ddbff47f4 Author: Weiqun Zhang Date: Thu Sep 3 20:53:44 2015 -0700 tiling Src/C_BaseLib/MultiFabUtil.cpp commit b3b6a47f8863e94f7f64e8ab71ef739ba1894bad Author: Max Katz Date: Thu Sep 3 23:38:33 2015 -0400 Fix minor bug in assertion Src/C_BaseLib/MultiFabUtil.cpp commit 70423254b1688c33412658baac2720f3dac3be8f Author: Michael Zingale Date: Thu Sep 3 21:17:33 2015 -0400 a bit more restructuring -- moving things into the suite class Tools/RegressionTesting/testnew.py commit 2a62e48f4040e1b8117288a9cdd6c5ac39d3ca9c Author: Weiqun Zhang Date: Thu Sep 3 16:11:53 2015 -0700 save local index in communication and local copy descriptors to avoid repeated calls to local_index Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_interface_stencil.f90 commit f603d5f1030e18ef2fb0b773a46da2382082cd7f Merge: 26d913e82 5112ec905 Author: Weiqun Zhang Date: Thu Sep 3 14:47:27 2015 -0700 Merge branch 'master' of github.com:BoxLib-Codes/BoxLib commit 5112ec905771fb43e9b0fc34fd1393bc69618ade Author: Brian Friesen Date: Thu Sep 3 13:15:59 2015 -0700 C_mk: updated Makefile flags for HPGMG to allow both pure V-cycles and pure F-cycles Tools/C_mk/Make.defs Tutorials/MultiGrid_C/GNUmakefile commit 26d913e828d25fe4257a32299a71fd30bd942866 Author: Weiqun Zhang Date: Thu Sep 3 13:08:17 2015 -0700 Added a few new utility functions to BoxLib namespace. Src/C_AMRLib/AmrLevel.H Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFabUtil.H Src/C_BaseLib/MultiFabUtil.cpp Src/C_BaseLib/MultiFabUtil_1d.f90 Src/C_BaseLib/MultiFabUtil_2d.f90 Src/C_BaseLib/MultiFabUtil_3d.f90 Src/C_BaseLib/MultiFabUtil_F.H commit f7f5de123273f49e7a6f672ecbd6d57baa559734 Author: Michael Zingale Date: Thu Sep 3 09:57:49 2015 -0400 start of what will become some basic unit tests -- nothing to see here now. Src/F_BaseLib/unittests/GNUmakefile Src/F_BaseLib/unittests/gr0_3d.1level Src/F_BaseLib/unittests/tests.f90 commit e0717fddd3a7f54d710c705903f3c7f3741d8874 Merge: ea3c6107f 266e1aee0 Author: Michael Zingale Date: Thu Sep 3 09:57:35 2015 -0400 Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib commit f981ba3516b11421a113fe9133f143fcf3ccbe55 Author: Weiqun Zhang Date: Wed Sep 2 20:40:23 2015 -0400 added bl_profiler MiniApps/PGAS_SMC/main.cpp commit 266e1aee0f4b1887f3f59450f4d802f5b6029735 Author: Weiqun Zhang Date: Wed Sep 2 10:44:38 2015 -0700 minor bug: used optional argument without checking Src/F_BaseLib/make_new_grids.f90 commit 22f812cf5ef0888215f717f85d2fdae31aa400d5 Merge: 83aa2b82a 5abc60ab0 Author: Brian Friesen Date: Tue Sep 1 16:13:26 2015 -0700 Merge branch 'port_hpgmg' This series of commits adds the ability to call the HPGMG multigrid solver written by Sam Williams. It is designed to be more or less a drop-in replacement for the in-house multigrid solver. There are a few caveats to using it, however: 1.) It is single-level only. No AMR. 2.) It is not nodal. 3.) It requires a cubic domain with cubic boxes. 4.) It does not support Neumann boundary conditions. Only periodic or Dirichlet. In addition, the version of HPGMG which Sam maintains will not work with this. You must use my "port" of it, which contains the necessary hooks. commit 5abc60ab022092045410177fa0ee50a91357ed70 Author: Brian Friesen Date: Tue Sep 1 14:21:55 2015 -0700 MultiGrid_C: add HPGMG as an example multigrid solver in the tutorial Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/README Tutorials/MultiGrid_C/main.cpp commit b2bc2eeee282c88c36c1a1300ab7c0d7d54ba914 Author: Brian Friesen Date: Tue Sep 1 12:29:38 2015 -0700 MultiFab: add static functions and hooks for using the HPGMG linear solver Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Tools/C_mk/Make.defs commit 0e12d1dda300ed37a9f10996f7f848312b42ea14 Author: Brian Friesen Date: Tue Sep 1 12:17:21 2015 -0700 Box: add static function isSquare() Checks that a Box is square (or cubic in 3-D). This is a convenient function to have when using the HPGMG solver, which requires cubic Boxes. Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit 83aa2b82a074305df72d5a1f6a3aec5616b40a80 Author: Weiqun Zhang Date: Tue Sep 1 17:46:04 2015 -0700 fixed intel compiler macro in last commit Src/C_BaseLib/BLBackTrace.H commit 99907183e4686a9e5a30e70bca56c63c6db9f015 Author: Weiqun Zhang Date: Tue Sep 1 17:44:51 2015 -0700 Cannot get threadprivate static class memeber work in Cray and Intel, so let's turn it off. Note that this would not cause race conditions unless we use BL_BACKTRACE_PUSH and POP for debugging. In that case, we have to use gcc. Src/C_BaseLib/BLBackTrace.H commit 1ce3f9801b756c1dc6e66edc0be19ffba3d33984 Author: Weiqun Zhang Date: Tue Sep 1 17:38:58 2015 -0700 option to turn on assertion if compiled with USE_ASSERTION=TRUE enven when DEBUG is FALSE. Src/C_BaseLib/BLassert.H Tools/C_mk/Make.defs commit cb86fba6ab3d8dc1e8e816c519a7c350ba6231ea Author: Weiqun Zhang Date: Tue Sep 1 17:24:38 2015 -0700 added -g to Cray Tools/C_mk/Make.Linux commit ea3c6107ff3d5e421f0d4f10f865f79ae2c3087f Merge: fcd46eb77 7a8a53088 Author: Michael Zingale Date: Tue Sep 1 19:35:39 2015 -0400 Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib commit fcd46eb777054faf5c4e578a32a9cdc2be0a86c3 Author: Michael Zingale Date: Tue Sep 1 19:35:15 2015 -0400 change multifab_equal to a function and check the layouts Src/F_BaseLib/multifab_f.f90 commit c7dbfb89ed7fb96759aa6848fcd493d333e5eaae Author: Weiqun Zhang Date: Tue Sep 1 14:19:46 2015 -0700 make Intel compiler happy MiniApps/PGAS_SMC/SMC_advance.cpp commit 7a8a530882089b7dd08169467c9ad88afcc49ab4 Author: Weiqun Zhang Date: Tue Sep 1 11:21:00 2015 -0700 Finished tiling in multifab_f. Roundoff errors are expected because this commit changes the order of sum. Src/F_BaseLib/multifab_f.f90 commit 5bb2e4d0c3baf827e73c37dc410682b05c26578f Author: Weiqun Zhang Date: Tue Sep 1 10:25:04 2015 -0700 added an assertion in mfiter Src/F_BaseLib/bl_error.f90 Src/F_BaseLib/multifab_f.f90 commit 3bf18a9c52e21519951602b7738ff8e3fc30a8c6 Merge: 15a52d089 6930a6b35 Author: Michael Zingale Date: Tue Sep 1 12:05:09 2015 -0400 Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib commit 6930a6b35ce8998abf58fe00ee100464e9796cdd Author: Michael Zingale Date: Tue Sep 1 12:00:24 2015 -0400 if there is no png file produced, then skip the copy Tools/RegressionTesting/testnew.py commit 15a52d0892307c44861868473b88c3dd28bfae2f Merge: b1ca0c239 9c962d1c2 Author: Michael Zingale Date: Tue Sep 1 11:50:05 2015 -0400 Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib commit b1ca0c239f064cbfa7212b0c0345d04ce24f3065 Author: Michael Zingale Date: Tue Sep 1 11:49:56 2015 -0400 add an equal method Src/F_BaseLib/multifab_f.f90 commit 9c962d1c2a8fd7edb11e2be614649ec168fdcde2 Author: Weiqun Zhang Date: Tue Sep 1 08:30:27 2015 -0700 fixed a new bug: forgot to build mfiter Src/F_BaseLib/multifab_f.f90 commit 4c8a14ea9fb271a958a36af99e4bff0b61bad48a Author: Weiqun Zhang Date: Mon Aug 31 17:44:20 2015 -0700 more tiling in multifab_f Src/F_BaseLib/multifab_f.f90 commit d23f672c4b4c4568b03b44f75497b55a820bbd6b Merge: 90a598b3c b1e9fe52d Author: vince Date: Mon Aug 31 17:19:02 2015 -0700 Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib commit 90a598b3cdb62ea2978980e8486596d9ca8f3dc2 Author: vince Date: Mon Aug 31 17:18:59 2015 -0700 some code cleanup. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/FabArray.H commit 439ba4044c9e689845aaec3b6adecef75425cdd5 Author: Weiqun Zhang Date: Mon Aug 31 16:02:54 2015 -0700 Fixed a very old in multifab_div_s_c. Fortunately, I don't think it is ever used by any codes. Src/F_BaseLib/multifab_f.f90 commit b1e9fe52d747b582c18de532c9dae23034dd05ba Author: Weiqun Zhang Date: Sat Aug 29 23:41:43 2015 -0700 fixed a new omp bug and cleanup Src/F_BaseLib/multifab_f.f90 commit dd986a0a2036c3faa19f131f2f7667b584dae8ae Author: Weiqun Zhang Date: Sat Aug 29 22:30:54 2015 -0700 fixed typo Src/F_BaseLib/multifab_f.f90 commit 34bc454266101d285615adfd1162486db2b61590 Author: Weiqun Zhang Date: Sat Aug 29 22:15:21 2015 -0700 more tiling and forgot to build mfiter Src/F_BaseLib/multifab_f.f90 commit ed06581dd8178f62e0498b4a8ed5e1db6509b947 Author: Weiqun Zhang Date: Sat Aug 29 21:53:48 2015 -0700 Multifab_fab_copy is serial only and I oon't think any codes are it, so it is removed. If it turns out some codes need to call it, we should implement a parallel version. Src/F_BaseLib/multifab_f.f90 commit 791a95df95a034f11d07a2656b1345ceece37282 Author: Weiqun Zhang Date: Sat Aug 29 21:46:48 2015 -0700 tiling in multifab_min Src/F_BaseLib/multifab_f.f90 commit 6e9de507b0ac244671cb9e1f747c3d4bf9e7a24e Author: Weiqun Zhang Date: Sat Aug 29 21:37:02 2015 -0700 tiling in multifab_val and removed allow_empty argument because mfiter skips empty box already Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_f.f90 commit d2254b328ac25b69ffdaf70ce7d532a508af4583 Author: Weiqun Zhang Date: Sat Aug 29 21:06:55 2015 -0700 It shouldn't be fab's responsibility to check if the caller passes in a box in fab_max_val and fab_min_val. Also note that in practice only the multifab module is supposed to call fab_max_val and fab_min_val. Src/F_BaseLib/fab.f90 commit ce00022119eb1037a51a216a9d9515702ab74893 Author: Weiqun Zhang Date: Fri Aug 28 17:01:48 2015 -0700 more tiling Src/F_BaseLib/multifab_f.f90 commit 3c83464587fc07a439bdbd47bc93b6eb562fabcb Author: Weiqun Zhang Date: Fri Aug 28 16:54:48 2015 -0700 no longer need to test empty box because mfiter will not hand out an empty box Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_f.f90 commit 5f0c809782930a5bd04bb8145f334d8928c0f602 Author: Weiqun Zhang Date: Fri Aug 28 16:52:02 2015 -0700 handle empty box in mfiter Src/F_BaseLib/layout.f90 commit 3550f7a84153dffbecaf3a3044508293d23008a9 Author: Weiqun Zhang Date: Fri Aug 28 16:18:13 2015 -0700 tiling and omp in multifab_f Src/F_BaseLib/multifab_f.f90 commit 2cc6fdf3524b121922c4a7f86eaefc8117f22326 Author: Weiqun Zhang Date: Fri Aug 28 15:16:32 2015 -0700 removed omp in fab.f90 because we are going to do it in multifab_f.f90 Src/F_BaseLib/fab.f90 commit 1d3dc73c93ee71fd205debc73e0d52c13dc5528d Merge: 156cd26bd 6cdabe5c9 Author: yzheng Date: Sat Aug 29 15:55:46 2015 -0700 Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas commit 4fc73359556090eedabdb23c92ebd4d68b81e1b5 Merge: 1af02ecf8 d89db3e6d Author: Max Katz Date: Sat Aug 29 01:51:10 2015 -0400 Merge branch 'master' of github.com:BoxLib-Codes/BoxLib commit 1af02ecf86d4ade6bf75416cb188d5cdcbc9c30a Author: Max Katz Date: Sat Aug 29 01:51:07 2015 -0400 Add a DIMENSION_AGNOSTIC variable to the makefile/defines; we'll use it in some cases for determining whether to call dimension agnostic Fortran functions. Also add a dimension agnostic version of the boundary function routines, similar to how we did this for the derive class. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Make.package Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp Tools/C_mk/Make.defs commit d89db3e6dc492a86956ab5bd13342c063984857e Author: Brian Friesen Date: Fri Aug 28 15:45:09 2015 -0700 ParallelDescriptor: put include of Analysis.H inside IN_TRANSIT ifdef Src/C_BaseLib/ParallelDescriptor.cpp commit 63036a25a575ff29e7cbf0e7714b88b003a7e359 Author: Brian Friesen Date: Fri Aug 28 15:42:52 2015 -0700 F_BaseLib: derive world_group communicator from m_comm instead of MPI_COMM_WORLD in parallel_create_communicator() This routine ultimately just wants the "parent" communicator from which to build sub-communicators. It shouldn't care whether the parent communicator is actually MPI_COMM_WORLD or anything else. Src/F_BaseLib/parallel.f90 commit 6cdabe5c98c8d26b3355f102a753ba48ab6e147e Author: Weiqun Zhang Date: Fri Aug 28 13:15:31 2015 -0700 split FillPeriodicBoundary_finish into two versions: MPI and UPCXX Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit d3b7e7e3a390367e320f9e5b8d61178bc3127dc0 Author: Brian Friesen Date: Fri Aug 28 12:10:16 2015 -0700 F_BaseLib: change parent communicator from MPI_COMM_WORLD to m_comm in parallel_create_communicator() Using MPI_COMM_WORLD breaks code which uses more than one MPI group. "m_comm" should be the correct pseudo-global communicator anyway, so this should work for any number of MPI groups. Src/F_BaseLib/parallel.f90 commit 8ed2642b6f37cb137bb4c386be68748a46118bae Author: Brian Friesen Date: Fri Aug 28 10:44:27 2015 -0700 F_BaseLib: remove assignment of m_comm to MPI_COMM_WORLD in parallel_finalize() This breaks the multigrid solver when running with the sidecars because the solver invokes many MPI collective routines which hang due to this. Src/F_BaseLib/parallel.f90 commit 763ba4d49b6394d29ec511527f687464006bc71d Author: Brian Friesen Date: Fri Aug 28 09:24:57 2015 -0700 ParallelDescriptor: move creation of InTransitAnalysis variable outside if/else section in SidecarProcess() Every type of analysis will use an InTransitAnalysis object, so rather than duplicating this line in every if/else case, just do it once at the beginning. Src/C_BaseLib/ParallelDescriptor.cpp commit fddeab5f255c416541df215dbaa142e6d1f707d3 Author: Brian Friesen Date: Fri Aug 28 07:21:37 2015 -0700 ParallelDescriptor: break out of while() loop immediately after sidecars receive quit signal Src/C_BaseLib/ParallelDescriptor.cpp commit 45789ea132a1576f536dae4d614d58daa6e4d4ec Author: Brian Friesen Date: Fri Aug 28 07:16:18 2015 -0700 ParallelDescriptor: use automatic allocation instead of new[] and delete[] in SidecarProcess() There's no reason to use pointers and allocate objects by hand. Let them come into and go out of scope automatically. Src/C_BaseLib/ParallelDescriptor.cpp commit e90ccdf0b5ff6e72110767c364ff91368e4249d6 Author: Brian Friesen Date: Fri Aug 28 07:06:16 2015 -0700 ParallelDescriptor: move sidecar completion message outside the signal if/else section This way we don't have to duplicate that message inside every if/else case. Src/C_BaseLib/ParallelDescriptor.cpp commit 8c89549a4222d91cee02ae84330c8a761a7492fe Author: Weiqun Zhang Date: Thu Aug 27 17:13:41 2015 -0700 split FillBoundary_finish into two versions: MPI and UPCXX Src/C_BaseLib/FabArray.H commit 156cd26bd6bbb292f9c9c39b15d4183b35ed2483 Merge: 84e9b950f 397e83ff7 Author: yzheng Date: Thu Aug 27 16:42:55 2015 -0700 Merge branch 'pgas' of github.com:BoxLib-Codes/BoxLib into pgas commit 84e9b950f7935d2eab4d482ef6e1bc12c4e9f131 Author: yzheng Date: Thu Aug 27 16:42:52 2015 -0700 Use UPC++ barrier for the UPC++ version MiniApps/PGAS_SMC/SMC.cpp commit 80140ecde6e9913fe4ede35b21d2021eae313589 Merge: 397e83ff7 801b617be Author: Weiqun Zhang Date: Thu Aug 27 16:24:34 2015 -0700 Merge branch 'master' into pgas commit 397e83ff7937c1ebc33cd559676095af0ef69233 Author: Weiqun Zhang 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 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 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 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 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 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: 6b8b68172 4e06e6b1b Author: Michael Zingale Date: Thu Aug 27 09:16:15 2015 -0400 Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib commit 6b8b68172b789d81f15b97eff96e46a8ab93ff65 Author: Michael Zingale Date: Thu Aug 27 09:15:16 2015 -0400 Fortran prints numbers with 3-digit exponents without the 'E' (i.e., 0.3979676757-175) Python/C don't know how to interpret this. Now we floor things with 1.d-99 Tools/Postprocessing/F_Src/fcompare.f90 commit a479b3ba6ecc57016666e412ce64d6bb976440a9 Merge: b5d1d12de 4e06e6b1b Author: Weiqun Zhang 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 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 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 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 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 Date: Wed Aug 26 10:25:50 2015 -0700 tidy MiniApps/PGAS_SMC/SMC.cpp commit cc5d3c0bda4cbfeff2887658228a8a2e52665221 Author: Weiqun Zhang Date: Wed Aug 26 10:19:50 2015 -0700 added some timers and some minor changes MiniApps/PGAS_SMC/SMC.H MiniApps/PGAS_SMC/SMC.cpp MiniApps/PGAS_SMC/SMC_advance.cpp commit bae28d55a3d36c647b5c1533accaa3af54885f24 Author: Weiqun Zhang Date: Tue Aug 25 17:31:04 2015 -0700 first version of PGAS_SMC MiniApps/PGAS_SMC/Make.package MiniApps/PGAS_SMC/SMC.H MiniApps/PGAS_SMC/SMC.cpp MiniApps/PGAS_SMC/SMC_F.H MiniApps/PGAS_SMC/SMC_advance.cpp MiniApps/PGAS_SMC/SMC_init.cpp MiniApps/PGAS_SMC/SMC_io.cpp MiniApps/PGAS_SMC/init_data.f90 MiniApps/PGAS_SMC/kernels.f90 MiniApps/PGAS_SMC/make_plot.f90 MiniApps/PGAS_SMC/transport_properties.f90 MiniApps/PGAS_SMC/variables.f90 commit 28f46dcd6e53e5a672e233bb503ee2da47d60549 Author: Weiqun Zhang Date: Tue Aug 25 17:29:41 2015 -0700 added MFGhostIter that iterates over ghost cells only Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 64064be9bea4012af0f0b6376406d7b2ab61ee2b Author: Brian Friesen Date: Tue Aug 25 16:21:49 2015 -0700 Analysis: started adding virtual Initialize() stubs for different kinds of analysis classes Different types of analyses require different types of input data, and at some point the compiler must know *something* about which data an analysis class requires. But we don't want to put the entire analysis code into BoxLib itself. Since we can't have virtual constructors, the compromise is to enumerate all the possible input sets via unique, virtual Initialize() stubs. BoxLib will not invoke a callback to Initialize() because it doesn't know which one to use. So the analysis class itself invokes its own Initialize(), and BoxLib will then invoke DoAnalysis() and Finalize(), since it is much easier to implement those functions for any analysis class with no arguments. Src/C_BaseLib/Analysis.H Src/C_BaseLib/ParallelDescriptor.cpp Tutorials/Sidecar_EX1/InTransitAnalysis.H Tutorials/Sidecar_EX1/InTransitAnalysis.cpp commit 94665db28cd82f2646de87b357396fb5afd6b114 Author: Brian Friesen Date: Tue Aug 25 15:57:08 2015 -0700 Analysis: created namespace "Analysis" and moved most stuff there from ParallelDescriptor Src/C_BaseLib/Analysis.H Src/C_BaseLib/Analysis.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tutorials/Sidecar_EX1/GridMoveTest.cpp commit 7ee82d882edc872cb22d2bd7a126c6e7e19ce3ba Author: Brian Friesen Date: Tue Aug 25 15:41:16 2015 -0700 Analysis: renamed generic class "Analysis" to "AnalysisContainer" Src/C_BaseLib/Analysis.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit b26fa9eb0eea002ab097d21d1fc7871245ad6dfb Author: Brian Friesen Date: Tue Aug 25 14:26:56 2015 -0700 ParallelDescriptor: compactify pointer allocation syntax in SidecarProcess() Src/C_BaseLib/ParallelDescriptor.cpp commit 8b9e73dcb7a3dbe40bbb76c15fca60c35f8df654 Author: Weiqun Zhang Date: Tue Aug 25 13:19:09 2015 -0700 fixed typos Src/C_BaseLib/BLPgas.H Src/C_BaseLib/BLPgas.cpp commit 1f1b768d763223b7e82a4ca7174c74a48ac05f2a Author: Brian Friesen Date: Tue Aug 25 12:49:39 2015 -0700 Tutorials: added #ifdef IN_TRANSIT to relevant parts of Sidecar_EX1 We want the code to run with or without sidecars. It's just that if you don't use the sidecars in this example, the code doesn't do anything interesting. Tutorials/Sidecar_EX1/GridMoveTest.cpp commit 205aadad75b58a649d6cefe628ee793534e303c2 Author: Amir Kamil Date: Tue Aug 25 15:38:01 2015 -0400 Split Send interface into Send and Request. Src/C_BaseLib/BLPgas.H Src/C_BaseLib/BLPgas.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 93ed9e20b57268608cd2f4f503bed1a64eb4db3d Merge: 3af81f606 023956613 Author: Brian Friesen Date: Tue Aug 25 12:35:07 2015 -0700 Merge branch 'add_sidecar_analysis' With these commits we return to a signal-based system for interacting with the sidecar MPI group. We have also moved to a callback-based system for performing the analysis so that the process of "registering" and executing a user-defined analysis routine with the sidecars can remain fairly generic. commit 02395661308319fa097d8f556dd351dca1915809 Author: Brian Friesen Date: Tue Aug 25 11:29:06 2015 -0700 Tutorials: removed Sidecar_EX2 example since Sidecar_EX1 has the same features Tutorials/Sidecar_EX2/GNUmakefile Tutorials/Sidecar_EX2/InSituAnalysis.H Tutorials/Sidecar_EX2/InSituAnalysis.cpp Tutorials/Sidecar_EX2/Make.package Tutorials/Sidecar_EX2/inputs_3d Tutorials/Sidecar_EX2/main.cpp commit 7dfda73ce337ceff2f8a4a4a9f91ab66707f559e Author: Brian Friesen Date: Tue Aug 25 09:13:48 2015 -0700 Sidecars: changed sidecar implementation back to signal-based, and updated Sidecar_EX1 tutorial accordingly Src/C_BaseLib/Analysis.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Sidecar_EX1/GridMoveTest.cpp Tutorials/Sidecar_EX1/InTransitAnalysis.H Tutorials/Sidecar_EX1/InTransitAnalysis.cpp Tutorials/Sidecar_EX1/Make.package commit 8022d0c677a69c333b567a99caecbd0c9cfdec8e Author: Weiqun Zhang Date: Mon Aug 24 17:23:27 2015 -0700 flesh out PGAS_SMC MiniApps/PGAS_SMC/Exec/ToyFlame/GNUmakefile MiniApps/PGAS_SMC/Exec/ToyFlame/Make.package MiniApps/PGAS_SMC/Exec/ToyFlame/Prob_3d.f90 MiniApps/PGAS_SMC/GNUmakefile MiniApps/PGAS_SMC/LiDryer.c MiniApps/PGAS_SMC/Make.package MiniApps/PGAS_SMC/SMC.H MiniApps/PGAS_SMC/SMC.cpp MiniApps/PGAS_SMC/SMC_F.H MiniApps/PGAS_SMC/SMC_advance.cpp MiniApps/PGAS_SMC/SMC_init.cpp MiniApps/PGAS_SMC/SMC_io.cpp MiniApps/PGAS_SMC/Source/Make.package MiniApps/PGAS_SMC/Source/SMC.H MiniApps/PGAS_SMC/Source/SMC.cpp MiniApps/PGAS_SMC/Source/SMCBld.cpp MiniApps/PGAS_SMC/Source/SMC_advance.cpp MiniApps/PGAS_SMC/Source/SMC_io.cpp MiniApps/PGAS_SMC/Source/SMC_setup.cpp MiniApps/PGAS_SMC/Source/main.cpp MiniApps/PGAS_SMC/chemistry_module.f90 MiniApps/PGAS_SMC/derivative_stencil.f90 MiniApps/PGAS_SMC/init_data.f90 MiniApps/PGAS_SMC/main.cpp MiniApps/PGAS_SMC/variables.f90 commit 3af81f60658bc0f173db56e2128f2e2ca30f9556 Author: Weiqun Zhang Date: Sat Aug 22 23:33:02 2015 -0700 align memory arena allocation to 16 bytes Src/C_BaseLib/Arena.H Src/C_BaseLib/Arena.cpp Src/C_BaseLib/CArena.cpp commit dfdfe3386dd788c108f58e2ef5908a413324fbbf Author: yzheng Date: Sat Aug 22 15:45:33 2015 -0700 Update BLPgas.cpp to use the latest version of UPC++ signaling put interface Src/C_BaseLib/BLPgas.cpp commit 78ee54183babdee46c65d5b78e22eb34f6db3f6b Author: Weiqun Zhang 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 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: 61d522c84 8c18d1e3e Author: Brian Friesen Date: Fri Aug 21 10:26:09 2015 -0700 Merge branch 'sidecar_improvements' This adds a few new static functions for sending various objects to the sidecars processes, and cleans up a few things as well. commit 8c18d1e3ebaa0353a3ade738fe3fbfc273da0e4a Author: Brian Friesen Date: Wed Aug 12 12:51:38 2015 -0700 MultiFab: change memcpy() to std::memcpy() in SendMultiFabToSidecars() memcpy() is a C function. To be consistent let's use the C++ version in STL. Src/C_BaseLib/MultiFab.cpp commit f7fbe8d95a5c5f7479862a7455d2b0b786bb554a Author: Brian Friesen Date: Wed Aug 12 12:04:18 2015 -0700 MultiFab: changed separate MPI_ROOT/MPI_PROC_NULL Bcast()s to a single Bcast() Src/C_BaseLib/MultiFab.cpp commit 493a2674a25400a55eadc508a75a0fba9a423e6a Author: Brian Friesen Date: Wed Aug 12 12:03:42 2015 -0700 Geometry: changed separate MPI_ROOT/MPI_PROC_NULL Bcast()s to a single Bcast() Src/C_BaseLib/Geometry.cpp commit d83fac4eabdfd604100e514ee9fbaf5ef6fb4d2b Author: Brian Friesen Date: Wed Aug 12 12:02:43 2015 -0700 DistributionMapping: changed separate MPI_ROOT/MPI_PROC_NULL Bcast()s to a single Bcast() Src/C_BaseLib/DistributionMapping.cpp commit e8ed87d3ae88114fbd21cb445ae4b2248333ae00 Author: Brian Friesen Date: Wed Aug 12 12:01:48 2015 -0700 BoxArray: changed separate MPI_ROOT/MPI_PROC_NULL Bcast()s to a single Bcast() Src/C_BaseLib/BoxArray.cpp commit 83d7fd630b6209d33a90b380d066149190f79cf4 Author: Brian Friesen Date: Tue Aug 11 13:49:15 2015 -0700 BoxArray, Geometry, MultiFab: change regular cast to const_cast in Bcast() The buffer in a Bcast() must not be a const, but some functions return consts. So const_cast them to be non-const wen we do the Bcast(). It's not pretty but it works. Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit 79db42d4246379b7c8a3d1d7d3272b704d4ee0f7 Author: Brian Friesen Date: Tue Aug 11 13:06:59 2015 -0700 DistributionMapping: add static function SendDistributionMappingToSidecars() When we move distributed data sets between the compute and MPI groups we send the FAB data using point-to-point communication, so each MPI group needs to know the distribution of FABs on the other group so that it knows who to Send() and Recv() from. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 1b2de8eaaddc8f7708f0382f77cc80c38da1d7fe Author: Brian Friesen Date: Tue Aug 11 11:15:03 2015 -0700 DistributionMapping: added define() to build a DM out of an Array This is useful if a DM is initialized with the default constructor and one wants to populate with a plain ol' array of ints. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 64dd430c74d412ac6cb0fca3db87df852b4a8e44 Author: Brian Friesen Date: Tue Aug 11 09:49:29 2015 -0700 BoxArray: added static function SendBoxArrayToSidecars() This clones a BoxArray onto the sidecar MPI group. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 7d8119a3679b9827704e16ffda9a6dbf56a27415 Merge: d662076d2 61d522c84 Author: Weiqun Zhang Date: Wed Aug 19 17:53:36 2015 -0700 Merge branch 'master' into pgas Conflicts: Src/C_BaseLib/FabArray.H Src/C_BaseLib/Make.package Tools/C_mk/Make.defs commit 61d522c84be722477d4bd47c5f611a031d76f22c Merge: 835c29d71 99d6969dd Author: Weiqun Zhang Date: Wed Aug 19 17:45:47 2015 -0700 Merge branch 'master' of github.com:BoxLib-Codes/BoxLib commit 835c29d7162c54e7081525d8dedcede22cd7ace2 Author: Weiqun Zhang Date: Wed Aug 19 17:22:47 2015 -0700 clean up MGT_Sover Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tutorials/MultiGrid_C/main.cpp commit 99d6969dd18fea3a9255eda83cf1f67740fcb99d Merge: 41da5318c 395fff20b Author: Brian Friesen Date: Wed Aug 19 16:01:40 2015 -0700 Merge branch 'add_analysis_abstract_base_class' This provides an abstract base class "Analysis" for doing data analysis during BoxLib simulations. It also provides a simple example of in-situ data processing executed on the sidecars. The actual analysis routines themselves must be provided by the user. commit 395fff20b2c4f4f2fedae044c075e2de07eff92c Author: Brian Friesen Date: Wed Aug 19 12:45:01 2015 -0700 Tutorials: added example "Sidecar_EX2" demonstrating use of Analysis class on sidecars Tutorials/Sidecar_EX2/GNUmakefile Tutorials/Sidecar_EX2/InSituAnalysis.H Tutorials/Sidecar_EX2/InSituAnalysis.cpp Tutorials/Sidecar_EX2/Make.package Tutorials/Sidecar_EX2/inputs_3d Tutorials/Sidecar_EX2/main.cpp commit 6e86d97059cf64947ba3a10d2c8152640568a259 Author: Brian Friesen Date: Wed Aug 19 12:24:30 2015 -0700 C_BaseLib: added abstract base class "Analysis" This class provides a platform for the user to do data analysis during BoxLib simulations. A class derived from Analysis should contain both functionality for doing the analysis itself, as well as storage for the results. Src/C_BaseLib/Analysis.H Src/C_BaseLib/Make.package commit 41da5318c0b1111c7f7afa15cc52ad998c6d4910 Author: Brian Friesen Date: Tue Aug 18 15:39:40 2015 -0700 C_mk: added missing "-mmic" flag for compiling Fortran files on MIC in debug mode Tools/C_mk/Make.Linux commit d662076d2c222950d29af719fb425e6f7fe19197 Author: Weiqun Zhang Date: Tue Aug 18 17:37:03 2015 -0700 started PGAS_SMC MiniApps/PGAS_SMC/Exec/Make.SMC MiniApps/PGAS_SMC/Exec/ToyFlame/GNUmakefile MiniApps/PGAS_SMC/Exec/ToyFlame/Make.package MiniApps/PGAS_SMC/Exec/ToyFlame/Prob_3d.f90 MiniApps/PGAS_SMC/Source/Make.package MiniApps/PGAS_SMC/Source/SMC.H MiniApps/PGAS_SMC/Source/SMC.cpp MiniApps/PGAS_SMC/Source/SMCBld.cpp MiniApps/PGAS_SMC/Source/SMC_advance.cpp MiniApps/PGAS_SMC/Source/SMC_io.cpp MiniApps/PGAS_SMC/Source/SMC_setup.cpp MiniApps/PGAS_SMC/Source/main.cpp commit 33b96aa4b5bb94a2c63479436c23df2eb7783e86 Author: Michael Zingale Date: Tue Aug 18 09:55:56 2015 -0400 add a subtitle to the main test page Tools/RegressionTesting/testnew.py commit 50b6a24b64adfbec80ecea3c9ff9f2ccba70f107 Author: Yili Zheng Date: Mon Aug 17 22:34:36 2015 -0700 Rewrite the PGAS version to use non-blocking signaling put and event-based point-to-point synchronization; thus removing the need of global barriers Src/C_BaseLib/BLPgas.H Src/C_BaseLib/BLPgas.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 5a96e4d68283bcb023789d84a5c4251ce6432207 Author: Michael Zingale Date: Mon Aug 17 16:02:19 2015 -0400 turn off inlining for pure PGI -- this generates an internal compiler error for knapsack.f90. Also drop down to -O2. This brings us more in line with what we use on the Cray's when we come in via the ftn wrapper. Tools/F_mk/comps/Linux_pgi.mak commit 14ee982afd07f5f12829dd394ba6de7846691c9b Merge: d43358759 6dbbd3caa Author: Michael Zingale Date: Mon Aug 17 15:04:58 2015 -0400 Merge branch 'master' of ssh://github.com/BoxLib-Codes/BoxLib commit d433587597891c02c2689917f372f086a0387d24 Author: Michael Zingale Date: Mon Aug 17 15:04:45 2015 -0400 get the compiler version working for pure PGI Tools/F_mk/comps/Linux_pgi.mak commit 6dbbd3caa6fe704f6a1e535a8814408423381b86 Author: Michael Zingale Date: Mon Aug 17 13:48:11 2015 -0400 make the tol 1.e-6 for highlighting Tools/RegressionTesting/testnew.py commit 15c393241ae627c000b092f7ba0ab583a97c1c20 Author: Michael Zingale Date: Mon Aug 17 13:31:39 2015 -0400 new test comparison table with highlighting Tools/RegressionTesting/testnew.py commit 8998acd991e62278848bc4732324ab7ca9ca24d3 Author: Michael Zingale Date: Mon Aug 17 10:53:31 2015 -0400 close an HTML header Tools/RegressionTesting/testnew.py commit d2873ed7e1ef4561c9d770e528e4e792eec4a7bd Author: Michael Zingale 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 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 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: 563fd4707 8a8ff836d Author: Ann Almgren Date: Fri Aug 14 10:29:43 2015 -0700 Merge branch 'master' of github.com:BoxLib-Codes/BoxLib commit 563fd470749f7861fd62653fd784f1644edc96e9 Author: Ann Almgren Date: Fri Aug 14 10:28:24 2015 -0700 Add another cycle type -- MG_FVCycle -- which is 1 F cycle followed by V cycles Src/LinearSolvers/F_MG/mg_tower.f90 commit 8a8ff836d2297951972dd03196933ca43c54a8ac Author: Weiqun Zhang Date: Thu Aug 13 11:32:21 2015 -0700 fixed periodic boundary and a local index bug Src/F_BaseLib/bndry_reg.f90 commit 0155e668db5814f3924502b88de6f101d3f87bd9 Author: Weiqun Zhang Date: Thu Aug 13 06:45:39 2015 -0700 delete removed variable 'id' from omp private Src/F_BaseLib/bndry_reg.f90 commit 731fff37e42deb6eb504bcd2ebb1696c9720c550 Author: Weiqun Zhang Date: Wed Aug 12 22:37:45 2015 -0700 avoid covered coarse cells in ml_interp_bcs; in order to to do that, mask is built in bndry register Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/ml_nd.f90 commit 7626e166aabc8eecb5eb4f8b1685774f3733707e Author: Weiqun Zhang Date: Wed Aug 12 11:11:27 2015 -0700 print more information Src/LinearSolvers/F_MG/ml_cc.f90 commit 3ae839d7ffdf826dc2c14f664d0871246b169eaf Author: Max Katz Date: Thu Aug 13 16:14:23 2015 -0500 Make Titan consistent with other Cray machines we're using by adding -lmpichf90. Tools/C_mk/Make.mpi commit 1fac90ac4aef4f0f2467081a1ba62f04dd71d91e Author: Ann Almgren Date: Thu Aug 13 13:27:21 2015 -0700 Oops -- committed the wrong expression for the stencil. Now works with Dirichlet as well as periodic. Src/LinearSolvers/C_CellMG/ABec_3D.F commit 2123b517be444d4937ad08f5dd69361bcf9f8daf Author: Ann Almgren Date: Thu Aug 13 13:00:08 2015 -0700 I have modified the 3D GSRB relaxation to use an over-relaxation factor of 1.15. This makes it the same as the smoother used in the F90 solver, and seems to consistently reduce the number of V-cycles needed. Src/LinearSolvers/C_CellMG/ABec_3D.F commit 75a6c59bcbb5a38461b892c1fa51a03c5152cf08 Author: Weiqun Zhang Date: Tue Aug 11 11:37:55 2015 -0700 use std::pair instead of std::make_pair because the latter does not work in C++11 due to template type deduction rules Src/C_BaseLib/FabArray.H commit 5e64772cee41eb4aea4753543c843a5b30954f5e Merge: e8954cf81 1b44cbefd Author: Weiqun Zhang Date: Mon Aug 10 17:43:43 2015 -0700 Merge branch 'weiqun' commit e8954cf81f29f07ea72fa4a382a38e8cd6df1b9f Author: Weiqun Zhang Date: Mon Aug 10 17:43:35 2015 -0700 allocate at lease 1 element if asked size is zero Src/C_BaseLib/mempool_f.f90 commit e161371d033a4ed3b3a4f6fee2e3f578ff68bc3e Author: Weiqun Zhang Date: Mon Aug 10 17:17:52 2015 -0700 fixed bugs in vector_i function that has never been used Src/F_BaseLib/vector_i.f90 commit f2958a6aaf9438af0b17643ef0a914fb99d9498b Merge: 2b4db8e31 009503a63 Author: vince Date: Mon Aug 10 12:58:10 2015 -0700 Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib commit 2b4db8e318c26d24e62badaed16ac27dcdbeecee Author: vince Date: Mon Aug 10 12:57:33 2015 -0700 code cleanup. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Utility.cpp commit 009503a63db2da581665a3aa34e2a407c08626cc Author: Brian Friesen Date: Mon Aug 10 11:24:49 2015 -0700 MultiFab: clean up SendMultiFabToSidecars() interface Now the only argument to MultiFab::SendMultiFabToSidecars() is a MultiFab pointer. In the Compute group this will point to a MultiFab with actual data filled in, whereas in the Sidecar group this will point to a MultiFab which is allocated but uninitialized prior to this function call. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Tutorials/Sidecar_EX1/GridMoveTest.cpp commit 1406a2c601cb3258103d1f1cbfc2608eddc584c0 Author: Brian Friesen Date: Mon Aug 10 11:02:34 2015 -0700 Geometry: clean up SendGeometryToSidecars() interface Now the only argument to Geometry::SendGeometryToSidecars() is a Geometry pointer. In the Compute group this will point to a Geometry with actual data filled in, whereas in the Sidecar group this will point to a Geometry which is allocated but uninitialized prior to this function call. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Tutorials/Sidecar_EX1/GridMoveTest.cpp commit 074781ba770bca63d6f037b092eeb3df7a14c339 Merge: f334cac5f 2df923040 Author: vince Date: Mon Aug 10 11:03:06 2015 -0700 Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib commit 1b44cbefd2ad2ddc8edeb851a7e3f400fbe09e07 Author: Weiqun Zhang Date: Mon Aug 10 10:59:04 2015 -0700 Avoided allocating temporary multifab in multifab parallel copy Src/F_BaseLib/multifab_f.f90 commit 68785531edeaa79f779a68801f1b6387ed7d7eb3 Author: Yili Zheng Date: Fri Aug 7 15:13:35 2015 -0700 Added SeqNum (tag) matching in BLPgas::Send; Changed map to multimap; Use unordered_multimap if C++11 is available; Enabled non-blocking UPC++ code in Geometry.H Src/C_BaseLib/BLPgas.cpp Src/C_BaseLib/Geometry.H commit 0a5d0b6586e3c18b998fd1d6fa56974c3abd032a Author: Weiqun Zhang Date: Thu Aug 6 14:57:48 2015 -0700 fixed typo Src/C_BaseLib/Geometry.H commit 77b2b36dfdbcdd9994790e7636948e5233cee632 Author: Weiqun Zhang Date: Thu Aug 6 14:38:27 2015 -0700 nonblocking version of FillPeriodicBoundary Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Tutorials/PGAS_HEAT/main.cpp commit 835fc68e681e462cc84e07f049f83e9b0bd96aeb Author: Weiqun Zhang Date: Thu Aug 6 11:15:57 2015 -0700 moved pgas send into new files Src/C_BaseLib/BLPgas.H Src/C_BaseLib/BLPgas.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Make.package commit e92de81e66f6f375f98b1aa228fa6847c1c9caa8 Author: Weiqun Zhang Date: Wed Aug 5 12:36:50 2015 -0700 added USE_UPCXX to makefile Tools/C_mk/Make.defs Tools/C_mk/Make.upcxx Tutorials/PGAS_HEAT/GNUmakefile commit d8ade2087159112d8ccf988bebabebb5d86ab2f1 Author: Weiqun Zhang Date: Wed Aug 5 12:22:33 2015 -0700 fixed merge Src/C_BaseLib/BoxLib.cpp commit f260a60c58188ef613980366d89f9943b3d06ac9 Merge: 3e5d35e86 2df923040 Author: Weiqun Zhang Date: Wed Aug 5 10:37:11 2015 -0700 Merge branch 'master' into pgas commit 2df9230407f01dcdd087161811600efc518b14e9 Author: Weiqun Zhang 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 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 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 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 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 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 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 Date: Tue Aug 4 12:15:36 2015 -0700 itac suffix. Tools/C_mk/Make.defs commit bc361948e69f9648361397d4ce7c546ea19a12cf Merge: 63d055aa7 f8083db82 Author: vince Date: Tue Aug 4 12:14:07 2015 -0700 Merge branch 'master' of https://github.com/BoxLib-Codes/BoxLib commit 3e5d35e86f45b4c03adedc76adc6fdcf260fc032 Merge: b03d062a1 f8083db82 Author: Weiqun Zhang 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 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 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 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 Date: Fri Jul 31 15:21:10 2015 -0700 made 1d gsrb truly rb Src/LinearSolvers/F_MG/cc_smoothers.f90 commit 526b09deadade958394423ab8540266fe02eac68 Merge: 6a2122636 4afa62fd8 Author: Marc Day 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 Date: Fri Jul 31 12:24:57 2015 -0700 Update release tag ID Tools/CMake/BoxLib_Version.cmake commit 4afa62fd8a688e79913e6ef37b48f3d6d1ec5727 Author: Weiqun Zhang Date: Fri Jul 31 11:06:39 2015 -0700 mfiter: fixed a special case in which there is no local boxes at all Src/F_BaseLib/layout.f90 commit 71924a551612ff495bd9451d70268e9e9ea363a4 Author: Michael Zingale Date: Fri Jul 31 13:17:12 2015 -0400 sometimes if there is a crash before output, then our check on the number of levels fails and we get a wordy error message in the overview table. Now we check if the result is an integer to prevent this Tools/RegressionTesting/testnew.py commit 6a80103f32394517d5e767cf5783b58a9fc62a1e Author: Michael Zingale Date: Fri Jul 31 13:01:09 2015 -0400 fix the storing of the diffDir if it paradoxically is a file Tools/RegressionTesting/testnew.py commit 5fd7d2afe2522c53a52986c1a32a0b9df7239282 Author: Michael Zingale 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 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 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 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 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 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 Date: Tue Jul 28 16:57:09 2015 -0700 fixed 2D tilearray_build Src/F_BaseLib/layout.f90 commit 87666d0beb7d9217b3de62bb26699969018a12dc Author: Weiqun Zhang Date: Tue Jul 28 16:29:35 2015 -0700 PGI: link to cpplib Tools/F_mk/comps/Linux_pgi.mak commit d0ccce487c27a1d3f3e9bdb8c4663467feeec798 Merge: 48297cb17 e552e303f Author: Weiqun Zhang Date: Tue Jul 28 15:32:31 2015 -0700 Merge branch 'mempool' of gamera.lbl.gov:/usr/local/gitroot/BoxLib into mempool commit 48297cb17ba681471e208dcdcba4c4c8fbed13dc Merge: c1e42db7e cb95de3d0 Author: Weiqun Zhang Date: Tue Jul 28 15:32:07 2015 -0700 Merge branch 'master' into mempool Conflicts: Src/F_BaseLib/multifab_f.f90 commit e552e303f78a23cba494e50fa8d35b060bd5a5dc Merge: f62a2b699 c1e42db7e Author: Weiqun Zhang 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 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 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 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: 580920963 cb95de3d0 Author: Weiqun Zhang Date: Mon Jul 27 17:06:58 2015 -0700 Merge branch 'master' into mempool Conflicts: Src/F_BaseLib/multifab_f.f90 commit 5809209638035fcc653c5a623b941ce8ce01872e Author: Weiqun Zhang Date: Mon Jul 27 16:42:39 2015 -0700 include C_BaseLib whenever F_BaseLib is included Src/F_BaseLib/GPackage.mak Tutorials/Tiling_Heat_F/GNUmakefile commit cb95de3d06d1e5a60847b88545832c7b2ee51402 Author: Weiqun Zhang Date: Mon Jul 27 16:36:24 2015 -0700 ability to handle restarting from and old checkpoint that does have the same number of states Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit a888edd3bd030cee2e0d2340ef76eab14a0df3ee Merge: fb9ffe60e 6927ff2b0 Author: Brian Friesen Date: Mon Jul 27 13:11:40 2015 -0700 Merge branch 'sidecar' This series of commits expands Vince's original stubs for in-situ performance monitoring framework. It introduces the notion of "sidecars", which are a set of MPI processes in a second, non-overlapping MPI group. They do not perform the "main" grunt work of the application -- this is undertaken by the "Compute" MPI group -- but rather can perform auxiliary tasks such as in-situ post-processing of MultiFab data, dynamic optimization and regridding strategies, etc. One annoying feature of this implementation is that the number of sidecars must be specified at compile time, not run time. This is because of the complicated initialization procedures in BoxLib and ParallelDescriptor which prevent the use of a ParmParse before MPI initialization has completed. This should definitely be fixed in the future if the sidecars become a popular tool. commit 6927ff2b04f2b9d5d667b0dbf393d842cc7caf61 Author: Brian Friesen Date: Fri Jul 24 15:31:47 2015 -0700 Tutorials: added example "Sidecar_EX1" to show how to send data to "sidecar" MPI group Tutorials/Sidecar_EX1/GNUmakefile Tutorials/Sidecar_EX1/GridMoveTest.cpp Tutorials/Sidecar_EX1/Make.package Tutorials/Sidecar_EX1/inputs_3d Tutorials/Sidecar_EX1/run.sh commit f0ea1627d915c44e63af55b5291422389a288fef Author: Brian Friesen Date: Fri Jul 24 15:16:17 2015 -0700 Geometry: add static function SendGeometryToSidecars() This clones a Geometry from the compute MPI group onto the "sidecar" MPI group. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 2c822ab81ac5519e1d27612f9d6e8c31d6222010 Author: Brian Friesen Date: Fri Jul 24 15:15:15 2015 -0700 MultiFab: add static function SendMultiFabToSidecars() This clones a MultiFab from the compute MPI group onto the "sidecar" MPI group. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 92e684cc9567e7f21327d6b7d0a5cfaf9938bde4 Author: Brian Friesen Date: Fri Jul 24 15:39:25 2015 -0700 ParallelDescriptor: add static function InCompGroup() This function is analogous to InSidecarGroup(). Src/C_BaseLib/ParallelDescriptor.H commit d8719919360b518bdab7098702359ebcfc84c873 Author: Brian Friesen Date: Tue Jul 21 13:45:12 2015 -0700 ParallelDescriptor:: remove some roll-call print statements Src/C_BaseLib/ParallelDescriptor.cpp commit 7b9c88477e4d27fe47c55d2c516d68b12686e246 Author: Brian Friesen Date: Fri Jul 24 15:29:55 2015 -0700 ParallelDescriptor: Communicator(), MyProc(), and NProcs() return values in the "local" communicator A large number of funtions assume the existence of only a single, global communicator, even though they operate on local objects. This approach worked fine until we introduced the notion of distinct MPI groups for computation and in-transit analysis. These MPI functions frequently break when operating on the in-transit processes because they request the computation communicator, which is undefined on those processes. Rather than introducing a million if-else's to all these functions, forcing them to explicitly return CommunicatorComp() or CommunicatorInTransit(), we just let Communicator() pick the correct communicator automatically. Src/C_BaseLib/ParallelDescriptor.H commit bc6eec4fdb0513d52a4d96722c9af292a73c339b Author: Brian Friesen Date: Fri Jul 24 15:12:55 2015 -0700 ParallelDescriptor:: rename "perfmon" -> "sidecar" Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 609a57546fa796ecb8d25e18f03b64577ff254fd Author: Brian Friesen Date: Tue Jul 21 13:37:10 2015 -0700 BLProfiler: remove perfmon stubs Src/C_BaseLib/BLProfiler.H Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BoxLib.cpp commit fb9ffe60e2eb7523a5c60ebe8ee7573e19d26399 Author: Michael Zingale Date: Mon Jul 27 10:07:54 2015 -0400 remove the old compareToolDir -- it is now part of BoxLib Tools/RegressionTesting/Maestro-tests.ini commit 012169ecb10c72245db547e432675b4e5df34f7f Author: Michael Zingale Date: Sat Jul 25 21:59:57 2015 -0400 add e-mail to the maestro-development group upon failure Tools/RegressionTesting/Maestro-tests.ini commit 772b8dddb8d13ea99210bdae069808b0fd7b034f Merge: 0b0854ba3 102b7c4b0 Author: Andy Nonaka Date: Fri Jul 24 12:59:08 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 0b0854ba38c00333a759402f907270b75243ebc5 Author: Andy Nonaka Date: Fri Jul 24 12:54:39 2015 -0700 created a fortran get_allnodaltilebox for nodal-in-all-dimensions boxes Src/F_BaseLib/multifab_f.f90 commit 0f271fba815491db8473646d8fa60eef1e56add5 Author: Weiqun Zhang Date: Wed Jul 22 17:07:14 2015 -0700 minor tweaks Src/F_BaseLib/boxlib_f.f90 Src/F_BaseLib/multifab_f.f90 Tools/F_mk/comps/Linux_intel.mak commit 18aa5bec14072784354ea28333761f98cb29c34d Author: Weiqun Zhang Date: Wed Jul 22 15:04:30 2015 -0700 added CXXFLAGS for Intel in Fortran makefile Tools/F_mk/comps/Linux_intel.mak commit eebd105f3ff87e84a373a6f98655eebe2ae56221 Author: Weiqun Zhang Date: Wed Jul 22 14:59:05 2015 -0700 each thread must destroy its own memory Src/F_BaseLib/layout.f90 commit 95c9ad785e599821fb8478544fcc395133f18c21 Author: Weiqun Zhang Date: Wed Jul 22 14:06:25 2015 -0700 new makefile for Fortran Src/C_BaseLib/GPackage.mak commit 1274f7c37943e4c2e7620281ecdeec5bcc7d82ff Author: Weiqun Zhang Date: Wed Jul 22 14:00:37 2015 -0700 started a branch that can use memory pool in Fortran BoxLib codes Src/C_BaseLib/BLassert.H Src/C_BaseLib/MemPool.cpp Src/C_BaseLib/mempool_f.f90 Src/F_BaseLib/boxlib_f.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak Tools/F_mk/comps/gfortran.mak Tutorials/Tiling_Heat_F/GNUmakefile commit 102b7c4b0ba77ac9906a5bfdb00594484328a9cb Author: Weiqun Zhang Date: Tue Jul 21 23:30:54 2015 -0700 Fortran mfiter: only let master do memory allocation and deallocation Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit ef3a00810888b8ebdfbee0de5276d63d38543075 Author: Weiqun Zhang Date: Tue Jul 21 17:27:42 2015 -0700 Fortran mfiter: save tilearray in layout Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit bf8814168e0e0f6134cff41b6ce3b3c84d703fa9 Author: Weiqun Zhang Date: Tue Jul 21 12:24:12 2015 -0700 Fortran mfiter: fixed a bug in tilearray checking and return the head if a tilearray is found. Src/F_BaseLib/layout.f90 commit 4215412c02685a29c2212dde9845da3398ef846a Author: Weiqun Zhang Date: Tue Jul 21 09:50:56 2015 -0700 rewrote Fortran mfiter; hopefully it's faster with multiple threads Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit d2e6961a9f32e592c1788b7cdb701a72ab413884 Author: Weiqun Zhang Date: Mon Jul 20 20:53:32 2015 -0700 identation Src/C_BaseLib/FabArray.cpp commit dd65a7e3b35e3e26c8c65848c825ecb4d37022d2 Author: Marc Day Date: Mon Jul 20 18:51:55 2015 -0700 Move .H and .cpp listings in the CMakelists.txt in C_Baselib Src/C_BaseLib/CMakeLists.txt commit cfadc04dfc88ff35425801b8319f23a92d398d7f Merge: a6e4f794e 1bcb01e95 Author: Marc Day Date: Mon Jul 20 18:49:52 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 63d055aa7a96f1e5418a1a84158397c7d306ac43 Author: vince Date: Mon Jul 20 16:45:19 2015 -0700 swap pair test. Src/C_AMRLib/Amr.cpp commit 1bcb01e95616b1ad5b3ed5e66bd462cab5b75d94 Author: Jessica Kawana Date: Mon Jul 20 16:19:04 2015 -0700 Included timing files and run script Tutorials/Tiling_Heat_F/results/babbage_omp.run Tutorials/Tiling_Heat_F/results/results.txt Tutorials/Tiling_Heat_F/results/t1a.txt Tutorials/Tiling_Heat_F/results/t1b.txt Tutorials/Tiling_Heat_F/results/t2a.txt Tutorials/Tiling_Heat_F/results/t2b.txt Tutorials/Tiling_Heat_F/results/t3a.txt Tutorials/Tiling_Heat_F/results/t3b.txt Tutorials/Tiling_Heat_F/results/t4a.txt Tutorials/Tiling_Heat_F/results/t4b.txt Tutorials/Tiling_Heat_F/results/t5a.txt Tutorials/Tiling_Heat_F/results/t5b.txt Tutorials/Tiling_Heat_F/results/t6a.txt Tutorials/Tiling_Heat_F/results/t6b.txt Tutorials/Tiling_Heat_F/results/t7a.txt Tutorials/Tiling_Heat_F/results/t7b.txt commit 652b4bae385626b8262e467c66b567fecc09abd2 Author: Jessica Kawana Date: Mon Jul 20 16:09:21 2015 -0700 Changed configuration to match tests on Babbage, includes some results Tutorials/Tiling_Heat_F/advance.f90 Tutorials/Tiling_Heat_F/inputs_3d Tutorials/Tiling_Heat_F/results.txt commit 54ffe9ddb577935883ef5c06693f724548fa04bb Author: Jessica Kawana Date: Mon Jul 20 13:18:05 2015 -0700 Added timer Tutorials/Tiling_Heat_F/advance.f90 commit 1aebdb969c75e8bc62cea116995ff168a0a5f13c Merge: 52dc3b8ab 3104d53e6 Author: vince Date: Mon Jul 20 12:09:59 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3104d53e63819dfe01e9152f857249d849921c47 Author: Weiqun Zhang Date: Mon Jul 20 10:54:53 2015 -0700 fixed uninitialized values to quiet valgrind; added some comments Src/F_BaseLib/layout.f90 commit 9b5255b025cfdc0912b1acd03c1eaab98e2bebde Author: Andy Nonaka Date: Mon Jul 20 10:51:00 2015 -0700 end if -> endif Tools/F_mk/GMakedefs.mak commit 86221be96f54977d73bca260d46a1ade921bd2aa Author: Andy Nonaka Date: Mon Jul 20 10:48:39 2015 -0700 if compiled with MIC=t, add .mic to executable Tools/F_mk/GMakedefs.mak commit 52dc3b8ab7c98a15ca29eca5f481c16f9ce066cd Merge: 81449569b acc5d3e07 Author: vince Date: Mon Jul 20 10:45:49 2015 -0700 merge conflict. commit acc5d3e0776ab757d9edbd6d8e0d67100f9e91a1 Author: Weiqun Zhang Date: Mon Jul 20 10:26:21 2015 -0700 fixed a new bug in FabSet: wrong source index Src/C_BoundaryLib/FabSet.cpp commit 5fed13edfd7db24f68635f2214d87d516bec55a7 Author: Weiqun Zhang Date: Mon Jul 20 06:56:16 2015 -0700 fixed another new bug in parallel copy Src/C_BaseLib/FabArray.H commit 566745cb1815c86b369d58c1be2a111e2aa7ed96 Merge: 75b5e7aca 31fbd4b0e Author: Weiqun Zhang Date: Mon Jul 20 06:16:52 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 75b5e7acafdf6cb19d7e8adf8fcd2e5ee8ed8cf2 Author: Weiqun Zhang Date: Mon Jul 20 06:16:42 2015 -0700 fixed a new bug in parallel copy: shouldn't set n_grow twice Src/C_BaseLib/FabArray.H commit 31fbd4b0e71fa9c42b48d86050762379ed6ec5f7 Author: Brian Friesen Date: Sun Jul 19 17:48:36 2015 -0700 Make: updated Babbage detection to work on any of the login nodes when selecting compiler flags in F_mk Tools/F_mk/comps/Linux_intel.mak commit fefd7b32e66e4024e969024a69655a63b3077f77 Author: Brian Friesen Date: Mon Jun 29 14:06:51 2015 -0700 Make: added Makefile variable "ITAC_TRACE" to define compiler flags and libs used with Intel Trace Analyzer and Collector Tools/C_mk/Make.Linux commit 0088baebef159bd3a53d01a0726be7026261a8a1 Author: Brian Friesen Date: Mon Jun 29 13:51:10 2015 -0700 Make: added "-xHost" flag to Intel compiler when compiling for Edison or the Xeon host on Babbage This flag generates the highest available instruction set on the native architecture. Without it, the compiler defaults to SSE2, while many newer instruction sets exist, including AVX, AVX2, SSE3, and SSE4.1/4.2. However, when compiling code for the MIC we can't use "-xHost" or any other instruction set request flag, hence all the logic around Babbage in this commit. Tools/C_mk/Make.defs Tools/F_mk/comps/Linux_intel.mak commit 4e298b046a919c0ae0fbb80e4b6ad9c96b9e75b5 Author: Brian Friesen Date: Mon Jun 29 13:56:04 2015 -0700 Make: added Makefile variable "MIC" for compiling native code for Intel MIC This adds the "-mmic" flag to the Intel compiler if the MIC variable is defined. Tools/C_mk/Make.Linux Tools/F_mk/comps/Linux_intel.mak commit 4d584f2995b548dd532d2c6419b7a23c45ee0faf Author: Brian Friesen Date: Tue Jun 9 12:20:25 2015 -0700 Make: use MPI compiler wrappers on orga No need to specify include/library directories by hand. Let the wrappers do all the work. Tools/C_mk/Make.mpi commit cbb1c3e88c10cf16515479f883de3e139fabd26b Author: Weiqun Zhang Date: Sun Jul 19 10:52:10 2015 -0700 Option to call dimension agnostic Fortran subroutines in deriving. Note that it is OK to mix the two types Fortran functions in the derive list. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp Src/C_BaseLib/ArrayLim.H commit 742cf9625500e11ed07cae7c8a9b633220f4e7ba Merge: 03e501ab5 9080603c5 Author: Weiqun Zhang Date: Sun Jul 19 06:55:19 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9080603c55391900bdb1f01682627a1d7b89d644 Author: Jessica Kawana Date: Fri Jul 17 17:21:59 2015 -0700 Swaps pointers between phi_old and phi_new instead of using actual multifab_copy to avoid allocating and de-allocating data. Tutorials/Tiling_Heat_F/advance.f90 commit 6990535aa1199be0089ef7b0eb98deb786284833 Author: Jessica Kawana Date: Fri Jul 17 16:59:06 2015 -0700 Combined compute_flux and update_phi subroutines into advance_phi. Tutorials/Tiling_Heat_F/advance.f90 Tutorials/Tiling_Heat_F/main.f90 commit 03e501ab5bdb6f229c15f8e07e54563bb21d0eb7 Author: Weiqun Zhang Date: Fri Jul 17 15:37:55 2015 -0700 Parallel copy can now include ghost cells for both source and destination. Note that it will not handle periodic boundary properly if the desitnation box includes ghost cells because MultiFab does not even know about periodicity. Src/C_BaseLib/FabArray.H Src/C_BoundaryLib/FabSet.cpp commit d3065390639a3727206e8bf7c830ba86a7e5b0ee Author: Weiqun Zhang Date: Fri Jul 17 14:50:11 2015 -0700 comment Src/C_BaseLib/MultiFab.H commit 086ebcdbec9b427217a7b6fa642a72595f71eaf8 Merge: 08de965ce 96d26c4f8 Author: Jessica Kawana Date: Fri Jul 17 13:08:16 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 08de965ce4872bb0334df6918c09895c18960494 Author: Jessica Kawana Date: Fri Jul 17 13:07:30 2015 -0700 Starting off Tiling_Heat_F as a copy of HeatEquation_EX1_F Tutorials/Tiling_Heat_F/GNUmakefile Tutorials/Tiling_Heat_F/GPackage.mak Tutorials/Tiling_Heat_F/advance.f90 Tutorials/Tiling_Heat_F/init_phi.f90 Tutorials/Tiling_Heat_F/inputs_2d Tutorials/Tiling_Heat_F/inputs_3d Tutorials/Tiling_Heat_F/main.f90 Tutorials/Tiling_Heat_F/write_plotfile.f90 commit 97b5aab3915f038a9c773fb9fe531806d02bb36b Author: Weiqun Zhang Date: Thu Jul 16 21:37:42 2015 -0700 added optional argument for number of ghost cells in parallel copy; this relieve the user's burden and avoids creating a temporary mulitfab. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BoundaryLib/FabSet.cpp commit 96d26c4f87178fc23a2596d6d119b3786f585c34 Author: Weiqun Zhang Date: Thu Jul 16 20:49:59 2015 -0700 added a new macro BL_TO_FORTRAN_N_3D provide by Max K. and moved ZFILL to ArrayLim.H Src/C_BaseLib/ArrayLim.H Src/C_BaseLib/BLFort.H commit bc3ba0fc1e58eff4b9c95cc8c46b911e8b46d886 Author: Weiqun Zhang Date: Thu Jul 16 15:34:44 2015 -0700 fixed a new bug Src/C_BaseLib/FabArray.cpp commit 84c5eeb162d9f0a7e0c7e07833cf64caf2d72486 Author: Weiqun Zhang Date: Thu Jul 16 15:11:04 2015 -0700 FillPatchIterator now interally has a normal MulitFab with non-overlapping grids Src/C_AMRLib/AmrLevel.cpp commit df445133f74b0f2db3405ffaa8e876c1cb6c7378 Author: Weiqun Zhang Date: Thu Jul 16 14:52:29 2015 -0700 allow MultiFab change n_grow without changing the data; this is useful for avoiding too local MultiFab to MultiFab copies in parallel copy, which only copies from valid to valid regions; Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit e8ffcb57a154ac3db874e634d3060c19e957cc21 Author: Weiqun Zhang 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 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 Date: Thu Jul 16 13:06:59 2015 -0700 more random cluster tests. Src/C_BaseLib/DistributionMapping.cpp commit 1a3057ea8836a677fc0cd3d57146bdba4ff68fba Author: vince Date: Thu Jul 16 12:23:49 2015 -0700 random cluster distribution test. Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 6aa65e7a3a739e5900086152b6446246f1d1bb02 Author: Weiqun Zhang Date: Thu Jul 16 10:47:27 2015 -0700 added a new macro ZFILL that in 1D and 2D take a real array like dx, make it three elements long, and fill the new elements with zero; it won't do anything in 3D Src/C_BaseLib/BLFort.H commit c7f210f45a177c72ff33dc2c886e8342f1d592e0 Author: Weiqun Zhang Date: Wed Jul 15 20:47:12 2015 -0700 MemPool: tidy Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/MemPool.H Src/C_BaseLib/MemPool.cpp Src/C_BaseLib/mempool_f.f90 commit 1df5aacba20673451eb699e4b45587becd7f4ed0 Author: Weiqun Zhang Date: Wed Jul 15 17:36:40 2015 -0700 revert my accident commit Tutorials/Tiling_Heat_C/advance_3d.f90 Tutorials/Tiling_Heat_C/init_phi_3d.f90 commit 9194883963124b6d842de1ecb0ca16fcfa3ebd74 Author: Weiqun Zhang Date: Wed Jul 15 17:21:27 2015 -0700 modified some macros to pass 3d integer index arrays right-filled with zeros in cased of 1d or 2d Src/C_BaseLib/ArrayLim.H Src/C_BaseLib/BLFort.H commit e283ae9fdfcf1b730acd349f4badb0d33d71a212 Author: Weiqun Zhang Date: Wed Jul 15 16:07:46 2015 -0700 Max's change that increases the optimization level of Cray compiler Tools/C_mk/Make.Linux Tutorials/Tiling_Heat_C/advance_3d.f90 Tutorials/Tiling_Heat_C/init_phi_3d.f90 commit 6e7927fa87626e4c329286695b5b4713d9e12e85 Author: Marc Day Date: Wed Jul 15 13:57:07 2015 -0700 Add kumonga to make system Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit f6bfa9ab94ec752bd39b35fe9b79b889e6093216 Author: vince Date: Tue Jul 14 15:03:13 2015 -0700 staggered cluster test. Src/C_BaseLib/DistributionMapping.cpp commit d057f983f778cf6e27ee7766bfdca0fee85a2d7d Author: Andy Nonaka Date: Tue Jul 14 10:20:33 2015 -0700 initialize the timers Tutorials/HeatEquation_EX1_F/main.f90 commit 44095aca66961d299288690e00fdcaa291e141da Author: Andy Nonaka Date: Tue Jul 14 09:44:29 2015 -0700 add some timers Tutorials/HeatEquation_EX1_F/advance.f90 commit 99c4ff052cb2f2802c6f1b14017b0bcfba907908 Author: vince Date: Mon Jul 13 16:56:22 2015 -0700 more staggered grids. Src/C_BaseLib/DistributionMapping.cpp commit 85116c6290ef03c0493e45948dbd361d72748466 Author: vince Date: Mon Jul 13 16:52:36 2015 -0700 more staggered grids. Src/C_BaseLib/DistributionMapping.cpp commit e2f2e308f51d8d7429e295b50eee33fde78d7150 Author: Weiqun Zhang Date: Mon Jul 13 16:27:28 2015 -0700 revert 'always use cray wrappers' because it causes problems for vtune Tools/C_mk/Make.Linux commit c977a996df7edb4727b1ff8309f31e21faaf268e Author: vince Date: Mon Jul 13 13:52:52 2015 -0700 added stagger option for mlpfc. Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H commit 98f6938c38c423660ffdd5a7366912263fb82682 Author: Weiqun Zhang Date: Sun Jul 12 22:27:05 2015 -0700 allow Intel compiler more memory and time Tools/C_mk/Make.defs commit c925bcdd1281baaada24edf9323a9baf2fbd6188 Author: Weiqun Zhang Date: Sun Jul 12 22:23:26 2015 -0700 always use cray wrappers Tools/C_mk/Make.Linux commit 40049f04f4a279d90fe610823299298cbb920abe Merge: 921e4bc85 ce2c315a6 Author: Weiqun Zhang Date: Sun Jul 12 22:22:09 2015 -0700 Merge branch 'mempool' commit ce2c315a68d947cc96855742b6ddaec8c8859219 Author: Weiqun Zhang Date: Sun Jul 12 20:33:15 2015 -0700 implemented a thread friendly memory pool that can be used in both C++ and Fortran to increase the speed of allocating and deallocating arrays inside OMP. Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/CArena.H Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/C_BaseLib/MemPool.H Src/C_BaseLib/MemPool.cpp Src/C_BaseLib/mempool_f.f90 commit 921e4bc85b93187b4fc9df8d65e36ff309ab293d Author: Andy Nonaka Date: Thu Jul 9 08:57:42 2015 -0700 works on any babbage login node now Tools/F_mk/GMakeMPI.mak commit 1887cd78d79b93f6625497b01768fcc60bad7005 Author: vince Date: Tue Jul 7 15:15:11 2015 -0700 some cleanup. Src/C_BaseLib/FabArray.H commit 3fc6bafd9bc1379a63cfd46a04a886d7995a8087 Author: vince Date: Tue Jul 7 13:46:00 2015 -0700 more multilevel distribution maps for moveallfabs. we now have full control. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H commit 51ec5bc17ad832ffd8185458af1b984490c1e58f Author: Weiqun Zhang Date: Tue Jul 7 12:50:02 2015 -0700 starting a new branch for PGAS and split FillBoundary into two functions Src/C_BaseLib/FabArray.H Tutorials/PGAS_HEAT/GNUmakefile Tutorials/PGAS_HEAT/Make.package Tutorials/PGAS_HEAT/advance_3d.f90 Tutorials/PGAS_HEAT/init_phi_3d.f90 Tutorials/PGAS_HEAT/inputs_3d Tutorials/PGAS_HEAT/main.cpp Tutorials/PGAS_HEAT/writePlotFile.H Tutorials/PGAS_HEAT/writePlotFile.cpp commit 62b07cd9cc6b04c8eb0e56d657403f9b0355c954 Author: Michael Zingale Date: Tue Jun 30 12:56:15 2015 -0400 remove debugging prints Tools/RegressionTesting/testnew.py commit b5e14617fd64389aa9bac077a1bfa0ad1043611c Author: Michael Zingale Date: Tue Jun 30 12:55:27 2015 -0400 catch AttributeError for the compilation failure too Tools/RegressionTesting/testnew.py commit 16f348309b39648fdd6f778e2b77054b5f377eae Merge: 0b6e6560e 2802ea126 Author: Adam Jacobs 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 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 Date: Mon Jun 22 13:30:10 2015 -0700 Changed path Tools/F_mk/GMakeMPI.mak commit a8ce9a1395826ef7b06d31d5782f9c6568a548a8 Author: Ann Almgren Date: Thu Jun 18 17:20:18 2015 -0700 Add 3D UniformVelocity test. Tools/RegressionTesting/BoxLib-tests.ini commit 51ffe8e476aaf9102d0f196812c9518a60bc82bc Merge: 6b04925b4 5be15104d Author: Ann Almgren 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 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: ad0d65813 3d537fe2f Author: Jessica Kawana Date: Thu Jun 18 14:31:16 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ad0d6581327d86e453df60947b5a2ce8989aece2 Author: Jessica Kawana Date: Thu Jun 18 14:30:43 2015 -0700 Turned off Intel compiler runtime warnings. Tools/F_mk/comps/Linux_intel.mak commit 3d537fe2f23c26b7a1cdc9a1491be693f85ceae1 Author: Michael Zingale Date: Thu Jun 18 11:49:37 2015 -0400 fix a bug I recently introduced that makes tests that were not run show up as failures in the suite overview webpage Tools/RegressionTesting/testnew.py commit 7c244bda48c2be174997c92d8cc500752ae82b15 Merge: b18250593 519d9132f Author: Ann Almgren 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 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 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 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 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 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 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 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 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 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: 9e0c93745 cbf205aa5 Author: vince Date: Mon Jun 15 13:17:36 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9e0c9374502afb8a564a08a435d013c62bd134e2 Author: vince Date: Mon Jun 15 11:53:30 2015 -0700 added function to move fabs to a new distribution map for all fabarrays sharing the same distribution map. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Tutorials/MultiFabTests_C/GridMoveTest.cpp commit ca0dbc9d720c971e8194cc021a2daca842dec465 Author: vince Date: Wed Jun 10 14:19:19 2015 -0700 added id for distmaps. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit cbf205aa53d816e2235694adf08cc5a167ccb6ea Author: Weiqun Zhang 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 Date: Tue Jun 9 13:27:44 2015 -0700 SMC: extra optimization flags for babbage MiniApps/SMC/GNUmakefile commit efea1b9840c56320d84ed92fbea091c456557f97 Author: Weiqun Zhang Date: Tue Jun 9 13:26:52 2015 -0700 added babbage to make system in Fortran Tools/F_mk/GMakeMPI.mak Tools/F_mk/comps/Linux_intel.mak commit 4c8e405f79232def461648c4cfabe65213349b8d Author: Weiqun Zhang 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 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 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: 6ebb02e18 7313a0444 Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Sat Jun 6 09:41:34 2015 -0700 minor cleanup of mfiter Src/F_BaseLib/multifab_f.f90 commit db79d9306c940dab44b2e1e81de90b7a8a471eff Author: Weiqun Zhang Date: Fri Jun 5 23:24:01 2015 -0700 started working on tiling in Fortran Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit 7920e8d9c0725f43e63acdef16d7fe7525b178f0 Author: Weiqun Zhang Date: Wed Jun 3 20:15:53 2015 -0700 rename FabArrayBase::fpb_boxarray_max_size to FabArrayBase::comm_tile_size (communication tile size) Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Tutorials/Tiling_Heat_C/inputs_3d commit dd095be0e1a1435bcc855de7b9f82ae511b5d561 Author: Weiqun Zhang Date: Wed Jun 3 17:40:38 2015 -0700 changed defaults Src/C_BaseLib/FabArray.cpp Tutorials/Tiling_Heat_C/inputs_3d commit e95854e20f444e1322694d0e7fb1ffdce36ae939 Author: Weiqun Zhang Date: Wed Jun 3 12:11:52 2015 -0700 removed an unnecessary std::max Src/C_BaseLib/BoxList.cpp commit a1378740da3f64dd53b80cc24ad4c4989abee377 Author: Weiqun Zhang Date: Wed Jun 3 11:28:14 2015 -0700 It turns out maxSize is not suitable for chopping a nodal box into small chunks in the recent changes in FabArray because maxSize() returns overlapping nodal boxes. So a new function is added to chop a box into a list of non-overlapping tile boxes. Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit 9abcff3203134392d9f4a383a674736afa7ab16b Author: Weiqun Zhang Date: Tue Jun 2 17:31:09 2015 -0700 no need to build boxarray if it's not used Src/C_BaseLib/FabArray.cpp commit a690fad4c6529c2540227d0ef655c8ca226f75fb Author: Michael Zingale Date: Tue Jun 2 20:16:42 2015 -0400 fix a bug with --single_tests pointed out by Ann Tools/RegressionTesting/testnew.py commit 647476b719534971b0afd2fb930c45d145806d3f Merge: 6c081424e 19d3b6723 Author: Brian Friesen Date: Tue Jun 2 16:13:45 2015 -0700 Merge branch 'fpb_thread_friendly' These commits improve thread efficiency when updating periodic boundary conditions by splitting Boxes which intersect domain edges into BoxArrays of smaller Boxes. Each individual thread then copies data from each smaller Box to the corresponding region elsewhere on the domain, rather than a single thread copying the entire intersecting Box while all the other threads spin idly. Preliminary tests using 120 threads on Babbage at NERSC have indicated a ~20x speedup for the boundary value update step, compared to the same number of threads updating boundary values using the old method. On systems with less concurrency the performance gain from these changes will likely be smaller. commit 19d3b67238d3406058b6a7a62b508566a47bd77f Author: Brian Friesen Date: Wed May 27 11:14:11 2015 -0700 FabArrayBase: split Boxes into BoxArrays in TheFB() for thread friendliness Src/C_BaseLib/FabArray.cpp commit b50e0a40e7f8d873512d7c16532e287b7a7b810b Author: Brian Friesen Date: Wed May 27 11:13:22 2015 -0700 FabArrayBase: split Boxes into BoxArrays in TheCPC() for thread friendliness Src/C_BaseLib/FabArray.cpp commit cc36b06bc230f4a22270e6b38f446ebec0ce0396 Author: Brian Friesen Date: Wed May 27 10:44:03 2015 -0700 Tiling_Heat_C: added timers to FillPeriodicBoundary() to test threading performance improvement Tutorials/Tiling_Heat_C/main.cpp commit 854777dbaa502cac5e6d87737edefbda886577cb Author: Brian Friesen Date: Tue May 26 14:45:47 2015 -0700 Geometry: changed box boundaries with periodic BCs to box arrays to improve performance with lots of threads Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Tutorials/Tiling_Heat_C/inputs_3d commit 6c081424e6c2f3577372805e1bf9ccb2d9544298 Author: Andy Nonaka Date: Mon Jun 1 14:30:36 2015 -0700 remove broken links in doc Docs/GettingStarted/GettingStarted.tex commit bc71cd8e8be4944ffa3ef657048f112e4d0540df Merge: 286febef3 a13067672 Author: Jessica Kawana Date: Mon Jun 1 14:03:29 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 286febef36a1e9cd27e11dd9935a865efdb338c2 Author: Jessica Kawana Date: Mon Jun 1 14:02:44 2015 -0700 Fixed typos Docs/GettingStarted/GettingStarted.tex commit a13067672eda84a5ee30f102a24f5d72fa87112b Author: Weiqun Zhang Date: Mon Jun 1 13:50:26 2015 -0700 added macros for calling dimension agnostic Fortran code Src/C_BaseLib/ArrayLim.H Src/C_BaseLib/BLFort.H commit 2bf9567a661119e0872b81b00e3926743016f197 Merge: cc3030f07 e251cb2a1 Author: Jessica Kawana Date: Mon Jun 1 10:12:20 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit cc3030f07af201a1a55c3a450c105a0b7e32da65 Author: Jessica Kawana Date: Mon Jun 1 10:10:55 2015 -0700 fixed a typo Docs/GettingStarted/GettingStarted.tex commit e251cb2a1efea41c8042ff6a931554bfbf31b071 Author: Ann Almgren Date: Fri May 29 18:29:22 2015 -0700 Further fixes for the 3d version of AMR_Advection_C. Tutorials/AMR_Advection_C/Exec/Make.ADR Tutorials/AMR_Advection_C/Source/Src_2d/Tagging_2d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/ACT_advection_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/Derive_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/trace_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/trans_3d.f90 commit 1513c6ec7525269500d9445d448a89f441b81f20 Author: Andy Nonaka Date: Fri May 29 11:49:43 2015 -0700 if plot_int <= 0, don't print any plotfiles Tutorials/HeatEquation_EX1_F/main.f90 Tutorials/HeatEquation_EX2_F/main.f90 Tutorials/HeatEquation_EX3_F/main.f90 Tutorials/HeatEquation_EX4_F/main.f90 Tutorials/HeatEquation_EX5_F/main.f90 commit c302ddc7d4e1934314971386c3268927baabfad8 Author: vince 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 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: f66591255 ad09dcceb Author: Ann Almgren Date: Sun May 24 15:24:54 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f66591255c159d25991ad212bc9f7b7100a2f731 Author: Ann Almgren Date: Sun May 24 15:24:36 2015 -0700 More changes for 3d plus cleaning up 2d. Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_3d.f90 Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.3d Tutorials/AMR_Advection_C/Exec/UniformVelocity/probin.3d Tutorials/AMR_Advection_C/Source/Src_2d/ACT_advection_2d.f90 commit f57828a8210870a9462fab3817729a265b8a69e4 Author: Ann Almgren Date: Sun May 24 15:24:04 2015 -0700 Fixing 3d source files ... Tutorials/AMR_Advection_C/Source/Src_3d/ACT_advection_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/EstDt_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/slope_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/trace_3d.f90 commit 48b3404ea6ccbb956380584148f9506c19701734 Author: Ann Almgren Date: Fri May 22 18:29:05 2015 -0700 This version compiles in 3d (and fixes a small bug in the transverse stuff in 2d) Tutorials/AMR_Advection_C/README Tutorials/AMR_Advection_C/Source/Src_2d/ACT_advection_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/Make.package Tutorials/AMR_Advection_C/Source/Src_2d/trans_2d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/ACT_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/ACT_advection_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/ACT_sums_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/Derive_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/EstDt_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/Make.package Tutorials/AMR_Advection_C/Source/Src_3d/React_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/Tagging_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/bc_fill_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/ext_src_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/fill_diff_coeff_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/slope_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/trace_3d.f90 Tutorials/AMR_Advection_C/Source/Src_3d/trans_3d.f90 commit ad09dccebe07dde5b548117225cdb6da25350047 Author: Brian Friesen Date: Fri May 22 17:55:58 2015 -0700 profiling: added Babbage run script for tiled version of heat solver Tutorials/Tiling_Heat_C/results/run-babbage.sh commit dfb721ede7c805d65eb21a3b6bc3ae1da14b1600 Author: Weiqun Zhang Date: Fri May 22 16:49:37 2015 -0700 added Intel 15 to make Tools/F_mk/GMakerules.mak Tools/F_mk/comps/Linux_intel.mak commit e2c77bad6f456575cababab6be9becd20aa0f90b Author: Weiqun Zhang Date: Fri May 22 16:23:21 2015 -0700 crayftn --> ftn, craycc --> cc Tools/C_mk/Make.Linux commit 64178d595cbca9f47c14fd9eae693c6ca2847346 Author: Weiqun Zhang Date: Fri May 22 15:57:50 2015 -0700 checked in job script and timing result Tutorials/Tiling_Heat_C/results/results.org Tutorials/Tiling_Heat_C/results/run-edison.sh commit a53cca19db1ffb13de094331be16082b879b7f0e Author: Weiqun Zhang Date: Fri May 22 15:45:11 2015 -0700 Revert "use allocatable arrays in the non-tiling version so that it does not cause stack overflow" because this made the non-tiling version much slower. This reverts commit 315454c51703f9e2eeb649f27b6412767811abfd. Tutorials/Tiling_Heat_C/advance_3d.f90 commit 315454c51703f9e2eeb649f27b6412767811abfd Author: Weiqun Zhang Date: Fri May 22 12:32:33 2015 -0700 use allocatable arrays in the non-tiling version so that it does not cause stack overflow Tutorials/Tiling_Heat_C/advance_3d.f90 commit da1effb675f37454bf7ce280fae4d0d38428dd51 Author: Weiqun Zhang Date: Fri May 22 12:31:39 2015 -0700 default USE_MPI to FALSE Tutorials/Tiling_Heat_C/GNUmakefile commit 0fbe6727d9a2e0331e72a9404d883636f121c924 Author: Brian Friesen Date: Thu May 21 14:43:05 2015 -0700 make: added support for Babbage, the Intel MIC testbed at NERSC This assumes you will be running natively on the MIC card, not on the Xeon host. NERSC recommends this approach since Cori will have a native MIC architecture with no co-processors. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 8d188a880333f311f4874cd204705dcf6e11c7eb Author: Weiqun Zhang Date: Thu May 21 14:14:18 2015 -0700 change default compilers to Intel in makefile Tutorials/Tiling_Heat_C/GNUmakefile commit 8f31ff4250a1926259b7568a12fa1f45d3cd6353 Author: Weiqun Zhang Date: Thu May 21 14:00:28 2015 -0700 added nowait for the omp on loops version Tutorials/Tiling_Heat_C/advance_3d.f90 commit 6ec1bdaaf16226eaf20cae9c2df79e6e3f90bf8a Author: Weiqun Zhang Date: Thu May 21 13:47:48 2015 -0700 a new tutorial code for tiling Tutorials/Tiling_Heat_C/GNUmakefile Tutorials/Tiling_Heat_C/Make.package Tutorials/Tiling_Heat_C/advance_3d.f90 Tutorials/Tiling_Heat_C/init_phi_3d.f90 Tutorials/Tiling_Heat_C/inputs_3d Tutorials/Tiling_Heat_C/main.cpp Tutorials/Tiling_Heat_C/writePlotFile.H Tutorials/Tiling_Heat_C/writePlotFile.cpp commit d9b8eb069ded3f3b528e72d0e312f8656188aea4 Merge: ef3f17dfe 111fbfd90 Author: Weiqun Zhang 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 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 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 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: 9cc016f4e 7cf282491 Author: vince 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 Date: Tue May 19 10:57:15 2015 -0700 added -lmpichf90 to bluewaters. Tools/C_mk/Make.mpi commit edb4fd3a738305d5856ab010a071334a12d07d06 Author: Michael Zingale Date: Tue May 19 12:17:03 2015 -0400 more cleaning Tools/RegressionTesting/testnew.py commit 644e747e2ac2731f5ea4eeb365ed05cc533d9db0 Author: Michael Zingale Date: Tue May 19 10:27:24 2015 -0400 return the compilatoin string in the build_f method Tools/RegressionTesting/testnew.py commit ddf434d8a391845975f34a140178475ff825f1bd Author: Michael Zingale Date: Mon May 18 22:09:45 2015 -0400 some pyflakes fixes Tools/RegressionTesting/testnew.py commit 2010ed3c963a2fe1ca6ff366e1e1a2b251422eec Author: Michael Zingale Date: Mon May 18 22:05:50 2015 -0400 remove the hack we used to encode the extra build directory in the build directory list by instead storing a tuple in the list. Tools/RegressionTesting/testnew.py commit 4626e6a24d915fdf452cf33584a017dd277a1e55 Author: Michael Zingale Date: Mon May 18 21:09:15 2015 -0400 rename classes to be more PEP-8-y Tools/RegressionTesting/testnew.py commit 31d8158aa8009b1e00879f4687363ced76a9a97e Author: Michael Zingale Date: Mon May 18 21:06:53 2015 -0400 add build_f() and make_realclean() methods to the suiteObj class. Tools/RegressionTesting/testnew.py commit ddd0f24053c7941ed9ac7eb4754fd3aa4d823393 Merge: 96acaf0cb 793376bcd Author: Andy Nonaka Date: Mon May 18 14:52:55 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 96acaf0cb82a6b69c25088fa887f451b6300bc74 Author: Andy Nonaka Date: Mon May 18 14:52:02 2015 -0700 print out # of MPI processes and # of threads, even with there is only 1 MPI proc (still useful info for OpenMP on one node) Src/F_BaseLib/boxlib_f.f90 commit 793376bcd2afe6eaa48bb7009ff10ab626e2b10f Author: Weiqun Zhang Date: Mon May 18 13:22:16 2015 -0700 Heat equation: fixed bug Tutorials/HeatEquation_EX4_F/main.f90 Tutorials/HeatEquation_EX5_F/main.f90 commit 0d3b8c7a98fd0d71e5a720d4a2c9d484479ac1b7 Author: Weiqun Zhang Date: Mon May 18 13:06:00 2015 -0700 fixed heat equation ex5 Tutorials/HeatEquation_EX5_F/main.f90 commit 6299f806676b067b4dfbdb17b53773543afc4390 Author: Weiqun Zhang Date: Mon May 18 12:55:46 2015 -0700 quiet valgrind Src/F_BaseLib/vector_i.f90 commit 918e575311bc91539bebc57d200dd227af26d67f Author: Weiqun Zhang Date: Mon May 18 12:54:56 2015 -0700 comment Tutorials/HeatEquation_EX4_F/main.f90 commit 95acf9cd301fd5a291dcde46bcbaa932adf65c41 Author: Weiqun Zhang Date: Mon May 18 12:32:00 2015 -0700 Fill ghost cells if tagging needs ghost cells Tutorials/HeatEquation_EX4_F/main.f90 commit 2f10f53d57b735633b5f932600ea44b302b5bf40 Author: Weiqun Zhang Date: Mon May 18 12:30:23 2015 -0700 fixed number of component. removed duplicated multifab_fill_boundary and physbc calls Src/F_BaseLib/regrid.f90 commit 76de0a013c1e6b09cf7181468ba07eea821f39a3 Author: Andy Nonaka Date: Mon May 18 10:17:28 2015 -0700 the 'tagging_needs_ghost_cells' option now has a call to multifab_fill_ghost_cells. fixes some problems where tagging is done with a gradient, but valgrind still complaining so no promises yet... Src/F_BaseLib/regrid.f90 commit 9cc016f4ed397fe74b94111f2e3447bd7b4de3f6 Merge: 025aa8583 516b3ae6f Author: vince 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 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 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 Date: Fri May 8 10:44:54 2015 -0400 some more simplifications Tools/RegressionTesting/testnew.py commit e88cdc058918ca5fa88050f59d06301a52634198 Merge: 1effdb399 a44325f64 Author: Michael Zingale 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 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 Date: Thu May 7 20:03:30 2015 -0400 fix the hydrostatic_adjust case Tools/RegressionTesting/Castro-SBU-tests.ini commit bd82028e14d3e5f1146dc9a1672a06712030aa35 Merge: 78d3db16c 29245a10a Author: Michael Zingale 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 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 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: 8b6bde7da fe2e663be Author: vince 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 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 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 Date: Tue May 5 19:21:23 2015 -0400 more simplification of the run commands Tools/RegressionTesting/testnew.py commit 5eb08b2d29a3b1f0adb4354468482322aab1c2d1 Merge: af91910c1 51819bdad Author: Michael Zingale 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 Date: Tue May 5 17:18:53 2015 -0400 remove redundant code Tools/RegressionTesting/testnew.py commit 51819bdad9fca5cf0cfb916f6355f83e8faa66a7 Author: Weiqun Zhang Date: Tue May 5 13:11:41 2015 -0700 OMP'd GetVolume and GetFaceArea Src/C_BaseLib/COORDSYS_1D.F Src/C_BaseLib/COORDSYS_2D.F Src/C_BaseLib/COORDSYS_3D.F Src/C_BaseLib/COORDSYS_F.H Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/Geometry.cpp commit 54a2e73eb68ae41b24b2aeb5f837dd0a92a7c2d5 Author: Michael Zingale Date: Tue May 5 15:04:12 2015 -0400 fix typo Tools/RegressionTesting/testnew.py commit 4c71c82b58b0df34693b4edf98124f974ea67010 Author: Michael Zingale Date: Tue May 5 14:59:00 2015 -0400 some more cleaning / modernization Tools/RegressionTesting/testnew.py commit f1ebe9db26050c3ccb5698c1d1cee429e6f18df7 Author: Michael Zingale Date: Tue May 5 14:13:42 2015 -0400 some more modernization with list comprehensions Tools/RegressionTesting/testnew.py commit 0a6576cdcf6f112af7910058b0986f8f694bc6a2 Merge: b2d8d31f7 17300fa05 Author: Michael Zingale 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 Date: Mon May 4 20:43:02 2015 -0400 more systemCall -> run() replacement Tools/RegressionTesting/testnew.py commit 17300fa05730b387932d6c216ecc4f6615764303 Author: Marc Day Date: Mon May 4 17:33:52 2015 -0700 Remove underflow protection code in LINCCINTERP. Was using a hardwired number, and overwrote crse data. Bad enough, but then appears to be totally unnecessary anyway. Let me know if this breaks someones code. Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F commit 7aa26fc5059fd5a25a50af5b2fb38dfb90f32c87 Merge: 267684fc9 3afd74b5d Author: vince Date: Mon May 4 14:58:04 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 267684fc91135f6d707d15a33fb89752e15cb58f Author: vince Date: Mon May 4 14:57:57 2015 -0700 ensure intermediate flushed database is complete. Src/C_BaseLib/BLProfiler.H Src/C_BaseLib/BLProfiler.cpp commit d07f855a1aa1219682b219041eb7d962d0c7b572 Author: vince Date: Mon May 4 11:34:56 2015 -0700 nostart option for var. Src/C_BaseLib/BLProfiler.H Src/C_BaseLib/BLProfiler.cpp commit 3afd74b5dcf73fd26cc0a770d5092e7d5e37b0a8 Author: Andy Nonaka Date: Mon May 4 08:05:47 2015 -0700 f90 mpi on atragon Tools/F_mk/GMakeMPI.mak commit 7d4873e709c07277d5203d0acff27a9238e2b7d0 Author: vince Date: Fri May 1 15:05:34 2015 -0700 removed buf size restriction in Concatenate. Src/C_BaseLib/Utility.cpp commit ab429bd6be23d10db34b224df0b1e77c363855be Merge: 02b9acd32 88e881b15 Author: Adam Jacobs 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 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: 1cc75c102 d6f575801 Author: Andy Nonaka 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 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: 33f4c20e2 d6f575801 Author: vince Date: Thu Apr 30 15:30:54 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit d6f5758014d3285f87c654b73faf806a3a92a729 Author: vince Date: Thu Apr 30 15:01:13 2015 -0700 another Bcast interface, additions for serial. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 33f4c20e218ffff3cbfe72735f74562ea9322edb Merge: b89095ca9 33c7336ba Author: vince 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 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 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 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 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 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 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: f86151f1f d8df7db52 Author: vince Date: Wed Apr 22 17:21:18 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f86151f1fc9c0573148555ddba6c126c1ddd927d Author: vince Date: Wed Apr 22 17:21:09 2015 -0700 nesting fix. Src/C_BaseLib/BLProfiler.cpp commit d8df7db524a1baf726bd0580beb980cc45cea251 Author: Weiqun Zhang Date: Wed Apr 22 16:42:16 2015 -0700 removed -target=linux for hopper Tools/C_mk/Make.Linux commit f4691440ab004a4f303ea93716bac6f580340b94 Author: Weiqun Zhang Date: Wed Apr 22 16:40:04 2015 -0700 added -lmpichf90 for edison and hopper. may need to do this for some other machines too, especially ones with cray mpich. Tools/C_mk/Make.mpi commit 35f7f3230804d02127a732fab7f29865362392e1 Author: Michael Zingale Date: Tue Apr 21 19:21:02 2015 -0400 some more clean-ups Tools/RegressionTesting/testnew.py commit 2759a86211d07777b5931b8db38780ffb63cbd78 Author: Weiqun Zhang Date: Tue Apr 21 15:23:46 2015 -0700 Fixed a problem on Windows. I do not have access to any Windows machines. But I believe the new overloaded functions in parallel module would not compile on Windows because c_long is the same as normal Fortran integer and the overloaded functions inside interface must have different kind. This also means the lastest BoxLib would not compile in the unlikely case that the compiler does not support long integer. Src/F_BaseLib/parallel.f90 commit 25443a5c9b77dee0554efc90e932879ecc55b558 Author: Weiqun Zhang Date: Tue Apr 21 12:31:47 2015 -0700 Let codes tell BoxLib the boundary functions are thread-safe. By default, BoxLib assumes that EXT_DIR is not thread safe, whereas other types are. Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp commit b28c94f7a52161244af5e5902f7bed623e10299a Author: Michael Zingale Date: Tue Apr 21 13:37:08 2015 -0400 more clean-ups -- eliminate some functions/logic in favor of list comprehensions Tools/RegressionTesting/testnew.py commit f60dc17e639d443a62d038aef7bf1324a8971b32 Author: Michael Zingale Date: Tue Apr 21 12:46:05 2015 -0400 some more cleaning -- especially to the restart execution string Tools/RegressionTesting/testnew.py commit acd85262c8d52aa4c6bc08d614ec394a03ab1efa Merge: 9f999bc4d 4552f323d Author: Michael Zingale Date: Tue Apr 21 12:05:52 2015 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib Conflicts: Tools/RegressionTesting/testnew.py commit 9f999bc4d4e7f85f3b672aeb22692ff87d38d5f6 Author: Michael Zingale Date: Tue Apr 21 12:03:00 2015 -0400 more clean-up -- now the run commands are greatly simplified (since aside from the MPI and OMP stuff, the command is the same in all cases). Also fix the single suite run output page (columns were mixed) Tools/RegressionTesting/testnew.py commit 4552f323dec6020ba4380e3a3a151575ae77ae6c Merge: ebfe9367b 419f8e692 Author: Weiqun Zhang Date: Mon Apr 20 21:51:32 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ebfe9367b81c36fda5db4d0b8ac2a1467561fe17 Author: Weiqun Zhang Date: Mon Apr 20 21:50:04 2015 -0700 Inflow boundary in IAMR and LMC is too complicated to be made thread safe. So an OMP critical region is added for EXT_DIR. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp commit 419f8e692b77598b94db316482317700a444f664 Author: Michael Zingale Date: Mon Apr 20 20:20:37 2015 -0400 remove some os.system() calls with shutil -- this is safer Tools/RegressionTesting/testnew.py commit c7bf2c8820c7814ff7051dc37b72e24de7c3c7dd Author: Weiqun Zhang Date: Mon Apr 20 16:55:28 2015 -0700 changes OMP approach in FillPatchIterator Src/C_AMRLib/AmrLevel.cpp commit f5d83082d23f3d6b677eae720ba60d6b10784ebf Author: Weiqun Zhang Date: Sun Apr 19 20:36:32 2015 -0700 tidy Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c commit 550a5e80a3a475425793d8caf29267348fc1b4ba Author: Weiqun Zhang Date: Sun Apr 19 17:28:48 2015 -0700 change user function in MPI_Op_create from fortran function to subroutine because it has no return value Src/F_BaseLib/parallel.f90 commit 3bfdac3956f792ea68780760630ff378dc4fd58d Author: Weiqun Zhang Date: Sun Apr 19 15:45:05 2015 -0700 create MPI_SUM, MIN and MAX for c_long in Fortran Src/F_BaseLib/parallel.f90 commit a4becda3c0cfea534c12a23258eaede231e4ff37 Author: Michael Zingale Date: Sun Apr 19 18:25:38 2015 -0400 call MPI_Type_create_f90_integer with 'r', not '5' -- fixes typo Src/F_BaseLib/parallel.f90 commit 080df2a6ea761e605924e65ca12b1f6a0d0b0e39 Author: Weiqun Zhang Date: Sun Apr 19 14:28:17 2015 -0700 use (C) long integer for offset and size in fabio so that i can handle large files Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c Src/F_BaseLib/particles_f.f90 Src/F_BaseLib/plotfile.f90 commit 94439f2ff2b603cdf2634151e9306d0992ac3cc6 Author: Weiqun Zhang Date: Sun Apr 19 14:24:16 2015 -0700 typo in comment Src/F_BaseLib/bl_types.f90 commit 2bff64d27f4fe535d27611d6cc606587a7d973f5 Author: Weiqun Zhang Date: Sun Apr 19 14:23:47 2015 -0700 add MPI support for (C) long integer in Fortran Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit b89095ca9e987d753839727d373451d001672951 Merge: 11e57eccc b013071c9 Author: vince 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 Date: Thu Apr 16 11:07:17 2015 -0700 fix a print statement Src/F_BaseLib/fab.f90 commit a099ee1097313e3bbd6c49ad7925d2f037aca776 Merge: d52fd1bea 20520f96e Author: vince Date: Wed Apr 15 14:42:58 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d52fd1bea88860d4b506bb1d5166b2f785f7e5ca Author: vince Date: Wed Apr 15 14:42:48 2015 -0700 more support for amrprof. Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 11e57eccc19e8a321e06d1a4b31fa81d53958878 Merge: bb70cfe43 20520f96e Author: vince 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 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: 559ad2fb4 935df63f8 Author: Michael Zingale 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 Date: Tue Apr 14 18:54:52 2015 -0400 switch fboxinfo over to run() Tools/RegressionTesting/testnew.py commit 559ad2fb4e69cf504a04a277f22400dc2f8efe4f Merge: 641d51625 d9e8754e5 Author: Michael Zingale 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 Date: Tue Apr 14 14:10:38 2015 -0400 some more run() Tools/RegressionTesting/testnew.py commit d9e8754e5b8c87a3e86dd0f2caa42e4b5d7aa44a Merge: c799bb3ae 56d895444 Author: vince Date: Thu Apr 9 15:52:13 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 56d895444c640990f64abaa80d4554c7098233e1 Author: Weiqun Zhang 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 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 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 Date: Mon Apr 6 14:01:08 2015 -0700 some perfmon cleanup. Src/C_BaseLib/ParallelDescriptor.cpp commit 68e6423532122c665d096c31dd74205d1a1ec929 Author: vince Date: Mon Apr 6 13:21:11 2015 -0700 some cleanup for perfmon. Src/C_BaseLib/ParallelDescriptor.cpp commit 26568227a2040c45785ca0422902b23adade072f Author: vince Date: Mon Apr 6 13:20:35 2015 -0700 fix for serial. Src/C_BaseLib/ParallelDescriptor.H commit 884a98299f55f5d286fb20574da1093e682564cf Merge: 9f021ad2b 6c8abf2d6 Author: Michael Zingale 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 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 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 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 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 Date: Thu Apr 2 14:45:12 2015 -0700 Uptick tagged version number Tools/CMake/BoxLib_Version.cmake commit cf034bebf40dda642ceb269292f453b2801dfbe0 Merge: 1783e2ea8 fad4b157c Author: Marc Day Date: Thu Apr 2 14:41:34 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit c8ce73fb1de3ce7b37c4b6215babfbea40f6b348 Author: vince Date: Wed Apr 1 18:22:11 2015 -0700 support for multiple perfmonproc processes. Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit c9d1d01398185b80f0c2a406fdb3adcacfbfdbb5 Author: vince Date: Wed Apr 1 18:18:45 2015 -0700 support for multiple perfmonproc processes. Src/C_BaseLib/BLProfiler.cpp commit fad4b157c0dc6f708f21d4c5e600e0592796c106 Author: Weiqun Zhang Date: Wed Apr 1 17:14:58 2015 -0700 Warn rather than Abort when both plot_int and plot_per are set Src/C_AMRLib/Amr.cpp commit 45cc74c4c2fa984831f467e0b32141c5dd745738 Author: Weiqun Zhang Date: Wed Apr 1 17:11:03 2015 -0700 fixed a couple of things so that we can compile with PRECISION=FLOAT Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit e92f198afbf1d4f2af36b9ec3966e783c744ccbf Author: Regression Tester account Date: Fri Mar 27 12:26:32 2015 -0700 update make file for battra again Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit e8995767635f9929b69a04029869c048f36411bd Author: Weiqun Zhang Date: Thu Mar 26 11:05:25 2015 -0700 updated makefile for battra Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 2ff86a93ef331de1371e2c8fe4c684d7452be76b Author: vince Date: Wed Mar 25 11:48:43 2015 -0700 added more profiling. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp commit 2d6307d007abed51bee75e93cd531dcb19d07890 Author: vince Date: Wed Mar 25 11:47:52 2015 -0700 checks for zero size arrays, percent for cov. Src/C_BaseLib/BLProfiler.cpp commit 9d09b7a4c0fedb839109d12d398cfab3b276f843 Author: vince Date: Thu Mar 19 12:49:12 2015 -0700 added coefficient of variation. Src/C_BaseLib/BLProfiler.cpp commit bb70cfe43c3669ec8120c5d6004e3c0b2cc06df5 Merge: 2e2a67307 d94cc43cd Author: vince Date: Wed Mar 18 15:33:11 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit d94cc43cd72e5c0a33f38ba939043e0fb64462a2 Merge: 4d94ec3be 539cb4064 Author: vince Date: Wed Mar 18 15:31:19 2015 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 4d94ec3be851c1da0012649de18ba77293de4f81 Author: vince Date: Wed Mar 18 15:30:56 2015 -0700 showpoint to avoid 0 parse. Src/C_BaseLib/BLProfiler.cpp commit 539cb4064c182b657d9bc4758aa781158a1a8f86 Author: Adam Jacobs Date: Mon Mar 16 14:39:05 2015 -0500 Update rules for Blue Waters compiling Tools/F_mk/GMakeMPI.mak commit 07f9e41482a0f9410df85b0c85702261f65e19a8 Merge: ddc3197fe 9c80caaaa Author: Adam Jacobs Date: Mon Mar 16 13:04:53 2015 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 9d7fd6b8b801c85ee1241eea25d9baed849a33ca Author: vince Date: Thu Mar 12 17:43:27 2015 -0700 makefile update. Tests/IOBenchmark/GNUmakefile commit 9c80caaaa45720e09a5fbda175c4f006cdd5117b Author: Weiqun Zhang Date: Thu Mar 12 17:20:20 2015 -0700 better name for turning on c++11 support Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit a786e8f1b72745307daa74eac11ab2755a5a819c Author: Weiqun Zhang Date: Thu Mar 12 17:16:35 2015 -0700 make c flags immediate so that we can later add c++ only flags Tools/C_mk/Make.defs commit 30d8bdeb66755164ff79ebb454f68815bd82d9dd Author: Weiqun Zhang Date: Thu Mar 12 17:14:52 2015 -0700 increased buffer size for backtracing Src/C_BaseLib/BLBackTrace.cpp commit 7a011c8ee0722a9da1a3e322a341d3eb30026fd1 Author: Michael Zingale Date: Tue Mar 10 15:27:09 2015 -0400 add a comment based on a question from a student Tutorials/WaveEquation_F/advance.f90 commit 1783e2ea8f8ec63ee1ceda5b47a8ca708dc1f968 Merge: deb1863f1 6a58f029f Author: Marc Day Date: Mon Mar 9 17:41:12 2015 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit c2e82b06b5b12f7e6fc999b05f043d2e5ab0ac07 Author: vince Date: Fri Mar 6 17:35:41 2015 -0800 extra send interface with comm. Src/C_BaseLib/ParallelDescriptor.H commit 6a58f029f128c3d252f5ae3853a0dc387a8e39cf Author: Weiqun Zhang 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 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: c8da6f0cc aa1c24709 Author: Marc Day 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 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 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 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: 3a7588387 7e2e3d3dc Author: Weiqun Zhang Date: Wed Mar 4 17:20:06 2015 -0800 Merge branch 'lazy' commit 3a75883876bef2cccceca1631bd4244c112ac8e7 Merge: 3fc24fc0a 6be72b810 Author: Weiqun Zhang Date: Wed Mar 4 17:16:22 2015 -0800 Merge branch 'lazy' commit 7e2e3d3dceae00b65a833d555f024ee6d456ea91 Author: Weiqun Zhang Date: Wed Mar 4 13:58:54 2015 -0800 fixed it for Intel Src/C_BaseLib/Lazy.H commit 6be72b810b5356122f914d8bcf5597cbb892aab9 Author: Weiqun Zhang Date: Wed Mar 4 13:55:23 2015 -0800 forgot to add new files Src/C_AMRLib/Make.package Src/C_BaseLib/Lazy.H Src/C_BaseLib/Lazy.cpp Src/C_BaseLib/Make.package commit 9bf26492062c003f0db1194cac8d591369a94909 Author: Weiqun Zhang Date: Wed Mar 4 13:42:40 2015 -0800 implemented prototype lazy evaluation that can delay MPI bulk synchronization till it hits a necessary bulk synchronization Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Make.package Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Tools/C_mk/Make.defs commit c8da6f0cc2f304c1ef3c80e6d939834b8f00fb8a Merge: c6f978975 3fc24fc0a Author: Marc Day Date: Wed Mar 4 13:15:52 2015 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit ddc3197febe5d2f734eddc5a2ff34c94c9223dc3 Merge: 9aa54a9fd 3fc24fc0a Author: Adam Jacobs Date: Wed Mar 4 10:53:34 2015 -0600 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 3fc24fc0adc453192f828899a26f3bedbeef9d22 Merge: a91e1fcc0 a023226e4 Author: vince Date: Tue Mar 3 12:46:16 2015 -0800 commit merge. Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a91e1fcc0a093d7b27707f1a3790be6f4550dc45 Author: vince Date: Tue Mar 3 12:46:06 2015 -0800 update the profiling doc. Docs/Readme.profiling commit a023226e4ffffde266ef77be0b03f91875c07558 Author: Michael Zingale Date: Tue Mar 3 09:39:02 2015 -0500 update some problem locations Tools/RegressionTesting/Maestro-tests.ini commit c6f978975022a87073c346239d628e2a336dc59e Merge: a0c480319 505c096fe Author: Marc Day 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 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: 8b84ef608 1da3a2c36 Author: vince Date: Mon Mar 2 11:59:47 2015 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1da3a2c369b29b85b2606e59fc6baad562a01f7b Author: Andy Nonaka Date: Sat Feb 28 05:56:22 2015 -0800 mpi on gamera Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 2e2a67307567f6a763cedfd6ccf93823326619c0 Merge: ffaeb61bd 8b84ef608 Author: vince 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 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 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: 465f51d7f 5db099fa9 Author: Marc Day Date: Fri Feb 27 12:49:51 2015 -0800 Merge master commit 5db099fa9ad5222bf02e55c16f1c609f57ce8f2c Author: Weiqun Zhang 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 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 Date: Tue Feb 24 09:23:07 2015 -0500 a little more cleaning Tools/RegressionTesting/testnew.py commit 4101571a4fdfc8517cd567f407289a19e87abc24 Author: Michael Zingale Date: Mon Feb 23 14:16:57 2015 -0500 more clean-up, remove some redundant/unused modules are reported by pyflakes Tools/RegressionTesting/testnew.py commit 5e7f9fe8c132aea2435014e344f07e9392e39dc9 Author: Michael Zingale Date: Mon Feb 23 12:52:19 2015 -0500 some more cleaning and PEP-8ing Tools/RegressionTesting/testnew.py commit 92254576dc98b641a3eee934f22e4d3ba80886c0 Author: Michael Zingale Date: Mon Feb 23 11:09:48 2015 -0500 a little bit of clean-up -- use setattr to set a lot of the suite-wide parameters instead of needing a separate elif for each. Still need to do this for the test stuff. Also add a purge_output option to delete all but the comparison plotfile from the output directory. Finally do a little PEP-8 cleaning. Tools/RegressionTesting/testnew.py commit dfcee6e2528b433cc34ac3907078dc09b63844fa Author: ajnonaka Date: Fri Feb 20 10:51:21 2015 -0800 gimantis MPI for f90 boxlib Tools/F_mk/GMakeMPI.mak commit 460d306d7936f0d95c3895162237b0428da04fb5 Author: vince Date: Fri Feb 20 10:36:20 2015 -0800 changes for gimantis. Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 3fcc394f2774d4dd80e974316327665672537eb5 Author: Michael Zingale Date: Wed Feb 18 10:14:15 2015 -0500 add some latex ignores .gitignore commit 4bc2946bda23f217590260a224bda871958b07b6 Author: Michael Zingale Date: Wed Feb 18 10:08:49 2015 -0500 remove stray } Tools/C_scripts/makebuildinfo_C.py commit c9141f75de8d9875f2f8ad858683656f1fe78df9 Author: Michael Zingale Date: Wed Feb 18 10:06:20 2015 -0500 update header with new functions Tools/C_scripts/buildInfo.H commit 6db0c2dc09b65579948531ee614db79b566e6024 Author: Michael Zingale Date: Wed Feb 18 09:58:19 2015 -0500 add a build_git_name and build_git_dir for problems that are built in special places... Tools/C_scripts/makebuildinfo_C.py commit b7c5e149434117b41a0534644a83258f8cd70b68 Author: Michael Zingale Date: Tue Feb 17 18:50:23 2015 -0500 if we set the extra directory (ASTRODEV_DIR for MAESTRO) and the directory doesn't actually exist, then handle this gracefully and still make a build_info.f90. Tools/F_scripts/makebuildinfo.py commit ea645f68c43a2baa75e6ac479c75cb1b7a3f19ae Author: ajnonaka 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 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 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 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 Date: Wed Feb 11 15:04:17 2015 -0500 make BOXLIB_HOME relative Tools/Postprocessing/F_Src/GNUmakefile commit 2a43fcc5a514dd9cff62516a62499e05c8207e66 Author: Michael Zingale Date: Wed Feb 11 14:50:39 2015 -0500 move these from AmrPostprocessing Tools/Postprocessing/F_Src/CASTRO_radiation/GNUmakefile Tools/Postprocessing/F_Src/CASTRO_radiation/fgaussianpulse.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/flgt_frnt1d.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradshock.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradsource.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/fradsphere.f90 Tools/Postprocessing/F_Src/CASTRO_radiation/frhdshocktube.f90 Tools/Postprocessing/F_Src/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/fsubchandra.f90 Tools/Postprocessing/F_Src/MAESTRO_sub_chandra/fsubchandra_mod.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_tests/fgaussianpulse.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/fmlcompare.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/fmlconverge.f90 Tools/Postprocessing/F_Src/MAESTRO_tests/fnorm.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_wdconvect/feint.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fthermo.f90 Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fthermo_driver.py Tools/Postprocessing/F_Src/MAESTRO_wdconvect/fwdconvect.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/GNUmakefile Tools/Postprocessing/F_Src/MAESTRO_xrb/fad_excess.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fbuoyancy.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fconv_slopes.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/frates.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fspec_total_mass.f90 Tools/Postprocessing/F_Src/MAESTRO_xrb/fspeciesmass.f90 Tools/Postprocessing/F_Src/Palette Tools/Postprocessing/F_Src/faverage.f90 Tools/Postprocessing/F_Src/fboxinfo.f90 Tools/Postprocessing/F_Src/fcompare.f90 Tools/Postprocessing/F_Src/fextract.f90 Tools/Postprocessing/F_Src/fextrema.f90 Tools/Postprocessing/F_Src/ffdcompare.f90 Tools/Postprocessing/F_Src/fsnapshot2d.f90 Tools/Postprocessing/F_Src/fsnapshot3d.f90 Tools/Postprocessing/F_Src/ftime.f90 Tools/Postprocessing/F_Src/fvarnames.f90 Tools/Postprocessing/F_Src/old_flame/GNUmakefile Tools/Postprocessing/F_Src/old_flame/fbubble_position.f90 Tools/Postprocessing/F_Src/old_flame/fbubble_position_3d.f90 Tools/Postprocessing/F_Src/old_flame/fcusp.f90 Tools/Postprocessing/F_Src/old_flame/fcylflame.f90 Tools/Postprocessing/F_Src/old_flame/fflamelength.f90 Tools/Postprocessing/F_Src/old_flame/finteg.f90 Tools/Postprocessing/F_Src/old_flame/fturbkin.f90 Tools/Postprocessing/F_Src/old_flame/fwidth.f90 Tools/Postprocessing/F_Src/python/README Tools/Postprocessing/F_Src/python/column_depth.py Tools/Postprocessing/F_Src/python/conv_slopes.py Tools/Postprocessing/F_Src/python/dumpparthistory.py Tools/Postprocessing/F_Src/python/eos_data.txt Tools/Postprocessing/F_Src/python/helmeos.py Tools/Postprocessing/F_Src/python/parseparticles.py Tools/Postprocessing/F_Src/python/test_helmeos.py Tools/Postprocessing/F_Src/python/test_parseparticles.py Tools/Postprocessing/F_Src/python/timestamp_00 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: 4e107169e b4d803084 Author: Michael Zingale Date: Wed Feb 11 14:49:31 2015 -0500 Merge branch 'master' of /home/zingale/temp/AmrPostprocessing commit b4d8030846736565aa6598ceeb808089817077e8 Author: Michael Zingale Date: Wed Feb 11 14:47:12 2015 -0500 moving F_Src/CASTRO_radiation/GNUmakefile F_Src/CASTRO_radiation/fgaussianpulse.f90 F_Src/CASTRO_radiation/flgt_frnt1d.f90 F_Src/CASTRO_radiation/fradshock.f90 F_Src/CASTRO_radiation/fradsource.f90 F_Src/CASTRO_radiation/fradsphere.f90 F_Src/CASTRO_radiation/frhdshocktube.f90 F_Src/GNUmakefile F_Src/MAESTRO_sub_chandra/GNUmakefile F_Src/MAESTRO_sub_chandra/fsubchandra.f90 F_Src/MAESTRO_sub_chandra/fsubchandra_mod.f90 F_Src/MAESTRO_tests/GNUmakefile F_Src/MAESTRO_tests/fgaussianpulse.f90 F_Src/MAESTRO_tests/fmlcompare.f90 F_Src/MAESTRO_tests/fmlconverge.f90 F_Src/MAESTRO_tests/fnorm.f90 F_Src/MAESTRO_wdconvect/GNUmakefile F_Src/MAESTRO_wdconvect/feint.f90 F_Src/MAESTRO_wdconvect/fthermo.f90 F_Src/MAESTRO_wdconvect/fthermo_driver.py F_Src/MAESTRO_wdconvect/fwdconvect.f90 F_Src/MAESTRO_xrb/GNUmakefile F_Src/MAESTRO_xrb/fad_excess.f90 F_Src/MAESTRO_xrb/fbuoyancy.f90 F_Src/MAESTRO_xrb/fconv_slopes.f90 F_Src/MAESTRO_xrb/frates.f90 F_Src/MAESTRO_xrb/fspec_total_mass.f90 F_Src/MAESTRO_xrb/fspeciesmass.f90 F_Src/Palette F_Src/faverage.f90 F_Src/fboxinfo.f90 F_Src/fcompare.f90 F_Src/fextract.f90 F_Src/fextrema.f90 F_Src/ffdcompare.f90 F_Src/fsnapshot2d.f90 F_Src/fsnapshot3d.f90 F_Src/ftime.f90 F_Src/fvarnames.f90 F_Src/old_flame/GNUmakefile F_Src/old_flame/fbubble_position.f90 F_Src/old_flame/fbubble_position_3d.f90 F_Src/old_flame/fcusp.f90 F_Src/old_flame/fcylflame.f90 F_Src/old_flame/fflamelength.f90 F_Src/old_flame/finteg.f90 F_Src/old_flame/fturbkin.f90 F_Src/old_flame/fwidth.f90 F_Src/python/README F_Src/python/column_depth.py F_Src/python/conv_slopes.py F_Src/python/dumpparthistory.py F_Src/python/eos_data.txt F_Src/python/helmeos.py F_Src/python/parseparticles.py F_Src/python/test_helmeos.py F_Src/python/test_parseparticles.py F_Src/python/timestamp_00 F_Src/python/timestamp_02 F_Src/tutorial/GNUmakefile F_Src/tutorial/fspeciesmass2d.f90 F_Src/tutorial/fwrite2d.f90 commit 4e107169e5bd1b631fb19fd7b15d17067e126d0a Author: Michael Zingale Date: Wed Feb 11 14:38:52 2015 -0500 update to reflect mainline Sod_stellar Tools/RegressionTesting/Castro-SBU-tests.ini commit ffaeb61bd839dbabde672c48c749b33135a86f5b Merge: afc15dddf 995f4e759 Author: Michael Zingale 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 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 Date: Tue Feb 10 14:08:48 2015 -0500 update for helmeos stuff Tools/RegressionTesting/Castro-SBU-tests.ini commit fb07c99075b41c2956a513ec821c4256171c64c5 Merge: 200c3cc5d 097dff288 Author: Michael Zingale 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 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 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 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 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 Date: Fri Feb 6 14:20:46 2015 -0800 fixed typo Docs/Readme.backtrace commit 3099e7396323432afe825dc50c703255a41f7ca9 Author: Weiqun Zhang Date: Fri Feb 6 13:59:12 2015 -0800 updated Reame.backtrace Docs/Readme.backtrace commit c7b0717ea104a51a93334154e0d8986a39106d19 Author: Weiqun Zhang Date: Fri Feb 6 13:48:55 2015 -0800 updated Readme.backtrace Docs/Readme.backtrace commit 77dafebabebde51598f8a42c720f09b117e44264 Author: Weiqun Zhang Date: Fri Feb 6 13:24:22 2015 -0800 better support of threads in BLBackTrace Src/C_BaseLib/BLBackTrace.H Src/C_BaseLib/BLBackTrace.cpp commit 1dad9a515a11e4235cdc53aed875f426bb912a17 Merge: 3beed2daa d30481527 Author: Weiqun Zhang 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 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 Date: Fri Feb 6 10:32:19 2015 -0800 moved -rdynamic flag to LDFLAGS Tools/C_mk/Make.defs commit 2629e1868b0da4d8849f82b0d3ac9dfb0116724d Author: Weiqun Zhang Date: Fri Feb 6 09:48:51 2015 -0800 fixed multithreading in BLBackTrace Src/C_BaseLib/BLBackTrace.cpp commit 75d2da368a0a9f2046d35f164f7ea37479dee898 Author: Weiqun Zhang Date: Thu Feb 5 21:09:14 2015 -0800 Implemented backtrace capability in case of segfault. See Docs/Readme.backtrace for details. Docs/Readme.backtrace Src/C_BaseLib/BLBackTrace.H Src/C_BaseLib/BLBackTrace.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Tools/C_mk/Make.defs commit 68dc5aa02c2c920ef6136d1546d22c9b48c37623 Author: ajnonaka 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 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 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: f72b1ea8e ca8596b76 Author: Weiqun Zhang Date: Fri Jan 30 16:42:49 2015 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f72b1ea8ebd8ba664e6e4bbfddb4fefd76610c0a Author: Weiqun Zhang Date: Fri Jan 30 16:42:42 2015 -0800 added a version of ParticleBase::NexID that does not contain omp critical Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit ca8596b760fe828aad442d946e822a5a7b7a13b4 Merge: 27310bfdb e8f19d366 Author: Michael Zingale 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 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 Date: Thu Jan 29 17:06:00 2015 -0800 removed some omp critical Src/C_BaseLib/MultiFab.cpp commit 0db952bacd126f1ce0a0b0c4a4b4c0080c1b4396 Author: vince Date: Thu Jan 29 15:38:38 2015 -0800 defs for new os. Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 851159f167b47ce16953bd93c9bd7c762893e8b2 Author: ajnonaka Date: Thu Jan 29 12:33:44 2015 -0800 update atragon mpi library directories lijewski no longer exists Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit db55b6542bb891d0946e04e048b8662b5a51768d Author: Weiqun Zhang Date: Thu Jan 29 10:56:38 2015 -0800 update makefile per Andy's suggestion after os upgrade Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit ee15f1c1d50ced7b5ab4161b14f3a08d235b3185 Author: Marc Day Date: Wed Jan 28 15:49:16 2015 -0800 Modify make config per Andy suggestion Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit a235af87d30cbfc721d4d7eb4da9b8daadeded7d Merge: 34b16c061 271a38754 Author: Matthew Emmett 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 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 Date: Wed Jan 28 12:45:41 2015 -0800 fixed assertion Src/F_BaseLib/multifab_f.f90 commit 8ccce3c12cfb8b593b1460a613c34b5163d31187 Merge: 5c85b0b69 9eea1d223 Author: Matthew Emmett 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 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 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 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 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 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 Date: Fri Jan 23 10:09:26 2015 -0800 removed an extra endif Tools/C_mk/Make.mpi commit d0eacd01e789b4ee4b73ec78b089f31241286605 Author: Weiqun Zhang Date: Fri Jan 23 10:04:43 2015 -0800 take a shortcut in make_particle_dmap Src/C_AMRLib/AmrLevel.cpp commit d0178cee85ecd85d0bc1ec862addf9c6d37cac35 Author: Ann Almgren Date: Fri Jan 23 09:48:21 2015 -0800 Make the manda options identical to the megalon options. Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit f587f2653eabf1f1304dd0b860a362762310db8a Merge: 543f44ada 434590420 Author: Weiqun Zhang 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 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 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 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 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 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 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 Date: Thu Jan 15 16:36:19 2015 -0800 fixed a typo Src/C_BaseLib/DistributionMapping.cpp commit c4402137b46f6aa7ee9d7cbd80d0f4118e2a33a4 Author: Weiqun Zhang Date: Thu Jan 15 16:30:03 2015 -0800 A new distribution mapping strategy called RRKS, which combines RoundRobin with KnapSack. It's not as greedy as KnapSack. It tries to keep the number of boxes balanced while considering box weights. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 28ff0ef76edb9102d62d001690c14b3f83bebb31 Author: Weiqun Zhang 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 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 Date: Wed Jan 14 20:52:16 2015 -0800 single quote to double Src/C_AMRLib/Particles.H commit 718c57256eb5a799542aba0c44ac62e9ba26d022 Author: Weiqun Zhang Date: Wed Jan 14 20:50:10 2015 -0800 new function that put distribution map in cache Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit ad512a17fe49f41df577d8e9e233a6d2f427b927 Author: Weiqun Zhang Date: Wed Jan 14 20:49:41 2015 -0800 added extra \n Src/C_AMRLib/Particles.H commit 2078ff0041bfa91a054d8d67d6f236cbeccc96fd Author: Weiqun Zhang Date: Wed Jan 14 20:11:17 2015 -0800 added new Amrlevel constructor and StateData::define that take distribution map Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit a619d9b88052bf6c79074d1d3ac9d66449783b84 Author: Michael Zingale Date: Wed Jan 14 22:18:15 2015 -0500 when writing the auxFiles to the webpage, remove the root. Also some neighboring pep-8 fixes Tools/RegressionTesting/testnew.py commit 722f6e63c8f01329dc0b0023817d6812e10eadd7 Author: Weiqun Zhang Date: Wed Jan 14 09:59:55 2015 -0800 fixed typo Src/C_AMRLib/MLSDCAmrEncap.cpp commit b6976cb11e073a6aed282a362ac3881d679c0ce8 Merge: 0bf873b1a 781bd8a4b Author: vince Date: Tue Jan 13 15:01:07 2015 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 781bd8a4b8713bad89e4fffa8fda18190fb2bbc3 Merge: 247366944 63e8d34cf Author: Weiqun Zhang Date: Tue Jan 13 14:57:19 2015 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 247366944b485235b226009a256e4114174c9b66 Author: Weiqun Zhang Date: Tue Jan 13 14:57:11 2015 -0800 more openmp Src/C_AMRLib/TagBox.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 63e8d34cf204e8cd42e3fa87dfc6d3f4146a01ef Merge: 49f4fd2ea 4f4250930 Author: Andy Nonaka Date: Tue Jan 13 13:23:10 2015 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 49f4fd2ea0eebcee022fc896721e409222ac3437 Author: Andy Nonaka Date: Tue Jan 13 13:22:30 2015 -0800 point to mpich on megalon... I can compile but get n instances of the program running Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 4f4250930c46056967cef22ced9f573a7c7a2e7c Author: Weiqun Zhang Date: Tue Jan 13 13:04:11 2015 -0800 fixed typo Src/C_BaseLib/iMultiFab.cpp commit 0e92c6e8dea4ee1b3ca3b8cc0df77003a891ae6a Author: Weiqun Zhang Date: Tue Jan 13 13:01:40 2015 -0800 added OMP to iMultiFab::min, max, and norm Src/C_BaseLib/iMultiFab.cpp commit ffaf6f8f281b1a6b4ea278c42290d9138a7e10df Author: Weiqun Zhang Date: Tue Jan 13 12:48:19 2015 -0800 fixed new bugs Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/iMultiFab.cpp commit 350c12d39261893278342b7c76cc1e717e5beb94 Author: Weiqun Zhang Date: Tue Jan 13 12:41:54 2015 -0800 fixed a new bug Src/C_BaseLib/MultiFab.cpp commit 58a0df604e74f50994e990d99f585918f5c40632 Author: Weiqun Zhang Date: Tue Jan 13 11:25:28 2015 -0800 added OMP to MultiFab norm, min, and max.... Src/C_AMRLib/MLSDCAmrEncap.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/SPECIALIZE_1D.F Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F commit 9e2f2bbda103dcd047b9232ee22c771b63df869b Author: Weiqun Zhang Date: Mon Jan 12 15:28:01 2015 -0800 removed an unstarted BL Profiler Src/LinearSolvers/F_MG/ml_cc.f90 commit 0bf873b1a46d1b1c9d79cab6013738bc73e310b0 Merge: 31efce2fa d083c8050 Author: vince Date: Mon Jan 12 14:50:09 2015 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 31efce2fa11f70fee638427b26fbade58382e04a Author: vince 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 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 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 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 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 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 Date: Sat Jan 10 12:33:56 2015 -0500 latest version Tools/RegressionTesting/Maestro-tests.ini commit a9dea1316fd267ded2700e84ab43b5375ed3b720 Author: Weiqun Zhang Date: Fri Jan 9 20:16:54 2015 -0800 For tiling version of derive, set xlo to the lower left corner of the tilebox Src/C_AMRLib/AmrLevel.cpp commit b35a7d0d7083db3faea5e5b8f36096b3a86b3b60 Author: Weiqun Zhang Date: Fri Jan 9 16:55:45 2015 -0800 in the new tiled derive, we should use the dst mf to initilize MFIter Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/MultiFab.cpp commit 2b7bd3711f5cc0df3db741cce44ae642436e780f Author: Weiqun Zhang Date: Fri Jan 9 15:39:32 2015 -0800 If CRSEGRNDOMP is defined, tile AmrLevel::derive. Src/C_AMRLib/AmrLevel.cpp commit 150db205e154481984a3f941032a9664326426a3 Author: Weiqun Zhang Date: Fri Jan 9 15:28:55 2015 -0800 fixed a bug in my last commit Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 5f6c97ecfc530e021f7a8b6e6e05d0b55d280ce8 Author: Weiqun Zhang Date: Fri Jan 9 15:06:19 2015 -0800 use the new FillPatch function Src/C_AMRLib/AmrLevel.cpp commit c1e2cfdbf2e6db06a3c1fbd5ca874d297ce02843 Author: Weiqun Zhang Date: Fri Jan 9 13:34:42 2015 -0800 Eliminated a few OMP critical directives by having threadprivate copies of variables like total_bytes_allocated_in_fabs. The trick is we can delay the summation of the numbers till we need them. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/DistributionMapping.cpp commit 12a95d0f6f35ac9565e78757a9745489d55df555 Author: Weiqun Zhang Date: Thu Jan 8 13:36:37 2015 -0800 fixed new bug Src/C_AMRLib/TagBox.cpp commit d8de0faf5a37b8701f578bb57274521332d00402 Author: Weiqun Zhang Date: Thu Jan 8 13:09:34 2015 -0800 added tiling functionality to TagBox Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 0ca6ec0412e549dbb296f3123c39893ea7af7f5f Author: Weiqun Zhang Date: Tue Jan 6 12:22:04 2015 -0800 fixed a bug I introduced two weeks ago Src/C_AMRLib/Particles.cpp commit fa0027cc224c6ffc93e85b822bdf52a0c2b691b4 Author: Weiqun Zhang Date: Mon Jan 5 21:32:07 2015 -0800 added an assertion Src/C_AMRLib/AmrLevel.cpp commit 14e97f649813e66f32d62cf0e28d33cd2b75feff Author: Weiqun Zhang Date: Mon Jan 5 20:53:51 2015 -0800 Added a static member function FillPatch to AmrLevel. This function takes the same argument as FillPatchIterator, but unlike FillPatchIterator, it fills the MultiFab. For example FillPatch(amrlevel,S_new,0,cur_time,State_Type,0,NUM_STATE); will fill-patch the MultiFab S_new. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/MultiFab.cpp commit 6f4fe13956c48b67c35ec7ea5df40c26e31a7890 Author: Weiqun Zhang Date: Sat Jan 3 07:58:32 2015 -0800 MFIter: rename fluxbox nodalbox for consistence Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp commit 1f56c8ddc474f4d6a39cdf682a67cad620008394 Author: Weiqun Zhang Date: Wed Dec 31 19:59:16 2014 -0800 added a new member function to FillPatchIterator t return the filled temporary MultiFab; this is useful for tiling loops that used to use FillPatchIterator Src/C_AMRLib/AmrLevel.H commit 90691c3cbf52bc4003b069ebc49c1dde9950bd64 Author: Weiqun Zhang Date: Wed Dec 31 14:22:47 2014 -0800 print out the smallest and biggest grid on each level after regrid if verbose > 0 Src/C_AMRLib/Amr.cpp commit 7824e7aac44826115b09864851a1b602a5a85284 Author: Weiqun Zhang Date: Sun Dec 28 21:06:55 2014 -0800 minor: use a more meaningful name Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit 1e216e469a0dd6d91d54015997e00ba3895455ba Author: Weiqun Zhang Date: Sun Dec 28 20:36:45 2014 -0800 fixed a new bug Src/C_BoundaryLib/FabSet.cpp commit f47ccf0f1aad0fc0089e2dfb69b0f1c8e3824e1c Author: Weiqun Zhang Date: Sun Dec 28 16:00:29 2014 -0800 added OMP to MGT_Solver Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit dcac0c0840bbe7791b6f3298037b77686732129b Author: Weiqun Zhang Date: Sun Dec 28 15:13:10 2014 -0800 added tiling and OMP in serveral palces Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/Geometry.cpp Src/C_BoundaryLib/FabSet.cpp Src/C_BoundaryLib/InterpBndryData.cpp commit 2a39a1118d454c146d0a548e6a20703f9ae4f7f3 Author: Weiqun Zhang Date: Wed Dec 24 15:35:06 2014 -0800 fixed similar OMP issue in C++ Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit ae6da048d55e2810fdd63be41d61406f06e5f62d Author: Weiqun Zhang Date: Wed Dec 24 10:37:22 2014 -0800 Fixed an omp bug in F90 fill_boundary of nodal multifab with periodic boundary. In this case, fill_boundary actually copyies from valid cells to valid cells. Src/F_BaseLib/layout.f90 commit 36a2f8e6bec380864d00baf319e3e4e9b5eb9dfc Author: Weiqun Zhang Date: Tue Dec 23 14:12:42 2014 -0800 removed an unintended nested OMP parallel region Src/C_BaseLib/MultiFab.cpp commit 3056d1391d7a4b0edb98b9204892d954aed417f8 Author: Weiqun Zhang Date: Tue Dec 23 13:16:32 2014 -0800 cleanup Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 729854ed53b0b9d315b91273234fcb0e0fa5d35b Author: Weiqun Zhang Date: Tue Dec 23 11:25:22 2014 -0800 implemented OMP in packing and unpacking for MPI Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit cc5465687732946e1c012a867ce9cbacc06fd046 Author: Weiqun Zhang Date: Mon Dec 22 20:06:25 2014 -0800 minor shortcuts Src/F_BaseLib/layout.f90 commit 18d793582bcaddfc6ca09a21be092613d8935545 Author: Weiqun Zhang Date: Mon Dec 22 16:35:01 2014 -0800 C++: work in progress: refactor OMP in packing and unpacking for MPI Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit 90d9c7507853fb062c8d7ab94832e2b65e26eebe Author: Weiqun Zhang Date: Mon Dec 22 15:50:33 2014 -0800 fixed a new bug Src/F_BaseLib/layout.f90 commit 3f47844b32bda69523af2abee5419d040c9e7ca1 Author: Weiqun Zhang Date: Mon Dec 22 15:09:03 2014 -0800 F90: Added thread safety flags for multifab copy and fill_boundary, and fixed a 2-year old OMP bug in multifab copy. Added OMP to sum_boundary. This might break some regression tests. Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit b1348fed1c6b99d00c727d02e83dceccf0569feb Author: Weiqun Zhang Date: Mon Dec 22 12:49:29 2014 -0800 fixed OMP data races introduced today Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit 86d544e75e458cbed4f7bd189fedd26426baba20 Author: Weiqun Zhang Date: Mon Dec 22 11:16:41 2014 -0800 removed random shuffle from FabArray because it is no longer used Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit b4a68f24e49b3d7ee12a1c0bc0262941ece70c23 Author: Weiqun Zhang Date: Mon Dec 22 11:14:00 2014 -0800 OMP in SumBoundary Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit 8aba9ac218ee01847281aba22eca3d20f78966ad Author: Weiqun Zhang Date: Fri Dec 19 14:28:55 2014 -0800 added a new distribution method, RRSFC, which do roundrobin on space filling curve. This is good for job balance in the case where the amount of work is correlated with position, such as Sedona. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 44c848f812eeca47403c851b1550c3c8c2ccf241 Author: Weiqun Zhang Date: Fri Dec 19 11:53:17 2014 -0800 moved memory allocation out of OMP parallel region Src/C_AMRLib/AmrLevel.cpp commit b756778325f858718fb7dda533b656515cc5d772 Author: Weiqun Zhang Date: Thu Dec 18 16:05:12 2014 -0800 minor optimization and clean up Src/C_BaseLib/FabArray.H Src/C_BaseLib/Utility.cpp commit 8731185fef12c9b38a7ff70774e5c0e2d4f68753 Merge: 2f08b1fae 0c11ec213 Author: Weiqun Zhang 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 Date: Thu Dec 18 11:23:50 2014 -0800 added timers Src/C_BaseLib/FabArray.cpp commit 0c11ec21345d1dc607d8cf0defceee037dc4deb4 Author: Weiqun Zhang Date: Wed Dec 17 16:42:42 2014 -0800 fixed a new bug in parallel copy Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit d9eebb72abb847077f2141b3b44922fb4fcd515e Author: Weiqun Zhang Date: Wed Dec 17 15:06:57 2014 -0800 OMP parallel copy Src/C_BaseLib/FabArray.H commit 51a873615777273e0b313e23b8c4eff0063665d4 Author: Weiqun Zhang Date: Wed Dec 17 13:57:52 2014 -0800 more OMP in FillPeriodicBoundary Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 12b44e6157669f1b8fed5355008d27b54aaa2dc5 Author: Weiqun Zhang Date: Wed Dec 17 13:05:40 2014 -0800 added OMP to FillPeriodicBoundary Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 6e919d149ee9963ddcd9c8ccf8c13cfef07a6c4a Author: Weiqun Zhang Date: Wed Dec 17 12:48:54 2014 -0800 option to turn off nested threading in MFIter Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 258f7ad577fb5c1563495a6a62d37a641cdfb697 Merge: 78312a445 3e090df7c Author: Weiqun Zhang Date: Wed Dec 17 10:38:41 2014 -0800 Merge branch 'master' into commopt commit 78312a44598e3eaec754c6be21b2e02ef3c2ab1d Author: Weiqun Zhang Date: Wed Dec 17 10:37:53 2014 -0800 more OMP in FillBoundary Src/C_BaseLib/FabArray.H commit 3e090df7cf883e218b692815e79dd898aaab86a7 Author: Weiqun Zhang Date: Tue Dec 16 21:19:12 2014 -0800 fixes for gcc 4.8 and above Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp commit bca2609e5869ca08b4cad8b017c53008abda9828 Author: vince Date: Tue Dec 16 17:20:10 2014 -0800 typo. Src/C_BaseLib/BLProfiler.cpp commit e85c1bbe0b7ac5b623276ddde7467c949c49f035 Author: Weiqun Zhang Date: Tue Dec 16 14:24:59 2014 -0800 OMP two loops in FillBoundary Src/C_BaseLib/FabArray.H commit 699e72b1332f1c31401e8be37388d2b3df0f6eaf Author: vince Date: Tue Dec 16 13:42:48 2014 -0800 array size. Src/C_BaseLib/BLProfiler.cpp commit 0884cfd6c4c4f9c99856f598ec6f29cb423f79c2 Merge: 01a608933 83c10c3c4 Author: Weiqun Zhang Date: Tue Dec 16 12:35:02 2014 -0800 Merge branch 'master' into commopt commit 83c10c3c45679db041cc96e3c23c5b79a9396a6f Author: Weiqun Zhang Date: Tue Dec 16 12:27:36 2014 -0800 removed the update argument and optimized Where() Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit aecb88cc2b8db590c514f17cd5685749cf640cc7 Author: Weiqun Zhang Date: Tue Dec 16 10:10:12 2014 -0800 Since particle can intersect with only one grid, we can set first_only=true in serveral calls to BoxArray::intersections Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 01a608933c2d8b227a005730b787c0cb4c7e7c69 Author: Weiqun Zhang Date: Tue Dec 16 09:51:37 2014 -0800 minor Src/C_BaseLib/FabArray.cpp commit edf539ea66b048a0d7ac0c8253152c3bfc70a600 Author: Weiqun Zhang Date: Fri Dec 12 14:13:00 2014 -0800 removed using std::isinf for Cray compiler on Hopper Src/LinearSolvers/C_CellMG/CGSolver.cpp commit a2cb52d3e74317bfda5fd34f952aaa5adc29f43e Author: Weiqun Zhang Date: Fri Dec 12 14:12:08 2014 -0800 removed tgmath.h and added std:: to sqrt for PGI on Hopper; tests show that it works for all compilers on Hopper and Edison, and my desktop with gcc 4.4.3 Src/C_BaseLib/BLProfiler.cpp commit 16940f74f4e80d17b35f8e6a5ca8892246fa4330 Author: vince Date: Fri Dec 12 13:58:04 2014 -0800 fix for sqrt, ioproc parens. Src/C_BaseLib/BLProfiler.cpp commit e358df5b1f6a26ab885fba2d714b06f5b63119f6 Merge: ab33f63b0 d84361b63 Author: vince Date: Fri Dec 12 11:56:31 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ab33f63b0bb92c66ee7bea1901ad1856ae5cd51a Author: vince Date: Fri Dec 12 11:56:16 2014 -0800 changed double to Real in SumPeriodicBoundary so PRECISION=FLOAT will compile. Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit d84361b63bc23e67b9de17819e8bba1ba907a377 Author: Weiqun Zhang Date: Thu Dec 11 17:25:07 2014 -0800 reverted my last change because it created new problems Tools/C_mk/Make.defs commit e1fcc42138a5861f64502ef2231465b507385245 Author: Weiqun Zhang Date: Thu Dec 11 16:30:39 2014 -0800 added -std=c++0x to gcc as needed by the new BLProfiler Tools/C_mk/Make.defs commit 67c94c42dcf41301572177f284bb2259aa99439b Author: vince Date: Thu Dec 11 11:04:02 2014 -0800 another donev machine. Tools/C_mk/Make.defs commit 9ee28b56cde48071dec3b0080562edbea6af80ff Author: vince Date: Wed Dec 10 15:35:21 2014 -0800 renamed Profiler to BLProfiler (class and files). Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Particles.H Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/BLProfiler.H Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/iMultiFab.cpp Src/C_BoundaryLib/FabSet.cpp Src/C_TowerLib/Layout.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tProfiler.cpp commit 38d7375179a18264c46b12be0a6fca4a881825dc Merge: 5b6e71a5d a4b0a0cf9 Author: vince Date: Tue Dec 9 14:33:23 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 5b6e71a5d09e3900258ca1a2fab1421541230552 Author: vince Date: Mon Dec 8 16:59:41 2014 -0800 added more statistics. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit a4b0a0cf9f9c5716b00a226f1e72c74c223ce7fc Author: Weiqun Zhang Date: Fri Dec 5 13:05:57 2014 -0800 fixed 2 new errors Src/C_AMRLib/Particles.cpp commit 782e47e953977be22810b10821560a572d00fd54 Author: Weiqun Zhang Date: Fri Dec 5 13:03:18 2014 -0800 fixed a new error Src/C_AMRLib/Particles.H commit 1f571643bae2d34cf53e00145034fd353b6d5d9b Author: Weiqun Zhang Date: Fri Dec 5 12:51:50 2014 -0800 more const T -->> const T& Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Utility.cpp Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/WaveEquation_C/main.cpp commit 8731e85444fa40242d8ab88e491b5aac0c7c292a Author: Weiqun Zhang Date: Fri Dec 5 12:27:09 2014 -0800 more const T -->> const T& Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BoundaryLib/InterpBndryData.cpp Src/C_BoundaryLib/MacBndry.cpp Src/C_TowerLib/Layout.cpp Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp Tools/C_util/ViewMF/viewMFdiff.cpp Tools/C_util/ViewMF/viewMFdiffHardWire.cpp Tools/C_util/WritePlotFile.cpp Tutorials/AMR_Advection_C/Source/ADR.cpp Tutorials/AMR_Advection_C/Source/Diffusion.cpp Tutorials/AMR_PETSc_C/Source/Darcy.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp commit 171196b707bea9d16329c080ca11b86d7910e4b2 Merge: 7b15734f3 5729afa91 Author: Weiqun Zhang Date: Thu Dec 4 21:55:58 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 7b15734f3015f791a0a0b4b001dc99d905071b67 Author: Weiqun Zhang Date: Thu Dec 4 21:06:07 2014 -0800 minor optimization using a nice feature of C++: temporary variable created as the rhs of assignment to const T& lhs has the same lifetime as the lhs variable. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/AuxBoundaryData.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/iMultiFab.cpp Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/InterpBndryData.cpp Src/C_TowerLib/Layout.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Tests/C_BaseLib/tBA.cpp commit 5729afa918fc3e30763070d16550f7b0848dbb3b Author: Weiqun Zhang Date: Thu Dec 4 06:13:04 2014 -0800 added -lquadmath for gcc 4.9 Tools/C_mk/Make.Linux commit 0262c2df8d6a2299ed42559e33a64e77f37965b9 Merge: df633b2b2 51c8c46f1 Author: Weiqun Zhang Date: Tue Dec 2 21:15:44 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit df633b2b2e699e0f17415d565e1a385ffc5aa41d Author: Weiqun Zhang Date: Tue Dec 2 21:02:00 2014 -0800 minor optimization Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/iMultiFab.cpp commit 51c8c46f14c15b06bb06c1307e2b1e5280866b78 Author: Weiqun Zhang 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 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 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: 40ebd9eee 7c6136db4 Author: Weiqun Zhang Date: Tue Dec 2 15:44:39 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 40ebd9eee387d0910bc938ca0d5b750218176500 Author: Weiqun Zhang Date: Tue Dec 2 15:40:28 2014 -0800 removed OMP from BaseFab saxpy so that we can do OMP on MultiFab Src/C_AMRLib/MLSDCAmrEncap.cpp Src/C_BaseLib/SPECIALIZE_3D.F commit 74d8b7bb95d5e4e5690ac6be94a3567e355a7683 Author: Weiqun Zhang Date: Tue Dec 2 15:31:59 2014 -0800 add tiling to FabSetIter and use it in FluxRegister::SumReg Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BoundaryLib/FabSet.H commit bf6b07fd247dd8edb61690816239d990081d5047 Author: Weiqun Zhang Date: Tue Dec 2 15:25:13 2014 -0800 cleanup Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 459b50f181fef59f62f7695c3c4fbb8970daa42b Author: Weiqun Zhang Date: Tue Dec 2 15:05:31 2014 -0800 tiled MultiFab::contains_inf and contains_nan Src/C_BaseLib/MultiFab.cpp commit aadb8abe1bc8c7afa383b2ca4b0dc7d3421f4569 Author: Weiqun Zhang Date: Tue Dec 2 14:49:27 2014 -0800 tiled a number of MultiFab functions Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/iMultiFab.cpp commit 9133dc02563685a157cd28004351f637a0ddc6c8 Author: Weiqun Zhang Date: Tue Dec 2 14:19:31 2014 -0800 minor optimization by moving omp critical out of MFIter loop Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp commit 7c6136db438d5f3febcad0b8df61bd9beaf1f621 Author: Weiqun Zhang Date: Tue Dec 2 12:31:25 2014 -0800 minor Src/C_BaseLib/BaseFab.H commit b871d80fb80e174f20001055fd3737983cc92894 Author: Weiqun Zhang Date: Tue Dec 2 12:04:53 2014 -0800 tiled setVal Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit d58a8c8827785e47e4a6c5c76cf0ac5ad440d40c Author: Weiqun Zhang Date: Tue Dec 2 11:51:15 2014 -0800 Added MFIter::growntilebox that returns the tile box grown to include ghost cells; cleanup Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit fabf904842684b5a76547c5d0ff09e3f13c40a25 Author: Weiqun Zhang Date: Mon Dec 1 17:01:38 2014 -0800 Do not set initialized to false in CGSolver and MultiGrid::Finalize so that we don not have to query ParmParse again and again. Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit af6b7d131edda1db8986ffb167d5f613113d4d3e Author: Weiqun Zhang Date: Mon Dec 1 16:56:17 2014 -0800 Do not set initialized to false in LinOp::Finalize so that we don not have to query ParmParse again and again. Src/LinearSolvers/C_CellMG/LinOp.cpp commit 17183ca8d75fdb4248715fa03d3611106705bdcd Author: Weiqun Zhang Date: Mon Dec 1 15:57:42 2014 -0800 more tiling in C_CellMG Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/LP_1D.F Src/LinearSolvers/C_CellMG/LP_2D.F Src/LinearSolvers/C_CellMG/LP_3D.F Src/LinearSolvers/C_CellMG/LP_F.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/MG_3D.F Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit e88fc3bbe0962c9c249e620e9e065cdb15f94142 Author: Weiqun Zhang 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 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 Date: Mon Dec 1 14:56:16 2014 -0800 added fluxbox to MFIter Src/C_BaseLib/FabArray.H commit 97d2b921b270edfdda0a890f1b29f36930122391 Author: Weiqun Zhang Date: Fri Nov 28 14:39:54 2014 -0800 BLMap: tidy Src/C_BaseLib/BLMap.H commit 50e9ea7f0dc243277d89ba427d73e02df3bdf961 Author: Weiqun Zhang Date: Fri Nov 28 14:15:53 2014 -0800 added local_size() function to FabArray.H; added reserve() to BLMap.H; fine tune BLMap::operator[] Src/C_BaseLib/BLMap.H Src/C_BaseLib/FabArray.H Src/C_BoundaryLib/FabSet.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit be3d9d36f2cf190a3dff95e8f6f66a5ee16a5840 Author: Weiqun Zhang Date: Thu Nov 27 23:30:56 2014 -0800 comments Src/C_BaseLib/BLMap.H commit 8fc65bf7f9d6bc427f3aa11148994ce60b1dbb18 Author: Weiqun Zhang Date: Thu Nov 27 23:22:39 2014 -0800 comments Src/C_BaseLib/BLMap.H commit cf0c63e0a280462b7bd93daf6dfdadfa03c42414 Author: Weiqun Zhang Date: Thu Nov 27 23:16:53 2014 -0800 added more comments Src/C_BaseLib/BLMap.H commit a9453dd308332240192cf07347dcee82b21bbe7b Author: Weiqun Zhang Date: Thu Nov 27 22:19:03 2014 -0800 added BLMap, a lightweight and thread-safe (in reading) class with some features of std::map; use BLMap instead of std::map in LinOp Src/C_BaseLib/BLMap.H Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit 3158500407ee451a73120ba4a3e71f15622850b5 Author: Weiqun Zhang Date: Wed Nov 26 20:47:49 2014 -0800 use std::lower_bound in local index search Src/C_BaseLib/FabArray.H commit 1b53e94e0b84239bb187436d164c1f75546cf6c0 Author: ajnonaka Date: Wed Nov 26 08:57:45 2014 -0800 plug a memory leak for the case when you try to use bottom_solver_type=4 but the grid layout isn't appropriate Src/LinearSolvers/F_MG/mg.f90 commit fab9bacbefeb2a167b32a46fc9fd5e03dec722a6 Author: Weiqun Zhang Date: Wed Nov 26 07:00:00 2014 -0800 tiled C_CellMG/GSRB Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/ABec_F.H commit 7bae0fb7a7a1d25f0da2b34e00e25555feeadacb Author: Ann Almgren Date: Tue Nov 25 13:41:23 2014 -0800 Add profiling to particle moveKick and moveKickDrift routines. Src/C_AMRLib/Particles.H commit cc9514c258a9e17c8e4a5ca7c4019963b598781a Author: Weiqun Zhang Date: Mon Nov 24 10:22:29 2014 -0800 more mf[mfi.index()] --> mf[mfi] Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tutorials/AMR_Advection_C/Source/ADR.cpp Tutorials/AMR_Advection_C/Source/ADR_advance.cpp Tutorials/AMR_Advection_C/Source/ADR_diffusion.cpp Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp Tutorials/MultiGrid_C/main.cpp commit d2f4f92a4c7ba7b03e09e3e27a01517894c545ba Author: Weiqun Zhang Date: Mon Nov 24 09:43:46 2014 -0800 more mf[mfi.index()] --> mf[mfi] Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/InterpBndryData.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/Python/src/boxlib_wrap_1.cpp Src/Python/src/boxlib_wrap_2.cpp Src/Python/src/boxlib_wrap_3.cpp Src/Python/swig/boxlib.i commit a77ce5091b4db713e9957e2d6deb74147ac6ed0a Author: Weiqun Zhang Date: Sun Nov 23 21:35:00 2014 -0800 fixed tiling bug in MFIter when inside OMP parallel region Src/C_BaseLib/FabArray.H commit c5b1467d98a9c6956b8706daa0287e26bd963827 Author: Weiqun Zhang Date: Sun Nov 23 20:43:47 2014 -0800 adde an omp atomic to fix a race condition Src/C_BaseLib/BaseFab.H commit b0f3dc0f465e3540371bf582066de1662f4fdf6f Author: Weiqun Zhang Date: Sun Nov 23 14:52:54 2014 -0800 clean up Src/C_BaseLib/FabArray.H commit 58406cf88a1a21259c294f24afebaba181ebf155 Author: Weiqun Zhang 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 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 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 Date: Fri Nov 21 22:10:07 2014 -0800 fixed another new bug Src/C_AMRLib/TagBox.cpp commit d75c10ed5be6680e549f47360b1959c955f0fc49 Author: Weiqun Zhang Date: Fri Nov 21 21:01:51 2014 -0800 fixed a new bug Src/C_AMRLib/AmrLevel.H commit 40ac1b0d4883dd181ffc2ef046631b19910493b7 Author: Weiqun Zhang Date: Fri Nov 21 19:17:21 2014 -0800 fixed a bug in localindex of the new vector based FabArray Src/C_BaseLib/FabArray.H commit ff99c3d7a922380b931cd68b0d7332c1f6a6ab60 Author: Weiqun Zhang Date: Fri Nov 21 17:01:39 2014 -0800 In many palce, use mfi instead of mfi.index() to access fab. This is now the preferred way because it is more efficient. MiniApps/MultiGrid_C/main.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/iMultiFab.H Src/C_BaseLib/iMultiFab.cpp commit 6d37ad94b5ca7196800feae4d6b3bd3452fae245 Author: Weiqun Zhang Date: Fri Nov 21 15:59:51 2014 -0800 In FabArray, use vector instead of map to store fab pointers. Src/C_BaseLib/FabArray.H commit dadd93badd192f60e32630d974100a06ffabba3a Author: Weiqun Zhang Date: Fri Nov 21 13:16:57 2014 -0800 Revert "tiled GSRB in C_CellMG" because of thread safety. The problem is C++ std::map::find is not thread safe. This reverts commit 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: 57e3776b3 3ea94eecb Author: Weiqun Zhang Date: Fri Nov 21 11:29:32 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3ea94eecb0fdab90cb4cfc783902ff8a51d5565f Author: vince Date: Fri Nov 21 11:19:23 2014 -0800 removed some debugging output. Src/C_BaseLib/DistributionMapping.cpp commit d4f16ed653e6b8df59787a08d8b9244fd2ab4f0b Author: vince Date: Fri Nov 21 11:11:48 2014 -0800 removed unused vars. Src/C_BaseLib/DistributionMapping.cpp commit 57e3776b305e98dfe8a6a858315721c88c6ca5de Author: Weiqun Zhang Date: Fri Nov 21 10:47:17 2014 -0800 tiled GSRB in C_CellMG Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/ABec_F.H commit b0c6b9d7bb37a8a46625964f381123489a32bf95 Author: Weiqun Zhang Date: Fri Nov 21 10:18:14 2014 -0800 added some timers to C_CellMG Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit d5268cc3b72b10c2393af654f6708b777c933e6b Author: Weiqun Zhang Date: Thu Nov 20 20:45:00 2014 -0800 added tilebox function to MFIter; added a parameter for controlling tile size via ParmParse; another MFIter constructor that used the default tile size. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Tutorials/Tiling_C/main.cpp commit 683b77907012921082ffb28bf9e45cff8964700e Author: Weiqun Zhang Date: Thu Nov 20 20:02:21 2014 -0800 fixed un-deleted heap memory to quiet valgrind MiniApps/MultiGrid_C/main.cpp Tests/LinearSolvers/ComparisonTest/main.cpp Tutorials/AMR_Trilinos_C/driver.cpp Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/MultiGrid_C/main.cpp Tutorials/WaveEquation_C/main.cpp commit b547b411f3087b68531b87bc20217674bada3624 Merge: ccc7a299a faff396e9 Author: vince Date: Thu Nov 20 17:23:35 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ccc7a299a24c7f096454456eb4951712d6fbd481 Author: vince Date: Thu Nov 20 17:23:25 2014 -0800 binary format for individual proc prof data. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit faff396e9ff672123f871a1df044fa49345c66e3 Author: Weiqun Zhang Date: Thu Nov 20 13:01:32 2014 -0800 validbox in MFIter must have the correct indexing type Src/C_BaseLib/FabArray.H commit 465f51d7fe6ff821ca2dde079f8d945d5d77134f Merge: 8db8e9e78 5d5c1dcdb Author: Marc Day Date: Thu Nov 20 10:39:49 2014 -0800 Merge branch 'master' into 4thOrderMG commit 5d5c1dcdb744ceaed9d33eaeb428c85a1237090c Author: Weiqun Zhang Date: Thu Nov 20 10:38:42 2014 -0800 added a tutorial code showing how tiling version of MFIter can be used. Tutorials/Tiling_C/GNUmakefile Tutorials/Tiling_C/Make.package Tutorials/Tiling_C/main.cpp Tutorials/Tiling_C/work.f90 commit 8db8e9e785f6e6e6f5e097c64bbabf20bb39ce6c Author: Marc Day Date: Thu Nov 20 10:37:58 2014 -0800 Initial commit of branch for 4th order mg Src/C_BaseLib/BLFort.H Src/C_BoundaryLib/BndryData.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG4/ABec2.H Src/LinearSolvers/C_CellMG4/ABec2.cpp Src/LinearSolvers/C_CellMG4/ABec2_2D.F Src/LinearSolvers/C_CellMG4/ABec2_3D.F Src/LinearSolvers/C_CellMG4/ABec2_F.H Src/LinearSolvers/C_CellMG4/ABec4.H Src/LinearSolvers/C_CellMG4/ABec4.cpp Src/LinearSolvers/C_CellMG4/ABec4_2D.F Src/LinearSolvers/C_CellMG4/ABec4_3D.F Src/LinearSolvers/C_CellMG4/ABec4_F.H Src/LinearSolvers/C_CellMG4/CMakeLists.txt Src/LinearSolvers/C_CellMG4/Make.package Src/LinearSolvers/C_CellMG4/OpenSource.txt Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Tools/C_mk/Make.mpi Tutorials/MultiGrid_C/COEF_2D.F Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/inputs.3d Tutorials/MultiGrid_C/main.cpp commit 035e96eb82b52d9535cc6404801f32153091706e Author: Weiqun Zhang Date: Thu Nov 20 10:20:23 2014 -0800 Implemented a tiling version of MFIter. This should not affect the results of any codes unless a tiling version of MFIter is actually used. Src/C_BaseLib/FabArray.H commit f05a9305ecba802085a3bcc634b6817b7ccf0f4a Author: Weiqun Zhang Date: Wed Nov 19 16:19:10 2014 -0800 commented out a cout Src/C_BaseLib/DistributionMapping.cpp commit f876859a2be417160ddbdc5f8cd1abe71dc8eb7f Author: vince Date: Wed Nov 19 14:54:58 2014 -0800 moved readBoxArray from StateData to BoxArray, removed dependencies in DistributionMapping. Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/DistributionMapping.cpp Tests/C_BaseLib/GNUmakefile commit 223fb9776100efe49f88dd7859a988654f10af4c Author: vince Date: Wed Nov 19 14:48:54 2014 -0800 added to the docs. Docs/Readme.profiling commit aa040a67ce6f21d7a9f3c4815c838c20f1c997e8 Merge: 42f7b239f dcbf1d8df Author: Weiqun Zhang Date: Wed Nov 19 13:30:48 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib Conflicts: Src/C_BaseLib/DistributionMapping.cpp commit 42f7b239fcdeeeb6665cf457fe060c439530774e Author: Weiqun Zhang 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 Date: Wed Nov 19 09:30:41 2014 -0800 removed an unused variable Src/C_BaseLib/threadbox.f90 commit dcbf1d8df20b79eb24f14a614f6962214e1adedc Merge: fb6721f6f c08554b28 Author: vince Date: Tue Nov 18 14:28:02 2014 -0800 more merge cleanup. commit fb6721f6f61185837643d6e959f30dc78aa0c412 Merge: 105a38657 9b5b6a886 Author: vince Date: Tue Nov 18 14:12:31 2014 -0800 merge resolution. commit d14c972dc3091c7e3ce03eba4cd426e76a0e3ef0 Author: Weiqun Zhang Date: Tue Nov 18 13:57:54 2014 -0800 minor Src/C_BaseLib/DistributionMapping.cpp commit c08554b28f3ec53ae3c1e86e8b4dde561de14249 Author: Weiqun Zhang Date: Tue Nov 18 13:23:08 2014 -0800 Removed the long long int stuff I recently committed and the long long int stuff in Particles I did a while ago. But I added a warning about the size of long int, if it is too small. I give up because: (1) there are many places that have to be changed if we really want to make sure BoxLib can handle really big runs on systems like Windows where long int is only 4-byte wide; (2) on most if not all Unix systems, long int is 8-byte wide. Src/C_AMRLib/Particles.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ccse-mpi.H commit 01795d3f2a5969cedfc9aa84b0daeee6f40deecd Author: Weiqun Zhang Date: Tue Nov 18 11:16:29 2014 -0800 minor cleanup: std::map::insert checks if the element to be inserted already existed, so we do not have to do it ourselves Src/C_BaseLib/DistributionMapping.cpp commit 105a386579446d3f0987e56244d3d83f4c448ecf Author: vince Date: Tue Nov 18 10:25:25 2014 -0800 some fortran profiling tests. Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/TPROFILER.F Tests/C_BaseLib/TPROFILER_F.H Tests/C_BaseLib/tProfiler.cpp commit 246687a6e6054f4809ff2bc1b5e61148e6dd0978 Author: vince Date: Tue Nov 18 10:24:03 2014 -0800 made regular profiling for ParallelDescriptor functions a special profiling option. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 29fca8e45a1502d3bb93c3dd2ea7e7ef3f4dc9a3 Author: vince Date: Tue Nov 18 10:22:21 2014 -0800 some cleanup before the merge. Src/C_AMRLib/Amr.cpp commit 99041f8b836079bd9e68cdb8ca8e7df1cf50c9f5 Author: vince Date: Tue Nov 18 10:21:44 2014 -0800 added faster fortran interface for functions with a large number of calls. Src/C_BaseLib/BLProfiler_F.f Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 9b5b6a88636c447c02db59183f180692413da9d0 Author: Weiqun Zhang Date: Tue Nov 18 06:26:45 2014 -0800 fixed typo and made it compile again. added comment on long long int. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/DistributionMapping.cpp commit 38b5b1a95f4d1a76eb06c67f60f55a740386ef16 Author: Weiqun Zhang Date: Mon Nov 17 16:43:13 2014 -0800 Make stable sort in LeastUsedCPUs truly stable. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 3ddd286d3726c3cf2b89b02e93caff688267a049 Author: Weiqun Zhang Date: Mon Nov 17 16:33:39 2014 -0800 Use long long int for storing the total bytes allocated. The maximum value of long int is only slightly larger than 2e9, whereas a compute node of Edison has 64 GB memory. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/DistributionMapping.cpp commit 3c8aef11a9ae58ec1f2758df917797a05fa50772 Author: Weiqun Zhang Date: Mon Nov 17 15:17:51 2014 -0800 comment Src/C_BaseLib/DistributionMapping.H commit 545c6a3e872b74be8dc86124115e921dc7829019 Author: Weiqun Zhang Date: Mon Nov 17 15:05:03 2014 -0800 Added one more digit to a few constants to achieve machine accuracy. For example, (1.d0/6.d0 .eq. 0.1666666666666667d0) is false, whereas (1.d0/6.d0 .eq. 0.16666666666666667d0) is true, if IEEE 754 is used. Src/C_BaseLib/CONSTANTS.H commit 3c77dbaabc2566d98fc5bbfe8433357afb649d0e Merge: 0ea96e660 cd402d553 Author: Weiqun Zhang Date: Mon Nov 17 12:07:35 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 0ea96e6606ce9a59cb84232a8024e9a55b4f12d3 Author: Weiqun Zhang Date: Mon Nov 17 12:05:54 2014 -0800 Fixed Box::isEmpty(). The old version would abort on an empty box in DEBUG mode because of an assertion. Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit d2a1767545f637f81fb80ce9895dd50a6b1681f3 Author: Weiqun Zhang Date: Mon Nov 17 11:04:59 2014 -0800 minor cleanup Src/C_BaseLib/Box.H commit f4b1e81cfb0b86ff539ca359b2424dc970dea95d Author: Weiqun Zhang Date: Fri Nov 14 13:26:02 2014 -0800 added long long type for number of points in a BoxArray Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 3a3843adfc8a8e09cc84110b38ee4342a94f7454 Author: Weiqun Zhang Date: Fri Nov 14 13:25:07 2014 -0800 modified comment Src/C_BaseLib/Pointers.H commit 5d2590547bcc18ed5dd9da28a78513adcc9a34e1 Author: Weiqun Zhang Date: Thu Nov 13 17:08:18 2014 -0800 clean up USE_F90_SOLVERS Tests/LinearSolvers/C_CellMG/GNUmakefile Tools/RegressionTesting/IAMR-tests.ini Tools/RegressionTesting/LMC-tests.ini commit 73f912357342dbe0f58a05664d28f106ef4b3f25 Author: Weiqun Zhang Date: Thu Nov 13 16:29:13 2014 -0800 removed an old obsolete file Src/C_BaseLib/std/limits commit 5fb46d4995ff74a97a0803e4fe008c44da37f743 Author: Matthew Emmett Date: Fri Nov 14 00:25:10 2014 +0300 PyBoxLib: Tidy a lot and use relative imports. Src/Python/F90/fboxlib/__init__.py Src/Python/F90/fboxlib/boxarray.py Src/Python/F90/fboxlib/fab.py Src/Python/F90/fboxlib/fabutils.py Src/Python/F90/fboxlib/layout.py Src/Python/F90/fboxlib/multifab.py Src/Python/F90/fboxlib/plotfile.py Src/Python/F90/fboxlib/regrid.py Src/Python/F90/fboxlib/utils.py Src/Python/F90/tests/regrid.py commit e1afb4a0e4579669e1140df71317562fc202094b Author: Matthew Emmett Date: Fri Nov 14 00:05:59 2014 +0300 PyBoxLib: Update README files and add test script. Src/Python/F90/README Src/Python/F90/setup.py Src/Python/F90/test.py Src/Python/README commit 5656433e56b36bcad8658cc5485a179cea7d0b84 Author: Matthew Emmett Date: Thu Nov 13 23:56:02 2014 +0300 PyBoxLib: Flesh out new wrapper, regridding works. Src/Python/F90/fboxlib/__init__.py Src/Python/F90/fboxlib/base.py Src/Python/F90/fboxlib/fab.py Src/Python/F90/fboxlib/layout.py Src/Python/F90/fboxlib/multifab.py Src/Python/F90/fboxlib/pybl.py Src/Python/F90/fboxlib/regrid.py Src/Python/F90/src/boxlib_numpy_c.c Src/Python/F90/src/boxlib_numpy_f.f90 Src/Python/F90/src/fboxlib.f90 Src/Python/F90/src/fboxlib_c.c Src/Python/F90/src/make_new_grids.f90 Src/Python/F90/src/tag_boxes.f90 commit a412db953a38ce26b0c49f9bf21e311b77958103 Author: Matthew Emmett Date: Thu Nov 13 16:27:04 2014 +0300 PyBoxLib: Begin new wrapper. Src/Python/F90/Makefile Src/Python/F90/fboxlib/__init__.py Src/Python/F90/fboxlib/boxarray.py Src/Python/F90/fboxlib/layout.py Src/Python/F90/src/fboxlib.f90 Src/Python/F90/src/fboxlib_c.c commit c6db4e20aeea61205dfcada904cc962d98b657c4 Author: Matthew Emmett Date: Thu Nov 13 12:21:31 2014 +0300 PyBoxLib: Add tagging callback throughout. Src/Python/F90/fboxlib/regrid.py Src/Python/F90/src/fboxlib.f90 Src/Python/F90/src/make_new_grids.f90 Src/Python/F90/src/regrid.f90 Src/Python/F90/src/tag_boxes.f90 commit 0f129b657dbb09fee1bef0e267a0f7d65692391f Author: Matthew Emmett Date: Thu Nov 13 10:47:11 2014 +0300 PyBoxLib: Mandatory boxes when creating a box array. Src/Python/F90/fboxlib/boxarray.py Src/Python/F90/fboxlib/pybl.py commit 7626eea0f7b1b729255af4f6860b67b93804cdc2 Author: Matthew Emmett Date: Thu Nov 13 10:46:43 2014 +0300 PyBoxLib: Add preliminary regrid capabilities. Src/Python/F90/fboxlib/__init__.py Src/Python/F90/fboxlib/regrid.py Src/Python/F90/src/fboxlib.f90 commit 397f8e21d5ff484aa5babc5ea821c23d9f9599ca Author: Matthew Emmett Date: Thu Nov 13 10:45:51 2014 +0300 PyBoxLib: Try to be a bit more defensive in `base.py`. Src/Python/F90/fboxlib/base.py commit f3e389f5161b7f3c716f4336ad9e1a4397085b22 Author: Matthew Emmett Date: Thu Nov 13 10:02:01 2014 +0300 regrid: Change an inout to an in, set nlevs_old properly. Src/F_BaseLib/regrid.f90 commit 63d7a7a193f3629a126ea160793b0233678bbe1b Author: vince Date: Wed Nov 12 18:04:56 2014 -0800 some profiling test codes. Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/TPROFILER.F Tests/C_BaseLib/TPROFILER_F.H Tests/C_BaseLib/tProfiler.cpp commit 1c1c345ee13a83d76eaf21b95debdea093648871 Merge: 21d5ebe18 6bccf4f5f Author: vince Date: Wed Nov 12 16:11:33 2014 -0800 Merge branch 'master' into commprof in ParallelDescriptor.cpp, readded the deleted BL_COMM_PROFILE calls before the calls to mpi functions, they are required. left the BL_PROFILE calls in the code but commented out. some after merge cleanup. Conflicts: Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp Src/F_BaseLib/bl_prof.f90 commit 21d5ebe1898bacfb285cd5c7747e09f488d7ac6c Author: vince Date: Wed Nov 12 15:24:07 2014 -0800 cleanup before merge. Tests/C_BaseLib/GNUmakefile Tutorials/MultiFabTests_C/GNUmakefile Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp commit 6bccf4f5f6987584fa7227057cc8f396520aa989 Author: Matthew Emmett Date: Wed Nov 12 23:13:32 2014 +0300 PyBoxLib: Fix installation of fboxlib. Src/Python/F90/Makefile Src/Python/F90/fboxlib/fab.py Src/Python/F90/fboxlib/pybl.py Src/Python/F90/setup.py commit 4feca5fd7292c1ee15a33a6f54e4dffda3444359 Author: Matthew Emmett Date: Wed Nov 12 17:25:43 2014 +0300 PyBoxLib: Tidy. Src/Python/GNUmakefile_F90.mak Src/Python/fsrc/blobjects.f90 Src/Python/fsrc/blobjects.py Src/Python/fsrc/boxlib_numpy_c.c Src/Python/fsrc/boxlib_numpy_f.f90 Src/Python/fsrc/fboxlib.f90 commit efdbaa3f5e4ee6bd962a1e7f9f90660674190641 Merge: 09eb19931 3332fc221 Author: Matthew Emmett 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 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 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 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 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 Date: Tue Nov 11 16:11:47 2014 +0300 PyBoxLib: Another fix for libgfortran. Src/Python/GNUmakefile_CXX.mak commit fdf0b26be5b5e0a54d13c38cbc880f3da5ae2fe0 Author: Matthew Emmett Date: Tue Nov 11 09:58:08 2014 +0300 PyBoxLib: Better gfortran detection (from Aron Ahmedia). Src/Python/GNUmakefile_CXX.mak commit cd550e54a678373beea34a702c0e582af8dd2bcf Author: Matthew Emmett Date: Tue Nov 11 09:57:21 2014 +0300 PyBoxLib: Revert back to distutils instead of setuptools. Src/Python/setup.py commit 9abcfa56867347305f3a0ad9674fb5ae1ec98ef6 Author: Matthew Emmett 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 Date: Sun Nov 9 07:10:06 2014 -0800 PyBoxLib: Tweak BOXLIB_HOME. Src/Python/GNUmakefile_CXX.mak commit 0d74e06100607d1a95bf59e2c05d9464cf622fed Author: Matthew Emmett Date: Sun Nov 9 05:15:30 2014 -0800 PyBoxLib: Get 'python setup.py develop' working. Src/Python/setup.py commit 01e9a09ff4061b881b4ad2485b761190caf70d54 Author: vince Date: Fri Nov 7 16:35:22 2014 -0800 typo, removed old code. Src/C_BaseLib/Profiler.cpp commit 8926a71546506fd5eaffea80c3e15f99922132f4 Author: Weiqun Zhang Date: Fri Nov 7 12:49:56 2014 -0800 put the new mpi_waitall code inside 'if' so that it won't break assertion in BaseFab Src/C_BaseLib/FabArray.H commit 6a51721ecc5e87fb7fff61e1be1a6aa4f5ad8c53 Author: Weiqun Zhang Date: Fri Nov 7 08:16:14 2014 -0800 fixed OMP in Jacobi smoother Src/LinearSolvers/C_CellMG/ABec_3D.F commit e99db1b1dd033612695fed7cf5b5682ec2532eb8 Author: Weiqun Zhang Date: Thu Nov 6 16:59:18 2014 -0800 C++: Use isend instead of send and replace waitsome with waitall. This makes fill boundary noticeably faster just we have observed in F90 codes. Note that MPI_Waitsome is always slower than MPI_Waitall because the former does a lot more testing, and unpacking the data is much cheaper than the overhead of waitsome. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit fd2517a2eb4b9e68594acf654de5275dc5033728 Author: Weiqun Zhang Date: Thu Nov 6 16:46:43 2014 -0800 shut down compiler warning by removing some unnecessary const prefixes to functions return plain numbers Src/C_BaseLib/Profiler.H commit f1440cc1cf4db3d4d464d183f60dda62ac89b304 Author: Weiqun Zhang Date: Thu Nov 6 16:43:34 2014 -0800 removed BL_PROFILE (not BL_COMM_PROFILE) from ParallelDescriptor because (1) there is already commprof; (2) this reduces clutter in the profiling report and gives a better idea about the cost of fill boundary and copy. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 355e8c1b26645dceb0d8854de381c15996cbcd33 Author: ajnonaka Date: Thu Nov 6 13:21:38 2014 -0800 call applyBC before calling jacobi smoother (now mirrors GSRB) Src/LinearSolvers/C_CellMG/LinOp.cpp commit 4ca1d1bb372d23fa9d443fcc442a329674210277 Author: ajnonaka Date: Thu Nov 6 13:20:27 2014 -0800 properly implement jacobi smoothing in 2d and 3d Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F commit e0496f13d82c7aaf1c2af36765f5b45d17c90acf Author: Weiqun Zhang Date: Wed Nov 5 20:39:14 2014 -0800 F90: send -> isend. We used to call irecv's followed by send's. Changing to isend makes multifab_copy and multifab_fill_boundary 20+% faster. Src/F_BaseLib/multifab_f.f90 commit a7f1abb1ab3a82c3eeddac1a545b3b6063b460f0 Author: Weiqun Zhang Date: Wed Nov 5 09:35:54 2014 -0800 F90: removed "intent(in)" from parallel_bcast because (1) it currently causes seg fault on Edison when compiled with gfortran; (2) it is incorrect: only for root rank that argument has intent(in), whereas it should be intent(out) for other MPI ranks. Src/F_BaseLib/parallel.f90 commit 0caf98360757264dd410dc66e1c67d112dc73fe1 Author: ajnonaka Date: Wed Nov 5 09:21:37 2014 -0800 cims.nyu.edu Tools/C_mk/Make.defs commit 42f99fa3a25919714b5bf09bddf9aff2c7684212 Author: Weiqun Zhang 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 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 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 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 Date: Mon Nov 3 14:08:41 2014 -0800 Donev updates Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 718e48b490d6ca683095be60d7ac63ac1098f5c1 Merge: 212d87dbe f5a5673f9 Author: Michael Zingale 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 Date: Fri Oct 31 14:46:03 2014 -0700 added comments Src/F_BaseLib/create_umac_grown.f90 commit d5d2ef0ac4fe4337b85b9d0534e7f11c9ef011b4 Author: Weiqun Zhang Date: Fri Oct 31 14:30:26 2014 -0700 fixed the fix Src/F_BaseLib/create_umac_grown.f90 commit fb6542a83f77ba3752bd6482548471eff65ffed9 Merge: c8f5704dd 401e42520 Author: Weiqun Zhang Date: Fri Oct 31 14:21:51 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c8f5704dd110cb6037e5d546189a38117cba6793 Author: Weiqun Zhang Date: Fri Oct 31 14:21:46 2014 -0700 fixed a new bug in create_umac_grown Src/F_BaseLib/create_umac_grown.f90 commit 401e425204df077e05577dcaf989cb1190cb759a Author: Ann Almgren Date: Fri Oct 31 14:20:38 2014 -0700 Add InitCosmo1ppcMultiLevel for IAG folks. Src/C_AMRLib/Particles.H commit 2ef059e4ef88e6b15cd500a7c7f4e8d27a7d7a71 Merge: ccbeba276 3ac16c1be Author: Weiqun Zhang Date: Thu Oct 30 17:35:27 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ccbeba2763280eeabc1da7045885c24e8f02fefc Author: Weiqun Zhang Date: Thu Oct 30 17:05:03 2014 -0700 removed one parallel copy from fill ghost cells Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 191392a779fcd3203012e3c4e22fa33016722801 Author: Weiqun Zhang Date: Thu Oct 30 16:35:19 2014 -0700 added argument to create_umac_grown to tell whether we need to fill fine boundaries Src/F_BaseLib/create_umac_grown.f90 commit 58e0846831fc718e4948d09597617c307f841549 Author: Weiqun Zhang Date: Thu Oct 30 16:29:03 2014 -0700 cleanup Src/F_BaseLib/create_umac_grown.f90 commit e20e3cc66b1011512efa2f1dff28100663bea892 Author: Weiqun Zhang Date: Thu Oct 30 16:06:06 2014 -0700 removed a parallel copy and fill_boundary from create_umac_grown Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/layout.f90 commit b5d2c2e59200781a73939a7fd417898cee43ad5e Author: Weiqun Zhang Date: Thu Oct 30 10:03:59 2014 -0700 merge ghstassoc with fgassoc Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/layout.f90 commit a0e5536198fdb37db54bc7fdbc320fadef11751f Author: Weiqun Zhang Date: Thu Oct 30 09:55:42 2014 -0700 simplify the boxarray in ghstassoc Src/F_BaseLib/layout.f90 commit 344102889238d3b1511ed56cf3a072d788d9b72b Author: Weiqun Zhang Date: Wed Oct 29 17:53:34 2014 -0700 work in progress for ghstassoc, which is intended to replace fgassoc Src/F_BaseLib/boxarray_f.f90 Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/layout.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit 3aa8cc705072fdfc6e81bc02c805905b19e4c3d0 Author: vince Date: Wed Oct 29 13:53:54 2014 -0700 put all output into one directory, bl_prof (or user specified name). write inclusive times option. trace flush threshold. directory creation cleanup. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 8bd20ee9a05a0a13c2117c498585e2a304f04fe2 Author: vince Date: Wed Oct 29 13:49:57 2014 -0700 optional barrier in ccd. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 8e1355728d22b5dd8774989ac06f83a5a6a542ba Author: vince Date: Wed Oct 29 12:51:23 2014 -0700 clean up directory creation. Src/C_AMRLib/Amr.cpp commit 39f41edf4ab24eb2209d903c55e3072916dcc4e5 Author: Weiqun Zhang Date: Wed Oct 29 12:14:50 2014 -0700 make ml layout strategy 1 more load balanced Src/F_BaseLib/fab.f90 Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/ml_layout.f90 Src/F_BaseLib/sort_i.f90 commit de72a561b652f3c32339225e2479091d061d7a97 Author: vince Date: Wed Oct 29 11:49:41 2014 -0700 create clean directory function. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 9aa54a9fd4bf806099e7944c6b629e287a11d7cf Merge: 5f498f217 3ac16c1be Author: Adam Jacobs 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 Date: Tue Oct 28 20:34:29 2014 -0700 removed some includes Tutorials/HelloWorld_C/GNUmakefile commit 9cbc3b532e29c8e3672a4dfb158f78616d133435 Author: Weiqun Zhang Date: Tue Oct 28 17:34:10 2014 -0700 Added a "hello world" type program for people to try tiling. Tutorials/HelloWorld_C/GNUmakefile Tutorials/HelloWorld_C/Make.package Tutorials/HelloWorld_C/main.cpp Tutorials/HelloWorld_C/work.f90 commit 212d87dbea1c78587f6bb6461ae3b368cdb0c647 Author: Michael Zingale Date: Tue Oct 28 20:21:51 2014 -0400 add a trim() fvarnames.f90 commit f5a5673f9b9c67756b1178e6e6297fb7c8995014 Author: Adam Jacobs Date: Tue Oct 28 17:10:52 2014 -0400 Add comparison temp histograms using the EoS. MAESTRO_sub_chandra/GNUmakefile MAESTRO_sub_chandra/fsubchandra.f90 MAESTRO_sub_chandra/fsubchandra_mod.f90 commit e22594e6282a7dc18df43d24956a291417fc3126 Author: Weiqun Zhang Date: Tue Oct 28 14:06:33 2014 -0700 F90 ml layout strategy 1: use prefilled version of knapsack for unassigned boxes. Src/F_BaseLib/ml_layout.f90 commit 7c96ed74a706076b387980af1742ebaf7edc9475 Author: Weiqun Zhang Date: Tue Oct 28 14:05:40 2014 -0700 F90: new knapsack that can have processors prefilled with boxes Src/F_BaseLib/knapsack.f90 commit bc18fd45264e8191ef3579d6c80b64d687da62de Author: vince Date: Mon Oct 27 15:38:12 2014 -0700 added call trace data flushing. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit ad4adf39dd5bd5117dac534000e153ac9f619197 Author: Weiqun Zhang Date: Mon Oct 27 15:17:18 2014 -0700 F90: fine tune ml layout strategy 2 Src/F_BaseLib/ml_layout.f90 commit 74a7030ef6a1861729245fe4f9b863f5af27a4ae Author: Weiqun Zhang Date: Mon Oct 27 14:59:56 2014 -0700 F90: fine tune ml layout strategy 2 Src/F_BaseLib/ml_layout.f90 commit 05848977ba471603c42d59c57c21c6bf6dfd7c40 Author: Weiqun Zhang Date: Mon Oct 27 14:20:28 2014 -0700 F90: implemented ml layout strategy 2 Src/F_BaseLib/ml_layout.f90 commit d35628e8db357c92a67f9d26677da8b488cef33e Author: Weiqun Zhang Date: Sun Oct 26 21:36:48 2014 -0700 cleanup Tutorials/HeatEquation_EX7_F/GNUmakefile commit 32d8f8990c5a7727931c05786d9bfebe0112a915 Author: Weiqun Zhang Date: Sun Oct 26 21:29:15 2014 -0700 update comments Src/F_BaseLib/ml_layout.f90 commit 468c8d3179cb6e246e407e4d9e5dba38364b2622 Author: Weiqun Zhang Date: Sun Oct 26 21:27:56 2014 -0700 F90: use the simple version for tutorial Tutorials/HeatEquation_EX5_F/main.f90 commit dbb5bfefd7c1e52b4ead08d358a8269b0d1f4057 Author: Weiqun Zhang Date: Sun Oct 26 21:20:25 2014 -0700 minor Tutorials/AMR_Adv_Diff_F/main.f90 commit b144f3c9e293570a0d575db2bbc6d8d34aca0a73 Author: Weiqun Zhang Date: Sun Oct 26 21:19:28 2014 -0700 fixed a bug in Tutorials/AMR_Adv_Diff_F Tutorials/AMR_Adv_Diff_F/compute_flux.f90 commit 246f58f816573dbfb5c01476f2053e049f81b86a Author: Weiqun Zhang Date: Sun Oct 26 19:38:01 2014 -0700 F90: destroy unused layouts Src/F_BaseLib/ml_layout.f90 commit 99b42169f6799c5613794a8b09891ff6abe018e3 Author: Weiqun Zhang Date: Sun Oct 26 15:15:18 2014 -0700 F90: back to use lower corner of boxes in sfc for testing, and some other minor changes MiniApps/AMR_Adv_Diff_F90/main.f90 Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/ml_layout.f90 commit 6f2518b854ed6a6ceb18fa6dc3641da626ea159f Author: Weiqun Zhang Date: Sun Oct 26 14:01:51 2014 -0700 F90: implemented the ignore_fine_in_layout_mapping strategy in ml_layout.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/ml_layout.f90 commit 3b3bdc9a33ee60991aca4faf07fb927b9bc6fe32 Author: Weiqun Zhang Date: Sun Oct 26 11:37:57 2014 -0700 F90: moved ml layout optimization stuff into ml_layout module, and do it when building ml_layout MiniApps/AMR_Adv_Diff_F90/main.f90 MiniApps/AMR_Adv_Diff_F90/write_plotfile.f90 Src/F_BaseLib/CMakeLists.txt Src/F_BaseLib/GPackage.mak Src/F_BaseLib/ml_layout.f90 Src/F_BaseLib/ml_optimization.f90 Src/F_BaseLib/ml_remap.f90 Src/F_BaseLib/regrid.f90 Tutorials/HeatEquation_EX5_F/main.f90 commit cdf9536cec640385288c2579dbc85b1f4e5d49e6 Author: Weiqun Zhang Date: Sat Oct 25 21:37:18 2014 -0700 renaming: ml_layout_remap --> ml_remap; and flesh out more interfaces Src/F_BaseLib/CMakeLists.txt Src/F_BaseLib/GPackage.mak Src/F_BaseLib/ml_layout_remap.f90 Src/F_BaseLib/ml_optimization.f90 Src/F_BaseLib/ml_remap.f90 commit b27c8c89f3fa25ea8b59473d22c1726802978905 Author: Weiqun Zhang Date: Sat Oct 25 20:36:13 2014 -0700 F90: cleaned up layout by removing obsolete pn_children Src/F_BaseLib/layout.f90 Src/F_BaseLib/ml_layout.f90 commit 681acfa47bcb9cd990546ae27b988af831dfff4f Author: Michael Zingale Date: Sat Oct 25 20:50:03 2014 -0400 add a 1-d routine, in prep for the Maestro flame problem. Also some styling syncing with that version Src/F_BaseLib/multifab_physbc.f90 commit 94b5e30e1eca2773b93c14f04d5a154c87883abf Author: Weiqun Zhang Date: Fri Oct 24 21:18:03 2014 -0700 F90: flesh out ml layout remapping Src/F_BaseLib/CMakeLists.txt Src/F_BaseLib/GPackage.mak Src/F_BaseLib/ml_layout_remap.f90 Src/F_BaseLib/ml_optimization.f90 Src/F_BaseLib/regrid.f90 commit aa4aac6c2ee0c8f8041a557d9184983085b9d188 Author: Weiqun Zhang Date: Fri Oct 24 17:17:36 2014 -0700 F90: use center of boxes instead of lower corner in sfc Src/F_BaseLib/knapsack.f90 commit 2d864feca536b34eff12def8293131781c07a3e9 Author: Weiqun Zhang Date: Fri Oct 24 16:35:31 2014 -0700 F90: split sfc_i into two functions, and save sfc order in layout Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/layout.f90 commit b2880812202e98af0316c65c24df8270439c91af Merge: b0acfa321 43a3e5967 Author: Adam Jacobs Date: Wed Oct 22 17:40:11 2014 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/AmrPostprocessing Conflicts: F_Src/MAESTRO_sub_chandra/fsubchandra_mod.f90 commit b0acfa32145eaaed3db3ab66e025ad745d0ba47f Author: Adam Jacobs Date: Wed Oct 22 17:38:02 2014 -0500 Add ability to handle full star geometries to sub-Chandra analysis routine. MAESTRO_sub_chandra/fsubchandra.f90 MAESTRO_sub_chandra/fsubchandra_mod.f90 commit 43a3e596715cce01e466509b1b1fa726efe74163 Merge: d0d4670be ac1a42fb8 Author: Adam Jacobs 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 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: 097732a57 4a77764da Author: Adam Jacobs Date: Tue Oct 21 15:37:49 2014 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib Conflicts: Tools/F_mk/comps/Linux_intel.mak commit 097732a57b711a2f5100fcfbee20a0cd4f50035a Author: Adam Jacobs Date: Tue Oct 21 15:34:15 2014 -0500 Add version 15 of the Intel compiler to Linux_intel.mak. This is the version on Blue Waters. Tools/F_mk/comps/Linux_intel.mak commit 4a77764da9551f9f1083e719d5fba3c1968c4c68 Author: Matthew Emmett 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 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 Date: Tue Oct 21 11:16:01 2014 -0700 added file Src/C_BaseLib/BLProfiler_F.f commit 450ae061c7a735f68310296374478552a093cf0e Author: vince Date: Tue Oct 21 10:50:12 2014 -0700 added proffort interface to master branch. Src/C_BaseLib/Make.package Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/bl_prof_stubs.f90 commit 56220a15ace9e2d30bbd41f15b42a038c379cef5 Author: vince Date: Mon Oct 20 13:37:54 2014 -0700 added step regions. Src/C_AMRLib/Amr.cpp commit 527e14ce603ef6df827e6d8a10d3dd26d37ee5a5 Merge: ccb37c7bc 873eecb2b Author: Weiqun Zhang 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 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 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: bcf8216dc a24ba7cbd Author: Michael Zingale 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 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 Date: Sun Oct 19 06:19:25 2014 -0700 kraken no longer exists (RIP...) Tools/F_mk/GMakeMPI.mak commit a24ba7cbd7af49ddd19dbf0b22c5173b07db8444 Author: Weiqun Zhang Date: Sat Oct 18 07:42:26 2014 -0700 F90: tweaked the copyassoc_check to make it go much faster; now we can afford to increase the maximum count of the copyassoc allowed Src/F_BaseLib/layout.f90 commit dad3d8db790a330b80244a048c06d2cb11347bce Author: Weiqun Zhang 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 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 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 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 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 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 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 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 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 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 Date: Thu Oct 16 11:55:18 2014 -0700 macros from the commprof branch. Src/C_BaseLib/Profiler.H commit 467d154897e39de70432c0ba0b47d3b915f59f97 Author: Adam Jacobs Date: Wed Oct 15 14:58:48 2014 -0500 Increase the maximum filename and full pathname from 128 character to 256 for the Fortran codebase. Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c Src/F_BaseLib/plotfile.f90 Src/F_BaseLib/ppm_util.f90 Src/F_BaseLib/ppm_util_c.c commit 2e45c68e62f891b29399de8f9b030a15c91ef748 Author: Weiqun Zhang Date: Wed Oct 15 11:15:04 2014 -0700 F90 linear solver: use the 8-byte integer versions of volume functions to find out if we cover the entire domain (if supported) Src/LinearSolvers/F_MG/mg.f90 commit bc166f9f83abb0331b8fb3d85020e0aa3d735891 Author: Weiqun Zhang Date: Wed Oct 15 11:13:01 2014 -0700 F90: added a 8-byte integer version of box volume function, and used it in boxarray volume function Src/F_BaseLib/box_f.f90 Src/F_BaseLib/boxarray_f.f90 commit 48041f250573aec4006791e3d475178b34d99c16 Author: Weiqun Zhang Date: Wed Oct 15 11:11:37 2014 -0700 F90: added query functions that return whether or not quad precision or 8-byte integer is supported Src/F_BaseLib/bl_types.f90 commit 4ce509e16c3177abc05da7fbfd4a3bd00dc024a0 Author: Weiqun Zhang Date: Tue Oct 14 20:33:14 2014 -0700 clean up the new ml_layout_build_la Src/F_BaseLib/ml_layout.f90 commit a9e464ee0049db3a6749d941822eef12a3c6b444 Author: Weiqun Zhang Date: Tue Oct 14 17:41:23 2014 -0700 new ml_layout_build that copies another layout Src/F_BaseLib/ml_layout.f90 commit 40d8a9e0e48945791fcd6072bd1c85d1c31ca209 Author: vince Date: Tue Oct 14 16:11:51 2014 -0700 better bounds checking for debug. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit b4231c8fdfbec9ca383d3506b53bbb1b549da195 Author: Weiqun Zhang Date: Tue Oct 14 15:43:43 2014 -0700 made the meaning of sfc_threshold in F90 consistent with C++ Src/F_BaseLib/layout.f90 commit 78a7012a4022f4b7768a9403680821394c80b1e0 Author: Weiqun Zhang Date: Tue Oct 14 15:30:55 2014 -0700 F90: only allow sfc to not sort in the least_used_cpus function Src/F_BaseLib/fab.f90 Src/F_BaseLib/layout.f90 commit d9814bc0208927099dc6bf9d0fc6aef630da12d9 Author: Weiqun Zhang Date: Tue Oct 14 15:20:13 2014 -0700 F90: removed an unused function that was recently added Src/F_BaseLib/fab.f90 commit 5c57292054107fe256814ff0b52504ee08056808 Merge: 32b4d4ea7 837cbfa78 Author: Matthew Emmett Date: Tue Oct 14 11:11:17 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 32b4d4ea793a08f8dfbb2445478f94f9eadc399b Author: Matthew Emmett Date: Tue Oct 14 11:09:46 2014 -0700 Add GetParticles method to ParticleContainer. Src/C_AMRLib/Particles.H commit 837cbfa788bdb624300ab3234b5313d48b26946b Author: Michael Zingale Date: Tue Oct 14 13:59:12 2014 -0400 add a description provided by Weiqun` Src/F_BaseLib/cluster_f.f90 commit 46a935a53676806dfe7d9eaf9653d7a2310c4b46 Author: Weiqun Zhang Date: Tue Oct 14 10:18:31 2014 -0700 F90: check allocation status of imask Src/F_BaseLib/cluster_f.f90 commit ccff20077bbe396521ab94d12454b15a3e7e6dc2 Author: Weiqun Zhang Date: Mon Oct 13 17:15:30 2014 -0700 fixed comments Src/LinearSolvers/F_MG/ml_solve.f90 commit 902c00908a2581b196d2132066e307d056df89d2 Author: Weiqun Zhang Date: Mon Oct 13 17:14:13 2014 -0700 F90: updated OMP for non-blocking multifab_fill_boundary so that it can be used for nodal mfs. Src/F_BaseLib/multifab_f.f90 commit eb39752be20c12aed19347903fd3256f5074734a Author: Weiqun Zhang Date: Mon Oct 13 13:26:50 2014 -0700 F90: speed up cluster a little bit Src/F_BaseLib/cluster_f.f90 Src/F_BaseLib/fab.f90 commit 8002bb34b2e1b19b03855bcb7ab4f7b1b403eda2 Author: vince Date: Mon Oct 13 12:21:44 2014 -0700 added several regions. Src/C_AMRLib/Amr.cpp commit aff2b6470eeacd7b9765e4633dfdaae7d3fed0e4 Author: vince Date: Mon Oct 13 12:15:46 2014 -0700 more regions and trace profiling, allow regions for commprof without traceprof. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 178b5087c974d7c2fb826dc2745c0c947b160476 Author: vince Date: Mon Oct 13 12:12:03 2014 -0700 added TRACE_PROFILE and new prof suffix and defs. Tools/C_mk/Make.defs commit 1a2c6206a52efbae2edf495c9ef6bfb64a09129f Author: Weiqun Zhang Date: Fri Oct 10 20:59:33 2014 -0700 F90: use merge sort rather than heap sort in SFC for speed Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/sort_i.f90 commit e649d09c3176b6ba7acfbc9b478e38999ff2cdde Author: vince Date: Fri Oct 10 17:06:04 2014 -0700 some reorg, relative minmax calltimes. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 07cf5390b436e1398539ddf57bd5688c794998c7 Author: Weiqun Zhang 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 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 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 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 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 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 Date: Thu Oct 9 16:46:38 2014 -0700 added const. Src/Extern/amrdata/AmrData.H commit 9f835f6c2b35cb0c8cb0a92178fcd752f3394945 Author: vince Date: Thu Oct 9 16:36:37 2014 -0700 added const. Src/Extern/amrdata/AmrData.H commit 9cf518ef043de6b9e29e9971b50538bdb96223c4 Author: Weiqun Zhang Date: Thu Oct 9 16:32:13 2014 -0700 F90: incresed maximum # of copyassocs from 25 to 50 Src/F_BaseLib/layout.f90 commit 8ac8dc220c09cbed78f1f0ba0ac395db3e37b94b Author: Weiqun Zhang Date: Thu Oct 9 14:55:53 2014 -0700 F90: rebuild fine layout too when not properly nested Src/F_BaseLib/regrid.f90 commit e60032f9cdcb5fd84e82df160dcb22a795bb6de4 Author: Weiqun Zhang Date: Thu Oct 9 14:42:02 2014 -0700 F90: new strategy for which item to remove when the copyassoc list is full Src/F_BaseLib/layout.f90 commit bee49d4233edf79edc9bc510c81c967cbc96e6a7 Author: Michael Zingale Date: Thu Oct 9 16:45:37 2014 -0400 prettification Tools/RegressionTesting/testnew.py commit 084af4f37ac76237f98949e26535079c51571f2d Author: Michael Zingale 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 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: 7a906c517 7778afd14 Author: Michael Zingale 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 Date: Wed Oct 8 20:38:14 2014 -0400 latest version Tools/RegressionTesting/Maestro-tests.ini commit ac1a42fb8a693eafbe34a7efd47d0da62c4e1591 Author: Michael Zingale Date: Wed Oct 8 20:25:22 2014 -0400 fix compilation fboxinfo.f90 commit 4ed45302b4dbbabbbbde0a6c412b0be6eae85b51 Author: Michael Zingale Date: Wed Oct 8 20:24:06 2014 -0400 add a -l option that only prints the number of levels -- I'm going to use this in the test suite shortly... fboxinfo.f90 commit 7778afd142f92eb74c4cae8245cb9f3a5239b502 Author: Weiqun Zhang 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 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 Date: Wed Oct 8 13:32:03 2014 -0700 tidy Src/F_BaseLib/regrid.f90 commit dfd7e0d2018744d83e188a4c1b93ea04ce94ffd8 Author: vince Date: Wed Oct 8 13:21:33 2014 -0700 made profiler output functions generic. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 5f913d5d04be7d135d4c2172a2c615b8d3e7f935 Author: Weiqun Zhang Date: Wed Oct 8 13:15:11 2014 -0700 Do not fill ghost cells in regrid unless told so by tag_boxes module. Do not call fillpatch if the new grids are the same as the original ones because a simple multifab copy is sufficient in this case. Src/F_BaseLib/regrid.f90 Src/F_BaseLib/tag_boxes.f90 commit bc636e228d0838c43f416e9aa11e7305e0d66992 Author: vince 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 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 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 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 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 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: 1bfaa270d b7f6467cb Author: Michael Zingale 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 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 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 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 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 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 Date: Mon Oct 6 15:42:15 2014 -0700 moved the new regid subroutine that does not change the base level into F_BaseLib MiniApps/AMR_Adv_Diff_F90/GPackage.mak MiniApps/AMR_Adv_Diff_F90/main.f90 MiniApps/AMR_Adv_Diff_F90/regrid.f90 Src/F_BaseLib/CMakeLists.txt Src/F_BaseLib/GPackage.mak Src/F_BaseLib/regrid.f90 Tutorials/AMR_Adv_Diff_F/GPackage.mak Tutorials/AMR_Adv_Diff_F/main.f90 Tutorials/AMR_Adv_Diff_F/regrid.f90 Tutorials/HeatEquation_EX4_F/GPackage.mak Tutorials/HeatEquation_EX5_F/GPackage.mak Tutorials/HeatEquation_EX5_F/regrid.f90 commit a00688229ca4454c972fbc9cb58edb9103c59ef8 Author: Weiqun Zhang Date: Mon Oct 6 14:59:38 2014 -0700 option to keep coarse layout when destroying multi-level layout Src/F_BaseLib/ml_layout.f90 commit ca7dd1be5ea9abc5835abc411b1f53ccf05be600 Author: Weiqun Zhang Date: Mon Oct 6 14:57:19 2014 -0700 added a new line in printf Src/C_AMRLib/Amr.cpp commit 370b48f2499a7a75c237c0353c06333d4174e070 Author: vince Date: Mon Oct 6 14:10:51 2014 -0700 fix for serial. Src/C_BaseLib/Utility.cpp commit 4dd0bad1bdf77375393824c48525144775291bf1 Author: Ann Almgren Date: Mon Oct 6 13:39:22 2014 -0700 Update to work with new restrictions files... Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 commit baf8b89b9f49cf0de64c7f986046f10f8cf81e45 Author: Ann Almgren Date: Mon Oct 6 13:02:53 2014 -0700 Initialize variable so we don't get compiler warning. Src/F_BaseLib/box_f.f90 commit 7f3d4bbeac88087b04d66d8b95e47740e04c6f92 Author: Ann Almgren Date: Mon Oct 6 12:59:20 2014 -0700 Remove unused variable. Src/F_BaseLib/fabio_c.c commit 64423961a2e46d6af43465e2ecad6fd0c261d996 Author: Ann Almgren Date: Mon Oct 6 12:47:40 2014 -0700 Remove unused variable. Src/F_BaseLib/layout.f90 commit 9ba4c92e1f2cba33886151aaf23e3bbd8926ebdd Author: Ann Almgren Date: Mon Oct 6 11:22:01 2014 -0700 Add test on plot_int < 0 so we can turn off plotfiles by setting plot_int negative in the inputs file MiniApps/AMR_Adv_Diff_F90/main.f90 commit c746d720e8929abba03428237a9fb0a10aaf3026 Author: vince Date: Fri Oct 3 12:52:03 2014 -0700 added function to sync sets of strings over procs. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 2c46931bb538475c84defef18cb6b876934ecd16 Author: vince Date: Thu Oct 2 11:10:40 2014 -0700 mask for NoRegion region. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 75bd8e606dfc9955559b26381c9fd3a7825a6e2b Author: vince Date: Wed Oct 1 14:46:29 2014 -0700 added time values and NoRegion to region prof. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 7dfe73e403ff741eb506f03faa4af5ce095afede Author: vince Date: Mon Sep 29 16:07:18 2014 -0700 streamlined binary callstats format. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit af04e63e716a8b2716f57f95d96f2d38d8e156c9 Author: Ann Almgren Date: Mon Sep 29 09:05:29 2014 -0700 Replace HeatEquation_EX6_F by AMR_Adv_Diff_F in documentation - this now correctly reflects what is in the code itself. Please enter the commit message for your changes. Lines starting Docs/F_AdvancedTopics/F_AdvancedTopics.tex commit f55f4cc18b99b68d00beb2aa8272bdaf3f57f116 Author: vince Date: Thu Sep 25 16:12:30 2014 -0700 binary format for trace data. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit e5f96414a1828d61412c66a34bef3d6b27266d7c Author: Marc Day Date: Wed Sep 24 17:47:02 2014 -0700 Set default for tecplot tool to not require tecplot bin libraries Tools/C_util/AmrDeriveTecplot/GNUmakefile commit d86dca967149a35699b2964a53b58ce887ffc450 Author: Marc Day Date: Wed Sep 24 17:39:38 2014 -0700 Add script to generate flattened pltfile format for Tecplot Tools/C_util/AmrDeriveTecplot/AmrDeriveTecplot.cpp Tools/C_util/AmrDeriveTecplot/GNUmakefile commit 25009c95a3ead625599a882d3030e05cb5c34b9b Author: Matthew Emmett Date: Wed Sep 24 11:26:11 2014 -0700 PyBoxLib: Add --disable-mpi build option. Src/Python/README Src/Python/setup.py commit 6023c0f415d58d6946e73a38e0b1292527a9ffc8 Author: Weiqun Zhang Date: Tue Sep 23 15:23:37 2014 -0700 fixed a bug in index of stencil array Src/LinearSolvers/F_MG/cc_ml_resid.f90 commit 583ed864bcd8d6275c73d3826eebe3d2f8327082 Author: Matthew Emmett Date: Tue Sep 23 13:14:37 2014 -0700 PyBoxLib: Honor USE_MPI environment variable. Src/Python/setup.py commit 747677fbec6e1eb31f35a3912aa0d41f8998a301 Author: Matthew Emmett Date: Tue Sep 23 12:50:37 2014 -0700 PyBoxLib: Add a more informative error message when mpicc can't be found. Src/Python/setup.py commit ea8f0722c55e3ad7e32f1de840f3b77fbc4bd01c Author: Weiqun Zhang Date: Mon Sep 22 16:51:52 2014 -0700 cleanup Src/F_BaseLib/ml_layout.f90 commit 3428935558f000090ead59ca9c7f7528f8440f79 Author: Weiqun Zhang Date: Mon Sep 22 15:25:25 2014 -0700 more cleanup Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 144f74de9a8c28992897fe4c33acb3b0868bdcbd Author: Weiqun Zhang Date: Mon Sep 22 15:16:46 2014 -0700 clean up Src/F_BaseLib/multifab_f.f90 commit 7aa7f9ae38eecfa4a53322c366f22c1ab25c46ba Author: Weiqun Zhang Date: Mon Sep 22 14:49:39 2014 -0700 removed pingpong.f90 from CMake Src/F_BaseLib/CMakeLists.txt commit 5700ab0d43c97dd5bde441e057fde4151af8e06a Author: Weiqun Zhang Date: Mon Sep 22 14:08:51 2014 -0700 F90 BoxLib: moved boxarray_intersection_bx into ml_boxarray and made it private because (1) it is only used by ml_boxarray; (2) the naive implementation works perfectly because bx intersects with every boxes in ba. Src/F_BaseLib/layout.f90 Src/F_BaseLib/ml_boxarray.f90 commit bc682fe123cb1685cb2d101aa7746d38531c2774 Author: Weiqun Zhang Date: Mon Sep 22 13:43:25 2014 -0700 F90 BoxLib: reimplemented boxarray-box intersection routines using the hash Src/F_BaseLib/layout.f90 commit 0fa8fecb012662e9f19edb5e2639cb2371c9f9ec Author: Weiqun Zhang Date: Mon Sep 22 11:17:34 2014 -0700 removed subroutines that do naive boxarray-box intersectin from boxarray module to layout module so that they can be reimplemented. Src/F_BaseLib/boxarray_f.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/ml_boxarray.f90 commit 1779e3212b9e77333c0b5b7fb23fc4cebeef5fb3 Author: Michael Zingale Date: Sun Sep 21 19:51:16 2014 -0400 we were using the wrong variable in the indxmap for the bndryreg j = indxmap(j) --> j = indxmap(i) Src/LinearSolvers/F_MG/cc_ml_resid.f90 commit 96b1c7e355e8af4f7a78079e9975791953a2958f Author: vince Date: Fri Sep 19 13:59:10 2014 -0700 added nooutput option. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 224e8f29e2db27c298332b164bb7c7c0698ca3c9 Author: vince Date: Thu Sep 18 11:56:21 2014 -0700 more region profiling. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 17134e99b6bf54875ed6184c88f228cb6fb128a1 Author: Marc Day Date: Tue Sep 16 14:36:12 2014 -0700 Uptick version number Tools/CMake/BoxLib_Version.cmake commit 72af319e46b4a358b3f025e032c5aac3dcc251b4 Author: Weiqun Zhang Date: Tue Sep 16 11:26:04 2014 -0700 minor cleanup Src/F_BaseLib/layout.f90 commit 62faf77edc2e11156bc8a237abc45ba94f838179 Author: Matthew Emmett Date: Mon Sep 15 22:13:16 2014 -0700 PyBoxLib: Fix inclusion of libgfortran and libquadmath. Src/Python/GNUmakefile_CXX.mak commit 6d76522c5692d16fab1a9dd462a1ee604ef89ef6 Author: Matthew Emmett 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 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 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 Date: Fri Sep 12 15:30:06 2014 -0700 PyBoxLib: Simplify PYLIBS. Src/Python/GNUmakefile_CXX.mak commit 3aac5cbbb60de1576d110fa3a7e0ae3bff2d0a76 Author: Matthew Emmett Date: Fri Sep 12 13:15:33 2014 -0700 PyBoxLib: More trickery for Darwin. Src/Python/GNUmakefile_CXX.mak Src/Python/setup.py commit 9aa9d65f0b29c2c5116d9ccaf3ed5f23e272d8bf Author: Matthew Emmett Date: Fri Sep 12 13:15:10 2014 -0700 Make.mpi: Don't change FC, F90 etc on Darwin. Tools/C_mk/Make.mpi commit 6f07ac5fe387103dd7c7779fc6483cb2ca8e28e3 Merge: 2ab9a79e6 d0d1804a5 Author: Matthew Emmett Date: Fri Sep 12 12:15:48 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 2ab9a79e6a2845d8921236aeb0e067a23240ba28 Author: Matthew Emmett Date: Fri Sep 12 12:15:37 2014 -0700 PyBoxLib: Move compiler defs to GNUmakefile and honor env CXX and CC. Src/Python/GNUmakefile Src/Python/GNUmakefile_CXX.mak commit b007d08249c2ff15a901f25dfd935b00f2135b20 Author: Matthew Emmett Date: Fri Sep 12 12:14:44 2014 -0700 Make.defs: Set defaults after checking USE_GCC, honor env CXX and CC if USE_GCC is true. Tools/C_mk/Make.defs commit d0d1804a5fcd8245e0238ee63027e34e6f61022f Merge: bde18b459 a05e9c7ab Author: Chris Malone Date: Fri Sep 12 12:39:07 2014 -0600 merge Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit bde18b4598120ca93ee1f4beb085b8c1f63f808b Author: Chris Malone Date: Fri Sep 12 12:39:02 2014 -0600 dont use libmpi_f77 on my Mac! Tools/C_mk/Make.mpi commit 35a84299208640e55c64f2612df57ded7c7024c6 Author: Michael Zingale Date: Fri Sep 12 14:34:15 2014 -0400 change option name fcompare.f90 commit 7bb7f71fe00044fc50337e1211ce5800bc8d68e5 Author: Michael Zingale 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 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 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 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 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 Date: Tue Sep 9 10:59:33 2014 -0700 remove some outdated comments Src/F_BaseLib/multifab_f.f90 commit 6d1769712fc62d3acd39bdbd6f62f21fa248e74e Author: ajnonaka Date: Tue Sep 9 08:59:53 2014 -0700 multifab_fill_boundary and multifab_physbc return if ng==0 Src/F_BaseLib/multifab_f.f90 Src/F_BaseLib/multifab_physbc.f90 commit 16f7db573430367f004cafafbefe97940915357b Author: Weiqun Zhang Date: Mon Sep 8 16:09:28 2014 -0700 added one moer argument to ml_restrict_and_fill so that n components can share one type of boundaries Src/F_BaseLib/ml_restrict_fill.f90 commit 57fc4432a6a678c0c146e78321390c1dba5fae5c Author: Weiqun Zhang Date: Mon Sep 8 14:00:53 2014 -0700 should not include ml_restric_fill_module in FParalleMG.mk Src/F_BaseLib/FParallelMG.mak commit 4d3235ef8c969d0234903ac5ae7cc344445a515d Author: Weiqun Zhang Date: Mon Sep 8 13:44:17 2014 -0700 update to the new flux register MiniApps/AMR_Adv_Diff_F90/GPackage.mak MiniApps/AMR_Adv_Diff_F90/advance.f90 MiniApps/AMR_Adv_Diff_F90/compute_flux.f90 MiniApps/AMR_Adv_Diff_F90/init_phi.f90 MiniApps/AMR_Adv_Diff_F90/main.f90 MiniApps/AMR_Adv_Diff_F90/reflux.f90 MiniApps/AMR_Adv_Diff_F90/regrid.f90 MiniApps/AMR_Adv_Diff_F90/update_phi.f90 commit b17a5e6e39b69d1ff61150280071423956ceb8d8 Author: Weiqun Zhang Date: Mon Sep 8 13:41:23 2014 -0700 forgot to add in last commit Src/F_BaseLib/ml_restrict_fill.f90 commit e26bbe732c785c0f1f829c64e6c5242bee183a08 Author: Weiqun Zhang Date: Mon Sep 8 13:16:31 2014 -0700 Added a new module for doing multi-level restriction and then fill all the boundaries because this needs to be done in so many places, and the new module saves half of fill_boundary calls for levels from 2 to nlevs-1. Src/F_BaseLib/CMakeLists.txt Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/GPackage.mak Tutorials/AMR_Adv_Diff_F/init_phi.f90 Tutorials/AMR_Adv_Diff_F/regrid.f90 Tutorials/AMR_Adv_Diff_F/update_phi.f90 Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX3_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/advance.f90 Tutorials/HeatEquation_EX4_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/regrid.f90 Tutorials/HeatEquation_EX5_F/advance.f90 Tutorials/HeatEquation_EX5_F/init_phi.f90 Tutorials/HeatEquation_EX5_F/regrid.f90 commit 302c356d44a93415e9b42249e88f6bf4004d9f27 Author: Weiqun Zhang Date: Sat Sep 6 21:44:06 2014 -0700 changed multifab_fill_ghost_cells to intentionally break (i.e., won't compile) codes that rely on the old behavior of ml_cc_restriction Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 40a9a340a27a64a96f72c83220f8a7319fc40387 Author: Weiqun Zhang Date: Fri Sep 5 17:40:39 2014 -0700 remove bl_error module from sort_i_module because bl_error_module uses sort_i_module Src/F_BaseLib/sort_i.f90 commit 0ba6747797ffae82acdf5348646730431b80ea96 Author: Weiqun Zhang Date: Fri Sep 5 17:32:34 2014 -0700 added a stable merge sort method Src/F_BaseLib/sort_i.f90 commit 4acef2d6f0bbe2a4b9ac5ab410d5b05def57ec47 Author: Weiqun Zhang Date: Fri Sep 5 15:55:10 2014 -0700 removed multifab_fill_boundary from ml_cc_restriction Src/F_BaseLib/ml_cc_restriction.f90 commit 9f96db6311c2c5325593c49c951c1a520d429edb Author: Weiqun Zhang Date: Fri Sep 5 14:10:23 2014 -0700 update due to new way of including mt19937ar.f90 Tutorials/MultiGrid_F/GNUmakefile Tutorials/MultiGrid_F/mt19937ar.f90 commit fc84b779e994f4395ac18b6a04c423d0f64ec63e Author: Weiqun Zhang Date: Fri Sep 5 13:46:15 2014 -0700 comments Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 9fae6ff55fbf8174813062fcbbb426f344dec62a Author: vince Date: Fri Sep 5 11:18:22 2014 -0700 made prof dir names user settable. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 5ddc6bf51294ba416d1c607570558fa38c4c8760 Author: Weiqun Zhang Date: Fri Sep 5 08:36:59 2014 -0700 added 'is up to date.' as an indication of successful compilation to regression test script Tools/RegressionTesting/testnew.py commit 3826da2fd31cb57eb78199f0ddeab30978c60698 Author: Weiqun Zhang Date: Fri Sep 5 08:26:54 2014 -0700 updated Tutorial/AMR_Adv_Diff_F due to flux register Tutorials/AMR_Adv_Diff_F/GPackage.mak Tutorials/AMR_Adv_Diff_F/advance.f90 Tutorials/AMR_Adv_Diff_F/compute_flux.f90 Tutorials/AMR_Adv_Diff_F/main.f90 Tutorials/AMR_Adv_Diff_F/reflux.f90 Tutorials/AMR_Adv_Diff_F/regrid.f90 Tutorials/AMR_Adv_Diff_F/update_phi.f90 commit 5b0fcce7be4f6b447a237f151039ea7de0e1c392 Author: Weiqun Zhang Date: Fri Sep 5 08:24:55 2014 -0700 added flux register for subcycling to F90 BoxLib Src/F_BaseLib/bndry_reg.f90 commit b7c6912e2a6709203af2e65ffe49dd71878c7802 Author: Weiqun Zhang Date: Fri Sep 5 08:22:25 2014 -0700 F90 BoxLib: fixed a memory leak in multifab_fill_ghost_cells_t for subcycling Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit cfb267b14706d95a887dc569db3192422a3fcbf4 Author: vince Date: Thu Sep 4 17:53:46 2014 -0700 added region profiling and parser support. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit f9d787e4a7ef4acdbcce6a2c90c5076fc8ad2158 Merge: ab8a6808a 065c75096 Author: Ann Almgren Date: Thu Sep 4 13:23:25 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ab8a6808af5ef835a293f0a341567704b01ee9ee Author: Ann Almgren Date: Thu Sep 4 13:21:42 2014 -0700 Have one test for implicit method and one for explicit method in the regression testing. Tutorials/HeatEquation_EX5_F/inputs-rt-expl Tutorials/HeatEquation_EX5_F/inputs-rt-impl commit 065c75096301a2e8532ae68fce1fda2c898bdac0 Merge: 37dab025e 3d53b47c4 Author: Chris Malone Date: Thu Sep 4 13:51:06 2014 -0600 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 37dab025e854417b5dc738f984e6dd5ba83a8c7d Author: Chris Malone Date: Thu Sep 4 13:50:48 2014 -0600 updates for my machine Tools/C_mk/Make.Darwin Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 3d53b47c47e1beffba50f77b4c98cda8293b4940 Author: Michael Zingale Date: Thu Sep 4 14:05:46 2014 -0400 if RANDOM is defined, then add mt19937.f90 to the f90sources Src/F_BaseLib/GPackage.mak commit 7d0da310d7e3b344c5169a70dac0c77fdb6a0ddf Author: Weiqun Zhang Date: Wed Sep 3 20:40:00 2014 -0700 commented on why OMP is removed in previous commit Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit 7db79010ca73fbdcff4acaf42cb9b73dc9a606d4 Author: Weiqun Zhang Date: Wed Sep 3 17:55:48 2014 -0700 removed another OMP PARALLEL DO becuase it is no longer safe in the new bndry_reg Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit 2a823fe17d7f29fae69815aba4b10e8a3a025329 Author: Weiqun Zhang Date: Wed Sep 3 17:54:34 2014 -0700 intent(inout) --> intent(in) Src/LinearSolvers/F_MG/cc_ml_resid.f90 commit 252e00b00abf0212aeffc2af6b41ba428e7735f5 Author: Weiqun Zhang Date: Wed Sep 3 17:02:27 2014 -0700 removed an OMP PARALLEL DO becuase it is no longer safe in the new bndry_reg Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 96da97b5c786865122e2a5e3d8e7bd6d59a217ff Author: Weiqun Zhang Date: Wed Sep 3 14:45:01 2014 -0700 F90 BoxLib bndry reg for cc linear solver: merged NDIM mulitfabs into one Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 0235a7cb572defa3da96d61fe4de9807c02dc921 Author: Weiqun Zhang Date: Wed Sep 3 12:29:58 2014 -0700 F90 BoxLib bndry reg for cc linear solver: merged the two faces into one so that it now contains NDIM multifabs instead of 2*NDIM multifabs. This amortizes a lot of works such as building copy assoc. Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 398b40a118051869d8d014e0469f09d3bee02a24 Author: Weiqun Zhang Date: Tue Sep 2 20:18:04 2014 -0700 F90 BoxLib: use boxhash in the subroutine for removing overlaps in a boxarray Src/F_BaseLib/boxarray_f.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/mt19937ar.f90 commit de54f06628e4c991f20cd13e081c2e8366f5c7eb Author: Weiqun Zhang Date: Fri Aug 29 15:45:04 2014 -0700 F90 BoxLib: (1) Added optional argument "all" to saxpy. (2) Added optional argument "ngsrc" to multifab copy. Parallel copy used to only copy from valid region to valid region, whereas now it copies from valid region + ngsrc ghost cells to valid region. The caller is responsible for having good data in ghost cells of the source multifab if ngsrc is not zero. Note that the destination is still valid region only for reasons I will not go into details. (4) fillpatch: If coarse multifab does not have ghost cells while fine grids touch physical domain, a temporary multifab with enough ghost cells will be built. This relieves the burden from the caller. (3) Refactored fillpatch_t and multifab_fill_ghost_cells_t. Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_f.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit e3947dff4aecd91401229b6fc880f15571d36c58 Merge: 9eaa4fbfb 5a30282cc Author: vince Date: Fri Aug 29 10:42:17 2014 -0700 conflict fix. commit 9eaa4fbfb74bc0181cb1edb151508ce9a4ac8f4d Author: vince Date: Fri Aug 29 10:36:52 2014 -0700 added profiling. Tutorials/MultiGrid_C/main.cpp commit d01e5bc06e4ab2056538ecbcfb74acd34ee5fb26 Author: vince Date: Fri Aug 29 10:35:44 2014 -0700 more f90 profiling. Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/bl_prof_stubs.f90 Src/F_BaseLib/layout.f90 Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/compute_defect.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/nodal_mg_tower_smoother.f90 commit 5a30282cc2b353eee71168f9cc53e5cbd98a47c2 Author: Weiqun Zhang Date: Thu Aug 28 20:30:13 2014 -0700 updated fillpatch_t too Src/F_BaseLib/fillpatch.f90 commit c018de6d306ffcf9e05fc07832250dc932263bdb Author: Weiqun Zhang Date: Thu Aug 28 20:03:27 2014 -0700 added assertion and cycle when cbx is empty in fillpatch Src/F_BaseLib/fillpatch.f90 commit 6a45fbd5e64640c3019eb089350331cb4352d6a2 Author: Weiqun Zhang Date: Thu Aug 28 20:01:47 2014 -0700 fixed a bug; did not set stencil_width when stencilwith_in is present Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit a2c36dea7d908d90c00982bbceefd1ba9ba9289e Merge: 2aaecc6da d5d6d1381 Author: vince Date: Thu Aug 28 18:12:10 2014 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 2aaecc6daa1d2e44aa3b71a30f8e88bcf9a82172 Author: vince Date: Thu Aug 28 18:11:43 2014 -0700 fixed array dim, k instead of 1. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit d5d6d13818869d8dfe110d4a3a14a74ef53ef964 Author: Chris Malone Date: Thu Aug 28 14:12:05 2014 -0600 this avoids an OSError if a repo doesnt exist Tools/C_scripts/makebuildinfo_C.py commit 6b9e8ce762c718bf84071d0b1569b43af9c24383 Author: Chris Malone Date: Thu Aug 28 10:55:43 2014 -0600 remove vestigial loop Src/C_AMRLib/Amr.cpp commit d782c727f35810dffc923f60ee395e3205c147ae Merge: 9ab74b206 cc235eb7e Author: Chris Malone 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 Date: Thu Aug 28 10:53:38 2014 -0600 updates for LANL machines Tools/C_mk/Make.mpi commit cc235eb7ecf20e95f86fc7e8ab4e383c96470c53 Author: Ann Almgren Date: Thu Aug 28 06:27:56 2014 -0700 Forgot to move define_bc_tower.f90 from the LinearSolvers/F_MG/FParallel.mak into the F_BaseLib/FParallel.mak Src/F_BaseLib/FParallelMG.mak Src/LinearSolvers/F_MG/FParallelMG.mak commit 430ebd8bd5a397788fd7527af3028a71c28893cf Author: Ann Almgren Date: Wed Aug 27 20:33:35 2014 -0700 Remove LinearSolvers/F_MG from the GNUMakefile ... this was kinda the point! Tutorials/AMR_Adv_Diff_F/GNUmakefile Tutorials/HeatEquation_EX3_F/GNUmakefile Tutorials/HeatEquation_EX4_F/GNUmakefile Tutorials/HeatEquation_EX7_F/GNUmakefile commit 2df91d9f562afaa1389c8f85acfcfd8c3a127cf1 Author: Ann Almgren Date: Wed Aug 27 20:29:53 2014 -0700 This is replaced by README_F Tutorials/README_HeatEquation_F commit 7dc3b5fb06f0b67d3686e94ab5cfcfe7ba0d68c2 Author: Ann Almgren Date: Wed Aug 27 20:29:11 2014 -0700 Fix up the Tutorials... Tutorials/AMR_Adv_Diff_F/advance.f90 Tutorials/AMR_Adv_Diff_F/compute_flux.f90 Tutorials/AMR_Adv_Diff_F/init_phi.f90 Tutorials/AMR_Adv_Diff_F/inputs_2d Tutorials/AMR_Adv_Diff_F/inputs_3d Tutorials/AMR_Adv_Diff_F/regrid.f90 Tutorials/AMR_Adv_Diff_F/update_phi.f90 Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX3_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/advance.f90 Tutorials/HeatEquation_EX4_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/regrid.f90 Tutorials/HeatEquation_EX5_F/advance.f90 Tutorials/HeatEquation_EX5_F/init_phi.f90 Tutorials/HeatEquation_EX5_F/regrid.f90 commit bc17c64390ac7115d933e303a5a607a9f9a1e489 Author: Ann Almgren Date: Wed Aug 27 18:56:55 2014 -0700 More fixes due to the recent changes ... with this version VARDEN now builds. Src/F_BaseLib/ml_nd_restriction.f90 Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit d018d1381eca70dc2419dceee31b1cb9f68fe398 Author: Ann Almgren Date: Wed Aug 27 18:43:30 2014 -0700 Oops ... missed two changes ... Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 commit e795e57708fb1808e47abac272cc23f706abfd69 Author: Ann Almgren Date: Wed Aug 27 18:36:49 2014 -0700 Move a bunch of files from LinearSolvers/F_MG to F_BaseLib because they are needed for multilevel operations (mostly restriction), in particular in subcycling codes, and not just in the linear solvers. We don't want to have to include everything in LinearSolvers/F_MG when we're not doing a linear solve. MiniApps/AMR_Adv_Diff_F90/GNUmakefile MiniApps/AMR_Adv_Diff_F90/advance.f90 MiniApps/AMR_Adv_Diff_F90/compute_flux.f90 MiniApps/AMR_Adv_Diff_F90/init_phi.f90 MiniApps/AMR_Adv_Diff_F90/inputs_2d MiniApps/AMR_Adv_Diff_F90/inputs_3d MiniApps/AMR_Adv_Diff_F90/regrid.f90 MiniApps/AMR_Adv_Diff_F90/update_phi.f90 Src/F_BaseLib/CMakeLists.txt Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bc_functions.f90 Src/F_BaseLib/cc_restriction.f90 Src/F_BaseLib/edge_restriction.f90 Src/F_BaseLib/ml_cc_restriction.f90 Src/F_BaseLib/ml_nd_restriction.f90 Src/F_BaseLib/nodal_neumann_bcs.f90 Src/F_BaseLib/nodal_restriction.f90 Src/F_BaseLib/nodal_stencil_bc.f90 Src/LinearSolvers/F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 58d9bc58925d6facedfbfdc6650390810e1822d1 Author: Ann Almgren Date: Wed Aug 27 18:00:47 2014 -0700 Dont have regression test in the miniap. MiniApps/AMR_Adv_Diff_F90/inputs-rt commit e176ed36c160904eea1c14cbf8de2525317eaf13 Author: Ann Almgren Date: Wed Aug 27 18:00:29 2014 -0700 Fixed in 3d. MiniApps/AMR_Adv_Diff_F90/compute_flux.f90 MiniApps/AMR_Adv_Diff_F90/init_phi.f90 commit a36e8d2df48a2931fb5cab8e502eedd89325e06c Author: Weiqun Zhang Date: Wed Aug 27 16:42:26 2014 -0700 F90 BoxLib: Assume grids are properly nested in fillpatch. So we no longer need to do the expensive O(N^2) check of whether one box array contains another box array. Src/F_BaseLib/fillpatch.f90 commit 3d0f4275855759aa34f38520bb7518294641d3b8 Author: Weiqun Zhang Date: Wed Aug 27 15:49:18 2014 -0700 added timer to boxarray_boxarray_contains function Src/F_BaseLib/boxarray_f.f90 commit 0a6774dc22acf13c84700c915d51ebe2c2292516 Author: vince Date: Wed Aug 27 15:33:48 2014 -0700 output cleanup. Src/C_AMRLib/StateData.cpp commit 1fbfb53d77fdcad99180d787fa79168d2823e302 Author: vince Date: Wed Aug 27 14:58:29 2014 -0700 remove redudnant resizes. Src/C_BaseLib/DistributionMapping.cpp commit 5e55387bc18ab6540dbc9338e527b85187cd63d8 Author: vince Date: Wed Aug 27 14:33:33 2014 -0700 redid defaults for pfc topology. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/DistributionMapping.cpp commit 24205dc4c54761f0aa676b31b55c8376f270c2c7 Merge: 2cbacf88d 3dfcdd21b Author: Weiqun Zhang 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 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 Date: Tue Aug 26 16:41:51 2014 -0700 Fix name of MultiFabTests to be consistent with others... Tutorials/MultiFabTests_C/GNUmakefile Tutorials/MultiFabTests_C/Make.package Tutorials/MultiFabTests_C/MultiFabReadWrite.cpp commit 1a21508d2abd8530088cad6efd619e83624b5693 Author: Ann Almgren Date: Tue Aug 26 16:36:27 2014 -0700 Fixed comment re particles leaving the domain. Src/C_AMRLib/Particles.H commit 21a7406fb9bf141a176821fb12b1001f46c2cf7b Author: Ann Almgren Date: Tue Aug 26 16:17:09 2014 -0700 Remove unused variable "ns_in" Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit aaa16e9b262281da56484c9f745188ee4c38ceeb Author: vince Date: Mon Aug 25 17:24:53 2014 -0700 more diagnostics. Src/C_BaseLib/DistributionMapping.cpp commit c54fd284d0bc2a4987c1d9f97a3a354a45552eaa Author: Ann Almgren Date: Fri Aug 22 12:42:53 2014 -0700 This directory was renamed AMR_Adv_Diff_F Tutorials/HeatEquation_EX6_F/GNUmakefile Tutorials/HeatEquation_EX6_F/GPackage.mak Tutorials/HeatEquation_EX6_F/advance.f90 Tutorials/HeatEquation_EX6_F/compute_flux.f90 Tutorials/HeatEquation_EX6_F/init_phi.f90 Tutorials/HeatEquation_EX6_F/inputs-rt Tutorials/HeatEquation_EX6_F/inputs_2d Tutorials/HeatEquation_EX6_F/inputs_3d Tutorials/HeatEquation_EX6_F/main.f90 Tutorials/HeatEquation_EX6_F/prob.f90 Tutorials/HeatEquation_EX6_F/reflux.f90 Tutorials/HeatEquation_EX6_F/regrid.f90 Tutorials/HeatEquation_EX6_F/tag_boxes.f90 Tutorials/HeatEquation_EX6_F/update_phi.f90 Tutorials/HeatEquation_EX6_F/write_plotfile.f90 commit 1701f4e1bf1c93ff449462ac3480505f87adee04 Author: Ann Almgren Date: Fri Aug 22 12:42:28 2014 -0700 Renamed some stuff, moved some stuff ... Tutorials/AMR_Adv_Diff_F/GNUmakefile Tutorials/AMR_Adv_Diff_F/GPackage.mak Tutorials/AMR_Adv_Diff_F/advance.f90 Tutorials/AMR_Adv_Diff_F/compute_flux.f90 Tutorials/AMR_Adv_Diff_F/init_phi.f90 Tutorials/AMR_Adv_Diff_F/inputs-rt Tutorials/AMR_Adv_Diff_F/inputs_2d Tutorials/AMR_Adv_Diff_F/inputs_3d Tutorials/AMR_Adv_Diff_F/main.f90 Tutorials/AMR_Adv_Diff_F/prob.f90 Tutorials/AMR_Adv_Diff_F/reflux.f90 Tutorials/AMR_Adv_Diff_F/regrid.f90 Tutorials/AMR_Adv_Diff_F/update_phi.f90 Tutorials/AMR_Adv_Diff_F/write_plotfile.f90 Tutorials/Exp_CNS_NoSpec_F/CNSEquations.tex Tutorials/Exp_CNS_NoSpec_F/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/GPackage.mak Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.c Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.h Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/bench.c Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/timer.h Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_c_c/timer.x86.c Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/Make.package Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_F/timer_c.c Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_cpp_c/Make.package Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/README Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/advance.f90 Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/HyptermKernel_f90_f90/main.f90 Tutorials/Exp_CNS_NoSpec_F/HyptermKernels/README Tutorials/Exp_CNS_NoSpec_F/README Tutorials/Exp_CNS_NoSpec_F/advance.f90 Tutorials/Exp_CNS_NoSpec_F/init_data.f90 Tutorials/Exp_CNS_NoSpec_F/inputs.jbb Tutorials/Exp_CNS_NoSpec_F/inputs_3d Tutorials/Exp_CNS_NoSpec_F/main.f90 Tutorials/Exp_CNS_NoSpec_F/write_plotfile.f90 Tutorials/README_F commit 8ee1a9a99c3c78f899a11b9211aa895993be1cd5 Author: Ann Almgren Date: Fri Aug 22 12:34:17 2014 -0700 Add a MiniApps/AMR_Adv_Diff_F90 directory as a MiniApp to be used for profiling, and rename the Tutorials/HeatEquation_EX6_F directory to be Tutorials/AMR_Adv_Diff_F to reflect the fact that it is an AMR code with subcycling in time that handles advective and explicit diffusive fluxes. MiniApps/AMR_Adv_Diff_F90/GNUmakefile MiniApps/AMR_Adv_Diff_F90/GPackage.mak MiniApps/AMR_Adv_Diff_F90/advance.f90 MiniApps/AMR_Adv_Diff_F90/compute_flux.f90 MiniApps/AMR_Adv_Diff_F90/init_phi.f90 MiniApps/AMR_Adv_Diff_F90/inputs-rt MiniApps/AMR_Adv_Diff_F90/inputs_2d MiniApps/AMR_Adv_Diff_F90/inputs_3d MiniApps/AMR_Adv_Diff_F90/main.f90 MiniApps/AMR_Adv_Diff_F90/prob.f90 MiniApps/AMR_Adv_Diff_F90/reflux.f90 MiniApps/AMR_Adv_Diff_F90/regrid.f90 MiniApps/AMR_Adv_Diff_F90/update_phi.f90 MiniApps/AMR_Adv_Diff_F90/write_plotfile.f90 Tutorials/HeatEquation_EX6_F/advance.f90 commit 6e7b42c742ae52e3b571374ceb8319e2302709b4 Author: vince Date: Fri Aug 22 12:26:23 2014 -0700 nstates. Src/C_BaseLib/DistributionMapping.cpp commit 11f1aa1a2d7a4663c802e1c926d35195cda1930e Author: Ann Almgren Date: Fri Aug 22 12:25:52 2014 -0700 These are updated to include advective fluxes and fixed previous bugs in the refluxing. Tutorials/HeatEquation_EX6_F/GPackage.mak Tutorials/HeatEquation_EX6_F/advance.f90 Tutorials/HeatEquation_EX6_F/compute_flux.f90 Tutorials/HeatEquation_EX6_F/main.f90 Tutorials/HeatEquation_EX6_F/prob.f90 Tutorials/HeatEquation_EX6_F/reflux.f90 Tutorials/HeatEquation_EX6_F/regrid.f90 Tutorials/HeatEquation_EX6_F/update_phi.f90 commit afd2e1e74668ba9f41f9371a0892ad99fe039c24 Author: vince Date: Thu Aug 21 17:02:48 2014 -0700 multilevel distribution map. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit ad3e5b8cd78e73e006525d0d55d6164a7490fee2 Author: Weiqun Zhang Date: Thu Aug 21 16:06:04 2014 -0700 Here, "rt" actually stands for regression test. Revert "Remove inputs.rt -- it didn't really do the RT problem" This reverts commit 4df26c59d4545be58573410010824a082eacb203. Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt commit 4df26c59d4545be58573410010824a082eacb203 Author: Ann Almgren Date: Thu Aug 21 15:02:36 2014 -0700 Remove inputs.rt -- it didn't really do the RT problem Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt commit 1f1b4a4cd2a05fe809a51f7905fb0e4d994b6885 Author: Weiqun Zhang Date: Tue Aug 19 17:24:41 2014 -0700 removed parallel_reduce in sanity check in fillpatch Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_f.f90 commit 014180e0931b862f17422e0ff4241bfe2bea9d0f Author: Weiqun Zhang Date: Tue Aug 19 17:10:50 2014 -0700 double precision --> dp_t for consistence Src/F_BaseLib/bl_constants.f90 Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/cutcells.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/multifab_physbc.f90 Src/F_BaseLib/particles_f.f90 Src/F_BaseLib/tag_boxes.f90 Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/cc_restriction.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/coarsen_coeffs.f90 Src/LinearSolvers/F_MG/compute_defect.f90 Src/LinearSolvers/F_MG/edge_restriction.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/nodal_applyop.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_newu.f90 Src/LinearSolvers/F_MG/nodal_restriction.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_apply.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 commit 2f25650574df7aaeb189b4dd56b1ed5774ba7b55 Merge: f6d15d3e1 b631255b0 Author: Weiqun Zhang Date: Thu Aug 14 22:12:58 2014 -0700 Merge branch 'master' into dev commit f6d15d3e10b76af2800c7206980afbaf2739a6f2 Author: Weiqun Zhang Date: Thu Aug 14 22:09:46 2014 -0700 added operator+= to BndryRegister class Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit b631255b010e038d9a9a792059a317187441f13b Merge: 9ccbaff9d 7f2ede7bf Author: ajnonaka Date: Thu Aug 14 12:34:08 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9ccbaff9d812bc4ee6050ea854775c3b65672eec Author: ajnonaka Date: Thu Aug 14 12:33:45 2014 -0700 CIMS machines Tools/C_mk/Make.defs commit 7f2ede7bf5995cb030be2da213e05b6d5fff834c Author: Ann Almgren Date: Thu Aug 14 11:24:02 2014 -0700 Fix the stupid typos from the last commit. Src/C_AMRLib/Amr.cpp commit 5596d482b201f2b8491545d0fee21ab1ebc22cad Author: Ann Almgren Date: Thu Aug 14 11:12:12 2014 -0700 Allow the user to set regrid_int = -1 as a signal not to regrid (at all or at that level) Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H commit 18ade79e8847f1ec597db32601f03ddcb97d7889 Author: vince Date: Wed Aug 13 16:24:22 2014 -0700 added function to read checkpoint headers. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit ea84920cb719b102d98ada3ef883ef832fd63761 Author: Matthew Emmett Date: Wed Aug 13 15:29:51 2014 -0700 PyBoxLib: Tidy up make files, pull in isinf and isnan from std on Darwin. Src/C_BaseLib/FArrayBox.cpp Src/Python/GNUmakefile_CXX.mak commit d7261903fcf40a9f6e3bacd91546a16ebc435fef Author: Ann Almgren Date: Wed Aug 13 12:49:11 2014 -0700 Add the option to use relativistic weighting of the mass (i.e. multiply by gamma) if the relativistic flag is set, which currently is only allowed if the NEUTRINO_PARTICLES flag is defined. Src/C_AMRLib/Particles.H commit a93d7777c9ca61bc99353ac57735c3105945232f Author: Ann Almgren Date: Tue Aug 12 13:56:34 2014 -0700 Add a README so we can keep track of the different F90 HeatEquation* examples in BoxLib/Tutorials. Tutorials/README_HeatEquation_F commit 20b852d49e5e94ac74d2573237964c3f0bbdef6a Author: Ann Almgren Date: Tue Aug 12 13:41:41 2014 -0700 Update subcycling description. Docs/F_AdvancedTopics/F_AdvancedTopics.tex commit 20542b726256602947deb55fa3ab9e3a3b01edf8 Author: Ann Almgren Date: Tue Aug 12 09:45:47 2014 -0700 Remove flags for ROSE compiler. Tutorials/HeatEquation_EX1_F/GNUmakefile Tutorials/HeatEquation_EX5_F/GNUmakefile commit 8afaec318b67f5a302fd105b5b4028763809c42f Author: Ann Almgren Date: Tue Aug 12 09:10:20 2014 -0700 Set NDEBUG = t Tutorials/HeatEquation_EX6_F/GNUmakefile commit 6055867ea40201743d80535576bba3151db63038 Author: Ann Almgren Date: Tue Aug 12 09:08:01 2014 -0700 Get 3d working ... Tutorials/HeatEquation_EX6_F/inputs_3d Tutorials/HeatEquation_EX6_F/reflux.f90 Tutorials/HeatEquation_EX6_F/tag_boxes.f90 commit d06098e2700b0608e509d01b10dee30ea6f9553c Author: Ann Almgren Date: Tue Aug 12 09:02:44 2014 -0700 set n_cell = 64 and max_levs = 3 in inputs file. Tutorials/HeatEquation_EX6_F/inputs_2d commit 4c9f90343aba8090b8e1de46b69663bd5fdf07dc Author: Ann Almgren Date: Tue Aug 12 09:01:36 2014 -0700 Fix bndry_reg copy when n > 1. Tutorials/HeatEquation_EX6_F/advance.f90 commit f822518eed014eab7d13b5746b98531ca751d0cf Author: Ann Almgren Date: Mon Aug 11 20:40:35 2014 -0700 Modify the Tutorials/HeatEquation_EX6_F code for explicit subcycling so that it uses new bndry_reg functions and new modified fillpatch and multifab_fill_ghost_cell routines. This works for max_levs = 2 but not yet for max_levs = 3. Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 Tutorials/HeatEquation_EX6_F/GNUmakefile Tutorials/HeatEquation_EX6_F/GPackage.mak Tutorials/HeatEquation_EX6_F/advance.f90 Tutorials/HeatEquation_EX6_F/cc_restriction.f90 Tutorials/HeatEquation_EX6_F/compute_flux.f90 Tutorials/HeatEquation_EX6_F/inputs_2d Tutorials/HeatEquation_EX6_F/main.f90 Tutorials/HeatEquation_EX6_F/ml_restriction.f90 Tutorials/HeatEquation_EX6_F/reflux.f90 Tutorials/HeatEquation_EX6_F/regrid.f90 Tutorials/HeatEquation_EX6_F/subcycling.f90 Tutorials/HeatEquation_EX6_F/tag_boxes.f90 Tutorials/HeatEquation_EX6_F/update_phi.f90 commit 878a412df36ac9f0b1d80cb4a2f873628f9a4780 Author: Matthew Emmett Date: Mon Aug 11 15:57:03 2014 -0700 PyBoxLib: Add python libs to linking stage. Src/Python/GNUmakefile_CXX.mak commit 6dcde9ac13549c7dfd80954281e74aac011a1abd Author: Weiqun Zhang Date: Fri Aug 8 12:25:53 2014 -0700 reduce the number of parallel reduce in Linear Solver Src/LinearSolvers/F_MG/ml_nd.f90 commit d0caacb5331fca64ccd1b0cb5da67928d4916d4c Author: Weiqun Zhang Date: Fri Aug 8 12:16:48 2014 -0700 fixed typo Src/LinearSolvers/F_MG/itsol.f90 commit 7caea75c48dc6f18cc148cebb24847279eeec7db Author: Weiqun Zhang Date: Fri Aug 8 12:13:31 2014 -0700 removed more unsafe saxpy; clean up Src/LinearSolvers/F_MG/itsol.f90 commit e211b62e103f755280573c6b05670bb18eac789d Author: Weiqun Zhang Date: Fri Aug 8 11:58:01 2014 -0700 Changed a potentially unsafe call to saxpy because Fortan arrays are not supposed to aliased. Src/LinearSolvers/F_MG/compute_defect.f90 commit 53bc43048345a0fe3aad107166622019bd063bb3 Author: Weiqun Zhang Date: Fri Aug 8 11:45:38 2014 -0700 reduced number of parallel reduce in multi-level nodal convergence check Src/LinearSolvers/F_MG/ml_nd.f90 commit aa6db09b8e0c1234f16edafa65ef6cecdf1dade3 Author: Weiqun Zhang Date: Fri Aug 8 11:19:05 2014 -0700 fixed a new bug Src/LinearSolvers/F_MG/cc_ml_resid.f90 commit d9789a27ce22d5637da95f2b55f6917182ef1866 Author: Weiqun Zhang Date: Fri Aug 8 10:37:13 2014 -0700 remove a multifab_fill_boundary in nodal solver Src/LinearSolvers/F_MG/ml_nd.f90 commit 7a1a2f19643f0be836c4822d083b4216df8af7c8 Author: Weiqun Zhang Date: Fri Aug 8 09:50:30 2014 -0700 removing more multifab_fill_boundary's in Linear Solver Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 0aa8e642fee01935346ca60af31b52aee5dd464d Author: Weiqun Zhang Date: Fri Aug 8 09:18:52 2014 -0700 cleanup Src/LinearSolvers/F_MG/ml_cc.f90 commit 9f69981543dfd21b7beb8c96cc3e324b40420337 Author: Weiqun Zhang Date: Fri Aug 8 09:07:43 2014 -0700 removed more multifab_fill_boundary's in Linear Solver Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/compute_defect.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit cc5c0596b380ed88d94eebd78822561f301191cd Author: Weiqun Zhang Date: Fri Aug 8 07:27:33 2014 -0700 renaming for consistence; removed more multifab_fill_boundary's Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit aad555467e36e1bbda0b8d532f5016c2a7958e8c Author: Weiqun Zhang Date: Thu Aug 7 21:50:31 2014 -0700 cleanup Src/LinearSolvers/F_MG/ml_cc.f90 commit 755904a853a318dc7cdf1fc2db64524426194969 Author: Weiqun Zhang Date: Thu Aug 7 21:38:38 2014 -0700 remove a number of redundant mf_fill_boundary calls Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit f216b9e07d1d1546dbc710eba0086d1c087d9455 Author: Weiqun Zhang Date: Thu Aug 7 18:03:22 2014 -0700 reduce the number of parallel reduce in checking multi-level convergence Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 65ea5ac81940031d3cf1db05961522a04ec14248 Author: Ann Almgren Date: Thu Aug 7 14:58:17 2014 -0700 Modify loops ... still some more to be done ... Src/F_BaseLib/bndry_reg.f90 commit 779b8cac1feb961b1c8211bf83d1283767f81bff Author: Weiqun Zhang Date: Thu Aug 7 13:56:24 2014 -0700 fixed a bug in new bndry_reg when fine box touches physical boundaries Src/F_BaseLib/bndry_reg.f90 commit 5dadf95d1d55b19c986515eb055b7c3e23054c8f Merge: f4ac7b1b5 ee33126bc Author: Weiqun Zhang 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 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 Date: Thu Aug 7 11:41:42 2014 -0700 Fix the section on the bndryreg Docs/GettingStarted/GettingStarted.tex commit 051007b33d53e6b7f1842130537847c4a33cefb5 Author: Weiqun Zhang 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 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 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 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 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 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 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 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 Date: Fri Aug 1 08:34:48 2014 -0700 Add this subcycling figure. Docs/F_AdvancedTopics/subcycling_algorithm.eps commit 071c456c3f59051980604ff726fe88baa8a46e50 Author: Ann Almgren Date: Thu Jul 31 18:34:03 2014 -0700 Add commentary about how subcycling is done in the F90 Tutorials example in HeatEquation_EX6_F. Docs/F_AdvancedTopics/F_AdvancedTopics.tex commit a8a98c259caf8cf1f4eb9b1b16292111e6682a6c Author: Ann Almgren Date: Thu Jul 31 18:33:25 2014 -0700 Modify these advance routines to look more like the one in the subcycling example, just so what changes is clearer. Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX4_F/advance.f90 Tutorials/HeatEquation_EX5_F/advance.f90 commit a8a1f20d7af61c8a681bc41df5562e01a23fae7a Author: Ann Almgren Date: Thu Jul 31 18:32:25 2014 -0700 Add a new Tutorials example which does subcycling in time for the explicit solution of the heat equation (an extension of HeatEquation_EX4_F). Tutorials/HeatEquation_EX6_F/GNUmakefile Tutorials/HeatEquation_EX6_F/GPackage.mak Tutorials/HeatEquation_EX6_F/advance.f90 Tutorials/HeatEquation_EX6_F/cc_restriction.f90 Tutorials/HeatEquation_EX6_F/init_phi.f90 Tutorials/HeatEquation_EX6_F/inputs-rt Tutorials/HeatEquation_EX6_F/inputs_2d Tutorials/HeatEquation_EX6_F/inputs_3d Tutorials/HeatEquation_EX6_F/main.f90 Tutorials/HeatEquation_EX6_F/ml_restriction.f90 Tutorials/HeatEquation_EX6_F/regrid.f90 Tutorials/HeatEquation_EX6_F/subcycling.f90 Tutorials/HeatEquation_EX6_F/write_plotfile.f90 commit b9007785d1a00cd2faba29b20ac945a8b5b44b3e Author: Ann Almgren Date: Thu Jul 31 18:14:54 2014 -0700 Modify the comment that subcycling is only in C++ since we have an F90 Tutorial example with subcycling. Docs/Introduction/Introduction.tex commit b598f581279be99ba07fe81c64c7e42601cbcfac Merge: 45f3ed75d 3e216cf76 Author: Ann Almgren Date: Thu Jul 31 17:40:38 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3e216cf766fdffc0c9246d2450dbd15b2e28f272 Author: Weiqun Zhang Date: Thu Jul 31 16:10:16 2014 -0700 more code consolidation in multilevel cell-centered solver Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit 645f5c302e2f8ab1e922e806a4c95745566e0acb Author: Weiqun Zhang Date: Thu Jul 31 15:55:53 2014 -0700 fixed a bug in bndry reg; minor cleanup Src/F_BaseLib/bc.f90 Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit 32880836c5f94e18eade5ec839278f3119756895 Author: Ann Almgren Date: Thu Jul 31 15:38:18 2014 -0700 We have changed the way we use bndry_reg in the multilevel cell-centered solves to make them much more efficient. Eliminated an extra parallel copy and consolidated code. Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit 45f3ed75d14fa50a1141434bae3751b983b2089c Author: Ann Almgren Date: Thu Jul 31 15:03:30 2014 -0700 Fix spelling error in comment. Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit 12d853d445a891013525693ef4da62b23cba42fc Author: Ann Almgren Date: Tue Jul 29 16:34:39 2014 -0700 Get this test code to work for cell-centered solve at multiple levels. Tests/LinearSolvers/F_MG/cc_multi.f90 commit e739f60b748475e93591262767dcf0625128fed4 Author: Weiqun Zhang Date: Fri Jul 25 15:32:52 2014 -0700 added USE_ACC to the make system Tools/C_mk/Make.Linux commit 1e91cc83cf37e55789227d5d0836c126a35e5b4e Author: Ann Almgren Date: Fri Jul 25 12:01:58 2014 -0700 Turns out the Cray compilers do not like the "isnan" function after all. Src/C_BaseLib/FArrayBox.cpp commit b24594a438715a7d1194a431766889794456d095 Author: Ann Almgren Date: Fri Jul 25 11:55:14 2014 -0700 Restore this file to the previous version -- turns out this wasn't really the problem with the cray compiler. Src/C_BaseLib/BLassert.H commit b1bb6b85f119941f8e83aed0a98657f9ba2ee65a Author: Weiqun Zhang Date: Thu Jul 24 22:34:31 2014 -0700 For cray compilers, always run the opertion in BL_ASSERT to get around a possible Cray compiler bug. Hopefully this will fix the crash of Castro compiled by cray. Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/BLassert.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/iMultiFab.cpp commit 85ad24c56b118d0b04011f61cfe3a2cb312cbcdf Merge: ce201b0f6 c61743c59 Author: Marc Day 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 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: d1d0f7ef9 453813efb Author: Michael Zingale 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 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 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 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: c07268824 25f509446 Author: vince Date: Tue Jul 22 16:19:19 2014 -0700 Merge branch 'master' into commprof commit 25f50944635873a8bf8755136567619264a1a5c0 Merge: b7433798b a25f8b4c6 Author: ajnonaka Date: Tue Jul 22 16:11:35 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit b7433798b38d5897e08040cc1aae79836b186350 Author: ajnonaka Date: Tue Jul 22 16:11:17 2014 -0700 comment out a broken timer until we figure out what's wrong Src/F_BaseLib/list_box.f90 commit a25f8b4c621874d3b39fa9fc7f6cc97852339838 Author: Ann Almgren Date: Tue Jul 22 15:39:54 2014 -0700 Change default to DEBUG = FALSE and add a pure-F90 inputs file. Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/inputs.f90.3d commit 0f7918cfa6aa4dccf43d604005a443840e0554e0 Author: ajnonaka 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 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: a3e8320e7 2bd19084a Author: Adam Jacobs 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 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 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 Date: Fri Jul 18 10:37:21 2014 -0700 added text for fortran90 interface. Docs/Readme.profiling commit 3b260c9bf898a29dc2540fe373417ed506bbbb16 Merge: e2354eb94 2b5e43bea Author: vince Date: Fri Jul 18 10:27:45 2014 -0700 Merge branch 'master' into commprof commit e2354eb9492852b1df730fe9b10be59455c30229 Author: vince Date: Fri Jul 18 10:26:41 2014 -0700 formatting. Src/C_BaseLib/Profiler.cpp commit b52ff318379bfb5dd862c2509d6f7555f4b715fe Author: vince Date: Thu Jul 17 16:55:16 2014 -0700 more call stack tracing. inclusive and exclusive times in the html tree output. collapse html call tree at depth > 4 by default. added function name map to store ints in CallStats instead of strings. added report for inclusive function times, recursive times are subtracted. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 2b5e43bea6b2d529532a9d19aa35b0ccd862fb71 Author: Michael Zingale Date: Wed Jul 16 19:57:55 2014 -0400 some cleanups Tools/F_scripts/makebuildinfo.py commit 0d7c698582fb42a0fafb8fddfad446b14f6b9393 Author: Michael Zingale Date: Wed Jul 16 19:57:28 2014 -0400 argparse -> getopt -- argparse requires the latext python 2.7 which is not available everywhere. Tools/C_scripts/makebuildinfo_C.py commit 0d56865ff24dbc01de9e476efb5a58ed8471a84a Merge: 1c9f051fa 326077234 Author: Ann Almgren Date: Tue Jul 15 11:23:03 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1c9f051fa12d36926289c96e257274365085d605 Author: Ann Almgren Date: Tue Jul 15 11:22:20 2014 -0700 Fix the use of Amr::UseFixedCoarseGrids -- the call to constructAreaNotToTag was missing in the AmrLevel constructor. Src/C_AMRLib/AmrLevel.cpp commit 326077234d783477cbb5f3a70edebbc1220c7953 Author: Weiqun Zhang Date: Mon Jul 14 13:48:45 2014 -0700 fixed makebuilinfo_C.py in case not all 3 git directories are set Tools/C_scripts/makebuildinfo_C.py commit ed5b71e27b09fe3119cacb0ce5c425378fa1e7ba Merge: 8a644a46f 780853b46 Author: Ann Almgren Date: Mon Jul 14 11:02:24 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 8a644a46fc69df022638101b4e7e7f8ad3a3da9a Author: Ann Almgren Date: Mon Jul 14 11:02:06 2014 -0700 Add "Vater" 9-pt nodal stencil in 2d only. Src/C_AMRLib/Particles.H Src/LinearSolvers/C_to_F_MG/stencil_types.H Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil_apply.f90 Src/LinearSolvers/F_MG/stencil_types.f90 commit 780853b46922792246e11496caf3ec8d7300194f Merge: ddaff3b70 6b1edc609 Author: Matthew Emmett 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 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 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 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 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 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 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 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 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 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: 862258d6d f12f52bd5 Author: vince Date: Tue Jul 1 16:44:06 2014 -0700 Merge branch 'master' into commprof commit 862258d6d0f0632bd84fcf531d6d2c75d654c900 Merge: e97d9f051 080b9725b Author: vince Date: Tue Jul 1 16:42:14 2014 -0700 Merge branch 'commprof' of gamera:/usr/local/gitroot/BoxLib into commprof commit e97d9f051b76a58ccad1dd472814b2f4f947d74d Author: vince Date: Tue Jul 1 16:42:02 2014 -0700 added inclusive and exclusive times to the call trace tree. Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit f12f52bd5c02060bfa819929260794e08f62d893 Merge: 574aee2f9 9bf14a832 Author: Ann Almgren Date: Mon Jun 30 17:37:30 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 574aee2f952fd9bf37eceeb30498f445357aa49f Author: Ann Almgren Date: Mon Jun 30 17:37:02 2014 -0700 Fix the add_rh_nodal stuff that is used in the initVortProj stuff in Projection.cpp Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 9bf14a83268a4c08fc9862b115d303fbc0d32041 Merge: ce158f688 5cca58b07 Author: Chris Malone 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 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 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 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 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 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 Date: Mon Jun 30 13:40:07 2014 -0700 Correct spelling in comment. Tutorials/HeatEquation_EX1_F/main.f90 commit ce0fbd7501113cb3b6caa30a1f40dfe1c49cd4c8 Author: Michael Zingale Date: Mon Jun 30 12:50:00 2014 -0400 change the definition of the relative norm. Before we were doing ||(A-B)/A||, now we do ||A-B||/||A|| -- this is more correct. fcompare.f90 commit 8d9b8abcd1dcdf2e7f20229aa06ef3e1f48a825c Author: Weiqun Zhang Date: Fri Jun 27 10:56:06 2014 -0700 made an essentially identity transformation to accommodate Cray compiler Src/LinearSolvers/F_MG/coarsen_coeffs.f90 commit c7fc604f4a5c4ac04f0e6f695d5d8d374ef14483 Author: ajnonaka Date: Wed Jun 25 08:45:57 2014 -0700 bugfix: in the nodal restriction, we assumed the mask multifabs had the same number of components as the thing you are restricting. the mask should only have 1 component Src/LinearSolvers/F_MG/ml_restriction.f90 commit 0119511cfa881b101b8731c91777f74a68db860b Merge: a23398f9c f3d38423d Author: ajnonaka Date: Wed Jun 25 06:25:38 2014 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit a23398f9c874541d68de5c72a17e789c08be5fe2 Author: ajnonaka Date: Wed Jun 25 06:25:08 2014 -0700 get this compiling again, won't affect results as fixed code wasn't being called by anything Src/LinearSolvers/F_MG/ml_restriction.f90 commit f3d38423d0077995254934a69d71cb058be79e9a Author: Weiqun Zhang Date: Wed Jun 25 06:22:02 2014 -0700 modified the interface of the new ml restriction wrapper so that the code can compile Src/LinearSolvers/F_MG/ml_restriction.f90 commit 014f1ee6f1e053ae30e022097aaaa96b2d566f31 Merge: 6900956dc 84f12efcf Author: ajnonaka Date: Tue Jun 24 17:01:58 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 6900956dc7f77f053cb42249822b4b034f23d3cf Author: ajnonaka Date: Tue Jun 24 17:00:42 2014 -0700 added a simplified interface to do direct injection nodal restriction that only requires an ml_layout, bc_tower, and bc_comp passed in. testing underway. Src/LinearSolvers/F_MG/ml_restriction.f90 commit 84f12efcf49d6e9bbb4306b2d629337b79eb2b2a Author: Michael Zingale Date: Mon Jun 23 14:15:09 2014 -0400 remove a parallel_reduce by doing the rh norm_inf (bnorm) locally and then packing it into the parallel reduce already in this code. Src/LinearSolvers/F_MG/ml_cc.f90 commit e11164c814cba460ecf3fb8da6f42b642e35382f Author: vince Date: Thu Jun 19 14:22:19 2014 -0700 added more mpi types. Src/C_AMRLib/Particles.H Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp Src/C_BaseLib/VisMF.cpp Src/C_TowerLib/Layout.cpp commit f35f8004ce120fa679b20f141306711e417c55a5 Author: ajnonaka Date: Thu Jun 19 08:45:54 2014 -0700 greatly simplified this cell-centered heat equation implicit example by hooking into the simple ml_cc_solve interface. no more building mg_towers, coefficients, etc., in the advance routine. comes up clean in my regression Tutorials/HeatEquation_EX5_F/advance.f90 commit c8b351a588a2cbb72f22b2e1e88e548c4d7200db Merge: cc4d7fd8d 842af460f Author: vince Date: Wed Jun 18 14:19:27 2014 -0700 merge fix. commit cc4d7fd8da0e10931b7517388801a3f2a5fa0394 Author: vince Date: Wed Jun 18 14:13:39 2014 -0700 bl loc. MiniApps/FillBoundary/GNUmakefile commit 401bb2ca183144702e4411fd51504bb4e2645f4c Author: vince Date: Wed Jun 18 14:05:00 2014 -0700 more pfc. Src/C_BaseLib/DistributionMapping.cpp commit 8249ad6b7678b2e68e9a0c3d8a7feffe538e80bd Author: vince Date: Wed Jun 18 14:01:15 2014 -0700 added function tracing. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 370e00eb3dfe86fa399ade3128a6f527a48587cb Author: vince Date: Mon Jun 2 16:22:44 2014 -0700 create default if no topological map is found. Src/C_BaseLib/DistributionMapping.cpp commit 842af460fc5180e896ff327f4aee7184acc72cf6 Author: Weiqun Zhang Date: Fri May 30 17:46:30 2014 -0700 fixed a number of memory leaks Src/C_AMRLib/Particles.H commit fd3afe6338dba347031138b9a45a965c3ce4f909 Merge: cafc9be28 9610d4720 Author: Weiqun Zhang Date: Fri May 30 16:59:14 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit cafc9be28609ce138805b9dfe9d905c4f4b4ae30 Author: Weiqun Zhang Date: Fri May 30 16:59:11 2014 -0700 Fixed invalid conversion from const MultiFab * to MultiFab * that is not tolerated by some compilers. Src/C_AMRLib/Particles.H commit 9610d4720fe783d4d3d4450ef70e7c47f10f8bd3 Author: Ann Almgren Date: Fri May 30 12:22:45 2014 -0700 nodal_enforce.f90 --> nodal_enforce_dirichlet_rhs.f90 Src/LinearSolvers/F_MG/CMakeLists.txt commit 66a529dd6fc56668fb92061ce213f7d7aa362776 Merge: 790804d51 a7870f703 Author: Ann Almgren Date: Thu May 29 12:00:09 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 790804d5110e98ee1118ca0cbea66664003f288f Author: Ann Almgren Date: Thu May 29 11:59:17 2014 -0700 Add new variable in Amr -- which_level_being_advanced -- with an access function level_being_advanced() so that the AmrLevel routines can know if post_regrid is being called within the advance for a level (which_level_being_advanced) which is different from lbase. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit a7870f703e2553923374ce50762ee0c6ddca9f7f Author: Ann Almgren Date: Wed May 28 16:36:22 2014 -0700 Need to allocate mgt%bottom_mgt inside a later test so that if we are unsuccessful in get_bottom_box_size we don't allocate it at all. Src/LinearSolvers/F_MG/mg.f90 commit 09a73522d0dd310b36202e99f3de18e003244fda Author: Ann Almgren Date: Wed May 28 16:31:00 2014 -0700 Remove un-needed print statements. Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 commit d47b8969fb90fcf3157cf344acdf55f1230947b3 Author: Ann Almgren Date: Wed May 28 14:54:04 2014 -0700 Version_One_Dot_Zero should default to reading *double* precision, not single. Src/C_AMRLib/Particles.H commit 9d12510f508d644b0f4ca4d0666a6a493ece0035 Author: vince Date: Wed May 28 11:39:48 2014 -0700 reindex. Src/C_BaseLib/DistributionMapping.cpp commit 30796730fafb42cd4263f9494607a006d43a9c2e Author: Weiqun Zhang Date: Fri May 23 15:41:59 2014 -0700 moved the code for regridding single-level run on restart to a function so that it can be called by derivative of Amr Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 9e41a766e5229c4a93a20d6d74444dd56a4fbb1e Author: Weiqun Zhang Date: Fri May 23 10:54:15 2014 -0700 use omp_lib --> include 'omp_lib.h' to make Cray compiler work Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/INTERP_3D.F commit d4001301fef59c8085169d0591a5f469a0270120 Author: vince Date: Thu May 22 13:38:19 2014 -0700 removed cout. Src/C_BaseLib/DistributionMapping.cpp commit be00d0b13ecbe5411a8b8dd794ab41669f0b184b Author: vince Date: Thu May 22 13:36:12 2014 -0700 added prof and commprof flags. Tests/C_BaseLib/GNUmakefile commit bfcc676719d02819632458919ed2a283b201e0a4 Author: vince Date: Thu May 22 13:33:10 2014 -0700 added tests. Tests/C_BaseLib/tFB.cpp commit 776258aadface133a28d8337145e7eb121ecaf40 Author: vince Date: Thu May 22 13:02:08 2014 -0700 added some profiling. MiniApps/MultiGrid_C/main.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 024a4bfe5159c0761105d5fe2f92df0c26cdbe0b Author: beckner2 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 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 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: 8dbad2ba2 6536829a5 Author: Marc Day Date: Tue May 13 20:36:31 2014 -0700 Resolve conflict in plotfile.f90 commit 8dbad2ba2e68484d5827d5d911216edae15fb4c4 Author: Marc Day Date: Tue May 13 20:34:22 2014 -0700 Add parameter to MultiGrid_C tutorial to avoid build f90 solvers Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/main.cpp commit 6577b5921327668d03cd2377cd10ba8bb8387275 Author: Marc Day 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 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 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 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: 8812a1b61 e4058b0aa Author: Michael Zingale 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 Date: Tue May 13 09:15:51 2014 -0400 add analysis Tools/RegressionTesting/Castro-SBU-tests.ini commit e4058b0aa925fc1b1777f616f6cfcf653107925f Merge: bbe297c8a b35aeacae Author: Weiqun Zhang 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 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 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 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 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 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 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 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 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 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: 8993142c7 0611941a7 Author: ajnonaka Date: Tue May 6 09:40:45 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 8993142c751c438871d82ed9845278270526c85d Author: ajnonaka Date: Tue May 6 09:40:12 2014 -0700 generalize make.defs to handle aliased gfortran versions Tools/C_mk/Make.defs commit 0611941a7cc2fe36cdb4282e1bc3813b168c95f0 Merge: 1155971fd 624e530ad Author: Ann Almgren Date: Mon May 5 16:07:11 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1155971fde263323d75dd76b2b1b72388155de1e Author: Ann Almgren Date: Mon May 5 16:05:44 2014 -0700 Modify enforce_outflow_on_divu_rhs to be enforce_dirichlet_rhs so that it sets the nodal rhs to zero anywhere the mask is dirichlet, not just at ouflow values. This takes care of setting the nodal rhs to zero at fine nodes at the coarse-fine interface. This routine is called inside of ml_nd_solve, so should not be called in codes which call ml_nd_solve. Moved the enforce... code out fo nodal_divu.f90 and into a new file: nodal_enforce_dirichlet_rhs.f90 Src/LinearSolvers/F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_enforce_dirichlet_rhs.f90 commit fe0aafebfe2778714fddcd87ae75c7a7853fe807 Author: Ann Almgren Date: Mon May 5 16:05:31 2014 -0700 Remove extra printing of tres in ml_cc.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 624e530ada953c6fc0e69a7c7b8c75d377d8fe7e Author: Weiqun Zhang Date: Mon May 5 14:39:55 2014 -0700 added a new function that returns whether a BoxArray intersects with a Box Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit aef0fba9a94273c344435e581db2acf32729382d Author: Marc Day Date: Wed Apr 30 12:21:12 2014 -0700 Increase max name length to 50 (from 20) for plotvars...probably should code this more robustly someday Src/F_BaseLib/plotfile.f90 commit ba0344314ca8287010dafed685be2962df0ca03e Merge: 3a45897a6 2880a3350 Author: Ann Almgren Date: Tue Apr 29 13:46:08 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3a45897a62a59b44bf41e068cdb8d6879376553f Author: Ann Almgren Date: Tue Apr 29 13:45:18 2014 -0700 1) Compute tres0 based on res, not rh 2) Use max_norm instead of bnorm in the first convergence test. Src/LinearSolvers/F_MG/ml_cc.f90 commit 2880a3350fba9972f702b488f9606cb1f7fca136 Author: Weiqun Zhang Date: Sat Apr 26 20:27:34 2014 -0700 updated make system for Edison Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/F_mk/GMakeMPI.mak Tools/F_mk/comps/Linux_intel.mak commit 98426666046fca27c0e71f552defe99ca404ee52 Author: ajnonaka Date: Tue Apr 22 16:14:33 2014 -0700 update to new solver interface Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 847667795fccb6fdecbf3f38a33a01c5cddc07d1 Author: Weiqun Zhang Date: Tue Apr 22 14:34:57 2014 -0700 added norm functions that can do multiple components so that MPI reduce calls can be aggregated Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit b2bf12460856ae2dc5e5f1c4188be9c6c8f6c41c Author: Ann Almgren Date: Fri Apr 18 12:29:22 2014 -0700 In mg_tower_cycle, use the cycle type "cyc" that is passed in, rather than using mgt%cycle_type. This allows us to use different cycle types for different iterations to test whether a combination of F- and V-cycles works better than pure F- or pure V-cycles. Src/LinearSolvers/F_MG/mg.f90 commit 9bfc179861656c2fb4b110b41dbc64f6e028b863 Author: Michael Zingale Date: Thu Apr 17 14:20:34 2014 -0400 only print the intepolation warning message from the IOProcessor Src/LinearSolvers/F_MG/ml_cc.f90 commit 844e679f607d5a05ad95106201a3003c12ddef13 Author: vince Date: Thu Apr 3 16:46:55 2014 -0700 reworked reduction tracking. Src/C_BaseLib/ParallelDescriptor.cpp commit d470c62a3e647dae037e11c59ee2444295f4000a Author: ajnonaka Date: Thu Apr 3 15:46:03 2014 -0700 stencil_apply_nodal_xd works now matter how many ghost cells the "dd" multifab has, where dd is the nodal result "L(phi)". Before it required 1 ghost cell, which doesn't make sense since it only returns dd on the valid region and the boundary nodes Src/LinearSolvers/F_MG/compute_defect.f90 Src/LinearSolvers/F_MG/nodal_stencil_apply.f90 commit 7e97e968f0b4e9d5f7c743be83da98684bb9b693 Author: vince Date: Thu Apr 3 12:31:23 2014 -0700 added error checking and reporting for the fortran interface. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 54fa42c1975eacbb9fdfa353fa8a255ab81eb116 Merge: 9c4b0edc5 55b4fd6dc Author: vince Date: Fri Mar 28 12:20:06 2014 -0700 Merge branch 'master' into commprof commit 9c4b0edc5caf4ac15106f5f25ce28deaad9d32e6 Author: vince Date: Fri Mar 28 12:18:25 2014 -0700 unconst Src/C_BaseLib/Profiler.H commit 55b4fd6dcae04fe7a3d84a74135597f5f0aa71c6 Merge: e242f127f b6cb92f13 Author: vince Date: Fri Mar 28 12:14:58 2014 -0700 streamretry tweaks. commit e242f127f01ade794c884eff44d4fae144e9b9e4 Author: vince Date: Fri Mar 28 12:10:31 2014 -0700 streamretry tweaks. Src/C_BaseLib/Utility.cpp commit b6cb92f13a7ad31f2280aa0b8e424dbfa2892626 Author: Weiqun Zhang Date: Thu Mar 27 16:04:22 2014 -0700 update make files for edison Tools/F_mk/GMakeMPI.mak Tools/F_mk/comps/Linux_intel.mak commit 2f892b2b477965af58bc22e928815dbd15ae9fad Author: ajnonaka Date: Tue Mar 25 16:13:49 2014 -0700 need to scale residual by -1 so nodal_applyop returns +del dot beta grad phi. appears to be working now Src/LinearSolvers/F_MG/nodal_applyop.f90 commit ef33bfd3fa5eba180e630b9856e8fa4b2fbf68f6 Author: ajnonaka Date: Tue Mar 25 15:48:51 2014 -0700 cleaning out cc_applyop Src/LinearSolvers/F_MG/cc_applyop.f90 commit 9d9513c30a6a250d9a78c263639f354d651956b2 Author: ajnonaka Date: Tue Mar 25 15:48:46 2014 -0700 add nodal_applyop.f90 Src/LinearSolvers/F_MG/GPackage.mak commit d68b2cb0f36317aff90841a867b86342526f05e9 Author: ajnonaka Date: Tue Mar 25 15:48:30 2014 -0700 writing a nodal_applyop... wip Src/LinearSolvers/F_MG/nodal_applyop.f90 commit c29e88eed2981934975495c542939c7d62be88b4 Merge: f9cbab930 8de9e3722 Author: ajnonaka Date: Tue Mar 25 09:57:17 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f9cbab9303c896b6a7a13706600501e1e78a9aca Author: ajnonaka Date: Tue Mar 25 09:57:03 2014 -0700 make ml_cc_applyop public Src/LinearSolvers/F_MG/cc_applyop.f90 commit 8de9e37220590417481609d034194f9acccf5403 Merge: c650d9dda 76b20a34a Author: Michael Zingale 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 Date: Tue Mar 25 12:15:56 2014 -0400 spelling Src/F_BaseLib/bl_constants.f90 commit 930b5843f9361cd703c5d5575304e3783c8f6860 Author: Michael Zingale Date: Tue Mar 25 12:15:08 2014 -0400 add TWELVTH and SEVEN12TH Src/F_BaseLib/bl_constants.f90 commit 76b20a34a1b624c27118eef76d54f164ead7e964 Author: ajnonaka Date: Tue Mar 25 08:36:52 2014 -0700 remove a comment Src/LinearSolvers/F_MG/ml_solve.f90 commit 2896d32dbee94d10fc4768002c2b466616cee3b9 Author: ajnonaka Date: Tue Mar 25 08:04:17 2014 -0700 update comments Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/mg.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/mg.f90 commit 5ac8dc6b22848ea2d5dc427477b670701c997e91 Author: ajnonaka Date: Tue Mar 25 08:02:16 2014 -0700 move mac_applyop into cc_applyop (delete mac_applyop.f90) and renname the function cc_applyop to be consistent with the rest of the mg naming convention. Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/mac_applyop.f90 commit b205af32b3035d7e5a8fb9b3e73f8c8f9efc3ff5 Author: ajnonaka Date: Mon Mar 24 16:31:30 2014 -0700 eliminate scale_residual subroutines and just use a mult_mult_s_c. bonuts points is that 3d is now openmp'd Src/LinearSolvers/F_MG/cc_applyop.f90 commit 420282e49d4e7fa34359543af7a737ba230e0c6d Merge: ac2f09c7a 574f92cb8 Author: ajnonaka Date: Thu Mar 20 15:44:35 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ac2f09c7ac84860ab749460f064dde45f3c17216 Author: ajnonaka Date: Thu Mar 20 15:44:14 2014 -0700 nodal_divu now works regardless of the number of ghost cells u or rh have Src/LinearSolvers/F_MG/nodal_divu.f90 commit 574f92cb8b915a1bd650e9fb40a84787e91704ad Author: lijewski 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 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 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 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 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: bafe1091f 89c279a8a Author: ajnonaka Date: Mon Mar 17 11:00:27 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit bafe1091f3640e3a93176437881672e2a12dda03 Author: ajnonaka Date: Mon Mar 17 11:00:00 2014 -0700 stencil_order is now an optional argument with a default value of 2 if not passed in Src/LinearSolvers/F_MG/mac_applyop.f90 commit 89c279a8adfb6acf773b7b8bffa4bf897e858797 Author: Marc Day Date: Mon Mar 17 10:56:54 2014 -0700 Uptick tag version number Tools/CMake/BoxLib_Version.cmake commit b7fba9e37c6b3c7c919d0404b0d82236543c2c9c Author: Marc Day Date: Mon Mar 17 10:54:08 2014 -0700 Explicitly cast the args in the pow function to quiet older compilers Src/C_BaseLib/IArrayBox.cpp commit b3c5f821cf2e1d8fb357f90e8c6b7632df072a0e Author: ajnonaka Date: Fri Mar 14 15:32:55 2014 -0700 mgt_nodal_solve() now takes in eps and abs_eps as arguments (as it used to earlier in the week) and copies these values into the mg_tower object Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit c9a0f494e0f55443e6a2aa04fc87b148d5cb6f5d Author: Ann Almgren Date: Thu Mar 13 21:31:55 2014 -0700 Modified BSD license stuff. README.txt license.txt commit af6511257bd2fa12c62e20eaa584fc0ca498905a Author: Ann Almgren Date: Thu Mar 13 21:30:25 2014 -0700 These are the new versions for our official modified BSD release of BoxLib version 02-28-2014. README.txt license.txt commit 36139c35f23843c485e8d7d4aba59d45e6e76bea Author: ajnonaka Date: Thu Mar 13 16:35:47 2014 -0700 added the flexibility to pass in optional "S" and subtract this from the RHS for nodal solves Src/LinearSolvers/F_MG/ml_solve.f90 commit 851e7e6275786ad94a1832a3b11163249e0a9ee4 Author: ajnonaka Date: Thu Mar 13 16:01:20 2014 -0700 cleanup only Src/LinearSolvers/F_MG/ml_solve.f90 commit c1206820680faa9f79f9e6d5976a4afc683da90c Author: ajnonaka Date: Thu Mar 13 15:56:13 2014 -0700 use new add_divu_to_rhs feature, fix comments Src/LinearSolvers/F_MG/ml_solve.f90 commit 51c492a8e9793d80118933cde3bf5cfb69b25d35 Author: ajnonaka Date: Thu Mar 13 15:46:33 2014 -0700 add optional logical argument to subtract_divu_from_rh to *add* rather than *subtract* Src/LinearSolvers/F_MG/nodal_divu.f90 commit 0fb969583aaa2193db566ba21853ae5acc348a77 Merge: 33aa4a56c 83efd743c Author: Ann Almgren Date: Thu Mar 13 15:20:12 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 33aa4a56c4be5bf9cef891ba8d614eb953ae86e7 Author: Ann Almgren Date: Thu Mar 13 15:19:12 2014 -0700 Make sure we use the tol and abs_tol that are passed in through the C++ interface -- they come in through the call from C++ in "mgt_solve" then are used to define mgts%mgt_eps and mgts%mgt_abs_eps which are actually used by the solver. Note that the C++ solvers always have to pass in the tolerance, they are not currently wired to use the default. Src/LinearSolvers/F_MG/cc_mg_cpp.f90 commit 83efd743c452e51fc0f282e3d5cacc34fb190a3c Author: ajnonaka Date: Thu Mar 13 14:28:40 2014 -0700 plug memory leak. also fix sign convention in rhs for nodal solve. still wip. varden works, need to check MAESTRO for nonzero S to see if the sign convention holds Src/LinearSolvers/F_MG/ml_solve.f90 commit 8a504d24d02caf13f0ccaab9dd3391a83a3e453b Author: ajnonaka Date: Thu Mar 13 13:12:18 2014 -0700 remove unnecessary optional arguments Src/LinearSolvers/F_MG/ml_solve.f90 commit 43f4592923cca4126dc8c1aa572a10f776e56c68 Merge: 28d83c763 90d7292de Author: ajnonaka Date: Thu Mar 13 13:02:59 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 28d83c763251935e91df687070f42fc3a26dc585 Author: ajnonaka Date: Thu Mar 13 13:02:33 2014 -0700 need to pass in a boundary register to cc solver interface. projections need the boundary flux of phi to update at CF interfaces Src/LinearSolvers/F_MG/ml_solve.f90 commit 90d7292de7fbed6eae69feb88f624e56fad89707 Author: Matthew Emmett Date: Thu Mar 13 11:45:50 2014 -0700 PyBoxLib: Add setup.py. Src/Python/GNUmakefile Src/Python/GNUmakefile_CXX.mak Src/Python/setup.py commit ad826963d62624663d62d033a377bbfbd668cd7a Author: Matthew Emmett Date: Thu Mar 13 11:12:53 2014 -0700 PyBoxLib: Update basic multifab test, tidy up a bit. Src/Python/read.py Src/Python/tests/test-multifab.py Src/Python/write.py commit 7e6c9c51370bc583816a8d9f8f64e4607e1d2329 Merge: f0cf19002 5d54592e5 Author: Matthew Emmett Date: Thu Mar 13 11:09:41 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f0cf190024b76b88e390302cd1b60eca4a7c2b83 Author: Matthew Emmett Date: Thu Mar 13 11:09:28 2014 -0700 PyBoxLib: Remove old Fortran wrappers, update C++ wrappers (very basic for now). Src/Python/GMakerules.mak Src/Python/GNUmakefile Src/Python/GNUmakefile_CXX.mak Src/Python/GNUmakefile_F.mak Src/Python/GPackage.mak Src/Python/README Src/Python/boxlib/__init__.py Src/Python/boxlib/bl1.py Src/Python/boxlib/bl2.py Src/Python/boxlib/bl3.py Src/Python/boxlib/fbl/__init__.py Src/Python/boxlib/fbl/base.py Src/Python/boxlib/fbl/boxarray.py Src/Python/boxlib/fbl/fab.py Src/Python/boxlib/fbl/fabutils.py Src/Python/boxlib/fbl/layout.py Src/Python/boxlib/fbl/multifab.py Src/Python/boxlib/fbl/plotfile.py Src/Python/boxlib/fbl/pybl.py Src/Python/boxlib/fbl/utils.py Src/Python/contrib/chemSupport.H Src/Python/contrib/chemSupport.cpp Src/Python/contrib/support.H Src/Python/contrib/support.cpp Src/Python/fsrc/blobjects.f90 Src/Python/fsrc/blobjects.py Src/Python/fsrc/boxlib_numpy_c.c Src/Python/fsrc/boxlib_numpy_f.f90 Src/Python/fsrc/fboxlib.f90 Src/Python/src/boxlib_wrap_1.cpp Src/Python/src/boxlib_wrap_2.cpp Src/Python/src/boxlib_wrap_3.cpp Src/Python/swig/boxlib.i commit 5d54592e5a1d0fd7feac13f86edfa9c6bb0a2e11 Author: Andy Nonaka Date: Wed Mar 12 16:55:16 2014 -0700 index bug fix in new cc solver Src/LinearSolvers/F_MG/ml_solve.f90 commit 280b35c2f787ab96654da5e1f29a5e578a2d7088 Author: Andy Nonaka Date: Wed Mar 12 15:49:12 2014 -0700 new interface for ml_nd_solve complete. now for testing Src/LinearSolvers/F_MG/ml_solve.f90 commit a1386031d5e627816ea659463471978de5f9a8c5 Author: Andy Nonaka Date: Wed Mar 12 14:51:15 2014 -0700 more progress on nodal solver interface. still not sure if sign convention on rhs is correct Src/LinearSolvers/F_MG/ml_solve.f90 commit 73acdae4e3faa158890160b73692840d2844b1f7 Author: Andy Nonaka Date: Wed Mar 12 12:12:48 2014 -0700 move enforce_outflow_on_divu_rhs to nodal_divu.f90 since each nodal projection code had its own local copy Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/nodal_divu.f90 commit 19dccdc0614d5072d029a613427bd5a9dd90b617 Author: Andy Nonaka Date: Wed Mar 12 10:46:03 2014 -0700 fixed a bug in the new cc multigrid interface... passing in wrong bc comp to mg_tower_build. some work on the new nd multigrid interface... WIP Src/LinearSolvers/F_MG/ml_solve.f90 commit d11d0f70c80cd291526717bf66b83452771dffc4 Author: Andy Nonaka Date: Wed Mar 12 10:32:51 2014 -0700 ml_cc_solve_1 internally figures out of the problem is parabolic now and sets is_singular to false in the call to mg_tower_build. for elliptic problems, no optional is_singular argument is passed in and mg_tower_build still checks the boundary conditions internally to see of the problem is singular Src/LinearSolvers/F_MG/ml_solve.f90 commit 621efa086864319739cc38a01da4c945c7784c3e Author: ajnonaka Date: Tue Mar 11 13:38:24 2014 -0700 clean up the interface to the cc solve, and add a new simple interface to call the cc f90 solver Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mac_applyop.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit cd1cfb81c81fdeff220959e27a5f2ae84b30cd8a Author: ajnonaka Date: Tue Mar 11 11:22:19 2014 -0700 cleanup only Src/LinearSolvers/F_MG/mg.f90 commit 0c1530540a557561c04af1206395e2765e0c04b0 Author: ajnonaka Date: Tue Mar 11 10:38:13 2014 -0700 interface changes to keep up with f90 solvers Src/LinearSolvers/F_MG/cc_mg_cpp.f90 commit 753617c9a067bde0de1b0eac26dff79c3c8afb69 Merge: a1e774b98 7e858fb54 Author: ajnonaka Date: Tue Mar 11 10:30:06 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a1e774b982617e8729b126cbe8e8684e7dc42750 Author: ajnonaka Date: Tue Mar 11 10:27:11 2014 -0700 don't pass in optional abs_eps and rel_eps arguments to ml_cc_solve and ml_nd_solve anymore and use the versions in the mg_tower object don't pass in ref_ratio anymore since it's available in the ml_layout Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Tutorials/HeatEquation_EX5_F/advance.f90 commit 7e858fb5462804b7c8112e511e0e516920a8c6b1 Merge: 8e4674344 97bb85239 Author: Matthew Emmett Date: Tue Mar 11 10:15:06 2014 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 8e46743441e9ea9ee3af2fcdcea9ebdfae83dfcf Author: Matthew Emmett Date: Tue Mar 11 10:14:51 2014 -0700 PyBoxLib: F90 version: Fold C routines into libpyfboxlib. Src/Python/GMakerules.mak Src/Python/GNUmakefile_F.mak Src/Python/GPackage.mak Src/Python/boxlib/fbl/fab.py Src/Python/fsrc/boxlib_numpy_c.c commit 84ab54fb249d24b829c95441bcc657c9515a8c60 Author: vince Date: Thu Mar 6 11:58:24 2014 -0800 merge with master. MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp commit 85313ab6a562a530ef462675282698bcf4048170 Merge: b384b52d5 97bb85239 Author: vince Date: Thu Mar 6 11:51:32 2014 -0800 Merge branch 'master' into commprof commit 97bb852391d58a78ac71deb92a157b9aeb6d3c3c Author: vince Date: Thu Mar 6 11:33:14 2014 -0800 removed dumpi vars, they are now in Tools/C_mk. MiniApps/FillBoundary/GNUmakefile commit 315544bce0f8d78285b03aea3ccdfd9763498b60 Author: vince Date: Thu Mar 6 11:31:55 2014 -0800 added dumpi support to make system. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit 2af23e2e8c1c0af6fdc03a6556b799dc6ba57884 Author: vince Date: Thu Mar 6 10:30:29 2014 -0800 new ncube code. MiniApps/MultiGrid_C/main.cpp commit c225104d6d66139a5f2b6cb73958eac285470abf Author: vince Date: Thu Mar 6 10:29:54 2014 -0800 added ipm, dumpi, prof flags. made more consistent with fillboundary. MiniApps/MultiGrid_C/GNUmakefile commit b384b52d53819207d07e1dc52dab73a09bfaa570 Merge: 2270d84a3 183ff1a4b Author: vince Date: Thu Mar 6 10:13:41 2014 -0800 merge with master. commit 183ff1a4b0516fd63a8fc783402ca9214e65f4fa Author: vince Date: Thu Mar 6 09:07:04 2014 -0800 iop around error output. MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp commit 94d9e35c57146c553d0723345fa2a1551751e195 Author: vince Date: Thu Mar 6 09:05:47 2014 -0800 we dont need the map since we are not going to reuse it. MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp commit 2270d84a365c63f383e9e870704cdf7b991cd6bb Merge: ad588e7b6 673b77fb2 Author: vince Date: Wed Mar 5 17:33:59 2014 -0800 merged with master. commit ad588e7b6880b20fe46edb9eda0fd7173ec9e7f9 Merge: efc31b9ee 91c938855 Author: vince Date: Wed Mar 5 17:29:37 2014 -0800 about to merge the latest versions. commit 673b77fb28c16179299812686362dd4d199050f8 Author: vince Date: Wed Mar 5 17:02:02 2014 -0800 added vector initialization for older compilers. rewrote the N cubed check with a simple map lookup for small values. exp(log...) breaks sometimes because of roundoff (nprocs = 1000 for example). yes, it is always something. MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp commit fccc382e05e5ed328c5908297b4dd5621dcfb1ca Author: vince Date: Wed Mar 5 17:01:34 2014 -0800 added new/old compiler flags and temporary dumpi support. MiniApps/FillBoundary/GNUmakefile commit c7df3a3d31e25ab717f885da2764ddb5505cc9a4 Merge: ac3e27715 b0ae7df8a Author: Adam Jacobs Date: Wed Mar 5 17:59:39 2014 -0500 Merge in sub-Chandra analysis routines in branch 'fsub_dev' commit b0ae7df8aef42c1ca827ef1dbcd9c678fa474ca1 Author: Adam Jacobs Date: Wed Mar 5 17:56:15 2014 -0500 Committing the latest version of the sub-Chandra analysis routines. MAESTRO_sub_chandra/GNUmakefile MAESTRO_sub_chandra/fsubchandra.f90 MAESTRO_sub_chandra/fsubchandra_mod.f90 commit 91c93885500965a9102cf142a12c57685f1f938b Author: vince Date: Wed Mar 5 12:24:26 2014 -0800 added run time. MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp commit efc31b9eed9ee4ff5f175ddaacdfd1a63c987d15 Merge: 4d8cee8f6 18407cd9b Author: vince Date: Wed Mar 5 11:44:16 2014 -0800 made these similar to the master branch versions. commit 18407cd9b2e6884aa1fb7bd982b433fa6628e4ac Author: vince Date: Wed Mar 5 11:27:13 2014 -0800 added other run sizes. MiniApps/FillBoundary/qsub.ipm.bat commit b2b52b5b02479089d726cd4634c4111dd29add31 Author: vince Date: Wed Mar 5 11:23:11 2014 -0800 changed filename. MiniApps/MultiGrid_C/README commit 8e098228fe54b1b94275defa9768181da6f7cbb6 Merge: 77ffa2a31 f1f05be32 Author: Matthew Emmett Date: Wed Mar 5 10:37:43 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 77ffa2a31f6015ada939f22ab6de0204bf4cf704 Author: Matthew Emmett Date: Wed Mar 5 10:37:35 2014 -0800 PyBoxLib: Move Fortran based version to its own directory. Begin importing C++ based version from Marc. Src/Python/GMakerules.mak Src/Python/GNUmakefile Src/Python/GNUmakefile_CXX.mak Src/Python/GNUmakefile_F.mak Src/Python/GPackage.mak Src/Python/boxlib/__init__.py Src/Python/boxlib/fbl/__init__.py Src/Python/boxlib/fbl/base.py Src/Python/boxlib/fbl/boxarray.py Src/Python/boxlib/fbl/fab.py Src/Python/boxlib/fbl/fabutils.py Src/Python/boxlib/fbl/layout.py Src/Python/boxlib/fbl/multifab.py Src/Python/boxlib/fbl/plotfile.py Src/Python/boxlib/fbl/pybl.py Src/Python/boxlib/fbl/utils.py Src/Python/fsrc/blobjects.f90 Src/Python/fsrc/blobjects.py Src/Python/fsrc/boxlib_numpy_c.c Src/Python/fsrc/boxlib_numpy_f.f90 Src/Python/fsrc/fboxlib.f90 Src/Python/pyboxlib/__init__.py Src/Python/pyboxlib/pybl.py Src/Python/swig/boxlib.i Src/Python/swig/numpy.i Src/Python/tests/test-multifab.py commit f1f05be3239ef04a2db8f7ad7d740d6152cc1e10 Author: Ann Almgren Date: Wed Mar 5 10:16:09 2014 -0800 1) Modify MultiGrid.H / MultiGrid.cpp so we can set a new flag (do_fixed_number_of_iters) in the MultiGrid class -- can only be set using SetFixedIter -- if this is set to 1 then the MultiGrid class will do exactly maxiter iterations without checking for convergence. The default value is 0, so if this is not set to 1 then the code will behave as before. 2) Modify the MiniApps/MultiGrid_C main.cpp so that it calls setFixedIter(1) to do just one iteration and stop without crashing. We also no longer need inputs.3d MiniApps/MultiGrid_C/inputs.3d MiniApps/MultiGrid_C/main.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 6dda885f2ec8b83286c2e07e6334901f96c5315c Author: Ann Almgren Date: Mon Mar 3 12:43:51 2014 -0800 Create a multigrid MiniApp that doesn't require any inputs file. It creates a single 64^3 grid on each MPI process, and requires that the number of processes be a perfect cube so that the domain is N*N*N grids where N = cube root of NProcs. MiniApps/MultiGrid_C/COEF_3D.F MiniApps/MultiGrid_C/COEF_F.H MiniApps/MultiGrid_C/GNUmakefile MiniApps/MultiGrid_C/Make.package MiniApps/MultiGrid_C/README MiniApps/MultiGrid_C/RHS_3D.F MiniApps/MultiGrid_C/RHS_F.H MiniApps/MultiGrid_C/inputs.3d MiniApps/MultiGrid_C/main.cpp MiniApps/MultiGrid_C/qsub.ipm.bat commit 614b6bde6bdef5d617a34e6cc84f9df8707cc76c Author: Ann Almgren Date: Mon Mar 3 10:33:53 2014 -0800 Add suggested numbers of processors. MiniApps/FillBoundary/README commit 4d8cee8f6aabc1e4974fa4eee15e88287bdcbc5d Author: Ann Almgren Date: Mon Mar 3 10:32:11 2014 -0800 Add suggested runs. MiniApps/FillBoundary/README commit a6b1fd6c7946f3756a2c6d4fbb59a35d00142c1e Author: vince Date: Fri Feb 28 14:29:49 2014 -0800 added ipm support for hopper. MiniApps/FillBoundary/GNUmakefile MiniApps/FillBoundary/README MiniApps/FillBoundary/qsub.ipm.bat commit 37b2e5ee8082d7a037bd508a8abc5eeb125b71e5 Author: vince Date: Fri Feb 28 13:21:31 2014 -0800 sanitized version for ipm/dumpi tracing. MiniApps/FillBoundary/GNUmakefile MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp MiniApps/FillBoundary/README commit a22aa946fa6fa3fc5e53ddd97c11a790683067b6 Author: vince Date: Fri Feb 28 12:23:57 2014 -0800 files from commprof. MiniApps/FillBoundary/GNUmakefile MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp MiniApps/FillBoundary/README commit c8681cd4b2c593c53f240fd4b4b67997a04c8204 Author: Ann Almgren Date: Fri Feb 21 00:12:33 2014 -0800 test3d --> fbtest3d MiniApps/FillBoundary/README commit ebf052d71c583eaa503382f872e1741df51d66ed Author: vince Date: Thu Feb 20 18:03:51 2014 -0800 squished into nested loops, added commprof tags. MiniApps/FillBoundary/GNUmakefile MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp commit 301b6a76d02783dd7917742d15d9d0af0b2bdb72 Author: vince Date: Thu Feb 20 17:59:54 2014 -0800 removed some diagnostic output. Src/C_BaseLib/DistributionMapping.cpp commit d3c8ea29ecd39dffd89fea73035289af7560dd94 Author: Ann Almgren Date: Thu Feb 20 16:07:36 2014 -0800 Fixed domain_hi. MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp commit 5d7a7cb33d7848e15e72ac051dea27129771d34a Author: Ann Almgren Date: Thu Feb 20 16:03:28 2014 -0800 Fixed. MiniApps/FillBoundary/MultiFabFillBoundaryTest.cpp commit 6746751707b8d39d2e4af505e31dbc6fbc1e5639 Author: Ann Almgren Date: Thu Feb 20 15:50:30 2014 -0800 Added info on how to build and run the code. MiniApps/FillBoundary/README commit fd1cbfa05c97d7747c080e87f5620d8757e69263 Merge: a52f0438c a89e7c545 Author: Ann Almgren 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 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 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 Date: Thu Feb 20 17:48:32 2014 -0500 allow for 2 extra build directories Tools/RegressionTesting/testnew.py commit ceb0ad6f5c3ce84dc78bf7d1b662079c341fe817 Merge: 3e5c6ca16 ee6e0d019 Author: vince Date: Wed Feb 19 10:23:28 2014 -0800 Merge branch 'master' into commprof commit ee6e0d0198d459abb58d24d5f93bfcbb9f93d478 Author: Michael Zingale Date: Wed Feb 19 13:14:02 2014 -0500 update of mostly comments + 1 parameter (time) in the wrong object Tools/RegressionTesting/testnew.py commit d78430667cb6bb3245d58952c41eed0dd6dd3941 Author: Michael Zingale Date: Wed Feb 19 11:59:42 2014 -0500 take care of the rarely encountered situation of having no active tests defined, in which case, we do not want to print a row in the main webpage Tools/RegressionTesting/testnew.py commit 3e5c6ca160a72309115ae06b133108d6263bcab4 Author: vince Date: Tue Feb 18 17:33:39 2014 -0800 added enum num. Src/C_BaseLib/Profiler.H commit d70eb8b880c8edd499630b243819261a48b5be41 Author: lijewski Date: Thu Feb 13 13:56:00 2014 -0800 I've been doing some experimentation regarding the order sends() in MPI Irecv/Send pairs. This code randomly shuffles the order of the sends. The idea is better spread the MPI traffic across the network. I'm checking the code in with the controlling variable defaulted to false. Got to gather more data to decide when/where it's really useful. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H commit aff8f6098f5dd3e41c4ae0706cb4c8c885c1ff94 Author: Marc Day Date: Wed Feb 12 15:59:32 2014 -0800 Uptick version Tools/CMake/BoxLib_Version.cmake commit 3838bd1d9d41f00969d57d4426f384c7122daf45 Author: Marc Day Date: Wed Feb 12 15:58:13 2014 -0800 Test mulitcomp Tests/C_BaseLib/tMF.cpp commit bd937ca0c8f098a2d8fc71e30bfe6c2ba4e1ff2d Author: vince Date: Wed Feb 12 12:59:48 2014 -0800 added timer for commstats flushing. Src/C_BaseLib/Profiler.cpp commit 9713a792faa33567defea08beae38572f90aa6ca Author: vince Date: Wed Feb 12 12:03:17 2014 -0800 removed some nametag tracing. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit ced059bd30dd6daa6cdca511c0203d7e4aa98932 Merge: 2cc06927e 9a4f8d779 Author: vince Date: Wed Feb 12 11:43:05 2014 -0800 fix merge conflict. commit 2cc06927e76ee01d6b4e39571e2b8ae9561ebf4c Author: vince Date: Wed Feb 12 11:28:57 2014 -0800 added -DDEBUG flag Tools/C_mk/Make.defs commit 65ed43095024a147aae9a64c435abb2cbb790666 Author: vince Date: Wed Feb 12 11:26:47 2014 -0800 temporary diagnostics for new mappings. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.cpp commit e4c6d4b8e9dc470ba2696e5528adfed7918ba3cf Author: vince Date: Wed Feb 12 11:24:51 2014 -0800 more work on proximity mapping, diagnostics are still in the code. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/Profiler.H commit 9a4f8d779691c93742e78eae2111ee4759c3fe06 Author: cmalone Date: Wed Feb 5 21:23:29 2014 -0800 shouldn't need libg2c anymore, if using GCC4.x+ Tools/C_mk/Make.CYGWIN_NT commit 930a8e0df84016e9e5c8cf86f317abe8d2b9c1fc Author: Weiqun Zhang Date: Wed Feb 5 14:16:21 2014 -0800 regression test script: added diff to restart test Tools/RegressionTesting/testnew.py commit e80e8c4028d646a3a58014adbef9ce366e7064b0 Author: Weiqun Zhang Date: Wed Feb 5 11:11:04 2014 -0800 get around an Intel compiler 14.0.1 bug Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit d19b4a8f472c4125dc2b809aa8f0ba99205dc83b Author: vince Date: Tue Feb 4 14:01:37 2014 -0800 mpi lib fix for mothra. Tools/C_mk/Make.mpi commit 8e70fe6780bfb011d78a484c6f673cfc6c38c987 Author: lijewski Date: Mon Feb 3 09:03:07 2014 -0800 Reverted out my latest mods; they were unnecessary given how we checkpoint. Src/C_AMRLib/Particles.H commit 708dc04bb9abf0db801a72bf4bb9cc341ff06c44 Author: lijewski Date: Fri Jan 31 10:06:42 2014 -0800 Comment out some debugging output. The Intel compiler doesn't like one of my format statements. Src/F_BaseLib/layout.f90 commit c475e5d32558e39e4382cc6e9550fff2bb07396c Author: lijewski Date: Thu Jan 30 14:13:34 2014 -0800 Merged Vince's stream retry idea into Checkpoint(). Src/C_AMRLib/Particles.H commit 8297fe3bd5f3e94dc4402d3d797139ab69b5b82c Author: lijewski Date: Thu Jan 30 14:12:44 2014 -0800 Added const std::string Unnamed to be used as default argument in ParallelDescriptor::Barrier() instead of creating a string on the fly. Src/C_BaseLib/ParallelDescriptor.H commit a4be50740f6b0e32480188a11d7b98a7fd7434ba Merge: 02662f59b 092ada2a6 Author: Marc Day 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 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 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 Date: Mon Jan 27 14:13:49 2014 -0800 Increased fabarray.maxcomp to 25. Src/C_BaseLib/FabArray.cpp commit 80b507e1d9b4356cb1782b126402ca6586fe4cb7 Author: vince Date: Fri Jan 24 16:12:23 2014 -0800 removed output. Src/C_AMRLib/Amr.cpp commit a9cdc809a68efd192d3a956f5d53887cda67a590 Author: Adam M. Jacobs Date: Fri Jan 24 15:50:42 2014 -0500 Modified fillpatch.f90 to safely handle empty boxes. Problems were noticed when attempting to refine the sub-Chandra MAESTRO problem to 4 levels. Src/F_BaseLib/fillpatch.f90 commit d414d85af44c6acb875895d1ade7a0f82057e725 Author: vince Date: Fri Jan 24 11:52:44 2014 -0800 comment. Src/C_AMRLib/Amr.cpp commit a33e841f4dc1a159572ffb96ae3bece3de7ae6d8 Merge: 262818137 0ab4eed05 Author: vince Date: Thu Jan 23 15:26:38 2014 -0800 Merge branch 'master' into streamretry commit 0ab4eed051c1abfecfb9227efce74974bee055f1 Merge: 3175d7569 4badd3224 Author: vince Date: Thu Jan 23 15:26:18 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 2628181376859157ec90443af91320fc86b91243 Author: vince Date: Thu Jan 23 15:25:33 2014 -0800 less verbosity. Src/C_AMRLib/Amr.cpp commit 976e725cabc2d0075a3fe4201868c5322a0241d7 Author: vince Date: Thu Jan 23 14:30:29 2014 -0800 changed temp file verbose output. Src/C_AMRLib/Amr.cpp commit 23e13c544ed3dd8680d93a7cfb8ebe35bb36fabd Author: vince Date: Thu Jan 23 13:55:44 2014 -0800 more stream information on retry. Src/C_BaseLib/Utility.cpp commit 4badd322415e97c58643c2f492833de43d584a9f Merge: d7382554e 92e5f0ab9 Author: Adam M. Jacobs Date: Thu Jan 23 14:32:28 2014 -0500 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit d7382554e665de39d9feead38d6685677d797432 Author: Adam M. Jacobs Date: Thu Jan 23 14:31:20 2014 -0500 add some optional arguments to allow for potentially empty boxes. These changes should not affect any output, but will be used for a safer fillpatch to come... Src/F_BaseLib/box_f.f90 Src/F_BaseLib/boxarray_f.f90 Src/F_BaseLib/multifab_f.f90 commit 3e2b61f3b8b8c06f03d3b2e9fcf6a50256dfc9e7 Author: vince Date: Wed Jan 22 15:36:26 2014 -0800 checkpoint and plotfiles now have temporary names until they are complete. then stream retry will rename them if there were stream errors. if the checkpoint or plotfile names exist, those directories are renamed with a random suffix. this includes the temporary file names. more output from stream errors. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 92e5f0ab95630a9e4e06eb2520fb1358993f97bb Author: lijewski Date: Wed Jan 22 11:22:28 2014 -0800 Modest reduction in memory use for TagBoxArray::collate(). This function collects all the tagged cells to the I/O processor, who then removes duplicates and broadcasts'm back, as part of the grid generation procedure. The tagged cells are passed around as arrays of IntVects. Duplicates are removed by first sorting the vector of IntVects. On the 9000 core LMC run I'm currently nursing on edison, I've got roughly 13000 grids at level 2. This leads to about 360000 tagged cells out of which about half turn out to be duplicates. This is a pretty large array to be sorting. Luckily the sort algorithm is NlogN. Src/C_AMRLib/TagBox.cpp commit 3175d75698ad37e7b12598d4d299a0233d887ecc Author: vince Date: Thu Jan 16 16:22:25 2014 -0800 make temporary filenames for plotfiles and checkpoints, then rename them only if they are complete. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit c4d7c89cb214f7b3509e965c6fe2e47b53aa5a0d Author: vince Date: Thu Jan 16 14:10:50 2014 -0800 delay reset of fab format. Src/C_AMRLib/Amr.cpp commit e19ed6d6cda7128de09f0fc30ca1a2bf05b0703f Author: Ann Almgren Date: Thu Jan 16 11:15:28 2014 -0800 Define the pd in line 200 of fillpatch rather than using the not-yet-defined "cdomain". Src/F_BaseLib/fillpatch.f90 commit 3368f5d092bebca7496995e964db19440da74a6c Author: lijewski Date: Thu Jan 9 14:56:52 2014 -0800 Some simplification. Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/ParmParse.cpp Src/C_BoundaryLib/FabSet.cpp commit 0abf5e1f6a3ac92e832ca9d9a2cf69c361580331 Merge: ba43b6f05 9f35cbdba Author: vince Date: Thu Jan 9 11:25:00 2014 -0800 Merge branch 'master' into commprof commit 9f35cbdba8af1621e8bd03a5ef24482498f8f3bb Author: lijewski Date: Tue Jan 7 09:48:07 2014 -0800 A little simplification. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit a2bf53a75d523f73cb131e1b120f764ea998f8cf Author: lijewski Date: Mon Jan 6 15:27:29 2014 -0800 Now print out particle byte spread in Redistribute if m_verbose > 0 instead of m_verbose > 1. Src/C_AMRLib/Particles.H commit e70a4064a9edfac32a2220d66b4b245ffd492a5a Author: lijewski Date: Mon Jan 6 13:42:34 2014 -0800 Some more cleanup to quite the compiler. Src/C_BaseLib/FabArray.H Tests/LinearSolvers/C_CellMG/GNUmakefile commit 22d40369450ae343b7d0bb4eadec1d4c25023f57 Author: lijewski Date: Mon Jan 6 12:34:00 2014 -0800 Always use F90 solvers. Tests/LinearSolvers/C_CellMG/MacOperator.cpp commit 94b782a883ad5fe2a56debfb9c7deb24be8253a1 Author: lijewski Date: Mon Jan 6 12:13:53 2014 -0800 Shut up compiler about "possible" uninitilized data. Src/F_BaseLib/bc.f90 commit 400f2336a7e3ce51563312bb9fffd4ecb481a1b7 Merge: 60cd4ddb7 92038f8c4 Author: ajnonaka Date: Thu Jan 2 15:22:18 2014 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 60cd4ddb7d3c2ee5629d2262866cfa03008fb22d Author: ajnonaka Date: Thu Jan 2 15:22:02 2014 -0800 add USE_WBAR option Tools/C_mk/Make.defs commit 92038f8c44c4c401e379cdfbb8a3e1c78a601a9a Merge: 963f1fa0f f134c1044 Author: Adam Jacobs 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 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 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 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 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 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 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 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 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: dc96c7fa4 c0f8756be Author: Marc Day Date: Thu Dec 19 15:36:20 2013 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit c0f8756be27cf5ccda21930538af611c4f4a4b77 Author: lijewski Date: Thu Dec 19 14:08:01 2013 -0800 Forgot to remove a debug statement. Src/C_BaseLib/FabArray.cpp commit 951475a20f2927b9643734c544c99b90f4035343 Merge: 52b1da2cb 036b8110b Author: lijewski Date: Thu Dec 19 14:03:34 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 52b1da2cb554d70eb5a62cc301b1a82a16a26abb Author: lijewski Date: Thu Dec 19 14:02:02 2013 -0800 Decreased the default sizes of the Fill_Boundary() and copy() caches to 25. This seems to get a majority of the reuse cases without leading to excessive metadata size. Src/C_AMRLib/AuxBoundaryData.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 036b8110b5380c73b7c7685eac287f30fce2d331 Author: Weiqun Zhang Date: Thu Dec 19 13:11:39 2013 -0800 fixed comment Src/C_BaseLib/FabArray.H commit 3a57e878f4b3a1bc67ada5cc88d8714455e1d6d7 Author: lijewski Date: Wed Dec 18 14:19:43 2013 -0800 Some cleanup. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BoundaryLib/BndryData.cpp commit 55a33339fa3133a6c0b203dfcd89c11b888c04dc Author: lijewski Date: Wed Dec 18 11:20:55 2013 -0800 Exclude the AuxBoundaryData parallel copy()s from being cached. Src/C_AMRLib/AuxBoundaryData.cpp Src/C_BaseLib/FabArray.cpp commit 0ea8d45f2b26cce6d85c5127f7b5a5bb5345fdca Author: lijewski Date: Wed Dec 18 10:35:41 2013 -0800 Added ability to specify not to cache the data patterns for parallel copy. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 580547bfc1ec131bb521b5c889d894471e057453 Author: lijewski Date: Wed Dec 18 09:03:51 2013 -0800 Removed a redundant line. Reduced the default max size of the copy cache from 200 -> 100. Might have to go even smaller unless I can squeeze out more memory from the BoxArrays. Or another route would be to not add the chemistry parallel copy()s to the cache. Src/C_BaseLib/FabArray.cpp commit 901d6dc73edc16ffb6cb8392c2479c8a560f48b6 Author: lijewski Date: Tue Dec 17 14:11:18 2013 -0800 Removed BoxArray::reserve(). As best I can tell this is not used anywhere. If someone is using it, you should be able to just delete the call to it and all should be well. It's really just a hint to the underlying containing to "reserve" memory for future operations on the BoxArray. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit ddacb5d444a0c6b833060430d14c852c7f688e2b Author: lijewski 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 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 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 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 Date: Mon Dec 16 16:41:53 2013 -0800 Cleaned up some verbose output. Src/C_AMRLib/Amr.cpp commit c1756e480a5a65dfb814eabd50dbe24a41174d23 Author: lijewski Date: Mon Dec 16 15:34:45 2013 -0800 Added counters for the high water mark of distinct BoxArrays and build hash tables. It looks like I've been overestimating the amount of data in hash tables. I missed a place in the code (hidden in the .H file not the .cpp file) where hash tables can go away. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit ba43b6f0561023989f9d12412ea773861368344f Merge: ea6ac6e9e 16e48dda7 Author: vince Date: Mon Dec 16 15:12:44 2013 -0800 Merge branch 'master' into commprof commit 16e48dda78ae5762532131fe06cd288dfe134db8 Author: lijewski Date: Mon Dec 16 13:58:19 2013 -0800 Squeezed out some more memory from the hash tables. Src/C_BaseLib/BoxArray.cpp commit 8a9ed72a2f1877466e2da1f370867936fff9c3f1 Author: lijewski Date: Mon Dec 16 12:28:08 2013 -0800 Added code to print out the high-water mark of bytes held in BoxArray hash tables at the end of each coarse time step (similar to FAB bytes spread). As best I can tell these hash tables are the only thing in the C++ code that grows as the total number of Boxes, not the total number of Boxes that a CPU owns. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 9b446e73de3cb3d678266d08162dc3e4c56b0f5a Author: Ann Almgren Date: Sun Dec 15 20:00:54 2013 -0800 Add an option to moveKick in Particles.H that allows one to store the acceleration at the particle location in the data of the particle. This option is only exercised if the component passed in is relevant, aka > the components of the data used to store the velocity. Src/C_AMRLib/Particles.H commit 98a75c520dcd9c5eaf102f9c154dd8d992d5383e Author: lijewski Date: Fri Dec 13 11:00:22 2013 -0800 More BoxHash statistics. Src/C_BaseLib/BoxArray.cpp commit 87103e9182f3f0799f651179c5ccf8e4213136bd Author: lijewski Date: Fri Dec 13 10:40:59 2013 -0800 Added a clear_hash_bin(). AddBox() calls intersections() ... Src/C_AMRLib/FluxRegister.cpp commit 3ac81d0aee2a8a93580b183455b6dc7577c753c6 Author: lijewski Date: Fri Dec 13 10:40:40 2013 -0800 Added a clear_hash_bin(). Src/C_AMRLib/TagBox.cpp commit ac3e27715461f914ab48f12b7b757a0dba7c9274 Merge: 184f40c8d 3d1eec256 Author: Michael Zingale 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 Date: Fri Dec 13 12:07:45 2013 -0500 don't require --infile1 --infile2 fcompare.f90 commit ee143ad65e95d61808926415b4cdc82757e77c07 Merge: 966b9c33a aba95cb1f Author: Ann Almgren Date: Thu Dec 12 21:06:01 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 966b9c33af81b018baff0f53a2b80ae336f4fd5b Author: Ann Almgren Date: Thu Dec 12 21:05:31 2013 -0800 Set default value of regrid_int = 1; you will now get a warning instead of an error if you don't set it in the inputs file. Src/C_AMRLib/Amr.cpp commit aba95cb1f29cc1a3ac9e8ebcf7c6b9e914171ac7 Author: lijewski Date: Thu Dec 12 15:30:07 2013 -0800 Some debugging stats for init_box_hash_bin(). I'd like to turn this into a "map" but it Fortran ... Src/F_BaseLib/layout.f90 commit f6700a83e939537246ec1d9fb723a273099da1e2 Author: Ann Almgren Date: Thu Dec 12 14:42:03 2013 -0800 Remove left over print statement. Src/C_AMRLib/Particles.H commit 3282494988f083c091922f81b689214705341e2e Merge: 82fa15909 c618d86fa Author: Ann Almgren Date: Thu Dec 12 14:37:29 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 82fa1590938ddfb12079a915f8a058b3a41664a4 Author: Ann Almgren Date: Thu Dec 12 14:31:09 2013 -0800 Add the access function GetParticleCPU. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/Particles.H commit c618d86faaf450d1da935ddb795a85bcbbb161b6 Merge: ead2de470 630788633 Author: lijewski Date: Thu Dec 12 13:39:00 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ead2de470709d356965172bef56427dd653aa190 Author: lijewski Date: Thu Dec 12 13:38:24 2013 -0800 Added more debugging statistics to box hash bin code. Src/C_BaseLib/BoxArray.cpp commit 63078863335e258f0e7be653e38cd75801a8ec5d Author: Ann Almgren Date: Thu Dec 12 13:37:09 2013 -0800 Modify the "GetParticle.." routines to change how we access the particle data, and pass it through the Amr object to the outside. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/Particles.H commit 186f011e6d8a3b8c85d9c0bd06aed0adcc2d214d Author: lijewski Date: Wed Dec 11 12:23:51 2013 -0800 On edison use -target=compute_node instead of -target=linux on compiles. Tools/C_mk/Make.Linux commit 96c86b1009012b14dece1e7b5b369e6097539720 Author: lijewski Date: Wed Dec 11 10:55:03 2013 -0800 Much more memory efficient implementation of the Box Hash stuff. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 4f52285789d34f7a7ef6fa4fa1c12d7ecf226b45 Merge: 76577ddfb 72e2483ee Author: lijewski Date: Tue Dec 10 17:56:23 2013 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 76577ddfb4a57cd1cf39dae2e0f46946a6a9b57d Author: lijewski Date: Tue Dec 10 17:55:00 2013 -0800 I'm adding back in the critical region that builds the hash bins. I seem to recall that the particle code needs this. Something along the lines of particles using BoxArray::contains() in OMPd loops, where contains() calls the intersect code under the covers. Src/C_BaseLib/BoxArray.cpp Src/F_BaseLib/layout.f90 commit 72e2483ee75a520b27348d4f7f23a9307ae79da9 Author: Ann Almgren Date: Tue Dec 10 17:21:40 2013 -0800 Removed commented line. Src/C_AMRLib/Particles.H commit 8f4cd9d9e6ecb2f73b1545912cf77078c465e0d8 Author: Ann Almgren Date: Tue Dec 10 17:18:08 2013 -0800 Add the virtual routine particle_redistribute so that we can call it from Amr::ParticleRedistribute. Src/C_AMRLib/AmrLevel.H commit a8b90f277d99a1c5c603f1d9127e0c2694a6e6a7 Author: Ann Almgren Date: Tue Dec 10 17:14:46 2013 -0800 1) Make the default ref_ratio be 2 for all directions and levels, instead of setting it to zero and having an error if not set in the inputs file. 2) Clean up the geometry stuff: we now define an external geometry by setting the intersection points of grid lines with the boundary in each coordinate direction (both hi and lo). This is a crude representation -- just one location for the face in each cell where it intersects. 3) Add Real coarseTimeStepDt which is the same as coarseTimeStep except it returns the dt that it used. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit e63cc29b01366154469a2607fe41d7e624a366fb Author: lijewski Date: Tue Dec 10 15:25:06 2013 -0800 Be a little more aggressive clearing box_hash_bin. Src/F_BaseLib/layout.f90 commit 6a921d778203b2f003746be0ab786ec121b18c5d Author: lijewski Date: Tue Dec 10 12:53:32 2013 -0800 Don't OMP loops containing layout_get_box_intersector calls. Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit a830de9f74994c7991ac6a873e2c898438340ebe Author: lijewski Date: Tue Dec 10 12:53:04 2013 -0800 Some cleanup. Src/C_BaseLib/BoxArray.cpp commit b3ed807387435003753ef4d17f91899e4047dc05 Author: lijewski Date: Tue Dec 10 12:24:34 2013 -0800 Some simplification. Also removed the critical section around the innards of intersections(). It's now no longer thread-safe. Hope I've found all places where I was trying to do intersections in threads and remomved'm. Src/C_BaseLib/BoxArray.cpp commit e5553e88b4fff1d306042abbea28fa8891c7c8f5 Author: lijewski Date: Mon Dec 9 21:51:31 2013 -0800 Increased verbosity level at which some debug output appears. Src/F_BaseLib/layout.f90 commit 43690fc09c81c1b85eba4afa7e9f8e30ef2305a2 Author: lijewski Date: Mon Dec 9 21:27:05 2013 -0800 Yet one more clear_hash_bin() call for the evening. Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 2d52f7549da9f2eb5d782c2df4d69263c0d5067a Author: lijewski Date: Mon Dec 9 21:24:14 2013 -0800 Inserted more clear_hash_bin() calls. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit 42f33bda143cfa80bf25af8d0d992c14958c4b2b Author: lijewski Date: Mon Dec 9 21:15:12 2013 -0800 Merged in some calls to BoxArray::clear_hash_bin(). Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/FabSet.cpp commit 57b0b76dc0f5670a59075254a342092a24022bfd Author: lijewski Date: Mon Dec 9 21:08:09 2013 -0800 Clear out the hash bin in a BoxArray after using intersections() to put a cached object into the FillBoundary() and parallel copy() caches. Src/C_BaseLib/FabArray.cpp commit 09da45f67fd950f115bd1aefe398085110131b60 Author: lijewski Date: Mon Dec 9 21:04:11 2013 -0800 Merged in call to clear_hash_bin(). Src/LinearSolvers/C_CellMG/LinOp.cpp commit c9afebd27b0195194b58605cea387cd64a5e1e6f Author: lijewski Date: Mon Dec 9 21:03:01 2013 -0800 Added BoxArray::clear_hash_bin(). Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit d8ae81efd1c0067ca3dc809ce8a513d2a6f06b9c Author: lijewski Date: Mon Dec 9 21:02:39 2013 -0800 Removed some debugging output. Src/F_BaseLib/layout.f90 commit 92b8d0981e68b526872ba9f386b2c96a653277a4 Author: lijewski Date: Mon Dec 9 20:40:35 2013 -0800 Compressed out some of the memory in the fast box intersection hash routine. This routine (and the one in F90) are looking like the metadata memory hogs that I've been searching for. I think there's more that can be done to cut down memory use here. Src/C_BaseLib/BoxArray.cpp commit dc5a6505dfc730830b0b66a2a5b301c9aee221e9 Author: lijewski Date: Mon Dec 9 15:08:34 2013 -0800 Added clear_box_hash_bin(). There may be some strategic places where we can call this routine to cut down on memory usage. Src/F_BaseLib/layout.f90 commit d3a114acd1f426bb10dba01de773a3ba762d6f39 Author: lijewski Date: Mon Dec 9 14:37:31 2013 -0800 Squeezed out some memory from the boxarray hash. Src/F_BaseLib/layout.f90 commit 39b4f9341a8e2c2a4e7f32b63ff5cd36c42e106a Author: lijewski Date: Mon Dec 9 12:48:21 2013 -0800 Added some code to calculate the maximum # of bytes in a boxassoc -- the structure that is used by layout for managing FillBoundary()s. Src/F_BaseLib/layout.f90 commit e87625fd1ab0450c0fc09400fc6cf6b7b1957584 Author: lijewski Date: Mon Dec 9 12:09:01 2013 -0800 Pulled something from the stack and put it on the heap. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 2438c4ea3a94283c7ef947a39cfbda79452b479c Author: lijewski Date: Mon Dec 9 10:44:37 2013 -0800 Some cleanup. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit e53944791524081eb25f7770dd78d351d97f5883 Merge: 852d9e455 a77623551 Author: lijewski Date: Mon Dec 9 10:22:22 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 852d9e455df3d80aae2ce570019a7ba376bfcbe2 Author: lijewski Date: Mon Dec 9 10:21:47 2013 -0800 Don't build the mask() lmultifabs in the ml_layout. They appear to only be used by the cell-centered code. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 6884575e39905e5021f0220e843b7f27cc958f33 Author: lijewski Date: Mon Dec 9 10:20:53 2013 -0800 Only try to delete the mask() lmultifabs if they've actually been built. Src/F_BaseLib/ml_layout.f90 commit a776235518314d4c6c7638142ad27d5f1e6bc046 Author: Ann Almgren Date: Sat Dec 7 12:12:18 2013 -0800 Add sanity checks and comments in ParticleContainer::addOneParticle() Src/C_AMRLib/Particles.H commit 0b15c631990e9ec7e8b18a537e999f8cf8f6bdc8 Author: lijewski Date: Fri Dec 6 14:14:47 2013 -0800 Fix typo. Src/C_BaseLib/FabArray.cpp commit 21e3ce87ac295283dcc01af236f5db862b834048 Merge: 74c2f5e06 2432e616b Author: lijewski Date: Fri Dec 6 13:54:51 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 74c2f5e062265e42baf305b4b830f79148b9e7cc Author: lijewski Date: Fri Dec 6 13:51:05 2013 -0800 Parallel copy() is now set up to do fabarray.maxcomp components at once. That is to say, we agglomerate MPI messages as always, but we only do fabarray.maxcomp (instead of ncomp) at one time. I'm occasionally getting killed by the Out-Of-Memory process of hopper. I'm wondering if it's because the internal MPI buffers are getting too big. So I want to do somewhat smaller MPI transfer. Large transfer happen, in particular, when we're rearranging state data for chemistry solves, amongst other times. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 2432e616b8ea6b69b474bad4ce3450818239c49e Author: Ann Almgren Date: Wed Dec 4 14:01:25 2013 -0800 Fix coefficients in tridiag. Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit db0609700fa3500334a0c6584f9b2e51249b4e87 Merge: d87999729 ff7ba31d9 Author: Ann Almgren Date: Tue Dec 3 16:20:23 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d879997299619919ee0bb1a3527dd37d5b633554 Author: Ann Almgren 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 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: 4dc4b042f 48d49251a Author: Weiqun Zhang Date: Mon Dec 2 21:27:22 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 4dc4b042f8ac1522a993dc41c547735cb174b17e Author: Weiqun Zhang Date: Mon Dec 2 21:27:15 2013 -0800 use OMP ATOMIC instead of OMP CRITICAL in a few places Src/C_AMRLib/Particles.cpp Src/C_BaseLib/BaseFab.H Src/F_BaseLib/bl_mem_stat.f90 commit 48d49251af16f1f9b8965b59f75ab53e169e5090 Author: Ann Almgren Date: Mon Dec 2 13:44:47 2013 -0800 DatasetClient.H no longer lives in this directory. Src/C_AMRLib/CMakeLists.txt commit 4b79909175406e318dbbbab16c0bd1bae6a129d3 Author: Ann Almgren Date: Mon Dec 2 13:22:35 2013 -0800 Add nodal_stencil_apply.f90 to CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt commit 34258cdc425a5e25afb69967a333eeab0c810437 Author: Ann Almgren Date: Mon Dec 2 13:19:02 2013 -0800 Add compute_defet.f90 to CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt commit 0f4d2e002d45e79b3902c29db49b214cd711203f Merge: d03cdd725 6a8e4a1dc Author: Ann Almgren Date: Mon Dec 2 13:01:23 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d03cdd725675d1ee7f62df47f6e3e4e440be283d Author: Ann Almgren Date: Mon Dec 2 13:01:02 2013 -0800 Update mg_tower_smoother.f90 --> nodal_mg_tower_smoother.f90 and cc_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/CMakeLists.txt commit 6a8e4a1dc054e5622f556be76979d4f3029d687c Author: Weiqun Zhang Date: Mon Dec 2 11:27:16 2013 -0800 Avoid using result, a Fortran keyword, as variable name although it is legal. Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit f19c451ade81e18e40c24bc27937ab3263a39b6b Author: Weiqun Zhang Date: Mon Dec 2 10:40:09 2013 -0800 fixed OMP bugs Src/LinearSolvers/C_TensorMG/MCLO_3D.F commit b6b4e54748391f9ec31748f2c6b33c315af83b37 Author: Weiqun Zhang 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 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 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 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 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 Date: Tue Nov 26 14:34:33 2013 -0800 fixed a minor OMP problem Src/C_BaseLib/BaseFab.H commit 4198681daad6aaffa92b8441435b2f0b4d431b5c Author: Weiqun Zhang Date: Mon Nov 25 20:11:39 2013 -0800 fixed OMP bugs in my recent commit that will lead to race condition if the number of threads is large Src/C_AMRLib/FLUXREG_3D.F commit d4627b1704fb3e3f4533e495627e0273b1fbceeb Author: lijewski Date: Mon Nov 25 20:00:51 2013 -0800 Some OMP fixes. Src/LinearSolvers/F_MG/ml_nd.f90 commit be5ae8effbbc10c02a58410da301885e69393e63 Merge: 714b43add 8b68cb9fc Author: Ann Almgren Date: Mon Nov 25 19:34:35 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib Conflicts: Src/LinearSolvers/F_MG/ml_nd.f90 commit 714b43add1ad03ac378fa1bfd21f4d4e85beb499 Author: Ann Almgren Date: Mon Nov 25 19:33:00 2013 -0800 Fix indices in nodal_stencil_norm. Src/LinearSolvers/F_MG/ml_nd.f90 commit 8b68cb9fc77e80bb5128280f750f17943616ef52 Author: lijewski Date: Mon Nov 25 19:24:16 2013 -0800 Some OMP bug fixes. Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil_apply.f90 commit d6f3af2df2a9c8ec4578d3763372eb49c8a093d8 Author: Ann Almgren Date: Mon Nov 25 17:42:41 2013 -0800 1) remove unused variable in nodal_smoothers. 2) fix nodal_stencil_norm. Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit 4d0bc68c9f74e6b6de8dd331c06add2881de3b27 Author: Ann Almgren Date: Mon Nov 25 16:58:06 2013 -0800 We need to use a different function for the stencil norm for the nodal solver. Src/LinearSolvers/F_MG/ml_nd.f90 commit 08b269fc1acc239e8fd6cc361139623bc914610d Author: Ann Almgren Date: Mon Nov 25 16:46:11 2013 -0800 Remove lp from OMP declaration where it isn't used Src/LinearSolvers/F_MG/cc_stencil.f90 commit ea6ac6e9e57d61191b370a037123aa529eebbd50 Author: vince Date: Mon Nov 25 14:34:15 2013 -0800 reset strategy fix. Src/C_BaseLib/DistributionMapping.cpp commit 53bc6d8a4a7f7c104ec2d0dbee6435a47905a9e7 Author: Weiqun Zhang Date: Mon Nov 25 13:32:00 2013 -0800 fixed a bug in nodal stencil Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 0791d360a1636992fc9094c42e662acef327a765 Author: Weiqun Zhang Date: Mon Nov 25 10:16:27 2013 -0800 Fixed new OMP bugs. Also added "collapse". If compilers have trouble with "collapse", we can take it out, and move "omp do" two loops down. Src/C_AMRLib/FLUXREG_3D.F commit daa3d2f96f4ddf944c30ead4744e8c9bbed0cc4b Author: lijewski Date: Mon Nov 25 08:53:00 2013 -0800 Make the C-F MG translation code understand CABiCG solver. Set it up so that it CG, BiCG and CABiCG get properly translated between C++ and Fortran. While in the C++ code we set cg_solver as cg.cg_solver we allow cg.cg_solver and mg.cg_solver. Default to CABiCG if nothing is set. If you want different bottom solvers in C++ and Fortran use mg.bottom_solver, set to the correct F90 value. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 787c846cec8a7a8585ec8c78b810feb42822706e Author: lijewski Date: Fri Nov 22 15:42:22 2013 -0800 Fixed typo. Src/LinearSolvers/F_MG/nodal_stencil.f90 commit cf587c51d9381865da76aff08429550e7074c3ef Merge: ccfb9b9f0 fbea799d2 Author: Ann Almgren Date: Fri Nov 22 15:35:42 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ccfb9b9f0b428edca5d8a06774d4c20d280377bb Author: Ann Almgren Date: Fri Nov 22 15:35:22 2013 -0800 Fix the way we impose Neumann bc's on sg in nodal stencil fill. Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit fbea799d248d80ba5ace093f105c50cac8d8fd7f Merge: a18f76a8d 3d69251cd Author: lijewski Date: Fri Nov 22 12:40:04 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a18f76a8d5ff8cccc3722feba0ddaaf4721f805d Author: lijewski Date: Fri Nov 22 12:37:21 2013 -0800 Added code so that we thread a couple of these routines if they're NOT called from within a parallel region. In general, the most common place to call these routines from is within FillPatch, where they're called by threading over boxes in C++. Src/C_AMRLib/INTERP_3D.F commit 3d69251cd06aabb444e19cc34ab8664cee4eb643 Author: Ann Almgren Date: Fri Nov 22 11:16:25 2013 -0800 Only have diagonalize=true for nodal solve. Src/LinearSolvers/F_MG/itsol.f90 commit 3f52768a9cfed4774196c58e4b3f4e6ac74206f8 Author: Ann Almgren Date: Fri Nov 22 11:09:09 2013 -0800 No longer pass ns into mg_tower_build. Tutorials/HeatEquation_EX5_F/advance.f90 commit 0490638368ba9a892df33ef0df8652e017055de6 Author: Ann Almgren Date: Fri Nov 22 11:03:08 2013 -0800 More changes to be compatibale with the new nodal stencil (and the fact that we no longer pass ns into mg_tower_build). Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 4cf8374aabd4cc88155915292bb932f2de6f503f Author: lijewski Date: Fri Nov 22 10:50:08 2013 -0800 Turns out there's an easy way to figure out whethe or not we're currently in an OMP parallel region. The FineAdd Fortran routines are now written to only thread if they're not in an OMP region. When the MultiFab version of FineAdd() is used we thread in C++ over the boxes and hence don't thread within the Fortran. When the FAB version of FineAdd() is called we thread the Fortran. More of this to come ... Src/C_AMRLib/FLUXREG_3D.F commit 6078399e2aca5b8928bcafdf869697e0d8885925 Author: Ann Almgren Date: Fri Nov 22 10:43:41 2013 -0800 ns --> mgt%ns Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/mg.f90 commit 5d0367a157e2526919de47a0e0b93ddffe38336d Author: Ann Almgren Date: Fri Nov 22 10:43:07 2013 -0800 These are the new versions of the nodal solver which carries the cell-centered coefficient rather than filling the nodal-based stencil. Src/LinearSolvers/F_MG/compute_defect.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_apply.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit ef86291d1ab894f7069850e3745f1ffb5a1715e6 Author: Ann Almgren 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 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: 389500a41 051471657 Author: Ann Almgren Date: Thu Nov 21 16:40:12 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 389500a41f9577daa0115084d3d8a703a327bef0 Author: Ann Almgren Date: Thu Nov 21 16:39:38 2013 -0800 Create a new directory: BoxLib/Tests/LinearSolvers/F_MG_Old_Nodal_Stencil to hold the source code and test code for the stencil-based nodal solver. Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/GNUmakefile Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/bc_interp.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/cc_edge_coeffs.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/cc_multi.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/cc_rhs.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/grids_2d_1lev Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/grids_2d_2lev Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/grids_3d_1lev Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/grids_3d_2lev Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/init_cell_coeffs.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/inputs.2d.nodal.cross Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/inputs.2d.nodal.dense Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/inputs.3d.nodal.cross Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/inputs.3d.nodal.dense Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/main.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/makefile Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_multi.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/nodal_rhs.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/regression Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/t_smoother.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/t_stencil.f90 Tests/LinearSolvers/F_MG_Old_Nodal_Stencil/wrapper.f90 commit 8aeb97027a30d621fbbd17879fab2d4a5d109f4d Author: Ann Almgren Date: Thu Nov 21 16:38:06 2013 -0800 No longer keep these scripts. Tests/LinearSolvers/F_MG/test_dir Tests/LinearSolvers/F_MG/test_script commit d101569b6356c97fdbf0906fc044e0adb243d5bb Author: Ann Almgren Date: Thu Nov 21 16:37:43 2013 -0800 These are the new test routines for the new sg-based nodal solver. Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/init_cell_coeffs.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/nodal_rhs.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 73cf58c59d06ea17ddf8d8bc7b7f283bda627c87 Author: Ann Almgren Date: Thu Nov 21 16:32:35 2013 -0800 More cleanup -- no functional change. Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/mac_applyop.f90 commit 05147165711f6ca554ee7741ae053aced57300b1 Author: Weiqun Zhang Date: Thu Nov 21 13:06:38 2013 -0800 fixed makefile in F_MG for C++ codes Src/LinearSolvers/F_MG/FParallelMG.mak commit 5323d990fe0733e36f19ab246306616e4a0de632 Author: Ann Almgren Date: Thu Nov 21 12:30:12 2013 -0800 These changes should not make any difference in the answers, they are just rearrangement and some renaming of subroutines. Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/compute_defect.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_apply.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 1c3450cfc8b8a4cd1e3b3431a565fa6e4bd99911 Author: Ann Almgren Date: Wed Nov 20 14:20:13 2013 -0800 Update the testing routines with new inputs*nodal* files and new grids files. Clean up the printouts as well. Tests/LinearSolvers/F_MG/grids_2d_1lev Tests/LinearSolvers/F_MG/grids_2d_2lev Tests/LinearSolvers/F_MG/grids_3d_1lev Tests/LinearSolvers/F_MG/grids_3d_2lev Tests/LinearSolvers/F_MG/init_cell_coeffs.f90 Tests/LinearSolvers/F_MG/inputs.2d.nodal.cross Tests/LinearSolvers/F_MG/inputs.2d.nodal.dense Tests/LinearSolvers/F_MG/inputs.3d.nodal.cross Tests/LinearSolvers/F_MG/inputs.3d.nodal.dense Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit b18d247295779459a946e8416a32a9bcf9dc8db7 Merge: 0d0235aed a8fbdd06f Author: Ann Almgren Date: Wed Nov 20 12:37:05 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 0d0235aed7abcd5946f93603e72142fd7d8ccb59 Author: Ann Almgren Date: Wed Nov 20 12:36:45 2013 -0800 Clean up of nodal multigird and the testing program in Tests/LinearSolvers/F_MG. Tests/LinearSolvers/F_MG/GNUmakefile Tests/LinearSolvers/F_MG/cc_edge_coeffs.f90 Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 53fa31fdbb5a2590075c633df00d7e4e23df0a41 Author: Ann Almgren Date: Wed Nov 20 12:36:08 2013 -0800 The filest are listed in GNUmakefile instead. Tests/LinearSolvers/F_MG/GPackage.mak commit 9923d1840ac3dd97f4367e2020f56f693954d779 Author: Ann Almgren Date: Wed Nov 20 12:33:32 2013 -0800 Get rid of Jacobi options within smoothers. Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit 12deadec217e7460f23c7c0c4b62bf34fe604e25 Author: Ann Almgren Date: Wed Nov 20 12:33:12 2013 -0800 Better formatting. Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 5692c902b30221d8d4cf1723313d1e21a29568d1 Author: Ann Almgren Date: Wed Nov 20 12:32:37 2013 -0800 Make sure rh has exactly one ghost cell. Src/LinearSolvers/F_MG/ml_nd.f90 commit bc518d99dccf0c9dec73ece74a3b251c0b38a5a3 Author: Ann Almgren Date: Wed Nov 20 11:28:47 2013 -0800 Get rid of Jacobi smoother. Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit a8fbdd06fbcf8a6d9cc60e5f6abc4ebc665513ac Author: lijewski Date: Tue Nov 19 12:03:37 2013 -0800 Verbose flags should be integer. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 53769811ca7573962452429875a8f7b35f83aee0 Author: lijewski Date: Tue Nov 19 09:50:47 2013 -0800 Added a verbose option, defaulted to false, to MGT_Solver. This way we can set the default on a case by case basis, instead of just using the ParmParsed valued of mg.v. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 149b79551780f18e0d75ade754af75e4878dc96d Author: lijewski Date: Mon Nov 18 15:08:48 2013 -0800 Example now shows how to reduce a map where the key is a structure. I use and IntVect since BoxLib knows how to sort IntVects. Tests/C_BaseLib/tMF.cpp commit 7eaf38ec5b62ce88a288f8ca258c873c2108bad0 Author: lijewski Date: Mon Nov 18 14:13:54 2013 -0800 A little cleanup. Tests/C_BaseLib/tMF.cpp commit 0b59f677575740b67530dd5da1528cc7bb0c2481 Author: lijewski Date: Mon Nov 18 14:10:38 2013 -0800 This test is now a simple example of how to reduce a std::map across CPUs. Tests/C_BaseLib/tMF.cpp commit 3196d1ffad20ca144ca7b41bc29e233b420771b2 Author: Ann Almgren Date: Fri Nov 15 12:18:53 2013 -0800 Add check on whether mf is nodal in build_nodal_dot_mask. Src/F_BaseLib/multifab_f.f90 commit 2e2c1600228eabc54e2351ad544a0462dbfca273 Author: vince Date: Wed Nov 13 15:42:37 2013 -0800 added proximity order diagnostic. added simulation of hopper distributions for testing locally. pfc order looks correct. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 820c6e30739548b2f3adc12e42408109f263adac Author: Weiqun Zhang Date: Wed Nov 13 11:19:41 2013 -0800 sum_integrated_quantities does not need to be virtual Tutorials/AMR_Advection_C/Source/ADR.H commit 3d1eec2561b843941eac0d5585d93ec6d0e9ee9c Author: Chris Malone Date: Tue Nov 12 18:23:52 2013 -0800 remove debug print statements MAESTRO_xrb/fbuoyancy.f90 commit fa8332ea9fd994ea558ea579f8c8213a659a28f2 Author: Ann Almgren Date: Tue Nov 12 16:18:17 2013 -0800 We no longer use mgt%st Src/LinearSolvers/F_MG/mg_tower.f90 commit ea13ae1dbd8e9c1b959148281a4d1d0d2f5cfe10 Author: Chris Malone Date: Tue Nov 12 15:21:44 2013 -0800 get this compiling again MAESTRO_xrb/fbuoyancy.f90 commit 17342cd7ea9f5bc2d470dc1acb6a875c206e46e4 Author: Marc Day Date: Mon Nov 11 18:13:16 2013 -0800 Redo solve_ function to look more like scalar solve, add access function to AmrData, uptick ccse lib version Src/Extern/amrdata/AmrData.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp Tools/CMake/BoxLib_Version.cmake commit abb197b36d43faca9f81c46c16d7294218a82f6d Author: vince Date: Mon Nov 11 12:00:18 2013 -0800 removed print. Tests/IOBenchmark/IOTest.cpp commit 1dd4f1b0d2d7c6b4568cd6e3f63dfa588317f3c1 Author: Weiqun Zhang Date: Mon Nov 11 11:53:16 2013 -0800 removed DatasetClient.H and .cpp from a couple of makefiles because DatasetClient has been moved to ArrayView Tools/C_util/Convergence/Make.package Tools/C_util/Statistics/Make.package Tools/C_util/ViewMF/Make.package commit 338b4262680a8d4899f235b0e742eb38021e83bd Author: lijewski 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 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 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: edc50bc81 365d0af7e Author: vince Date: Mon Nov 4 12:09:31 2013 -0800 Merge branch 'master' into commprof commit 99780b9ce4a005cb5a6becd312db6ddaa14ae893 Author: Chris Malone Date: Fri Nov 1 09:42:41 2013 -0700 new routine to calculate the total mass on the grid for all species MAESTRO_xrb/fspec_total_mass.f90 commit edc50bc8102379ce86236cf8aeb99c9f07696f82 Merge: 2cfa64c63 bfd874231 Author: vince Date: Thu Oct 31 11:23:55 2013 -0700 Merge branch 'commprof' of gamera:/usr/local/gitroot/BoxLib into commprof commit 365d0af7e4df9787cfe1cc48947eb92c62331fc4 Merge: e0bc9532a 993d6a3be Author: vince Date: Tue Oct 29 16:30:21 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e0bc9532a3d649035e10c4b7073766fbf0f75600 Author: vince 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 Date: Mon Oct 28 17:02:11 2013 -0400 actually add a usage statement MAESTRO_xrb/frates.f90 commit 993d6a3be68eb3d16c02be75fc3a956cb4da9dee Merge: 9afecb0e9 d53e06b7f Author: lijewski Date: Mon Oct 28 09:23:19 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d53e06b7fe4ed8a655b10e3e800dd77e0366abda Author: lijewski Date: Sun Oct 27 10:32:53 2013 -0700 Examine NERSC_HOST as well as uname for the hostname. Currently edison doesn't appear in 'uname -a'. Tools/C_mk/Make.defs commit 9afecb0e925fbdf962069dfd5f462340840c196d Author: lijewski Date: Fri Oct 25 14:58:08 2013 -0700 Added version of bCoefficients() that takes a FArrayBox and grid # instead of a MultiFab. Also ZeroACoefficients(); it's equivalent to a call of aCoefficients() where the passed MultiFab was setVal()d to zero, without having to build the MultiFab. Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_TensorMG/DivVis.H Src/LinearSolvers/C_TensorMG/DivVis.cpp commit 2cfa64c63f5bd79d1c5aae5f7fd1fc36b6ba3166 Author: vince Date: Fri Oct 25 11:42:22 2013 -0700 close file. Src/C_BaseLib/VisMF.cpp commit f508df09f3382c5d6ea2e5133176bdafe2f4cfb1 Author: vince Date: Fri Oct 25 11:42:05 2013 -0700 close file. Src/C_BaseLib/DistributionMapping.cpp commit bfd874231501a484aa38d9e4fecfc74299ae3b3a Author: vince Date: Thu Oct 24 15:28:35 2013 -0700 hopper test. Src/C_BaseLib/DistributionMapping.cpp commit 2ed1278b8bca1268868d4cf6a19ac125b1b411d9 Author: Marc Day Date: Thu Oct 24 12:37:40 2013 -0700 Add code to fill corner cells at phys corners...if0 it out, but leave it around for later use Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 3e179dd23ddb5c14d4232f6d98ae5cb7433ec3b9 Author: vince Date: Wed Oct 23 15:54:22 2013 -0700 hopper test. Src/C_BaseLib/DistributionMapping.cpp commit 8ca8c28c5c51ccecb7bea1fd8d170920bfe1794f Author: vince Date: Wed Oct 23 15:14:29 2013 -0700 procname. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 7536fdae3151b43c7d36a0161a2737e3303352bb Author: vince Date: Wed Oct 23 14:51:30 2013 -0700 no report for zero perfmon procs. Src/C_BaseLib/ParallelDescriptor.cpp commit e43b4cfd470ab15eeb9fa27747d61e76b87b8016 Author: vince Date: Wed Oct 23 14:30:38 2013 -0700 hopper fix. Src/C_BaseLib/Profiler.cpp commit e396c403efbad0d00e657ea1400fb63d1e404b5d Author: vince Date: Wed Oct 23 14:19:58 2013 -0700 more proximity mapping. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/Profiler.cpp commit 4a8d665c37f67e07d21255f06c4b450b6d41db8c Author: Ann Almgren Date: Mon Oct 21 09:58:46 2013 -0700 No more DatasetClient.cpp in CMakeList... Src/C_AMRLib/CMakeLists.txt commit 9adfbcc7f69f6f7e5483230b2f35d915d4f49d9e Merge: b6db08b4c 43acee06e Author: vince Date: Fri Oct 18 15:16:25 2013 -0700 Merge branch 'master' into commprof commit 43acee06e0795cf68aca91c64575a33e9191cb8c Author: vince Date: Fri Oct 18 15:12:47 2013 -0700 added arrayview support. Tools/C_mk/Make.defs commit 839c7f3e8a12c6fa9cde1844c61dcfd8f77a2950 Author: vince Date: Fri Oct 18 15:10:50 2013 -0700 added arrayview support. Src/C_AMRLib/DatasetClient.H Src/C_AMRLib/DatasetClient.cpp commit b6db08b4c9193a8b55b80b1b5740c4bedecaae53 Author: vince Date: Tue Oct 15 14:22:50 2013 -0700 more proximity mapping. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit ad5a3b4504cbb64dd035bdc120e21fc4be852178 Merge: e338a51ce 6a51cba9a Author: vince Date: Fri Oct 11 15:12:08 2013 -0700 Merge branch 'master' into commprof commit e338a51ce401786d58f2c1c071add58d0238a9cb Author: vince Date: Thu Oct 10 16:10:41 2013 -0700 helper functions for proximity ranking. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 6a51cba9a2e537c35ff30c879818ec85ba7bdb81 Merge: ab740a0e1 46d89ca34 Author: lijewski Date: Wed Oct 9 13:28:05 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ab740a0e18d37276043a1413297e62cc24c51ce6 Author: lijewski Date: Wed Oct 9 11:02:23 2013 -0700 Added version of contains_nan() and contains_inf() that take an IntVect that gets set to a relevant cell when the routines return true. Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp commit 46d89ca3400bdf46501df2b7a8fd672546de08c1 Merge: c897aabf5 b8cc570a6 Author: Matthew Emmett Date: Wed Oct 9 10:33:45 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c897aabf5431930dcbffd0a6d39d90d4debc6a26 Author: Matthew Emmett Date: Wed Oct 9 10:33:34 2013 -0700 AmrLevel: Add fineRatio. StateData: Remove unused setMidData. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit b8cc570a6c6302ee92e6bd50b5744b09c7ad45da Author: Ann Almgren Date: Tue Oct 8 21:48:18 2013 -0700 Only print the warning (about not using linear interp if ref_ratio = 4 instead of 2) once per solve rather than once per v-cycle. Src/LinearSolvers/F_MG/ml_cc.f90 commit 311e94e3e8fee28387d661b1227c249f038904c6 Author: Ann Almgren Date: Tue Oct 8 12:29:27 2013 -0700 Remove the Tests/LinearSolvers/C_NodalMG directory since we no longer support the code that this tests. Tests/LinearSolvers/C_NodalMG/files.2d Tests/LinearSolvers/C_NodalMG/files.3d Tests/LinearSolvers/C_NodalMG/gt_breaks_27pt Tests/LinearSolvers/C_NodalMG/inputs Tests/LinearSolvers/C_NodalMG/proj.cpp Tests/LinearSolvers/C_NodalMG/test_grids/3d_4_level.grids Tests/LinearSolvers/C_NodalMG/test_grids/gr.11 Tests/LinearSolvers/C_NodalMG/test_grids/gr.15 Tests/LinearSolvers/C_NodalMG/test_grids/gr.16 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19l3 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s2 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s2.4 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s4 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s4.1 Tests/LinearSolvers/C_NodalMG/test_grids/gr.292.11 Tests/LinearSolvers/C_NodalMG/test_grids/gr.292.25 Tests/LinearSolvers/C_NodalMG/test_grids/gr.7 Tests/LinearSolvers/C_NodalMG/test_grids/gr.8 Tests/LinearSolvers/C_NodalMG/test_grids/gr.8a Tests/LinearSolvers/C_NodalMG/test_grids/gr.ann.1 Tests/LinearSolvers/C_NodalMG/test_grids/gr.sstanley.1 Tests/LinearSolvers/C_NodalMG/test_grids/gr0 Tests/LinearSolvers/C_NodalMG/test_grids/gr0a Tests/LinearSolvers/C_NodalMG/test_grids/gr0b Tests/LinearSolvers/C_NodalMG/test_grids/gr1 Tests/LinearSolvers/C_NodalMG/test_grids/gr1mike.thin Tests/LinearSolvers/C_NodalMG/test_grids/gr1rick2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2.0 Tests/LinearSolvers/C_NodalMG/test_grids/gr2.1 Tests/LinearSolvers/C_NodalMG/test_grids/gr2.inf Tests/LinearSolvers/C_NodalMG/test_grids/gr2a2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2a4 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.l0 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.l1 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.l2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p1 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p3 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p4 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p5 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p6 Tests/LinearSolvers/C_NodalMG/test_grids/gr2b Tests/LinearSolvers/C_NodalMG/test_grids/gr2c Tests/LinearSolvers/C_NodalMG/test_grids/gr2cross Tests/LinearSolvers/C_NodalMG/test_grids/gr2d Tests/LinearSolvers/C_NodalMG/test_grids/gr2d2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2d4 Tests/LinearSolvers/C_NodalMG/test_grids/gr2dave Tests/LinearSolvers/C_NodalMG/test_grids/gr2e Tests/LinearSolvers/C_NodalMG/test_grids/gr2f Tests/LinearSolvers/C_NodalMG/test_grids/gr2g Tests/LinearSolvers/C_NodalMG/test_grids/gr2h Tests/LinearSolvers/C_NodalMG/test_grids/gr2mike Tests/LinearSolvers/C_NodalMG/test_grids/gr2mike1 Tests/LinearSolvers/C_NodalMG/test_grids/gr2mike2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2mike3 Tests/LinearSolvers/C_NodalMG/test_grids/gr2r1 Tests/LinearSolvers/C_NodalMG/test_grids/gr2r2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2r3 Tests/LinearSolvers/C_NodalMG/test_grids/gr3.rz Tests/LinearSolvers/C_NodalMG/test_grids/gr3a Tests/LinearSolvers/C_NodalMG/test_grids/gr3ann Tests/LinearSolvers/C_NodalMG/test_grids/gr3ann2 Tests/LinearSolvers/C_NodalMG/test_grids/gr3b Tests/LinearSolvers/C_NodalMG/test_grids/gr3c Tests/LinearSolvers/C_NodalMG/test_grids/gr3mike Tests/LinearSolvers/C_NodalMG/test_grids/gr3mike.3 Tests/LinearSolvers/C_NodalMG/test_grids/gr3rick Tests/LinearSolvers/C_NodalMG/test_grids/gr3rick2 Tests/LinearSolvers/C_NodalMG/test_grids/gr4 Tests/LinearSolvers/C_NodalMG/test_grids/gr4level Tests/LinearSolvers/C_NodalMG/test_grids/gt.32 Tests/LinearSolvers/C_NodalMG/test_grids/gt.bill1 Tests/LinearSolvers/C_NodalMG/test_grids/gt.inputs.3d.spin.grids Tests/LinearSolvers/C_NodalMG/test_grids/gt.jbb.1 Tests/LinearSolvers/C_NodalMG/test_grids/gt.sas Tests/LinearSolvers/C_NodalMG/test_grids/gt.scott.1 Tests/LinearSolvers/C_NodalMG/test_grids/gt.sstanley_2.32 Tests/LinearSolvers/C_NodalMG/test_grids/gt.sstanley_2.64 Tests/LinearSolvers/C_NodalMG/test_grids/gt.sstanley_3 Tests/LinearSolvers/C_NodalMG/test_grids/gt0 Tests/LinearSolvers/C_NodalMG/test_grids/gt010 Tests/LinearSolvers/C_NodalMG/test_grids/gt012 Tests/LinearSolvers/C_NodalMG/test_grids/gt016 Tests/LinearSolvers/C_NodalMG/test_grids/gt05 Tests/LinearSolvers/C_NodalMG/test_grids/gt1 Tests/LinearSolvers/C_NodalMG/test_grids/gt12 Tests/LinearSolvers/C_NodalMG/test_grids/gt12.2 Tests/LinearSolvers/C_NodalMG/test_grids/gt12.3 Tests/LinearSolvers/C_NodalMG/test_grids/gt2 Tests/LinearSolvers/C_NodalMG/test_grids/gt2t1 Tests/LinearSolvers/C_NodalMG/test_grids/gt2t3 Tests/LinearSolvers/C_NodalMG/test_grids/gt2t4 Tests/LinearSolvers/C_NodalMG/test_grids/gt3 Tests/LinearSolvers/C_NodalMG/test_grids/gt3ann Tests/LinearSolvers/C_NodalMG/test_grids/gt3ann2 Tests/LinearSolvers/C_NodalMG/test_grids/gt4 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s2 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s2.4.4 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s2a Tests/LinearSolvers/C_NodalMG/test_grids/gt4s4 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s4.2.4 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s4.4.2 Tests/LinearSolvers/C_NodalMG/test_grids/gt5 Tests/LinearSolvers/C_NodalMG/test_grids/gt5s2 Tests/LinearSolvers/C_NodalMG/test_grids/gt5s4 Tests/LinearSolvers/C_NodalMG/test_grids/gt6 Tests/LinearSolvers/C_NodalMG/test_grids/gt6s Tests/LinearSolvers/C_NodalMG/test_grids/gt6s2 Tests/LinearSolvers/C_NodalMG/test_grids/gt6s4 Tests/LinearSolvers/C_NodalMG/test_grids/gt7a Tests/LinearSolvers/C_NodalMG/test_grids/gt7aa Tests/LinearSolvers/C_NodalMG/test_grids/gt8 Tests/LinearSolvers/C_NodalMG/test_grids/gt8a Tests/LinearSolvers/C_NodalMG/test_grids/gt8b Tests/LinearSolvers/C_NodalMG/test_grids/gt8c Tests/LinearSolvers/C_NodalMG/test_grids/gt8ms2 Tests/LinearSolvers/C_NodalMG/test_grids/gtbig Tests/LinearSolvers/C_NodalMG/test_grids/gtbig2 Tests/LinearSolvers/C_NodalMG/test_grids/gtbig3 Tests/LinearSolvers/C_NodalMG/test_grids/gtbig4 Tests/LinearSolvers/C_NodalMG/test_grids/gtbig5 Tests/LinearSolvers/C_NodalMG/test_grids/gtclearlarge Tests/LinearSolvers/C_NodalMG/test_grids/gtclearsmall Tests/LinearSolvers/C_NodalMG/test_grids/gtgrav2 Tests/LinearSolvers/C_NodalMG/test_grids/gtgrav4 Tests/LinearSolvers/C_NodalMG/test_grids/gtjbb Tests/LinearSolvers/C_NodalMG/test_grids/gtjbb2 Tests/LinearSolvers/C_NodalMG/test_grids/gtpfail Tests/LinearSolvers/C_NodalMG/test_grids/gtrick commit dc1e35566d731727ee57c01f5d1851affb300c91 Author: Ann Almgren Date: Tue Oct 8 12:28:47 2013 -0700 Removing the Src/LinearSolvers/C_NodalMG directory since this code is no longer used by any of the applications. Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/OpenSource.txt Src/LinearSolvers/C_NodalMG/RegType.H Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real2d.2.f Src/LinearSolvers/C_NodalMG/amr_real2d.f Src/LinearSolvers/C_NodalMG/amr_real3d.2.f Src/LinearSolvers/C_NodalMG/amr_real3d.f Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_avg2d.f Src/LinearSolvers/C_NodalMG/hg_avg3d.f Src/LinearSolvers/C_NodalMG/hg_cg.cpp Src/LinearSolvers/C_NodalMG/hg_cg2d.f Src/LinearSolvers/C_NodalMG/hg_cg3d.f Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.f Src/LinearSolvers/C_NodalMG/hg_multi2d_full.f Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.f Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.f Src/LinearSolvers/C_NodalMG/hg_multi3d_full.f Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.f Src/LinearSolvers/C_NodalMG/hg_proj2d.f Src/LinearSolvers/C_NodalMG/hg_proj3d.f Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.H Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit f128d84bd70ef5a4f31ec66220a59455b4dc7c3c Merge: 18a498ebf 0eed263fd Author: Michael Zingale 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 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: 0bed6d2ef 89e87bb77 Author: lijewski Date: Mon Oct 7 16:21:42 2013 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 0bed6d2ef1df803b1da469596f42bd1f99ec6718 Author: lijewski Date: Mon Oct 7 16:20:47 2013 -0700 Don't thread over calls to setPhysBoundaryValues(). It doesn't play well with the Inflow code. Src/C_AMRLib/AmrLevel.cpp commit 89e87bb77edb41881a59dfbece896d1d7feb0e12 Author: Ann Almgren Date: Mon Oct 7 14:13:23 2013 -0700 Put comments in the inputs.3d.nodal.dense and set ba_maxsize = 128 so at first this will have only one grid. Tests/LinearSolvers/F_MG/inputs.3d.nodal.dense commit a7aa21b7e769e4c8e0b5365c11b3d5e5dc426b53 Author: Ann Almgren Date: Mon Oct 7 14:08:11 2013 -0700 Create a new 3d nodal dense smoother -- subroutine nodal_smoother_3d_opt -- that can be used to experiment with optimizations having to do with not storing the stencils. Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit 06782ac54efebee4be74ad85f408011ea7662c67 Author: lijewski Date: Mon Oct 7 13:28:06 2013 -0700 Inputs for nodal dense stencil test. Tests/LinearSolvers/F_MG/inputs.3d.nodal.dense commit 2ab88b31b48d7b6a802db21406b37df17c260fbf Author: Michael Zingale Date: Sun Oct 6 20:38:36 2013 -0400 change the way the defaults are indicated -- now we do a logical and output "[*]" via a merge instead of printing the default value alongside the current value. This is a lot easier to read. Tools/F_scripts/write_probin.py commit 1c957c006aa73a3dd647f95a928259bc13a270f0 Author: Ann Almgren Date: Fri Oct 4 17:04:45 2013 -0700 We can now restart from a plotfile if the appropriate data has been stored in the plotfile. This works for both grid data and particles, but the application must be in charge of making sure it can find the data that it needs. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Particles.H commit 580e8f0e4ff97d4e90ebe44f012301174f5f1780 Author: lijewski Date: Thu Oct 3 14:53:18 2013 -0700 Uses can now choose single -vs- double precision at compile time. The C preprocessor symbol BL_SINGLE_PRECISION_PARTICLES, when defined at compile time causes floating point particle data to be stored as floats instead of the default, which is doubles. Src/C_AMRLib/Particles.H commit ef4db703005dede233fa29317026883245f282d4 Author: lijewski Date: Thu Oct 3 14:27:59 2013 -0700 I'm now appended "single" or "double" to the version string in checkpoint files for particles. This allows me to know how they were written so that I can properly read them in. It thus gives us the ability to decide at compile time whether to use single or double precision for storing floating point data in particles. As of this commit all you have to do is edit Particles.H and change one typedef. To come will be a way to do this when compiling. The default floating-point precision as of this commit is back to double precision. Src/C_AMRLib/Particles.H commit f591bcb40b690fbfb021dd37a6ea83bc5530aae6 Merge: a90db6929 963787a8f Author: Michael Zingale 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 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 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 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 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 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 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 Date: Tue Oct 1 16:27:45 2013 -0700 More work on double -> float conversion. Src/C_AMRLib/Particles.H commit 5fedf8834306e0d4807044f9b4dc96ba2d55be62 Author: lijewski Date: Tue Oct 1 16:18:27 2013 -0700 Some work storing/using real data in particles as float instead of double. Src/C_AMRLib/Particles.H commit 8125a578b873356c8ce6e1c2d627582323f1265e Author: Ann Almgren Date: Tue Oct 1 15:18:38 2013 -0700 This change defines USE_PARTICLES instead of BL_USE_PARTICLES -- this is the flag that is seen in the rest of the code. Tools/CMake/CCSEOptions.cmake commit bea6d1b2afdfa912678c183aa887991423f8be6a Author: Ann Almgren Date: Tue Oct 1 11:12:40 2013 -0700 Add ParticleBoxArray option for AdvectWithUmac. Src/C_AMRLib/Particles.H commit 1163d71b3e5ad8be744d3c596b96a0e7a2ee7d2e Author: Ann Almgren Date: Mon Sep 30 21:36:53 2013 -0700 Must remember to make the particle DistributionMap on restart as well as on initialization -- put that section of code into a new routine, make_particle_dmap, which is called from init and from restart. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 909155c1bf1310f4b0957e8f1de5ba243e5ce5b5 Author: Ann Almgren Date: Mon Sep 30 16:54:56 2013 -0700 Decided we don't need to worry about copy on ghost cells as long as we copy after the temporary mf has completed SumBoundary. Src/C_AMRLib/Particles.H commit a0fa1d54b0777de9e759b3000b2b87e61be2742c Author: Ann Almgren Date: Mon Sep 30 16:38:42 2013 -0700 This version has the working multilevel AssignDensity which allows for particle_grids != grids. Still not sure what to do about ghost cell copies though. Src/C_AMRLib/Particles.H commit 960eea93241a5984459755719b55bf24ccea4f2f Merge: a60870593 5530bdcd6 Author: Ann Almgren Date: Mon Sep 30 12:44:53 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a60870593db1eea3e11a8763fb3f73a52c8e2efb Author: Ann Almgren Date: Mon Sep 30 12:43:14 2013 -0700 Inside addOneParticle, if a particle seems to be on the domain boundary we move it slightly inside. Src/C_AMRLib/Particles.H commit 5530bdcd66511988e5015fa55d8004744a11ce09 Author: Matthew Emmett Date: Mon Sep 30 09:57:36 2013 -0700 Remove MLSDC from BoxLib (moved to RNS). Src/C_AMRLib/MLSDCAmr.H Src/C_AMRLib/MLSDCAmr.cpp Src/C_AMRLib/MLSDCAmrEncap.cpp Src/C_AMRLib/Make.package commit 0cdc484807a6a966ddb0183bf996cb9c833a5221 Author: Matthew Emmett Date: Mon Sep 30 09:54:45 2013 -0700 Add setMidData. Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 510ce4f26db37b0c1c34bc7e9ed92de15db8949d Author: Ann Almgren Date: Mon Sep 30 08:59:27 2013 -0700 Back out latest changes to get this to work again. Src/C_AMRLib/Particles.H commit b515c42bd789d195418c6222d9dbaad8ce2be5c3 Author: Ann Almgren Date: Mon Sep 30 08:50:39 2013 -0700 Allow the particles to live on a different boxarray than the grid data lives -- this is particle_grids as opposed to grids. The default for now is that the boxarrays are identical. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 6956653e20a132b9875ab50327657b8f27749ae1 Author: Weiqun Zhang Date: Fri Sep 27 13:22:47 2013 -0700 optimization of the 5th-order interpolator Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F commit 10a12b95e3bc67b8a2fbb0c456268dec5f957929 Author: Weiqun Zhang Date: Fri Sep 27 11:07:09 2013 -0700 5th-order interpolation in 3D Src/C_AMRLib/INTERP_3D.F commit bd924155e060233fc7f01f70191da13d7941a0ba Merge: 45ed89856 6f553ef12 Author: Ann Almgren Date: Fri Sep 27 08:23:27 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 45ed89856243a7c4d1b2d2a780b241499d107daa Author: Ann Almgren Date: Fri Sep 27 08:22:29 2013 -0700 Modify the test at the end of moveKickDrift so that particles at level 0 flying along at cfl > 1 can leave a grid and not have their velocities and positions correctly updated, but still not get lost entirely. Src/C_AMRLib/Particles.H commit 6f553ef1251fa6eec5eb042ab296e61219af5abb Merge: 5fad865f2 ef1d54d73 Author: Weiqun Zhang Date: Thu Sep 26 22:17:42 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 5fad865f27d9a529c14bc186982787e0d8b3c5fb Author: Weiqun Zhang Date: Thu Sep 26 22:12:29 2013 -0700 added 5th-order interpolation based on quartic polynomial dimension by dimension; so far 1D and 2D are implemented; Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp commit ef1d54d738f858a4fcae202a3b2939c03c2634fa Author: lijewski 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 Date: Thu Sep 26 15:41:53 2013 -0700 Added some verbosity. Src/C_AMRLib/Particles.H commit ff0b75eaeccf344416430f0401363e1739ff9a62 Author: lijewski Date: Thu Sep 26 15:38:42 2013 -0700 Added InitFromBinaryMetaFile(). Src/C_AMRLib/Particles.H commit 178971219322ecb5bf6843601c45ac6498878599 Author: Ann Almgren Date: Thu Sep 26 12:52:02 2013 -0700 Restore DistributionMapping.{H,cpp} to be the same as before the previous commit -- we don't need that extra define after all. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 1f50252d92bb476dc94ab258ccb1ef1544b58904 Author: vince Date: Thu Sep 26 11:16:14 2013 -0700 proximity mapping tests. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.cpp Tools/C_mk/Make.Linux commit 6e19668c2b5aa84b636da059be3642feddb96065 Author: Ann Almgren Date: Thu Sep 26 10:07:47 2013 -0700 Remove left-over print statement when particles left the domain before being periodically shifted back in. Src/C_AMRLib/Particles.cpp commit 8a0c50868aca28827ff8a30f83dda7b16a69cd06 Author: Ann Almgren Date: Thu Sep 26 09:17:24 2013 -0700 Add a new version of DistributionMapping::define which takes an already-made pmap as an argument. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 160a59122b0cc8ed57f55756de8e4e9ca2c6c107 Merge: 7620ebd70 ce172ca1d Author: vince Date: Tue Sep 24 12:44:58 2013 -0700 Merge branch 'master' into commprof commit ce172ca1dc64a418ff43be452caa20c9041db699 Author: Michael Zingale Date: Tue Sep 24 10:07:54 2013 -0400 update Maestro tests Tools/RegressionTesting/Maestro-tests.ini commit e44fc2d85f4f2e1649c7dff2eafe0cd5cec6ce1b Author: Michael Zingale Date: Fri Sep 20 13:50:00 2013 -0400 fix globalAddToExecString Tools/RegressionTesting/testnew.py commit 561bdd52c3b7d80459e940824327d632967ab7ca Author: lijewski Date: Fri Sep 20 09:29:40 2013 -0700 Remove GETPLANE. Src/F_BaseLib/fabio_c.c commit f0dd557d629be2e4b01c3cd1882f086255c46236 Merge: a91c8dc7d 015a2fba1 Author: jbb Date: Thu Sep 19 20:06:27 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a91c8dc7d5ca6d330f8e946611232872d0ab151b Author: jbb Date: Thu Sep 19 20:05:46 2013 -0700 fixed bug in check of uniform mesh Src/LinearSolvers/F_MG/mg.f90 commit 015a2fba1c734b6b2a7a17ab90ff41d83431d4b7 Author: Weiqun Zhang Date: Thu Sep 19 17:12:46 2013 -0700 made the regression testing script write out correct html page in the case variables names contain special characters "<" and ">". Tools/RegressionTesting/testnew.py commit 0d0d4974991c37a5cedb8fefb8603bc6f5206a0d Merge: b72cb6d58 4a8594538 Author: jbb Date: Thu Sep 19 10:47:34 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 4a8594538cb83dd4a7d12a7a983d5bf1c8465077 Merge: d6de81dc3 5edabd632 Author: Marc Day 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 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: 2c7110983 909e626c7 Author: Ann Almgren Date: Wed Sep 18 15:58:36 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 2c71109831c55a590a5233a3b228ef75e7b1d1bb Author: Ann Almgren Date: Wed Sep 18 15:57:35 2013 -0700 Fixed up the case when the domain is not periodic and particles live in the cell next to the domain boundary. Before this wasn't allowed; now if we set the flag "allow_particles_near_boundary" to true then the particles can live in those cells, but the part of their contribution to AssignDensity that falls outside the domain will be ignored. Src/C_AMRLib/Particles.H commit 909e626c7c29a19858a9d7fbcc86e16d0c6f516f Merge: 5e578b8e1 fc2c77a18 Author: lijewski Date: Wed Sep 18 15:20:30 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 5e578b8e1fda27cf8f3c4ae36c302cc6f0383e66 Author: lijewski Date: Wed Sep 18 15:18:10 2013 -0700 Some work on FORT_GETPLANE(). This is needed to implement INFLOW on the F90 side of the house. It's a translation of IAMR/Source/INFLOW/inflow.cpp. It's not done yet as there's an issue with "long" int values. We don't currently use such things, but the offsets into turbulence files in 3D get bigger than can be held in a standard Fortran integer. Src/F_BaseLib/fabio_c.c commit fc2c77a18a90a9d2c67a3aa901116be7f4121d96 Author: Marc Day Date: Wed Sep 18 12:49:45 2013 -0700 up the tagged version num Tools/CMake/BoxLib_Version.cmake commit 6356be7e1aee8da83fbb9e102f8141d74f685e9d Author: lijewski Date: Wed Sep 18 12:46:52 2013 -0700 Changed mpi module name to fboxlib_mpi so not to conflict with system-supplied names. Src/F_BaseLib/parallel.f90 Src/F_BaseLib/pingpong.f90 commit e6983ab620c7cf0f6b84e18a311ddef92bcdafa7 Author: Marc Day Date: Mon Sep 16 16:58:13 2013 -0700 Redo CMake stuff to more properly use command-line options to the cmake command for setting/overriding defaults CMakeLists.txt Tools/CMake/CCSEOptions.cmake Tutorials/MultiGrid_C/CMakeLists.txt commit 35ae2af53a127c38ee3dafd2af74bc24319cace1 Author: Weiqun Zhang Date: Mon Sep 16 09:29:39 2013 -0700 Made AmrLevel::addOneParticle not pure so that classes derived from AmrLevel can be instantiated without implementing addOneParticle. Src/C_AMRLib/AmrLevel.H commit 606e47f3014797e07381ef3653c817283249b560 Merge: 99b38e869 1674226c0 Author: Ann Almgren Date: Fri Sep 13 11:43:29 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 99b38e8691bab67c721c17c29b24f27f1da03102 Author: Ann Almgren Date: Fri Sep 13 11:42:43 2013 -0700 Modify Amr and Particle classes to allow Amr to be defined from an outside class and not to read from inputs file. Also allow particles to be copied in one by one. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 1674226c0b6735cf5812f0274c21da18ac7d8788 Author: lijewski Date: Fri Sep 13 10:04:14 2013 -0700 Added constructors to FabArray and MultiFab that take a DistributionMap. This way folks don't have to do the usual two-step process of creating a MultiFab and then calling define() if they want to specify their own DistributionMap. Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 8ccd5122cde53b9f9746ce15a30b51a6d0adf9c2 Merge: 5cbc021fb 539beb055 Author: Ann Almgren Date: Thu Sep 12 16:00:13 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 5cbc021fb69d8a7bb72b8ec294dfad5c1b78ccef Author: Ann Almgren Date: Thu Sep 12 15:59:54 2013 -0700 Make the minimum physical box size 1.e-8 instead of 1.e-6. Src/C_BaseLib/RealBox.cpp commit 7620ebd70757f693076524e1ffbf8b1b5dbb95f4 Author: vince Date: Thu Sep 12 15:44:17 2013 -0700 procnums and names. Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 539beb0553474dd37152cc3fbccb0eb121062123 Author: Marc Day Date: Thu Sep 12 12:29:08 2013 -0700 Add usage comment, remove debugging note CMakeLists.txt Tools/CMake/InstallManager.cmake Tutorials/MultiGrid_C/CMakeLists.txt commit 2819e118b9213e145d4458d8f8fe044e6d7191a4 Merge: 306eeab74 da4259961 Author: Marc Day 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 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 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 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 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: a112aaf3b fb587de91 Author: Ann Almgren Date: Wed Sep 11 17:19:32 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a112aaf3bf0d43e5c9199ccb485739a01213d25f Author: Ann Almgren Date: Wed Sep 11 17:18:45 2013 -0700 Add versions of init, initialInit and defBaseLevel that take both a BoxArray and a pmap. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit fb587de91f0305b46f04f15c9f9a0f7a013fa5cb Author: Marc Day Date: Wed Sep 11 16:48:49 2013 -0700 Update version file Tools/CMake/BoxLib_Version.cmake commit 38f460235ae7027382fc1c1c7bcb20eae98fb93c Author: Marc Day Date: Wed Sep 11 16:42:55 2013 -0700 ick...more hacking on cmake CMakeLists.txt Tools/CMake/BoxLib_Version.cmake Tools/CMake/InstallManager.cmake commit 475251acb7d1edf6e370ea37068e64209a90ec30 Merge: 21fc6426e c56e36564 Author: Marc Day 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 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: 1d0a6654f 135904384 Author: lijewski Date: Wed Sep 11 15:18:35 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1d0a6654f4211fc7da42cc5031b30043e3087184 Author: lijewski Date: Wed Sep 11 15:17:23 2013 -0700 Added ability to pre-load the distribution mapping cache by simply building a DistributionMapping with a pmap and asking for it to be added to the cache. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 1359043843dce946759141ebfa1edf9e5eca2317 Author: Ann Almgren Date: Wed Sep 11 14:16:02 2013 -0700 Make the first lines of DM/Header in a plotfile be the same as the first lines of DM/Header in a checkpoint file. Src/C_AMRLib/Particles.H commit 68028afe93d2661616c625a435a4e1dd605071a4 Author: Ann Almgren Date: Wed Sep 11 13:07:29 2013 -0700 Clean up Solver.cpp and add contact info for Tulin. Tutorials/AMR_Trilinos_C/README Tutorials/AMR_Trilinos_C/Solver.cpp commit 97aaa120bb070f4f268013a0d18bf35529ac2295 Author: Marc Day Date: Wed Sep 11 10:31:46 2013 -0700 More tweaks to CMake files Src/F_BaseLib/CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt Tools/CMake/CCSEOptions.cmake commit 7ed7f6d13d762e96d33ad0bf11cf34301b19ac17 Author: Marc Day Date: Wed Sep 11 10:16:38 2013 -0700 Add a couple tests to the CCSEOptions to be sure stuff is defined Tools/CMake/CCSEOptions.cmake commit 5f6c46c13c1f84ccc13ad15f655bec1a29a8c1e5 Author: Marc Day Date: Wed Sep 11 09:45:30 2013 -0700 Small mods working with Andreas Src/C_AMRLib/Particles.H Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/FabSet.H commit 31a715c322a21bdfad93641bcd8ad3273b576bd5 Author: Marc Day Date: Wed Sep 11 01:18:03 2013 -0700 CMake install the mod files Src/CMakeLists.txt commit f303baa3773e7d1e90d6c8d8d36b56ffbe06b2fb Author: Marc Day Date: Wed Sep 11 00:41:49 2013 -0700 Start to collect BL_DEFINEs throughout, and set some defaults CMakeLists.txt Tools/CMake/CCSEOptions.cmake commit 241eed3c92d40f9052f2c957952d14707f16602e Author: Marc Day Date: Tue Sep 10 23:56:02 2013 -0700 Add buildInfo.H to install CMakeLists.txt commit f4c238be632bd1ad105f5f1c019d0fe6cdb43f6a Author: Marc Day Date: Tue Sep 10 18:47:50 2013 -0700 Add Particles.cpp and Particles.H to CMakeLists Src/C_AMRLib/CMakeLists.txt commit bd7569a05e174a5b88f8ce584491f4192629f6f8 Author: Marc Day Date: Tue Sep 10 18:12:24 2013 -0700 Consolidate all the CMake-built C++ libs into one using the OBJECT library feature post 2.8.8 CMakeLists.txt Src/CMakeLists.txt Src/C_AMRLib/CMakeLists.txt Src/C_BaseLib/CMakeLists.txt Src/C_BoundaryLib/CMakeLists.txt Src/LinearSolvers/C_CellMG/CMakeLists.txt Src/LinearSolvers/C_TensorMG/CMakeLists.txt Src/LinearSolvers/C_to_F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt commit 0c26d27df85b83df2fc1f4da90db4dd22f608240 Merge: 3f8312d59 77cba4079 Author: Marc Day Date: Tue Sep 10 15:31:01 2013 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 77cba407956bb3bea68db004745a6b2260ce4de3 Merge: 6e0d0e484 7cc961dc4 Author: lijewski Date: Tue Sep 10 14:57:12 2013 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 6e0d0e484fb8c588a87aeb923f75d0c07f35fd56 Author: lijewski Date: Tue Sep 10 14:56:26 2013 -0700 Some cleanup using latest gnu compiler on edison. Src/F_BaseLib/boxarray_f.f90 Src/F_BaseLib/cluster_f.f90 commit 3f8312d593f6f2d7fde71d65f01875c2a4a15049 Author: Marc Day Date: Tue Sep 10 14:26:45 2013 -0700 Working cmake a bit...in progress CMakeLists.txt Src/CMakeLists.txt Src/LinearSolvers/C_TensorMG/CMakeLists.txt Tools/CMake/CCSEOptions.cmake commit 7cc961dc4cf66990ae6d40c8eb4d3417c5255e2b Author: Ann Almgren Date: Tue Sep 10 13:23:33 2013 -0700 Add comment about RHS and SOLN and visualizing these. Tutorials/AMR_Trilinos_C/README commit d8363ad054587ef86fb3e773e9f0e10580102d7b Merge: 86de1b584 03edb7ee3 Author: Ann Almgren Date: Tue Sep 10 13:21:11 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 86de1b584f8669d809bb03186b3a2aa3a9615e11 Author: Ann Almgren Date: Tue Sep 10 13:20:48 2013 -0700 Tutorial example of how to call a Trilinos solver (Epetra) from a BoxLib C++ code. Tutorials/AMR_Trilinos_C/GNUmakefile Tutorials/AMR_Trilinos_C/Make.package Tutorials/AMR_Trilinos_C/README Tutorials/AMR_Trilinos_C/Solver.H Tutorials/AMR_Trilinos_C/Solver.cpp Tutorials/AMR_Trilinos_C/SolverBoundary.cpp Tutorials/AMR_Trilinos_C/driver.cpp Tutorials/AMR_Trilinos_C/inputs Tutorials/AMR_Trilinos_C/writePlotFile.H Tutorials/AMR_Trilinos_C/writePlotFile.cpp commit 03edb7ee3773370acda82c00e6850a6c812378a9 Author: Weiqun Zhang 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 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 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 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 Date: Fri Sep 6 13:01:41 2013 -0400 find the / detection fextract.f90 commit a98683be907c9a16c2029f07d0a868aabc2ad615 Author: lijewski Date: Wed Sep 4 15:15:02 2013 -0700 Reduced the amount of data transferred via MPI in the Reflux() routines to the bare minimum. Previously Cy noticed that we "ship" more data than needed. We were sending a full FluxRegister boundary data set whenever some coarse FAB needed any of its data. This was due to the difficulty of figuring out intersections of cell-centered entities with face-centered ones. I've checked it with HyperCLaw and LMC. We'll see if the regression tests turn up anything. Src/C_AMRLib/FluxRegister.cpp commit ddd46eb0f139a0d031830b1e76cd00049c1f90a6 Author: vince Date: Tue Sep 3 14:04:07 2013 -0700 added interface callable from f90. Src/C_BaseLib/BLProfiler_F.f Src/C_BaseLib/Make.package Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit e24505cd767723b8e53221c8acc55fdbaad27e5b Author: Ann Almgren Date: Fri Aug 30 12:26:30 2013 -0700 Add interface to estTimeStep in Particles.H that doesn't take "a" Src/C_AMRLib/Particles.H commit db44236d373e59edbf86d584cd3584829342ff19 Author: lijewski Date: Fri Aug 30 08:23:29 2013 -0700 Minor bug fix. Wasn't properly indicating "good" failure of CABiCGStab back to the MG solver when we want to do additional smooths. I noticed this when a case I was running was doing additional bottom smooths in the BiCG case but was not in the CABiCG case. Curiously, in that case, both the CiCG and the CABiCG MG solves converged in the same number of iterations. The additional smooths done when the BiCG didn't solve the bottom problem to the requested precision, didn't do much of anything, except waste time. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit a6f9fa646c2c5fe5f6f77e0b93fb5091256c3676 Merge: 6b11003d5 d275a9770 Author: Marc Day 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 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 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 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 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 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 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 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 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 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 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 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: 44eb1480b 88bde8dd8 Author: vince Date: Thu Aug 22 12:41:25 2013 -0700 Merge branch 'master' into commprof commit 88bde8dd85518effb256312164ada78daf47cebc Author: Matthew Emmett Date: Tue Aug 20 14:59:28 2013 -0700 Make regrid virtual, add InitAmr routine to avoid repetition. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 44eb1480b0be84cf5716892ec38b374afee8c8f7 Author: vince Date: Fri Aug 16 15:51:16 2013 -0700 more in-situ, on/off, noprof, prof, commprof. Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 93cfaaa2f0eaccfa2a6e8849283d9b92f9a4ac89 Author: Jonathan Wang Date: Fri Aug 16 10:38:43 2013 -0700 Changed REaDME Tutorials/MultiGrid_F/README commit f8b7e88e65ba05f8034eb8003b4fcca9f7518ef3 Author: Jonathan Wang Date: Fri Aug 16 10:37:50 2013 -0700 Added 3d inputs files Tutorials/MultiGrid_F/inputs_fmg_lin_3d Tutorials/MultiGrid_F/inputs_fmg_pc_3d Tutorials/MultiGrid_F/inputs_v_lin_3d Tutorials/MultiGrid_F/inputs_v_pc_3d commit 325ff3aa1217cf2fe680ca702cd99021e2ee110b Author: vince Date: Thu Aug 15 14:55:11 2013 -0700 more in-situ support. Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp Src/C_BaseLib/ccse-mpi.H commit e27d900962fef19943c481ff960e04c97e905a1f Merge: 78bafd9dc d732127f9 Author: Jonathan Wang Date: Thu Aug 15 13:16:58 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 78bafd9dc40a56a8c4a2e32ab3b8ad5c881073cd Author: Jonathan Wang Date: Thu Aug 15 13:16:05 2013 -0700 Remove executables; added parallel_IOProcessor to fmg_cycle.f90 Tutorials/MultiGrid_F/fmg_cycle.f90 Tutorials/MultiGrid_F/main.Linux.gfortran.exe Tutorials/MultiGrid_F/main.Linux.gfortran.mpi.exe commit d732127f9df80edb26d0bb7ac43cf9c910d9590d Author: Ann Almgren Date: Thu Aug 15 11:13:34 2013 -0700 Only print memory stats if we set memory_verbose = .true. Tutorials/MultiGrid_F/main.f90 commit f9638da29b903dab35c923827ebe597c73cb3ae1 Author: Ann Almgren Date: Thu Aug 15 11:08:41 2013 -0700 1) Don't want to have executables in the repo. 2) Don't need GPackage.mak since the files are listed in the GNUmakefile. Tutorials/MultiGrid_F/GNUmakefile Tutorials/MultiGrid_F/GPackage.mak Tutorials/MultiGrid_F/main.Linux.gfortran.exe Tutorials/MultiGrid_F/main.Linux.gfortran.mpi.exe commit c1e78af163733b10a873c6cd0f3e178c298e0345 Merge: 6641ec7d0 dd9f03060 Author: Jonathan Wang Date: Thu Aug 15 11:03:39 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 6641ec7d06c2fe6c1228510c463a470838700b54 Author: Ann Almgren Date: Thu Aug 15 11:01:32 2013 -0700 New Tutorial for fortran 90, multigrid, Jonathan Tutorials/MultiGrid_F/GNUmakefile Tutorials/MultiGrid_F/GPackage.mak Tutorials/MultiGrid_F/README Tutorials/MultiGrid_F/constants.f90 Tutorials/MultiGrid_F/cycle_tower.f90 Tutorials/MultiGrid_F/fmg_cycle.f90 Tutorials/MultiGrid_F/init_coeffs.f90 Tutorials/MultiGrid_F/init_rhs.f90 Tutorials/MultiGrid_F/inputs_fmg_lin_2d Tutorials/MultiGrid_F/inputs_fmg_pc_2d Tutorials/MultiGrid_F/inputs_v_lin_2d Tutorials/MultiGrid_F/inputs_v_pc_2d Tutorials/MultiGrid_F/main.Linux.gfortran.exe 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 Date: Wed Aug 14 09:52:40 2013 -0700 and an mpilib.... Tools/F_mk/GMakeMPI.mak commit b8970d804517aa12a5141ea074631541bfb51f75 Author: vince Date: Wed Aug 14 09:48:54 2013 -0700 and for fortran. Tools/F_mk/GMakeMPI.mak commit b2c1d2e3e354588baa82518c54473f3c99c9cdfb Author: vince Date: Wed Aug 14 09:45:00 2013 -0700 fix for gigan. Tools/C_mk/Make.mpi commit 47abfaa1a89f7debdd3f2b6284929e9c60e2136a Merge: 3802df5d9 001a1039a Author: vince Date: Thu Aug 8 15:06:42 2013 -0700 Merge branch 'master' into commprof commit 3802df5d9356b62986d032345c08d6c3c6eb4b6e Author: vince Date: Thu Aug 8 12:48:40 2013 -0700 working version of in-situ mpi process for dynamic optimization. the process doesn't do much yet, just rides along. not yet tested with the finalize function stack not empty. Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 001a1039aa97bc1af99d668a282812d88d6aaa8b Author: lijewski Date: Wed Aug 7 10:41:02 2013 -0700 Removed the qaxpy() stuff. It didn't appear to work properly. Not a big deal anyway. The dots() and sums() are the important stuff. Now to see if it makes any difference on real problems in parallel. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit e5cff7835f97d7675652cd528ba910634bdd96d5 Author: lijewski Date: Tue Aug 6 14:33:05 2013 -0700 In qsotxy() do the parallel reduction in quad precision by sending all the partial sums to the IO processor and having it do the sum in quad precision and then broadcast it back to the other processors. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit cea0fab7ebac08b7cf9782036bfc13951a9e6c37 Author: lijewski Date: Tue Aug 6 13:57:33 2013 -0700 Some code rearrangement to get XBLAS & non-XBLAS code to coexist. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit bb474d0505c9746cbd7cacbe3e08202a2e439bcd Author: lijewski Date: Tue Aug 6 13:42:48 2013 -0700 Added qdotxy(). Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 8902719bb281aba84ae1ea0ccb7c7c6afc0abdd1 Author: lijewski Date: Tue Aug 6 12:31:13 2013 -0700 Some work on adding a version of CABiCGStab that uses the quad precision routines from XBLAS. It's disabled at the moment so it shouldn't affect anyone. My plan is to see if a more accurate bottom solver can solve some problems with fewer iterations. It may also be the case that with a more accurate bottom solver we can up the max "S" in the CABiCGStab from 4 -> 8 or somesuch. Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 7c801bba2b708e95d770ad058e4f48e1bf2f4ace Author: lijewski Date: Mon Aug 5 15:02:10 2013 -0700 Some code rearrangement to make some multi-level testing I'm doing easier. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 660b1a179ea51a0e53a6b17756cd1ea9b65366f3 Author: lijewski Date: Mon Aug 5 14:59:49 2013 -0700 Checked in some code that builds cfine in the cfine -> fine multilevel prolongation routines with one grow cell so that the interpolation doesn't have to do piecewise-constant interp on the grid boundaries. It's disable for now until I do more testing. Also added similar code for the nodal multi-level prolongate. Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 63d775ddcc7d6d0d0af135ef0885ec0860ca3d88 Author: lijewski Date: Mon Aug 5 12:46:50 2013 -0700 Make lininerp the default for cell-centered interpolators. Src/LinearSolvers/F_MG/mg_tower.f90 commit 217c63b93f4a0461be7d9c3d6d3b9a4810ae67a2 Author: lijewski Date: Mon Aug 5 11:41:15 2013 -0700 Just a little code rearrangement. Src/LinearSolvers/F_MG/mg.f90 commit 40ef685b98f9a1d61c418c09ef5b715fabf5796b Author: lijewski Date: Mon Aug 5 11:22:06 2013 -0700 Changed how I impose BCs for #D CC interpolators. Src/LinearSolvers/F_MG/mg.f90 commit 642fe94b6358ba86c20ef1dd8246cbd3f4d3e4b7 Author: lijewski Date: Mon Aug 5 09:50:38 2013 -0700 Changed how I impose 2D BCs for CC interpolators. Src/LinearSolvers/F_MG/mg.f90 commit 52f0bd84d605a9080d90b8370e7d1c4461b60706 Author: lijewski Date: Thu Aug 1 15:22:05 2013 -0700 Some code rearrangement. Put the lininterp pys BC stuff into their own routines. Src/LinearSolvers/F_MG/mg.f90 commit 1a6bade001e25aa1708d60f762ed64db4707e72a Author: lijewski Date: Thu Aug 1 14:08:32 2013 -0700 Some work on edges & corners for 3D lininterp. Src/LinearSolvers/F_MG/mg.f90 commit 28c5715e8e88ac7348dd65feb866eddedf032eeb Author: lijewski Date: Thu Aug 1 10:26:51 2013 -0700 Work on getting corners right for 2D interp. Still got to do corners & edges for 3D. I'm checking this stuff in with the lininterp defaulting to FALSE. I want to get it pushed to the repo before I get too ahead of myself. Soon we'll want to default to lininterp but I'm not yet ready. Src/LinearSolvers/F_MG/mg.f90 commit 3c2a83aa55f16b06b22681151d6a8b437b5a5b1e Author: lijewski Date: Thu Aug 1 09:20:42 2013 -0700 Can now set linear or piecewise constant on command line or inputs file. Tests/LinearSolvers/F_MG/wrapper.f90 commit 356ca7291d3bb37899968c7c4666270742fc1ad2 Author: lijewski Date: Thu Aug 1 08:59:51 2013 -0700 mg tower now takes a "ptype" and we can set it on the command line or inputs file. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit f375ef92a90a6725095e129ceb2904c209c4bb3d Author: lijewski Date: Thu Aug 1 08:06:49 2013 -0700 Added phys BCs to mg tower. Need'm to get BCs for lininterp. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 commit 419e49501d44edd18c07de271924bdfbbdd36258 Author: lijewski Date: Wed Jul 31 13:30:25 2013 -0700 Added use_lininterp to mg_tower, defaulting to false. In mg_tower_build, if not passed as an argument, set it to true for 3D. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 04836f40290547005b4cee45cef1ad32f107420b Author: lijewski Date: Wed Jul 31 13:29:46 2013 -0700 Removed a reference to ml_cc_prolongation which isn't called from here. Src/LinearSolvers/F_MG/cc_applyop.f90 commit 4cbc69a5d903430c161a926ea05258effd03e809 Author: lijewski Date: Wed Jul 31 10:35:50 2013 -0700 Consolidated where all the various parameters for prolongaton are set. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit e0e55541b4972e41817df08acb20e51087d330ba Author: lijewski Date: Tue Jul 30 17:04:31 2013 -0700 Fixed a calling sequence bug I recently introduced. Made the calling sequences for PC on linterp look like the stuff in mg.f90. Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 2aacddc05d75929b9c208db24f7ce072c68d3fd5 Author: lijewski Date: Tue Jul 30 16:56:16 2013 -0700 A little cleanup. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit feccdf0061edcc1f59433cdb783eefe8d0533e14 Author: lijewski Date: Tue Jul 30 16:09:51 2013 -0700 Some code rearrangement in mg_tower_prolongation. We should think about making linear interp the default for cell-centered. Src/LinearSolvers/F_MG/mg.f90 commit e983a7c7a430692610b463214001c0c42cf408d3 Author: lijewski Date: Tue Jul 30 15:55:21 2013 -0700 Changed the cell-centered lininterp routines to use ghost cells or not depending on how they're called. If the coarse fab has one grow cell it will use it, otherwise it'll use PC interp on the face cells and linear interp on the interior. Moved the setting of cc_ptype and nodal_cubic into mg_tower_prolongation. My testing showed that lininterp is a benefit, but only if you do it in both the F and V-cycles. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 953784b78df701e9cfef981e9896711e7b4a9d3e Author: lijewski Date: Tue Jul 30 14:55:45 2013 -0700 Bug fix. Src/LinearSolvers/F_MG/mg.f90 commit b9b2bd8c0c93cecacca4da03602ed9524e044f24 Author: lijewski Date: Tue Jul 30 13:45:54 2013 -0700 Added some commented out debugging code. Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 41e6de9662db42c11ae776b98f9c5ae11d194fef Author: lijewski Date: Tue Jul 30 13:36:14 2013 -0700 Tricubic interpolation also doesn't assume it has ghost cells. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 2bbc0be66ca6424e629c3bcc1e7b4bc1a4f383a6 Author: lijewski Date: Tue Jul 30 13:30:06 2013 -0700 The bicubic will now call linear interp if it doesn't have enough grow cells, and then call itself on the interior. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit e00a6e5a1b5f89a3c7bcdb597f46ac822e1fe4b9 Author: lijewski Date: Tue Jul 30 11:12:13 2013 -0700 Separated out the [bi,tri] cubic nodal prolongation stuff into own functions. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 23ccee4f498606ae2750fa336ead802bbeae2ee3 Author: lijewski Date: Mon Jul 29 15:34:38 2013 -0700 Added some debugging code. Src/LinearSolvers/F_MG/ml_nd.f90 commit 64b85dc81f5153c98cf18c77e06a1285513b59d3 Author: lijewski Date: Mon Jul 29 15:33:44 2013 -0700 mg.cycle_type is now ParmParse'd so we can pass it to F90 MG. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit a12f017a97228aceee6191dce8a59c0542f72dcd Author: lijewski Date: Mon Jul 29 15:33:12 2013 -0700 Print out cycle_type when outputting settngs. Src/LinearSolvers/F_MG/mg.f90 commit 2f1914ddf8d60127ee8e954fbb06c4624c67f788 Author: lijewski Date: Mon Jul 29 12:29:39 2013 -0700 Some cleanup. Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit 160ce7630e9ed22534afc9fa694bfe881351f643 Author: lijewski Date: Fri Jul 26 17:38:49 2013 -0700 I "think" the tricubic interpolators are working. Still got more testing to do though. Checking'm in so I don't lose'm over the weekend. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 78b2d5fbfbee2fc2bca5a3028075c1dcff3d6f3b Author: lijewski Date: Fri Jul 26 17:14:26 2013 -0700 bicubic wasn't quite right on high nodes. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 8c091e47affba52a9c5d6a6a6f1a5cc010181b8c Author: lijewski Date: Fri Jul 26 16:56:51 2013 -0700 More work on tricubic. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 commit a68873b39bb0af2c718b56ba46530dc051306463 Author: lijewski 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 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 Date: Fri Jul 26 15:25:39 2013 -0700 Removed some divides. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit d4bab1cac66356d34af9ef1b15e093790c924e52 Author: lijewski Date: Fri Jul 26 14:44:56 2013 -0700 Merged back in specialized unrolled PC interpolators for ir=2. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit f3d783c3586d27639394aab28f93dcbee67de014 Merge: b744b6e48 a94302267 Author: lijewski Date: Fri Jul 26 14:22:54 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit b744b6e4855e9786c2c9457857b53ebc109830ed Author: lijewski Date: Fri Jul 26 14:15:27 2013 -0700 The multi-level solves now have the ability to call either the piecewise constant or linear prolongators, just like in the multigrid code proper. Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 724ed423e488dea769f958102ebc3fa1e6d16e48 Author: lijewski Date: Fri Jul 26 14:01:46 2013 -0700 Made the multigrid and multi-level solves both call the same piecewise constant cell-centered prolongators. Used the interface of the multi-level solves and integrated those into the multigrid ones. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit a94302267f7b938d838c86b55da424501907d062 Author: vince Date: Fri Jul 26 10:32:03 2013 -0700 fix for intel on gimantis. Tools/C_mk/Make.defs commit 7ae3cd77a78540b40df143185ed2d17b84a0d650 Merge: 840d2a325 f6f6c8478 Author: lijewski Date: Thu Jul 25 15:28:11 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 840d2a32558d6cd4ef41a47f513414cb86d50c71 Author: lijewski Date: Thu Jul 25 15:25:56 2013 -0700 Checked in specialized nodal_prolongation_2d(). This mirrors the 3D one in that it minimized the number of arithmetic operations. It was my starting point for developing the bicubic. Might as well use it when ir=2. It'll be faster, but both it and the 3D version may produce slightly different numbers due to floating point roundoff compared to the more general versions. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 65aaac7538828bb7cf2bb25cd80f39a15ba833c6 Author: lijewski Date: Thu Jul 25 15:11:47 2013 -0700 Specialized version of nodal_prolongation_3d that assumes ir=2. It minimizes the number of arithmetic operations and doesn't need a temporary allocatable array. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 401eda9502f1de648431912be354dab40aa3e3da Author: lijewski Date: Thu Jul 25 14:45:40 2013 -0700 Got bicubic working again (but checked in disabled). Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 4c54023e4896d174c0ccb6214909c8d6b48ddde2 Author: lijewski Date: Thu Jul 25 12:30:19 2013 -0700 We now use the nodal prolongators in mg_prolongate. Got to do the same for cell-centered. Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 86dbe528fcb27e47da213d1d5e51cd0d4b1dc940 Author: lijewski Date: Thu Jul 25 11:18:25 2013 -0700 Rewrote interfaces to nodal prolongation routines. I want to call the routines in mg_prolongation in ml_prolongation. No need to have duplicated routines lying around. I like to see if bicubic has any effect in 2D multi-level solves too. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 commit f6f6c84784ce1a689f49794faaebc648489dd9a7 Author: Matthew Emmett Date: Thu Jul 25 10:40:16 2013 -0700 MLSDC: Add multi-level SDC files (work in progress). Src/C_AMRLib/MLSDCAmr.H Src/C_AMRLib/MLSDCAmr.cpp Src/C_AMRLib/MLSDCAmrEncap.cpp Src/C_AMRLib/Make.package Tutorials/.gitignore Tutorials/AMR_Advection_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Advection_C/Source/main.cpp commit 0299238ac61b3a90a8697c9ac2fc083ebbea8097 Author: lijewski Date: Wed Jul 24 17:08:40 2013 -0700 Had a bug in how cc() was dimensioned in nodal progate 3D. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 commit d72fb9a56e39ab01764d4b69c9a3a74de80bfa1c Author: lijewski Date: Wed Jul 24 16:47:26 2013 -0700 Implemented classic #D full-weighting restriction. Src/LinearSolvers/F_MG/nodal_restriction.f90 commit 489a3fcbe1cd223900704727c45b43dcb9fc50c2 Author: lijewski 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 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 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 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 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 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 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 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 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 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: d94495a7a 12633de05 Author: lijewski Date: Tue Jul 23 10:05:46 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 12633de0560fdf0ab0894c83c19e5ceacfa658d7 Author: Ann Almgren Date: Mon Jul 22 12:37:15 2013 -0700 Add new file cc_edge_coeffs.f90 Tests/LinearSolvers/F_MG/GNUmakefile commit 438616f07fbc74cd0043b6a419d001221796e36a Author: Ann Almgren Date: Mon Jul 22 11:48:38 2013 -0700 We now have coeffs_type = 0: constant coefficients ( = 1) coeffs_type = 1: variable coefficients in [1,11] coeffs_type = 2: variable coefficients in [1,101] Tests/LinearSolvers/F_MG/cc_edge_coeffs.f90 commit 896a0273cdb0d567c062413f2cc969b2593d957b Author: Michael Zingale Date: Mon Jul 22 14:19:57 2013 -0400 squash some compiler warnings: lwb(), upb(), and get_dx() all return arrays of the actual dimensionality rather than MAX_SPACEDIM. This was picked up by the debug flags, but there is no real memory issue here. fextract.f90 commit 8c7d5d3a1d5832789edd7ce43cc285e923c4e1cc Author: Ann Almgren Date: Mon Jul 22 10:36:54 2013 -0700 Change the default value of nub from 10 to 0. This is the number of smooths that are automatically done after a CG or BiCG bottom solve has reduced the residual by the requested orders of magnitude. In theory we shouldn't need to do any relaxations here, but one can always set it in the inputs file to 10 or higher if needed. Src/LinearSolvers/F_MG/mg_tower.f90 commit 477b7222a90013c423ff12fd0483bd3b71cb384f Author: Ann Almgren Date: Sun Jul 21 07:09:22 2013 -0700 If you set coeffs_type = 1 now you get variable coefficients for the solve -- currently they vary by about 1:100. Tests/LinearSolvers/F_MG/cc_edge_coeffs.f90 Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/test_script Tests/LinearSolvers/F_MG/wrapper.f90 commit d94495a7a198624a9149331041e58b1fcd39d5b1 Author: lijewski Date: Sat Jul 20 21:35:21 2013 -0700 Added specialized versions of pc interp & restrict operators in 2D & 3D for ir==2. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit cb151fc25dd0b92e0fbd1222974141700146b215 Author: lijewski Date: Sat Jul 20 21:34:08 2013 -0700 Added specialized versions of pc interp operators in 2D & 3D for ir==2. Src/LinearSolvers/F_MG/cc_restriction.f90 commit 882d3755ee061ec0033f1f01c1387cc587130848 Author: lijewski Date: Fri Jul 19 17:07:08 2013 -0700 Removed the need for a fill_boundary on prolongation. The linear interpolators do PC interp on faces & linear on interior. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 9009890e22bf1dc38e22f70710436d12daa28d9f Author: lijewski Date: Fri Jul 19 14:52:44 2013 -0700 Little more cleanup. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit f248f79ab22d8a4092e1d504de30ac5b55af183c Author: lijewski Date: Fri Jul 19 13:45:05 2013 -0700 Some cleanup of new linear prolongation operators. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit bbfeb862ef57dd3c5df7e65253d002ad9764ebbc Author: lijewski Date: Fri Jul 19 12:04:18 2013 -0700 Removed unnecessary fill_bounary() in special bottom solver. Src/LinearSolvers/F_MG/mg.f90 commit ea9200968c41e8ea6061971a8598d1e5a072af05 Author: lijewski Date: Fri Jul 19 11:14:05 2013 -0700 Removed some unnecessary neumann stuff from 1D nodal restriction. Src/LinearSolvers/F_MG/nodal_restriction.f90 commit e6c99fceaf50545b32aa9b9a1afe35ae19ddd078 Merge: 7fe3c4c18 a5a470571 Author: Ann Almgren Date: Fri Jul 19 10:45:51 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 7fe3c4c1843a797c47a4d34e53796cfe9d3bff62 Author: jmwang214 Date: Fri Jul 19 10:44:28 2013 -0700 Add random nmber RHS for Tests/LinearSolvers/F_MG. Tests/LinearSolvers/F_MG/cc_rhs.f90 commit a5a470571ef9b200095f35666030b58abaabf462 Author: lijewski Date: Fri Jul 19 10:28:53 2013 -0700 Added optional argument "eps" to mg_tower_bottom_solver(). I want to test the effect of bottom solver tolerances on the F cycle. Src/LinearSolvers/F_MG/mg.f90 commit 321516692171b1020e78fb4ae346466019cb70f1 Author: lijewski Date: Fri Jul 19 10:21:44 2013 -0700 Some cleanup. Removed unnecessary mg_defect() calls from fmg_cycle. Removed bl_timer routines from mg_tower. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 commit b7dd2b75e3b787fddaa347b8a9f17a1607bbc753 Author: Ann Almgren Date: Thu Jul 18 15:59:39 2013 -0700 Add inputs for the new problem with Dirichlet bc's Tests/LinearSolvers/F_MG/inputs.2d.fcycle.dir Tests/LinearSolvers/F_MG/inputs.2d.vcycle.dir Tests/LinearSolvers/F_MG/inputs.3d.fcycle.dir Tests/LinearSolvers/F_MG/inputs.3d.vcycle.dir commit b1a802a8df6ed5cb552abf7566e9e130e18e9418 Author: Ann Almgren Date: Thu Jul 18 15:58:34 2013 -0700 Add test problem where we start with exact phi, compute the Laplacian, then use that as the RHS. This works with Dirichlet bc's. Tests/LinearSolvers/F_MG/cc_rhs.f90 Tests/LinearSolvers/F_MG/test_dir commit fac7171aa1cf6c04870dc1f82857e80abc9fd59e Author: Ann Almgren Date: Thu Jul 18 15:56:48 2013 -0700 Add options for linear interpolation in 2d and 3d. Currently the linear only works for ref_ratio = 2. Default is still to use piecewise constant so this shouldn't change anything. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 commit f47a0731728f2512b2adee9a2a668a9a2fb505cb Author: Ann Almgren Date: Thu Jul 18 14:06:25 2013 -0700 Fix up this code so it is easier to run different test problems, with different rhs or using F- vs V-cycle Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/cc_rhs.f90 Tests/LinearSolvers/F_MG/inputs Tests/LinearSolvers/F_MG/inputs.2d.fcycle Tests/LinearSolvers/F_MG/inputs.2d.vcycle Tests/LinearSolvers/F_MG/inputs.3d.fcycle Tests/LinearSolvers/F_MG/inputs.3d.vcycle Tests/LinearSolvers/F_MG/test_script Tests/LinearSolvers/F_MG/wrapper.f90 commit 9ac40b68057b4dc5c184460219696a86fe04ffb0 Author: Ann Almgren Date: Thu Jul 18 13:10:32 2013 -0700 Separate out the rhs routines from nodal_multi.f90 and cc_multi.f90 Tests/LinearSolvers/F_MG/GNUmakefile Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/cc_rhs.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/nodal_rhs.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 19576081fb0b3b462ec7d0516b1a1fee1d0350ba Merge: aeb277324 7bf6bfd49 Author: Michael Zingale 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 Date: Wed Jul 17 08:54:11 2013 -0400 add FIVE3RD Src/F_BaseLib/bl_constants.f90 commit 7bf6bfd4937afeff9c6350f5d314e7be69c760fa Author: lijewski Date: Tue Jul 16 15:08:15 2013 -0700 Nodal FMG cycle now seems to be working. At least it takes no more cycles than does V-cycle. Src/LinearSolvers/F_MG/mg.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 182afceec7ef80b8a1893383889db2c569a90f90 Author: Weiqun Zhang Date: Tue Jul 16 10:06:28 2013 -0700 omega is no longer part of mg_tower Tutorials/HeatEquation_EX5_F/advance.f90 commit 93bb923fe7843c8c67fb9b374a74ccc0938f83d5 Author: Ann Almgren Date: Mon Jul 15 15:32:49 2013 -0700 Add timer stuff to f_cycle. Src/LinearSolvers/F_MG/mg.f90 commit 0577a802d2c8aaa11d34b0023f8f700b9ecdb891 Author: Ann Almgren Date: Mon Jul 15 15:30:57 2013 -0700 Remove unused nodal_flag in fmg_cycle. Src/LinearSolvers/F_MG/mg.f90 commit 4809d1651451e34268f188404b82b2e731967a77 Author: lijewski Date: Mon Jul 15 14:54:23 2013 -0700 Removed the GS_LEX smoother stuff. Never used. Just use GSRB. Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 commit 7a76e3b900ba28ef7c8efc6204a9515e553d7a88 Author: lijewski Date: Mon Jul 15 14:37:43 2013 -0700 Omega is no longer a part of the mg_tower. Nor is omega passed to the smoother routines. The smoother routines now use their own omega. Also removed the unused lgs_* smoother routines added by Chuck long ago. Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit fcc9754c0ec3eabbbdafe771c465961e591437d3 Author: lijewski Date: Mon Jul 15 13:43:20 2013 -0700 Only set mgt%face_type if nodal. Src/LinearSolvers/F_MG/mg.f90 commit 4e2afe6241778a3798fa6bddab6bc4e67e52e67f Author: lijewski Date: Mon Jul 15 13:22:28 2013 -0700 Skewed stuff. Src/LinearSolvers/F_MG/mg_tower_smoother.f90 commit 56ab461ce41bec8900a22b381898b3bf7489d3d9 Author: lijewski Date: Mon Jul 15 13:21:43 2013 -0700 Only build mgt%skewed and mgt%skewed_not_set if cell-centered. Src/LinearSolvers/F_MG/mg.f90 commit f4fb330d250e2a804a768838e666e608e94fe402 Author: lijewski 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 Date: Mon Jul 15 12:11:37 2013 -0700 Added --cycle_type. Tests/LinearSolvers/F_MG/wrapper.f90 commit c73e1db6ec693d5b7351584a0b813908a9696476 Author: vince Date: Mon Jul 15 11:41:51 2013 -0700 spacing. Src/C_BaseLib/Profiler.cpp commit a6f3fd4ca01b5293fc800942487f53ca263e49c5 Author: vince Date: Mon Jul 15 10:46:01 2013 -0700 optimized nametags. Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 32f9d6a1025bb8c0df88d63de7eafe33fead5d24 Author: Weiqun Zhang Date: Thu Jul 11 07:42:26 2013 -0700 updated some tests due to the removal of gamma from mg_tower_build interface Tests/LinearSolvers/F_MG/wrapper.f90 Tutorials/HeatEquation_EX5_F/advance.f90 commit 4d3be1fe98f254628b1f5d1ee7ca159096074d97 Author: ajnonaka 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 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 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 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 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 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 Date: Mon Jul 8 15:52:40 2013 -0700 Declare mgt%visited. Src/LinearSolvers/F_MG/mg_tower.f90 commit b7381559b2455abb2c0b590d99ed3acb5f698a51 Author: Ann Almgren Date: Mon Jul 8 15:52:27 2013 -0700 Try to fix the logic for the F-cycle. Src/LinearSolvers/F_MG/mg.f90 commit 53e05eb7d845a5983cd0f100171608d46f10b0c2 Merge: 58b5bbb3c a8aed6002 Author: Ann Almgren Date: Mon Jul 8 13:34:06 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a8aed6002f7d9cd9e0c5b2981239c5b26d579c86 Author: lijewski Date: Mon Jul 8 10:13:21 2013 -0700 More work speeding up nodal_restriction; hadn't done all cases. Src/LinearSolvers/F_MG/nodal_restriction.f90 commit 4ccdeca95ee2ffcb0fe35c96239da028a979652b Author: lijewski Date: Mon Jul 8 09:33:49 2013 -0700 Rearranged the nodal_restriction code to be faster & more memory efficient. Src/LinearSolvers/F_MG/nodal_restriction.f90 commit 58b5bbb3c209be2016fa1a7f31198d60cd5ff887 Author: Ann Almgren Date: Sat Jul 6 10:01:34 2013 -0700 We were printing the wrong final number of iterations. Src/LinearSolvers/F_MG/ml_cc.f90 commit b105800b6e9f28843d849f1632ca0493598ebac9 Merge: 2a613f62b 714551bbb Author: lijewski Date: Sat Jul 6 09:27:49 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 714551bbb19c3946b792d1b46924147dcd55da09 Author: Michael Zingale Date: Fri Jul 5 09:19:20 2013 -0400 remove duplicate tests (if any) when using the --tests "..." argument. Otherwise we crash Tools/RegressionTesting/testnew.py commit 2a613f62b3d3a237aa36aca5c6968d92b40ced15 Merge: 4932bece7 8da5f10a3 Author: lijewski Date: Tue Jul 2 14:54:21 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 8da5f10a310649677b12a0dd77683e616d19e8cb Author: Ann Almgren Date: Tue Jul 2 13:45:57 2013 -0700 Add WritePlotFile in Particles.H Src/C_AMRLib/Particles.H commit 4932bece7152507e5e54ea85bf63eb104f5f2b3c Merge: 786d24eb7 a16bbc76f Author: lijewski Date: Tue Jul 2 11:05:40 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a16bbc76fde8b7e0db48f8fde9fa0431e0039f29 Author: ajnonaka Date: Tue Jul 2 10:59:43 2013 -0700 don't prevent nodal solves from reducing to a global 2x2 bottom solve. certain bc's means this becomes a problem with 1 unknown which we've seen can stall multigrid Src/LinearSolvers/F_MG/mg.f90 commit 786d24eb7626bfea3479e43d60e6cc92589cb5fe Author: lijewski Date: Mon Jul 1 15:21:55 2013 -0700 Moved the memory stats stuff till after we've flushed the copyassoc cache. Checked it in commented out. Tests/LinearSolvers/F_MG/main.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 9de67f2fd397d0163ab6dc3cd15272061e6fd704 Author: lijewski Date: Mon Jul 1 13:05:37 2013 -0700 Reverting right back out the four-color dense 2D GS smoother. Sometimes better smoothers aren't necessarily a win; especially when they're so much more communication intensive. Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit de62800c3ea546a4da06eaa70b62a02edbb8bffa Author: lijewski Date: Mon Jul 1 13:02:15 2013 -0700 I've implemented four-color GS scheme for the dense nodal 2D stencil. I'm checking it in here to document it. I'm going to immediately revert out these files to their previous contents. Turns out doing four FillBoundary()s per smooth is a serious lose in 2D. On my test case my nodal solves were about 20% slower on 64 cores on hopper, and about 50% slower on 512 cores. This despite the four-color scheme being a "better" smoother, sometimes leading to fewer V-cycles in the MG. Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit aa0608c319ef2b6ebae171fce81e6779fcb2c89a Author: lijewski Date: Mon Jul 1 12:41:48 2013 -0700 Made the bottom solve timer work for bottom_solver=4. Src/LinearSolvers/F_MG/mg.f90 commit def0336d981e10866f54447b029754c3597e6cff Merge: e1b9cb938 f278203e7 Author: ajnonaka Date: Mon Jul 1 10:36:23 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e1b9cb938ea2f1a96288c3e9df8f20de72ddecd0 Author: ajnonaka Date: Mon Jul 1 10:35:57 2013 -0700 fixed some mg level calculation weirdness that prevented cc fancy bottom solver from converging Src/LinearSolvers/F_MG/mg.f90 commit f278203e7ef2f1a80bfa598bf2e846541154addd Author: Weiqun Zhang Date: Mon Jul 1 08:30:55 2013 -0700 get around a PGI compiler bug Src/F_BaseLib/multifab_f.f90 commit 9100a79ed4aed3574bce691727009ec53f1cc702 Author: ajnonaka Date: Mon Jul 1 08:16:52 2013 -0700 fixed logic to handle the case when you try to invoke the fancy bottom solver and you have between 1 and (2**dm)-1 grids... in this case you can't use it so revert to bottom_solver_type=1 Src/LinearSolvers/F_MG/mg.f90 commit b0d52a253a8b58eedfe11a9ddd9cc58413b57145 Author: ajnonaka Date: Fri Jun 28 16:01:22 2013 -0700 change default value of max_bottom_nlevel to 3 so fancy bottom solver coarsens two levels (i.e., reducing # grids by factor of 8) Src/LinearSolvers/F_MG/mg_tower.f90 commit 738994822f85cb0dcee361580d5fc46836cdf73e Author: ajnonaka Date: Fri Jun 28 15:59:36 2013 -0700 eliminated some fancy bottom solver logic that was a) preventing the fancy bottom solver from ever being used if there are exactly 8 grids in the original bottom solve b) always forcing the max number of new levels to be 3. this should be controlled by max_bottom_nlevel, which will be default 3 Src/LinearSolvers/F_MG/mg.f90 commit 4fbfd3c5d9f83e393285c2b7034e584743392740 Author: ajnonaka Date: Fri Jun 28 15:07:11 2013 -0700 when calling_tower_build, you can pass in an optional argument "fancy_bottom_type_in" that controls the bottom solver for bottom_solver type 4. This is useful if you would rather do smooths than the default BiCGStab Src/LinearSolvers/F_MG/mg.f90 commit e2a1cdd8895424145a3d6383e346cfaa2dc3ff3d Author: lijewski Date: Wed Jun 26 11:12:26 2013 -0700 Rearranged lin_cc_interp_3d to do fewer allocate()s and be more cache efficient. Src/F_BaseLib/interp.f90 commit d91fcdc5e75876de1abced925830ba88f9ff4f2c Author: lijewski Date: Wed Jun 26 11:08:28 2013 -0700 Removed some trim() calls on string comparisons. Tutorials/AMR_Advection_C/Source/network.f90 commit d32858a52e13f8e27ddab807fe838296a5673a01 Author: lijewski Date: Wed Jun 26 08:11:33 2013 -0700 Got another 20% out of fourth_order_interp_2d(). Src/F_BaseLib/interp.f90 commit 43b08071ee921a5e06670930cef462905d635c04 Merge: 11bf3db90 b0da2f95d Author: lijewski Date: Tue Jun 25 15:38:10 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit b0da2f95ddb90c1188fb42a62617a0455337ccd6 Author: vince Date: Tue Jun 25 14:52:15 2013 -0700 added nametags. Src/C_BoundaryLib/FabSet.cpp commit 329d2bc9905a35be72fe3bf0fdccd5d5547f3e61 Author: vince Date: Tue Jun 25 14:51:20 2013 -0700 added nametags. Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit 98bf4d3893cb08628ac81c95ac8403248e559834 Author: vince Date: Tue Jun 25 14:48:15 2013 -0700 added nametags. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp commit d100d8d76f5fe89869c16d0d7837ac00ca30ee79 Author: vince Date: Tue Jun 25 14:41:41 2013 -0700 added to docs for comm profiling. Docs/Readme.profiling commit 11bf3db9077d315c21522758cdde511bafdca90c Author: lijewski Date: Tue Jun 25 10:40:52 2013 -0700 Build and use a local copy of the transpose of A2 in the fourth order interpolator. Src/F_BaseLib/interp.f90 commit 8dbbada1e1485f174f37697a5a54c4c71c98d952 Merge: 4357fcd62 dc0ceee7a Author: lijewski Date: Mon Jun 24 16:21:27 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 4357fcd6226605580812d6b929f5d9f2ccf4ea42 Author: lijewski Date: Mon Jun 24 16:17:38 2013 -0700 Made fourth_order_interp_2d() more cache efficient by declaring the tmp variable c(:,:,:,:) such that the first dimension holds the values at each cell, not the last dimension. It could be made more efficient if A2 in fourth_order_interp_coef_module were defined as A2(15,0:3) instead of the other way around. But that could only be done all routines using it were changed as well. Src/F_BaseLib/interp.f90 commit dc0ceee7a50d0cdd4317fce3c66fc735cef92fdd Author: cmalone 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 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 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 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: db0d03851 5bd0b350c Author: Weiqun Zhang Date: Sun Jun 23 21:45:48 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit db0d038517d34af15ab7dc864887dae8c1521c37 Author: Weiqun Zhang Date: Sun Jun 23 15:17:48 2013 -0700 fixed a minor memory issue Tutorials/AMR_Advection_C/Source/ADR_setup.cpp commit 5bd0b350c38192996223034f648fbed2ad717e4b Merge: 7211c1ea0 13cb18a54 Author: lijewski Date: Sun Jun 23 07:57:50 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 7211c1ea01ab7a553630395f639ab6107c2e3d66 Author: lijewski Date: Sun Jun 23 07:57:30 2013 -0700 Mod to parallel_create_communicator(). Src/F_BaseLib/parallel.f90 commit 13cb18a54e67b6228bde070d29885638b67c8e3b Author: Ann Almgren Date: Fri Jun 21 15:56:23 2013 -0700 Update the Tutorials/AMR_Advection_C/Exec/UniformVelocity test problem. Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_2d.f90 Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt Tutorials/AMR_Advection_C/Exec/UniformVelocity/probdata.f90 Tutorials/AMR_Advection_C/Exec/UniformVelocity/probin.2d Tutorials/AMR_Advection_C/Source/ADR_setup.cpp commit 9caac1e5cbdc7d381adfdf9c6a0065a477341923 Author: lijewski Date: Fri Jun 21 14:20:36 2013 -0700 Added back in Ann's tweak to get_bottom_box_size(). Src/LinearSolvers/F_MG/mg.f90 commit c125c81a370729b4da569120c19d49eaa3a5ff19 Author: lijewski Date: Fri Jun 21 14:18:54 2013 -0700 Can't use bl_error_module; just print & abort by hand. Src/F_BaseLib/parallel.f90 commit 2a40dd3758401f99e6bc73dec9c0bba67627efed Author: lijewski Date: Wed Jun 19 15:26:06 2013 -0700 Some cleanup. Src/LinearSolvers/F_MG/mg.f90 commit d31115348b8105c22ab04ba98809ea8d7927d201 Author: lijewski Date: Wed Jun 19 15:25:38 2013 -0700 Added signatures for functions I recently added to parallel.f90. Src/F_BaseLib/parallel_stubs.f90 commit 38d682600d99c61530c869f4a57b0de04f654fab Author: lijewski Date: Wed Jun 19 14:56:50 2013 -0700 Added parallel_null_communicator(). Added optional comm argument to parallel_ioprocessor(). Src/F_BaseLib/parallel.f90 Src/LinearSolvers/F_MG/itsol.f90 commit 41f9a4f801f7d89f786a8a0f75772c21c8f30000 Author: lijewski Date: Wed Jun 19 14:37:46 2013 -0700 Used parallel_communicator() instead of MPI_COMM_WORLD. Src/LinearSolvers/F_MG/mg.f90 commit a18a92091ee2d66c46d9f070028697b6d339acc9 Author: Matthew Emmett Date: Wed Jun 19 14:33:06 2013 -0700 BaseFab: Tidy SAXPY signature, fix SAXPY domain bug. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp commit ca7d98f3add60ebd535e9f5d60070b7fda0ec88d Author: lijewski Date: Wed Jun 19 14:30:28 2013 -0700 Added parallel_create_communicator() and parallel_free_communicator(). Src/F_BaseLib/parallel.f90 Src/LinearSolvers/F_MG/mg.f90 commit db02b8f90d988e49aabb928771ba72372e09c8a6 Author: Matthew Emmett Date: Wed Jun 19 14:18:02 2013 -0700 BaseFab: Add SAXPY. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/SPECIALIZE_1D.F Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit 1154fa043f8db4e171703d00f8bf5bf5e2cc7c82 Author: lijewski Date: Wed Jun 19 13:57:28 2013 -0700 Some initial work getting bottom_solver=4 to use its own communicator. Src/LinearSolvers/F_MG/mg.f90 commit 14c178a96c506bebedbb4ead72eb2aa3eaf9633b Author: lijewski Date: Wed Jun 19 13:55:12 2013 -0700 First cut at making BICGStab and CABiCGStab work with a given MPI communicator instead of the default one: MPI_COMM_WORLD. Src/LinearSolvers/F_MG/itsol.f90 commit 72be4104ab91aa6fdc4b19dc3d7febce99662859 Author: lijewski Date: Wed Jun 19 13:52:35 2013 -0700 Changed the default of max_bottom_nlevels from 10 -> 4. Added an MPI communicator data member that will be set in the mg_tower that does the bottom solve for the bottom_solve=4 case. The idea is that we pick a communicator that includes only those MPI procs involved in the bottom solve and pass it to routines that do global reductions to make those reductions go faster. Src/LinearSolvers/F_MG/mg_tower.f90 commit 36fca427106f7716d4cf08bfe2d17cb1869f77da Author: lijewski Date: Wed Jun 19 13:51:34 2013 -0700 multifab_dot() and multifab_norm_inf() now take optional MPI communicators. Src/F_BaseLib/multifab_f.f90 commit 12536f5634e27ea7f0acfbf189cbd830c52a13ea Merge: bbdfe5459 1602225c5 Author: Matthew Emmett Date: Wed Jun 19 12:17:43 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit bbdfe5459ade46aaec5b337311be5f4c7dcec814 Author: Matthew Emmett Date: Wed Jun 19 12:17:35 2013 -0700 Amr.H: Mark timeStep as virtual, sync parameter names with Amr.cpp. Src/C_AMRLib/Amr.H commit 1602225c5ee89a8207e65474094ed9936d2c3550 Author: Chris Malone Date: Wed Jun 19 11:52:50 2013 -0700 updates for hyades.ucsc.edu Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi commit 1ab064adfad76bd92b0b04ed6bbe4a3e56d7ba92 Author: lijewski Date: Wed Jun 19 08:00:34 2013 -0700 3d nodal dense test case on 256^3 base grid with 64^3 grids for Legion folks. Tests/LinearSolvers/F_MG/inputs.simple.3d commit 056d4bccf10e449afbb90eb35a4d75dc0c79f453 Author: lijewski Date: Wed Jun 19 08:00:02 2013 -0700 Set up for non-MPI non-OpenMP for Legion folks. Tests/LinearSolvers/F_MG/GNUmakefile commit ce0b32af4855b79f9822f0606a1bb4ca0f6faf58 Merge: 5ccb3871e bfaea73b9 Author: Ann Almgren Date: Tue Jun 18 14:17:50 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 5ccb3871e12a295cc2c424b64d8f7cacdab5c52d Author: Ann Almgren Date: Tue Jun 18 14:17:26 2013 -0700 Remove unneded "use" statements. Tests/LinearSolvers/F_MG/main.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 371fe1de14ab3e9b22d777ec923e5a7bbbd58ba7 Author: Ann Almgren Date: Tue Jun 18 14:06:44 2013 -0700 Updated which modules are included. Tutorials/WaveEquation_F/main.f90 commit bfaea73b95780a3f3b81011485487d7a6c06130a Author: lijewski Date: Mon Jun 17 16:26:03 2013 -0700 Some mods to get it to compile again. Tests/LinearSolvers/C_CellMG/main.cpp commit 69b32fa6e6a83ffac38a4ed343636b242ecc79ad Author: lijewski Date: Mon Jun 17 16:24:32 2013 -0700 Thread sxay() over FABs in the MultiFab. The FABs themselves are too small to make threading over their Fortran boxes cost effective. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 11d856e690ffb00c6ab82f09a5c0dd381156680a Author: lijewski Date: Mon Jun 17 16:08:38 2013 -0700 Removed the multiply by alpha in axpy() since it's always one. Likewise optimized gemv() knowing alpha==1.0 and beta==0.0. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit fe2ec96a6859a384567dc5a3c4cc4ffe585b48f6 Merge: a92f9ce7a 6c256b24b Author: lijewski Date: Mon Jun 17 14:40:54 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a92f9ce7a6df22c1404ce9523cabdc07cfdba63f Author: lijewski Date: Mon Jun 17 14:40:26 2013 -0700 Removed grow cells on MultiFabs in BiCGStab that weren't needed. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 3574bba09a703acc872e6b6bf7c3eb14a76b6233 Author: lijewski Date: Mon Jun 17 14:22:51 2013 -0700 Beefed up error checking in CABiCGStab. Also removed ghost cells from MultiFabs where not needed. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 3700fc70c407b6669925050f473c848deff61691 Author: lijewski Date: Mon Jun 17 14:11:17 2013 -0700 FApply() didn't correctly use src_comp, dst_comp and num_comp. Src/LinearSolvers/C_CellMG/Laplacian.cpp commit 6c256b24b7be0865ede37a7e059f56d9fed09ad4 Author: Ann Almgren Date: Mon Jun 17 11:50:14 2013 -0700 Fix some comments only. Src/LinearSolvers/F_MG/cc_stencil_apply.f90 commit 426d832f42b7d92b025be46ff25f2c4d116fd3ac Author: lijewski Date: Fri Jun 14 18:48:08 2013 -0700 Little more OMP tweaking of my previous mod. Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/itsol.f90 commit cb27cce466d063d907e56752d6a8dea0f21cff73 Merge: 123ef66a8 790e00953 Author: lijewski Date: Fri Jun 14 15:19:32 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 123ef66a8c38f16a3d59d9fc65cf8541568ec19c Author: lijewski Date: Fri Jun 14 15:17:57 2013 -0700 Make itsol_defect() aware when it's being called from the bottom solver. Src/LinearSolvers/F_MG/itsol.f90 commit 2f7ebdff44129bc7ece830dcc115d00e6c9cd111 Author: lijewski Date: Fri Jun 14 15:11:28 2013 -0700 We now pass a flag to itsol_stencil_apply() indicating whether or not we're doing a bottom solve. It passes that flag to the relevant 3d apply routine, which then threads its loops if it's NOT in a bottom solve. This threads better for fewer boxes than threading over the calls to the apply op itself. Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 46f1d5503b3d425e14428515689aa30a56782744 Author: lijewski Date: Fri Jun 14 14:18:55 2013 -0700 Changed the name of a constant. Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 2a6d836746e15ce7988a632cb9c57dd5143019f1 Author: lijewski Date: Fri Jun 14 11:58:44 2013 -0700 Attempted to make some of the minion stencils more memory efficient by doing as much work as possible on them in one pass instead of multiple passes. Also, OMP over the bit twiddling in mask. Src/LinearSolvers/F_MG/cc_stencil.f90 commit 438e679074aaece9790e7feda12182d861514668 Author: lijewski Date: Fri Jun 14 10:52:40 2013 -0700 Some OMP tweaking. Src/LinearSolvers/F_MG/cc_stencil.f90 commit 790e00953bd6bf04f1e3117ea2ad70d5a3593263 Author: Weiqun Zhang Date: Thu Jun 13 21:33:10 2013 -0700 fixed a bug in my new code; now fillpatch seems to be working in cases that don't need interpolation in time (which is the case for multi-level SDC) Src/C_AMRLib/StateData.cpp commit 64689c15cc8d811e6941b77a2985d2292d8522e0 Author: Weiqun Zhang Date: Thu Jun 13 17:56:30 2013 -0700 added multi-level SDC nodes Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/BaseFab.cpp commit 84ee0b81b1749b5d3b0726a3adaf596697a285d4 Author: lijewski Date: Thu Jun 13 17:16:22 2013 -0700 Added some barriers. Tests/C_BaseLib/tFB.cpp commit 39b20d22173f392a7e6432c6962855483bb16e2d Merge: 6cdda2589 0cbea00c9 Author: lijewski Date: Thu Jun 13 12:58:22 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 6cdda2589ac71491e772250819f2a239ca918112 Author: lijewski 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 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 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 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 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 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 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: c668eac52 e503b0c19 Author: lijewski Date: Wed Jun 12 14:08:37 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c668eac525136aa123f65cf8fb50d88414b9f68c Author: lijewski Date: Wed Jun 12 14:08:15 2013 -0700 Mods due to formal argument changes. Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 6ee6cfccb53d6b751c59e48ce4159d705b31c8f6 Author: lijewski Date: Wed Jun 12 13:46:04 2013 -0700 Destroy a boxarray. Tests/LinearSolvers/F_MG/wrapper.f90 commit 55db139289b2b9f7a3d41f9c7fabb4e7597a3d4e Author: lijewski Date: Wed Jun 12 12:54:13 2013 -0700 Removed a bunch of unused variables and formal arguments. Really trying to get the code to compile clean in debug mode. Src/F_BaseLib/multifab_f.f90 Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 9f19927c261cbea6b034a9dc6de0bf3c2c51dbd3 Author: lijewski Date: Wed Jun 12 11:01:27 2013 -0700 Fix bug in s_simple_1d_nodal(). Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 797ef77b26dfa82f9fe55623448dd82ce40679fd Author: lijewski Date: Wed Jun 12 10:54:30 2013 -0700 Fixed bug in stencil_set_bc_nodal(). Added set_faces_edges_corners_2d(). Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 1695d0f8675e36d592ff13ad0125b2e7e789c9cb Author: lijewski Date: Wed Jun 12 10:30:08 2013 -0700 Some OMP tweaking. Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 commit e503b0c19f64f4d7eedebc172795f01ff58edb9e Author: Weiqun Zhang Date: Tue Jun 11 21:41:58 2013 -0700 pass SDC node times into StateData Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 33c5295d776fb227e7d2113aeaad6cd038b48366 Author: Weiqun Zhang Date: Tue Jun 11 17:45:46 2013 -0700 added SDC nodes information to Amr Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit f1c5af2405cf3a678fad67f0bde07732a5c265b5 Author: Weiqun Zhang Date: Tue Jun 11 15:28:56 2013 -0700 added mid_data to StateData class for the storge of SDC middle nodes Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_BaseLib/PArray.H commit c0db0c7f17ff1e8eedde56b4f51d73b28975a2af Author: lijewski Date: Mon Jun 10 10:37:41 2013 -0700 A little memory cleanup. Src/C_AMRLib/StateData.cpp commit a5b7ad7d261e4a89d0eb65cbd08e94b685e2136c Author: lijewski Date: Mon Jun 10 10:29:06 2013 -0700 Fixed OMP bug. Src/C_AMRLib/AmrLevel.cpp commit 4c0c9bd13b58c007ce527f8a65943d08b7f15289 Author: lijewski Date: Sun Jun 9 19:29:07 2013 -0700 Added version of linInterp() in which the two src boxes & the dest box are all the same. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/MultiFab.cpp commit f042e44f770952d7c2476ce98d4dd7438155027d Author: lijewski Date: Sun Jun 9 18:56:18 2013 -0700 Added specialized version of BaseFab::sum() for Reals. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/SPECIALIZE_1D.F Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit 94afa49e716e474b032f80a384bebade8906d2c5 Author: lijewski Date: Sun Jun 9 17:38:28 2013 -0700 Added some profilers. Src/C_AMRLib/AmrLevel.cpp Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BndryRegister.cpp commit a21da84aca22c0deaa28456623f13e5a14ab6eff Author: lijewski Date: Thu Jun 6 13:46:24 2013 -0700 Reverting out the eight-color nodal dense smoother. With the number of fill_boundary()s required it's a lose. Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit 73a42622c1761b3559767e1a6b478d7c15db00ae Author: lijewski Date: Thu Jun 6 13:13:21 2013 -0700 Removed the OMP from multifab_dot_cc(). Do the calculaton as a sum of partial sums. Src/F_BaseLib/multifab_f.f90 commit ee3dddcf85d4a29336d163c82b31dc8e2337956d Author: lijewski Date: Thu Jun 6 13:13:02 2013 -0700 Named the critical section. Src/C_BaseLib/BaseFab.H commit 4ce4d9558951b47e1f3a8cd1746632911513427e Author: lijewski Date: Thu Jun 6 12:56:20 2013 -0700 Had to add a critical region around the code in BaseFab::define() in which we maintain global track of the amount of data allocated in FABs. Multiple threads can hit this code at the same time. Src/C_BaseLib/BaseFab.H commit c2490d4f51701ef97a0ed9545044de1c081123d8 Author: lijewski Date: Thu Jun 6 07:30:35 2013 -0700 Fixed OMP bug. Src/F_BaseLib/multifab_f.f90 commit cafc252f44d53c834dfd498accd3b5f1e8e54d81 Merge: 3f24251a4 3a50328bb Author: lijewski Date: Wed Jun 5 14:14:55 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3f24251a4875a23d8e86416b644d4ff07a9fbccc Author: lijewski Date: Wed Jun 5 14:08:50 2013 -0700 OMP over operations on boxes in boxarray. Src/F_BaseLib/boxarray_f.f90 commit 580f62519eea2302a993e6353f950f858ffb5929 Author: lijewski Date: Wed Jun 5 13:51:20 2013 -0700 OMP over the various loops in BoxArray that operate on all the boxes. This appears to be a win a modest # of boxes. Should be a big win with very large box counts. Src/C_BaseLib/BoxArray.cpp commit 3a50328bbea51e3057ddfa6ab25f459046b7a7df Author: Ann Almgren Date: Wed Jun 5 12:06:29 2013 -0700 Need different template depth if USE_IN_SITU is true. Tools/C_mk/Make.defs commit 32119f256154e4b3b1dd95f2147ad456ad4c8c2f Author: lijewski Date: Wed Jun 5 11:00:09 2013 -0700 Explicitly write out the sum() operation in multifab_dot_cc(). Src/F_BaseLib/multifab_f.f90 commit 28ad2081a304210423a57665a8078b8619b3eeaf Author: lijewski Date: Wed Jun 5 10:26:27 2013 -0700 A little cleanup. Src/C_AMRLib/AmrLevel.cpp commit 1e603f7e921950ede47ef3f61b1800c56330d30f Author: lijewski Date: Wed Jun 5 10:05:19 2013 -0700 OMP over number of boxes when building proper grid for FabSets. Src/C_BoundaryLib/BndryRegister.cpp commit 6a1407f1b961447eede7391632012eabd5654d45 Author: lijewski 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 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 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 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 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 Date: Tue Jun 4 19:30:32 2013 -0700 Fixed OMP bug. Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 1b0f0876b0850fb2c17e64b2bbea86d6eecac9ed Author: lijewski Date: Tue Jun 4 17:09:46 2013 -0700 Fixed OMP bug. Src/F_BaseLib/multifab_f.f90 commit 1ab4e7ce5056bef6f18c6156859a9f5759f09b95 Author: lijewski Date: Mon Jun 3 17:45:29 2013 -0700 The stencil apply functions are only called by the bottom solver. The boxes are too small to profitably OMP. Instead OMP over FABs. Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 3bc5b9db6faf8ca0bd05e4b2b397ca1f807226fc Author: lijewski Date: Mon Jun 3 17:18:47 2013 -0700 Use cpy_d() instead of generic pointer copy assignment. Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 1b6dfe31c98e44b11051447cfaf42de97d51cd4a Author: lijewski Date: Mon Jun 3 16:33:52 2013 -0700 Some OMPing. Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 448aab707c3f0b4d0c8567edd4a169e6cddb3b55 Author: lijewski Date: Mon Jun 3 14:59:39 2013 -0700 Now print out solve time and accumulated time in the bottom solver. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 2ffa8f8fae99bbd868eed1e7676496a9d8316899 Author: lijewski Date: Mon Jun 3 10:59:04 2013 -0700 Some cleanup. Src/F_BaseLib/multifab_f.f90 commit bbf950c08d832f24a9882627847bbb94627879fe Author: lijewski Date: Mon Jun 3 10:36:07 2013 -0700 Added multifab_norm_l2_doit(). Src/F_BaseLib/multifab_f.f90 commit 9da8efe4dcb9ef3cdf2504abd04eb237ae91b2b2 Author: lijewski Date: Mon Jun 3 10:24:40 2013 -0700 Thead over FABs in multifab_dot(). They're almost always called with tiny boxes that can't be threaded over individually. Src/F_BaseLib/multifab_f.f90 commit dff1e0b6f715cebe5f1629ab5a902db7e4f307e5 Author: lijewski Date: Mon Jun 3 09:18:09 2013 -0700 Tweaking the OMP IF constaints on some loops. Src/F_BaseLib/multifab_f.f90 commit 3a7f487c917cc14179866240d01be0a4d62270e3 Author: lijewski Date: Wed May 29 16:17:37 2013 -0700 Can now call gs_lex_dense_smoothers in mg_tower_smoother. Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 commit 54c0a103dc72d666a0fb8af6e0511432a7421ec4 Author: lijewski Date: Wed May 29 16:00:43 2013 -0700 Some cleanup. Also, make sure mg_tower_smoother calls the fourth order smoothers the proper number of times. Only the 2-D HO cross stencil does red-black; the others do a full sweep. Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 commit 096e32f62ca9912ff407326f97715e2a3cbb6441 Author: lijewski Date: Wed May 29 15:14:15 2013 -0700 Only use the 8-color dense nodal smoother if OMP=t and don't have enough FABs. Src/LinearSolvers/F_MG/mg_tower_smoother.f90 commit 38101f54aca6a9f1ea8e95b091a9526a48ae923f Author: lijewski Date: Wed May 29 15:13:31 2013 -0700 Can now use the F90 omp_module from the C++/Fortran side of things. Src/F_BaseLib/FParallelMG.mak commit dd9a855847c5fd44a1a7d8b4d4a14f0a5df95693 Author: lijewski Date: Wed May 29 13:51:03 2013 -0700 Added an 8-color GS nodal dense smoother for 3D that's OMP'd. It's only called when the number of FABs in the multifab is fewer than the maximum number of threads available. Otherwise we thread over the FABs in the multifab when calling the nodal dense smoothers. Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit 7da8bbfe4c7dd473e0f31d360b0c5c1567e12022 Author: lijewski Date: Wed May 29 12:26:36 2013 -0700 I'm partially backing out some of my recent OMP changes. I want to use the old threading model over FAB boxes, and the new way of threading over multifabs only when the FAB box can't be threaded. Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit bf0e54d82cb488b19c457743e9ffaac5f638b3f5 Author: Weiqun Zhang Date: Tue May 28 21:21:32 2013 -0700 Fixed an assertion bug in initializing random number generator. Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 0df6d874f273c1dc48af26475ba16eaff204ca35 Author: lijewski Date: Tue May 28 18:24:22 2013 -0700 Back to old way of doing some OMP. Nesting has too much overhead. Src/F_BaseLib/multifab_f.f90 commit 4e04d617e0ebfa5ab703f90ec7c3c5f6020259f1 Author: lijewski Date: Tue May 28 16:50:47 2013 -0700 Had a tmp array in BuildGramMatrix() dimmensioned too small. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 6a7b00a968de43ebf312c6d8ae13085130d96688 Author: lijewski 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 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 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: 64400c10c 132b40ecd Author: Weiqun Zhang Date: Tue May 28 14:21:36 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 64400c10cc58edb05996b9ffdd2f3d610dfe5ac3 Author: Weiqun Zhang Date: Tue May 28 14:18:35 2013 -0700 In mf_fb_fancy_*, turn off some unsafe OMP parallel regions for nodal multifabs. In principle, the unsafe scenario could also happen for cell-centered multifabs that have overlapped valid cells. Src/F_BaseLib/multifab_f.f90 commit 132b40ecd880706a18a55bc0e63c4d100bdfb110 Author: lijewski Date: Tue May 28 13:55:52 2013 -0700 Only reduce the upper triangle of the Gram matrix. After reduction fill in the rest via symmetry. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 1eabaade19578f03e0bf9d78cdf9422c1906eb35 Author: lijewski Date: Tue May 28 13:06:23 2013 -0700 Only reduce the upper triangular part of the Gram matrix in the CABiCGStab instead of the whole matrix. Use symmetry to fill it in after the allreduce(). Src/LinearSolvers/F_MG/itsol.f90 commit 3654e02a035c58e60a2782e636b5ba88b15bc57c Author: lijewski Date: Tue May 28 11:25:04 2013 -0700 Some OMPing. Src/LinearSolvers/F_MG/ml_solve.f90 commit 226bb7377af99452b448c8422ad6fcbebf64a8c1 Author: lijewski Date: Tue May 28 10:22:34 2013 -0700 Remove boxarray_boxarray_diff() and its synonym boxarray_complementIn(). Force people to use layout_boxarray_diff(). Src/F_BaseLib/boxarray_f.f90 commit cc88917e587855345f03bd95a0d537581d2723fa Author: lijewski Date: Tue May 28 10:22:16 2013 -0700 Use layout_boxarray_diff() instead of boxarray_boxarray_diff(). Src/F_BaseLib/make_new_grids.f90 commit b477550a9030fe67982a0c243a4a69beb07856fe Author: lijewski Date: Tue May 28 09:11:48 2013 -0700 OMP over call to ml_interface_[123]_crse() that include calls to layout_get_box_intersector(). Not sure what I tweak exactly to make this work but I'm going with it. Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit 9e0883955c5c7614ee1928340cea428c8a1384e7 Author: lijewski Date: Tue May 28 09:11:13 2013 -0700 Further refinement of critical region placement for layout_get_box_intersector(). Src/F_BaseLib/layout.f90 commit 2b0ead018d675153b8ed943fafe76002ad14bea6 Author: lijewski Date: Mon May 27 18:40:25 2013 -0700 Refined the critical area in layout_boxarray_diff(). I'd really like to understand why I can't call layout_get_box_intersector() directly in an OMP loop. Src/F_BaseLib/layout.f90 commit 7773951a2ceb456daa20bc0b1651e8e8afbff3c6 Merge: c3de69f6f 9a6d4f143 Author: lijewski Date: Mon May 27 17:52:53 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c3de69f6f20704120ea5d4f14c32c1a2904b55ff Author: lijewski Date: Mon May 27 17:52:13 2013 -0700 Removed some OMP loops in the multifab_sync routines. Src/F_BaseLib/multifab_f.f90 commit 9a6d4f1439e731bf378c14dcfd3cc791628eb200 Author: lijewski Date: Mon May 27 16:56:41 2013 -0700 Fixed bug I recently introduced. Src/F_BaseLib/multifab_f.f90 commit 951dfa15f33f7602f511c90687e7e8728def5b05 Author: lijewski Date: Mon May 27 13:40:40 2013 -0700 Moved critical section to inside of layout_boxarray_diff() instead of around it. I still don't understand why layout_get_box_intersector() isn't thread-safe. Src/F_BaseLib/layout.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 2b6c314341b4af4af0c14917eaacf836cdb5b71a Author: lijewski Date: Mon May 27 11:11:18 2013 -0700 Made some internal layout routines much more efficient for large boxarrays. Src/F_BaseLib/layout.f90 commit 722dd4418d62422399077a6cccf316f9cb4c9a02 Author: lijewski Date: Mon May 27 10:34:01 2013 -0700 Added layout_boxarray_diff(). This is a much more efficient version of boxarray_boxarray_diff(). Use this in place of the latter, which I'll be removing soon. Src/F_BaseLib/layout.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit adb204210f62ba7b01e59e7d9a253958b1b1c5c3 Merge: 1a78c9622 3ab615d34 Author: lijewski Date: Sun May 26 18:26:17 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3ab615d344d279410ff595ce402ff1dffcc19ef4 Author: lijewski Date: Sun May 26 18:06:07 2013 -0700 Fix typo. Src/LinearSolvers/F_MG/itsol.f90 commit 1a78c9622f3976b2c36746544a9b903c8651ca8b Author: lijewski Date: Sun May 26 10:39:01 2013 -0700 Moved most of the OMP for MG over the FAB in a multifab. This turns out to be a big win. We do a lot more calls of the smooth() and apply() on very small boxes. And as problems get bigger this will only increase. It doesn't help the extreme case (much) where you only have one grid per MPI process, but for multilevel problems where you almost certainly have multiple grids per MPI process it's a clear win. Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/edge_restriction.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit 66a475922146087cb1e65a8bcb1a8fcefbd0e215 Author: lijewski Date: Sun May 26 10:22:54 2013 -0700 Fixed typo. Src/F_BaseLib/multifab_physbc.f90 commit b5aa9ad6fc6d5c54017f8af476f5593f952ad8c5 Author: lijewski Date: Sat May 25 22:09:53 2013 -0700 Some more OMPing. I'm lifting OMP loops out of simple routines and writing loops around nfabs() or nboxes() instead in cases where the amount of work to do in the original OMP loops is small. Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 commit 1ef2abc3d3cb0c53176afc1618d63bd3ee8fe168 Author: lijewski Date: Sat May 25 20:19:39 2013 -0700 More OMP polishing. Src/F_BaseLib/multifab_f.f90 Src/LinearSolvers/F_MG/itsol.f90 commit 0378c582d1693f3a5fec6bba42521c97131cbe02 Author: lijewski Date: Sat May 25 20:18:59 2013 -0700 Make the memory statistics stuff thread safe using critical regions. Src/F_BaseLib/bl_mem_stat.f90 commit f1628a9b01659c48edea08a832c5ecabb75d2ca7 Author: lijewski Date: Sat May 25 19:09:20 2013 -0700 Don't OMP the interp routines. Instead OMP over all the typically small grids in routines like fillpatch, make_umac_grown and fill_ghost_cells. Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 Src/F_BaseLib/multifab_physbc.f90 commit fa120810211351a868cb3be78c16491fb37a9392 Author: lijewski Date: Sat May 25 11:29:05 2013 -0700 Don't thread dot() or saxpy(); they're mostly used on really small boxes. Src/F_BaseLib/multifab_f.f90 commit b6fdc16e97cfee59078f17a7443ceffd0fd75d72 Author: lijewski Date: Sat May 25 10:23:45 2013 -0700 Tweak to CABiCGStab. Needed to fill both components of "ph" with "uu" at start. Src/LinearSolvers/F_MG/itsol.f90 commit a25117100200f43afb0e7816ba6a83ff1644a002 Author: lijewski Date: Fri May 24 15:06:57 2013 -0700 Removed some OMP loops that were effectively nested. Src/LinearSolvers/F_MG/itsol.f90 commit 11e5f77e0cbcdae6bd3764db7a99053ef4e52883 Author: lijewski Date: Fri May 24 14:46:25 2013 -0700 OMPing across FABs instead of within FABs on MG routines that often use small boxes. Src/LinearSolvers/F_MG/cc_restriction.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/coarsen_coeffs.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/nodal_restriction.f90 commit 0eab51a2c459abf7c15789a64d3dfbaca93cdbd4 Author: lijewski 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 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 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 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 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 Date: Wed May 22 17:03:28 2013 -0700 OMP's part of BuildGramMatrix(). Src/LinearSolvers/F_MG/itsol.f90 commit 67d19501465683ad52826171fdbb1d3c44c09c8e Author: lijewski Date: Wed May 22 16:19:14 2013 -0700 Call itsol_apply_stencil() on pp & rr together in the CA algorithm. Cuts out half the fill_boundary() calls. Src/LinearSolvers/F_MG/itsol.f90 commit 976a65377ab9b00f22dec3e9d826773d4d352fd7 Author: lijewski Date: Wed May 22 15:44:46 2013 -0700 Some OMP loop polishing. Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 28457b58dc5d3192420d8ef8465317de47bea457 Author: lijewski Date: Wed May 22 15:15:39 2013 -0700 Put some small arrays on the stack instead of the heap. Polished up some of the OMP loops. Src/LinearSolvers/F_MG/cc_smoothers.f90 commit 4baf41909ed6f256cb1aa2098a9a48cfe33288d7 Author: lijewski Date: Wed May 22 14:24:43 2013 -0700 Removed some unnecessary setval()s. Src/LinearSolvers/F_MG/itsol.f90 commit 90168ceb447c57354ffa7800f73d0101891f686f Author: lijewski Date: Wed May 22 14:05:53 2013 -0700 More cleanup. Src/LinearSolvers/F_MG/itsol.f90 commit 49f03c5f66fc88f81476b1470c31a0cd11f34f67 Author: lijewski Date: Wed May 22 13:28:10 2013 -0700 Some cleanup. Src/LinearSolvers/F_MG/itsol.f90 commit 78d2a9d97eaf91d894dcea712c6c078fab1f17fd Author: lijewski Date: Wed May 22 13:01:11 2013 -0700 Added is_an_inf() and is_a_nan() routines for checking single double values. Src/F_BaseLib/fab.f90 Src/LinearSolvers/F_MG/itsol.f90 commit 34e55b4398a913b53259d3914c1fcb0e89b50859 Author: lijewski 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 Date: Wed May 22 12:21:37 2013 -0700 Integrated in isinf() stuff. Src/LinearSolvers/F_MG/itsol.f90 commit 7952390542446c4e5a4f167870e158f3e024b819 Author: lijewski Date: Wed May 22 12:09:32 2013 -0700 Added val_is_nan() and val_is_inf() routines. Src/F_BaseLib/fabio_c.c commit c2a19c54caf394344c6dd0e6ed39f7a921d4f09a Author: lijewski Date: Wed May 22 10:54:29 2013 -0700 Elided some multiplies via strategic use of parentheses. Src/LinearSolvers/F_MG/nodal_restriction.f90 commit e7205738cd1730eda5fbb5a27901f43e16f4a7bc Merge: 148b73d0b 9ad7447eb Author: lijewski Date: Tue May 21 16:13:09 2013 -0700 Merge branch 'CA' commit 9ad7447eb94e6c302df22eedc01417c962ccf647 Author: lijewski Date: Tue May 21 16:08:17 2013 -0700 Fixed bug I recently introduced. Src/F_BaseLib/multifab_f.f90 commit 894194b67bf4e89dd1e7827e2349e0e5c9dc13ce Author: lijewski Date: Tue May 21 16:02:53 2013 -0700 More cleanup of unused formal subroutine parameters. Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 148b73d0bb74ce5471d52145c694eb5b2147a0f8 Author: Ann Almgren Date: Tue May 21 15:42:21 2013 -0700 Fixed the cc wrapper and removed the memory print statements. Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit e738a00f9dc8125df32960c38a36179458724ecb Author: lijewski Date: Tue May 21 15:30:37 2013 -0700 Cleaned up some unused formal subroutine arguments. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit d9c0f582813a5f07b9cfbc4c33da635052bc5244 Author: lijewski Date: Tue May 21 15:21:09 2013 -0700 Removed the unused "uu" argument to itsol_converged(). Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 commit 71a600e91100f48199a5e2d680c795876d4a4091 Author: lijewski Date: Tue May 21 15:16:13 2013 -0700 Some more cleanup. Src/LinearSolvers/F_MG/itsol.f90 commit f7c56e0b7e3a92360f091562dee8bb4f6006ff20 Author: lijewski Date: Tue May 21 15:01:05 2013 -0700 Seems to work; at least for a simple nodal solve. Src/LinearSolvers/F_MG/itsol.f90 commit fccc5b301d06a9a75c30556b501e1bd3049c44db Author: lijewski Date: Tue May 21 14:46:24 2013 -0700 Still working on CABiCGStab. Src/LinearSolvers/F_MG/itsol.f90 commit 590cfa942b32a77dfca5b30155a9b1bd854aef8a Author: lijewski Date: Tue May 21 13:56:33 2013 -0700 Yet more progress on CABiCGStab. Src/LinearSolvers/F_MG/itsol.f90 commit 4a25c354af37b117f3f37d8d282b1a3940746cb8 Author: lijewski Date: Tue May 21 13:01:36 2013 -0700 Added a optional args nodal_mask and local to multifab_dot_cc. Now multifab_dot_c() and multifab_dot() both call that routine. Src/F_BaseLib/multifab_f.f90 Src/LinearSolvers/F_MG/itsol.f90 commit 69fc0393be96206f859e1d02cfd4179702d9c5a2 Author: lijewski 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 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 Date: Tue May 21 09:27:14 2013 -0700 Elided some more reductions. Src/LinearSolvers/F_MG/itsol.f90 commit 6b39f1f5b2451427fb25ef7a21a2434eb94e7eea Author: lijewski Date: Tue May 21 08:58:14 2013 -0700 Some cleanup on the way ... Src/LinearSolvers/F_MG/itsol.f90 commit 7f1f9bf0adc6a3fbb1e648ebed86d6494a8a1c61 Author: lijewski Date: Mon May 20 13:34:33 2013 -0700 Some cleanup of DGEMV(). Src/LinearSolvers/F_MG/itsol.f90 commit ee32b3587d37d68bd9d71bbe6b86d069043ea7f7 Author: lijewski Date: Mon May 20 13:28:48 2013 -0700 Merged in slightly simlified version of the BLAS DGEMV() matrix-vector multiply routine. Src/LinearSolvers/F_MG/itsol.f90 commit 7ff6e9defa6761187e754c545555cc0104243188 Author: lijewski Date: Mon May 20 11:28:19 2013 -0700 Added SetMonomialBasis(). Src/LinearSolvers/F_MG/itsol.f90 commit a46b0dcc4c7d45fde6007d857f85f1382534ef5f Author: lijewski 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 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 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 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 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 Date: Fri May 17 10:22:50 2013 -0700 Removed some divisions. Src/LinearSolvers/F_MG/nodal_divu.f90 commit 2b7f3625acb2ae88fcecbec570a2e5e1f4c5634b Author: lijewski 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 Date: Thu May 16 22:12:49 2013 -0700 More OMPing. Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 commit d343ee49c79767d617b898d6600677a63e0b37aa Author: lijewski Date: Thu May 16 21:09:31 2013 -0700 Some OMPing. Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90 commit 67fcafeba36fbb81109fb0d6aa2538a5f781411d Merge: 69e4e47c5 9a2af1787 Author: lijewski Date: Thu May 16 20:19:56 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9a2af17876e458936e0d1a268d2465f87b684121 Author: Ann Almgren Date: Thu May 16 19:15:57 2013 -0700 This is a cleaned up version that appears to work, for the nodal dense stencil in 2d anyway (using inputs.simple) Tests/LinearSolvers/F_MG/GNUmakefile Tests/LinearSolvers/F_MG/cc_single.f90 Tests/LinearSolvers/F_MG/inputs.simple Tests/LinearSolvers/F_MG/main.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/nodal_single.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 69e4e47c5e4d06f79507e6f1d5beef877341bf97 Author: lijewski Date: Thu May 16 15:44:51 2013 -0700 Regularized some constants in the code. Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 commit 371e587606502a51a863085621471a32f10df232 Author: lijewski Date: Thu May 16 14:30:31 2013 -0700 Removed some divides. Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_newu.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit a502c9a32fc97c04214e98ddbe63ee73cafd0626 Author: Weiqun Zhang Date: Thu May 16 12:25:40 2013 -0700 added functions to reset random number seed Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 4ef86ac01f873184b0943aaa10ff8161cb7c716d Author: lijewski Date: Wed May 15 14:11:31 2013 -0700 Some code cleanup. Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit 961705032ddcb24de296b23365b69c50c649b405 Author: lijewski Date: Wed May 15 13:34:33 2013 -0700 Now can print out solve time for tensor solve. Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit e01709b8d7dc76217de5d42a2dae6bf7c1dad6c8 Author: lijewski Date: Wed May 15 13:34:21 2013 -0700 Tweak to output. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 5cc9af0c0da1931f62967d5bf6c2c0ec976e1595 Author: Matthew Emmett 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 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 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 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 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 Date: Mon May 13 12:27:20 2013 -0700 Removed unused variable. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 7f7ddc284542807f21f5af0a6ab21ce069dd70d7 Merge: 77cbae25d a51a9bf5e Author: lijewski Date: Mon May 13 11:26:36 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a51a9bf5e4ee48daa3262478bfcf22c7c64e1f8c Author: Weiqun Zhang Date: Mon May 13 11:12:58 2013 -0700 minor changes to the initialization of random number seeds Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Utility.cpp commit 77cbae25d8986f3611cf30d2b3929341e934791c Author: lijewski Date: Mon May 13 10:58:48 2013 -0700 More MPI_Allreduce() elimination/reduction. Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 3506f17e4e7cb9a4de59a95d20f32f69214a081f Merge: ebd6c680c 24ca69841 Author: lijewski Date: Mon May 13 10:58:29 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 24ca69841f6849eaf0eb48fb94b2158ff9ed5d0e Author: Weiqun Zhang Date: Mon May 13 10:55:09 2013 -0700 made random number generator thread safe Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit ebd6c680cd436791be2246ff881d746d341ec831 Author: lijewski Date: Mon May 13 10:11:02 2013 -0700 Little more OMPing. Src/LinearSolvers/F_MG/cc_stencil.f90 commit e36a72d42c466c0ec1bd6cab83d003d062f1fcea Author: lijewski Date: Mon May 13 10:02:10 2013 -0700 For stencil_norm and max_of_stencil_sum we thread on fab boxes not within fab boxes. Src/LinearSolvers/F_MG/cc_stencil.f90 commit 43327ff56ff64090578a1d2bfe9da6b81235c34a Author: lijewski Date: Fri May 10 20:35:59 2013 -0700 Simiplification. Src/F_BaseLib/fab.f90 commit 8978baf2fd302eb42c7ac9d094d341cf79857fb6 Author: lijewski Date: Fri May 10 20:35:26 2013 -0700 Fixed a bug I introduced earlier. Src/LinearSolvers/F_MG/cc_stencil.f90 commit c5d1f770cd3d3295d709f557d569f3dad41e3b39 Author: lijewski Date: Fri May 10 20:10:03 2013 -0700 OMP'd max_of_stencil_sum(). Src/LinearSolvers/F_MG/cc_stencil.f90 commit b84ab0827e712c71b973a9c7d8d46b818a5900f7 Author: lijewski 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 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 Date: Fri May 10 14:19:44 2013 -0700 Elided more reductions. Src/LinearSolvers/F_MG/ml_cc.f90 commit 702fc911f82c794d77ee040e2358580d04573914 Author: lijewski Date: Fri May 10 14:19:17 2013 -0700 Added optional "local" flag to max_of_stencil_sum(). Src/LinearSolvers/F_MG/cc_stencil.f90 commit 1cf3baeb2153b043d5bbc4ad698071d1633743cd Author: lijewski 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 Date: Fri May 10 13:31:14 2013 -0700 Some parallel reduction elimination. Src/LinearSolvers/F_MG/mg.f90 commit 9c441778fdc0e56bde6bee5152665d9990ca7ee5 Author: lijewski Date: Fri May 10 13:30:11 2013 -0700 Added optional "local" flag to ml_norm_inf(). Src/LinearSolvers/F_MG/ml_norm.f90 commit a18d0e078faae604f9272f14f3061ffa7a74c2f2 Author: lijewski Date: Fri May 10 10:47:57 2013 -0700 More debugging & performance analysis output. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 1fe43e67e9bc4005cb6dc37c1ca946773113b969 Author: lijewski Date: Thu May 9 22:40:59 2013 -0700 Elided some global reductions. Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 47207b01e3b828d93c48e8ac67d4350928c90da4 Author: lijewski Date: Thu May 9 21:50:46 2013 -0700 Now can print out the multigrid time and accummulated bottom solver times. Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit c2eb369e12524e37e41e293a7b9faa9c3f8762d2 Author: lijewski Date: Thu May 9 17:21:51 2013 -0700 Removed multifab "sh" from BiCGStab; reuse "ph" instead. Src/LinearSolvers/F_MG/itsol.f90 commit fbb52b6ba2f664bf2d837e6d4831def1062f2bc8 Author: lijewski Date: Thu May 9 14:50:03 2013 -0700 Some cleanup and code simplification. Src/LinearSolvers/F_MG/itsol.f90 commit adbb38a653e834e9bebcf4c04eb1581a6cd48631 Author: lijewski 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 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 Date: Wed May 8 17:22:51 2013 -0700 added -lmpich back Tools/C_mk/Make.mpi commit 5a844aafbf2e0ac7a130312edb9c4f769f38b2a1 Merge: 7253b6e04 81d4ab64b Author: Weiqun Zhang Date: Wed May 8 16:24:22 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 7253b6e047a98d1d14a242ff0191c188ab4fdd29 Author: Weiqun Zhang Date: Wed May 8 16:21:05 2013 -0700 Added long long to Mpi_typemap. Use long long for total number of particles in some functions. Some were not updated because it would require more significant changes. Src/C_AMRLib/Particles.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ccse-mpi.H commit 81d4ab64be3f07210b7cdb4c8c3b4f8e7b98fbc0 Author: Michael Zingale 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 Date: Wed May 8 19:19:57 2013 -0400 ok -- for real now... Tools/RegressionTesting/testnew.py commit 64790a9df098f365b111cc9a613850254b088cff Author: Michael Zingale Date: Wed May 8 19:03:57 2013 -0400 self -> suite in the enw parameter Tools/RegressionTesting/testnew.py commit 75724a208a94e766e5f091b9f6f259adb050156a Author: Michael Zingale Date: Wed May 8 18:56:36 2013 -0400 add globalAddToExecString argument to allow a runtime option to be appended to all jobs. For Maestro, e.g., this is useful for forcing all plotfiles to be double precision via: globalAddToExecString = "--single_prec_plotfiles F" also fix a bug in the recent git updates that didn't work with the external build directories. Tools/RegressionTesting/testnew.py commit f4e01c450af9a9316356fb88ccf79fc3cc771abe Author: lijewski 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 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 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: a01919b13 dd524262c Author: vince Date: Wed May 8 10:01:24 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit dd524262c633d80ee13ddb4813ca35a9e9c5ca22 Author: lijewski Date: Tue May 7 15:31:42 2013 -0700 Some cleanup and improved comments. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit e434d16040fb3417f4fd140fc119487c62f39367 Author: lijewski Date: Tue May 7 14:58:34 2013 -0700 Changed some of my verbose output. No longer try and calculate the norm_inf(r). Just go with the L2_resid as calculated by the algorithm. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 3e3dc98688127339a485ac9457c84aab2d85582d Author: lijewski 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 Date: Tue May 7 14:35:42 2013 -0700 prof def. Tools/C_mk/Make.defs commit 2ef28d3731801663df798edbac25ffeb07739d3f Merge: 44050d41c c098ccbad Author: vince Date: Mon May 6 12:25:06 2013 -0700 Merge branch 'master' into commprof commit 471201209d31bac2197ea912a69a10e2eee6f5ff Merge: 0ff9112f7 f8dfb7ae3 Author: Chris Malone 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 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: e97c3037f 12f7007da Author: vince Date: Mon May 6 11:28:04 2013 -0700 Merge branch 'master' into commprof commit c098ccbad32adc3d6fa1fecab5794e7ea780ffa6 Author: lijewski Date: Mon May 6 11:25:38 2013 -0700 Still more include "file" -> include Thought I had all of'm earlier. Src/LinearSolvers/C_CellMG/CG_1D.F Src/LinearSolvers/C_CellMG/CG_2D.F Src/LinearSolvers/C_CellMG/CG_3D.F commit e97c3037f3daf4bf729b84e3a8ba8a2d612d4bdc Author: vince Date: Mon May 6 11:24:07 2013 -0700 profiling doc. Docs/Readme.profiling commit 207f834e43f9b98396ddf3cfdbe5b4e588b5e4d9 Author: lijewski Date: Mon May 6 10:40:46 2013 -0700 A little code rearrangment. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 12f7007da5691798ab9c7733640f28dcd921a382 Author: lijewski Date: Mon May 6 10:07:34 2013 -0700 The "S" in the CABiCGStab is now an input variable. It's currently limited to be in the range: [1,4]. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit ca705cd1d2d0edeaece43367faced8ecc85a6be5 Author: lijewski Date: Fri May 3 16:05:17 2013 -0700 Cut the number of apply() calls in CABiCG by two by doing each of the powers of p and r together in a single call instead of one call for each of the powers of p and r separately. Mostly this cuts down on FillBoundary() calls and should be a win in parallel. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit e16c033b28e53d7a662f82774297b8cd5bff1058 Author: lijewski Date: Fri May 3 16:03:46 2013 -0700 Removed a number of num_comp==1 assertions. I wanted to be able to call apply() with more than one component. Appears to work. Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp commit 17840884621799089b7e4ce1e02b5a3b5057a373 Author: lijewski Date: Fri May 3 14:17:53 2013 -0700 Changed some ifndef clauses to the more natural ifdef. Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 387713cb85ab3782890e968556b75b9c7fc35ae2 Author: lijewski Date: Fri May 3 13:58:58 2013 -0700 Some more work on convergence criteria for CABiCG. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit b5933d22a140fd12276edc12d3acc544990929c9 Author: lijewski Date: Fri May 3 09:56:17 2013 -0700 Be a little more careful about convergence tests. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 66879ba7c63922398265d0b3a808e0e49b17583c Author: lijewski Date: Fri May 3 09:05:18 2013 -0700 Removed some unneeded code. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 06e7663c74b229d3c9e030722b07d086ac7e61c6 Author: lijewski Date: Thu May 2 19:57:04 2013 -0700 Some refinrements and bug fixes. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 8595a8351c6a587292c3149a13f596331c0c7bc4 Author: lijewski Date: Thu May 2 16:06:04 2013 -0700 A little code rearrangement. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 7b4e51fdd5d15dc688d5b4723fbda33afcbb2128 Author: lijewski Date: Thu May 2 15:39:28 2013 -0700 Some work on making CABiCGStab output like BiCGStab output. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 175035e00fc9a1c8f68a6694f81038c3c123ae8a Author: vince Date: Thu May 2 14:19:33 2013 -0700 fix for serial. Src/C_BaseLib/Profiler.cpp commit edc5704f3f735189695cd17c2b67b53c6b4ce30c Author: vince Date: Thu May 2 14:09:20 2013 -0700 added mf test code. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 31be56d7d8ba9a629a8f4b2d481a25fe321e93e4 Merge: e50480231 a0064c941 Author: vince Date: Thu May 2 14:08:17 2013 -0700 merge issue. commit 7a7345eec0e3002e18096cfbfa5dbcbbf2efe15b Author: lijewski Date: Thu May 2 14:06:15 2013 -0700 Added some profiler calls. Seems to work in parallel. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 561b456a58529c32b79b5f212e507cd4fb9f0072 Author: lijewski Date: Thu May 2 12:49:54 2013 -0700 Looks to be more-or-less working! Src/LinearSolvers/C_CellMG/CGSolver.cpp commit febf34dba7cc701a78c73e16a543f062cf36d587 Author: lijewski Date: Wed May 1 17:20:46 2013 -0700 Getting closer ... Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 5e991b8da18ba638acb91ee9a437f2b2c85fafee Author: lijewski 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 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 Date: Wed May 1 15:39:59 2013 -0700 Added BuildGramMatrix() code. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit c0b0eb745f4436aa2db05b9c9934fb48d93ce6dd Merge: 08269643f 9fd0aba43 Author: lijewski Date: Wed May 1 14:51:55 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 08269643fc73491835985cf1a4d785defe18c492 Author: lijewski Date: Wed May 1 14:51:41 2013 -0700 More work ... Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 8b42d53eb1f2d2ff68b3ea616c9b131726a4f57c Author: lijewski Date: Wed May 1 14:42:24 2013 -0700 A little more progress. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit b438010dfa1b79dcf6ce3dde7a6825cb23213739 Author: lijewski 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 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 Date: Wed May 1 13:07:51 2013 -0700 Changes for Blue Waters Cray compiler. Tools/C_mk/Make.Linux commit c243c05f9e7506bad3397409774e4227fdec29c1 Author: lijewski Date: Wed May 1 12:58:24 2013 -0700 Some work on CA BiCGStab. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 99cc2911d360a9f06075ca4a8fcdf2b0900d52e6 Author: lijewski Date: Wed May 1 12:24:53 2013 -0700 A little cleanup. Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp commit f891f99279cf90d0045705fe7a6aacdcbc0fb7fd Author: lijewski Date: Wed May 1 11:13:21 2013 -0700 Some setup to try & implement a communication avoiding BiCGStab solver. Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp commit d498593a3c402ef476434d5cba63461a20cc5e15 Author: lijewski Date: Wed May 1 11:12:48 2013 -0700 Removed stuff for setting default CG solver. It's now only in one place: in the CG code itself. Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 45c81dc7cfea1ec0d44e25dbcfbb410d06c0885f Author: Weiqun Zhang Date: Tue Apr 30 14:40:46 2013 -0700 Added optional argument verbose to ParticleBase::Reset so that we can turn off a print statement. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit ddc5679364051c4d64eda4faafe7ce3588e074d7 Author: Weiqun Zhang Date: Tue Apr 30 14:19:03 2013 -0700 Added latex file describing equations solved by Exp_CNS_NoSpec. Tutorials/Exp_CNS_NoSpec/CNSEquations.tex commit a0064c941d8c661eebff80c7bc207a416a0fc976 Author: beckner2 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 Date: Wed Apr 24 16:05:07 2013 -0700 fixed ivLevel, ivLoc. Src/Extern/amrdata/AmrData.cpp commit dfddc5e4d79dc2e154ce2761f9f2ab0ac37c4201 Author: Weiqun Zhang Date: Wed Apr 24 13:02:03 2013 -0700 Added more functions for random numbers. In addition to the old Real BoxLib::Random() that returns a number belonging to [0,1], Real BoxLib::Random1() returns a real number that belongs to [0,1); Real BoxLib::Random2() returns a real number that belongs to [0,1); unsigned long BoxLib::Random_int(unsigned long n) returns an integer belonging to [0,n). Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 157ec8b6874f848d9e17dd07b646972b9c4e975b Merge: 1f5bc582d cf1bd9648 Author: lijewski Date: Fri Apr 19 16:31:55 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1f5bc582d5b5062a15effdc354baf0d167a2d5d6 Author: lijewski Date: Fri Apr 19 16:24:05 2013 -0700 Removed an unnecessary setVal(). Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit c4ee28517991d07ac074ab6e7a7837e3a801bc30 Author: vince Date: Thu Apr 18 15:03:02 2013 -0700 before/after call changes. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.cpp commit cf1bd9648b6fa8eee58509ee3e579e0637b988bf Author: Matthew Emmett Date: Wed Apr 17 15:49:08 2013 -0700 Add parallel_set_comm. Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit 1752c72c714999d5c84d3fb1b28cf4319fcd70fc Author: vince 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 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 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 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 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 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 Date: Fri Apr 5 13:33:09 2013 -0700 beforecall. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit d41405989f32615bfafcbcd460812bf8be410cce Author: lijewski Date: Thu Apr 4 15:13:35 2013 -0700 Yet more replacements of divisions by multiplications. Src/LinearSolvers/C_TensorMG/DV_3D1.F Src/LinearSolvers/C_TensorMG/DV_3D4.F commit 040e63992bee1d43b551ce9963b823392c4990c8 Author: lijewski 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 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 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 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 Date: Thu Apr 4 10:51:21 2013 -0700 Elide some reductions in BiCGStab. Src/LinearSolvers/F_MG/itsol.f90 commit 387fbf5ef6fdbb7e3613a0cb34285207c23e6b12 Author: lijewski Date: Thu Apr 4 10:51:00 2013 -0700 stencil_norm() now takes an optional "local" flag. Src/F_BaseLib/multifab_f.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 commit b46f26e91887e56943f0ed9f01ae76801414afb5 Author: lijewski Date: Thu Apr 4 10:05:43 2013 -0700 Added optional argument "local" to norm_inf() so we can calculate the local value of the norm without doing the parallel reduce. Src/F_BaseLib/multifab_f.f90 commit d93bdcbc25a9d56e625eafd46e2542d1980956e7 Author: lijewski Date: Wed Apr 3 16:16:50 2013 -0700 Elided another reduction in BiCGstab by calculating the local values of two norms() and then reducing them together. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit b50f2a69abca2f2a188fef5dfeeca76a57b5df05 Author: lijewski Date: Wed Apr 3 15:28:27 2013 -0700 More eliding of divides. Src/LinearSolvers/C_TensorMG/DV_3D1.F Src/LinearSolvers/C_TensorMG/DV_3D2.F commit 1ddbb0e143f0a2c67a3fd183a97b459564d3942c Author: lijewski Date: Wed Apr 3 15:00:39 2013 -0700 Replaced most divides by multiplies in apply(). Src/LinearSolvers/C_TensorMG/DV_3D1.F commit 1aadec77b71c2d701c0b0fac320b63942300c2a7 Author: vince Date: Wed Apr 3 13:30:26 2013 -0700 nfiles for headers. smaller header files. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Profiler.cpp commit faf12c76e3601367807cb572cf5f663c8826ff33 Merge: 825de481f 366cc6184 Author: Chris Malone 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 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 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 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 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 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 Date: Mon Apr 1 16:40:33 2013 -0700 fixed nfiles init. Src/C_BaseLib/VisMF.cpp commit 300a680b619b58947004a5ef7a3a1c5aa9c5ff58 Author: beckner2 Date: Mon Apr 1 16:39:12 2013 -0700 fixed init nfiles. Src/C_AMRLib/Amr.cpp commit b72cb6d588301ba84c226723302e8b437bd20bfa Merge: 793dc7be6 826e47a33 Author: jbb Date: Mon Apr 1 15:07:19 2013 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 793dc7be6da2c3ef3558a946e682900741c47416 Author: jbb Date: Mon Apr 1 15:06:56 2013 -0700 fixed mpi path on mothra Tools/F_mk/GMakeMPI.mak commit 77a4d077f000a99bd18a4bc6bf8e61cdae14a5e7 Merge: e2856a1a5 966077330 Author: beckner2 Date: Mon Apr 1 14:55:23 2013 -0700 hera. commit 9660773309011e99ef174fd59955e0fa3d5c969d Merge: 8ad8e193d 826e47a33 Author: vince Date: Mon Apr 1 14:48:55 2013 -0700 Merge branch 'master' into commprof commit 8ad8e193dab091f173d2065c6da5925afbaee330 Author: vince Date: Mon Apr 1 14:47:45 2013 -0700 tweak for waitsome. Src/C_BaseLib/Profiler.cpp commit 826e47a33e08cce9d2eb51581b082f23c8a9a4b4 Author: lijewski Date: Mon Apr 1 14:08:39 2013 -0700 A little cleanup. Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/LP_3D.F commit 279fdcfa07430ceb2679ed028f9054ba0a239257 Author: lijewski Date: Mon Apr 1 13:42:54 2013 -0700 Elided one of the global reduction operations in the BiCGStab by doing the "local" part of two dot products and then calling one global reduction on the "pair" of values. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit e2856a1a5ca31328f8d681b425c0e5d47f345446 Author: Vincent Eric Beckner Date: Mon Apr 1 11:51:53 2013 -0700 hera. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 2d70b9b6759409c9518b9c6485408337272f4d69 Author: lijewski Date: Mon Apr 1 11:11:31 2013 -0700 Removed OpenMP stuff. Not enough work in bottom solver to be worth it. Src/LinearSolvers/C_CellMG/CG_3D.F commit 8d398f598da36c5261c7164a992d93b00d606648 Author: vince Date: Fri Mar 29 17:20:45 2013 -0700 more support for send recv and nametags. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit da914bb7c0bf83ee307d71a5eba1f4fe86b8ec78 Author: lijewski Date: Fri Mar 29 09:20:22 2013 -0700 Changed many of the divides to multiplies for a modest speedup. Src/LinearSolvers/C_TensorMG/DV_3D3.F commit 1a1e9bfd9acc37b6449afcfa3b6595c17048f7f1 Author: vince Date: Wed Mar 20 16:18:04 2013 -0700 improved flushing. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 3c106e75fbabb5849c053681ef238aa294c920a8 Author: lijewski Date: Wed Mar 20 15:59:49 2013 -0700 Don't need -ftree-vectorize for gnu. It's implied with -O3. Tools/C_mk/Make.defs commit f3ad326fc27fa80b4c4da4ff9d69b202429bd6df Author: vince Date: Wed Mar 20 10:42:56 2013 -0700 added more profiling. Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/StateData.cpp commit 60633b76ff88d852ca6b459bbfa3aedb182b2988 Merge: 024965a93 c259ab401 Author: lijewski 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 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 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 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 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 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 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 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 Date: Thu Mar 14 13:38:47 2013 -0700 A little cleanup. Tools/C_mk/Make.defs commit 6b01d33aebfee08a107f60591dfdbf041eff4c06 Author: lijewski Date: Thu Mar 14 12:56:37 2013 -0700 Make sure C flags are same as C++ flags for gnu. Tools/C_mk/Make.defs commit 4f349682d28733aa12c55203f88ac1fbe4215489 Author: vince Date: Tue Mar 12 16:19:57 2013 -0700 verified flushing, allow profiling without comm, named more barriers, cached times to header. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.cpp Tools/C_mk/Make.defs commit 73493ac184493dac606206ccd6f76fe139712a2c Author: vince Date: Mon Mar 11 16:21:37 2013 -0700 made call orders consistent. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 8ca4d061887c0f6ecedb3b26d1af9d71a7f84500 Author: vince Date: Fri Mar 8 13:22:21 2013 -0800 merged interfaces, added calls. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit f8dfb7ae394673ef67df01b8e7469a311904a4c4 Author: Weiqun Zhang Date: Mon Mar 4 13:00:08 2013 -0800 Option to dump a plotfile for errors in finite-difference fcompare ffdcompare.f90 commit 5890360fb18d9746e22bedaea0f93056d4619e21 Author: vince Date: Fri Mar 1 14:51:53 2013 -0800 added tracking of reduction wait times. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 9332aed6a6840277207161f8a031c6c92dfae170 Merge: 3f2e95eae 9b251b45a Author: Matthew Emmett Date: Thu Feb 28 13:31:30 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3f2e95eaedfc00ce1608f5e0607be5143bd18724 Author: Matthew Emmett Date: Thu Feb 28 13:31:24 2013 -0800 Add profiling to multifab_saxpy_3. Src/F_BaseLib/multifab_f.f90 commit 91c02a2ebfeddfad376a21606ffe05b7d38ac824 Author: vince Date: Thu Feb 28 12:01:51 2013 -0800 barrier changes. Src/C_BaseLib/Profiler.cpp commit 95f5e1338ccdddbbd21d0f013299014fbd26a985 Author: vince Date: Thu Feb 28 11:24:38 2013 -0800 more tags, reduced function parameters. Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 9b251b45a80485f5bfe095b59c6e5cdf192f86f4 Author: ajnonaka Date: Thu Feb 28 10:22:01 2013 -0800 cleanup of max_mg_nlevels. also fixed the single-grid case, which was not allowing for a 2x2 bottom solve due to some messed up logic that was protecting us in the (unused to my knowledge) minwidth=1 case Src/LinearSolvers/F_MG/mg.f90 commit 3881653a26edf916b66ca57f0133eadfe718a2ad Author: lijewski Date: Tue Feb 26 09:08:23 2013 -0800 Added "-fp-model precise" to the optimization options for both the C++ and Fortran flags for Intel. This fixes an optimization bug in the DME_jet problem on edison. Weirdly, the default for Intel is to allow extensive floating point rearrangement during optimization. The above option disables enough of that such that the problem appears to run correctly. Tools/C_mk/Make.defs commit 80f34879688937a2c373f940b86af362d9be11d6 Author: lijewski Date: Tue Feb 26 07:21:39 2013 -0800 A workaround to the tellp() bug we found on edison.nersc.gov. Hopefully it doesn't break anything else :-) Src/C_BaseLib/VisMF.cpp commit 9d4649330339d566f6b077d01d01d77767ae0bf9 Author: Weiqun Zhang Date: Mon Feb 25 13:37:14 2013 -0800 fcompare for finite-difference results ffdcompare.f90 commit f0c00a0ac18ad7bbf34689e53a27ccda11f7f421 Author: Ann Almgren Date: Sat Feb 23 17:19:02 2013 -0800 Add GetParticleData access routine. Src/C_AMRLib/Particles.H commit dbae66051298f1ca8183eda4d85b41a6cc91ff03 Author: Michael Zingale Date: Fri Feb 22 19:18:58 2013 -0500 add -h fp0 to all the Cray optimized flags. Experimentation on Titan has shown that this prevents strange compilation errors resulting in crashes in BoxLib. This forces the compiler not to do any crazy optmizations that violate the floating point standard. Tools/C_mk/Make.Linux commit 38bfb172a48fc88086cdf85bf3c30e9a1c30590e Author: lijewski Date: Thu Feb 21 16:49:10 2013 -0800 A little cleanup. Tools/C_mk/Make.defs commit a1eb3051c3eac2c490330d756462a4bdbf61bd5c Author: lijewski Date: Thu Feb 21 14:58:35 2013 -0800 Merged in GhostParticleID and VirtualParticleID and cleaned up CreateVirtualParticles() and CreateGhostParticles() a bit. Src/C_AMRLib/Particles.H commit a278ee2a5a6dbe80fa403ce326e687c6d8692798 Merge: 4275788b5 7624abc0d Author: lijewski Date: Wed Feb 20 12:54:05 2013 -0800 Merge branch 'redistribute' commit 4275788b576d8c2a415efcc6783db10e8bfb9eb9 Author: lijewski Date: Wed Feb 20 08:38:53 2013 -0800 Removed IF() qualifiers on OMP PARALLEL DO loops. I recently found an example on edison where the presence of one of these qualifiers caused a compile to take 100x longer than when it's not present. I just don't think the compiler can be doing anything good/useful in that time. Src/LinearSolvers/F_MG/cc_restriction.f90 Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/edge_restriction.f90 Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_restriction.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 commit dccc407d89aa581b3de904d32fb5c77766c2ee45 Author: vince Date: Tue Feb 19 17:36:57 2013 -0800 added user filtering and name tags to separate parts of the code for easier communication analysis. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 8ccc515e0b063f342a3666373589d5023fba11cf Author: lijewski Date: Tue Feb 19 15:11:23 2013 -0800 Got this stuff to compile again; it's been a while. Not sure whether it works or not. Some of the stuff with the new way to specify stencils may require some modification. Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/cc_single.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/nodal_single.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 0e7465f1c492430ae5851c66c1c90bfec00c4ab0 Author: lijewski Date: Tue Feb 19 15:10:31 2013 -0800 Added edison stuff to mirror hopper. Tools/F_mk/GMakeMPI.mak commit 604b151e08337cb57dd9dd09163facbf1b606ee1 Author: vince Date: Tue Feb 19 14:59:47 2013 -0800 implemented flushing of the commstats. Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit d11e171d6f9fe243bfe95272e0bd75b690f3c25c Author: lijewski Date: Tue Feb 19 13:58:14 2013 -0800 Remove some COLLAPSE() stuff I recently added. The Intel compiler on edison generates bad code. Src/C_BaseLib/SPECIALIZE_3D.F commit 3775471547d77db2a85912fe38ea90c1fde7680a Author: lijewski Date: Tue Feb 19 12:35:13 2013 -0800 Revert out all the recent OMP COLLAPSE stuff. The lastest Intel compiler on edison (13.0.1) produces bad code. Hopefully I can find a simple example that illustrates the bug to pass on to Intel. Src/F_BaseLib/fab.f90 Src/F_BaseLib/multifab_f.f90 commit c1cd4951826853042a6c729d37e34858d83f6ec2 Author: lijewski Date: Tue Feb 19 09:08:15 2013 -0800 Add -openmp flag for Intel C compiler when USE_OMP=TRUE. Tools/C_mk/Make.defs commit 939ab6896902adbe59677a10b133ac4de853f4d3 Author: lijewski Date: Tue Feb 19 09:04:41 2013 -0800 Wrapped omp pragmas with ifdef _OPEN to shut up warnings when OpenMP is not enabled. Src/F_BaseLib/fabio_c.c commit 05c043a87facb899b9387296f40094ebe67ee90c Author: lijewski Date: Tue Feb 19 08:18:11 2013 -0800 Duplicated hopper stuff for edison. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit 7624abc0d210bc021402b264ab325b895ac0066d Author: lijewski Date: Sat Feb 16 21:19:27 2013 -0800 Fixed bug in commit for case where boundaries aren't all periodic. Src/C_AMRLib/Particles.H commit 8515b4de012706fb2c9ca72325c3c9eee3d6721d Author: lijewski Date: Sat Feb 16 19:08:13 2013 -0800 Some cleanup. Src/C_AMRLib/Particles.H commit 3f6cc2a0782ca958664fbe51301e31799f38bc66 Author: vince Date: Thu Feb 14 15:25:14 2013 -0800 named barriers, local message filtering, all/none filtering. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp Src/C_BaseLib/VisMF.cpp commit 65161c9643c88e2821429dadcd76f5e5d7a701c1 Author: lijewski Date: Thu Feb 14 11:22:43 2013 -0800 A little cleanup. Src/C_AMRLib/Particles.H commit 85c702ddb88375e12b70884a759a3a8dc43306f6 Merge: 3fcf2c414 ea6123309 Author: Chris Malone 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 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: fe48fb4d2 572c6fa76 Author: lijewski Date: Wed Feb 13 16:02:13 2013 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit fe48fb4d235d3f00f1c9d00d8fc936d813b33ce6 Author: lijewski Date: Wed Feb 13 16:01:55 2013 -0800 Made the destructor for ErrorRec virtual. Src/C_AMRLib/ErrorList.H commit e57d15421cd4da966fe4d6c0ab2d583fd4ded9b3 Author: lijewski Date: Wed Feb 13 15:53:24 2013 -0800 Little more work on AssignDensityDoit(). Still needs testing. Src/C_AMRLib/Particles.H commit 8d64711803f7887f73057fee5eb43451e3be875e Author: lijewski Date: Wed Feb 13 15:14:08 2013 -0800 More work on AssignDensityDoit(). Src/C_AMRLib/Particles.H commit 572c6fa76f852784f50db0673ee8039b8cfe01bd Author: Chris Malone Date: Wed Feb 13 17:33:08 2013 -0500 generalize the fix for PGAS error for Cray versions >= 8.1.2 Tools/C_mk/Make.mpi commit 77d59c903811cef6709ca81f698e971c332a1a44 Author: lijewski Date: Wed Feb 13 14:32:47 2013 -0800 Some work on AssignDensityDoit() to use send/recv pairs instead of Alltoallv(). Src/C_AMRLib/Particles.H commit c24266ef90e048512423999b27602658961c2787 Merge: e1689575c a672ff233 Author: lijewski Date: Wed Feb 13 13:07:35 2013 -0800 Merge branch 'redistribute' commit a672ff23362b41879e78701280acc6341dda27ea Author: lijewski Date: Wed Feb 13 13:04:15 2013 -0800 Merged RedistributeMPI() into AddParticlesAtLevel(). Src/C_AMRLib/Particles.H commit e1689575c6998daef05df10b3e81328344c7ae18 Author: Weiqun Zhang Date: Wed Feb 13 12:47:58 2013 -0800 got around Cray compiler bug Src/F_BaseLib/multifab_f.f90 commit 125d3c1cdbfd8e28fc0dbe873e6c124537ee4bd0 Author: lijewski Date: Wed Feb 13 12:25:52 2013 -0800 Merged in RedistributeMPI(). Src/C_AMRLib/Particles.H commit bcca699258f1db9b0f2bdc0c729634cc0f6939fc Author: lijewski Date: Wed Feb 13 10:45:49 2013 -0800 Finished Redistribute(). Now uses Send/IRecv instead of Alltoallv(). AddParticlesAtLevel() needs to be redone as well. Src/C_AMRLib/Particles.H commit c06a9bcf16d85f2eeb1f1aafe83f0afea01c1720 Merge: 7e9cdc826 e08b52493 Author: vince Date: Tue Feb 12 16:52:13 2013 -0800 Merge branch 'master' into commprof commit 7e9cdc826e086e717612820dff8b2b107a40f8d6 Author: vince Date: Tue Feb 12 16:51:10 2013 -0800 some changes to the output format. Src/C_BaseLib/Profiler.cpp commit 9f4fc50722b94d92a774950eb90c66f2029cc9fe Merge: 90779ab3d 12ca0c07d Author: vince Date: Tue Feb 12 11:03:52 2013 -0800 Merge branch 'master' into commprof commit 90779ab3ddab750077297534f253125c89e95c0f Author: vince Date: Tue Feb 12 11:03:35 2013 -0800 more support for the output parser. Src/C_BaseLib/Profiler.cpp commit 2ef3a07d3fb1af8aea4e189f7b2dd0261655ca03 Author: lijewski Date: Mon Feb 11 21:14:25 2013 -0800 Looking good. Redistribute() now uses Send/IRecv pairs instead of Alltoallv. Src/C_AMRLib/Particles.H commit 7c462d5e5380cbdf93a3505f5a3aeff6697ee17b Author: lijewski Date: Mon Feb 11 20:50:33 2013 -0800 Closer still. Appears to work. A little more refining to go. Src/C_AMRLib/Particles.H commit 16d4d8f92d16c1f9b8a25e7bed8f11e3e98443b8 Author: lijewski Date: Mon Feb 11 19:55:41 2013 -0800 More work on Redistribute(). Getting close. Src/C_AMRLib/Particles.H commit 88e42c14a834ee906be74d77a3dafc5f551e004b Author: lijewski Date: Mon Feb 11 19:24:06 2013 -0800 Yet more work on Redistribute(). Src/C_AMRLib/Particles.H commit 741831bc81710424183d3dd4f7713eb296b4d7e9 Author: lijewski Date: Mon Feb 11 18:59:35 2013 -0800 More work on Redistribute(). Src/C_AMRLib/Particles.H commit c1377b1b5cc2fb775294e8b7be7d4970c3cedafc Author: lijewski Date: Mon Feb 11 18:21:59 2013 -0800 Some work on Redistribute(). Src/C_AMRLib/Particles.H commit 34a763c9a1c5665be193dc36b60382ed3f3e3815 Author: vince Date: Fri Feb 8 14:58:46 2013 -0800 binary nfile output with header. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit e08b5249366da9e54349348079173708ac36ff41 Author: lijewski Date: Fri Feb 8 14:56:25 2013 -0800 Reverting out previous mod. Src/C_AMRLib/FLUXREG_3D.F commit 16c58e149add2f89fd2b3f444e6b4b54992404cd Author: lijewski Date: Fri Feb 8 14:03:51 2013 -0800 Some OMP tweaking. Src/C_AMRLib/FLUXREG_3D.F commit 1e91342411fc339295201b6b18f07a28f9b2f45b Author: lijewski Date: Fri Feb 8 13:45:58 2013 -0800 Some OMP tweaking. Src/C_BaseLib/SPECIALIZE_3D.F commit 2c3a232c307a0d89f5bb4268a9be3d55483e2b5c Merge: d3081ba20 18dea5885 Author: ajnonaka Date: Fri Feb 8 10:31:24 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d3081ba20aff11eeca17d46d92ac89fa15cbf3bd Author: ajnonaka 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 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 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 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 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 Date: Thu Feb 7 11:41:20 2013 -0500 More faverage edits/fixes to the RMS calculations faverage.f90 commit 77cefe1f80c3417de4b390a495c273c8a150acbc Author: vince Date: Wed Feb 6 17:22:53 2013 -0800 added more message tagging support. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 38e6ddea5257306bb372b36fb5d5bec9fc6df94f Author: vince Date: Wed Feb 6 16:19:02 2013 -0800 implemented nfiles for bl_prof output from all procs. Src/C_BaseLib/Profiler.cpp commit 45e5d650a6b927d392fb029c965d59fa3de5c80a Author: Weiqun Zhang Date: Wed Feb 6 16:14:52 2013 -0800 added OMP to setval in F_BaseLib Src/F_BaseLib/fab.f90 commit f333857d01b7e4f337e5c6671cb662ba9f109a5b Author: Weiqun Zhang Date: Wed Feb 6 16:14:00 2013 -0800 added OMP to sum_d in F_BaseLib Src/F_BaseLib/multifab_f.f90 commit 20edf70cb5d2a66a59e80f73c16e240505f705b7 Author: vince Date: Wed Feb 6 15:30:50 2013 -0800 added more counters. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 5149ee87dbb63819fe6c7945a06d8c74ab15b5cc Author: Adam Jacobs Date: Wed Feb 6 17:38:56 2013 -0500 Fixed AmrPostprocessing/F_Src/faverage.f90 so that it properly weighs data from coarse cells. faverage.f90 commit 9ac927beb5db2cc274cf965e4b8de7efcab13533 Author: Weiqun Zhang Date: Wed Feb 6 14:23:54 2013 -0800 OMP multifab copy in F_BaseLib Src/F_BaseLib/multifab_f.f90 commit 148ce3ba54c552eacc3750c528187541f8a3797f Merge: 58097fdf3 ac241eecb Author: Weiqun Zhang Date: Wed Feb 6 13:08:26 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 58097fdf3756d749c6b08dd99e7a652fa30be7e7 Author: Weiqun Zhang Date: Wed Feb 6 13:07:25 2013 -0800 Collapsed some OMP DO's. Src/F_BaseLib/multifab_f.f90 commit ac241eecb151740562be88e69e1473fbc0a24f9c Author: cmalone Date: Wed Feb 6 12:00:30 2013 -0600 updates for BW Tools/C_mk/Make.defs Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit e877f5d61610254e13d436343117314c51db5594 Author: vince Date: Tue Feb 5 16:32:46 2013 -0800 more handling profiled names that are not on the ioproc. Src/C_BaseLib/Profiler.cpp commit 7d407b1b3cb0d4e64fe4ee53e7ad3ac6ea036511 Author: vince Date: Tue Feb 5 15:58:15 2013 -0800 handle profiled names that are not on the ioproc. Src/C_BaseLib/Profiler.cpp commit 99c5f77c12ff07e229972af1b758bee8a4b58cd6 Author: vince Date: Mon Feb 4 15:05:19 2013 -0800 synced profiled names list across procs. Src/C_BaseLib/Profiler.cpp commit 13d89772ba000a86fec0e8002b419ad47ee24d46 Author: vince Date: Fri Feb 1 14:11:32 2013 -0800 nfiles for commstats, cleaner init. Docs/Readme.profiling Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 4c2fd37875d699f4b5ade58a48da2de60c430890 Merge: 6c2ec659e 744471833 Author: Ann Almgren Date: Fri Feb 1 13:51:28 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 6c2ec659ef23d017647ef1dbfe0661edae35e182 Author: Ann Almgren Date: Fri Feb 1 13:51:16 2013 -0800 Add more functions to ParticleContainerBase. Src/C_AMRLib/Particles.H commit 744471833e4a5c292624f9da6409d0166f216240 Author: Michael Zingale Date: Fri Feb 1 15:02:11 2013 -0500 one more clean-up -- there were two separate blocks for the GNU compilers, one invoked if we did COMP=gcc and the other for COMP=g++ -- they both did the same thing. Now we define a variable USE_GCC if we come in with either of these COMPs, and have a single block for the GNU compilers. Tools/C_mk/Make.defs commit 9234f2877ce1cf6137919df659f4fe21f2d5c083 Merge: f5768a85a feb2d00b0 Author: Michael Zingale 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 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 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 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 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 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 Date: Thu Jan 31 10:13:11 2013 -0800 Tweaks to InitFromBinary(). Src/C_AMRLib/Particles.H commit bbe234933c6774f679d0656a5f0ea64d3f3400a3 Author: lijewski Date: Thu Jan 31 09:54:30 2013 -0800 Added non-template abstract base class ParticleContainerBase from which the templatized ParticleContainer class now publicly inherits. This is so we can maintain a list (or vector) of pointers to ParticleContaiers as ParticleContainerBases. Any functions we wish to call using those pointers need to be declared as pure virtual functions in the base class, exactly matching the signature in the ParticleContainer class itself. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 58f1cdb29aa8548dca67e81d6b38d7863c78c3f6 Author: vince Date: Wed Jan 30 17:19:50 2013 -0800 barrier tagging, named comm types. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 5c370b577b1a62e7b42ebfffc2b86254cc72e330 Author: Ann Almgren Date: Wed Jan 30 13:43:39 2013 -0800 Correction to new impose_refine_grid_layout call (must pass in lbase as new_finest) Src/C_AMRLib/Amr.cpp commit 2634747cdc011ae2bc39dce8106a881549b4fc42 Author: Ann Almgren Date: Wed Jan 30 13:42:22 2013 -0800 Impose refine_grid_layout at level 0 earlier in the grid_places routine so that it is still imposed even if we return with fixed_grids. Src/C_AMRLib/Amr.cpp commit 75acffefbc0b98bcee358249fa42683d4fed72f8 Author: lijewski Date: Tue Jan 29 16:47:45 2013 -0800 An attempt to better distribute the NReader processes in IntFromBinaryFile() by building a set of NReaders processes from the full range [0,NProcs) using a random number generator. The idea is to minimize the number of reader processes per Node, so that each reader can use more of the available memory on the Node. Src/C_AMRLib/Particles.H commit 1da5946d54ba4f4067328688ca037c5dddbab1e0 Author: vince Date: Tue Jan 29 15:48:06 2013 -0800 more communications profiling. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 12ca0c07d7cfc275a5f534376e271a3808c676f6 Author: Ann Almgren Date: Tue Jan 29 15:03:37 2013 -0800 If we can't use mg.bottom_solver = 4 then just set it to one instead of aborting with an error. Src/LinearSolvers/F_MG/mg.f90 commit dc824bc2e6222e504e481a91b78c2c8358907703 Author: Ann Almgren Date: Tue Jan 29 10:29:42 2013 -0800 Fix comment about Nprocs > ngrids. Src/C_AMRLib/Amr.cpp commit ee3de04615987764b7e8c185df027119018cb5b0 Author: Ann Almgren Date: Tue Jan 29 10:21:49 2013 -0800 We now impose the refine_grid_layout criterion (breaking up grids into smaller chunks if nprocs > ngrids) in a call from defBaseLevel as well as in a call from regrid so we fix the grids at level 0 at the initial time (unlike before) and if max_level = 0 (unlike before). Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 2548a77c865d493384939f59ab232986e78d718d Author: vince Date: Mon Jan 28 11:31:09 2013 -0800 start of comm profiling. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp commit 1909ba20e7029cf8759ae213d1a89921891813b8 Author: vince Date: Fri Jan 25 14:20:34 2013 -0800 eliminated warnings. Tests/RoseTests/CPP/NullTransTest/PROB_3D.F commit a7eb867e646425930fd626b6140353f2504e82a5 Merge: b530a9669 0ac36b671 Author: Marc Day Date: Fri Jan 25 14:15:49 2013 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 0ac36b671119171203d90e254dcbedf0147b30bf Author: vince Date: Fri Jan 25 14:13:49 2013 -0800 added code to gracefully exit on user stop request, so the profiling will still print. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit b530a9669bfccce50dfb35890da5bc3b3cffc02b Author: Marc Day Date: Fri Jan 25 13:42:21 2013 -0800 Fixed other remnants of multi-component operator data Src/C_BoundaryLib/InterpBndryData.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp commit 51dc44e104d9f04689939bdaf6c46c5e697406cc Merge: fd5561989 28e0d6ae9 Author: Marc Day 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 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 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 Date: Thu Jan 24 09:21:11 2013 -0800 Update makefile for Intel 13 Tools/F_mk/comps/Linux_intel.mak commit 4d8a71d97b550f2b2f10f54242be3637a74e053f Merge: d852bc8db d573eaa80 Author: Marc Day Date: Wed Jan 23 18:37:46 2013 -0800 Merge commit 'd573eaa' commit d573eaa80bed94e3812ddc6174516ff5caa453e0 Author: Marc Day Date: Wed Jan 23 18:36:29 2013 -0800 Modify interface to a number of linear solver support structures to generalize access/usage Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit d852bc8db22b510d4e1e8cf10e591526ce8b5727 Author: Weiqun Zhang Date: Wed Jan 23 11:01:39 2013 -0800 More OMP to the nonblocking multifab_fill_boundary Src/F_BaseLib/multifab_f.f90 commit f9139d1589d48baf50ef1b70e671635c14c65e3f Author: Chris Malone Date: Wed Jan 23 12:54:14 2013 -0500 fix how we capture version number for Cray; this is a hack Tools/C_mk/Make.mpi commit 65918d5cd55b34dbfc97bbfe63810bd6fe0e1d9f Author: Christopher Malone Date: Wed Jan 23 12:40:15 2013 -0500 titan updates Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi commit 259ade08c4e2342ef9d21013e26e2df830df3819 Author: Weiqun Zhang Date: Tue Jan 22 13:41:01 2013 -0800 OpenMP part of nonblocking fill_boundary Src/F_BaseLib/multifab_f.f90 commit 72f3d964dffcdd787a182295755185f197ef3a04 Author: Weiqun Zhang Date: Tue Jan 22 13:13:13 2013 -0800 OpenMP FAB_CONTAINS_NAN and INF Src/F_BaseLib/fabio_c.c commit 63db3471e7d60d26b9b7e7a8261ddcff6c37a659 Author: Michael Zingale Date: Sun Jan 20 18:53:04 2013 -0500 remove python_plotfile python_plotfile/vis.in commit fb04d09cf5d79cb98f85079614e16f4909b0a163 Merge: 021ac572e a1e5c2d39 Author: Michael Zingale 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 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 Date: Sun Jan 20 16:10:02 2013 -0500 fix a comment python_plotfile/plotsinglevar.py commit 653b8856fba5055df2a77d60ade77a2e4976f760 Author: Michael Zingale Date: Sun Jan 20 16:08:55 2013 -0500 greatly simplify the GNUmakefile -- we only really need the BoxLib F_Src python_plotfile/GNUmakefile commit 3f53bad9815681187777ff8dd5a2f5ea2d43ef38 Author: Michael Zingale Date: Sun Jan 20 13:32:16 2013 -0500 sample runtimevis.py inputs file python_plotfile/vis.in commit 99b6f7281191aa2776181c0bd8af8c084c3d636a Author: Michael Zingale Date: Sun Jan 20 13:31:44 2013 -0500 add tight_layout -- this really makes things look better. Also fix the problem if the plt file ends in / python_plotfile/runtimevis.py commit b23fd6586125274ace6895e4f4ed6b74c28e96d2 Author: Ann Almgren Date: Wed Jan 16 13:31:59 2013 -0800 Remove XGRAPH stuff for BoxLib version of this. Tutorials/AMR_Advection_C/Source/main.cpp commit 4146900c2a5d8454fad9a5ad175e440daaf2c8af Author: Regression Tester account Date: Wed Jan 16 09:58:58 2013 -0800 Regression Testing script: added capability of switching to non-master branches Tools/RegressionTesting/testnew.py commit c93cd91c0e31f3756a15d389afbd38ae8def76ad Author: vince Date: Tue Jan 15 16:05:14 2013 -0800 changed flags for fortran. Tests/RoseTests/CPP/NullTransTest/GNUmakefile commit 45d311bb0bee7f40300816f6b81549c38c1dd3e8 Author: vince Date: Mon Jan 14 15:21:46 2013 -0800 added some simple rose translation tests. see weiqun for the f90 parts. Tests/RoseTests/CPP/NullTransTest/GNUmakefile Tests/RoseTests/CPP/NullTransTest/PROB_3D.F Tests/RoseTests/CPP/NullTransTest/PROB_F.H Tests/RoseTests/CPP/NullTransTest/README Tests/RoseTests/CPP/NullTransTest/RoseNullTest.cpp Tests/RoseTests/F90/Readme Tests/RoseTests/F90/test1/GNUmakefile Tests/RoseTests/F90/test1/main.f90 Tests/RoseTests/F90/test2/GNUmakefile Tests/RoseTests/F90/test2/main.f90 Tests/RoseTests/F90/test3/GNUmakefile Tests/RoseTests/F90/test3/bc.f90 Tests/RoseTests/F90/test4/GNUmakefile Tests/RoseTests/F90/test4/main.f90 Tests/RoseTests/F90/test5/GNUmakefile Tests/RoseTests/F90/test5/main.f90 Tests/RoseTests/F90/test6/GNUmakefile Tests/RoseTests/F90/test6/main.f90 Tests/RoseTests/F90/test6/omp.f90 Tests/RoseTests/F90/test7/GNUmakefile Tests/RoseTests/F90/test7/main.f90 Tests/RoseTests/F90/test7/probin.f90 Tests/RoseTests/F90/test7/runtime.f90 Tests/RoseTests/F90/test8/GNUmakefile Tests/RoseTests/F90/test8/init_data.f90 Tests/RoseTests/F90/test8/main.f90 commit 244eba0af80874f9bb56812409e9317bd48a5ac0 Author: lijewski Date: Mon Jan 14 10:00:33 2013 -0800 Compile fillfab.f into tFillFab. Tests/C_BaseLib/GNUmakefile commit 89943ef523db39f1c682f267a2339fe7600ad791 Author: Michael Zingale Date: Sun Jan 13 21:16:34 2013 -0500 add time python_plotfile/runtimevis.py commit 088f60c564482444511be55fc7f3acd86cfb741c Author: Michael Zingale Date: Sun Jan 13 20:44:15 2013 -0500 looking prettier now python_plotfile/runtimevis.py commit 958d8f47c126673122b0a23070c82c9ac3aea90a Author: Michael Zingale Date: Sun Jan 13 20:29:57 2013 -0500 basic functionality working python_plotfile/runtimevis.py commit 14a0236bb6b693854a9a482f532f8bb6adb9d6e5 Author: Michael Zingale Date: Sun Jan 13 18:21:10 2013 -0500 more progress python_plotfile/runtimevis.py commit 7a884a82f0c45448c137f13ae8862b0147f45277 Merge: 5a5a16ab5 23ec5ddc0 Author: Michael Zingale 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 Date: Sun Jan 13 18:00:08 2013 -0500 start of a runtime vis script python_plotfile/runtimevis.py commit bc6b95a682ca1d6f43dcbebfc2de1427c11d0f05 Merge: 4df0ea425 17ca07d9f Author: ajnonaka Date: Thu Jan 10 16:52:27 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 4df0ea4255715ca6fdf2609411fd11ba498e7ee9 Author: ajnonaka Date: Thu Jan 10 16:51:06 2013 -0800 introducing HOM_DIR bc type. certain problems need to distinguish between EXT_DIR (e.g., for inflow) and HOM_DIR (e.g., for velocity at a wall) Src/F_BaseLib/bc.f90 commit 17ca07d9fe5f6afe51abbcf9ba22682cc6e54579 Merge: 512f17e24 40a5cdbc9 Author: Ann Almgren Date: Wed Jan 9 15:21:54 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 512f17e242bd692298664d9d6ec6db07c808aab5 Author: Ann Almgren Date: Wed Jan 9 15:21:39 2013 -0800 local_only --> only_local so declarations match. Src/C_AMRLib/Particles.H commit 40a5cdbc91958e240afe9f0325dd24cde700b425 Merge: 4e0ff4498 32f22dbe5 Author: vince Date: Wed Jan 9 14:49:16 2013 -0800 Merge branch 'streamretry' commit 32f22dbe5022870475461a1e6716c55e8dff60d6 Author: vince Date: Tue Jan 8 16:15:19 2013 -0800 stream retry for checkpoint and plotfiles. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 4e0ff449815c11d4bebacfe26e0ef69490b70566 Author: lijewski Date: Tue Jan 8 09:23:45 2013 -0800 Check in with tMF enabled not tFillFab. Tests/C_BaseLib/GNUmakefile commit 24b443dbcdd195378c05b8fb4b25a0931e598729 Merge: 461a347f0 5ef5b891d Author: lijewski Date: Tue Jan 8 09:05:16 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 461a347f0e583ba0886369405b8fab866cb69db6 Author: lijewski Date: Tue Jan 8 09:04:49 2013 -0800 Added FillFab stuff to add values from a file into a fab. Only works for 2D at the moment. Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/fillfab.f Tests/C_BaseLib/tFillFab.cpp commit 5ef5b891d45a5993bf62e142da8020f37138c921 Author: ajnonaka 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 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: e04311fe6 bb2bbb79b Author: ajnonaka Date: Fri Jan 4 15:38:32 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e04311fe68b6768955c5ef999a07d8029693bec2 Author: ajnonaka Date: Fri Jan 4 15:37:33 2013 -0800 added the option for the code to *not* abort if you have reached the maximum number of v-cycles, as controlled by abort_on_max_iter in mg_tower.f90. Fixed a bug in the ml_cc solver where on the *last* v-cycle, the solver didn't actually do any smooths Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit bb2bbb79b4c14120f673bec32e45adf55c06e2c0 Author: Weiqun Zhang Date: Thu Jan 3 16:40:08 2013 -0800 Made make for ROSE again. Tools/F_mk/GMakedefs.mak commit 90b87096d92b66f74a26b595dd804a9375a9c361 Author: Weiqun Zhang Date: Thu Jan 3 16:26:45 2013 -0800 Fixed a bug in the make system introduced by me today. The perl scripts require a space after "-I". Tools/F_mk/GMakedefs.mak commit 1cb1b764c7406167170b3e044cde90cf3a77179d Author: Weiqun Zhang Date: Thu Jan 3 16:13:28 2013 -0800 Minor changes to make the code more readable and ROSE happy, because ROSE cannot handle d%d. Src/F_BaseLib/cutcells.f90 Src/F_BaseLib/vector_i.f90 commit 7df762f58437c1e113d25dc61ac4dbc87577466f Author: lijewski Date: Thu Jan 3 12:11:44 2013 -0800 Fixed OMP bug. Src/F_BaseLib/create_umac_grown.f90 commit c1fc023b538ab23afe01665ee08cf5538fd42d21 Merge: 1d48013ee 06319b1af Author: Weiqun Zhang Date: Thu Jan 3 10:45:58 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1d48013ee9ae746c5baf62606e22cefcb8c114eb Author: Weiqun Zhang Date: Thu Jan 3 10:44:51 2013 -0800 Rose support for F_mk Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/gfortran.mak Tools/F_mk/comps/rose.mak Tutorials/HeatEquation_EX1_F/GNUmakefile Tutorials/HeatEquation_EX5_F/GNUmakefile commit 06319b1affdf3905365f01dab85b8b663d3767d3 Author: ajnonaka Date: Thu Jan 3 08:42:36 2013 -0800 interface changes to simplify mac_applyop Src/LinearSolvers/F_MG/mac_applyop.f90 commit 61772f83e41e086d03d103a7eaaed5eb6011650f Merge: 3c411ee6f ccdc04d9d Author: ajnonaka Date: Thu Jan 3 08:26:29 2013 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3c411ee6f66b73e39c4fbd4b1065a5cb2ea1d331 Author: ajnonaka Date: Thu Jan 3 08:24:53 2013 -0800 move mac_applyop from VARDEN and MAESTRO into BoxLib/Src/LinearSolvers/F_MG... more applications will be needing this Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/mac_applyop.f90 commit ccdc04d9d5ceacda2f5981f882e751d5c5ff35bc Author: Michael Zingale Date: Wed Jan 2 19:05:39 2013 -0500 explain Real in C++ and dp_t in F90 Docs/GettingStarted/GettingStarted.tex commit 152e05f999fbcb28b40da8a1ea3e8fa24f1dd2d0 Author: Weiqun Zhang Date: Wed Jan 2 14:31:48 2013 -0800 Get around an Intel compiler bug that makes unnecessary copy when a_pointer(a_type%a_integer:) is passed to the first argument of parallel_isend and parallel_irecv. Src/F_BaseLib/multifab_f.f90 commit 1e65c3085945486b3f9c5dc26d3d13250bd36cb9 Author: Weiqun Zhang Date: Thu Dec 20 21:31:28 2012 -0800 Use -h noomp rather than -h thread0 to disable OMP for craycc Tools/F_mk/comps/Linux_cray.mak commit 133151e6c4a6cfd847248608850cd78d8b7013a2 Author: Weiqun Zhang Date: Thu Dec 20 17:34:04 2012 -0800 Explicitly disable OMP for Cray C compiler when OMP is not defined. Tools/F_mk/comps/Linux_cray.mak commit 59d79b962506492ffedc6fc1120d4dc369a0a5f7 Author: Weiqun Zhang Date: Thu Dec 20 17:25:10 2012 -0800 CFLAGS must also have -openmp when OMP is defined, otherwise SMC will fail when built with OMP using Intel. Tools/F_mk/comps/Linux_intel.mak commit 8cf767958888d158473d7f9102582d491b1f4879 Merge: 6b4e6a01c d7d6096ea Author: vince Date: Wed Dec 19 16:12:26 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 6b4e6a01cd699a548ef501ca05a1fbf64b2baf3a Author: vince Date: Wed Dec 19 16:12:12 2012 -0800 added rose support for mk. Tools/C_mk/Make.defs Tools/F_mk/GMakedefs.mak Tools/F_mk/comps/rose.mak commit 23ec5ddc038f93cfd25fbaffc14a0587fab8143a Author: Michael Zingale Date: Wed Dec 19 09:26:59 2012 -0800 use tight_layout() if it exists. Also reduce the number of tick labels for very narrow domains python_plotfile/plotsinglevar.py commit d7d6096ea9cde70521ed2682107a8324ce4ca2ba Author: Ann Almgren Date: Tue Dec 18 08:14:12 2012 -0800 Modify how we deal with initial_grids_file and regrid_grids_file -- we now read in the boxarrays soon after we parmparse the names of the files, and store these as static BoxArrays. Then later when they are needed in grid_places() we have them stored and do not read them in again. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit b74c7559777ab885d59661a563f1c5beaa24b176 Author: ajnonaka Date: Mon Dec 17 13:02:57 2012 -0800 a note about space/time-dependent boundary conditions in multifab_physbc Docs/F_AdvancedTopics/F_AdvancedTopics.tex Docs/Introduction/Introduction.tex commit 9e66e3bf514d9860c91c9aedd60bc2edad100992 Author: ajnonaka Date: Mon Dec 17 12:31:00 2012 -0800 added optional arguments: time, dx(:), prob_lo(:), prob_hi(:) for space/time-dependent boundary conditions Src/F_BaseLib/multifab_physbc.f90 commit 87b1d9fb96b632f2213517d02bc4b9faab1328eb Author: Ann Almgren Date: Fri Dec 14 15:33:10 2012 -0800 Add the option to set amr.initial_grid_file = as well as amr.regrid_file = This is similar to the regrid_file option, except that: 1) it is only used to set the initial grids file; there is no file specified for later regrids. 2) the max_grid_size criterion is not enforced on the initial grids generated this way, rather it is imposed after the grids are read. The point is to allow us to initially read in grids specified by an external routine which did not know about max_grid_size. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 0051502ffd2c47acb44277045c37f64ee45f52f7 Merge: cd6009883 7b4de0b0d Author: Weiqun Zhang 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 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: 349205204 cbf39e333 Author: lijewski Date: Thu Dec 13 11:00:06 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3492052044897b9a06c9b28431e95e780d0541a4 Author: lijewski Date: Thu Dec 13 10:58:08 2012 -0800 Added ParticleBase::MaxParticlesPerRead() for use in InitFromBinaryFile(). It's the number of particles that each reader should try to read before everyone does a Redistribute(). Currently it's defaulted to 100000. It's ParmParse-able as particles.nparts_per_read. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit cbf39e333cdcc04cf6fd5fa8fa9ffd68457e17a1 Merge: 30d784d45 be842ccfa Author: Michael Zingale 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 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 Date: Wed Dec 12 16:16:06 2012 -0800 More work on InitFromBinaryFile(). Src/C_AMRLib/Particles.H commit d7809cad5d32ecb4713f9549153c150b460feb1a Author: lijewski Date: Wed Dec 12 15:57:52 2012 -0800 A little more tweaking on InitFromBinaryFile(). Src/C_AMRLib/Particles.H commit 62e4239feb44f4002f565fae4a1c7a0e8abb7e2f Author: lijewski Date: Wed Dec 12 15:52:27 2012 -0800 More work on InitFromBinaryFile(). Src/C_AMRLib/Particles.H commit 2393c0a7c890519f94f8982e34f4fbe356cef5da Author: lijewski Date: Wed Dec 12 14:44:01 2012 -0800 Some work making InitFromBinaryFile() faster in parallel with large numbers of particles. Src/C_AMRLib/Particles.H commit f73c8c9d353307c9be9d1508fab0a1a7650fcb6c Author: Ann Almgren Date: Tue Dec 11 11:32:02 2012 -0800 Added writePlotNow routine to Amr.cpp and to AmrLevel. In Amr this routine now contains the various tests on whether to write a plotfile at this timestep. In AmrLevel it allows the application at level 0 to tell Amr to write a plotfile now. There should be no changes in the default behavior. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 7297bdb45b8638af5ccd26082d2c864f32835e6e Author: Marc Day Date: Mon Dec 10 14:26:05 2012 -0800 Virtualize a couple of functions to allow easier extensions into derived classes. Src/C_AMRLib/Amr.H Src/C_AMRLib/ErrorList.H commit 2cc1cafe172ea29b9c4f3621b634eb3ee37ed36c Author: vince Date: Fri Dec 7 16:19:52 2012 -0800 writeavg pct fix. Src/C_BaseLib/Profiler.cpp commit 4f9841bd9f6baa312b7455aab10922972d2361dd Merge: 0f0481031 43d6fbdac Author: vince Date: Fri Dec 7 15:07:00 2012 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 0f04810313ba6679973c5164595c512b002bb372 Author: vince Date: Fri Dec 7 15:06:28 2012 -0800 fixed writeavg percent. Src/C_BaseLib/Profiler.cpp commit 43d6fbdacc4c485e63299252a44f03fb5a1dd434 Author: lijewski Date: Fri Dec 7 14:53:38 2012 -0800 some profiling tweaks Src/C_AMRLib/Amr.cpp Src/C_BaseLib/ParallelDescriptor.cpp commit 67a0b7721855a1d6271160e2f91250f4b7b18e57 Author: lijewski Date: Fri Dec 7 13:19:38 2012 -0800 Added profilers to SFC & KNAPSACK. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 545dc0d24927b34f97e383c1738cb1a54fcfb0d3 Author: lijewski Date: Fri Dec 7 12:41:29 2012 -0800 added some Profilers Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BoundaryLib/FabSet.cpp commit bac2c145e6fa3ffb4676e4ab73d20bde9b050927 Author: lijewski Date: Thu Dec 6 15:11:28 2012 -0800 Comment out the "-warn all" stuff for Intel Fortran compiler. The EGLib stuff is just to old & crufty to pass this test. Tools/C_mk/Make.defs commit d9a0afb2fe1bdb60bd04792b0ee82bb1c53ad5d6 Author: lijewski Date: Thu Dec 6 10:40:04 2012 -0800 Add more compile time checking when using Intel fortran compiler. Tools/C_mk/Make.defs commit f27aab14022907461677c075fada9f2ea3c4c3a6 Author: Weiqun Zhang Date: Wed Dec 5 11:45:06 2012 -0800 Made the nonblocking multifab_fill_boundary safer in case it is not used properly. Src/F_BaseLib/multifab_f.f90 commit 818df3051bc4ab0421de15c9003e5d2c7a27ab46 Author: Weiqun Zhang Date: Tue Dec 4 16:02:43 2012 -0800 Switch the order of isend and irecv in the nonblocking multifab_fill_boundary. In principle, posting irecvs before isends is the right thing to do. Src/F_BaseLib/multifab_f.f90 commit e9f844b534edfd960515e9f04dbe169a1d238bae Author: Weiqun Zhang Date: Tue Dec 4 10:12:21 2012 -0800 Fix typo Tools/Release/release.py commit 41a8bbe9cff4f0a263b13c57bda2e503dbe450cc Author: vince Date: Mon Dec 3 12:07:31 2012 -0800 added stream retry for some output. Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 2c84c1ef211d4c05992c03baf5794e97842ee879 Merge: a4dc8483a 44d38ec20 Author: Matthew Emmett 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 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 Date: Tue Nov 27 17:36:11 2012 -0800 update to the i/o benchmark. Tests/IOBenchmark/IOTestDriver.cpp commit 42298f4470b094f00b83522d1b1d67116c48d1af Author: vince Date: Tue Nov 27 17:31:54 2012 -0800 tweaked the profiling output. Src/C_BaseLib/Profiler.cpp commit 08c58fb991636f4cb1429267e9b585dfcf1bcc16 Author: Weiqun Zhang Date: Tue Nov 27 14:48:12 2012 -0800 Special treatment for the case of no MPI jobs in the nonblocking multifab fill boundary. Src/F_BaseLib/multifab_f.f90 commit bad069d2dca50387a454aa731477d798920c7f55 Merge: 0fb9bb794 176048bfb Author: Weiqun Zhang Date: Tue Nov 27 12:20:42 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 0fb9bb794d25acdc85013284f794bdcccc12a070 Author: Weiqun Zhang Date: Tue Nov 27 12:17:56 2012 -0800 Changed the default sfc_threshold from 4 to 0 for F_BaseLib. This is a win for many tests. Also, F_BaseLib is now consistent with C_BaseLib. Src/F_BaseLib/layout.f90 commit 176048bfb80ed2671228a928aea4d4a34e55983d Author: lijewski Date: Tue Nov 27 10:54:47 2012 -0800 Changed the default for sfc_threshold from 4 to 0. This way, even if we have fewer grids than cores we'll get the Space Filling Curve distribution. Tests on hopper indicate this is a win. Src/C_BaseLib/DistributionMapping.cpp commit 2bfde03f60b6008d27c56a1c4d675172fbc9c13c Author: Weiqun Zhang Date: Mon Nov 26 17:06:32 2012 -0800 Fix a bug in parallel_test_one. I don't think anyone ever used this function. Src/F_BaseLib/parallel.f90 commit 862e9c003196570bc8d7c458bd3749407a740204 Author: Ann Almgren Date: Sun Nov 25 10:01:03 2012 -0800 Cleaned up version. Src/C_AMRLib/Particles.H commit d84bb130a610bc238dde54bf0cfa743b5f8ca08c Author: Weiqun Zhang Date: Wed Nov 21 10:41:19 2012 -0800 Fix a bug in my last commit. Src/F_BaseLib/multifab_f.f90 commit 3a1cddac41d49225e16e84fb02ad33fa10bb7c23 Merge: 5fa641b09 403dc58d0 Author: Weiqun Zhang Date: Wed Nov 21 10:32:12 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 5fa641b09ab39f3d6d53b343db97fa7a16c71171 Author: Weiqun Zhang Date: Wed Nov 21 10:29:51 2012 -0800 Add multifab_fill_boundary_waitrecv that will return when messages are received regardless the status of sending messages. Src/F_BaseLib/multifab_f.f90 commit 403dc58d09ef3dc3cb843eb64f138485d89e1f74 Merge: b12069727 2965e36e1 Author: Ann Almgren Date: Tue Nov 20 17:27:51 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit b120697275f4d92590c56eacbb0890877266ed3a Author: Ann Almgren Date: Tue Nov 20 17:27:37 2012 -0800 Add new access functions in Particles.H Src/C_AMRLib/Particles.H commit 2965e36e1cb2b823dfe9602dd73a164cf1ba43cb Author: vince Date: Tue Nov 20 15:43:59 2012 -0800 moved readme to docs. Docs/Readme.profiling commit bb7cae32ca175a758d59265983ae189f03646514 Author: vince Date: Tue Nov 20 15:35:43 2012 -0800 rewrote the c++ boxlib profiler. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/Profiler.H Src/C_BaseLib/Profiler.cpp Src/C_BaseLib/Readme.profiling commit b2854e00727e1bf278f0db67ba26a6e06a8b19fb Author: Ann Almgren Date: Fri Nov 16 15:16:45 2012 -0800 Add GetParticleVelocities routine. Src/C_AMRLib/Particles.H commit 07fc698cf652b54f7b571a9190f29bde33853ec8 Author: Ann Almgren Date: Tue Nov 13 14:29:50 2012 -0800 If bottom_solver type is not defined by the calling routine, then set default to BiCGStab (type 1) rather than type 3 which no longer exists. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 77ce5827a7448ccb367ef9a44ad6bcc25c8ffaa3 Author: Weiqun Zhang Date: Tue Nov 13 13:35:35 2012 -0800 For nonblocking multifab_fill_boundary_nowait, MPI tag is passed in as argument. Src/F_BaseLib/multifab_f.f90 commit 9fcaacbd11507f6b6672643d50713077e34621dd Author: Weiqun Zhang Date: Tue Nov 13 08:14:19 2012 -0800 Option to initialize MPI with thread support Src/F_BaseLib/boxlib_f.f90 Src/F_BaseLib/multifab_f.f90 Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit dc56abe8bb5763c84a2b65a9c6553bea169b026a Author: Weiqun Zhang Date: Mon Nov 12 17:24:11 2012 -0800 real "add mpi_test to the nonblocking multifab_fill_boundary" Src/F_BaseLib/multifab_f.f90 commit bb1213402966fee5240ef862a7f55eca632c2c43 Author: Weiqun Zhang Date: Mon Nov 12 17:21:52 2012 -0800 Revert "add mpi_test to the nonblocking multifab_fill_boundary" because I accidently committed some files. This reverts commit 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 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: 7549250e2 4e974a3d7 Author: vince Date: Thu Nov 8 17:25:26 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 7549250e2d28be2cd9bf23d983d966561392b6ad Author: vince Date: Thu Nov 8 17:25:15 2012 -0800 added random initialization, mb2, and more compact boxarray. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp Tests/IOBenchmark/README commit 4e974a3d736013b001ed359313aa258ba6986fa1 Merge: 6aaa57657 8f81bf74c Author: Weiqun Zhang Date: Thu Nov 8 17:12:06 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 6aaa576578c424583116d1561b922068c93b0e26 Author: Weiqun Zhang Date: Thu Nov 8 17:11:31 2012 -0800 Revert my previous change because it does not make any difference in performance Src/F_BaseLib/multifab_f.f90 commit 8f81bf74c3c142c08e11cc42083271c9e55713ca Merge: 8aef5f06c 98eef2970 Author: Michael Zingale 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 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 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 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 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 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 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 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 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 Date: Fri Nov 2 22:41:23 2012 -0700 minor improvement of the new fill_boundary Src/F_BaseLib/layout.f90 commit b3194b061f9531f2394a736137401f873a6aae41 Merge: b771dd30b 47536525a Author: Weiqun Zhang Date: Fri Nov 2 22:31:01 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit b771dd30b61072e97073200436e1261ca7bc7e0d Author: Weiqun Zhang Date: Fri Nov 2 22:30:52 2012 -0700 force cross to be true when idim .ne. 0 in the new multifab_fill_boundary Src/F_BaseLib/multifab_f.f90 commit 47536525a1037944b540488d38badc5cf6e55d62 Author: ajnonaka 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 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 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 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 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 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 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 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: f226be5ff a895aaff2 Author: Marc Day 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 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 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 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: e0e06b010 88947b7da Author: Ann Almgren Date: Thu Oct 25 15:23:30 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e0e06b010fc01c4c5739edeef1f8748fc186649f Author: Ann Almgren Date: Thu Oct 25 15:23:13 2012 -0700 Make the GetParticleLocationsAndMass new routine work in parallel. Src/C_AMRLib/Particles.H commit 88947b7daa00bdd22158c0b517c5c2a2b8f48fe4 Merge: 36f60c171 5dc34a5c0 Author: Marc Day 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 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 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: 633771fa7 f01b50174 Author: Michael Zingale 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 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: 3de93be49 72b8d1fd3 Author: Ann Almgren Date: Wed Oct 24 15:39:08 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3de93be49f72dcd8768ba7bab9718a95613c518e Author: Ann Almgren Date: Wed Oct 24 15:35:47 2012 -0700 1) Added TotalNumberOfParticles to return total number of particles. 2) Add GetParticleLocationsAndMass to return this data to an outside routine. 3) Fix abs --> std::abs in estTimeStep so that we use the real, not integer, version of abs. Src/C_AMRLib/Particles.H commit 72b8d1fd391bc3f2851f2c66626e75857c0d0487 Author: Michael Zingale Date: Wed Oct 24 16:36:43 2012 -0400 build_hash -> build_git_hash Tools/F_scripts/makebuildinfo.py commit 15fce1bad1d55af0d35c3be91aeec39f7426f9a4 Author: Michael Zingale Date: Wed Oct 24 16:31:45 2012 -0400 python version of make_build_info -- the shell version was getting hard to maintain. This one adds yet another git hash if it detects that we are compiling in a directory that is not part of the source tree, i.e. MAESTRO_Exec/ instead of MAESTRO/Exec/ Tools/F_scripts/makebuildinfo.py commit bb48d2abf9fc8d5fce806b872c77ad5f5094f2f2 Author: Weiqun Zhang Date: Mon Oct 22 17:09:19 2012 -0700 print more information Tools/RegressionTesting/reg_test_blame.py commit 2451eeedc7df7a4258d4ae73bc15f2b7c1391952 Author: Marc Day Date: Mon Oct 22 10:22:17 2012 -0700 Minor tweaks to solver interface Tutorials/AMR_PETSc_C/Source/Darcy.cpp Tutorials/AMR_PETSc_C/Source/DarcySNES.H Tutorials/AMR_PETSc_C/Source/DarcySNES.cpp commit 73bad4eea0de4676ca32fa4fb75519e3983f9808 Merge: cb477586f 1a1cf7fc9 Author: Marc Day 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 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 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 Date: Wed Oct 17 17:58:58 2012 -0400 get this compiling again tutorial/GNUmakefile commit cb477586fe791c4491b5ed7acf132ae2a6cdb994 Merge: 46153187f 5f13721f7 Author: Marc Day 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 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 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 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: 635c998e4 adf395089 Author: Weiqun Zhang Date: Thu Oct 11 14:53:41 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 635c998e4b08479d6c1d82ba3b296dc3c25e5c72 Author: Weiqun Zhang Date: Thu Oct 11 14:48:47 2012 -0700 Commented out some debug print statements that are not thread safe. Src/C_AMRLib/INTERP_3D.F commit adf39508954dcf6a011fca7b48b36d0707a33fd8 Author: ajnonaka Date: Thu Oct 11 14:11:23 2012 -0700 comment out the C++ stuff until we have something more substantial to say Docs/UsersGuide.tex commit 18c96d7b14538a2ac534a5e1e2782bd0d5988004 Author: lijewski Date: Wed Oct 10 15:48:04 2012 -0700 Fix long-standing bug in GSRB found as race-condition by helgrind. Src/LinearSolvers/C_TensorMG/DV_3D3.F commit 7ebf60c4da91a2a085952519ed191ab0dc79b313 Author: lijewski 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 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 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 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 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 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 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 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 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: 9af27fe6f 67c13e4fe Author: Michael Zingale 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 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 Date: Wed Oct 3 21:38:42 2012 -0700 Releasing tool: Fix the taget repo. Tools/Release/release.py commit 38f4fde25f183b8f2ad2ec8e66cc6134f3345cfe Author: Weiqun Zhang 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 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: 22cce5059 c9596ebfb Author: Ann Almgren Date: Wed Oct 3 12:31:34 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 22cce5059c289999c76e0534617c7fc7821d93d2 Author: Ann Almgren Date: Wed Oct 3 12:31:25 2012 -0700 Get this compiling again. Tests/F_BaseLib/t_main.f90 commit c9596ebfba6a06922f640d2fde0d4ed0f1809106 Author: Weiqun Zhang Date: Wed Oct 3 11:55:11 2012 -0700 Regression testing script: add reportActiveTestsOnly option Tools/RegressionTesting/BoxLib-tests.ini Tools/RegressionTesting/Castro-tests.ini Tools/RegressionTesting/IAMR-tests.ini Tools/RegressionTesting/LMC-tests.ini Tools/RegressionTesting/Nyx-tests.ini Tools/RegressionTesting/testnew.py commit 5b61067f069b3032e983d7c751a813982c8de83e Author: lijewski Date: Mon Oct 1 12:23:05 2012 -0700 Fixed typos. Src/F_BaseLib/multifab_f.f90 commit 67c13e4febc7c1fe4e13a64f36af6d30bf53163b Author: Weiqun Zhang Date: Mon Oct 1 10:35:04 2012 -0700 fcompare: Fix 2D case fcompare.f90 commit 5c3318dbfc8eba4f37b7105dc2d19e349104750c Author: lijewski Date: Mon Oct 1 09:42:23 2012 -0700 Added contains_inf() and contains_nan() for multifabs to match calls for fab routines. Src/F_BaseLib/multifab_f.f90 commit bf485bad689443ee498a82cdc72a6a14b473bfa5 Merge: d7e702c1d e3f5d5260 Author: Weiqun Zhang Date: Sun Sep 30 21:25:22 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/AmrPostprocessing commit e3f5d5260e3d16d2ee3fdf512531092c53750b58 Author: Michael Zingale Date: Sat Sep 29 12:53:49 2012 -0400 not supported fIDLdump.f90 fIDLdump3d.f90 commit 97ee63b49be67f1f21d191a38723793356a049f3 Author: Michael Zingale Date: Sat Sep 29 11:34:40 2012 -0400 add NaN detection fcompare.f90 commit 6ae50ec4b8999ebccf06910b052d5106ebaeabc1 Author: lijewski Date: Fri Sep 28 15:49:48 2012 -0700 Substituted a select case statement for a long if/elseif string. Src/LinearSolvers/C_TensorMG/DV_3D3.F commit 103f9221620e2b9b313d36255ed88ee49ed0d391 Author: ajnonaka Date: Thu Sep 27 14:48:15 2012 -0700 only providing OMP support for 3D in the base infrastructure now Docs/GettingStarted/GettingStarted.tex Docs/UsersGuide.tex Tutorials/HeatEquation_EX1_C/advance_2d.f90 Tutorials/HeatEquation_EX1_F/advance.f90 Tutorials/HeatEquation_EX1_F/init_phi.f90 Tutorials/HeatEquation_EX2_F/advance.f90 Tutorials/HeatEquation_EX2_F/init_phi.f90 Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX3_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/advance.f90 Tutorials/HeatEquation_EX4_F/init_phi.f90 Tutorials/HeatEquation_EX5_F/advance.f90 Tutorials/HeatEquation_EX5_F/init_phi.f90 commit a38e1e57fbc0d4bba0361d75594c78cd3db00daf Author: ajnonaka Date: Thu Sep 27 10:43:11 2012 -0700 Fix regrid so that we delete the old multifabs before we delete the layouts on which they are based. Tutorials/HeatEquation_EX5_F/regrid.f90 commit f87f6cc08c2e83c00593406614ae9aa8d0e37671 Author: Ann Almgren Date: Thu Sep 27 08:36:25 2012 -0700 Move CASTRO_hydro routines into Castro/Diagnostics/Sedov. CASTRO_hydro/GNUmakefile CASTRO_hydro/fsedov1d.f90 CASTRO_hydro/fsedov2d_cart.f90 CASTRO_hydro/fsedov2d_cyl_in_cartcoords.f90 CASTRO_hydro/fsedov2d_cyl_in_cylcoords.f90 CASTRO_hydro/fsedov2d_sph_in_cylcoords.f90 CASTRO_hydro/fsedov3d_cyl.f90 CASTRO_hydro/fsedov3d_sph.f90 commit a1512d7749fc01b40b517d5655700a3772bcd9e2 Author: Ann Almgren Date: Wed Sep 26 13:35:34 2012 -0700 Add protections against divide by 0, and clean up 1d/2d/3d a little. fcompare.f90 commit 2f45661a202a3cb8499745adcb488ef3741d93be Author: Ann Almgren Date: Mon Sep 24 12:16:34 2012 -0700 Updated Nyx regression testing. Tools/RegressionTesting/Nyx-tests.ini commit 82492c0c8c868bb72e05f4aa142bfba05052c7c0 Author: Ann Almgren Date: Mon Sep 24 12:15:36 2012 -0700 Fix regrid so that we delete the old multifabs before we delete the layouts on which they are based. Tutorials/HeatEquation_EX4_F/regrid.f90 commit 1d7759d242ad7ba44b42753e4127b45d60001b20 Author: Ann Almgren Date: Mon Sep 24 12:10:52 2012 -0700 When we take only 1/8 of the particles in WriteCoarsenedAsciiFile we want the mass in the domain to be unchanged (more or less) so we multiply each remaining particle's mass by 8. Src/C_AMRLib/Particles.H commit d43cf734365b3b1d79a0f61b8d467d8e31f4e6b3 Author: Ann Almgren Date: Mon Sep 24 11:27:26 2012 -0700 Moved these files into Castro/Diagnostics. CASTRO_gravity/GNUmakefile CASTRO_gravity/fdustcollapse1d.f90 CASTRO_gravity/fdustcollapse2d.f90 CASTRO_gravity/fdustcollapse3d.f90 commit b8eb9e11c9f8acc88091a478c9cbc989fc659725 Author: Matthew Emmett Date: Mon Sep 24 12:41:59 2012 -0400 PyBoxLib: Simplify utils. Src/Python/pyboxlib/utils.py commit 2d9e04d12316fbe84b1b47ef3fe97e0c46e6aa2e Author: Ann Almgren Date: Mon Sep 24 08:33:01 2012 -0700 Need to include PArray.H -- now compiles again. Src/LinearSolvers/C_NodalMG/amr_multi.H commit d2486309cfda64c682ba637b37a8c901855629c0 Author: Ann Almgren Date: Fri Sep 21 17:56:14 2012 -0700 Replace CoarsenAndPrint by WriteCoarsenedAsciiFile which writes nparticles then only the particles from even cells into a new ascii file. Src/C_AMRLib/Particles.H commit 65bcfb2f557fff9277eaeb60b95eda430252a531 Merge: 807d57247 6adb2be20 Author: Ann Almgren Date: Fri Sep 21 17:41:41 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 807d5724786858611ae94fa6f88a245c11c049e6 Author: Ann Almgren Date: Fri Sep 21 17:41:05 2012 -0700 Add a routine which writes out particles from every other cell -- this is useful when creating coarser versions of existing particle files. Src/C_AMRLib/Particles.H commit 6adb2be206611f86a70232cc3a402a77d17d34bc Merge: dd7183f77 6ff592e75 Author: Weiqun Zhang Date: Fri Sep 21 16:35:41 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 6ff592e75ead229fd254639f9fb02bb59c144800 Merge: 591216ffc 1eb933a5f Author: cmalone Date: Fri Sep 21 16:32:36 2012 -0700 Merge branch 'master' of https://ccse.lbl.gov/pub/Downloads/BoxLib commit 591216ffc08ef48326451fcab7144aac9e1207a5 Author: cmalone Date: Fri Sep 21 16:32:22 2012 -0700 hanlde ifndef blocks properly Tools/ppCleanup/ppCleanup.py commit dd7183f77e7023b5c3027b29525e0a2297e9127a Author: Weiqun Zhang Date: Fri Sep 21 16:31:30 2012 -0700 a new ppCleanup python script for cleaning up IFDEF regions Tools/Release/cleanWords.txt Tools/Release/ppCleanup.py Tools/ppCleanup/ppCleanup.py commit 1eb933a5f47c7ef7784c1d723eeb4f549c82be43 Author: Mike Lijewski Date: Fri Sep 21 18:00:33 2012 -0400 Cleaned up some warning messages from g++. Src/C_AMRLib/ErrorList.H Src/C_BaseLib/FabArray.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/F_MG/itsol.f90 commit 3aae27d2cd217a512f92d55830c9fad66d06cb70 Author: cmalone Date: Fri Sep 21 11:48:21 2012 -0700 I *think* this is working for the pathological nested cases Tools/ppCleanup/ppCleanup.py commit a574b8499b891decfa2e6f1fd865f8bc85a76612 Author: cmalone Date: Fri Sep 21 11:17:16 2012 -0700 fix character eating with -o option Tools/ppCleanup/ppCleanup.py commit 3fe289704ba6c6b5c63cf2c2ceed7bbef3c55010 Author: Chris Malone Date: Thu Sep 20 19:49:44 2012 -0700 no longer need to have version 2.7.X Tools/ppCleanup/README commit 7a9aa6c18c3b1558eb35f1366f0973f74fdd76ea Author: Chris Malone Date: Thu Sep 20 19:44:27 2012 -0700 workaround for versions less than 2.7 arg parsing Tools/ppCleanup/ppCleanup.py commit 4e60f3f0dcc6638cd765b39866ec6bee8e2b6b72 Author: Ann Almgren Date: Thu Sep 20 15:02:18 2012 -0700 These are the ifdef sections we want to eliminate for the first public release of CASTRO. Tools/ppCleanup/cleanWords.txt commit a2f6a971683f34ae28a62ebc82b60f5c3063b5f5 Author: Marc Day Date: Wed Sep 19 13:45:42 2012 -0700 Fix up CMake files Src/F_BaseLib/CMakeLists.txt Src/LinearSolvers/C_to_F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt commit d151cf266235dc90016112078d6a83275059a77c Author: Michael Zingale Date: Tue Sep 18 18:12:08 2012 -0400 forgot to commit this originally Src/F_BaseLib/bl_prof_backtrace.f90 commit a472cd430b4991780e88d95dd28848d0c3a0fbb7 Author: Michael Zingale Date: Tue Sep 18 13:03:58 2012 -0400 bl_error cannot include the bl_prof stuff needed for a stacktrace, because when we run with PROF=t, we get circular dependencies. Now create a separate bl_error just for the backtracing stuff. Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_error.f90 Src/F_BaseLib/bl_error_backtrace.f90 commit 370462023534c3c8fcf0d5d90fdfc283369531da Author: Matthew Emmett Date: Mon Sep 17 20:58:15 2012 -0400 PyBoxLib: Various updates to run utilities and fabric utilities. Src/Python/pyboxlib/__init__.py Src/Python/pyboxlib/fabutils.py Src/Python/pyboxlib/plotfile.py Src/Python/pyboxlib/utils.py commit d7e702c1db21065e95b02114adf76400b0c50e9d Merge: f2bc68c8d 0f55a5689 Author: Weiqun Zhang Date: Mon Sep 17 13:50:34 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/AmrPostprocessing commit fe6bce435144b207b2dab9039dd8edd2f076bfb0 Author: lijewski Date: Mon Sep 17 13:49:06 2012 -0700 Include Tutorials/AMR_Advection_C/Source/ADR.cpp commit c3222db34dff6db5584f0aae7c4215a83fc3a6e7 Author: Ann Almgren Date: Mon Sep 17 13:39:33 2012 -0700 Fix GNUmakefile in AMR_Advection_C Tutorial. Tutorials/AMR_Advection_C/Exec/UniformVelocity/GNUmakefile commit 71fb05e0091c29d634a7beaff5361262c7bc1750 Author: Ann Almgren Date: Mon Sep 17 09:58:57 2012 -0700 Modify 1d and 3d versions of diagonalization as well as 3d. Src/LinearSolvers/F_MG/itsol.f90 commit 49834d80a40af1910b7b93300a9e1b9fde64629d Author: Ann Almgren Date: Mon Sep 17 09:57:21 2012 -0700 Protect against divide by zero in diagonalization. Src/LinearSolvers/F_MG/itsol.f90 commit 4e5ffc6a84d436ed1d84235a09d5d0f1d34a923d Author: Weiqun Zhang Date: Fri Sep 14 18:03:57 2012 -0700 Fix C_Src part of regression testing script Tools/RegressionTesting/testnew.py commit d2ed1e7bfd9f754a443e1e5aa96f6b1a2bdd4872 Author: vince Date: Fri Sep 14 16:31:16 2012 -0700 instrumented the unoptimized hypterm. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/advance.f90 commit 3646103599c5dfe8b60f5b2640a6c6ba070dc80c Merge: 78ab4218b 161684dce Author: lijewski Date: Fri Sep 14 09:37:05 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 161684dce8fd960f98097bf868cac22fc67b74e4 Author: Michael Zingale Date: Fri Sep 14 11:06:35 2012 -0400 latest Maestro tests Tools/RegressionTesting/Maestro-tests.ini commit bd6d8106a47209846289fca4b0a6a65b864ae423 Author: Michael Zingale Date: Fri Sep 14 10:54:20 2012 -0400 add support for debug tests Tools/RegressionTesting/testnew.py commit 78ab4218b7d8a2181035bee009b86809200e02af Merge: 9a07ac2ff f5510f3f3 Author: lijewski Date: Thu Sep 13 20:44:51 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9a07ac2ff0131a87da450c5f2c805a8ee8e0535b Author: lijewski Date: Thu Sep 13 20:44:31 2012 -0700 Specialized copyToMem() and copyFromMem() for Real. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/SPECIALIZE_1D.F Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit 8be7a7de07c9a19304620a746f680454e5195cbe Author: lijewski Date: Thu Sep 13 19:48:01 2012 -0700 Merged in copyFromMem(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 35e69b94b09eb6a4139044db57eb6cd795ac94c6 Author: lijewski Date: Thu Sep 13 19:47:25 2012 -0700 Added copyFromMem() to complement copyToMem(). Src/C_BaseLib/BaseFab.H commit 0cdfecbf8598b526a2779c5f4222ab618e0b1497 Author: lijewski Date: Thu Sep 13 19:13:16 2012 -0700 Merged in new copyToMem() calls in place of doing a copy to a temporary fab and then a memcpy(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit c64f29148b14b52bf0ab5000baecc12706ca5afc Author: lijewski Date: Thu Sep 13 19:12:07 2012 -0700 Renamed MemCopy() -> copyToMem() and made it a member function not a static member function. Src/C_BaseLib/BaseFab.H commit 26c596c3e3f9aae9966ed4ad325ae38965e5a16d Author: lijewski Date: Thu Sep 13 17:31:53 2012 -0700 Added static BaseFab::MemCopy(). Specialized version of copy() that goes from a FAB to a raw T* memory location. Src/C_BaseLib/BaseFab.H commit f5510f3f3290339fd6c44837fd485f3070050605 Merge: 2a17d8e23 adcc65729 Author: ajnonaka Date: Thu Sep 13 15:00:16 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 2a17d8e23dddece3d5ac45cc9fdd37c5c347a855 Author: ajnonaka Date: Thu Sep 13 14:59:32 2012 -0700 changed the_bc_tower class to use local indices for boundary conditions instead of global indices. Changed the rest of the source code to refer to the local indices. Src/F_BaseLib/define_bc_tower.f90 Src/F_BaseLib/multifab_physbc.f90 Src/F_BaseLib/multifab_physbc_edgevel.f90 commit adcc65729baf6fd8b946941e29bc5c550734d0b3 Author: Matthew Emmett Date: Thu Sep 13 16:41:09 2012 -0400 PyBoxLib: Remove (empty) utils. Src/Python/pyboxlib/fabutils.py commit 6ccf72e2ec132787a6d5acaf347e022b5a8a8093 Author: Matthew Emmett Date: Thu Sep 13 16:40:22 2012 -0400 PyBoxLib: Print warning if libpycboxlib.so can't be loaded. Src/Python/pyboxlib/fab.py Src/Python/pyboxlib/pybl.py commit 19bbd5d2c2aa7599a214651d49104ffb2fc2090f Author: Matthew Emmett Date: Thu Sep 13 16:35:39 2012 -0400 PyBoxLib: Try again... Src/Python/pyboxlib/pybl.py commit 4f43bb2272961df90ed04050d74073c47ed5d5ca Author: Matthew Emmett Date: Thu Sep 13 16:33:50 2012 -0400 PyBoxLib: Print warning of libpyboxlib.so can't be loaded. Src/Python/pyboxlib/pybl.py commit fdce994c0068cdd40e9c8d7245a95f7d5a89023f Author: Matthew Emmett Date: Thu Sep 13 13:57:54 2012 -0400 PyBoxLib: Add fabutils.py. Src/Python/pyboxlib/fabutils.py commit 2d3d1f53537d7d8ddbd4031bf815059ee1b5f4db Author: ajnonaka Date: Thu Sep 13 10:27:03 2012 -0700 bugfix: during regrid, after building the level 1 layout, you need to call bc_tower_level_build on level 1 so that the bc arrays are consistent with a possibly new layout Tutorials/HeatEquation_EX4_F/regrid.f90 Tutorials/HeatEquation_EX5_F/regrid.f90 commit 0c454a3f67808f88bc5ad4ad78e5e107165a9c28 Author: vince Date: Thu Sep 13 10:16:34 2012 -0700 updates for new boxlib changes. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/advance.f90 Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/main.f90 commit 8f059468bb5a4423d1c40bfe2bb629930982edef Author: Matthew Emmett Date: Thu Sep 13 11:22:54 2012 -0400 PyBoxLib: Finish plotfile support and add "compare" routines. Src/Python/pyboxlib/__init__.py Src/Python/pyboxlib/fab.py Src/Python/pyboxlib/multifab.py Src/Python/pyboxlib/plotfile.py Src/Python/src/boxlib_numpy_c.c Src/Python/src/boxlib_numpy_f.f90 Src/Python/src/fboxlib.f90 commit 4fc121b9cd8e374d2b8f10d595b642e17ddb2fcb Merge: 5d47eece8 c4b5b52ff Author: Matthew Emmett Date: Thu Sep 13 11:23:15 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit c4b5b52ff4e0a18227e1c84256cd2cf05ec0ff2c Merge: 41b132266 489d7b42b Author: ajnonaka Date: Wed Sep 12 14:23:13 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 41b13226621a178aa49d678904cf242480d00e61 Author: ajnonaka Date: Wed Sep 12 14:22:39 2012 -0700 fix multilevel bug. after ml_restricted_build, la_array is not consistent with mla%la. Therefore we must redefine/build the_bc_tower stuff Tutorials/HeatEquation_EX4_F/main.f90 Tutorials/HeatEquation_EX5_F/main.f90 commit 489d7b42bc0eef58c66ce0c94f319b12bcab84f3 Author: Marc Day Date: Wed Sep 12 13:14:19 2012 -0700 Fix templatization issues in FillBoundary calls and add inline funcs in Amr Src/C_AMRLib/Amr.H Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit 212f8f156afc7699de85402ae4fa43909a4b2fb7 Author: Marc Day Date: Wed Sep 12 11:55:07 2012 -0700 Try again to fix cmake Src/F_BaseLib/CMakeLists.txt commit 523406e5c3780ff925d5c71b33020b26d94ca65e Author: Marc Day Date: Wed Sep 12 11:42:36 2012 -0700 Fixup CMakeLists.txt files in fort folders Src/F_BaseLib/CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt commit b1488a5b005bd1e82e760301481d30dada8412c8 Author: Marc Day Date: Wed Sep 12 11:19:20 2012 -0700 update CMakeLists file in F_Baselib Src/F_BaseLib/CMakeLists.txt commit 5d2c480548495f6dee61746faf7fed0379341a3f Merge: 2b39e82a0 0f3cd3c34 Author: Marc Day 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 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 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: af236db04 c9019d717 Author: Marc Day Date: Wed Sep 12 10:07:37 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit c9019d717c819d9ad3ecd0a080171d3dfd7d5442 Author: ajnonaka Date: Wed Sep 12 09:35:20 2012 -0700 some cleanup of define_bc_tower allocation/deallocation. ngrids is also no longer part of the_bc_level. prep work for upcoming switch to use local indices for bc stuff Src/F_BaseLib/define_bc_tower.f90 commit af236db04fece752fbc79c1104afe229728efc05 Merge: 1f274a353 0ebed9030 Author: Marc Day Date: Wed Sep 12 08:35:55 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 0ebed90306706557d54e2412096c57f6041d1d1e Author: ajnonaka Date: Wed Sep 12 08:01:29 2012 -0700 bugfix... changed do i = 1, nboxes(fine%la) call push_back(pbl, box_nodalize(get_box(fine,i),fine%nodal)) end do to do i = 1, nboxes(fine%la) call push_back(pbl, box_nodalize(get_box(fine%la,i),fine%nodal)) end do Src/F_BaseLib/fillpatch.f90 commit 57e627c47032587b21b1492abb3de93bcdab8d69 Author: Michael Zingale Date: Wed Sep 12 09:47:11 2012 -0400 add the backtrace stuff if we call bl_error. For this to work, we need to set BACKTRACE := t in the GNUmakefile. Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_error.f90 Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/bl_prof_stubs.f90 commit 41aa4a2a4ddc748b25dad548049caae6a7be80c8 Author: ajnonaka Date: Tue Sep 11 14:48:06 2012 -0700 local/global indexing bugfix Src/LinearSolvers/F_MG/cc_stencil.f90 commit fb65b6a7e50ab0efcd4cf8e69ab28ac18315f2ba Author: lijewski Date: Tue Sep 11 12:39:30 2012 -0700 A little cleanup. Src/LinearSolvers/F_MG/nodal_divu.f90 commit 5d47eece82aacd4db41c2b25a7a71e14bc1d102c Merge: 76f96159d 0ce350b32 Author: Matthew Emmett 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 Date: Tue Sep 11 15:30:39 2012 -0400 MODDEP: Ignore iso_c_binding module. Tools/F_scripts/moddep.pl commit 0ce350b3251c701990140f1306b2345e77147818 Merge: d2a3e8bfa da51c7297 Author: lijewski Date: Tue Sep 11 12:09:37 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d2a3e8bfa627efe1bda158603dc156c6c71c1e3b Author: lijewski Date: Tue Sep 11 12:07:42 2012 -0700 Forgot to pass the multifab nodal flags to a couple box_nodalize() calls. For some weird reason the nodal flag argument to box_nodalize() is optional :-( Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit da51c729748b41d03214e62d857723dcf6ecb40b Author: Ann Almgren Date: Tue Sep 11 11:00:51 2012 -0700 Add README file for new Tutorial example. Tutorials/AMR_Advection_C/README commit b7ef7da0571010c03152959da6f165c0c14aa8df Merge: dc66a9b08 1c70749b5 Author: Ann Almgren Date: Tue Sep 11 10:57:55 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit dc66a9b08436015d0efd1503576365700846f3fa Author: Ann Almgren Date: Tue Sep 11 10:57:03 2012 -0700 Add new example to BoxLib/Tutorials -- this is a multilevel ADR problem in the C++ framework. About as simple as you can make an AmrLevel-type application. Tutorials/AMR_Advection_C/Exec/Make.ADR Tutorials/AMR_Advection_C/Exec/UniformVelocity/GNUmakefile Tutorials/AMR_Advection_C/Exec/UniformVelocity/Make.package Tutorials/AMR_Advection_C/Exec/UniformVelocity/Prob_2d.f90 Tutorials/AMR_Advection_C/Exec/UniformVelocity/amrvis.defaults Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.2d Tutorials/AMR_Advection_C/Exec/UniformVelocity/inputs.rt Tutorials/AMR_Advection_C/Exec/UniformVelocity/probdata.f90 Tutorials/AMR_Advection_C/Exec/UniformVelocity/probin.2d Tutorials/AMR_Advection_C/Source/ADR.H Tutorials/AMR_Advection_C/Source/ADR.cpp Tutorials/AMR_Advection_C/Source/ADRBld.cpp Tutorials/AMR_Advection_C/Source/ADR_F.H Tutorials/AMR_Advection_C/Source/ADR_advance.cpp Tutorials/AMR_Advection_C/Source/ADR_diffusion.cpp Tutorials/AMR_Advection_C/Source/ADR_error.cpp Tutorials/AMR_Advection_C/Source/ADR_nd.f90 Tutorials/AMR_Advection_C/Source/ADR_react.cpp Tutorials/AMR_Advection_C/Source/ADR_setup.cpp Tutorials/AMR_Advection_C/Source/Derive_F.H Tutorials/AMR_Advection_C/Source/Diffusion.H Tutorials/AMR_Advection_C/Source/Diffusion.cpp Tutorials/AMR_Advection_C/Source/Make.package Tutorials/AMR_Advection_C/Source/Src_2d/ACT_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/ACT_advection_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/ACT_sums_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/Derive_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/EstDt_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/MGutils_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/Make.package Tutorials/AMR_Advection_C/Source/Src_2d/React_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/Tagging_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/bc_fill_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/ext_src_2d.f90 Tutorials/AMR_Advection_C/Source/Src_2d/fill_diff_coeff_2d.f90 Tutorials/AMR_Advection_C/Source/burner.f90 Tutorials/AMR_Advection_C/Source/extern_probin.template Tutorials/AMR_Advection_C/Source/interpolate.f90 Tutorials/AMR_Advection_C/Source/main.cpp Tutorials/AMR_Advection_C/Source/meth_params.f90 Tutorials/AMR_Advection_C/Source/network.f90 Tutorials/AMR_Advection_C/Source/prob_params.f90 Tutorials/AMR_Advection_C/Source/sum_integrated_quantities.cpp commit 1c70749b56e3b2b86c306cd73655c371757c70fa Author: ajnonaka Date: Tue Sep 11 09:59:44 2012 -0700 fix the boundary conditions so we refer to the global index. seems to run fine now in parallel Src/F_BaseLib/multifab_physbc.f90 Src/F_BaseLib/multifab_physbc_edgevel.f90 Tutorials/HeatEquation_EX4_F/init_phi.f90 Tutorials/HeatEquation_EX5_F/init_phi.f90 commit f44830cb349a52bf20eba449331500c2ad2ccb79 Author: lijewski Date: Mon Sep 10 18:00:57 2012 -0700 Moved some of the new multifab code into layout. Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 commit 642c4efa898678f798776ab66fcd97b0f2a46401 Merge: 5b60c2dce 8edbafb96 Author: lijewski Date: Mon Sep 10 17:54:42 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 8edbafb963c6df2145bbbe2aa16f7514d17f5eb6 Author: ajnonaka Date: Mon Sep 10 17:06:16 2012 -0700 fix lall option of multifab_volume Src/F_BaseLib/multifab_f.f90 commit 5b60c2dce1252287d6e1b7a175f77708559d2a98 Merge: 375cf06aa 462516a52 Author: lijewski Date: Mon Sep 10 16:16:05 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 462516a523d528dc75f8cdee0ffc56a739e8e6a9 Author: Weiqun Zhang Date: Mon Sep 10 15:25:16 2012 -0700 Fixed a very old bug that was exposed by the recent changes. Src/F_BaseLib/bndry_reg.f90 commit 8cf1e5fb330b680be473864108b9bb6fae780afb Author: Weiqun Zhang Date: Mon Sep 10 14:59:58 2012 -0700 Update MG CC solver for the latest nfabs changes. Src/LinearSolvers/F_MG/cc_mg_cpp.f90 commit 375cf06aa8bd5b573bf478c375f2771f9fa37b42 Author: lijewski Date: Mon Sep 10 14:53:13 2012 -0700 Now using the same gfortran options as they use in the F90 side of the code. Tools/C_mk/Make.defs commit aa57279710b4fd994a529e8af6aed2f131beb4ac Author: ajnonaka Date: Mon Sep 10 14:49:21 2012 -0700 update all fortran tutorials and documentation to update latest way to loop over grids Docs/F_AdvancedTopics/F_AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex Tutorials/Chemotaxis_F/advance.f90 Tutorials/Chemotaxis_F/chemotaxis.f90 Tutorials/Exp_CNS_NoSpec/advance.f90 Tutorials/Exp_CNS_NoSpec/init_data.f90 Tutorials/HeatEquation_EX1_F/advance.f90 Tutorials/HeatEquation_EX1_F/init_phi.f90 Tutorials/HeatEquation_EX2_F/advance.f90 Tutorials/HeatEquation_EX2_F/init_phi.f90 Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX3_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/advance.f90 Tutorials/HeatEquation_EX4_F/init_phi.f90 Tutorials/HeatEquation_EX5_F/advance.f90 Tutorials/HeatEquation_EX5_F/init_phi.f90 Tutorials/WaveEquation_F/advance.f90 Tutorials/WaveEquation_F/init_data.f90 commit fc284c8bfa7f2e98ae806afff3f4ce10a6c13765 Merge: 20a4316c3 39c3c5291 Author: ajnonaka Date: Mon Sep 10 14:42:21 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 20a4316c32b63c91497c6ce3bca9774d5ee5f97e Author: ajnonaka Date: Mon Sep 10 14:41:36 2012 -0700 fixed buggy paralle logic in ml_interface_c Src/LinearSolvers/F_MG/cc_interface_stencil.f90 commit 39c3c52911535138579f0a223e6cc44649517bd9 Author: lijewski Date: Mon Sep 10 13:26:29 2012 -0700 Shut up a couple warnings about unused variables. Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp commit f16039ee9bfa10bbea34518410e34cc66a00f8f3 Author: Weiqun Zhang Date: Mon Sep 10 13:16:12 2012 -0700 nboxes => nfabs Src/F_BaseLib/multifab_physbc.f90 Src/F_BaseLib/tag_boxes.f90 commit 8e9d240cddc5d3c3637db6741556e80d04c4f82b Author: lijewski Date: Mon Sep 10 12:59:12 2012 -0700 MAESTRO appears to work with new multifab stuff. Src/F_BaseLib/cluster_f.f90 Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 Src/F_BaseLib/multifab_physbc_edgevel.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit 0fb26c8a5917b843a86b7c8d22e8858049f34be0 Author: lijewski 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 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 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 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 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 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 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 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 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 Date: Fri Sep 7 16:35:26 2012 -0700 Tweak to local_index(). Src/F_BaseLib/multifab_f.f90 commit 76507d4a9ef430a5f181d760e98c42e1027ac2ca Author: lijewski Date: Fri Sep 7 16:23:03 2012 -0700 Merged in local_index() calls. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 53ee2c6cfa6969ee2beae2b554c274a75069590b Author: lijewski Date: Fri Sep 7 16:04:31 2012 -0700 Got things to compile & run in serial. Almost surely there's parallel issues to be found. Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/ml_multifab.f90 Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/coarsen_coeffs.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 Src/LinearSolvers/F_MG/nodal_newu.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 0addc281775d97532dd9e28defc7de5351aba8f4 Author: lijewski Date: Fri Sep 7 13:02:09 2012 -0700 get_[ip]*box() work on local indices. Src/F_BaseLib/multifab_f.f90 commit 2b6cf463e9b0226ed9eaae462da9cc4e7203750f Author: lijewski Date: Fri Sep 7 10:41:33 2012 -0700 Merged in local_index(). Src/F_BaseLib/multifab_f.f90 commit 1e9555362ecb84772bd1ce304578c84dd850b94f Author: lijewski Date: Fri Sep 7 10:07:26 2012 -0700 Added local_index(). Still need to merge into all the right places. Src/F_BaseLib/multifab_f.f90 commit c5d624fd047e7e831cdfdae3f7c58749be80f5b3 Author: lijewski Date: Fri Sep 7 09:27:54 2012 -0700 Removed "most" remote() calls. Got a couple that are more tricky to do. Src/F_BaseLib/multifab_f.f90 commit 9f31e3d56cfdbdf85c20108f2826ff748d0993e9 Author: lijewski Date: Fri Sep 7 09:07:10 2012 -0700 fbs(:) is now sized to be just the local fabs. idx(:) are the global boxarray indices for the local fabs. Removed remote() and local() functions. Src/F_BaseLib/multifab_f.f90 commit b83d8a83eb9b66b0b96f6c4ce295f5763c5fd4bb Author: lijewski Date: Thu Sep 6 15:23:23 2012 -0700 Removed the Do_AllToAllV code. This is unlikely to be useful as we move to exascale. I left the multifab_set_alltoallv() function since I "think" that may be callable by some input parsing code -- it does nothing now. Src/F_BaseLib/multifab_f.f90 commit 7631189eeeb80fcc883aeeb2e13a869636951ce6 Author: lijewski Date: Thu Sep 6 12:52:27 2012 -0700 Reverted out an ill-advised numcomp -> ncomp substitution. Src/C_AMRLib/FluxRegister.cpp commit 28e51281ae5996cbf23dbdf74b3607aed79748ed Author: Weiqun Zhang Date: Wed Sep 5 20:45:44 2012 -0700 Fix a minor bug in make system I just introduced. Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 22fee0ed185bac9fc2a74c0a3919cc4ae76b0f69 Author: Weiqun Zhang Date: Wed Sep 5 14:52:35 2012 -0700 The make system can handle dependence of "include" lines in f90 files now. Tools/C_mk/Make.defs Tools/C_mk/Make.rules Tools/C_scripts/moddep.pl Tools/F_mk/GMakerules.mak Tools/F_scripts/moddep.pl commit 65e664aa2adc33f41627c737214653012efabf1f Author: lijewski Date: Wed Sep 5 14:31:26 2012 -0700 Made the CrseInit() that takes FABs a bit more memory efficient. Src/C_AMRLib/FluxRegister.cpp commit c257fadfdf260401996ec7eb83a7b2cc831a739e Author: lijewski Date: Wed Sep 5 09:02:51 2012 -0700 Pulled some computation out of an inner loop. Src/C_AMRLib/FluxRegister.cpp commit 99d8b31c0ed87fd92613c37dcef51dc2bb42888b Merge: 0748ce818 663b15af1 Author: lijewski Date: Tue Sep 4 15:01:01 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 0748ce818c1ff1cf2d1c4629c35cb84a4b8368cb Author: lijewski Date: Tue Sep 4 15:00:48 2012 -0700 Simplified mapPeriodic() a bit. Src/C_AMRLib/TagBox.cpp commit 663b15af1bdf212d21cd887b5fc63733fe36f6cc Author: Ann Almgren Date: Tue Sep 4 14:11:48 2012 -0700 Fix test on ref_ratio -- we were just doing the wrong test on whether all the components were the same ... (was previously testing across levels, just meant to test across 1:dm) Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit b381d3a5a7df159baf7f9974feaaae5cf179324c Author: lijewski Date: Tue Sep 4 12:25:19 2012 -0700 Replaced the specialized CrseInit() parallel implementation with one that uses parallel copy()s. I'd like to do the same for the parallel implementation of Reflux() but that's more complicated ... Src/C_AMRLib/FluxRegister.cpp commit f8c45d71cc0a9f7dc2b43c90fc60cd99ca746fe9 Author: Mike Lijewski Date: Sat Sep 1 14:47:53 2012 -0400 Yet more early exits from nested loops. This about finishes (hopefully) my rewrite of our MPI communication and caching infrastructure. We should be ready for exascale. Metadata has been minimized & should not be an issue. The new code is also significantly faster than the new, with the difference increasing as the number of MPI processors increases. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit 5a8ab4ed62bacce67b1a3405ce5bbbe9f7fd9e8e Merge: db8d6509d bb5877daf Author: lijewski Date: Fri Aug 31 13:39:43 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit bb5877daff8b52d51ef6b663b645bf42aa7133ad Author: vince Date: Fri Aug 31 13:37:55 2012 -0700 more make and output tweaks. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/advance.f90 commit db8d6509de52acdfa651d155b5b75132bc16ff7c Author: lijewski Date: Fri Aug 31 12:28:15 2012 -0700 More short-circuiting out of loops. Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit ee6c6a3f49cfcf5826fc30d55bc07256eb5c31ef Merge: 9daf040ff d61ca5996 Author: lijewski Date: Fri Aug 31 10:56:28 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9daf040ffedc5b911eeb2c812d5988e3b436f01d Author: lijewski Date: Fri Aug 31 10:53:45 2012 -0700 Have Finalize() flush cache. Src/C_BaseLib/DistributionMapping.cpp commit d61ca5996086d8b102c11270d82a192bedc1fca6 Author: vince Date: Thu Aug 30 17:34:09 2012 -0700 set up the makefiles to allow local setting of optimization flags. there is something wrong with the f90 flux minmax output for rho. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/bench.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile commit 0cf31ca5e3c2664656876da44a2b3b0750cb3e17 Author: lijewski Date: Thu Aug 30 15:44:20 2012 -0700 Refinement of the count of bytes held by the caches. I was overcounting. Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit fdcb53499139e24b8a09cfecf3e0254e4fd42632 Author: lijewski Date: Thu Aug 30 15:22:09 2012 -0700 Some speedups. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 65ae89dc229cb00fe3be3e131d63446601dd0ed5 Author: vince Date: Thu Aug 30 13:23:58 2012 -0700 added openmp flag for c. Tools/C_mk/Make.defs commit 697740dbf7002eefc4a965dd31c9f13fc92b9056 Author: vince Date: Wed Aug 29 16:13:28 2012 -0700 undid some changes from hopper. Tools/C_mk/Make.defs commit 608e45fe54da0c95a5d3f91afb60481f186e2cdf Author: vince Date: Wed Aug 29 16:07:07 2012 -0700 set omp flag for regular c. Tools/C_mk/Make.defs commit 85810c15b0fbcb5b146178d49364bb8e54c04b6a Author: vince Date: Wed Aug 29 15:54:22 2012 -0700 omp fix. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F commit 2415e3a5c58fd52b9dc64bfedb29bfd6f33d9f69 Author: vince Date: Wed Aug 29 15:24:03 2012 -0700 made the output more consistent between cases. cleaned up some code. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/bench.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/advance.f90 Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/main.f90 commit d4dd2a3344eaedeca54e96a22f59bf527a580960 Author: vince Date: Wed Aug 29 12:59:21 2012 -0700 reused files. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly_F.F Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly_F.H Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/bench.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.h Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.x86.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer_c.c commit ea17ff7b5499c20856237b628a22f0abf2faea81 Author: lijewski Date: Wed Aug 29 11:06:36 2012 -0700 Some cleanup. Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H commit 9660f8dbabf6309a923f2abe0443d6c7cd634466 Author: lijewski Date: Wed Aug 29 10:36:03 2012 -0700 For now always print out the DistributionMapping cache stats; i.e. ignore whether or not verbose is set. I want to get a good handle on the total amount of metadata being used. Src/C_BaseLib/DistributionMapping.cpp commit b9bfc3147a81cd139eb52b818394766c9eeb0805 Author: lijewski Date: Wed Aug 29 10:28:29 2012 -0700 Little code cleanup. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryRegister.H commit cd944109d88ff9d0ec335ac71ee0dc0e61f86956 Author: lijewski Date: Wed Aug 29 10:13:03 2012 -0700 Simpler (but equally good) key calculation for copy cache. Src/C_BaseLib/FabArray.cpp commit dfc463e761f322f5f251830b2cf0a00b7be6af38 Author: lijewski Date: Wed Aug 29 10:10:31 2012 -0700 Moving short inlines directly into class declaration. This seems to make the code a little easier to read and cut down total amount of code. Src/C_AMRLib/Amr.H Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AuxBoundaryData.H Src/C_AMRLib/BCRec.H Src/C_AMRLib/Cluster.H Src/C_AMRLib/StateData.H commit f3a9feacfb7a2f10a81a411d127dfcbe8643ca50 Author: lijewski Date: Wed Aug 29 08:52:08 2012 -0700 Wrapped some long lines. Src/C_BaseLib/Array.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/CoordSys.H Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/Orientation.H Src/C_BaseLib/Pointers.H commit 5f3c8e0f9482b167ed873aaf306a6687c1da0968 Merge: bbd68cac4 dbeb69737 Author: lijewski Date: Tue Aug 28 16:49:25 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit bbd68cac40e9b3089268d6d28468c19cdb9d35fe Author: lijewski Date: Tue Aug 28 16:46:21 2012 -0700 Some simplification. Src/C_BaseLib/Array.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/CoordSys.H Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/IndexType.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/Orientation.H Src/C_BaseLib/PArray.H Src/C_BaseLib/Pointers.H Src/C_BaseLib/RealBox.H Src/C_BaseLib/Tuple.H Src/C_BaseLib/UseCount.H commit dbeb69737ad80ea4b8a914e1e361862a740733ab Author: vince Date: Tue Aug 28 13:16:41 2012 -0700 some cleanup. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/bench.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.h Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.x86.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/README commit ad20735aaf6ed4e862e96a3247e4262c97b0e125 Author: vince Date: Tue Aug 28 13:05:13 2012 -0700 they should all be working now. stil need to sync timings and consolidate duplicate files. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/bench.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly_F.F Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly_F.H Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/Make.package Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.h Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.x86.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/advance.f90 Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/main.f90 commit 96893aca1b7d5c39a523487d738fbbfe750c7b75 Author: lijewski Date: Tue Aug 28 11:17:54 2012 -0700 A little cleanup of some output I had left in. I'd Key used in the copy cache is better than previously, but SyncRegister::FineAdd() can generate a number of distinct calls to plusFrom() that all yield the same Key :-(. Src/C_BaseLib/FabArray.cpp commit bee39c643e93617b82efefb0b80cae74b10e3731 Author: lijewski Date: Tue Aug 28 11:03:57 2012 -0700 Came up with better Key into the multimap for the caches in an attempt to minimize the search time. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 9e314edf7da121b21f3f056dbefe8e8dc0c6c749 Author: lijewski Date: Mon Aug 27 17:16:21 2012 -0700 Shortcut out of a nested loop a little earlier than before. Src/C_BaseLib/Geometry.cpp commit bc7e450453c5a1415e6eb2ea4bf036d388600466 Author: lijewski Date: Mon Aug 27 16:56:02 2012 -0700 Increase max size of FillPeriodicBoundary() cache. Src/C_BaseLib/Geometry.cpp commit da7bd02eb73b507609609ac8424fac0d32f84d3c Merge: 9a5f6853e 12a69810b Author: lijewski Date: Mon Aug 27 16:44:14 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9a5f6853ede15333fe422afb21f14145b0f97845 Author: lijewski Date: Mon Aug 27 16:43:41 2012 -0700 Implemented SunBoundary() using intersection & communcation info from the FillBoudary() cache. Src/C_BaseLib/MultiFab.cpp commit 12a69810b330ea1bd276f118fa510cd28ad5ae33 Author: vince Date: Mon Aug 27 16:15:04 2012 -0700 added u and q initialization, fixed loop and pencil ranges. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/FakeWriteMultifab.h Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/bench.c commit 90fbd81e6e9215c5a13761c29dedfe979336b446 Author: lijewski Date: Mon Aug 27 15:29:24 2012 -0700 Some code consolidation. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit 5044d9a87fd13723c4583f3bd1b9739e68fda7e2 Author: lijewski Date: Mon Aug 27 15:07:24 2012 -0700 Increased the size of the caches to 100 entries. Refined the count of number of bytes contained by the caches. Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp commit d9b89f4e7b4fc77ce430eeeabbc5b87c212712b9 Author: lijewski Date: Mon Aug 27 14:18:01 2012 -0700 New implementationof copyFrom()/plusFrom() that uses FabArray::copy(). This means that it'll be able to use the copy cache & all that entails. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/FabArray.H Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 1b336fcdee6e06cf99396d47e5f14fc5a65d53b5 Merge: fe909fa37 134434043 Author: lijewski Date: Mon Aug 27 12:18:06 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 134434043da61fab2419a45455a7109a137f74ba Author: Weiqun Zhang Date: Mon Aug 27 10:59:42 2012 -0700 Fix a bug in getRecentFileName in regression testing python script Tools/RegressionTesting/testnew.py commit fe909fa3790d2654c79f129ed43dfcf1c0035c58 Author: lijewski Date: Sun Aug 26 13:52:48 2012 -0700 Call FabSet::Cache() on regrid of level 0. Src/C_AMRLib/Amr.cpp commit 982a5b125dfba7f06615b86beabf5260dfabb021 Author: lijewski Date: Sun Aug 26 13:51:40 2012 -0700 Added a cache for the grid intersection & communication info for copyFrom() and plusFrom(). Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit a1b1950d9de0ada605a90e4b22df054875033d82 Author: lijewski Date: Sun Aug 26 12:47:31 2012 -0700 Generalized the copy cache stuff so I can maintain separate copy caches for different purposes. I want to have a copy cache for FabSet::copyFrom() and FabSet::plusFrom(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit c5d0f7b22773764d163041f19b08f6ba17ad68ce Author: lijewski Date: Sun Aug 26 09:55:55 2012 -0700 Simplified Reflux(). Src/C_AMRLib/FluxRegister.cpp commit 6cfa536b68cee797e48fe95b6e0404f3443106f1 Author: lijewski Date: Sun Aug 26 09:21:48 2012 -0700 Simplified CrseInit(). Removed CrseInitDoit(). Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit bdf8ba1f5284730750bc236068266634e2ba81a8 Author: lijewski Date: Sat Aug 25 19:43:54 2012 -0700 Attempt to get a little communication/computation overlap. Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit e894a538e79881caba9032e82ed6b290e28c895e Author: lijewski Date: Sat Aug 25 19:11:41 2012 -0700 Yet more code consolidation. Src/C_BaseLib/FabArray.H commit 58a30f1e74ca08b699ebf88a9bd6857b76d3c197 Author: lijewski Date: Sat Aug 25 15:06:31 2012 -0700 Found my bug. Back to the hand-optimized version of Reflux(). Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 4b9fb43a75545f680c3caa0a1e67cafbd8d2ba26 Author: lijewski Date: Fri Aug 24 22:42:14 2012 -0700 I'm reverting back to a slightly older version. Something's weird. Running a single timestep multiple times on 256 cores on hopper, the FAB byte spread varies from run to run. Unfortunately it should be the same for identical runs. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 512e849b796864c5a02da2a938c5c2cac7e5ff06 Author: lijewski 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 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 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 Date: Fri Aug 24 16:53:39 2012 -0700 Removed some #if 0 code. Src/C_BaseLib/FabArray.cpp commit 74e470a62623f65f1134ea26a312039e66155ca2 Author: lijewski Date: Fri Aug 24 16:46:45 2012 -0700 Minor performance mod to periodicShift(). Src/C_BaseLib/Geometry.cpp commit f4b1a5c6bb8862390f659672d850853697dc7dcf Author: lijewski Date: Fri Aug 24 16:11:12 2012 -0700 Changed some static member functions of FabArrayBase to member template functions and was able to consolidate more of the recent communication code I wrote. Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.cpp commit e8a4941f216050f1057eeae16abaec494a127627 Author: lijewski Date: Fri Aug 24 14:09:50 2012 -0700 A little more refinement. Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.cpp commit 84de73bc1a6e502528f061bf6524c2ec5e961277 Author: lijewski Date: Fri Aug 24 13:30:35 2012 -0700 A little more refinement. Src/C_AMRLib/FluxRegister.cpp commit 474e3eac259eff15adee2f36c0e18293400f3bd1 Author: lijewski Date: Fri Aug 24 13:13:09 2012 -0700 Handcoded optimized parallel Reflux routine. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit e4b62153fd090963a8c536a4a378a4114d2d5b03 Author: lijewski Date: Thu Aug 23 17:35:59 2012 -0700 Further simplification. Src/C_AMRLib/FluxRegister.cpp commit 2190d260217d7a4754b2290e74f9100bc0f7ce32 Author: lijewski Date: Thu Aug 23 15:58:04 2012 -0700 Some more cleanup of Reflux(). I added another argument to FORT_FRREFLUX() -- an IntVect shift. It's (0,0,0) if it's being called when the two boxes concerned overlap, but it's how much the dest fab must be shifted when being updated due to periodic shifts. Src/C_AMRLib/FLUXREG_1D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 4e29d28d9908392627aeeb214fd7bd64ac1c2b30 Author: lijewski Date: Thu Aug 23 13:21:04 2012 -0700 Very modest simplification of Reflux(). Src/C_AMRLib/FluxRegister.cpp commit afe8c4375bf392f61fff5a48d0afba531454ee01 Author: lijewski Date: Wed Aug 22 15:47:34 2012 -0700 More typedef regularization. Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit 7ecb281614b9e92cb5a59c480a736e82a35169f2 Author: lijewski Date: Wed Aug 22 15:35:51 2012 -0700 Regularized some typedefs. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 84a88dd336c2a7317e505dfbdeaa6b8f65d6d055 Author: lijewski Date: Wed Aug 22 15:19:15 2012 -0700 Some simplification. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 0e3c3405bfc971a3223e01e150b0997d4eb3b5f1 Author: vince Date: Wed Aug 22 12:49:59 2012 -0700 our cpp calling sam's c hypterm. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly_F.F Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/HyptermOnly_F.H Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/Make.package Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/hyptermbench.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.h Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer.x86.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_c/timer_c.c commit ebeb824a82a32cccac719495874211da22d529cc Author: vince Date: Wed Aug 22 12:37:42 2012 -0700 sam's c_c version. need to check the answers. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/bench.c Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/timer.h Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_c_c/timer.x86.c commit a4384cd1dc176b68c1ee7a5c1e3146641ee0daf6 Author: lijewski Date: Wed Aug 22 12:27:28 2012 -0700 Inlined some stuff that seems to matter at high CPU counts. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit d8298cef94146005c1c72252c97170ddad741c3e Author: lijewski Date: Wed Aug 22 11:11:31 2012 -0700 OMP'd couple routines over ncomp. At least for LMC ncomp is sometimes NSPECIES or BL_SPACEDIM so OMP "might" give us a nudge. Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/FluxRegister.cpp commit f48114e2dfe2f5be1608c770f449c2e289e37e50 Author: lijewski Date: Wed Aug 22 10:54:38 2012 -0700 Made the constant volume Reflux() call the more general one. Was able to get rid of a lot of code. I'd like to simplify the more general Reflux() routine enough that I can provide a hand-optimized parallel version. Src/C_AMRLib/FLUXREG_1D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/FluxRegister.cpp commit f8a03a63dd8b741fa6302d0bed8bbeeebcffc426 Author: lijewski Date: Wed Aug 22 09:44:26 2012 -0700 Removed PIRec and PIRMVector stuff -- no longer used. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 283edce059ee20673f1319995eb6d1cb34575eb1 Author: lijewski Date: Wed Aug 22 09:37:16 2012 -0700 Handcoded optimized parallel routine for SumPeriodicBoundary(). Src/C_BaseLib/Geometry.cpp commit 68e92ee8b5724e85cf7730e26a3664fa70dbf071 Author: lijewski 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 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 Date: Tue Aug 21 19:30:31 2012 -0700 Removed SIRec structure -- no longer used. Src/C_BaseLib/FabArray.H commit ae6d0770113a469f3342a1f668eaae3e7af436e8 Author: lijewski Date: Tue Aug 21 19:27:24 2012 -0700 More code consolidation. Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.cpp commit 5437e22a487d3ed50d6883dd2a81fb8b7fd7e8f1 Author: lijewski Date: Tue Aug 21 17:45:26 2012 -0700 Some code consolidation. Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.cpp commit e6d8f05b61584ac85ae05db500545e81aba11466 Author: lijewski Date: Tue Aug 21 16:38:05 2012 -0700 Handcoded parallel routine for SumBoundary(). Src/C_BaseLib/MultiFab.cpp commit f374de43061bcd1afb6c1fc9c93c41a76c13b4dc Merge: 2dcae2309 1cfb636fb Author: lijewski Date: Tue Aug 21 16:37:45 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1cfb636fb07ca37d7013a1367b0940ce13a8eaed Author: vince Date: Tue Aug 21 16:05:29 2012 -0700 the cpp_F version. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly.cpp Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.F Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/HyptermOnly_F.H Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/Make.package Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_cpp_F/timer_c.c commit ff8da35a597965a27e6ba5048e226ac763808de6 Author: vince Date: Tue Aug 21 15:53:41 2012 -0700 the f90_f90 version. Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/GNUmakefile Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/README Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/advance.f90 Tutorials/Exp_CNS_NoSpec/HyptermKernels/HyptermKernel_f90_f90/main.f90 commit 2dcae2309c63304b39b37c68854e67c735d523af Author: lijewski Date: Tue Aug 21 15:02:17 2012 -0700 Removed a data structure no longer used by CollectData(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 21b85f0b9527ae8c80f47ed84541d8d3bd20b929 Author: Ann Almgren Date: Tue Aug 21 13:41:17 2012 -0700 Fix order of tests on bottom solver type when setting up mg_tower because in some cases the bottom solver type is set to 4 but we override that and set it to 1. We need to make sure we make the nodal_mask after that change. Src/LinearSolvers/F_MG/mg.f90 commit a61dded61450a388103a97a01adc2ef72b4f472a Merge: 500109700 a53272407 Author: lijewski Date: Tue Aug 21 10:48:26 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 5001097001846cac63c4513758d39687c02f24f7 Author: lijewski Date: Tue Aug 21 09:22:08 2012 -0700 Consolidated two CrseInit() functions into single CrseInitDoit() that they both call. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit af1d6eecf18369d575411862e3e3e46d2c1fb496 Author: lijewski Date: Mon Aug 20 21:59:18 2012 -0700 Handcoded parallel routine for copyFrom(). Added an assertion that wasn't in the old code: I now check that ngrow <= src.nGrow(). I found one place in MacProj.cpp where it was calling copyFrom() on a src MultiFab and asking to fill more ghost cells than the MultiFab had. I could have silently done the right thing in my code, but it just didn't seem right to allow people to ask for filling with more ghost cells than the MultiFab contains. Hopefully MacProj.cpp is the only code that did that :-) Src/C_BoundaryLib/FabSet.cpp commit a53272407108fcc6262c044f2fd416add7898b48 Author: ajnonaka Date: Mon Aug 20 19:59:32 2012 -0700 add support for USE_LMC_SDC. Will compile in #ifdef LMC_SDC items Tools/C_mk/Make.defs commit ff5c1a139420efe03fd6f07d0f0d9be3d2214070 Author: lijewski Date: Mon Aug 20 19:26:12 2012 -0700 Some cleanup. Two Reflux() functions still call CollectData(). I'll eventually get to them but they're a tad more complicated than the CrseInit()s. I'll work my way up to'm. Src/C_AMRLib/FluxRegister.cpp commit 76500feff119ab12182d1462eee05a16329ee45e Author: lijewski Date: Mon Aug 20 17:19:39 2012 -0700 Handcoded special parallel routine for other CrseInit() -- the one that takes an area MultiFab. Src/C_AMRLib/FluxRegister.cpp commit bda454d14bc7007227bf58efec782c371dff5be5 Author: lijewski Date: Mon Aug 20 15:55:07 2012 -0700 Handcoded parallel routine for FluxRegister::CrseInit(). This avoids the MPI_alltoall and MPI_alltoallv routines in CollectData(). Src/C_AMRLib/FluxRegister.cpp commit 458ae45d4cbfd5578eece227789ea33775289d86 Author: lijewski Date: Mon Aug 20 13:26:08 2012 -0700 Deleted some no-longer-used static variables. Increased the maximum size of the caches. We could "probably" go without limiting their size in any way, as they're cleared every level zero regrid. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 2620d1cda8ea4cba9918190bcdcd44cd53c97b2f Author: lijewski 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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: 6c1615c34 3b41737ee Author: lijewski Date: Fri Aug 17 13:56:51 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 6c1615c344bb015313990dbc516fb55d60d62815 Author: lijewski Date: Fri Aug 17 13:55:19 2012 -0700 Moved the do_alltoallv stuff in copy() into its own function. I'm thinking of removing the do_alltoallv stuff entirely. It's hard for me to imagine as we run on larger & larger machines & communication patterns get sparser that MPI_Alltoallv can beat MPI_Irecv/MPI_Send pairs. Src/C_BaseLib/FabArray.H commit a0a342913e74ec8e5258a5cd8737d14580cec749 Author: lijewski Date: Fri Aug 17 13:33:00 2012 -0700 Moved the portion of CollectData() that uses do_alltoallv into its own helper function. Src/C_BaseLib/FabArray.H commit 3b41737ee90450b2f1597088428a7c0db9087c36 Merge: 5a096355d a26a96e51 Author: vince Date: Fri Aug 17 13:22:53 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 5a096355d4d659176ed65b292e1192456ff6c0a6 Author: vince Date: Fri Aug 17 13:22:23 2012 -0700 gnu. Tutorials/Exp_CNS_NoSpec/GNUmakefile commit a26a96e512693d2021b63ab2c52f0bb0f368cbef Author: Mike Lijewski Date: Fri Aug 17 13:37:32 2012 -0400 Use SameRefs() in copy & fillboundary() cache code. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit df398fd8484023c97ca324a6df40937d54d7697e Author: Mike Lijewski Date: Fri Aug 17 13:35:26 2012 -0400 Added static functon SameRefs() to test if the underlying reference counted pointers are the same. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit f6ff299b7c0c24a2a7528e531bfeddcaa471b4c6 Author: Mike Lijewski Date: Fri Aug 17 13:32:08 2012 -0400 Inline operator==() in reference counted pointer class for testing if underlying pointers are the same. Src/C_BaseLib/Pointers.H commit ba285bd39cede4a841a36756020142e526d1953e Author: lijewski Date: Thu Aug 16 19:48:35 2012 -0700 Built a map of iterators into FabComTagContainer to avoid a modest N^2 loop when receiving FAB data in CollectData(). Src/C_BaseLib/FabArray.H commit 9cd023f2cd6a0c717bc9884b6ebd4793ad99ca9b Author: lijewski Date: Thu Aug 16 19:18:26 2012 -0700 More performance tweaking in CollectData(). Got one more thing I wnat to try before pushing this stuff. Src/C_BaseLib/FabArray.H commit e4fb985a8c6c12df7256658ae65a95d902118b0e Author: lijewski Date: Thu Aug 16 18:03:10 2012 -0700 More tweaks to CollectData(). Src/C_BaseLib/FabArray.H commit d3219ab6ac872ff588501e9423f85d032d72954d Merge: 419146ff6 bf7c2e46f Author: lijewski Date: Thu Aug 16 14:47:02 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 419146ff6cc7df89c1401c40f778655cda2a3e92 Author: lijewski Date: Thu Aug 16 14:46:49 2012 -0700 Squished out more memory from CollectData(). Src/C_BaseLib/FabArray.H commit 92d311cb511ff447f3653c2cda30cf7197a19f6d Author: lijewski Date: Thu Aug 16 13:03:21 2012 -0700 Removed unused variable. Src/C_BaseLib/FabArray.cpp commit bf7c2e46f87a2442495ac3ef54bf394df5f85c4f Author: Ann Almgren Date: Thu Aug 16 11:50:53 2012 -0700 Add extra assertions and comments to make sure we understand the deletion of ghost particles at the end of moveKickDrift in Particles.H Src/C_AMRLib/Particles.H commit 04ceb6cc3a02070fd0ff942bd234576afe27ecf5 Author: lijewski Date: Thu Aug 16 10:44:45 2012 -0700 Changed how caches are passed to CollectData() to cut down on memory allocations. Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H commit a0de0205e7d523f466f314cc0b0da6f0672ac6a0 Author: lijewski Date: Thu Aug 16 10:04:00 2012 -0700 Changed the send count cache used by FillBoundary & FillPeriodicBoundary() from an Array to std::map. This'll keep the size of the cache entries from growing as the number of cores grows. Hence we can increase the size of the cache a bit w/o much problem. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit fecebcc120f1ead7e6bc7dd4bf6e82d4627d629c Merge: 1a90437f7 d2588c3f5 Author: Weiqun Zhang Date: Tue Aug 14 16:23:58 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d2588c3f5fdcad47e1afde09c836ea4bdb0c249c Author: lijewski Date: Tue Aug 14 16:02:43 2012 -0700 Added an optional third argument to KnapSackProcessorMap(). It's a pointer to a double into which the efficiecy will be placed if it's not NULL. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 1a90437f7904e234245bfb1116a3a5c499addbd5 Merge: dd9138b62 e3f54c6ee Author: Weiqun Zhang Date: Tue Aug 14 10:37:31 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit dd9138b6235b6c30892c1a268804bf48d7e9df32 Author: Weiqun Zhang Date: Tue Aug 14 10:37:18 2012 -0700 Fix a comment Tools/RegressionTesting/testnew.py commit e3f54c6ee6f004a2427051ab392e60406e28481d Merge: 84e0716de 9553fce6c Author: lijewski Date: Tue Aug 14 09:35:59 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 84e0716de61eb51e78e8e1171dc7f064619ccb3b Author: lijewski Date: Tue Aug 14 09:11:08 2012 -0700 Set verbose to false. Src/C_AMRLib/AuxBoundaryData.cpp commit 9553fce6cfbf721efae915ac4a198d8c0ef434ea Author: Matthew Emmett Date: Tue Aug 14 11:57:56 2012 -0400 Add 'build' and 'destroy' interfaces to BC tower. Src/F_BaseLib/define_bc_tower.f90 commit 16402f204b94cbc95fcac6838b295eee8b61b557 Author: Weiqun Zhang Date: Mon Aug 13 22:18:33 2012 -0700 Fix a bug in regression testing script for the case when extSrcGitHash is used Tools/RegressionTesting/testnew.py commit 21856cb8e95fd3afaa5f6caa5c9a54d527a2dbef Author: Matthew Emmett Date: Mon Aug 13 19:03:14 2012 -0400 PyBoxLib: Begin adding plotfile support. Src/Python/pyboxlib/base.py Src/Python/pyboxlib/fab.py Src/Python/pyboxlib/multifab.py Src/Python/pyboxlib/plotfile.py Src/Python/src/blobjects.f90 Src/Python/src/blobjects.py Src/Python/src/fboxlib.f90 Src/Python/tests/test-multifab.py commit 2f36539e319d2576dc760c1671f9856c10a9701d Author: Matthew Emmett Date: Mon Aug 13 19:09:11 2012 -0400 HeatEqaution: Tweak regrid. Tutorials/HeatEquation_EX4_F/regrid.f90 Tutorials/HeatEquation_EX5_F/regrid.f90 commit 0f55a568964aa1d1aca4d8ac540c634e74fa5fc8 Author: Michael Zingale Date: Wed Aug 8 21:10:40 2012 -0400 some minor fixes (deallocates, comments) python_plotfile/fsnapshot.f90 commit 40a2ea134d6f194dfe717beba0a076f143472036 Author: Matthew Emmett Date: Wed Aug 8 19:35:28 2012 -0400 CHEMOTAXIS: Tidy, use first-order stencils. Tutorials/Chemotaxis_F/README Tutorials/Chemotaxis_F/advance.f90 Tutorials/Chemotaxis_F/chemotaxis.f90 Tutorials/Chemotaxis_F/chemotaxis.py Tutorials/Chemotaxis_F/chemotaxis.tex Tutorials/Chemotaxis_F/codegen/README Tutorials/Chemotaxis_F/codegen/__init__.py Tutorials/Chemotaxis_F/codegen/compile.py Tutorials/Chemotaxis_F/codegen/polyquad.py Tutorials/Chemotaxis_F/codegen/symbolic.py Tutorials/Chemotaxis_F/dtypes.f90 Tutorials/Chemotaxis_F/inputs.mwe Tutorials/Chemotaxis_F/kernels.f90 Tutorials/Chemotaxis_F/kernels.py Tutorials/Chemotaxis_F/kernels.tmpl.f90 commit ff14d31f3716358a1d6bda8a1aebba27bada56ed Author: Michael Zingale Date: Wed Aug 8 16:14:05 2012 -0400 add new routine to make a plot of several variables from a flame_1d plotfile python_plotfile/plot1dflame.py commit a4ed93f696f2373068527dc5a2e27594fc029781 Author: Michael Zingale Date: Wed Aug 8 14:37:34 2012 -0400 add methods to get at the variable names python_plotfile/fsnapshot.f90 commit 8085200159435601f063a7f98b3b1828cf82fb51 Author: Michael Zingale Date: Wed Aug 8 12:48:08 2012 -0400 add support for 1d data, for flame plotting python_plotfile/fsnapshot.f90 commit dbb7011c6b5acf96ef2aba2a825feb49b37ed21f Author: lijewski Date: Tue Aug 7 20:28:35 2012 -0700 Added extra constructor that takes a pointer to BndryData. We want to be able to reuse BndryData types in linear solves. Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit e7c430257585f6a7f3145156bdf93e81225f07b6 Author: lijewski Date: Tue Aug 7 18:53:03 2012 -0700 A little cleanup of the BndryData hierarchy. Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp Src/C_BoundaryLib/MacBndry.H Src/C_BoundaryLib/MacBndry.cpp commit 8f3613052005f1cd7583036c4c366487520338bc Merge: e81f65100 7f8d82365 Author: lijewski Date: Tue Aug 7 18:50:39 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 7f8d82365722e524fad6caea903adc19f311c42e Merge: ca6fa36e1 974aeb1ba Author: Weiqun Zhang Date: Tue Aug 7 17:28:04 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ca6fa36e1a107b1b8d0cbafc9b9283b5fee4d1e1 Author: Weiqun Zhang Date: Tue Aug 7 17:27:53 2012 -0700 Increase the precision of numbers written to Header Src/F_BaseLib/fabio.f90 commit e81f65100bc4a73bdef2f47ba55d21102e70bdc6 Author: lijewski Date: Tue Aug 7 10:31:53 2012 -0700 Attempt to allow so reuse of BndryData objects. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp commit 974aeb1ba65bcd68aede07ae99fb5317173ba2e0 Merge: 676abbddd a9a3ebcd5 Author: Matthew Emmett Date: Tue Aug 7 10:13:10 2012 -0400 Merge branch 'chemotaxis' commit a9a3ebcd5c2a588f7cedc008bdf9041a4856e956 Author: Matthew Emmett Date: Tue Aug 7 10:11:46 2012 -0400 CHEMOTAXIS: Add codegen, tweak some parameters. Tutorials/Chemotaxis_F/GPackage.mak Tutorials/Chemotaxis_F/advance.f90 Tutorials/Chemotaxis_F/chemotaxis.f90 Tutorials/Chemotaxis_F/codegen/README Tutorials/Chemotaxis_F/codegen/__init__.py Tutorials/Chemotaxis_F/codegen/compile.py Tutorials/Chemotaxis_F/codegen/polyquad.py Tutorials/Chemotaxis_F/codegen/symbolic.py Tutorials/Chemotaxis_F/dtypes.f90 Tutorials/Chemotaxis_F/inputs.mwe Tutorials/Chemotaxis_F/kernels.f90 Tutorials/Chemotaxis_F/kernels.py Tutorials/Chemotaxis_F/kernels.tmpl.f90 commit 676abbddd21c429182bf578b2f6a1cda2546eddf Author: Matthew Emmett Date: Tue Aug 7 10:12:21 2012 -0400 PyBoxLib: Bug fix. Src/Python/pyboxlib/fab.py commit 3dd46fda1fbe8924198c9143fb2b4432fac2ba06 Author: cmalone Date: Mon Aug 6 14:06:29 2012 -0700 ppCleanup is a C PreProcessor macro cleanup script that removes unwanted code associated with specified macros. This is useful for stripping out bits of code before releasing it to the masses. Currently this requires python 2.7.X to run; let me know if this is a problem... Tools/ppCleanup/README Tools/ppCleanup/cleanWords.txt Tools/ppCleanup/ppCleanup.py commit 155901569aaa141fd287a8495a82f969cb21f2b5 Merge: 6d0c685ed 194a91136 Author: Weiqun Zhang Date: Sat Aug 4 20:52:32 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 194a91136df5ff3e80a630f8771adf3204c47a1f Author: lijewski Date: Sat Aug 4 13:56:24 2012 -0700 Changed define() so that we can reuse BndryData and derived types. This way in LMC (and other codes) where we diffuse a raft of species, we can reuse these objects instead of building a new one for each component we diffuse. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp commit 6d0c685edfa51ef346097b193a5ed148754592ca Merge: 3c4e9b8dd 12fc2bf4c Author: Weiqun Zhang Date: Fri Aug 3 10:49:19 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 12fc2bf4cc45a108b37b378f38eb8840f9ffcdf1 Author: ajnonaka Date: Fri Aug 3 10:41:58 2012 -0700 revert Src/F_BaseLib/define_bc_tower.f90 commit 3ce2731d0f5afed02d938b352a6e14a6265284b1 Author: ajnonaka Date: Fri Aug 3 10:41:15 2012 -0700 revert Src/F_BaseLib/fabio.f90 commit 3c4e9b8dded9f232b879744f9745832c71562140 Merge: 23e458897 8e8312285 Author: Weiqun Zhang Date: Thu Aug 2 21:16:10 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 23e45889755e4d53ff4d70334ec53496e5d185cd Author: Weiqun Zhang Date: Thu Aug 2 18:18:20 2012 -0700 Update stencil_types.H according to stencil_types.f90. Src/LinearSolvers/C_to_F_MG/stencil_types.H commit 25b835afc7135fe2722fb4ec82875a426eaf09d7 Author: Weiqun Zhang Date: Thu Aug 2 18:13:55 2012 -0700 Due to a bug in either etags or Emacs (on my Ubuntu 10.04?), absolute path has to be used in tagging. Tools/F_mk/GMakerules.mak commit 8e8312285bf8d22bfd86f252871c7ff909728795 Merge: d8b422f03 6c86a20da Author: Sandra May Date: Thu Aug 2 16:51:12 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d8b422f030f432e2580f8f2cfdb65f469f1f895c Author: Sandra May Date: Thu Aug 2 16:48:50 2012 -0700 typos Docs/F_AdvancedTopics/F_AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex Docs/Introduction/Introduction.tex commit 6c86a20dad2e24792ec2b865eeddce4f0aa0691f Author: ajnonaka Date: Thu Aug 2 16:37:51 2012 -0700 test commit Tutorials/HeatEquation_EX5_F/main.f90 commit 10f93ea6599b282eae90874ab03bace98806ccbb Author: Weiqun Zhang Date: Thu Aug 2 14:03:10 2012 -0700 Fix a bug. "if (stencil_type .eq. 1)" is no longer good. Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 65ba033fd5fd317f7a4490df539150513555c011 Author: lijewski Date: Wed Aug 1 21:19:08 2012 -0700 Fixed the assignment of the "nodal" data member in [ilz]multifab_build() in the presence of an optional argument. Interestingly, it was correct for multifab_build(). Src/F_BaseLib/multifab_f.f90 commit 01a2f314b94fc32060817419c41b883775e097d0 Author: Michael Zingale Date: Wed Aug 1 19:57:57 2012 -0400 add a diffOpts attribute to tests -- this is the flags we want to invoke diff with when comparing plain text files (through diffDir). This is useful for instance to ignore comment lines in the output Tools/RegressionTesting/testnew.py commit d05778a3db3a24e852d63779d2fab72aaed27a39 Merge: 3a56fe746 4853fce34 Author: lijewski Date: Wed Aug 1 14:45:31 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3a56fe74698dd58f35554e5f510f8ec0d72678ce Author: lijewski Date: Wed Aug 1 14:45:07 2012 -0700 Didn't have src_comp & dst_comp quite right in new compFlux(). Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp commit 4853fce34ee366e8eb05896c3e1e80fc4851a059 Merge: 8383125bf d8b0dc424 Author: Ann Almgren Date: Wed Aug 1 14:36:08 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 8383125bf1ae591d70d92fb337ca681389ebbf57 Author: Ann Almgren Date: Wed Aug 1 14:35:48 2012 -0700 More transition from size(ss) to using stencil_type. Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/stencil_types.f90 commit d8b0dc42419b93d80af56f64dddee27708d929a2 Merge: 4cb851c06 255f630df Author: lijewski Date: Wed Aug 1 13:38:10 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 4cb851c06b4e5a63d39bdfa35fd09d165c1eea33 Author: lijewski Date: Wed Aug 1 13:34:16 2012 -0700 More general compFlux(). Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp commit 764754d2de1ffb18473189dc3ed9088d2c3a1777 Author: lijewski Date: Wed Aug 1 13:33:55 2012 -0700 Fixed typo in my previous fix. Src/C_BoundaryLib/BndryData.cpp commit f9a4149a80112ecb28e670cad88c1921c79795c1 Author: lijewski Date: Wed Aug 1 12:51:54 2012 -0700 Added scomp, dcomp & ncomp to compFlux() with obvious defaults. Src/LinearSolvers/C_CellMG/LinOp.H commit ee24b14f3fc3ffbec2f3cd24364357ddd21b5d3b Author: lijewski 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 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: c27f9f572 f902913e8 Author: Sandra May Date: Wed Aug 1 11:13:14 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f902913e899922eaf37bda61cee846c3cedbecd9 Author: ajnonaka 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 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 Date: Tue Jul 31 19:32:02 2012 -0700 Had argument order switch. Src/C_BaseLib/MultiFab.cpp commit 82d5b68f0d222423365505eea37b6051dcb48591 Author: lijewski Date: Tue Jul 31 18:40:15 2012 -0700 Enable cross=true for FillBoundary() in LinOp::applyBC(). My test indicate it isn't needed. We'll see what the regression tests say ... Src/LinearSolvers/C_CellMG/LinOp.cpp commit 6e41c7704b83e792c5a950d17ec3f83bb925a270 Author: lijewski Date: Tue Jul 31 17:33:03 2012 -0700 Work on adding the "cross" idea to the C++ FillBoundary from FORTRAN. Then will have to add the add the calls to use it when appropriate. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit c58cd32ac61fdcb5ebbace68bbf2d49a03c6f751 Author: Matthew Emmett Date: Tue Jul 31 16:34:49 2012 -0400 Chemotaxis: Implement SDC time-stepping. Tutorials/Chemotaxis_F/advance.f90 Tutorials/Chemotaxis_F/chemotaxis.f90 Tutorials/Chemotaxis_F/inputs.mwe Tutorials/Chemotaxis_F/main.f90 commit c27f9f572cf10cf0ec33cf5ea69aeb6371a61ab3 Merge: dd0d3dabd 2475496ca Author: Sandra May Date: Tue Jul 31 12:32:30 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 2475496cab253d18e4252b2f3efa624bdb5c6223 Author: Matthew Emmett Date: Tue Jul 31 15:16:09 2012 -0400 Chemotaxis: Minimal model working. Tutorials/Chemotaxis_F/GNUmakefile Tutorials/Chemotaxis_F/GPackage.mak Tutorials/Chemotaxis_F/advance.f90 Tutorials/Chemotaxis_F/chemotaxis.f90 Tutorials/Chemotaxis_F/dtypes.f90 Tutorials/Chemotaxis_F/inputs.mwe Tutorials/Chemotaxis_F/kernels.f90 Tutorials/Chemotaxis_F/main.f90 commit 6e008af670a5eeff0e375ea6dc3dae609c0df2a3 Author: Matthew Emmett Date: Tue Jul 24 10:27:17 2012 -0400 CHEMOTAXIS: WIP. Tutorials/Chemotaxis_F/chemotaxis.py commit 198f2b97dfd94c06621b45c6f6d16a54aa44a22c Author: Matthew Emmett Date: Tue Jul 24 09:59:00 2012 -0400 CHEMOTAXIS: WIP. Tutorials/Chemotaxis_F/GPackage.mak Tutorials/Chemotaxis_F/advance.f90 Tutorials/Chemotaxis_F/chemotaxis.f90 Tutorials/Chemotaxis_F/chemotaxis.py Tutorials/Chemotaxis_F/chemotaxis.tex Tutorials/Chemotaxis_F/dtypes.f90 Tutorials/Chemotaxis_F/inputs.mwe Tutorials/Chemotaxis_F/main.f90 Tutorials/Chemotaxis_F/sdcquad.f90 commit 07fd4adb40fc0bb4d8fac27ce82da1b2e8e15d79 Author: Matthew Emmett Date: Fri Jul 20 21:02:21 2012 -0400 CHEMOTAXIS: Create skeleton chemotaxis example. Tutorials/Chemotaxis_F/GNUmakefile Tutorials/Chemotaxis_F/GPackage.mak Tutorials/Chemotaxis_F/chemotaxis.f90 Tutorials/Chemotaxis_F/inputs.mwe Tutorials/Chemotaxis_F/main.f90 Tutorials/Chemotaxis_F/write_plotfile.f90 commit 421cce52970f43ae2e942377d969d7e24dedbe1b Author: Matthew Emmett Date: Tue Jul 31 15:24:33 2012 -0400 PyBoxLib: Update make structure, fix indexing with multiple components. Src/Python/GMakerules.mak Src/Python/GNUmakefile Src/Python/GPackage.mak Src/Python/pyboxlib/fab.py Src/Python/pyboxlib/pybl.py commit 3109955e41a2feae036b3096d0a9b6e2d90153d3 Author: Ann Almgren 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 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 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 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: e2c8ef913 1dbaf45d6 Author: Sandra May Date: Mon Jul 30 10:11:04 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1dbaf45d6b513f42b8d2a9e86a544bcb6e0b8e92 Author: ajnonaka Date: Sun Jul 29 22:00:16 2012 -0700 get this compiling and running again with latest interfaces changes to mg_tower_build Tutorials/HeatEquation_EX5_F/advance.f90 commit 9c59dcef9a18775b36616c78ba302c50f8ab4604 Merge: e5fc8be69 506891d3a Author: Michael Zingale 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 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 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: 90b4e6105 d508b85e2 Author: Weiqun Zhang Date: Sat Jul 28 07:28:39 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 90b4e61059aa1dd640361bbc4545fdc531295ba5 Author: Weiqun Zhang Date: Fri Jul 27 22:29:30 2012 -0700 Simplify the make_build_info script and add more comments Tools/C_scripts/make_build_info_cpp commit d508b85e2ad94e02cd50ca963654c54fbe9d8b06 Author: Ann Almgren Date: Fri Jul 27 21:59:46 2012 -0700 Start to use stencil_type rather than ncomp of the stencil to know which stencil we're actually using. Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 commit e509176939f9d0b4f44c0abeea44ece271852227 Author: Ann Almgren Date: Fri Jul 27 21:43:28 2012 -0700 We now define a stencil_type and lcross as part of the mg_tower. We will use stencil_type rather than testing on ncomp of the stencil to decide which stencil we're actually using. Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/mg_tower_smoother.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit c797c028961361e93103acbf7c46811e26863a05 Author: Weiqun Zhang Date: Fri Jul 27 17:04:22 2012 -0700 minor update of usage string Tools/RegressionTesting/testnew.py commit d2833df779bbab7f20ac53eff64758c49b24b43b Author: Weiqun Zhang Date: Fri Jul 27 16:31:08 2012 -0700 Add git hash to job_info file in plotfiles Tools/C_scripts/buildInfo.H Tools/C_scripts/make_build_info_cpp commit 2155c62e324f10c95fc2aea2c7a793e995e8df72 Author: Ann Almgren Date: Fri Jul 27 14:31:32 2012 -0700 Add stencil_types.f90 Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/stencil_types.f90 commit e449ae53559ebdde0f4eae3bafc3bdeaff34357c Author: Ann Almgren Date: Fri Jul 27 14:29:05 2012 -0700 We now pass the stencil_type explicitly through from the calling routine to the F90 multigrid -- this requires a change in the calling sequence from each application. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/C_to_F_MG/Make.package Src/LinearSolvers/C_to_F_MG/stencil_types.H commit c3b8c05694c96c196442d8c11991329d8986e9f1 Author: vince Date: Fri Jul 27 11:48:16 2012 -0700 added debug checks for varnames. Src/Extern/amrdata/AmrData.cpp commit f0d4b6dd14bb106f0a062a2056493dfe851b9df0 Merge: 260be6ef4 7eaf3b82c Author: lijewski Date: Fri Jul 27 08:42:49 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 260be6ef4bba8911b79623158fa727913589efc3 Author: lijewski Date: Fri Jul 27 08:42:29 2012 -0700 Some simplification. Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit 7eaf3b82c9dffa87d5b01106a70f62994beb4cad Author: Michael Zingale Date: Thu Jul 26 22:38:47 2012 -0400 really fix it now... Tools/F_scripts/make_build_info commit 9c6aaa8b51340faa9371e8a11683f553757a1476 Author: Michael Zingale Date: Thu Jul 26 22:37:49 2012 -0400 fix compilation Tools/F_scripts/make_build_info commit ac7138adb4bdd5334fed703a11889af96ea318ec Author: Michael Zingale Date: Thu Jul 26 22:31:17 2012 -0400 add git hashes for boxlib, source (e.g. Maestro). and extra (e.g. AstroDev) Tools/F_scripts/make_build_info commit b8d4b7d41c410c9a6629d5880a4b0fb439b6487d Author: Regression Tester account Date: Thu Jul 26 16:35:50 2012 -0700 Add restart tests Tools/RegressionTesting/IAMR-tests.ini Tools/RegressionTesting/LMC-tests.ini Tools/RegressionTesting/Nyx-tests.ini commit c4ae93e6296cf380dc7fe6a43c0a1715f3de5978 Author: Regression Tester account Date: Thu Jul 26 14:39:58 2012 -0700 Add some regression restart tests Tools/RegressionTesting/Castro-tests.ini Tools/RegressionTesting/Nyx-tests.ini Tools/RegressionTesting/radiation-tests.ini Tools/RegressionTesting/testnew.py commit 54499346dfcc5b42e9a2b2d1bcac7eeec8057c49 Author: Weiqun Zhang Date: Thu Jul 26 13:09:21 2012 -0700 The precision of Checkpoint Header is changed to 17 from 15. According to IEEE 754, if a double precision number is saved in clear text and is then convected back to double precision number, the clear text number must have at least 17 significant decimal for the new number to exactly match the original. Src/C_AMRLib/Amr.cpp commit dfa27bad3fd6836f3fa95d65adfcfb584ab76a01 Author: lijewski Date: Tue Jul 24 13:56:09 2012 -0700 More cleanup & simplification. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BoundaryLib/FabSet.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit d48102247e916f17a9aac369d50eb1cdca45927f Author: Regression Tester account Date: Tue Jul 24 12:11:15 2012 -0700 inputs files for regression tests Tests/LinearSolvers/ComparisonTest/inputs-rt-Dir Tests/LinearSolvers/ComparisonTest/inputs-rt-Neu Tutorials/HeatEquation_EX5_F/inputs-rt commit bf27bd82de2d3bd5aa7b8efe6d0c2233e2930cd0 Author: Weiqun Zhang Date: Tue Jul 24 12:03:39 2012 -0700 Update README for regression testing scripts. helmeosDir is no longer required for a test suite that does not have any tests using helmeos. Tools/RegressionTesting/BoxLib-tests.ini Tools/RegressionTesting/Castro-tests.ini Tools/RegressionTesting/IAMR-tests.ini Tools/RegressionTesting/LMC-tests.ini Tools/RegressionTesting/Nyx-tests.ini Tools/RegressionTesting/README Tools/RegressionTesting/radiation-tests.ini Tools/RegressionTesting/test-Ubuntu.py Tools/RegressionTesting/testnew.py commit 681838b19f2deaa80f8841dfbf652888909df95b Author: Ann Almgren Date: Tue Jul 24 10:29:02 2012 -0700 These have a more general interface to s_dense_2d_nodal. Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit ca1b5620f7b75e775f7aa68793a18baeabaf1832 Author: Michael Zingale Date: Tue Jul 24 12:32:18 2012 -0400 revamp the NEEDS_EOS_NETWORK stuff -- now it will work with stuff in AstroDev/ and also pull in the proper dependencies GNUmakefile commit 409ab742fd987dcb7ffd07d68a3e3dd756288d9d Author: Matthew Emmett Date: Tue Jul 24 10:28:12 2012 -0400 PyBoxLib: Add is_periodic argument to layout creation routines. Src/Python/pyboxlib/layout.py Src/Python/pyboxlib/pybl.py Src/Python/src/fboxlib.f90 commit 10d9e991d15f10039cf4a2b38b10b11f6ddc1cf6 Author: Matthew Emmett Date: Tue Jul 24 10:00:55 2012 -0400 PyBoxLib: Added bxrange to fab and switched to global indexing. Src/Python/pyboxlib/fab.py commit 79421977cb522ac051e971d98ae1d3f3500cd7ee Merge: 00c67237c 735ba4138 Author: Michael Zingale 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 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: b9b222b25 9e57e62d2 Author: Weiqun Zhang Date: Mon Jul 23 18:23:03 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9e57e62d2ded550fbf2884abf22cc0394e8a4da6 Author: lijewski Date: Fri Jul 20 16:33:15 2012 -0700 Using the new BoxArray::const_iterator. Src/C_BoundaryLib/FabSet.cpp commit e4d012f70eaef2bcc03af2aa63ceddb431035306 Author: lijewski Date: Fri Jul 20 16:32:18 2012 -0700 Using the new BoxArray::const_iterator. Src/C_BaseLib/DistributionMapping.cpp commit 3855aeb038b186aaa9957f90d7056ae9edcb7c5a Author: lijewski Date: Fri Jul 20 15:56:27 2012 -0700 Added const_iterators to BoxArray. They can now be used like a const STL container. We don't allow non-const iterators because BoxArrays are reference counted and we don't want folks to modify them without using the regular BoxArray interface. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit b9b222b250f7fc7dd4a1e314d9209553c402afd5 Merge: 7cfd2c851 844756022 Author: Weiqun Zhang Date: Fri Jul 20 14:51:01 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 844756022516a895ad9f8a4e7ae1e4afe4088dee Author: lijewski Date: Fri Jul 20 14:45:51 2012 -0700 Used iterators more extensively. Src/C_AMRLib/AmrLevel.cpp commit 7cfd2c8512317a4e19ee40d901649c714016fea9 Merge: 14951ed07 b4b31715e Author: Weiqun Zhang Date: Thu Jul 19 07:05:01 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 14951ed07c84624d548e259f7326220325540ea4 Author: Weiqun Zhang Date: Thu Jul 19 07:04:54 2012 -0700 Add baragon to F_mk Tools/F_mk/GMakeMPI.mak commit b4b31715e87c220d3bb0af91c44e892d4ee48ebf Author: Michael Zingale Date: Wed Jul 18 23:54:59 2012 -0400 add aux1 and aux2 to hold additional build information Tools/C_scripts/buildInfo.H Tools/C_scripts/make_build_info_cpp commit ece0088b47e135b79730ba1f441e65755762bdec Author: Michael Zingale Date: Wed Jul 18 23:34:19 2012 -0400 add COMP and FCOMP Tools/C_scripts/buildInfo.H Tools/C_scripts/make_build_info_cpp commit 24e2115656336e236c3d0df9a09c31236021ee7c Merge: 5e06064dd 680388f6c Author: Michael Zingale 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 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 Date: Wed Jul 18 16:13:53 2012 -0700 Just a minor tweak. Src/C_BaseLib/FabArray.H commit 1b583c3354e7904384a2ba57a7ac1dbff7620c2d Author: lijewski Date: Wed Jul 18 15:04:54 2012 -0700 Be more sophisticated when inserting elements into std::map<>s in those cases when we "know" the index is increasing, say when the index corresponds to the index into a BoxArray. Src/C_AMRLib/AmrLevel.cpp Src/C_BoundaryLib/BndryData.cpp commit b2e44f706e688910d56c091b7c982adb6729d59b Merge: 1ce42ec74 b73802823 Author: lijewski Date: Wed Jul 18 12:14:10 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1ce42ec7464481c3095ab8645a41e23b977396de Author: lijewski Date: Wed Jul 18 12:12:14 2012 -0700 Fixed bug I introduced yesterday. I was using the std::vector::back() function to refer to the last element in a vector. That's fine as it goes but the reference returned can be invalidated if the vector is resize()d with the addition of new elements. Also shorted the names of some data members of FillPatchIteratorHelper. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 46153187fee8e7781665384e90ffafd1f4ca7606 Merge: d2081ba76 b73802823 Author: Marc Day 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 Date: Wed Jul 18 12:02:33 2012 -0700 need quadmath on Marcs laptop Tools/C_mk/Make.Darwin commit b7380282315f4b89731d65899e348c9e5e3151c1 Author: Michael Zingale Date: Wed Jul 18 09:27:48 2012 -0400 writes had an extra ',' in them -- Cray doesn't like this. Get this compiling again. Src/F_BaseLib/cutcells.f90 commit 1f274a353cbd2a5280eadf086a15cd508d6fd93f Merge: 4ce643967 3e414575a Author: Marc Day Date: Tue Jul 17 22:57:27 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 3e414575a3e7f15258b22ca4ffa4098a0bdafcfa Author: lijewski Date: Tue Jul 17 14:21:50 2012 -0700 Added defineDoit() to consolidate two define() functions. Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit 08cf2346b9d479c5193faaaf2e26338aacd5d277 Author: lijewski Date: Tue Jul 17 14:21:07 2012 -0700 Simplifed class declaration a bit. Since we really only wrap an integer let the compiler generate copy constructor & assignment operator. Src/C_BoundaryLib/BoundCond.H commit 9aa3885857775898420cdb3953abd8cec3a64284 Merge: 67709eceb 6b4dc6b91 Author: lijewski Date: Tue Jul 17 13:26:24 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 67709eceb4cc20e0f877c68369d723e21b26ee79 Author: lijewski Date: Tue Jul 17 13:26:08 2012 -0700 Squeezed out a little more memory. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 4ce64396757951c36e9a9aa07e6c46ca6c33c217 Merge: a4c3068c9 6b4dc6b91 Author: Marc Day 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 Date: Tue Jul 17 11:23:39 2012 -0700 add TagBox include file Tools/C_util/ViewMF/viewMF.cpp commit b23a99c43bf47b55684c1e172748f12cc0d67e41 Author: Marc Day Date: Tue Jul 17 11:23:07 2012 -0700 Add special rules for hedorah Tools/F_mk/GMakeMPI.mak commit 6b4dc6b91d9d78dba0bce85b3beef5af692ad221 Author: Weiqun Zhang Date: Tue Jul 17 10:52:22 2012 -0700 Fixed a bug due to underestimating the complexity of git history. Tools/RegressionTesting/reg_test_blame.py commit 940bde4c962e1a7e95d83d34370cb461c695aca2 Merge: 63860b2e7 c4ef4db23 Author: ajnonaka Date: Tue Jul 17 08:34:41 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 63860b2e7b69b246dc0cd8fc1e2390b6872d42fb Author: ajnonaka Date: Tue Jul 17 08:34:21 2012 -0700 alpha and beta going into cc solve do not need ghost cells Tutorials/HeatEquation_EX5_F/advance.f90 commit c4ef4db23c377e416e51b4ddc8729f8d48cabda0 Author: Michael Zingale Date: Mon Jul 16 16:43:44 2012 -0400 get this working with the latest version of the test suite -- in particular, the extSrc replacing AstroDev stuff Tools/RegressionTesting/Maestro-tests.ini commit 0af64ddb08e75990510a02ab8e49ae5cd8529904 Author: lijewski Date: Mon Jul 16 10:36:47 2012 -0700 Provide a specialization of invert() for Real. The implementation is an OpenMP'd Fortran function. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/SPECIALIZE_1D.F Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit 9c2c1e1ca30954b3074afe9e7c15322ecfa256d6 Author: lijewski Date: Fri Jul 13 16:52:37 2012 -0700 Pass MultiFabIDs by value not const reference. They're just integers. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 710799820a92f0031f7d816ab4c787405382e1c1 Author: lijewski Date: Fri Jul 13 16:51:42 2012 -0700 Inline the default constructor. Contrary to the previous documentation it does nothing. Src/C_AMRLib/BCRec.H Src/C_AMRLib/BCRec.cpp commit a5f102f7c8ff75e21a13c9dd258902e5bb15f511 Author: lijewski Date: Fri Jul 13 16:51:05 2012 -0700 Inline the FluxRegister::Rec constructors. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 2fe86a29f0ce2237051ef761952e2f7a92a28192 Author: lijewski Date: Fri Jul 13 16:05:48 2012 -0700 Got rid of the "len" member data in RealBox. Had to throw out the length() member function. Calculate the len(dir) on the fly. Also had to throw out the length() member function in Geometry. This latter doesn't appear to have been used anywhere I could find. Src/C_BaseLib/Geometry.H Src/C_BaseLib/RealBox.H Src/C_BaseLib/RealBox.cpp commit b1736020e8f04d9ea987b45e0a358ef545852d46 Author: lijewski Date: Fri Jul 13 15:50:00 2012 -0700 Pass Orientations and IndexTypes by value not const reference. They're just fancy integers. Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit 29decf7ab90769748c00795bd544bca2887acfe7 Author: lijewski Date: Fri Jul 13 13:56:39 2012 -0700 Minor cleanup. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit c38b71b494ed1d92cb4d41d60b49f6afd42bdde5 Merge: e925dac74 5451cac3f Author: Weiqun Zhang Date: Fri Jul 13 13:26:44 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e925dac7456fc03614925c22ccca31d2ae86ea9d Author: Weiqun Zhang Date: Fri Jul 13 13:25:11 2012 -0700 minor updated Tools/RegressionTesting/testnew.py commit 5451cac3fc9977e70fe8196b126ab8346c7a5310 Merge: 64c530dae c3be672d7 Author: lijewski Date: Fri Jul 13 13:01:08 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 64c530daefbf59fd2b74373df55d4c126bee2a66 Author: lijewski Date: Fri Jul 13 13:00:00 2012 -0700 In BndryData changed the following member data: PArray masks[2*BL_SPACEDIM]; to std::map masks; Also, changed the following member function: const PArray& bndryMasks (const Orientation& face) const; to const MaskTuple& bndryMasks (int igrid) const; using to the following typedef: typedef Tuple MaskTuple; In MCLinOp.H, changed the following member data: Array< Array< Array< Mask*> > > maskvals; to Array< std::map > maskvals; Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/InterpBndryData.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit c3be672d72cdd420ccf653cc9a1712fd2e8bfbb5 Author: Weiqun Zhang Date: Fri Jul 13 12:59:05 2012 -0700 another bug Tools/RegressionTesting/testnew.py commit 4a932e09719e52ccfac04248af37a7bb501db071 Author: Weiqun Zhang Date: Fri Jul 13 12:43:22 2012 -0700 fix bug Tools/RegressionTesting/testnew.py commit 8195cddf7ee146fc407686fe38e7d54086c3af74 Author: Weiqun Zhang Date: Fri Jul 13 12:21:42 2012 -0700 testnew.py now takes --no_update=value, where the case-insensitive "value" can "all" or "none" or a list of names separated by ",", such as "Castro,AstroDev". reg_test_blame.py now supports an extra git source other than the main source code and BoxLib. Tools/RegressionTesting/reg_test_blame.py Tools/RegressionTesting/testnew.py commit 5a2790b09389d1ac37991432425da78b80dd8d87 Author: Weiqun Zhang Date: Thu Jul 12 16:33:38 2012 -0700 Fix outputFile. Add a new script called reg_test_blame.py that will find out which commit of either the main source code or BoxLib to blame. Tools/RegressionTesting/reg_test_blame.py Tools/RegressionTesting/testnew.py commit e2c8ef9137a70e5f0137bc1a8a876c5b7dcd04f8 Author: Sandra May Date: Thu Jul 12 15:38:08 2012 -0700 changes to enable inflow and outflow b.c. Src/F_BaseLib/define_bc_tower.f90 commit 0d281aca286e5c831b1e5c5871b37adfb839a2a9 Merge: 1c01e0e71 30327b84e Author: lijewski Date: Thu Jul 12 14:29:58 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 1c01e0e7157a4baf1293e25f4dbfe7cf49c306de Author: lijewski Date: Thu Jul 12 14:27:57 2012 -0700 Prototype of BndryData::bndryConds() changed from const Array& bndryConds (const Orientation& face, int igrid) const; to const Array< Array >& bndryConds (int igrid) const; The "new" outer dimension is over Orientation. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 88a8631bea8525a4d8e2f8a79e8ace4ba9bd26aa Author: lijewski Date: Thu Jul 12 14:08:15 2012 -0700 Changed the prototype of BndryData::bndryLocs() from Real bndryLocs (Orientation face, int igrid) const; to const RealTuple& bndryLocs (int igrid) const; where RealTuple is defined: typedef Tuple RealTuple; Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit f0b33579a19cf13c16cb7022aafa327c1760741e Author: lijewski Date: Thu Jul 12 13:45:18 2012 -0700 bcond is now a single map instead of an array of'm. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/MacBndry.cpp commit 30327b84e6d8e976722c7c76d8f39c0ce5b3fb15 Author: vince 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 Date: Thu Jul 12 12:37:41 2012 -0700 Used std::map for bcloc instead of Array> to cut down on memory overhead. If we write the inner loops on Orientation this also puts data used per grid together. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/MacBndry.cpp commit ed4b766b06a98a79799bf83337cb51325eebd2f8 Merge: 7728eb416 3febd0391 Author: lijewski Date: Thu Jul 12 11:00:07 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 7728eb416d54f24db3a355dffaf83da6d508b04c Author: lijewski Date: Thu Jul 12 10:59:01 2012 -0700 To further cut memory overhead, maskvals & lmaskvals use a Tuple instead of Array for each grid they own. Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit e1a83ee8f6df15fba22b9fe6880dda67417a36d1 Author: lijewski Date: Thu Jul 12 10:38:48 2012 -0700 Squeezed out more memory by using std::map<>s for maskvals and lmaskvals. Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit 026761eedf5b521b8ea56f74369247e3bc5448eb Author: Sandra May Date: Thu Jul 12 09:59:22 2012 -0700 added integer parameter to define FLOW, SOLID, IRRFLOW Src/F_BaseLib/cutcells.f90 commit 8c8e392e44d53f6dc68e23cf99626c61f864f392 Author: lijewski Date: Thu Jul 12 09:22:27 2012 -0700 Replaced some uses of std::vector with Array. The former is great if you're trying to save storage, but it does bit twiddling which is more expensive than just accessing an integer. Src/C_AMRLib/StateDescriptor.H Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_TensorMG/DivVis.H commit 3febd0391250f4245ffc86827d2fc636a82a5c29 Author: Matthew Emmett Date: Thu Jul 12 11:35:10 2012 -0400 PyBoxLib: Add read/write. Tidy Makefiles. Src/Python/.gitignore Src/Python/GMakerules.mak Src/Python/GNUmakefile Src/Python/GPackage.mak Src/Python/Makefile Src/Python/README Src/Python/pyboxlib/fab.py Src/Python/pyboxlib/layout.py Src/Python/pyboxlib/multifab.py Src/Python/pyboxlib/pybl.py Src/Python/read.py Src/Python/src/boxlib_numpy_c.c Src/Python/src/boxlib_numpy_f.f90 Src/Python/src/fboxlib.f90 Src/Python/write.py commit 3a467dd828971e5b2831ad227c7643ae6bde1d85 Merge: 3b10a0f28 d0142db51 Author: Matthew Emmett 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 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: 74438db39 59dc8f31b Author: Ethan Van Andel Date: Wed Jul 11 18:18:55 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 59dc8f31b8cfe0812ac69f34997c4aef52dd9c8f Author: lijewski Date: Wed Jul 11 16:46:21 2012 -0700 In BndryData, change the following member data: Array bcloc[2*BL_SPACEDIM]; to std::map bcloc[2*BL_SPACEDIM]; Changed the following member function: const Array& BndryData::bndryLocs (const Orientation& _face) const to const Array& BndryData::bndryLocs (const Orientation& _face, int igrid) const Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/MacBndry.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 14455d20c2121cc85f28690a4b53c4c26d506df3 Author: lijewski Date: Wed Jul 11 15:56:42 2012 -0700 In BndryData, change the following member data: Array< Array > bcond[2*BL_SPACEDIM]; to std::map< Array > bcond[2*BL_SPACEDIM]; Changed the following member function: const Array< Array >& bndryConds (const Orientation& face) const; to const Array& bndryConds (const Orientation& face, int igrid) const; Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/MacBndry.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 74438db39a7aa65ce1372b303d34e968eb8e7c9c Author: Ethan Van Andel Date: Wed Jul 11 14:57:07 2012 -0700 Fixed PList pop. Src/C_BaseLib/PList.H commit 5b326422ef0d2e5347e1090cbbbb5d1337f5679a Author: lijewski Date: Wed Jul 11 14:16:22 2012 -0700 Got rid of the following data member in StateData.cpp: Array< Array > bc; Got rid of the member function: Array& StateData::getBCs(); Changed the member function StateData::getBC() from const BCRec& getBC (int comp, int i) const; to const BCRec getBC (int comp, int i) const; This latter changes means that instead of writing: const int* b_rec = state[State_Type].getBC(strt_comp+n,gridno).vect(); you'll have to write: BCRec bcr = state[State_Type].getBC(strt_comp+n,gridno); const int* b_rec = bcr.vect(); I "think" I've made all necessary changes to stuff I have access to in the GIT repository. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/BCRec.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 726e11e50af42f32b30d4836fcc9f9328f6b6ef1 Author: Ethan Van Andel Date: Wed Jul 11 13:28:17 2012 -0700 Added PList class for memory-managed lists of pointers. Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/Make.package Src/C_BaseLib/PList.H commit 4b2f5d3e0a78c1dd925d712e354d9f4e46073107 Author: lijewski Date: Wed Jul 11 12:25:13 2012 -0700 Squeezed out some memory when running in parallel by using std::map<>s instead of Array<>s based on the length of the BoxArray. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 851402278e750eb7cac441a6a9164720f0a1363c Author: lijewski Date: Wed Jul 11 09:13:34 2012 -0700 A little simplification. Src/C_AMRLib/AmrLevel.cpp commit 506365e743dcba8bbfbae124142656370f51c99e Author: Sandra May Date: Tue Jul 10 18:28:23 2012 -0700 changed 2 things to be able to use the CartGrid option of amrvis Src/F_BaseLib/fabio.f90 commit a6b7285babb244db8e2ed4e8580e3c886bcd6dc3 Author: lijewski Date: Tue Jul 10 16:25:15 2012 -0700 Cached a little more stuff for multifab copy(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 757b99ec5bec2618052ff386dce1512d1ff6bc86 Author: Sandra May Date: Tue Jul 10 13:06:54 2012 -0700 added 2d option Src/F_BaseLib/cutcells.f90 commit 77ad27235997bf433b1b73ebcd5bae97880ae7ad Author: lijewski Date: Mon Jul 9 20:11:26 2012 -0700 Removed unused variable. Src/C_BaseLib/FabArray.H commit 064630d31f450265070b5dbc47ee8c07503ec12c Merge: c52a04326 4035d67eb Author: Mike Lijewski 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 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 Date: Mon Jul 9 16:37:43 2012 -0700 changed comp to gfortran Tutorials/Exp_CNS_NoSpec/GNUmakefile commit 4e13222985d86368e7d66c7962dac5f20da96c37 Author: Ethan Van Andel Date: Mon Jul 9 12:17:54 2012 -0700 Removed debug messages Src/C_AMRLib/Particles.H commit 57a1e292f45ad655efe1e0c2cc91f12c094d28b9 Merge: 1d5ceb51d a1869d8f2 Author: Ethan Van Andel Date: Mon Jul 9 11:10:00 2012 -0700 Merge branch 'master' into hybrid_sub commit 1d5ceb51d8e20ffec04f1e1c91b63ef11413123d Author: Ethan Van Andel Date: Mon Jul 9 11:09:11 2012 -0700 Added finest_level option to AssignDensity Src/C_AMRLib/Particles.H commit a1869d8f2acca615c9f87c3f9ec22f358e32acb9 Author: ajnonaka Date: Mon Jul 9 10:02:47 2012 -0700 a call to FillPeriodicBoundary with do_corner=true now fills all corners, including those at periodic boundaries. previously the corners were only filled if they were behind physical boundaries Src/C_BaseLib/Geometry.H commit cec7c17b0e90c7d4f6dd62eb4faf853f8cc4da0d Author: lijewski Date: Fri Jul 6 20:25:38 2012 -0700 Sped up Checkpoint() by eliding work when no particles at a level. Src/C_AMRLib/Particles.H commit 866079b6b73c73b52bb0c3e4fcbe1925a1a86766 Author: smay Date: Fri Jul 6 10:26:37 2012 -0700 added many arguments to the cutcell module, modified the build and print command Src/F_BaseLib/cutcells.f90 commit 93c38d997299ce55140b30bed3ce92c436533320 Author: lijewski Date: Fri Jul 6 09:41:14 2012 -0700 Turn off some uninformative Cray C++ compiler warning messages. Tools/C_mk/Make.Linux commit bb6012e6dcc2bf570237b610e571331f4150e570 Author: lijewski Date: Fri Jul 6 09:21:02 2012 -0700 Going with the NERSC-recommended Cray optimization flags: no explicit flags. Tools/C_mk/Make.Linux commit f272f5a39b541ae0cb69a819fd0cb180fa9aa684 Author: cmalone Date: Thu Jul 5 12:41:52 2012 -0700 file not used in docs Docs/Preface/preface.tex commit be71463d98a9aff1179a788784cad14c01293b3f Merge: 3ee573133 1c8dda49a Author: Michael Zingale 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 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 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 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 Date: Tue Jul 3 15:40:43 2012 -0700 added mf read benchmark. Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit 6799bac447291864a84859848af3595a953ec112 Merge: 9091b7b63 34015a8f9 Author: vince Date: Tue Jul 3 14:09:11 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9091b7b6306ec0d4a4c1a58c64495997f0c7a864 Author: vince Date: Tue Jul 3 14:08:44 2012 -0700 changed VisMF::How and updated io benchmark. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Tests/IOBenchmark/IOTest.cpp Tests/IOBenchmark/IOTestDriver.cpp commit 34015a8f95425debc870ec614c5ba3c1a0ff6893 Merge: 193656bb8 212361e7a Author: lijewski Date: Tue Jul 3 13:59:03 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 193656bb84ce6c737273b964232167596b5cf40a Author: lijewski 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 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: 51b328902 482c363db Author: Michael Zingale Date: Tue Jul 3 15:16:24 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 482c363dbb53ed838578ccd394ccf3bdc64dbf5d Author: lijewski Date: Tue Jul 3 09:52:44 2012 -0700 Added ParticleContainer::NumberOfParticlesAtLevel(). Src/C_AMRLib/Particles.H commit 8a7f0a8847fda955cf3dd35c063e9e7b24daf360 Author: lijewski Date: Tue Jul 3 09:52:20 2012 -0700 Change the default value for verbosity from true to false. Src/C_BaseLib/DistributionMapping.cpp commit 69b92f866c36cf8271ac8da629f647b4c39aaec7 Merge: 94a732e03 12d2c40b7 Author: lijewski Date: Mon Jul 2 12:53:42 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 94a732e034ab6837bb9dc62cb6a14e9cb47283aa Author: lijewski Date: Mon Jul 2 12:51:27 2012 -0700 Some better memory management. Now KNAPSACK time also includes time spent in LeastUsedCPUs() which does an MPI_Allgather(). SFC time already included that time. I'd been wondering why SFC time was so much greated that KNAPSACK time when running large parallel jobs. They should now be more comparable. Src/C_BaseLib/DistributionMapping.cpp commit b84727067af995b7e138c1bcf42cd11fbb143f0c Author: lijewski Date: Mon Jul 2 10:52:18 2012 -0700 Added a couple more typedefs to facilitate possible future tweaks. Removed some debugging code I left in. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 12d2c40b79b291c9d8d46ad5ad3974e8e2a3f963 Author: Ethan Van Andel Date: Mon Jul 2 10:45:41 2012 -0700 Added setDtLevel for specific level. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit c1b37c461f9b743b3698ea28a75e6aa12dd12142 Author: lijewski Date: Mon Jul 2 09:59:07 2012 -0700 Check that at most one of do_alltoall & do_async_send can be true. Src/C_BaseLib/FabArray.H commit 671e628bd313f5832a4e3a844c97ced04df4aa3a Author: Ann Almgren Date: Sat Jun 30 09:08:39 2012 -0700 Fix the bottom_solver = 4 option, hopefully for real this time! Src/LinearSolvers/F_MG/mg.f90 commit 51b32890295fda6ff7d6043e713ad95e2a726fb5 Merge: e705bbd2e 085a6905b Author: Michael Zingale 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 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 Date: Fri Jun 29 14:37:01 2012 -0700 addition for ipm gnu Tools/C_mk/Make.Linux commit fe4f6b7b461d3b251b1f140364b40df0d10d10df Author: vince Date: Fri Jun 29 14:20:02 2012 -0700 instrumented the code with bl_prof. Src/F_BaseLib/bl_prof.f90 Tutorials/Exp_CNS_NoSpec/advance.f90 Tutorials/Exp_CNS_NoSpec/main.f90 commit 308ebd9cffbfbcb38dc6d86ed9231e90a647b041 Merge: f7f7e7910 baf1213b8 Author: vince Date: Fri Jun 29 13:57:27 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit baf1213b8515ce7fb35c18ad270cb39b78c7a71b Author: lijewski Date: Fri Jun 29 13:26:06 2012 -0700 Fixed something I just broke; forgot to test non-MPI. Src/C_BaseLib/ParallelDescriptor.cpp commit 4d6a7def907a9ce6e3959de3aa96de4724b36580 Author: lijewski Date: Fri Jun 29 13:25:40 2012 -0700 Defined MPI_DATATYPE_NULL for non-MPI builds. Src/C_BaseLib/ccse-mpi.H commit fdd8d8ca8c8f19bd096bb81a3e80684fe4edb37c Author: lijewski Date: Fri Jun 29 13:08:42 2012 -0700 Moved "struct RF" from an unnamed namespace in the .cpp file into the class definition of FluxRegister. Also renamed it to "Rec". This way we can reuse this struct in other code. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 1320e357a4950125856802fad695a9c7fe9d0a2c Author: lijewski Date: Fri Jun 29 12:51:21 2012 -0700 Fixed typo. Src/C_BoundaryLib/FabSet.cpp commit 58aadfbd96f6c4805c347b64e5c1f2e5f96e8bdb Author: lijewski Date: Fri Jun 29 12:37:01 2012 -0700 Removed some redundant code. Src/C_BoundaryLib/FabSet.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp commit 8e6c035afcd8958716d62ec5bb4367305543f995 Merge: 7926b533d 5fb7f49a0 Author: lijewski Date: Fri Jun 29 11:26:46 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 7926b533d8f13b41ff2ce136ae24ccbd79a344a3 Author: lijewski Date: Fri Jun 29 11:26:35 2012 -0700 Removed some redundant code. Src/C_BaseLib/BoxArray.cpp commit 5fb7f49a044276a529c56da20103283160ddf68f Merge: 20f774de3 83ff0f006 Author: Ethan Van Andel Date: Fri Jun 29 11:19:38 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 20f774de39a8d4dbfaa80b5718a62b84b8601887 Author: Ethan Van Andel Date: Fri Jun 29 11:18:28 2012 -0700 Fix to initial timestep fix. It now pays attention to regridding -and- checks input flags Src/C_AMRLib/Amr.cpp commit 83ff0f00665d2163fd937f4a66aaa24f7855734c Author: lijewski Date: Fri Jun 29 10:20:49 2012 -0700 Added skeleton for cut cells stuff. Src/F_BaseLib/GPackage.mak Src/F_BaseLib/cutcells.f90 commit 94a870b3f95d91aebda33c109599eeb1ba5991a2 Author: lijewski Date: Fri Jun 29 10:17:08 2012 -0700 Removed the isects.reserve() calls. They're now embedded in the BoxArray intersections() calls. Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/FabSet.cpp commit 4f7ecbb995b75c0f61c31f8c787b416e7170acbf Merge: 6460cfd29 00199574f Author: lijewski Date: Fri Jun 29 09:59:09 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 00199574f77ef7f5b0294b10d785789a472eb3de Merge: e55ba734e c72dade6f Author: Ethan Van Andel Date: Fri Jun 29 09:56:19 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e55ba734e91c3ad01d75abed3eadf6b4cf669c60 Author: Ethan Van Andel Date: Fri Jun 29 09:54:46 2012 -0700 Fixed bug where Level 0 initData could be called multiple times. Src/C_AMRLib/Amr.cpp commit 6460cfd292d699b9bb273c0fd31ad119cc63c3c3 Author: lijewski Date: Fri Jun 29 09:40:47 2012 -0700 A final bit of polishing. Src/C_BaseLib/FabArray.H commit a2b58bc1fa4cb10651c3f9953ebe389e6b7eaba6 Author: lijewski Date: Fri Jun 29 09:14:45 2012 -0700 Inlined & simplified some stuff. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit c72dade6f2ab27bbc78617946102461be3518e4b Author: lijewski Date: Thu Jun 28 17:37:28 2012 -0700 Inlined a few things. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 735f0a65fe61a3ccbd42518e066d854ea31c3bf3 Author: lijewski Date: Thu Jun 28 17:08:43 2012 -0700 Use std::deque<> for fabComTagList and fabCopyDescList instead of std::vector<>. Src/C_BaseLib/FabArray.H commit 8762865b76e89e275867dbe7920d69baa0a8d286 Author: lijewski Date: Thu Jun 28 15:47:26 2012 -0700 Squished out some more memory. Also added some new typedefs. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit f2c6f123598e71c82d8b31af8502178ae9cdd6da Merge: e7792f66c 0611d1291 Author: lijewski Date: Thu Jun 28 15:45:07 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e7792f66c6474899b6fdd62c12ea0f8c762e4cb0 Author: lijewski Date: Thu Jun 28 15:24:03 2012 -0700 Squished out a little more memory. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 0611d129125e9010641e44999338f570ffed2e5d Merge: ecf5281b6 42bfb4209 Author: Ethan Van Andel Date: Thu Jun 28 15:18:54 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ecf5281b688964044bd36175dbfd02e6698db3b2 Author: Ethan Van Andel Date: Thu Jun 28 11:17:55 2012 -0700 Subcycling bugfixes and a change to initial dt computation. This change may slightly change the size of the first timestep and break regression tests. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Particles.H commit 42bfb42097383b288f89c42a83833f20a7ebcbf7 Author: Michael Zingale Date: Thu Jun 28 15:48:55 2012 -0400 all repos are now git. Make the changelogs work for all the git and finish the AstroDev inputs Tools/RegressionTesting/testnew.py commit 38c8af034014f2579dd0ba46c8ce489d1656ea3c Author: Ethan Van Andel Date: Wed Jun 27 15:17:20 2012 -0700 Optimal Subcycling added. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 281cb403cabc567a04ef71efc01a3685e296f28b Author: lijewski Date: Wed Jun 27 13:59:23 2012 -0700 A little more cleanup. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/MultiFab.cpp commit 78c1bb984d269c4cba941d1ec010c1f39a7352e5 Author: lijewski Date: Wed Jun 27 12:45:11 2012 -0700 Minor efficiency improvements. Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp commit 211b113c398b741406734c8db95325cc9c1900fc Author: lijewski Date: Wed Jun 27 12:26:46 2012 -0700 Some memory efficiency improvements. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit d2023dc690937cfda5c50cc60f197095fca4a97f Merge: 77441ac81 cbfca81cb Author: Ethan Van Andel Date: Wed Jun 27 12:26:06 2012 -0700 Merge branch 'master' into opt_sub commit cbfca81cbe47e8dd4a682c5fe78d81acda93f2fb Author: Ethan Van Andel Date: Wed Jun 27 11:28:53 2012 -0700 One more ADDI fix. Src/C_AMRLib/Particles.H commit 0e9299180d9c6799d8cc996b559568efacbb474b Author: Ethan Van Andel 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 Date: Wed Jun 27 10:35:41 2012 -0700 One more small virtual numbering change. Src/C_AMRLib/Particles.H commit 369956b112c634241b60f8fa82c72d009cccfedb Merge: b95fe450c ca54cfced Author: Ethan Van Andel Date: Wed Jun 27 10:30:56 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit b95fe450c1a1df83465da80a8f550d32b9ada59e Author: Ethan Van Andel Date: Wed Jun 27 10:30:02 2012 -0700 Fix to AddParticlesAtLevel and virtual/ghost particle numbering. Src/C_AMRLib/Particles.H commit 77441ac813d1430f35d96b9887d143982f135e77 Author: Ethan Van Andel Date: Wed Jun 27 10:29:24 2012 -0700 Work on optimal subcycling Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit ca54cfced38fcd48edc4989c1d77fb7911bb49f8 Author: lijewski Date: Tue Jun 26 17:35:57 2012 -0700 Minor simplification to collate(). Src/C_AMRLib/TagBox.cpp commit 466074e67491014109414201f1c5cf1e43cbfafe Author: lijewski Date: Tue Jun 26 17:11:06 2012 -0700 Some cleanup of minIndex() and maxIndex(). Src/C_BaseLib/MultiFab.cpp commit 0665a823242cbb895b1dd26e5775ba72ad262903 Author: lijewski Date: Tue Jun 26 16:34:47 2012 -0700 Cut down on number of heap allocations. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 5dffbe6563cd52072d936aac27768dce9c76aa55 Author: lijewski Date: Tue Jun 26 14:42:50 2012 -0700 Improved the memory efficiency of copy() and CollectData(). Trying to miniminze the number of NProc size arrays needed. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 76cd743059bda73018935c6918a5ad323020584e Author: lijewski Date: Tue Jun 26 14:14:32 2012 -0700 Replaced as many uses of std::list<> with std::deque<> as possible for efficiency reasons. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/VisMF.cpp commit 36ec3340b84b9111d94b5dda238e9c6b7e895cc8 Author: Michael Zingale Date: Tue Jun 26 13:07:31 2012 -0400 better way to do the labels python_plotfile/contourcompare.py commit 31dd2e32ff5f3623fb16d50364d43967663612c3 Author: lijewski Date: Fri Jun 22 14:12:56 2012 -0700 We now have the capability to switch between using synchronous MPI sends and asynchronous MPI sends in CollectData() and copy(), controlled by ParmParse'd variables. The default is to use synchronous sends as we've been using for years. I had a vague hope that the asynchronous sends might be faster on hopper, but that doesn't appear to be the case. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 2f109e0688d0efcaa4b333873f5d7a88eaec7ef8 Author: lijewski Date: Fri Jun 22 09:07:26 2012 -0700 Cleaned up some warnings. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 4c08f8fe57e63c6a17a5dff022584a7c6a2d53a2 Author: Weiqun Zhang 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 Date: Thu Jun 21 15:27:25 2012 -0700 Fix makefile for this tutorial Tutorials/MultiGrid_C/GNUmakefile commit d48739a7bcb1a23191b1f555c59ef36a7ede57b8 Author: Weiqun Zhang Date: Thu Jun 21 15:16:11 2012 -0700 Add @echo SUCCESS so that regression testing would know whether or not the compilation is successful. Tests/LinearSolvers/ComparisonTest/GNUmakefile Tutorials/MultiGrid_C/GNUmakefile commit 4001987431545d7fdeab43e2e5de09774c7615d1 Merge: d077aa09e 2316c0d03 Author: Michael Zingale 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 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 Date: Wed Jun 20 16:46:19 2012 -0700 fix for battra. Tools/C_mk/Make.mpi commit 87d976a3d88e3f00f63ff0c0eaaa8ad356c14309 Author: ajnonaka Date: Wed Jun 20 15:13:10 2012 -0700 fixed error in makefile documentation Docs/GettingStarted/GettingStarted.tex commit ec58b183abfa7d012509d70284e1ae1e31789275 Author: ajnonaka Date: Wed Jun 20 14:41:52 2012 -0700 note about makefiles Docs/GettingStarted/GettingStarted.tex commit 14f996c077fb4b6f02860556c1c712e27ee9082e Author: Ethan Van Andel Date: Wed Jun 20 10:49:21 2012 -0700 Added method for computing optimal subcycling. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit ef32878b8001d89faa4358d1de4fdaa97966307f Author: Ann Almgren Date: Wed Jun 20 09:35:59 2012 -0700 Fix logic for whether we can use bottom_solver = 4 in the F90 mg -- it should only be used when the grids completely fill their bounding box. Src/LinearSolvers/F_MG/mg.f90 commit a5ec4a9eda17ccd864d38ea8df4fb9f8ddeb4d2d Author: Ann Almgren Date: Tue Jun 19 17:33:24 2012 -0700 Somehow the bottom_solver = 4 option can create more rather than fewer grids at the bottom level. If this happens, ignore the new grids and use bottom_solver = 1 instead. Src/LinearSolvers/F_MG/mg.f90 commit c1432d62ee9345eb875316a0a1d9be5b083e568d Author: Ann Almgren Date: Tue Jun 19 16:23:49 2012 -0700 Force a full regrid if we change n_cycle on restart (this is a prelude to optimal subcycling) Src/C_AMRLib/Amr.cpp commit 5f8d95a8e99bccb0f9bd6590abe5fa6df37a45ba Author: lijewski Date: Tue Jun 19 14:35:07 2012 -0700 Merged in new BoxArray::intersections(). Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/FabSet.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp commit 4fedde37eaa72171f4ca76d20d02c3ae96579e57 Merge: a900da3a6 4c467d694 Author: lijewski Date: Tue Jun 19 14:30:52 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a900da3a625e423619e378f7cddbd59f9ae8c251 Author: lijewski Date: Tue Jun 19 14:13:13 2012 -0700 Added new version of intersections() that takes the std::vector<...> as an argument, instead of returning it. For codes that use intersections() a lot (like Particle codes) this'll make things run faster. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 4c467d694b920827b4e8629558d81d94001e4f88 Author: Ann Almgren Date: Tue Jun 19 13:28:59 2012 -0700 Fix typo: "ghost" --> "ghosts" Src/C_AMRLib/Particles.H commit a7b098d373fe566f5a772d91433602204ef55ce3 Merge: 890997708 c712e3df4 Author: Ann Almgren 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 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: a79ea8030 479499de5 Author: Michael Zingale Date: Tue Jun 19 15:55:43 2012 -0400 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 479499de5f568386334cb15bdd8fca9e1162cb15 Author: lijewski Date: Tue Jun 19 12:48:17 2012 -0700 Pass PBoxes by reference in a few routines where they were being passed by copy. Fixed some bugs in AddParticlesAtLevel(). Src/C_AMRLib/Particles.H commit a79ea8030050d6d6623b2c6f4f928ca811edff34 Merge: b59402144 255990a71 Author: Michael Zingale 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 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 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 Date: Tue Jun 19 10:36:44 2012 -0700 Simplified RemoveParticlesNotAtFinestLevel() & RemoveParticlesAtLevel() among other minor tweaks. Src/C_AMRLib/Particles.H commit 2316c0d03bb0927fd54ca212970b2204908232ad Merge: eeeba07b8 3d038b0e3 Author: Michael Zingale Date: Tue Jun 19 13:09:16 2012 -0400 tweaking of the makefile commit eeeba07b84fb81f999052f277137171e9a1aa8e1 Author: Michael Zingale Date: Tue Jun 19 13:04:27 2012 -0400 get this compiling again GNUmakefile commit ad56e065e47404e08b8d4543c5d7137b3772417a Author: lijewski Date: Tue Jun 19 09:27:37 2012 -0700 Try to be a little more const correct. In FineCellsToUpdateFromCrse() use resize(0) instead of clear() to cut down on memory allocation. Src/C_AMRLib/Particles.cpp commit 7c4b77b2de45bc5351387f1cb19c54e4ebb6f5bb Author: lijewski Date: Mon Jun 18 15:20:01 2012 -0700 Call CIC_Cells_Fracs_Basic() from CIC_Cells_Fracs() when dx_geom == dx_part. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 32271a1a717c3076a6b84d99fc59f0fbc655d2a5 Author: lijewski Date: Mon Jun 18 14:42:47 2012 -0700 Un-inlined ParticleBase::CIC_Cells_Fracs(). Other minor cleanup. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit dfef3a64d2761f1995a2d1fc1b33975f5885b2f0 Author: Ethan Van Andel Date: Mon Jun 18 10:17:26 2012 -0700 More cleanup Src/C_AMRLib/Particles.H commit 32d43a77b48ae662c2746cd94a85794a5e37d04c Author: Ethan Van Andel Date: Mon Jun 18 10:16:21 2012 -0700 Pre-push cleanup Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Particles.H commit a8bef047f312f4ecb038073a71f5aa74113d15fb Merge: 2050bc829 9fd402397 Author: Ethan Van Andel Date: Mon Jun 18 09:40:35 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9fd402397ebbb85ec569d83f466295215cbdd1fa Author: Chris Malone Date: Fri Jun 15 19:51:48 2012 -0700 add libquadmath for all gfortran's in Darwin Tools/C_mk/Make.Darwin commit 991ead74dd38245f8551d5367cb5c6935717bdd0 Author: Chris Malone Date: Fri Jun 15 19:19:51 2012 -0700 add the optional do_finalize_MPI input to parallel_finalize calling sequence to sync up with parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit 2050bc829d7df053aa7f1246352b752c1cf4ce83 Author: Ethan Van Andel Date: Fri Jun 15 17:59:58 2012 -0700 Minor refactoring and debugs to variableSetup Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 247252f1ec29651dfadfda886893bd1c36366c81 Author: Ethan Van Andel Date: Fri Jun 15 16:56:15 2012 -0700 Minor additions to subcycling parse logic. Src/C_AMRLib/Amr.cpp commit a04f6273c858cc867faca8f3c18dc490c7612c18 Author: Ethan Van Andel Date: Fri Jun 15 16:20:23 2012 -0700 Big Commit. Added new subcycling controls/logic. Documentation to follow. Fixed a sneaky bug in nosubcycling AssignDensity. Added Particle Aggregation for virtual particles. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit ac7d972332077cf24befbf1a09c7990151dd1d2d Author: Marc Day Date: Fri Jun 15 15:56:06 2012 -0700 The MPI_Comm_Free call seems to cause a core dump...so for now, we will live with a small mem leak Src/F_BaseLib/parallel.f90 commit 90db26a959bba8caf6dd1efd1dbba96725bff218 Merge: fbe700735 85dca7c88 Author: Marc Day 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 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: 74ac6907d 2d69e7c1e Author: Michael Zingale 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 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 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 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 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 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: f44de4027 3d3c77868 Author: Michael Zingale 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 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: 75601eb08 3d3c77868 Author: Ethan Van Andel Date: Mon Jun 11 09:30:05 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 3d3c77868db4f2212a164246dc8847a6f471d57d Author: Ann Almgren Date: Sat Jun 9 17:35:34 2012 -0700 Enforce that MGTSolver always sends a status flag to mgt_solve; note that ml_cc still has to take on if present(status) because the F90 codes may call ml_cc directly. But mgt_solve is only called from MGTSolver so we can safely modify that interface. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit df364a45c4005e0afa07a7949cf28fa8cb121c6d Merge: ad6841f9a b7fda4c45 Author: Ann Almgren Date: Sat Jun 9 15:09:40 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ad6841f9a7786249c1db5b6cde59c03e543efe2b Author: Ann Almgren Date: Sat Jun 9 15:09:09 2012 -0700 Now the mgt_solve version does *not* take a status flag and mgt_solve_stat does. Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 39f5bd2ee2b8ae8fa53cc5cb070dc8d3c293057b Author: Ann Almgren Date: Sat Jun 9 15:07:47 2012 -0700 Need to differentiate between the ones that take a status flag and the ones that don't. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 75601eb0874314596e1b30fabdd2374fff46d8a7 Author: Ethan Van Andel Date: Fri Jun 8 16:38:32 2012 -0700 DERP fix. Src/C_AMRLib/Amr.cpp commit 1da913a4f2bebb2d86921a3f0cee75f48129d6c4 Author: Ethan Van Andel Date: Fri Jun 8 15:35:16 2012 -0700 Fixed nosub setting in Amr.cpp, particle tweaks. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Particles.H commit 0801b25866d51e354a1768877ede86d730545871 Author: Ethan Van Andel Date: Fri Jun 8 14:33:04 2012 -0700 Fixes to subcycling assign density. Src/C_AMRLib/Particles.H commit b7fda4c45af930d09428d9d90fdff7ea3a5ead7d Author: Michael Zingale Date: Fri Jun 8 10:23:54 2012 -0400 remove references to nan -- we can use BOXLIB_USE_MPI_WRAPPERS now Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 10d2f62861d61bc60b79f6e773a08ba55297ff11 Author: Ethan Van Andel Date: Thu Jun 7 16:23:19 2012 -0700 Minor fix to periodic ghost cell densities. Src/C_AMRLib/Particles.H commit 79818822af9aa1794d10f0a30fbc9e3afc46262f Author: Ethan Van Andel Date: Thu Jun 7 11:04:36 2012 -0700 Debug to nonsybcycling redistribute. Src/C_AMRLib/Particles.H commit f3099a1f7b3dcbb626bcfafa3b5ed913c4d6dcfc Author: Ethan Van Andel Date: Thu Jun 7 10:44:24 2012 -0700 Modifications for working DM particle subcycling. - Ghosts, Virtuals - CIC for particles with arbitrary radii (at the CIC level, not the assign density level) Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 3d038b0e3f595dc14fbb07b102ee371fccaa8b60 Author: Christopher Malone Date: Thu Jun 7 11:28:44 2012 -0400 get this working with updated make system GNUmakefile commit 5e5bddfa03c675811e56d207304ea90180a7dc17 Merge: 3d76feafa 4d37e80e0 Author: Marc Day 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 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 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 Date: Tue Jun 5 13:01:05 2012 -0700 One more merge fix. Src/C_AMRLib/Particles.H commit cc1ba810715e8dde57c4f96ecc6e8e683244789d Merge: 59b11008c 3b21290aa Author: Ethan Van Andel Date: Tue Jun 5 12:56:41 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib Conflicts: Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 3b21290aa9d4a376291d042993990f95741829e0 Author: Ann Almgren Date: Tue Jun 5 11:47:30 2012 -0700 Modify NReaders and NRedist in Particles.H in order to be able to read large particle files when N_processor >= 4K Src/C_AMRLib/Particles.H commit d423bc8da6a0982b48b5845ccdd0a90db0614428 Author: lijewski Date: Tue Jun 5 10:39:28 2012 -0700 Added finest_level argument to Where() and PeriodicWhere() that defaults to -1. The -1 implies to use m_amr->finestLevel(). Changed Redistribute() and AssignDensity() to the effective finest level, not to blindly use m_amr->finestLevel(). Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 89d96e9bb2bae63e35dbb68ed60272bc68831afc Author: ajnonaka Date: Tue Jun 5 08:13:42 2012 -0700 give multifab_build_edge and multifab_build_nodal the optional "stencil" argument Src/F_BaseLib/multifab_f.f90 commit 24a91d1c5d32cfc4fc0ac940bf8250dde9eb879a Author: ajnonaka Date: Tue Jun 5 07:53:29 2012 -0700 added subroutine multifab_build_nodal Src/F_BaseLib/multifab_f.f90 commit 382029737051e5a624f8a35aabb32b47aa23cfdb Merge: 9989f76d8 821232fed Author: Michael Zingale 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 Date: Mon Jun 4 17:17:03 2012 -0700 Working Ghost particles, debugs. Src/C_AMRLib/Particles.H commit 9989f76d8cc55667308082b1ac3db31b59791e2b Author: Michael Zingale 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 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 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 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: 010083040 72f613edb Author: Michael Zingale 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 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 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 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: 6891882c3 c53ec80ea Author: vince Date: Fri Jun 1 14:29:40 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 6891882c32dd0a035d95dee77856f6f0864596ee Author: vince Date: Fri Jun 1 14:29:19 2012 -0700 changes for battra and naphta. Tools/F_mk/GMakeMPI.mak commit f2bc68c8d95e7b9e1fcff135818ff2fbd6f05f87 Merge: 7bdc6c310 821232fed Author: Weiqun Zhang Date: Fri Jun 1 13:04:34 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/AmrPostprocessing commit 7bdc6c310748ece7ee07a440c05f6508b0587d7c Author: Weiqun Zhang Date: Fri Jun 1 13:04:11 2012 -0700 chmod a+x plotsinglevar.py python_plotfile/plotsinglevar.py commit c53ec80ea9dbe6f18fe86905336c4438313417ac Merge: 0e208d92f e69c6bdf0 Author: Michael Zingale 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 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 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 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 Date: Thu May 31 09:54:56 2012 -0700 No longer need cvs scripts. Tools/F_scripts/cvs2cl.pl commit 540b6f1819015d01e5a1152e5d0afccbd12c77c7 Author: Ann Almgren Date: Thu May 31 09:54:13 2012 -0700 Remove Tools/F_scripts/idlbl directory completely -- we don't want to support IDL stuff. Tools/F_scripts/idlbl/README Tools/F_scripts/idlbl/batch.pro Tools/F_scripts/idlbl/color.pro Tools/F_scripts/idlbl/color_index.pro Tools/F_scripts/idlbl/colorbar2.pro Tools/F_scripts/idlbl/dump_surface.pro Tools/F_scripts/idlbl/flamelength.pro Tools/F_scripts/idlbl/flash_colors.tbl Tools/F_scripts/idlbl/get_idlbl_path.pro Tools/F_scripts/idlbl/nolabel.pro Tools/F_scripts/idlbl/partvelvec.pro Tools/F_scripts/idlbl/plotflash.pro Tools/F_scripts/idlbl/plotraw.pro Tools/F_scripts/idlbl/rawread.pro Tools/F_scripts/idlbl/rawread3d.pro Tools/F_scripts/idlbl/scale_color.pro Tools/F_scripts/idlbl/start_linux.pro Tools/F_scripts/idlbl/tvimage.pro Tools/F_scripts/idlbl/vcolorbar.pro Tools/F_scripts/idlbl/xaverage.pro commit 66d612c53bd8ccb4704e47d4475ce9a832d61c23 Author: Ann Almgren Date: Thu May 31 09:53:13 2012 -0700 Move Tools/C_util/regtests to Tools/RegressionTesting Tools/RegressionTesting/Castro-tests.ini Tools/RegressionTesting/Maestro-tests.ini Tools/RegressionTesting/README Tools/RegressionTesting/gen_compile_test.sh Tools/RegressionTesting/radiation-tests.ini Tools/RegressionTesting/test-Ubuntu.py Tools/RegressionTesting/test.py Tools/RegressionTesting/testnew.py commit 25643bf9f0271277328e42c84d28d844a37bcebc Merge: 0a875389a 1232211ff Author: Ethan Van Andel Date: Tue May 29 10:46:54 2012 -0700 Merge branch 'subcycling' commit 1232211ff46ec47bd9270058b0db71fadd08c860 Author: Ethan Van Andel Date: Tue May 29 10:43:52 2012 -0700 Minor fix to Where Src/C_AMRLib/Particles.cpp commit cc0d084a07aeecaf9a8938ffb387d825c24355ec Author: Ethan Van Andel Date: Tue May 29 09:55:15 2012 -0700 Removed redundant method declarations, changed to default param. Src/C_AMRLib/Particles.H commit 0a875389aef2915532ee8f59f6b12196df9efde0 Author: lijewski Date: Thu May 24 13:02:16 2012 -0700 Changes for Aleks. Tools/F_mk/GMakeMPI.mak commit afa02079e7ffb62e2a9ea81864066594c6ee94a0 Author: ajnonaka Date: Wed May 23 21:16:36 2012 -0700 builds correctly now after Ethan's re-org to add C_AdvancedTopics Docs/GNUmakefile commit af4058867f8242ef0ae3c51288a5bc594b703ed9 Author: Ethan Van Andel Date: Wed May 23 15:07:58 2012 -0700 Added support for particles leaving the domain across a non-periodic boundary (they are invalidated and removed at the coarse timestep). Src/C_AMRLib/Particles.H commit 712baa3b2ed3d1c12f8ead06ca671df820c64d8a Author: Ethan Van Andel Date: Wed May 23 15:05:00 2012 -0700 Important bugfix to 2d hoextraptocc (seldom used) Src/C_AMRLib/FILCC_2D.F commit bd14f4cfd42be340a22e69ec0a0bd1f12c47d9f5 Author: Ethan Van Andel Date: Tue May 22 14:30:34 2012 -0700 Debug fixes to particle subcycling Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit e20daad2d5638784d2d5d2c0d5cdc9c5eb1df2b9 Merge: cd6749fe0 ceb063cdc Author: vince Date: Tue May 22 13:20:35 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit cd6749fe0554fd1ea7e80c3d42837d445684aaca Author: vince Date: Tue May 22 13:19:20 2012 -0700 changed default PLOTPER test. Src/C_AMRLib/Amr.cpp commit ceb063cdc0c3a5d83aa3473e32c379770f47b109 Merge: 56054f7e6 bbf2ab392 Author: Ann Almgren Date: Tue May 22 11:08:16 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 56054f7e6047dd094e1e57465b02102379be6cc8 Author: Ann Almgren Date: Tue May 22 11:07:49 2012 -0700 1) Formatting in mg.f90 2) We no longer allow the dense stencil in 2D since the multilevel divergence operator is known to be wrong. Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/F_MG/mg.f90 commit bbf2ab39298902895eda07dce395fc12dbb088d9 Merge: 6d2ed2fa0 451dea88f Author: ajnonaka Date: Tue May 22 10:25:14 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 6d2ed2fa05c32d88afca7a415bdcc46ee511d9c8 Author: ajnonaka Date: Tue May 22 10:25:02 2012 -0700 fixed a comment Tutorials/HeatEquation_EX5_F/advance.f90 commit 451dea88f654c33ab3a6317c975e7726b65d4240 Author: Michael Zingale Date: Tue May 22 09:59:24 2012 -0400 add OpenMP support for fParallel jobs Tools/C_util/regtests/Maestro-tests.ini Tools/C_util/regtests/testnew.py commit 17ee12a0deb996d8ce758b8be0990342ec53cc06 Author: Ethan Van Andel Date: Mon May 21 17:02:28 2012 -0700 Seemingly working particle subcycling; more tests needed. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit c62e4cc066894184a2bc29b12e4d55c60adc0477 Author: Marc Day Date: Mon May 21 16:37:03 2012 -0700 Some small (hopefully ineffectual) changes to minimize redundant code Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 8754726883a876f01533c6871a7917ca86349edd Merge: fdc92bfc2 2d04bb064 Author: Ethan Van Andel Date: Mon May 21 12:03:21 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 2d04bb064d89cbd4a2c8800090b6c876b94b3565 Author: Michael Zingale Date: Mon May 21 11:27:56 2012 -0400 remove explicit inf section Tools/F_mk/GMakeMPI.mak commit d0d9d98c6e6dbcbc578ed0ddf1ed8b5947f4aa9f Merge: 6a6787bd1 bca983a69 Author: Michael Zingale 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 Date: Mon May 21 11:19:08 2012 -0400 remove xrb specific section Tools/F_mk/GMakeMPI.mak commit 6a6787bd133f00101dc428d6823881910b40c3b6 Author: Michael Zingale Date: Mon May 21 11:06:42 2012 -0400 remove sn specific make -- use the generic BOXLIB_USE_MPI_WRAPPERS now Tools/F_mk/GMakeMPI.mak commit c84606868b8876a6a0cec893267160c12901da7b Author: Michael Zingale Date: Mon May 21 10:56:37 2012 -0400 MAESTRO -> BOXLIB :) Tools/F_mk/GMakeMPI.mak commit c51e7c9585d797f0fcccd73fc47a9bcb37e153cc Author: Michael Zingale Date: Mon May 21 10:55:19 2012 -0400 remove the nan-specific entry. Add a generic Linux MPI that is more general than the old one -- now look for the environment MAESTRO_USE_MPI_WRAPPERS Tools/F_mk/GMakeMPI.mak commit 36c3f731d2213e470c85dc75c21b938f2d251730 Merge: 3d0941937 0610b80a9 Author: Michael Zingale 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 Date: Mon May 21 10:33:04 2012 -0400 some pretty printing stuff Tools/F_mk/GMakedefs.mak commit fdc92bfc269693fa6b1d00d8c90eb6c42238ef5f Author: Ethan Van Andel Date: Fri May 18 14:31:02 2012 -0700 More doc additions. Docs/C_AdvancedTopics/C_AdvancedTopics.tex commit 0ab9ff2fd3b38dcfd053e05508bc9f4a09d5852a Merge: 48820a9c6 0610b80a9 Author: Ethan Van Andel Date: Thu May 17 15:38:12 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 0610b80a99ce863b3d6a08c86339b8e853adabe2 Author: ajnonaka Date: Thu May 17 13:47:58 2012 -0700 linear solver note Docs/AdvancedTopics/AdvancedTopics.tex commit 48820a9c61c2ad9456090d62a62ec0f48575f77f Merge: 71e44f371 9962debb1 Author: Ethan Van Andel Date: Thu May 17 13:46:26 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 71e44f371cab7cb76e6f82763989fd1e9ae458c3 Author: Ethan Van Andel Date: Thu May 17 13:45:57 2012 -0700 Added Assertions to check vcomp validity. Src/C_AMRLib/Particles.H commit e074473779ee4a798160e3297351b156d3678bac Author: Ethan Van Andel Date: Thu May 17 13:42:51 2012 -0700 Added empty Users Guide section for "State Data" Docs/C_AdvancedTopics/C_AdvancedTopics.tex commit fc7a53e31f9b58dc4507576b1f3bbdd42c111251 Author: Ethan Van Andel Date: Wed May 16 16:45:36 2012 -0700 Typo correction to main page, additions to particle documentation. Docs/C_AdvancedTopics/C_AdvancedTopics.tex Docs/UsersGuide.tex commit bbc5ce94ae537cb45390d04dc773a1c652ef698b Author: Ethan Van Andel Date: Wed May 16 16:13:29 2012 -0700 Added a UsersGuide Stub chapter for Advanced Topics with C++ that will cover particles. Docs/C_AdvancedTopics/C_AdvancedTopics.tex Docs/F_AdvancedTopics/F_AdvancedTopics.tex Docs/F_AdvancedTopics/bc_example1.eps Docs/F_AdvancedTopics/bc_example1.fig Docs/F_AdvancedTopics/bc_example2.eps Docs/F_AdvancedTopics/bc_example2.fig Docs/F_AdvancedTopics/bc_example3.eps Docs/F_AdvancedTopics/bc_example3.fig Docs/F_AdvancedTopics/hopper_omp.run Docs/GettingStarted/GettingStarted.tex Docs/Introduction/Introduction.tex Docs/UsersGuide.tex commit 1d695f9b508e5c454a1c057c6ceba5abc3599b51 Author: Ethan Van Andel Date: Wed May 16 14:19:35 2012 -0700 Added vcomp parameter to allow offset velocity storage in mdata. Minor documentation additions. Src/C_AMRLib/Particles.H commit 704e65b2d732ef2793df216a8c242c30ae6c76ee Author: Ethan Van Andel Date: Wed May 16 11:21:40 2012 -0700 Added Periodic particle motion to AdvectWithUMAC. Minor Documentation additions. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 9962debb1b6e26544bf613f05e226f1539bf7e29 Author: Marc Day Date: Wed May 16 09:19:45 2012 -0700 Rearrange so that solver fails give slightly more info Src/LinearSolvers/F_MG/ml_cc.f90 commit 5e1524b60a6c8492f2217784dc3dde988d3da5ba Author: lijewski Date: Sat May 12 19:14:49 2012 -0700 InitFromBinaryFile() appears to be working. Note that I didn't carry over the "Nrep" argument from InitFromAsciiFile(). If that's really needed it should just be a simple cut & paste. Src/C_AMRLib/Particles.H commit ba72d50c4dd242b0816868a741129dd9e1cb6718 Author: lijewski Date: Sat May 12 17:23:15 2012 -0700 A first cut at InitFromBinaryFile(). Src/C_AMRLib/Particles.H commit 2aa25131d9618841c4b432f8940caba50bed9305 Merge: 453bea1ba 2a5bc74bc Author: Ann Almgren 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 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: fc5701324 32cd0c490 Author: Mike Lijewski 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 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 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 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 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: 6644b702f 4cab11e34 Author: Marc Day 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 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 Date: Tue May 8 13:13:11 2012 -0700 Merged in protected_divide() to AssignDensity(). Src/C_AMRLib/Particles.H commit a93857b7c9df3c1887bb8ac2ded473739b433b48 Author: lijewski Date: Tue May 8 13:11:33 2012 -0700 Added protected_divide(). This is similar to divide() except it only does the division if the denominator is "true" or non-zero. In does nothing in the case where the denominator is not "true" or non-zero. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/SPECIALIZE_1D.F Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit 1882f77e408d5ea224a41d69f816049d4c92ad63 Author: Ann Almgren Date: Tue May 8 10:35:05 2012 -0700 Fix the placement of velocities onto the grid in AssignDensityAndVels -- we need to sum up momenta then divide by total mass in the cell rather than summing up velocities Src/C_AMRLib/Particles.H commit 47dd2fad9f3e7739f01445f4ede1576829dc318b Author: lijewski Date: Tue May 8 08:59:14 2012 -0700 Also constrain mult() in single-level AssignDensity() as previous commit. Src/C_AMRLib/Particles.H commit 35b713aa0cfe1643ace4264711608369f29500e4 Author: Ann Almgren Date: Tue May 8 08:52:31 2012 -0700 In AssignDensityAndVels in Particles.H, we divide the mass by volume to get density, but don't divide the velocities by volume. Src/C_AMRLib/Particles.H commit 186e6f39ddb40d93eddfdf88770099dac2126062 Author: lijewski Date: Mon May 7 15:10:02 2012 -0700 Inlined some ParticleBase routines. Now go about 10% faster on my SantaBarbara test case on my machine with g++/gfortran. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 8c930a6ddde8e4512d80408d5e4ed84d94b6094f Author: lijewski Date: Mon May 7 10:31:08 2012 -0700 Some more BL_ASSERT()s. Src/C_AMRLib/Particles.H commit c02d3fc3d8b03806711643d1fa525c10dac009f1 Author: lijewski Date: Sun May 6 08:10:35 2012 -0700 Got AssignDensity() working in parallel for > 1 components. Had to move it from ParticleBase to ParticleContainer. Now use ncomp components of m_data instead of m_pos. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 20c6420992edd5c0b61930fbb38859b4b48b15c9 Author: Ann Almgren Date: Sat May 5 08:38:06 2012 -0700 Add the option in Particles.H to initialize the gas velocities as well as density from the particle file. Src/C_AMRLib/Particles.H commit a768e14a63d404521edd820efa38cbeca7d5b545 Merge: aa2dff1f7 5fe1b8e52 Author: Ann Almgren Date: Fri May 4 17:42:22 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit aa2dff1f739dfa1e75dc571550214b9743caac52 Author: Ann Almgren Date: Fri May 4 17:41:50 2012 -0700 One more place to add max_L0_growth so that it is passed through from inputs file to ml_cc.f90 Src/LinearSolvers/F_MG/cc_mg_cpp.f90 commit 5fe1b8e5217068ca0f53aa076288f7ebf140d25a Author: Marc Day Date: Fri May 4 17:20:09 2012 -0700 manual update of version textfile BoxLib_Version.txt commit 6ba1a4cc62fdd54e971eb8ffbcbe433b3d2ee623 Merge: 80f587ae5 83540a42d Author: Ann Almgren Date: Fri May 4 16:50:11 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 80f587ae52631d08ece6f9386124b0321a13a60c Author: Ann Almgren Date: Fri May 4 16:49:11 2012 -0700 Modify the mg stuff so that the max_L0_growth defaults to -1 and isn't used, but should be able to be set from the C++ inputs file. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/mg_tower.f90 Src/LinearSolvers/F_MG/ml_cc.f90 commit 83540a42df2d5d76da897171ea22fe93f3fcc57b Author: lijewski Date: Fri May 4 14:53:11 2012 -0700 Changed some large 2-D stack allocated arrays to be allocatable. Some OpenMP. Src/F_BaseLib/create_umac_grown.f90 commit 66220caaccab3eb8a23139576745ee9904b03869 Author: Marc Day Date: Fri May 4 13:26:57 2012 -0700 addition solved case Src/LinearSolvers/F_MG/ml_cc.f90 commit 4e0be3cdfec38d52399e6cdae974333c2679cff7 Author: lijewski Date: Fri May 4 10:23:38 2012 -0700 I've checked in an OpenMP'd Jacobi solver for the dense stencil into nodal_smoother_3d(). It's in the "else" part of a "if (.true.) then else endif" chunk of code so that the usual Gauss-Seidel solver is still used at the moment. We'd like to give folks the option of using either Jacobi or Gauss-Seidel, with the code defaulting to Jacobi if OMP=t. Got to think about how to do that. Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit 9aa3afdf7d76ffa8101505fb8a69d98ccb5eef26 Author: ajnonaka Date: Thu May 3 13:45:03 2012 -0700 some VisIt documentation Docs/GettingStarted/GettingStarted.tex Docs/GettingStarted/VisIt_2D.eps Docs/GettingStarted/VisIt_3D.eps commit f452b228fa3944d2f3930ecdf69600d895820e9d Author: ajnonaka Date: Thu May 3 13:10:29 2012 -0700 fix variable name Tutorials/HeatEquation_EX1_C/writePlotFile.cpp commit 47f4c9087a28c9607f05d7d47febd5f2a5b0ba35 Merge: 67b3bda30 212215655 Author: Marc Day 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 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 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 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 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 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 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 Date: Tue May 1 11:19:22 2012 -0700 A little cleanup. Src/C_BaseLib/FabArray.cpp commit 1c21cca08cc15f0f56a92f5b8d650ebee1c65cfa Author: lijewski Date: Tue May 1 10:37:52 2012 -0700 Shortcut out of TagBoxArray::mapPeriodic() if there's no parallel work. Src/C_AMRLib/TagBox.cpp commit 5efc3ca5c264ca9804a5a8b137f14353f78176c1 Author: lijewski Date: Tue May 1 10:02:32 2012 -0700 Shortcut out of FillPeriodicBoundary() and SumPeriodicBoundary() if there's no work to do. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 8fdf0a141c5c6f7488560f1ca756717df79a7d46 Merge: 624695ac1 0a27a8d89 Author: lijewski Date: Mon Apr 30 17:07:12 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 624695ac1feac5040453d3e80b3c8daac73ed0bf Author: lijewski Date: Mon Apr 30 17:06:55 2012 -0700 Some simplification & cleanup after merging in new sum_boundary() stuff. Src/F_BaseLib/multifab_f.f90 commit a341435c02b9af54324f0121b7da8fdb31df3a0a Author: lijewski 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 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 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: 3b5156323 ef541e1a2 Author: lijewski Date: Mon Apr 30 13:23:06 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ef541e1a2f7bda8c844c5cad8b0a90b1cfd3e4ac Author: Marc Day Date: Mon Apr 30 13:20:25 2012 -0700 Fixup CMake files to deal with DEBUG=TRUE/FALSE via standard CMake variables BoxLib_Version.txt Tools/CMake/CCSEOptions.cmake commit 3b5156323ce61171c4b98ef443a313cb47481a8c Author: lijewski Date: Mon Apr 30 13:19:52 2012 -0700 Merged new boxassoc_build() call that also can build optimized sumassoc structures into [l]multifab_sum_boundary(). Src/F_BaseLib/multifab_f.f90 commit 1d204bcccc27142e3bb62470290ebfb436551419 Author: lijewski Date: Mon Apr 30 13:17:47 2012 -0700 Added sumassoc_build_innards(). This routine does all the calculations needed to minimize the number of MPI communication needed for a sum_boundary() call. It's called from boxassoc_build() when passed the appropriate flag. I haven't (yet) made a cache of these. Src/F_BaseLib/layout.f90 commit 8e6157e60622a3520bc69a3742a71df5d9854530 Author: lijewski Date: Mon Apr 30 12:07:07 2012 -0700 Split out the box intersection stuff in boxassoc_build() into boxassoc_build_innards() in anticipation of adding an option to boxassoc_build() to build the appropriate optimized MPI structure for sum_boundary(). Src/F_BaseLib/layout.f90 commit 485a3d1523ebdf8971a097aeec5b9ef7d2804ff3 Author: ajnonaka 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 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 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: 9722377b8 b7ee8797a Author: Marc Day Date: Fri Apr 27 09:53:40 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit b7ee8797a846862d6df53ccd90656fe538051ab5 Merge: eec86a8a2 8d30c31a7 Author: ajnonaka Date: Thu Apr 26 17:11:50 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit eec86a8a2ffd0d7c5cd316daacfc919d7ef3639e Author: ajnonaka Date: Thu Apr 26 16:59:24 2012 -0700 some User's Guide updates Docs/Introduction/Introduction.tex Docs/UsersGuide.tex commit 8d30c31a790b8c35f81b6e8e5030fca1809538ef Merge: 4ed154495 71333cf94 Author: lijewski Date: Thu Apr 26 15:53:09 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 4ed154495c92fe66205badbcb7721ebdab590dbe Author: lijewski Date: Thu Apr 26 15:52:36 2012 -0700 Consolidated all the info for calculating CIC stuff into minimum number of required routines. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 8b1dd172ff2ec3fe1c49c2232455edb560813628 Author: lijewski Date: Thu Apr 26 14:18:33 2012 -0700 Some cleanup. Src/C_AMRLib/Particles.H commit 894daaf35e5b972a77c13cd688141914068ebc99 Author: ajnonaka Date: Thu Apr 26 14:15:21 2012 -0700 comments Tutorials/HeatEquation_EX5_F/advance.f90 commit 71333cf94f615bed396e0d064cb80508aeb25f23 Author: ajnonaka Date: Thu Apr 26 13:40:35 2012 -0700 remove print statement Src/F_BaseLib/cluster_f.f90 commit df2834a50c306b81f571dd63e43c737fbb8ce7b6 Author: lijewski Date: Thu Apr 26 13:21:03 2012 -0700 Use sum_boundary() and fill_boundary() to enforce a logical .or. on overlapping ghost & valid cells. Src/F_BaseLib/cluster_f.f90 commit 8d7a7dc31fe01003a8d26838ca08d448fc793d3e Author: lijewski Date: Thu Apr 26 08:06:32 2012 -0700 Added lmultifab_sum_boundary(). It does a logical "or" of all ghost cells that overlay valid cells with those valid cells. Should be useful in error tagging. Src/F_BaseLib/multifab_f.f90 commit 87b5d03d22be81360ce912e56e0344bf29295856 Author: lijewski Date: Thu Apr 26 07:55:32 2012 -0700 Mods to get to compile again. Tests/F_BaseLib/t_cls.f90 Tests/F_BaseLib/t_main.f90 commit 071ca932333b3bbdac89aaf3cbe31843dc10838c Author: ajnonaka Date: Thu Apr 26 06:02:31 2012 -0700 put WaveEquation examples back until I make a multivariable tutorial based on HeatEquation with all the bells and whistlesZ Tutorials/WaveEquation_C/GNUmakefile Tutorials/WaveEquation_C/Make.package Tutorials/WaveEquation_C/advance_2d.f90 Tutorials/WaveEquation_C/advance_3d.f90 Tutorials/WaveEquation_C/init_data_2d.f90 Tutorials/WaveEquation_C/init_data_3d.f90 Tutorials/WaveEquation_C/inputs_2d Tutorials/WaveEquation_C/inputs_3d Tutorials/WaveEquation_C/main.cpp Tutorials/WaveEquation_C/writePlotFile.H Tutorials/WaveEquation_C/writePlotFile.cpp Tutorials/WaveEquation_F/GNUmakefile Tutorials/WaveEquation_F/GPackage.mak Tutorials/WaveEquation_F/advance.f90 Tutorials/WaveEquation_F/init_data.f90 Tutorials/WaveEquation_F/inputs_2d Tutorials/WaveEquation_F/inputs_3d Tutorials/WaveEquation_F/main.f90 Tutorials/WaveEquation_F/write_plotfile.f90 commit 1c7a76fef6cababcf298877446c53a34a2538b89 Merge: 659726fab e40ac7cf7 Author: ajnonaka Date: Wed Apr 25 15:44:06 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 659726fabcebc6c13fef4ac91f3a2c5a25ac23ac Author: ajnonaka Date: Wed Apr 25 15:42:56 2012 -0700 temporary band-aid to get proper nesting to work properly. You will lose information about buffered tagged cells that should have been passed to the valid regions of neighboring grids. fix for that coming tomorrow. Src/F_BaseLib/cluster_f.f90 commit e40ac7cf73288527207bab383e24f3a67343ef7e Merge: 609601b08 e89b81f22 Author: lijewski Date: Wed Apr 25 13:51:27 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 609601b0841425bc9c4c22acedf6d91c285cbd89 Author: lijewski Date: Wed Apr 25 13:50:01 2012 -0700 Inlined Box::operator&=(Box), Box::operator&(Box) and Box::intersects(Box). This greatly speeds up some BoxArray operations. Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit e89b81f228b61c8dfa18dd73781fd7ad4ccac71e Merge: a67a0b836 800d75a19 Author: ajnonaka Date: Wed Apr 25 13:43:51 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 800d75a19e5798c8d257d1f790a65bbcffcfe46c Merge: 282c629c3 9fc5bce23 Author: lijewski Date: Wed Apr 25 13:38:51 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 282c629c38ff041478f6e8ba4241281bc0bf4c9f Author: lijewski Date: Wed Apr 25 13:38:38 2012 -0700 Inlined some Box stuff. Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit 9fc5bce23e8323b352a51e47d728d88ca83cef22 Author: vince Date: Wed Apr 25 11:59:25 2012 -0700 added comments clarifying creating a distmap with an array. Src/C_BaseLib/DistributionMapping.H Tutorials/MultiFabTests/MultiFabReadWrite.cpp commit 58122a511b60b71b0ca6c3ab4605bea693275174 Author: lijewski Date: Wed Apr 25 11:56:25 2012 -0700 Final fix to FineToCrse() and hence AssignDensity(). Problem was yet one more place where coarsening & refining don't quite work right when indices go negative. This looks to be the last bug in this code :-) Src/C_AMRLib/Particles.cpp commit a67a0b83659f574a8257b08ca992e0ef0a90f583 Author: ajnonaka Date: Wed Apr 25 11:06:09 2012 -0700 min_eff to 0.7 Tutorials/HeatEquation_EX4_F/inputs_3d Tutorials/HeatEquation_EX5_F/inputs_3d commit 27dbe2ed6e9c7b6541db2183db1ac515c1bf49e8 Author: ajnonaka Date: Wed Apr 25 10:54:46 2012 -0700 update docs Docs/AdvancedTopics/AdvancedTopics.tex commit 5ec5da06aaf478268a60e7d736b8cb10d2cce0cb Author: ajnonaka Date: Wed Apr 25 10:27:15 2012 -0700 shake out some bugs in implicit example Tutorials/HeatEquation_EX5_F/advance.f90 Tutorials/HeatEquation_EX5_F/inputs_2d Tutorials/HeatEquation_EX5_F/inputs_3d commit b3fb98e4619821f1109323f2a4e088191ac9f9a4 Author: ajnonaka Date: Wed Apr 25 09:43:27 2012 -0700 linear solver progres Tutorials/HeatEquation_EX5_F/advance.f90 commit 9722377b8cb088f83865e85e8a6ed7d9b8859459 Author: Marc Day Date: Wed Apr 25 09:21:29 2012 -0700 Add some robustness stuff in AmrData::FlushGrids, handling the case when it is called before any data is actually read Src/Extern/amrdata/AmrData.cpp commit 92cadbf7f85954ad0f1b5b2d12e53953e1180c55 Author: ajnonaka Date: Wed Apr 25 09:20:23 2012 -0700 include ml_solve.f90 in F_MG/GPackage.mak Src/LinearSolvers/F_MG/GPackage.mak commit 612a8782ebfbbcbdb8617fdfce0a096c27f23f8f Author: Michael Zingale Date: Wed Apr 25 10:20:15 2012 -0400 add compiler version Tools/F_mk/comps/Linux_cray.mak commit ae1e4cf398b432c66763c3742351f3c989a605fa Merge: 0dcd55b72 908c1a76f Author: Michael Zingale 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 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 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: 6d8ebcfcc 168e559dc Author: ajnonaka Date: Tue Apr 24 16:58:58 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 6d8ebcfccd602827264385da566262755fba7ce0 Author: ajnonaka Date: Tue Apr 24 16:58:39 2012 -0700 implicit example, just starting Tutorials/HeatEquation_EX5_F/GNUmakefile Tutorials/HeatEquation_EX5_F/GPackage.mak Tutorials/HeatEquation_EX5_F/advance.f90 Tutorials/HeatEquation_EX5_F/init_phi.f90 Tutorials/HeatEquation_EX5_F/inputs_2d Tutorials/HeatEquation_EX5_F/inputs_3d Tutorials/HeatEquation_EX5_F/main.f90 Tutorials/HeatEquation_EX5_F/regrid.f90 Tutorials/HeatEquation_EX5_F/write_plotfile.f90 commit 168e559dc2d56b0de9fc601a312ef7ebff40fd2f Merge: 3d9abcad4 f73a8b22b Author: lijewski Date: Tue Apr 24 16:55:30 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f73a8b22b359dba93eed61478568e79452cd969d Merge: 73709895e 1a57bbe22 Author: vince Date: Tue Apr 24 16:08:52 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 73709895e3340d2b792951bc4ace0c35392d2f94 Author: vince Date: Tue Apr 24 16:08:29 2012 -0700 fix for FlushGrids. Src/Extern/amrdata/AmrData.cpp commit 3d9abcad4bd878db7d00326754709b57045810ef Author: lijewski Date: Tue Apr 24 15:33:36 2012 -0700 Make sure the most common case can be accessed quickly. Src/C_AMRLib/Particles.H commit 86d960ec3c1bc8a0ff23d75f8ab5fee948052e9b Author: lijewski Date: Tue Apr 24 15:01:27 2012 -0700 Yet more cleanup. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 070f846fab343a9b2d8e133d26163bfced2e910f Author: ajnonaka 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 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 Date: Tue Apr 24 13:14:35 2012 -0700 Some cleanup. Src/C_AMRLib/Particles.H commit 1a57bbe229149092fe9846821ccf0221ddcbbcdc Author: lijewski Date: Tue Apr 24 09:38:40 2012 -0700 An attempt to minimize excessive memory allocation/deallocation in AssignDensity. I'm allocating arrays in outer routines & passing'm into inner routines. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 6c731388968b5ed31dd08129fab5e3dea94c99c2 Author: lijewski Date: Tue Apr 24 09:15:44 2012 -0700 When shifting periodically into the fine level, I was using the coarsened version of the fine shift. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit f79f4663665cf2dca43b33affeaa4112c67a08f8 Author: lijewski Date: Mon Apr 23 20:48:04 2012 -0700 Call the single level version of AssignDensity from the multi-level version if there's only one level. It's likely much faster. Src/C_AMRLib/Particles.H commit 751c5bba94709117e4c8455bd6311056e8c8f38f Author: lijewski Date: Mon Apr 23 15:29:46 2012 -0700 I'm going to push this stuff. I'm getting really close to having the various period special cases finished. I don't want to lose what I've got to date. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 7eea992ed0ca2d8a5d9223976afca0c0f6d22836 Author: lijewski Date: Mon Apr 23 14:55:43 2012 -0700 Dealt with the special case where the fine grids totally covers the coarse. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 444b39bad3d62de1451389ae5e0f93d51f71b9d0 Author: lijewski Date: Mon Apr 23 13:41:24 2012 -0700 More work on C-F periodic overlap. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 1939a427607705e0760c73bd3d433b948b12e61b Merge: efcf06c4e c985bde71 Author: lijewski Date: Mon Apr 23 08:51:32 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c985bde7118efd720f3cf27d68796d967c608e4f Author: lijewski Date: Mon Apr 23 08:50:15 2012 -0700 Simplify Make.mpi a tad to help someone's old version of make. Tools/C_mk/Make.mpi commit efcf06c4eaca00b1509cda4c9c6c86adea444961 Author: lijewski Date: Sun Apr 22 19:37:09 2012 -0700 Some changes I want to save; still not soup yet! Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 5c650255cc43b8c723aeb10da772a72d2a48cbfc Merge: bcd119b46 23cef6596 Author: lijewski Date: Sun Apr 22 16:45:08 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit bcd119b469cbd912a21841a2f9147df6d7ddcefe Author: lijewski Date: Fri Apr 20 16:26:32 2012 -0700 More progress on Fine->Crse periodic. The case when level 1 is fully refined works. Other cases not so much. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 23cef65968bd4afc076872eabdf3ab997a0082f6 Author: ajnonaka Date: Fri Apr 20 14:04:34 2012 -0700 update to point to new HeatEquation tutorials in Fortran and C++ Docs/AdvancedTopics/AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex Docs/GettingStarted/hopper.run Docs/UsersGuide.tex commit c0e71b33dcf7d002f9d9e57f6811bd454156878f Author: ajnonaka Date: Fri Apr 20 14:03:56 2012 -0700 WaveEquation tutorials are now replaced by HeatEquation Tutorials/WaveEquation_C/GNUmakefile Tutorials/WaveEquation_C/Make.package Tutorials/WaveEquation_C/advance_2d.f90 Tutorials/WaveEquation_C/advance_3d.f90 Tutorials/WaveEquation_C/init_data_2d.f90 Tutorials/WaveEquation_C/init_data_3d.f90 Tutorials/WaveEquation_C/inputs_2d Tutorials/WaveEquation_C/inputs_3d Tutorials/WaveEquation_C/main.cpp Tutorials/WaveEquation_C/writePlotFile.H Tutorials/WaveEquation_C/writePlotFile.cpp Tutorials/WaveEquation_F/GNUmakefile Tutorials/WaveEquation_F/GPackage.mak Tutorials/WaveEquation_F/advance.f90 Tutorials/WaveEquation_F/init_data.f90 Tutorials/WaveEquation_F/inputs_2d Tutorials/WaveEquation_F/inputs_3d Tutorials/WaveEquation_F/main.f90 Tutorials/WaveEquation_F/write_plotfile.f90 commit 8fdb58b4eeaa492cd3e41246e0c982f1622e93ff Author: lijewski Date: Fri Apr 20 13:58:02 2012 -0700 More work on periodic in AssignDensity(). Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit bbf5f6147b04e37b6b912cbaca9f9ea6071c1f31 Author: ajnonaka Date: Fri Apr 20 13:35:54 2012 -0700 added geom.FillPeriodicBoundary. Now gives exactly same answer in 2D and 3D as fortran tutorial Tutorials/HeatEquation_EX1_C/main.cpp commit eb3435be43c96c938b645586aa7411eea5ad2151 Author: ajnonaka Date: Fri Apr 20 13:24:39 2012 -0700 index bug Tutorials/HeatEquation_EX1_C/advance_2d.f90 Tutorials/HeatEquation_EX1_C/advance_3d.f90 commit 7182a5288e966cb1bbc34b0d70527f732f1d55a0 Author: ajnonaka Date: Fri Apr 20 12:45:52 2012 -0700 C version compiles and runs, but doesn't give correct answer yet Tutorials/HeatEquation_EX1_C/GNUmakefile Tutorials/HeatEquation_EX1_C/Make.package Tutorials/HeatEquation_EX1_C/advance_2d.f90 Tutorials/HeatEquation_EX1_C/advance_3d.f90 Tutorials/HeatEquation_EX1_C/init_phi_2d.f90 Tutorials/HeatEquation_EX1_C/init_phi_3d.f90 Tutorials/HeatEquation_EX1_C/inputs_2d Tutorials/HeatEquation_EX1_C/inputs_3d Tutorials/HeatEquation_EX1_C/main.cpp Tutorials/HeatEquation_EX1_C/writePlotFile.H Tutorials/HeatEquation_EX1_C/writePlotFile.cpp commit 0926f26fbc5c50babf73fe97b1aad8a9db1dbeab Merge: beabd798a 95a034233 Author: ajnonaka Date: Thu Apr 19 20:51:31 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit beabd798ada15803bf675e28686b34d3f7a6c940 Author: ajnonaka Date: Thu Apr 19 20:51:02 2012 -0700 note about new example Docs/AdvancedTopics/AdvancedTopics.tex commit 95a0342339ae5bb687e8bf75ce4bc5cfb5f105af Author: Ann Almgren Date: Thu Apr 19 15:22:25 2012 -0700 Set ng = nghost(uu) rather that using mgt%ng in calls to smoothers. Src/LinearSolvers/F_MG/mg_tower_smoother.f90 commit f426bdfea6e3a0a6623a2ac9e9367ea7d58167a4 Merge: 0f4b6acc7 d21efc20d Author: lijewski Date: Thu Apr 19 13:29:23 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 0f4b6acc7e726437c370f91eda475519ceb29bc2 Author: lijewski Date: Thu Apr 19 13:24:16 2012 -0700 Contains Ann's latest changes to finetocrse. This is possibly as best as we can do. Also moved the SumBoundary() and SumPeriodicBoundary() into own loop after ParticleBase::AssignDensityDoit(mf,data) call. Src/C_AMRLib/Particles.H commit d21efc20dfed9bdf0d742911347b012c6df76250 Author: ajnonaka Date: Thu Apr 19 13:12:46 2012 -0700 turn off OMP and MPI by default Tutorials/HeatEquation_EX1_F/GNUmakefile Tutorials/HeatEquation_EX2_F/GNUmakefile Tutorials/HeatEquation_EX3_F/GNUmakefile Tutorials/HeatEquation_EX4_F/GNUmakefile commit ee67042946923d1ec4c919cf71b9910a38c0674f Merge: 7b3610e85 5b43709c9 Author: ajnonaka Date: Thu Apr 19 12:37:45 2012 -0700 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 7b3610e85c07d7ae63085ff817fc3eae6726cd3e Author: ajnonaka Date: Thu Apr 19 12:37:11 2012 -0700 adaptive gridding works Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX3_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/advance.f90 Tutorials/HeatEquation_EX4_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/inputs_2d Tutorials/HeatEquation_EX4_F/inputs_3d Tutorials/HeatEquation_EX4_F/main.f90 Tutorials/HeatEquation_EX4_F/regrid.f90 commit c274eec8ebaab74e1f793d1959444d9e197e8d03 Author: ajnonaka Date: Thu Apr 19 11:31:30 2012 -0700 regridding seems to work - still needs cleanup. other various multilevel cleanups Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX3_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/GPackage.mak Tutorials/HeatEquation_EX4_F/advance.f90 Tutorials/HeatEquation_EX4_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/main.f90 Tutorials/HeatEquation_EX4_F/tag_boxes.f90 commit 5b43709c9883a13e452e9b347fd26a52c5f5e816 Merge: 94d370d18 b33276d87 Author: lijewski Date: Thu Apr 19 10:41:00 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 94d370d184958acc49a7c087d6e2f8976418f2d0 Author: lijewski Date: Thu Apr 19 10:40:19 2012 -0700 More refinement to finetocrse. May be the best we can do for now. Still have to deal with fine grid on periodic boundary ... Src/C_AMRLib/Particles.H commit b33276d8799fb8214e38a8290aafdc53c4b934be Author: ajnonaka Date: Thu Apr 19 10:12:37 2012 -0700 clean up some parallelization and memory issues Tutorials/HeatEquation_EX1_F/main.f90 Tutorials/HeatEquation_EX2_F/main.f90 Tutorials/HeatEquation_EX3_F/main.f90 Tutorials/HeatEquation_EX4_F/main.f90 Tutorials/WaveEquation_F/main.f90 commit e8c0619c08eb9bba0cbe582198442803ed664355 Author: ajnonaka Date: Wed Apr 18 16:50:08 2012 -0700 more AMR progress, updating older examples Tutorials/HeatEquation_EX1_F/main.f90 Tutorials/HeatEquation_EX2_F/main.f90 Tutorials/HeatEquation_EX3_F/main.f90 Tutorials/HeatEquation_EX4_F/inputs_2d Tutorials/HeatEquation_EX4_F/inputs_3d Tutorials/HeatEquation_EX4_F/main.f90 Tutorials/HeatEquation_EX4_F/tag_boxes.f90 commit 5c56d01899aa6b6d60028ca2eec358ccbcf0e554 Author: ajnonaka Date: Wed Apr 18 16:12:55 2012 -0700 using the 'max_levs' convention that the AMR example will inherit Tutorials/HeatEquation_EX3_F/inputs_2d Tutorials/HeatEquation_EX3_F/inputs_3d Tutorials/HeatEquation_EX3_F/main.f90 commit 8aed01d21a9cfac7fad3ff42d39ef2439e35146c Merge: 9d7e33ebe 10a1429b3 Author: Ann Almgren Date: Wed Apr 18 15:29:43 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9d7e33ebe014715f4039aff1b12c871aaf8748d5 Author: Ann Almgren Date: Wed Apr 18 15:29:02 2012 -0700 New improved version of how particles assign their density at coarse-fine interfaces. This one works better at faces but still is "off" at edges and corners. It does not currently work for multiple fine grids. Src/C_AMRLib/Particles.H commit 10a1429b36c3284b55baa9703a10017cdea80229 Merge: 60edad2ec 6f77ef960 Author: lijewski Date: Wed Apr 18 15:17:54 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 60edad2ec9a19d09f77cc3f213d54fe5f50b3cef Author: lijewski Date: Wed Apr 18 15:16:03 2012 -0700 Integrated FineToCrsePeriodic() into FineToCrse(). FineToCrse() now considers fine cells that are outside the fine domain and only considers them a FineToCrse boundary if that fine cell won't be periodically shifted into a valid fine region. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 7dcc738ed300b0b6a34b7fea0a4e6930c085478d Author: lijewski Date: Wed Apr 18 13:56:45 2012 -0700 A little cleanup. Src/C_AMRLib/Particles.cpp commit f6e1cc92517bb5cb95a6b7dc7ba80dc0ec6db9a8 Author: lijewski Date: Wed Apr 18 13:33:56 2012 -0700 Added FineToCrsePeriodic(). Need to integrated into AssignDensity(). Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 6f77ef96015b4899b50b938e13b3999ebaa443cc Author: ajnonaka Date: Wed Apr 18 13:24:02 2012 -0700 minwidth is now the minimum length on a side for any newly created fine regions. before minwidth was applied to the blocking_factor-coarsed tagboxes logical multifab, so the min length on a side was minwidth*blocking_factor Src/F_BaseLib/cluster_f.f90 commit d65120f92f0ed09775addf2d9b000f28058e1ce1 Author: ajnonaka Date: Wed Apr 18 11:02:16 2012 -0700 saving progress - lots of AMR work Tutorials/HeatEquation_EX4_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/inputs_2d Tutorials/HeatEquation_EX4_F/inputs_3d Tutorials/HeatEquation_EX4_F/main.f90 Tutorials/HeatEquation_EX4_F/tag_boxes.f90 commit 30997f0eb204505bf05876b2412b4c650ea8618c Author: ajnonaka Date: Wed Apr 18 09:19:25 2012 -0700 AMR example Tutorials/HeatEquation_EX4_F/GNUmakefile Tutorials/HeatEquation_EX4_F/GPackage.mak Tutorials/HeatEquation_EX4_F/advance.f90 Tutorials/HeatEquation_EX4_F/init_phi.f90 Tutorials/HeatEquation_EX4_F/inputs_2d Tutorials/HeatEquation_EX4_F/inputs_3d Tutorials/HeatEquation_EX4_F/main.f90 Tutorials/HeatEquation_EX4_F/tag_boxes.f90 Tutorials/HeatEquation_EX4_F/write_plotfile.f90 commit 0a2f540b2cb907df0047f97ff25538c3886dc43e Author: ajnonaka Date: Wed Apr 18 09:17:57 2012 -0700 tidying up Tutorials/HeatEquation_EX3_F/main.f90 commit 380bff01cd8f3b6c944be363ec64456ef4959425 Author: ajnonaka 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 Date: Wed Apr 18 08:51:25 2012 -0700 comment Src/F_BaseLib/tag_boxes.f90 commit fd19cb3dcbc3ca49640b0a415c81745f1ab92d80 Author: ajnonaka Date: Wed Apr 18 07:10:39 2012 -0700 comments in ml_layout.f90 Src/F_BaseLib/ml_layout.f90 commit 69796f5f67fac49506411ad7dd809960e95e4da5 Author: ajnonaka Date: Tue Apr 17 20:01:09 2012 -0700 some cleanup of tutorials Tutorials/HeatEquation_EX1_F/advance.f90 Tutorials/HeatEquation_EX1_F/init_phi.f90 Tutorials/HeatEquation_EX1_F/main.f90 Tutorials/HeatEquation_EX2_F/advance.f90 Tutorials/HeatEquation_EX2_F/init_phi.f90 Tutorials/HeatEquation_EX2_F/main.f90 Tutorials/HeatEquation_EX3_F/main.f90 Tutorials/WaveEquation_F/advance.f90 Tutorials/WaveEquation_F/init_data.f90 Tutorials/WaveEquation_F/main.f90 Tutorials/WaveEquation_F/write_plotfile.f90 commit 71b5dd80b20db01daba4e4d64c2759a5bf46e6dc Author: lijewski Date: Tue Apr 17 13:48:26 2012 -0700 More work on parallelization of AssignDensity(). Seems to work but could use more testing. Still have to do the special Fine->Crse periodic case. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit b178158fff36c1c4a037ecce48109d7b2737ef50 Author: lijewski Date: Tue Apr 17 13:16:32 2012 -0700 Some work making new AssignDensity() work in parallel. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit bffce84589a880bb4ab266893c870ec55670dfdc Author: lijewski Date: Mon Apr 16 13:03:45 2012 -0700 Some cleanup. Removed all OpenMP references in multi-level AssignDensity(). Just doens't seem worth it to try & OpenMP. Src/C_AMRLib/Particles.H commit 176aba0f52d033fb7ad8ff89416ca565136b41e7 Author: ajnonaka Date: Sun Apr 15 20:40:33 2012 -0700 tweak the tutorial example by moving initial Gaussian profile slighly off-center (greatly helps with examining the effects of non-periodic boundary conditions) Docs/AdvancedTopics/AdvancedTopics.tex Tutorials/HeatEquation_EX1_F/init_phi.f90 Tutorials/HeatEquation_EX2_F/init_phi.f90 Tutorials/HeatEquation_EX3_F/init_phi.f90 Tutorials/HeatEquation_EX3_F/main.f90 commit 725a1daf3badce7077d6b029c825baba3edc90ac Author: lijewski Date: Fri Apr 13 13:56:36 2012 -0700 Factored some stuff in ParticleBase routines. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit b31a9583435afc148a612ab45219092952b5e0da Author: lijewski Date: Fri Apr 13 13:12:27 2012 -0700 Simplified FineToCrse(). Removed "some" ref_ratio==2 assumptions. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit e4cdaf63cfb52a6b58fddd597c553ed507267eac Author: lijewski Date: Fri Apr 13 12:41:52 2012 -0700 Damn! I've had this correct for some time. I forgot that I changed the offset in init.cpp from .5 -> .49 for some previous debugging. You can't have uniform distribution if the particles aren't uniformly distributed. Src/C_AMRLib/Particles.H commit ce00d5da92ae70a6e836b4b6b71d9e19c1ad5642 Author: lijewski Date: Fri Apr 13 10:07:05 2012 -0700 Didn't have my CrseFine fractions -> Fine correct. Src/C_AMRLib/Particles.H commit 24f4e711d42a8beff1b288d5574f7eb221bbdc18 Author: lijewski Date: Fri Apr 13 09:16:08 2012 -0700 Some more debugging tests. Src/C_AMRLib/Particles.H commit 7c7b1c10e2508bdb11f44bd0d9cf8579ee803920 Author: Michael Zingale Date: Thu Apr 12 20:21:16 2012 -0400 add support for 3 plotfiles python_plotfile/contourcompare.py commit 99ece003b29af6e1698650a7e4cc49871d0e29a0 Author: lijewski Date: Wed Apr 11 16:12:04 2012 -0700 I "think" I've come up with a way to calculate the fine cells and their respective fractions in the case when moving some mass from a coarse cell to a fine cell. I'm still don't appear to be getting constant density. More to do ... Src/C_AMRLib/Particles.H commit 94dc612b3e81b96fa911428b162b3f0efcb2e9cb Author: lijewski Date: Wed Apr 11 08:30:22 2012 -0700 I'm going to commit and push the new AssignDensity(). It isn't correct but it's close. The fine->crse stuff is OK (with the possible exception when coarse & fine overlap at a periodic boundary). It also doesn't work in parallel if you try with more than one level. I'll get it working in parallel after it's totally done. The sticking point is when we're at a coarse level and have some mass that wants to be placed on the fine level: how to calculate the cell indices & fractions for the fine level? Src/C_AMRLib/Particles.H commit de1ec0fe4796a54b5b74d4553660f5c7f894fa59 Author: lijewski Date: Tue Apr 10 16:02:46 2012 -0700 Crse->Fine is looking better. Still not quite right. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit d6ccda35d362b65ce198b568d3723469fe9fe96d Author: lijewski Date: Tue Apr 10 14:10:35 2012 -0700 I'm feeling pretty good about the Fine->Crse code. It's still serial but that can be fixed. The Crse->Fine still needs work. Src/C_AMRLib/Particles.H commit 1cd4b38c13c121e75f9889ee3349cd97adbd7ee2 Author: lijewski Date: Tue Apr 10 10:13:09 2012 -0700 The Fine->Crse stuff "might" be working in serial. Little hard to tell till the Crse->Fine is also working the the RH array in TestAdiabatic comes out looking uniform. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 497861ea6a411b13b3a39c2260747fd7a97c2189 Merge: 2cb87cd2f e76980477 Author: lijewski Date: Mon Apr 9 17:33:56 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 2cb87cd2f8a73918a0560aa08c0fc4256fbfec98 Author: lijewski Date: Mon Apr 9 11:15:15 2012 -0700 A little cleanup. Still more to do on AssignDensity(). Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit e769804776586e55d5f68b044268584161ea1727 Author: ajnonaka Date: Mon Apr 9 11:09:59 2012 -0700 a few more additions Docs/AdvancedTopics/AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex Docs/UsersGuide.tex commit 3c7dbd9b388056d071e122ad8492fbec2d0598cc Author: lijewski Date: Mon Apr 9 10:50:23 2012 -0700 CrseToFine() and FineToCrse() now use AssignDensityCoeffs(). which is now a bool[]. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit d65d66a713296b6bfb0956988c39a7ee3f658de7 Author: lijewski Date: Mon Apr 9 09:32:25 2012 -0700 Removed AssignDensityDoit(). Implemented the single level & multi-level AssignDensity() separately. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit c451dcc982d850d69a0a3f64828d059b1f70baa2 Author: lijewski Date: Sun Apr 8 10:28:30 2012 -0700 Added some more comments to direct my future work on Crse->Fine. Src/C_AMRLib/Particles.H commit 96326f32058323d89480e019fef8917707c40d8c Author: lijewski Date: Sun Apr 8 10:21:28 2012 -0700 Some work on Crse->Fine issue in AssignDensity. More to do. I've disable threading in AssignDeisntyDoit() for now. Once it's working I'll make sure threading works. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit e175c298b217a132ca5187ff9ebbb1144111234f Author: lijewski Date: Sat Apr 7 19:05:23 2012 -0700 Integrated in AssignDensityCoeffs(). The Fine->Crse stuff looks good. Crse->Fine to go. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit ff25d19614406ede500a8a45d15150b67218d2a5 Author: lijewski Date: Sat Apr 7 10:18:37 2012 -0700 Some work on AssignDensity() Fine-Crse issue. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 46519366b98d4293225f22bcdea212ae0e0ed959 Author: lijewski Date: Sat Apr 7 08:29:22 2012 -0700 Final (hopefully) tweak to FineToCrse(). Src/C_AMRLib/Particles.cpp commit 9c2aae8c8c997dd1e9ee48a49f41829b28fba0fc Author: lijewski Date: Sat Apr 7 08:26:55 2012 -0700 Refined FineToAdd(). Src/C_AMRLib/Particles.cpp commit 7c2ac0856d37ff74275cef72be4cf4ef87723f9b Author: ajnonaka Date: Fri Apr 6 21:21:28 2012 -0700 more User's Guide and Tutorial progress. In pretty good shape now. Docs/AdvancedTopics/AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex Docs/Introduction/Introduction.tex Docs/Preface/Preface.tex Tutorials/HeatEquation_EX1_F/advance.f90 Tutorials/HeatEquation_EX2_F/advance.f90 Tutorials/HeatEquation_EX3_F/advance.f90 commit db12646d4dd3557083b4a451ab0552b6cda63605 Author: ajnonaka Date: Fri Apr 6 16:55:29 2012 -0700 tutorial Docs/AdvancedTopics/AdvancedTopics.tex commit 29d366224b644afadd8f3005d5bc9ad93ca10e94 Author: ajnonaka Date: Fri Apr 6 16:39:14 2012 -0700 fix comments, get the multilevel example working by hooking into the F_MG restriction calls Tutorials/HeatEquation_EX2_F/advance.f90 Tutorials/HeatEquation_EX2_F/init_phi.f90 Tutorials/HeatEquation_EX3_F/GNUmakefile Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX3_F/init_phi.f90 Tutorials/HeatEquation_EX3_F/inputs_2d Tutorials/HeatEquation_EX3_F/inputs_3d Tutorials/HeatEquation_EX3_F/main.f90 commit 6a8cf291e2b60605f54741f5c24b275135351c43 Merge: 7cf62ebba 7a5f4e21d Author: lijewski Date: Fri Apr 6 15:52:59 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 7cf62ebba890ab615581a17eb5705f5a44050920 Author: lijewski Date: Fri Apr 6 15:50:44 2012 -0700 Added ParticleBase::FineToCoarse(). Needed by AssignDensityDoit(). Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 7a5f4e21d096f9dd6d50c5c4f765d0350377fd4a Author: ajnonaka Date: Fri Apr 6 15:50:29 2012 -0700 forgot to add init_phi.f90 Tutorials/HeatEquation_EX3_F/init_phi.f90 commit e3b79c0453068e0dbbec6e5e4e59734d6c6df21f Author: ajnonaka Date: Fri Apr 6 15:50:06 2012 -0700 this is as far as I can go before I move the restriction stuff into F_BaseLib Tutorials/HeatEquation_EX3_F/advance.f90 commit 529ea6e4c4c59e56315894827c08e9266e85a5cb Author: ajnonaka Date: Fri Apr 6 15:39:15 2012 -0700 first cut at multilevel extension of HeatEquation_EX2. This one uses ml_layouts and ml_boxarrays instead of just arrays of layouts and boxarrays Tutorials/HeatEquation_EX3_F/GNUmakefile Tutorials/HeatEquation_EX3_F/GPackage.mak Tutorials/HeatEquation_EX3_F/README Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX3_F/init_data.f90 Tutorials/HeatEquation_EX3_F/initialize.f90 Tutorials/HeatEquation_EX3_F/inputs_2d Tutorials/HeatEquation_EX3_F/inputs_3d Tutorials/HeatEquation_EX3_F/main.f90 Tutorials/HeatEquation_EX3_F/make_fluxes.f90 Tutorials/HeatEquation_EX3_F/write_plotfile.f90 commit a37a564c0c50f590b289bad4cbcf903ab248597d Author: ajnonaka Date: Fri Apr 6 15:00:13 2012 -0700 destory the_bc_tower Tutorials/HeatEquation_EX2_F/main.f90 commit 092ea38bd6bbef0ab3fede9dcecdc35b88ab1592 Author: ajnonaka Date: Fri Apr 6 14:20:31 2012 -0700 more Tutorial updates Docs/AdvancedTopics/AdvancedTopics.tex commit 1f037503a95febb773cc400bf8ed445c341f4495 Author: ajnonaka Date: Fri Apr 6 13:38:07 2012 -0700 bugfix; the ncomp feature wasn't implemented in multifab_physbc.f90 Src/F_BaseLib/multifab_physbc.f90 commit 4235e69d631d19c6b7893ad5eb9ab7a824364fd9 Author: ajnonaka Date: Fri Apr 6 13:32:59 2012 -0700 pass in hi to physbc_2d/3d instead of computing it with fortran size() tricks within Src/F_BaseLib/multifab_physbc.f90 commit 798d370dc28cc939cc6199296bac9b04cb8af952 Author: ajnonaka 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 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 Date: Thu Apr 5 22:22:44 2012 -0700 bug in 2d bc's Tutorials/HeatEquation_EX2_F/advance.f90 commit f2fbff443ea41a00c476e394fa04ba69605aa854 Author: ajnonaka Date: Thu Apr 5 22:06:38 2012 -0700 spruced up the first two heat equation examples. the boundary condition example is finished, with options for a 'source' dirichlet wall, outflow (phi_n=0) and periodic Src/F_BaseLib/define_bc_tower.f90 Src/F_BaseLib/multifab_physbc.f90 Tutorials/HeatEquation_EX1_F/init_phi.f90 Tutorials/HeatEquation_EX1_F/main.f90 Tutorials/HeatEquation_EX2_F/advance.f90 Tutorials/HeatEquation_EX2_F/init_phi.f90 Tutorials/HeatEquation_EX2_F/main.f90 commit 0d9b6a177402df18b3c5056a49c452299d514ed2 Author: ajnonaka Date: Thu Apr 5 19:22:33 2012 -0700 more bc example progress Src/F_BaseLib/define_bc_tower.f90 Tutorials/HeatEquation_EX2_F/inputs_2d Tutorials/HeatEquation_EX2_F/inputs_3d Tutorials/HeatEquation_EX2_F/main.f90 commit ae04300fe8ac87d0518477bdc8c6ab6b50ea8e67 Author: ajnonaka Date: Thu Apr 5 18:13:41 2012 -0700 some documentation updates Docs/AdvancedTopics/AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex commit a1d7e5ab52cc3eb36f346bc6b2d65b13d319d228 Author: ajnonaka Date: Thu Apr 5 18:12:47 2012 -0700 start the HeatEquation_EX2_F boundary condition example by copying the EX1 example. Tutorials/HeatEquation_EX2_F/GNUmakefile Tutorials/HeatEquation_EX2_F/GPackage.mak Tutorials/HeatEquation_EX2_F/advance.f90 Tutorials/HeatEquation_EX2_F/init_phi.f90 Tutorials/HeatEquation_EX2_F/inputs_2d Tutorials/HeatEquation_EX2_F/inputs_3d Tutorials/HeatEquation_EX2_F/main.f90 Tutorials/HeatEquation_EX2_F/write_plotfile.f90 commit 7ca08631bd506414e824fa803feb30feb4ef7f8d Author: ajnonaka Date: Thu Apr 5 18:11:50 2012 -0700 renname example Tutorials/HeatEquation_EX3_F/GNUmakefile Tutorials/HeatEquation_EX3_F/GPackage.mak Tutorials/HeatEquation_EX3_F/README Tutorials/HeatEquation_EX3_F/advance.f90 Tutorials/HeatEquation_EX3_F/init_data.f90 Tutorials/HeatEquation_EX3_F/initialize.f90 Tutorials/HeatEquation_EX3_F/inputs_2d Tutorials/HeatEquation_EX3_F/inputs_3d Tutorials/HeatEquation_EX3_F/main.f90 Tutorials/HeatEquation_EX3_F/make_fluxes.f90 Tutorials/HeatEquation_EX3_F/write_plotfile.f90 commit 2a03e8425e77437250c8fe5fc2befb737c31fbfb Author: ajnonaka Date: Thu Apr 5 17:07:42 2012 -0700 first attempt at a generic boundary condition type Src/F_BaseLib/define_bc_tower.f90 Src/F_BaseLib/multifab_physbc.f90 commit 15d3d3f53b454adedc98a53382cf2c3b761c3695 Author: ajnonaka Date: Thu Apr 5 17:07:13 2012 -0700 don't need to include files already in F_BaseLib/GPackage.mak Tutorials/HeatEquation_F/GPackage.mak commit 33ba0848c5e7364697b6609bfb6c5a889c760b9e Author: ajnonaka Date: Thu Apr 5 15:00:56 2012 -0700 HeatEquation_F will use F_BaseLib boundary condition stuff Tutorials/HeatEquation_F/define_bc_tower.f90 Tutorials/HeatEquation_F/multifab_physbc.f90 commit 1f57c910a56a3c2b4208abe91d21d59ad88622a9 Author: ajnonaka Date: Thu Apr 5 15:00:17 2012 -0700 f90sources += create_umac_grown.f90 f90sources += define_bc_tower.f90 f90sources += fillpatch.f90 f90sources += multifab_fill_ghost_cells.f90 f90sources += multifab_physbc_edgevel.f90 f90sources += multifab_physbc.f90 Src/F_BaseLib/GPackage.mak commit 6b75f233e221e2b1ca35e3c59e67958e6b4c2d0b Author: ajnonaka Date: Thu Apr 5 14:59:07 2012 -0700 add define_bc_tower and multifab_physbc to F_BaseLib. Still need to clean these up to be the 'simplest' case for use in HeatEquation tutorials. Now, the F_BaseLib/GPackage.make contains f90sources += create_umac_grown.f90 f90sources += define_bc_tower.f90 f90sources += fillpatch.f90 f90sources += multifab_fill_ghost_cells.f90 f90sources += multifab_physbc_edgevel.f90 f90sources += multifab_physbc.f90 so local codes won't have to Src/F_BaseLib/define_bc_tower.f90 Src/F_BaseLib/multifab_physbc.f90 commit 13ffabbb0a5fb20fbf6bf7706145e9bb06ba3e99 Author: lijewski Date: Thu Apr 5 14:13:31 2012 -0700 Little cleanup. Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp Tutorials/HeatEquation_F/main.f90 commit 37676d98c1737a09613f5f6ed8251042911eb80d Merge: 7a47cb261 742f31372 Author: Ann Almgren Date: Thu Apr 5 13:45:22 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 7a47cb261a67a1cf3a1e9d6ff6b427f40a985d09 Author: Ann Almgren Date: Thu Apr 5 13:45:13 2012 -0700 Fix call to layout_build_ba. Src/LinearSolvers/F_MG/ml_solve.f90 commit 742f31372f32d1bf3cabd8941116524fdfdd5ee9 Author: ajnonaka Date: Thu Apr 5 13:36:13 2012 -0700 completely eliminate the string "setbc" from all files and filenames in the fBoxLib source and HeatEquation tutorial Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 Src/F_BaseLib/multifab_physbc_edgevel.f90 Tutorials/HeatEquation_F/GPackage.mak Tutorials/HeatEquation_F/multifab_physbc.f90 Tutorials/HeatEquation_F/setbc.f90 commit 127a64a3cc05d1030ecda6b8529ca692aa838c50 Author: ajnonaka Date: Wed Apr 4 15:38:47 2012 -0700 latest Docs/AdvancedTopics/AdvancedTopics.tex commit 8f91b26363aba509b1907dffd8deb422e67d105d Author: ajnonaka Date: Wed Apr 4 15:38:23 2012 -0700 forgot to commit this Docs/AdvancedTopics/hopper_omp.run commit 623c4fb80a087095ab6e22c18e3abc4bde091778 Author: ajnonaka Date: Wed Apr 4 13:52:15 2012 -0700 finished section on OMP and accompanying example code Docs/AdvancedTopics/AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex Docs/GettingStarted/hopper.run Docs/Introduction/Introduction.tex Docs/UsersGuide.tex commit fc001cacd70e4310111febb37a35dd9b561dfb48 Author: ajnonaka Date: Wed Apr 4 13:28:08 2012 -0700 code comments Tutorials/HeatEquation_EX1_F/advance.f90 commit b4a06457c0e53d192ffa2b2cdd9687bc41df30ed Author: ajnonaka Date: Wed Apr 4 13:26:57 2012 -0700 comments Tutorials/HeatEquation_EX1_F/advance.f90 Tutorials/HeatEquation_EX1_F/main.f90 commit 83582dd591477f6eb406f505a284e56a21981668 Author: ajnonaka Date: Wed Apr 4 12:47:24 2012 -0700 more progress on User's Guide Docs/AdvancedTopics/AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex commit 83cb73aa1ece771d366dd633f76d6a90b737e665 Author: ajnonaka Date: Wed Apr 4 12:46:54 2012 -0700 some cleanup of WaveEquation_F Tutorials/WaveEquation_F/advance.f90 Tutorials/WaveEquation_F/init_data.f90 commit 7528cafa42546610d8f12bff21892e92943d58de Author: ajnonaka Date: Wed Apr 4 12:45:13 2012 -0700 simple OMP-enabled heat equation example Tutorials/HeatEquation_EX1_F/GNUmakefile Tutorials/HeatEquation_EX1_F/GPackage.mak Tutorials/HeatEquation_EX1_F/advance.f90 Tutorials/HeatEquation_EX1_F/init_phi.f90 Tutorials/HeatEquation_EX1_F/inputs_2d Tutorials/HeatEquation_EX1_F/inputs_3d Tutorials/HeatEquation_EX1_F/main.f90 Tutorials/HeatEquation_EX1_F/write_plotfile.f90 commit e6c3b207456f91d924dbebfd3253f8d2f4706b9c Merge: 6bf50c19e 443482136 Author: ajnonaka Date: Wed Apr 4 10:55:44 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 6bf50c19e46998ae87b80ca7bc399ca9c081e611 Author: ajnonaka Date: Wed Apr 4 10:55:19 2012 -0700 rewriting advanced topics chapter Docs/AdvancedTopics/AdvancedTopics.tex Docs/UsersGuide.tex commit 93241b4c58e49e5888128239d36acfc719b01423 Author: ajnonaka Date: Wed Apr 4 10:31:17 2012 -0700 update to the new layout_build_ba interface Tutorials/WaveEquation_F/main.f90 commit 4434821360ae62ff54ef539779121a44636a82e0 Author: Ann Almgren Date: Wed Apr 4 10:28:39 2012 -0700 Fix the call to layout_build_ba. Tutorials/Exp_CNS_NoSpec/main.f90 commit 44e38f803aa4be0a5cf6a6d3d4e63744683d86b6 Merge: f8a6c0800 42596e528 Author: Ann Almgren Date: Wed Apr 4 10:26:03 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f8a6c0800885de0c2d65688ee6862c487109b970 Author: Ann Almgren Date: Wed Apr 4 10:25:34 2012 -0700 Add boxarray_bbox(ba) to the layout build calls where needed since the problem domain argument is no longer optional. Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/cluster_f.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_f.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit 42596e528fc550d4759a8f9e4deebdc5cabddc07 Author: lijewski Date: Wed Apr 4 10:12:31 2012 -0700 Destroy the_bc_tower and call layout_flush_copyassoc_cache() to keep valgrind happy. Tutorials/HeatEquation_F/main.f90 commit 3645722c0054fbe8ce4bc248f1ff88a7514ec26b Merge: f6b98b596 514040f9f Author: lijewski Date: Wed Apr 4 10:12:16 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 514040f9fa8b16a865b2f0eb9aee25bfe7326993 Author: Ann Almgren Date: Wed Apr 4 10:09:06 2012 -0700 The problem domain argument (pd) is no longer optional in the call to layout_build_ba in layout.f90 Src/F_BaseLib/layout.f90 commit f6b98b596613694409ba9badb05babf862959a32 Author: lijewski Date: Wed Apr 4 09:59:35 2012 -0700 OMP'd. Tutorials/HeatEquation_F/advance.f90 Tutorials/HeatEquation_F/init_data.f90 Tutorials/HeatEquation_F/make_fluxes.f90 commit ff19364c0dcb1f65801988651e4763e9f6dda6e2 Author: Ann Almgren Date: Wed Apr 4 09:15:48 2012 -0700 Add 3d inputs file. Tutorials/HeatEquation_F/inputs_3d commit 1f6035cf10332880fb5dd6db9475d50a9e62a044 Author: Ann Almgren Date: Wed Apr 4 09:15:24 2012 -0700 Get 3d version working. Tutorials/HeatEquation_F/GNUmakefile Tutorials/HeatEquation_F/init_data.f90 Tutorials/HeatEquation_F/make_fluxes.f90 commit 47ae657a2ae4f5f730b2cd7ddb27d1a2faf456fc Author: Ann Almgren Date: Wed Apr 4 08:02:14 2012 -0700 Don't let nlevs > 3 for now just because we haven't defined grids at the higher levels. Tutorials/HeatEquation_F/main.f90 commit af079ee7bbb12d9b984e3716330166e191091452 Author: Ann Almgren Date: Wed Apr 4 08:01:15 2012 -0700 Added README. Tutorials/HeatEquation_F/README commit 0196078ef89ba993ea631e269d4a691db22a85af Author: Ann Almgren Date: Wed Apr 4 07:57:50 2012 -0700 More cleanup... Tutorials/HeatEquation_F/define_bc_tower.f90 Tutorials/HeatEquation_F/main.f90 commit 2f0e4082f36fe0bf37ff5543d49964a0d8e97708 Author: Ann Almgren Date: Wed Apr 4 07:55:23 2012 -0700 Add more comments. Tutorials/HeatEquation_F/main.f90 commit a73975856df21b4f98849d7f97b454475266b531 Author: Ann Almgren Date: Wed Apr 4 07:45:49 2012 -0700 This is a multilevel explicit solver for the heat equation using forward Euler. The boxes are currently hardwired in the main.f90 routine. Tutorials/HeatEquation_F/GNUmakefile Tutorials/HeatEquation_F/GPackage.mak Tutorials/HeatEquation_F/advance.f90 Tutorials/HeatEquation_F/define_bc_tower.f90 Tutorials/HeatEquation_F/init_data.f90 Tutorials/HeatEquation_F/initialize.f90 Tutorials/HeatEquation_F/inputs_2d Tutorials/HeatEquation_F/main.f90 Tutorials/HeatEquation_F/make_fluxes.f90 Tutorials/HeatEquation_F/multifab_physbc.f90 Tutorials/HeatEquation_F/setbc.f90 Tutorials/HeatEquation_F/write_plotfile.f90 commit 04a458206dfc0a389aa54a0024ba5e46ad33bc74 Author: Marc Day Date: Tue Apr 3 12:41:31 2012 -0700 What the heck...declare v1.0.0 BoxLib_Version.txt commit 2fc4bd3a77807d0a5f054135d1000472ed2c0206 Author: lijewski Date: Thu Mar 29 15:51:34 2012 -0700 Changed := -> : in a couple places. Tools/C_mk/Make.defs commit 56ad6f9df48abb6a9ebcc888eddbc0e7c96cbda2 Author: Marc Day Date: Thu Mar 29 13:55:28 2012 -0700 Generalize refinement and derive functionality to allow user to build at runtime BoxLib_Version.txt Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp Src/C_AMRLib/ErrorList.H Src/C_AMRLib/ErrorList.cpp commit f333a72a1cd74813fb32cdd9eeff77eacca7f18e Author: Marc Day Date: Thu Mar 29 13:24:48 2012 -0700 Modify where data pulled in simpleg stencils to avoid creating inconsistent edge data Src/LinearSolvers/F_MG/cc_stencil.f90 commit 39296ce3cb58c67df08a9722f4841cbfe0830c6b Merge: 2675ff663 9f44ff907 Author: lijewski Date: Thu Mar 29 07:17:21 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 2675ff663158711b8678f75c5a7be905de7df5aa Author: lijewski Date: Thu Mar 29 07:16:48 2012 -0700 Fix from Manuel Cotelo. Src/C_BaseLib/FabArray.H commit 9f44ff907c8a64f21342c979bdd5019c7946f548 Merge: 427e2ee6a 045289947 Author: vince Date: Wed Mar 28 10:38:03 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 427e2ee6a2690c74b4d7a23badff954f77ca786d Author: vince Date: Wed Mar 28 10:37:43 2012 -0700 added FillBoundary. Tutorials/MultiFabTests/MultiFabReadWrite.cpp commit 045289947b8e41a20e2c8e77a82f34926e1ad605 Merge: eed78a66c 052eaa8d8 Author: lijewski Date: Wed Mar 28 10:33:21 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit eed78a66ca694f0a75cd27c88495203d6534b839 Author: lijewski Date: Wed Mar 28 10:32:41 2012 -0700 Mods requested by Donev. Tools/C_mk/Make.defs Tools/F_mk/GMakeMPI.mak Tools/F_mk/comps/gfortran.mak commit 052eaa8d82bd5de60128ab97fdd3b09781511d32 Author: vince Date: Tue Mar 27 17:55:18 2012 -0700 example to do multifab functions. Tutorials/MultiFabTests/GNUmakefile Tutorials/MultiFabTests/Make.package Tutorials/MultiFabTests/MultiFabReadWrite.cpp commit c14baf6d8e8af32b56537e5c61b8b5aea5acb04e Author: ajnonaka Date: Thu Mar 22 12:35:26 2012 -0700 mothra no longer overrides GNUmakefile to force Intel compilers Tools/F_mk/GMakeMPI.mak commit 1e075a4fa187b574a6139d9cc9688c2354f5957f Author: Matthew Emmett Date: Thu Mar 22 14:04:10 2012 -0400 PyBoxLib: Tweak imports, add multifab.get_info method. Src/Python/pyboxlib/__init__.py Src/Python/pyboxlib/base.py Src/Python/pyboxlib/multifab.py commit 880d095df1edb33a09efd1ac2446558f2ea32444 Author: Ann Almgren Date: Fri Mar 16 12:32:24 2012 -0700 Fix bug where RelaxType was called instead of RAPType in the Hypre stuff. Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp commit b57df6d8ff1f497e2d34167c3254830ef66ca421 Author: Marc Day Date: Thu Mar 15 18:22:29 2012 -0700 Shoops....forgot the box transform for the derive source data. Src/C_AMRLib/AmrLevel.cpp commit 280ad87841a0387d3573b59f3acf2e22e355f5ee Author: Marc Day Date: Thu Mar 15 17:56:37 2012 -0700 Fix the derive function that does not use a Fortran function, specifically for the case that the source data needs to be larger than the derived data. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp commit 37ecccc56b3d29139a40e6cd1cd0fdcbc0cf618a Author: Michael Zingale Date: Thu Mar 15 19:02:32 2012 -0400 add functions to convert between the integer bc names to strings and vice-versa Src/F_BaseLib/bc.f90 commit 115a3d43d02dd929c06792b416c8458d007cd650 Merge: f233bf4e0 3a5b8aefd Author: lijewski Date: Thu Mar 15 14:13:05 2012 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f233bf4e0552283cd62dd03e101370c004222142 Author: lijewski Date: Thu Mar 15 14:12:24 2012 -0700 When splitting grids we split on Z then Y then X. Then tends to be more efficient cache-wise than X -> Y-> Z. Src/C_AMRLib/Amr.cpp commit 3a5b8aefd7c24779e7ee590499e3cdf2603ef5c1 Author: Marc Day 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 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 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: 4bc5ddc87 c72eb8724 Author: Michael Zingale 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Thu Mar 1 14:22:07 2012 -0800 Add REAME for the multigrid tutorial. Tutorials/MultiGrid_C/README commit 46ff83b4021704ecf58a2d2666cdbe1f44dc79fe Merge: 0452a2552 cc9236e49 Author: Weiqun Zhang Date: Wed Feb 29 16:38:30 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit cc9236e49a9b2d9babaff2bd1cc4a42e6b14f82e Author: lijewski 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 Date: Wed Feb 29 11:17:16 2012 -0500 get this compiling again python_plotfile/GNUmakefile commit 4f9614fc9fc649881ac7450b192748fde8afdcd8 Author: Michael Zingale Date: Mon Feb 27 19:20:00 2012 -0500 add projection, eos, and incompressible tests. Also update to the new data_processing location Tools/C_util/regtests/Maestro-tests.ini commit ae66a9ab804723415aec22e3a7cd2d3c02a11c9a Author: Michael Zingale Date: Mon Feb 27 19:06:31 2012 -0500 more sensible (optional) fParallel location to get this to compile if you have a MAESTRO checkout at the same level as AmrPostprocessing GNUmakefile commit 5681ff56f8f569cd7598d0920792517f3718db0a Author: Ann Almgren Date: Fri Feb 24 13:10:20 2012 -0800 Fix the quadratic terms in subroutine FORT_CQINTERP in INTERP_2D.F. They were missing the 1/2 in front of phi_xx * dx^2 term. Src/C_AMRLib/INTERP_2D.F commit 51e5a3c1c1a94734fa89723cbc464d69dabbb1ea Author: lijewski Date: Thu Feb 23 15:07:11 2012 -0800 BOXLIB_HOME default should be ../../.. not ../.. Tutorials/MultiGrid_C/GNUmakefile commit 179448c17609121d570366aa28dbc7beee73683c Author: lijewski Date: Thu Feb 23 15:04:54 2012 -0800 Make the BndryData member a const reference instead of a concrete data member. This means that the BndryData object passed to the constructor had better not be destroyed before we use it. The "right" way to do this would be to pass a reference-counted pointer to a BndryData. I'll put that on my list ... Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.H commit f78e11d9b1a5de57e0f685d99d08c02e22ce6465 Author: lijewski Date: Thu Feb 23 15:02:59 2012 -0800 Disallow some copy constructors and assignment operators. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp commit 5c940c11d5afba1508e340bdc749793b4e84e85f Author: lijewski Date: Thu Feb 23 13:45:58 2012 -0800 Make copy constructor & assignment operator private. Src/C_BoundaryLib/FabSet.H commit 53de5fac7da00066329441f45e7c5d31bc786268 Author: lijewski Date: Thu Feb 23 13:29:38 2012 -0800 Use PArrayNoManage instead of PArrayManage to cut down on copy()ing. Tutorials/MultiGrid_C/main.cpp commit d6cacd007daef8f26f5a9c751317471ee93bba2b Author: Michael Zingale Date: Tue Feb 21 21:29:19 2012 -0500 add the ability to add a string to the compilation command -- useful for forcing the code to use alternate microphysics. Tools/C_util/regtests/testnew.py commit 0452a25525b6ddf5722b591d9a31c5da19cf2089 Merge: 53d48d791 121ab03d5 Author: Weiqun Zhang Date: Tue Feb 21 15:40:31 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 121ab03d54c2a7488f13203d5fb35b2205e95fd9 Author: John Bell 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 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 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 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 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 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 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 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 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 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 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 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 Date: Tue Feb 14 15:53:05 2012 -0800 Fixed typo. Tutorials/Exp_CNS_NoSpec/write_plotfile.f90 commit b3dd826a12e437b68f052c78e516c6c2da3dac4b Author: lijewski Date: Tue Feb 14 15:52:12 2012 -0800 Made write_plotfile() more generic. Tutorials/Exp_CNS_NoSpec/main.f90 Tutorials/Exp_CNS_NoSpec/write_plotfile.f90 commit d9f12caf29f8b0b133cf4a3b948dc8f89b908983 Author: lijewski Date: Tue Feb 14 15:35:59 2012 -0800 Moved final output statement before boxlib_finalize(). Tutorials/Exp_CNS_NoSpec/main.f90 commit ae5a621f27287ff6d66374fe064e1edf67abe4b5 Author: lijewski Date: Tue Feb 14 14:26:42 2012 -0800 Some code rearrangement. Tutorials/Exp_CNS_NoSpec/advance.f90 commit ac650ebac49d68674949df907b6148ca12cca719 Author: lijewski Date: Tue Feb 14 13:44:12 2012 -0800 New inputs file. Tutorials/Exp_CNS_NoSpec/inputs.jbb commit 704c64152a1de7ae562084f8a95b86c6c472a164 Author: lijewski Date: Tue Feb 14 13:43:54 2012 -0800 More like what JBB wanted. Tutorials/Exp_CNS_NoSpec/init_data.f90 Tutorials/Exp_CNS_NoSpec/inputs_3d commit 154f3e1a91111c608812d5b7ecfde2ab8d278ad0 Author: lijewski Date: Tue Feb 14 13:26:18 2012 -0800 Replaced some divides with multiplies. Tutorials/Exp_CNS_NoSpec/advance.f90 commit 11f5bdcfefe5ff8c2acfe58d8237355fa0b9bcda Author: lijewski Date: Tue Feb 14 13:03:45 2012 -0800 Some memory and performance improvements. Tutorials/Exp_CNS_NoSpec/advance.f90 commit 51c07ce5ce2945a6e56f19e2695da3e332d63c75 Author: lijewski Date: Tue Feb 14 12:34:50 2012 -0800 Some cleanup. Tutorials/Exp_CNS_NoSpec/advance.f90 Tutorials/Exp_CNS_NoSpec/init_data.f90 commit ee134688620c874e7896c230970f0d44b758c3b3 Merge: d84057616 0b4702e74 Author: lijewski Date: Tue Feb 14 11:12:14 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d84057616f447f2a41196ea68783ac817b866c1a Author: lijewski Date: Tue Feb 14 11:12:04 2012 -0800 OMP init_data Tutorials/Exp_CNS_NoSpec/init_data.f90 commit 0b4702e7491873e40d2d6defcf5f4aad7518594c Author: Michael Zingale Date: Tue Feb 14 13:49:29 2012 -0500 new main page format -- makes it easier to view many tests Tools/C_util/regtests/testnew.py commit b7d54afbbdc3f4ca433f9b20c929509fe05ce478 Author: lijewski Date: Tue Feb 14 10:48:54 2012 -0800 Some OMP tweaking. Tutorials/Exp_CNS_NoSpec/advance.f90 commit 71ec1b3d993ae7d89413d76323d146aa89f0f68d Author: lijewski Date: Tue Feb 14 10:23:10 2012 -0800 OMP'd diffterm(). Tutorials/Exp_CNS_NoSpec/advance.f90 commit 9c8e925b574dea8cc2d8b2729d12bd13b3528c17 Author: lijewski Date: Tue Feb 14 10:01:44 2012 -0800 OMP'd hypterm(). Tutorials/Exp_CNS_NoSpec/advance.f90 commit 08faa433272cba5b2213550ef0b9a5b552786d2c Author: lijewski Date: Mon Feb 13 21:23:05 2012 -0800 Some renaming and added newer namelist stuff to example inputs file. Tutorials/Exp_CNS_NoSpec/inputs_3d Tutorials/Exp_CNS_NoSpec/main.f90 commit 623b8940699a726d6da44871d41fa33b87434982 Author: lijewski Date: Mon Feb 13 20:58:08 2012 -0800 Now write out when outputing a plotfile. Add more things to the namelist so they can be set in an input file. Some more cleanup. Tutorials/Exp_CNS_NoSpec/advance.f90 Tutorials/Exp_CNS_NoSpec/main.f90 Tutorials/Exp_CNS_NoSpec/write_plotfile.f90 commit d8b6c68402d378563cc08c023aa7c6c2ee7f85ee Merge: 4877c5587 f11d3be3a Author: lijewski Date: Mon Feb 13 20:28:22 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 4877c5587d3daa7682072cf10740040ae2fcf908 Author: lijewski Date: Mon Feb 13 20:27:52 2012 -0800 Fixed bug; now appears to be working. Did some cleanup as well. Tutorials/Exp_CNS_NoSpec/advance.f90 Tutorials/Exp_CNS_NoSpec/init_data.f90 Tutorials/Exp_CNS_NoSpec/inputs_3d Tutorials/Exp_CNS_NoSpec/main.f90 commit 3cc1401c74bce16cbb60934e12a11d4cbfb95e99 Author: lijewski Date: Mon Feb 13 17:49:49 2012 -0800 Fixed bug in difflux(). Now calculate dt based on CFL/courno. Tutorials/Exp_CNS_NoSpec/advance.f90 Tutorials/Exp_CNS_NoSpec/init_data.f90 Tutorials/Exp_CNS_NoSpec/main.f90 commit f11d3be3ac1ac18cc29acfbcbb8a8c5c59d72f78 Merge: 521d1fd6a 4e8ec03af Author: Michael Zingale 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 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 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 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 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 Date: Mon Feb 13 15:48:12 2012 -0800 Some work getting diffterm(). Tutorials/Exp_CNS_NoSpec/advance.f90 commit 9ad9192e9e0e264a8271cba0be2e02c8e4cca409 Author: lijewski Date: Mon Feb 13 15:20:48 2012 -0800 Actually call ctoprim() & hypterm(). Tutorials/Exp_CNS_NoSpec/advance.f90 commit e7a3df79ab7f8d42db923bf6db256bb118f7aa3b Author: lijewski Date: Mon Feb 13 14:47:28 2012 -0800 Brought in ctoprim() and hypterm(). Tutorials/Exp_CNS_NoSpec/advance.f90 Tutorials/Exp_CNS_NoSpec/init_data.f90 Tutorials/Exp_CNS_NoSpec/main.f90 Tutorials/Exp_CNS_NoSpec/write_plotfile.f90 commit 6eeb24926850a2dc704c12789f7a05d575f173b6 Author: lijewski Date: Mon Feb 13 12:11:40 2012 -0800 Removed various flags used to turn off C++ exceptions. The various compilers on jaguarpf really want exceptions enabled. Shouldn't really effect performance. Tools/C_mk/Make.Linux commit d6fbcf1834bd345af83339b24740907b1aa80c15 Author: Marc Day Date: Fri Feb 10 20:45:11 2012 -0800 Virtualize a couple functions to support more generic control of plotfile and checkpoint output BoxLib_Version.txt Src/C_AMRLib/Amr.H Tools/C_scripts/gen_release_tarball commit 4c0a400aacdb34c30d6fcdb391aca35639dae19f Merge: 1e03915a1 c7830e6c7 Author: Marc Day Date: Fri Feb 10 20:44:45 2012 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit c7830e6c77a33ad6187e159d9f2ef770aecea032 Author: lijewski Date: Fri Feb 10 16:02:04 2012 -0800 Some cleanup. Tutorials/Exp_CNS_NoSpec/advance.f90 commit 6357e1abb9ff8153ccda2909ee544608ecfb8cca Author: lijewski Date: Fri Feb 10 16:01:49 2012 -0800 Plug a couple memory leaks. Tutorials/Exp_CNS_NoSpec/main.f90 Tutorials/WaveEquation_F/main.f90 commit 5d55ea7fc30c18f79831e64c76c8a24188884161 Author: lijewski Date: Fri Feb 10 15:26:35 2012 -0800 Some work on RK3 algorithm. Tutorials/Exp_CNS_NoSpec/advance.f90 Tutorials/Exp_CNS_NoSpec/main.f90 commit c8d26c262ad2d249f971120f1d46a25ca890801d Author: lijewski Date: Fri Feb 10 14:12:38 2012 -0800 A little more cleanup. Still just WaveEquation. Tutorials/Exp_CNS_NoSpec/advance.f90 Tutorials/Exp_CNS_NoSpec/init_data.f90 commit 5d5ef8d6e1e73ae94a91f57f722eeefa3224769d Author: lijewski Date: Fri Feb 10 14:06:26 2012 -0800 A little cleanup. Tutorials/Exp_CNS_NoSpec/inputs_2d Tutorials/Exp_CNS_NoSpec/inputs_3d Tutorials/Exp_CNS_NoSpec/main.f90 commit bbd95909a171e491648b8884824e2ec5f125cdd2 Author: lijewski Date: Fri Feb 10 13:38:49 2012 -0800 Just copied files from WaveEquation_F. Tutorials/Exp_CNS_NoSpec/GNUmakefile Tutorials/Exp_CNS_NoSpec/GPackage.mak Tutorials/Exp_CNS_NoSpec/advance.f90 Tutorials/Exp_CNS_NoSpec/init_data.f90 Tutorials/Exp_CNS_NoSpec/inputs_2d Tutorials/Exp_CNS_NoSpec/inputs_3d Tutorials/Exp_CNS_NoSpec/main.f90 Tutorials/Exp_CNS_NoSpec/write_plotfile.f90 commit 74d3da57ac3a0633c05bbe183c63a504e2056586 Author: lijewski Date: Fri Feb 10 09:03:54 2012 -0800 Some patches from Chris for Macs. Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 4695e77d9f41b6f445408315c0fa4c4475ecee6a Author: Ann Almgren Date: Fri Feb 10 08:26:27 2012 -0800 Put Mike's fixes in for gcc/g++. Tools/C_mk/Make.defs commit 42db55787ce633e95fcd3bb952eaa0abcb4bae9b Author: Michael Zingale Date: Thu Feb 9 16:31:03 2012 -0500 add a sort to the test problem Tools/C_util/regtests/testnew.py commit d13bf9506a878f001a41c5e25a2361e01aef7eea Author: Ann Almgren Date: Thu Feb 9 12:58:19 2012 -0800 The alpha term was incorrectly included in s_minion_cross_fill_2d and s_minion_cross_fill_3d Src/LinearSolvers/F_MG/cc_stencil.f90 commit 054ac4696b0e1e08435723314bf408e5f16c1856 Author: Michael Zingale Date: Wed Feb 8 20:02:30 2012 -0500 fix some typos Tools/F_scripts/write_probin.py commit f95cbd6017915fa9901126a25bc3b0f50835daa3 Author: Michael Zingale Date: Wed Feb 8 20:00:43 2012 -0500 make the problem names more unique. Eliminate docs Tools/C_util/regtests/gen_compile_test.sh commit 3c3fefcd7fa4382fc5d5689616e1d3dfbdae0ce0 Author: lijewski Date: Wed Feb 8 09:14:26 2012 -0800 A little more generalization in support of Aleks. Tools/C_mk/Make.defs commit 2b9da5fe2278c31728555b1e83cad5f3d1c7088c Merge: 9844778fe ab7751740 Author: Michael Zingale 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 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 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 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 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 Date: Tue Feb 7 10:05:24 2012 -0800 BOXLIB_HOME macro wasn't quite right. Tests/LinearSolvers/ComparisonTest/GNUmakefile commit 7ed675942b5d05bb6430e3fcbabd0ffbe88114c2 Merge: cf4caaba7 0ba36a85a Author: Weiqun Zhang Date: Mon Feb 6 14:10:14 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit cf4caaba7e07233dddd91577bb20dc6faf290d15 Author: Weiqun Zhang Date: Mon Feb 6 14:09:21 2012 -0800 OpenMP the sync residue subroutines. Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 0ba36a85a76eec3951ca3c8a22abbcdbeef138e2 Author: Michael Zingale Date: Mon Feb 6 14:09:53 2012 -0500 add RT, update build directories to reflect new directory structure Tools/C_util/regtests/Maestro-tests.ini commit a415f6cecc4fdd0ec6e478805f27127861a13038 Author: Michael Zingale Date: Mon Feb 6 14:09:35 2012 -0500 if we fail to compile during a normal test, show the make output Tools/C_util/regtests/testnew.py commit 1d98cb2eb1f28356fa5dbfd6f2f3f5bae3dfa336 Author: Ann Almgren Date: Sun Feb 5 16:38:27 2012 -0800 Define lo_inflow(:) and hi_inflow(:) instead of lo_inflow(3) and hi_inflow(3) in nodal_divu.f90/subroutine divu. Src/LinearSolvers/F_MG/nodal_divu.f90 commit f6cc9ed18fe1f1337b32537b124d10ecf0d03bf5 Author: Weiqun Zhang Date: Thu Feb 2 17:59:22 2012 -0800 Support the case when fine grids touch inflow boundaries. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit cea650320323a69818dffe5f316a33eaf791f0a7 Author: Weiqun Zhang Date: Thu Feb 2 15:42:52 2012 -0800 Call bl_error if nonuniform grids are used in the F90 nodal solver. Src/LinearSolvers/F_MG/mg.f90 commit 686cd540f2f91c3b60bc72f6ff5f4f165fb1f9cd Author: Weiqun Zhang Date: Thu Feb 2 13:41:17 2012 -0800 Pass velocity in ghost cells into the F90 nodal solver in order to support inflow boundary. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 877210180c8b8a413ce36f45034ed0898f21373d Author: Weiqun Zhang Date: Wed Feb 1 17:00:03 2012 -0800 put subtract_divu_from_rh back Src/LinearSolvers/F_MG/nodal_divu.f90 commit ca02edb9d8a6fa2d38f5cbf1be77bca4c7daad0f Author: Weiqun Zhang Date: Wed Feb 1 14:09:03 2012 -0800 Fix a bug in computing the new u in 3D nodal projection. The bug was due to confusing rho and sigma (which is 1/rho). Src/LinearSolvers/F_MG/nodal_newu.f90 commit a2d6cdca3d04fe8702d9dac4f7e20636976d82ef Author: Weiqun Zhang Date: Wed Feb 1 13:31:59 2012 -0800 Fix a bug in 3D nodal projection with the dense stencil. MG towers were used before they were built. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit cd5e5ef1b5c42edadace7394a72485050dc26a6b Author: Weiqun Zhang Date: Wed Feb 1 12:50:39 2012 -0800 Fix a bug in 3D nodal projection Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/nodal_divu.f90 commit 4a943b9c62ccc99befff52e903546d8aaab3e5f5 Merge: 306e286be aa2f7db79 Author: Weiqun Zhang Date: Tue Jan 31 17:27:36 2012 -0800 Merge branch 'dev' commit aa2f7db79e32ef57218b86014dbc6af639481e08 Author: Weiqun Zhang Date: Tue Jan 31 16:11:21 2012 -0800 3D support for have_divu Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 306e286be05863043669bf4e810d5aa7796290ff Merge: e836c3128 19de476e6 Author: Michael Zingale 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 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 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 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 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: c7881bbb2 6173aa36b Author: Weiqun Zhang Date: Fri Jan 27 13:15:47 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 6173aa36b71032c29040502b9493a36c4c5eb678 Merge: b785eb0b7 ea544ba8f Author: vince Date: Fri Jan 27 13:12:27 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit b785eb0b7e495fb729b94f91b0a0017bfc93c80c Author: vince 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 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 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 Date: Thu Jan 26 13:49:50 2012 -0800 Add some comments Src/LinearSolvers/F_MG/nodal_divu.f90 commit fe231bdc5bcb32704314c7542557eaa080dde525 Author: Weiqun Zhang Date: Thu Jan 26 13:43:26 2012 -0800 clean up Src/LinearSolvers/F_MG/nodal_divu.f90 commit 4445d01ec5b196f38c71dbd978fe0f90a8603cb4 Author: Weiqun Zhang Date: Wed Jan 25 17:51:13 2012 -0800 support have_divu Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 1e03915a1827a80de7b811cf2a75c9d40140c4c9 Merge: 2cdd6eaa1 94f30abbf Author: Marc Day 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 Date: Wed Jan 25 16:35:24 2012 -0800 Remove CMake hack suggested by one of the Amanzi folks CMakeLists.txt commit 94f30abbfb6674169a7ea366a101f2f81b78235f Merge: 30bd8eb93 bf3bb541d Author: Weiqun Zhang Date: Fri Jan 20 13:24:31 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 30bd8eb9336009461a9e6c58efbfa87f411ca1f3 Author: Weiqun Zhang Date: Fri Jan 20 13:23:38 2012 -0800 Fix a parallel bug Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit bf3bb541d409227d5959d26fa6eaa56df1891099 Merge: e2c5b3a79 d9344e6f5 Author: Michael Zingale 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 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: 14eafc8ea 9a5bb1dd0 Author: Weiqun Zhang Date: Thu Jan 19 17:17:14 2012 -0800 Merge branch 'dev' commit 9a5bb1dd0c42d2877b6d77b3047f1ce74ea4a80b Author: Weiqun Zhang Date: Thu Jan 19 17:10:50 2012 -0800 3D implemented for nodal sync residue. Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 14eafc8eab3b6b6262f44d867a5889c7dcf4dad0 Author: vince Date: Thu Jan 19 17:00:14 2012 -0800 rle update pubtest 4 Tests/IOBenchmark/README commit c75b87ac1bb85d3dbbfa198cc57d01bcecda9e3f Author: vince Date: Thu Jan 19 16:46:28 2012 -0800 rle update pubtest 3 Tests/IOBenchmark/README commit 4a253b7365e0c1a0ed947847a8c99185c85bd2ff Author: vince Date: Thu Jan 19 16:43:18 2012 -0800 rle update pubtest 2 Tests/IOBenchmark/README commit 98235ea264bb643ab08a99a50a788c6b9055df90 Author: vince Date: Thu Jan 19 16:38:05 2012 -0800 rle update pubtest Tests/IOBenchmark/README commit ae9be45fc966bb7cecd45da405765240de4cc81d Merge: 232484954 e383f0b7c Author: vince Date: Wed Jan 18 15:49:48 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 2324849545f7f83bffa0a81b0011db04da609b74 Author: vince Date: Wed Jan 18 15:49:28 2012 -0800 rme update 3 Tests/IOBenchmark/README commit e383f0b7cf0dbfb337f387eabcfe96df5d5b3457 Merge: cef5902a4 23620784b Author: Weiqun Zhang Date: Wed Jan 18 15:34:42 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit cef5902a468455af7f566c8076e21b55782c7dc9 Author: Weiqun Zhang Date: Wed Jan 18 15:33:55 2012 -0800 Fix a few memory leaks. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 23620784baeffe76099f7af97354b577f4b25029 Author: vince Date: Wed Jan 18 11:19:14 2012 -0800 rme update 2 Tests/IOBenchmark/README commit 620d0dad51d7418cf6be0b9ebc214b984520cc1d Author: vince Date: Wed Jan 18 11:08:17 2012 -0800 rme update Tests/IOBenchmark/README commit 82ef714d345a8208027d6efeb4431127421f69a6 Author: Michael Zingale 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 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: 521c2aa49 b843d64ab Author: Weiqun Zhang Date: Fri Jan 13 14:26:40 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 521c2aa49cb5cf8bcb2a8e452592ef8a4040abbd Merge: 2efda7d65 37fb65783 Author: Weiqun Zhang Date: Fri Jan 13 14:26:23 2012 -0800 Merge branch 'dev' commit 37fb657834a1ca6c157ab899434d7618295e7876 Author: Weiqun Zhang Date: Fri Jan 13 14:23:16 2012 -0800 change the size of zero_rh from (nlevs) to (2:nlevs) because rh(1) was never used. Src/LinearSolvers/F_MG/ml_nd.f90 commit b843d64ab6f6dd75c23dcb90316cda81e40d30ec Author: lijewski Date: Fri Jan 13 08:25:43 2012 -0800 Some cleanup. Tools/C_mk/Make.defs commit 9f78fc730467518a7b5c14818d8461b9f58c88c7 Merge: 7676f02bb 57ac1a196 Author: lijewski Date: Thu Jan 12 21:03:39 2012 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 57ac1a1967fc3590b03f1dd0a248f93e28733972 Merge: bdbacfe34 0564f8fbd Author: lijewski Date: Thu Jan 12 20:27:37 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 7676f02bb3e348bbeaa03a9b4a439c9bab118bdb Author: lijewski Date: Thu Jan 12 20:24:27 2012 -0800 Minor tweak to get .mod files in the right place on hopper. Tools/C_mk/Make.defs commit 0564f8fbd996aea0c4cf9a57096d763c2ae8da43 Merge: d49e265e0 2efda7d65 Author: Marc Day 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 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 Date: Thu Jan 12 17:17:18 2012 -0800 switch mpi on hedorah Tools/C_mk/Make.mpi commit 9b4eb6e605a2351ce62e78d29f0a2ac19a9ef488 Author: Marc Day Date: Thu Jan 12 17:15:11 2012 -0800 Allow 2D in solver tutorial Tutorials/MultiGrid_C/COEF_2D.F Tutorials/MultiGrid_C/RHS_2D.F commit bdbacfe342bb2ce4117c6b990f0e0db27700ace7 Author: lijewski Date: Thu Jan 12 16:48:12 2012 -0800 Fix to GNU FC stuff to get .mod files written to the appropriate place on hopper. The problem was that the "-J" flag was being set on the FC and fC lines, which are overwritten on Cray computers with ftn. Solution was to move all those flags set together with the compiler into [fF]FLAGS. Tools/C_mk/Make.defs commit 2efda7d6569005aa3d03b254e1292dcfe7f778d6 Merge: d7d4c021b 66213b92d Author: Weiqun Zhang Date: Wed Jan 11 16:58:12 2012 -0800 Merge branch 'dev' commit 66213b92da3767b1a5ae2dd82a7eafa044d9de8d Author: Weiqun Zhang Date: Wed Jan 11 16:54:59 2012 -0800 Change the way of getting sync resid from the MG solver for safety. Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit d7d4c021be3c0c77ca1577a5a0a1244fe303b08f Merge: 8fde59bdd 8435b76cf Author: Weiqun Zhang Date: Wed Jan 11 15:35:28 2012 -0800 Merge branch 'dev' commit 8435b76cfc242940071770cf14e2af2adf8a234e Author: Weiqun Zhang Date: Wed Jan 11 15:32:01 2012 -0800 Fix a bug. The ghost cells of sync_resid should be set to zero. Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 8fde59bdd029b689b93990149258ed69bd1c8581 Merge: 201c5ad00 64314f2d9 Author: Weiqun Zhang Date: Wed Jan 11 11:00:41 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 201c5ad000003229842628c4f982493b3d3364bd Author: Weiqun Zhang Date: Wed Jan 11 10:52:53 2012 -0800 Remove the hack in nodal smoother that try to match the C++ nodal solver. The 2D hack had a bug. Moreover, the old way is also problematic because the color (i.e., red or black) depends upon the layout of grids. Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit 64314f2d96518256173d5f1dacc9d35c3c7695c3 Author: ajnonaka Date: Tue Jan 10 17:41:17 2012 -0800 boundary condition figures Docs/AdvancedTopics/bc_example1.eps Docs/AdvancedTopics/bc_example1.fig Docs/AdvancedTopics/bc_example2.eps Docs/AdvancedTopics/bc_example2.fig Docs/AdvancedTopics/bc_example3.eps Docs/AdvancedTopics/bc_example3.fig commit 7510803ad377fff3656e5f1cfc1905b73389deea Author: ajnonaka 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 Date: Tue Jan 10 16:35:45 2012 -0800 moving this Docs/GettingStarted/hopper.run commit a237ef60928ea7224152a7e2e1ad4a76cfd9623a Author: ajnonaka Date: Tue Jan 10 16:35:33 2012 -0800 moving this Docs/AdvancedTopics/hopper.run commit 69c83c282a777dba8826414f760a5db97c08fede Merge: 46b0ffeef 46106c0ea Author: Weiqun Zhang Date: Tue Jan 10 12:50:28 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 46b0ffeef910e32b93219cf41bf7e2262b559c7f Author: Weiqun Zhang Date: Tue Jan 10 12:48:54 2012 -0800 cleanup Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 46106c0ea3b1ad86c1dd6c2cdf7e12378203f940 Author: ajnonaka Date: Mon Jan 9 17:40:42 2012 -0800 minor updates Docs/AdvancedTopics/AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex Docs/Introduction/Introduction.tex Docs/UsersGuide.tex commit fe0f46152b50b6c41a4e8a17ca1eb6a22a4750cc Author: Weiqun Zhang Date: Mon Jan 9 17:35:14 2012 -0800 It works for the simple problem now. Cleanup is needed. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_sync_resid.f90 commit 3d21a34d7bf26f8cb7fdda269d07bcd7400ae2d8 Author: Weiqun Zhang Date: Mon Jan 9 14:30:52 2012 -0800 Turn on do_diagnostics when mg.v >= 4. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 919ad433e6506db8ca49f67eb0cc20608a0ec0f7 Author: Weiqun Zhang Date: Mon Jan 9 14:26:40 2012 -0800 Allow MGT_Solver change smoother. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 6a729c98339eb9035a0dafc364cda5a7c68d58db Author: Weiqun Zhang Date: Mon Jan 9 13:59:18 2012 -0800 There are cases that err = ml_residual is zero while err = ml_cycle is not. Src/LinearSolvers/C_NodalMG/amr_multi.cpp commit 138a2b186ffe39046d98d25a8471170980c77363 Author: Michael Zingale Date: Sat Jan 7 17:09:52 2012 -0500 add bender Tools/F_mk/GMakeMPI.mak commit 7cba34de3d61a4788a5455cd8bbae00710c7385a Merge: cdd044f6c 5d5e01c41 Author: Michael Zingale 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 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 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 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: c4690f508 119ce3fe3 Author: Weiqun Zhang Date: Thu Jan 5 17:21:17 2012 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit c4690f508c9d792b52e1e82807adcd4b56370cdd Author: Weiqun Zhang Date: Thu Jan 5 17:20:01 2012 -0800 Fixed a bug. one_sided_ss should be built with stencil=.true. Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 119ce3fe36fc89f560581b7eb327e5a34e548f27 Author: vince Date: Thu Jan 5 16:10:10 2012 -0800 added rodan. Tools/C_mk/Make.mpi commit 66992034ec62ffcf885be5697f77ab17fbec90b0 Merge: fe2cfa8b1 1a9bd7993 Author: lijewski Date: Wed Jan 4 14:07:59 2012 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit fe2cfa8b1e6c3af8923b6beb673fcdb174ae7907 Author: lijewski Date: Wed Jan 4 14:07:41 2012 -0800 GNUmakefile for use with DUMPI trace package on hopper. Tests/LinearSolvers/C_CellMG/GNUmakefile.dumpi commit 1a9bd79938df655d6cf82768a6ce1d917234eed0 Author: Marc Day Date: Wed Jan 4 13:52:42 2012 -0500 Add mpi stuff for LENS at ORNL Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 3eba53a80224f80ff92d8a6a2234e08b5048bcc1 Author: Ann Almgren Date: Tue Jan 3 14:42:36 2012 -0800 Change verbosity test in Amr.cpp to verbose>0 instead of verbose>1 when use_efficient_regrid=1. Src/C_AMRLib/Amr.cpp commit 96a1fa2ea68588544c70edd2ff3174ff1d18e6af Author: Ann Almgren Date: Tue Jan 3 13:13:16 2012 -0800 Add use_efficient_regrid flag which allows us to not recreate existing AmrLevels when the regridding process does not change the boxArray. Src/C_AMRLib/Amr.cpp commit 1574e6991d0d6c3dddf2c2a2c20870bc6a9b94b8 Author: Matthew Emmett Date: Sat Dec 31 21:10:30 2011 -0500 PyBoxLib: Add "read" and "copy" methods to multifab class. Src/Python/pyboxlib/base.py Src/Python/pyboxlib/multifab.py Src/Python/src/fboxlib.f90 Src/Python/test.py commit 29c238b19bc1c7c7a8259f69207641314b93efc3 Author: Matthew Emmett Date: Sat Dec 31 01:37:28 2011 -0500 PyBoxLib: Add "write" method to multifab class. Src/Python/pyboxlib/multifab.py Src/Python/src/fboxlib.f90 commit 0e7435273168d52f700f3cac9de126068db23f60 Author: Matthew Emmett Date: Fri Dec 30 23:44:29 2011 -0500 PyBoxLib: Add "nboxes" and "local_boxes" methods to layout class. Src/Python/GMakerules.mak Src/Python/pyboxlib/fab.py Src/Python/pyboxlib/layout.py Src/Python/pyboxlib/multifab.py Src/Python/src/fboxlib.f90 commit 7b9343e21ce0bdc78520817891c1ac8f1aba9509 Merge: 758269311 c8e22c93f Author: Ann Almgren 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 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 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 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 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: 61cf7f0af 79acec6c5 Author: Ann Almgren 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 Date: Wed Dec 21 08:49:10 2011 -0800 Fix defaults for NReaders and NRedist. Src/C_AMRLib/Particles.H commit 79acec6c58221eaed8b41ad9a97850d3283abec6 Author: ajnonaka Date: Tue Dec 20 17:41:45 2011 -0800 staggered grid convergence tester complete Tools/C_util/Convergence/AVGDOWN_2D.F Tools/C_util/Convergence/AVGDOWN_3D.F Tools/C_util/Convergence/AVGDOWN_F.H Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp commit 5a1dd1a5df21a855409d3973f556cab9be2fa8d4 Author: ajnonaka Date: Tue Dec 20 16:16:17 2011 -0800 good progress on the staggered grid convergence utility. works now for x-direction, need to generalize to all directions and ref_ratios Tools/C_util/Convergence/AVGDOWN_2D.F Tools/C_util/Convergence/AVGDOWN_3D.F Tools/C_util/Convergence/AVGDOWN_F.H Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp Tools/C_util/Convergence/GNUmakefile commit 0faeb762d0edd3d50fc2b925f2a6c9ae3f229314 Author: ajnonaka Date: Tue Dec 20 09:50:28 2011 -0800 fix comments, check in new template for staggered grid convergence testingZ Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameDomainRefinedStag.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp commit b831b864b8b446e6d52efe9dcb2dab9aea656592 Author: ajnonaka Date: Mon Dec 19 12:20:33 2011 -0800 clean this up Tools/C_util/Convergence/GNUmakefile commit fdac7fee6aa73d9cf77ada046bfaa7d93ff3a5c4 Author: lijewski Date: Thu Dec 15 09:12:51 2011 -0800 Added a critical section around the std::cout call in Reset() just to be safe. Src/C_AMRLib/Particles.cpp commit b3d93cf0fd91df231dc4632b5b09cf11152bf6c6 Author: lijewski Date: Wed Dec 14 22:14:26 2011 -0800 Added a critical section around that part of intersections() that builds the hash table. Src/C_BaseLib/BoxArray.cpp commit 27187d63fc3dede4c9e71c2938714c61eca66914 Author: lijewski Date: Wed Dec 14 13:15:09 2011 -0800 More mods for Gunther. Src/C_BaseLib/GNUmakefile commit 3b2937b1c20fc95ef6333aa0acacc5de92bac112 Merge: 694cf96dc cc6e1512f Author: Michael Zingale 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 Date: Mon Dec 12 18:51:46 2011 -0500 fix cray path Tools/F_mk/GMakedefs.mak commit cc6e1512f22aa71219a5dc76eed231a517d16005 Author: Ann Almgren Date: Mon Dec 12 12:46:49 2011 -0800 Add domlo and domhi to interface for ErrorFunc2. Src/C_AMRLib/ErrorList.H commit 3576f724d31d963588ae9a5c771f62a413edd0ab Author: Matthew Emmett Date: Mon Dec 12 12:01:27 2011 -0500 PyBoxLib: Add "interleave" flag to multifab create method. This allows PyBoxLib to create interleaved FABs, which are indexed according to (c,i,j,k) instead of (i,j,k,c). Src/Python/pyboxlib/fab.py Src/Python/pyboxlib/multifab.py Src/Python/src/boxlib_numpy.c Src/Python/src/boxlib_numpy.f90 Src/Python/src/fboxlib.f90 commit ec2ebc2be594b79297d6632591984745c83cf867 Author: Weiqun Zhang Date: Fri Dec 9 18:41:33 2011 -0800 Add a couple of functions to MGT_Solver. It now gets a cell center mask from Projection. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit 2ba36e0b3c83aa0c0cd3fb0c29e0bd7b5f2f3991 Author: lijewski Date: Fri Dec 9 16:36:59 2011 -0800 Inlined some one liners. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit c8adb2db1a31baccc7a7dfd83a9f37fe22702bd7 Merge: 830475865 da53d9186 Author: lijewski Date: Fri Dec 9 15:37:54 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 8304758651fec2e56745c4da29c98ab02fb22bd8 Author: lijewski Date: Fri Dec 9 15:37:37 2011 -0800 Mods requested by Gunther for VisIt. Src/C_BaseLib/GNUmakefile Src/C_BaseLib/Make.package commit da53d918616a8ba9b71a70f600b2cf406c42c865 Merge: e3a0ebb31 ae8c47fd9 Author: Weiqun Zhang Date: Thu Dec 8 17:25:36 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e3a0ebb3126a0722d2d30705ff6a081dca735427 Author: Weiqun Zhang Date: Thu Dec 8 17:25:09 2011 -0800 undo change in .gitignore .gitignore commit 1371f4ea700f54c7ef46df37f5460d517ec7ab1d Author: Weiqun Zhang Date: Thu Dec 8 17:22:06 2011 -0800 If both rhs and v are provided, the nodal solver will use rhs + div v as RHS. If only v is provided, it will use div v as RHS, as before. .gitignore Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit ae8c47fd9acbe8e14645dff16cc7cc25d315ceb2 Author: Ann Almgren Date: Thu Dec 8 14:56:47 2011 -0800 Remove defined-but-unused "gridloc" Src/C_AMRLib/Particles.H commit 147eef2def11489f58ebc33332d2e61fd80a66b3 Merge: 5ef337ae0 5e0eb1d79 Author: Ann Almgren 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 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: 19218c3a2 a246b8867 Author: Weiqun Zhang Date: Thu Dec 8 13:32:58 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 19218c3a2089dc212de506dc4b67d2e65d28b0c8 Author: Weiqun Zhang Date: Thu Dec 8 13:32:53 2011 -0800 Fix a typo/bug when BL_FORT_USE_UPPERCASE Src/LinearSolvers/F_MG/mg_cpp_f.h commit a246b88670cda1aeac8b12c61eb92aac4b75ee47 Merge: 484fd0f25 e15c03629 Author: Ann Almgren 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 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 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 Date: Wed Dec 7 20:21:39 2011 -0500 pretty it up some more Tools/C_util/regtests/testnew.py commit 3f18f2d096ac6083165cdeb8c8858e3abb000e07 Merge: 41002b9ef e535678c0 Author: Michael Zingale 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 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: 201610315 41feff82f Author: Marc Day 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 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 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 Date: Tue Dec 6 10:11:31 2011 -0800 Need to fix NRedist default. Src/C_AMRLib/Particles.H commit 6dda459bae7a60af869a3e4ca245a6259a9f9d59 Merge: b47507b94 6d32518b3 Author: Weiqun Zhang Date: Mon Dec 5 14:42:31 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 6d32518b3bc58de92bd13eec74c0e84efc261df1 Merge: 49a787204 d94d63364 Author: ajnonaka Date: Mon Dec 5 14:41:57 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 49a787204f2d1a96a98ff498022f77f92c1d8d26 Author: ajnonaka Date: Mon Dec 5 14:41:39 2011 -0800 back out of some of Ann's solvability changes Src/LinearSolvers/F_MG/ml_cc.f90 commit b47507b940c74f30a33221b6a1230d6dff6593b1 Author: Weiqun Zhang Date: Mon Dec 5 14:32:48 2011 -0800 Fix a bug in deallocating multifabs for the nodal solver with the dense stencil. The one_sided_ss multifab is not allocated in that case. The communication between MGT_Solver and the underlying F90 solver is changed so that the multifabs in the MGT_Solver can have an arbitrary number of components. This saves memory because we do not have to copy the state data into the MGT solver. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 commit d94d63364d53dd0f693e74414485b87673c83255 Merge: 90ed7e598 1d9765202 Author: Weiqun Zhang Date: Mon Dec 5 14:31:04 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 90ed7e598530073bc7b12071f24fb6e035424f6b Author: Weiqun Zhang Date: Mon Dec 5 14:28:40 2011 -0800 Fine tune the setup of Hypre AMG solver according to the recommendation of Ulrike Meier. Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp commit 1d97652020e3a0d14f8f86515596a1278ec4f5ea Author: lijewski Date: Mon Dec 5 13:15:45 2011 -0800 Shut up a compiler warning about a possibly unset variable. Src/C_AMRLib/Particles.H commit 9f199f53eb595e38eaaeb461180eb514a12d3304 Merge: 730d22347 37ca7adfd Author: Marc Day Date: Fri Dec 2 10:11:02 2011 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 730d2234731db401fb934b102e16697d25652d4d Merge: 91ceeff13 05e230acf Author: Marc Day Date: Fri Dec 2 10:08:28 2011 -0800 Merge branch 'master' of /home/marc/src/CCSE/tmp/../BoxLib commit 05e230acf801011e50af4a9e4338e42eda4d4454 Author: Marc Day 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 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 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 Date: Mon Nov 28 21:27:52 2011 -0800 Fix up InitFromAsciiFile. Src/C_AMRLib/Particles.H commit aadc1b399dca0c8a79c653e4984e62aef1c97512 Author: Ann Almgren Date: Mon Nov 28 19:27:59 2011 -0800 This version breaks up the Redistribute calls into chunks in InitFromAsciiFile in Particles.H Src/C_AMRLib/Particles.H commit 449e35083b353dcb1253592bec2f3860b3a5dd62 Author: lijewski Date: Mon Nov 28 17:08:05 2011 -0800 Revert m_id & NextID() back to int. Keep num_particles and num_particles_read as longs. NextID() now checks if we try to read/initialize more than INT_MAX particles per any MPI process. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit bcb93e381fee7756f1957d8eeba545c5ee6c0a65 Author: Ann Almgren Date: Mon Nov 28 15:33:20 2011 -0800 One more int --> long in Particles.H Src/C_AMRLib/Particles.H commit bc618d626f20db6c731dc98c1590e5956506cf73 Author: Ann Almgren Date: Mon Nov 28 15:32:12 2011 -0800 One more int --> long in Particles.H Src/C_AMRLib/Particles.H commit 98e48cd941bcb89699a93a003a02e66a4827028d Author: Ann Almgren Date: Mon Nov 28 15:27:54 2011 -0800 We need m_id and next_id to be long instead of int for the case when we have lots and lots of particles. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit a89fc79a149ed60e3cd506ffaf4bc78c045b8bfc Merge: 6e713b2ea 6c4cdf0c2 Author: Ann Almgren Date: Mon Nov 28 15:17:22 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 6e713b2ea3f49f2d23324de21a9e8c822bf604fa Author: Ann Almgren Date: Mon Nov 28 15:17:13 2011 -0800 Fix error print statement. Src/C_AMRLib/Particles.H commit 6c4cdf0c2fa9ace75a82511f7bfb874a1153db3b Merge: 8fbe03efc 50b273c43 Author: Michael Zingale 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 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 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 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 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 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 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 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 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 Date: Wed Nov 23 10:39:14 2011 -0800 Remove random debug statement. Src/C_AMRLib/Particles.H commit 38c2f2269dc67445d5457ce88a1f6dca4142ab2c Author: Ann Almgren Date: Wed Nov 23 10:38:11 2011 -0800 Fix test for print statement. Src/C_AMRLib/Particles.H commit e06387da5d83e83b851b15ba057243a17df00d4b Author: Ann Almgren Date: Wed Nov 23 10:35:25 2011 -0800 Fix typo with lNrep... Src/C_AMRLib/Particles.H commit 1998fbdbdcd6dff1ffeff779d9d0160185c22125 Author: lijewski Date: Wed Nov 23 10:23:31 2011 -0800 Changed the Nrep argument to InitFromAscii() to const IntVect* and defaulted it to zero. Src/C_AMRLib/Particles.H commit 3316244707ed9562ab4abd6930ec0511f028e4da Merge: 47ea2d18b 3c66da0e3 Author: lijewski Date: Wed Nov 23 09:43:26 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 47ea2d18bd6f96ece1cf882524d9bc8ea3c5b7f8 Author: lijewski Date: Wed Nov 23 09:42:33 2011 -0800 Use -O1 instead of -O0 for gcc/g++ when DEBUG=TRUE. This still gives good debugging info but yields much faster code. Tools/C_mk/Make.defs commit 3c66da0e32d57399982176bc9e87f36b024e9671 Author: Ann Almgren Date: Wed Nov 23 09:39:43 2011 -0800 Pass Nrep through the calling sequence instead of hard-wiring it. Src/C_AMRLib/Particles.H commit b823629eeaef184ef274523ebe90783512fa51cb Author: ajnonaka Date: Wed Nov 23 08:03:37 2011 -0800 more progress - wrote parallel jobs section Docs/AdvancedTopics/AdvancedTopics.tex Docs/AdvancedTopics/hopper.run Docs/GettingStarted/GettingStarted.tex Docs/UsersGuide.tex commit adc71bb4e3d0b8a48a21a7b0154d7d3002ccd292 Author: Michael Zingale Date: Tue Nov 22 20:41:20 2011 -0500 frontmatter page numbers should be roman, main page numbers normal Docs/UsersGuide.tex commit b0499e4aa60841b14e2b34eff9d579c79f36c72f Author: Ann Almgren Date: Tue Nov 22 14:44:53 2011 -0800 Change defaults for how far the bottom solver can go -- we now limit by keeping the min in any direction to be 8 rather than by number of levels. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 commit 64104cbc58cadabe5bf3c380e700d6d74af647c5 Author: ajnonaka Date: Tue Nov 22 14:08:41 2011 -0800 new color scheme. fixed typo Docs/GettingStarted/GettingStarted.tex Docs/Introduction/Introduction.tex Docs/UsersGuide.tex commit 201d08ec73534348fcc8126306bc3cdfffdc5c15 Author: Ann Almgren Date: Tue Nov 22 11:54:05 2011 -0800 Allow for the option of replicating the domain in InitFromAsciiFile. Src/C_AMRLib/Particles.H commit 3306205caca4acdc35b6ef7d552a8017f04bf080 Author: ajnonaka Date: Tue Nov 22 11:21:25 2011 -0800 getting started section complete Docs/GettingStarted/GettingStarted.tex commit b87bf023c303265ff811464130fb394cbc00bf19 Author: ajnonaka Date: Tue Nov 22 10:25:04 2011 -0800 more progress Docs/AdvancedTopics/AdvancedTopics.tex Docs/GettingStarted/GettingStarted.tex Docs/UsersGuide.tex commit 2108f2485a5584f02e6f0446d8e3a677c7c2f4a8 Author: ajnonaka Date: Tue Nov 22 08:38:11 2011 -0800 more progress and some re-org Docs/GNUmakefile Docs/GettingStarted/GettingStarted.tex Docs/Introduction/Introduction.tex Docs/UsersGuide.tex commit dffffeb26fcb6b3326e5d0bd1b6f483f6c7ab7a6 Author: ajnonaka Date: Tue Nov 22 08:37:53 2011 -0800 new section Docs/AdvancedTopics/AdvancedTopics.tex commit 13f0096e50c3a7da0e4cb6b78a6de1df85b72093 Author: ajnonaka Date: Tue Nov 22 08:06:44 2011 -0800 turn off MPI by default Tutorials/WaveEquation_C/GNUmakefile Tutorials/WaveEquation_F/GNUmakefile commit 6964bb8db84965d3cd4e57d683afff7d6748e150 Author: ajnonaka Date: Tue Nov 22 07:19:01 2011 -0800 clean these up a bit Docs/GettingStarted/GettingStarted.tex Docs/Introduction/Introduction.tex Docs/Introduction/index_grid.odg Docs/Introduction/index_grid2.eps Tutorials/WaveEquation_C/GNUmakefile Tutorials/WaveEquation_C/Make.package Tutorials/WaveEquation_F/GNUmakefile Tutorials/WaveEquation_F/GPackage.mak commit e0a4d8b53779a07c9cd83a16728b86480a4ae427 Author: ajnonaka Date: Mon Nov 21 15:42:25 2011 -0800 starting to take shape Docs/GettingStarted/GettingStarted.tex Docs/Introduction/Introduction.tex Docs/Introduction/index_grid.odg Docs/Introduction/index_grid2.eps Docs/UsersGuide.tex Tutorials/WaveEquation_F/main.f90 commit b2908d56c1694d55b27d0a7ccaf6aa08b0cb58b2 Author: ajnonaka Date: Mon Nov 21 14:34:16 2011 -0800 new fig Docs/Introduction/AMR.eps Docs/Introduction/Introduction.tex commit 1422087b19b344e076c724de649992488601152e Merge: d4dccce42 d01ad1707 Author: ajnonaka Date: Mon Nov 21 13:40:32 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d4dccce42599d80c2e0aecea03b8d77182e3309e Author: ajnonaka Date: Mon Nov 21 13:40:12 2011 -0800 fixed to use regular old layouts and boxarrays Tutorials/WaveEquation_F/advance.f90 Tutorials/WaveEquation_F/init_data.f90 Tutorials/WaveEquation_F/main.f90 Tutorials/WaveEquation_F/write_plotfile.f90 commit d01ad1707993eec099a5987b124f85b127d8c25c Merge: cce69f934 f21d5a80b Author: lijewski Date: Mon Nov 21 12:42:11 2011 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit cce69f93485a627a459f888fe41a78fd8b111b01 Author: lijewski 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 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 Date: Mon Nov 21 09:37:20 2011 -0800 now this builds again Docs/Introduction/Introduction.tex commit aa92dcf60c2fa8930168de9696406a7e87b8c5dc Author: ajnonaka Date: Mon Nov 21 09:35:37 2011 -0800 more playing around with git - hope this works Docs/Overview/Overview.tex Docs/Overview/boxlib_directory_bw2.eps Docs/Overview/castro_scaling.eps Docs/Overview/data_loc.odg Docs/Overview/data_loc2.eps Docs/Overview/index_grid.odg Docs/Overview/index_grid2.eps Docs/Overview/lmc_scaling.eps Docs/Overview/maestro_scaling.eps commit 3fa44c6b57cce24a55016b22eecc0c864e88f949 Author: ajnonaka Date: Mon Nov 21 09:35:07 2011 -0800 more playing with git. hope this works Docs/GNUmakefile Docs/GettingStarted/GettingStarted.tex Docs/Introduction/Introduction.tex Docs/Introduction/boxlib_directory_bw2.eps Docs/Introduction/castro_scaling.eps Docs/Introduction/data_loc.odg Docs/Introduction/data_loc2.eps Docs/Introduction/index_grid.odg Docs/Introduction/index_grid2.eps Docs/Introduction/lmc_scaling.eps Docs/Introduction/maestro_scaling.eps Docs/UsersGuide.tex commit 008a0622fbef621a925468b893dbf8f0869804a8 Author: ajnonaka Date: Fri Nov 18 17:33:20 2011 -0800 lots of comments in code, wrote small section in User's guide. This could actually be released now Docs/GettingStarted/GettingStarted.tex Tutorials/WaveEquation_F/main.f90 Tutorials/WaveEquation_F/write_plotfile.f90 commit ccf821fc5fbdd87c81fd37b317bb10cb2d8feff8 Author: ajnonaka Date: Fri Nov 18 13:44:22 2011 -0800 fortran version of WaveEquation_C. fully working (I think) Tutorials/WaveEquation_F/GPackage.mak Tutorials/WaveEquation_F/advance.f90 Tutorials/WaveEquation_F/init_data.f90 Tutorials/WaveEquation_F/inputs_3d Tutorials/WaveEquation_F/main.f90 Tutorials/WaveEquation_F/write_plotfile.f90 commit 0bd82fc4b746e534fd99b606dd966fbe8f7f883a Author: ajnonaka Date: Fri Nov 18 12:31:43 2011 -0800 remove unused variables Tutorials/WaveEquation_C/init_data_2d.f90 commit 97cece503026d5714a5e65ecc6ab5adc77b1d6c3 Author: lijewski Date: Fri Nov 18 12:30:09 2011 -0800 datalog is now a Managed PArray instead of UnManaged so it gets properly cleaned up on exit. Src/C_AMRLib/Amr.cpp commit 60e49e8887c11ef51d1e178c0c5e6c78dd95df33 Merge: 7a134e64c 089f34994 Author: Weiqun Zhang Date: Fri Nov 18 12:14:32 2011 -0800 Merge branch 'hypre' commit 089f3499427013eedae833e5a97045f094e536b2 Author: Weiqun Zhang Date: Fri Nov 18 12:13:36 2011 -0800 Minor changes in input file Tests/LinearSolvers/ComparisonTest/inputs.3d commit 7a134e64cbb590fed2f7e6a23a3c99cd2bb1db59 Merge: abfa7d69a 864b3cd1e Author: Weiqun Zhang Date: Fri Nov 18 12:12:02 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit abfa7d69aec6dbe9f67cd79fc069a8f1c32e3d7f Author: Weiqun Zhang Date: Fri Nov 18 12:10:51 2011 -0800 Collect more timing info. Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp commit 864b3cd1e128f7b1ff40bf96242685197f7b8537 Merge: 533705b6e ddc99b7aa Author: lijewski Date: Fri Nov 18 10:58:18 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 533705b6e479c651d9f8a75396a80db201b4a07c Author: lijewski 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 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 Date: Fri Nov 18 10:35:32 2011 -0800 Remove a useless statement. Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp commit 1b2767e18ffa88317ea7f616901dd983f3f8508d Merge: 5c8115578 ddc99b7aa Author: Weiqun Zhang Date: Fri Nov 18 10:19:41 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 5c81155787a1ef2a5d4ab73fd70ae3524bb05cb6 Author: Weiqun Zhang Date: Fri Nov 18 10:18:55 2011 -0800 Fix typo in a variable name. Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp commit ddc99b7aaf280b82b44f45c0662d544879c00d73 Author: Weiqun Zhang Date: Fri Nov 18 10:08:27 2011 -0800 delete BndryData objects in the destructor of HypreABecLap Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp commit 4f4b88299f587d92f658fe6a32b258f9dd4d2e4d Author: lijewski Date: Fri Nov 18 09:44:56 2011 -0800 Be a little smarter about which cached copyassocs to delete when the cache hits the maximum size. The max copyassoc cache size now defaults to 25 instead of 50. Src/F_BaseLib/layout.f90 commit 55f782362f8bba46fa83860367548c9a807eb37f Author: lijewski Date: Fri Nov 18 09:21:27 2011 -0800 Added -lmpl for my machine. Tools/F_mk/GMakeMPI.mak commit 601bcdb325c712f0b3761e29121099cca262f63a Merge: 5f2a2582f 30356b5b9 Author: Michael Zingale 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 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 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: 2edeec88a ded697878 Author: ajnonaka Date: Thu Nov 17 17:51:10 2011 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 2edeec88ab457fee5a59e98ef8f186e391c20d0c Author: ajnonaka Date: Thu Nov 17 17:50:49 2011 -0800 tidy this tutorial up a biZ Tutorials/WaveEquation_C/GNUmakefile Tutorials/WaveEquation_C/inputs_2d Tutorials/WaveEquation_C/inputs_3d commit ded6978783361298ba77a8b0eace6dcf4f478689 Merge: 155d46f78 cd1fff349 Author: Weiqun Zhang 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 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 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 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: 7ec0f902d fa7cbff48 Author: ajnonaka Date: Thu Nov 17 15:29:33 2011 -0800 Merge branch 'master' of gamera.lbl.gov:/usr/local/gitroot/BoxLib commit 7ec0f902ddf6a850ad0843e5a1c9e37d394406e5 Author: ajnonaka 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 Date: Thu Nov 17 15:24:24 2011 -0800 new section Docs/GettingStarted/GettingStarted.tex commit 878cdfdfc4520f5b536c4c0a7a89e052849e4549 Author: ajnonaka Date: Thu Nov 17 15:23:02 2011 -0800 re-org Docs/GNUmakefile Docs/UsersGuide.tex commit 8d1f3ae3888833c1c420ae4e59778fb3d393fa39 Author: ajnonaka Date: Thu Nov 17 15:22:14 2011 -0800 re-org Docs/Preface/Preface.tex commit 06baaa3305175f69939b21fedceddb27c8298972 Author: ajnonaka Date: Thu Nov 17 15:21:41 2011 -0800 re-org Docs/Preface/preface.tex commit 769a4c1b27dfdc02fa15d2f63fbdca7813fb0bd8 Author: ajnonaka Date: Thu Nov 17 15:21:22 2011 -0800 re-org Docs/Overview/Overview.tex Docs/Overview/boxlib_directory_bw2.eps Docs/Overview/castro_scaling.eps Docs/Overview/data_loc.odg Docs/Overview/data_loc2.eps Docs/Overview/index_grid.odg Docs/Overview/index_grid2.eps Docs/Overview/lmc_scaling.eps Docs/Overview/maestro_scaling.eps commit 1130ea23c1b3fdf12bc708218954d12dc29a45d5 Author: ajnonaka Date: Thu Nov 17 15:20:58 2011 -0800 re-org Docs/BoxLib/Overview.tex commit 2ad363cf5c8788b56211882d18fe7feb65fb5e1f Author: ajnonaka Date: Thu Nov 17 14:52:06 2011 -0800 updates Docs/BoxLib/boxlib.tex commit fa7cbff4834b2d173a6ed8d3bd46473ab0e1808a Merge: 37b345c6f c76202d09 Author: Weiqun Zhang Date: Thu Nov 17 12:59:37 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 37b345c6f1c0830b1e4014c9d3c838d8a4b18a92 Author: Weiqun Zhang Date: Thu Nov 17 12:58:49 2011 -0800 Add timing information Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp commit c76202d098b98506d9d01a78d227a25348bfe97d Author: ajnonaka Date: Thu Nov 17 12:19:35 2011 -0800 updates Docs/BoxLib/boxlib.tex Docs/preface/preface.tex commit 006862404d90c0c5600f12d4a94c0463aa2804f7 Author: ajnonaka Date: Thu Nov 17 12:17:52 2011 -0800 scaling figs Docs/BoxLib/castro_scaling.eps Docs/BoxLib/lmc_scaling.eps Docs/BoxLib/maestro_scaling.eps commit fa649f8ce88617eaae6fc24adbfc74eefc30996d Author: ajnonaka Date: Thu Nov 17 11:06:43 2011 -0800 moved file Src/C_AMRLib/OpenSource.txt commit f1b97850e63bbbebc0930d7ebda477185f5e9e83 Author: ajnonaka Date: Thu Nov 17 11:05:45 2011 -0800 boxlib tree figure Docs/BoxLib/boxlib_directory_bw2.eps commit 55dfcaa077aee5485f29cba52e8df62288d7dfc2 Author: ajnonaka Date: Thu Nov 17 11:05:19 2011 -0800 updating doc Docs/BoxLib/boxlib.tex Docs/GNUmakefile Docs/README Docs/UsersGuide.tex Docs/preface/preface.tex commit 6671913aa8d85aa02deb15b314b70bea092e06d1 Author: ajnonaka Date: Thu Nov 17 11:04:12 2011 -0800 moved license from C_AMRLib license.txt commit e7c1330b9f52db002dbef832d9e266e57991a0f3 Author: ajnonaka Date: Thu Nov 17 10:15:31 2011 -0800 renamed UsersGuide.tex Docs/paper.tex commit 657e80439f7cac20a560187a73f03f57b0c4117e Author: ajnonaka Date: Thu Nov 17 10:11:52 2011 -0800 updating in progress... Docs/BoxLib/boxlib.tex Docs/BoxLib/maestro_directory.odg Docs/GNUmakefile Docs/UsersGuide.tex commit af4064da45d071b3d64a408dffd5317c29a9d802 Author: ajnonaka Date: Thu Nov 17 09:27:55 2011 -0800 eliminating option for building sub-directories within the main documentation. someone can add this back in if they actually see a reason for this Docs/BoxLib/GNUmakefile commit 68e80a8d6a16c2530ad915a9378cd4a4cf029543 Author: ajnonaka Date: Thu Nov 17 09:27:24 2011 -0800 git rid of these too Docs/BoxLib/mac.odg Docs/BoxLib/mac2.eps commit 82b0ed43eb89b24ff7d0aa06f140465cd3a60fcc Author: ajnonaka Date: Thu Nov 17 09:24:39 2011 -0800 get rid of this too Docs/BoxLib/maestro_directory2.eps commit f7451f0e101526236c0b87a0d9369e54ddc8255d Author: ajnonaka Date: Thu Nov 17 09:23:27 2011 -0800 no idea why this was here Z Docs/BoxLib/paper.tex commit aadd3b5703cc2bc8325627cfeaf6519f257e3c22 Author: lijewski Date: Thu Nov 17 07:44:42 2011 -0800 Just a little code rearrangement & reformatting in InitFromAscii(). Src/C_AMRLib/Particles.H commit e17396dd7fe08ceac8750f8b24c00edd67ca6382 Author: Michael Zingale Date: Thu Nov 17 09:18:38 2011 -0500 add xrb Tools/F_mk/GMakeMPI.mak commit 3d736e90138b35e6cd3f883ad68a64ef2dfeda3c Author: Michael Zingale Date: Wed Nov 16 22:25:03 2011 -0500 add defaults for the input param strings -- this is needed for CASTRO Tools/F_scripts/write_probin.py commit 022a0ec15214e5f07c3ed2adcf2f46b6bd4e9181 Merge: 5d2e7336d e560e401c Author: Ann Almgren Date: Wed Nov 16 18:16:06 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 5d2e7336d0003600f58caa6c8b197f54c053fc55 Author: Ann Almgren Date: Wed Nov 16 18:15:07 2011 -0800 In InitFromAsciiFile in Particles:H, we now read the file using at most 64 processors; this speeds things up dramatically for nprocs > 64. Src/C_AMRLib/Particles.H commit e560e401c33ab8a3b48d2107c7f4988354d53f6d Author: lijewski Date: Wed Nov 16 16:19:32 2011 -0800 A little optimization & cleanup. Src/C_AMRLib/Particles.H commit 9a6c8131fba941cc9f30ae5b81652083a35191ba Author: Ann Almgren Date: Wed Nov 16 14:41:13 2011 -0800 We were not calling post_regrid when using regrid_on_restart with finest_level = 0. Now we are. Src/C_AMRLib/Amr.cpp commit 0316344b00f4a1e148be64efe28c8c9e05a52588 Merge: bf7f4dfc4 b31073de0 Author: Weiqun Zhang Date: Wed Nov 16 10:52:57 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit bf7f4dfc4592b24910f296e8cfecfeff15caf056 Author: Weiqun Zhang Date: Wed Nov 16 10:51:26 2011 -0800 Add Hypre to the comparison test Tests/LinearSolvers/ComparisonTest/COMP_NORM_1d.f90 Tests/LinearSolvers/ComparisonTest/COMP_NORM_3d.f90 Tests/LinearSolvers/ComparisonTest/COMP_NORM_F.H Tests/LinearSolvers/ComparisonTest/GNUmakefile Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.H Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABecLap.cpp Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_3D.F Tests/LinearSolvers/ComparisonTest/HypreABecLap/HypreABec_F.H Tests/LinearSolvers/ComparisonTest/HypreABecLap/Make.package Tests/LinearSolvers/ComparisonTest/Make.package Tests/LinearSolvers/ComparisonTest/compute_norm.cpp Tests/LinearSolvers/ComparisonTest/inputs.3d Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp Tests/LinearSolvers/ComparisonTest/solve_with_hypre.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.H Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp commit b31073de0c62326bcea7ae932596e0d78dbdcbc0 Author: lijewski 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 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 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 Date: Mon Nov 14 10:30:14 2011 -0800 untrack tag files .gitignore commit 8872f0853150ce375a7219e06a7308d0fdd1cd3f Merge: d386485ff 4c6336fea Author: Weiqun Zhang Date: Mon Nov 14 10:27:38 2011 -0800 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d386485ff77954e160f2417db507acc6db81a2f0 Author: Weiqun Zhang Date: Mon Nov 14 10:23:20 2011 -0800 Add 1D case. Tests/LinearSolvers/ComparisonTest/main.cpp commit 6dec8a2c5d3d30f424905e8afb43542aa02241ef Author: Weiqun Zhang Date: Mon Nov 14 10:21:15 2011 -0800 Add 1D test. Tests/LinearSolvers/ComparisonTest/COEF_1D.F Tests/LinearSolvers/ComparisonTest/COEF_F.H Tests/LinearSolvers/ComparisonTest/COMP_NORM_1d.f90 commit eceec14553c3c61803d807f475d77cab55c7ec6f Author: Weiqun Zhang Date: Mon Nov 14 10:18:33 2011 -0800 Minor changes to make it more generic, in case the physical dome is not from 0 to 1. Tests/LinearSolvers/ComparisonTest/COEF_3D.F commit fdcb893436be392fd5a4f61d867dd99971acf179 Author: Weiqun Zhang Date: Mon Nov 14 10:15:41 2011 -0800 Add 1D case to mg_tower_print. Src/LinearSolvers/F_MG/mg.f90 commit 9a9495624d6ee89127443adcbe6b82356eb8265a Author: Weiqun Zhang Date: Mon Nov 14 10:06:43 2011 -0800 Fix the subroutines names in the calls to mgt_verify. Fix the size of arrays in a 1D routine. Src/LinearSolvers/F_MG/cc_mg_cpp.f90 commit 4c6336fea97a0e761674ea3a3e917f3af692c53d Author: Ann Almgren Date: Fri Nov 11 08:37:07 2011 -0800 1) Modify default stencil_order (sets order of boundary condition stencils) to be 2 instead of 1 when the F90 solver is called from C++. 2) Removed commented lines from stencil routine. Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 commit bb82920ab1f81b71b389c341b1a7eeadbd1784b7 Author: Ann Almgren Date: Thu Nov 10 10:27:26 2011 -0800 These are changes for how the Hypre solver is called -- from Rob Falgout. Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp Tutorials/MultiGrid_C/inputs.3d commit 3dcd64acd92fe836e30c04359d42d8218cf20b67 Author: Ann Almgren Date: Wed Nov 9 15:42:35 2011 -0800 Made the test in AmrData.cpp on whether the grids fit in the domain be an explicit test rather than a BL_ASSERT. Src/Extern/amrdata/AmrData.cpp commit 230fb283cf1ef7158fdd05876054740ea569a777 Author: lijewski Date: Mon Nov 7 19:37:16 2011 -0800 Applied patches supplied by Steffen Klemer. Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit b1211ea2ed028adfd3c97d32d2bb72a6f4684650 Author: lijewski 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 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 Date: Fri Nov 4 10:15:12 2011 -0700 1000.0 => 1000.0D0 Src/F_BaseLib/interp.f90 commit f5fbadb6baa1d499a45ae5a1bbde7de3965632d0 Merge: e5991002f 5e222f906 Author: Ann Almgren 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 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 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 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 Date: Thu Nov 3 19:44:06 2011 -0400 add comments Tools/F_scripts/findparams.py commit b4bf17e1bcd2085ba64b1cef1023166e3f804496 Author: Michael Zingale Date: Thu Nov 3 15:53:02 2011 -0400 slight prettification Tools/F_scripts/findparams.py commit 729986137648a21b5208db8d0fa936d85445764d Author: Michael Zingale Date: Wed Nov 2 14:23:06 2011 -0400 a simple script to search a list of directories for _parameters files and print the resulting list to stdout. This is used by makefiles to provide the list of dependencies for write_probin.py Tools/F_scripts/findparams.py commit 4b33ad937d49eb8747147998fad26ea33d6c53cd Author: Michael Zingale Date: Wed Nov 2 10:28:27 2011 -0400 move the write_probin.py script from the MAESTRO source to here so it can be used by other BoxLib codes (like CASTRO) Tools/F_scripts/write_probin.py commit 4583135213e2cb1ce9d85a0b79d41799995e17ab Author: Matthew Emmett Date: Sat Oct 29 09:06:56 2011 -0400 PyBoxLib: Silence some warning, minor tweaks to build system. Src/Python/GMakerules.mak Src/Python/mkpyfboxlib Src/Python/src/boxlib_numpy.c commit 4568b590dd5df866b555202cc0afa3a6a61f95a9 Author: lijewski Date: Fri Oct 28 09:33:43 2011 -0700 Moved the initialization of "ss" in s_minion_full_fill_3d() to before the OMP PARALLEL DO loop. Src/LinearSolvers/F_MG/cc_stencil.f90 commit 03380a3099bb47f4aed6cd6b6b99563937c881ae Author: lijewski Date: Fri Oct 28 08:53:21 2011 -0700 A little note explaining why this directory exists. Tests/LinearSolvers/C_CellMG/dumpi/NOTE commit 8f833d714f383cd92575e940f1b8bc00d831ea3c Author: lijewski Date: Fri Oct 28 08:44:53 2011 -0700 A little cleanup. Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.4096core Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.512core Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.64core Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.8core commit 648d13ab7df788a163f952f3b62a5e8e5f555dff Author: lijewski Date: Fri Oct 28 08:42:24 2011 -0700 Now accepts n_cells and max_grid_size. If n_cells is defined will make a domain that long in each direction and then split it up based on max_grid_size. Otherwise expects to read in a file containing the initial BoxArray. Tests/LinearSolvers/C_CellMG/main.cpp commit 2f03144be46c9d5bd45a0cbb022e6bbda00ab07e Author: lijewski Date: Thu Oct 27 14:32:51 2011 -0700 Renamed the exascale directory -> dumpi since I really used these inputs files for the dumpi test with Joe Kenny. Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.4096core Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.512core Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.64core Tests/LinearSolvers/C_CellMG/dumpi/inputs.3d.8core commit e40aec28e6bbf4c76b760e1f2c2c711837eb83b1 Author: lijewski Date: Thu Oct 27 14:30:49 2011 -0700 I meant to put these input files into the exascale directory. Tests/LinearSolvers/C_CellMG/exascale/inputs.3d.4096core Tests/LinearSolvers/C_CellMG/exascale/inputs.3d.512core Tests/LinearSolvers/C_CellMG/exascale/inputs.3d.64core Tests/LinearSolvers/C_CellMG/exascale/inputs.3d.8core commit d38d9856c7a863fae3c51f51d69357d22ad2ee95 Author: lijewski Date: Thu Oct 27 14:25:29 2011 -0700 Inputs files I used when running the MG test for dumpi that I passed to Joe Kenny. Tests/LinearSolvers/C_CellMG/inputs.3d.4096core Tests/LinearSolvers/C_CellMG/inputs.3d.512core Tests/LinearSolvers/C_CellMG/inputs.3d.64core Tests/LinearSolvers/C_CellMG/inputs.3d.8core commit 3f693e5b7912a48a7a6d09978d674321a96686a7 Merge: 86c7e69aa 73eb59861 Author: vince Date: Wed Oct 26 15:35:03 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 86c7e69aaf677defc37a081ec446d05a4786a932 Author: vince Date: Wed Oct 26 15:33:29 2011 -0700 added Amrvis namespace. updated files to use the namespace. fixed memory leak. Src/Extern/amrdata/AmrData.H Src/Extern/amrdata/AmrData.cpp Src/Extern/amrdata/AmrvisConstants.H Src/Extern/amrdata/DataServices.H Src/Extern/amrdata/DataServices.cpp Tools/C_mk/Make.mpi Tools/C_util/Convergence/DiffSameDomainRefined.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGrid2.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileNormB.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/Statistics/PltFileFluxAve.cpp Tools/C_util/Statistics/PltFileList.cpp Tools/C_util/Statistics/PltFileStat.cpp Tools/C_util/Statistics/PltFileXAve.cpp commit cb48ec6e773ceb223324a26e6cea4349442211ab Author: vince Date: Wed Oct 26 15:25:57 2011 -0700 fixed boxlib path. Tools/C_util/Convergence/GNUmakefile Tools/C_util/Statistics/GNUmakefile commit 73eb59861af4433b9054c7e8dede0d579e2ce47c Author: Ann Almgren Date: Wed Oct 26 14:38:56 2011 -0700 Fix Redistribute so that empty boxes do not generate seg faults. Src/C_AMRLib/Particles.H commit 7c569c28436be896601316de4d5ecb55c8e02657 Merge: 34d014fb1 988925f7d Author: lijewski Date: Mon Oct 24 14:01:48 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 34d014fb151b9e8ef3ae1b666c0e3ab5dca0e200 Author: lijewski Date: Mon Oct 24 14:01:01 2011 -0700 Deprecate CrseInit(FArrayBox&,...); spew a warning if used. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 35c8f0f67b4da689b2bf5fde54764f03addad11e Author: lijewski Date: Mon Oct 24 14:00:24 2011 -0700 If blocking_factor or max_grid_size are not explicitly defined, use supplied defaults. Src/C_AMRLib/Amr.cpp commit 988925f7d3ae669b1121efd2c75abc7b2f086c56 Author: Ann Almgren Date: Mon Oct 24 13:29:11 2011 -0700 Get this Tests/LinearSolvers/F_MG test code to compile again. No guarantee that it works correctly. Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/cc_single.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/nodal_single.f90 commit ee552ff4374df9eec96d0347a40f5f39bba8ee30 Author: lijewski Date: Mon Oct 24 12:23:30 2011 -0700 Closer to compiling with new GIT layout. Tests/LinearSolvers/F_MG/GNUmakefile Tests/LinearSolvers/F_MG/GPackage.mak Tests/LinearSolvers/F_MG/cc_multi.f90 Tests/LinearSolvers/F_MG/cc_single.f90 Tests/LinearSolvers/F_MG/nodal_multi.f90 Tests/LinearSolvers/F_MG/nodal_single.f90 Tests/LinearSolvers/F_MG/t_smoother.f90 Tests/LinearSolvers/F_MG/t_stencil.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 2803d5f6b4819acc0d91b75d16238b2393b9f6b9 Author: lijewski Date: Mon Oct 24 12:22:59 2011 -0700 Add t/ to ignore list. .gitignore commit acc172852ef671997dfc67609e87002b404dea81 Merge: afbce3a60 42e5f79d8 Author: lijewski Date: Mon Oct 24 10:42:50 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit afbce3a60fb36634736695e11a2620bbde6ca037 Author: lijewski Date: Mon Oct 24 10:41:41 2011 -0700 Replaced saxpy(a,ONE,b) with plus_plus(a,b) calls. Replaced saxpy(a,-ONE,b) with sub_sub(a,b) calls. Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 commit 42e5f79d8fbc4eb577980fcc54100bdd8aafeac2 Author: Ann Almgren Date: Mon Oct 24 10:20:19 2011 -0700 Fix bug in reading max_grid_size and blocking_factor arrays -- we need to read max_level+1 values, but we were only reading max_level values (when number of values > 1 in the inputs file) Src/C_AMRLib/Amr.cpp commit 1a7d04f042c3793081e06bdcfd9467b7c4f4a991 Author: lijewski Date: Fri Oct 21 15:57:38 2011 -0700 Modest speedup to simplify_doit(). Src/C_BaseLib/BoxList.cpp commit 4c30fa0db73b55d00995383ff984c9b5ec6b4db3 Author: lijewski Date: Fri Oct 21 14:44:20 2011 -0700 Got MPI working on my upgraded machine. Tools/C_mk/Make.mpi commit 8418c17e843c0fc93fa44aedc4ca2c868cc7a7f6 Merge: 2fafc8abd 110e38e50 Author: lijewski Date: Fri Oct 21 13:56:20 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 2fafc8abdee5be08b72b287638a618d988a67b12 Author: lijewski Date: Fri Oct 21 13:55:43 2011 -0700 Added .gitignore that ignores d f o directories as well as *o *a and a few other things. .gitignore commit 110e38e50d3c9599b83b70bc3100e16edae38c6f Author: Ann Almgren Date: Fri Oct 21 13:54:16 2011 -0700 Add the line p_n_comp[i].simplify(); inside the grid_places() routine. This reduces the number of grids dramatically when doing regridding with low lbase and high finest_level. Saves a factor of over 100 in test with lbase=2 and finest_level=7. Src/C_AMRLib/Amr.cpp commit b3906daa5ccf835f882fd0651ac35a881b1e7a94 Author: lijewski Date: Fri Oct 21 13:47:26 2011 -0700 Use BoxList::catenate() instead of BoxList::join() when possible. The former is more memory efficient. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.cpp Src/Extern/amrdata/AmrData.cpp commit 6b4e094845656d5aadf5216e4621822efea65abb Author: Matthew Emmett Date: Thu Oct 20 15:35:40 2011 -0400 PyBoxLib: Add ml_layout wrapper. Src/Python/GMakerules.mak Src/Python/pyboxlib/__init__.py Src/Python/pyboxlib/layout.py Src/Python/src/blobjects.py Src/Python/src/fboxlib.f90 commit d95fd5c7e0af6c32b01c387e264f5d06c85a0840 Author: Matthew Emmett Date: Thu Oct 20 14:26:07 2011 -0400 PyBoxLib: Change makefile structure to mimic BoxLib, remove extraneous files. Src/Python/GMakerules.mak Src/Python/GPackage.mak Src/Python/Makefile Src/Python/mkpyfboxlib Src/Python/src/blobjects.f90 Src/Python/src/boxlib_numpy.c Src/Python/src/fboxlib.pyf Src/Python/src/pyfboxlib.m4 Src/Python/src/pyfboxlib.pyf commit bcfb7b58576bfd735e6ea02a5f570a9b72fd445e Author: Matthew Emmett Date: Thu Oct 20 11:36:12 2011 -0400 PyBoxLib: Add Src/Python. Src/Python/Makefile Src/Python/README Src/Python/pyboxlib/__init__.py Src/Python/pyboxlib/base.py Src/Python/pyboxlib/boxarray.py Src/Python/pyboxlib/fab.py Src/Python/pyboxlib/layout.py Src/Python/pyboxlib/multifab.py Src/Python/src/blobjects.f90 Src/Python/src/blobjects.py Src/Python/src/boxlib_numpy.c Src/Python/src/boxlib_numpy.f90 Src/Python/src/fboxlib.f90 Src/Python/src/fboxlib.pyf Src/Python/src/pyfboxlib.m4 Src/Python/src/pyfboxlib.pyf Src/Python/test.py commit 5a34bbe8b48e6fac6d1f79a80d6277b2c0e75a54 Author: Ann Almgren Date: Wed Oct 19 19:27:05 2011 -0700 Add options for Zarija's machine, stribog. Tools/C_mk/Make.mpi commit a2fe501abf74b4a06a99a0b1b8009e55e1320c65 Author: Weiqun Zhang Date: Tue Oct 18 11:28:19 2011 -0700 Add a space to the ouput message Tools/C_util/regtests/testnew.py commit 537419220029d0d441484ae6e18943f96dcaf67c Author: Ann Almgren Date: Mon Oct 17 14:20:41 2011 -0700 This has latest greatest InitCosmo from Jan Frederik. Src/C_AMRLib/Particles.H commit 35bb875236768e7dc6ee7ad79d84fae9a8117cca Author: gilet Date: Mon Oct 17 12:27:53 2011 -0700 added -lmpl for orga Tools/F_mk/GMakeMPI.mak commit f5318cd38a6c967623e607b37423b5de4727e0a8 Author: Ryan Orvedahl Date: Sat Oct 15 17:59:29 2011 -0400 add support for sn.astro.sunysb.edu Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit d44483341d681b9d4a2afdcf8a87f1b8c4eab750 Merge: f6a4cda91 16462549d Author: Michael Zingale 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 Date: Fri Oct 14 15:12:06 2011 -0400 add MPI stuff for sn Tools/F_mk/GMakeMPI.mak commit 16462549dc5c0c3255510d5a69de51e175dc8df4 Author: Ann Almgren Date: Fri Oct 14 12:11:54 2011 -0700 Change int to long in i = 0 to truesize in clear (already did this in define). Src/C_BaseLib/BaseFab.H commit e3960aa58fbc39a03d46af4e2550f97215a9c4fc Author: Ann Almgren Date: Fri Oct 14 11:35:09 2011 -0700 Replace int by long in BaseFab::define so that it can handle very large (e.g, 1024^3) boxes. Src/C_BaseLib/BaseFab.H commit 8571c67fd2f6e3f2fd2c68e16a039af9356471a8 Author: Ann Almgren Date: Fri Oct 14 11:34:39 2011 -0700 Fix mpi for manda. Tools/C_mk/Make.mpi commit 7b0fa08efc81d39d9bad37b0da8ca5b761119ad2 Author: lijewski Date: Thu Oct 13 14:26:03 2011 -0700 Un-inlined some stuff that didn't need to be inlined. Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/UseCount.H Src/C_BaseLib/UseCount.cpp commit 207606d4c205a8d0cc1f9f7ed45860fd4b3a89a9 Author: lijewski Date: Thu Oct 13 13:59:03 2011 -0700 Merged the std::stable_sort() and std::reverse() into a static function Sort(). Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit aed2c69cfe2ca8b3fe2e2d72ddf1c79789573bdb Author: lijewski Date: Thu Oct 13 12:59:39 2011 -0700 More protected => private for some data members. Un-inlined some stuff. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/Orientation.H Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit aed3a358951146e68b40a9f21c08baaa18f69353 Merge: 200a8b17e 2c38d0867 Author: lijewski Date: Wed Oct 12 13:54:36 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 200a8b17ec39e705a3c697f5b7f485134f91ca4a Author: lijewski Date: Wed Oct 12 13:53:40 2011 -0700 Made as much "protected" data "private" as possible. Removed unneeded "virtual" on some member functions. Src/C_AMRLib/AuxBoundaryData.H Src/C_AMRLib/BCRec.H Src/C_AMRLib/Derive.H Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/StateData.H Src/C_AMRLib/StateDescriptor.H Src/C_BaseLib/Box.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/Orientation.H Src/C_BaseLib/PArray.H Src/C_BaseLib/ParmParse.H Src/C_BaseLib/RealBox.H Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/FabSet.H Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/MultiGrid.H commit 2c38d08674fdc983d9493d00c70c96bb97b56722 Author: lijewski Date: Tue Oct 11 15:08:30 2011 -0700 Use -O3 instead of -Ofast with PathScale to work-around current 4.0.9 bug in IPA on hopper. Tools/C_mk/Make.Linux commit 9199eccc7efec74c64f1b95a047ccaefd2b44aa9 Author: lijewski Date: Tue Oct 11 15:01:01 2011 -0700 -Ofast no longer works on latest PathScale on hopper. Use -O3 instead. Tools/F_mk/comps/Linux_pathscale.mak commit b8851cc9682eebaeb22e8466350b013ab625ce11 Author: lijewski Date: Mon Oct 10 13:16:59 2011 -0700 Changes to work around PathScale bug. PathScale has problems with file scope C++ standard strings in MPI programs. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Tools/C_mk/Make.Linux commit ecfcf1e544ed3ad8acdca615f7b3b214ab3d535c Merge: 0ce370416 7c22d5a0c Author: Marc Day Date: Fri Oct 7 16:34:47 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib Conflicts: Tools/C_mk/Make.defs commit 0ce370416a3dda399d6bcb5b628faccaf1c45005 Author: Marc Day Date: Fri Oct 7 16:26:22 2011 -0700 update for ascem with sub-comm in fBox BoxLib_Version.txt Tools/C_scripts/gen_release_tarball.txt commit 7c22d5a0c6c6e68069650861c48bdb59e9d8e215 Author: lijewski Date: Fri Oct 7 15:59:15 2011 -0700 std::snprintf() => snprintf() to get to compile with PGI. Src/C_BaseLib/ParallelDescriptor.cpp commit 44ff6a3c4815f4511add42f354631eb6d3dbbc5b Author: lijewski Date: Fri Oct 7 15:12:55 2011 -0700 Now always calls the mgt_init() that takes a single argument. We want to support George Pau who needs the ability to pass in an MPI_Communicator that is not MPI_COMM_WORLD. Added Finalize() that gets called on BoxLib::Finalize() which'll reset initialized to false. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit da9a293b5800a1f870b406aca9c5128620d14e3d Author: lijewski Date: Fri Oct 7 15:10:02 2011 -0700 mgt_init() now takes a single integer argument "comm". Removed the saved logical variable that only called parallel_initialize() on the first call. Instead MGT_Solver only calls mgt_init() when it needs to. Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 3d907e46e81d9121e9296effbdf26a840fd91abf Author: lijewski Date: Fri Oct 7 15:06:21 2011 -0700 parallel_initialize() now takes an optional integer "comm" argument. If it's present we use it instead of MPI_COMM_WORLD as the MPI communicator. Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit e32a61ceb6c82272573308b8dd484a1566e83c20 Author: Michael Zingale Date: Fri Oct 7 15:10:57 2011 -0400 add the compilation and execution commands to the web output Tools/C_util/regtests/testnew.py commit 250a9d19d46ae3e77e6f2b183beede879917ec1e Author: lijewski Date: Thu Oct 6 14:38:59 2011 -0700 More tweaking on removeOverlap(). There's got to be a better way to do this but I don't see it just yet. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 407404a044029c0b360b9d8bbbd22ea5e0397648 Author: lijewski Date: Thu Oct 6 12:40:52 2011 -0700 Instead of just calling std::list::clear() our version of clear() employs the swap() trick to really get rid of any extra memory hanging around due to stray Boxes. Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit c06be835b829a81d4aae78ae6194c6997c3dc6fb Author: lijewski Date: Thu Oct 6 12:30:18 2011 -0700 removeOverlap() no longer returns a BoxList. Instead it's a void function. We now though fix up the resultant BoxArray so it doesn't have holes. We then can use the boxList() function to get a good non-overlapping list of boxes. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.cpp commit 3e161ca704c5da15ff0eb7da7969526065934a9b Author: lijewski Date: Thu Oct 6 11:06:58 2011 -0700 This has most of the previous tweeks put back in. What I broke was something in removeOverlap() which I'm still thinking about. It's weird. Src/C_BaseLib/BoxArray.cpp commit 3b67bea29d3e7c86b1acc296763aa321f4784272 Author: lijewski Date: Thu Oct 6 10:34:33 2011 -0700 I broke BoxArray somehow. I'm reverting to this earlier copy from Parallel/BoxLib till I figure out what I did. Src/C_BaseLib/BoxArray.cpp commit 92fdbc84a1883ecaa28d4de00f400e2837042b76 Author: Ann Almgren Date: Wed Oct 5 20:03:05 2011 -0700 Changes to InitCosmo in Particles.H only. Src/C_AMRLib/Particles.H commit 686858aefbd4a8c6365aef956710b74d99e94821 Author: lijewski 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 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 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 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 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 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 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 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 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 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 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 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 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: 39537a808 f6ab0d901 Author: Weiqun Zhang Date: Fri Sep 30 11:43:25 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 39537a80834f6a1eaf6c42efc1fd50b493299d6e Author: Weiqun Zhang Date: Fri Sep 30 11:35:12 2011 -0700 If the link files are absolute path, the old version would fail. This is now fixed. The link files can now be either absolute path or just basename. The old version used gmake. But on some systems the GNU amke is just "make". In the new version, MAKE is a variable that can be changed in the input file for the script. Also, numMakeJobs is added so that several make jobs can run simultaneously. Tools/C_util/regtests/testnew.py commit f6ab0d9014c9b4fa430c32de33c5b5f63d131498 Author: lijewski Date: Thu Sep 29 16:08:02 2011 -0700 Quiet compiler warning. Src/C_AMRLib/DatasetClient.cpp commit 3276cf0c8be88ac08522ca79f5f81546af8e75e5 Author: lijewski Date: Thu Sep 29 13:42:06 2011 -0700 Removed all the wrappergen stuff. This is a third-party library for profiling MPI calls. The only reason it was in our original CVS repository was because Chuck made some modifications to it. Tools/C_util/wrappergen/Makefile Tools/C_util/wrappergen/PROTO Tools/C_util/wrappergen/README Tools/C_util/wrappergen/args.c Tools/C_util/wrappergen/args.h Tools/C_util/wrappergen/doc.c Tools/C_util/wrappergen/doc.h Tools/C_util/wrappergen/driver.c Tools/C_util/wrappergen/expandingList.h Tools/C_util/wrappergen/mpifn Tools/C_util/wrappergen/petsccfg.h Tools/C_util/wrappergen/prof.c Tools/C_util/wrappergen/prof_wrapper.c Tools/C_util/wrappergen/readproto.c Tools/C_util/wrappergen/sample.c Tools/C_util/wrappergen/sample.w Tools/C_util/wrappergen/system.c Tools/C_util/wrappergen/system.h Tools/C_util/wrappergen/tools.h Tools/C_util/wrappergen/wrappergen.c Tools/C_util/wrappergen/wrappergen.h Tools/C_util/wrappergen/write_proto.c commit 171f6444f686e6ff269ff01ff18866aa6e7ecdd2 Author: lijewski Date: Thu Sep 29 09:17:09 2011 -0700 sprintf() => snprintf() This allows us to specify the size of the buffer into which we're writing so that we don't overflow the buffer & write arbitrary memory. We also can tell when the buffer when the buffer is too small to contain everything we wanted to write and abort if necessary. Src/C_AMRLib/DatasetClient.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Utility.cpp Src/Extern/amrdata/AmrData.cpp Src/Extern/amrdata/DataServices.cpp Src/F_BaseLib/fabio_c.c commit d971268f105b47536662e1b8d9bbaa86e356c342 Author: lijewski Date: Wed Sep 28 15:48:15 2011 -0700 Oops. Forgot a semi-colon. Src/C_AMRLib/Particles.H commit 0775ec172e43c6647c6697939f59172b3cdf4a5f Author: lijewski Date: Wed Sep 28 15:40:36 2011 -0700 Changed as many sprintf() calls to BoxLib::Concatenate() as possible. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Particles.H Src/C_AMRLib/StationData.cpp Src/C_BaseLib/VisMF.cpp Src/C_BoundaryLib/BndryRegister.cpp Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/Statistics/PltFileFluxAve.cpp Tools/C_util/Statistics/PltFileList.cpp Tools/C_util/Statistics/PltFileStat.cpp Tools/C_util/Statistics/PltFileXAve.cpp Tools/C_util/WritePlotFile.cpp Tutorials/MultiGrid_C/writePlotFile.cpp Tutorials/WaveEquation_C/writePlotFile.cpp commit a5f3345328158031d47fe4f7086086c36e4b97eb Author: lijewski Date: Wed Sep 28 15:40:11 2011 -0700 Cut at new GNUmakefile for GIT. Tools/C_util/Statistics/GNUmakefile commit 99413d31bb6c2830dab7b204ec7a9aae859af037 Author: lijewski Date: Wed Sep 28 15:36:08 2011 -0700 Cut at working GNUmakefile for new GIT repositories. Will needs to be fixed a tad once AmrData stuff is in it's correct place. Tools/C_util/Convergence/GNUmakefile commit b2a1bb8d2ca590317c02b5454d391223074abc72 Author: lijewski Date: Wed Sep 28 15:10:18 2011 -0700 Change [fF]DEBF from -O0 => -O1 for gfortran. Some version of gfortran get internal compiler error with -O0 on some hgproj code. Tools/C_mk/Make.defs commit 3a91b0e2266d899b8278c741fb0142e96b4834e0 Author: lijewski Date: Wed Sep 28 14:56:14 2011 -0700 Removed some unused variables. Tutorials/WaveEquation_C/main.cpp commit 090fe46083ee54d0a5de9b2d7a9ce9937197e490 Author: lijewski Date: Wed Sep 28 09:16:56 2011 -0700 -O -> -O0 when debugging. Will produce slower but "truer" code. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit 7d09ccf29d04579abeebd067f17eb86ece9f3f20 Author: Weiqun Zhang Date: Tue Sep 27 16:15:24 2011 -0700 BoxLib_F with Dirichlet boundary works for both level solve and composite solve. Periodic and Neumann boundaries do not work yet. Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp commit a62ff46c318be5d6b2871db98edc50f0f2d7d3b2 Author: Weiqun Zhang Date: Tue Sep 27 16:12:01 2011 -0700 MGT_Solver::set_vis_coefficients(PArray& aa, Array >& bb, const Real& beta, Array< Array >& xa, Array< Array >& xb, int index_order=0); Add an optional argument index_order. If index_order == 0, bb[dim][level] else, bb[level][dim] The second way is consistent with other set_?_coefficients. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 27563b647757f05150ca53509cee36671b4f1f94 Author: Weiqun Zhang Date: Tue Sep 27 14:23:50 2011 -0700 add routines for computing norms to makefile Tests/LinearSolvers/ComparisonTest/Make.package Tests/LinearSolvers/ComparisonTest/main.cpp commit 6b6b106f0ddbcb57745ccb02952256cb1c8df797 Merge: 3c0659975 bc9613a7c Author: Weiqun Zhang Date: Tue Sep 27 14:21:39 2011 -0700 Merge branch 'boxarray' commit bc9613a7c6b31b4770bb78573c83a74064b61d16 Author: Weiqun Zhang Date: Tue Sep 27 14:20:52 2011 -0700 compute 2-norm and max-norm Tests/LinearSolvers/ComparisonTest/COMP_NORM_3d.f90 Tests/LinearSolvers/ComparisonTest/COMP_NORM_F.H Tests/LinearSolvers/ComparisonTest/compute_norm.cpp commit 3c06599753845035bf17942ed4fa4e84a4693c68 Merge: 0c00d87b4 af836b0a4 Author: lijewski Date: Tue Sep 27 14:02:34 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 0c00d87b48c4758a30569954448e768c9f1fb405 Author: lijewski Date: Tue Sep 27 14:01:29 2011 -0700 Removed a couple gfortran warning flags on the f90 debug line that weren't supported by gfortran version 4.3.3 or anything earlier. Tools/C_mk/Make.defs commit 733901080ac93bb9d83716ecc46d20dc795a9cb8 Author: lijewski Date: Tue Sep 27 13:58:53 2011 -0700 Removed some new/deletes and replaced with Array operations. Src/C_AMRLib/TagBox.cpp commit be03abf3dda7dd16595e976faf12fa9e6ac65ca1 Author: lijewski Date: Tue Sep 27 13:58:24 2011 -0700 Disabled the copy assignment operator and copy constructor. We don't want folks copying BaseFabs. Src/C_BaseLib/BaseFab.H commit af836b0a489897f67f5c89584f14e6ee99813b6b Merge: f31ffcf0a dc23a56a4 Author: Weiqun Zhang Date: Tue Sep 27 12:49:41 2011 -0700 Merge branch 'master' into boxarray commit f31ffcf0ac3147899392a51f3393aa3e54d5df5a Author: Weiqun Zhang Date: Tue Sep 27 12:48:23 2011 -0700 a file containing calls to BoxLib_F Tests/LinearSolvers/ComparisonTest/solve_with_F90.cpp commit dc23a56a4d009898dff0af54b5c2be1bf8db2a86 Merge: f74218209 b13e4c3ed Author: Weiqun Zhang Date: Tue Sep 27 12:37:10 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f742182099fe785f7f1aa1201f37596041ec7839 Author: Weiqun Zhang Date: Tue Sep 27 12:36:50 2011 -0700 write plotfile Tutorials/MultiGrid_C/writePlotFile.H Tutorials/MultiGrid_C/writePlotFile.cpp commit 3118d92daa0bfba6d527a0d54b6398b8f50d2e58 Author: Weiqun Zhang Date: Tue Sep 27 10:35:16 2011 -0700 Fix a bug: phys_bc was created by new BCRec, but was deleted. Tutorials/MultiGrid_C/main.cpp commit b13e4c3eddd17416ae3b7311184b5c2fce706443 Merge: bf0450f99 c206b9315 Author: Ann Almgren 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 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 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: 911058ab0 5fa07424f Author: Weiqun Zhang Date: Mon Sep 26 15:55:59 2011 -0700 Merge branch 'master' into boxarray commit 911058ab0281d101ad182e3f0f5a424d66bf219c Author: Weiqun Zhang Date: Mon Sep 26 15:54:59 2011 -0700 BoxLib_F runs. But not sure whether or not the boundaries are set correctly. Tests/LinearSolvers/ComparisonTest/COEF_3D.F Tests/LinearSolvers/ComparisonTest/COEF_F.H Tests/LinearSolvers/ComparisonTest/GNUmakefile Tests/LinearSolvers/ComparisonTest/Make.package Tests/LinearSolvers/ComparisonTest/inputs.3d Tests/LinearSolvers/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/writePlotFile.H Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp commit 5fa07424f076b657e186014221cbc84c0fa8a4b4 Author: lijewski Date: Mon Sep 26 13:47:06 2011 -0700 Changed the way Arenas are allocated. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/FabArray.H Tests/LinearSolvers/C_NodalMG/proj.cpp commit 3af755e10172e50145c71bf03a2087aa35090c50 Author: Weiqun Zhang Date: Fri Sep 23 18:28:37 2011 -0700 Started the linear solver comparison test The setup of multilevel grids, coefficients, rhs and exact solutions are done. It can also write a plotfile. Tests/LinearSolvers/ComparisonTest/writePlotFile.H Tests/LinearSolvers/ComparisonTest/writePlotFile.cpp commit 89082af8d0737c0a7b3708ac1a3eac331d71c26f Merge: ce2215486 84b153aad Author: Ann Almgren Date: Fri Sep 23 10:15:21 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ce22154867b7cacf0f7596b7867df227568b9a68 Author: Ann Almgren Date: Fri Sep 23 10:14:56 2011 -0700 We now pass vel_fac into Particles::InitCosmo() instead of computing it inside. Src/C_AMRLib/Particles.H commit 84b153aadbcf819c5af970512b735a743232bb8b Author: Michael Zingale Date: Fri Sep 23 12:09:08 2011 -0400 add support for link files (link1File, link2File, link3File). These are linked into the run directory instead of copied. Tools/C_util/regtests/testnew.py commit dd1159cf6982401e59c56a8ffbcebe265969ae3a Author: Michael Zingale Date: Fri Sep 23 10:43:06 2011 -0400 do a symlink for helm_table.dat instead of copying it Tools/C_util/regtests/testnew.py commit 0ba92b526653a6d1498d0037197b147729bd80fb Author: Michael Zingale 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 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 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 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 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 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: c9129be8f 481abb529 Author: Michael Zingale 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 Date: Thu Sep 22 15:20:00 2011 -0400 add more checks Tools/C_util/regtests/testnew.py commit 481abb5297a5f40fc6ee84a2eaa2bfd5391658f2 Author: Weiqun Zhang Date: Wed Sep 21 16:41:36 2011 -0700 Give warning when both of the following are true: ifndef CG_USE_OLD_CONVERGENCE_CRITERIA mg. use_Anorm_for_convergence = 0. This appears to be a bad combination at least for the hard test in MG tutorial. Src/LinearSolvers/C_CellMG/MultiGrid.cpp Tutorials/MultiGrid_C/GNUmakefile commit 6b6fae2d8871b42df6e0bdbd75bb71010cdd0e0f Merge: a14094a20 1c450406f Author: Weiqun Zhang Date: Wed Sep 21 15:56:53 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit a14094a20e02573dad55dfa809d3f159c8df2fe8 Author: Weiqun Zhang Date: Wed Sep 21 15:53:40 2011 -0700 It seems too verbose that all the grids are printed out when mg.verbose>2. The threshold is now >4. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 7986da139a58e7f5fef6a868cc836ae90fa7243e Author: Weiqun Zhang 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 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 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: 5412bd75b ee979881f Author: Aleks Donev 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 Date: Wed Sep 21 16:28:33 2011 -0400 Added Courant systems to Makefile Tools/F_mk/GMakeMPI.mak commit ee979881f4b91e0c1d1d48f6305f75b448f3036f Author: Michael Zingale Date: Wed Sep 21 12:22:57 2011 -0400 add support for BOXLIB_HOME. Finish cleaning things up. Tools/C_util/regtests/testnew.py commit a03fc3fa757170c3d071e8b29f8621e9761ad17b Author: Michael Zingale Date: Wed Sep 21 12:00:08 2011 -0400 add BOXLIB_DIR to the list of information held by this module. Tools/F_scripts/make_build_info commit 5256c0efea8efc4c6220d90034a215abf48999d6 Author: Weiqun Zhang Date: Tue Sep 20 11:08:18 2011 -0700 Added SMG solver for Hypre Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp Tutorials/MultiGrid_C/inputs.3d commit 95473e2fcfcf26e63d44fcd9c52e5b093ed57cfb Merge: 27393a8a4 446a5dbfa Author: Marc Day Date: Mon Sep 19 17:19:18 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 27393a8a43599e1ea363cb764e0338dcdc6519cb Author: Marc Day Date: Mon Sep 19 17:18:55 2011 -0700 Replace Wall with everything but unused-dummy-arguments Tools/C_mk/Make.defs commit 179de187e7c91d3c984ffe8705c5fc4e72e68576 Author: Weiqun Zhang Date: Mon Sep 19 15:18:40 2011 -0700 Two parameters are introduced in the setup of problems. We now can run test problems with variable diffusion coefficient. Tutorials/MultiGrid_C/COEF_3D.F Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/RHS_3D.F Tutorials/MultiGrid_C/RHS_F.H Tutorials/MultiGrid_C/inputs.3d Tutorials/MultiGrid_C/main.cpp commit 446a5dbfaeed6eb6b7cdf31bf535d5648a62cf88 Merge: 4bb5994a2 cb8b4bb81 Author: Ann Almgren Date: Mon Sep 19 13:50:40 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 4bb5994a294d8b72b09b418b5004e387303a076f Author: Ann Almgren Date: Mon Sep 19 13:49:30 2011 -0700 Tests/StencilOrder: Add this new test program (with accompanying README file) to demonstrate the difference in timings that we see by simply modifying the ordering of the indices in multigrid stencils, from ss(i,j,k,n) to ss(n,i,j,k) demonstrates a roughly factor 5 speedup for this example stencil with 21 entries. Tests/StencilOrder/README Tests/StencilOrder/program.f90 commit cb8b4bb81fadb4c58299486e7aff7bf6d2ef7e35 Merge: 7f9dd74f8 d959e2c94 Author: lijewski Date: Mon Sep 19 13:07:46 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 7f9dd74f852a11cdfefae5cb6e371eafb2238ff8 Author: lijewski Date: Mon Sep 19 13:07:14 2011 -0700 Some endian test stuff for Darwin from Chris Malone. Tools/F_mk/GMakedefs.mak commit d959e2c9468a6ddf544563c719198229b33384b4 Merge: 9826b5873 fc456301f Author: Michael Zingale 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 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 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 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 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 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: bd7f979dd 8a5c81305 Author: Weiqun Zhang Date: Fri Sep 16 16:19:56 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit bd7f979dd84f5393fede8f92c84f12c236df5cc5 Author: Weiqun Zhang Date: Fri Sep 16 16:12:54 2011 -0700 fix a problem in inputs Tutorials/MultiGrid_C/inputs.3d commit 8a5c813050fc481c50e4d78a6c54b39db706c19a Author: Ann Almgren Date: Fri Sep 16 15:38:59 2011 -0700 Add a flag "use_Anorm_for_convergence" that allows us to control whether or not we use the Anorm in the convergence test. This allows us to test convergence against the F90 solver and the Hypre solver. Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 3771253dae9c1537a2aff7d02bb365b1083c8317 Author: Ann Almgren Date: Fri Sep 16 15:26:15 2011 -0700 Fix test for print statements regarding convergence Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit b866af072ceef9b4033a98e239a0a5edb53a08db Author: Ann Almgren Date: Fri Sep 16 15:04:57 2011 -0700 Clean up print statements for convergence test. Src/LinearSolvers/F_MG/ml_cc.f90 commit c992133785f25a9a6cf4ddd016c82537aa01a163 Author: Ann Almgren Date: Fri Sep 16 14:33:24 2011 -0700 Add additional output (if verbose > 0) so we know what convergence criterion was used. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 2f9a7a5d3f14209d15f5e566f9b454667d0a62db Author: Ann Almgren Date: Fri Sep 16 14:31:23 2011 -0700 GNUmakefile: Add much more commentary about how to set variables so this will compile. Tutorials/MultiGrid_C/GNUmakefile commit 904298f01c8a13af7670a17bfb8a810208be720e Author: Weiqun Zhang Date: Fri Sep 16 13:13:06 2011 -0700 pass high-order boundary parameter to Fortran Tutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F commit 2cfd0849953447c836351af2906d8b3d851b2f16 Author: Weiqun Zhang Date: Fri Sep 16 12:04:40 2011 -0700 make the stencil index in hypre consistent with what returned by BoxLib bndlib Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp Tutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F Tutorials/MultiGrid_C/HypreABecLap/HypreABec_F.H commit 57bb6e98e68b969c5836f0ffcf8e328da719a18d Merge: ef8caaee1 2c203da57 Author: Weiqun Zhang Date: Fri Sep 16 10:45:48 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ef8caaee1209bb26c7c2ecd2b9fb61053d7a97bc Author: Weiqun Zhang Date: Fri Sep 16 10:45:40 2011 -0700 minor cleanup Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp commit db8bff7285e0f202952a308fd6b2998cd32fb510 Author: Weiqun Zhang 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 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 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 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 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: f37c1548a 402c4507d Author: Weiqun Zhang Date: Thu Sep 15 17:35:53 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib Conflicts: Tutorials/MultiGrid_C/main.cpp commit f37c1548ac30085748d55bcd39d17e43f14c93f5 Author: Weiqun Zhang Date: Thu Sep 15 15:55:46 2011 -0700 Make bc_type and solver_type enum type rather than string type. Using string is more error-prone due to typos in the string. Move to the part that sets boundaries to a function. Bot BoxLib_C and Hypre use it. Tutorials/MultiGrid_C/main.cpp commit 402c4507d933431fac2bcd665e1358845899bef5 Merge: 1fd6890c3 ecc71f63e Author: Ann Almgren 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 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 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 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 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 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: 0fca70a5b 21ab65eac Author: Marc Day Date: Thu Sep 15 08:46:57 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 0fca70a5b852b6c620952ef8eaf3b6c00987a5d4 Author: Marc Day Date: Thu Sep 15 08:46:44 2011 -0700 Clean up screen dump during build using C_mk stuff: if the GNUmakefile (or make cmd line) contains VERBOSE=FALSE or VERBOSE=OFF, the build line will not be echoed to the screen. Added a line to simply say ...Building XXX... , commented out strip72 warning text, removed warning about unused dummy arguments in gfortran. Comment out silly echo SUCCESS, since it reports success regardless - tests based on the presence of this string should be restructured. Tools/C_mk/Make.defs Tools/C_mk/Make.rules Tools/C_scripts/strip72 commit 21ab65eacd01206899e8be2512ec23c3dce655c3 Author: lijewski Date: Thu Sep 15 08:44:40 2011 -0700 A little simplification; make the swap() call for clearing memory one liners. Src/C_AMRLib/Particles.H commit 6cc3450aff163bcae028488be5b6a18dd0a07a78 Author: Ann Almgren Date: Wed Sep 14 21:28:46 2011 -0700 1) Fix boundary conditions for BoxLib_C solver in Tutorials/Multigrid_C 2) Change multifab_remote --> remote in all places for consistency Src/LinearSolvers/F_MG/cc_applyop.f90 Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/coarsen_coeffs.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_newu.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 Tutorials/MultiGrid_C/main.cpp commit ca596ac233c710651f857ff41e328fde28e28ab9 Merge: 064e8540f e5d1f1ef2 Author: Weiqun Zhang Date: Wed Sep 14 18:20:48 2011 -0700 merge commit 064e8540f8a9071d1641485c11a542583af09ab5 Author: Weiqun Zhang Date: Wed Sep 14 18:12:03 2011 -0700 hypre A matrix is no longer symmetric Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp Tutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F Tutorials/MultiGrid_C/inputs.3d Tutorials/MultiGrid_C/main.cpp commit e5d1f1ef29f8e083f8f35b51119773e87d5db0a5 Author: lijewski Date: Wed Sep 14 17:11:11 2011 -0700 More mods from Chris Malone. Tools/F_mk/GMakedefs.mak commit b303351e9b19db103b2cbb9a6aeca0a0e17d86f4 Author: lijewski Date: Wed Sep 14 16:51:48 2011 -0700 Added Darwin_intel.mak from Chris Malone. Tools/F_mk/comps/Darwin_intel.mak commit 54caef468b819921d73cbb8ab41534ee7994a68a Author: Ann Almgren Date: Wed Sep 14 14:19:49 2011 -0700 Add comments about verbosity flags. Tutorials/MultiGrid_C/inputs.3d commit e251f094cadddc0c34becdfb6e6651b99a95d7c6 Merge: 55af7b122 9cf4e460a Author: Ann Almgren Date: Wed Sep 14 13:29:35 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 9cf4e460a1bcbe76be002aef78d640d3b3c22408 Author: Weiqun Zhang Date: Wed Sep 14 12:51:39 2011 -0700 fix default BOXLIB_HOME Tutorials/MultiGrid_C/GNUmakefile commit 899f5b6917608215cd010e06254bbd7bf827150d Author: Weiqun Zhang Date: Wed Sep 14 12:08:01 2011 -0700 clean up Tutorials/MultiGrid_C/COEF_3D.F Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp Tutorials/MultiGrid_C/inputs.3d Tutorials/MultiGrid_C/main.cpp commit e9e21416bc4ca8e54c79ccb6294422071023af50 Author: Weiqun Zhang Date: Wed Sep 14 10:19:25 2011 -0700 add the iostream and iomanip headers to HypreABecLap Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H commit 59b01e5a147a01c47e62d12bcc827d876e78fe73 Author: Weiqun Zhang Date: Wed Sep 14 10:14:54 2011 -0700 Add USE_HYPRE to GNUmakefile so that the code can be compiled without hypre. Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/main.cpp commit 55af7b1221be96e984d2aa37a62de9eb0361cd1e Merge: 2842e2cde d7f4e737d Author: Ann Almgren Date: Wed Sep 14 08:29:26 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d7f4e737de464fba0b0e169d9268c39d64c921a6 Author: Weiqun Zhang Date: Wed Sep 14 06:18:21 2011 -0700 rename solvers to BoxLib_C and BoxLib_F Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/inputs.3d Tutorials/MultiGrid_C/main.cpp commit b384a47ac9d3f362b15b045b478f41cd74bfb8e4 Merge: d0d2fcb33 dbd51e3ba Author: Weiqun Zhang Date: Wed Sep 14 05:38:55 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d0d2fcb338e4c6f9d94d1a1174770588d1d2a59d Author: Weiqun Zhang Date: Wed Sep 14 05:38:15 2011 -0700 check in hypre driver Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.H Tutorials/MultiGrid_C/HypreABecLap/HypreABecLap.cpp Tutorials/MultiGrid_C/HypreABecLap/HypreABec_3D.F Tutorials/MultiGrid_C/HypreABecLap/HypreABec_F.H Tutorials/MultiGrid_C/HypreABecLap/Make.package commit 2842e2cdec5d82c12418057e5e9cc4fc1bc7f069 Merge: 433581d40 dbd51e3ba Author: Ann Almgren Date: Tue Sep 13 22:08:12 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e0e6504fe7aad096d52907c2771fa62a43b63916 Author: Weiqun Zhang Date: Tue Sep 13 18:12:45 2011 -0700 8 combinations work. The one doesn't work is C++ with periodic boundary. Tutorials/MultiGrid_C/COEF_3D.F Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/inputs.3d Tutorials/MultiGrid_C/main.cpp commit dbd51e3ba2a46a7d030f34b022de89c025f15272 Author: Marc Day Date: Tue Sep 13 13:40:31 2011 -0700 modify install procedure to clean up how an external code might link to the libraries CMakeLists.txt Src/C_AMRLib/CMakeLists.txt Src/C_BaseLib/CMakeLists.txt Src/C_BaseLib/ParmParse.H Src/C_BoundaryLib/CMakeLists.txt Src/Extern/amrdata/CMakeLists.txt Src/Extern/gslib/CMakeLists.txt Src/F_BaseLib/CMakeLists.txt Src/LinearSolvers/C_CellMG/CMakeLists.txt Src/LinearSolvers/C_to_F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt Tools/CMake/CCSEConfig-install.cmake.in Tools/CMake/CCSEConfigReport.cmake Tools/CMake/CCSEConfigVersion-install.cmake.in Tools/CMake/CCSELinkLine.cmake Tools/CMake/CCSEOptions.cmake Tools/CMake/InstallManager.cmake Tools/CMake/MakefileConfig.export.in Tools/CMake/ParseLibraryList.cmake Tools/CMake/TransformVersion.cmake Tools/C_scripts/boxlib-build.sh commit 433581d40ccc2ddc75132bb4051ac2513962c758 Author: Ann Almgren Date: Tue Sep 13 13:15:18 2011 -0700 This now has the working 3d 4th order variable coefficient stencil. Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 commit a52c141bdbe3a50962fc9935ec113aa719d9abb6 Author: lijewski Date: Tue Sep 13 11:05:04 2011 -0700 Do a maxSize() on the BoxArrays to get more grids. Tests/C_BaseLib/tMFcopy.cpp commit 22b9473cd7a908cfac60d6c4ca6613169c16721d Author: lijewski 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 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 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 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: ec0a883e7 33413e65c Author: Ann Almgren Date: Mon Sep 12 14:53:52 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit ec0a883e7a0364095da0cbd0545c427d5f6f2b7c Author: Ann Almgren Date: Mon Sep 12 14:53:00 2011 -0700 1) Broke cc_stencil.f90 into two files -- cc_stencil.f90 and cc_stencil_apply.f90 2) Added 4th order stencil for variable coefficients in 3d (61 terms in stencil) Src/LinearSolvers/F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/cc_ml_resid.f90 Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_apply.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit 33413e65cacbdbba82379bee4bea4bb3eb739357 Merge: e6dcb173b 5beed29d6 Author: lijewski Date: Mon Sep 12 14:31:11 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit e6dcb173b2ea6bae3e3c12454ebb0f04bd582b96 Author: lijewski Date: Mon Sep 12 14:30:59 2011 -0700 Fixed typo in comment. Tests/C_BaseLib/tMFcopy.cpp commit be6349c1429cd137a6ed7fabba39d4e602ab5f4f Author: lijewski Date: Mon Sep 12 14:30:02 2011 -0700 Added SFC_Threshold() functions to set/get the sfc_threshold. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 8ac97f486cc1ca2e10874f1e227a2a0a539616cf Author: lijewski Date: Mon Sep 12 14:28:23 2011 -0700 Added new test routine that tests parallel copy between two multifabs whose boxarrays cover the same area but have different number of boxes and hence different distribution. Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tMFcopy.cpp commit 5beed29d65613c0aeaa61cafb52d9ebc341c248b Author: Ann Almgren Date: Mon Sep 12 12:55:35 2011 -0700 Remove extra arguments so this compiles. Src/LinearSolvers/F_MG/cc_stencil_fill.f90 commit 98e04d0b35240c803d55d99588b89b5c3ba7c9b9 Author: Ann Almgren Date: Mon Sep 12 12:54:41 2011 -0700 Need to declare the new variables so this compiles (though still not working) Src/LinearSolvers/F_MG/cc_stencil.f90 commit c6d6896b276b6fbe4d5b03fa7eb1b19ed646f31d Author: Ann Almgren Date: Mon Sep 12 12:06:36 2011 -0700 1) New improved version of subroutine minion_fill_full_2d 2) Introduced subroutine minion_fill_full_3d but it is not yet complete. 3) Modified call to minion_full_fill_3d to test on whether ns = 61, not 125. Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 commit e14967c1f6355a9009577f3856e4918b64a8a9fa Author: Ann Almgren Date: Sat Sep 10 09:32:52 2011 -0700 Latest version -- added choice of bc_type -- still not fully working. Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/inputs.3d Tutorials/MultiGrid_C/main.cpp commit 28ce486a549cd6bf0e767b9ac081e40a1871cbff Author: Ann Almgren Date: Fri Sep 9 21:54:36 2011 -0700 New Tutorials directory -- a C++ MultiGrid driver that will call the C++ solver, the F90 solver and the Hypre solver. Tutorials/MultiGrid_C/COEF_3D.F Tutorials/MultiGrid_C/COEF_F.H Tutorials/MultiGrid_C/GNUmakefile Tutorials/MultiGrid_C/Make.package Tutorials/MultiGrid_C/inputs.3d Tutorials/MultiGrid_C/main.cpp commit c029a76578d71a39ee8220d33af09e3f56c29105 Author: Ann Almgren Date: Fri Sep 9 17:25:13 2011 -0700 No need to copy mf into plotMF Tutorials/WaveEquation_C/writePlotFile.cpp commit 2d1f88296b3e39250040e3b68f7881cf037719b9 Author: Ann Almgren Date: Thu Sep 8 11:10:30 2011 -0700 Keep this file here but don't put it in GPackage.mak Signed-off-by: Ann Almgren Src/F_BaseLib/mt19937ar.f90 commit b5982ce6397f962f60c80d995ad18d461d476892 Author: Ann Almgren Date: Thu Sep 8 09:49:30 2011 -0700 Include options for the Gottingen machines. Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi Tools/F_mk/GMakedefs.mak commit 1f976bf6558eb1b54f1ae7c9c80121668d78ac20 Author: Marc Day Date: Wed Sep 7 19:15:59 2011 -0700 version/release info BoxLib_Version.txt Tools/C_scripts/gen_release_tarball.txt commit c4ce57b990c33b57b0a721cd8b584d5952ab5175 Author: Marc Day Date: Wed Sep 7 18:41:58 2011 -0700 Add gslib files here to simplify distribution for ASCEM Src/Extern/gslib/CMakeLists.txt Src/Extern/gslib/acorni.f Src/Extern/gslib/backtr.f Src/Extern/gslib/beyond.f Src/Extern/gslib/blue.f Src/Extern/gslib/chknam.f Src/Extern/gslib/chktitle.f Src/Extern/gslib/cova3.f Src/Extern/gslib/dlocate.f Src/Extern/gslib/dpowint.f Src/Extern/gslib/dsortem.f Src/Extern/gslib/gauinv.f Src/Extern/gslib/gcum.f Src/Extern/gslib/getindx.f Src/Extern/gslib/getz.f Src/Extern/gslib/green.f Src/Extern/gslib/hexa.f Src/Extern/gslib/ksol.f Src/Extern/gslib/ktsol.f Src/Extern/gslib/locate.f Src/Extern/gslib/nscore.f Src/Extern/gslib/numtext.f Src/Extern/gslib/ordrel.f Src/Extern/gslib/picksupr.f Src/Extern/gslib/powint.f Src/Extern/gslib/psfill.f Src/Extern/gslib/psline.f Src/Extern/gslib/pstext.f Src/Extern/gslib/rand.f Src/Extern/gslib/red.f Src/Extern/gslib/resc.f Src/Extern/gslib/scal.f Src/Extern/gslib/setrot.f Src/Extern/gslib/setsupr.f Src/Extern/gslib/sortem.f Src/Extern/gslib/sqdist.f Src/Extern/gslib/srchsupr.f Src/Extern/gslib/strlen.f commit bb0c52ff2653fac67f9ab057189935478368ab59 Author: Marc Day Date: Wed Sep 7 18:40:50 2011 -0700 Add some amrdata files here as a temporary measure until amrvis available elsewhere Src/Extern/amrdata/AmrData.H Src/Extern/amrdata/AmrData.cpp Src/Extern/amrdata/AmrvisConstants.H Src/Extern/amrdata/CMakeLists.txt Src/Extern/amrdata/DataServices.H Src/Extern/amrdata/DataServices.cpp Src/Extern/amrdata/FABUTIL_2D.F Src/Extern/amrdata/FABUTIL_3D.F Src/Extern/amrdata/Make.package commit 8ed8f3c60b7f4f9cb4eebaebf4a4cf3f38156417 Author: Marc Day Date: Wed Sep 7 18:38:40 2011 -0700 Add support for CMake builds CMakeLists.txt Src/CMakeLists.txt Src/C_AMRLib/CMakeLists.txt Src/C_BaseLib/CMakeLists.txt Src/C_BoundaryLib/CMakeLists.txt Src/F_BaseLib/CMakeLists.txt Src/LinearSolvers/C_CellMG/CMakeLists.txt Src/LinearSolvers/C_to_F_MG/CMakeLists.txt Src/LinearSolvers/F_MG/CMakeLists.txt Tools/CMake/CCSEConfigReport.cmake Tools/CMake/CCSEOptions.cmake Tools/CMake/CMakeParseArguments.cmake Tools/CMake/ExampleBoxLibConfig.cmake Tools/CMake/ExampleCMakeLists.txt_CCSEApp Tools/CMake/PreprocessBoxLibFortran.cmake Tools/CMake/TestManager.cmake Tools/C_scripts/boxlib-build.sh commit 317490ddfd150c21486b3de05c3d046e68f2c462 Merge: 41a2e6843 ea561a2c1 Author: Marc Day Date: Wed Sep 7 18:34:43 2011 -0700 Merge branch 'master' of /home/marc/src/CCSE/BoxLib commit 41a2e68432f6483b50f90e74f95dd3d02842e6da Author: Marc Day Date: Wed Sep 7 18:32:09 2011 -0700 Add Utility.H Src/C_AMRLib/SlabStat.cpp commit ea561a2c1a6dc8c17d543e93eb639c73661b05f6 Author: lijewski Date: Tue Sep 6 09:51:38 2011 -0700 Got rid of explicit copy constructors and copy assignment operators. Use the compiler generated ones. Src/C_BaseLib/IndexType.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/Orientation.H commit 08a1d7974e1a655f736b0295701f35ae8f87f23f Author: cmalone Date: Tue Aug 30 15:04:33 2011 -0700 get rid of all the *.mod files in the CWD Signed-off-by: lijewski Tools/C_mk/Make.Darwin commit 74449ac63d05a1c5bfcc66d191bf48ac6dcb11a9 Author: lijewski Date: Tue Aug 30 13:52:19 2011 -0700 workd with USE_F90_MG=TRUE Tests/LinearSolvers/ComparisonTest/GNUmakefile commit 3134b51ddd29a848aadfe986eb2be796906b0858 Author: lijewski Date: Tue Aug 30 12:59:41 2011 -0700 A wad of simplification and consolidation. Removed BL_USECLOSE -- always assume true. Removed BL_USEOLDREAD -- always assume false. Always use the ReadAndBcastFile() stuff whether or not USE_MPI=TRUE. Always use the fancy probin reader regardless of whether or not USE_MPI=TRUE. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Particles.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/VisMF.cpp commit 87af60426e14f78d88e8f8e0623c142ed3f30bb8 Author: Ann Almgren Date: Tue Aug 30 09:03:02 2011 -0700 Added Tutorials directory with first example: WaveEquation_C, a simple program that uses BoxLib stuff with the C++ make system to run a single-level wave equation evolution routine. Tutorials/WaveEquation_C/GNUmakefile Tutorials/WaveEquation_C/Make.package Tutorials/WaveEquation_C/advance_2d.f90 Tutorials/WaveEquation_C/advance_3d.f90 Tutorials/WaveEquation_C/init_data_2d.f90 Tutorials/WaveEquation_C/init_data_3d.f90 Tutorials/WaveEquation_C/inputs_2d Tutorials/WaveEquation_C/inputs_3d Tutorials/WaveEquation_C/main.cpp Tutorials/WaveEquation_C/writePlotFile.H Tutorials/WaveEquation_C/writePlotFile.cpp commit c042e7c56cc5e6b890dac68ce70f363a360b15c0 Author: lijewski Date: Mon Aug 29 14:51:27 2011 -0700 Added Initialize()/Finalize() functions to ensure static variables are initialized properly. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 765947bd0286e574d3c95d34cb664250ae8b565f Merge: f4e754d1f df774945f Author: ajnonaka Date: Fri Aug 26 16:12:38 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit f4e754d1f95ea74ba1cc7252672a711b42a0ec88 Author: ajnonaka Date: Fri Aug 26 16:11:59 2011 -0700 Chris' mod for macs Tools/F_mk/GMakeMPI.mak commit e905c1d4ecf7a85d543ff6ff4dafd9f735379dce Author: ajnonaka Date: Fri Aug 26 16:11:37 2011 -0700 Chris' mod for mac's Tools/C_mk/Make.Darwin commit df774945f241d13b70ec953508541594611d04f8 Author: lijewski Date: Fri Aug 26 16:11:27 2011 -0700 0.0 -> 0.0d0 in a few places. Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/LinearSolvers/C_TensorMG/DV_2D.F commit b92c343a694a2bfad207d1086dbdf762938ca882 Author: Theodore Kisner Date: Thu Aug 25 15:58:55 2011 -0700 Had to modify this commit because BoxLib.f90 was named FBoxLib.f90 in Ted's work and boxlib_f.f90 in Ann's work. We kept it as boxlib_f.f90. Old message: Rename BoxLib.f90 to FBoxLib.f90 to avoid name conflicts in the output object files when building outputs in the top level of the source tree. Signed-off-by: lijewski Src/F_BaseLib/GPackage.mak commit a9ab1ce1a92366736366fce1cc750a3a18435366 Author: Theodore Kisner Date: Thu Aug 25 15:15:03 2011 -0700 Convert Cray vector merge functions to modern fortran merge syntax. Signed-off-by: lijewski Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/LinearSolvers/C_CellMG/ABec_1D.F Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/LO_1D.F Src/LinearSolvers/C_CellMG/LO_2D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LP_1D.F Src/LinearSolvers/C_CellMG/LP_2D.F Src/LinearSolvers/C_CellMG/LP_3D.F Src/LinearSolvers/C_TensorMG/DV_2D.F Src/LinearSolvers/C_TensorMG/DV_3D4.F commit 50cadd0ec72a99ec0ba541965da0a6f3cce404c4 Author: lijewski 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 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 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 Date: Thu Aug 25 15:13:51 2011 -0700 1) Rename six files so they no longer have name conflicts with the C++ file. So ... box.f90 --> box_f.f90 boxarray.f90 --> boxarray_f.f90 cluster.f90 --> cluster_f.f90 BoxLib.f90 --> boxlib_f.f90 multifab.f90 --> multifab_f.f90 particles.f90 --> particles_f.f90 Note that this does not affect other files as these are included by module name, not file name. 2) Also remove from F_MG/FParallelMG.mak the files which are in F_BaseLib/FParallel.mak Src/F_BaseLib/FParallelMG.mak Src/F_BaseLib/GPackage.mak Src/F_BaseLib/box_f.f90 Src/F_BaseLib/boxarray_f.f90 Src/F_BaseLib/boxlib_f.f90 Src/F_BaseLib/cluster_f.f90 Src/F_BaseLib/multifab_f.f90 Src/F_BaseLib/particles_f.f90 Src/LinearSolvers/F_MG/FParallelMG.mak commit caf3f9ebf19e2de5a1870f7532ddfa7c383169df Author: lijewski 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 Date: Tue Aug 23 14:04:30 2011 -0700 Update the GNUmakefile in Tests/LinearSolvers/ComparisonTest Tests/LinearSolvers/ComparisonTest/GNUmakefile commit 40232598e1319dda44652d831a338469697fc362 Author: vince Date: Tue Aug 23 14:00:08 2011 -0700 email push test 0. v. Tests/C_BaseLib/tVisMF.cpp commit de7c0e8d8b6f3180a5184e074e4a59d73ebee607 Author: lijewski Date: Thu Aug 18 14:12:34 2011 -0700 Quieted some warnings. Src/C_AMRLib/ErrorList.H Src/C_AMRLib/ErrorList.cpp Src/C_BaseLib/BoxLib.cpp commit 093ff163bde1998b30cd10db1f7a087c291d74e0 Author: lijewski Date: Thu Aug 18 13:44:14 2011 -0700 Cleaned up the Make stuff. Removed all hints of installing things since we don't do that anymore. Tools/C_mk/Make.defs Tools/C_mk/Make.rules Tools/C_scripts/install-sh commit 8949f1b4cf432f2d2ac49afe3466212f0ed8c2ea Author: lijewski Date: Thu Aug 18 13:23:14 2011 -0700 Removed all .dsp stuff for generating Microsoft-compatible Makefiles. Also got rid of ckread.pl since we no longer generate tranfiles from ChemKin itself. Tools/C_mk/Make.rules Tools/C_scripts/ckread.pl Tools/C_scripts/dsp.lib.mak Tools/C_scripts/dsp.mak commit ae55f73d3a53feb12d0f1b9d55df47c2d9539aa3 Author: Ann Almgren Date: Wed Aug 17 13:14:08 2011 -0700 Fixed comments to refer to new directory structure. Src/F_BaseLib/FParallelMG.mak commit 2a821bbf99b3132dc1e752d00910713a76120ce5 Author: Ann Almgren Date: Wed Aug 17 13:10:37 2011 -0700 Make Tests/C_BaseLib and Tests/F_BaseLib both up to date. Tests/C_BaseLib/GNUmakefile Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/mt19937ar.f90 commit 8cef4c250a5d531bd21eacd25334c0664776213f Author: Ann Almgren Date: Wed Aug 17 13:03:39 2011 -0700 This now compiles. Tests/LinearSolvers/C_TensorMG/GNUmakefile commit 328f191a92ca01bf0080f788b381e5ccca0a69a4 Author: Ann Almgren Date: Wed Aug 17 13:01:56 2011 -0700 Remove reference to iamrlib. Tests/LinearSolvers/C_CellMG/GNUmakefile commit d2c2c38d18201ea98550804c9f2e0445c8d454ee Author: Ann Almgren 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 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: e2456d183 35d9c4087 Author: Ann Almgren Date: Wed Aug 17 12:38:39 2011 -0700 Merge branch 'master' of almgren@gamera:/usr/local/gitroot/BoxLib commit e2456d18349b729e74a2be13400cef507e1d599e Author: Ann Almgren Date: Wed Aug 17 12:38:23 2011 -0700 slight clean-up Tests/LinearSolvers/ComparisonTest/main.cpp commit 35d9c408794a22e947792c2dd8af048402e75dd2 Merge: 3cf0ba963 73ece674b Author: Marc Day Date: Wed Aug 17 12:37:05 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 73ece674b9afeafc8847727836170e2b419ec7f0 Author: Ann Almgren Date: Wed Aug 17 12:36:02 2011 -0700 Dont need our own copies of MacBndry* -- they're in C_BoundaryLib. Tests/LinearSolvers/ComparisonTest/MacBndry.H Tests/LinearSolvers/ComparisonTest/MacBndry.cpp commit f9b0b3dcf09973a7cadb21f22058becb704c95fb Author: Ann Almgren Date: Wed Aug 17 12:33:48 2011 -0700 Now compiles with F90 solvers turned on as well. Tests/LinearSolvers/ComparisonTest/GNUmakefile Tests/LinearSolvers/ComparisonTest/main.cpp commit f2466e6ba5a3c11cf9db9880777b6911a8342da7 Author: Ann Almgren Date: Wed Aug 17 12:27:53 2011 -0700 This now compiles with the new BoxLib format. Tests/LinearSolvers/ComparisonTest/GNUmakefile Tests/LinearSolvers/ComparisonTest/main.cpp commit 367f14eb7ed804d4b26e00a8bd81a1b5716a5e18 Author: Ann Almgren Date: Wed Aug 17 12:12:03 2011 -0700 Changes to try to get this to compile. Tests/LinearSolvers/ComparisonTest/GNUmakefile commit 3cf0ba963542df0eae03c6064d73ea4d8359d304 Author: Marc Day Date: Wed Aug 17 11:00:33 2011 -0700 Remove bibtex command Docs/GNUmakefile commit 92aa3d5100f4610172362a352d2b9e8d45dddddf Author: lijewski Date: Wed Aug 17 08:32:12 2011 -0700 Removed a couple weird Crutchfield scripts. Tests/LinearSolvers/C_TensorMG/doit Tests/LinearSolvers/C_TensorMG/dotest commit 9884a83ee14b9a1a7df495d5a5e26db3aface7ef Author: lijewski Date: Wed Aug 17 08:22:21 2011 -0700 Removed instances of PROFILE={TRUE,FALSE} in GNUmakefiles. Left the PROFILE rule in Make.rules. Tests/C_BaseLib/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/ComparisonTest/GNUmakefile Tools/C_mk/Make.T3E Tools/C_util/Convergence/GNUmakefile Tools/C_util/Convergence/GNUmakefile.temp Tools/C_util/Statistics/GNUmakefile Tools/C_util/ViewMF/GNUmakefile Tools/C_util/dbgTools/GNUmakefile commit a6089d48ab34d894d485d4b0fb7534bbadf917f3 Merge: c071cfcd2 47ee822fa Author: lijewski Date: Wed Aug 17 08:10:59 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit 47ee822fa1adb96d1e63279205c2c8967c540940 Author: Ann Almgren Date: Tue Aug 16 20:59:36 2011 -0700 PBOXLIB_HOME --> BOXLIB_HOME Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/ComparisonTest/GNUmakefile commit 51c03405a0bf4a75b89a569072897da840c4eb8e Author: Ann Almgren Date: Tue Aug 16 20:58:33 2011 -0700 1) PBOXLIB_HOME --> BOXLIB_HOME 2) Get rid of ComparisonTest from Src/LinearSolvers/C_CellMG -- it is already in Tests/LinearSolvers/C_CellMG Src/LinearSolvers/C_CellMG/ComparisonTest/COEF_3D.F Src/LinearSolvers/C_CellMG/ComparisonTest/COEF_F.H Src/LinearSolvers/C_CellMG/ComparisonTest/GNUmakefile Src/LinearSolvers/C_CellMG/ComparisonTest/MacBndry.H Src/LinearSolvers/C_CellMG/ComparisonTest/MacBndry.cpp Src/LinearSolvers/C_CellMG/ComparisonTest/Make.package Src/LinearSolvers/C_CellMG/ComparisonTest/inputs.3d Src/LinearSolvers/C_CellMG/ComparisonTest/main.cpp commit e393c7f125dc74719d27e735ac55a8e0e034351b Author: Ann Almgren Date: Tue Aug 16 20:53:16 2011 -0700 PBOXLIB_HOME --> BOXLIB_HOME Tests/C_BaseLib/GNUmakefile commit caae5456da98c941b79a6e138ee8e2d16afe6ad3 Author: Ann Almgren Date: Tue Aug 16 20:51:40 2011 -0700 Change PBOXLIB_HOME --> BOXLIB_HOME Src/LinearSolvers/F_MG/GPackage.mak Tools/C_util/Convergence/GNUmakefile Tools/C_util/Convergence/GNUmakefile.temp Tools/C_util/Statistics/GNUmakefile Tools/C_util/ViewMF/GNUmakefile Tools/C_util/dbgTools/GNUmakefile commit c1bbaf67fa33de4cc8c6a3fe17c9da8ec455017f Author: Ann Almgren Date: Tue Aug 16 20:48:37 2011 -0700 PBOXLIB_HOME --> BOXLIB_HOME. Tools/C_mk/Make.IRIX64 Tools/C_mk/Make.T3E Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 11ce5675a6cd6f7dd3a6d15915b14b28cf3ea306 Author: Ann Almgren Date: Tue Aug 16 18:18:00 2011 -0700 Better for new BoxLib structure... Tools/F_mk/GMakedefs.mak commit c071cfcd2976cda7ce37af3ace85b0a8a7320d7b Author: lijewski Date: Tue Aug 16 16:34:11 2011 -0700 No longer keeping around the POSIX Pthread stuff. Src/C_BaseLib/Thread.H commit 08b4e376a60c1a9f8e0f39dea5b2077a0941fc13 Merge: d9b487c60 8942fb1ee Author: lijewski Date: Tue Aug 16 16:25:05 2011 -0700 Merge branch 'master' of gamera:/usr/local/gitroot/BoxLib commit d9b487c60310ddd014c8b2cd8eb8069f7a251303 Author: lijewski Date: Tue Aug 16 16:24:09 2011 -0700 Removed all BL_PROFILE stuff. Left a bare-boned Profiling.H so code that still have BL_PROFILE stuff in them will compile. Also got rid of the POSIX Pthread stuff. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/StateData.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/BLMpi.cpp Src/C_BaseLib/BLMpi.w Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.cpp Src/C_BoundaryLib/FabSet.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp Tests/C_BaseLib/tMinCommCosts.cpp commit 8942fb1ee1cef682a5102c9454a1de6eb449f6a5 Author: ajnonaka 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 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 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 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 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 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 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 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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 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 Date: Mon Aug 15 15:26:16 2011 -0700 This test directory is now in Tests/C_BaseLib. 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Reformatted some stuff to make it easier to read. 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Src/C_AMRLib/FLUXREG_2D.F Src/C_BaseLib/BLParmParse_F.f Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/t8BIT.cpp Src/C_BaseLib/test/tCArena.cpp Src/C_BaseLib/test/tDir.cpp Src/C_BaseLib/test/tFAC.cpp Src/C_BaseLib/test/tFB.cpp Src/C_BaseLib/test/tMF.cpp Src/C_BaseLib/test/tParmParse.cpp Src/C_BaseLib/test/tVisMF.cpp Src/C_BaseLib/test/tread.cpp Src/F_BaseLib/fabio_c.c Src/F_BaseLib/ppm_util_c.c Src/F_BaseLib/timer_c.c Src/LinearSolvers/C_CellMG/GNUmakefile Src/LinearSolvers/C_CellMG/Test/Make.package Src/LinearSolvers/C_CellMG/Test/macprojTest.cpp Src/LinearSolvers/C_CellMG/Test/main.cpp Src/LinearSolvers/C_NodalMG/GNUmakefile commit b64c6562ee8f7cc0e2a02409e8ba004219bde137 Author: mjlijewski@lbl.gov Date: Mon Aug 15 11:26:00 2011 -0700 Removed BLVERSION.H file. Src/C_BaseLib/BLVERSION.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Make.package commit a88c944ff43d29d9f020078586c9df6903ee9192 Author: mjlijewski@lbl.gov Date: Mon Aug 15 11:18:02 2011 -0700 Removed some WorkQueue and Thread stuff. All the WorkQueue stuff is gone. Most of the POSIX Thread stuff is gone, but not the files themselves. BLProfiler still used the THread stuff. Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/BLWorkQueue.cpp Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/WorkQueue.H Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/tProfiler.cpp Src/C_BaseLib/test/tWorkQueue.cpp Src/LinearSolvers/C_CellMG/ComparisonTest/main.cpp Src/LinearSolvers/C_CellMG/Test/macprojTest.cpp Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tProfiler.cpp Tests/C_BaseLib/tWorkQueue.cpp commit 2ea54a393b2f80e119624c7e479617e08d00a381 Author: Ann Almgren 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 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 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 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 Date: Sat Aug 13 15:45:28 2011 -0700 Remove cvs tags. 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Src/LinearSolvers/C_TensorMG/DivVis.H Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/DivVis_F.H Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLO_2D.F Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp Src/LinearSolvers/C_TensorMG/Make.package commit 7470963748594addac6aaed1a1c416e4e071d916 Author: Ann Almgren Date: Sat Aug 13 15:28:11 2011 -0700 Remove cvs tags. Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABec_1D.F Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/ABec_F.H Src/LinearSolvers/C_CellMG/ABec_UTIL.F Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/CG_2D.F Src/LinearSolvers/C_CellMG/CG_3D.F Src/LinearSolvers/C_CellMG/CG_F.H Src/LinearSolvers/C_CellMG/LO_2D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LO_F.H Src/LinearSolvers/C_CellMG/LP_2D.F Src/LinearSolvers/C_CellMG/LP_3D.F Src/LinearSolvers/C_CellMG/LP_F.H Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MG_2D.F Src/LinearSolvers/C_CellMG/MG_3D.F Src/LinearSolvers/C_CellMG/MG_F.H Src/LinearSolvers/C_CellMG/Make.package Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG/lo_bctypes.fi Src/LinearSolvers/C_NodalMG/Make.package commit 1045ed9d8e72715cb29aa0aa0c53f7a94fb35be9 Author: Ann Almgren 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 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 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 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 Date: Fri Aug 12 19:32:57 2011 -0700 changed script Tools/C_mk/Make.rules commit 39c83ae9990acfc20434902adc1fd2fee6410d04 Author: Ann Almgren Date: Fri Aug 12 19:28:33 2011 -0700 changed script location Tools/C_mk/Make.rules commit 7b4725caff4607cbcfa8196c467a5c30ccd1b754 Author: Ann Almgren Date: Fri Aug 12 18:57:18 2011 -0700 Needed to fix the paths for mk and scripts. Tools/C_mk/Make.IRIX64 Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 774eac855d0a663b87bbc838421a63c7934adff7 Author: Ann Almgren Date: Fri Aug 12 18:17:15 2011 -0700 Modifying C_mk/Make* to reflect the new path for C_mk Tools/C_mk/Make.IRIX64 Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit dbb2cf44a4e78b49d6b22a9ec7c9a4b03923279f Author: almgren Date: Thu Aug 11 13:47:16 2011 +0000 This now includes the particles. Src/C_AMRLib/Make.package commit 7c645e6c22e78a7e1e5275d51fe50c7a822462ff Author: almgren Date: Wed Aug 10 22:11:31 2011 +0000 Fix oops. Src/C_BaseLib/Make.package commit 5674ef7050fc42a42d414176ce7769dff7aba872 Author: ajnonaka Date: Wed Aug 10 20:33:52 2011 +0000 added support for Intel12 on hopper Tools/F_mk/comps/Linux_intel.mak commit 363d9153cc5d5bf52f4916ec5505228cc1c664fb Author: 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 Date: Wed Aug 10 20:18:57 2011 +0000 Added RealBox, CoordSys, Geometry stuff. Src/C_BaseLib/Make.package commit 5545e5760409c9aa0aa0fb2f905ca780dee3f539 Author: almgren Date: Wed Aug 10 19:40:14 2011 +0000 Remove reference to Minion stencil in nodal stencil. Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 16723e91d437860e201271fa28abc9e058f688e8 Author: almgren Date: Wed Aug 10 19:27:09 2011 +0000 Comment out all SPARSKIT files since we no longer build in the sparse solver capability. Src/LinearSolvers/F_MG/FParallelMG.mak commit da611c7af56b0a8896bf71cae7f116657418b3e8 Author: lijewski Date: Tue Aug 9 21:47:18 2011 +0000 more Initialize()/Finalize() foo fah Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 6fdd4e5d4b61af386b54f95a3d513e72ed48e83b Author: lijewski Date: Tue Aug 9 21:32:45 2011 +0000 added clear() to DeriveList Src/C_AMRLib/Derive.H commit 0f091e4f9fd05c6fe06f4152b2240fb8594288f6 Author: lijewski Date: Tue Aug 9 16:36:54 2011 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp commit cda44e2ca8a6aa571f7549251774172ef25bdf42 Author: lijewski Date: Tue Aug 9 16:30:16 2011 +0000 fix to clear(); have to also do a resize(0) to fully clear a StateDescriptorList Src/C_AMRLib/StateDescriptor.cpp commit 8d7d258a0601c335ce4e501bfd559a62fc81ccb7 Author: lijewski Date: Tue Aug 9 15:51:53 2011 +0000 yet more work on Initialize()/Finalize() Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit cd99a72952d76d217d23c423da18af0b8a569e17 Author: lijewski Date: Tue Aug 9 00:00:01 2011 +0000 yet more work on Initialize()/Finalize() Src/C_BaseLib/Arena.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp commit 06f9820e1d8f25042cebcb24444204a9bae24050 Author: lijewski Date: Mon Aug 8 21:23:34 2011 +0000 more work on Initialize()/Finalize() Src/C_BaseLib/BLWorkQueue.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp commit 9fe43bac57ae0d3013384c6a23f797ea38628c50 Author: lijewski Date: Mon Aug 8 20:47:45 2011 +0000 more work on Initialize()/Finalize() Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 5182942ce238ae1dec64b64b0a53529cffd4c90f Author: lijewski Date: Mon Aug 8 20:37:25 2011 +0000 more work on Initialize()/Finalize() Src/C_AMRLib/Amr.cpp commit 1262f30784175f8fe04766180381dea5ddbed8aa Author: lijewski Date: Mon Aug 8 17:24:24 2011 +0000 put 'initialized' into unnamed namespace instead of static member Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 6a873f0b16d64137869cdf1bc1586aa69a80f413 Author: lijewski Date: Mon Aug 8 16:58:44 2011 +0000 add clear() to ErrorList Src/C_AMRLib/ErrorList.H commit e45e13fe10f8419199fb44c402f40d94bf0ad016 Author: lijewski Date: Sat Aug 6 02:57:14 2011 +0000 turn on/off cache statistics with geometry.verbose Src/C_BaseLib/Geometry.cpp commit 98def4c308bd32a77af45914a1bd991590225e21 Author: lijewski Date: Sat Aug 6 02:56:31 2011 +0000 turn on/off cache statistics with fabarray.verbose Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 06a835e73f7ed81c0daa7445646218c19615bca4 Author: almgren Date: Sat Aug 6 00:34:08 2011 +0000 Allow us to use DistributionMapping.v as well as DistributionMapping.verbose to control the verbosity. Src/C_BaseLib/DistributionMapping.cpp commit b93b8cfe11c2b3143adcb947643e7772a5018513 Author: lijewski Date: Fri Aug 5 23:14:10 2011 +0000 new way of doing Finalize() Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit db783b7f28b6fbe76a3f93b8b07fc87514c060d1 Author: lijewski Date: Fri Aug 5 22:56:49 2011 +0000 new way of doing Finalize() Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit d2ba695c2157a2aaefbb91f68708a8ba7bd651c1 Author: almgren Date: Fri Aug 5 22:28:02 2011 +0000 Needed ParmParse.H ... Src/C_AMRLib/Particles.H commit f378f62bca28e667d7e67c35425703ce1ea43dd6 Author: lijewski Date: Fri Aug 5 22:21:16 2011 +0000 some cleanup Src/C_BoundaryLib/InterpBndryData.cpp commit 25da41aa71ae5908bdee5cc6f791808e30ef3859 Author: lijewski Date: Fri Aug 5 22:21:05 2011 +0000 new way of doing BoxLib::Finalize() Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 215a39433faa50dfdaf3bc68e3a9047623eba742 Author: lijewski Date: Fri Aug 5 22:20:28 2011 +0000 BoxLib now maintains a stack of functions that should be called on BoxLib::Finalize(). Initialization functions that set defaults or that build global data that needs to be cleared out on BoxLib::Finalize() should define a function of the form: void (fp) () that performs necessary cleanup, and then register those functions via BoxLib::ExecOnFinalize(fp). Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParmParse.cpp commit 18cb705fb09783c558e6ac373bb853ea74c9a109 Author: almgren Date: Fri Aug 5 22:04:38 2011 +0000 Allow a new type of ErrorFunc so that we can have different argument lists for the error tagging functions. Src/C_AMRLib/ErrorList.H Src/C_AMRLib/ErrorList.cpp commit 51adc18f2e20bf3888e915616396e06609f16503 Author: lijewski Date: Thu Aug 4 21:13:49 2011 +0000 more Initialize()/Finalize() foo fah Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.cpp commit a9cc80ae4f3b36828e151cfde51f1759d041d41d Author: lijewski Date: Thu Aug 4 20:25:44 2011 +0000 Added Initialize()/Finalize() but not yet integrated into BoxLib.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit df55e9fbd3585d0891c92d316bfbdb58e03c3b7d Author: 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Wed Jul 20 14:37:52 2011 +0000 Add BC_GEOM. Src/LinearSolvers/F_MG/bc_functions.f90 commit 4730bbbe0e6c734ebbd591de6ef0ec7dca621ae7 Author: mzingale Date: Wed Jul 20 14:10:56 2011 +0000 add missing "implicit none". No longer compiles. Src/LinearSolvers/F_MG/bc_functions.f90 Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90 commit 0f548887d21ba25aa4af1e83a651e2ed664f9bc1 Author: almgren Date: Wed Jul 20 05:25:44 2011 +0000 Separate restriction modules. Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/cc_restriction.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/nodal_restriction.f90 commit 65297acc1299e66e3eacb9eb73070758bb6b3782 Author: 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 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 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 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 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 Date: Wed Jul 20 04:06:00 2011 +0000 Forgot multifab_module. Src/LinearSolvers/F_MG/ml_norm.f90 commit 81adbb460e1eccb4d09d9fa51c41e12ccecf085f Author: almgren Date: Wed Jul 20 04:04:35 2011 +0000 Catch these up with other changes. Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 commit 21c10ac23f16e1be7e67133636c2efa497c4feea Author: almgren Date: Wed Jul 20 04:04:08 2011 +0000 ml_util.f90 --> ml_norm.f90 Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/ml_norm.f90 Src/LinearSolvers/F_MG/ml_util.f90 commit ec2390c4e1eecc51a3e1273bc0607d6d2c3d07eb Author: almgren Date: Wed Jul 20 03:54:05 2011 +0000 Keep up with new files. Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak commit 80058bed05e6f2accbdc3b36d105e367da044b7f Author: almgren Date: Wed Jul 20 03:53:53 2011 +0000 Break up ml_interface_stencil.f90 into nodal and cc. Src/LinearSolvers/F_MG/cc_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_interface_stencil.f90 commit 1fb6070c2bb1366231526eed54410f461b97f583 Author: almgren Date: Wed Jul 20 01:51:56 2011 +0000 Get ml_prolongation started to separate. Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 3d341cba69a59f5b209dbbe49ab2db22f36ac7aa Author: almgren Date: Wed Jul 20 01:43:24 2011 +0000 mg_nodal_cpp --> nodal_mg_cpp Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak commit 36a1462fbe24410e18b04540cfb091927e99cb34 Author: almgren Date: Wed Jul 20 01:42:44 2011 +0000 Changed name. Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit a69f976d31a04b0763742443d8cf08b99c726c60 Author: almgren Date: Wed Jul 20 01:40:31 2011 +0000 add bl_error_module... Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 Src/LinearSolvers/F_MG/tridiag.f90 commit c1eb5723c800d27301e46f464eef59085cdb1cc5 Author: almgren Date: Wed Jul 20 01:36:49 2011 +0000 Fix nodal_newu... Src/LinearSolvers/F_MG/GPackage.mak commit 1753ffc34b166da6dbf83fd7e53f6464350b6cd2 Author: almgren Date: Wed Jul 20 01:34:45 2011 +0000 Clean up ... Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 commit 19e612d3c3d4303d0d47b9eb6eacec37b3fa86fc Author: almgren Date: Wed Jul 20 01:32:31 2011 +0000 Remove ST_FILL... they were never used. Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 commit e8d079b25c5b51eeefae21c189a7bd5b28eb4e56 Author: almgren Date: Wed Jul 20 01:29:44 2011 +0000 stencil --> ... Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit f1d0622175afc8c95f1202f83cfd4585506bcbfc Author: almgren Date: Wed Jul 20 01:29:18 2011 +0000 stencil_module --> ... Src/LinearSolvers/F_MG/mg_tower.f90 commit 5a7ae4eb96603b30a632658f17d8d3f1d43324c4 Author: almgren Date: Wed Jul 20 01:28:43 2011 +0000 stencil -->... Src/LinearSolvers/F_MG/ml_util.f90 commit 556d3711389736629317787bfc1279e2d1b854af Author: almgren Date: Wed Jul 20 01:27:28 2011 +0000 fix oops. Src/LinearSolvers/F_MG/bc_functions.f90 commit 2208b4a405e3175f55279abcb6753303098b5f7a Author: almgren Date: Wed Jul 20 01:26:43 2011 +0000 add bl_spacedim. Src/LinearSolvers/F_MG/bc_functions.f90 commit 92d5b68fca546a6a8d0197963faf25fdbc54ad8d Author: almgren Date: Wed Jul 20 01:25:21 2011 +0000 move BC_BIT... Src/LinearSolvers/F_MG/bc_functions.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 commit 8fdfa1eba96556286eea356217ac4653f0ad980e Author: almgren Date: Wed Jul 20 01:23:43 2011 +0000 Extra bc_neumann, bc_dirichlet, etc, from cc_stencil.f90 Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/bc_functions.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 commit fec4f78936511d14ad59c36ff16b4f45be6bb301 Author: 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 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 Date: Wed Jul 20 00:59:59 2011 +0000 impose_neumann_bcs.f90 --> nodal_neumann_bcs.f90 Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/nodal_neumann_bcs.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 Src/LinearSolvers/F_MG/tridiag.f90 commit d337c3a6f2907cdf6104a7dfaa38986acd6a72cb Author: almgren Date: Wed Jul 20 00:56:30 2011 +0000 Separate cc from nodal in the stencil* files. Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/cc_mg_cpp.f90 Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/cc_stencil.f90 Src/LinearSolvers/F_MG/cc_stencil_fill.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/nodal_mg_cpp.f90 Src/LinearSolvers/F_MG/nodal_stencil.f90 Src/LinearSolvers/F_MG/nodal_stencil_fill.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 commit bc66ffd2168a0be05df0400fdf8562c52ca3424a Author: almgren Date: Wed Jul 20 00:44:13 2011 +0000 Clean up from previous changes.. this now compiles with CASTRO... Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 Src/LinearSolvers/F_MG/tridiag.f90 commit 9b85f71813d366774497ffda52d07473353940be Author: 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 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 Date: Wed Jul 20 00:35:38 2011 +0000 Separate mg_smoother.f90 into separate files -- cc_smoothers.f90 and nodal_smoothers.f90 Src/LinearSolvers/F_MG/cc_smoothers.f90 Src/LinearSolvers/F_MG/nodal_smoothers.f90 commit d99b33d5a5213eb20ff367b9afee89d62db0fd59 Author: almgren Date: Wed Jul 20 00:32:58 2011 +0000 Separate mg_smoother.f90 into nodal_smoothers.f90 and cc_smoothers.f90, and separate tridiag.f90 into a separate file. Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/tridiag.f90 commit e3047a371edb76ea781ba19842b28a779b7c62f8 Author: lijewski Date: Tue Jul 19 21:12:32 2011 +0000 use -O3 for optimizing with gfortran instead of -O2 Tools/C_mk/Make.defs commit ad54a1e611571480aee0e65054866a0722317d21 Author: almgren Date: Tue Jul 19 17:17:29 2011 +0000 These are the files I'm using to compare C++ to F90 solvers. Src/LinearSolvers/C_CellMG/ComparisonTest/COEF_3D.F Src/LinearSolvers/C_CellMG/ComparisonTest/COEF_F.H Src/LinearSolvers/C_CellMG/ComparisonTest/GNUmakefile Src/LinearSolvers/C_CellMG/ComparisonTest/MacBndry.H Src/LinearSolvers/C_CellMG/ComparisonTest/MacBndry.cpp Src/LinearSolvers/C_CellMG/ComparisonTest/Make.package Src/LinearSolvers/C_CellMG/ComparisonTest/inputs.3d Src/LinearSolvers/C_CellMG/ComparisonTest/main.cpp Tests/LinearSolvers/ComparisonTest/COEF_3D.F Tests/LinearSolvers/ComparisonTest/COEF_F.H Tests/LinearSolvers/ComparisonTest/GNUmakefile Tests/LinearSolvers/ComparisonTest/MacBndry.H Tests/LinearSolvers/ComparisonTest/MacBndry.cpp Tests/LinearSolvers/ComparisonTest/Make.package Tests/LinearSolvers/ComparisonTest/inputs.3d Tests/LinearSolvers/ComparisonTest/main.cpp commit c3b66a45c2df14219273f16a71a15fbe9e8d408e Author: marc Date: Tue Jul 19 17:11:07 2011 +0000 Fix up fParallel calls Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/main.cpp commit c0ee0f0d7024949354f23c6e107c1c66a2cb9374 Author: almgren Date: Tue Jul 19 00:07:05 2011 +0000 Remove unused variables in George's new stencils to quiet warnings... Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 commit 0c3cec3bb85fd777d9333d9a40ca4a811de0174d Author: almgren Date: Mon Jul 18 23:45:01 2011 +0000 Remove unused variables. Src/LinearSolvers/F_MG/stencil.f90 commit 61b7c4524b0358eac0c09de67f29a3e40c65b02b Author: lijewski Date: Mon Jul 18 20:51:17 2011 +0000 substitute istringstream for deprecated istrstream Src/C_AMRLib/Amr.cpp commit 685b23ae3612d29e4ee14bfad64489b412ab9669 Author: lijewski Date: Mon Jul 18 19:52:05 2011 +0000 substitute istringstream for deprecated istrstream Src/C_BaseLib/VisMF.cpp commit 3e1246abb615e01bcecd73f0d9be3b6c14e5dd49 Author: lijewski Date: Mon Jul 18 16:39:54 2011 +0000 deal with losing an AmrLevel on a regrid() in Redistribute() Src/C_AMRLib/Particles.H commit f9faba62dca6845506ca028879b0033a8b992b28 Author: lijewski Date: Sat Jul 16 16:02:14 2011 +0000 in Redistribute() must remove from the level map empty particle containers Src/C_AMRLib/Particles.H commit 6a46c0192080964df74c5f3ba2eda12358a4e1cd Author: lijewski Date: Sat Jul 16 04:10:21 2011 +0000 added m_particles.reserve() calls to the various init routines Src/C_AMRLib/Particles.H commit 53b796f19fffc43f820719cf6e6aace7f918220f Author: almgren Date: Sat Jul 16 04:01:36 2011 +0000 Change tcmf -> new_cmf so that we dont re-use MultiFab after clear -- turns out that clear does not delete the boxarray... Src/C_AMRLib/Particles.H commit ca453237c5b36fce71eac881eddbbd54f7e5b3ba Author: almgren Date: Sat Jul 16 03:50:17 2011 +0000 Add m_particles.resize() in Redistribute if m_particles.size() < m_amr.finestLevel()+1. Src/C_AMRLib/Particles.H commit 140d275d9bac9576a357f6c448eb9a2d574f3389 Author: lijewski Date: Thu Jul 14 23:32:18 2011 +0000 cut scalar time in Redistribute() by roughly a factor of two Src/C_AMRLib/Particles.H commit 091de5cbace1e356fd9e50ba509c8696700a605e Author: gilet Date: Thu Jul 14 22:13:07 2011 +0000 add note that this script is not for use on Jaguar Tools/F_scripts/extract.parallel commit 5b7487a65ff75d2026fd9b78b05f00613dcf8347 Author: 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 Date: Thu Jul 14 21:24:11 2011 +0000 Add LO_UTIL.F Src/C_BoundaryLib/Make.package commit a690a0e114be17aab84e68decc68edbc0c345763 Author: lijewski Date: Thu Jul 14 16:53:26 2011 +0000 ByteSpread() now also prints out total particle count. Src/C_AMRLib/Particles.H commit 195279b900be55a2f4b9244cd573de67bc56691a Author: lijewski Date: Wed Jul 13 22:42:01 2011 +0000 Bypass the MPI_Alltoall() calls in Redistribute() if there's no parallel work to do by doing a ReduceLongMax() on the number of particles I have that aren't mine. Src/C_AMRLib/Particles.H commit dcd41c87c1f69396eeebfb03555ec208f741a6dd Author: mzingale Date: Wed Jul 13 21:31:22 2011 +0000 have the timestamp routine that an optional argument, vel_mf, which contains the velocites. If this mf is present, then output the velocity of the zone where the particle lives along with the other data Src/F_BaseLib/particles.f90 commit eb62c53b045cfde29172927f2c64613f55bd3f67 Author: almgren Date: Wed Jul 13 21:28:03 2011 +0000 No longer need Make_nyx.package since we've moved those files into bndrylib. Src/LinearSolvers/C_CellMG/Make_nyx.package commit b5551be643ee4106634f9cf9117e13588f264b20 Author: 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 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 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 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 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 Date: Tue Jul 12 16:54:30 2011 +0000 beefed up OK() a bit more Src/C_AMRLib/Particles.H commit 8e53caed16247af61d90fbe1c3bf2c14d286ce51 Author: lijewski Date: Mon Jul 11 20:29:08 2011 +0000 Modest speedup to Redistribute(). Previously we only passed m_cpu and m_id via MPI and recalculated m_lev, m_grid and m_cell using Where(). Now Redistribute() sends all the integral data via MPI and recalculates nothing. For large numbers of particles this is a modest speedup. Src/C_AMRLib/Particles.H commit 947fb706c2b6d8955a6037921cb844cacd153f12 Author: 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 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 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 Date: Fri Jul 8 17:15:56 2011 +0000 quiet some compiler warnings Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 5dbf4118285883df575ff1cb9e682551ba9fdb1d Author: lijewski Date: Fri Jul 8 16:42:38 2011 +0000 quiet some compiler warnings Src/C_BaseLib/Looping.H commit 983bc0f0763dd1fb8e0a5507d75da4f2693a0fea Author: lijewski Date: Fri Jul 8 16:19:06 2011 +0000 quiet some compiler warnings Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit ceb3f24a1a829cb2f179bb0fd83c171cd9554fbc Author: lijewski Date: Fri Jul 8 16:03:40 2011 +0000 removed some unused variables Src/C_BaseLib/BaseFab.H commit 00a22d5ede723cb57de43480773162a1452a3972 Author: lijewski Date: Fri Jul 8 16:02:51 2011 +0000 cut number of random number calls in MoveRandom() by half Src/C_AMRLib/Particles.H commit bba19e122adcc51b93b0065200ac4929e87c2097 Author: mzingale Date: Fri Jul 8 15:54:28 2011 +0000 add a function particle_global_numparticles to return the total number of active particles -- for diagnostics Src/F_BaseLib/particles.f90 commit 391d413b7db96d72fa1c47ecabc11ac1ac2ec004 Author: 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 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 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 Date: Wed Jul 6 21:31:14 2011 +0000 Fix periodic wraparound in multilevel AssignDensity. Src/C_AMRLib/Particles.H commit 88e7662bdffc6f364abebdf9ae3a210311bf57b9 Author: almgren Date: Wed Jul 6 17:13:28 2011 +0000 Fix the case in AssignDensity where we need to copy from fine ghost cells onto coarse valid regions. Src/C_AMRLib/Particles.H commit 7d7f5cbee5c8c29480d252d03101f5752dca889b Author: almgren Date: Wed Jul 6 07:31:34 2011 +0000 Allow us to enforce solvability even for multilevel solves -- just enforce it at amr level = 0, not the higher levels. Src/LinearSolvers/F_MG/ml_cc.f90 commit 22838cfcc8270dbf64b2880754c92f681c4953ee Author: almgren Date: Wed Jul 6 02:59:40 2011 +0000 Eliminate GetRhoFromParticles -- this was replaced by AssignDensity and other source in CastroParticles.cpp Src/C_AMRLib/Particles.H commit 1354ed707c676d73c84f12074aef5038f506aac4 Author: almgren Date: Wed Jul 6 02:58:57 2011 +0000 Add new routine -- MultiplyParticleMass -- used in SantaBarbara initialization. Src/C_AMRLib/Particles.H commit 25df466454bd540ea7f092ef8a3f20526b4ff0df Author: almgren Date: Tue Jul 5 20:43:16 2011 +0000 Fix to GetRhoFromParticles when lev > 1 -- we need to count the contributions from particles at level lev-1 which might contribute to the density at level lev. Src/C_AMRLib/Particles.H commit 2c06cb640c8d5453db8936ada92b10393c7b38bb Author: almgren Date: Tue Jul 5 20:41:01 2011 +0000 Add new subroutine part_sumdensup, which is just like subroutine part_summassup, but differs in that it does not multiply the coarse contributions by volfrac since it works with density instead of mass. Src/C_AMRLib/Particles_1D.F Src/C_AMRLib/Particles_2D.F Src/C_AMRLib/Particles_3D.F Src/C_AMRLib/Particles_F.H commit ec0e20457e242a13276d959ceb3944ee67f95abc Author: 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 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 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 Date: Fri Jul 1 23:10:54 2011 +0000 to facilitate derivation, if necessary Src/C_BaseLib/ParmParse.H commit 6fd6b0712b6e1cd865e0df952b6227b7dcd8370d Author: marc Date: Fri Jul 1 22:50:54 2011 +0000 add hedorah to the list of special cases Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 009eb0af4410952e00ab3acfa080f9b22e936d73 Author: almgren Date: Fri Jul 1 19:11:24 2011 +0000 Fix ml_layout_build_la_array so instead of copying the entire mba, we only copy nlevel levels of it (as is done in ml_layout_build_n). Src/F_BaseLib/ml_layout.f90 commit 5ad33e6c7ba99b91d028721b91055b46bc8a349c Author: almgren Date: Fri Jul 1 06:06:03 2011 +0000 Don't print all the particles in InitFromAscii. Src/C_AMRLib/Particles.H commit 023cb64f8d417e25788a568c1078b198b777b22f Author: almgren Date: Thu Jun 30 21:59:46 2011 +0000 Add new way of building ml_layout -- ml_layout_build_la_array -- which allows us to copy existing la_array(n) instead of making new ones. Src/F_BaseLib/ml_layout.f90 commit 9be548bb4d7282bc794b5892e4a3bd927e53705f Author: almgren Date: Thu Jun 30 21:24:09 2011 +0000 Destroy ba_new once we're done with it (elminated leftover layout in MEMORY STATS) Src/F_BaseLib/make_new_grids.f90 commit 832f075efd6467c5512e241b191b89b740ce1e72 Author: lijewski Date: Wed Jun 29 16:10:50 2011 +0000 Fixed bug in InitFromAscii() when running in parallel. There was in essence an off-by-one counting bug which caused the last particle read in by cpu 0 to be the first particle read in by cpu 1, and the last particle in the file to not be read in by cpu N was not read in at all. Src/C_AMRLib/Particles.H commit d1f8921e333351b68b32f255bba16d3959ce4b1f Author: lijewski Date: Wed Jun 29 15:10:42 2011 +0000 got rid of some unused variables in Timestamp() Src/C_AMRLib/Particles.H commit bda6db560ad4a0c39913fadcd2ee8b545ff2d4a2 Author: 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 Date: Wed Jun 29 13:12:13 2011 +0000 switch to latest MPI for nan Tools/C_mk/Make.mpi commit 7b95af193539583622c41532042aa106546b10c4 Author: lijewski Date: Wed Jun 29 05:23:51 2011 +0000 remove some debugging I/O Src/C_AMRLib/TagBox.cpp commit e7d78bb0a9a7c1bb7fcc7547659bdc4c8e4f16a4 Author: lijewski Date: Wed Jun 29 05:21:17 2011 +0000 fix to previous mod when USE_MPI=FALSE Src/C_AMRLib/TagBox.cpp commit 6138342c2c7821cd8f33cc89aa214cbb5c9f7ff7 Author: lijewski Date: Wed Jun 29 04:40:38 2011 +0000 remove potential problem with send/recv args to MPI_Gatherv() being the same on the root processor Src/C_AMRLib/TagBox.cpp commit c865ef2ec22796fb676ee12d03cdc04c3cfebbb5 Author: mzingale Date: Tue Jun 28 21:51:33 2011 +0000 no -module flag for nan Tools/C_mk/Make.Linux commit 16aecd6dc69f4477c30047509f29626423ce5662 Author: mzingale Date: Tue Jun 28 21:15:01 2011 +0000 add MPI instructions for nan. Need -DMPICH_SKIP_MPICXX to make things happy Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 01ca6e3e67f39e4eaf66df68139b261b877f24f3 Author: almgren Date: Tue Jun 28 19:09:34 2011 +0000 Remove characters from word. Src/F_BaseLib/tag_boxes.f90 commit aa9445e4cbd258f6acebf33432365299d83ac41d Author: marc Date: Fri Jun 24 23:13:09 2011 +0000 Add some arguments for parallel stuff Src/C_BaseLib/.cvsignore Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ParmParse.H commit 6aab3239d31273a7665637c2e05a72e7001c1a8e Author: marc Date: Fri Jun 24 22:59:07 2011 +0000 add hg file to list Src/C_BoundaryLib/.cvsignore commit 2815573c274a7a23225abd98462e6898c5fd37db Author: marc Date: Fri Jun 24 22:40:28 2011 +0000 stupid cast that seems to be needed for idiotic GNU compiler Src/C_BoundaryLib/BndryData.cpp commit 6b151be00d98f6a8a5adb338ac71bcf1fa9e5680 Author: lijewski Date: Fri Jun 24 21:03:23 2011 +0000 more OMPing Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 5db3de4f63e56974efc9ee90481fe31e4b8a21f4 Author: lijewski Date: Fri Jun 24 21:01:36 2011 +0000 some more OMPing Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 7e81f612a845fe9c7b8581dddf3351d2e13f050f Author: lijewski Date: Fri Jun 24 21:01:02 2011 +0000 some more OMPing and moved temp from stack to allocatable Src/LinearSolvers/F_MG/mg_prolongation.f90 commit adfe9a5c3fba81944e84d123a810bf019cd33bc3 Author: lijewski Date: Fri Jun 24 21:00:21 2011 +0000 make lr, tb and fb allocatable instead of building on the stack Src/LinearSolvers/F_MG/mg_smoother.f90 commit 486514ce6d1d91e71630486ffc6c1170ef65cb41 Author: lijewski Date: Thu Jun 23 23:42:44 2011 +0000 little more OMPing Src/LinearSolvers/F_MG/mg_prolongation.f90 commit ed54327e6d0ecd0b1a50b7be90b5a0b3627d603a Author: lijewski Date: Thu Jun 23 20:10:33 2011 +0000 *** empty log message *** Src/LinearSolvers/F_MG/ml_restriction.f90 commit 1b969ad882e799db0ba660f146bebc7cc0c4aef6 Author: lijewski Date: Wed Jun 22 23:13:49 2011 +0000 single-precision constants -> double-precision constants Src/F_BaseLib/fourth_order_interp_coeffs.f90 commit 7cdf73b872c7a7756b09c606ec74ee6dd1913cc0 Author: lijewski Date: Wed Jun 22 22:11:27 2011 +0000 0 -> 0.0_dp_t in a few places Src/F_BaseLib/multifab.f90 commit 14f5f41fe96df69697ae3d85e0dfd79cb74d696a Author: lijewski Date: Wed Jun 22 21:19:15 2011 +0000 More work on periodic_add_copy(): Replace array assignments w/ calls to cpy_d() and additions with calls to cpy_d() using ml_restrict_copy_sum() as a filter. Likewise replace saxpy() calls with multifab_copy() calls using ml_restrict_copy_sum() as a filter. Src/LinearSolvers/F_MG/ml_restriction.f90 commit 0f68a8e274847fba2a47e3865195d9da0384ff20 Author: lijewski Date: Wed Jun 22 18:11:33 2011 +0000 little more simplificaton to periodic_add_copy(); can't be readily cached due to synced argument Src/LinearSolvers/F_MG/ml_restriction.f90 commit 6dd119b948d6ede093f11d006c6032881c19952f Author: almgren Date: Wed Jun 22 01:27:02 2011 +0000 max --> std::max Src/C_AMRLib/Particles.H commit 3d6742502d029487f8a05e2de72f54c064f70152 Author: almgren Date: Wed Jun 22 01:24:55 2011 +0000 Fix typo. Src/C_AMRLib/Particles.H commit cf29429bd23db382febfaf64a943e5b472423ae1 Author: almgren Date: Wed Jun 22 01:20:58 2011 +0000 Change estTimestep so that we satisfy dt = cfl * a * dx / mag_vel where mag_vel is the maximum of a component in any one direction, not the magnitude of the velocity. Src/C_AMRLib/Particles.H commit 13eeccd14962d0cf9c37e8ed0877b1b17b3a0f32 Author: almgren Date: Wed Jun 22 00:51:11 2011 +0000 estTimestep now takes a CFL in the argument list which specifies what maximum fraction of a cell the particle can cross in a timestep. Src/C_AMRLib/Particles.H commit edd57d610f3b2afc19d4a0a2a3733237be55ef07 Author: lijewski Date: Wed Jun 22 00:01:51 2011 +0000 use O2 when optimizing Tools/F_mk/comps/gfortran.mak commit 1f946cb9e799adbd645a7482ea87e60245565ee4 Author: gilet Date: Tue Jun 21 19:16:42 2011 +0000 add script to extract multiple files from HSI at a time Tools/F_scripts/extract.parallel commit 4e63435d3861384b29fa62a01621324cd20c4436 Author: lijewski Date: Tue Jun 21 19:05:17 2011 +0000 early exit from periodic_add_copy() when not periodic Src/LinearSolvers/F_MG/ml_restriction.f90 commit c6250667a9894072bd57a0ba3fc7bf0b804e4394 Author: lijewski Date: Tue Jun 21 19:04:51 2011 +0000 removed comment Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 commit d71bb0ce659081e86102bbe48b177f2f79bb8b38 Author: celdred Date: Tue Jun 21 18:25:32 2011 +0000 added gojira entry Tools/F_mk/GMakeMPI.mak commit 11cdd46a1aa18c76f4b82ba15f5a703aea88f992 Author: lijewski Date: Thu Jun 16 16:30:26 2011 +0000 removed some unused code Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Tuple.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit fd9dd5fb9dc16b56a45c75609e9adb2e5d6b8e80 Author: lijewski Date: Thu Jun 16 15:51:30 2011 +0000 removed some XT3 junk Src/C_BaseLib/Utility.cpp commit f78280aced463907b7b46e21bf70067366baeb62 Author: lijewski Date: Tue Jun 14 20:35:53 2011 +0000 remove option for calling bicubic interp on state data Src/C_AMRLib/Particles.H commit 9291908019b7aba1599c48e2d626085289c6fd24 Author: lijewski Date: Tue Jun 14 20:35:35 2011 +0000 *** empty log message *** Src/C_AMRLib/Particles_2D.F commit b677cf7587a15ced834bf165da452992bc577c70 Author: ajnonaka Date: Tue Jun 14 16:44:03 2011 +0000 now printing lo/hi/avg FAB byte spread Src/F_BaseLib/fab.f90 commit 74364aabaa73068b2b50e0ae6d6d732c95cfece7 Author: almgren Date: Mon Jun 13 20:20:35 2011 +0000 Need more files than we thought. Src/LinearSolvers/C_CellMG/Make_nyx.package commit c565ecfc4760a5857bb6503fbcd01629cf50d160 Author: almgren Date: Mon Jun 13 20:03:47 2011 +0000 Only include what we need for running NYX. Src/LinearSolvers/C_CellMG/Make_nyx.package commit b5da222c60158862ede94203fdb97b0fbb1a7a59 Author: lijewski Date: Fri Jun 10 23:48:03 2011 +0000 quiet some unsed variable warnings Src/C_AMRLib/Particles.H commit baec2180b9dddc6fcc1092c0fb372ddc88c4e6a6 Author: lijewski Date: Fri Jun 10 23:45:29 2011 +0000 we store the average advected velocity in particles that use AdvectWithUmac() for LMC Src/C_AMRLib/Particles.H commit dea4af6351150aae43f1d51484f8ac8903b37667 Author: lijewski Date: Fri Jun 10 23:39:54 2011 +0000 *** empty log message *** Src/C_AMRLib/Particles_2D.F commit 6d4f807926cfa4174c705f99a816666bac623e14 Author: lijewski Date: Fri Jun 10 17:43:22 2011 +0000 make it explicit that we are using cell-centered data in bicubic Src/C_AMRLib/Particles_2D.F commit 299689332e319dcd6799916d75a27d328318801a Author: wqzhang Date: Fri Jun 10 16:23:59 2011 +0000 more radiation benchmarks added Tools/C_util/regtests/radiation-tests.ini Tools/C_util/regtests/test-Ubuntu.py commit 8a8203e98e3a3adcdd4a64617ec76c33a52bef46 Author: lijewski Date: Thu Jun 9 23:25:54 2011 +0000 *** empty log message *** Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles_2D.F Src/C_AMRLib/Particles_F.H commit 07853c1cf9a5d074a30ef790ce54855573bb7827 Author: lijewski Date: Wed Jun 8 21:40:33 2011 +0000 more work on AdvectWithUmac(); now Redistribute between predictor and corrector Src/C_AMRLib/Particles.H commit fc7a2c2e658c1805561089a1731d97027c64aa93 Author: lijewski Date: Wed Jun 8 19:50:12 2011 +0000 *** empty log message *** Src/C_AMRLib/Particles.cpp commit b708b6397377646257a3c023af59c9055d8b8949 Author: mzingale Date: Wed Jun 8 17:46:17 2011 +0000 add a generic catch for a linux machine with the generic localhost name (like a typical laptop), with an MPIHOME defined to an mpich directory. Tools/F_mk/GMakeMPI.mak commit bf08fe9b9de2000311598d8680bcd8888c8813cd Author: 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 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 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 Date: Mon Jun 6 22:15:21 2011 +0000 oops. Src/F_BaseLib/interp.f90 commit a28690dca4260c488fec8451d8a203079553960a Author: almgren Date: Mon Jun 6 22:13:37 2011 +0000 fix name of interp_coeffs_module -> fourth_order_interp_coeffs_module. Src/F_BaseLib/interp.f90 commit f53119a5e3707b9000c73ecb52a1af38c9a16455 Author: lijewski Date: Mon Jun 6 21:38:58 2011 +0000 didn't have vel interp quite right in AdvectWithUmac() Src/C_AMRLib/Particles.H commit 857a7129fe46af8de66fc1b6171da0d939a07249 Author: lijewski Date: Mon Jun 6 19:51:29 2011 +0000 Pulled the core of Interp() into InterpDoIt() which is now called by AdvectWithUmac(). Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 85587e65aa23b18ad932427ed3d66ab36d4e4a4b Author: 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 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 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 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 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 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 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 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 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 Date: Thu May 26 21:11:27 2011 +0000 *** empty log message *** Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit f2ff9233380c7bedff8f678b94d4922ede4a26f4 Author: lijewski Date: Thu May 26 20:57:34 2011 +0000 don't build lasrctmp in fluxassoc_build() if not really needed Src/F_BaseLib/layout.f90 commit 7e77e659fe84654e42c6509a6917a62b5a0276b9 Author: lijewski Date: Thu May 26 20:30:27 2011 +0000 don't build latmp in boxassoc_build() if not really needed Src/F_BaseLib/layout.f90 commit 776e4b688568cec5148d53d8a7da5f7fe92daf7c Author: lijewski Date: Thu May 26 19:29:57 2011 +0000 multifab_sum_boundary() now used layout_get_box_intersector() stuff Src/F_BaseLib/multifab.f90 commit e5fedf82f39e37f4aba0a7d3af6117f042d0105a Author: 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 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 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 Date: Mon May 23 20:52:14 2011 +0000 Fix error message. Src/F_BaseLib/particles.f90 commit db784ca3967dde67177ad3c3b9f94289a8cdb432 Author: 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 Date: Mon May 23 18:42:30 2011 +0000 Add comment. Src/F_BaseLib/particles.f90 commit 83b9a8ca54af6185f5bb45c7648f16f4b86b06cf Author: almgren Date: Thu May 19 19:47:51 2011 +0000 Added some debugging to InitCosmo. Src/C_AMRLib/Particles.H commit 05fc949f4be1061453164d76ca63d78f1aea509c Author: almgren Date: Thu May 19 18:21:52 2011 +0000 New version of InitCosmo(). Src/C_AMRLib/Particles.H commit ac4a76c37a96ee91a5d97d66b3754ee6581d1fc5 Author: lijewski Date: Wed May 18 20:49:11 2011 +0000 IncrementWithTotal() now returns a long not an int. Ints are only guaranteed to hold numbers up to 2^31-1. All callers of this routine should change their return value from int to long as well. Src/C_AMRLib/Particles.H commit 9de2aeba25aa82479f6a0296a7ef831bf2d2541b Author: almgren Date: Wed May 18 19:19:22 2011 +0000 Make a version of MoveRandom that takes level as an argument. Src/C_AMRLib/Particles.H commit 6ee09ccef5acf10e09ff3089a72f6cd85a6bd85c Author: lijewski Date: Wed May 18 16:07:38 2011 +0000 AdvectWithUmac() now assumes we have at least one ghost cell in umac. This means we only have to do one Redistribute() per call instead of two. It also means that particles that cross a periodic boundary work properly. Src/C_AMRLib/Particles.H commit bf573df91f390d32dac33f51de47b6d0d2047df7 Author: lijewski Date: Mon May 16 22:54:34 2011 +0000 delta in move_advect() didn't take into account a non-zero problo Src/F_BaseLib/particles.f90 commit 6ced58a03ae655f315fb156e4431754b9969499c Author: lijewski Date: Mon May 16 22:47:19 2011 +0000 delta in MoveKick[Drift] routines didn't take account of possibility of non-zero problo Src/C_AMRLib/Particles.H commit b550f28bfec6cbe649d60cfcc4a771b82e7f5cd8 Author: lijewski Date: Mon May 16 21:48:02 2011 +0000 fixed my typo Src/C_AMRLib/Particles.H commit d5d55215e957a53d7fd7e2a93943049f97a37d74 Author: almgren Date: Mon May 16 21:13:58 2011 +0000 Remove unused "grid" Src/C_AMRLib/Particles.H commit 3d9d0fdfad0d5b7837677e92b18ada3b5fc56523 Author: lijewski Date: Mon May 16 17:25:21 2011 +0000 removed unused variable Src/C_AMRLib/Particles.H commit d8b7b689bb9e8cc0e928f39b7c8cbc68da905921 Author: 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 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 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 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 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 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 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 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 Date: Thu May 12 22:20:33 2011 +0000 removed names from Timestamp Src/C_AMRLib/Particles.H commit bac09666619461957d350cfe0f2d9f82fd45360d Author: lijewski Date: Thu May 12 20:58:44 2011 +0000 close() Timestamp file after flush() Src/C_AMRLib/Particles.H commit b464cf223e59b0fe2953c6da4430c0db95aa0d15 Author: lijewski Date: Wed May 11 17:55:40 2011 +0000 exist ASAP from Timestamp() if no work to do Src/C_AMRLib/Particles.H commit 8bc648e3df6c18aa746bd727e524bc72e81db0a3 Author: lijewski Date: Tue May 10 22:36:04 2011 +0000 make AssignDensityDoIt() work with non zero-based prob domain like Interp() Src/C_AMRLib/Particles.H commit 60c408f21723411568f8c111e80455e1e792e94b Author: lijewski Date: Tue May 10 22:34:35 2011 +0000 make sure frac is in [0,1] in a floating-point way Src/C_AMRLib/Particles.cpp commit 2bab199c83876a4f26c0fe090e5d4ae0f350c249 Author: lijewski Date: Tue May 10 18:56:30 2011 +0000 frac calculation in Interp now works with non zero-based prob domain Src/C_AMRLib/Particles.cpp commit cdf1d28eb7f3cef4d29a3c8899a225efd1cb095c Author: lijewski Date: Tue May 10 04:55:21 2011 +0000 *** empty log message *** Src/C_AMRLib/Particles.H commit 11496dbf99136717cf8d5cf6b6dbb1090238538d Author: lijewski Date: Mon May 9 20:03:29 2011 +0000 *** empty log message *** Src/C_AMRLib/Particles.cpp commit 4ecef25f64d4b2d08c1ca0d2e784e0ef3c788dbe Author: lijewski Date: Mon May 9 19:48:36 2011 +0000 just use MyProc when setting initial m_cpu Src/C_AMRLib/Particles.H commit a6e3de95f52692fb1abe0f2dc02455b182f40e1e Author: lijewski Date: Mon May 9 17:27:45 2011 +0000 removed lev argument from Interp() Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit a7b2b08a76ceff86fe04b242cae3e458972b3251 Author: lijewski Date: Mon May 9 16:43:30 2011 +0000 Timestamp() must now be passed the MultiFab to be sampled Src/C_AMRLib/Particles.H commit 005328d7cff938296d72e97ec29b9ed8a207f93c Author: lijewski Date: Mon May 9 05:51:58 2011 +0000 some I/O mods Src/C_AMRLib/Particles.H commit c66fd71313ac93f59e3e022ff20423bf9f0e686f Author: lijewski Date: Mon May 9 05:51:03 2011 +0000 removed some I/O Src/C_AMRLib/Particles.cpp commit 6d3e4367263341da38b978551a64a77e1cff3047 Author: 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 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 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 Date: Mon May 9 00:09:20 2011 +0000 refinement to Timestamp() Src/C_AMRLib/Particles.H commit 90c2093d82551068d67d5348d8b99832cca73770 Author: lijewski Date: Sun May 8 20:04:49 2011 +0000 Undefaulted the second argument to InitFromAsciiFile(). This way is someone updates to the latest code and tries to use it, they'll get an error, until I've gotten around to fixing all calling sequences. Src/C_AMRLib/Particles.H commit a68a43c985e9340e7aafc954608048639697ae02 Author: lijewski Date: Sun May 8 19:37:15 2011 +0000 Apparently InitFromAsciiFile() has changed since I wrote it. Instead of just reading in the position data, N bytes of m_data where also being read it. Not sure how reading in all those bytes could possibly make sense since some of those bytes are there only to hold temporary position data in AdvectWithUmac(), but I had to change it a bit in order to make the routine work when I only want to read in positions: I added a default integer argument "extradata", that defaults to zero, which is the number of bytes of data in m_data to read in for each particle. It MUST be <= N. The default way to use InitFromAsciiFile() is now to read in just positions. If you want to get "extra" data read in for each particle, you must specify the count as the second argument of the call. Src/C_AMRLib/Particles.H commit e6d4706e9297c294f364e87beb63a992431431c1 Author: lijewski Date: Sun May 8 19:02:58 2011 +0000 remainder of particles in InitFromAscii() needs to go to last CPU not IOProc Src/C_AMRLib/Particles.H commit cfc3e121f6c54dfc5f9f384187138ae93a4569ec Author: 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 Date: Fri May 6 21:52:07 2011 +0000 changed AdvectWithUmac() to John's satisfaction Src/C_AMRLib/Particles.H commit a75884e390c97f0ef40b138d181efc3b780d6fec Author: 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 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 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 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 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 Date: Wed May 4 19:46:04 2011 +0000 early exit from Increment() Src/C_AMRLib/Particles.H commit 605884642822b536f131d7e843ecd0aa3223b8c6 Author: lijewski Date: Wed May 4 17:10:37 2011 +0000 added RemoveParticlesNotAtFinestLevel() needed by HeatTransfer Src/C_AMRLib/Particles.H commit 693f459f4d079dcd967bb6f95dd1bc688465d55a Author: lijewski Date: Tue May 3 21:01:37 2011 +0000 removed some excess whitespace when printing in verbose Src/C_AMRLib/Particles.H commit 82e41c43b9c2ef8ae5ae975443ea370c89013b3c Author: lijewski Date: Tue May 3 20:00:00 2011 +0000 no longer force Timestamp() to have non-empty names and indices Src/C_AMRLib/Particles.H commit 02695422061820d45873bc32039f617256c94c6c Author: 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 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 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 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 Date: Thu Apr 28 21:59:53 2011 +0000 Correct criterion for destroying gcrse. Src/F_BaseLib/fillpatch.f90 commit e9d8f693f9d1d7e360910b00a2548e5b72a3287e Author: almgren Date: Thu Apr 28 20:56:38 2011 +0000 Changes by Ann & Mike L. which hopefully fix the problems we were seeing. Still not clear if this will work in all cases; we are assuming that proper nesting covers situations. Src/F_BaseLib/fillpatch.f90 commit 28650c3c29d14ce24d9cdfdbd6a269a0ded7fbc8 Author: almgren Date: Thu Apr 28 19:33:36 2011 +0000 If ng = 0 define ncomp(crse) components of gcrse (used to default to 1). Src/F_BaseLib/fillpatch.f90 commit 0f7222451b2ef7c3674389623b76f0bb4a8ffa4a Author: almgren Date: Sun Apr 24 21:17:11 2011 +0000 Allow for fourth order stencil with stencil_width = 2. Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 9d9d75484b1c8f8a0cbdc5fa43c1c80588cb2d15 Author: almgren Date: Sun Apr 24 21:09:14 2011 +0000 If fourth_order = .true. then call fourth_order_interp instead of lin_cc_interp. Src/F_BaseLib/fillpatch.f90 commit 09cb63fe4a26628c69f2b40c26f121c0d2555424 Author: 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 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 Date: Fri Apr 22 21:37:17 2011 +0000 changed some 0 -> ZERO Src/LinearSolvers/F_MG/stencil.f90 commit 2adea4dba94b682c675f8417f3b80d147b5f0c55 Author: almgren Date: Fri Apr 22 21:35:20 2011 +0000 1) Pass through optional argument stencil_width_input. 2) Send ng=0 to fillpatch -- no need to create ghost cells of the buffer region mf's around the fine grids. Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 4a8196886bf909425d84d1e2a7f96ccb375e3b63 Author: almgren Date: Fri Apr 22 21:29:06 2011 +0000 Allow for a more general stencil_width (still defaults to one) Src/F_BaseLib/fillpatch.f90 commit b0aa3d5d85f7c77112d8fbb46b178b7ff02c574b Author: almgren Date: Fri Apr 22 20:18:52 2011 +0000 Fix test on whether coeffs sum to zero (used for whether we enforce solvability) Src/LinearSolvers/F_MG/ml_cc.f90 commit a52813126f4ecb792a0ebafa76e10a77fc894aba Author: almgren Date: Fri Apr 22 20:07:27 2011 +0000 Add new function -- "max_of_stencil_sum" that looks just like stencil_norm but doesn't take the absolute value of each component before summing. Src/LinearSolvers/F_MG/stencil.f90 commit 6ad77c451b572c5a0916b660410bd41dec7f421e Author: 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 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 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 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 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 Date: Wed Apr 13 21:15:20 2011 +0000 some OMP Src/C_AMRLib/FLUXREG_3D.F commit a97fe5d304dba7becaf09145fc4cba82dceaed0f Author: lijewski Date: Wed Apr 13 21:03:26 2011 +0000 minor performance improvement Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F commit 55eb06b7dc53fbcb3d9e091e88c9a2b438a6c24f Author: 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 Date: Fri Apr 8 01:34:01 2011 +0000 *** empty log message *** Tools/C_util/ViewMF/viewMFcol.cpp commit f5f4666586a88cc56957fcd518011c69336505e1 Author: lijewski Date: Thu Apr 7 21:18:19 2011 +0000 removed all references to USE_THREADS Src/C_BaseLib/test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/GNUmakefile Tests/C_BaseLib/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile Tools/C_mk/Make.AIX Tools/C_mk/Make.OSF1 Tools/C_mk/Make.defs commit f12fbc91d63c458b990fdbbff06c025f874eda04 Author: lijewski Date: Sat Apr 2 23:26:07 2011 +0000 minor simplification of AssignDensity() Src/C_AMRLib/Particles.H commit 82ab1bb973d33b8cb3ce36d007589084d6c2aa8f Author: lijewski Date: Fri Apr 1 23:15:23 2011 +0000 *** empty log message *** Tools/C_mk/Make.mpi commit f457f3aecf5f59bf196d84646b1ec060e8c634d1 Author: lijewski Date: Fri Apr 1 17:36:21 2011 +0000 added GPROF stuff Tools/F_mk/comps/gfortran.mak commit 89933d91bd53141c6933fca0489ad05681415747 Author: almgren Date: Thu Mar 31 18:03:47 2011 +0000 Add comments about which MoveKick or MoveKickDrift function we're calling -- the one with gravity at cell centers or the one with the normal components of gravity on faces. Src/C_AMRLib/Particles.H commit e861d88b762ecb67f4cec33291376ac9198dba81 Author: 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 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 Date: Wed Mar 30 23:59:27 2011 +0000 integrated in new SumPeriodicBoundary(dstmf,srcmf) Src/C_AMRLib/Particles.H commit eefb2ed9f75c078b31f106fc8442c7a14bfcd066 Author: lijewski Date: Wed Mar 30 23:58:51 2011 +0000 Wrote SumPeriodicBndry() taking a srcmf and dstmf. Still needs to be tested. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 164218bfd121a1fcc83a701d98b98dd301e0215d Author: lijewski Date: Wed Mar 30 21:42:56 2011 +0000 more work on AssignDensity(); still not right for level 1 grid abutting periodic boundary Src/C_AMRLib/Particles.H commit 86b7ff10c1f6690ed1038ce96100088f00a510b9 Author: almgren Date: Wed Mar 30 19:27:13 2011 +0000 1) Change verbosity threshhold. 2) If there are no particles at a level then return a negative est_dt for that level. Src/C_AMRLib/Particles.H commit fa2704113bfdcdabdfa927ee71e3e69305ffd387 Author: almgren Date: Wed Mar 30 18:28:55 2011 +0000 if particles.verbose > 0 then print out total number of particles when reading from ascii file. Src/C_AMRLib/Particles.H commit 42740248cc895aea2657556a44f310fdb87432c2 Author: 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 Date: Wed Mar 30 17:44:22 2011 +0000 Add setval of tcmf. Src/C_AMRLib/Particles.H commit 639adad40603a008ed1e6a7eb85e36df63567751 Author: almgren Date: Wed Mar 30 17:08:00 2011 +0000 Make sure to call multifab_fill_boundary on crse mf when filling bndry_reg. Src/F_BaseLib/bndry_reg.f90 commit 1449b4475e85b435c1e55708a7339070ac31e17d Author: 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 Date: Tue Mar 29 20:35:46 2011 +0000 more work on multi-level AssignDensity() Src/C_AMRLib/Particles.H commit 2e607c6ec3c47588f94d9efc76ca681fd73a9900 Author: lijewski Date: Tue Mar 29 20:24:20 2011 +0000 more work on multi-level AssignDensity() Src/C_AMRLib/Particles_1D.F Src/C_AMRLib/Particles_2D.F Src/C_AMRLib/Particles_3D.F commit 1ff8b6c60beea137c5bc0c00dec796c32a2711b5 Author: lijewski Date: Tue Mar 29 17:43:39 2011 +0000 more work on multi-level AssignDensity() Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles_F.H commit efa64dda0100f8c22a6937a18b76089f95944f3c Author: lijewski Date: Tue Mar 29 17:28:13 2011 +0000 some work on multi-level AssignDensity() Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles_1D.F Src/C_AMRLib/Particles_2D.F Src/C_AMRLib/Particles_3D.F Src/C_AMRLib/Particles_F.H commit df8f39e69bf64e688be67dbf6fac14113a4443ac Author: lijewski Date: Mon Mar 28 23:00:26 2011 +0000 *** empty log message *** Src/C_AMRLib/Particles_3D.F commit 546dc04d610a66ffa2ade5411840500312715619 Author: lijewski Date: Mon Mar 28 23:00:13 2011 +0000 added AssignDensityDoIt() Src/C_AMRLib/Particles.H commit 33521bafebe5b344063677ca39b2028d63365af3 Author: lijewski Date: Mon Mar 28 22:37:45 2011 +0000 *** empty log message *** Src/C_AMRLib/Particles_1D.F Src/C_AMRLib/Particles_2D.F commit daf83bee7ed0c0fe46ddc72600d3469b0cef00cf Author: lijewski Date: Mon Mar 28 22:20:08 2011 +0000 added part_summassup() Src/C_AMRLib/Particles_3D.F Src/C_AMRLib/Particles_F.H commit deeef1897a44aba4a4faa4e53755439cae10d5e1 Author: lijewski Date: Mon Mar 28 20:32:42 2011 +0000 added part_sumdown() Src/C_AMRLib/Particles_3D.F Src/C_AMRLib/Particles_F.H commit 51ba655bac551c1aa9ed204644295def2755f583 Author: lijewski Date: Mon Mar 28 16:19:35 2011 +0000 mod to quiet g++ Src/C_AMRLib/Particles.H commit 146912ef7a3289d09b79be4154cc0dcf7df1ee3a Author: lijewski Date: Fri Mar 25 18:01:48 2011 +0000 some OMP refinement Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/stencil.f90 commit afc37515da2d136cf9c2c40ab4a442e9b5dae86b Author: lijewski Date: Fri Mar 25 17:11:38 2011 +0000 some OMP refinement Src/F_BaseLib/fab.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/multifab.f90 commit bed95c1771e0162447b847c7e30b3ea48bda9700 Author: lijewski Date: Thu Mar 24 21:27:31 2011 +0000 some OMP refinement Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/CG_3D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LP_3D.F commit 9044bb515ab7073fbd6ce16a13426c00d1bc300b Author: lijewski Date: Thu Mar 24 20:50:43 2011 +0000 some OMP refinement Src/C_AMRLib/INTERP_3D.F commit 21353eb59ea6f4ef48088a3a7803744bf8d8af49 Author: lijewski Date: Thu Mar 24 20:37:37 2011 +0000 some OMP refinement Src/C_BaseLib/SPECIALIZE_3D.F commit 2140cb837261be7410fbdecf6466f6d2791996a7 Author: lijewski Date: Tue Mar 22 20:24:56 2011 +0000 some cleanup Src/C_AMRLib/Amr.cpp Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/interface.cpp commit 8e36d2b91ba4644c9d591a08d6b1338f7930bd44 Author: lijewski Date: Tue Mar 22 20:02:48 2011 +0000 No longer need to call AddToCache() to recache some MultiFabs. DistributionMapping::FlushCache() now only removes DMs that are not referenced by any MultiFabs. Src/C_AMRLib/Amr.cpp commit 260f9bf32f587a4506fc589c30ca791a3227d4e1 Author: lijewski Date: Tue Mar 22 20:01:39 2011 +0000 The cache is now a std::map instead of a std::vector. FlushCache() now only removes DMs that are not referenced by any MultiFabs. Removed AddToCache(). Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 66488df6e0ed070dd1cbc5c48dc2bd07c34a8c07 Author: almgren Date: Sun Mar 20 17:42:38 2011 +0000 Make the minion smoother be GSRB, for now anyway. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 commit 2417f0eab67ab7cb83ff6577fd634cd19cdf9267 Author: almgren Date: Sun Mar 20 15:36:34 2011 +0000 Add crse flux construction for Minion's 2D cross stencil (ns = 9 as opposed to 7). Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit a362034c826b262715bea55938327e4ed16cd339 Author: almgren Date: Sun Mar 20 15:35:56 2011 +0000 Add flux construction for Minion's 2D cross stencils (ns = 9 as opposed to 7) Src/LinearSolvers/F_MG/stencil.f90 commit 8750d3d4279eab462a7444e63f4b6ae853669717 Author: almgren Date: Sun Mar 20 15:29:42 2011 +0000 Fix typo. Src/LinearSolvers/F_MG/ml_cc.f90 commit bb3be359ed62d543b91ca7d4911ad760002341e4 Author: almgren Date: Sun Mar 20 15:26:43 2011 +0000 Clean up how we test whether we should enforce solvability. Src/LinearSolvers/F_MG/mg.f90 commit 063c6ec9b2274f439875dc176434a318f5e413a4 Author: almgren Date: Sun Mar 20 15:25:59 2011 +0000 Use new coeffs_sum_to_zero flag to decide whether to enforce solvability. Src/LinearSolvers/F_MG/ml_cc.f90 commit 46db06e6f82a444333a9ce83d20e1024f688bde0 Author: almgren Date: Sun Mar 20 15:25:33 2011 +0000 Add coeffs_sum_to_zero flag in mgt Src/LinearSolvers/F_MG/mg_tower.f90 commit fb822cea060a2e912c938c110a1862e9f07a2c38 Author: almgren Date: Sun Mar 20 02:51:00 2011 +0000 Need to allow for nghost > 1. Src/F_BaseLib/create_umac_grown.f90 commit f9dc28eec61dc7ec015c1d09241399ed26d688e1 Author: almgren Date: Sat Mar 19 20:15:17 2011 +0000 Grow the fine region by ng_fill instead of 1 so that we fill the right zone of ghost cells. Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 297f684479389da634491e64e33c31b70a8ded84 Author: almgren Date: Sat Mar 19 01:24:04 2011 +0000 Remove unused variable. Src/LinearSolvers/F_MG/ml_cc.f90 commit d1dbfe9f37d9e7113cf9cabfc14398deaf3ece97 Author: almgren Date: Fri Mar 18 23:59:32 2011 +0000 Comment out the making of bottom_singular until I figure out how to differentiate MAC solves from viscous/diffusive solves. Src/LinearSolvers/F_MG/mg.f90 commit 9359d5c6dc4c8cec356c27bcafc1c05463c31dbd Author: lijewski Date: Fri Mar 18 16:40:29 2011 +0000 removed some too-little-work OMP loops Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/stencil.f90 commit ee4a5a8651742057c8e25f24146a4e06187e49a5 Author: lijewski Date: Fri Mar 18 16:03:41 2011 +0000 removed some too-little-work OMP loops Src/F_BaseLib/fab.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/multifab.f90 commit cd7454eb59e27aedd83f089737e3277f2cf7ac22 Author: lijewski Date: Thu Mar 17 22:11:14 2011 +0000 removed some too-little-work OMP loops Src/LinearSolvers/C_NodalMG/amr_real3d.f Src/LinearSolvers/C_NodalMG/hg_avg3d.f commit 338fa647ea9003dd64569043104e88ba2d70dbea Author: lijewski Date: Thu Mar 17 21:13:01 2011 +0000 removed some too-little-work OMP loops Src/C_BaseLib/COORDSYS_3D.F commit 7cb36dbe8cf80a87ad378e3939e0184f2cad4a0e Author: lijewski Date: Thu Mar 17 21:00:23 2011 +0000 removed some too-little-work OMP loops Src/C_AMRLib/FILCC_3D.F Src/C_AMRLib/INTERP_3D.F commit e45a546d4b670e0e183fa89a21dd282247465ddc Author: lijewski Date: Thu Mar 17 20:52:50 2011 +0000 removed some too-little-work OMP loops Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/CG_3D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LP_3D.F commit cf12f0a8b1f6afb20e7224f7d33d0a609218a5e5 Author: almgren Date: Wed Mar 16 19:50:38 2011 +0000 We now allow crse to have more than one ghost cell (before required exactly one) and we only copy what is needed for interpolation. Src/F_BaseLib/create_umac_grown.f90 commit cb72fe9926711677eedeae9acc0d26ef2e478288 Author: almgren Date: Wed Mar 16 17:56:35 2011 +0000 Convert is_singular from integer to logical. Src/LinearSolvers/F_MG/mg.f90 commit 1238084fb571304a614ebc13ff7909b733aa9963 Author: almgren Date: Wed Mar 16 17:34:59 2011 +0000 Add "is_singular" optional argument to mg_tower_build so that you can over-ride the local test for solvability. Src/LinearSolvers/F_MG/mg.f90 commit 40b92c9e79cf0ce927c3400d4cee847ecad57683 Author: nazgul Date: Tue Mar 15 23:56:12 2011 +0000 Adding ability to specify DistributionMapping when defining FluxRegisters. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 6496454e9463a50842fd81c2ce5cbc287a7ebc6b Author: nazgul Date: Tue Mar 15 23:55:15 2011 +0000 Adding ability to specify DistributionMapping when defining these objects, in case the correct map has been flushed from the cache. Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 4c3e728e0161dbe06274a5b75cc6e81392a75362 Author: almgren Date: Thu Mar 10 23:42:04 2011 +0000 Add pleiades stuff. Tools/C_mk/Make.mpi commit 9e9ac222bf00746da9d412e516df37b71c8d2bc3 Author: wqzhang Date: Wed Mar 9 23:54:05 2011 +0000 Some new features. If one types "touch dump_and_continue" in the run directory, a checkpoint file and a plot file will be generated and then the run will continue. The "dump_and_continue" file will be deleted. If one types "touch stop_run" in the run directory, the run will stop without generating a checkpoint. The "stop_run" file will be deleted. If one types "touch dump_and_stop" in the run directory, a checkpoint file and a plot file will be generated and then the run will stop. The "dump_and_stop" file will be deleted. Src/C_AMRLib/Amr.cpp commit 4b563eed384008f151d3235e57a095a77236ec48 Author: ajnonaka Date: Wed Mar 9 13:32:07 2011 +0000 typo in output string Src/F_BaseLib/fab.f90 commit 1fab0e02a30478beff2acdf79d2552cdc498545a Author: almgren Date: Tue Mar 8 21:04:50 2011 +0000 Modify the verbosity tests so that the "particles added per processor" print only happens if verbosity > 1. Src/C_AMRLib/Particles.H commit 6d3094e5eb4a2a731ec26e7bda3ba216e6cd4935 Author: marc Date: Tue Mar 8 18:47:47 2011 +0000 *** empty log message *** Tools/C_util/ViewMF/GNUmakefile Tools/C_util/ViewMF/mfMinMax.cpp commit 9ecdc4aedd638a06172ec165897fb7626e0f93c4 Author: lijewski Date: Tue Mar 8 02:09:14 2011 +0000 little mod to previous OMP reorg of estTimestep() Src/C_AMRLib/Particles.H commit 4aab43cc31ace18a6bb5c04a9eded8087e4e5c8e Author: almgren Date: Tue Mar 8 01:32:18 2011 +0000 Mike L's fixes to estTimestep make this work with PGI + OMP. Src/C_AMRLib/Particles.H commit 171bf8c3b5dadfed8fa9a3f5b279ae3457681b91 Author: almgren Date: Mon Mar 7 03:39:11 2011 +0000 Add additional solvability enforcement -- *before* we start the V-cycle. We might even be able to use this only and eliminate the tests inside the V-cycles .... but for now we'll leave them in. Src/LinearSolvers/F_MG/ml_cc.f90 commit 02f7c6714f89e5586e6cd22edea08ad77c615748 Author: 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 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 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 Date: Thu Mar 3 23:19:38 2011 +0000 Verbose --> SetVerbose Src/C_AMRLib/Particles.H commit decf8586bec23f742edaddc1499f895f8e468496 Author: 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 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 Date: Wed Mar 2 23:21:49 2011 +0000 Comment out print statement. Src/LinearSolvers/F_MG/mg.f90 commit 10148680c4c97961f463e4165a46c14023c7afa5 Author: almgren Date: Wed Mar 2 23:21:08 2011 +0000 Make the cell-centered single-level solver solvable if singular -- EACH V-cycle. Src/LinearSolvers/F_MG/ml_cc.f90 commit 36697343c540ba3bbe0bd08a25d1fc3f7a6b86f1 Author: almgren Date: Wed Mar 2 23:20:11 2011 +0000 Fix print statement. Src/LinearSolvers/F_MG/itsol.f90 commit 092c96ddaf873fa943cc8539db1e5c38770ddd59 Author: lijewski Date: Tue Mar 1 17:12:29 2011 +0000 simplified AdvectWithUMac() Src/C_AMRLib/Particles.H commit 0056194423bd84c11fb7a3cc76dcafccf9587a00 Author: lijewski Date: Tue Mar 1 17:09:07 2011 +0000 simpler but equivalent formulas for delta and vel in move_advect Src/F_BaseLib/particles.f90 commit 15359151ffd1f62f4bf3351fd19c2bd95ad3e180 Author: wqzhang Date: Mon Feb 28 23:10:19 2011 +0000 test.py does not work on Ubuntu (at least 10.04 LTS) because os.system calls dash instead of bash Tools/C_util/regtests/test-Ubuntu.py commit a13afe27106e45a63ad41d932f6795067f69cbfc Author: wqzhang Date: Mon Feb 28 23:05:34 2011 +0000 *** empty log message *** Tools/C_util/regtests/radiation-tests.ini commit 76a3ed532b637df8bb0aa26f49d7ce6664960dfa Author: lijewski Date: Mon Feb 28 21:17:26 2011 +0000 removed an assertion Src/C_AMRLib/Particles.H commit a276abdc90f9e195149013cbb196e5a02abbcef6 Author: mzingale Date: Mon Feb 28 21:06:53 2011 +0000 the predictor and corrector in the advection were both doing almost the same thing -- remove redundant code by looping over the velocity interpolation and redistribution Src/F_BaseLib/particles.f90 commit 202d43019f5c85f7d01c68bccb5a2139f59fa87f Author: lijewski Date: Mon Feb 28 19:03:52 2011 +0000 bit more simplification Src/C_AMRLib/Particles.H commit da99837d45613ef4482d2618c7b632c60bf486b1 Author: 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 Date: Mon Feb 28 18:23:43 2011 +0000 some cleanup & speedups Src/C_AMRLib/Particles.H commit b9113d8337669d092906e46006a0853485e8aec2 Author: lijewski Date: Mon Feb 28 17:49:31 2011 +0000 added code to check to infs mirroring nan code Src/F_BaseLib/fab.f90 Src/F_BaseLib/fabio_c.c commit 8191987436b691a83be2c3d0b44392f01b1a57a1 Author: almgren Date: Sat Feb 26 01:59:18 2011 +0000 Remove extraneous definition. Src/C_AMRLib/Particles.H commit ecc0a32a9959a6a70cf29f4974e0bcfe780e25bd Author: almgren Date: Sat Feb 26 01:50:11 2011 +0000 Change default in estTimeStep to be 0.5 rather than 0.1 Src/C_AMRLib/Particles.H commit ad32e4b18ad64991c9fab3090ac95b174b138847 Author: almgren Date: Sat Feb 26 01:45:33 2011 +0000 Added another version of moveKick and moveKickDrift that takes edge-based gravity components rather than cell-based. Src/C_AMRLib/Particles.H commit fb3267b96504790cbf9114432ed804ad6e612f4b Author: almgren Date: Sat Feb 26 00:03:02 2011 +0000 Remove print statement. Src/LinearSolvers/F_MG/itsol.f90 commit fefb50e6c1ecbb58b1e9eca675c6d0eb832d2911 Author: lijewski Date: Fri Feb 25 22:39:33 2011 +0000 FAB_CONTAINS_NAN now works for gcc; need to test on __GNUC__ macro Src/F_BaseLib/fabio_c.c commit c793cbf2566a0a9c93f73be7c84d2414b61ef9fc Author: lijewski Date: Fri Feb 25 22:13:25 2011 +0000 contains_nan_bx_c() Src/F_BaseLib/fab.f90 commit a3d1537258146a33d020563b145f6e36506e7a97 Author: 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 Date: Fri Feb 25 21:10:52 2011 +0000 added contains_nan_c() Src/F_BaseLib/fab.f90 commit b93d6a7a7c8466b1876e10bd823070d8bb651734 Author: lijewski Date: Fri Feb 25 18:47:10 2011 +0000 some simplification of add_point() Src/F_BaseLib/particles.f90 Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit c49682e5717c7fac9d38eb694ad23efbe4d5dc7a Author: mzingale Date: Fri Feb 25 16:52:21 2011 +0000 remove the conditional_add routine -- it required that all processors call it at the same time -- this is not how we do the particle adds in MAESTRO. Instead, implement a less ambitious version by adding the "conditional" logical optional argument to the normal pointwise add routine. If true, then this will only add the particle if there is not already one in the same zone/level. Src/F_BaseLib/particles.f90 commit da0d39fa20dcefb72658a32b5d48935ef5baf468 Author: marc Date: Thu Feb 24 01:06:52 2011 +0000 *** empty log message *** Tools/C_util/ViewMF/viewMF.cpp commit e754a154e1dac939fcfac94c9d6b6f582d01dc57 Author: almgren Date: Tue Feb 22 23:53:07 2011 +0000 Make sure to do singular adjustment *before* diagonal preconditioning. Src/LinearSolvers/F_MG/itsol.f90 commit b36e5e07bc95c3c7939f8f8501c320f080f8bc64 Author: 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 Date: Tue Feb 22 21:48:34 2011 +0000 Change Init --> InitFromAsciiFile Src/C_AMRLib/Particles.H commit d45146841a13d705b7e98791a1c4fdd1fb895f7e Author: mzingale Date: Sun Feb 20 15:45:19 2011 +0000 first cut at a "conditional add" routine -- only add a particle if it is some distance (dr) away from any existing particle. Needs more testing, but seems to work. Src/F_BaseLib/particles.f90 commit ec735c5b5208b57c5f092168b512eb147dc51d28 Author: almgren Date: Fri Feb 18 21:28:34 2011 +0000 1) Wrapped printing of read time for PROBINIT inside verbose>1 test. 2) Added sanity checks when restarting to check n_cell and ref_ratio from inputs file against what is in checkpoint file. If the index-space domains at all levels don't match then the code aborts on restart. Src/C_AMRLib/Amr.cpp commit 51144f0206314ae2ae58bcb35f4851d7493c869c Author: lijewski Date: Thu Feb 17 17:14:24 2011 +0000 more specialized versions of contains_nan() and contains_inf() Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp commit 3b36953818e096536b48b416dda94b38e019bddd Author: lijewski Date: Thu Feb 17 00:02:18 2011 +0000 changes to debugging interface Src/F_BaseLib/particles.f90 commit c6e4a3ec1522655239e36a34ebb70909961d1567 Author: almgren Date: Tue Feb 15 22:38:43 2011 +0000 Forgot commas. Src/C_AMRLib/Particles.H commit 753ee107fdb96631044fe272a7221382d1aeb404 Author: almgren Date: Tue Feb 15 22:33:16 2011 +0000 Fix typos. Src/C_AMRLib/Particles.H commit 9394334f629e51ba6f0b717fb83a604194b0425a Author: almgren Date: Tue Feb 15 20:55:18 2011 +0000 This has the correct time stepping now (fingers crossed) Src/C_AMRLib/Particles.H commit 8fc6d3eca6346901387f6f3105a1b9b0525c57a9 Author: 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 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 Date: Sat Feb 12 03:17:19 2011 +0000 Integrate changes from Test_90Mpc version. Src/C_AMRLib/Particles.H commit 066b496b2a4796e883fe18819873e5977d101b86 Author: lijewski Date: Fri Feb 11 22:30:02 2011 +0000 some cleanup Src/C_AMRLib/Particles.H commit 9820e1f703baf3a36fe4a23f3c1230bb75cac6dc Author: lijewski Date: Fri Feb 11 21:50:34 2011 +0000 added WriteAsciiFile() Src/C_AMRLib/Particles.H commit 1d6773edf0754278edf55f8a080d31b38690523e Author: marc Date: Thu Feb 10 19:15:21 2011 +0000 adjust usage of numLevelsMAX to be consistent with its name, was allowing one extra level Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 010fb60a7449ae71ff633bee3e6da4771022f54c Author: lijewski Date: Thu Feb 10 00:06:50 2011 +0000 fixed issue with Timestamp() Src/C_AMRLib/Particles.H commit 1ff197a7cb6f3337b5fa9804d447a74eb7483db5 Author: lijewski Date: Wed Feb 9 23:42:03 2011 +0000 *** empty log message *** Src/C_AMRLib/Particles.H commit 57f06b41befa0fc1f1a752e1f01028e414d7934d Author: lijewski Date: Wed Feb 9 23:21:15 2011 +0000 some work on advectWithUMac() Src/C_AMRLib/Particles.H commit 83c98742ce84a1905af56178698809277970cc01 Author: lijewski Date: Tue Feb 8 23:01:50 2011 +0000 bit more work on Timestamp() -- appears to be working Src/C_AMRLib/Particles.H commit 1d44bf67d4d27d058c79bae2d2c0465d9939e85d Author: 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 Date: Tue Feb 8 19:19:01 2011 +0000 more work on Timestamp() Src/C_AMRLib/Particles.H commit 36eb78f73485bf89f1f96d44a7cc8a3c47ba30a6 Author: lijewski Date: Tue Feb 8 19:05:22 2011 +0000 some work on Timestamp() Src/C_AMRLib/Particles.H commit 7a69276e0928c2ca225efff9391fc149c702b7f0 Author: mzingale Date: Sun Feb 6 03:07:39 2011 +0000 first attempt at doing second-order in time advection of the particles. A new field, origpos(), was added to the particle datatype to store the position of the particle at the start of the time integration. Redistribution is now done twice -- once at the half-time and then after the final movement of the particle. Src/F_BaseLib/particles.f90 commit 1cfb9ac8ad1c1ae641b8d97119a85d1194f99025 Author: lijewski Date: Fri Feb 4 23:20:33 2011 +0000 we now checkpoint/restart the max value of particle_id Src/F_BaseLib/particles.f90 commit 6960604d56982e3e3fbb58049e5e484292412061 Author: lijewski Date: Fri Feb 4 22:46:21 2011 +0000 we now checkpoint/restart the max value of NextID() Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 2cfae6126c8237ca57b5fe4377a9969e9e6b0d65 Author: lijewski Date: Fri Feb 4 22:30:24 2011 +0000 Init() can now be called on restart too - doesn't assume there are no existing particles in container Src/C_AMRLib/Particles.H commit 02f2c51091b16cac95b89a7e25e9056b5b0a0f2d Author: lijewski Date: Fri Feb 4 21:32:06 2011 +0000 do NOT use the update arg to Where() after PeriodicShift() Src/C_AMRLib/Particles.H commit 4acd736c44b3b951520540649ff01ee07e5b942d Author: lijewski Date: Fri Feb 4 21:31:25 2011 +0000 PeriodicShift() now only tries a particular dir if you're periodic in that dir Src/C_AMRLib/Particles.cpp commit cad83c1ba8cd1f9cb47aac175a46aeeb2614cb55 Author: 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 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 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 Date: Fri Feb 4 16:44:00 2011 +0000 added a BL_ASSERT() Src/C_AMRLib/Particles.H commit a6554e10ec5e1caad6739693d43e7edb3965f299 Author: 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 Date: Wed Feb 2 01:42:16 2011 +0000 *** empty log message *** Tools/C_mk/Make.mpi commit d67e0c21e31df0b528985988a96fac7237e98e22 Author: mzingale Date: Sun Jan 30 02:45:07 2011 +0000 change the header names to contain no spaces so it is easier to parse Src/F_BaseLib/particles.f90 commit 06ea0c878ba9ce8b551458e43e009a3afd35397b Author: mzingale Date: Sat Jan 29 20:13:12 2011 +0000 add a header to the top of the timestamp files that lists the name of each column. This requires that a names() array is passed through giving the name of each data field. Src/F_BaseLib/particles.f90 Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 408c4522f7929a2efce9b4e3d8584fb55af9c67d Author: ajnonaka Date: Sat Jan 29 01:59:27 2011 +0000 created a tidy interface for adding a single particle at a point Src/F_BaseLib/particles.f90 commit 8c2407bad4bcf8e1c88c0ce7d659b5d3cfb2f247 Author: ajnonaka Date: Fri Jan 28 18:12:27 2011 +0000 generalized piecewise bilinear advection of particles using mac velocities to 1d/2d/3d Src/F_BaseLib/particles.f90 commit 97e1496134e7c74ea31aea6c69149b3b6aa78985 Author: 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 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 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 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 Date: Thu Jan 27 23:19:50 2011 +0000 more error checking Src/F_BaseLib/vector_i.f90 commit fa8f593fc9616dc5f4966014c84ab1502fcca930 Author: ajnonaka Date: Thu Jan 27 22:53:08 2011 +0000 changed problo/hi -> prob_lo/hi to make consistent with VARDEN and MAESTRO Src/F_BaseLib/fabio.f90 Src/F_BaseLib/particles.f90 commit 793278eba90fa491451c1700430cbda0d7ad5bee Author: ajnonaka Date: Thu Jan 27 22:46:20 2011 +0000 added an advect function Src/F_BaseLib/particles.f90 commit b1a6fee9ddc2360255388a11909ccc22ba729490 Author: lijewski Date: Thu Jan 27 22:31:22 2011 +0000 more error checking Src/F_BaseLib/particles.f90 commit 35f05e1a007215f81547ec8626771855d560e5e3 Author: lijewski Date: Thu Jan 27 22:13:30 2011 +0000 brought up-to-date with latest particle changes Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit bfa95841f2da0da4ed46702ea06218a3c7ab52e4 Author: lijewski Date: Thu Jan 27 21:27:57 2011 +0000 mods for MAESTRO Src/F_BaseLib/particles.f90 commit 6866556f33baf7fb91c16945f77e21e4ca35f720 Author: 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 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 Date: Wed Jan 26 21:12:13 2011 +0000 add f90sources += particles.f90 Src/F_BaseLib/GPackage.mak commit d849e3d80066fb6d26b492e6e4a11bb8a7297d8e Author: lijewski Date: Wed Jan 26 17:11:47 2011 +0000 added dataptr() Src/F_BaseLib/particles.f90 Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 5f5cc418453a3f337ce32dd1ffcf39aa448fab68 Author: marc Date: Tue Jan 25 23:50:22 2011 +0000 Add placeholder for max_order...ordre of tangential interpolant...supporting only 1 and 3 at the moment Src/C_BoundaryLib/INTERPBNDRYDATA_2D.F Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F Src/C_BoundaryLib/INTERPBNDRYDATA_F.H Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp commit 7d08a25cee9226319a770ea2ef94b9741b8a2e6d Author: lijewski Date: Tue Jan 25 23:26:33 2011 +0000 some simplification Src/F_BaseLib/particles.f90 Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 4ebccc21f7bb4011b7ced2ed8b13d84b684f0322 Author: lijewski Date: Tue Jan 25 22:26:54 2011 +0000 2D now appears to work also Src/F_BaseLib/particles.f90 Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 9fb9e098439849a193b915a77f9de94eb3481a18 Author: lijewski Date: Tue Jan 25 18:44:57 2011 +0000 some simplification Src/F_BaseLib/particles.f90 commit d92e7996959a376a82a072f19bf92cefafe82cd3 Author: lijewski Date: Tue Jan 25 17:16:44 2011 +0000 particle_vector -> particle_container Src/F_BaseLib/particles.f90 Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 35e9855c36bd1ed7f42db8fa70416f5cf4ca70e7 Author: lijewski Date: Tue Jan 25 00:04:21 2011 +0000 little more cleanup Src/F_BaseLib/particles.f90 commit 0f896f5a3aba2be62728f1dbb7af198072d3ccfa Author: lijewski Date: Mon Jan 24 23:56:30 2011 +0000 remove empty timestamp files after each series of writes Src/F_BaseLib/particles.f90 Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 79ef8c32de4a6213608aa3beef55499fada19c6f Author: lijewski Date: Mon Jan 24 23:55:59 2011 +0000 added some unlink() code for empty files used by particle code Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c commit d6d7dc83cd692cbb73efd79b19245942e8789f77 Author: lijewski Date: Mon Jan 24 23:08:26 2011 +0000 can now set/unset verbosity and debugging via function calls Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 6ec088427b03ea52a928dac38310433f83c5a081 Author: lijewski Date: Mon Jan 24 23:07:58 2011 +0000 some cleanup Src/F_BaseLib/particles.f90 commit 021d126a42e06a6e43fda6ba19a08a3b77525559 Author: lijewski Date: Mon Jan 24 22:36:05 2011 +0000 added some timestamp() tests Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 54d069772cf48b2306577dbe051ca8db4f071152 Author: lijewski Date: Mon Jan 24 22:35:42 2011 +0000 timestamp() appears to be working Src/F_BaseLib/particles.f90 commit 0f7ddc22273de44115b69ad2e0c4f401da0845af Author: lijewski Date: Mon Jan 24 22:22:58 2011 +0000 timestamp() closer to working Src/F_BaseLib/particles.f90 commit 898c78342a8d04421dfe68d74c30163260100b1f Author: lijewski Date: Mon Jan 24 21:06:56 2011 +0000 *** empty log message *** Src/F_BaseLib/fabio_c.c commit 4b5bb86d2e0a5ee6047f1df56fbbc3be424cfaa2 Author: lijewski Date: Mon Jan 24 21:06:42 2011 +0000 some work on timestamp() Src/F_BaseLib/particles.f90 commit aba76452d148a3eaf5be20f6ffcd719bfe701216 Author: lijewski Date: Fri Jan 21 21:23:59 2011 +0000 added couple more functions needed by particle code Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c commit 4b83cf01f208d667245d775dbb9c9bb0f2294713 Author: lijewski Date: Fri Jan 21 21:22:03 2011 +0000 some cleanup Src/F_BaseLib/particles.f90 commit 2441c7cd9e3f2518891ae362536ba7606894bffd Author: lijewski Date: Fri Jan 21 20:59:15 2011 +0000 *** empty log message *** Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 7030025520e245ae5235288524be68abd3e5da4e Author: lijewski Date: Fri Jan 21 20:52:04 2011 +0000 some code to test restart() Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 044e7d90f94dfff32fca14b036ff582e22995735 Author: lijewski Date: Fri Jan 21 20:51:52 2011 +0000 restart appears to be working Src/F_BaseLib/particles.f90 commit fcca1e3fd4b895f6df52a11e8f6188b29d8bcab3 Author: lijewski Date: Fri Jan 21 01:21:27 2011 +0000 *** empty log message *** Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 9871b024787e61946e720fe2cd9ae7a60e7a6ecc Author: lijewski Date: Fri Jan 21 01:21:16 2011 +0000 some work on restart() Src/F_BaseLib/particles.f90 commit 4b6f198a27c4aef8959451569b13b7d43f183fbf Author: 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 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 Date: Wed Jan 19 23:51:18 2011 +0000 yet more work on checkpoint() Src/F_BaseLib/particles.f90 commit 450135d72fb4b5ba7fef6838e460637b0d1371a7 Author: lijewski Date: Wed Jan 19 23:50:27 2011 +0000 moved interface for particle write routines from particles.f90 to here Src/F_BaseLib/fabio.f90 commit bc08374707f7d752c7d84dcc564a0e2fec807e4b Author: lijewski Date: Wed Jan 19 23:37:33 2011 +0000 added couple C I/O functions needed by particle code Src/F_BaseLib/fabio_c.c commit 9e24f9c5cdac9615d00d72524827b101e998e4fa Author: lijewski Date: Wed Jan 19 23:37:09 2011 +0000 yet more work on checkpoint() Src/F_BaseLib/particles.f90 commit 34dcae34170bea43e7b92dec38a9c329b6cd59fa Author: lijewski Date: Wed Jan 19 22:26:51 2011 +0000 some more work on checkpoint() Src/F_BaseLib/particles.f90 commit 8cdcacccae1f1647f43f1cd93eda3b1cb634e4fc Author: lijewski Date: Wed Jan 19 21:43:22 2011 +0000 some work on checkpoint() Src/F_BaseLib/particles.f90 commit 9ec9f68ce28ddd092ba66882784c3cf9c1eb6a96 Author: 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 Date: Thu Jan 13 19:13:20 2011 +0000 redistribute() appears to be working Src/F_BaseLib/particles.f90 commit 1d16e087d9af21bdea2ef33d825558b8cea78886 Author: lijewski Date: Thu Jan 13 19:12:58 2011 +0000 *** empty log message *** Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 30e05579aaf617425fb672e77b5c121959a16c0d Author: 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 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 Date: Thu Jan 13 00:18:13 2011 +0000 some work on redistribute() - not finished Src/F_BaseLib/particles.f90 commit a9d924603278973e37859a737133446a3b96936e Author: lijewski Date: Wed Jan 12 22:12:29 2011 +0000 Figured out the Intel -vs- gfortran issue. I wasn't setting the rr(n,:) component of the ml_boxarray. That should really be passed as part of build_n(). Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit ba7c173e60df7c00d98e57de52f52ca0b592772d Author: lijewski Date: Wed Jan 12 21:49:57 2011 +0000 move_randomo() implemented; works with gfortran but not Intel 11.1 ??? Src/F_BaseLib/particles.f90 commit 1b2347d1c4da8f4d71ab1431290bf8324aa62bbc Author: lijewski Date: Wed Jan 12 21:49:24 2011 +0000 test code for move_random() Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 8999d5e16a4add74b3bbadea3f72e70003053d94 Author: lijewski Date: Wed Jan 12 17:55:14 2011 +0000 multi-level mla's appear to work OK Src/F_BaseLib/particles.f90 commit 6c817629eb7e53c96f2be62febd0acf6e78a5a95 Author: lijewski Date: Wed Jan 12 17:54:41 2011 +0000 added test for multi-level mla Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit ccf577809346848cc3e1be7ab8c8beb5d37c6418 Author: lijewski Date: Wed Jan 12 03:09:37 2011 +0000 fixed bug -- how did it work for me before? Src/F_BaseLib/particles.f90 commit a03164472ba68378ddaeed2b239e8285a917e04a Author: 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 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 Date: Tue Jan 11 23:56:23 2011 +0000 wrote init_random() -- untested yet Src/F_BaseLib/particles.f90 commit 62ac6b9ba8e33f889b5a6a296bbd59002f792f1e Author: lijewski Date: Tue Jan 11 22:24:08 2011 +0000 wrote particle_index() and particle_where(); now to test ... Src/F_BaseLib/particles.f90 commit 4741b3debed1f30e50351d26aac42d2c8df8237c Author: 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 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 Date: Tue Jan 11 18:25:28 2011 +0000 added particle_vector Src/F_BaseLib/particles.f90 commit b45cfa8f81244d0c5747c32b722e0c943e7a335b Author: lijewski Date: Tue Jan 11 17:02:19 2011 +0000 added particles stuff Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/main.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/main.f90 commit 7187ab287dbac198d273661d2a4d6fa044b84375 Author: lijewski Date: Tue Jan 11 17:01:50 2011 +0000 particles test code Src/F_BaseLib/test/t_particles.f90 Tests/F_BaseLib/t_particles.f90 commit 7df9d2c335f29bb3c16a334955ada3c6a6eae26c Author: lijewski Date: Tue Jan 11 17:01:11 2011 +0000 added particles.f90 Src/F_BaseLib/GPackage.mak commit 6ae26882e0b475619250202303e23ac8433f00cc Author: lijewski Date: Tue Jan 11 17:00:47 2011 +0000 Just getting started ... Src/F_BaseLib/particles.f90 commit 64c1d3862458024004442155d8f2cf2b0b97e817 Author: almgren Date: Thu Jan 6 23:05:44 2011 +0000 Add JFE's InitCosmo() routine which sets up initial conditions a la Martin White. Src/C_AMRLib/Particles.H commit 51f3b9ce40e031405c8b2f71b4957fb01bb0195f Author: almgren Date: Mon Jan 3 21:35:05 2011 +0000 Add a to estTimestep. Src/C_AMRLib/Particles.H commit ebc94aee6ffa46230fbc9b0164d9a56f5e83d9f7 Author: almgren Date: Mon Jan 3 20:49:31 2011 +0000 Fix... Src/C_AMRLib/Particles.H commit 31b31408a973951dcb0d24121e82f67b01115f51 Author: almgren Date: Mon Jan 3 20:48:00 2011 +0000 Add versions of moveKick and moveKickDrift that include the comoving coordinate stuff. Src/C_AMRLib/Particles.H commit 88dfccf64427cde51113d91593b48d8c155df152 Author: almgren Date: Mon Jan 3 20:26:30 2011 +0000 This doesn't compile. Src/C_AMRLib/Particles.H commit 8e1334a37bdbb336830e3048bcaece46e08d5bd0 Author: gpau Date: Wed Dec 22 23:46:58 2010 +0000 *** empty log message *** Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/GNUmakefile commit 579daae447b79f8d1183eb25fe5d804c67dd06f0 Author: ajnonaka Date: Tue Dec 21 18:38:02 2010 +0000 added ability to pass in aux multifab to tagging routines Src/F_BaseLib/make_new_grids.f90 Src/F_BaseLib/tag_boxes.f90 commit 465bb870714fc6f6519d22f82aea45b4ef957654 Author: 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 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 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 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 Date: Thu Dec 9 00:53:21 2010 +0000 fix for pgCC oddity Src/C_BaseLib/BaseFab.cpp commit 374d27fce8038d14e4faba493b13804d2b208625 Author: lijewski Date: Wed Dec 8 23:07:06 2010 +0000 mods for compiling VisIt with Microsoft Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/winstd.H commit 036231f5daaf6f9d3090afe33eb79df3b15bfd09 Author: lijewski Date: Wed Nov 24 02:50:25 2010 +0000 Yet another downgrade of the Cray optimization options. I've finally managed to get Castro/ParticleTest working with the Cray compiler on grace. The C++ used "-O 1 -h noexceptions" and the Fortran "-O 1,vector0 -h noomp". This is strictly with MPI not with OMP. It takes roughly twice as long per timestep as does PGI. Tools/C_mk/Make.Linux commit 6a8feccc1f719d6873cb062e6f0e6f1c81f57a91 Author: lijewski Date: Sat Nov 20 21:50:29 2010 +0000 Downgrade Cray optimization from -O 2 -> -O 1. Still can't get Castro/ParticleTest to run. It's dying in the first gravity solve. Weird since MAESTRO/wdconvect works with -O 1. Tools/C_mk/Make.Linux commit e732667011ef231c471b2532675631b13930bd3e Author: lijewski Date: Sat Nov 20 20:21:26 2010 +0000 Downgrade optimization from -O2 -> -O1. -O2 hits an OMP bug though -O2 works fine with just MPI. Weirdly -O1 appears to produce slight faster code (just a few percent). Tools/F_mk/comps/Linux_cray.mak commit ec85ba75a9371d680b3013013628e270f7d00e0d Author: mzingale Date: Sat Nov 20 01:42:58 2010 +0000 add a 1-d version to get flame_1d running again Src/F_BaseLib/multifab_physbc_edgevel.f90 commit f69e436e21ac9b11d005b06fb86d2e38b8454b9e Author: lijewski Date: Fri Nov 19 18:06:59 2010 +0000 dm wasn't being initialized Src/F_BaseLib/test/t_bxasc.f90 Tests/F_BaseLib/t_bxasc.f90 commit fd20966736ec945991c5d2f935be1bd8de576fad Author: lijewski Date: Thu Nov 18 20:14:12 2010 +0000 tweaks to Cray options to work around a bug Tools/C_mk/Make.Linux commit 7db322e0c33adf87ea5259dbb0a8b5cbcfc773a7 Author: ajnonaka Date: Mon Nov 15 20:50:51 2010 +0000 default max_bottom_nlevel=3 instead of 1024 Src/LinearSolvers/F_MG/mg_tower.f90 commit 05404c58f1e98116b48e7d38fabe731a15428d41 Author: lijewski Date: Mon Nov 15 19:23:57 2010 +0000 speedup to InitRandom() Src/C_AMRLib/Particles.H commit 1b89204fbe3c20a24c26cba5c7a3d30b510c3599 Author: vince Date: Mon Nov 15 19:13:37 2010 +0000 couts. Src/C_AMRLib/StationData.cpp commit b933c1cfd4a3bd039cc5c22bcc9473b6fa2826e4 Author: lijewski Date: Thu Nov 11 21:08:56 2010 +0000 parallel_abort() was ignoring the optional string argument Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit 7d99a64c37a7ca3d9974035bc5888343d6f3e361 Author: ajnonaka Date: Thu Nov 11 17:54:39 2010 +0000 fixed USE_OLDPLOTPER Tools/C_mk/Make.defs commit c487c7ea18909f44d52c84abcbb8be44bdd4cf25 Author: ajnonaka Date: Thu Nov 11 17:48:44 2010 +0000 add support for USE_OLDPLOTPER=TRUE in makefile Tools/C_mk/Make.defs commit 34369ca97c3ba3e73a92211c3ec8f0bc8ea282d2 Author: ajnonaka Date: Thu Nov 11 17:48:24 2010 +0000 change "BL_USEOLDPLOT_PER" to "BL_USE_OLDPLOTPER" to be consistent with other cases Src/C_AMRLib/Amr.cpp commit 02dd446f78166bcd17ce12630371a1b19c074d7f Author: 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 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 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 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 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 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 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 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 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 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 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 Date: Fri Nov 5 21:00:44 2010 +0000 fixed bug I just introduced Src/C_AMRLib/Particles.H commit cbf6d34a7e961f36ab118895ae89819a809fb00d Author: 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 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 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 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 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 Date: Thu Nov 4 16:24:40 2010 +0000 some more error checking Src/C_AMRLib/Particles.H commit 72684afbb7ea1d69c108c2be628bc0b1caabba89 Author: lijewski Date: Wed Nov 3 06:01:07 2010 +0000 changed the byte spread output to refer to MPI processes instead of CPUs Src/F_BaseLib/fab.f90 commit 03cfa026aedfd1b53d7e5714e4fd664b104a50f0 Author: 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 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 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 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 Date: Mon Nov 1 20:57:00 2010 +0000 some performance tweaks Src/C_AMRLib/Particles.H commit 1411cd0485927f1ccc044b8c42d92bec954246a9 Author: lijewski Date: Mon Nov 1 18:04:36 2010 +0000 no longer write p.m_lev and p.m_grid to disk -- they can be easily recreated given how we write checkpoint files Src/C_AMRLib/Particles.H commit a1ad4cf64a59656d72ef5a3dd01078d059ce9316 Author: lijewski Date: Mon Nov 1 17:22:41 2010 +0000 I've redone how particles are stored. Instead of a single deque we now have a deque per grid per level. This makes most of the algorithms that operate on particles containers more memory efficient since they almost always work on a level by level and grid by grid basis. Src/C_AMRLib/Particles.H commit d19ced8db8759c2eebb1f081dc83ad53039e3d3a Author: lijewski Date: Mon Nov 1 17:16:55 2010 +0000 some IPM stuff for hopper Tools/C_mk/Make.Linux commit 47ca92460b111674f4b5d94becda416ff765a1e9 Author: lijewski Date: Fri Oct 29 22:50:41 2010 +0000 added ability to sort particles -- not yet used Src/C_AMRLib/Particles.H commit a6fa5c893abd0df8c0afa1a12ca5befd26f5ae00 Author: lijewski Date: Fri Oct 29 21:39:15 2010 +0000 *** empty log message *** Src/LinearSolvers/F_MG/ml_cc.f90 commit a2c528428bd15616e30532d2804d593174dfe61c Author: almgren Date: Fri Oct 29 21:16:41 2010 +0000 Add code to print "sum of rhs" *only* for all periodic bc's and cell-centered. Src/LinearSolvers/F_MG/ml_cc.f90 commit c48e6f06d2e7deea90b8b8ce9aa34d363ca26dc9 Author: lijewski Date: Fri Oct 29 20:36:14 2010 +0000 added serialize option to InitRandom() Src/C_AMRLib/Particles.H commit cfc48b8c917be36dbd1916c32244601c3487c94d Author: lijewski Date: Fri Oct 29 17:22:04 2010 +0000 *** empty log message *** Src/C_AMRLib/Particles.cpp commit f04e94647d924f0b86d67bb2697966e103f18156 Author: 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 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 Date: Wed Oct 27 22:04:34 2010 +0000 simplified the OMP scheme for sumParticleMomentum() Src/C_AMRLib/Particles.H commit c0be065d433ff7206653b04546d57843466d59eb Author: lijewski Date: Wed Oct 27 21:56:03 2010 +0000 OMPd sumParticleMomentum() Src/C_AMRLib/Particles.H commit 6c71f397461189c44936765f7589601fc906dbca Author: lijewski Date: Wed Oct 27 21:25:55 2010 +0000 came up with a way to OMP AssignDensity() Src/C_AMRLib/Particles.H commit 4f77026d5e1d9ae2e142ecc6fb83b16143f0f820 Author: lijewski Date: Wed Oct 27 20:45:39 2010 +0000 sumParticleMomentum() now calculates all BL_SPACEDIM momemtums at once Src/C_AMRLib/Particles.H commit 7147d6d4df1f54bebf1a3ee384f9305cffbc7946 Author: lijewski Date: Wed Oct 27 19:41:04 2010 +0000 mods for PathScale Tools/C_mk/Make.Linux commit bdad9c9db4e9791b17a284014f50d4f75c999017 Author: 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 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 Date: Tue Oct 26 22:09:17 2010 +0000 decrease Cray optimization intensity Tools/F_mk/comps/Linux_cray.mak commit d4920dca1894f54daeab5f9d1d4ab55866f7be26 Author: 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 Date: Tue Oct 26 20:21:33 2010 +0000 mods to quiet Cray compiler Src/C_AMRLib/Particles.H commit 07cd56f74dc3254a03fc14b2803a8eafef3b7fee Author: lijewski Date: Mon Oct 25 23:36:18 2010 +0000 OMPd estTimestep() Src/C_AMRLib/Particles.H commit c4a4a983120c88fd4d38b98599d585c908efc45f Author: almgren Date: Mon Oct 25 22:10:07 2010 +0000 Fix indexing of cell vs csect in AssignDensity... Src/C_AMRLib/Particles.H commit 1ab78da01b160aa4f93efe85c8031bae44458634 Author: almgren Date: Mon Oct 25 22:01:54 2010 +0000 Fix up getGravity Src/C_AMRLib/Particles.cpp commit ea4151f491c61752ed04bf2154e7c0c6da9319ce Author: lijewski Date: Mon Oct 25 20:06:33 2010 +0000 getParticleGrav() -> ParticleBase::GetGravity() Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit bc9b83affba9cf1d6d06b23603a9612fda7fcf16 Author: almgren Date: Mon Oct 25 18:47:48 2010 +0000 This now includes Jan's updates which use getParticleGrav to interpolate the gravity onto particle locations instead of using the cell-centered value. Src/C_AMRLib/Particles.H commit 1f411ab5e706032e5236e50e2841e5c98331dac5 Author: lijewski Date: Mon Oct 25 03:43:11 2010 +0000 little cleanup Src/C_AMRLib/Particles.H commit f5b55c0106b7f82a58ab9190abb2768d9cb5b0f7 Author: lijewski Date: Mon Oct 25 01:59:43 2010 +0000 std::list -> std::deque as the latter is more amenable to OMPing Src/C_AMRLib/Particles.H commit 93fa83226be2bfa117a889822b14469c41e0657a Author: lijewski Date: Sun Oct 24 23:41:46 2010 +0000 some OMPing Src/C_AMRLib/Particles.H commit e635c870b4448a70ab4dac1c69dc1fe9d5d206ca Author: lijewski Date: Sun Oct 24 22:45:29 2010 +0000 minor performance tweaks Src/C_AMRLib/Particles.H commit cca09a3d9e373142bc5a6ea774c47e8b775c1da0 Author: lijewski Date: Sun Oct 24 22:07:10 2010 +0000 add some more timers Src/C_AMRLib/Particles.H commit 93dd81491112a8d4f981c4ac2a84ca66fd7d6203 Author: lijewski Date: Fri Oct 22 23:25:30 2010 +0000 more Cray tweaks Tools/C_mk/Make.Linux commit 905dfc24b8ffe0a8f42647826c940eb8d59a25b9 Author: lijewski Date: Fri Oct 22 22:26:31 2010 +0000 fixed bug in AssignDensity() when DIM=3 - be good if Jhon could confirm Src/C_AMRLib/Particles.H commit e1657e8780492c6b131425518e5ab0363a8bc622 Author: wqzhang Date: Fri Oct 22 21:10:12 2010 +0000 added my desktop baragon Tools/C_mk/Make.defs commit 0e402335de03e6053d27995301edb225ad3ede17 Author: ajnonaka Date: Fri Oct 22 20:31:36 2010 +0000 if USE_LEVELSET=T, at .LevelSet suffix to executable name Tools/C_mk/Make.defs commit 39a5d403027d92d8511243cce596dd95caa8ac5a Author: lijewski Date: Fri Oct 22 20:26:10 2010 +0000 more Cray stuff Tools/C_mk/Make.Linux commit a13bca42cf898079677b3f48306161ac0cdb0a10 Author: lijewski Date: Fri Oct 22 16:48:51 2010 +0000 some work adding Cray Tools/C_mk/Make.Linux commit 9c23cefc5becaf4f9ddf14596cdbbde5dd1e02de Author: lijewski Date: Fri Oct 22 15:34:29 2010 +0000 added -Minline flag Tools/F_mk/comps/Linux_pgi.mak commit 4ef1e55f01d7c94cd9f361a0d1368cc49eefec44 Author: lijewski Date: Thu Oct 21 20:59:14 2010 +0000 for Cray compilers Tools/F_mk/comps/Linux_cray.mak commit 23bfbc8384952aa45d81521cd5e875d0623800cc Author: 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 Date: Thu Oct 21 18:21:39 2010 +0000 added grace Tools/F_mk/GMakeMPI.mak commit a7630a69256ac207b765a5083d213abc2aec4d75 Author: lijewski Date: Wed Oct 20 23:17:09 2010 +0000 tweaked the PGI optimization flags Tools/C_mk/Make.Linux commit 91681b72b57cd0563234dd5dd65122bd4d351003 Author: lijewski Date: Wed Oct 20 23:15:22 2010 +0000 added GRACE Tools/C_mk/Make.defs commit 3f9e34e18ef417cecc487e3f0bfb6e1e9023923b Author: ajnonaka Date: Wed Oct 20 13:58:53 2010 +0000 mpi for my home machine Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit 699296f89d4ed42db03736a3b17026b94be5905f Author: mzingale Date: Wed Oct 20 13:54:55 2010 +0000 add support for kraken Tools/F_mk/GMakeMPI.mak commit 7c420e6e21e12e9649a374d8e5e74486d4b84472 Author: wqzhang Date: Tue Oct 19 22:48:32 2010 +0000 *** empty log message *** Tools/C_mk/Make.rules commit 4b376771d07635394baab35c6afa0828d8735aba Author: ajnonaka Date: Tue Oct 19 00:04:05 2010 +0000 MPI for ebirah Tools/F_mk/GMakeMPI.mak commit 8cd95fd8565f30cabfbffc2ea871f888e325b795 Author: almgren Date: Mon Oct 18 21:48:52 2010 +0000 We do not need those lines for compiling with intel on ranger. Tools/C_mk/Make.mpi commit ace12b459ae4b24b7d2745b50db5ffff0dbe7ea0 Author: lijewski Date: Mon Oct 18 21:09:32 2010 +0000 introduced version string for checkpoint/restart files Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 9a35210d1497cb72a784cc678f6fe38308ae7e37 Author: lijewski Date: Mon Oct 18 20:02:18 2010 +0000 some performance tweaking Src/C_AMRLib/Particles.H commit bda8decbfcdff2146d2da8902586ef1350b5fb27 Author: lijewski Date: Mon Oct 18 19:18:49 2010 +0000 a little cleanup Src/C_AMRLib/Particles.H commit db5fb9fb0efc49201208e70543857f2f9f65cfef Author: lijewski Date: Mon Oct 18 18:26:32 2010 +0000 now unlink() zero-length data files but not directories Src/C_AMRLib/Particles.H commit 013e613060d25cc8d542de14a26907c7d325b6ec Author: lijewski Date: Mon Oct 18 17:14:17 2010 +0000 non-backward compatible performance change to particle checkpoint/restart files Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 004ff2311d1908247127d054adbda22004db6c90 Author: almgren Date: Fri Oct 15 22:55:19 2010 +0000 Add orion. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 7f608cec15614f1082fb79c0e8653bcc4eda43aa Author: 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 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 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 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 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 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 Date: Thu Oct 14 23:50:37 2010 +0000 a little cleanup Src/C_AMRLib/Particles.H commit 45e68c8b71ca3d6e3e4369cbbaccbb043c1ace5e Author: lijewski Date: Thu Oct 14 23:34:34 2010 +0000 OK() is now more thorough Src/C_AMRLib/Particles.H commit 9d86b374ab6e6c178e1a53b52f4c279a74c2aff7 Author: lijewski Date: Thu Oct 14 23:13:04 2010 +0000 yet more work on Checkpoint() Src/C_AMRLib/Particles.H commit 1901783cc450c81f58f807063abfe267caac1212 Author: lijewski Date: Thu Oct 14 22:37:31 2010 +0000 more work on Checkpoint() Src/C_AMRLib/Particles.H commit dbdc78e5254ed57695365cf084ac4b2da54e3a42 Author: 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 Date: Thu Oct 14 17:34:43 2010 +0000 some optimization Src/C_AMRLib/Particles.H commit e1e161c89abb3539f0d89d8cfe8a7ce980b13ad0 Author: 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 Date: Sat Oct 9 19:16:31 2010 +0000 Add verbose to test for output... Src/C_AMRLib/Particles.H commit 2e5835f505ed67597d8e274eb0125e3653e04345 Author: almgren Date: Sat Oct 9 16:31:01 2010 +0000 Make sure to set bottom_singular = .true. if the boundary conditions for the current solve are all periodic. Src/LinearSolvers/F_MG/mg.f90 commit e934ce022e92adde473b015de4df04a970ca81e0 Author: almgren Date: Fri Oct 8 20:50:57 2010 +0000 These appear to actually work with clumping particles in 2d. Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit 01aedbaf9ba4d00404a2b11408ea8cff334c3207 Author: almgren Date: Fri Oct 8 17:03:28 2010 +0000 Latest updates from JF. Src/C_AMRLib/Particles.H commit c4dd3d4cdac940584afca35cea9e3aea32fa48be Author: almgren Date: Thu Oct 7 16:49:54 2010 +0000 Change the default particle to have the first real component have value = 1 (and all the others are zero). Src/C_AMRLib/Particles.H commit 14be603f02e57e14d5d56ace2f81f9c1921ffe88 Author: almgren Date: Wed Oct 6 22:05:14 2010 +0000 Add Particles_F.H Src/C_AMRLib/Particles_F.H commit 607c40956248a34d97f16680d7fc731eaf37fbc2 Author: almgren Date: Wed Oct 6 21:14:44 2010 +0000 This is a merge of Mike's latest and Jan's latest -- it has everything as of now. Src/C_AMRLib/Particles.H commit 96368a67b4f244f36c8b6a89cad845f35f54be9d Author: almgren Date: Wed Oct 6 20:17:48 2010 +0000 Moved Particles.* from amrlib to particles directory. Src/C_AMRLib/Make.package Src/C_AMRLib/Particles.H Src/C_AMRLib/Particles.cpp commit f85de47915842a1a30059f2029f0a1584019a21b Author: vince Date: Wed Oct 6 20:01:22 2010 +0000 added new machines. Tools/C_mk/Make.mpi commit 511263a4974b7133f05af6222fe4e21554ac6ace Author: lijewski Date: Wed Oct 6 15:44:20 2010 +0000 little code rearrangement Src/C_BaseLib/FabArray.H commit 84db0fa66d0d581fee32c4472da7c7cbe41574bd Author: lijewski Date: Wed Oct 6 15:38:30 2010 +0000 little code rearrangement in SumPeriodicBoundary() Src/C_BaseLib/Geometry.cpp commit 8f2776af708cd403e1689171c5cf6d75fd41f067 Author: lijewski Date: Wed Oct 6 15:31:30 2010 +0000 use intersections() in SumBoundary() Src/C_BaseLib/MultiFab.cpp commit b43e60333e519c5657418237ca9ad78df52e03c9 Author: lijewski Date: Wed Oct 6 15:14:27 2010 +0000 minor code motion Src/C_BoundaryLib/BndryData.cpp commit a6bcb87153b36fa75e39bc10f1e927c37577f6b2 Author: lijewski Date: Wed Oct 6 15:14:27 2010 +0000 minor code motion Src/C_AMRLib/FluxRegister.cpp Src/C_BoundaryLib/FabSet.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp commit 69546ec70e6e895ec5ad788986bb81c7e6ab7b7e Author: lijewski Date: Tue Oct 5 23:00:00 2010 +0000 added initial cut of SumBoundary() Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 16b40b9b494ae663ace6f023435eddf830d0aca6 Author: 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 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 Date: Sun Oct 3 23:32:29 2010 +0000 donev in Makefile Tools/C_mk/Make.mpi commit 31b7045112f1462cc91fc27aedf25736d708377a Author: ajnonaka Date: Fri Oct 1 23:13:06 2010 +0000 more makefile hacking Src/F_BaseLib/GPackage.mak Src/F_BaseLib/multifab_physbc_edgevel.f90 commit 23e75b9be1ebcd018f6ee2dc90ba54843a11099c Author: ajnonaka Date: Fri Oct 1 22:41:37 2010 +0000 in progress hacking to get the initial model stuff to compile Src/F_BaseLib/GPackage.mak Src/F_BaseLib/multifab_physbc_edgevel.f90 commit f292b253025921032f52e0efc5fe82ca09a42718 Author: marc Date: Fri Oct 1 21:55:40 2010 +0000 Add win include Src/C_BaseLib/IntVect.H commit 2cdac7e3efe399cd82753f55be39b6181f5ff63f Author: marc Date: Fri Oct 1 21:54:57 2010 +0000 Rename macro for excluding fortran functions from boxlib build Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/GNUmakefile Src/C_BaseLib/Make.package commit 17c95e390429d07c689ea084567d095d16b13ac9 Author: ajnonaka Date: Fri Oct 1 21:54:18 2010 +0000 moved MAESTRO/Source/impose_phys_bcs_on_edge_vels into /boxlib/ and rennamed it multifab_physbc_edgevel. create_umac_grown.f90 now calls multifab_physbc_edgevel on the coarsest and the current fine level Src/F_BaseLib/GPackage.mak Src/F_BaseLib/create_umac_grown.f90 Src/F_BaseLib/multifab_physbc_edgevel.f90 commit bed6cb58df43b10043b1f7df7c1a0f77fc6b0708 Author: lijewski Date: Fri Oct 1 21:44:47 2010 +0000 brought back from the dead Src/C_BaseLib/GNUmakefile commit 4271dd0d25039be17c88c19493127403652ef89d Author: ajnonaka Date: Fri Oct 1 21:14:33 2010 +0000 need to pass the_bc_level into create_umac_grown so we can call impose_phys_bcs_on_edges Src/F_BaseLib/create_umac_grown.f90 commit 40ca155204a341b50e2fdaa8fb8a44cea0b38f1a Author: ajnonaka Date: Fri Oct 1 20:40:21 2010 +0000 it would help if i actually added this file to the repository Src/F_BaseLib/create_umac_grown.f90 commit e234e1b5a2b8cbb770c967e20e53f6b47d235982 Author: ajnonaka Date: Fri Oct 1 19:34:31 2010 +0000 move create_umac_grown.f90 into /boxlib/ and removed these local copies Src/F_BaseLib/GPackage.mak commit a35d17cfd95db2d325cc07b034f7d13be65518b4 Author: almgren Date: Fri Oct 1 17:40:07 2010 +0000 We need to back out this change from v1.36 to v1.37 or the CASTRO codes don't build anymore Tools/C_mk/Make.rules commit 0342844f3301c1c76d8a972a83c729b7bcb8b865 Author: lijewski Date: Thu Sep 30 22:41:03 2010 +0000 some VisIt changes from Gunther Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/FPC.cpp Src/C_BaseLib/Make.package Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 0b6cb900ceffd9fef061e8b8ab3f730545e67ce0 Author: ajnonaka Date: Thu Sep 30 05:00:39 2010 +0000 remove unused variables Src/F_BaseLib/fab.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit 14e011b1a93a61b2599c6691acf69f3f27f95e95 Author: ajnonaka Date: Thu Sep 30 01:08:20 2010 +0000 turn on gfortran compiler warnings if you are in debug mode. it will warn you about uninitialize and unused variables Tools/F_mk/comps/gfortran.mak commit e4de48465afea8d24e4ff137eea33692f8a46e3c Author: marc Date: Wed Sep 29 23:16:18 2010 +0000 removing files that were renamed to avoid name collisions Src/LinearSolvers/C_NodalMG/cg.cpp Src/LinearSolvers/C_NodalMG/cg_2d.f Src/LinearSolvers/C_NodalMG/cg_3d.f commit 8831c4a3be3348ba3ed6256fb59f3a2e467273c1 Author: 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 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 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 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 Date: Wed Sep 29 03:46:35 2010 +0000 *** empty log message *** Tools/C_mk/Make.CYGWIN_NT commit e4efb88b979d73acac5a9e78584b90b09663daac Author: adonev Date: Mon Sep 27 23:28:22 2010 +0000 Added host donev Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 22bbfe0b44f13da00d39ddea4e266bb4ae8d3dc9 Author: adonev Date: Mon Sep 27 21:22:18 2010 +0000 Added host donev Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak commit a529bc8014dfc340cb4ec2ee2c3e2977f3c2a3ef Author: lijewski Date: Mon Sep 27 21:11:33 2010 +0000 more particle stuff Src/C_AMRLib/Make.package commit 6ad5817ec0aec986897d5ee9a9fcfa875e04d24f Author: gpau Date: Wed Sep 22 04:47:04 2010 +0000 Doing function provided by ViscBndry differently: do not need ViscBndry in solve. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit a003a1e01bddf388fa6b50603da9b5432caedaae Author: 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 Date: Thu Sep 16 21:29:17 2010 +0000 Fixed a comment Src/C_BaseLib/IntVect.H commit b2ddf346fc1da0ad0a51d2c00b01830ec865f426 Author: ajnonaka Date: Thu Sep 16 17:56:36 2010 +0000 Chris' fix to get PathScale working on atlas Tools/F_mk/GMakeMPI.mak commit ccaa62ebc2d682073546dbe4929e8ab99f75949c Author: marc Date: Mon Sep 13 20:33:30 2010 +0000 fix PathScale second underscore thing Tools/C_mk/Make.Linux commit 8616318751812416775435c75a6d1d28d93612ba Author: lijewski Date: Fri Sep 10 23:05:34 2010 +0000 beefed up FULLWARN for g++ Tools/C_mk/Make.defs commit 2a135e619f582121cd4a6988f5b452ab898c2811 Author: lijewski Date: Fri Sep 10 22:34:20 2010 +0000 now passes g++ -pedantic -Wall Src/C_AMRLib/Amr.cpp Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BoundaryLib/BndryData.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 6930f58a911770263d0f9b4898805b4b65b454a6 Author: lijewski Date: Fri Sep 10 20:24:52 2010 +0000 added -fbacktrace flag when debugging with gfortran Tools/F_mk/comps/gfortran.mak commit 280fa58ae08981cf5c75b518c0da0c5c38562150 Author: lijewski Date: Thu Sep 9 16:47:29 2010 +0000 unOMPd setval() Src/F_BaseLib/fab.f90 commit da39749fe0f526ee4032b9d7d1841b6241123632 Author: lijewski Date: Thu Sep 9 16:27:10 2010 +0000 removed some unused dummy arguments and unOMPd SETVAL Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/SPECIALIZE_1D.F Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit 17fab4f6bbc51ad420af20c838767766b856ab93 Author: almgren Date: Wed Sep 8 16:47:35 2010 +0000 Add kraken stuff. Tools/C_mk/Make.Linux commit 75299b5aaa380d8f736336f058a00f5bd82ae564 Author: almgren Date: Wed Sep 8 16:46:48 2010 +0000 Add kraken info. Tools/C_mk/Make.defs commit 288527260ed37727f60ba77a76adff9c22c514ce Author: gpau Date: Tue Sep 7 18:03:14 2010 +0000 *** empty log message *** Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 530f5b60ccbbecc813fa1128035cb165d6592e97 Author: almgren Date: Thu Sep 2 23:35:06 2010 +0000 Fix bug in stencil_norm inside if present(mask) test. Src/LinearSolvers/F_MG/stencil.f90 commit d419c5bd440786ef295861e542094b5a1c1a7c02 Author: ajnonaka Date: Tue Aug 31 15:21:08 2010 +0000 MPI on my home machine Tools/F_mk/GMakeMPI.mak commit ed3928691807dabe708f0a130afb668967f8be1e Author: ajnonaka Date: Tue Aug 31 15:21:01 2010 +0000 MPI on my home machin Tools/C_mk/Make.mpi commit 94ea214989b8f8d259bfb9bc078f636f402344c1 Author: ajnonaka Date: Fri Aug 27 23:02:54 2010 +0000 added -fno-range-check for gfortran to get the fParallel/extern/random/mt19937ar.f90 stuff to compile Tools/C_mk/Make.defs commit f760fe9bd0adab2ae59b62183702e80e741eb376 Author: ajnonaka Date: Fri Aug 27 22:43:02 2010 +0000 new install of mpi. Fixed to work with gfortran on atragon Tools/C_mk/Make.mpi commit 106038a8f392307314d17c84788482f812339fb9 Author: ajnonaka Date: Fri Aug 27 22:32:11 2010 +0000 new install of mpi. Fixed to work with gfortran on atragon Tools/F_mk/GMakeMPI.mak commit 68767687a2bae8161b462edbf1e18f2d44e89b7d Author: almgren Date: Fri Aug 27 21:54:47 2010 +0000 This modifies the convergence criterion for the solver in ml_cc so that it stops when res < eps * MAX(bnorm,tres0) instead of res < eps * bnorm. Here bnorm = norm(rhs) and tres0 = norm(resid0). Src/LinearSolvers/F_MG/ml_cc.f90 commit c6fd0dc65ac69db837f93550c5e95a395fcf8dbc Author: ajnonaka Date: Thu Aug 26 21:33:27 2010 +0000 printing out fancy bottom solver grids even when mg_verbose=0 Src/LinearSolvers/F_MG/mg.f90 commit 2abb2890caf57d98b13068cc8e48168e40976d54 Author: nazgul Date: Thu Aug 26 00:15:56 2010 +0000 Commenting out iters.f, as it causes build problems for Castro and does not appear to be used. Louis Src/LinearSolvers/F_MG/FParallelMG.mak commit f7bca0357aeb645235d6c68ee788f76328cc54ee Author: 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 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 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 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 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 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 Date: Tue Aug 24 20:30:31 2010 +0000 end if --> endif Src/C_BaseLib/BoxLib.cpp commit 948a8181a1ab1b84861173c2cdd2f79df15e666d Author: almgren Date: Tue Aug 24 20:12:38 2010 +0000 Print out many MPI processes even if only one. Src/C_BaseLib/BoxLib.cpp commit c71e59a2892ba6c87bbb753ad133a7384aedb603 Author: lijewski Date: Tue Aug 24 20:12:00 2010 +0000 removed all nocomm stuff and some OMP loops of dubious usefulness Src/F_BaseLib/multifab.f90 commit aead63ff2827ad21c6d2e6fc91aa046f4657852a Author: almgren Date: Tue Aug 24 20:08:19 2010 +0000 Wrap the statement "MPI initialized..." with #ifdef BL_USE_MPI Src/C_BaseLib/BoxLib.cpp commit 6300eabc2e5d75855bfa71bac75a666abafe998d Author: lijewski Date: Tue Aug 24 17:46:28 2010 +0000 removed ml_layout_build_la() -- not used by any current code Src/F_BaseLib/ml_layout.f90 commit b852c5281e3c582ddd70405faafac9471a44cf5a Author: lijewski Date: Tue Aug 24 17:31:57 2010 +0000 Added destroy_all_layouts member to ml_layout. This is so we can distinguish between the two main ways of building ml_layouts. In most f90 code we use build() which forces the layouts of higher levels to be owned by the one at the coarsest level, via proper nesting. In the MGT code however the layouts are build level by level and hence in destroy() we must destroy all of them, not just the one at the coarsest level. Src/F_BaseLib/ml_layout.f90 commit dcce444829a4570fa6c1c7ec79bdc600270f1cd2 Author: ajnonaka Date: Mon Aug 23 23:36:14 2010 +0000 upgraded the fancy bottom_solver_type 4 to allow an even coarsen bottom solve for this bottom solver. ultra complicated and will get some details in the user's guide when I figure out a clean way of describing it Src/LinearSolvers/F_MG/mg.f90 commit 2d2d0344bb9cc50e4f9c46c533d85151d710b448 Author: lijewski Date: Mon Aug 23 23:30:51 2010 +0000 got rid of OMP shared variable warnings via firstprivate Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/stencil.f90 commit c8dbe1da99619aadc5550ab71647657d25eb28ee Author: ajnonaka Date: Mon Aug 23 20:35:00 2010 +0000 some cleanup - preparing to make the new bottom solver more robust by allowing more levels in certain cases. Example: we would like a 20^3 problem to be able to go down to a 5^3 rather than the 10^3 it would currently do. Src/LinearSolvers/F_MG/mg.f90 commit fcde7f4c4f9ffdabebf01d41337639d2d15f4b1c Author: lijewski Date: Fri Aug 20 17:30:30 2010 +0000 some cleanup Src/LinearSolvers/F_MG/ml_solve.f90 commit 75264e4526a635be0f582142cb4cc35f90b3ef62 Author: lijewski Date: Fri Aug 20 17:03:27 2010 +0000 unOpenMPd set_faces_edges_corners_3d - probably not a win Src/LinearSolvers/F_MG/stencil_nodal.f90 commit b1f5c864cb35752d502e90a06ea2cc34638b33ae Author: lijewski Date: Fri Aug 20 16:46:50 2010 +0000 some more OpenMPing Src/LinearSolvers/F_MG/stencil.f90 commit cbb3f9129ec1b20a47999d2a0d74040a938aea74 Author: lijewski Date: Thu Aug 19 23:45:25 2010 +0000 removed some unused routines & made some private Src/LinearSolvers/F_MG/stencil.f90 commit 1aedf33e9ebf227cc2db640b8abde257b4256294 Author: lijewski Date: Thu Aug 19 22:56:32 2010 +0000 refined public interface Src/LinearSolvers/F_MG/nodal_mask.f90 commit abce4934d0c8e2b38882933f6a43fd0070face59 Author: 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 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 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 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 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 Date: Thu Aug 19 21:30:06 2010 +0000 some OpenMPing Src/LinearSolvers/F_MG/itsol.f90 commit 12db264079513f77842aca5df518a844f2f9ca1f Author: lijewski Date: Thu Aug 19 21:19:17 2010 +0000 some OpenMPing Src/LinearSolvers/F_MG/nodal_newu.f90 commit c2ca381fe5a736f8c7a960aa1c543b2470e4b461 Author: almgren Date: Thu Aug 19 00:37:34 2010 +0000 Modified the nodal solver output to more closely match the MAC solver -- specifically, it now prints F90mg: Final Iter. 7 resid/resid0 = 0.33106928E-11 rather than MG finished at 7 iterations at the end of the solve. Src/LinearSolvers/F_MG/ml_nd.f90 commit fb7ba108b94f8c48c628ca1d9ff989381f050e8b Author: lijewski Date: Wed Aug 18 22:10:12 2010 +0000 attempt to shut up 'possible uninitialized variable' msgs Src/F_BaseLib/multifab.f90 Src/F_BaseLib/plotfile.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 3bc6ca71589b6d5b2b298298cc1f661737e34c38 Author: lijewski Date: Wed Aug 18 20:15:12 2010 +0000 0 -> 0_dp_t and removed a print statement Src/F_BaseLib/multifab.f90 commit 1f9999920509e1e48203de4ed7d0f890263467b7 Author: ajnonaka Date: Tue Aug 17 13:44:07 2010 +0000 in MAESTRO/Source/ rennamed cluster_min_width to minwidth so it matches what's in boxlib/cluster.f90 now you can set blocking_factor in the inputs file both blocking_factor and minwidth default to 8 in both MAESTRO and cluster.f90 Src/F_BaseLib/cluster.f90 commit f529a0652e527cf96d8670dcb5fd0cb7f65f184a Author: ajnonaka Date: Tue Aug 17 13:09:04 2010 +0000 output says "MPI initialized with XXXX MPI processes" instead of CPUs Src/F_BaseLib/BoxLib.f90 commit 768c329836d3e9910e439d34c5dde29de36139ae Author: lijewski Date: Mon Aug 16 20:02:11 2010 +0000 plugged memory leak Src/F_BaseLib/fabio.f90 commit 9f20a9685cb3dca6826a968f191a97940b7bf33b Author: 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 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 Date: Fri Aug 13 21:44:26 2010 +0000 some OpenMPing Src/LinearSolvers/F_MG/nodal_divu.f90 commit f5909642f1be94b2ac895b3b519aebf612712de9 Author: lijewski Date: Fri Aug 13 20:30:07 2010 +0000 some OpenMPing Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 93d7cc34ac04c5b387cc57f3b3fb1852c738db87 Author: lijewski Date: Fri Aug 13 20:18:08 2010 +0000 some OpenMPing Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 235bc7141a3efa55d6b93a9dfd61b4c9010c5249 Author: lijewski Date: Fri Aug 13 17:21:51 2010 +0000 some OpenMPing Src/LinearSolvers/F_MG/mg_restriction.f90 commit ac1170ad718d735b52e887551d751fdfac8a491a Author: lijewski Date: Fri Aug 13 17:05:32 2010 +0000 some OpenMPing Src/LinearSolvers/F_MG/coarsen_coeffs.f90 commit d8115d3ce0ecd124f90f247e6a8e97ad018e4e48 Author: lijewski Date: Fri Aug 13 16:33:13 2010 +0000 some code rearrangement Src/F_BaseLib/sort_box.f90 commit 84fd7fda33c261f086f02367cc4ff828f37de640 Author: lijewski Date: Fri Aug 13 16:24:31 2010 +0000 some OpenMPing Src/F_BaseLib/interp.f90 commit 7a5724bcaef7a86c3b2c99f5387bedb3f16c7603 Author: ajnonaka Date: Fri Aug 13 15:16:41 2010 +0000 test commit for cvs email notifications Src/F_BaseLib/make_new_grids.f90 commit 0c065b307246b062d6891a15cd85d9e697f00001 Author: ajnonaka Date: Fri Aug 13 14:38:54 2010 +0000 New probin variables that let you set max_grid_size as a function of level. They are max_grid_size_1, max_grid_size_2, and max_grid_size_3. Note max_grid_size_base has been replaced by max_grid_size_1. These default to max_grid_size if they are not set. max_grid_size_1 is max_grid_size for the coarsest level, "level 1" max_grid_size_2 is max_grid_size for the first level of refinement, "level 2" max_grid_size_3 is max_grid_size for the second level of refinement and beyond, "level 3 and beyond" Modified inputs files to reflect this. Also, setting the default value of cluster_min_width to 8. 16 gave horrifically blocky looking grid structures, even for very hi-res problems. The averaging procedure just works better if you get more form-fitting grids. Still need to update local copies of initialize.f90, regrid.f90, and make_new_grids.f90 Src/F_BaseLib/make_new_grids.f90 commit 270506f74cc54425835d77af9509ef8dd8cd2f26 Author: lijewski Date: Thu Aug 12 23:36:20 2010 +0000 removed pc_cc_interp and pr_cc_interp routines Src/F_BaseLib/interp.f90 commit 68df84af8b8ed585a3bb0004ddf51c6cc24f18f5 Author: 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 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 Date: Thu Aug 12 21:04:28 2010 +0000 workaround for dumb IBM xlf bug Src/F_BaseLib/fillpatch.f90 commit 9ac4e5bbd69ee842341ff8b6d31e911a5c275c99 Author: almgren Date: Thu Aug 12 19:45:38 2010 +0000 Anything to do with the sparse solver is now commented out in mg.f90 and mg_tower.f90 and we no longer include sparse_solve.f90 in GPackage.mak Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_tower.f90 commit 27442eb5fcee8b83fcf01e45eadd65d8d95c3bc1 Author: lijewski Date: Thu Aug 12 19:33:22 2010 +0000 OpenMP'd min_val and max_val routines Src/F_BaseLib/fab.f90 commit 137c2ed9ce257fdf2665a91e100af3cd945fdeaf Author: lijewski Date: Thu Aug 12 17:41:18 2010 +0000 OpenMP'd sub_sub and plus_plus routines Src/F_BaseLib/multifab.f90 commit e64eb4a9ad58d404d6b171e3ad45f61cd5939bda Author: lijewski Date: Thu Aug 12 17:27:38 2010 +0000 OpenMP'd mult_mult routines Src/F_BaseLib/multifab.f90 commit db8184d4b6064a02e8cd7e1799eaead3a813f394 Author: lijewski Date: Thu Aug 12 17:18:03 2010 +0000 OpenMP'd div_div routines Src/F_BaseLib/multifab.f90 commit a4d2edb5c42597baa843218cbc6f502fe6b583e3 Author: lijewski Date: Thu Aug 12 16:06:17 2010 +0000 some code simplification Src/F_BaseLib/multifab.f90 commit 32e769269f1937067db055c2af65f4851c0e5b43 Author: ajnonaka Date: Thu Aug 12 13:47:07 2010 +0000 -O for franklin, -Ofast for everyone else, regardless of what the OMP flag is set to Tools/F_mk/comps/Linux_pathscale.mak commit f8cde24b29bfc48463754ea652ef950ffbd41b44 Author: gpau Date: Thu Aug 12 00:12:50 2010 +0000 *** empty log message *** Tools/C_util/Convergence/ComputeAmrDataNorms.H Tools/C_util/Convergence/ComputeAmrDataNorms.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/GNUmakefile Tools/C_util/Convergence/PltFileNorm.cpp commit a6fd2824e5f01a149aee7ff2e14fd692c208307b Author: gpau Date: Wed Aug 11 22:46:45 2010 +0000 added multilevel support for visc_coefficients Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit cc935fbedc36cbdebfee17a6fbaa1b3b1e343394 Author: mzingale Date: Fri Aug 6 19:31:13 2010 +0000 update to new file and dir locations Tools/C_util/regtests/Maestro-tests.ini commit d74844a335cee80c066ec6987ca371b3055ea0af Author: lijewski Date: Thu Aug 5 15:53:24 2010 +0000 compiles now Tools/C_util/Convergence/DiffSameGrid2.cpp commit 5a5504cd03d6a27df34c4739ccf6d3a3c947fe3b Author: mzingale Date: Tue Aug 3 15:32:19 2010 +0000 add support for NYBlue -- note, now we do COMP=xlf Tools/F_mk/comps/xlf.mak commit fbfce1f4a2588d011ebbd40604b435af5888fd42 Author: almgren Date: Fri Jul 30 23:25:33 2010 +0000 rho_xy,rho_yz,rho_xz were not being used. Src/LinearSolvers/C_CellMG/ABec_3D.F commit c30a693f25bd562d7bf5d757cfb5589515bf8180 Author: almgren Date: Fri Jul 30 21:41:06 2010 +0000 Fix an oops. Src/C_AMRLib/INTERP_1D.F commit 0648074cad647b19fe4cc50f139b8a05b36e1de8 Author: almgren Date: Thu Jul 29 16:33:28 2010 +0000 Reused "actual_state" twice, first should have been "actual_comp" Src/C_AMRLib/INTERP_F.H commit 3560d96bb960dc04d12ef3ff8c256fd9b6ad7fd9 Author: almgren Date: Wed Jul 28 01:21:08 2010 +0000 Fix another oops. Src/C_AMRLib/INTERP_2D.F commit 614aaa2b1b195a02cdc8ed9ace8b7825a0eec4e0 Author: almgren Date: Wed Jul 28 01:17:57 2010 +0000 Typo before. Src/C_AMRLib/INTERP_2D.F commit ecbd4f7d285d43683bbc93e4d5bddab649cea6b5 Author: almgren Date: Wed Jul 28 01:07:23 2010 +0000 Pass actual_comp and actual_state to the Fortran interp routines, through the Interpolater::interp(...) routines. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp commit 7892155f2b42a8896fbe2a110431f3d6b2f39494 Author: gilet Date: Wed Jul 28 00:50:55 2010 +0000 Change MPIHOME for orga so things work again Tools/F_mk/GMakeMPI.mak commit 54cfa6c50806b21948b13362670dc528cb037e08 Author: almgren Date: Mon Jul 26 23:56:09 2010 +0000 Moved ml_fill_all_fluxes back from mg_cpp.f90 into stencil.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/stencil.f90 commit d682444a61747a68c93cd9e970e9e26941ba6ff0 Author: almgren Date: Mon Jul 26 16:54:04 2010 +0000 Start to put use_hypre option in. Src/LinearSolvers/F_MG/mg.f90 commit 0c2520bde636838695c6004491e9be49310db696 Author: lijewski Date: Fri Jul 23 23:14:46 2010 +0000 some g++ and gfortran mods Tools/C_mk/Make.defs commit 12d9a7694994a00fb095b85b7df1caf711ea3b2b Author: lijewski Date: Fri Jul 23 18:21:28 2010 +0000 some cleanup prompted by gfortran -Wall Src/F_BaseLib/interp.f90 Src/F_BaseLib/list_box.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 commit 4a718b26437a0fc6d76bdbc903f3251ee6cbcb28 Author: lijewski Date: Fri Jul 23 17:00:40 2010 +0000 add -fopenmp if OMP Tools/F_mk/comps/gfortran.mak commit c009f2485aef70b297639721d1facb70a618a8c6 Author: almgren Date: Fri Jul 23 16:31:01 2010 +0000 Modify to let this work on hicegate0, Wolfram Schmidt's machine. Tools/C_mk/Make.mpi commit 586b7f289003f23304fbb13db2cf249b9c337fde Author: almgren Date: Fri Jul 23 16:24:28 2010 +0000 Fix the eps stuff we pass in to ml_nd_solve and ml_cc_solve. Src/LinearSolvers/F_MG/ml_solve.f90 commit 05259a44efb44ac89894ab46f66ae869596f4203 Author: 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 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 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 Date: Thu Jul 22 14:34:43 2010 +0000 Removed quotes around included files. Tools/F_mk/GMakedefs.mak commit 332ba211461c98717ed36890a2bdec33e80e48fb Author: almgren Date: Wed Jul 21 21:46:16 2010 +0000 Put each compiler's options into a separate file in comps/*.mak Tools/F_mk/GMakedefs.mak commit 688401ca2be2c3e8b5d086e794d32db098513474 Author: almgren Date: Wed Jul 21 21:44:11 2010 +0000 Use this to simplify the makefile system -- these are included in Gmakedefs.mak Tools/F_mk/comps/Darwin_ibm.mak Tools/F_mk/comps/Linux_catamount.mak Tools/F_mk/comps/Linux_intel.mak Tools/F_mk/comps/Linux_lahey.mak Tools/F_mk/comps/Linux_nag.mak Tools/F_mk/comps/Linux_pathscale.mak Tools/F_mk/comps/Linux_pgi.mak Tools/F_mk/comps/Linux_sunstudio.mak Tools/F_mk/comps/Linux_xt4.mak Tools/F_mk/comps/aix.mak Tools/F_mk/comps/crayx1.mak Tools/F_mk/comps/g95.mak Tools/F_mk/comps/gfortran.mak Tools/F_mk/comps/irix64.mak Tools/F_mk/comps/osf1.mak Tools/F_mk/comps/xlf.mak commit 06076f617dd72c1d1d521555506d037e6509e23b Author: lijewski Date: Wed Jul 21 19:28:28 2010 +0000 fix where to find mpi stuff for my machine Tools/F_mk/GMakeMPI.mak commit d188e8d8ff880681b76a2a4e57dd693caaf6b527 Author: lijewski Date: Wed Jul 21 19:03:55 2010 +0000 fix for when not all levels defined Src/F_BaseLib/ml_layout.f90 commit 6b1ff2c853bfd29076935c9fe25fc4c76112e1bb Author: almgren Date: Tue Jul 20 21:35:12 2010 +0000 Need this to compile from C++ Src/LinearSolvers/F_MG/mg_cpp.f90 commit 4b356fb143c8bf8eb176c7edb4363861377f246e Author: almgren Date: Tue Jul 20 20:59:33 2010 +0000 Use local form of dnrm2 so we don't have to link with LAPACK. Src/LinearSolvers/F_MG/sparse_solve.f90 commit 348fea521c6137a2d91838db07bd637364ff3be7 Author: almgren Date: Tue Jul 20 19:58:40 2010 +0000 More clean-up of use modules... Src/LinearSolvers/F_MG/ml_solve.f90 commit 8fbdb79edeec394b40c24143fb11a71737743bbd Author: almgren Date: Tue Jul 20 19:56:50 2010 +0000 More clean-up... Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit 3da572b38f5636596f2699b1e9167b75a102044e Author: almgren Date: Tue Jul 20 19:54:26 2010 +0000 Clean up "use" statements. Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 commit 5acedd98a7eaa6d4268bf054b57cc213c30bc831 Author: almgren Date: Tue Jul 20 19:35:22 2010 +0000 Moved ml_fill_all_fluxes from ml_util into mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/ml_util.f90 commit 3893c6099a08b3ced41adb5713c6c0e90a328177 Author: almgren Date: Tue Jul 20 19:32:44 2010 +0000 No more mlmg.f90 Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak commit 2e7b2e8a5c0dcc9cef947bf358f3a2ab09b74533 Author: almgren Date: Tue Jul 20 19:22:48 2010 +0000 Fix oops. Src/LinearSolvers/F_MG/ml_nd.f90 commit fc6339d8696449edb78644a106bba15c130a780e Author: almgren Date: Tue Jul 20 19:03:17 2010 +0000 Fix oops... Src/LinearSolvers/F_MG/ml_nd.f90 commit 6870145a34ee6a7af7092655f459abb4604f1051 Author: 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 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 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 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 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 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 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 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 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 Date: Mon Jul 19 18:10:08 2010 +0000 Works now for ranger. Tools/C_mk/Make.Linux commit 10ebef18880b0ff7b8bea5825bb64503af8391dc Author: lijewski Date: Mon Jul 19 16:56:47 2010 +0000 mods in preparation for making the components of multifabs private Src/LinearSolvers/F_MG/ml_nd.f90 commit 9a5ecdc99746f5cb492ef1b28cc61ffceb1ac04f Author: lijewski Date: Sat Jul 17 00:51:01 2010 +0000 mods to quiet gfortran std=f95 warnings Src/F_BaseLib/fabio_c.c Src/F_BaseLib/ppm_util_c.c Src/F_BaseLib/system_util_c.c Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 917247d1ffbb5f87afa7f1712306acab12c6ae38 Author: lijewski Date: Sat Jul 17 00:05:27 2010 +0000 mods in preparation of making the components of multifabs private Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/cluster.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/make_new_grids.f90 Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/multifab.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 Src/LinearSolvers/F_MG/coarsen_coeffs.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 666b36f825891a0ddb4366ef72c699eff62b6984 Author: lijewski Date: Thu Jul 15 20:29:51 2010 +0000 the components of type fab are now private and only accessible via function calls Src/F_BaseLib/fab.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 198ba5378c9520d82d19b64e1c8a9f4fda9b3c3c Author: almgren Date: Thu Jul 15 04:01:29 2010 +0000 Add Amr::blockingFactor (int lev) which returns blocking_factor[lev]. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 77ef622690ebf5464a76049b6ccf9ca7331116ac Author: lijewski Date: Wed Jul 14 23:27:45 2010 +0000 the components of type boxarray are now private and only accessible via function calls Src/F_BaseLib/box.f90 Src/F_BaseLib/box_util.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/list_box.f90 Src/F_BaseLib/make_new_grids.f90 Src/F_BaseLib/ml_boxarray.f90 Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit dee5a7e22a171bd5a0ef3f8a820c58c1b8ddf6a7 Author: 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 Date: Tue Jul 13 22:16:48 2010 +0000 made component types private Src/F_BaseLib/bl_stream.f90 commit 2f93ad35bf355820cc73303239e5094ebaa43bc1 Author: 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 Date: Tue Jul 13 21:22:33 2010 +0000 removed pingpong.f90 Src/F_BaseLib/GPackage.mak commit 3d3a038ecff7df32c8d71224f2802e55a4e2b4ed Author: lijewski Date: Tue Jul 13 21:15:56 2010 +0000 made sfc_greater_i() private Src/F_BaseLib/knapsack.f90 commit 4943188442707a67f61f2bb5857ec04210135869 Author: 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 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 Date: Tue Jul 13 20:50:49 2010 +0000 removed unused module variable Src/F_BaseLib/box.f90 commit a0f4a9d8b22e1a267d923257cb9b256f999d6cac Author: 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 Date: Wed Jun 30 22:35:46 2010 +0000 add back in KnapSack to initialize() Src/C_AMRLib/AuxBoundaryData.cpp commit 7d84ce28ab6600533fa1d8b08a500d043899f971 Author: lijewski Date: Wed Jun 30 22:16:36 2010 +0000 do a maxSize() after the simplify() in initialize() Src/C_AMRLib/AuxBoundaryData.cpp commit 436d9889ccc3eb41433db5c13e5eb4d04532231c Author: lijewski Date: Tue Jun 29 20:19:45 2010 +0000 sped up boxlist_simplify() and boxarray_simplify() Src/F_BaseLib/list_box.f90 commit fb611f234fbec0253720af8ab8cc4d2544153ca3 Author: ajnonaka Date: Tue Jun 29 15:25:44 2010 +0000 changed the plot_per functionality to print the plotfile *after* you pass plot_per, rather than before. This matches the MAESTRO functionality and also prevents the code from printing two plotfiles in a row at the end of a simulation. Src/C_AMRLib/Amr.cpp commit a2bdfd1461d66245919e06fe13282777822c5df2 Author: lijewski Date: Mon Jun 28 20:44:24 2010 +0000 do NOT force the use of KnapSack in initialize() Src/C_AMRLib/AuxBoundaryData.cpp commit f261d602c5d1d03ab4d017c019ef2241405f6501 Author: lijewski Date: Mon Jun 28 18:25:12 2010 +0000 initialize() now calls GetBndryCells() Src/C_AMRLib/AuxBoundaryData.cpp commit 5f4750bb48d68d4995608c8c0a3fbc690d698d1a Author: lijewski Date: Mon Jun 28 18:24:45 2010 +0000 make better use of faster simplify() in GetBndryCells() Src/C_BaseLib/BoxArray.cpp commit 6152aaaf743a0dcbf25e1e41a0931e285f3c2ae0 Author: 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 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 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 Date: Fri Jun 25 22:36:07 2010 +0000 added some diagnostics and a sync. Src/C_BaseLib/VisMF.cpp commit f7093103802a3a469f200452208587f268ff244f Author: lijewski Date: Wed Jun 23 22:02:06 2010 +0000 use std::fabs() instead of std::abs() in a couple places Src/C_BaseLib/FArrayBox.cpp commit 07dcb53541dc506d6c096f8f16d9138e270e3f6b Author: almgren Date: Sun Jun 20 00:47:24 2010 +0000 Get rid of daxpy.f and ddot -- these are in BLAS... Src/LinearSolvers/F_MG/FParallelMG.mak commit 5fc7cd4ae88fb229c3ee8153454d38081fa4f2e3 Author: almgren Date: Sun Jun 20 00:23:19 2010 +0000 Change the interface for set_mac_coefficients, set_visc_coefficients, set_porous_coefficients so we don't have to pass a MacBndry, instead we pass xa and xb directly. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 32b9050471b0c62d0bc0bd566e353f63e8e645e5 Author: almgren Date: Sun Jun 20 00:15:07 2010 +0000 Add these files so we can stop including the Make.package from LAPACK, SPARSKIT and BLAS. Hope this works! Src/LinearSolvers/F_MG/FParallelMG.mak commit f33e821c05c018f4955ac87561d4cdef5ef5eb28 Author: 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 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 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 Date: Fri Jun 11 19:48:58 2010 +0000 Add kiryu. Tools/F_mk/GMakeMPI.mak commit a4f46996848194ecfb20a3878e155569d49764f4 Author: marc Date: Thu Jun 10 20:29:13 2010 +0000 Mods for marcs account on the TUe computer Tools/C_mk/Make.mpi commit 807caec85cdc7d5c96116828d085217aaf14da5e Author: almgren Date: Thu Jun 10 00:34:46 2010 +0000 Remove unused variable. Src/LinearSolvers/F_MG/ml_cc.f90 commit b94f519160d2b0107ab62258b16d145fea0775f3 Author: almgren Date: Wed Jun 9 19:59:36 2010 +0000 Modified amr.regrid_int so that we only need max_level values of it (instead of max_level+1), and we don't need it at all if max_level = 0. Also add print statement that says "Successfully read inputs file" (analogous to "Successfully read probin...") Src/C_AMRLib/Amr.cpp commit de0d9ae6e7a7576b83a243ff360d4b09dbdb1bde Author: mzingale Date: Wed Jun 9 16:57:12 2010 +0000 update to allow for the cvs updates to work when fParallel is not in the top level directory Tools/C_util/regtests/test.py commit bad0b869f2ca6b65b7a8654390e671fffab95280 Author: gpau Date: Wed Jun 9 16:56:26 2010 +0000 added an optional argument for Reflux function that allows the flux to be multiplied by a fixed value regardless of the face direction. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 45aa055d33f7b474b0982a519693124bc2ba4852 Author: mzingale Date: Wed Jun 9 00:48:16 2010 +0000 remove the old NMake stuff Tools/F_mk/NMakedefs.mak Tools/F_mk/NMakerules.mak commit 06f81c33d6a171a524e012d4acd1d4843216e94a Author: almgren Date: Tue Jun 8 21:34:32 2010 +0000 Dont maintain NPackage.mak anymore. Src/F_BaseLib/NPackage.mak commit fd58b47053d7a7e206235190f628afd8b37ee173 Author: ajnonaka Date: Tue Jun 8 20:05:38 2010 +0000 back of compiler optimization for franklin with pathscale and openmp. -Ofast won't even compile so going back to -02 Tools/F_mk/GMakedefs.mak commit c0d61a746ad1bc56b7253cd6e8b6979df9d9efa2 Author: almgren Date: Mon Jun 7 19:59:39 2010 +0000 Remove unused variable. Src/LinearSolvers/F_MG/stencil.f90 commit c2cfc2830adec2ba7ccaa9de6bbe407652c6013e Author: ajnonaka Date: Mon Jun 7 19:41:23 2010 +0000 added a .MAESTRO to the executable suffix list if we are building with USE_MAESTR_INIT=TRUE Tools/C_mk/Make.defs commit 9d4865fef2d1307504c3a5f4f1ba6bdf90d03da0 Author: almgren Date: Sun Jun 6 20:07:22 2010 +0000 Fix this. Src/LinearSolvers/F_MG/FParallelMG.mak commit 4f0f78eecc34870a072a443c35e1bf0928caf49d Author: gpau Date: Sat Jun 5 02:10:53 2010 +0000 updated to handle new operator Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 commit af14fd8be6fbe1adf7653393df5ff8cc459c870a Author: gpau Date: Sat Jun 5 02:06:46 2010 +0000 updated to handle new operator. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 4ceaae39e5da9e6933f2afad201bf220087a2069 Author: adonev Date: Fri Jun 4 23:16:23 2010 +0000 Added host angilas Tools/F_mk/GMakeMPI.mak commit 875838b5c50696da5f9afefa0f170f81456b4f25 Author: almgren Date: Fri Jun 4 21:42:45 2010 +0000 Latest ... Docs/BoxLib/boxlib.tex Docs/paper.tex commit 0018f85531179f9d6087f582c455cdf243d5bc9e Author: almgren Date: Fri Jun 4 21:39:28 2010 +0000 We just keep making it better... Docs/BoxLib/boxlib.tex commit 4aaaa0ed59ab94573b55782276e2fa8a46293122 Author: almgren Date: Fri Jun 4 21:39:15 2010 +0000 These are just the framework for building the docs. Docs/GNUmakefile Docs/paper.tex commit a042e68e6ca78b9e2547aee98ed8ccb33f7ea43d Author: almgren Date: Fri Jun 4 21:16:00 2010 +0000 Copied from MAESTRO/docs/architecture then modified. Docs/BoxLib/GNUmakefile Docs/BoxLib/boxlib.tex Docs/BoxLib/data_loc.odg Docs/BoxLib/data_loc2.eps Docs/BoxLib/index_grid.odg Docs/BoxLib/index_grid2.eps Docs/BoxLib/mac.odg Docs/BoxLib/mac2.eps Docs/BoxLib/maestro_directory.odg Docs/BoxLib/maestro_directory2.eps Docs/BoxLib/paper.tex commit 3cd8e4513d1b942b9554c798ac09d141b2a981e7 Author: 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 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 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 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 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 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 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 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 Date: Wed Jun 2 02:00:01 2010 +0000 removed some unused variables Src/LinearSolvers/F_MG/mg.f90 commit 663b4d64cc66702c11071aee6bf51c8160288f4a Author: lijewski Date: Wed Jun 2 01:49:57 2010 +0000 removed some unused variables Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 9cc92b3ac37828934a5c9f7dc4f9c3e6eacc3bef Author: lijewski Date: Wed Jun 2 01:25:23 2010 +0000 removed some unused variables Src/LinearSolvers/F_MG/mg.f90 commit b4ee73f4b936cdcba69c7376d1327dfeb7f15f45 Author: ajnonaka Date: Wed Jun 2 00:53:13 2010 +0000 backing out of a previous change which mysteriously breaks the multigrid on Ann's and my machine Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit b5326cd6d5b9ae41ef33e4fe2f94296240819366 Author: vince Date: Tue Jun 1 21:50:06 2010 +0000 paths for kiryu. Tools/C_mk/Make.mpi commit 64663863101ff8d4e4d6d19990394163e7ee1842 Author: almgren Date: Mon May 31 19:40:23 2010 +0000 Modify the amr.verbose > 1 option so that it calls printGridSummary instead of not printing any grid info. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit a6f4f9a352e9ba62c82713d4d5debe4ec0c8e772 Author: almgren Date: Mon May 31 18:33:06 2010 +0000 Replace "verbose" by "verbose > 0" in most cases, but "verbose > 1" in cases which controlled a call to printGridInfo. Src/C_AMRLib/Amr.cpp commit 6a5fcd1076844b5d3ac8318309774a8425742e79 Author: lijewski Date: Mon May 31 15:52:09 2010 +0000 plugged memory leak Src/F_BaseLib/cluster.f90 commit 1ff62e70a9ecdcce3df43f81cf5701635dd245be Author: almgren Date: Mon May 31 03:38:54 2010 +0000 Add checkpoint_on_restart flag which only happens if doing regrid_on_restart. Src/C_AMRLib/Amr.cpp commit b34105aa870ac5e8f31e4228d396e0d5c43eb816 Author: almgren Date: Mon May 31 03:29:16 2010 +0000 Fix indentation. Src/C_AMRLib/Amr.cpp commit 0a5391988ee06710297528d28c742c105f40fbf1 Author: almgren Date: Sun May 30 23:07:43 2010 +0000 I believe that this version of cluster correctly uses blocking_factor when making grids, both in serial and in parallel. It works for a simple 2d test in varden anyway. Src/F_BaseLib/cluster.f90 commit 31509bab5e79bf45e611a2de677e50a8a9e82240 Author: lijewski Date: Fri May 28 23:39:28 2010 +0000 removed some unused variables Src/F_BaseLib/pingpong.f90 commit 82a3a29c319b0b7db85e76ca92ec996b100a8dc1 Author: lijewski Date: Fri May 28 23:31:09 2010 +0000 cleaned up some unused variables Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 5b7436543d4a1f483308b7fe059c22c6b02d95cc Author: lijewski Date: Fri May 28 21:58:13 2010 +0000 removed some unused variables Src/F_BaseLib/box_util.f90 Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/multifab.f90 Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_bx.f90 Src/F_BaseLib/test/t_bxasc.f90 Src/F_BaseLib/test/t_cls.f90 Src/F_BaseLib/test/t_knapsack.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_bx.f90 Tests/F_BaseLib/t_bxasc.f90 Tests/F_BaseLib/t_cls.f90 Tests/F_BaseLib/t_knapsack.f90 Tests/F_BaseLib/t_main.f90 commit 51921159917355c87068c505e44b9e58fe7e6b0f Author: lijewski Date: Thu May 27 22:23:32 2010 +0000 moved tagboxes_coarsen() from tag_boxes.f90 -> cluster.f90 Src/F_BaseLib/cluster.f90 Src/F_BaseLib/tag_boxes.f90 commit 5157143439e5b17503504e26f81b2a91e5b9f218 Author: lijewski Date: Thu May 27 22:16:30 2010 +0000 bit more cleanup Src/F_BaseLib/tag_boxes.f90 commit 88baa8c6b4e6000d6c04a33966e0506ab254339c Author: lijewski Date: Thu May 27 22:15:02 2010 +0000 got rid of some unused variables Src/F_BaseLib/make_new_grids.f90 commit f6b0283e965ab4fa67b01e71c626927b26c636bf Author: 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 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 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 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 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 Date: Tue May 25 21:56:21 2010 +0000 One more fix... Tools/C_util/Convergence/DiffSameDomainRefined.cpp commit 3891a1c5771511a29e246f164cd32ef2d7eb9c12 Author: almgren Date: Tue May 25 21:47:45 2010 +0000 Try again... Tools/C_util/Convergence/DiffSameDomainRefined.cpp commit 6481c0e9f5e7c01fd4aa25cd16b093e2e7f123ca Author: almgren Date: Tue May 25 21:39:24 2010 +0000 Fix mistakes. Tools/C_util/Convergence/DiffSameDomainRefined.cpp commit bef1f55cb6f5a9f4f2cd0ba6fc183c85802324c0 Author: 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 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 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 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 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 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 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 Date: Fri May 21 22:36:02 2010 +0000 Remove unused variable. Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit 6ff6bcbf2a542c2e3eb21b888024c85bc24925cc Author: mzingale Date: Fri May 21 18:59:26 2010 +0000 comment tweaks Tools/F_scripts/make_build_info commit c9400fb21ada46e1aa68eaec1f9e472d457c11c7 Author: mzingale Date: Fri May 21 17:20:07 2010 +0000 change how build_info works. It is now a module (which is safer for the string length matching) and therefore, it now needs to be detected by the moddep.pl script, so the dependences in GMaestro.mak are updated. This seems to work. When you recompile, it rewrites build_info.f90 and recompiles it (as we want). Note that now build_info.f90 is deleted once it is built. Tools/F_scripts/make_build_info commit e89b30278c2564ebe38466d3bb4bf0648c71a308 Author: mzingale Date: Thu May 20 23:50:48 2010 +0000 fix a line-length issue -- should really wrap the modules line Tools/F_scripts/make_build_info commit f47822b93e8c04936300a51675fd84c9bfa5a60a Author: mzingale Date: Thu May 20 22:10:41 2010 +0000 store the list of "modules" (e.g. reaction network, EOS, ...) compiled into the code in the job_info file. Tools/F_scripts/make_build_info commit 60d1d73ed74ca3061e27b2c96c068ecfb56e8a4a Author: mzingale Date: Thu May 20 19:52:54 2010 +0000 move the stuff that makes build_info.f90 out of the general mk/ stuff and into GMaestro.mak, since this is only used by Maestro. This will give us more control over it. Tools/F_mk/GMakerules.mak commit 0c3a9c66550da0653302a0bd066e684f060427ee Author: ajnonaka Date: Mon May 17 22:46:49 2010 +0000 OMP fix Src/LinearSolvers/F_MG/itsol.f90 commit 8b6ffc976e1c1917bafbeee126e4676f9160bcd4 Author: almgren Date: Sat May 15 01:12:56 2010 +0000 Fix the way max_bottom_nlevel is handled. Src/LinearSolvers/F_MG/mg.f90 commit b9900b99c5c4580dce9f07e4b2d9944671718c8a Author: 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 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 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 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 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 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 Date: Wed May 12 20:48:04 2010 +0000 removed some unused drek Src/F_BaseLib/box.f90 commit 0ca63e7ac9abc027c1146c89c7c54ffcf1cb200a Author: lijewski Date: Wed May 12 20:35:26 2010 +0000 removed some unused drek Src/F_BaseLib/boxarray.f90 commit e9783133d200cf09e73455d319942de677857c16 Author: almgren Date: Wed May 12 18:05:46 2010 +0000 Put print statements before and after reading probin so that we can tell if we die there -- dying while reading probin always just gives an Abort with no error message, so this at least lets you know you are there. Only prints with amr.v >= 1. Src/C_AMRLib/Amr.cpp commit 88bfca30c3f7f9cdb014a425d1b0987a0ea09fc3 Author: lijewski Date: Wed May 12 16:45:22 2010 +0000 removed aveassoc stuff - no longer used by average.f90 Src/F_BaseLib/layout.f90 commit 6ab993142d35547d23e3b658d8b0903c99d0200f Author: lijewski Date: Wed May 12 16:29:17 2010 +0000 removed mcc stuff -- SFC is the way to go Src/F_BaseLib/knapsack.f90 commit 7cc7035340912d28630f01c005b67eefbb0cafd8 Author: 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 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 Date: Fri May 7 20:44:26 2010 +0000 Add one line of comment... Src/LinearSolvers/F_MG/mg.f90 commit f87d7687708257587b1a1c8d08d96d4c4645ce55 Author: 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 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 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 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 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 Date: Thu May 6 01:58:28 2010 +0000 Fix definitions of hi. Src/LinearSolvers/F_MG/mg_smoother.f90 commit 718f2242b73ed75e738dd97ad31e0caa278c0a71 Author: almgren Date: Thu May 6 01:58:04 2010 +0000 Add st_type as a member of mg_tower. Src/LinearSolvers/F_MG/mg_tower.f90 commit 73da9f4d113c57b1807de90277f95681328fb573 Author: almgren Date: Thu May 6 01:38:58 2010 +0000 Fixes for minion routines plus getting rid of more "stencil" stuff. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 6aa733f0e8fc88a9424160b5171162eab67753be Author: almgren Date: Wed May 5 21:38:45 2010 +0000 AmrLevel::computeNewDt now takes post_regrid_flag as a final argument. Src/C_AMRLib/AmrLevel.H commit e80ff5f49e3784dbb07f946cb93385dd90a8e896 Author: almgren Date: Wed May 5 21:38:24 2010 +0000 1) Amr::timeStep now takes stop_time as the final argument. 2) There is a new flag, compute_new_dt_on_regrid (default=0) which, if true, tells the code to call computeNewDt after a regrid with base level 0. This is needed in particular in codes like CASTRO which call an EOS routine to compute the sound speed which is used in computing dt. 3) AmrLevel::computeNewDt now takes an integer flag, post_regrid_flag, which tells the routine whether it is being called after a regrid. If so, then dt_min[i] is "minned" with dt_level[i], rather than change_max*dt_level[i]. Src/C_AMRLib/Amr.cpp commit 6ffda162a89528d3af78672fc2d26475e2c2c7e0 Author: almgren Date: Wed May 5 21:36:11 2010 +0000 Amr::timeStep now takes stop_time as the final argument. Src/C_AMRLib/Amr.H commit dc1ffc3fc1fcf4692800d938f04d509feb6fb1ea Author: 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 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 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 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 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 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 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 Date: Fri Apr 30 15:05:03 2010 +0000 no, really add inf... Tools/F_mk/GMakeMPI.mak commit 05b66078785e39acb96df6d5393c9d87378e8e95 Author: mzingale Date: Fri Apr 30 15:03:55 2010 +0000 add inf Tools/F_mk/GMakeMPI.mak commit 38ef8c0b3ce66aa09efce9e46d9af511ed377e76 Author: almgren Date: Thu Apr 29 21:38:05 2010 +0000 Modify print statement to be more similar to Initial error print. Src/LinearSolvers/F_MG/mg.f90 commit d0d9f705b0330e8249c3b47d762b460b76a11706 Author: 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 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 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 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 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 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 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 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 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 Date: Wed Apr 28 13:53:36 2010 +0000 FINAL TEST COMMIT Src/LinearSolvers/F_MG/stencil_fill.f90 commit 4cfcded2a154c574740858e78a77480541111799 Author: ajnonaka Date: Wed Apr 28 13:52:00 2010 +0000 TEST COMMIT 3 Src/LinearSolvers/F_MG/stencil_fill.f90 commit 11776e6fc079d7e8c67ba653fddfc347b33cd2ae Author: ajnonaka Date: Wed Apr 28 13:49:48 2010 +0000 TEST COMMIT 2 (almost done - sorry for the spam) Src/LinearSolvers/F_MG/stencil_fill.f90 commit e566bec070944aaff2c9247753d00f48c1c08345 Author: ajnonaka Date: Wed Apr 28 13:46:45 2010 +0000 TEST COMMIT Src/LinearSolvers/F_MG/stencil.f90 commit 42b0c154321936ffabb96bbbafd86ad3a2c1cc2a Author: ajnonaka Date: Wed Apr 28 13:40:49 2010 +0000 commit to test log messages - no changes Src/LinearSolvers/F_MG/stencil.f90 commit 2fcb4844c3c3490c77e426a7da565eb612f0484c Author: almgren Date: Wed Apr 28 00:01:43 2010 +0000 If doing XGRAPH stuff (1d) then allow Amr::init to call setPlotVariables so we can use it in the xgraph stuff. Src/C_AMRLib/Amr.cpp commit 6db052890e275670d5ebd9aeffb8f0f0b215029d Author: lijewski Date: Tue Apr 27 23:01:54 2010 +0000 plugged memory leaks in bottom_solver==4 Src/LinearSolvers/F_MG/mg.f90 commit 240b53a5ca4990d34605ffbf935e4fd8eb87f10c Author: mzingale Date: Tue Apr 27 19:18:31 2010 +0000 add a routine write_a_hgproj_grid to complement read_a_hgproj_grid. This is useful for dumping out a grid structure from MAESTRO for debugging in the test_average problem. Src/F_BaseLib/box_util.f90 commit 8e7668d7f1563612a21d4512099b99928908ce5a Author: almgren Date: Mon Apr 26 21:26:15 2010 +0000 There was duplication of code that didn't need to be there, inside the bottom solver stuff. Src/LinearSolvers/F_MG/stencil_fill.f90 commit fc755c030a5b6e22193a78ef03f32bcf537a9243 Author: gpau Date: Mon Apr 26 19:13:01 2010 +0000 updated the porous stuff Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 4b1fa65b01d115b904e96c4addf29b443b6ad0d7 Author: almgren Date: Mon Apr 26 19:10:26 2010 +0000 This version compiles... Src/LinearSolvers/F_MG/mg_cpp.f90 commit 770ea54542113050cb493ad3901a3ae6d4faca36 Author: almgren Date: Mon Apr 26 19:00:08 2010 +0000 Fix the definition of nlevel -- it's number of mglevels, not amr levels, when used for cell_coeffs and edge_coeffs. Src/LinearSolvers/F_MG/mg_cpp.f90 commit b2e1b2cc9c0ac40f5f07d337ccfd5855d5c1bf9b Author: almgren Date: Mon Apr 26 17:23:07 2010 +0000 st_coeffs --> coarsen_coeffs Src/LinearSolvers/F_MG/FParallelMG.mak commit c2225fa88c66ee77ecfdf90c56251638ebd0dd79 Author: 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 Date: Sat Apr 24 13:42:12 2010 +0000 line wrap error Src/LinearSolvers/F_MG/stencil.f90 commit abc0cf7c9dbb0afe1e22fce0c0dff0045feef1f8 Author: almgren Date: Sat Apr 24 05:13:53 2010 +0000 Fix bug in 3d averaging of x-edge coefficients. Src/LinearSolvers/F_MG/coarsen_coeffs.f90 commit ef2e139c58074bbf0c4cd5a207b15aadaa34dd4e Author: almgren Date: Sat Apr 24 01:34:49 2010 +0000 Remove print statement. Src/LinearSolvers/F_MG/stencil_fill.f90 commit 743960500674bb382f8ac274a4e6b85e0aa4ca26 Author: almgren Date: Sat Apr 24 01:16:13 2010 +0000 We no longer have a single coeffs(:) array, we now have cell_coeffs and edge_coeffs. Src/LinearSolvers/F_MG/coarsen_coeffs.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 commit 3134128407204972e679aa9879ddcf31f0d0680e Author: 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 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 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 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 Date: Sat Apr 24 00:07:01 2010 +0000 Typo ex --> dx Src/F_BaseLib/tag_boxes.f90 commit c48f309a3739cb0176baa7973d79bcce8e9b1fe0 Author: ajnonaka Date: Fri Apr 23 23:41:55 2010 +0000 for intel 9, reverting to a less optimized mode, which actually runs faster (go figure) and is less susceptible to the plotfile pi bug I've been struggling with Tools/F_mk/GMakedefs.mak commit 10909bb536dced456dad7833240c851903a1351d Author: ajnonaka Date: Fri Apr 23 22:36:32 2010 +0000 rewritten in gfortran-friendly way Src/F_BaseLib/layout.f90 commit fdd9cdc6fc1d3e5369d9640c997078ab4d8f53c4 Author: ajnonaka Date: Fri Apr 23 22:29:28 2010 +0000 pass in dx to tag_boxes so you can refine based on location Src/F_BaseLib/make_new_grids.f90 Src/F_BaseLib/tag_boxes.f90 commit 8d74bfa9a7c16b813acf43867b825649fe791330 Author: almgren Date: Fri Apr 23 21:34:20 2010 +0000 Add multifab_build_edge routine. Src/F_BaseLib/multifab.f90 commit 0f7a102cbc5cb1b1156d7363d94d4947ae1a43f3 Author: lijewski Date: Fri Apr 23 20:16:46 2010 +0000 removed some dead code Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ccse-mpi.H commit 708db30edc69bc870a57f4596b58dfd0922a9641 Author: almgren Date: Fri Apr 23 18:33:18 2010 +0000 Renamed st_coeffs.f90 --> coarsen_coeffs.f90 Src/LinearSolvers/F_MG/GPackage.mak commit 2e3300b437f0a1782b3093bbecbfb034ce1975a8 Author: almgren Date: Fri Apr 23 18:24:47 2010 +0000 Rename st_coeffs.f90 --> coarsen_coeffs.f90 and modify it to put in more comments and make it work for the porous media stencils. Src/LinearSolvers/F_MG/coarsen_coeffs.f90 commit 7bf63d38e64312fb77e68c2bbaf87ff7907a705d Author: almgren Date: Fri Apr 23 18:24:00 2010 +0000 1) Include coarsen_coeffs_module instead of coeffs_module. 2) Start to make the number of components more general so we can accomodate the porous media stuff. Src/LinearSolvers/F_MG/stencil_fill.f90 commit 035f2fa353bcd9dd2d6fe1d0336049b82d872386 Author: almgren Date: Fri Apr 23 18:21:05 2010 +0000 Doesn't need to include coeffs_module. Src/LinearSolvers/F_MG/nodal_mask.f90 commit 6d75c2b01649cb6dfa97aba6f66915ef8b514866 Author: mzingale Date: Fri Apr 23 15:29:17 2010 +0000 mgt%dh was being indexed incorrectly when initializing coarse_dx Src/LinearSolvers/F_MG/mg.f90 commit eb0a3eb7cec65d2d713f35ca9fccbcef7ab1f515 Author: gilet Date: Wed Apr 21 16:30:17 2010 +0000 added stuff for orga Tools/F_mk/GMakeMPI.mak commit 4df043d6ddbfa92e0c2cf49586632ab978b6047d Author: almgren Date: Wed Apr 21 04:00:44 2010 +0000 Pass in bottom_solver Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 175dc9fd7675ced09f7da3d9c44f09cbe53a3c11 Author: 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 Date: Wed Apr 21 03:57:48 2010 +0000 Remove unused statements. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 70c32e7022b07cfcadda7805f04a812732051ea3 Author: ajnonaka Date: Tue Apr 20 21:55:41 2010 +0000 xlf library location mysteriously moved in the last hour Tools/C_mk/Make.mpi commit a741b73a1f3a45878cfd4478fd38e7f0bb1c3da5 Author: almgren Date: Tue Apr 20 21:36:42 2010 +0000 Need to set coeffs%nc equal to coeffs(maxlev)%nc, NOT ss%nc. Src/LinearSolvers/F_MG/stencil_fill.f90 commit aaa81902be8a8bc539efed6a336764964a42f31f Author: almgren Date: Tue Apr 20 21:30:33 2010 +0000 One more call to fix. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit fff7307b7146bf03375df55d697c2398fbd2ddf6 Author: 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 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 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 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 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 Date: Tue Apr 20 20:31:06 2010 +0000 Fix line 157. Src/LinearSolvers/F_MG/mg.f90 commit 91dadbf8400d4440a1d35992ed35f3f3b8dd63b0 Author: ajnonaka Date: Tue Apr 20 20:22:34 2010 +0000 forgot to include impose_neumann_bcs.f90 Src/LinearSolvers/F_MG/FParallelMG.mak commit a27d111b2b14b4756bf9bbcbdb026b3ec31cbd97 Author: almgren Date: Tue Apr 20 20:12:56 2010 +0000 Dont need to pass pd into stencil_fill. Src/LinearSolvers/F_MG/stencil_fill.f90 commit 4a034f087266ce8d9c0e222e2dc38bb4302f7052 Author: ajnonaka Date: Tue Apr 20 19:43:52 2010 +0000 omp now compiles on intrepid with xlf; whether it works or not is currently unknown Tools/C_mk/Make.mpi commit 7df24f54f9218376c3b0ed6388adfb004df475eb Author: ajnonaka Date: Tue Apr 20 19:35:49 2010 +0000 oops, guess it doesn't work yet, but this fixes one library Tools/C_mk/Make.mpi commit 69a9121bef43873beb31ccb055657935ac6b38c9 Author: ajnonaka Date: Tue Apr 20 19:34:27 2010 +0000 omp now compiles on intrepid with xlf; whether it works or not is currently unknown Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi commit 155b277949c13bc3f15ab8df107bf3d1bac9661b Author: almgren Date: Tue Apr 20 19:31:59 2010 +0000 Add stencil_fill_minion_all_mglevels which enables bottom_solver=4 for the minion stencil as well. Src/LinearSolvers/F_MG/stencil_fill.f90 commit 46571fceab7721ccc02f55b88463b762971c997e Author: almgren Date: Tue Apr 20 18:59:55 2010 +0000 Added some new files. Src/LinearSolvers/F_MG/GPackage.mak commit c1efe4714b655f81f640eb5df3301892a7301525 Author: almgren Date: Tue Apr 20 18:53:58 2010 +0000 Changes so that all of the bottom_solver=4 stuff is now created in files in this directory rather than needing to be passed in. Src/LinearSolvers/F_MG/impose_neumann_bcs.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_fill.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit d3fda8b0f2db34149960fcbf6dc3a5acc11fcdc6 Author: 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 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 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 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 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 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 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 Date: Thu Apr 15 21:17:10 2010 +0000 carver.nersc.gov stuff Tools/F_mk/GMakeMPI.mak commit e77850990aa0ace1af2ae32311a2c31f4fd575f2 Author: 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 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 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 Date: Tue Apr 13 23:14:54 2010 +0000 added extern/random stuff Tests/LinearSolvers/F_MG/GNUmakefile commit 962c8b3c09833846f173b8f3860337cae2f4545e Author: almgren Date: Mon Apr 12 18:39:33 2010 +0000 Move mt19937ar.f90 from boxlib to extern/random so we don't have to compile it every time -- it takes a long time. Src/F_BaseLib/GPackage.mak Src/F_BaseLib/mt19937ar.f90 commit 5ccc3bd361ef22edab88c64e9be75621f1ab51b5 Author: adonev Date: Fri Apr 9 22:15:57 2010 +0000 stochastic_varden now compiles OK Src/F_BaseLib/GPackage.mak commit 0b2323ee9871fdf6a8c7122e47889f78734e6800 Author: ajnonaka Date: Wed Apr 7 19:03:39 2010 +0000 xlf on interpid with omp now compiles Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit 3670809b263e39227e627ac5a103576fe925967d Author: vince Date: Tue Apr 6 20:48:05 2010 +0000 fixed default MPI_HOME. Tools/C_mk/Make.mpi commit b89f03e249032f371b575f51ac4dc0e12c1baa4f Author: ajnonaka Date: Tue Apr 6 20:41:44 2010 +0000 turned of auto threading on intrepid Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit f73d0058ef86c54c901b5ff0960ebb2153904bb1 Author: ajnonaka Date: Tue Apr 6 20:14:57 2010 +0000 for some reason the mpi compiler on intrepid needs its own OMP statements Tools/F_mk/GMakeMPI.mak commit fae1830465684d8f992a4185ded246e561ef74c6 Author: 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 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 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 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 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 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 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 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 Date: Fri Mar 26 20:33:02 2010 +0000 fixed parallel bug Src/LinearSolvers/C_NodalMG/amr_multi.cpp commit 055f7e71ecf5ba8dc1898710e0a0b9a83b4b6ae3 Author: almgren Date: Thu Mar 25 21:44:46 2010 +0000 Allow a "dump_old" flag to be passed through AmrLevel into StateData so we have the option not to write both the old and new data. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 58a0dec142983c4598104f3efe73a5dbba039569 Author: lijewski Date: Thu Mar 25 20:33:42 2010 +0000 mods for carver.nersc.gov Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit b4ec1a1244d52a33409761d34fc19fed17307671 Author: gpau Date: Wed Mar 24 23:53:44 2010 +0000 fixed an error with the pressure solve Src/LinearSolvers/F_MG/stencil.f90 commit 851a2987446b3fd67a88f39b0aa20810592b6eed Author: gpau Date: Wed Mar 24 19:29:43 2010 +0000 fixed the stencil to loop over ncomp of density Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/stencil.f90 commit def0d12a075b69351564e36d22935a442e0c0b69 Author: gpau Date: Wed Mar 24 19:28:47 2010 +0000 updated the porous Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 110da6e43b7a9f84e9cb074daf3a5cc765ed7089 Author: lijewski Date: Tue Mar 23 19:17:33 2010 +0000 hmmmm Src/C_BaseLib/BoxList.cpp commit b29a994fb50711afd040d08a11efcea5bf0d5fb7 Author: gpau Date: Tue Mar 23 19:10:35 2010 +0000 removed bad BL_ASSERT() Src/C_BaseLib/BoxList.cpp commit 498f6e5344284af087b12c824021fab3c2381c7f Author: mzingale Date: Sun Mar 21 20:55:41 2010 +0000 add support for self-tests (like Maestro's test_advect). These are tests that diagnose themselves, so no comparison to a benchmark is needed. Tools/C_util/regtests/Maestro-tests.ini Tools/C_util/regtests/test.py commit 25331b056d1c00f4bfdebb746a7ae30aabc54115 Author: mzingale Date: Fri Mar 19 20:21:00 2010 +0000 add -fltconsistency to the -mp1 for Intel 10 and 11 -- this fixes errors that test_advect showed. Tools/F_mk/GMakedefs.mak commit 180683da6704811f314b1eb4395e24849cc59705 Author: ajnonaka Date: Fri Mar 19 19:23:06 2010 +0000 mods for PGI and jaguar Tools/C_mk/Make.Linux commit c3427103935a87c179729aaf590b28dcc5a1f551 Author: gpau Date: Fri Mar 19 18:05:17 2010 +0000 fixed a bug in the simplen_2d Src/LinearSolvers/F_MG/stencil.f90 commit b9b445573d6f8721535996b1d218696b5c4b7435 Author: mzingale Date: Fri Mar 19 14:01:08 2010 +0000 add some error handling for the visualization if no output file is produced Tools/C_util/regtests/test.py commit f9d8185836e15ffc5785dc9c990e6c0fc334d6a1 Author: almgren Date: Thu Mar 18 21:48:00 2010 +0000 Move "finest_level = new_finest_level" to be before the call to amr_level->post_restart in Amr::restart. Src/C_AMRLib/Amr.cpp commit 56f12bed53bd0c00d27784acc5797e656bcc7fb8 Author: 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 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 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 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 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 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 Date: Thu Mar 18 16:52:49 2010 +0000 latest test suite Tools/C_util/regtests/Maestro-tests.ini commit 979375ae5ea84d6682cdb4efc42a217fe9c079f7 Author: mzingale Date: Thu Mar 18 16:52:14 2010 +0000 pretty-up the output (now in color) Tools/C_util/regtests/test.py commit 8cd993b15429b2181cb8f6b7db915407d5312333 Author: 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 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 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 Date: Tue Mar 16 19:16:12 2010 +0000 syntax fix Src/LinearSolvers/F_MG/mg.f90 commit 35eac60a974a38332bb619b9c84da383b52d5a19 Author: almgren Date: Tue Mar 16 19:10:32 2010 +0000 Fix bottom_solver_type = 4 so that it now works with PGI on franklin -- problem before was that mg_tower_bottom_solve was effectively called recursively from mg_tower_cycle --> mg_tower_cycle --> mg_tower_bottom_solve --> mg_tower_cycle --> mg_tower_bottom_solve. We have fixed this by renaming the routine that is called when bottom_mgt is present -- that is now "do_bottom_mgt", and the routine mg_tower_bottom_solve only does bottom_solver_type = 1,2 or 3. Src/LinearSolvers/F_MG/mg.f90 commit b2e9db5ca467d128636ede135a7fe7fef1e9d14b Author: lijewski Date: Mon Mar 15 21:24:19 2010 +0000 removed commented out vestiges of OMP in hgrlxu() Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit 5a5f3177b1f3a4d6d85d0db24e71ccf828e332a7 Author: 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 Date: Mon Mar 15 01:15:22 2010 +0000 added fredom stuff Tools/C_mk/Make.Linux commit 7825121247448df072727755ca2c6917b5128fab Author: lijewski Date: Mon Mar 15 01:13:15 2010 +0000 removed some OMP stuff that PGI gets wrong Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit 72b98effe065706d613a6d17861263f8add6fa2e Author: lijewski Date: Sun Mar 14 22:01:46 2010 +0000 freedom added Tools/C_mk/Make.defs commit d8d601951081950fefaf2a5b0756e6f6bf03c91d Author: lijewski Date: Sat Mar 13 01:24:22 2010 +0000 OMP mods to compile with PGI Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit d971e7dce9b7a52aae8eb9b463abe4737096cf1d Author: lijewski Date: Fri Mar 12 21:07:59 2010 +0000 changed -O -> -fast for PGI Tools/F_mk/GMakedefs.mak commit c799b95142024ec5a08ffc6b9b60b5532b2629dc Author: lijewski Date: Thu Mar 11 22:28:09 2010 +0000 remove OMP loop -- Intel didn't like it :-( Src/LinearSolvers/F_MG/mg_restriction.f90 commit 51fbfa76709c0718edeeea630267a53a102e3c47 Author: mzingale Date: Thu Mar 11 03:38:22 2010 +0000 fix a bug introduced during an optimization Src/LinearSolvers/F_MG/stencil.f90 commit 9c37fd65388bec5250a2922b099b0c65cda24f93 Author: ajnonaka Date: Wed Mar 10 21:18:08 2010 +0000 get rid of SMP stuff so nobody gets the (false) impression that it actually works Tools/C_mk/Make.mpi Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit fec5f80532389c3b7833b4c94622abe774bb6202 Author: almgren Date: Tue Mar 9 18:23:25 2010 +0000 Remove print statements. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 79a9983eeef9131e70576705c4333cc96a4228cb Author: 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 Date: Mon Mar 8 19:02:52 2010 +0000 *** empty log message *** Tests/LinearSolvers/F_MG/nodal_multi.f90 commit 3224970e045b26f8f113613f939b79b369e464b7 Author: almgren Date: Sat Mar 6 22:40:05 2010 +0000 Now allow multicomponent coefficients. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit c0b139380c497694427c67df5f8878d79e28d3bd Author: almgren Date: Sat Mar 6 22:39:38 2010 +0000 Now allow multicomponent betax, betay. Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/stencil.f90 commit 64ea68ac519687d7a1950824dc6cff7791143570 Author: almgren Date: Sat Mar 6 04:25:35 2010 +0000 Remove unused variables. Src/F_BaseLib/multifab.f90 commit bb22403c674f9d2ee316a8e318320801d54adb1f Author: lijewski Date: Sat Mar 6 00:15:55 2010 +0000 use our cpy_[dilz] routines instead of compiler generated ones Src/F_BaseLib/multifab.f90 commit 27ac6582b095c8f67ca9655079ff95786ed0e076 Author: lijewski Date: Fri Mar 5 23:46:58 2010 +0000 bit more OMP Src/F_BaseLib/multifab.f90 commit 72909a6542987c16cdbf51ea8c174301ba2ff854 Author: lijewski Date: Fri Mar 5 23:28:10 2010 +0000 OMPd fab_setval_c() Src/F_BaseLib/fab.f90 commit 34869373b82e62230e3f7405b9a0310e8ea8860b Author: lijewski Date: Fri Mar 5 23:05:05 2010 +0000 OMP'd norm_inf Src/F_BaseLib/multifab.f90 commit b6427871074c9aab5514edc41060c91841671aa7 Author: lijewski Date: Fri Mar 5 21:52:58 2010 +0000 more OMPing Src/F_BaseLib/multifab.f90 commit 1354d5044558910d6e7a0afd92750000ab265a7d Author: lijewski Date: Fri Mar 5 20:40:21 2010 +0000 little code rearrangement Src/LinearSolvers/F_MG/stencil.f90 commit ed5abbd35391fbefdcc1b1d5c9009d6408ba45e7 Author: lijewski Date: Fri Mar 5 18:58:48 2010 +0000 some code consolidation Src/LinearSolvers/F_MG/stencil_nodal.f90 commit c3181a5fdde782df8bf0227c0310576cfc00d934 Author: lijewski Date: Fri Mar 5 18:19:11 2010 +0000 some more OMPing Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 593f986ef8c21662fcf484365f68832777b706a8 Author: 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 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 Date: Thu Mar 4 22:03:50 2010 +0000 removed itsol_breakdown() -- not used Src/LinearSolvers/F_MG/itsol.f90 commit 290e9e99b208a545808a5eaa19cd4a5122d2b6df Author: lijewski Date: Thu Mar 4 22:00:53 2010 +0000 some cleanup Src/F_BaseLib/multifab.f90 commit d6efe30b2b0bd84f795e3721482d7c15e29df615 Author: lijewski Date: Thu Mar 4 17:35:13 2010 +0000 Commented out a bunch of OMP directives that Chuck put in. They were over boxes which is not the right way to do things. Got to eventually go back over these and OMP over the fortran instead. Src/F_BaseLib/multifab.f90 commit bfdb349e3e850e61bc03d3b927a8a3227bb42991 Author: lijewski Date: Thu Mar 4 17:33:36 2010 +0000 OCVS: ---------------------------------------------------------------------- Removed couple OMP directives on loops over boxes that Chuck put in some time ago. It's not the right way to do things. It was leading to nested thread calls which was killing PathScale. Src/LinearSolvers/F_MG/mg.f90 commit 7d143ba543f5b1e309db7d937da8f7d2b7590230 Author: 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 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 Date: Wed Mar 3 23:17:39 2010 +0000 some OMPing Src/LinearSolvers/F_MG/nodal_divu.f90 commit ce9d354acb2ff110ee7d169e5ca20df4e1ddc7fa Author: lijewski Date: Wed Mar 3 23:13:07 2010 +0000 OPM'd Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 4255b7c2e9a83d0cc3e19405246885f2974a2096 Author: lijewski Date: Wed Mar 3 21:15:01 2010 +0000 Removed bunch of duplicate functions by making single module private version. Src/LinearSolvers/F_MG/itsol.f90 commit d00854ceb3c542114118c481f011c62fd6131154 Author: lijewski Date: Wed Mar 3 21:06:03 2010 +0000 more OMP and cleanup Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 498acd3bdfe8f3507f52a7d8a57c0ed64b8a4c9c Author: 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 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 Date: Tue Mar 2 23:49:03 2010 +0000 some OPMing Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 2d8f1aba27c5b2c9b35cf494152e13fdd8ab89b4 Author: lijewski Date: Tue Mar 2 23:20:41 2010 +0000 some OMP Src/LinearSolvers/F_MG/mg_restriction.f90 commit c11a35cda09c9932706daf007876576f44edd5b2 Author: lijewski Date: Tue Mar 2 23:08:27 2010 +0000 more function eliding Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 3450c5650323ed8f34f8fbeac42f897115768d68 Author: lijewski Date: Tue Mar 2 21:06:00 2010 +0000 yet more eliding of bc_neumann() and bc_dirichlet() Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 265a72ed327e5370d2d5bca6940665efa15eb2a2 Author: lijewski Date: Tue Mar 2 19:05:19 2010 +0000 more eliding of bc_neumann() and bc_dirichlet() Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 7314f9e5e78ea5b00d7fdce15f49d82b9401821b Author: lijewski Date: Tue Mar 2 18:16:47 2010 +0000 Rearranged code to remove bunch of bc_neumann() calls. More to be done ... Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 93e12e5587df3d17e374852db2c2d97ef39066df Author: 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 Date: Mon Mar 1 23:10:17 2010 +0000 some OMP Src/LinearSolvers/F_MG/ml_prolongation.f90 commit caee6b388fe9d5f4509f2db80aa843ea727efb52 Author: lijewski Date: Mon Mar 1 22:43:58 2010 +0000 yet more OMP Src/LinearSolvers/F_MG/stencil.f90 commit 8b4ab52cbfcaa272dd2cdd28a237a5ff5076b7e9 Author: lijewski Date: Mon Mar 1 22:22:02 2010 +0000 some OMP Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 693d83cd18376b1df263af1cf915c3a7999f30b7 Author: lijewski Date: Mon Mar 1 22:15:57 2010 +0000 some OMP Src/LinearSolvers/F_MG/mg_smoother.f90 commit 72d94ddcbc6b2da968b9a4947fd526bf6cf5ee55 Author: lijewski Date: Mon Mar 1 22:02:03 2010 +0000 brought up-to-date Tests/LinearSolvers/F_MG/main.f90 Tests/LinearSolvers/F_MG/wrapper.f90 commit 65cdb3dda7150b02fe6e4ce96a9fcabf6a90af17 Author: lijewski Date: Mon Mar 1 22:00:11 2010 +0000 Got rid of -stand f95 for intel; complains about OMP loops. Added appropriate stuff for OMP with Intel. Changed -mp --> -mp1 Tools/F_mk/GMakedefs.mak commit 272910eb9ad7dfdabc4a8b55c16f419ec65d2b85 Author: lijewski Date: Mon Mar 1 20:12:14 2010 +0000 speedup to gs_rb_smoother_3d Src/LinearSolvers/F_MG/mg_smoother.f90 commit 594ddeb94343fc9862f3d251f6f34a8e8bbd54f5 Author: almgren Date: Fri Feb 26 22:23:37 2010 +0000 Remove unused variable: IntVect b1_length = b1.size(); Src/C_AMRLib/TagBox.cpp commit 8adc964d67678a40e977cc5718c0dfd20784000a Author: almgren Date: Fri Feb 26 21:57:04 2010 +0000 Modify Amr, AmrLevel and Make.package so that we don't generically include SlabStat and StationData stuff. You must now define USE_SLABSTAT or USE_STATIONDATA to get those (respectively). Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Make.package commit 4f7467b63279338532a4d663db717cccf088d337 Author: lijewski Date: Fri Feb 26 21:33:58 2010 +0000 minor efficiency tweaks Src/C_BaseLib/BoxList.cpp commit 09e955a8181919b798036d1d0ba068508013ca55 Author: lijewski Date: Fri Feb 26 21:14:00 2010 +0000 minor tweaks to add() Src/C_BaseLib/BoxDomain.cpp commit e630d63e8164d7327e72230e6146fc96cd80b174 Author: lijewski Date: Thu Feb 25 22:34:34 2010 +0000 use LnClassPtr instead of CpClassPtr Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit c3a0b5bc234fe1f45d411f2e810475062388bdd3 Author: lijewski Date: Thu Feb 25 20:59:23 2010 +0000 undrrelxr now uses LnClassPtr instead of CpClassPtr Src/LinearSolvers/C_CellMG/LinOp.H commit 0a46529825fceb21e5246af37e6b616fd7c39bc6 Author: lijewski Date: Tue Feb 23 21:37:42 2010 +0000 minor tweak to how intersections() is used Src/C_AMRLib/AuxBoundaryData.cpp Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/FabSet.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp commit ed5c1530ba0bedc52e46954792e5a665a9c4a34e Author: lijewski Date: Tue Feb 23 21:08:02 2010 +0000 remove unused constructor & use reserve() on vector members Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit c974efeb44b9c18bfbbb63052719237a1e2cf92a Author: lijewski Date: Tue Feb 23 20:09:48 2010 +0000 use a std::list instead of std::vector for PIRMList type Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 1cea6f82fc47ea06dee33a715df76fdfdf8402b7 Author: lijewski Date: Tue Feb 23 18:36:07 2010 +0000 added swap() Src/C_BaseLib/BaseFab.H commit 6ebf9e8c60c12baa27b51fbb79c3dcf92ea2bcda Author: 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 Date: Sun Feb 21 16:28:19 2010 +0000 efficiency mods to simplify() Src/C_BaseLib/BoxList.cpp commit 964ed5ff1f96d8931fdc03c19b7f59f4eb49b616 Author: almgren Date: Fri Feb 19 23:40:10 2010 +0000 These now compile. Tools/C_util/Convergence/Add.cpp Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/GNUmakefile Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileNormB.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp commit 9b443be98f48f14093ef75e77044d4f8198b9703 Author: ajnonaka Date: Fri Feb 19 23:04:42 2010 +0000 prints out norms now - that are properly normalized as well (as noted in the output stream)! Tools/C_util/Convergence/DiffFab.cpp commit ed0babdcc7400e46294a14c542689bc206cf8c1d Author: almgren Date: Fri Feb 19 22:45:04 2010 +0000 Start to make these compile again. Tools/C_util/Convergence/Add.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileNormB.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp commit 435415dde25c7f81ff5272dc3647091b2c78ade1 Author: 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 Date: Fri Feb 19 22:36:05 2010 +0000 compiles again Tools/C_util/Convergence/DiffFab.cpp commit 347345acf80e750e7d6c0eb545864fd1fdb2c83b Author: lijewski Date: Fri Feb 19 21:19:34 2010 +0000 minor refinement of execute() Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit ace11fa8dfc102aafe5dc538e6c81a8e85dafc7b Author: lijewski Date: Fri Feb 19 18:18:34 2010 +0000 a bit more const-correctness Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit f3481fcf61853daf9277ac3211099dea9833be4d Author: almgren Date: Fri Feb 19 18:16:11 2010 +0000 Add -DBL_PLEIADES so we know if we are on pleiades. Tools/C_mk/Make.Linux commit e4d889612f0ef233f3b84d53af13a2c70876bfda Author: lijewski Date: Fri Feb 19 17:59:07 2010 +0000 removed BFProxy stuff Src/C_BaseLib/BaseFab.H commit cc12d50e562296a720fbff95bb607cc5cebc544d Author: almgren Date: Thu Feb 18 17:49:08 2010 +0000 Fix print statements. Src/LinearSolvers/F_MG/mg.f90 commit 15953644e28d55c5ccda2fe086c12153bd45006b Author: lijewski Date: Wed Feb 17 16:49:54 2010 +0000 integrated back in FORT_HGRESU and FORT_HGRLXU for the time being Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit 24a7d4ed3b1655ba336f140e337399154918d43e Author: lijewski Date: Tue Feb 16 18:41:07 2010 +0000 removed some virtuals -- FabArrayBase is a concrete class Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit a421807911ab68cb5172b163e03e9a53d670ae98 Author: lijewski Date: Tue Feb 16 18:15:50 2010 +0000 remove some temporaries Src/C_BaseLib/BoxList.cpp commit e38413400a46fe354c5c64ab57e75964e17732f9 Author: lijewski Date: Tue Feb 16 18:15:17 2010 +0000 enforce stricter const-correctness Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/Orientation.H commit a64839b99d0c446f2d34bdc847a0af6d9fa47ee0 Author: 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 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 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 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 Date: Tue Feb 16 17:42:46 2010 +0000 *** empty log message *** Src/C_AMRLib/Cluster.cpp commit 39e82ffdd4a346ad1c989144fd505fdf7410ba0d Author: lijewski Date: Sat Feb 13 23:06:18 2010 +0000 added cg.cpp Src/LinearSolvers/C_NodalMG/Make.package commit 7c36b7b016363342b5a38b4f6e04732f7f7a7f83 Author: lijewski Date: Sat Feb 13 22:50:17 2010 +0000 some efficiency mods Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AuxBoundaryData.cpp Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/Derive.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.cpp commit 40b35b26b0b66dd1b8a64b7ac5ea35c8c58dc90e Author: almgren Date: Sat Feb 13 01:41:39 2010 +0000 Remove unused variables. Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit a15a9e5a51dc392a168afc3258631c6bdccf7339 Author: almgren Date: Sat Feb 13 01:17:54 2010 +0000 Moved gt_breaks_27pt to the Test directory. Src/LinearSolvers/C_NodalMG/Test/gt_breaks_27pt Tests/LinearSolvers/C_NodalMG/gt_breaks_27pt commit 3a937963a8ad0c5b70bc3e5f09b88f101e8e93fc Author: almgren Date: Sat Feb 13 01:15:26 2010 +0000 Moved 3d_4_level.grids to the tests directory. Src/LinearSolvers/C_NodalMG/tests/3d_4_level.grids Tests/LinearSolvers/C_NodalMG/test_grids/3d_4_level.grids commit 6119c0b82851e1b06d9f5bd87f232cfb34ac5aca Author: almgren Date: Sat Feb 13 01:14:08 2010 +0000 Moved files.2d and files.3d to the Test directory. Src/LinearSolvers/C_NodalMG/Test/files.2d Src/LinearSolvers/C_NodalMG/Test/files.3d Tests/LinearSolvers/C_NodalMG/files.2d Tests/LinearSolvers/C_NodalMG/files.3d commit 44bdfe67a7c29541e76b4ff04c9c57f1eff7ad7f Author: almgren Date: Sat Feb 13 01:12:33 2010 +0000 Moved proj.cpp and inputs to the Test directory. Src/LinearSolvers/C_NodalMG/Test/inputs Src/LinearSolvers/C_NodalMG/Test/proj.cpp Tests/LinearSolvers/C_NodalMG/inputs Tests/LinearSolvers/C_NodalMG/proj.cpp commit 464e294d149a4a29bbf0f3a0bbded1e598ce3f0d Author: almgren Date: Sat Feb 13 01:10:35 2010 +0000 No clue what hgproj.pg was for. Src/LinearSolvers/C_NodalMG/hgproj.pg commit 777e12089e0ed7952dfe4f39b83ed311db137fc9 Author: almgren Date: Sat Feb 13 00:53:07 2010 +0000 Move cgsolve out of hg_multi3.cpp and into a separate file, cg.cpp Src/LinearSolvers/C_NodalMG/cg.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 50e45ac8c85160bd272eba3e16a5f2402da2d701 Author: almgren Date: Sat Feb 13 00:47:47 2010 +0000 Removed unused subroutines and renamed HGRESUR to HGRES_CROSS. Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit d91b862ab1933719b8282a45c4c5abe75adcc7a0 Author: almgren Date: Sat Feb 13 00:47:07 2010 +0000 Moving subroutines around to make it easier to keep track of things. Created cg_2d.f and cg_3d.f to hold the subroutines used for the CG bottom solve. Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/cg_2d.f Src/LinearSolvers/C_NodalMG/cg_3d.f Src/LinearSolvers/C_NodalMG/hg_multi2d.f Src/LinearSolvers/C_NodalMG/hg_multi2d_full.f Src/LinearSolvers/C_NodalMG/hg_multi3d.f Src/LinearSolvers/C_NodalMG/hg_multi3d_full.f commit f724e396c3504cfe31fe3d278e9c46c78f63f84f Author: almgren Date: Fri Feb 12 23:36:42 2010 +0000 Added more print statements to make it look more like f90 version. Doesn't change execution and should be the same with Pcode = 0 or 1. Src/LinearSolvers/C_NodalMG/amr_multi.cpp commit 47e6d409d6d77a6abec8a90cd92335f42a29356f Author: almgren Date: Fri Feb 12 23:34:40 2010 +0000 Remove unused routines (ones with unrolled loops) and modified print statements. Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit f6a8aeb898047f4dc47d0f99fbebc5ec02a30319 Author: almgren Date: Fri Feb 12 23:34:04 2010 +0000 Remove unused variables, unused subroutines, and the unrolled versions of the cross-stencil relaxation routines. Src/LinearSolvers/C_NodalMG/hg_multi2d.f Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit 56f97bc7c32d3733513dda6b39a34018dd548f75 Author: lijewski Date: Thu Feb 11 23:38:05 2010 +0000 some inlining Src/C_AMRLib/BCRec.H Src/C_AMRLib/BCRec.cpp Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp commit fa7854bc451422f4b46417955d501fc4883785d2 Author: lijewski Date: Thu Feb 11 23:15:08 2010 +0000 some inlining Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/RealBox.H Src/C_BaseLib/RealBox.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit fe34d39f9d2955c293c04e14701d40c19e8dc625 Author: lijewski Date: Thu Feb 11 22:22:34 2010 +0000 some inlining Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/IndexType.H Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/UseCount.H Src/C_BaseLib/UseCount.cpp commit f868b912c916c78e77c6f79458a590256bb49a2b Author: almgren Date: Wed Feb 10 22:19:52 2010 +0000 1) Back out the introduction of "just_solve" 2) Add an extra argument (Rhs) to nodal_project. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 86c1e5d390cf07794def26da845d77475b323079 Author: almgren Date: Wed Feb 10 21:46:57 2010 +0000 Add additional option for solve which doesn't take a BndryData Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 09de753af5ac1e79b03bc3400f61ce56597728c7 Author: lijewski Date: Wed Feb 10 21:22:23 2010 +0000 some refinement to Distribute() Src/C_BaseLib/DistributionMapping.cpp commit 46544a5792251f35ca6cbac9904fe8aa19e71976 Author: almgren Date: Wed Feb 10 20:44:49 2010 +0000 Modified print statements to be more aligned with current mglib. Src/LinearSolvers/F_MG/mg.f90 commit 39a765832f5f0c8c63f3edcd7fc38df78474a993 Author: almgren Date: Wed Feb 10 20:42:24 2010 +0000 Modified verbosity controls to make output more similar to that of F90 solvers. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit d0af494542496d85b579875fefda27dceebc2b52 Author: almgren Date: Wed Feb 10 20:31:43 2010 +0000 Remove unused variable. Src/LinearSolvers/F_MG/mg_cpp.f90 commit d220743937059824e8ccb4f66a1582528fbeab9a Author: 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 Date: Tue Feb 9 23:04:49 2010 +0000 added to get sprintf() Src/C_BoundaryLib/BndryRegister.cpp commit cfb8d82c00b3f5504647dc31fc5ed69905bbc802 Author: 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 Date: Tue Feb 9 21:00:42 2010 +0000 Hopper Tools/F_mk/GMakeMPI.mak commit 1eb07ad3ba3512bf492dc327e4b753b90b734d56 Author: lijewski Date: Tue Feb 9 20:29:04 2010 +0000 use a std::map instead of a std::vector for the cache Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 9340f95aab244c8641204dd728ccb69cf8e8ccd2 Author: lijewski Date: Tue Feb 9 18:22:09 2010 +0000 removed unused BL_ASSERT() Src/C_AMRLib/TagBox.cpp commit d8f3bc089f4615a5b19c70aba7f095f4bce5913a Author: lijewski Date: Tue Feb 9 18:19:35 2010 +0000 *** empty log message *** Src/C_AMRLib/FluxRegister.cpp commit 3106bcabd7dd5a5c0fedce275992b1b6f98968d5 Author: lijewski Date: Tue Feb 9 17:33:59 2010 +0000 added some reserve() calls Src/C_BoundaryLib/FabSet.cpp commit 45c4b9434da0caf5724c47bcee6e2ae6222a83bb Author: 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 Date: Tue Feb 9 06:32:27 2010 +0000 some memory consolidation Src/C_AMRLib/TagBox.cpp commit 051acd89638951ebf07bd5ddfa19f9c9c2c33ec1 Author: lijewski Date: Tue Feb 9 06:05:55 2010 +0000 use vector::reserve() Src/LinearSolvers/C_NodalMG/interface.cpp commit c53a5fbdd9ddc795731426fdb48a0d529579e7a6 Author: lijewski Date: Tue Feb 9 03:59:25 2010 +0000 removed unused function Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 45d9daa80be0666d52d67b336c99fa1d9cb081a8 Author: lijewski Date: Tue Feb 9 01:08:39 2010 +0000 now use vector::reserve() Src/C_AMRLib/AuxBoundaryData.cpp commit 0c7787c2a19adda9c443cbcbe1f8982fe427c734 Author: lijewski Date: Tue Feb 9 00:50:26 2010 +0000 use vector::reserve() a bit Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit d593ca08223433cdc50dea3816103e57f9f0a9c9 Author: lijewski Date: Mon Feb 8 23:39:53 2010 +0000 use std::vector::reserve() in places Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit bbefcdb2432a95d1f72301dfbef81a3277b10443 Author: lijewski Date: Mon Feb 8 23:39:13 2010 +0000 some simplification Src/C_BaseLib/BoxList.cpp commit 4822ae757387222f0650f98857ddabd0a4e894fb Author: lijewski Date: Mon Feb 8 21:05:04 2010 +0000 replace std::vector with std::list in a number of places Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit a0fbf90744d567e1cff56c630a5598f6f3d77654 Author: almgren Date: Mon Feb 8 19:01:38 2010 +0000 Add shift operator for BoxArray that takes an IntVect. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit e9288e69e1df6ae1db33cedb675d5367d5997931 Author: ajnonaka Date: Tue Feb 2 19:15:06 2010 +0000 turn on Ann and Andy's unused variable warnings for C++ and fortran Tools/C_mk/Make.defs commit 8a816da077f5f22157eb6ffd010b5e51e266f5a7 Author: ajnonaka Date: Tue Feb 2 14:45:19 2010 +0000 turn on unused variable check in debug mode using gfortran Tools/C_mk/Make.defs commit 5e306a4b55a89ba4419c89d872d23c4e906b7b06 Author: ajnonaka Date: Tue Feb 2 14:10:58 2010 +0000 when compiling in debug mode with intel 9, you now get unused variable warning messages Tools/F_mk/GMakedefs.mak commit da21a61d985e93f23859ed33a357b273bcfd7005 Author: ajnonaka Date: Tue Feb 2 13:01:47 2010 +0000 reverting back to 1/29/10 - otherwise Castro doesn't compile with Intel10 in DEBUG mode Src/C_BaseLib/CArena.cpp commit 2efe084620abf0967fb4a4b04423b1fead9e75cd Author: ajnonaka Date: Tue Feb 2 12:56:23 2010 +0000 need to declare freeblock before using - was causing compiler error in debug Src/C_BaseLib/CArena.cpp commit d0a24f67f32ba9014becb0e3d5d0b02241abc469 Author: lijewski Date: Fri Jan 29 21:14:02 2010 +0000 additional optimization options for PathScale Tools/C_mk/Make.Linux commit 94efa1030dfffefcf27927e7e65c6ea86f06ee84 Author: lijewski Date: Fri Jan 29 20:42:04 2010 +0000 some cleanup Src/C_AMRLib/Amr.cpp Src/C_BaseLib/CArena.cpp Src/C_BaseLib/VisMF.cpp commit 7a610c6a4c61a5841ff8390e41b895c975afc519 Author: mzingale Date: Thu Jan 21 17:53:51 2010 +0000 add xmin, ymin, ... to the coordinates vector to account for domains that don't start at 0 Tools/F_scripts/idlbl/rawread.pro Tools/F_scripts/idlbl/rawread3d.pro commit af5bcacd09de476fcfb40bdb874d5921d53ad2f5 Author: nazgul Date: Wed Jan 20 19:21:49 2010 +0000 Added read and write functions to support FluxRegister checkpoint/restart. Louis Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit c7ebd0d658469c3165e6f76a09ce5b31d920461b Author: nazgul Date: Wed Jan 20 19:20:11 2010 +0000 Read and write functions to support flux register checkpoint/restart. Louis Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 33d1c3627bd4b68f7a3a6eff2a1aa0c482be928e Author: almgren Date: Tue Jan 12 22:51:34 2010 +0000 Make sure to set abs_eps based on what we've defined in the mgt. Src/LinearSolvers/F_MG/ml_cc.f90 commit 16a220e3da70cc0920d6180d5386ae247463c629 Author: 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 Date: Wed Jan 6 01:11:50 2010 +0000 *** empty log message *** Tools/C_mk/Make.mpi commit 876b1799e1e2e8a9a1408581cef80a6e710af0f8 Author: 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 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 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 Date: Mon Dec 21 20:36:20 2009 +0000 removed stdnormal_cdf() Src/C_BaseLib/Utility.cpp commit 0d05884ad2edc7a726da5deeed5da5cc08b46226 Author: lijewski Date: Mon Dec 21 20:36:04 2009 +0000 removed Output_CPU_Comm_Costs() Src/C_BaseLib/DistributionMapping.cpp commit 9d6470f2e72b9c62f524197db6c5b52a4fd028cf Author: almgren Date: Mon Dec 21 17:44:10 2009 +0000 Added stuff for ranger, a machine that Jason Nordhaus uses. Tools/C_mk/Make.mpi commit 8e242c70c04836489413732bedb97182e29e77af Author: almgren Date: Mon Dec 21 17:42:40 2009 +0000 Added ranger (a Texas machine which Jason Nordhaus uses). Tools/C_mk/Make.defs commit 9886ad560753c60793775f1d1841b9eaf221faf8 Author: 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 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 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 Date: Mon Dec 14 21:13:58 2009 +0000 disable the MFRead:: output Src/C_BaseLib/VisMF.cpp commit 509117d07672038849d806166cd231e9c270318d Author: lijewski Date: Fri Dec 11 03:05:08 2009 +0000 some cleanup of InvNormDistBest() Src/C_BaseLib/Utility.cpp commit c95f9bb47fab0e23e1f2b0ab210e724e6318eb38 Author: lijewski Date: Fri Dec 11 01:06:49 2009 +0000 Added InvNormDistBest(). This is used instead of the previous "best" option to InvNormDist(). The algorithm is from Applied Statistics Algorithm 241 by Michael Wichura and the C++ implementation by John Burkardt. It provides machine precision and is much faster than the previous "best" option. It's only about 30% slower than InvNormDist(). Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit e05b1df5f526d9dca20eb0910c94564915588942 Author: vince Date: Thu Dec 10 22:49:30 2009 +0000 added code for more file system friendly restarts. Src/F_BaseLib/fabio.f90 commit a4a6f2bdacf3becf035e084221cc1f38dbc1c205 Author: almgren Date: Thu Dec 10 22:18:47 2009 +0000 We need to delete fluxes which we have created through a call to mgt_compute_flux. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 7a270eb52b095b1d1604ff89d1edbfb12857f2de Author: almgren Date: Thu Dec 10 22:18:27 2009 +0000 We need to be able to delete fluxes which are built in mgt_compute_fluxes. Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 8f05eb45d616e9bc63b297bdeeb503c86b604185 Author: almgren Date: Wed Dec 9 19:15:15 2009 +0000 Allow us to read in a single value for n_error_buf, to be used for all levels, or an array for n_error_buf with a distinct value for each level. Src/C_AMRLib/Amr.cpp commit dbbdcc6b06df0398efadfb84090e7ce69c4dc3a5 Author: lijewski Date: Wed Dec 9 17:41:57 2009 +0000 Added d2_value() from latest MT folks. Faster implementation of d[12]?_value() according to latest MT stuff. Changed names: d1_value -> d_value and d_value -> d1_value to match MT. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 6568e4b1ac4df44e6813892988520f2d1362497f Author: lijewski Date: Wed Dec 9 06:37:50 2009 +0000 modest speedup to mt19937 code Src/C_BaseLib/Utility.cpp commit f48a119138e5bf9c7e72287504c74f9afdc68be9 Author: 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 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 Date: Tue Dec 8 19:23:14 2009 +0000 added blinitrand() entry point Src/C_BaseLib/Utility.cpp commit 8f88b8002cdcbd0ed7f8049145b461d3a6fcc617 Author: almgren Date: Fri Dec 4 20:18:50 2009 +0000 Add empty line after Final Iter print statement for easier readability. Src/LinearSolvers/F_MG/ml_cc.f90 commit eba5908d25a9510a948e7b00961a2a074250867a Author: lijewski Date: Fri Dec 4 18:21:56 2009 +0000 fixed bug I introduced yesterday Src/C_BaseLib/Geometry.cpp commit 2eb5c494c60c3d87d4897801171754e25b2b3774 Author: lijewski Date: Fri Dec 4 17:35:13 2009 +0000 *** empty log message *** Src/C_AMRLib/Amr.cpp commit ff6ed3e354fecc58610552b970300c18484d256f Author: lijewski Date: Thu Dec 3 19:12:28 2009 +0000 can now set periodicity on construction Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 1e2fd5d64b606b66d865f58aefe40f1f24112802 Author: mzingale Date: Thu Dec 3 02:25:59 2009 +0000 fix the C compiler on Atlas, add optimizations for Intel 11 Tools/F_mk/GMakedefs.mak commit 57aac64b6177b2e78e66d3d94d61f6db31167b54 Author: 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 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 Date: Sat Nov 28 00:23:19 2009 +0000 fixed stencil Src/LinearSolvers/F_MG/stencil.f90 commit 03a439e763265f448cc857469dec83d268fc1bd0 Author: 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 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 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 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 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 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 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 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 Date: Tue Nov 17 22:14:46 2009 +0000 yet more OpenMP Src/LinearSolvers/C_NodalMG/amr_real3d.f commit de6bf740e099634e7ef69ffb3645514378f924ea Author: lijewski Date: Tue Nov 17 21:52:53 2009 +0000 yet more OpenMP Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit 9c7df66a9d7715a66667d975131b51150bc7b096 Author: lijewski Date: Tue Nov 17 21:40:58 2009 +0000 more OpenMP Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit f395a3f4a4cb39f379fde51c7f5f0d9e4553f62d Author: lijewski Date: Tue Nov 17 21:19:20 2009 +0000 more OpenMP Src/LinearSolvers/C_NodalMG/hg_avg3d.f commit 8d49e1e3d87ff07e78ec73591150cd0d08662424 Author: lijewski Date: Tue Nov 17 18:57:50 2009 +0000 changed FAB byte string to say MPI nodes not CPUs Src/C_AMRLib/Amr.cpp commit f396b90bd359a81b89013288ee734647aa4e0cc4 Author: mzingale Date: Tue Nov 17 04:39:36 2009 +0000 get create_nodal_mask_1d to compile Src/LinearSolvers/F_MG/ml_solve.f90 commit 435c9668a172179a935d1487db5a670fa4351a14 Author: almgren Date: Tue Nov 17 03:04:27 2009 +0000 Add 1d versions. Src/LinearSolvers/F_MG/ml_solve.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 commit f2625d79d368a65c48897c6079e5b52895c0068b Author: almgren Date: Tue Nov 17 03:01:00 2009 +0000 Add 1d version. Src/LinearSolvers/F_MG/nodal_newu.f90 commit b2d134e97ffeac5622d8985120e3f425ed00313d Author: gpau Date: Mon Nov 16 18:16:27 2009 +0000 *** empty log message *** Tools/C_util/Statistics/ComputeAmrDataStat.H Tools/C_util/Statistics/ComputeAmrDataStat.cpp Tools/C_util/Statistics/GNUmakefile Tools/C_util/Statistics/PltFileStat.cpp commit 877cf57ae28f595f9bc8d49df9fa1fc077803eb9 Author: gpau Date: Sun Nov 15 17:01:53 2009 +0000 added functionality to PltFileList: now reads in multifab instead of just plotfiles. Tools/C_util/Statistics/GNUmakefile Tools/C_util/Statistics/PltFileList.cpp commit bea7fcb556ca90d80781c18b2416d72629a98878 Author: gpau Date: Sun Nov 15 00:06:43 2009 +0000 update the outputfile Tools/C_util/Statistics/PltFileStat.cpp commit 374e8982126a26ec5d00cee47caff4989f5b316f Author: almgren Date: Sat Nov 14 01:17:23 2009 +0000 Hack the mg driver so that in 1d the code calls the line solve at the top level and does not enter the V-cycle or call the bottom solver. Src/LinearSolvers/F_MG/mg.f90 commit 9ad00e0b814dd5bd5b13a6bcac8d0dae77a57953 Author: almgren Date: Sat Nov 14 01:16:39 2009 +0000 Fix the Neumann boundary conditions in the nodal_line_solve_1d. Src/LinearSolvers/F_MG/mg_smoother.f90 commit 7fe039c2c42c1c3c45c60fc9c47c2d6d10605e9b Author: gpau Date: Fri Nov 13 22:47:04 2009 +0000 handles multifab variogram Tools/C_util/Statistics/ComputeAmrDataStat.H Tools/C_util/Statistics/ComputeAmrDataStat.cpp Tools/C_util/Statistics/PltFileStat.cpp commit 11b2a13bacb7814728c5fabdcc854e6d4acedc20 Author: gpau Date: Thu Nov 12 21:57:09 2009 +0000 *** empty log message *** Tools/C_util/Statistics/ComputeAmrDataStat.H Tools/C_util/Statistics/ComputeAmrDataStat.cpp Tools/C_util/Statistics/GNUmakefile Tools/C_util/Statistics/PltFileStat.cpp commit 85dae7c2e4c8b742f30d756d52c90517609536ff Author: almgren Date: Wed Nov 11 22:26:38 2009 +0000 Replaced cycle by cycle_type. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit db3d42a8414898f93effb45aa6f3ffc271845abc Author: almgren Date: Wed Nov 11 22:19:52 2009 +0000 Just a cleanup.. Src/LinearSolvers/F_MG/mg_prolongation.f90 commit 4870a71bbab3efcced6242275c3d8cf33e66419e Author: ajnonaka Date: Wed Nov 11 21:53:06 2009 +0000 fixed the pesky bottom_solver=4 once and for all Src/LinearSolvers/F_MG/mg.f90 commit e49932319029023d9ba58586488035732a64d359 Author: lijewski Date: Wed Nov 11 20:37:02 2009 +0000 add -fpconstant to Intel fortran and some simplification Tools/C_mk/Make.defs commit 61fa4cdb85eb2ce5718e2166c4639a5e0a74c0a9 Author: lijewski Date: Wed Nov 11 20:20:36 2009 +0000 decrease Intel optimization -O3 and -ip are buggy Tools/C_mk/Make.defs commit d3c57e86c849536a2223d526e88724d09c64d0d2 Author: gpau Date: Tue Nov 10 23:26:05 2009 +0000 *** empty log message *** Tools/C_util/Statistics/PltFileList.cpp commit 324bbef71c214ac92dc4f44a9f2505642676edd4 Author: gpau Date: Tue Nov 10 22:19:48 2009 +0000 *** empty log message *** Tools/C_util/Statistics/PltFileList.cpp commit 2d1ef1513d2ec82984d753740ece28d719595212 Author: lijewski Date: Tue Nov 10 21:44:13 2009 +0000 now use a map instead of a PArray to hold FABs Src/C_AMRLib/TagBox.cpp Src/C_BoundaryLib/FabSet.H commit 85d6a0a0e908d3ebee9842a3e55848249dbc3120 Author: lijewski Date: Tue Nov 10 21:43:44 2009 +0000 now us a map instead of a PArray to hold FABs Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit b47707c1c07f118ed34a490c037af97891e6b3c4 Author: gpau Date: Tue Nov 10 21:39:32 2009 +0000 *** empty log message *** Tools/C_util/Statistics/PltFileList.cpp commit a40abdeeb407fb51d308c39140f555f9fb912ce3 Author: gpau Date: Tue Nov 10 21:10:53 2009 +0000 *** empty log message *** Tools/C_util/Statistics/GNUmakefile Tools/C_util/Statistics/PltFileList.cpp commit b6d6ddc516c41502c7b86ca69bd8e33060de7734 Author: gpau Date: Tue Nov 10 20:42:17 2009 +0000 updated with some GSLIB stuff Tools/C_util/Statistics/ComputeAmrDataStat.H Tools/C_util/Statistics/ComputeAmrDataStat.cpp Tools/C_util/Statistics/GNUmakefile Tools/C_util/Statistics/PltFileStat.cpp commit 55f02c7787a2f8b5544cc87494e4cf70ec90f8fc Author: nazgul Date: Tue Nov 10 19:45:40 2009 +0000 For della, use mpich by default. openmpi version commented out. Louis Tools/C_mk/Make.mpi commit 4516e1fed1a061c731eacff7118e947f487485da Author: 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 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 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 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 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 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 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 Date: Fri Nov 6 20:06:43 2009 +0000 replaced some usages of MFIter::fabbox() Src/C_AMRLib/FluxRegister.cpp commit 49bf957831f66508f4fd27f60cb7c471bd702a2a Author: lijewski Date: Fri Nov 6 18:33:23 2009 +0000 some cleanup Src/C_BaseLib/FabArray.cpp commit 197f3b44b7f0e9835f1d02d26d0b9427fa97fa7e Author: lijewski Date: Fri Nov 6 16:44:43 2009 +0000 g++ 4.4.1 thinks strrchr() returns const char* Src/C_BaseLib/VisMF.cpp commit daeed7514d0b210059f9a810f3b850e8cd3e8beb Author: 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 Date: Thu Nov 5 23:34:18 2009 +0000 more OpenMP mumbo-jumbo Src/LinearSolvers/C_CellMG/LO_3D.F commit 3d06b1da3eac3e12e5040584d23567e0662dd361 Author: 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 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 Date: Thu Nov 5 22:45:37 2009 +0000 OpenMP'd Src/C_BaseLib/COORDSYS_3D.F commit 4b2605e0dc12206b0fadac139572e1e104fe765d Author: 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 Date: Thu Nov 5 21:30:53 2009 +0000 more OpenMPing Src/C_BaseLib/SPECIALIZE_3D.F commit eae53271303197c06c2b0e18e19b3e676396506c Author: lijewski Date: Thu Nov 5 07:50:40 2009 +0000 commented out one pragma omp that kills PathScale Src/C_AMRLib/FluxRegister.cpp commit 7e0a110f731bc73f12dd66818471d4acbbebc22f Author: almgren Date: Thu Nov 5 04:01:13 2009 +0000 Modify the test on max_grid_size vs blocking_factor -- we now only require that max_grid_size >= blocking_factor, not . *not* that max_grid_size >= blocking_factor*ref_ratio Src/C_AMRLib/Amr.cpp commit 590893d22db433961ec1122063de0878a7622a39 Author: lijewski Date: Wed Nov 4 21:35:24 2009 +0000 OpenMP the .cpp not the .F when possible Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/FluxRegister.cpp commit 6cc63ee482b409ad8dbfcfeec0a0568f854a24a6 Author: lijewski Date: Wed Nov 4 18:50:35 2009 +0000 now thread across FABS in applyBC() Src/LinearSolvers/C_TensorMG/DV_3D4.F Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit a6be3f01aecc63cabab1f87d8ab0af4a62d4e43b Author: lijewski Date: Wed Nov 4 18:14:56 2009 +0000 now do all faces of given FAB at a time in applyBC() Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 2f57b8e3739880e88ea8af4e1b98e4a41fa556e9 Author: 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 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 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 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 Date: Tue Nov 3 21:37:29 2009 +0000 more OpenMP stuff Tools/C_mk/Make.defs commit b7acbcb7a5d22eb33bbe6e9191fcc31323ceae7c Author: lijewski Date: Tue Nov 3 16:35:22 2009 +0000 OpenMp LinOp::applyBC() over face calls to FORT_APPLYBC() Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LinOp.cpp commit 5bf4242e44b5e1160e8d833cdda5c3e4df558c37 Author: nazgul Date: Fri Oct 30 23:51:19 2009 +0000 Using what appears to be the preferred mpi on della. Louis Tools/C_mk/Make.mpi commit 9e20b0e8168117d6404d6a65edbf2b50ad7700d9 Author: 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 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 Date: Tue Oct 27 21:05:48 2009 +0000 more OpenMPing Src/LinearSolvers/C_NodalMG/hg_proj3d.f commit 9a48bfff893f64c5502380328cea5fadacce0b98 Author: lijewski Date: Tue Oct 27 20:45:56 2009 +0000 some cleanup Src/LinearSolvers/C_NodalMG/hg_multi2d.f Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.f Src/LinearSolvers/C_NodalMG/hg_multi3d_full.f Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.f commit f0d3555054aeec9f1f0c2233fa58010feb47a5fc Author: lijewski Date: Tue Oct 27 20:06:01 2009 +0000 more OpenMPing Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit 602f7e441e1fe074dea29f1d11343d87b70498f9 Author: lijewski Date: Tue Oct 27 19:37:59 2009 +0000 more OpenMPing Src/LinearSolvers/C_NodalMG/amr_real3d.f commit 77125099a334565419fbda317792d6c41363ab83 Author: lijewski Date: Tue Oct 27 19:09:12 2009 +0000 more OpenMPing Src/C_AMRLib/FLUXREG_3D.F commit c059664f9a0b8c42113483708e940bb906c3f99b Author: lijewski Date: Tue Oct 27 04:55:45 2009 +0000 some OpenMP Src/LinearSolvers/C_NodalMG/hg_avg3d.f commit 4c400148bd7882ead59d65a05f19858b40dd1678 Author: lijewski Date: Tue Oct 27 04:43:04 2009 +0000 some OpenMPing Src/C_AMRLib/FLUXREG_3D.F commit c54a6c9a1b71a7a8315ea00a190601790549647e Author: lijewski Date: Mon Oct 26 21:58:40 2009 +0000 print out size as well as initialize() time Src/C_AMRLib/AuxBoundaryData.cpp commit f354024b21c990d59ef4a27682b656dbf1b02e51 Author: lijewski Date: Mon Oct 26 20:26:53 2009 +0000 add some PathScale options for when BL_NOFAST=TRUE Tools/C_mk/Make.Linux commit e3493b274827c735f8d0943b970e48c822415bf5 Author: lijewski Date: Fri Oct 23 20:12:29 2009 +0000 *** empty log message *** Tools/C_mk/Make.defs commit 9a4c2b086a3aa3e0110739e4cd3d3d89d599b534 Author: lijewski Date: Fri Oct 23 19:57:50 2009 +0000 OpenMP mods for Intel 11 Tools/C_mk/Make.defs commit ed62805ce598790acbbccddeb3711c8d59601196 Author: lijewski Date: Thu Oct 22 21:00:30 2009 +0000 removed OpenMP directives from FORT_NBINTERP() - buggy Src/C_AMRLib/INTERP_3D.F commit 80be497c5f9db7a00560190473eb9178fe191c0a Author: vince Date: Thu Oct 22 19:24:32 2009 +0000 added the new mothra. Tools/C_mk/Make.mpi commit b468a81f49c76aea85821b331cec26a55032b400 Author: lijewski Date: Tue Oct 20 22:47:35 2009 +0000 *** empty log message *** Src/LinearSolvers/C_TensorMG/MCLO_3D.F commit b7e414649466239df5fe23b83bdd9ae3cd7ff5de Author: lijewski Date: Tue Oct 20 02:37:46 2009 +0000 rearranged OpenMP directives for Intel 11.1 Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F commit 4d74a9ef671f8c80ff9e049babfc9a46ddae40be Author: 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 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 Date: Thu Oct 15 21:57:39 2009 +0000 Remove print statement. Src/LinearSolvers/F_MG/mg_restriction.f90 commit 69cfea3713ac21f1370f71c1f092a32941bcd1f9 Author: almgren Date: Thu Oct 15 21:57:21 2009 +0000 Fix 1d version. Src/LinearSolvers/F_MG/mg_restriction.f90 commit d6efd48f83a94807127b0850ba4a90cd86c19cdd Author: 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 Date: Mon Oct 12 21:40:17 2009 +0000 *** empty log message *** Src/C_BaseLib/BaseFab.H commit b818bbcae55a86b7d41a9ce825e3d7566cdf0bed Author: lijewski Date: Mon Oct 12 21:37:41 2009 +0000 New versions of fortran-specialized functions that can be OpenMP'd in 3D. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/SPECIALIZE_1D.F Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit c0ba4ef4d6a6174e876838af41f45f9e1db30b99 Author: 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 Date: Thu Oct 8 22:50:52 2009 +0000 removed a bug Tools/C_util/Statistics/PltFileXAve.cpp commit f6a92cd0ffb004c6419e2efc55e89600340c0d1b Author: lijewski Date: Thu Oct 8 22:10:56 2009 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.f commit 2e42b725677a4ee02bb731614616b3c368c1322b Author: lijewski Date: Thu Oct 8 21:50:46 2009 +0000 more OpenMP Src/LinearSolvers/C_NodalMG/hg_proj3d.f commit 6487fdcbb581665f6e44e4383cd3366077aa7ae7 Author: lijewski Date: Thu Oct 8 21:38:47 2009 +0000 more OpenMP stuff Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit bd7507f1e0b46f6d7845f329037e3e77c9f0a11e Author: 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 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 Date: Thu Oct 8 20:29:52 2009 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit 49e1c9ad0ce6bbc3ec4ae47fca03fb57b87e9433 Author: lijewski Date: Thu Oct 8 17:58:43 2009 +0000 mods to work with PGI OpenMP Src/LinearSolvers/C_TensorMG/DV_3D4.F commit 88bd7f66b1358412f3d02d944a698410745bf6d7 Author: lijewski Date: Thu Oct 8 17:41:02 2009 +0000 *** empty log message *** Src/LinearSolvers/C_TensorMG/DV_3D1.F commit 1d20ebec2d9f87324950435d216fb70c423faae3 Author: lijewski Date: Thu Oct 8 17:40:47 2009 +0000 more OpenMP Src/LinearSolvers/C_TensorMG/DV_3D2.F commit 65a4f8366a2562e36cbbcdcd361f65a94cb36c54 Author: lijewski Date: Wed Oct 7 22:14:01 2009 +0000 more OpenMP directives Src/LinearSolvers/C_TensorMG/DV_3D1.F commit 400946386ceeff68cea7e44a77fd41546a9aa9a0 Author: gpau Date: Wed Oct 7 21:24:49 2009 +0000 updated file reflect variable phi Tools/C_util/Statistics/GNUmakefile Tools/C_util/Statistics/PltFileXAve.H Tools/C_util/Statistics/PltFileXAve.cpp commit e989cc894374c4946acbc14d754b2e9d11362f4d Author: lijewski Date: Wed Oct 7 21:19:17 2009 +0000 more OpenMP junk Src/LinearSolvers/C_TensorMG/DV_3D4.F commit d49bb271bdb47758424f137745588f8068d3f90b Author: lijewski Date: Wed Oct 7 21:00:43 2009 +0000 OpenMP'd Src/LinearSolvers/C_TensorMG/DV_3D4.F commit 6a3a04c57bca7110d4c48165527c82f3f44581ed Author: lijewski Date: Wed Oct 7 20:24:37 2009 +0000 more OpenMP directives Src/LinearSolvers/C_TensorMG/DV_3D3.F commit 18d38aec276197592e32041f7c3a0ae6c095fdc9 Author: lijewski Date: Wed Oct 7 18:06:04 2009 +0000 added some d0's on constants Src/LinearSolvers/C_TensorMG/MCLO_3D.F commit eb22a2f65149e29403b37f3371989930f1a7333c Author: lijewski Date: Wed Oct 7 17:58:54 2009 +0000 added some d0's on constants Src/LinearSolvers/C_TensorMG/DV_3D4.F commit 26ba8674706868673a564315fd30bed3eb9816c9 Author: lijewski Date: Wed Oct 7 17:58:29 2009 +0000 little simplification Src/LinearSolvers/C_CellMG/LO_3D.F commit 0fa95dc5ecaafec3c19b0bbb4d0504cae8d0adb7 Author: 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 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 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 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 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 Date: Tue Oct 6 21:37:14 2009 +0000 OpenMP'd Src/LinearSolvers/C_TensorMG/DV_3D3.F commit 88e66a141f673ea8f6968fcc0121c9f2eca23cfd Author: 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 Date: Tue Oct 6 20:00:31 2009 +0000 addend angilas support for mpi. Tools/C_mk/Make.mpi commit 0b35f673e04bdfe93a03e86a2501e706899f10a3 Author: lijewski Date: Tue Oct 6 16:02:18 2009 +0000 OpenMP'd Src/LinearSolvers/C_TensorMG/DV_3D2.F commit e51320eb6ca4e7df0a91943daa42857ddf2a57a4 Author: lijewski Date: Mon Oct 5 22:49:21 2009 +0000 OpenMP'd Src/LinearSolvers/C_TensorMG/DV_3D1.F commit 7ee06f6c2044de46cfc7d1681fc737fafb290ef7 Author: almgren Date: Mon Oct 5 21:51:07 2009 +0000 Added 1D versions of all the routines. Src/LinearSolvers/F_MG/nodal_divu.f90 commit 79802855937cbbaa0a388b783ded7ed8b4647adb Author: lijewski Date: Mon Oct 5 21:47:50 2009 +0000 OpenMP'd Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F commit 0b3ded9d1c1b9fd4756cf4fb51b9e79164ef513f Author: lijewski Date: Mon Oct 5 21:13:20 2009 +0000 OpenMP'd Src/LinearSolvers/C_TensorMG/MCLO_3D.F commit a39e4e29466c057114349e68404c8d7a0d506c3b Author: lijewski Date: Mon Oct 5 20:42:30 2009 +0000 more OpenMP stuff Src/LinearSolvers/C_NodalMG/hg_multi3d.f Src/LinearSolvers/C_NodalMG/hg_proj3d.f commit bdbb3f467f717b10305f9caace4408c5372211ee Author: 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 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 Date: Thu Oct 1 21:20:40 2009 +0000 OpenMP'd node_bilinear_interp Src/C_AMRLib/INTERP_3D.F commit d37282849f1613bb84ad5b60dbf1b987cdd5bf2a Author: lijewski Date: Thu Oct 1 20:51:08 2009 +0000 *** empty log message *** Src/C_AMRLib/INTERP_3D.F commit 7c9397a8049800cce5d05c8dad07fac9a2a615b2 Author: lijewski Date: Thu Oct 1 19:30:58 2009 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/MG_3D.F commit 3213772f7601cbfa63f0c7a04e498745f3d10892 Author: lijewski Date: Thu Oct 1 18:18:10 2009 +0000 Added specialized version of 0 & 1 norms for Real in Fortran Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit 7e9bb2f108992965495776bc86522d165f8678a1 Author: lijewski Date: Tue Sep 29 20:42:36 2009 +0000 removed WorkQueue stuff Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp commit e7a7e4c109fd860ad2358dd5190a11bb7fac25ba Author: lijewski Date: Mon Sep 28 21:29:25 2009 +0000 removed all BL_THREAD junk Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp commit 86519b50dae37adcf345a47ae8eb20c51312b1df Author: 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 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 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 Date: Mon Sep 28 20:14:48 2009 +0000 some simplification of APPLYBC() Src/LinearSolvers/C_CellMG/LO_3D.F commit 48ab6df446a9a19174290f1952bfbd0e0828c899 Author: lijewski Date: Mon Sep 28 19:23:01 2009 +0000 more OpenMP tweeking Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LP_3D.F commit 5c2730e829110e4bd6132250783ad9950e532a45 Author: lijewski Date: Mon Sep 28 19:13:53 2009 +0000 OpenMP'd Src/LinearSolvers/C_CellMG/ABec_3D.F commit d6e105f05a0a47a9640ecbeec321a11fc30a80fb Author: lijewski Date: Mon Sep 28 18:09:11 2009 +0000 yet more OpenMP tweeking Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F commit 4df2f04ef1c225e0a01535ba0c2e7627a1c06e5b Author: lijewski Date: Mon Sep 28 17:57:54 2009 +0000 more OpenMP tweeking Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F commit 6ecea4d686f385d4feb8b1f21894f4ab0ea65158 Author: lijewski Date: Mon Sep 28 17:51:35 2009 +0000 OPenMP'd Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F Src/LinearSolvers/C_CellMG/MG_3D.F commit db127c7c113a2d65592b71179f870533319991f8 Author: nazgul Date: Mon Sep 28 17:06:21 2009 +0000 Updated compiler options for Atlas. -mp is deprecated. Using -fp-model fast=2 instead. Louis Tools/C_mk/Make.Linux commit 351ed7dcd1f70a56680095e09331d9e051d75a22 Author: lijewski Date: Mon Sep 28 17:05:50 2009 +0000 removed OpenMP directives -- slowed down test case Src/LinearSolvers/C_CellMG/CG_3D.F commit f2e82b1c253031bdcd97987c5bdb784bb5fe6dea Author: lijewski Date: Mon Sep 28 16:46:16 2009 +0000 added some OpenMP macros Src/LinearSolvers/C_CellMG/CG_3D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LP_3D.F commit e409fda5a5fd4c50c375b4f8e654918fb6d1c3b5 Author: lijewski Date: Fri Sep 25 23:18:53 2009 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 88dd1854afdf2132f7c0075dc417b50307506190 Author: lijewski Date: Fri Sep 25 21:24:22 2009 +0000 disable -Ofast for PathScale C++ compiler - causes bug in mglib on franklin Tools/C_mk/Make.Linux commit a9bb3cae07fd5c80513da2613ca5c75b77af13ae Author: lijewski Date: Fri Sep 25 18:04:31 2009 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/inputs.3d Tests/LinearSolvers/C_CellMG/inputs.3d commit 638640ae292cb3a55e99976559479da16eb22b42 Author: lijewski Date: Fri Sep 25 03:50:56 2009 +0000 rearranged some OpenMP stuff Src/C_AMRLib/INTERP_3D.F commit ee4ff2b74444c7a5018786e6e6395b2a5241cba8 Author: 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 Date: Wed Sep 23 21:59:07 2009 +0000 some OMP stuff Tools/C_mk/Make.Linux commit b3d4c2cd6d2a805925ab7980727164931f01b3a4 Author: lijewski Date: Fri Sep 18 22:10:33 2009 +0000 some OpenMP stuff Tools/C_mk/Make.defs commit 6f70f0283d1d9cb0c554413087927f3bd6aeb270 Author: 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 Date: Fri Sep 11 18:20:09 2009 +0000 more 11.1. Tools/C_mk/Make.defs commit 5e9da5df15e6bca7951e2d121099cf23b8086bcc Author: vince Date: Fri Sep 11 18:13:19 2009 +0000 intel 11.1. Tools/C_mk/Make.defs commit b4ec7e42dab71ce96418672243662f4a642c1d6d Author: ajnonaka Date: Thu Sep 10 22:20:02 2009 +0000 on franklin with pathscale, now you can turn on openmp with OMP=t in your make line Tools/F_mk/GMakedefs.mak commit d34ef67b4c3b9884a6e252a7b389b50103d7abb2 Author: lijewski Date: Wed Sep 2 17:50:59 2009 +0000 now pass problo and probhi optionally to ml_multifab_write Src/F_BaseLib/fabio.f90 commit c047e8998f41a80842e8ff1b4dba819a4e08fba5 Author: mzingale Date: Wed Sep 2 16:27:58 2009 +0000 no longer abort if a plotfile variable is not found in plotfile_var_index, instead just return -1. The calling program should test on the output. This allows you to test for the presence of variables. Src/F_BaseLib/plotfile.f90 commit 1f6187e4f4f041b4cfeadcecbba7b6e316db5a80 Author: 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 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 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 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 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 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 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 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 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 Date: Fri Aug 14 22:28:31 2009 +0000 Fix indexing in 1d. Src/LinearSolvers/F_MG/stencil.f90 commit 674716acc8876b505c6ed52c30672d6d5f00e35d Author: almgren Date: Fri Aug 14 22:21:48 2009 +0000 Fix typo. Src/LinearSolvers/F_MG/stencil.f90 commit 016c6c193c4c5e6d72051061c66d69ae6fd178af Author: almgren Date: Fri Aug 14 22:21:05 2009 +0000 Fix stencil_apply_1d. Src/LinearSolvers/F_MG/stencil.f90 commit b2aae0d067b188f9cc41f35427b81b46abd6edd3 Author: almgren Date: Fri Aug 14 22:20:18 2009 +0000 1) Fix bug in stencil_1d_apply 2) Modify stencil_1d_apply and stencil_2d_apply to take lo and hi as inputs so we can more easily debug with the actual indices. Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 613cce2f70d86f340f9b0e0de053d914b351c13f Author: almgren Date: Fri Aug 14 22:09:47 2009 +0000 Added 1d capability. Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/interp.f90 commit 2006b6408e2cc33284f5839a273feaf92892d911 Author: almgren Date: Wed Aug 12 22:38:28 2009 +0000 Use lo(:),hi(:) instead of nx,ny,nz for easier debugging. Src/LinearSolvers/F_MG/stencil.f90 commit b7c9dc1e5bbe84d10f12925d63262c6fa9ed594f Author: almgren Date: Tue Aug 11 20:28:28 2009 +0000 Explicitly add climits. Src/C_AMRLib/TagBox.cpp commit 592cd0d9642dc96410fad94cb2b5cfc5de1600ae Author: almgren Date: Tue Aug 11 17:11:19 2009 +0000 Fixed a bug -- we didn't use to call crse_fine_residual from applyop so the coarse grid cell next to a fine grid had the wrong residual. Src/LinearSolvers/F_MG/ml_cc.f90 commit 207f1705fa6df77a7a907eaf7eb4953cda0d7542 Author: ajnonaka Date: Fri Aug 7 17:16:29 2009 +0000 added .smp to executable if smp is true Tools/F_mk/GMakedefs.mak commit 92f01599045aa7816afbfd8379ea4ea6e86c0427 Author: mzingale Date: Fri Aug 7 15:15:04 2009 +0000 add some error checking to the copying of inputs, probin, and the auxfiles Tools/C_util/regtests/test.py commit 55df2de0de028f6868f31720dfb5751a612a9454 Author: almgren Date: Thu Aug 6 21:51:36 2009 +0000 Fixed the Minion "full" stencil which is used for variable density. Src/LinearSolvers/F_MG/stencil.f90 commit bc4941e6dc1ecb03e5802e346d75d807543009be Author: mzingale Date: Tue Aug 4 19:17:19 2009 +0000 update to reflect new directory locatios Tools/C_util/regtests/Castro-tests.ini commit 4da70e99a219082e2b43584df84c60c76c8e46bc Author: mzingale Date: Tue Aug 4 18:58:49 2009 +0000 on second thought, update -d for CASTRO is a bad idea Tools/C_util/regtests/test.py commit 03c22373481342bb9fab26f3126669a1ead491a9 Author: mzingale Date: Sun Aug 2 14:37:03 2009 +0000 do a CVS update -d to capture new directories. only take the file name (not relative path) for the auxFiles when copying to the web directory Tools/C_util/regtests/test.py commit b6b12a02139b24ef3f01666a04fead0571a38973 Author: mzingale Date: Sun Aug 2 00:59:32 2009 +0000 update to reflect new directory structures and no more grid files Tools/C_util/regtests/Maestro-tests.ini commit 0dc500228673389562bfa5619592643aef41f19b Author: mzingale Date: Thu Jul 30 19:44:28 2009 +0000 add a check that if there is a floating point constant that it be a double precision constant. At the moment, it catches a bunch, but has too many false positives Tools/F_scripts/fcheck.py commit 84864e9dccd6be466c397f41a138c70c9a52cce7 Author: mzingale Date: Thu Jul 30 17:19:13 2009 +0000 the start of a simple script to check that quantities are allocated correctly in our Fortran code. At the moment, it looks for all the 'real' variables that aren't 'dp_t'. Next up is checking all the constants. Tools/F_scripts/fcheck.py commit 3f2e68813ca700788e2373eedeaf851e0de9cb41 Author: ajnonaka Date: Thu Jul 30 15:58:14 2009 +0000 on franklin, hpctoolkit will compile in if you add "USE_HPCTOOLKIT=t" when you make Tools/F_mk/GMakedefs.mak commit a332d711947ed81c9d9111ee2d930145e72a9b12 Author: 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 Date: Mon Jul 27 21:50:16 2009 +0000 Remove unused variable. Src/LinearSolvers/F_MG/ml_cc.f90 commit 1c69cd032c2e7fe4d9f103d0d334dc747f783d4c Author: 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 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 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 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 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 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 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 Date: Tue Jul 21 21:19:21 2009 +0000 fixed bug in grid_places() Src/C_AMRLib/Amr.cpp commit e2b50aa4df96ce1943e37dee0e3769db0cd827ce Author: lijewski Date: Thu Jul 16 18:01:27 2009 +0000 break up crse domain using maxSize() Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp commit a4975648399e1bca89bd8881216b4f6bfd86136d Author: lijewski Date: Thu Jul 16 17:37:20 2009 +0000 *** empty log message *** Src/LinearSolvers/C_TensorMG/Test/inputs3D Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Tests/LinearSolvers/C_TensorMG/inputs3D Tests/LinearSolvers/C_TensorMG/testVI.cpp commit f4a2d46c044d3a02a1ce8c691d81a4e963c1aad9 Author: lijewski Date: Thu Jul 16 16:59:51 2009 +0000 *** empty log message *** Src/LinearSolvers/C_TensorMG/Test/grids/gr.3_2x3x4 Src/LinearSolvers/C_TensorMG/Test/grids/gr16.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr16x8.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr2D Src/LinearSolvers/C_TensorMG/Test/grids/gr32.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr32x8.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr64.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr8.dog Src/LinearSolvers/C_TensorMG/Test/inputs3D Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Tests/LinearSolvers/C_TensorMG/grids/gr.3_2x3x4 Tests/LinearSolvers/C_TensorMG/grids/gr16.dog Tests/LinearSolvers/C_TensorMG/grids/gr16x8.dog Tests/LinearSolvers/C_TensorMG/grids/gr2D Tests/LinearSolvers/C_TensorMG/grids/gr32.dog Tests/LinearSolvers/C_TensorMG/grids/gr32x8.dog Tests/LinearSolvers/C_TensorMG/grids/gr64.dog Tests/LinearSolvers/C_TensorMG/grids/gr8.dog Tests/LinearSolvers/C_TensorMG/inputs3D Tests/LinearSolvers/C_TensorMG/testVI.cpp commit b48f5ac079ee403d72d790c6c5bea87d08cb9ef5 Author: lijewski Date: Thu Jul 16 16:32:44 2009 +0000 first cut at bringing up-to-date Src/LinearSolvers/C_TensorMG/Test/GNUmakefile Src/LinearSolvers/C_TensorMG/Test/Make.package Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.cpp Src/LinearSolvers/C_TensorMG/Test/main_F.H Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/C_TensorMG/Make.package Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp Tests/LinearSolvers/C_TensorMG/main_F.H Tests/LinearSolvers/C_TensorMG/testVI.cpp commit 87daa0dfb938de07c0d2aeea49c5913af5284d2e Author: lijewski Date: Mon Jul 13 20:18:28 2009 +0000 removed simplify() in initialize() Src/C_AMRLib/AuxBoundaryData.cpp commit 301362eeb80f01ff73f210d90b42091613bd906b Author: lijewski Date: Mon Jul 13 20:17:24 2009 +0000 removed simplify() in GetBndryCells Src/C_BaseLib/BoxArray.cpp commit 14702fe97c7b9d1404012c739e915842f02b9704 Author: lijewski Date: Sun Jul 12 00:38:32 2009 +0000 fpb_cache_max_size now defaults to 10. Src/C_BaseLib/Geometry.cpp commit 599ff3793b747b13368c3dae299a482e4f20fbdd Author: lijewski Date: Sat Jul 11 03:01:19 2009 +0000 max_live_tasks now defaults to 50. Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 3de6b9cf8706234911005d7e68dfef32780f976e Author: 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 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 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 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 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 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 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 Date: Fri Jun 19 21:07:13 2009 +0000 SMP -> USE_SMP=TRUE Tools/C_mk/Make.mpi commit 302a157d41fd48cd55a3a8c819e399190f9820c2 Author: 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 Date: Thu Jun 18 17:16:36 2009 +0000 more work on intrepid Tools/C_mk/Make.mpi commit b8395e8941db769bf19a610fecdc152bb9c51c11 Author: lijewski Date: Thu Jun 18 16:54:34 2009 +0000 some work getting HyperCLaw to compileon intrepid Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi commit 51ba47ef8ceb8419dd590fe504170e58befa4637 Author: lijewski Date: Wed Jun 17 15:54:28 2009 +0000 *** empty log message *** Src/C_AMRLib/AuxBoundaryData.cpp commit 2a08582386b0addfce1a7aa20553efc1abb3772d Author: almgren Date: Tue Jun 16 23:04:38 2009 +0000 Add Barrier calls at the end of Amr::writePlotFile and Amr::checkPoint. Hopefully this fixes the problems we've been having on della.princeton.edu Src/C_AMRLib/Amr.cpp commit 7459c78b87befee105718ccb85054d125c75785e Author: mzingale Date: Wed Jun 3 21:02:03 2009 +0000 update to reflect current problem setups Tools/C_util/regtests/Maestro-tests.ini commit 3897e8b118431e95aff938210b31aa4740b6a3d6 Author: ajnonaka Date: Wed Jun 3 16:34:09 2009 +0000 added parallel_barrier call to parallel_initialize to give timers better performance Src/F_BaseLib/parallel.f90 commit 0e8d7f58ab3597b8b6752c686cc8bb8732e63eb3 Author: ajnonaka Date: Tue Jun 2 21:38:51 2009 +0000 made timer output much more readable added additional timers in put_1d_array_... Src/F_BaseLib/bl_prof.f90 commit edb7fe14d97e25cc5de69d42aaf67d47edef3f46 Author: lijewski Date: Tue Jun 2 02:51:02 2009 +0000 Added new version of CrseInit() that takes a single MultiFab. This is meant to replace the weird version that takes a FArrayBox and has to be followed by a call to CrseInitFinish(). Codes should set themselves up to use this version, as the FArrayBox version appears to use too much memory in high CPU/high grid count scenarios. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 4cc373d1e999b278b25e99e36f8b31ca9a08e511 Author: 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 Date: Fri May 29 23:15:57 2009 +0000 some instrumentation for CrseInitFinish() Src/C_AMRLib/FluxRegister.cpp commit 318e773a3d26d6514f588f5a40b2268382a356d5 Author: ajnonaka Date: Fri May 29 21:57:03 2009 +0000 #pathscale friendly Src/C_BaseLib/FabArray.H commit c8b8393d67654db0d5ac42135be0892f35eec601 Author: lijewski Date: Fri May 29 21:54:15 2009 +0000 more instrumentation Src/C_BaseLib/FabArray.H commit 11c18d8a0af2a0b22e48b37766085db249457c5a Author: lijewski Date: Fri May 29 21:13:35 2009 +0000 added some instrumentation to CollectData() Src/C_BaseLib/FabArray.H commit 1846d1adb4ecb8501974ac9d594dbcd307f5b18e Author: lijewski Date: Wed May 27 21:36:59 2009 +0000 parallel speedup to linComb() Src/C_BoundaryLib/FabSet.cpp commit 9ceeb3995a2d9da3f8f949892812a2eade7d8d7c Author: 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 Date: Tue May 26 21:02:40 2009 +0000 added timer to initialize() Src/C_AMRLib/AuxBoundaryData.cpp commit 346674bdf9c8e0e1367e237778303856c84d3eb0 Author: lijewski Date: Tue May 26 20:40:00 2009 +0000 verbose flag and some timers Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit a914af7888eb829cb0ccfa473306db7bb3a68c54 Author: lijewski Date: Tue May 26 20:20:52 2009 +0000 some timers Src/C_AMRLib/AmrLevel.cpp commit 6a3dac2372525e537da7a8d5e3289d20b116a920 Author: almgren Date: Tue May 26 17:19:02 2009 +0000 Remove unused variables bxa_src and bxa_dst. Src/F_BaseLib/layout.f90 commit 0552a063cfb4f0a079279cd7bdadb1ef7f2e4a6c Author: 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 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 Date: Mon May 11 20:57:52 2009 +0000 added f90sources += mt19937ar.f90 Tests/LinearSolvers/F_MG/GPackage.mak commit cd450103545d2c4f8f6b26898220a3a6e2d07d4e Author: almgren Date: Sun May 10 05:11:16 2009 +0000 Added 3d Minion stencil. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 7f69454d13c73b52d14b72d439fd5fe7e08dd435 Author: lijewski Date: Fri May 8 18:07:31 2009 +0000 attempt to deal with empty case Src/C_AMRLib/AuxBoundaryData.H Src/C_AMRLib/AuxBoundaryData.cpp commit c99c6487b5becf30b8ff66cdb8198e6ab290dbdd Author: almgren Date: Wed May 6 23:50:04 2009 +0000 Put the minus sign back into minion_full_fill_2d. Src/LinearSolvers/F_MG/stencil.f90 commit c2419fe10c9627b915eca643e3f642fd0dbc8c37 Author: almgren Date: Wed May 6 23:40:12 2009 +0000 Fix up stencil... Src/LinearSolvers/F_MG/stencil.f90 commit f24404069e17b1011e49c7284c479af6992d6cdf Author: almgren Date: Wed May 6 22:50:02 2009 +0000 Generalize to coeffs having more than one ghost cell. Src/LinearSolvers/F_MG/stencil.f90 commit 50860bd8a3ff5f48fa423f6e3bece4afb03817a9 Author: almgren Date: Wed May 6 21:49:33 2009 +0000 Uncomment lines. Src/LinearSolvers/F_MG/stencil.f90 commit 384efd5793bd224367cc8c03fbd645a66ca2db99 Author: almgren Date: Wed May 6 21:37:40 2009 +0000 Fix stencil in stencil_minion_full_fill. Src/LinearSolvers/F_MG/stencil.f90 commit 2285fedf469b069c6063f027d38e4aa77c6eb581 Author: almgren Date: Wed May 6 20:56:00 2009 +0000 Add stencil for 25-point minion solve. Src/LinearSolvers/F_MG/stencil.f90 commit 59ead0993997adb87346c005d239d18a75869c63 Author: 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 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 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 Date: Sat May 2 00:40:33 2009 +0000 *** empty log message *** Tools/C_util/Statistics/PltFileXAve.cpp commit 967049379251b590d3ce360db54e6d60015fdc84 Author: almgren Date: Thu Apr 30 22:04:28 2009 +0000 Fix print statement for going down in V-cycle. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit a5657c1020e907f9db4aa3f85a7ed884fa25ea13 Author: lijewski Date: Thu Apr 30 17:34:34 2009 +0000 disallowed copy constructor & assignment operator Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp commit eb88eccf2620b33ffab5ea8f6120c5269be7fdc0 Author: gpau Date: Fri Apr 24 19:21:35 2009 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 18e6f200075056ae69db86af5dd87dd430997c47 Author: almgren Date: Tue Apr 21 19:40:00 2009 +0000 Fixed verbosity again. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 16ed91fefd875f181aa16e66ecea7c6f5c3921e8 Author: almgren Date: Tue Apr 21 19:21:16 2009 +0000 Modified verbosity -- added extra verbosity to Multigrid when verbose > 1.Z Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit b84fbc08b5df91689e584283bf10942c73839f55 Author: ajnonaka Date: Tue Apr 21 17:22:08 2009 +0000 boxassoc deallocate statements weren't being counted properly Src/F_BaseLib/layout.f90 commit 75bada19d838019b6e4ac4c780c9dbab6193fa25 Author: ajnonaka Date: Tue Apr 21 17:04:25 2009 +0000 plugged memory leak Src/LinearSolvers/F_MG/mg.f90 commit 119b8b0e1a9ef5a23689fafb39f031a5d710ae4b Author: 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 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 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 Date: Mon Apr 20 17:38:34 2009 +0000 Formatting only. Src/LinearSolvers/F_MG/mg_smoother.f90 commit 9d136865b83ad8cff233e471ef8122929f653b43 Author: almgren Date: Sat Apr 18 03:21:20 2009 +0000 Dont think we need to include mlmg.f90 in a make... do we? Src/LinearSolvers/F_MG/GPackage.mak commit b1ee9d14d3de5e90f3fb0d47d22acd84132a0169 Author: almgren Date: Sat Apr 18 03:20:11 2009 +0000 Fix case where we set bottom_solver_eps = eps when only one mg_level -- we only want this in the case when it's not being called as a bottom solver for another mgt, so here we test on volume ... this should work well enough for now. Src/LinearSolvers/F_MG/mg.f90 commit 59a5967a80de77616226339e7fc8dda26d143e70 Author: almgren Date: Fri Apr 17 21:36:12 2009 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg.f90 commit d65df552fe0f58106948b818ddc49d3b222dec55 Author: almgren Date: Fri Apr 17 21:20:46 2009 +0000 IF nodal and using CG or BiCG as bottom solver then build the nodal mask at the bottom solver level ahead of time and pass it in to the BiCG or CG routine so that they can pass it into the multifab_dot routine so we don't build it every time the dot routine is called. Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 commit b39d3551b9ba1b4e0d06360d68150904ed820186 Author: almgren Date: Fri Apr 17 21:19:14 2009 +0000 Added optional nodal_mask argument to multifab_dot which computes a dot product. Without the nodal_mask argument present the multifab_dot function still builds and destroys the nodal mask every time it is called. Src/F_BaseLib/multifab.f90 commit 2cb9fb3e74b5e812261101592947373ea9d29236 Author: ajnonaka Date: Thu Apr 16 22:20:08 2009 +0000 plugged memory leak Src/LinearSolvers/F_MG/mg.f90 commit 1f6c1dc15e57fc4ef2223a3b089366ffada8e2e4 Author: almgren Date: Thu Apr 16 21:44:46 2009 +0000 Make sure to allocate bottom_uu and bottom_rh as nodal if need be. Src/LinearSolvers/F_MG/mg.f90 commit 681bd58ecf875ff85a3708ee26442998310b2939 Author: 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 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 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 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 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 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 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 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 Date: Tue Apr 7 17:37:20 2009 +0000 updated gojira. Tools/C_mk/Make.mpi commit c3c3a9a1a14d806566d73acc5a6c029469fb7b3b Author: gpau Date: Sun Apr 5 15:28:42 2009 +0000 *** empty log message *** Tools/C_util/Statistics/PltFileXAve.cpp commit 70e6cbf531af3087cd8130b5d58274bcf36b3d04 Author: 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 Date: Fri Apr 3 20:19:05 2009 +0000 *** empty log message *** Tests/LinearSolvers/F_MG/inputs commit c35b0d9372d7d197eeceac78fe9bf054b697723d Author: lijewski Date: Fri Apr 3 20:15:11 2009 +0000 some simplification Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 666a5f55233dd7d7346d2e5d69d49fbd501f2511 Author: ajnonaka Date: Fri Apr 3 20:02:53 2009 +0000 changed the bl_timer output width to 40 characters so you can actually see what's being called... Src/F_BaseLib/bl_prof.f90 commit 682b4f6e1355caa728b0b06d14bd5cb43daddf83 Author: lijewski Date: Thu Apr 2 19:31:52 2009 +0000 more verbose output Src/F_BaseLib/layout.f90 commit 9d0d95b6e8ca78be2eeed4f968572e3ae3ed83e9 Author: lijewski Date: Thu Apr 2 17:20:29 2009 +0000 added simple hash to speed up copyassoc matches Src/F_BaseLib/layout.f90 commit 22c09fc4739227fdf2845d20b4132d99aff37cf0 Author: lijewski Date: Thu Apr 2 05:10:18 2009 +0000 back to simpler way of limiting copyassoc cache size Src/F_BaseLib/layout.f90 commit 8a586e5e342b802d85536e959dfd05cb021c5c41 Author: lijewski Date: Wed Apr 1 20:54:14 2009 +0000 more sophisticated cache clearing strategy Src/F_BaseLib/layout.f90 commit 327be62db3f5c5c841896585d9335f4343480a11 Author: lijewski Date: Wed Apr 1 20:24:24 2009 +0000 smarter about what to delete from copy cache Src/F_BaseLib/layout.f90 commit 1eeaa91ab8ac85940e471907be19f7faada993fe Author: 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 Date: Wed Apr 1 18:12:35 2009 +0000 copyassoc cache refinements Src/F_BaseLib/layout.f90 commit c9cc1b4a6f715c3ad7e96d53266041c19cce1537 Author: almgren Date: Tue Mar 31 17:37:06 2009 +0000 Don't need to compute residual on the way back up the V-cycle *after* the relaxation at that level -- we can compute it later when we need it. Left in that we do compute it if do_diagnostics is on. Src/LinearSolvers/F_MG/ml_cc.f90 commit 9df2b60113c9f3b45ace1cb8177e97c4618e8c68 Author: ajnonaka Date: Tue Mar 31 17:24:05 2009 +0000 fix comment Src/F_BaseLib/make_new_grids.f90 commit 9e71ff410498c1773dac529c0668d5dbfba49ba1 Author: ajnonaka Date: Tue Mar 31 17:09:01 2009 +0000 fixed a comment Src/F_BaseLib/ml_boxarray.f90 commit 377327506c52b27046ed12e746a258981dc4d9dd Author: lijewski Date: Mon Mar 30 22:01:29 2009 +0000 bypass distribution mapping calculation when possible Src/F_BaseLib/make_new_grids.f90 Src/F_BaseLib/ml_boxarray.f90 commit 4edc638758e12f5b4ba59c8cd0f832b79262c21f Author: lijewski Date: Mon Mar 30 21:49:55 2009 +0000 bypass distribution mapping calculation when possible Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit 471403705caa75958824a5ebf9ccea332b0903c9 Author: ajnonaka Date: Mon Mar 30 21:34:59 2009 +0000 modified calls to multifab_fill_ghost_cells to not call multifab_fill_boundary for the crse data when the ghost cells have previously been filled. no change to results. Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit fdecf5123521090841aea784035f1c665946988b Author: almgren Date: Mon Mar 30 21:12:12 2009 +0000 Move call to multifab_fill_boundary out of ml_interp_bcs and into ml_cc which is calling ml_interp_bcs 2*BL_SPACEDIM times. Should reduce the time in multifab_fill_boundary by factor of 2*BL_SPACEDIM. Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 603752e1557ef8fac438a1c38325e73847967e2b Author: ajnonaka Date: Mon Mar 30 19:31:19 2009 +0000 sfc_threshold=4 actually is a better idea now that we have turned off the knapsack minimize communication cost optimization Src/F_BaseLib/layout.f90 commit 58419fb5d4b77c8646adcf04c4f1ce2aa7494af4 Author: almgren Date: Mon Mar 30 17:56:57 2009 +0000 Add new smoother type -- "efficient GSRB" -- doesn't do a fill boundary between the red and black sweeps. Src/LinearSolvers/F_MG/mg.f90 commit fdd442328422596b2d0cc75087d593b51b314695 Author: 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 Date: Mon Mar 30 17:47:33 2009 +0000 turn off do_mcc by default Src/F_BaseLib/knapsack.f90 commit 417cc25b5e91267550d7a72fe730894b9dd282d5 Author: lijewski Date: Mon Mar 30 16:03:20 2009 +0000 reverted out the removal of profile timers Src/LinearSolvers/F_MG/mg_smoother.f90 commit cff9a168a492703d361e6f5577145394a4456c18 Author: 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 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 Date: Fri Mar 27 20:06:42 2009 +0000 remove bl_prof_timers Src/LinearSolvers/F_MG/mg_smoother.f90 commit ef541865fd6068b6394ec1b91dc8ecad1dc516dd Author: lijewski Date: Thu Mar 26 21:58:34 2009 +0000 modest speedup to SSFC stuff Src/C_BaseLib/DistributionMapping.cpp commit 7594644bc2ef73630546711da7aa67f972e7cc85 Author: 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 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 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 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 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 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 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 Date: Sat Mar 21 00:07:10 2009 +0000 made knapsack verbosity false by default Src/F_BaseLib/knapsack.f90 commit d5061d679355910dcc8a93e275a2ebe02b642a3f Author: lijewski Date: Fri Mar 20 22:20:59 2009 +0000 plot_nfiles=-1 or checkpoint_nfiles=-1 ==> really use ParallelDescriptor::NProcs(). Src/C_AMRLib/Amr.cpp commit dbe393cf17eb978cb9f51d7ccc5d59d1c2d5059c Author: almgren Date: Tue Mar 17 17:03:10 2009 +0000 This DiffPlot is obsolete -- has been replaced by other Diff... routines. Tools/C_util/Convergence/DiffPlot.cpp commit 94ebf575c10d5dc0c455becd9771faa8e463b26b Author: vince Date: Fri Mar 13 20:32:58 2009 +0000 added hyperion. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 0fbdcebfc5bf5f43ec2c1f1460ea7ae914adb573 Author: almgren Date: Fri Mar 13 18:01:25 2009 +0000 Add a new routine -- tags_and_untags, which copies both the CLEAR and the SET values instead of just the SET values. Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 56225ac7e0dcfd644d48f51e519602eab9d61a10 Author: vince Date: Thu Mar 12 01:11:37 2009 +0000 squished denorm mins to zero when writing the header. this is for aix. Src/C_BaseLib/VisMF.cpp commit f91de45446707f6f32403e92677ec7c02269b7e1 Author: lijewski Date: Wed Mar 11 16:44:17 2009 +0000 Removed the grid_loc data member of AmrLevel. Also the corresponding accessory function gridLocations(). Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StationData.cpp commit db86c16fa8c682ee1373513fa2a1f738a7028510 Author: almgren Date: Tue Mar 10 20:09:21 2009 +0000 Make the derive functions virtual. Src/C_AMRLib/AmrLevel.H commit f0c59916a95b818b76f9992c550206e29ddfc895 Author: lijewski Date: Mon Mar 9 16:05:03 2009 +0000 mods for yana at LLNL from Mike Singer Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit d437ce703ab207671763d0bf593a28954544bfcb Author: lijewski Date: Tue Mar 3 20:34:29 2009 +0000 some cleanup Src/C_BaseLib/DistributionMapping.cpp commit d7615cba6246feb9d3f1ebe609be64e84aa0f6de Author: lijewski Date: Mon Mar 2 23:23:13 2009 +0000 more namespace cleanup Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BoundaryLib/FabSet.cpp commit 967b59f691fc1cfd487ee949511901a641d98707 Author: lijewski Date: Mon Mar 2 22:38:56 2009 +0000 some namespace cleanup Src/C_AMRLib/Amr.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BoundaryLib/FabSet.cpp commit c176a6cf8ab5566678527b7b442c28ed73d3b380 Author: lijewski Date: Mon Mar 2 21:18:37 2009 +0000 put FSRec in unnamed namespace Src/C_BoundaryLib/FabSet.cpp commit a4db4d1abba5c43777e9a24b1aa6aebe310173e3 Author: 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 Date: Mon Mar 2 21:17:29 2009 +0000 put struct in unnamed namespace Src/C_AMRLib/FluxRegister.cpp commit b652594b5a92d0845f7311e88b42357ac8d1eb64 Author: lijewski Date: Mon Mar 2 21:04:12 2009 +0000 put BoxCmp in unnamed namespace Src/C_BaseLib/BoxList.cpp commit 551b2e2e779039f9b4f762218483169072de201a Author: lijewski Date: Mon Mar 2 21:00:59 2009 +0000 put SFCToken in unnamed namespace Src/C_BaseLib/DistributionMapping.cpp commit 2dfac20eb407fc1f40623e0965ca9ee5a0c6cb6a Author: 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 Date: Fri Feb 27 23:21:11 2009 +0000 catch mpi for lawrencium Tools/C_mk/Make.mpi commit b242781a43707f6324a122f4c8ca6c94bdd16052 Author: marc Date: Fri Feb 27 00:44:10 2009 +0000 CYGWIN does support the -f option, move HOSTNAME call Tools/C_mk/Make.defs commit 6ed34cc6b7610636613b772eeb4243646e3f74f6 Author: ajnonaka Date: Tue Feb 24 18:49:43 2009 +0000 Our makefiles for MAESTRO and MAESTRO_paper4 were starting to diverge. Brought these almost back into sync now - one more possible change coming Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit ac55e2122fe9b76da72d2670b14c14872484304f Author: mzingale Date: Mon Feb 23 18:51:57 2009 +0000 if making benchmarks + compileTest, nothing to report Tools/C_util/regtests/test.py commit 1f2066822b3c1aa56e2c91daf1c15db8f0961235 Author: mzingale Date: Fri Feb 20 20:43:53 2009 +0000 for some reason the BL_AIX flag never made it in for intrepid Tools/F_mk/GMakeMPI.mak commit b20c1f5f422577071a6b8aaaaa5d47283a871bbc Author: lijewski Date: Fri Feb 20 18:20:15 2009 +0000 update for pleiades Tools/C_mk/Make.Linux commit 187b2bcac1af192286f81051521b9943b3c0417a Author: almgren Date: Thu Feb 19 18:34:45 2009 +0000 Fixed settings for pleiades. Tools/C_mk/Make.mpi commit f4724add99430c816bbdac6addaf29543c244c00 Author: lijewski Date: Wed Feb 18 22:03:19 2009 +0000 can now use space-fill-curves instead of knapsack Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/layout.f90 commit 26b256405fc3968d12b6b8215a61e015891e1cba Author: 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 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 Date: Fri Feb 13 16:39:52 2009 +0000 *** empty log message *** Tools/F_mk/GMakeMPI.mak commit 65fec44ed0374be368ca2dba2b2ea7352595b9be Author: almgren Date: Thu Feb 12 21:13:02 2009 +0000 Add BL_USECLOSE for pleiades. Tools/C_mk/Make.mpi commit c4e291f0fcad55a502d72a6b3f4a8d5687313fe2 Author: almgren Date: Thu Feb 12 21:11:32 2009 +0000 Add special case for pleiades. Tools/C_mk/Make.Linux commit c7af4cb7ba75ada87fab2076e16074803953f1e0 Author: vince Date: Thu Feb 12 20:51:51 2009 +0000 added option for explicit file closing. Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp commit f5d3a017772a869f9b0e80f2134ee571d6ae2f5d Author: mzingale Date: Thu Feb 12 19:48:47 2009 +0000 fix the logic for deciding if a test is successful Tools/C_util/regtests/test.py commit fe3f89be2650fa8e797ee51a287e6888e9ebe553 Author: marc Date: Wed Feb 11 23:06:50 2009 +0000 fix data type Src/C_BaseLib/ParallelDescriptor.cpp commit 201593cb05d37f6f7413e613a3bf42e4c01c1fe4 Author: 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 Date: Wed Feb 11 01:44:06 2009 +0000 replaced STOP with bl_abort() Src/C_BaseLib/BLutil_F.f commit 67145c6c1aabf7046eceb139b95e490fd1731de3 Author: 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 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 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 Date: Mon Feb 9 20:30:54 2009 +0000 works for Lawrencium mpi Tools/F_mk/GMakeMPI.mak commit 123204860dec4c424cc18ce74891e581bb1378dc Author: mzingale Date: Mon Feb 9 15:09:26 2009 +0000 archive the output fix a restart issue for Parallel rename chk files for fParallel jobs using the new commandline setting Tools/C_util/regtests/test.py commit ad193dae2966734c655bed3fe4f878666934b8e5 Author: mzingale Date: Fri Feb 6 23:10:50 2009 +0000 add xlf stuff so we can compile analysis routines on the Intrepid frontend Tools/F_mk/GMakedefs.mak commit 5e348a53ae88a10164676b191ea8883c1c96ff76 Author: vince Date: Fri Feb 6 22:57:03 2009 +0000 changes for lijewski. Tools/C_mk/Make.mpi commit 7107e49148d62fc90c26ae0d5120ed8e544e334f Author: lijewski Date: Fri Feb 6 22:14:38 2009 +0000 Do_AllToAllV is now settable Src/F_BaseLib/multifab.f90 commit 093bf5ba34bbd9da5641689815ea63615839e3c7 Author: 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 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 Date: Fri Feb 6 20:46:19 2009 +0000 Fix previous fix. Src/C_BaseLib/ParallelDescriptor.cpp commit 6cd0bbac9c8f1d4f342fc8d0c0930d25961b6ba8 Author: lijewski Date: Fri Feb 6 19:17:04 2009 +0000 added allreduce() operations on vectors Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 0001436b2a14356c00aea3d10802513bf2252285 Author: mzingale Date: Fri Feb 6 16:30:50 2009 +0000 more clean-ups Tools/C_util/regtests/test.py commit 78aab489f1a223c77a60746f76e8bedb764c4e7b Author: mzingale Date: Fri Feb 6 16:02:04 2009 +0000 -module and -I are now picked up from the PathScale entry in GMakedefs.mak so we don't need to repeat them here Tools/F_mk/GMakeMPI.mak commit 079ecbb4ecf1d0d1c73fc46b09d553baf12cee03 Author: mzingale Date: Fri Feb 6 15:03:50 2009 +0000 some code clean up + add the ability to override the compiler for fParallel. Tools/C_util/regtests/test.py commit d835c161557b0111512a61ec9a4cc075f507e682 Author: mzingale Date: Thu Feb 5 20:22:04 2009 +0000 neither $HOST nor uname contain "intrepid" on intrepid, so define HOSTNAMEF which is the output of hostname -f, which does contain "intrepid". THis is used in GMakeMPI.mak to define the compilers. Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit 26eb725829abff46e324720b89de5ca90c973fb4 Author: mzingale Date: Thu Feb 5 19:49:36 2009 +0000 for some reason, on jaguar with PathScale, we were explicitly not putting in the module path and include path flags for compiling. This means that any .mod files were in the . instead of in t/XXX/m/. We don't need a special case for jaguar here. Note: this doesn't affect an MPI build, since that uses the jaguar stuff setup in GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit 065daa5cf3339f40a3d617943e9c939c83e3110e Author: lijewski Date: Tue Feb 3 17:08:10 2009 +0000 note in comments that if you want Array use std::vector Src/C_BaseLib/Array.H commit 5f63a477a7f593a97837c50a7149cb6f4c9cccdd Author: vince Date: Mon Feb 2 20:50:44 2009 +0000 intel 11. Tools/C_mk/Make.defs commit 0c9a08845607a01c3d718d69dcfa8bc07186194a Author: mzingale Date: Sat Jan 31 20:04:00 2009 +0000 add a comment Tools/F_scripts/make_build_info commit a9d95e2b89af9a1054f0ff2438313c0f5d25b734 Author: mzingale Date: Sat Jan 31 19:13:25 2009 +0000 switching over to uname instead of relying on setting HOST in a makefile automagically makes MPI compiling work on nan Tools/F_mk/GMakeMPI.mak commit 80a07b4cf4b745e4650b266b7037decd536b2fdd Author: lijewski Date: Thu Jan 29 21:13:24 2009 +0000 added BL_NOFAST to turn off maximum optimization Tools/C_mk/Make.Linux commit b5d6d1f0d4be6d4dc2a0693c4126686614f2e500 Author: lijewski Date: Thu Jan 29 17:47:15 2009 +0000 removed STRCTLY stuff Tools/C_mk/Make.defs commit 96887610be23373bceeba6433c1cf01c2775f184 Author: mzingale Date: Thu Jan 29 15:02:31 2009 +0000 make realclean before building the comparison and vis tools Tools/C_util/regtests/test.py commit 9b722c15832e68b985b48f7f412facbbf393db70 Author: 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 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 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 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 Date: Thu Jan 22 21:21:02 2009 +0000 f90 -> f95 on intrepid Tools/F_mk/GMakeMPI.mak commit 16826b2716aeb647fe230d44e6d469b5c5fcdb77 Author: 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 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 Date: Mon Jan 12 22:19:31 2009 +0000 Removed unused variable. Src/LinearSolvers/F_MG/ml_cc.f90 commit d24b33412d353ae0d29c7f019766f02829fca685 Author: gpau Date: Sat Jan 10 00:05:56 2009 +0000 parallelized PltFileXAve.cpp Tools/C_util/Statistics/GNUmakefile Tools/C_util/Statistics/PltFileList.cpp Tools/C_util/Statistics/PltFileStat.cpp Tools/C_util/Statistics/PltFileXAve.cpp commit 2601ae6bd9a8426ce714fc4ec8736bf957676733 Author: 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 Date: Mon Jan 5 21:12:15 2009 +0000 added varan. Tools/C_mk/Make.mpi commit b4f846ae4b8e9061cb7b3dfb14c71efabbed9791 Author: mzingale Date: Sat Jan 3 19:39:33 2009 +0000 for nan, if we are doing mpi, use mpif90 and mpicxx Tools/F_mk/GMakeMPI.mak commit 6ed8278a5837779116731c4002b56e75fdf767ff Author: 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 Date: Sat Dec 27 01:47:51 2008 +0000 Clean up some memory. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 64298f3f524fa414f46647f0175a9bba14e09067 Author: lijewski Date: Fri Dec 19 22:48:51 2008 +0000 added contains_nan() Src/F_BaseLib/fab.f90 Src/F_BaseLib/fabio_c.c commit 82c47066bc0dfc637a30d32f70d45afe0a66b83f Author: vince Date: Wed Dec 17 21:52:22 2008 +0000 added F90 for franklin. Tools/C_mk/Make.Linux commit 71972fc320ace9dd31dca1c64e7ba80408fa06ad Author: lijewski Date: Wed Dec 17 21:00:35 2008 +0000 *** empty log message *** Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit a2f76dcdd10e9fac3309a68a7e58870e3e299cf2 Author: almgren Date: Mon Dec 8 21:41:59 2008 +0000 Let us call CellBilinear if not in 3-d -- it appears to work in 2d anyway. Src/C_AMRLib/Interpolater.cpp commit d6744cb896abf9c675685fc651fd82047f552415 Author: ajnonaka Date: Thu Dec 4 18:54:14 2008 +0000 need to specify which optional argument is going into ml_cc() Src/LinearSolvers/F_MG/ml_solve.f90 commit 753e47c79da33eba57ec9490fab9a1e1855db9ee Author: almgren Date: Thu Dec 4 18:41:11 2008 +0000 Actually use abs_eps for a change. Src/LinearSolvers/F_MG/ml_cc.f90 commit b55945aa26da79b1633c00a4381f7934c50098cc Author: almgren Date: Thu Dec 4 18:40:43 2008 +0000 Pass abs_tol through into solver. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 6a7f1823c2e15f5d5e6953ed9bea82029a3328a8 Author: almgren Date: Tue Dec 2 01:51:59 2008 +0000 Cleaned up SETAREA. Src/C_BaseLib/COORDSYS_1D.F commit c8ecbcabcc529c74e90619ac06b049d0dfa55358 Author: almgren Date: Tue Dec 2 01:51:28 2008 +0000 Cleaned up SETAREA Src/C_BaseLib/COORDSYS_2D.F commit 191633c6d3bb4441ff2f9dc359bcdf9ed74ece24 Author: almgren Date: Tue Dec 2 01:49:30 2008 +0000 Cleaned up SETDLOGA. Src/C_BaseLib/COORDSYS_2D.F commit 1478959eb1ec056d7a10f1a96937e264ee8b7284 Author: almgren Date: Tue Dec 2 00:46:54 2008 +0000 Fix SETDLOGA and improve the formatting of the others. Src/C_BaseLib/COORDSYS_1D.F commit 4681df6eb8c1910bd65703189f89e070e39954f1 Author: lijewski Date: Mon Nov 17 23:45:55 2008 +0000 ParmParse do_full_knapsack Src/C_BaseLib/DistributionMapping.cpp commit 16d92f480062c4071e3e5c44678bcd8fa9868779 Author: lijewski Date: Mon Nov 17 23:45:39 2008 +0000 set copy_cache_max_size default to 100 Src/C_BaseLib/FabArray.cpp Src/C_BoundaryLib/FabSet.cpp commit bc4d107d8799ba47a25d34f062db133c2b4c7328 Author: lijewski Date: Thu Nov 13 16:57:52 2008 +0000 print out reusage rate of various caches Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BoundaryLib/FabSet.cpp commit c6c9e38196aade7a4f6f02709ebae3ef7beffe14 Author: lijewski Date: Wed Nov 12 21:34:52 2008 +0000 -1 implies no limit on cache size Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BoundaryLib/FabSet.cpp commit f19ca1d83d07c1b7343464b50e7803f85587c8be Author: lijewski Date: Wed Nov 12 04:27:32 2008 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/Geometry.cpp commit 435ac2b24ce2c1af897715e23d8c34b489875447 Author: almgren Date: Tue Nov 11 00:53:56 2008 +0000 Only define final_resnorm from ni_res if it's been included in the calling sequence. Src/LinearSolvers/F_MG/ml_cc.f90 commit bb5bf0a570a2f739d26a3e1148fa53b3895339a9 Author: almgren Date: Mon Nov 10 22:56:26 2008 +0000 Add final_resnorm to calling sequence for mgt_solve and ml_cc. This can be used to pass the final resnorm back to the calling routine -- this can be used later as a test for correction solves. Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/ml_cc.f90 commit b2fd11f6b1b45845cc620a4631bd33fdde4ab6ab Author: almgren Date: Mon Nov 10 22:54:38 2008 +0000 Add final_resnorm to calling sequence for mgt_solve. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit c65db7f1fb0210875101f9898140a0a6670d3369 Author: almgren Date: Thu Nov 6 17:26:10 2008 +0000 Add additional verbosity about which convergence criterion was satisfied. Src/LinearSolvers/F_MG/ml_cc.f90 commit b3391798c74762a79ec6e9650a668e8587bf5d78 Author: lijewski Date: Thu Nov 6 17:14:49 2008 +0000 Added do_full_knapsack flag which defaults to false. The default implies that we skip the triply nested loop which swaps boxes trying to get the efficiency above the threshold. We just sort the boxes and pass them out in the most efficient manner we can and let that suffice. Src/C_BaseLib/DistributionMapping.cpp commit efb6dc75b797f5d594e07109567b494870ba26ba Author: almgren Date: Wed Nov 5 18:07:36 2008 +0000 In gs_rb_smoother_1d, do lexicographical rather than GSRB smoothing -- GSRB just wasn't working... Src/LinearSolvers/F_MG/mg_smoother.f90 commit bbc057ae27ac5186789d8e3fefe5cfa0f4d6b530 Author: almgren Date: Wed Nov 5 18:07:08 2008 +0000 Don't call line solve for DIM=1 and more than one box -- call gs_rb_smoother_1d instead. Src/LinearSolvers/F_MG/mg.f90 commit 16a4cabe1eda0664983a425c598f167786851094 Author: lijewski Date: Wed Nov 5 00:10:43 2008 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit 323b27654e7699b2acb1862d2606dacd524079fe Author: lijewski Date: Mon Nov 3 23:33:30 2008 +0000 Now count & output # of passes thru core of knapsack() algorithm. max_efficienty now defaults to 0.9 and sfc_threshold to 6. Src/C_BaseLib/DistributionMapping.cpp commit f6c35a25196b4290ef4bc4358a81299bff4ee05a Author: lijewski Date: Mon Nov 3 20:22:52 2008 +0000 refine_grid_layout now defaults to true. ---------------------------------------------------------------------- removed automatically CVS: CVS: Committing in . ---------------------------------------------------------------------- Src/C_AMRLib/Amr.cpp commit c23bcecf408d89b73c0b6098797c909d03a85147 Author: lijewski Date: Fri Oct 31 20:40:02 2008 +0000 Moved template statics set via ParmParse into FabArraBase & set'm via BoxLib::Initialize(). Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 93dafa147ae8dcbb8f8341feb9ca5f5754175db6 Author: lijewski Date: Thu Oct 30 20:03:31 2008 +0000 Added refine_grid_layout, but it defaults to false for the time being. Src/C_AMRLib/Amr.cpp commit ae50b387bb185ecb1ec7a254db7d373c3bcc3f30 Author: sepp Date: Wed Oct 29 16:50:44 2008 +0000 1) add MultiFab Divide operation similar to Subtract Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 96dc30c89092a8e1e100b2f09ae048f1a432c7de Author: sepp Date: Tue Oct 28 21:51:50 2008 +0000 1) add a Multiply operation similar to Subtract Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit d49756f1c210065569cd195782c75394d8882df7 Author: lijewski Date: Fri Oct 24 21:05:35 2008 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit 74e65e566c81b7750392918b9c4aa16f805262b5 Author: 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 Date: Thu Oct 23 19:56:37 2008 +0000 added gigan. Tools/C_mk/Make.mpi commit 679e912bfc76e05b4ca3edb14cbe90446a9a01c0 Author: 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 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 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 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 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 Date: Thu Oct 16 18:13:23 2008 +0000 reverted back out recent GetBndryCells() changes Src/C_BaseLib/BoxArray.cpp commit 9b8b5dd7b03407c366e307c0937f9b58a3bec6ac Author: lijewski Date: Thu Oct 16 16:03:01 2008 +0000 Do a maxSize(64) after simplify() in GetBndryCells(). Src/C_BaseLib/BoxArray.cpp commit 346ff2b71a7f5b2bf3cd0b1f016e3fdb7d4bbf99 Author: lijewski Date: Thu Oct 16 16:02:32 2008 +0000 Do a maxSize(64) after simplify() in initialize(). Src/C_AMRLib/AuxBoundaryData.cpp commit d55a8de59e1208c7b270daccb28e019e7c606c7f Author: lijewski Date: Wed Oct 15 22:45:30 2008 +0000 GetBndryCells() now does a simplify(). Src/C_BaseLib/BoxArray.cpp commit 2d79a45edbc47d3e6aedf4ed341cf2b73f6d05fb Author: 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 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 Date: Fri Oct 10 23:31:57 2008 +0000 now use Ofast for PathScale optimization Tools/C_mk/Make.Linux commit bb5f1d11d40764465429f215571cd8a616ace70a Author: lijewski Date: Fri Oct 10 22:35:41 2008 +0000 FillPeriodicBoundary() is now a template in BoxLib namespace on FabArray ---------------------------------------------------------------------- automatically CVS: CVS: Committing in . CVS: CVS: Modified Files: CVS: Geometry.H Geometry.cpp CVS: ---------------------------------------------------------------------- Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 25ca197400ff679d1a365238017d8fea3639a3d1 Author: lijewski Date: Mon Oct 6 20:22:09 2008 +0000 use 'fast' instead of 'O' for optimization with PGI Tools/C_mk/Make.Linux commit 8fa248285f8f4b29008685fb4cdfd311e134222c Author: ajnonaka Date: Mon Oct 6 17:13:07 2008 +0000 using -Ofast optimization - seems to give a few more percent speed bonus Tools/F_mk/GMakedefs.mak commit a573d1eb2896ee8ab6acdfeb8b5c96217a8ad908 Author: ajnonaka Date: Mon Oct 6 16:33:38 2008 +0000 adding -ipa flag back in, so that means you need to module swap pathscale pathscale/3.2 on franklin before next week, when 3.2 becomes the default. Testing shows -ipa runs faster Tools/F_mk/GMakedefs.mak commit 0e3b4503be4f911e751f220c018389fbca73c953 Author: ajnonaka Date: Sun Oct 5 00:05:26 2008 +0000 i've permanently disabled the -ipa flag. now the default pathscale compilers (3.1) work on jaguar AND franklin. 3.2 should work as well, but I'm going back to the default 3.1 Tools/F_mk/GMakedefs.mak commit 4ea4a97ed0768e62a6da82b07eaeb9cd162f31da Author: ajnonaka Date: Sat Oct 4 23:12:47 2008 +0000 oops; franklin's hostnane is nid*. works now Tools/F_mk/GMakedefs.mak commit c41cbdaeb6535d6ef660bed9ecfca3a6b77ae64d Author: ajnonaka Date: Sat Oct 4 23:05:39 2008 +0000 if franklin, disable -ipa flags. after a make realclean, MAESTRO compiles on franklin again Tools/F_mk/GMakedefs.mak commit c5aa39ae49e3c6ddba36740b06126fc4defb7acb Author: almgren Date: Thu Oct 2 19:10:33 2008 +0000 Impose a limit on how many times you regrid on initialization. Previously one could go on regridding indefinitely; now there's a limit of 4 times through the regridding process. The integer MaxCnt is locally defined and arbitrarily set to 4; we could ParmParse this later if needed. Src/C_AMRLib/Amr.cpp commit baf0d347a536aba67f09f2fe7a7198e03e0762ec Author: almgren Date: Wed Oct 1 18:20:07 2008 +0000 Added an option to generate a runlog_terse which prints only the step number, time and dt, with no words. It is set by amr.run_log_terse = filename in the inputs file. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 26145cd254806f9d92a118f85c04b7b5d9db1c6e Author: lijewski Date: Tue Sep 30 20:48:29 2008 +0000 mods for when there are no bndry cells; i.e. triply periodic Src/C_AMRLib/AuxBoundaryData.cpp commit 4b448b76e601e3fe7f39f2524121b9e901054326 Author: lijewski Date: Tue Sep 30 17:17:04 2008 +0000 FillBoundary() is now in FabArray Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 3be26e3dec7ea32ebb9a525b350fda6ef4ab4265 Author: mzingale Date: Tue Sep 30 14:28:49 2008 +0000 an updated version of the changelog script (taken from http://www.red-bean.com/cvs2cl/). This version seems to work better with recent CVS changes. Tools/F_scripts/cvs2cl.pl commit d00932bed7b8b930cd0ff8f2c5014e8152f52165 Author: almgren Date: Fri Sep 26 21:01:27 2008 +0000 For nodal_smoother_3d, Jacobi iteration, only update uu = uu_temp if we've actually defined uu_temp. Src/LinearSolvers/F_MG/mg_smoother.f90 commit 45c555c585ac3fae52bf09b447aa289a516272ea Author: vince Date: Thu Sep 25 22:50:21 2008 +0000 strstream update. Src/C_AMRLib/DatasetClient.cpp commit fc9995ace0dca662a08376f1331667c1a1358f27 Author: sepp Date: Tue Sep 23 14:45:01 2008 +0000 1) reverse Ann's change that turns off icc for v 9.0 of compiler Tools/C_mk/Make.defs commit aa310321f9cc5166d2d12c27686161757e70a0f9 Author: ajnonaka Date: Mon Sep 22 18:40:03 2008 +0000 #f90sources += mt19937ar.f90 putting local copy in wdconvect instead since this sompiles so slowly Src/F_BaseLib/GPackage.mak commit 5fc0995501fc05611a2e4dda02b1183fc44eb105 Author: ajnonaka Date: Mon Sep 22 18:35:33 2008 +0000 f90sources += mt19937ar.f90 Src/F_BaseLib/GPackage.mak commit e9c9e70773fe04a735da91fc91ff1f33fbbacfeb Author: ajnonaka Date: Wed Sep 17 20:49:05 2008 +0000 added mpi capabilities for atragon Tools/F_mk/GMakeMPI.mak commit 5d68e5215856ab722f56ae402f659140091e3cf3 Author: vince Date: Wed Sep 17 20:01:52 2008 +0000 added atragon and gojira. Tools/C_mk/Make.mpi commit 67978532c439d3c95381e5d204031f0ceaef165d Author: ajnonaka Date: Thu Sep 11 15:19:00 2008 +0000 aligned the tabs so the logic reads easier Src/LinearSolvers/F_MG/mg.f90 commit e4897a6163114380b828a3a86c6ab5995bf6be16 Author: ajnonaka Date: Wed Sep 10 21:11:44 2008 +0000 fixed a line of code that didn't work with intel compiler version 9.1.043 Src/F_BaseLib/fillpatch.f90 commit 8bcfd2c3b8ffcc01cb41cc62b0466e6c9ad4ebab Author: ajnonaka Date: Wed Sep 10 21:11:17 2008 +0000 made the cpy_ functions public Src/F_BaseLib/multifab.f90 commit a90c425976f93210c6814b5a22047173905826e5 Author: ajnonaka Date: Mon Sep 8 19:39:20 2008 +0000 works for ng = 0 Src/F_BaseLib/fillpatch.f90 commit 035dbab7063e7e23489ec5964ff2c85480fea5df Author: 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 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 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 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 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 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 Date: Thu Aug 28 17:41:48 2008 +0000 made 2d consistent with 3d Src/F_BaseLib/tag_boxes.f90 commit 23bd38798627082c9514cbff581862c8ca6690a7 Author: ajnonaka Date: Wed Aug 27 23:04:11 2008 +0000 Every instance of tag_boxes.f90 that was not in boxlib was identical. So I removed them all from the local directories and made the default version in boxlib the same as the removed copies. Src/F_BaseLib/tag_boxes.f90 commit ce7f03654efcfce24f62e6c9a39398f942d59ec0 Author: ajnonaka Date: Wed Aug 27 22:57:30 2008 +0000 Fixed a bug where nothing would ever be tagged for level 4 or greater. Also, the comments did not match the code. The code did a nonsensical tagging, so I made the code match the comments, which did make sense. Src/F_BaseLib/tag_boxes.f90 commit 84316eb951ed7fc7dd10ebabd9eacfbd9c1967f3 Author: mzingale Date: Tue Aug 26 15:18:39 2008 +0000 add the 2-d gaussian diffusion problem Tools/C_util/regtests/Castro-tests.ini commit a66c30c22d9d7e39f6a76594f77709df8d5a5b5f Author: almgren Date: Mon Aug 25 23:08:04 2008 +0000 Replace "area" by "coeffs" in set_gravity_coefficients. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 0b45ae200ecbbd67ffd5f6d933ac7d2815794e6d Author: almgren Date: Mon Aug 25 23:07:31 2008 +0000 Replace "area" by "coeffs" Src/LinearSolvers/C_to_F_MG/MGT_Solver.H commit f80d6385d4c0d71471a979f112a1dfebae6926ae Author: almgren Date: Mon Aug 25 23:06:52 2008 +0000 Remove geom from call to set_gravity_coefficients. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 4061b1840c7af057d4447c0fdc2fb1639ee849f7 Author: mzingale Date: Mon Aug 25 20:56:41 2008 +0000 fix a crash if the benchmark file was not found Tools/C_util/regtests/test.py commit 646f8b4fab30a69ba1e669f26c089154c8800080 Author: 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 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 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 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 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 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 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 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 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 Date: Tue Aug 12 00:09:49 2008 +0000 added battra. Tools/C_mk/Make.mpi commit fafe59ebf67ddba4c93477b8fa86759ab67547ca Author: vince Date: Mon Aug 11 19:18:06 2008 +0000 changes for manda. Tools/C_mk/Make.mpi commit 8d2a74a0e1cf675c16c5fe7a65cb8c0b386fce17 Author: almgren Date: Thu Aug 7 21:30:12 2008 +0000 Create pmask from la_array(1), not la_array(nlevs) Src/F_BaseLib/make_new_grids.f90 commit 48b21e006a6732ddf233718ed03f5e05e6b65921 Author: almgren Date: Thu Aug 7 21:18:52 2008 +0000 1) Fix regridding and proper nesting. 2) Move min_eff and minwidth to cluster and add functionality to set them through probin. Src/F_BaseLib/cluster.f90 Src/F_BaseLib/make_new_grids.f90 commit cf07c6d2dc671087be5a82cf77900291e584f0bc Author: almgren Date: Thu Aug 7 21:15:22 2008 +0000 Don't need cluster_2d.f90 anymore -- we use cluster.f90 for 2d and 3d. Src/F_BaseLib/cluster_2d.f90 commit 7755c58a31472bcfa1f703c3e49b43c5151ccc81 Author: almgren Date: Wed Aug 6 21:58:09 2008 +0000 Move the test on being close to the domain boundary *after* instead of *before* the proper nesting test. Src/F_BaseLib/make_new_grids.f90 commit d91ad504193d67ef7baae780f4ca4fc72569dbfc Author: almgren Date: Wed Aug 6 21:43:05 2008 +0000 If a fine grid is within 2 fine cells of a physical non-periodic boundary, then make the grid touch the boundary instead of staying 2 cells away. We don't know how to fillpatch the third ghost cell if it's outside the domain but the grid doesn't touch the domain boundary. Src/F_BaseLib/make_new_grids.f90 commit 485a63857ae0e44a584bbb2a1cbc0f050f04bdc8 Author: vince Date: Wed Aug 6 19:38:44 2008 +0000 changes for naphta. Tools/C_mk/Make.mpi commit 1adb427518e94f75ee99fc0f1f60c3bf1e4b5cf4 Author: almgren Date: Wed Aug 6 19:35:26 2008 +0000 Only do proper nesting test if there are in fact grids at the finer level. Src/F_BaseLib/make_new_grids.f90 commit 7d2531b735fc08e4c2364e7b92873c2ed76c5e58 Author: almgren Date: Wed Aug 6 19:29:38 2008 +0000 Dont call cluster if there are no tagged points. Src/F_BaseLib/make_new_grids.f90 commit e4b4232cd1f23401501249eec7ce16d65f4c42eb Author: vince Date: Wed Aug 6 18:30:25 2008 +0000 change for naphta. Tools/C_mk/Make.mpi commit 708db2a10156407659a68fd4707aef58f4c688a6 Author: lijewski Date: Wed Aug 6 16:16:23 2008 +0000 destroy() tagboxes in enforce_proper_nesting() Src/F_BaseLib/make_new_grids.f90 commit a8418e407cce6a50095fb3badfcdd9155f742480 Author: almgren Date: Wed Aug 6 03:09:43 2008 +0000 1) Removed probin_module from enforce_proper_nesting. 2) Modified enforce_proper_nesting so it calls the clustering algorithm to create the new grids, instead of just adding small grids to the existing one. This allows us to use the minwidth criteria already in cluster. Src/F_BaseLib/make_new_grids.f90 commit aa8ca7f75373d482b9d43e805ec93e77ea224bf2 Author: almgren Date: Wed Aug 6 00:03:57 2008 +0000 Modify the call to the proper_nested routine. Src/F_BaseLib/ml_boxarray.f90 commit 68e4e88d203c538e81c69c463eaa2372b75d8bba Author: almgren Date: Wed Aug 6 00:03:36 2008 +0000 Moved enforce_proper_nesting into here. Src/F_BaseLib/make_new_grids.f90 commit 225134ef0651f0d76ce54bc7bf09a71437fa94cd Author: almgren Date: Tue Aug 5 23:01:46 2008 +0000 Set minwidth = 4 instead of 2. Src/F_BaseLib/make_new_grids.f90 commit 83153f9de14832df7d604d57d3b6cff9fab5d7c0 Author: almgren Date: Tue Aug 5 21:10:22 2008 +0000 Hopefully we fixed the case where multifab_fill_ghost_cells asks fillpatch to fill a box which is completely outside the domain. Src/F_BaseLib/fillpatch.f90 commit 5389d911545b12561bcfa2070d1a67e30f1502bc Author: gilet Date: Tue Aug 5 18:08:43 2008 +0000 mpich now works on gigan Tools/F_mk/GMakeMPI.mak commit a7934c8e6cc9ceda0f97b0fa9f5e01fee738086a Author: almgren Date: Mon Aug 4 23:19:06 2008 +0000 *** empty log message *** Src/LinearSolvers/F_MG/stencil.f90 commit 640ac8416263be1510ba7a3e63cfa64e68e19067 Author: almgren Date: Mon Aug 4 23:13:02 2008 +0000 Fix a typo. Src/LinearSolvers/F_MG/stencil.f90 commit f3d5f0250ca80c94c823236ff048ac8c698be699 Author: almgren Date: Mon Aug 4 23:09:49 2008 +0000 1) Use the beta's since they carry the viscous coefficients for the viscous/diffusive solves. 2) Add the alpha -- forgot that last time. Src/LinearSolvers/F_MG/stencil.f90 commit 2b6258d09dc0bcf0b8f8e8e07e53e00bde7a4928 Author: almgren Date: Mon Aug 4 22:59:43 2008 +0000 Put full 9-pt cross stencil back in. Src/LinearSolvers/F_MG/stencil.f90 commit 790357b38c9182f0c6ac549db579345957a0cfc1 Author: almgren Date: Mon Aug 4 22:45:16 2008 +0000 I have added the functionality to do Minion's 4th order constant density stencil -- the coefficients are independent of beta for now, and the 1-d stencil would be (i-2,j), (i-1,j), (i,j), (i+1,j) (i+2,j) and analogously in 2d. Only 2d is coded. Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 3c09bf2e7a9541165ca6d50dcfae76c3e5c2c973 Author: almgren Date: Fri Aug 1 23:11:45 2008 +0000 Remove unused "proc" Src/F_BaseLib/cluster.f90 commit bdfb9e9ff13bfedad200e2ee412e1095963fdf6e Author: almgren Date: Fri Aug 1 23:11:02 2008 +0000 Remove unused ibxs(:) Src/F_BaseLib/cluster.f90 commit 6b62b6f60f27978bc7a10fe9dd0fa05e4d3c517f Author: mzingale Date: Fri Aug 1 17:49:14 2008 +0000 the C99 standard moves std::abort into cstdlib and std::strerror into cstring, so these header files need to be added in the appropriate places. This allows Castro to compile with GCC 4.3 Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/ParallelDescriptor.cpp commit f35bf0d517568ada0905378d9067499ea1e7472e Author: lijewski Date: Thu Jul 31 21:55:48 2008 +0000 added version of GetVolume() taking a FArrayBox Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 0f9a1945b8d73fe37b17a11f08c21647bb961955 Author: 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 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 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 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 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 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 Date: Wed Jul 30 01:10:47 2008 +0000 littlea cleanup Src/C_BaseLib/BaseFab.H commit a6e64fa65437b8c283b68fd65a0a444c9e26f405 Author: lijewski Date: Wed Jul 30 00:54:45 2008 +0000 fixed bug related to calculating FAB byte spread and clear() calls Src/C_BaseLib/BaseFab.H commit c71ddb25e26de9099ca2fed8184da7f586b2a47c Author: almgren Date: Tue Jul 29 19:32:04 2008 +0000 Remove stray line -- no change in functionality (caught by Candace G) Src/F_BaseLib/multifab.f90 commit b1ce4d38555d751232e27b5ee2e8c3b4f8caadc2 Author: 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 Date: Wed Jul 23 21:38:57 2008 +0000 some memory cleanup Src/C_AMRLib/AmrLevel.cpp commit 4c2b27f5743cb65bf69cd8a6be8611f9507ac826 Author: lijewski Date: Wed Jul 23 17:18:34 2008 +0000 *** empty log message *** Tools/C_mk/Make.defs commit ed2dd69a7ef144605aa7ac15342f870dee855d8e Author: 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 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 Date: Mon Jul 21 19:28:27 2008 +0000 new compare tool Tools/C_util/regtests/Maestro-tests.ini commit 06d566d5d7ca8e7c3c6da2df940f32c8971709d0 Author: mzingale Date: Mon Jul 21 19:27:59 2008 +0000 switch over to using fParallel/data_processing/fcompare to do the comparisons -- this works even if the list of variables changes, so a better comparison can be done on those that remain. It also does 1-,2-, and 3- all in one executable. Tools/C_util/regtests/test.py commit af86adf04d5b329540c1dffcb83b19dfe28bf03a Author: almgren Date: Fri Jul 18 23:57:31 2008 +0000 1) Added gs_rb_smoother_1d as well as line solve -- use gsrb if more than one grid at the level, it works better with V-cycle. 2) Moved defn of mgt%dim to the top because it was getting used before it was defined. Src/LinearSolvers/F_MG/mg.f90 commit 3377bdc8e2b69342bcf072fa1927bdcfaff686b5 Author: almgren Date: Fri Jul 18 23:45:30 2008 +0000 Add gs_rb_smoother_1d for 1d gsrb relaxation -- need to use this instead of line solve for multiple grids, otherwise mg v-cycles seem to have a hard time. Src/LinearSolvers/F_MG/mg_smoother.f90 commit 5cf07700120338b376e2e9696d503f4c37e59b2b Author: ajnonaka Date: Thu Jul 17 14:10:14 2008 +0000 fixed multilevel, 3d, out-of-bounds bug Src/LinearSolvers/F_MG/ml_prolongation.f90 commit c9017bd391716ebacc81a4280af8239096f5baf0 Author: marc Date: Wed Jul 16 22:48:41 2008 +0000 marc hacking for gigan Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit 037141b3444c5386fd6731a41558b5e4f5a431e3 Author: almgren Date: Wed Jul 16 20:57:52 2008 +0000 Made same changes for 1d as already done for 2d and 3d in setting stencils at interior grid boundaries. Src/LinearSolvers/F_MG/stencil.f90 commit 12d640b569f9e122b123a8f0c7f2862a21be2eca Author: almgren Date: Wed Jul 16 17:48:57 2008 +0000 Introduced new integer member of Amr : file_name_digits. This defaults to 5, but can be set in parmparse. This is the number of digits used in plotfile names and checkpoint file names. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 847dc590773bc04110e6ebc49506acbbe265bf3b Author: lijewski Date: Wed Jul 16 17:40:24 2008 +0000 added mindigits 3rd arg to Concatenate() that defaults to 5 Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 251b35b2fa7f9f7bd184c64361d3c9b0a224f16e Author: lijewski Date: Tue Jul 15 20:58:20 2008 +0000 mods for intel -- needs more stuff than xlf95 says it should Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/layout.f90 commit 0e0589f4f8876fb5ce5e9cf5fed20640ab0107d1 Author: lijewski Date: Tue Jul 15 20:30:49 2008 +0000 now compile with no complaints with xlf95 -qlanglev=95std Src/F_BaseLib/bl_stream.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 2063b6c2bdc82d3d9641294cef8a0f46977a07e1 Author: 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 Date: Thu Jul 10 23:24:16 2008 +0000 removed unneeded module usage Src/F_BaseLib/make_new_grids.f90 commit ae249cc2ce280dfd3997721d012788e0c7b6c571 Author: lijewski Date: Thu Jul 10 20:17:39 2008 +0000 plugged memory leak & make boxes via copy() Src/F_BaseLib/make_new_grids.f90 commit 98021f6e5906dba352ca7eda32c6449e0b04eb17 Author: 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 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 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 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 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 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 Date: Thu Jul 10 16:55:57 2008 +0000 document the MPI stuff Tools/C_util/regtests/test.py commit 491b3f02ad53cf5eabc1e2c830cb762b6caaa023 Author: lijewski Date: Thu Jul 10 16:10:14 2008 +0000 Moved some list_box routines that were private in boxarray to list_box. More could be done but I'm hitting an Intel compiler error. Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/list_box.f90 commit f1f0c573eb6f1e038313cbdcecc10d91b4255cc9 Author: mzingale Date: Thu Jul 10 14:21:17 2008 +0000 add parallel: Tools/C_util/regtests/Castro-tests.ini commit b5972f65a1b27fd16ddd09369ede3773683ccd0d Author: mzingale Date: Thu Jul 10 14:20:52 2008 +0000 get initial MPI stuff in the test suite to do parallel tests Tools/C_util/regtests/test.py commit ea1193bff9a7dba3dee15944b5416eb71c9decc2 Author: mzingale Date: Thu Jul 10 13:48:18 2008 +0000 only store ChangeLog.Parallel if we are doing a Parallel/ test Tools/C_util/regtests/test.py commit a622089a2976aa2e4fa860f34647d0de10b8e0aa Author: lijewski Date: Thu Jul 10 05:57:52 2008 +0000 removed couple unused & broken routines Src/F_BaseLib/boxarray.f90 commit 715c9f0a8a672d60c86505f3636e77c83cccabc0 Author: almgren Date: Thu Jul 10 01:25:37 2008 +0000 Fixed subroutine buffer. Src/F_BaseLib/make_new_grids.f90 commit d8530bbe1ef0c958bc939a94408c5dca036cbc8a Author: almgren Date: Wed Jul 9 22:32:28 2008 +0000 Set the setval back to true in subroutine buffer. Src/F_BaseLib/make_new_grids.f90 commit 2c20a24e108512c9036f55dc97bdb432d5677167 Author: almgren Date: Wed Jul 9 22:30:44 2008 +0000 Added machine della (Adam Burroughs' machine at Princeton) as an option. Tools/C_mk/Make.defs commit 95b464619fa404072bc5102b339a565dc8b69632 Author: almgren Date: Wed Jul 9 22:28:57 2008 +0000 Add machines manda and DELLA as new options. Tools/C_mk/Make.mpi commit 481627e08cdb0fedfdd2b48b674d9c3abc96fb07 Author: 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 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 Date: Wed Jul 9 00:04:58 2008 +0000 Renamed regrid.f90 --> make_new_grids.f90 Src/F_BaseLib/make_new_grids.f90 commit a19cba9792fa81be52d72d66fa8271ee338b9c21 Author: almgren Date: Tue Jul 8 23:53:01 2008 +0000 Separated the tag_boxes functionality out of regrid -- new files tag_boxes.f90 Src/F_BaseLib/regrid.f90 Src/F_BaseLib/tag_boxes.f90 commit 438704d400645df6ac1448c434bae5cc5540a038 Author: almgren Date: Tue Jul 8 23:39:52 2008 +0000 Remove commented line. Src/F_BaseLib/boxarray.f90 commit 3f3cbdfa1838d334e830b46ad97a5082855dce08 Author: lijewski Date: Tue Jul 8 23:08:13 2008 +0000 tiny bit of cleanup Src/F_BaseLib/multifab.f90 commit ca428d39938f2c068f38d4e2df7b835f4912ede1 Author: lijewski Date: Tue Jul 8 21:54:12 2008 +0000 first cut at map_periodic() Src/F_BaseLib/cluster.f90 commit 35ecf29d2b844be0aa262f988e5fa22bbd23eaf3 Author: almgren Date: Mon Jul 7 18:05:26 2008 +0000 This takes max_grid_size as an argument to make_new_grids, and some other changes.. Src/F_BaseLib/regrid.f90 commit b47b24bc9e56532b646a6239982a1c79c66ace06 Author: almgren Date: Thu Jul 3 21:32:39 2008 +0000 Replace set_const_gravity_coefficients by a flagged version of set_gravity_coefficients. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 401a1a39db95bf510b0fde14672677ccb532f750 Author: almgren Date: Thu Jul 3 00:05:28 2008 +0000 Add another sanity check for proper nesting. Src/F_BaseLib/ml_boxarray.f90 commit 8f285f7e5310ab83d99380a3112192093ea7e325 Author: almgren Date: Thu Jul 3 00:04:30 2008 +0000 Modify properly nested test to take optional arguments: min_level and max_level, so can test just between two levels. Src/F_BaseLib/ml_boxarray.f90 commit 8ceda966e24088e551717c2fa67db8348a4baec3 Author: almgren Date: Wed Jul 2 23:15:57 2008 +0000 Removed commented line. Src/F_BaseLib/fabio.f90 commit ea6dcd424043fe0e03b2c15db58cdefe384e2d8a Author: 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 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 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 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 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 Date: Mon Jun 30 22:05:03 2008 +0000 minimize copy()ing Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit cbe2fdfed5874a1732578d421fe31b4a7b4cbde5 Author: lijewski Date: Thu Jun 26 23:04:34 2008 +0000 slight reworking of ml_boxarray_properly_nested() Src/F_BaseLib/ml_boxarray.f90 commit 5a67691aeb1c7b9a488b7d4be05c15401651c9cd Author: lijewski Date: Thu Jun 26 21:02:48 2008 +0000 more efficient periodic tests in properly_nested() Src/F_BaseLib/ml_boxarray.f90 commit eb7de21cf3417eae17a54cc8d35a655fd294096a Author: lijewski Date: Thu Jun 26 20:45:21 2008 +0000 no need to grow box by ng before passing to box_periodic_shift() Src/F_BaseLib/fillpatch.f90 commit b38d8a0306816ea59303cd7ad7d5988f6982788b Author: lijewski Date: Thu Jun 26 15:58:19 2008 +0000 *** empty log message *** Src/F_BaseLib/boxarray.f90 commit 61fa51333ce5e72ff6d790c28079d8b483f64276 Author: lijewski Date: Thu Jun 26 15:57:56 2008 +0000 added couple uses of boxarray_contains() Src/F_BaseLib/test/t_knapsack.f90 Tests/F_BaseLib/t_knapsack.f90 commit 32a4e9ce3bf754a132291aee67712eba80cf7cd0 Author: almgren Date: Thu Jun 26 05:38:50 2008 +0000 I believe we now have a correct implementation of ml_boxarray_properly_nested. Only limited testing has been done, but it seems good. Src/F_BaseLib/ml_boxarray.f90 commit bf654d4188b3742cbef23f43221443385949f9cb Author: ajnonaka Date: Thu Jun 26 03:51:35 2008 +0000 added "use_bl_error_module". Code compiles again. Src/F_BaseLib/boxarray.f90 commit 72b801590e3819401b683df119759b83afd4e776 Author: almgren Date: Wed Jun 25 23:31:30 2008 +0000 New functions added: 1) function boxarray_boxarray_contains(ba1,ba2) returns true if ba1 contains ba2 2) function boxarray_box_contains(ba1,ba2) returns true if ba contains bx Src/F_BaseLib/boxarray.f90 commit 1bf25b6685afcdd82d5784b64f20993df67ede95 Author: almgren Date: Wed Jun 25 22:11:05 2008 +0000 Replace the box_grow_i_m function by box_grow_n_m which actually makes the lo lower and the hi higher, unlike the previous box_grow_i_m, which made the lo lower and the hi lower (go figure). Src/F_BaseLib/box.f90 commit d3d32346454aa95feb74c2c98eff973aa2bfe351 Author: almgren Date: Wed Jun 25 21:19:50 2008 +0000 Fix ml_boxarray_properly_nested so that it correctly works *except* for periodic cases. It takes an integer, nproper, which is how many grow cells are needed at the fine level to be contained by the coarser boxarray. Src/F_BaseLib/ml_boxarray.f90 commit ca0badbff30c4bc77af6814ccabb25607970e33c Author: almgren Date: Wed Jun 25 19:14:47 2008 +0000 Change ml_boxarray_properly_nested_new --> ml_boxarray_properly_nested and ml_boxarray_properly_nested --> ml_boxarray_properly_nested_old Src/F_BaseLib/ml_boxarray.f90 commit 2e696263f83b32cd9e721094ca2005318b3012b1 Author: almgren Date: Wed Jun 25 18:04:29 2008 +0000 Slight change in the test for creating maximum number of multigrid levels. One of the criteria for stopping the coarsening is now if the volume of the entire boxarray is less than or equal to 2**dim. This makes the single-base-grid XRB initial divu iterations converge. Hopefully it won't break anything else (?). Src/LinearSolvers/F_MG/mg.f90 commit 73f7d020101471e7cb5bd3d18dc1a325dd0bb29d Author: lijewski Date: Wed Jun 25 17:25:51 2008 +0000 some cleanup Src/F_BaseLib/cluster.f90 commit 7007010538cd7bf3435a1f4e71eb8c82dfaa6e17 Author: almgren Date: Wed Jun 25 15:12:05 2008 +0000 Should use bchi instead of bclo in test on whether is BC_INT -- oops! Src/LinearSolvers/F_MG/stencil.f90 commit b53c15ade4793c3da874f53be0f8ce9f30238bb5 Author: almgren Date: Wed Jun 25 05:25:05 2008 +0000 Changed the way we define the stencil at interior boundaries of grids -- this only changes the stencil values at the level of machine precision, but it helps in debugging ... now the stencils will be identical whether there is a single grid or multiple grids covering the same region. Src/LinearSolvers/F_MG/stencil.f90 commit 31cced15781a353d85a0e66ddbd8715487164b77 Author: lijewski Date: Tue Jun 24 22:29:58 2008 +0000 fixed another parallel gotcha -- seems OK but more testing required Src/F_BaseLib/cluster.f90 commit b54676384b38813cb188e0a33fe72ac3c079c41c Author: almgren Date: Tue Jun 24 20:09:01 2008 +0000 Fix ml_edge_restriction to correctly handle the periodic fix. Src/LinearSolvers/F_MG/ml_restriction.f90 commit d2a8c3176c5e80b88a9a6e4f9a40024ad8dbb9e3 Author: almgren Date: Tue Jun 24 17:03:08 2008 +0000 Remove fillpatch and multifab_fill_ghost_cells -- returning to previous approach where these are included in the directory where define_bc_tower lives... Src/F_BaseLib/GPackage.mak commit f33bd47fea847b82e8332c7e5d7693b2130d9bcc Author: almgren Date: Tue Jun 24 05:29:58 2008 +0000 Divide max_grid_size by ref_ratio since we create the new grids at the coarser resolution but we want max_grid_size to hold at the fine resolution. Src/F_BaseLib/regrid.f90 commit 37c916862c61966b3dc2d332a31d39df27ac3a59 Author: almgren Date: Mon Jun 23 23:29:56 2008 +0000 Impose boxarray_maxsize on the new boxarray before making the new multifabs. Src/F_BaseLib/regrid.f90 commit ab0b08e63567acab10babfe490f893fcd2c817d3 Author: almgren Date: Mon Jun 23 22:00:19 2008 +0000 Take max_grid_size as an input into make_new_grids. Src/F_BaseLib/regrid.f90 commit a62fe8c2ee4ab5190a58697ddc28c4ca543ec0e4 Author: lijewski Date: Mon Jun 23 21:54:35 2008 +0000 removed setval_mask() functions - not apparently used anywhere Src/F_BaseLib/fab.f90 Src/F_BaseLib/multifab.f90 commit 5e798361b32ff9d6512df8f76cd43be990829e86 Author: almgren Date: Mon Jun 23 21:42:34 2008 +0000 Added fillpatch.f90 and multifab_fill_ghost_cells.f90 to GPackage.mak since we took them out of varden/GPackage.mak Src/F_BaseLib/GPackage.mak commit a1dffa108bc48d9c8bd45972f9b644c653dcddb7 Author: lijewski Date: Mon Jun 23 21:29:27 2008 +0000 removed potentially troublesome where constructs Src/F_BaseLib/box.f90 commit 9fc44c6ea8e623ce63aca305486c2124faa8d6cf Author: ajnonaka Date: Mon Jun 23 20:07:52 2008 +0000 in function box_grow_i_m, loop over dimensions instead of assuming dim=3 Src/F_BaseLib/box.f90 commit 7adbf45eb1e95c58a350c2566ccb3a97f2dd399b Author: ajnonaka Date: Mon Jun 23 19:41:05 2008 +0000 loop over l(i) instead of using where construct Src/F_BaseLib/box.f90 commit 901802abe9558533736f07dc1c72995e8a904784 Author: lijewski Date: Sun Jun 22 18:02:27 2008 +0000 *** empty log message *** Src/F_BaseLib/cluster.f90 commit 50990ab23dc1204f4d0b1b7e731c9a5f88ea654d Author: lijewski Date: Fri Jun 20 16:34:52 2008 +0000 clustering now works in parallel Src/F_BaseLib/cluster.f90 commit c84e14abf774563699f944eb214ffb85d8f17553 Author: lijewski Date: Fri Jun 20 16:33:50 2008 +0000 changed verbosity defaults Src/F_BaseLib/knapsack.f90 commit dbe8d247e12318dc4938fd6fa474aa88bb861f14 Author: lijewski Date: Mon Jun 16 20:50:56 2008 +0000 *** empty log message *** Tools/F_mk/GMakedefs.mak commit 3bf2525f291e3ce77ed228aa00a6f02c7382142c Author: 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 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 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 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 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 Date: Mon Jun 9 23:50:40 2008 +0000 fix a model file Tools/C_util/regtests/Maestro-tests.ini commit e692b0458101d477949c99dfb08bb1bb121c50de Author: almgren Date: Mon Jun 9 17:40:02 2008 +0000 1) Cleaned up the crse/fine resid routine. 2) We now include fine fluxes on periodic boundaries -- this seems to work for now. Src/LinearSolvers/F_MG/nodal_divu.f90 commit fb80ba863a94656ed8e8b26c297d61ed01386a64 Author: mzingale Date: Sun Jun 8 22:30:57 2008 +0000 update to reflect changes to the spherical problems Tools/C_util/regtests/Maestro-tests.ini commit f79d558559bd400fb348a88fc6d06d6cb896734a Author: lijewski Date: Tue Jun 3 23:45:09 2008 +0000 some simplification of VisMF::Write Src/C_BaseLib/VisMF.cpp commit 07e15d44487a86c182d2ca089ea9237c8b883f91 Author: aaspden Date: Tue Jun 3 20:09:14 2008 +0000 Added a Barrier to prevent running out of PER_PROC message packets (happened on Jagwar) Src/C_BaseLib/VisMF.cpp commit b64099265853ec4bed4cb95b23c11d7909b3930b Author: almgren Date: Tue Jun 3 19:44:30 2008 +0000 Change mla and la from intent "inout" to intent "in" Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_solve.f90 commit da858ea952627d65565ba01cda0ff472e2944385 Author: 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 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 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 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 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 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 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 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 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 Date: Fri May 9 17:28:58 2008 +0000 Remove unneeded variables. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 8178539b07346703ed87ff6e007a717e609ad88c Author: almgren Date: Fri May 9 17:26:17 2008 +0000 Small code cleanup. Src/LinearSolvers/F_MG/stencil.f90 commit 571e96ee03bae9456afe06faed203000c44ff2f8 Author: almgren Date: Wed May 7 20:20:10 2008 +0000 Removed unused variables. Src/C_BaseLib/COORDSYS_1D.F Src/F_BaseLib/layout.f90 commit 521c1d3e23aea836945331bf49877de5953ff6b4 Author: almgren Date: Wed May 7 20:19:34 2008 +0000 Removed unneeded "lenx". Src/C_AMRLib/FLUXREG_1D.F commit a0a4993c63fa04a890111a526dad8c57069eb0f9 Author: almgren Date: Fri Apr 25 21:06:54 2008 +0000 Changed the length in BoxLib::Concatenate from 4 to 5 -- this will make pltfiles and chkfiles now use 5 spaces instead of 4 for the step number. Src/C_BaseLib/Utility.cpp commit 4d1adefb266489029795c15aee83ec149daca4b6 Author: almgren Date: Fri Apr 25 20:45:49 2008 +0000 Can't use 0.d0 Src/C_BaseLib/MultiFab.cpp commit 223014f0386233cf38ae0b5c8058424635fdc3fb Author: almgren Date: Fri Apr 25 19:30:49 2008 +0000 Added a norm2 function to MultiFab (analogous to norm0). Doesn't use ghost cells. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 875ae127bddc67ff5940d9a65f708b40ce713b5f Author: 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 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 Date: Thu Apr 17 23:10:54 2008 +0000 Gimantis update Tools/C_mk/Make.defs commit f0e5708f89b5601064b54f7f742176407115f6db Author: mzingale Date: Tue Apr 15 14:43:23 2008 +0000 Castro uses a different # of digits in the plotfile name Tools/C_util/regtests/test.py commit 4ec073a566408de1421d699db6fe0a767a4ca860 Author: mzingale Date: Mon Apr 14 21:07:09 2008 +0000 get the Castro test suite back up to date with the latest changes Tools/C_util/regtests/Castro-tests.ini commit d92c901531c1d46f8237d1933b1f240cb79a67fc Author: mzingale Date: Mon Apr 14 21:04:33 2008 +0000 don't generate Parallel Changelog for an fParallel run remove useFParallel for Parallel builds -- it is always needed now. Tools/C_util/regtests/test.py commit 1075a9f3dd51a04360f998a9b8d79161f9ee44e4 Author: almgren Date: Fri Apr 11 20:30:10 2008 +0000 Another fix of sign error on lo side in stencil_all_flux_3d. Src/LinearSolvers/F_MG/stencil.f90 commit 1720acacb6752504e7d4d702f300814c0d21a6e0 Author: almgren Date: Fri Apr 11 20:28:32 2008 +0000 Fill sign error for lo side in stencil_all_flux_3d. Src/LinearSolvers/F_MG/stencil.f90 commit a149483935db93818944a2cb50b79ef2c3aa5c11 Author: 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 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 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 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 Date: Wed Apr 2 20:39:43 2008 +0000 modest touch-up to norm0() Src/C_BaseLib/MultiFab.cpp commit de0f714f34d91ddb6127011ff178c693e7e7dec6 Author: almgren Date: Wed Apr 2 19:21:23 2008 +0000 Added norm0 function which takes the inf norm of a multifab using no ghost cells. Optional comp argument (defaults to zero). Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 24e40c47a947bbf12c0276c3fc2b6e7d211cc847 Author: almgren Date: Tue Apr 1 20:02:11 2008 +0000 1) Move the functions which call the mt19937ar random stuff from box_util.f90 into mt19937ar.f90 2) Remove mt19937ar.f90 from GPackage.mak and NPackage.mak so that they are not included in general. They can still be included as needed in the boxlib/test directory (the only place I can found where the make_random_box routines are actually called) Src/F_BaseLib/GPackage.mak Src/F_BaseLib/NPackage.mak Src/F_BaseLib/box_util.f90 Src/F_BaseLib/mt19937ar.f90 commit 3c2fed79cf9dd04e04bd516620272aaec5f9a53b Author: almgren Date: Mon Mar 31 20:39:13 2008 +0000 Changes by Candace in making varden truly adaptive. Src/F_BaseLib/fabio.f90 Src/F_BaseLib/regrid.f90 commit 4ae48b41428784f54870ad15262f910986a97adf Author: vince Date: Fri Mar 21 22:24:16 2008 +0000 i/o float fix. Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp commit 2bf3deaeec624e2172488a5e3273a1c2a32a7c09 Author: vince Date: Fri Mar 21 22:07:37 2008 +0000 i/o fix. Src/C_BaseLib/RealBox.cpp commit 21027fb55efcd7cdc083eba2b073dbfe3961d5f4 Author: almgren Date: Tue Mar 18 19:54:58 2008 +0000 Candace's changes to regrid -- buffer subroutine not complete, but this does multiple levels. Src/F_BaseLib/regrid.f90 commit be0ab32a17d8255c5d4a6329998a64d45a7ebbfb Author: 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 Date: Sat Mar 8 00:56:53 2008 +0000 added mpi link for gimantis Tools/F_mk/GMakeMPI.mak commit 8cd11b1d05c26ca1dbad890e096922172aada956 Author: mzingale Date: Tue Mar 4 20:03:12 2008 +0000 fix jaguar compiling -- now it handles modules correctly. Tools/F_mk/GMakeMPI.mak commit 2146ec424b5bf42bc540888091ab75b0457ddeab Author: lijewski Date: Tue Mar 4 18:41:19 2008 +0000 removed some profilers Src/F_BaseLib/multifab.f90 commit cae88ed3c1ce767fca48f2ced0392c3906c1cfa6 Author: ajnonaka Date: Mon Mar 3 22:07:23 2008 +0000 fixed a comment Src/LinearSolvers/F_MG/ml_nd.f90 commit 90cfd64598321a73cea95c032295c1fedaa30b2c Author: mzingale Date: Mon Mar 3 20:51:19 2008 +0000 update homer to use MPICH2 Tools/C_mk/Make.Linux Tools/C_mk/Make.mpi commit 27bdbb22ad9cb235a918bffbbd93ab9fb77f13d6 Author: almgren Date: Mon Mar 3 18:03:07 2008 +0000 Remove print statement. Src/LinearSolvers/F_MG/nodal_divu.f90 commit f9308ace521793abc4ab32f1bc90050c5fcf20ee Author: jbb Date: Mon Mar 3 17:38:15 2008 +0000 Add case for mothra. Tools/F_mk/GMakeMPI.mak commit a81132814c99a6310bb76d97e289f259600a060a Author: 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 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 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 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 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 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 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 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 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 Date: Thu Feb 21 21:06:52 2008 +0000 works for jaguar now Tools/F_mk/GMakeMPI.mak commit f89ec7c26876e68822b86798c3100734a0e62d0b Author: 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 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 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 Date: Wed Feb 13 21:24:57 2008 +0000 more gimantis additions. Tools/C_mk/Make.defs commit 40c3570a6b2105cdf637fb9e7ef5b5de60fa688c Author: vince Date: Mon Feb 11 23:54:22 2008 +0000 additions for gimantis. Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 3c17ab3146a26d8a0162c2ba9f8da6292233e596 Author: marc Date: Fri Feb 8 20:56:10 2008 +0000 *** empty log message *** Tools/C_mk/Make.defs commit 7b982b7c14872b00c184d663c5bedcb49f44e46e Author: jbb Date: Fri Feb 8 20:22:31 2008 +0000 make mothra work Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 0685351c868453936970e03fb491dc685da65acb Author: lijewski Date: Fri Feb 8 18:15:11 2008 +0000 added some implicit none statements Src/C_BaseLib/COORDSYS_2D.F Src/C_BaseLib/COORDSYS_3D.F commit c19691b1b16a5cbcb14804cfcddeae1584b86e15 Author: lijewski Date: Fri Feb 8 18:08:01 2008 +0000 added some implicit none statements Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/CG_2D.F Src/LinearSolvers/C_CellMG/CG_3D.F Src/LinearSolvers/C_CellMG/LO_2D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LP_2D.F Src/LinearSolvers/C_CellMG/LP_3D.F Src/LinearSolvers/C_CellMG/MG_2D.F Src/LinearSolvers/C_CellMG/MG_3D.F commit 18e3d0d6fcf82a5b3e962dba297c86ddc364f8d8 Author: lijewski Date: Fri Feb 8 17:48:46 2008 +0000 added some implicit none statements Src/C_AMRLib/FILCC_1D.F Src/C_AMRLib/FILCC_2D.F Src/C_AMRLib/FILCC_3D.F Src/C_AMRLib/FLUXREG_1D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/MAKESLICE_3D.F commit 906e5b19700e3c3688416d081016d042b490e2a6 Author: lijewski Date: Thu Feb 7 23:48:08 2008 +0000 some cleanup Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F commit ddd8b331ebdc6b2b55c1cd1f57690390e8bdfaa6 Author: lijewski Date: Tue Feb 5 21:28:18 2008 +0000 make explicit that we use O2 not Ofast with PathScale Tools/F_mk/GMakedefs.mak commit decfd04f09a11335fd3ea9e96b59f8c1985f0a02 Author: lijewski Date: Tue Feb 5 21:25:50 2008 +0000 use -O2 -ipa with PathScale to be consistent with stuff in fParallel Tools/C_mk/Make.Linux commit fba3c4a450447864a660d6989ab7dd27a91eeea0 Author: 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 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 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 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 Date: Thu Jan 31 18:58:36 2008 +0000 += instead of = Tools/C_mk/Make.Linux commit 843a8e3c2a57eabd44bac6fd0bc2b14347d51a08 Author: marc Date: Thu Jan 31 18:50:17 2008 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/Make.package commit c40af9d17590bc866ef4a429a7b29aee290b35ff Author: lijewski Date: Thu Jan 31 18:31:02 2008 +0000 more IO wraps Src/F_BaseLib/multifab.f90 commit 6d4e2872fb7ff881ad1ef9682249f0dc60d4e65a Author: lijewski Date: Thu Jan 31 18:25:46 2008 +0000 parallel_IOProcessor() wraps in print() Src/F_BaseLib/multifab.f90 commit 0f60c9785f63968b85ba259c5fac50e525906234 Author: marc Date: Thu Jan 31 18:20:54 2008 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit 21b3f84f095bd4adaaf37503b43dc2d2e576a8a7 Author: 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 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 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 Date: Thu Jan 24 23:54:18 2008 +0000 PathScale bug fix Tools/C_mk/Make.Linux commit b1c77f2432b44dea21d77092f3db3b71259af00f Author: mzingale Date: Thu Jan 24 22:07:34 2008 +0000 fix the permissions at the end of the suite run so other users can see the files Tools/C_util/regtests/test.py commit d73d3a8e12ef3b7902094f45de474fccad2304fb Author: mzingale Date: Thu Jan 24 19:42:45 2008 +0000 update the grid file for test_smallscale Tools/C_util/regtests/Maestro-tests.ini commit 533d0280c5c86f2ec0df3b7e6c144b98bbcd1304 Author: lijewski Date: Thu Jan 24 17:13:30 2008 +0000 reverting out some changes -- not particularly useful Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 44d33cb58ccd6511066bfb2ddf477030c17149dc Author: lijewski Date: Wed Jan 23 23:33:42 2008 +0000 got rid of gs_rb_smoother_3d_transpose() Src/LinearSolvers/F_MG/mg_smoother.f90 commit e1bb6ffc5a953e013570403d2d45cf32a5232656 Author: lijewski Date: Wed Jan 23 22:10:49 2008 +0000 unrolled 3d cross stencil for modest speed improvement Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit ae4f9c8cdcd391c417dbda2c3078882b5836164c Author: 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 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 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 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 Date: Sun Jan 20 21:46:03 2008 +0000 add compilation rules for homer Tools/F_mk/GMakedefs.mak commit 69af824cbdfe7ea24ec43b6efabe6466486cd6ae Author: lijewski Date: Fri Jan 18 21:18:02 2008 +0000 now have minimize communication costs ability in knapsack Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/layout.f90 commit c2c4b2b9988c8926fe051b48b0d11e19684739af Author: mzingale Date: Wed Jan 16 21:18:47 2008 +0000 turn on -mp for Intel, and turn on warnings for Intel 10 in debug mode Tools/F_mk/GMakedefs.mak commit 9fffcf1dfde6febb6474a7ea58a8a6aceff3ed8e Author: 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Fri Jan 11 22:52:28 2008 +0000 *** empty log message *** Src/F_BaseLib/fab.f90 commit 6f276a40c651ccf23df4d2c8d9f5b1b7549a661c Author: lijewski Date: Fri Jan 11 22:30:06 2008 +0000 use least_used_cpus() when assigning boxes to CPUs Src/F_BaseLib/layout.f90 commit 8e37b6081cc4ff106dde8f4a4f730d99225ab55f Author: lijewski Date: Fri Jan 11 22:29:36 2008 +0000 added least_used_cpus() Src/F_BaseLib/fab.f90 commit 4bebbd7ae67e30c1095fc92f5ae2cd331c2dd541 Author: lijewski Date: Fri Jan 11 18:23:57 2008 +0000 added MPI_Allgather functionality Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit 1c1b24fe29a6e30e4e14333427b4c22240061fa0 Author: mzingale Date: Tue Jan 8 21:45:23 2008 +0000 make the restart work again (i.e. we need to keep the checkpoint files around) Tools/C_util/regtests/test.py commit fa1518bd7206be6894ba97321d80692a4376250f Author: mzingale Date: Mon Jan 7 21:13:27 2008 +0000 enable bounds checking for gfortran Tools/F_mk/GMakedefs.mak commit 000be82c45646cc79124fed04fba71c74d8009e3 Author: lijewski Date: Thu Jan 3 23:44:21 2008 +0000 fabs no longer have an ng component Src/LinearSolvers/F_MG/stencil.f90 commit 5a6e671c4b40fe2f9a381fdf650261e875d9e730 Author: lijewski Date: Thu Jan 3 23:43:59 2008 +0000 Removed multifab_debug_fill(). Src/F_BaseLib/multifab.f90 commit e4ebb2e4cb3369644b030ae137596b2b0b72c1fa Author: lijewski Date: Thu Jan 3 23:43:37 2008 +0000 Removed the "ng" component of fabs. Removed the set_border_val() routines & fab_debug_fill(). Src/F_BaseLib/fab.f90 commit 9c78de614b5918cf5466798a777725d2e62ea4fa Author: lijewski Date: Thu Jan 3 23:39:22 2008 +0000 removed multifab_debug_fill() call Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/t_main.f90 commit 1a595143b4ef41f9796fae7ccca3d117f60caabd Author: lijewski Date: Thu Jan 3 06:11:53 2008 +0000 *** empty log message *** Src/F_BaseLib/fab.f90 commit 1bfc5fcfc324bf900b560df821e7c3588131965b Author: 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 Date: Tue Jan 1 21:04:37 2008 +0000 fixed more parallel bugs Src/LinearSolvers/F_MG/itsol.f90 commit b75a8fc72188ac09f5aba2878b59684d213290fe Author: lijewski Date: Tue Jan 1 17:15:53 2008 +0000 added aveassoc stuff Src/F_BaseLib/layout.f90 commit 2d35dd6b75df6d4c368f58aa12df0c052fdf19de Author: lijewski Date: Tue Jan 1 16:28:45 2008 +0000 added sort_i.f90 Src/F_BaseLib/GPackage.mak commit fd6eabdef1316399760e93ad0c84d027c9f8e0a5 Author: mzingale Date: Mon Dec 31 15:44:18 2007 +0000 switch to realclean instead of clean don't output checkpoint files (to save space) Tools/C_util/regtests/test.py commit 90b08a5c5b9c9fd45d6b2cc6bb86a8aad4ae4306 Author: 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 Date: Wed Dec 26 20:32:02 2007 +0000 more mem_stat refinement Src/F_BaseLib/fab.f90 commit 2e36895a1728131ca5d3f268f406562b0c864bb1 Author: lijewski Date: Wed Dec 26 19:49:18 2007 +0000 *** empty log message *** Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit e0284c83bc9624db57a6ed8d767cbc9bf7a79135 Author: lijewski Date: Wed Dec 26 19:32:31 2007 +0000 more work on mem_stats for cached data Src/F_BaseLib/layout.f90 commit 893e7415daadeaf259dd7e577ccb68ebae47d551 Author: lijewski Date: Wed Dec 26 02:25:05 2007 +0000 more mem_stats stuff Src/F_BaseLib/layout.f90 commit 46787417ee2114ec0bab0f506c30a69bbbcea681 Author: lijewski Date: Wed Dec 26 01:05:31 2007 +0000 now calculates min/max cnt & min/max alloc across CPUs Src/F_BaseLib/bl_mem_stat.f90 commit 80f65a0b11d567234d0d9e34b8adfeba51039656 Author: almgren Date: Wed Dec 26 00:50:36 2007 +0000 Need bl_constants_module now that we're using "ZERO" Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit 4b3ef2f0807997b4b5eec42460783ceacb29a0ab Author: lijewski Date: Wed Dec 26 00:19:25 2007 +0000 mem_stats was NOT taking number of components into account Src/F_BaseLib/fab.f90 Src/F_BaseLib/multifab.f90 commit 071dcfc581c30b8d7916098926ebbc708f629a3c Author: lijewski Date: Tue Dec 25 20:40:27 2007 +0000 added flags to put modules in correct place for PGI Tools/F_mk/GMakeMPI.mak commit 80009724202022339b20cf48a328025ddaacbb5f Author: lijewski Date: Mon Dec 24 20:36:34 2007 +0000 run boxarray_maxsize() on boxarray stored in fgassoc Src/F_BaseLib/layout.f90 commit cdd0b938a1c1bd701c3c2f61e7b6c11454cd20d1 Author: lijewski Date: Mon Dec 24 18:09:48 2007 +0000 removed unimplemented routine Src/F_BaseLib/list_box.f90 commit 998d2cbe913d52b46f0afa16c4e7c57d0e495064 Author: 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 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 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 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 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 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 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 Date: Wed Dec 19 20:42:10 2007 +0000 needed bl_constants_module Src/LinearSolvers/F_MG/nodal_newu.f90 commit d107891b92d4ee0f338a1272d8512a98ed9ca29a Author: lijewski Date: Wed Dec 19 20:38:27 2007 +0000 ml_norm_inf() and ml_norm_l2() are now in ml_util_module Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_util.f90 commit 44c68d4afdea8d28b93214c549d49e05b2193511 Author: lijewski Date: Wed Dec 19 17:20:51 2007 +0000 mods to compile with Intel 9.0 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/layout.f90 commit 9b494b50ff53258db67c21223e27cfbaea6abddb Author: lijewski Date: Wed Dec 19 06:11:09 2007 +0000 some cleanup of use statements Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 Src/LinearSolvers/F_MG/nodal_newu.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 Src/LinearSolvers/F_MG/stencil.f90 commit ad67d7bc8ed11a736a6ca4a5dddffa9d2426fa82 Author: lijewski Date: Wed Dec 19 04:47:27 2007 +0000 more careful with use statements Src/F_BaseLib/bl_error.f90 Src/F_BaseLib/bl_mem_stat.f90 Src/F_BaseLib/bl_parmparse.f90 Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/bl_stream.f90 Src/F_BaseLib/bl_string.f90 Src/F_BaseLib/bl_timer.f90 Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/box.f90 Src/F_BaseLib/box_util.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/cluster.f90 Src/F_BaseLib/cluster_2d.f90 Src/F_BaseLib/fab.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/list_box.f90 Src/F_BaseLib/ml_boxarray.f90 Src/F_BaseLib/ml_layout.f90 Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/mt19937ar.f90 Src/F_BaseLib/multifab.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 Src/F_BaseLib/plotfile.f90 Src/F_BaseLib/ppm_util.f90 Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/t_bx.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/t_bx.f90 Tests/F_BaseLib/t_main.f90 commit 64e75777491acdd6ea72a018700a5aa8ed90ff2b Author: lijewski Date: Wed Dec 19 02:54:45 2007 +0000 some franklin/PathScale mods Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit 12e76f3e5070a58086b9737c0f7a7bb53e97c11e Author: lijewski Date: Wed Dec 19 02:52:19 2007 +0000 mods to compile on franklin with PathScale Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 commit de2878967470594fbf20a2471b9ca349c322ddf1 Author: lijewski Date: Tue Dec 18 17:40:05 2007 +0000 *** empty log message *** Tools/F_mk/GMakedefs.mak commit fe0cba25695baad37787885cea8e9c19db526406 Author: lijewski Date: Tue Dec 18 17:24:37 2007 +0000 *** empty log message *** Tools/F_mk/GMakedefs.mak commit 6b790f13e2a846bb1aff728d37ca4feb520a1a14 Author: 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 Date: Mon Dec 17 23:10:53 2007 +0000 fixed bug in boxarray_same_q() Src/F_BaseLib/boxarray.f90 commit b86096ce2e424b8550df295b8739729d0c912073 Author: lijewski Date: Mon Dec 17 21:40:00 2007 +0000 used new fgassoc stuff from layout Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit fb90da12211d28cee4916ad2e2d840f3c203136f Author: lijewski Date: Mon Dec 17 21:39:43 2007 +0000 added fgassoc to cache ghost cell boxarray used by mf_fill_ghost_cells() Src/F_BaseLib/layout.f90 commit 1686d5da257d4b579fc9aa9091a55d7f8415c2e5 Author: lijewski Date: Mon Dec 17 21:39:11 2007 +0000 more cleanup Src/F_BaseLib/boxarray.f90 commit 3ffb1869dba7657512087ad20aa8547dd3866c66 Author: lijewski Date: Mon Dec 17 19:22:07 2007 +0000 came up with simpler way to remove overlap Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit dadb70fcf9c75dfd1aeebdff800e004aa57bceb8 Author: lijewski Date: Mon Dec 17 19:11:40 2007 +0000 removed some unused stuff Src/F_BaseLib/boxarray.f90 commit 57ff637c2cc18408f2e85027ae5d162ea973100b Author: lijewski Date: Mon Dec 17 18:24:07 2007 +0000 cleanup & bug fix in boxarray_add_clean_boxes() Src/F_BaseLib/boxarray.f90 commit 67a0cc903eb983a504538bcc38742ee04af4444d Author: lijewski Date: Mon Dec 17 18:23:41 2007 +0000 remove overlap in internal ghost multifab Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 8951ab4510b34a230685af4e1f08149bdacfbed9 Author: ajnonaka Date: Fri Dec 14 21:13:10 2007 +0000 a couple minor 3d bugs fixed. cslope_lo and hi need to have 3 components a reference to fvcy has been changed to fvcz for a dm=3 case Src/F_BaseLib/fillpatch.f90 commit 20e59719b02c6dd65cd4b048bbdf5a1134b127ba Author: ajnonaka Date: Fri Dec 14 20:55:21 2007 +0000 inverted the meaning of lim_slope so lim_slope .eq. .true. means use limited slopes. Change the behavior of the code by leaving the default value as true. Added lim_slope_input and lin_limit_input as optional input arguments to fillpatch to change the behavior Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 06333597977a55d064ba4d8918c4ed58977e7b93 Author: ajnonaka Date: Fri Dec 14 20:33:46 2007 +0000 fillpatch now takes icomp_fine and icomp_coarse as inputs instead of just icomp. The old way, which used just icomp, didn't work if the coarse and fine components didn't have the same index Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 7ff38b6455e3bc298c5a8fbd9dcc9b458ba3f0dd Author: lijewski Date: Thu Dec 13 18:24:23 2007 +0000 call bl_error when proc trees are NOT identical Src/F_BaseLib/bl_prof.f90 commit fcf29f72afc8c6e311729bd07f1500e7a8ee12f3 Author: lijewski Date: Thu Dec 13 18:23:58 2007 +0000 removed some profilers Src/F_BaseLib/interp.f90 commit c0e74a010f23689eca87b57e7cd0fd0686432448 Author: lijewski Date: Wed Dec 12 20:28:07 2007 +0000 added TODO note Src/LinearSolvers/F_MG/nodal_divu.f90 commit f097679c4f88a96e081e1139061af8056196c7be Author: lijewski Date: Wed Dec 12 00:12:03 2007 +0000 use box_intersector stuff in periodic_add_copy() Src/LinearSolvers/F_MG/ml_restriction.f90 commit 525ec2ecc55c212435d45d89b4f1502687faa8d4 Author: lijewski Date: Tue Dec 11 23:47:19 2007 +0000 now use box_intersector in ml_crse_divu_contrib() Src/LinearSolvers/F_MG/nodal_divu.f90 commit f3d058be8132376ee68bd97c9a02a69862ecb72d Author: 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 Date: Tue Dec 11 22:21:30 2007 +0000 added needed type casts Src/F_BaseLib/mt19937ar.f90 commit f5c4d826dc0f9c6065ad823eb9b63c237e23bd3f Author: lijewski Date: Tue Dec 11 22:21:05 2007 +0000 some type cleanup Src/F_BaseLib/ml_boxarray.f90 commit bbe0967370ef2bf209a4c8fbd686981b3d0aeccd Author: lijewski Date: Tue Dec 11 22:20:44 2007 +0000 some cleanup Src/F_BaseLib/layout.f90 commit 338b6b79cf2865ae0072e0c4416101d54e35b4f2 Author: lijewski Date: Tue Dec 11 22:20:26 2007 +0000 removed unused declaration Src/F_BaseLib/fillpatch.f90 commit df4f2d143dc9b1aa5024894c0501a6e75a4223e8 Author: lijewski Date: Tue Dec 11 22:19:38 2007 +0000 fixed type issue Src/F_BaseLib/bl_timer.f90 Src/F_BaseLib/box_util.f90 Src/F_BaseLib/cluster.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 commit a23802ab7a6c696e5b227f861cea6e4e54425167 Author: lijewski Date: Tue Dec 11 21:19:28 2007 +0000 check for overflow in box_volume; no longer elemental Src/F_BaseLib/box.f90 commit 3215fc2964c1f403a802400d0615cb5430d676ac Author: lijewski Date: Tue Dec 11 18:52:48 2007 +0000 some cleanup Src/F_BaseLib/box.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/layout.f90 commit 49ef743c84add4bace62c43f8f9467568420ef2d Author: lijewski Date: Tue Dec 11 18:52:34 2007 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg.f90 commit 5327bde909bb522a53120637b55a0c2fb7b021d7 Author: lijewski Date: Tue Dec 11 01:13:28 2007 +0000 added some bl_prof timers Src/F_BaseLib/knapsack.f90 commit 4ed60bb6f7e28eb364e60abf8ef93e8cee2a07e3 Author: lijewski Date: Tue Dec 11 01:01:23 2007 +0000 added some bl_prof timers Src/F_BaseLib/interp.f90 commit 3749ddebe90f1cf1d21cf9eb3a5161ec607f694d Author: lijewski Date: Tue Dec 11 00:42:19 2007 +0000 added some bl_prof timers Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit d901ebb3a9b7570e04bd787592225bb413736b02 Author: lijewski Date: Mon Dec 10 23:56:18 2007 +0000 added some profile timers Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 commit f4b27c609250f2382eb12bed5770671bb68b9d3d Author: 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 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 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 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 Date: Sun Dec 9 00:38:44 2007 +0000 some cleanup Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 893c39c2be080a92b265ec3f55f4947c5f73d83c Author: almgren Date: Sat Dec 8 00:49:01 2007 +0000 Added multifab_fill_boundary(crse) after restriction. Src/LinearSolvers/F_MG/ml_restriction.f90 commit b3fcf3fe4c37b5db8c9d718da1148895084d8d9e Author: almgren Date: Fri Dec 7 21:28:56 2007 +0000 Put prototype regridding algorithm here. Src/F_BaseLib/regrid.f90 commit ed3a447db19364c8335b7aa90e65f0f8442e89d9 Author: 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 Date: Fri Dec 7 19:58:14 2007 +0000 mg test commit Src/LinearSolvers/F_MG/GPackage.mak commit d48121e84c4d74c3e9f238825988c72f667a4cb9 Author: lijewski Date: Fri Dec 7 18:00:25 2007 +0000 added parallel check in ml_crse_divu_contrib() Src/LinearSolvers/F_MG/nodal_divu.f90 commit b4e12ae6910339907be15138f5b6af97f8d6f3ad Author: almgren Date: Fri Dec 7 17:39:53 2007 +0000 Need to add multifab_fill_boundary for full_soln after we create it. Src/LinearSolvers/F_MG/ml_cc.f90 commit 40f7713210a466896c21d440e50dd1d14928230a Author: almgren Date: Thu Dec 6 21:57:47 2007 +0000 Separated out crse and fine parts of ml_interface_stencil -- only tested in 2d. Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 0284ca40c17e18e176ad6cd9b93da3ec7a68d96c Author: almgren Date: Thu Dec 6 21:41:36 2007 +0000 Needed to add multifab_fill_boundary for multilevel solve to get right convergence -- I think it's only needed for periodic but not 100% sure. Src/LinearSolvers/F_MG/ml_cc.f90 commit 42dbd95c142060e6e23eca8591f9b99b318f893c Author: almgren Date: Thu Dec 6 20:39:40 2007 +0000 formatting cleanup. Src/LinearSolvers/F_MG/mg.f90 commit 401bc162e009192b3884edfe6bab50b8b0753f21 Author: almgren Date: Thu Dec 6 20:39:25 2007 +0000 Removed commented line. Src/LinearSolvers/F_MG/ml_cc.f90 commit db2c11ac1cd247eb8128a10ec57ed4b905630f82 Author: almgren Date: Thu Dec 6 20:38:59 2007 +0000 Fix ml_interface for the periodic case. Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 0afddac083f560c24f07572cacac8ac60b7e4909 Author: 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 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 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 Date: Wed Dec 5 19:00:27 2007 +0000 Removed commented line. Src/F_BaseLib/layout.f90 commit 45e79a6fdc5fd3ba6dd4a9dd522c6372afad5ad4 Author: almgren Date: Wed Dec 5 18:36:21 2007 +0000 Remove ng from bndry_reg_copy calls. Src/F_BaseLib/bndry_reg.f90 commit 67a9bf6b64b9a7478f3df8493975c13f932b6ecb Author: lijewski Date: Wed Dec 5 02:23:07 2007 +0000 more work on parallel-aware more efficient version Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 01f671d6430d5da043a1925b214164ce841b3685 Author: lijewski Date: Wed Dec 5 01:41:59 2007 +0000 special case when can fill periodic ghost cells from given fine data Src/F_BaseLib/fillpatch.f90 commit 4c4e110c847bb8a970f33383ef818262f8923415 Author: lijewski Date: Tue Dec 4 23:48:40 2007 +0000 some cleanup Src/F_BaseLib/fillpatch.f90 commit 2b334505a45f882d3662727fb6e68f140b14e920 Author: 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 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 Date: Tue Dec 4 22:26:35 2007 +0000 start on making fillpatch periodically-aware Src/F_BaseLib/fillpatch.f90 commit 016624ef7ac8c370491af091e9491d3773e03dc2 Author: lijewski Date: Tue Dec 4 00:33:39 2007 +0000 more error checking Src/F_BaseLib/fillpatch.f90 commit 6f228ca90ca2e1fecc5b0b801de0d03206b5539e Author: lijewski Date: Tue Dec 4 00:29:26 2007 +0000 start on more efficient parallel version -- more to do ... Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit bb0bd7beb2cef018c0fc5e03eccd7d09ced1afdb Author: lijewski Date: Tue Dec 4 00:27:35 2007 +0000 modest fixes -- still periodic issues Src/F_BaseLib/fillpatch.f90 commit 99a521c4d62addad5d7b99d83914caf166ca1a61 Author: mzingale Date: Mon Dec 3 22:27:05 2007 +0000 add a "/" to the end of the paths as required Tools/C_util/regtests/test.py commit 1e8b22bad344c2503a2e5ca55fa3badb72b2e8f5 Author: lijewski Date: Mon Dec 3 22:18:48 2007 +0000 modest bug fix Src/F_BaseLib/fillpatch.f90 commit d3f9b2c7eff7352cbf6944eccbc67973d5a3edda Author: lijewski Date: Mon Dec 3 17:37:30 2007 +0000 mods from Mike Singer Tools/C_mk/Make.mpi commit c33d08a3aefaf3a511b65cf2a6b0334a2c6b7a1f Author: lijewski Date: Mon Dec 3 17:28:39 2007 +0000 mods from Mike Singer Src/C_BoundaryLib/LO_BCTYPES.H commit 61954f66502fa0c12e398d9a8c9fdefa8bedc5ec Author: lijewski Date: Sun Dec 2 00:49:44 2007 +0000 layout_get_box_intersector() now call init_box_hash_bin() automagically if needed Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/layout.f90 commit 725b1ba43522f365e15331e18d1bfc8e373870b9 Author: lijewski Date: Sat Dec 1 00:21:44 2007 +0000 little cleanup Src/F_BaseLib/fillpatch.f90 commit 5a4d113c149ac6dc1aaa653e52671ae375addd0c Author: almgren Date: Fri Nov 30 22:52:03 2007 +0000 Don't include fillpatch and multifab_fill_ghost_cells in the make stuff because they depend on stuff in the varden/MAESTRO directories. Src/F_BaseLib/GPackage.mak Src/F_BaseLib/NPackage.mak commit 87dac27cf95bd9efa75ccb6e5cb039ca4a0fe1ef Author: almgren Date: Fri Nov 30 22:14:18 2007 +0000 Add fillpatch and multifab_fill_ghost_cells to GPackage and NPackage. Src/F_BaseLib/GPackage.mak Src/F_BaseLib/NPackage.mak commit 1c116d9a8afafe61f4845dae8b1fa94c7fec3726 Author: almgren Date: Fri Nov 30 22:12:59 2007 +0000 Move fillpatch and multifab_fill_ghost_cells from varden/MAESTRO into boxlib. Src/F_BaseLib/fillpatch.f90 Src/F_BaseLib/multifab_fill_ghost_cells.f90 commit 4a73c494e2d33f5dc353b02821b5c1e401416654 Author: almgren Date: Fri Nov 30 22:08:59 2007 +0000 Fixed bug in lin_cc_interp_2d -- was using xok(1) instead of xok(2) for yslope. Src/F_BaseLib/interp.f90 commit 69be5a43d8840b54e74271c3f673407bdd8bb8ed Author: mzingale Date: Sun Nov 25 15:34:32 2007 +0000 new main webpage -- now it lists each test up front in separate columns Tools/C_util/regtests/test.py commit d03247ad46cd393740c1c777d6f633d9106dd565 Author: mzingale Date: Mon Nov 19 03:05:24 2007 +0000 add a --note option and also fix a crash when making benchmarks and we have a restart test Tools/C_util/regtests/test.py commit 04441420aa37339581d32821e9d994f467fff04e Author: ajnonaka Date: Sun Nov 18 06:08:35 2007 +0000 created ml_edge_restriction_c. ml_edge_restriction calls ml_edge_restriction_c, which loops over all components in the coarse multifab by default. I believe the code only restricted the 1st component of coarse before. Src/LinearSolvers/F_MG/ml_restriction.f90 commit d62560be857affd7d607b16727e260c965e8ef50 Author: mzingale Date: Sun Nov 18 02:57:06 2007 +0000 add the ability to do restart tests. Make the script behave gracefully when we fail compiling. Tools/C_util/regtests/Maestro-tests.ini Tools/C_util/regtests/test.py commit 2511da0a0a45821882398cff325166becf0ad68d Author: ajnonaka Date: Sat Nov 17 01:53:49 2007 +0000 cleaned up code for easier reading Src/LinearSolvers/F_MG/ml_restriction.f90 commit 3c366d29d301ab3356f29c5f542019a12613c156 Author: lijewski Date: Wed Nov 14 22:20:53 2007 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit 285097eb8da5ccd2f536003808eb28c617a97c04 Author: lijewski Date: Wed Nov 14 21:04:25 2007 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit 6b826b61cde333a457d0b64d4d0f81cec0ab50d1 Author: lijewski Date: Wed Nov 14 20:33:03 2007 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit 4f544fb2e733a09eca52bb171d123a1b69a5e97c Author: lijewski Date: Wed Nov 14 18:42:15 2007 +0000 *** empty log message *** Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit 64e33b0da48482aa9719c02ae0c208bc28c98e1f Author: lijewski Date: Wed Nov 14 03:51:45 2007 +0000 centralized PGI and PathScale stuff Tools/C_mk/Make.Linux commit 35125ec746decf875101490d73d30015cd19fcfb Author: 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 Date: Tue Nov 13 15:48:56 2007 +0000 turn off debugging Tools/C_util/regtests/test.py commit 6e5c5e518273b59f046c996c8d20b8af1ebe325d Author: mzingale Date: Tue Nov 13 15:01:34 2007 +0000 add an entry for nan.astro.sunysb.edu Tools/F_mk/GMakeMPI.mak commit a73af2db3978cfec878157fcd7ca29e903d60b5a Author: 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 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 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 Date: Wed Nov 7 00:38:58 2007 +0000 *** empty log message *** Tools/C_mk/Make.defs commit 9479217588812d1db2d7591b7c8e8d0732f14376 Author: lijewski Date: Mon Nov 5 23:00:55 2007 +0000 *** empty log message *** Tools/F_mk/GMakeMPI.mak commit 77990c41aaed91e5e4137f7f00a5ceaf83cc29a7 Author: almgren Date: Mon Nov 5 19:08:39 2007 +0000 Stuff to debug Castro 1d. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/stencil.f90 commit a2ced314fc1a20aa39375898a214a4253fbe30f2 Author: almgren Date: Mon Nov 5 18:54:41 2007 +0000 New stuff to enable 1d. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit bccee1710c0479ffbc1b51403eac2b13522caa0e Author: ajnonaka Date: Thu Nov 1 17:29:54 2007 +0000 added commented out jacobi option for 7 point 3d nodal smoother Src/LinearSolvers/F_MG/mg_smoother.f90 commit 0e9acd4081828454df1a7e08c4a39485d6df7b60 Author: ajnonaka Date: Thu Nov 1 00:45:25 2007 +0000 added some commented out code to give a jacobi option for gs_rb_smoother_3d Src/LinearSolvers/F_MG/mg_smoother.f90 commit 4c6fd5f6082e71c25f263ad02a605b36774dd522 Author: 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 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 Date: Tue Oct 30 20:50:27 2007 +0000 Adding 1d routines. Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit dc32245e95db0f66bd3067169b22fba68eecb6dd Author: almgren Date: Tue Oct 30 20:47:09 2007 +0000 Making 1d stuff compile. Src/LinearSolvers/C_CellMG/ABec_1D.F Src/LinearSolvers/C_CellMG/ABec_F.H Src/LinearSolvers/C_CellMG/CG_F.H Src/LinearSolvers/C_CellMG/LO_F.H Src/LinearSolvers/C_CellMG/LP_1D.F Src/LinearSolvers/C_CellMG/LP_F.H Src/LinearSolvers/C_CellMG/MG_F.H commit e14f200078860cbafa98531beb9c17e17372428a Author: almgren Date: Tue Oct 30 20:29:03 2007 +0000 Need this in 1d. Src/LinearSolvers/C_CellMG/LP_1D.F Src/LinearSolvers/C_CellMG/MG_1D.F commit 03be5dd822e84f856f952c16fa63f8798a443a94 Author: 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 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 Date: Tue Oct 30 20:10:19 2007 +0000 Need this in 1d. Src/C_BoundaryLib/INTERPBNDRYDATA_1D.F commit b124ea735becde12f15475efee94105ef022f010 Author: almgren Date: Tue Oct 30 19:59:55 2007 +0000 Need to have one of these in 1d as well. Src/LinearSolvers/C_CellMG/CG_1D.F commit c3976590901e0442120601769554a4e59dcd6b19 Author: almgren Date: Tue Oct 30 19:43:55 2007 +0000 New 1-d version of ABec*.F Src/LinearSolvers/C_CellMG/ABec_1D.F commit f1b29261978b395c59537d92f4ab8c80d7c73441 Author: 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 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 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 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 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 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 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 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 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 Date: Mon Oct 22 20:29:20 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/CGSolver.cpp commit e3c37d81534f954a9098a5f03f341b3c9b6d89e3 Author: almgren Date: Mon Oct 22 20:27:04 2007 +0000 New version of diagonal (aka Jacobi) preconditioning for solve_bicgstab. Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/ABec_F.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG/Test/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile commit ab3338c0c7d7bc830942ac4c0339a555a056a7a8 Author: almgren Date: Mon Oct 22 03:47:32 2007 +0000 Put in commented code which actually should work much better. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 22c7ccc25225b40f9579af7f12ae957b268c6a6e Author: almgren Date: Mon Oct 22 02:49:57 2007 +0000 Added the capability for the BiCG solver in CGSolver.cpp to do a Jacobi relaxation as a preconditioner. Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/ABec_F.H Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 87bf8b8ac707c7924003a9639693427864086f95 Author: almgren Date: Fri Oct 19 21:22:05 2007 +0000 Code was just wrong -- it was computing the diff into a FAB but never putting it into the "error" MultiFab. Tools/C_util/Convergence/DiffUniform.cpp commit 508b9beaa618fd45b47a6d7e6d7c389b7421bf98 Author: marc Date: Thu Oct 18 00:00:02 2007 +0000 fix CVS screwup Tools/C_mk/Make.mpi Tools/C_mk/Make.rules commit 06fead4879a66cac399ed27360a802f2db662eee Author: marc Date: Wed Oct 17 23:43:53 2007 +0000 *** empty log message *** Tools/C_mk/Make.mpi Tools/C_mk/Make.rules commit d885427a29e5ee43697f0f13fe408f7cec44f49c Author: mzingale Date: Tue Oct 16 18:41:40 2007 +0000 add links to allow for navigation between the test page and individual tests Add ChangeLogs Tools/C_util/regtests/test.py commit e24fc09419b818d1813624d36d4f541b05242ef0 Author: 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 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 Date: Mon Oct 15 21:11:12 2007 +0000 added -lrt for FRANKLIN Tools/C_mk/Make.Linux commit d8f090440a3c01d4b7b8c6bf04242c7698dc44ac Author: almgren Date: Thu Oct 11 20:33:23 2007 +0000 Commented code which does Jacobi instead of GSRB relaxation for 2d cell-centered and 2d nodal. As is the code does GSRB, but one can uncomment certain lines to do Jacobi instead. Src/LinearSolvers/F_MG/mg_smoother.f90 commit 9798cc658206d269d0909839121bc717183512b9 Author: lijewski Date: Tue Oct 9 21:59:01 2007 +0000 *** empty log message *** Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_util.f90 commit befd45a7deb66141eb1623e81ecd9a8a65a723d2 Author: lijewski Date: Tue Oct 9 21:39:45 2007 +0000 *** empty log message *** Src/F_BaseLib/cluster.f90 Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_bxasc.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_bxasc.f90 Tests/F_BaseLib/t_main.f90 commit 0902136e6b22b588d2a28bf3fceae93a518dd6e8 Author: 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 Date: Tue Oct 9 00:30:39 2007 +0000 *** empty log message *** Tools/C_mk/Make.CYGWIN_NT commit 055bdc3f4517230bb198c5a7b5dc5789ba432db0 Author: lijewski Date: Fri Oct 5 21:52:52 2007 +0000 more franklin mods for Castro Tools/C_mk/Make.Linux commit 5d4579e5e1cccbc0b445b3947aa109bfaaccf593 Author: lijewski Date: Fri Oct 5 21:09:37 2007 +0000 automagically identify franklin in Make.defs/Make.Linux Src/LinearSolvers/C_CellMG/Test/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile commit 1af8f098035d08e224477dfdc5161c4d93fcdfa4 Author: lijewski Date: Fri Oct 5 21:04:46 2007 +0000 treat franklin as Linux machine Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit af01d1325d8032550b3c8e0ac4d3a0651fcf99da Author: almgren Date: Fri Oct 5 17:07:30 2007 +0000 Added new mult functions to multifab and ml_multifab. Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/multifab.f90 commit 9322cb8eed76bb76a58178046d95009b412e2401 Author: lijewski Date: Thu Oct 4 22:44:21 2007 +0000 ansi C++-ified Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 1586ce83037c7bbb84152505ee64feb04e3059c9 Author: lijewski Date: Thu Oct 4 22:41:20 2007 +0000 commented out pedantic -- conflicts with something in mpi.h Tools/C_mk/Make.defs commit c5ef13f401b3eb5a455f3bbcd5f169c7320d49c2 Author: lijewski Date: Thu Oct 4 22:31:27 2007 +0000 some cleanup Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/SlabStat.cpp Src/C_AMRLib/TagBox.cpp commit c7d0c6404346a3afdd2aea2286b6bb73fe8b572e Author: lijewski Date: Thu Oct 4 22:31:17 2007 +0000 added -pedantic to g++ Tools/C_mk/Make.defs commit 2749a439256500656eb86435f6d53fa74c4c16d4 Author: mzingale Date: Mon Oct 1 14:08:04 2007 +0000 add a comment when the benchmarks are updated so we log the reason for the change in the solution Tools/C_util/regtests/test.py commit 18ab2f4db6cab8eb9a5378935019f2103e8f2bef Author: almgren Date: Thu Sep 27 18:16:11 2007 +0000 Fix the copy in ml_multifab to match that in multifab, i.e. you can pass number of ghost cells but can no longer pass "all". Src/F_BaseLib/ml_multifab.f90 commit 9110a14c6641c40d211e2532be08ba16c4ef3b87 Author: lijewski Date: Tue Sep 25 20:34:13 2007 +0000 AIX mods Tools/F_mk/GMakedefs.mak commit 65a5b4e73f8d350094fd312b95c107e921256796 Author: almgren Date: Tue Sep 25 17:57:39 2007 +0000 Replace all by ng in bndry_reg copy functions. Src/F_BaseLib/bndry_reg.f90 commit 9f2dca77fd3ea4c31356c8b0f61df8062731dc83 Author: lijewski Date: Mon Sep 24 21:29:35 2007 +0000 added xt4 block for franklin Tools/F_mk/GMakedefs.mak commit 809c6b717f698bedc1d3cfeebd87c651e73ac597 Author: 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 Date: Sun Sep 23 16:44:06 2007 +0000 inf & nan stuff works on AIX Src/C_BaseLib/FArrayBox.cpp commit 47ead16da484dbc0729d6cf16d215b065984ff02 Author: lijewski Date: Sat Sep 22 15:05:31 2007 +0000 added nan & inf detection code Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 03fc2bf0383cb51968582482f68ea119373fe762 Author: lijewski Date: Sat Sep 22 15:05:12 2007 +0000 removed debug stuff from MFIter Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 86224db16b3c20c44f93099a089de7ce2f0b0231 Author: almgren Date: Tue Sep 18 20:17:22 2007 +0000 Didn't mean to commit all the changes in stopping criteria, just wanted the change in copy calls. Src/LinearSolvers/F_MG/itsol.f90 commit e8450fed55acd1bc271dcc14db8528ef1726368d Author: lijewski Date: Tue Sep 18 20:03:57 2007 +0000 force Headers to use scientific notation for floating point values Src/C_BaseLib/VisMF.cpp commit ad8c69d88af751cd8adab7e16e2288b80613e988 Author: lijewski Date: Tue Sep 18 19:57:29 2007 +0000 floating point format change: es30.20 -> es25.15 Src/F_BaseLib/fabio.f90 commit 991daf6e1371c1f2e84ce94bb23c6fa1868e57d9 Author: almgren Date: Tue Sep 18 19:42:36 2007 +0000 Replaced "all" argument by "ng" argument in multifab_copy and multifab_copy_c. Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 commit dac8519056662baaa08a62046b5dd50cbdf92fe6 Author: lijewski Date: Mon Sep 17 21:37:27 2007 +0000 simplified _nfiles stuff previously added Src/C_AMRLib/Amr.cpp commit 6448464f14cafff770489492edf20e8b87c983f9 Author: 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 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 Date: Fri Sep 7 23:01:43 2007 +0000 can now regrid single-level calculation Src/C_AMRLib/Amr.cpp commit ba361e2f63d9424026d8358535614b10ee2391d1 Author: almgren Date: Fri Sep 7 17:09:14 2007 +0000 These versions of mg.f90 and mg_smoother.f90 actually compile. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 commit 1e25255b3f9ee926e4699660faa477b06685ea62 Author: almgren Date: Fri Sep 7 17:07:31 2007 +0000 Modify 2d- and 3d- nodal smoother calls so that when using cross stencil, with red-black Gauss-Seidel, we make sure to do a multifab_fill_boundary between the red and black sweeps. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 commit 61d642d1c88e302d991b3bf2d60bff78a4882a12 Author: lijewski Date: Thu Sep 6 20:27:16 2007 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit bc6692574107efbdf54a7239565664225283ae89 Author: marc Date: Tue Sep 4 21:31:40 2007 +0000 Do not include wait.h on Columbia...makes Intel compiler unhappy...do we need this elsewhere?? Src/C_BaseLib/Utility.H commit 055ebe55e5457570619bdd061a25f68fec774802 Author: marc Date: Tue Sep 4 21:25:12 2007 +0000 Remove wait.h include, already dealt with in Utility.H Src/C_BaseLib/Utility.cpp commit 4fc697882a3578a81d6eb13cd3751dd5c7c1a36c Author: lijewski Date: Tue Sep 4 19:50:10 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/grids/in.3_512cubed Tests/LinearSolvers/C_CellMG/grids/in.3_512cubed commit a82ffa5953a147e7d7a204fff1aa81260745d022 Author: lijewski Date: Tue Aug 28 22:18:55 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/grids/in.2_256squared Tests/LinearSolvers/C_CellMG/grids/in.2_256squared commit d9ccc6310172565a1a41fe41581813d80bc2819b Author: lijewski Date: Tue Aug 28 21:38:13 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/grids/in.2_256squared Tests/LinearSolvers/C_CellMG/grids/in.2_256squared commit 83f9ae5c1bb1ee44a37b09f0ec6398de2a32b955 Author: lijewski Date: Tue Aug 28 19:37:45 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 0ddb88546b289bdabbef0906cdba24905eb79e90 Author: almgren Date: Fri Aug 24 19:27:48 2007 +0000 Add option to set variable coefficients in solve, flag is use_variable_coef which defaults to false. Src/LinearSolvers/C_CellMG/Test/COEF_2D.F Src/LinearSolvers/C_CellMG/Test/COEF_3D.F Src/LinearSolvers/C_CellMG/Test/COEF_F.H Src/LinearSolvers/C_CellMG/Test/Make.package Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/COEF_2D.F Tests/LinearSolvers/C_CellMG/COEF_3D.F Tests/LinearSolvers/C_CellMG/COEF_F.H Tests/LinearSolvers/C_CellMG/Make.package Tests/LinearSolvers/C_CellMG/main.cpp commit 3a5c82e9fb500d4715d0ec6378907a6f3e1429ea Author: mzingale Date: Fri Aug 24 14:57:43 2007 +0000 add the ability to do only a single test, if desired Tools/C_util/regtests/test.py commit e1b671f7d7711ef0595a53fd8a575cbd209f5cf5 Author: mzingale Date: Thu Aug 23 14:10:48 2007 +0000 make it work with python 2.3 switch to inf norm for fParallel builds, feed in MPI= to disable MPI in the make add the time and date of the CVS update to the webpage Tools/C_util/regtests/test.py commit 9e2ea598fa2aca4636e431fb77ae2ed715621b6b Author: lijewski Date: Tue Aug 21 21:49:42 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/grids/in.2_256squared Src/LinearSolvers/C_CellMG/Test/grids/in.3_128cubed Src/LinearSolvers/C_CellMG/Test/grids/in.3_256cubed Tests/LinearSolvers/C_CellMG/grids/in.2_256squared Tests/LinearSolvers/C_CellMG/grids/in.3_128cubed Tests/LinearSolvers/C_CellMG/grids/in.3_256cubed commit 40e8fe853a67710d9d97ebfec37c9ed077a02d16 Author: almgren Date: Tue Aug 21 21:43:42 2007 +0000 Two more 3-d grids with a domain just broken up into same-size boxes. Src/LinearSolvers/C_CellMG/Test/grids/gr.3_256cubed Src/LinearSolvers/C_CellMG/Test/grids/gr.3_512cubed Tests/LinearSolvers/C_CellMG/grids/gr.3_256cubed Tests/LinearSolvers/C_CellMG/grids/gr.3_512cubed commit 343099aff40261ac0daa360d50697d1159928b7a Author: mzingale Date: Tue Aug 21 20:36:35 2007 +0000 echo SUCCESS upon a successful build -- this will be seen by the regression test framework (Parallel/util/regtests/) to detect that compilation worked. Tools/C_mk/Make.rules commit 723757c1fe4d5e65843f235d8b02e4c9203755b9 Author: almgren Date: Tue Aug 21 18:21:53 2007 +0000 Clean this up... Src/LinearSolvers/C_CellMG/Test/grids/in.3_128cubed Tests/LinearSolvers/C_CellMG/grids/in.3_128cubed commit 587a3c961c7c27e0491bd00c92f00694d0e6f6ea Author: almgren Date: Tue Aug 21 18:21:10 2007 +0000 These are the ones we're testing superlu with. Src/LinearSolvers/C_CellMG/Test/grids/gr.2_256squared Src/LinearSolvers/C_CellMG/Test/grids/in.2_256squared Tests/LinearSolvers/C_CellMG/grids/gr.2_256squared Tests/LinearSolvers/C_CellMG/grids/in.2_256squared commit e99dc22c282347994a982c6845df924bb7037884 Author: almgren Date: Tue Aug 21 17:41:11 2007 +0000 Finished changing mult,div,plus,sub calls take ng instead of "all" now. Src/F_BaseLib/multifab.f90 commit 3004e15edc29d01a244b3fe9172d3c9fbbbf47d1 Author: mzingale Date: Tue Aug 21 14:48:28 2007 +0000 add the initial version of the regression testing framework, developed initially for Castro. The Castro-tests.ini file sets up some pure hydro tests. Maestro-tests.ini will setup a single test for Maestro (in the fParallel framework). Tools/C_util/regtests/Castro-tests.ini Tools/C_util/regtests/Maestro-tests.ini Tools/C_util/regtests/README Tools/C_util/regtests/test.py commit 54ad330a534f637cbea364da453bb2c17f069912 Author: ajnonaka Date: Mon Aug 20 23:32:11 2007 +0000 finished Ann's implementation for mandatory ghost cells for plus_plus, div_div, and mult_mult Src/F_BaseLib/ml_multifab.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 9d3441fb20d978a8c9fb282d761578154c092d45 Author: almgren Date: Mon Aug 20 23:05:20 2007 +0000 We are now changing the calling sequence to operations on multifabs which used to take "all" as an optional argument -- they now take ng. Src/F_BaseLib/multifab.f90 commit 5e49193b5f9c89056796ddbfd52ae3b487bd554d Author: mzingale Date: Fri Aug 10 17:59:22 2007 +0000 add the compressor script from the Parallel tree to help tame our plot/chk directories Tools/F_scripts/compressor commit b791b42339476c2cbf7870c821c1f3823d6bda4f Author: almgren Date: Mon Aug 6 22:24:41 2007 +0000 Shouldn't test on rnorm in cg or bicg solve if stopping criterion was reached before any iterations. Src/LinearSolvers/F_MG/itsol.f90 commit 78fbe4dd056443cdfd9bc3881ac906e30df49a28 Author: mzingale Date: Sat Aug 4 23:54:40 2007 +0000 determine if the files agree by looking at the absolute norms and print out a message that the regression suite can detect. Tools/C_util/Convergence/DiffSameGrid2.cpp commit 2eba167f30172dc54789ccb550f59e5b2028d7aa Author: mzingale Date: Fri Aug 3 17:37:12 2007 +0000 change the make clean rule from $(RM) $(EBASE)$(optionsSuffix).ex to $(RM) $(executable) so it works when we invoke make as gmake executable=Castro.exe to rename the executable. Tools/C_mk/Make.rules commit f03c59b90114d99d16dfd85632989cebbf1c89fa Author: mzingale Date: Thu Aug 2 17:40:00 2007 +0000 switch over to using a lock file to guarantee that build_info.f90 is regenerated and built each time. This now means that at any make invocation, it gets rebuilt (i.e. not only when some other file has changed), but it avoids some circular dependencies that I couldn't track down. Tools/F_mk/GMakerules.mak commit eec0968fac9057949d2c663675145dbf3b33b98e Author: mzingale Date: Wed Aug 1 21:23:42 2007 +0000 add a new rule for build_info.f90, so that we are sure that it is regenerated any time we recompile. Previously, the script was not rerun when a file changed, so the build info could be out of date. Now there is a new class of files, sf90sources, that do not get the dependency check done to them. Rightnow, build_info.f90 is the only such example of this type of file. This allows it to have as dependencies all of the other files, thus guarranting that it gets regenerated. Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak commit 5c3e933d4376e712d0963eaba6bd6c4b2be941f9 Author: mzingale Date: Wed Aug 1 15:19:55 2007 +0000 make this compile with compilers that don't allow > 132 columns Tools/F_scripts/make_build_info commit dd114a9aaf49c99537077edb31a0fbdd9295b0ee Author: almgren Date: Tue Jul 31 23:56:29 2007 +0000 Added multifab_print_c and fab_print_c which print only a single component of the multifab or fab. Src/F_BaseLib/fab.f90 Src/F_BaseLib/multifab.f90 commit bfdfb64deb561270e05914cab8a22dca8055184b Author: almgren Date: Mon Jul 30 18:18:10 2007 +0000 Missed a few places for the BL_ASSERT(num_comp > 0); statement. Src/C_BaseLib/MultiFab.cpp commit c3e6c7cbeaf29cc8d2cd9e78d9e7dd4490bb23b0 Author: almgren Date: Mon Jul 30 18:10:58 2007 +0000 Added BL_ASSERT(num_comp > 0); to a number of the plus/minus - type calls... Src/C_BaseLib/MultiFab.cpp commit c1987f970807c4eb5ff82c73383e46b278520aa7 Author: almgren Date: Sat Jul 28 22:24:05 2007 +0000 Fixed stencil_all_flux_3d to match sign convention of 2d version. Src/LinearSolvers/F_MG/stencil.f90 commit 145e5e7e9db211df660f0b65f8bc5eed0731e122 Author: mzingale Date: Wed Jul 25 20:34:31 2007 +0000 make the string length a script parameter Tools/F_scripts/make_build_info commit c5720ea4e3785ad55b6e5f086b06e4a3145ead4f Author: marc Date: Wed Jul 25 01:07:35 2007 +0000 *** empty log message *** Tools/C_mk/Make.CYGWIN_NT commit c89b062764143930c093290aff7c750bf037e8e9 Author: 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 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 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 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 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 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 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 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 Date: Tue Jul 17 05:15:37 2007 +0000 Fix small typos. Src/LinearSolvers/F_MG/mg_cpp_f.h commit ff1b5693c7377b4c5b57aca4763bfe4f1725ceb6 Author: almgren Date: Tue Jul 17 05:06:33 2007 +0000 Needed 3d instead of 2d... Src/LinearSolvers/F_MG/mg_cpp_f.h commit 76fe970bf5143d05c4ce42a953595be21f1fa671 Author: almgren Date: Tue Jul 17 04:46:18 2007 +0000 Remove print statement. Src/LinearSolvers/F_MG/stencil.f90 commit 7ca08308b319b85186284e51296fee6d8b171f88 Author: almgren Date: Tue Jul 17 04:42:12 2007 +0000 Add mgt_compute_residual routine which calls new ml_resid. Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 49ef3a5a2419a8e26f2f5fa8cf81ba2c981b5733 Author: almgren Date: Tue Jul 17 04:41:39 2007 +0000 Added compute_residual routine. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 6e7c7f7747aff070a77421560c61ce75edbc124c Author: 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 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 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 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 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 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 Date: Sat Jul 14 00:16:46 2007 +0000 Remove print statements. Src/LinearSolvers/F_MG/mg_cpp.f90 commit cc05121eb62801ee55c803ca6db59757061656fe Author: almgren Date: Fri Jul 13 22:56:49 2007 +0000 New code to work for gravity in Castro. Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 8eadcecc8082623170481464b8d5cabe62076d83 Author: almgren Date: Fri Jul 13 22:56:17 2007 +0000 New stuff to work for gravity in Castro. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit f20ff73120d3a87bd22815928110f0211599b4d6 Author: mzingale Date: Fri Jul 13 16:34:39 2007 +0000 create a rule to make build_info.f90. You need to add f90sources += build_info.f90 to your GPackage.mak to get this rule to execute Tools/F_mk/GMakerules.mak commit 043ed38d0229483082982a0c33beadffa6f828ed Author: mzingale Date: Fri Jul 13 15:15:50 2007 +0000 a script that automagically generates a Fortran subroutine that returns the name of the machine we compiled on, the build date/time, and the directory that we built in. Tools/F_scripts/make_build_info commit 8b42615f5bd17c833584560956cc9a3e3438a9b7 Author: almgren Date: Tue Jul 10 21:15:06 2007 +0000 When need_grad_phi is true, make sure we fill periodic and fine-fine ghost cells as well as interpolating from crser grid. Src/LinearSolvers/F_MG/ml_cc.f90 commit 5eacacf3e92dcfbd2152b35d5b0f7d6793020ffc Author: ajnonaka Date: Mon Jul 9 18:27:27 2007 +0000 This is a dummy checkin to verify my CVS works. Tools/F_scripts/coco/coco.pl commit 3546b63aca105b385312b661a1cf5a187d40da01 Author: almgren Date: Fri Jul 6 01:04:01 2007 +0000 Fixed bug for multiple grids per level above 0. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit a07c1a10a0263248bf388a07f3381b1c12f8ac63 Author: lijewski Date: Thu Jul 5 20:59:05 2007 +0000 *** empty log message *** Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit 55201d704c732512c3b1f260828306addb349f4a Author: almgren Date: Thu Jul 5 20:51:20 2007 +0000 Get rid of unused gbox in assertions. Src/LinearSolvers/C_CellMG/CGSolver.cpp commit d3f1290b7f42162e3f2b5ea942efde60b07e0457 Author: almgren Date: Thu Jul 5 20:50:32 2007 +0000 Get rid of unused stuff in assertions. Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp commit 1f143e98d4827a70544070d827e544c87126e3b7 Author: almgren Date: Thu Jul 5 20:49:18 2007 +0000 Fix up the MyProc stuff. Src/C_BoundaryLib/FabSet.cpp commit 3b24bf6b6f9bbda70db6881b1954e0472d1faa8f Author: lijewski Date: Thu Jul 5 20:43:08 2007 +0000 *** empty log message *** Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/StationData.cpp commit 4f3198393055a9cfa83e612fec32e219cb494fdc Author: lijewski Date: Thu Jul 5 20:02:11 2007 +0000 *** empty log message *** Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Derive.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/StateDescriptor.cpp Src/C_AMRLib/StationData.cpp Src/C_BoundaryLib/FabSet.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile commit 6e9eca51bf4623f7c7b4d75684122c234f42cca1 Author: lijewski Date: Thu Jul 5 17:02:00 2007 +0000 *** empty log message *** Src/C_AMRLib/Amr.H Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/LevelBld.H commit 8e0135b01e104b1a807ad9ce8ae4d33d51a5f9af Author: lijewski Date: Tue Jul 3 21:54:58 2007 +0000 *** empty log message *** Src/C_BaseLib/COORDSYS_3D.F Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F Src/LinearSolvers/C_CellMG/LO_3D.F commit 48dc62e9ac5952bd7ed609909ab48bb072fe07c3 Author: lijewski Date: Tue Jul 3 21:22:57 2007 +0000 *** empty log message *** Tools/C_mk/Make.defs commit 83dd3209220924f53f20bb6bd854dddb36c5a88b Author: almgren Date: Tue Jul 3 21:05:31 2007 +0000 This main.cpp has a RHS that sums to zero, so it is solvable with all-Neumann or all-periodic bc's as well as with Dirichlet. Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 1d0cd47cee590ae52ed9d66b125baf1843b2b9f9 Author: almgren Date: Tue Jul 3 20:41:45 2007 +0000 New files with 128 cubed divided into 64 patches of 32 cubed. Src/LinearSolvers/C_CellMG/Test/grids/gr.3_128cubed Src/LinearSolvers/C_CellMG/Test/grids/in.3_128cubed Tests/LinearSolvers/C_CellMG/grids/gr.3_128cubed Tests/LinearSolvers/C_CellMG/grids/in.3_128cubed commit ab9125ff53fabd9ec3001988f1ab98ebe3193574 Author: lijewski Date: Tue Jul 3 20:10:56 2007 +0000 g95 stuff Tools/C_mk/Make.defs commit 95e1a6a6e4f65522f6b640ef0e9da838a1cdf4f0 Author: lijewski Date: Tue Jul 3 19:50:33 2007 +0000 removed extraneous OutOfMemory Src/C_BaseLib/BoxLib.cpp commit dc084c10230144693998c3956cad4a0bf1783c79 Author: 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 Date: Tue Jul 3 03:13:09 2007 +0000 *** empty log message *** Tools/C_mk/Make.defs commit e8221def5fed47c26b3ea7f0df9770585750262c Author: lijewski Date: Tue Jul 3 03:10:38 2007 +0000 some cleanup Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/box.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/fab.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 Src/LinearSolvers/F_MG/stencil.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 68824b03f8853d869bdb977ada9329051dd8f8d4 Author: lijewski Date: Mon Jul 2 23:00:14 2007 +0000 some cleanup Src/C_AMRLib/INTERP_2D.F Src/C_BoundaryLib/INTERPBNDRYDATA_2D.F Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/LO_2D.F Src/LinearSolvers/C_CellMG/LP_2D.F Src/LinearSolvers/C_CellMG/LP_F.H commit 89b95736137485ff704b81898beec60dfffadf37 Author: almgren Date: Mon Jul 2 17:53:31 2007 +0000 Comment out the printing of f90 mg settings (for now) Src/LinearSolvers/F_MG/mg_cpp.f90 commit 4d336d4c5ecf8959894d812d53b6fe0440bc578d Author: almgren Date: Sun Jul 1 21:49:17 2007 +0000 Must take multilevel norm of initial residual. Src/LinearSolvers/F_MG/ml_cc.f90 commit 5857a4cd2867c2532a236ccf92ffb3c5efcb82d9 Author: almgren Date: Sun Jul 1 21:14:54 2007 +0000 Need to pass ng into mgt_get_uu so that we can pass the ghost cells of the fine grid solution back from the f90 to the C++. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 88dc7c1c24e7dd7fb996dbd2b3c8bf64c9f9f425 Author: almgren Date: Sun Jul 1 21:14:09 2007 +0000 Need to pass ng into mgt_get_uu so that we can pass the ghost cells of the fine grid solution back to the C++. Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit c9cc54d569bbf8d97fe3d6545556596b40c78a20 Author: almgren Date: Sat Jun 30 00:30:12 2007 +0000 Added need_grad_phi argument to mgt_solve Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 4e54a883d614f342b617b3187ca815f36a6f7cb1 Author: almgren Date: Sat Jun 30 00:29:58 2007 +0000 Added need_grad_phi argument to MGT_Solver::solve and mgt_solve Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 6c9fcb8005d56cb045a648cbc68ac0c5e9ac9498 Author: almgren Date: Fri Jun 29 21:34:45 2007 +0000 *** empty log message *** Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit ebba28515abb61695c8ef743ad840e25f5410b66 Author: mzingale Date: Fri Jun 29 17:33:16 2007 +0000 clean up the printing some to now output the variable names Tools/C_util/Convergence/DiffSameGrid.cpp commit ba5906adcb53e87c2043551b3445c4725d8ddc06 Author: sepp Date: Fri Jun 29 17:06:45 2007 +0000 1) more adjustment of spaces in comments Src/C_AMRLib/BC_TYPES.H commit dd611f01c79fad385b60c7236ea7237448fefedf Author: sepp Date: Fri Jun 29 17:01:53 2007 +0000 1) adjusted spaces in table so columns line up exactly Src/C_AMRLib/BC_TYPES.H commit ea0cd0ac16913dd306353d7f1dcc86ef5ecfb04f Author: 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 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 Date: Thu Jun 28 19:41:07 2007 +0000 Removed print statement. Src/LinearSolvers/F_MG/mg_cpp.f90 commit 5bcd584817c7a1eb740851c81b8a6d528fc78e3b Author: 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 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 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 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 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 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 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 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 Date: Tue Jun 12 12:20:21 2007 +0000 add Intel 10.0 compiler support Tools/C_mk/Make.defs commit da394d5f116b6cfa1c11394fa714dc8d35e0dedb Author: almgren Date: Thu Jun 7 22:23:07 2007 +0000 Use -mp flag for all Intel compilers -- doesn't allow optimization to screw up the precision. Tools/F_mk/GMakedefs.mak commit 4966cc88cffb4c52ff8f2822eec9a92564ee5c45 Author: almgren Date: Fri May 11 17:45:04 2007 +0000 mg_jacobi_smoother now does nu1 relaxations instead of 1. Src/LinearSolvers/F_MG/mg.f90 commit 452a67ccfe4c0d3895ee796ba9aabd6d7a35c880 Author: almgren Date: Wed May 9 21:30:59 2007 +0000 Added mg_jacobi_smoother to be called at end of solve... Src/LinearSolvers/F_MG/mg.f90 commit 5071974b7d63ba389267010cb74a9562290aa19a Author: 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 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 Date: Wed May 9 17:55:29 2007 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit 449bf8c4f5c3cede01d25406ed22b2da4b8365c9 Author: lijewski Date: Tue May 8 21:01:15 2007 +0000 faster sort() in simplify() Src/C_BaseLib/BoxList.cpp commit 92c1996b2b8b0252563bdbb5d5354f8fc2a939a0 Author: lijewski Date: Tue May 8 20:08:21 2007 +0000 *** empty log message *** Src/C_AMRLib/Amr.cpp commit 084ffa6cc8b8c9093c889d9d7c14f002622f159f Author: lijewski Date: Tue May 8 19:28:35 2007 +0000 Added strategically placed simplify()s simplify() scales better than complementIn() in grid_places. Basically we're simplify()ing before complementIn(). Src/C_AMRLib/Amr.cpp commit 31be6c2c25b9753116be385c8a58e88605a6e8c8 Author: lijewski Date: Tue May 8 19:26:35 2007 +0000 now simplify() in batches of 50 not 250 Src/C_BaseLib/BoxList.cpp commit b6d9d835835716e2e1a3c22e40f08d67826834e7 Author: lijewski Date: Tue May 8 19:02:45 2007 +0000 assert ngrow>=0 Src/C_BaseLib/FabArray.H commit 82586616075cf95b1cf73c7537c22b6bdb310ed4 Author: 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 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 Date: Sat May 5 20:54:12 2007 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/interface.cpp commit d2cc24e0b46fe729d5f2bb0de2d2323253710c21 Author: lijewski Date: Fri May 4 23:21:24 2007 +0000 *** empty log message *** Src/C_BaseLib/BoxList.cpp commit 2152c0b8e454343555b1fa254d13a82b92a4c1b9 Author: lijewski Date: Fri May 4 23:00:51 2007 +0000 *** empty log message *** Src/C_AMRLib/Cluster.cpp Src/C_BaseLib/BoxArray.cpp commit 8455340dc3e4c5e2a1d7cceec18d3d9ff4ba9526 Author: almgren Date: Fri May 4 20:29:49 2007 +0000 This one works on atlas as well as manda (I think). Tools/F_mk/GMakedefs.mak commit fba93fa3c5efc4493d92719291ca732d8c1465e8 Author: almgren Date: Fri May 4 20:24:05 2007 +0000 Include specifics for using mpi on manda.lbl.gov Tools/F_mk/GMakeMPI.mak commit 5c0c75d9a60cd676335516a77ef6738da5c3e065 Author: lijewski Date: Fri May 4 19:08:48 2007 +0000 *** empty log message *** Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.cpp commit 5e7834214c96b7e24b79cb472eca7c95c0b0f594 Author: lijewski Date: Thu May 3 23:29:59 2007 +0000 changed BL_PROFILE() a bit Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.cpp commit 861db38e4f24c6c8558fdf848ff5c7f0bc586668 Author: lijewski Date: Wed May 2 21:53:15 2007 +0000 added FastContins() Src/C_AMRLib/Cluster.cpp commit e178ee01979a36cd758c39e1c88e74e5fece4910 Author: 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 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 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 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 Date: Tue May 1 22:42:34 2007 +0000 *** empty log message *** Src/C_BaseLib/BoxList.cpp commit 60e2d138ff17ba9839283fe30936458df8f9ad57 Author: lijewski Date: Tue May 1 22:26:03 2007 +0000 comment out simplify in grid_places() for now Src/C_AMRLib/Amr.cpp commit a78b8bddb5559600dbe77594d95ab6c075730795 Author: lijewski Date: Tue May 1 21:54:43 2007 +0000 commented out simplify() in removeOverlap() for the time being Src/C_BaseLib/BoxArray.cpp commit 1e5eaf26fcc1276598589ccc0757f5dd747f19f1 Author: lijewski Date: Tue May 1 20:11:02 2007 +0000 *** empty log message *** Src/C_AMRLib/Amr.cpp commit acb00607d0fcda635bd41ea9f7120227fcfd7c8a Author: lijewski Date: Tue May 1 03:12:50 2007 +0000 ProjPeriodic() now does a simplify() Src/C_AMRLib/Amr.cpp commit 83aa2764ec2f5403f31237d239be495ed9fe2152 Author: lijewski Date: Tue May 1 02:59:57 2007 +0000 Initialize() now does full simplify() Src/C_AMRLib/AuxBoundaryData.cpp commit f29560f565ee0bb16c7d9dc569edf463f76d7d2a Author: lijewski Date: Tue May 1 02:59:32 2007 +0000 complementIn() now does full simplify() Src/C_BaseLib/BoxList.cpp commit 4fe7164d4d413c5bf7d4611f604ba5fdfe8ed51b Author: lijewski Date: Tue May 1 02:59:20 2007 +0000 removeOverlap() now does full simplify() Src/C_BaseLib/BoxArray.cpp commit b8fed644ff5bc924c72130414fd96e4577728372 Author: 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 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 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 Date: Wed Apr 25 20:02:34 2007 +0000 *** empty log message *** Tools/F_mk/GMakedefs.mak commit 7bf9c341375658a68e894cced36db92f4126e6bb Author: almgren Date: Wed Apr 25 19:38:09 2007 +0000 Change in calling sequence to stencil_fill_nodal (no longer pass h_finest) Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit 43234e5ca1bf3b4b12b54af0abfbe76d414af67b Author: 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 Date: Tue Apr 24 21:12:42 2007 +0000 improved SFC; sfc_threshold now 10 Src/C_BaseLib/DistributionMapping.cpp commit 0dd0c8c16f28298dcd345b06adfbab7b1ef9d356 Author: lijewski Date: Tue Apr 24 21:05:46 2007 +0000 *** empty log message *** Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/ba.23925 Src/C_BaseLib/test/tDM.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/ba.23925 Tests/C_BaseLib/tDM.cpp commit a17d3683edc0d513106f9804f81d40add84aa5ca Author: lijewski Date: Tue Apr 24 19:43:47 2007 +0000 uncomment simplify() till further notice Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.cpp commit f62c7dcfbb5a8348b3f43bab972a07d32dfa8bc2 Author: almgren Date: Tue Apr 24 17:45:28 2007 +0000 Fix in function stencil_norm to workaround bug in Intel compiler for large single arrays. Src/LinearSolvers/F_MG/stencil.f90 commit ccd278d17a7ceb4774cb0dbff1d2be8248861344 Author: 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 Date: Tue Apr 24 01:13:20 2007 +0000 commented out complementIn() in removeOverlap() Src/C_BaseLib/BoxList.cpp commit d7a2f6db4a65332e83d1eed6347202caea08b47c Author: lijewski Date: Tue Apr 24 01:13:06 2007 +0000 commented out simplify() in removeOverlap() Src/C_BaseLib/BoxArray.cpp commit 83dc414139a409859d12447678e64e3863c60093 Author: nazgul Date: Mon Apr 23 20:44:48 2007 +0000 Commenting out a section of code that appears to be unnecessary and makes it impossible to have a Tuple. The offending code also conflicts with the comments. If this code really is necessary let me know and we can work something else out. Louis Howell Src/C_BaseLib/Tuple.H commit e1e6336a9fc339f7af2129ae89a4e7b8d95ae993 Author: nazgul Date: Mon Apr 23 16:46:52 2007 +0000 Minor bug fixes for 1D. (Doesn't look like 1D gets used very much.) Louis Src/C_BaseLib/COORDSYS_1D.F Src/C_BaseLib/CoordSys.cpp commit 8b1c8c74b4452e9775ddc889804a59b2dc987dc8 Author: lijewski Date: Sat Apr 21 03:32:11 2007 +0000 yet further refinements to FAB data uniformization Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 7e925e972683a274d17673466011fd616d258baa Author: lijewski Date: Sat Apr 21 00:51:57 2007 +0000 further refinements to FAB data uniformization Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit f9a784d6ac733e978bef05bbd082452d2d9d4423 Author: 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 Date: Fri Apr 20 20:55:44 2007 +0000 verbose now defaults to true Src/C_BaseLib/DistributionMapping.cpp commit 103da9ee73c80dc9c406633f152ab2343c984712 Author: lijewski Date: Fri Apr 20 19:13:58 2007 +0000 *** empty log message *** Src/C_AMRLib/Amr.cpp commit 94de005abcbc104e3bf8f2392c78610add28f8a7 Author: lijewski Date: Fri Apr 20 02:49:08 2007 +0000 print out FAB byte high-water-mark at end of timestep Src/C_AMRLib/Amr.cpp commit 783f46821775fb46d2f9e92a3442d49edcd76c88 Author: lijewski Date: Fri Apr 20 02:48:33 2007 +0000 now maintain FAB byte high-water-mark Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp commit 1ad917d5be758fed4499be1bdebc2a3d5261e7d5 Author: 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 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 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 Date: Thu Apr 19 00:17:49 2007 +0000 added code to limit probin opens. Src/C_AMRLib/Amr.cpp commit 6e1f042345e8316d5bcb484e01fd534a6618f992 Author: lijewski Date: Wed Apr 18 17:51:08 2007 +0000 Must check DistributionMaps, as well as BoxArrays, when deciding on caching. Src/C_BoundaryLib/FabSet.cpp commit 26565df2e2cebe1e2c499cfa369ad3c09bfc29e7 Author: lijewski Date: Wed Apr 18 17:37:08 2007 +0000 Must look at DistributionMapping, not just BoxArray, in FillBoundary(). Src/C_BaseLib/MultiFab.cpp commit 29706d1a803d3de38b9227d6ef04e9c0d1674ffe Author: lijewski Date: Wed Apr 18 17:29:15 2007 +0000 Need to look at DistributionMapping, in addition to BoxArray, when caching FPBs. Src/C_BaseLib/Geometry.cpp commit e72baa65d5df91303ae3bbf04791548683e55c46 Author: lijewski Date: Wed Apr 18 17:28:03 2007 +0000 *** empty log message *** Tools/C_mk/Make.mpi commit 155a0e88006db106b72a28fefd4b664ad70ce059 Author: lijewski Date: Wed Apr 18 17:27:28 2007 +0000 added -Wno-deprecated for g++ Tools/C_mk/Make.defs commit 34bdea67fe23c8862df5e5bb7ff6cfde85fa4f60 Author: lijewski Date: Wed Apr 18 15:40:23 2007 +0000 *** empty log message *** Src/C_BaseLib/test/tBA.cpp Tests/C_BaseLib/tBA.cpp commit 1af6469ca5f3b7e1f2b4850992873e92ef46721a Author: lijewski Date: Tue Apr 17 18:12:14 2007 +0000 added AuxBoundaryData Src/C_AMRLib/Make.package commit deaca49594e733fc454b26f843f2c8be8e3c5ec8 Author: lijewski Date: Tue Apr 17 16:56:12 2007 +0000 stripped out of LMC, nova & Castro Src/C_AMRLib/AuxBoundaryData.H Src/C_AMRLib/AuxBoundaryData.cpp commit 9a6cb64cda7cb9865ff9b3c1d75a9a324c3265cc Author: lijewski Date: Tue Apr 10 20:16:27 2007 +0000 needed Src/C_BaseLib/ParallelDescriptor.H commit 8c255ccffdc0d70888404b2038573432cabb516d Author: lijewski Date: Mon Apr 9 20:29:45 2007 +0000 *** empty log message *** Tools/F_mk/GMakedefs.mak commit 2746b0ee389686501d94cff17692227a60b0c7ad Author: vince Date: Fri Apr 6 22:31:42 2007 +0000 another friendly read. Src/C_BaseLib/ParmParse.cpp commit 7eb5ef4292ac8c8131da7a51a88bef355fbaa98a Author: vince Date: Fri Apr 6 19:57:12 2007 +0000 implemented a mechanism to limit the total number of open files when reading a multifab. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit c737e279be241242160246b1f453bf01b26c9c56 Author: lijewski Date: Wed Apr 4 05:14:10 2007 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit bce34c7fa6833d459222710b29de22e550e1b8dd Author: lijewski Date: Tue Apr 3 23:36:58 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/grids/in.grids.15456 Src/LinearSolvers/C_CellMG/Test/grids/in.grids.213 Src/LinearSolvers/C_CellMG/Test/grids/in.grids.25600 Src/LinearSolvers/C_CellMG/Test/grids/in.grids.5034 Tests/LinearSolvers/C_CellMG/grids/in.grids.15456 Tests/LinearSolvers/C_CellMG/grids/in.grids.213 Tests/LinearSolvers/C_CellMG/grids/in.grids.25600 Tests/LinearSolvers/C_CellMG/grids/in.grids.5034 commit b63e80657a15438dd89c0a09caa1802f2da03f89 Author: 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 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 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 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 Date: Thu Mar 29 18:08:50 2007 +0000 XT3 stuff Src/C_BaseLib/Utility.cpp commit 4bdc2c36e71303c0303ff6e4593ad0dda4baeb1d Author: lijewski Date: Thu Mar 29 17:57:25 2007 +0000 XT3 stuff Src/C_BaseLib/Utility.cpp commit e15e9970fda6edea417d398b83f0d5ffbe66dd6c Author: lijewski Date: Wed Mar 28 21:33:38 2007 +0000 added XT3 stuff Src/LinearSolvers/C_CellMG/Test/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile commit c2100b0f8c7209b26c6a2b8d5efe80d084f5bea9 Author: lijewski Date: Mon Mar 26 17:31:37 2007 +0000 now cognizant of amount of FAB data per CPU Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit f760a8a1eeee4e07ba64ace526c08d5eec1851be Author: lijewski Date: Thu Mar 22 16:24:40 2007 +0000 *** empty log message *** Src/C_BaseLib/BaseFab.H commit 9b91aa0bf31515769ce46fb98272f87948c25312 Author: lijewski Date: Thu Mar 22 04:21:20 2007 +0000 add total_bytes_allocated_in_fabs Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp commit 1b13c4c02ad1f99176c6ea82b6051b9c83248807 Author: almgren Date: Mon Mar 19 19:15:51 2007 +0000 Need this to work on Ann and Andy's machines... Tools/F_mk/GMakedefs.mak commit 74763270b81554e61f6f04d464fa6fbeed1823f2 Author: lijewski Date: Wed Mar 14 01:17:37 2007 +0000 Knapsack called beneath SFC when too few grids for SFC, can now do MinimizeCommCosts(). Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 240d35f35fd3f9752f9a9e52171dabf53fd6c703 Author: lijewski Date: Tue Mar 13 21:35:54 2007 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit ff04a5c947efab92e3c15de02e707c0db1d86365 Author: lijewski Date: Tue Mar 13 17:01:23 2007 +0000 SFC is now the default Src/C_BaseLib/DistributionMapping.cpp commit 2722b88f65696221163badfb9978e31c45cef799 Author: lijewski Date: Fri Mar 9 04:40:43 2007 +0000 removed nProcsCFD() stuff Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 405a72db47994157a98e34f5bb8bd1096c5450ec Author: lijewski Date: Fri Mar 9 04:21:05 2007 +0000 array versions of REDUCE operators Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit e39f0a146bb3c4d9c99c8c98b5569e7d381c95f4 Author: 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 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 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 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 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 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 Date: Fri Feb 23 23:05:57 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 6a8a7109e2b5eb7b60b8b0fd95957736a9057038 Author: lijewski Date: Fri Feb 23 22:38:31 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit e02311abc7ce92ae727e1f9b9a67586c3856f02b Author: 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 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 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 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 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 Date: Wed Feb 21 17:19:34 2007 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/CGSolver.cpp commit cf8f201f0b3028909d5cc72413d9e5b78263e661 Author: 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 Date: Fri Feb 16 21:18:22 2007 +0000 set eps_rel to 1e12 Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 527bd14f4104df279d68ab3ec0ab8bebf2e7b202 Author: lijewski Date: Fri Feb 16 00:21:29 2007 +0000 Added version of FillPeriodic that doesn't do any parallelism to support use_jbb_precond in CGSolver.cpp. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 7438688d246e65db63d4809f119a7b6f3b85108a Author: lijewski Date: Fri Feb 16 00:19:19 2007 +0000 added version of FillBoundary that doesn't do parallel Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit d855590437cc587927bf49b53b1e47209b1b1955 Author: lijewski Date: Fri Feb 16 00:15:01 2007 +0000 Hash the mask calculations. Added stuff needed for use_jbb_precond. Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit aff4aa5096152f718dc56050d6598015ef5fe91d Author: lijewski Date: Fri Feb 16 00:12:58 2007 +0000 Removed CG_Alt and Automatic stuff. Added stuff needed for use_jbb_precond. Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp commit e5f1683f63605ec62c04e30c1f7e615ecf810ae7 Author: lijewski Date: Fri Feb 16 00:09:16 2007 +0000 stuff needed for use_jbb_precond Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp commit a5f038c21ea7a79b9c8b34ada2e4cc176eb119f8 Author: lijewski Date: Fri Feb 16 00:03:14 2007 +0000 removed CG_Alt stuff Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit d2e4d44a32c0c50f4dcf04c716e1bcc149ecb3ba Author: 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 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 Date: Fri Jan 26 20:16:45 2007 +0000 ParmParse'd fpb_cache_max_size Src/C_BaseLib/Geometry.cpp commit e815a67b82dffdb6b5bfbc58b971b3fddd965efa Author: lijewski Date: Fri Jan 26 19:23:40 2007 +0000 *** empty log message *** Src/C_BaseLib/MultiFab.cpp commit f35ee336f07db3b809525c60558375924636c75b Author: 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 Date: Fri Jan 26 19:03:14 2007 +0000 *** empty log message *** Src/C_BoundaryLib/FabSet.cpp commit 4bce76e693c18b43a56d0aa5a065d40b2a2e70f9 Author: 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 Date: Fri Jan 26 18:26:04 2007 +0000 ParmParse'd copy_cache_max_size Src/C_BaseLib/FabArray.cpp commit 1734bde3900c772a27c31b483afad528b052aa08 Author: lijewski Date: Wed Jan 24 18:11:28 2007 +0000 turn on some cache stats Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.cpp commit f6ecab07a285c8a606a18432d9352332fd750968 Author: lijewski Date: Thu Jan 18 17:22:19 2007 +0000 extra assertion in define() Src/C_BaseLib/FabArray.H commit 775a826538e3797348612edf4ece8b4aa0dc6d9c Author: lijewski Date: Thu Jan 18 17:22:04 2007 +0000 added copy constructor & assignment operator Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit cacb232aec2592fa496a4f0a3456436960f63a03 Author: almgren Date: Fri Jan 12 20:53:59 2007 +0000 Changed default nub from 0 to 10 so that after CG or BiCG bottom solver the code will do 10 relaxations -- this to deal with case when CG or BiCG just doesn't converge (and I don't know why). Src/LinearSolvers/F_MG/mg.f90 commit efb08bbbeaf0ebe6b0eddbfd7856498bb4026c6d Author: lijewski Date: Thu Jan 4 20:43:26 2007 +0000 oops Src/C_AMRLib/FluxRegister.cpp commit 7aeb75a42883ee29bad9135b9241e88eae505fa1 Author: 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 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 Date: Fri Dec 8 20:40:29 2006 +0000 changed some verbose stuff Src/C_BaseLib/DistributionMapping.cpp commit f5b960794ffee797a4723f9cd03fd1ec2109559e Author: almgren Date: Mon Dec 4 22:30:08 2006 +0000 Move multifab_remote after loop thru filenames -- checkpoint reading now works in parallel. Src/F_BaseLib/fabio.f90 commit 33f71937ecdc839ccff5ca7760000270f9661ca0 Author: almgren Date: Mon Dec 4 20:57:53 2006 +0000 Fix to make ml_multifab_read_d work in parallel... Src/F_BaseLib/fabio.f90 commit 8ce0c6582e1fc8803904189496a37ceb446a3ccd Author: mzingale Date: Fri Dec 1 15:45:33 2006 +0000 some gfortran fixes Tools/F_mk/GMakedefs.mak commit 3e824591b3a86ac2afe56344f49559ba8c03b47e Author: lijewski Date: Wed Nov 22 21:10:58 2006 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/grids/in.2_19boxes Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_3x2 Src/LinearSolvers/C_CellMG/Test/grids/in.2_big Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_d Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_e Src/LinearSolvers/C_CellMG/Test/grids/in.2_small_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_small_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_d Src/LinearSolvers/C_CellMG/Test/grids/in.2per_2x2_c Src/LinearSolvers/C_CellMG/Test/grids/in.3_2boxes_a Src/LinearSolvers/C_CellMG/Test/grids/in.3_2x3x4 Src/LinearSolvers/C_CellMG/Test/grids/in.3_big Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_a Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_b Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_c Src/LinearSolvers/C_CellMG/Test/grids/in.3_mac_tst Src/LinearSolvers/C_CellMG/Test/grids/in.3_shiftedUp Src/LinearSolvers/C_CellMG/Test/grids/in.3_small_a Src/LinearSolvers/C_CellMG/Test/grids/in.3_stack_a Src/LinearSolvers/C_CellMG/Test/grids/in.3per_2x3x4 Src/LinearSolvers/C_CellMG/Test/grids/in.grids.213 Src/LinearSolvers/C_CellMG/Test/grids/in.grids.5034 Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/grids/in.2_19boxes Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_a Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_b Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_c Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_a Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_b Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_c Tests/LinearSolvers/C_CellMG/grids/in.2_3x2 Tests/LinearSolvers/C_CellMG/grids/in.2_big Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_a Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_b Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_c Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_d Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_e Tests/LinearSolvers/C_CellMG/grids/in.2_small_a Tests/LinearSolvers/C_CellMG/grids/in.2_small_b Tests/LinearSolvers/C_CellMG/grids/in.2_stack_a Tests/LinearSolvers/C_CellMG/grids/in.2_stack_b Tests/LinearSolvers/C_CellMG/grids/in.2_stack_c Tests/LinearSolvers/C_CellMG/grids/in.2_stack_d Tests/LinearSolvers/C_CellMG/grids/in.2per_2x2_c Tests/LinearSolvers/C_CellMG/grids/in.3_2boxes_a Tests/LinearSolvers/C_CellMG/grids/in.3_2x3x4 Tests/LinearSolvers/C_CellMG/grids/in.3_big Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_a Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_b Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_c Tests/LinearSolvers/C_CellMG/grids/in.3_mac_tst Tests/LinearSolvers/C_CellMG/grids/in.3_shiftedUp Tests/LinearSolvers/C_CellMG/grids/in.3_small_a Tests/LinearSolvers/C_CellMG/grids/in.3_stack_a Tests/LinearSolvers/C_CellMG/grids/in.3per_2x3x4 Tests/LinearSolvers/C_CellMG/grids/in.grids.213 Tests/LinearSolvers/C_CellMG/grids/in.grids.5034 Tests/LinearSolvers/C_CellMG/main.cpp commit c3bebdd6a2beba4d119acf61212d12f6c65e968c Author: lijewski Date: Tue Nov 21 23:38:57 2006 +0000 changed sfc_threshold: 4 ==> 8 Src/C_BaseLib/DistributionMapping.cpp commit ac29bbc595772ce78c802c654b5ccf1d3f2d2897 Author: lijewski Date: Tue Nov 21 06:25:50 2006 +0000 more SFC tweaks Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 5a065a55a49e0addd3479c02de20a206d589a0ff Author: lijewski Date: Sun Nov 19 04:09:13 2006 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit 361fea84c0fd2cf5bb608e29ba05feb1a713a360 Author: lijewski Date: Sat Nov 18 05:07:25 2006 +0000 removed embedded CVS ID Src/C_BaseLib/DistributionMapping.H commit 7a7bbb18e9237aaadfbe3dbc1b7f3aab6fe51de7 Author: lijewski Date: Sat Nov 18 05:05:46 2006 +0000 initial cut at space filling curve mapping; more work to do ... Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 5c7d27314f831c90b9a5495031f7c5804127c896 Author: almgren Date: Sat Nov 11 05:57:26 2006 +0000 Fixed print statement so don't print NaN if res0 = 0. Src/LinearSolvers/F_MG/ml_cc.f90 commit 7743810d8dff738690a5fa4167042eaa8914e4b0 Author: marc Date: Thu Oct 12 16:45:12 2006 +0000 *** empty log message *** Tools/C_mk/Make.defs commit 2b32ab247e7a3161cf264df582bc7c9fee1308d2 Author: lijewski Date: Wed Oct 11 18:15:08 2006 +0000 added defined() Src/C_BaseLib/FabArray.H commit 9b807943fb99b02c50815ea9142422dd71c883e3 Author: sepp Date: Tue Oct 10 20:52:16 2006 +0000 1) added stuff for davinci that was checked over my Mike Tools/C_mk/Make.mpi commit e5a0578d4b34d08dd0582aa09dd985ace6881471 Author: 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 Date: Wed Oct 4 22:27:04 2006 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit 69ccf2d188d2f64e20915931ca08b2d6c4608e85 Author: lijewski Date: Sun Sep 24 00:40:19 2006 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit fbb75c95498eba237995ccd7d107eaa5b89251f9 Author: 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 Date: Sat Sep 16 03:20:59 2006 +0000 Fixed extra endif. Src/LinearSolvers/F_MG/mg_smoother.f90 commit 6db4a5ec58478b28fde9e6084116e824b576c5be Author: almgren Date: Sat Sep 16 00:52:54 2006 +0000 Fix weighting of different stencils. Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 25d5f0ec8fa549e5e23570967a022276cd7af50c Author: almgren Date: Sat Sep 16 00:52:35 2006 +0000 Fix weighting of residual for coarsening operations... Src/LinearSolvers/F_MG/ml_nd.f90 commit addb5daabdb98ba79f96b763ada39ad4dc4989a3 Author: almgren Date: Sat Sep 16 00:52:01 2006 +0000 Fix calling sequence to stencil_one_sided. Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit 8a5a1584811325f916f99f197eb0da8df5bfda05 Author: almgren Date: Sat Sep 16 00:51:35 2006 +0000 Small cleanup. Src/LinearSolvers/F_MG/nodal_divu.f90 commit d96ae34547005e07053994ab21bf668ffba6ce61 Author: almgren Date: Sat Sep 16 00:50:39 2006 +0000 Better write statements, also test in gsrb2d on whether any skewed... Src/LinearSolvers/F_MG/mg_smoother.f90 commit 02af82104b06271d78e3ab115dbad0b385e001cb Author: almgren Date: Fri Sep 15 23:57:51 2006 +0000 Fix print statement. Src/LinearSolvers/F_MG/mg.f90 commit 0de7e31b9c907e22cda8ae369b4a588243764490 Author: almgren Date: Thu Sep 14 21:03:49 2006 +0000 Remove "NXC" print statement. Src/F_BaseLib/interp.f90 commit 02ae4bdbe7ef0debb69472796dc2c04243cc25b3 Author: lijewski Date: Thu Sep 14 19:57:27 2006 +0000 *** empty log message *** Tools/C_util/Convergence/GNUmakefile commit 6f605244afcce7a89286f40ecb795b6a9685c3e9 Author: lijewski Date: Thu Sep 14 19:50:46 2006 +0000 *** empty log message *** Tools/C_util/Convergence/ComputeAmrDataNorms.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/GNUmakefile commit ed200285f17ce81f87d32ecd953201575f8029e6 Author: lijewski Date: Wed Sep 13 20:28:00 2006 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit e3128968528cee436cc1144c3dec464520059094 Author: lijewski Date: Wed Sep 13 18:03:22 2006 +0000 cleaned up some compiler warnings Src/C_BaseLib/BLThread.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit a59a02cba92fdbe0cd45b56b29098fa1de8d06f1 Author: lijewski Date: Tue Sep 12 22:51:04 2006 +0000 refinement to FPB caching Src/C_BaseLib/Geometry.cpp commit 9a34a49dee49973658cfe610e34d76d3e01ab826 Author: lijewski Date: Tue Sep 12 21:50:09 2006 +0000 refinements to caching Src/C_BoundaryLib/FabSet.cpp commit 393c70d5c1b319b660f68ae80840b8636e0f5484 Author: lijewski Date: Tue Sep 12 21:38:45 2006 +0000 *** empty log message *** Src/C_BaseLib/MultiFab.cpp commit 4378d712289e9d0c7abd5d27c40204d843d6067b Author: lijewski Date: Tue Sep 12 20:46:46 2006 +0000 refinement to FillBoundary caching Src/C_BaseLib/MultiFab.cpp commit 4a41e4035435623d65a2f282599de27e3652a84c Author: lijewski Date: Tue Sep 12 20:01:16 2006 +0000 refinement to copy caching Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit d053719564df013263ffe76b1b00604501ff201f Author: lijewski Date: Mon Sep 11 21:43:39 2006 +0000 flush copy() cache on regrid Src/C_AMRLib/Amr.cpp commit f417de25ca058949715ebfc93fe63f259ab1c679 Author: lijewski Date: Mon Sep 11 21:43:20 2006 +0000 added copy() caching Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit e30769dad88a75c430c2415394a1f5fdddfa3e16 Author: vince Date: Fri Sep 8 23:17:20 2006 +0000 change for jvn. Src/C_BaseLib/VisMF.cpp commit 112143b8f019ad0d23677ac1b299c8a0ee9a1f17 Author: vince Date: Fri Sep 8 20:44:02 2006 +0000 added support for specifying at run time the number of files written for a multifab. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit f9146825ff22b0da3b47624df71dba132b1671e6 Author: almgren Date: Thu Sep 7 18:30:22 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/GPackage.mak commit c8f63ceb12775c2155b6515ce50e8d8f20805d81 Author: lijewski Date: Wed Sep 6 17:26:53 2006 +0000 Box::length() -> Box::size() Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/Looping.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 91ed7ebe277faaf69089e4f19cf465a8e95b0f02 Author: lijewski Date: Fri Sep 1 23:10:36 2006 +0000 shut up some compiler message Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp commit 33959afafc331447dadf20acf7ffb2384c888e52 Author: lijewski Date: Fri Sep 1 21:28:06 2006 +0000 reverted out fillpatch caching Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp commit 552cb18f27869a34aecd14653d6b5126f24a547d Author: lijewski Date: Fri Sep 1 21:20:51 2006 +0000 DistributionMappings are now reference counted Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit d8d1d806806b8ed56dd1fa6623de78a84cca82c3 Author: almgren Date: Fri Sep 1 18:14:39 2006 +0000 Added absolute tolerance as optional argument to itsol_converged. Src/LinearSolvers/F_MG/itsol.f90 commit 5ecfc8cf81b78b2178b4357931376786103359e1 Author: almgren Date: Fri Sep 1 18:13:54 2006 +0000 Added abs_eps (absolute tolerance) in addition to rel_eps (relative tolerance). Also fixed weighting for dense stencil. Src/LinearSolvers/F_MG/mg.f90 commit a157b0c1bb835dbffef83d042ffaba1b385ce9c1 Author: almgren Date: Fri Sep 1 18:09:59 2006 +0000 Hopefully this has correctly weighted stencils for 2d and 3d, cross and dense... Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 75ec3b29c6d38008c6fefd7ce1eb5662a6f7c2ce Author: lijewski Date: Fri Sep 1 16:24:17 2006 +0000 removed METIS stuff Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 63399f7fc0cdadaf3729ce182309bd88064c5162 Author: mzingale Date: Fri Sep 1 15:09:29 2006 +0000 a useful script to aggregrate CVS logs into a nice GNU-style ChangeLog format Tools/F_scripts/cvs2cl.pl commit 48eae2f061e707cf5ed5119b84ff213684075bb0 Author: mzingale Date: Thu Aug 31 18:57:53 2006 +0000 add nodal_divu.f90 to the list of packages Src/LinearSolvers/F_MG/GPackage.mak commit 3fedc02adfdb891635f14d69b63558a6ab74bafa Author: lijewski Date: Wed Aug 30 00:39:20 2006 +0000 some consolidation of caching -v- no caching in CollectData Src/C_BaseLib/FabArray.H commit 85c990ef47c1ab39ba8ffb6a6536d0eb72acdb5a Author: lijewski Date: Tue Aug 29 19:52:49 2006 +0000 added ParmParse'd variable to disable caching in CollectData Src/C_BaseLib/FabArray.H commit 9fc7b4111501111b47f63061e7e51082c0ce3d86 Author: lijewski Date: Mon Aug 28 18:28:42 2006 +0000 some caching of FillPatch stuff Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 962f3b744e4ff800f3427250353f6ce2fa5b6b52 Author: lijewski Date: Sat Aug 26 03:47:42 2006 +0000 added amr_real[23]d.2.f to help work around columbia bug Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/amr_real2d.2.f Src/LinearSolvers/C_NodalMG/amr_real2d.f Src/LinearSolvers/C_NodalMG/amr_real3d.2.f Src/LinearSolvers/C_NodalMG/amr_real3d.f commit 15c14c7f8d22b67b65caf93fab7104b13a4678eb Author: almgren Date: Fri Aug 25 22:04:03 2006 +0000 Modified verbosity and removed extraneous argument "solver" Src/LinearSolvers/F_MG/mg.f90 commit 8dc45d0708e7a10e75a755de26b9a1c9657ab3d6 Author: almgren Date: Fri Aug 25 22:03:29 2006 +0000 Modified verbosity in ml_nd... Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 7023135bad54c17895897b6bdeb7b0184e4d8c14 Author: almgren Date: Fri Aug 25 22:02:25 2006 +0000 Modified the scaling for cross-stencil in 2d and 3d. Gives same answers in 3d as in 2d. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit dcd011f9e06f639582af493c36cb1c2d98cb7468 Author: almgren Date: Fri Aug 25 22:01:55 2006 +0000 This nodal_divu is now called from f90 varden codes as well as from mg_nodal_cpp.f90 Src/LinearSolvers/F_MG/nodal_divu.f90 commit 1c6a329b73b087c100fb012e571a8e8bd0829f60 Author: almgren Date: Fri Aug 25 22:01:17 2006 +0000 Turned off special nodal stopping criterion in CG solve. Src/LinearSolvers/F_MG/itsol.f90 commit f9c28f077e40468c775e9b332154ba3f3fd8afec Author: 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 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 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 Date: Sat Aug 19 03:47:04 2006 +0000 didn't have caching quite right Src/C_BaseLib/FabArray.H commit 6012f6c8db04be84e235d1e32ee2740eff676c40 Author: 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 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 Date: Fri Aug 18 22:05:44 2006 +0000 Small change in formatting. Src/LinearSolvers/F_MG/mg_cpp.f90 commit ee76cba30582767ea66acef21e73d466b22b1318 Author: almgren Date: Fri Aug 18 22:04:38 2006 +0000 Added "save" to mgts declaration. Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit 0cb66662056e3a52451ef23f2f275184edb26737 Author: almgren Date: Fri Aug 18 20:29:01 2006 +0000 New interface for bc's. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit fa761ab908cdc4c0194bda849ae950b9f2417e25 Author: lijewski Date: Wed Aug 16 20:41:32 2006 +0000 can now ParmParse between send/recv & alltoallv in copy & collectdata Src/C_BaseLib/FabArray.H commit 75fbfaf9462cca20b09a62f06ad6e65ca5945b62 Author: almgren Date: Wed Aug 16 19:53:49 2006 +0000 Added new functionality to do diffusive solves as well as MAC solves. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 commit 7555ae44ec3c5c059d97e39d3dd5a12d7e5c4176 Author: 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 Date: Tue Aug 15 19:16:47 2006 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.f commit 631f73c51ed2ccf447c880c3cf852d8fcbdadd67 Author: almgren Date: Tue Aug 15 19:14:18 2006 +0000 Fix definition of nx,ny,nz in grid_divu_3d. Src/LinearSolvers/F_MG/nodal_divu.f90 commit 40ebc5ac0abb6fca376b0440feb56872d480f1c4 Author: 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 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 Date: Tue Aug 15 19:10:30 2006 +0000 commented out couple prints Src/LinearSolvers/F_MG/mg_cpp.f90 commit 2d36dd465e5d9ae735200f65aa6f3b3e1418510f Author: 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 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 Date: Tue Aug 15 04:40:00 2006 +0000 Fixed typo. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 7f7f8788ef35beba7eb220f4d04eeae3584f39ad Author: lijewski Date: Tue Aug 15 02:30:43 2006 +0000 Can now ParmParse whether or not to use alltoallv in copy(). Src/C_BaseLib/FabArray.H commit 3448e61489b73f605474ee0abd7b3332487cc14b Author: almgren Date: Tue Aug 15 02:18:18 2006 +0000 Latest version which calls cc and nodal multigrid solvers. Src/LinearSolvers/C_to_F_MG/MGT_Solver.H commit 88cc62d4822066c22d5630f29749b7936ba119d9 Author: almgren Date: Tue Aug 15 02:17:52 2006 +0000 Latest version which calls nodal as well as cc multigrid solvers. Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 4435398f132d85293e909b6664d41b22ac398180 Author: almgren Date: Tue Aug 15 02:15:51 2006 +0000 Latest stuff to enable cc and nodal multigrid calls from IAMR. Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_nodal_cpp.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit c20c70dcc51a36b6d02282edb079bed7640b56a2 Author: lijewski Date: Tue Aug 15 01:19:15 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg.f90 commit 3fc1dde8f4d889c24a65e129cbd0d42087756882 Author: almgren Date: Mon Aug 14 21:15:03 2006 +0000 Remove commented line. Src/LinearSolvers/F_MG/mg.f90 commit 1bd1956e99750d05f121bcdb5bff530919f06742 Author: almgren Date: Mon Aug 14 20:27:02 2006 +0000 Added new files... Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/GPackage.mak commit 3348963cfc10f3e8460a2f1235ee43be7651008c Author: almgren Date: Mon Aug 14 20:26:44 2006 +0000 New routines to handle calls from IAMR. Src/LinearSolvers/F_MG/nodal_divu.f90 Src/LinearSolvers/F_MG/nodal_mask.f90 Src/LinearSolvers/F_MG/nodal_newu.f90 commit 1aad05ff744384ab4b705fb8791152dbaf386ce8 Author: lijewski Date: Mon Aug 14 20:22:12 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg_smoother.f90 commit 9a3195f67a9ee33867ad1bf6df99939ec064546d Author: almgren Date: Mon Aug 14 20:07:44 2006 +0000 Make mgt%skewed(nlev,ngrids) a member of mgt instead of calculating every time we call the smoother... Src/LinearSolvers/F_MG/mg.f90 commit 6d4ed5cf4049941a8b168a06797b7d8ddc901b8b Author: 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 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 Date: Wed Aug 9 18:00:41 2006 +0000 do NOT do alltoallv() by default Src/F_BaseLib/multifab.f90 commit 4997b0e71976bc1a40dcfb56e773d8d57612a50b Author: lijewski Date: Wed Aug 9 04:20:14 2006 +0000 merged in nocomm=.true. in copy() & fill_boundary() Src/LinearSolvers/F_MG/sparse_solve.f90 commit bd69519ae725a56fcbfbfadbd5bd33a86ece9353 Author: 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 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 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 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 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 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 Date: Mon Aug 7 18:23:00 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg.f90 commit 78f986e1ae4829ee1b59c003df85c372a155f29f Author: lijewski Date: Mon Aug 7 18:22:45 2006 +0000 only call MPI_Init() if MPI_Initialized() is false Src/F_BaseLib/parallel.f90 commit 1eb6e2064d001eaab7363e418ef1e62803be8e0d Author: lijewski Date: Fri Aug 4 22:33:01 2006 +0000 removed weird embedded comment Src/F_BaseLib/parallel.f90 commit f96ecbaebd1184df0b2490e73bc1e118d947876d Author: lijewski Date: Fri Aug 4 22:26:57 2006 +0000 moved mpi.f into parallel.f90 Src/F_BaseLib/GPackage.mak Src/F_BaseLib/parallel.f90 commit 69c527c49637869648bee94ad816ecf505a5b455 Author: lijewski Date: Fri Aug 4 22:26:18 2006 +0000 *** empty log message *** Src/F_BaseLib/mpi.f commit ba601449e5f67a9004f8686c25080ed5104242cc Author: 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 Date: Fri Aug 4 22:25:34 2006 +0000 removed mpi.f Src/LinearSolvers/F_MG/FParallelMG.mak commit 2f5a66a282e5d6d8beb077f4edbf8d5308b85657 Author: lijewski Date: Fri Aug 4 22:24:03 2006 +0000 f90 stuff Tools/C_mk/Make.AIX Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit f8266e666d24b081033738fba0222a62c063f571 Author: 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Fri Jul 21 22:16:39 2006 +0000 cfe3 -> cfe Tools/C_mk/Make.defs commit 981f3aa3627010a40f90d789b80fe2d903c361ad Author: 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 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 Date: Tue Jul 18 03:56:30 2006 +0000 optimization flags for columbia Tools/C_mk/Make.Linux commit 73c6e3016ad5c3e1ce774d04fbf579152f960323 Author: lijewski Date: Tue Jul 18 03:55:34 2006 +0000 turn off a bunch of Intel stuff that doesn't always work Tools/C_mk/Make.defs commit 9ef3aa382957fdd4ef81cf573f213e01e41925dc Author: lijewski Date: Thu Jul 13 21:08:56 2006 +0000 ipo -> ip for Columbia Tools/C_mk/Make.Linux commit 2044330744c8a6f510ea85d5af73aedab29ac303 Author: 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 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 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 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 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 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 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 Date: Tue Jun 27 20:24:52 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg_smoother.f90 commit 16263e580645ea754263fee3fb3f9f35f3248b75 Author: 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 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 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 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 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 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 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 Date: Thu Jun 22 22:15:46 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg_smoother.f90 commit fb63ac5ed1a73d3240c3b3a6ca4901579a8751f9 Author: almgren Date: Thu Jun 22 21:37:01 2006 +0000 Now has capability for 7-point (3d cross) nodal stencil. Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 6daa59fe617d437af377302ed0b557a052f8c709 Author: almgren Date: Thu Jun 22 21:30:59 2006 +0000 Now has capability for 7-point (cross stencil in 3d) Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 0b7754bbd8fcb931ef04163e58843de93a70376e Author: car Date: Thu Jun 22 19:28:13 2006 +0000 closer Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 778dfb439d6b905025e4d47921cc8e0f88de0157 Author: car Date: Thu Jun 22 19:27:37 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit b8d2cc1428cfa82d4326df80b980ba5a259fe011 Author: car Date: Thu Jun 22 19:27:26 2006 +0000 stop using optional unit Src/F_BaseLib/layout.f90 commit fdf74ee15d74ae7f587370ac87ecd09693ce8abd Author: almgren Date: Thu Jun 22 02:37:12 2006 +0000 Fix calling sequence for first subroutine. Src/LinearSolvers/C_NodalMG/amr_real3d.f commit a32467c6d8e4a72371ab91e7e8e2db124f09b802 Author: car Date: Wed Jun 21 22:52:15 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg_cpp.f90 commit 74b48fae8e0c2dda5e3b6a213a29bdd7779b0b9e Author: 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 Date: Wed Jun 21 17:40:12 2006 +0000 mods for cfe3 Tools/F_mk/GMakeMPI.mak commit cc0e3aeeeac0a69bcd004c892d50cef29776a621 Author: lijewski Date: Tue Jun 20 19:36:38 2006 +0000 *** empty log message *** Tools/F_mk/GMakedefs.mak commit 0448c0c2ff12f76728b5d1c5206521a5f8c9cb16 Author: car Date: Tue Jun 20 16:42:03 2006 +0000 changes for c++/f90 Src/F_BaseLib/ml_boxarray.f90 Src/F_BaseLib/ml_layout.f90 Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/main.cpp Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/ml_nd.f90 Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/main.cpp Tools/C_mk/Make.defs commit 923c7b8cebebad60cebd5ea760ff52a412ee1eb9 Author: almgren Date: Tue Jun 20 06:50:14 2006 +0000 Put abs() around quantities in convergence test. Src/LinearSolvers/F_MG/itsol.f90 commit 1594d9c525005ac243f940ead27dd36884bda043 Author: lijewski Date: Mon Jun 19 21:06:57 2006 +0000 removed ml_crse_contrib_easy() Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit f08d82bca3134b30d0f5fd953ee7d5da480ff159 Author: lijewski Date: Fri Jun 16 22:08:13 2006 +0000 -Ofast => -O2 for PathScale Tools/F_mk/GMakedefs.mak commit b285d554af674d09fb5cd754f837954ec1d92275 Author: lijewski Date: Fri Jun 16 21:24:35 2006 +0000 *** empty log message *** Src/F_BaseLib/layout.f90 commit ba2e3dcee65e894b909adee5df45b358dafabdba Author: lijewski Date: Fri Jun 16 20:57:52 2006 +0000 fixed bug in fluxassoc_build Src/F_BaseLib/layout.f90 commit 5b3dce23ea1d4223066cc3eff62bb7da37270fce Author: 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 Date: Thu Jun 15 20:34:10 2006 +0000 removed all 'easy' functions Src/F_BaseLib/multifab.f90 commit cf0907374307fb9f3f45e99cdf6f3316008388ed Author: 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 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 Date: Wed Jun 14 22:13:12 2006 +0000 PGI fixes Src/F_BaseLib/layout.f90 commit 04cb170d0c1aaeaf96db7e54d3adac19f09c6c1d Author: lijewski Date: Wed Jun 14 22:06:59 2006 +0000 fixes for PGI Src/F_BaseLib/knapsack.f90 commit bc29730a71a9f027af4668f99d86bc7649c27c89 Author: lijewski Date: Wed Jun 14 20:55:54 2006 +0000 PGI mods Tools/F_mk/GMakedefs.mak commit f17c254f4af153361cc868b8f38e386be9fe08ec Author: lijewski Date: Tue Jun 13 22:20:29 2006 +0000 initial cut at XT3 (catamount) Tools/F_mk/GMakedefs.mak commit 004882171889825a7cfa45e47ba235991273d44a Author: lijewski Date: Tue Jun 13 22:19:31 2006 +0000 fixes for jaguar (XT3) Src/F_BaseLib/bl_types.f90 Src/F_BaseLib/sort_box.f90 commit f3c606bccec3c38f1c2df0fcac358e581f593e22 Author: lijewski Date: Tue Jun 13 20:45:46 2006 +0000 sped up boxassoc_build Src/F_BaseLib/layout.f90 commit cf8e75da153c4ae30974e8e38de33ad2fa78bd20 Author: lijewski Date: Tue Jun 13 18:23:29 2006 +0000 speed up of unique_cover Src/F_BaseLib/layout.f90 commit 8fad29ae3cf95345af2d1f9afd56d00383e55a83 Author: lijewski Date: Tue Jun 13 18:00:48 2006 +0000 added optional sort arg to boxarray_build_l Src/F_BaseLib/boxarray.f90 commit a255e65ba4bfabf254c5267249607ef45f729e9d Author: lijewski Date: Tue Jun 13 18:00:10 2006 +0000 *** empty log message *** Src/F_BaseLib/bndry_reg.f90 commit ea719b9d80d047ab2ef42cedbfb635a0115ebfdd Author: car Date: Tue Jun 13 17:07:10 2006 +0000 test of knapsack Src/F_BaseLib/test/ball_def.14656 Tests/F_BaseLib/ball_def.14656 commit 0c57d5f6bdfae445cb45bc92c57c9b04db5f40cd Author: car Date: Tue Jun 13 16:46:20 2006 +0000 changes for c++/fortran Src/F_BaseLib/ml_layout.f90 Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp commit 4c0c739241df01a97503847da9c9329b87c6bc02 Author: car Date: Tue Jun 13 16:46:04 2006 +0000 changes for fortran/c++ Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/ml_cc.f90 commit 7d173b48a10eb375ee151f25c0b4629fbf3ae89e Author: 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 Date: Tue Jun 13 15:41:28 2006 +0000 bug fix for hash stuff Src/F_BaseLib/layout.f90 commit 251a709af51d9aaf4459365e87301cb9e62e2bc6 Author: lijewski Date: Tue Jun 13 03:43:51 2006 +0000 added more timers Src/F_BaseLib/bndry_reg.f90 commit f31e713a82bc89d8fc105bb31beabe48a53b515d Author: lijewski Date: Mon Jun 12 23:25:48 2006 +0000 check (a hack) that call trees are the same across CPUs Src/F_BaseLib/bl_prof.f90 commit dac1bc7ab84e0bdf86443e1835e82e58eaa4fa52 Author: lijewski Date: Mon Jun 12 22:32:03 2006 +0000 *** empty log message *** Src/F_BaseLib/bl_timer.f90 commit 9bf87ab80c1429c570da26938f9efb0472341a6f Author: lijewski Date: Mon Jun 12 22:31:42 2006 +0000 removed ba_bndry_periodic timer Src/F_BaseLib/layout.f90 commit 54eec73461e481252e6f9c64e599b3c6862bd12b Author: lijewski Date: Mon Jun 12 21:04:10 2006 +0000 commented out private statement Src/F_BaseLib/bl_timer.f90 commit 8ed9119c2bbac9d94360e83ebde7b921f5457a30 Author: lijewski Date: Mon Jun 12 17:14:14 2006 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Utility.cpp commit e046bab253a64fee7617ef586a50b8c8527496a7 Author: almgren Date: Fri Jun 9 23:06:00 2006 +0000 1) added construction of singular flag 2) added two relaxations at bottom level after the CG solver is called (to match results of Parallel/hgproj code) Src/LinearSolvers/F_MG/mg.f90 commit c387497128c0bccbf81f59c852ef3bc68c5cda96 Author: almgren Date: Fri Jun 9 22:34:19 2006 +0000 Modify the CG and BiCG solvers to take a flag which says if the problem is singular. If true, then subtract off the average of the RHS from each value of the residual to make it solvable. The flag is optional. Src/LinearSolvers/F_MG/itsol.f90 commit 11aef1c08276469c573aa7032ab29a964e12e9e9 Author: almgren Date: Fri Jun 9 22:32:50 2006 +0000 In the multilevel convergence test, we were incorrectly computing the residual on the coarsest level if there were more than two levels, because the level 1 residual was averaged down to level 0 before the coarse-fine corrections (from the level 1-2 interface) were used to modify the level 1 residual. This is now fixed. Src/LinearSolvers/F_MG/ml_nd.f90 commit c7f84c0958a1f551d77939770990655f15ad1243 Author: almgren Date: Thu Jun 8 20:53:12 2006 +0000 This file is a simpler case than gtbig3 of a case that breaks the Parallel/hgproj 3-d 27-point (dense) solver - the solver will not converge because values of the solution on different grids are different. Src/LinearSolvers/C_NodalMG/gt_breaks_27pt commit a3fce98eb4a860133c1a7ef3939e7c55467c515a Author: lijewski Date: Wed Jun 7 22:15:40 2006 +0000 added verbose flag Src/F_BaseLib/layout.f90 commit b6cf26110ede30756c9e7719c9d53be52abb1782 Author: lijewski Date: Wed Jun 7 22:15:10 2006 +0000 removed nocomm stuff Src/F_BaseLib/multifab.f90 commit 6d0e9bdfae4d609e32c98b50e1b4619b36677d35 Author: lijewski Date: Wed Jun 7 19:33:11 2006 +0000 cleanup & simplification Src/F_BaseLib/multifab.f90 commit db4ef8eb0cf7bb31d27efc666f80aadf7bfdb04d Author: 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 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 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 Date: Mon Jun 5 21:39:51 2006 +0000 added alltoall() for integer data Src/F_BaseLib/parallel.f90 commit 308c42d8a31c9757d3dbf5566d0bd79c385db88d Author: car Date: Mon Jun 5 21:25:15 2006 +0000 pointer, intent conflict Src/F_BaseLib/layout.f90 commit 47c149a00666b35c02fb917b3a8015885d446bf3 Author: 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 Date: Fri Jun 2 16:35:49 2006 +0000 little cleanup Src/F_BaseLib/bndry_reg.f90 commit 45cbe976ec681c96e989780b71e8265082e513b4 Author: lijewski Date: Thu Jun 1 22:23:37 2006 +0000 fast parallel internal_sync Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab.f90 commit 4344b91cdc8ed386ef66fa389457b54d6be3a089 Author: 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 Date: Thu Jun 1 20:18:58 2006 +0000 made a private member public Src/F_BaseLib/boxarray.f90 commit 155db2d5ea977ddc18d444e2d74735060340be44 Author: lijewski Date: Wed May 31 20:42:49 2006 +0000 AIX mods Tools/F_mk/GMakedefs.mak commit 6ff889b9643c794098becc12779ff4be70fc8a03 Author: lijewski Date: Wed May 31 20:16:49 2006 +0000 tad simplification Src/LinearSolvers/F_MG/ml_restriction.f90 commit d4e94ecde1f35d60fd2bff9037198ebec8bd4d74 Author: 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 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 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 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 Date: Tue May 30 17:47:44 2006 +0000 added timer to boxarray_add_clean Src/F_BaseLib/boxarray.f90 commit e8e93fb76a23b931b037d5f7fb7eb564bb589721 Author: lijewski Date: Tue May 30 17:47:23 2006 +0000 sped up stencil_fill_nodal for periodic Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 3524c04144af5d85c8ca4880554fea8a189c068b Author: lijewski Date: Sat May 27 17:59:24 2006 +0000 memory management cleanup; expanded copy_sum() Src/LinearSolvers/F_MG/ml_restriction.f90 commit d656cc1dcc6077510f2de79f2d4e9bee251878ed Author: lijewski Date: Sat May 27 05:12:00 2006 +0000 remove dull_copy_d(); use cpy_d(); more remote()s Src/F_BaseLib/multifab.f90 commit 7a54d66bbee4dfbdf8d3f97f51cdae71090eb3b4 Author: 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 Date: Sat May 27 03:44:25 2006 +0000 added timer to internal_sync Src/F_BaseLib/multifab.f90 commit 7b518a12a4fe0f9534ce8527148305480e1b2312 Author: lijewski Date: Fri May 26 23:39:18 2006 +0000 added timers Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 94d97f0c7bbec260acffbb34a1a87a76e6bc6796 Author: lijewski Date: Fri May 26 23:20:55 2006 +0000 added a remote() cycle test Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 7a9d38fb00e028d9adf78ddae3ab4272ee705cd3 Author: lijewski Date: Fri May 26 23:20:25 2006 +0000 moved fill_boundary() around Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_util.f90 commit e95f365419ac1a60f36f10eb243055dd0c1378d1 Author: 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 Date: Fri May 26 20:42:44 2006 +0000 changed name of timer Src/F_BaseLib/layout.f90 commit a4422a93a14e9a59fa4cb0f23217126f2433c654 Author: almgren Date: Fri May 26 19:23:21 2006 +0000 Fixed bug in indexing in nodal_restriction_3d (ONLY 3D). Src/LinearSolvers/F_MG/mg_restriction.f90 commit 452892d37cb316a7b4c08985d9e052fa0048b438 Author: lijewski Date: Fri May 26 18:23:43 2006 +0000 removed async stuff & added timers Src/F_BaseLib/multifab.f90 commit 6b5a20092aee9a4afc4fe7af8596b5541e853422 Author: lijewski Date: Fri May 26 18:23:16 2006 +0000 added some timers Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 11bcaf81ed74570ef32c40026ba168b9d40aa775 Author: car Date: Fri May 26 18:11:14 2006 +0000 unused variable Src/C_BaseLib/ParmParse.cpp commit 066cf855bae1c850cff92674417c0e0a77052629 Author: lijewski Date: Thu May 25 21:50:26 2006 +0000 merged periodic_add_copy()s Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 commit e29a79b0c06a15fe5a78972310574bc7ff5a4d3f Author: almgren Date: Thu May 25 20:11:41 2006 +0000 We need to have two different periodic_add_copy routines, depending on whether the multifab src is already synced up at overlapping nodes. Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 commit f718b1fe0d15eae694b1ba5cb45e1f97b89d35d7 Author: lijewski Date: Thu May 25 19:19:51 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 commit 40f94ec0822240936ca5645e61f7873a28db838c Author: 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 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 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 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 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 Date: Tue May 23 04:40:22 2006 +0000 some cleanup Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 55f2c8729bac9a6c7dcfaf97ba5f52cfe0ca2732 Author: 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 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 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 Date: Mon May 22 20:48:03 2006 +0000 some cleanup Src/LinearSolvers/F_MG/ml_nd.f90 commit a679eb206ec8d084ad7e025ec88a714c99c42fbd Author: almgren Date: Mon May 22 20:42:53 2006 +0000 Moved periodic_add_copy functionality from ml_nd into ml_restriction for first call anyway...will still need to deal with 2nd call to periodic_add_copy... Src/LinearSolvers/F_MG/ml_restriction.f90 commit 14749623548993b87ba05e7de354bb9bbd7465ce Author: lijewski Date: Mon May 22 20:37:42 2006 +0000 think I got ml_crse_contrib() parallelized Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 1f8aac76145a0cd1879c69d183519537a7ec9eca Author: lijewski Date: Mon May 22 17:19:21 2006 +0000 some cleanup; not yet parallel-ready Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 750bb1aaa6f3479bb79468696ccaaf441fa7859d Author: 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 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 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 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 Date: Fri May 19 00:14:09 2006 +0000 fixed '>' sign. Src/C_AMRLib/INTERP_3D.F commit b5f5f139c93777c005446559916f03dbccbb9b9b Author: car Date: Thu May 18 21:15:24 2006 +0000 mgt_solver suppt Src/LinearSolvers/C_CellMG/Make.package Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/main.cpp commit 17a5a778bee048919a6a0101035ae00b7def3306 Author: car Date: Thu May 18 21:14:49 2006 +0000 *** empty log message *** Src/LinearSolvers/C_to_F_MG/MGT_Solver.H Src/LinearSolvers/C_to_F_MG/MGT_Solver.cpp Src/LinearSolvers/C_to_F_MG/Make.package commit 44ec6604f4f7c705b86a2a791a37da37583d14da Author: vince Date: Wed May 17 21:34:13 2006 +0000 gatherv fix for romulus. Src/C_AMRLib/Amr.cpp commit 0b3291b0f064d26f4b0d10c19dfde04fc6271d38 Author: almgren Date: Wed May 17 19:53:40 2006 +0000 Necessary corrections to handle periodic bcs. This has been tested for all combinations of bc's with grids in data/hgproj_grids. Src/LinearSolvers/F_MG/ml_nd.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 7467a081e915e711c7d9e5fe46adc07272cbb9fa Author: lijewski Date: Tue May 16 22:28:37 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/ml_nd.f90 commit 3040b62dbf63e2af3b8760815de83147f32b749c Author: lijewski Date: Tue May 16 21:50:21 2006 +0000 *** empty log message *** Src/LinearSolvers/F_MG/ml_nd.f90 commit ccbdb6f8d6373e5641b156e4141add27afe53ae5 Author: 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 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 Date: Tue May 16 21:17:59 2006 +0000 *** empty log message *** Tools/F_mk/GMakeMPI.mak commit dd8a57753304a62dfec5ac980643025334c3e4e5 Author: 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 Date: Tue May 16 21:03:14 2006 +0000 Needed correction for periodic. Src/LinearSolvers/F_MG/ml_util.f90 commit e40f584b151d0b94b48157a40a541ce6ff797dd5 Author: car Date: Mon May 15 21:10:35 2006 +0000 a print function Src/F_BaseLib/ml_layout.f90 commit d189ec9aec0cea272b1756181a43e6e1ce0cbe6c Author: car Date: Fri May 12 23:01:24 2006 +0000 needed Src/F_BaseLib/test/t_bl_prof.f90 Tests/F_BaseLib/t_bl_prof.f90 commit 6be5654342348c790b1cdeaf1b0ca3f18e609047 Author: car Date: Fri May 12 23:01:14 2006 +0000 some parallel support Src/F_BaseLib/bndry_reg.f90 commit de2dde80397b29a837a9f3e6c461c7f46e3bc85e Author: car Date: Fri May 12 23:01:05 2006 +0000 extra printouts Src/F_BaseLib/layout.f90 commit 6633bbf816200c3aef896bf31df7948ff0f77b78 Author: car Date: Fri May 12 23:00:48 2006 +0000 should use bnd reg for flux reg Src/F_BaseLib/GPackage.mak Src/F_BaseLib/flux_reg.f90 commit d9bc7a2d171063dbeae04679ea2f1636f15c21d8 Author: car Date: Fri May 12 23:00:15 2006 +0000 nil Src/F_BaseLib/flux_reg.f90 commit 8ee1fcc2afdbb13af739624720794d6aaab989bd Author: 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 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 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 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 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 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 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 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 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 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 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 Date: Wed May 3 18:19:29 2006 +0000 removed length limit on tokens Src/C_BaseLib/ParmParse.cpp commit 387bc9a8972eeb895819439a5346292af7d6844d Author: lijewski Date: Tue May 2 21:25:33 2006 +0000 *** empty log message *** Src/C_AMRLib/Amr.cpp commit 773af358f840598efafaa7e844d0c3bc0eafae12 Author: car Date: Tue May 2 18:41:38 2006 +0000 *** empty log message *** Src/C_BaseLib/SPECIALIZE_1D.F commit f4d9676992ba70295a3d0879b8fbfcc439d1b300 Author: lijewski Date: Tue May 2 18:01:15 2006 +0000 no Src/C_AMRLib/INTERP_1D.F commit 53693f577dd6b9019bb04f2db6927fa1b2d0cde4 Author: lijewski Date: Tue May 2 16:47:05 2006 +0000 from Greeno Src/C_AMRLib/ARRAYLIM_1D.F Src/C_AMRLib/SLABSTAT_1D.F commit 7302f6fe08a3cf726f478ed66b534d13c903225d Author: lijewski Date: Tue May 2 16:39:25 2006 +0000 removed some BL_LANG_CC stuff Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H Src/C_BaseLib/Utility.H commit 2e9bd456af2b7dd5e469a08affede8047544da70 Author: lijewski Date: Mon May 1 20:26:34 2006 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Utility.cpp commit 2bca812703597a66bc76581c79cafba50ec60403 Author: lijewski Date: Mon May 1 19:19:13 2006 +0000 up from 200 to 100000 to accomodate long material_input entries in geodyne Src/C_BaseLib/ParmParse.cpp commit cec8d87c3fc09c4f2fa40952c34fcaf88a8bb260 Author: car Date: Mon May 1 19:19:12 2006 +0000 not sure i'll need this Tests/LinearSolvers/F_MG/bc_interp.f90 commit 64912f65e5e4d852a1260ad9eef720b8435b0d6b Author: lijewski Date: Thu Apr 27 21:22:01 2006 +0000 bug fix Src/C_BaseLib/FabArray.H commit b1e912e0f289482517ab201dfc55494bca58c0c9 Author: car Date: Thu Apr 27 21:03:08 2006 +0000 gfortran bug work-around Src/F_BaseLib/list_box.f90 commit 46293460425014524097e8c76f78e3656185b0f2 Author: 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 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 Date: Mon Apr 24 22:36:31 2006 +0000 more tweaks to CollectData() Src/C_BaseLib/FabArray.H commit f0bc86bf134c3fc3b310ced898ab457515f65422 Author: lijewski Date: Mon Apr 24 21:11:03 2006 +0000 added #ifdef BL_MPI ... #endif Src/C_BaseLib/FabArray.H commit 8d1f0b4ee4365ea6e9ac8df036c812a67bfa28b8 Author: lijewski Date: Mon Apr 24 17:27:49 2006 +0000 now uses MPI group operations Src/C_AMRLib/FluxRegister.cpp commit 994e649bcad5f289903d0c78e4c2fd00fb8c80fb Author: car Date: Fri Apr 21 20:16:57 2006 +0000 parallel safe printing Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 447809865cb0b7edee492b22aadfe03996e30f72 Author: lijewski Date: Thu Apr 20 20:15:38 2006 +0000 slight tweak to CollectData() Src/C_BaseLib/FabArray.H commit 48144677369929b588e02fbc823f6bb8343cc658 Author: 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 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 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 Date: Sat Apr 8 00:01:42 2006 +0000 use MPI_Gatherv() in VisMF::Write() Src/C_BaseLib/VisMF.cpp commit d0bb2a59fe32c29775651ec0a10e5fc66adc9858 Author: lijewski Date: Fri Apr 7 20:51:59 2006 +0000 use gatherv() instead of send()/recv() for Header build Src/C_BaseLib/VisMF.cpp commit 49004c894b41e46ecfd73e9f12195d822e9284f9 Author: car Date: Thu Apr 6 13:52:53 2006 +0000 reformat Src/F_BaseLib/ml_multifab.f90 commit 9b43671b95c2fde38d69d13d1e4adc283294f3fd Author: car Date: Thu Apr 6 13:52:23 2006 +0000 lall needed to protect all Src/F_BaseLib/multifab.f90 commit 788d190390bfff0f25b0d3acf23962b7cf26ce9c Author: almgren Date: Tue Apr 4 20:15:51 2006 +0000 Made same fixes for 3d as well. Src/LinearSolvers/F_MG/mg_smoother.f90 commit 85786394d0784fb354b11f7c28445b09607e6848 Author: almgren Date: Tue Apr 4 20:11:14 2006 +0000 Fix to bug in gs_rb_smoother_2d which caused crash at lowest MG level in non-square grid. Src/LinearSolvers/F_MG/mg_smoother.f90 commit 4c005cbd52fdbcfffbc749762492f3f618176733 Author: marc Date: Fri Mar 31 22:27:35 2006 +0000 reduce precision Src/C_AMRLib/Amr.cpp commit e08cc248099f0f9d77b6a6df2f51032207c651da Author: 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 Date: Fri Mar 31 21:42:50 2006 +0000 add a couple of timers Src/C_BaseLib/VisMF.cpp commit 2a2f89ba760f71d7b8d10cf5c11a12fdff9ea9dd Author: vince Date: Thu Mar 30 21:52:12 2006 +0000 test for old style box. Src/C_BaseLib/Box.cpp commit b0c63803e163608335b2d51c2e7cace3fca5435a Author: car Date: Tue Mar 28 00:05:30 2006 +0000 *** empty log message *** Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_knapsack.f90 Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_knapsack.f90 commit 6bb08baedfc5844076f901b78a2805e25564ed10 Author: car Date: Mon Mar 20 20:06:28 2006 +0000 test for ann Src/F_BaseLib/multifab.f90 commit e3c07c28d21e6af07df42157b91a22de3210c16e Author: vince Date: Thu Mar 16 19:04:34 2006 +0000 additions for columbia. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 8b5bd3fd275f801ae90ba2d33b41c4544e3b3ba0 Author: 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 Date: Mon Mar 6 22:23:50 2006 +0000 forward decls needed Src/C_BaseLib/FabArray.H commit 530011db83fdce7510d3875cc02360f74f58ca7e Author: car Date: Mon Mar 6 19:24:44 2006 +0000 missing declarations Src/C_BaseLib/VisMF.H commit 18776ab510aacbaf89a3fe8f514c06400fe9d9cf Author: 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 Date: Tue Feb 14 18:56:23 2006 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit 8fc0005ac6a6fdf726679004494d8bb482070bd3 Author: car Date: Fri Feb 10 22:18:40 2006 +0000 fewer includes when not profiling Src/C_BaseLib/Profiler.H commit 86d7f09893c3261959616714b47852f9e6e1a8f2 Author: car Date: Fri Feb 10 22:18:17 2006 +0000 need string include Src/LinearSolvers/C_NodalMG/RegType.H commit cea4b7710ee109333ea9a8687a370920540a7be6 Author: car Date: Fri Feb 10 17:22:02 2006 +0000 some code needing further testing Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit c1cc3eef684eb5ad17303167e82ad23b97bb7107 Author: car Date: Fri Feb 10 17:20:22 2006 +0000 cleaned up makefile Src/LinearSolvers/C_NodalMG/GNUmakefile commit 30454112db1b2737300555a3807c741ff8eacdf5 Author: car Date: Fri Feb 10 17:10:31 2006 +0000 naphta Tools/C_mk/Make.mpi commit 2eccfd29060cf4a004ce24136da60b394830fa6a Author: car Date: Fri Feb 10 17:10:11 2006 +0000 BROWSE Tools/C_mk/Make.rules commit c9f645efff9018faddad31b872270b1db42431f8 Author: car Date: Thu Feb 9 23:00:12 2006 +0000 need iostream... Src/C_AMRLib/StateData.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit eeb5406ce0cde91a2d6e19ea1101e7e6845450ab Author: car Date: Thu Feb 9 21:40:58 2006 +0000 can now turn of profiling more completely Src/C_BaseLib/Make.package Src/C_BaseLib/Profiler.H commit 552bd7b88ea7ae840588ad4ebac70d5039bad63b Author: car Date: Thu Feb 9 21:40:02 2006 +0000 iostream... Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 6a446337b3eb4545c14844049fcb620f5d38a894 Author: car Date: Thu Feb 9 21:13:58 2006 +0000 iostream... Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 326a8ab05a9cb0828b772977549a28069c4f7842 Author: car Date: Thu Feb 9 21:08:25 2006 +0000 include needed for iostream Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 6074e61c0678f1ec9a430a3960f10160f4e09739 Author: car Date: Wed Feb 8 21:38:05 2006 +0000 PGI->BL_PGI Src/C_BaseLib/Thread.H commit d642b2362a87850797c09c1837f1bdfdb683b58f Author: car Date: Wed Feb 8 21:37:26 2006 +0000 wsecond on XT3 Src/C_BaseLib/Utility.cpp commit 7c30b2a644e43b199886fca6361d46bfc03bb6c3 Author: car Date: Wed Feb 8 21:36:12 2006 +0000 PGI flag not needed re template specialization Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp commit ee0ec82a756dbdef563c500a38193137c716e01c Author: lijewski Date: Mon Jan 30 18:03:18 2006 +0000 commented out some BL_PROFILE()s Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 7547473bf96a9d90911f1dfc2590afee79285ba2 Author: lijewski Date: Fri Jan 27 23:25:38 2006 +0000 *** empty log message *** Src/C_BaseLib/test/tMinCommCosts.cpp Tests/C_BaseLib/tMinCommCosts.cpp commit 2cccfc7c8bf08cd14729270b9ef741525ca65f53 Author: lijewski Date: Fri Jan 27 23:24:38 2006 +0000 speedup of MinimizeCommCosts() Src/C_BaseLib/DistributionMapping.cpp commit 8626ce13cb3289497aa9d7fe46cdca358b554e26 Author: car Date: Thu Jan 26 23:51:58 2006 +0000 machinefile not needed Src/LinearSolvers/C_NodalMG/machinefile.mpi commit 3cf485ca437eca1c237f7ba9a006c25f856f602a Author: lijewski Date: Thu Jan 26 00:12:17 2006 +0000 zeroed out Execute() Src/C_BaseLib/Utility.cpp commit e17d917866600d88ce7a42116a9d531b49bd450f Author: lijewski Date: Thu Jan 26 00:09:26 2006 +0000 *** empty log message *** Src/C_BaseLib/Make.package commit 4f246033f8ce281a136bad6f2e336ba1c7f2ba41 Author: lijewski Date: Wed Jan 25 23:58:03 2006 +0000 more profiling Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 0692fc8a2a2698a035461b7cba9541405860c996 Author: lijewski Date: Mon Jan 23 22:14:00 2006 +0000 speedup to add() Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp commit a2726e12f493e9e2a833e5a49e81459aa20b66cf Author: lijewski Date: Fri Jan 13 20:26:28 2006 +0000 use O3 with Fortran & PathScale Tools/C_mk/Make.Linux commit 1aef407f6b34649154850f12131bd0994947c129 Author: car Date: Tue Jan 10 22:05:28 2006 +0000 Added another assert. Src/C_BaseLib/BoxArray.cpp commit 9534b7eee2384d8d04516da28e5d546f418ed276 Author: car Date: Tue Jan 10 22:05:08 2006 +0000 Fixed ixType() bug in minimalBox(). Also added a bunch more asserts. Src/C_BaseLib/BoxList.cpp commit 457319502f5724018617c04454aaf54e7610ee41 Author: lijewski Date: Mon Jan 9 19:18:48 2006 +0000 removed some simplify()s Src/C_AMRLib/Amr.cpp commit 85d3e377740fece5333ed2f1a399c43e2caa1c81 Author: lijewski Date: Mon Jan 9 19:17:24 2006 +0000 minimize() -> simplify() Src/C_BaseLib/BoxArray.cpp commit 62ee9b199de864fab81f0b0cca5a246105bfc763 Author: 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 Date: Mon Jan 9 18:05:16 2006 +0000 more speedups Src/C_BaseLib/BoxList.cpp commit e75c0e252c6d03c1740d6a2b48fa563da4a84312 Author: 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 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 Date: Mon Jan 9 04:23:37 2006 +0000 speedup of add(BoxList) Src/C_BaseLib/BoxDomain.cpp commit 644bbaa4088eea44d382fb41d1ba6cd71b8c690e Author: 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 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 Date: Sat Jan 7 20:35:20 2006 +0000 think it's finally right Src/C_BaseLib/BoxList.cpp commit 8539fb49876b917fa9d9615a1b987d8d2e856888 Author: lijewski Date: Sat Jan 7 18:57:30 2006 +0000 think I fixed complementIn() Src/C_BaseLib/BoxList.cpp commit 331938db52e22d5230db3de181fa5744549c3f4a Author: lijewski Date: Sat Jan 7 16:27:05 2006 +0000 oops, got some weird recursion to work out Src/C_BaseLib/BoxList.cpp commit 55b3bc82a1a556516cf16564ced9a8fc4fdd5a9f Author: lijewski Date: Sat Jan 7 01:22:09 2006 +0000 more scalable version of complementIn() Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit 9ecedd012faaec1001731eeecfadd744de98e9ce Author: lijewski Date: Fri Jan 6 22:58:21 2006 +0000 one complementIn() now calls other Src/C_BaseLib/BoxList.cpp commit 5b846a3b683eb5f418554bb97596dc0fa6907dd2 Author: lijewski Date: Fri Jan 6 18:47:26 2006 +0000 efficiency back to .95 Src/C_BaseLib/DistributionMapping.cpp commit 5b8263b4670781d33a0611afdee9b9b9028579e0 Author: 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 Date: Fri Jan 6 17:59:40 2006 +0000 mem improvement for knapsack Src/C_BaseLib/DistributionMapping.cpp commit 3a3f907c96c69476e572fd63a535ad6f2f8d55b4 Author: lijewski Date: Fri Jan 6 05:34:24 2006 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit f664fb1e785c600c9685b8bdc9d39a4b25cb3581 Author: lijewski Date: Thu Jan 5 23:53:10 2006 +0000 added timers to grid_places() Src/C_AMRLib/Amr.cpp commit 5d31405ebdca5a6c0b1bb008913d0ab01b631ee2 Author: 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 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 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 Date: Tue Nov 22 22:15:05 2005 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit bf9da3ed3309c484557a7fa475068771c26e9343 Author: marc Date: Tue Nov 22 22:14:47 2005 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit 928b9ae779942f0e473faec06d4a4336009cce2f Author: car Date: Fri Nov 18 22:52:16 2005 +0000 *** empty log message *** Src/F_BaseLib/ml_multifab.f90 commit 9e84d1b8da2caec801fd6c3f3e4a10fcd1711a0e Author: car Date: Fri Nov 11 18:47:46 2005 +0000 *** empty log message *** Src/F_BaseLib/ml_multifab.f90 commit d49f9a2f87f7bfcad4c911f992344b399254268e Author: car Date: Thu Nov 10 23:42:16 2005 +0000 *** empty log message *** Tools/F_mk/GMakeMPI.mak commit 5d5093fa0dcd456c5351cabe8bc4a3c60c666fd0 Author: 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 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 Date: Thu Nov 10 23:16:32 2005 +0000 greenstreet mpi Tools/F_mk/GMakeMPI.mak commit 21976547a10bf1f8bec4b93ffdb92c4bbc6702fe Author: car Date: Thu Nov 10 23:11:28 2005 +0000 farg Tools/F_mk/GMakeMPI.mak commit a3f7ed08a14b6488612f254f08c31f1e19f46523 Author: car Date: Thu Nov 10 23:03:39 2005 +0000 *** empty log message *** Tools/F_mk/GMakeMPI.mak commit 4f6b2b21a706b6aecb9aa86f961d13664247c8f7 Author: car Date: Thu Nov 10 22:51:18 2005 +0000 farg in extern Tools/F_mk/GMakeMPI.mak commit 241edfe4406442a31fde2e3d8d701909358e39f6 Author: car Date: Wed Nov 9 17:26:29 2005 +0000 fix for parallel stats Src/F_BaseLib/bl_prof.f90 commit f33b01dcce0afabf4579146b9259e97062cca8ef Author: car Date: Wed Nov 9 16:53:55 2005 +0000 new MPI config method Tools/F_mk/GMakeMPI.mak Tools/F_mk/GMakedefs.mak commit 2f96daf4f55fc633ef20f38c90831339a09b8690 Author: car Date: Tue Nov 8 16:23:57 2005 +0000 *** empty log message *** Tools/F_mk/GMakedefs.mak commit 0f04a10c668624dd932f812dbf232e33d70ae2d4 Author: 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 Date: Wed Nov 2 23:49:30 2005 +0000 barrier after mkdir Src/F_BaseLib/fabio.f90 commit 7c06096cdfe23ea6780732ad947a787dafcb7937 Author: marc Date: Wed Nov 2 01:41:00 2005 +0000 Add stuff to build on Jacquard Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 2f30abd1f7b5a0a044a3fab5843225dcb6d7afdb Author: car Date: Mon Oct 31 17:19:49 2005 +0000 more support for dft; and bl_prof for longer running programs Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/multifab.f90 commit f86ed331aaec1bad5919d476e2f53ed7ee3ee9a2 Author: lijewski Date: Wed Oct 26 18:20:46 2005 +0000 removed sndcnt/rcvcnt args to startup() Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 604cc7acb16173c7376b97a2ea787c4db9d80294 Author: lijewski Date: Tue Oct 25 22:13:13 2005 +0000 some simplification of execute() Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 025b9c21ddf959cdac97a22c43da6dd0193deb3e Author: 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 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 Date: Sat Oct 22 19:41:09 2005 +0000 default for verbose is now false Src/C_BaseLib/DistributionMapping.cpp commit b66bcee76dcf4fa5ab92ada2adc4ed4cd353cfec Author: lijewski Date: Fri Oct 21 03:27:42 2005 +0000 removed timer & freshened code Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 98e69f27bcf4f5724b9b3da6c8faa59d66e318e7 Author: 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 Date: Tue Oct 18 18:19:57 2005 +0000 some speedups to alloc() Src/LinearSolvers/C_NodalMG/interface.cpp commit 60ae9197f1b6129fc7df3c461f805071bfda8529 Author: lijewski Date: Tue Oct 18 15:57:34 2005 +0000 *** empty log message *** Src/C_BaseLib/BoxArray.cpp commit 9c648c3dcb7045a05ffc69734fdf5317b56076d9 Author: lijewski Date: Tue Oct 18 15:49:57 2005 +0000 *** empty log message *** Src/C_BaseLib/BoxArray.cpp commit 161c6ef690941c8d3bb6f05856d63c62df1c7695 Author: car Date: Mon Oct 17 19:52:48 2005 +0000 *** empty log message *** Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_bx.f90 Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_bx.f90 commit 3ba14fddae4d6d74c156e68dc0ecbd56ca1a6e21 Author: 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 Date: Mon Oct 17 17:50:34 2005 +0000 merged in intersections() Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 74aed413eae6d4ba962c42164b802abf56047561 Author: lijewski Date: Mon Oct 17 17:50:22 2005 +0000 added some timers Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit fe56e82d765ce4960b303a30ae0e25e8f2a6398d Author: 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 Date: Mon Oct 17 02:21:05 2005 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit bfb68543c14c262d7c6e4badefcad83efaa7b80d Author: 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 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 Date: Thu Oct 13 20:14:16 2005 +0000 reverting out some previous mods Src/C_BaseLib/BoxArray.cpp commit add7016e1df1927893614e51cc60ebb2f3af6426 Author: lijewski Date: Thu Oct 13 16:51:04 2005 +0000 oops Src/C_BaseLib/BoxArray.cpp commit 520e14b85b1c22ccabe6a2aaef1e66164d75dff1 Author: lijewski Date: Wed Oct 12 18:01:48 2005 +0000 merged in BoxMSet Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp commit f46d038b59c22cd839c026d41f25da6ef56ff7e8 Author: lijewski Date: Wed Oct 12 04:26:31 2005 +0000 more uses of intersections() Src/C_BaseLib/BoxArray.cpp commit ceae194d133d77cec0e6807a0578f49bbe7d4bdc Author: lijewski Date: Wed Oct 12 02:54:55 2005 +0000 slight speed mods Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 778850471ab1b8880bded59a6b1f0167831b9a06 Author: 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 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 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 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 Date: Tue Oct 11 16:07:18 2005 +0000 turned off FillPatch verbosity Src/C_AMRLib/AmrLevel.cpp commit 60734ebbe19a4fa3e3f83410ad1a514541353cb2 Author: car Date: Tue Oct 11 02:32:09 2005 +0000 added a few timers Src/LinearSolvers/C_NodalMG/interface.cpp commit a9e0d23f6e98ef3a8b8bf9c07f18eb2243e2d36e Author: lijewski Date: Mon Oct 10 22:28:51 2005 +0000 *** empty log message *** Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/tBA.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tBA.cpp commit e7980b38c352ba93a48cce537ac91d83f1975119 Author: lijewski Date: Mon Oct 10 21:25:33 2005 +0000 added removeOverlap() Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit 26eae7c48b17f792c85c3c6534adfdaa303283e5 Author: lijewski Date: Mon Oct 10 21:00:23 2005 +0000 added timer to FillPatch::Initialize() Src/C_AMRLib/AmrLevel.cpp commit 485fd8f86738b1fe34cc1bc1710e00a1822353fe Author: car Date: Mon Oct 10 18:20:36 2005 +0000 remove inclusion of BoxDomain.H where not needed Src/C_AMRLib/Amr.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/TagBox.H commit a3689e3ebb5ef6b73944d66ebf8f6759717c2914 Author: car Date: Mon Oct 10 18:01:23 2005 +0000 help find g77 library Tools/C_mk/Make.defs commit bb9748e767d7ba18a9b4db414ae1a59956074976 Author: lijewski Date: Sun Oct 9 03:08:33 2005 +0000 inlined min()/max() Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp commit 5777ca53ff2862595f3b2dbbeec79cc5f3144ef9 Author: 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 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 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 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 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 Date: Fri Oct 7 21:50:29 2005 +0000 *** empty log message *** Src/C_BaseLib/BoxArray.cpp commit 2ac8cd73e77c7d7b3114e3db37a827268e97a78a Author: 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 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 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 Date: Thu Oct 6 17:26:16 2005 +0000 now use intersections() in CrseInit(Fab) Src/C_AMRLib/FluxRegister.cpp commit feceeef67263287618efc14e1b9098b016b958fa Author: car Date: Wed Oct 5 22:45:56 2005 +0000 timers Src/C_AMRLib/FluxRegister.cpp commit d6e915ffdc97e3e9842cefc5dc4b5ac598c1bf13 Author: lijewski Date: Wed Oct 5 21:44:12 2005 +0000 use intersections() in FillBoundary Src/C_BaseLib/MultiFab.cpp commit 55070c604ff233b21b3045ab9572b9f3654c9c33 Author: lijewski Date: Wed Oct 5 21:22:14 2005 +0000 use intersections() in copy() Src/C_BaseLib/FabArray.H commit 4690e464cddbfdc74c0ac7e0f9a0ebb007dffd53 Author: car Date: Wed Oct 5 20:28:48 2005 +0000 pathscale wrong about shared(filter) Src/F_BaseLib/multifab.f90 commit d19c79e4f3b7115dc818699479fc8d227c7afef4 Author: car Date: Wed Oct 5 20:25:05 2005 +0000 shared fcns? Src/F_BaseLib/multifab.f90 commit 55bf3830699b71b279fc1be42b0cf25ba602392f Author: car Date: Wed Oct 5 19:53:03 2005 +0000 *** empty log message *** Src/F_BaseLib/layout.f90 Src/F_BaseLib/test/t_bx.f90 Tests/F_BaseLib/t_bx.f90 commit 3fe615ad2b2667fbf0ed587331285e16c579c40a Author: 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 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 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 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 Date: Tue Oct 4 17:33:05 2005 +0000 *** empty log message *** Tools/C_mk/Make.defs commit e7ed9d4d718bcbb82ad0a1b96411eedf3b5812c3 Author: lijewski Date: Fri Sep 30 19:26:42 2005 +0000 *** empty log message *** Src/C_BaseLib/bl_flush.f commit bb78205e3d0ee2a9324872bd751bc1b9d80debe3 Author: lijewski Date: Fri Sep 30 17:41:56 2005 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.cpp commit c9b0649d698993190a1ec2b6d79bdfe9ad8d6978 Author: lijewski Date: Fri Sep 30 17:41:39 2005 +0000 add flush(6) Src/C_BaseLib/BLBoxLib_F.f commit 11be5d5b12a8b4b5459e3db04671984be5b8a3e2 Author: 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 Date: Fri Sep 30 16:50:20 2005 +0000 cerr message on abort Src/C_AMRLib/StateData.cpp commit 58743341897a2204d8f0de800fa3e7c9a94d862b Author: car Date: Fri Sep 30 16:47:39 2005 +0000 cout --> cerr Src/C_AMRLib/StationData.cpp commit d39916944f126c0a7d792fa40eba61e3411bf414 Author: car Date: Thu Sep 29 15:56:25 2005 +0000 slight time improvement for boundaries in 3d only at this time Src/LinearSolvers/F_MG/mg_smoother.f90 commit 929d8cdb0fe568c68c1c42a67e2d23b93b8a6da7 Author: car Date: Thu Sep 29 15:55:17 2005 +0000 timer Src/LinearSolvers/F_MG/stencil.f90 commit 4c7907e51c230e3b5c9cc524bd53ba37f8f58cd5 Author: car Date: Thu Sep 29 15:53:54 2005 +0000 *** empty log message *** Src/F_BaseLib/box.f90 Src/F_BaseLib/test/t_bx.f90 Src/LinearSolvers/F_MG/mg.f90 Tests/F_BaseLib/t_bx.f90 commit 7a938e549024eacaffa8e50a0642c52034e41950 Author: car Date: Wed Sep 28 20:59:07 2005 +0000 *** empty log message *** Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/box_util.f90 Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_bx.f90 Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_bx.f90 commit 7de62d6652da770938dda4ecad53b30901f9308a Author: car Date: Wed Sep 28 17:48:08 2005 +0000 speed up of boxarray_boxarray_diff; for 5000 box case stencil_fill_cc is 3 x faster Src/F_BaseLib/box.f90 Src/F_BaseLib/boxarray.f90 commit 78571d1109d9dfcf47b37b0bef8821a39c392156 Author: car Date: Tue Sep 27 18:12:04 2005 +0000 ba_coarsen Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 2ea338d1559f99ee33ae2a50deaf0e8a44955be6 Author: car Date: Tue Sep 27 16:42:11 2005 +0000 gcc 4.0 support Tools/C_mk/Make.defs commit 587aff0e39ca472b367f217aedc934551eb0226d Author: car Date: Tue Sep 27 16:40:09 2005 +0000 *** empty log message *** Src/C_BaseLib/.cvsignore commit a3b5a6619defc8f00afadfa9c4413239c906b204 Author: 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 Date: Fri Sep 23 15:40:07 2005 +0000 max min and count Src/F_BaseLib/bl_prof.f90 commit 70d6c10b855328537a256b43bbe9b92ade3dc006 Author: car Date: Thu Sep 22 22:39:43 2005 +0000 remove testing smoothers Src/LinearSolvers/F_MG/mg_smoother.f90 commit 765b6e0c93701111004b1b9d2aa9c874600c1914 Author: lijewski Date: Thu Sep 22 22:23:40 2005 +0000 optimized copyassoc_build() Src/F_BaseLib/layout.f90 commit 961934b61096b7ac755099ec3f898c07a84c1e1a Author: 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 Date: Thu Sep 22 20:00:01 2005 +0000 in serial, use cpu time Src/F_BaseLib/bl_prof.f90 commit 85fec4b34caf6f6431d89eb408049ee54d127e63 Author: car Date: Thu Sep 22 19:59:05 2005 +0000 new smoother, doesn't seem faster Src/LinearSolvers/F_MG/mg_smoother.f90 commit 1f8e44f021da3ed2fd1eba075654c113f0aaa72b Author: 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 Date: Wed Sep 21 20:11:28 2005 +0000 *** empty log message *** Src/F_BaseLib/bl_prof.f90 commit 3052f25763a3200970e80014f3a5e8fb8c574353 Author: car Date: Wed Sep 21 19:52:13 2005 +0000 finally fixed Src/F_BaseLib/bl_prof.f90 commit 6fd9a71b258ae3af082b575ef04231cfae455082 Author: lijewski Date: Wed Sep 21 19:34:53 2005 +0000 hueristic for chunksize Src/F_BaseLib/layout.f90 commit feccecbc55c0c1040e47e445046c8f75956eed17 Author: car Date: Wed Sep 21 19:25:54 2005 +0000 better bl_prof Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/test/t_bl_prof.f90 Tests/F_BaseLib/t_bl_prof.f90 commit c923e338e339c38deb4a87c5c2c9a22de9858007 Author: car Date: Wed Sep 21 18:59:20 2005 +0000 *** empty log message *** Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_bl_prof.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_bl_prof.f90 commit bd4580ef39679e3647b6692cd2bdb7b121215a8c Author: lijewski Date: Wed Sep 21 17:47:50 2005 +0000 merge two nested loops into one in boxassoc_build() Src/F_BaseLib/layout.f90 commit 4f8a78c3c42b2a71cf371383524733cecebae192 Author: car Date: Wed Sep 21 16:22:13 2005 +0000 no more do_atav Src/F_BaseLib/multifab.f90 commit a8f59503e430c2615d29391db21ad7fc8bfdb35d Author: car Date: Wed Sep 21 01:01:21 2005 +0000 *** empty log message *** Src/F_BaseLib/bl_prof.f90 commit 7b3bfe47b001bedba3db599c33566692542885aa Author: car Date: Wed Sep 21 00:27:01 2005 +0000 fix for reduction Src/F_BaseLib/bl_prof.f90 commit 0d1ec18d3950f3d84d9e13c0f48f67ad1c44bd03 Author: lijewski Date: Tue Sep 20 22:42:34 2005 +0000 got do_atav working Src/F_BaseLib/multifab.f90 Src/F_BaseLib/parallel.f90 commit 263b6ddabc02a93e66b7594521956f09dff80932 Author: car Date: Tue Sep 20 20:12:15 2005 +0000 parallel_alltoall Src/F_BaseLib/multifab.f90 Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit 4dbf74b94aff5cd3f0f58b8f930320184f580fa6 Author: car Date: Tue Sep 20 17:22:56 2005 +0000 *** empty log message *** Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_bxasc.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_bxasc.f90 Tests/F_BaseLib/t_main.f90 Tools/F_mk/GMakedefs.mak commit 0454f9cf1cb698662494f0f61662e2834f15bce7 Author: lijewski Date: Tue Sep 20 16:40:30 2005 +0000 added timer around boxassoc_build Src/F_BaseLib/layout.f90 commit 4e652cebf9eb307dc3aef2c298dd7f572d609244 Author: car Date: Tue Sep 20 00:09:29 2005 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg_smoother.f90 commit 24050f9e80a91b3f40226886d443371d274a6a1d Author: car Date: Tue Sep 20 00:09:04 2005 +0000 cpy_d improves things Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_prof.f90 Src/F_BaseLib/multifab.f90 commit d6baff9f26984336588a1e2ec75393494e0f2f32 Author: almgren Date: Mon Sep 19 20:51:01 2005 +0000 Bug fix in ml_interface_stencil_3d. Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit bc3943e1d5e257f3f7aaf365b0e89bd7be7c3f0b Author: car Date: Mon Sep 19 20:46:33 2005 +0000 norm profiling Src/F_BaseLib/multifab.f90 commit dd7be6d39ca3b41cd7e7bf7527ee8aa2b5330014 Author: car Date: Mon Sep 19 19:50:24 2005 +0000 summary stats Src/F_BaseLib/bl_prof.f90 commit b4524c5e33a2044eca7ecef192aac1fc27860b14 Author: car Date: Sun Sep 18 23:54:13 2005 +0000 more profiling Src/F_BaseLib/cluster.f90 Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 5a2691f1e7bb52980adf294ed25995e5125f5d86 Author: car Date: Sun Sep 18 21:53:11 2005 +0000 profiling Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 927408cd9b6a0053ceb0ccffbb5646f9e2707bd5 Author: 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 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 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 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 Date: Sat Sep 17 13:58:41 2005 +0000 tweak for reduce Src/F_BaseLib/bl_timer.f90 commit dd6fa0e2bda37020a0b49bb8d3ecd6c41adc56b8 Author: car Date: Sat Sep 17 13:57:58 2005 +0000 mg_tower_print Src/LinearSolvers/F_MG/mg.f90 commit d361a1ffb369e8b9dfdeb62f53ae7f9bed5f4d6f Author: almgren Date: Fri Sep 16 19:26:41 2005 +0000 Cleaner implementation that looks more like ml_interface_3d_divu in varden/hgproject.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 60d8a86e6b81e784fbe904c2bf1f225172940106 Author: 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 Date: Mon Sep 12 14:12:19 2005 +0000 *** empty log message *** Tools/F_mk/GMakedefs.mak commit c5e86cc321ed54fd2ad2770803e38cedc9938fff Author: car Date: Fri Sep 9 20:35:16 2005 +0000 tweaks for f90 and Intel 9 Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 2655e1ec9dd1fef746f11dbe0275c3c33d5897db Author: almgren Date: Thu Sep 8 21:55:46 2005 +0000 An attempt to make CG_solve and BiCG_solve not create huge answers when the problem is almost completely solved. Src/LinearSolvers/F_MG/itsol.f90 commit 42a2aef77695ab9789316f4d2a351ea2a6989d74 Author: car Date: Thu Sep 8 19:35:22 2005 +0000 pure is a stumbling block for PathScale, save for later Src/F_BaseLib/ml_multifab.f90 commit eafd68222209c46f1584bda0e2a62713eb9a40a8 Author: jbb Date: Wed Sep 7 21:13:00 2005 +0000 Oops - typo in previous INTERP_2D.F Src/C_AMRLib/INTERP_2D.F commit 90836f771cfeda8d9f6034a15d6c54d8351d1da8 Author: jbb Date: Wed Sep 7 21:11:47 2005 +0000 Fix in LINCC_INTERP (and set-up for it) so that the routine which sets alpha loops over all of the fine cells in each coarse grid cell, not just the ones to be interpolated. This was needed because of a umac_periodic_bust because regions of different size were setting alpha differently. Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/Interpolater.cpp commit 817b8121a26f90473c75a06063ad69195ab4666b Author: 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 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 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 Date: Wed Sep 7 17:02:14 2005 +0000 *** empty log message *** Tools/C_scripts/moddep.pl commit 2043e8569c0e008378a4eee4142cefbc2a44ab20 Author: car Date: Tue Sep 6 22:52:23 2005 +0000 Intel9 support Tools/F_mk/GMakedefs.mak commit c9df1f7d77f0c60e609a22473318eedfa94de0f9 Author: car Date: Tue Sep 6 22:51:54 2005 +0000 *** empty log message *** Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit 4411172eb1105e4fbe57b895719c13d7c67c4355 Author: car Date: Tue Sep 6 22:06:27 2005 +0000 *** empty log message *** Src/LinearSolvers/F_MG/FParallelMG.mak Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h commit f544a43fec109c2a933c597f7a544d8c23016c46 Author: car Date: Tue Sep 6 21:06:25 2005 +0000 mg_cpp changes Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_cpp_f.h Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 26a4099fc1234e5fb3cad173237bf0a4b30fab83 Author: almgren Date: Thu Sep 1 21:35:00 2005 +0000 Needed to make same index fixed in lin_cc_interp_3d as in lin_cc_interp_2d. Src/F_BaseLib/interp.f90 commit 4aef65bc74727e1b7d5e3e88537edc232d509b9c Author: almgren Date: Thu Sep 1 19:18:24 2005 +0000 I believe this is the correct scaling for 3-d nodal. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 631177770fbfb013da506dfdf5af2380ffa849a8 Author: almgren Date: Thu Sep 1 17:57:38 2005 +0000 The ml_layout_build from a ml_boxarray was not correctly passing the problem domain to the layout...instead the problem domain was being defined as the bounding box at that level. Now the problem domain from the ml_boxarray is passed through the layout_build call. Src/F_BaseLib/ml_layout.f90 commit c219663a4d3549ae312bf88a33a9ef12d04e4fc3 Author: car Date: Tue Aug 30 20:34:07 2005 +0000 dead code elimination Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/boxarray.f90 commit 0668c523f27259fac9317132c6b96ff646ef9c1e Author: 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 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 Date: Wed Aug 24 20:22:46 2005 +0000 added cluster_2d.f90, temporarily Src/F_BaseLib/GPackage.mak commit 3b06f5fccd9264590caf3c5bd86f1556ba46c2bb Author: 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 Date: Tue Aug 23 19:02:29 2005 +0000 better error control Src/LinearSolvers/F_MG/itsol.f90 commit dadf98f49fd09ae1e7b5d435bfd627f5de57644e Author: car Date: Tue Aug 23 18:18:32 2005 +0000 hack to fix cg/bicg when r.a.r is zero Src/LinearSolvers/F_MG/itsol.f90 commit b8da19766396ac1aaec3f4f377fa2abe94878f66 Author: 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 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 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 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 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 Date: Sat Aug 20 16:39:57 2005 +0000 cluster should be debugged Src/F_BaseLib/cluster.f90 commit c673065973778d4a1e0d5fafcbb3c9204061bd4b Author: almgren Date: Sat Aug 20 05:27:28 2005 +0000 2D version of cluster.f90 used by Ann until cluster.f90 is debugged. Src/F_BaseLib/cluster_2d.f90 commit a1cc8f64131586f52f7bc42e35d159e2c731c0ca Author: car Date: Fri Aug 19 23:08:32 2005 +0000 tweaks for mpi Tools/F_mk/GMakedefs.mak commit 285e718277e0220b0098236dc647619d0f36a3be Author: car Date: Fri Aug 19 23:08:08 2005 +0000 get_boxarray Src/LinearSolvers/F_MG/mg.f90 commit 530c3a343bb73e727419435293f29b8a653b8f8b Author: car Date: Fri Aug 19 23:07:49 2005 +0000 *** empty log message *** Src/F_BaseLib/box.f90 Src/F_BaseLib/cluster.f90 Src/F_BaseLib/test/t_cls.f90 Tests/F_BaseLib/t_cls.f90 commit 02f06319a5676078691e6acbcadce0f1d9a3fb66 Author: car Date: Wed Aug 17 13:29:56 2005 +0000 *** empty log message *** Src/F_BaseLib/fab.f90 Src/F_BaseLib/multifab.f90 commit e31f5e9fd5287f54a7d4cd40eb98eef061f02096 Author: car Date: Sat Aug 13 15:47:54 2005 +0000 missed some Src/F_BaseLib/parallel.f90 commit 28862e8e3634e4ad6510b8e6ca545e76045492d9 Author: car Date: Fri Aug 12 17:28:32 2005 +0000 intel is too permissive... Src/F_BaseLib/multifab.f90 Src/F_BaseLib/parallel_stubs.f90 commit 204eda4433ca10dcf15d69d28d239666e86089b5 Author: car Date: Fri Aug 12 17:21:57 2005 +0000 oops Src/F_BaseLib/parallel_stubs.f90 commit 526b15c0165ad28a5f05fe4a9cb302254daaaccf Author: car Date: Fri Aug 12 16:50:19 2005 +0000 more complex support Src/F_BaseLib/multifab.f90 Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit 4cea41f4325c6b0e05844313a4dd945c62644448 Author: car Date: Thu Aug 11 23:43:10 2005 +0000 fab, multifab complex for fmm Src/F_BaseLib/fab.f90 Src/F_BaseLib/multifab.f90 commit fe66adad57bfa80ec52bd9c6bcf34456c09dd3c3 Author: car Date: Wed Aug 3 20:25:32 2005 +0000 oops Src/F_BaseLib/ml_layout.f90 commit 19a9fdb7460b2f80ba20a0eb838361abdff16d62 Author: car Date: Wed Aug 3 14:43:43 2005 +0000 extra vars Src/F_BaseLib/multifab.f90 Src/F_BaseLib/test/t_cls.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/t_cls.f90 Tests/F_BaseLib/t_main.f90 commit d9a0ca35309acf5ee271782ed5902053623164d9 Author: car Date: Wed Aug 3 14:43:09 2005 +0000 ml_layout Src/F_BaseLib/layout.f90 Src/F_BaseLib/ml_layout.f90 commit b8d1e1b3c2a09717501203ea3bf879335363c4e0 Author: car Date: Fri Jul 29 21:34:27 2005 +0000 fix for 3d Src/F_BaseLib/cluster.f90 Src/F_BaseLib/test/t_cls.f90 Tests/F_BaseLib/t_cls.f90 commit 9d3952f9f9a67ce14786891b3fecd645263dbea8 Author: almgren Date: Fri Jul 29 20:53:13 2005 +0000 Make sure to set the boxarray%dim = 2 in the 2d case... Src/F_BaseLib/cluster.f90 commit dfa0927c62f265e9bab4fb3f1a8094661d5e5440 Author: car Date: Fri Jul 29 19:13:19 2005 +0000 mask out ghostcells, more debugging Src/F_BaseLib/cluster.f90 Src/F_BaseLib/test/t_cls.f90 Tests/F_BaseLib/t_cls.f90 commit 60fa7a7318361f5be2f0d67134cc968ab4fb45e8 Author: car Date: Fri Jul 29 17:10:05 2005 +0000 i think a fixed cluster Src/F_BaseLib/cluster.f90 Src/F_BaseLib/multifab.f90 Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_cls.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_cls.f90 Tests/F_BaseLib/t_main.f90 commit d32ea0d09bdf62f6d45f4f7bcfcdfa2ee984e956 Author: almgren Date: Thu Jul 28 19:34:04 2005 +0000 Dont need to test on (n>1) on the way back up because that code is only called for n = 2,...nlevs. Src/LinearSolvers/F_MG/ml_cc.f90 commit de7d04559f0b3dabb7c98ae231b6dfec9b7aa746 Author: almgren Date: Thu Jul 28 19:33:19 2005 +0000 Make sure to use "mini_cycle" instead of mg_tower_cycle when relaxing at a fine AMR level so that the smoother and not the bottom solver will be called. Src/LinearSolvers/F_MG/ml_cc.f90 commit b78182062bfe83a57d3bfdcff09801c506d09edd Author: almgren Date: Wed Jul 27 20:26:09 2005 +0000 Index bug... Src/F_BaseLib/cluster.f90 commit 814c5204ea1724cd28455a4d7e5f0ef4b3542a1b Author: car Date: Wed Jul 27 17:12:58 2005 +0000 some fixes Src/F_BaseLib/cluster.f90 Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit 9f4c3c2075932baab80cd349faa6a3ec21350cdf Author: 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 Date: Thu Jul 21 18:13:13 2005 +0000 complex fabs Src/F_BaseLib/fab.f90 commit f66d7b6d50b1a0b00c1cdb6a963a425663121320 Author: lijewski Date: Wed Jul 13 19:56:31 2005 +0000 Some mods for Portland Group C++ compiler. I'm using PGI as a placeholder for the "appropriate" predefined compiler symbol. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/Thread.H commit 6d302c95ff1126d853f8a6e015a22e790e6f15ba Author: car Date: Mon Jul 4 23:12:22 2005 +0000 *** empty log message *** Src/F_BaseLib/bl_types.f90 commit d30a62674ddfce953ae6c20765944fa17e0440d9 Author: car Date: Mon Jul 4 22:52:01 2005 +0000 endian test Src/F_BaseLib/bl_types.f90 commit d69fa57d9d69f6bd1c198eb50d826d0d948a02c9 Author: car Date: Thu Jun 23 16:50:22 2005 +0000 some multicomponent adjustments Src/F_BaseLib/fab.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/multifab.f90 commit fd0648d398f1f68f10034e71e332b31c03d8bde4 Author: lijewski Date: Tue Jun 21 21:42:03 2005 +0000 added Plot_Files_Output() Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 71192f64f0a8c34e7ffc4338b390b9dd9d89a86e Author: lijewski Date: Tue Jun 21 20:09:47 2005 +0000 fixed the bug in the speed upgrades Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 7a6d871f6e9935d6641fa8bb229ffad5aee340da Author: car Date: Sat Jun 18 19:04:36 2005 +0000 *** empty log message *** Src/F_BaseLib/test/t_boxlib.dsp Src/F_BaseLib/test/t_boxlib.dsw Tests/F_BaseLib/t_boxlib.dsp Tests/F_BaseLib/t_boxlib.dsw commit 927e32a60cafcca76df11f65dd063ed2dd4a0414 Author: car Date: Fri Jun 17 17:08:31 2005 +0000 OMP fix Src/LinearSolvers/F_MG/stencil.f90 commit 921c5509c171a067a91a89c33d69443924ad4c4c Author: car Date: Fri Jun 17 02:03:28 2005 +0000 new mech for intrisics Tools/F_mk/GMakedefs.mak commit 8441fd9c5bc6f49a97c31fcf02da8f9f3f8d861e Author: car Date: Thu Jun 16 22:53:14 2005 +0000 box_projectable Src/F_BaseLib/box.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/ppm_util.f90 commit 9c50fb92de721f323d5b7553ec98e4e2aff57b42 Author: car Date: Tue Jun 14 20:00:24 2005 +0000 support for Intel 9 Tools/F_mk/GMakedefs.mak commit 3a1b997e7115239cf44e0d2ea751605cf42afc58 Author: car Date: Tue Jun 14 16:30:11 2005 +0000 not need external on iagc Src/F_BaseLib/f2kcli.f90 commit 162353772f53d9587d99ec6c7d3465bf92a29f57 Author: car Date: Tue Jun 14 16:23:08 2005 +0000 Lahey checking Tools/C_mk/Make.Linux commit eb979c2dec93a2639c8d7f2fb7b38ff44533fba8 Author: car Date: Tue Jun 14 16:22:54 2005 +0000 icpc/ifort version 9 Tools/C_mk/Make.defs commit d16bb0a168a56f11a57bedb51a0fe61595791530 Author: car Date: Fri Jun 10 16:56:28 2005 +0000 reversion to April 1, 2005 Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real2d.f Src/LinearSolvers/C_NodalMG/amr_real3d.f Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 4c2ee23d86089a9757daef8e63aa7cfc9d5aaea6 Author: lijewski Date: Thu Jun 9 17:27:56 2005 +0000 some simplification Src/F_BaseLib/cluster.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/sparse_solve.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit bbc6cd6634d9e0558523ba99049eb377c694d9ca Author: almgren Date: Thu Jun 9 00:08:58 2005 +0000 Fix to the problem of one-cell thick domains getting the boundary nodes incorrectly set to nodal. Fix is in combination to fix to box_contains function... Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 03e220b804d3046ea473de194bf255a84b3ff139 Author: almgren Date: Thu Jun 9 00:08:04 2005 +0000 "Contains" now checks lo against lo and hi, and hi against lo and hi. Src/F_BaseLib/box.f90 commit f569dff58c5bd2d954fc9c4ad77eb9d764f0ce3e Author: lijewski Date: Wed Jun 8 21:50:04 2005 +0000 ml_nodal_restriction is now parallelized Src/LinearSolvers/F_MG/ml_restriction.f90 commit b7e3d074d91a3256da05e1099e4bd30cc47768ab Author: 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 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 Date: Tue Jun 7 18:09:53 2005 +0000 added nodal zero routines Src/LinearSolvers/F_MG/mg_restriction.f90 commit 3181d81999d05c74c3818d6a557691bd2cb1c036 Author: almgren Date: Tue Jun 7 18:03:31 2005 +0000 Formatting... Src/LinearSolvers/F_MG/ml_nd.f90 commit b7c3d86f22bdfe8136738f55b665f8c19b595223 Author: almgren Date: Tue Jun 7 16:33:03 2005 +0000 Fix to how we zero the crse array before restriction. Src/LinearSolvers/F_MG/ml_restriction.f90 commit f32cf7fda9fcc194e2710c514123f84f98e01375 Author: car Date: Mon Jun 6 18:17:43 2005 +0000 lnc Src/F_BaseLib/multifab.f90 commit 8cb459eac46f8a11675c86201727f0f64743c8a9 Author: almgren Date: Mon Jun 6 16:37:06 2005 +0000 Put the same changes in lin_cc_interp_3d as in lin_cc_interp_2d to get indexing thru crse and fine correct. Src/F_BaseLib/interp.f90 commit 6b086d4f401ce69ecb93a41900375d425daeeb51 Author: almgren Date: Sun Jun 5 21:06:58 2005 +0000 Fixed lin_cc_interp_2d...NOTE: 3d needs to be fixed as well!!! Src/F_BaseLib/interp.f90 commit 8723b24e6e0e49b213d4fa74a693c8dbba427ba8 Author: 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 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 Date: Fri Jun 3 19:39:49 2005 +0000 parallelized ml_edge_restriction Src/LinearSolvers/F_MG/ml_restriction.f90 commit 325ae184f8da47ef5472d8fb83f882c46d003caa Author: lijewski Date: Fri Jun 3 19:16:51 2005 +0000 *** empty log message *** Src/LinearSolvers/F_MG/ml_restriction.f90 commit bd4028b9211fde9e45e32043d1ade0a99af3b703 Author: lijewski Date: Fri Jun 3 17:45:16 2005 +0000 moved destroy code to after final uses Src/LinearSolvers/F_MG/ml_cc.f90 commit 039d86a03e06a52e2185748fbcc9ffd227b218f3 Author: almgren Date: Fri Jun 3 05:16:26 2005 +0000 Pass "n" thru calling sequence instead of looping over. Note that multifabs coming in are now edge-based. Src/LinearSolvers/F_MG/ml_restriction.f90 commit 8d8eaa4675690034d4fbd2263c9b6f249891595c Author: lijewski Date: Thu Jun 2 20:35:36 2005 +0000 a little cleanup Src/LinearSolvers/F_MG/mg_prolongation.f90 commit b15676667bd11efe5269f4e4177cf0d8a4f5c2bf Author: lijewski Date: Thu Jun 2 16:38:39 2005 +0000 out -> inout in a couple places Src/LinearSolvers/F_MG/mg_cpp.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 commit b7e5c97eeaa13a9d723b6ac7e12ea1e7f8169732 Author: vince Date: Thu Jun 2 00:28:08 2005 +0000 added support for jvn. Tools/C_mk/Make.Linux Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit 1603587bc1ec13d3f5fbf06b2a20ac64422b4ac3 Author: lijewski Date: Wed Jun 1 22:28:52 2005 +0000 some cleanup Src/LinearSolvers/F_MG/mg_restriction.f90 commit 374b8c75a8cfa03e0ae139d7ead705bd10f907f6 Author: car Date: Wed Jun 1 21:40:35 2005 +0000 should read ml_boxarray with != rr properly Src/F_BaseLib/box_util.f90 commit 99101c835143c68b7a291b1eda259809dfbafd06 Author: almgren Date: Wed Jun 1 21:08:56 2005 +0000 Fix problem in defn of jbot vs jtop. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit eebe9672e9ca65963415b8342e0dbb1c037964ad Author: lijewski Date: Wed Jun 1 20:14:38 2005 +0000 parallelized ml_prolongation Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 7b26e9a7a741300b166cf6e539556a8ee188b011 Author: lijewski Date: Wed Jun 1 16:44:16 2005 +0000 messed up something in ml_nodal_restricton Src/LinearSolvers/F_MG/ml_restriction.f90 commit b86de26ea7a09adf34ac1163ff4c12fdd261d0d0 Author: lijewski Date: Tue May 31 21:38:19 2005 +0000 some cleanup Src/LinearSolvers/F_MG/mg_restriction.f90 commit d0e19f050874e96a6b99edb7ff087072295371e9 Author: 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 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 Date: Tue May 31 17:21:44 2005 +0000 more ignorance Tests/LinearSolvers/F_MG/.cvsignore commit b32d15a42d1c585669c3422e17804ffc55b3b5d5 Author: 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 Date: Fri May 27 21:58:11 2005 +0000 BC_UNDEF Src/F_BaseLib/bc.f90 commit 8be2ac04ed1ce6271a1338679337dfc2c28bffff Author: 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 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 Date: Thu May 26 16:42:02 2005 +0000 memory leak Src/LinearSolvers/F_MG/ml_cc.f90 commit ba7ee51884eadb3c0698d124eb7ef903bf32bee0 Author: almgren Date: Wed May 25 21:10:38 2005 +0000 Was bug in how we were computing ML residual within the iteration loop. Now appears to work on 2-level and 3-level problems. Src/LinearSolvers/F_MG/ml_cc.f90 commit 03526f92ca7ab9ba00e038e983541919e8c5b16a Author: 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 Date: Tue May 24 22:31:22 2005 +0000 added the_copyassoc_head Src/F_BaseLib/layout.f90 commit 3eda9853c40be9ef03342e05498b1a882616d47b Author: lijewski Date: Mon May 23 21:21:44 2005 +0000 *** empty log message *** Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 commit bd740614943c8cb98365721cc39a6146556006ce Author: lijewski Date: Mon May 23 20:08:28 2005 +0000 ml_interp_bcs now calls ml_interp_bcs_c Src/LinearSolvers/F_MG/ml_prolongation.f90 commit 9e76bd20d1810674e5c7c81df65096a0d6b2ba62 Author: lijewski Date: Mon May 23 19:43:11 2005 +0000 ml_cc_restriction now call ml_cc_restriction_c Src/LinearSolvers/F_MG/ml_restriction.f90 commit 5b82f49dd8d823215ca0a681f69a45877b6e0179 Author: lijewski Date: Fri May 20 21:30:11 2005 +0000 removed local_boxes stuff Src/F_BaseLib/layout.f90 commit f69621cccc4432e57ca449f9d70a2683856fd0a3 Author: lijewski Date: Fri May 20 20:42:29 2005 +0000 added multifab_internal_sync_c Src/F_BaseLib/multifab.f90 commit 654d02f2f3daf07f7abbc92fc3fd21702e7b6707 Author: lijewski Date: Fri May 20 18:22:09 2005 +0000 more copyassoc stuff Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab.f90 commit 715ab5a1d2136a6e99c0e987051f261c724ac179 Author: lijewski Date: Wed May 18 21:57:16 2005 +0000 some work toward a fancy parallel copy Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab.f90 commit 712c890599b75c03c399b40df661bc3eb087debb Author: car Date: Wed May 18 21:16:28 2005 +0000 try to get the alpha term right Src/LinearSolvers/F_MG/stencil.f90 commit 8d8cf1419283ebe6e5c5527c46d3b1df757357fb Author: lijewski Date: Tue May 17 22:03:17 2005 +0000 copy fixes Src/F_BaseLib/multifab.f90 commit 505c83fc32011603b539ceffab36249d83a631a8 Author: lijewski Date: Tue May 17 22:02:53 2005 +0000 added component to debug output Src/F_BaseLib/fab.f90 commit 0c73e0b8a4c4bab40cb14afeaf22f508946afd3a Author: car Date: Tue May 17 20:46:41 2005 +0000 false alarm Src/F_BaseLib/fab.f90 commit 601c7a23874bfc4f75ad60b5068ccf3c58580f79 Author: car Date: Tue May 17 20:19:05 2005 +0000 make sure multicomponet fabs print correctly in 1 and 2 dimensions Src/F_BaseLib/fab.f90 commit 845dbd1a2ce001b6404575573134c48b5fdc862f Author: car Date: Sun May 15 21:11:52 2005 +0000 more multicomponent fixes Src/F_BaseLib/bl_constants.f90 Src/F_BaseLib/multifab.f90 commit 12628509b6f3cd547a59393aca3362a334d415b0 Author: 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 Date: Tue May 10 22:11:11 2005 +0000 simple abec code Src/LinearSolvers/F_MG/stencil.f90 commit 8c80088739a29dbdb5d8eb90baff071f641b49ef Author: car Date: Tue May 10 13:51:28 2005 +0000 single component applicators Src/LinearSolvers/F_MG/stencil.f90 commit 239ce091447c1ed4d1a5b60ec65b540588a11139 Author: car Date: Fri May 6 19:59:11 2005 +0000 select bottom level Src/LinearSolvers/F_MG/mg.f90 commit bdc3397e953fc6186c9583165b5c1dcf1024c6ab Author: car Date: Thu May 5 22:32:58 2005 +0000 more suger Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/multifab.f90 commit fa73ff57b108d37d3b61f2f97ac68719c1fff317 Author: car Date: Thu May 5 22:32:47 2005 +0000 more options to output plotfiles Src/F_BaseLib/fabio.f90 commit b04476eef0be369dc574cc8446013758af20bd02 Author: car Date: Thu May 5 22:32:14 2005 +0000 not needed modules Src/LinearSolvers/F_MG/ml_cc.f90 commit b6cc62cec353a1f397cb577948d4a3924be81b52 Author: car Date: Thu May 5 20:29:11 2005 +0000 PROF only uses BLMpi.cpp Src/C_BaseLib/Make.package commit 085d869eb2d0c468608660c67c182635988647c9 Author: car Date: Thu May 5 04:35:01 2005 +0000 more suger Src/F_BaseLib/ml_multifab.f90 commit 7269347d2f545f96619d8e65acf9edf075d7e615 Author: car Date: Wed May 4 21:06:15 2005 +0000 more helper fcns Src/F_BaseLib/bl_constants.f90 Src/F_BaseLib/ml_layout.f90 Src/F_BaseLib/ml_multifab.f90 commit 3f9c22f4b5396a142c417f63ccff4a3e0d9c899f Author: lijewski Date: Tue May 3 17:46:01 2005 +0000 oops Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 2224e50c0b413a2cf4a31e1c178b4dfea6aeedda Author: car Date: Fri Apr 29 20:34:15 2005 +0000 layout lev 1 owns finer level layouts Src/F_BaseLib/ml_layout.f90 commit fe3101bd51670cbcdd4b8e653d345098cb57b937 Author: lijewski Date: Thu Apr 28 23:09:13 2005 +0000 memory cleanup Src/F_BaseLib/ml_layout.f90 commit 7a0d7b087f95295ade30388984bb33485d29bab8 Author: lijewski Date: Thu Apr 28 22:15:41 2005 +0000 memory cleanup Src/LinearSolvers/F_MG/ml_nd.f90 commit ffae07ae0a0f0d54dbdbdc1d62618c4b1cbfb734 Author: lijewski Date: Thu Apr 28 18:29:49 2005 +0000 memory cleanup Src/F_BaseLib/fabio.f90 Src/F_BaseLib/ml_layout.f90 Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit b9cc765a043be4df9623028722d1a8b811bf35d6 Author: almgren Date: Thu Apr 28 16:54:25 2005 +0000 ml_layout_build can now take periodic flag pmask...(passes flag through into layout_build) Src/F_BaseLib/ml_layout.f90 commit 4d9352a3415b9865596e06445d8ae6a8154de25f Author: 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 Date: Thu Apr 28 16:31:12 2005 +0000 simplification of buildFPB() Src/C_BaseLib/Geometry.cpp commit f1eeb40d8594cd1d7842d7e57e2e783fde0a6938 Author: lijewski Date: Mon Apr 25 18:25:56 2005 +0000 nodal fix to set_bc_nodal Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 60ac15e4b1cec652cda97ac98a436ecacb216147 Author: car Date: Sat Apr 23 19:49:49 2005 +0000 sparse data distribution speed up Src/C_BaseLib/FabArray.H commit ee07e3f054e0d70267cb7a5800c2908fa69fd8d2 Author: lijewski Date: Fri Apr 22 20:59:22 2005 +0000 mods to speedup interface_residual Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H commit f2d78dfe4c29a17009e26c1e0840094e8ea23d9f Author: car Date: Fri Apr 22 17:24:16 2005 +0000 added profiler Src/C_AMRLib/AmrLevel.cpp commit 8dd6aa0529e4f3ab333d8a33318f5b013c78d7ae Author: lijewski Date: Fri Apr 22 02:35:30 2005 +0000 Array -> Array for did_work storage Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 70da6521c0da7695ec28299a18ea5d63549cb609 Author: lijewski Date: Fri Apr 22 02:01:10 2005 +0000 speedup for fill_internal_borders Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp commit d57b6d2b53bdcba71f9a6b422bad31cef7188c4c Author: lijewski Date: Thu Apr 21 19:53:49 2005 +0000 speedups to fill_interface() Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit de69f187aff907e2dd85c06fd1b26bedff1a3174 Author: almgren Date: Thu Apr 21 17:08:48 2005 +0000 Use ml_layout mla instead of array of layouts la_tower(:) Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit 0bb03f62223efc12d5d33b231b82b9a2f8beb426 Author: almgren Date: Thu Apr 21 16:22:21 2005 +0000 Add option to fix boundary conditions on solution so we can correctly compute the gradient afterwards. Src/LinearSolvers/F_MG/ml_cc.f90 commit 64e1180097ddd92f7d5f7684f2d9693a2f2236d6 Author: almgren Date: Thu Apr 21 15:12:44 2005 +0000 New ml_cc routine (called by cc_multi), and modifications to ml_cc and ml_nd so that we don't test on the full multilevel residual unless the fine residual is already converged. Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/ml_cc.f90 Src/LinearSolvers/F_MG/ml_nd.f90 commit edf02c7aa0af9912fddaeefe324974621a654b54 Author: almgren Date: Thu Apr 21 14:45:57 2005 +0000 Add restriction of rh in beginning, and better convergence criteria. Src/LinearSolvers/F_MG/ml_nd.f90 commit d5628fb125b19bd0000375c7a32fa943b04c19ca Author: almgren Date: Wed Apr 20 18:04:41 2005 +0000 Fixed bug in stencil_flux_2d for lo-j sides. Src/LinearSolvers/F_MG/stencil.f90 commit 96d1df6ec0d8f8b2304f5bbb7ca5d531b59b4468 Author: car Date: Tue Apr 19 21:04:20 2005 +0000 can no turn of all i/o; improves grid_places for large numbers of grids Src/C_AMRLib/Amr.cpp commit 5bd69fb0e8b19d7799e7bdfedeb90830a251212a Author: car Date: Tue Apr 19 20:42:24 2005 +0000 fill_patch::restrict_level: seems to speed up cases with > 1000 grids Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real2d.f Src/LinearSolvers/C_NodalMG/amr_real3d.f Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit de542e2d4effacb9c477ad7152db8758cd739ecb Author: car Date: Tue Apr 19 03:32:37 2005 +0000 hate assert Src/F_BaseLib/bl_error.f90 Src/F_BaseLib/boxarray.f90 commit 72e0d1f75bc67ea758f6e18f6b0daf68a5aa3dfc Author: lijewski Date: Mon Apr 18 19:21:21 2005 +0000 fix to box_periodic_shift when nodal. ---------------------------------------------------------------------- removed automatically CVS: CVS: Committing in . ---------------------------------------------------------------------- Src/F_BaseLib/box.f90 commit af7852e432f1f64387689ed5b35c4f44adc2f56d Author: lijewski Date: Mon Apr 18 18:26:39 2005 +0000 Checked in some mask code for dealing with periodicity; not fully working. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 0bf4a39511ace0c9ea88ad8a5be0d6444558e727 Author: car Date: Mon Apr 18 16:25:57 2005 +0000 ml_nd Src/LinearSolvers/F_MG/GPackage.mak commit a70dd034735009f32191aa6158070a56b658a65a Author: almgren Date: Mon Apr 18 00:51:20 2005 +0000 Use bl_constants_module instead of redefining constants. Src/LinearSolvers/F_MG/ml_nd.f90 commit 6deb4f58af1b6ee2f83bf98fb700920f93107ede Author: almgren Date: Fri Apr 15 21:05:54 2005 +0000 This contains the multilevel loop that does nodal multilevel multigrid solves. Src/LinearSolvers/F_MG/ml_nd.f90 commit e5971e090e4c9d4d8c25442ebfad099ab82e1b2c Author: almgren Date: Fri Apr 15 17:06:14 2005 +0000 Intersect box with the problem domain in stencil_set_bc so that Neumann boundary conditions are not over-written by coarse-fine loop. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit b8b5522b61bcd039b556a9fc4308acbfb29c923d Author: lijewski Date: Thu Apr 14 23:22:36 2005 +0000 fixed typo Src/F_BaseLib/multifab.f90 commit 059eaedfa80f8f95c98cec177bd65ec2a7385556 Author: 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 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 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 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 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 Date: Wed Apr 13 15:59:26 2005 +0000 fixed some typos Src/F_BaseLib/parallel.f90 commit 8fdfa67b83958ae584a29dd86aa44c5ea764da43 Author: car Date: Tue Apr 12 23:25:27 2005 +0000 fix for vector bcast Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit e9f7803fbc9b2b44f2ffa0ab7508b1426aeed1c0 Author: car Date: Tue Apr 12 23:21:01 2005 +0000 bcast error condition Src/LinearSolvers/F_MG/mg.f90 commit 86a5a06b734fc26873c0821b4ac17fb1f2785da0 Author: car Date: Tue Apr 12 23:20:23 2005 +0000 broadcast of scalars Src/F_BaseLib/parallel.f90 Src/F_BaseLib/parallel_stubs.f90 commit dec55c0d8d84c70b8a7548f4d3ca45c316c91c74 Author: 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 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 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 Date: Mon Apr 11 17:57:26 2005 +0000 Fixed bug in copy() routines. Src/F_BaseLib/multifab.f90 commit 00e7fa3fa3970175e418c9c1b943a723cab871f2 Author: car Date: Mon Apr 11 17:33:07 2005 +0000 parallel Src/LinearSolvers/F_MG/sparse_solve.f90 commit 0c7608df8c18edba3963d0a47c5f260455be3943 Author: car Date: Mon Apr 11 16:31:47 2005 +0000 reclaim memory Src/LinearSolvers/F_MG/mg.f90 commit 03d9ebda05e573cc35922d96338746d57955e446 Author: 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 Date: Thu Apr 7 22:51:31 2005 +0000 -O4 buggy on AIX Tools/F_mk/GMakedefs.mak commit 9d3df7efb8cc39d13909ed95654cab9c8f48c877 Author: lijewski Date: Wed Apr 6 16:58:42 2005 +0000 Always do fill_boundary()s using asynchronous recv's. Src/F_BaseLib/multifab.f90 commit 61fd8f7bb99e268a0b56738b31a8832ff39cb4b9 Author: car Date: Tue Apr 5 16:54:47 2005 +0000 change of calling sequence to stencil_fill_cc; pxa and pxb are the locations of the 'physical boundary' relative to the celll geometry edge; normally, these are set to ZERO Src/LinearSolvers/F_MG/stencil.f90 commit afc844ce9f47ff0f5e8a92d9c55180299fb1d655 Author: lijewski Date: Mon Apr 4 21:43:12 2005 +0000 Call fab_destroy() unconditionally to fix mem_stats bug. Src/F_BaseLib/multifab.f90 commit fb1c69eba5de3a114bef6a09662d0ca41a911a88 Author: almgren Date: Mon Apr 4 17:28:32 2005 +0000 Don't use mg_bc.f90 any more. Src/LinearSolvers/F_MG/GPackage.mak commit e48625c76e93dc011f88fbdf3497f3b5250a83e5 Author: car Date: Fri Apr 1 22:15:17 2005 +0000 seem to have 2nd order adaptive 'working' Src/F_BaseLib/bl_error.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/ml_boxarray.f90 Src/F_BaseLib/ml_layout.f90 Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/test/t_main.f90 Src/LinearSolvers/F_MG/mg.f90 Tests/F_BaseLib/t_main.f90 commit c478355cb44d554451771036e1445567fc4a56bc Author: car Date: Thu Mar 31 18:44:14 2005 +0000 ml operations added Src/LinearSolvers/F_MG/stencil.f90 Tools/F_mk/GMakedefs.mak commit 7f2bc428b0c22f02771c7474bbc30b99c2b1d31b Author: car Date: Thu Mar 31 18:43:57 2005 +0000 *** empty log message *** Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_constants.f90 Src/F_BaseLib/box_util.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/ml_boxarray.f90 Src/F_BaseLib/ml_layout.f90 Src/F_BaseLib/ml_multifab.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/t_main.f90 commit 30d24161f084eb36287d2a1e2ec8fa7bab8ce56a Author: welcome Date: Wed Mar 30 01:49:01 2005 +0000 Added "probStartTime" data member to Amr class to record the system time just before init/restart was called. Needed for "Time since start(restart)" value printed when dumping plotfile. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit f46cb0467abc7ff5fc62459910a59c56ab7a456c Author: lijewski Date: Thu Mar 24 21:39:23 2005 +0000 Got working on Jacquard with PathScale compiler. Src/F_BaseLib/mboxarray.f90 Tools/F_mk/GMakedefs.mak commit 2549f66d12bddc021a77a31df59b38c2197ce002 Author: lijewski Date: Thu Mar 24 17:49:51 2005 +0000 Added pretty printing for mask arrays. Fixed a bug in the Z-direction stuff in *_aaa(). Src/LinearSolvers/F_MG/stencil.f90 commit 431aef71b54a1bf666969c5fd5ae506de0c19cfc Author: car Date: Tue Mar 22 22:59:07 2005 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg.f90 commit 30b44913d257d9975dbb10fe2522781f51f4e36d Author: lijewski Date: Tue Mar 22 21:40:32 2005 +0000 Just more goo from periodic testing. Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/t_main.f90 commit 5fa4d71f44f1abc0b29e8cde200f036e864feca4 Author: lijewski Date: Tue Mar 22 21:38:04 2005 +0000 Modified arguments to stencil_fill_bc_st() Tests/LinearSolvers/F_MG/t_stencil.f90 commit e33db700f956accb727755d58f1a7dda1438fd73 Author: lijewski Date: Tue Mar 22 21:23:18 2005 +0000 Set mg.v=2 & added ability to set periodicity. Src/LinearSolvers/C_CellMG/Test/grids/in.2_19boxes Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_3x2 Src/LinearSolvers/C_CellMG/Test/grids/in.2_big Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_d Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_e Src/LinearSolvers/C_CellMG/Test/grids/in.2_small_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_small_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_d Tests/LinearSolvers/C_CellMG/grids/in.2_19boxes Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_a Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_b Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_c Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_a Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_b Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_c Tests/LinearSolvers/C_CellMG/grids/in.2_3x2 Tests/LinearSolvers/C_CellMG/grids/in.2_big Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_a Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_b Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_c Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_d Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_e Tests/LinearSolvers/C_CellMG/grids/in.2_small_a Tests/LinearSolvers/C_CellMG/grids/in.2_small_b Tests/LinearSolvers/C_CellMG/grids/in.2_stack_a Tests/LinearSolvers/C_CellMG/grids/in.2_stack_b Tests/LinearSolvers/C_CellMG/grids/in.2_stack_c Tests/LinearSolvers/C_CellMG/grids/in.2_stack_d commit 6284cf110b8e2b8da04c7cdcf38382aea3731d28 Author: lijewski Date: Tue Mar 22 21:22:53 2005 +0000 Changed the default tol & made dump_VisMF default to true. Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit c855c190cec7a9ba95df8496081d743893c4dfee Author: 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 Date: Thu Mar 17 23:34:52 2005 +0000 *** empty log message *** Src/LinearSolvers/F_MG/stencil.f90 commit a9eb87f03f6583beefc67862d10299dd2347f061 Author: lijewski Date: Thu Mar 17 22:05:51 2005 +0000 Work needed to add "cross" argument to fill_boundary. Src/F_BaseLib/layout.f90 commit 50c617983f30fe6eb9da9e66fbe4561a166303e6 Author: lijewski Date: Thu Mar 17 21:57:25 2005 +0000 slight code rearrangment Src/F_BaseLib/boxarray.f90 commit 63d189941796cdf39c425db3f70dee322dd9e6ae Author: 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 Date: Wed Mar 16 23:33:59 2005 +0000 corner/edge extrap Src/LinearSolvers/F_MG/stencil.f90 commit e0a5c1ba7a6361330e9197f3937d95f049779132 Author: lijewski Date: Wed Mar 16 21:56:00 2005 +0000 Added boxarray_box_corners() Src/F_BaseLib/boxarray.f90 commit 8fbafa6ad02ae7d0f5b74db554c488db974e8ac0 Author: car Date: Wed Mar 16 19:00:42 2005 +0000 OMP syntax fixes Src/F_BaseLib/multifab.f90 commit c382b7dad97d5d93cfdaebb69a86429e9ebe74ca Author: car Date: Wed Mar 16 17:30:23 2005 +0000 *** empty log message *** Src/LinearSolvers/F_MG/stencil.f90 commit d015d860820ec5b6eb372747ed98ce9cca6d2adc Author: lijewski Date: Tue Mar 15 21:43:34 2005 +0000 Better test for early return from multifab_internal_sync_shift Src/F_BaseLib/multifab.f90 commit 7d07d35b542792d5999b4a51d587d156a17a8dcd Author: lijewski Date: Tue Mar 15 21:00:30 2005 +0000 internal_sync's now appear to work for periodic. Src/F_BaseLib/multifab.f90 commit 8bc9e888620bc9863cbf70f5245348bb86dd7550 Author: lijewski Date: Tue Mar 15 20:59:38 2005 +0000 slight change in notation Src/F_BaseLib/box.f90 commit 347af29371a229892b5b99ba22644c7e0f837b00 Author: car Date: Tue Mar 15 19:14:00 2005 +0000 think i've fixed ann's checkpoints Src/F_BaseLib/fabio.f90 Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_main.f90 commit 7f81cd25274dd2eb189d582996b2915a4d09e6a6 Author: car Date: Mon Mar 14 22:56:37 2005 +0000 denodalize Src/F_BaseLib/box.f90 commit d82cd85c187342f544e07e27ef090e70c596152b Author: almgren Date: Mon Mar 14 20:58:35 2005 +0000 Remove nodal from the writing of the bounding box in fabio_ml_multifab_write_d. Src/F_BaseLib/fabio.f90 commit b78b3d3d021a100f42ca822e185f4f8cf126b85c Author: car Date: Mon Mar 14 20:45:11 2005 +0000 add flux_reg.f90 Src/F_BaseLib/GPackage.mak commit ea66d591c989c57b49dac9a8b3c8884503e379f4 Author: car Date: Mon Mar 14 20:44:50 2005 +0000 read nodal mf Src/F_BaseLib/box.f90 Src/F_BaseLib/fabio.f90 commit 3a5230cdb54eeaaa25ba51a5f43732e7cf0e91b6 Author: almgren Date: Mon Mar 14 20:29:12 2005 +0000 New flux register code - this differs from boundary registers in that these are defined in fine index space at the boundaries of fine grids. Src/F_BaseLib/flux_reg.f90 commit d1479ef5168ded053be25fd0916ce760a878ea00 Author: car Date: Sat Mar 12 19:43:51 2005 +0000 cvs strings Src/F_BaseLib/ppm_util_c.c Src/F_BaseLib/timer_c.c commit 44120521c83f23091ed5a58bb47695094aeeb285 Author: 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 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 Date: Sat Mar 12 00:23:34 2005 +0000 A little simplification. Src/F_BaseLib/layout.f90 commit 924d07072ac7aad52ab20911f784a0cf2f996078 Author: lijewski Date: Sat Mar 12 00:22:31 2005 +0000 periodic_shift() -> box_periodic_shift() Src/F_BaseLib/box.f90 commit 7afce3f74b647b2b3edde7f7b360145e6bd19491 Author: lijewski Date: Fri Mar 11 22:28:16 2005 +0000 Added box_contains_strict() Src/F_BaseLib/box.f90 commit facbf2546309ab6a5ba09efa3ff60d5f915c9784 Author: lijewski Date: Fri Mar 11 19:20:37 2005 +0000 Didn't have easy() functions quite correct for nodal MultiFabs. Src/F_BaseLib/multifab.f90 commit 5e58d7012de230336cdd7225f1fe3bea34165e46 Author: lijewski Date: Thu Mar 10 23:00:05 2005 +0000 Made the easy() functions in multifab fill_boundary periodic-aware. Src/F_BaseLib/multifab.f90 commit 64610e073a663da624aa8ee0908b4cd28d894255 Author: lijewski Date: Tue Mar 8 21:50:44 2005 +0000 Some progress on making fill_boundary periodic-aware. Src/F_BaseLib/layout.f90 commit 5f98228a49bf7ede464547465d347892e098619d Author: almgren Date: Tue Mar 8 17:29:13 2005 +0000 Fix for 3d so now works correctly with Neumann bcs. Src/LinearSolvers/F_MG/sparse_solve.f90 commit 3cd413d31764582e6437603defcf31e60ded960f Author: lijewski Date: Mon Mar 7 23:11:41 2005 +0000 Looking good. Src/F_BaseLib/box.f90 commit 9d03035567a6e9cd50e628bdd1874c171d3d7954 Author: almgren Date: Mon Mar 7 22:16:01 2005 +0000 Works now in 3-d for Dirichlet bc's, still broken for 3-d Neumann. Src/LinearSolvers/F_MG/sparse_solve.f90 commit e0da2122c4da8727499536e990a3967ea78a8db5 Author: 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 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 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 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 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 Date: Fri Mar 4 20:25:48 2005 +0000 remove extraneous print statments Src/LinearSolvers/F_MG/stencil.f90 commit 643db54ba72e4577925314af1984dd0dbffd51bc Author: lijewski Date: Thu Mar 3 23:35:38 2005 +0000 Added periodic_shift. Still got to test it a tad more. Src/F_BaseLib/box.f90 commit ff4a0e251f1998d1990b5a55ad74d2d3d4ea6271 Author: almgren Date: Thu Mar 3 19:18:31 2005 +0000 Fixed some bugs in order to run on more than one grid. Runs on multiple grids with Dirichlet bc's but not yet working for Neumann. Src/LinearSolvers/F_MG/sparse_solve.f90 commit 7acfa510f0fac5ab69b6ca0110c030603dca1eb5 Author: 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 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 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 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 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 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 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 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 Date: Tue Mar 1 20:03:25 2005 +0000 Clean-up... Src/LinearSolvers/F_MG/sparse_solve.f90 commit 1bb5d5437dae70a59025981e0be280b97fb2aafb Author: car Date: Fri Feb 25 16:27:24 2005 +0000 somedebugging Src/F_BaseLib/GPackage.mak Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Tools/F_mk/GMakedefs.mak commit fb893953604dc54a038454f54307c447844eb9cf Author: car Date: Sun Feb 20 16:51:34 2005 +0000 fixes for dft Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/fab.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/multifab.f90 Src/F_BaseLib/test/t_bx.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/t_bx.f90 Tests/F_BaseLib/t_main.f90 commit 7577f4214fd6e1054cd3a790986e220521f6ef34 Author: car Date: Sun Feb 20 16:50:57 2005 +0000 *** empty log message *** Src/LinearSolvers/F_MG/stencil.f90 commit 8edcef40a24e07ee9a6c58cd65f4f15ac3dd5478 Author: car Date: Fri Feb 18 14:25:53 2005 +0000 *** empty log message *** Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_bx.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_bx.f90 commit 7fff51f57a925beb0ba18322fbe02f6a5d60ee65 Author: car Date: Thu Feb 17 23:21:09 2005 +0000 debug and opt flags for IBM on Mac Tools/F_mk/GMakedefs.mak commit 223576640b62ab5f1d8e7e207539a809d990a93b Author: car Date: Thu Feb 17 22:03:31 2005 +0000 no stinking mutex's Src/C_AMRLib/AmrLevel.cpp commit 78fcf3e4826886bace690d4c6d7bf77b944387b1 Author: car Date: Wed Feb 16 23:10:40 2005 +0000 more arithmetic in multifab Src/F_BaseLib/multifab.f90 commit 2dc1d5251a33ff9dbefe7d9d7ba211739f5ba731 Author: car Date: Tue Feb 15 21:54:19 2005 +0000 more dft debug changes Src/F_BaseLib/multifab.f90 commit 77f35293566112fa0740bedf329889e03d9138cd Author: 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 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 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 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 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 Date: Wed Jan 26 23:20:30 2005 +0000 Got rid of std::pow(). Src/C_BoundaryLib/InterpBndryData.cpp commit 2b0085a76d76a4461504789a4f3807755d799a2b Author: lijewski Date: Wed Jan 26 22:52:54 2005 +0000 Fix for Jacquard. Src/C_BoundaryLib/InterpBndryData.cpp commit 4694b7376b40e4af2981ce264d977ad19383160b Author: car Date: Wed Jan 26 16:33:15 2005 +0000 fancy gfortran Tools/C_mk/Make.defs commit 1886c91b2b00a4ca3bbee7527d7a2bc39b9abf8c Author: car Date: Wed Jan 26 16:31:27 2005 +0000 fancy gfortran Tools/C_mk/Make.defs commit 31af8966f0588b7c0c4e8e595f4172a7bc9a3692 Author: car Date: Wed Jan 26 00:20:31 2005 +0000 crafty way of getting path to libf95.a Tools/C_mk/Make.defs commit 9a6a458e7d026de6650ddcf8ff29b5d4330da476 Author: lijewski Date: Tue Jan 25 21:27:19 2005 +0000 Mod for PathScale when USE_MPI=TRUE on jacquard. Tools/C_mk/Make.Linux commit b2b8b12138bbcb4ab0e9438345cb629915f2d982 Author: lijewski Date: Tue Jan 25 18:45:00 2005 +0000 Mods to PathScale to compile on NERSC's jacquard system. Tools/C_mk/Make.Linux commit 52df063b8527b250cbb76b99ad1cf1389dce8a2f Author: car Date: Mon Jan 24 23:54:32 2005 +0000 *** empty log message *** Src/F_BaseLib/fabio_c.c Src/F_BaseLib/pingpong.f90 Src/F_BaseLib/ppm_util_c.c Src/F_BaseLib/test/main.f90 Tests/F_BaseLib/main.f90 commit a7b134be839c399a3e2675f93cf224eda45f10fe Author: almgren Date: Tue Jan 11 21:48:30 2005 +0000 Put trim(names(i)) instead of names(i) so that amrvis can read the names of the variables without the extra white spaces... Src/F_BaseLib/fabio.f90 commit 0ff436a8493e00a59a66ffba75a446135aa322f0 Author: car Date: Mon Jan 10 22:04:45 2005 +0000 White Space Fix dos->unix Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit d87e8956480f87356fa944e67fcf3cfbed22a790 Author: lijewski Date: Fri Jan 7 17:38:55 2005 +0000 fix to operator= Src/C_BoundaryLib/BndryRegister.cpp commit ba43c235da5d003c18bdc7e0f8dcddd73d2f9112 Author: lijewski Date: Thu Jan 6 22:18:50 2005 +0000 extra gunk for LAM Tools/C_mk/Make.mpi commit dd4300d1e0e80fbc607ab8e1086cb8615ea4edea Author: lijewski Date: Wed Jan 5 22:19:46 2005 +0000 fix to operator= Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BndryRegister.cpp commit d373c725ebfde4f08178062fe480b22de8c4cb29 Author: lijewski Date: Wed Jan 5 21:53:21 2005 +0000 fix to operator= Src/C_BaseLib/Tuple.H commit 80a757a63aac918a136c8d4e31783714b2bfa567 Author: 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 Date: Tue Jan 4 22:36:15 2005 +0000 name map Tools/C_mk/Make.frank commit 41f3ce57f65e219df6a8c838ffec2f3103089866 Author: car Date: Tue Jan 4 22:10:41 2005 +0000 frank archive file Tools/C_mk/Make.frank commit 3056e90423b8113e74ddde99d0eacfc82b0dccf4 Author: 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 Date: Tue Dec 21 15:32:03 2004 +0000 darwin Src/F_BaseLib/GPackage.mak commit 6f648d485d3bee84095fa75b6c3ea165ae999cda Author: car Date: Tue Dec 21 15:22:58 2004 +0000 some minor fixes to silence warnings Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/fabio.f90 Tools/F_mk/GNUmakefile Tools/F_mk/makefile commit e693758a45bdab651d08ac546e66f161d97bdf68 Author: car Date: Fri Dec 17 21:53:05 2004 +0000 *** empty log message *** Src/F_BaseLib/bl_constants.f90 Src/F_BaseLib/bl_string.f90 Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/mboxarray.f90 Src/F_BaseLib/parallel_stubs.f90 commit 83e65108d6ffaa8c6976cd45d7f194376486191d Author: car Date: Fri Dec 17 17:33:53 2004 +0000 MF_DEBUG_FILL: untested Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real2d.f Src/LinearSolvers/C_NodalMG/amr_real3d.f commit d91e017a0c3d15a8e984aa1a3a497d48b510a50a Author: 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 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 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 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 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 Date: Fri Dec 3 18:54:52 2004 +0000 clean/realclean not as painful Tools/C_mk/Make.rules commit eeba26b049c5062575ff49c37b14bba8d10f5ad7 Author: car Date: Fri Dec 3 17:44:04 2004 +0000 *** empty log message *** Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak commit d0d14639316f7e02ca18358858595bd6d3ab3d42 Author: almgren Date: Wed Dec 1 18:37:17 2004 +0000 Need change in setting up mba%rr in order to be consistent with new mboxarray_build_rr routine. Src/F_BaseLib/box_util.f90 commit 698757470244c1323ecfe9575926d19633144132 Author: lijewski Date: Tue Nov 30 19:21:09 2004 +0000 added Compare class Src/C_BaseLib/IntVect.H commit e3085ac168606d5f87e8633faf1d5535a97f4f64 Author: almgren Date: Mon Nov 29 22:42:16 2004 +0000 Use bc_module as opposed to mg_bc_module. Src/LinearSolvers/F_MG/stencil.f90 commit 3991c95a3899a00b4bfa745d7f93b75f33c9b77e Author: almgren Date: Mon Nov 29 22:40:55 2004 +0000 Added edge restriction. Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 commit 9eaf9909e5164f76ffb2331aaaf0d07f1deab45a Author: almgren Date: Mon Nov 29 22:40:30 2004 +0000 Removed print statements. Src/LinearSolvers/F_MG/mg_smoother.f90 commit 0453e2a5dd7e98454154b88a8500b26b9d911661 Author: car Date: Mon Nov 29 20:53:24 2004 +0000 bc interp renewed Src/F_BaseLib/GPackage.mak commit a6bbf95cff76072abe1159ea9b937d631fcdbec7 Author: almgren Date: Mon Nov 29 20:14:32 2004 +0000 bc.f90 holds the definitions of the bc type parameters. lincc_interp2d in interp.f90 has a bug fix. Src/F_BaseLib/bc.f90 Src/F_BaseLib/interp.f90 commit a4db5825943beb3e0c42baec181ef51c16541af5 Author: car Date: Sat Nov 27 20:28:09 2004 +0000 fix for totalview Src/F_BaseLib/GPackage.mak Src/F_BaseLib/interp.f90 Src/F_BaseLib/mboxarray.f90 commit 732f381f49c7a13e78d5d67d8e52b27fbfb20feb Author: 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 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 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 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 Date: Wed Nov 17 20:08:25 2004 +0000 using lbound,ubound should work Src/F_BaseLib/multifab.f90 commit 6c288d3720622d32e4a3c0c8704a68f007a62801 Author: car Date: Wed Nov 17 19:09:22 2004 +0000 multifab_fab_copy Src/F_BaseLib/multifab.f90 commit 5e5813233225f3972f1aade0d2fe8f86114532d7 Author: car Date: Wed Nov 17 16:29:36 2004 +0000 FreeBSD Tools/F_mk/GMakedefs.mak commit f1a903a5c8d37a60405e85bc5ddef7afac822759 Author: car Date: Tue Nov 16 23:56:24 2004 +0000 order of include Darwin? Src/F_BaseLib/timer_c.c commit 316c6675e78db7903fe7f4d36fb7e85c29b87fcf Author: 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 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 Date: Fri Nov 12 20:55:33 2004 +0000 gotta go home Src/LinearSolvers/F_MG/stencil.f90 commit b746b42a3428baa38e3864238f9e3936b792704a Author: car Date: Thu Nov 11 22:31:29 2004 +0000 *** empty log message *** Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_util.f90 commit 5edf0ed64e25afd7f298396ef19acf1888ac05c0 Author: car Date: Thu Nov 11 22:24:34 2004 +0000 *** empty log message *** Src/F_BaseLib/box.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/fab.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/mboxarray.f90 Tools/F_mk/GMakedefs.mak commit 39c5d7f49cd42bf4476638508ce1a6993303df30 Author: car Date: Wed Nov 10 22:39:14 2004 +0000 minor tweaks Src/F_BaseLib/bl_constants.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 5ea8c2b4f571f5a3d4d7adb6381396816118baac Author: car Date: Mon Nov 8 22:33:33 2004 +0000 minor tweaks for F Src/F_BaseLib/bl_mem_stat.f90 Src/F_BaseLib/bl_stream.f90 Src/F_BaseLib/bl_string.f90 Src/F_BaseLib/bl_timer.f90 Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/box.f90 Src/F_BaseLib/box_util.f90 Src/F_BaseLib/boxarray.f90 Src/F_BaseLib/cluster.f90 Src/F_BaseLib/fab.f90 Src/F_BaseLib/interp.f90 Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/mt19937ar.f90 Src/F_BaseLib/multifab.f90 Src/F_BaseLib/pingpong.f90 Src/F_BaseLib/plotfile.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 commit 38376488dbd1f0ce201d9554e5829fd9d3993ad1 Author: 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 Date: Thu Oct 28 19:17:15 2004 +0000 tweak Tools/F_mk/GMakedefs.mak commit b59f423a4e337ad097760bbb10cfbc099ffb387b Author: car Date: Thu Oct 28 17:27:37 2004 +0000 *** empty log message *** Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/t_main.f90 commit 71e542453f0335ca124d5dc65376dbc92849f6dc Author: car Date: Fri Oct 15 21:36:35 2004 +0000 *** empty log message *** Src/F_BaseLib/fabio.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/t_main.f90 commit cf6a5d03406c1f624bfbe8b26aa35b4911e5db97 Author: car Date: Fri Oct 15 20:34:51 2004 +0000 more changes for eigenproblem Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/ml_util.f90 Tools/F_mk/GMakerules.mak commit d6108e7e002f8771f9afc37023c3b00a44d41409 Author: car Date: Fri Oct 15 20:31:58 2004 +0000 first cut at ml_multifab_read Src/F_BaseLib/bl_stream.f90 Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/list_box.f90 Src/F_BaseLib/multifab.f90 Src/F_BaseLib/plotfile.f90 Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_main.f90 commit c89e9175809c9167744d9a822ce90a50f3060b9e Author: lijewski Date: Wed Oct 13 21:52:22 2004 +0000 Set default for "verbose" to true for the time being. Added "only_heaviest_cpu". Src/C_BaseLib/DistributionMapping.cpp commit bde5769088e68fda4a56b1b96c211b427acb2abc Author: lijewski Date: Wed Oct 13 20:57:03 2004 +0000 output a bit more stuff Src/C_BaseLib/DistributionMapping.cpp commit 59f5d7867122d506f8689399c9c45d045cdeaad2 Author: car Date: Tue Oct 12 15:44:07 2004 +0000 If the number of processors is <= 8 then use the 'better' metis partitioner. Src/C_BaseLib/DistributionMapping.cpp commit ef0afc70ebdf783397110feea8ee7f51b0f6c067 Author: car Date: Mon Oct 11 23:26:35 2004 +0000 If metis_opt is != 0 then use edgeweights in addition to vertex weights. The edgeweights are equal to the volume of the intersection of the target box grown by one and the source boxs. Src/C_BaseLib/DistributionMapping.cpp commit 8cc383b24a19da81507a4baabe5d3495fe68a70b Author: lijewski Date: Mon Oct 11 22:45:37 2004 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit a2147c43f35e4a9db339db6d4ca2e11a7c2201f9 Author: lijewski Date: Mon Oct 11 22:00:12 2004 +0000 Fixed Chuck's bug Src/C_BaseLib/DistributionMapping.cpp commit c7007acb6a3b385e7f0a9b2be20afb0bdfec781a Author: lijewski Date: Mon Oct 11 21:57:09 2004 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit 05ac385569218889d221395c31d87e28aface89b Author: lijewski Date: Mon Oct 11 21:47:03 2004 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp commit c01ae1f75894a8e8cc3ca61aa1884952e07bbf71 Author: car Date: Mon Oct 11 21:17:13 2004 +0000 for metis Tools/C_mk/Make.defs commit 7c6af15f41bbd82c173242d01cfc4e8ba8ebe5d2 Author: car Date: Mon Oct 11 20:33:17 2004 +0000 ops Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/test/GNUmakefile Tests/C_BaseLib/GNUmakefile commit f1b7d50f6738532d13e8ee101e79c52333bc5fc0 Author: 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 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 Date: Tue Oct 5 01:41:46 2004 +0000 minor fixes Src/F_BaseLib/fabio_c.c commit c5939d3e5e635000f51e8e54a8fcb7950e6c579c Author: car Date: Tue Oct 5 01:40:56 2004 +0000 windows fixes Src/F_BaseLib/plotfile.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/stencil.f90 commit a79560c415793171bf9ab8efa91a2b17c154b292 Author: car Date: Mon Oct 4 19:41:54 2004 +0000 ml changes Src/F_BaseLib/multifab.f90 commit 5d9dc9e2fcb206bf501f157952142d4d46e31393 Author: car Date: Sat Oct 2 22:49:41 2004 +0000 *** empty log message *** Src/F_BaseLib/filler.f90 Src/F_BaseLib/mt19937ar.f90 Src/F_BaseLib/multifab.f90 Src/F_BaseLib/plotfile.f90 Src/F_BaseLib/test/main.f90 Src/LinearSolvers/F_MG/stencil.f90 Tests/F_BaseLib/main.f90 Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak commit 4373c344a33b2d134c32e5e566de5fbeb17db016 Author: car Date: Thu Sep 30 19:02:41 2004 +0000 corrected fab dimensions Src/F_BaseLib/fabio.f90 commit 5015be84b9445ca2af35023ac0989a1d74661175 Author: car Date: Tue Sep 28 17:56:35 2004 +0000 formatted io for plotfiles Src/F_BaseLib/fabio.f90 commit 52e52ac63ea9d3e1c2730c22c0dce956a50f8fb5 Author: car Date: Wed Sep 22 17:53:41 2004 +0000 more constants Src/F_BaseLib/bl_constants.f90 commit 79f4dec7a53485da670fca9994461c115824e1a9 Author: car Date: Tue Sep 21 17:38:17 2004 +0000 fixes for ia64 Src/F_BaseLib/mt19937ar.f90 commit cbb241d709212f9dc94dc19db954f05755c2c7e5 Author: 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 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 Date: Fri Sep 17 20:30:36 2004 +0000 Make.IRIX64 Tools/C_mk/Make.IRIX64 commit 26d496ec631acd25b6eff18b4a2d4691b7f4b9c8 Author: car Date: Thu Sep 16 16:12:45 2004 +0000 intel8 bug fixes Src/F_BaseLib/bl_constants.f90 Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/box.f90 Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_main.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_util.f90 Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_main.f90 Tools/F_mk/GMakedefs.mak Tools/F_mk/GNUmakefile commit 9762316222b4e634c71ae3232e994f30a39f25b2 Author: car Date: Wed Sep 15 22:22:18 2004 +0000 windows fixes Src/F_BaseLib/NPackage.mak Tools/F_mk/NMakedefs.mak Tools/F_mk/NMakerules.mak commit 0ddeb1aeae75f1c7b16424535c3266bfd2a3b3cb Author: car Date: Mon Sep 13 19:55:34 2004 +0000 *** empty log message *** Src/F_BaseLib/f2kcli_crayx1.f90 commit 67ab67e1bb2f57d2dc17dfda7cbe7823a7032de2 Author: vince Date: Mon Sep 13 19:02:23 2004 +0000 flags for cxx. Tools/C_mk/Make.OSF1 commit 23a9eeec7f700aa4a6cdf0a39771ffbd5efec269 Author: car Date: Thu Sep 9 16:35:08 2004 +0000 more spinning Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 Tools/F_mk/GMakedefs.mak commit c1dc0557dcbcf63d9f02764c88db1d30e9a232c9 Author: car Date: Tue Sep 7 16:22:00 2004 +0000 minor changes Src/F_BaseLib/layout.f90 Src/F_BaseLib/multifab.f90 Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_main.f90 Src/LinearSolvers/F_MG/itsol.f90 Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/stencil.f90 Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_main.f90 Tools/F_mk/GMakedefs.mak commit a8218a6fc0d4a8f45eacf7d8c1e27c72525a5884 Author: vince Date: Fri Sep 3 23:59:19 2004 +0000 added check for capfinestlevel. Src/C_AMRLib/StationData.cpp commit b80413555b22bf2570226bc24d4596d3ad1b7bc0 Author: welcome Date: Fri Aug 27 17:47:57 2004 +0000 Changed options for CRAYX1 removed -O in C++, does nothing Default C++ optimization is -O2 Added options for loopmark listings to see where vectorization happens. Tools/C_mk/Make.CRAYX1 commit e6f95a0f1464dc26551f6b567062dfe3a54e0b24 Author: car Date: Wed Aug 25 19:32:27 2004 +0000 FCOMP=g77 Tools/C_mk/Make.defs commit 77e3d3f9be567375b6bdfbe5a2d78b8893caee51 Author: car Date: Tue Aug 24 22:33:16 2004 +0000 Intel/Lahey fix Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit e724fd8e98d5df9ea42ecc341bfeb47f68933fd7 Author: marc Date: Mon Aug 16 22:40:50 2004 +0000 Add test for max ref ratio in PROTECT_INTERP Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F commit d49870db16594ffaaec9011ab8741f575a3b9913 Author: car Date: Thu Aug 5 22:21:54 2004 +0000 slight changes Src/F_BaseLib/knapsack.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_util.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 7495cfe27fbac5933b9d0bf68722a93a120601f5 Author: car Date: Thu Aug 5 16:45:18 2004 +0000 windows fixes Src/F_BaseLib/bl_IO.f90 Src/F_BaseLib/cluster.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 4603f3057f21cd04bb09188190b0b292ec654fb8 Author: car Date: Wed Aug 4 22:46:08 2004 +0000 *** empty log message *** Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 commit beb03c69a5d2880111ec3c80e8d9cef4c5149f15 Author: car Date: Wed Aug 4 19:53:26 2004 +0000 more mboxarray stuff Src/F_BaseLib/mboxarray.f90 commit 5c98f8e4903d5476b2625f57a2265de860a3d1fc Author: car Date: Wed Aug 4 00:52:04 2004 +0000 windows update Src/LinearSolvers/F_MG/stencil_nodal.f90 commit 88e7d21b2ad008090cace5fee834ca8a8d5f4ced Author: car Date: Tue Aug 3 22:47:17 2004 +0000 *** empty log message *** Src/F_BaseLib/bndry_reg.f90 Src/LinearSolvers/F_MG/stencil.f90 commit 64c7fbc68d16979f09288a7be375737d75e0da14 Author: car Date: Mon Aug 2 22:11:38 2004 +0000 *** empty log message *** Src/LinearSolvers/F_MG/stencil.f90 commit 022ad48784ea49cd2db7498bb7c129f24e25847e Author: car Date: Fri Jul 30 18:01:29 2004 +0000 minor tweaks Src/LinearSolvers/F_MG/mg_smoother.f90 Tools/F_mk/GMakedefs.mak commit 4eef4aeeb736f685561989965fd5654e9abdd8fc Author: car Date: Fri Jul 30 17:46:49 2004 +0000 smaller files Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/mg_prolongation.f90 Src/LinearSolvers/F_MG/mg_restriction.f90 Src/LinearSolvers/F_MG/ml_interface_stencil.f90 Src/LinearSolvers/F_MG/ml_prolongation.f90 Src/LinearSolvers/F_MG/ml_restriction.f90 Src/LinearSolvers/F_MG/ml_util.f90 commit 3f27bdf455485d13eb19634a0efcef334fdcb678 Author: car Date: Thu Jul 29 20:32:23 2004 +0000 altrix Tools/C_mk/Make.defs commit c04d52dab2fe46440104468f5e99dc2773cfde47 Author: car Date: Thu Jul 29 18:53:12 2004 +0000 altix Src/C_BaseLib/FPC.cpp commit 442726a9614a3ad6c48f15cf7a308d5cff0b7f7c Author: car Date: Thu Jul 29 15:35:03 2004 +0000 crayx1 Tools/C_mk/Make.CRAYX1 commit 4f555c329e2dc41ea3684b54b73e15eddba53d68 Author: welcome Date: Wed Jul 28 20:48:30 2004 +0000 Modification for NEC SX6. Needed to explicitly strip-mine the main loops in hgrlxu. Brain-dead Sx6 compiler partially vectorizes the loop but needs to allocate temporary array. Makes an assumption about the max length of the loop and generates a run-time error if the actual length is larger than the assumption. Can request larger array with pragma, but only up to about 15000. New function only called on SX6, since not very well tested. Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit f84dbf86452e727cdbe861fb8ae26f5c2b4ac35e Author: welcome Date: Wed Jul 28 20:20:24 2004 +0000 try again to update makefiles for NEC SX6 Tools/C_mk/Make.SUPERUX Tools/C_mk/Make.defs commit 80fdd17621677eeec7909651cd14c711171f3efd Author: welcome Date: Wed Jul 28 19:52:18 2004 +0000 Minor updates for NEC SX6 Src/C_BaseLib/BaseFab.H Src/C_BaseLib/FPC.cpp commit 8710d2bc54febf3f7bc4493d7c3b5647d5d34fc2 Author: car Date: Wed Jul 28 18:06:05 2004 +0000 fixes for X1 Tools/C_mk/Make.CRAYX1 commit 65e55237e971c6e1b3eac5610ee6d9ea6fa7cf15 Author: vince Date: Tue Jul 27 22:51:25 2004 +0000 added std:: Src/C_AMRLib/DatasetClient.cpp commit 96d012f269fd1b69dda8642f4d39ec3460b22310 Author: vince Date: Mon Jul 26 22:24:29 2004 +0000 call fix for arrayview. Src/C_AMRLib/DatasetClient.cpp commit 6b8b6a101c04688d26e5a057dba307754a8a8c4f Author: car Date: Mon Jul 26 20:49:39 2004 +0000 *** empty log message *** Src/F_BaseLib/bl_types.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/t_main.f90 commit 446b995f0adcc43ac003959e8d741bc9df1f2b40 Author: car Date: Mon Jul 26 20:49:09 2004 +0000 gfortran trial Tools/F_mk/GMakedefs.mak commit 9f15aa3de73bca64c1ff4d578da9de1c18d15bbc Author: car Date: Mon Jul 26 20:48:18 2004 +0000 cray x1 fixes Src/F_BaseLib/f2kcli_crayx1.f90 Tools/F_mk/GMakedefs.mak commit 70f528b3a225b78e47361144d6ce48fd3d88128a Author: car Date: Mon Jul 26 19:37:21 2004 +0000 ihi->ilo Src/F_BaseLib/interp.f90 commit 7d277ee899088f80007ff44381da042a84db603f Author: car Date: Mon Jul 26 19:36:59 2004 +0000 pointer association, not Src/F_BaseLib/cluster.f90 commit 4a70d1e85b0e15670f7f3eabf5eb2d7205868d52 Author: car Date: Mon Jul 26 19:25:57 2004 +0000 broken unitialized variables on IRIX Tools/F_mk/GMakedefs.mak commit 8d5942de36aba6db1cfe709e57e36a6a7154cf8b Author: car Date: Fri Jul 23 23:37:28 2004 +0000 cray bug work around Src/F_BaseLib/boxarray.f90 commit a290b2b64576fc2e44c961fdf2c14d9c8be43d41 Author: 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 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 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 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 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 Date: Fri Jul 2 19:59:25 2004 +0000 new types definitions Src/F_BaseLib/bl_types.f90 commit 0de502bb2893474f5d056c87330e76d5bae34b63 Author: car Date: Wed Jun 30 22:10:48 2004 +0000 testing purposes Src/F_BaseLib/bl_types.f90 Src/F_BaseLib/multifab.f90 commit 9b04d71a56755cf3f29df36e0226c7aee4ae0580 Author: 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 Date: Tue Jun 29 19:58:48 2004 +0000 Removed print statements. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit dcdceecd14df0b1c0e4d3561ae4a78df5cad8c4c Author: car Date: Mon Jun 28 16:00:30 2004 +0000 minor fixes Src/F_BaseLib/BoxLib.f90 Src/F_BaseLib/bndry_reg.f90 Src/F_BaseLib/test/fornberg_weights.f90 Tests/F_BaseLib/fornberg_weights.f90 Tools/F_mk/GMakedefs.mak commit 6c0ad5b1d8b169ddb052777a479d169aadb08f3f Author: car Date: Mon Jun 28 15:57:33 2004 +0000 *** empty log message *** Src/F_BaseLib/bl_IO.f90 Tools/F_scripts/coco/coco.pl Tools/F_scripts/coco/e1.FF Tools/F_scripts/coco/e1.II commit 8e41fe7ac969317c011e9a26722e37f1f3a5c15a Author: almgren Date: Fri Jun 25 22:38:30 2004 +0000 Typo: had ny instead of nx. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit acdbf6089214f2f5a09cc546f973861d1d6d58a0 Author: almgren Date: Fri Jun 25 20:01:32 2004 +0000 Changes to accomodate Neumann bcs in the case of factor 4 refinement. Change also relevant for factor 2 but that already worked. This uses values inside the domain instead of those reflected outside by Neumann condition (which didn't exist for factor 4). Src/LinearSolvers/F_MG/mg.f90 Src/LinearSolvers/F_MG/stencil_nodal.f90 commit ac44dd382d49fb9c634e5f1d5ee49d137543c3d7 Author: almgren Date: Thu Jun 24 22:06:30 2004 +0000 Fix in nodal_restriction_2d which gives same (working) result for factor 2 refinement but fixes the (broken) factor 4 refinement. Only fixed in 2d for now. Src/LinearSolvers/F_MG/mg.f90 commit df6b9ad6b1cb988ce025fa0af4e94b4ffa16f6d4 Author: almgren Date: Thu Jun 24 20:23:14 2004 +0000 Fixed code for Neumann boundary conditions in 2d and 3d. Src/LinearSolvers/F_MG/stencil_nodal.f90 commit fbf4f926ab1b605006b87d0e6b2136d4112d818d Author: almgren Date: Thu Jun 24 20:22:32 2004 +0000 Typo mis-spelling corrected. Src/LinearSolvers/F_MG/stencil.f90 commit e38dfe967994adc89a395c9e3523645bf47f0e1e Author: car Date: Wed Jun 23 17:23:42 2004 +0000 bl_kiss not needed Src/F_BaseLib/GPackage.mak Src/F_BaseLib/NPackage.mak Src/F_BaseLib/bl_kiss.f90 Src/F_BaseLib/test/.cvsignore Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/.cvsignore Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_main.f90 commit 23c6934f1e448841fa53d0f68a5fc8b887a0affa Author: car Date: Tue Jun 22 16:42:05 2004 +0000 *** empty log message *** Tools/F_scripts/coco/coco_e.FF Tools/F_scripts/coco/e1.FF Tools/F_scripts/coco/e1.II commit d573fc321d34f6d3c3ade270cc1f2ee2f296765a Author: car Date: Tue Jun 22 16:42:05 2004 +0000 *** empty log message *** Tools/F_scripts/coco/coco_e.II commit acf74a2c568b193072d3c9162aceb5c794e89dbc Author: car Date: Tue Jun 22 16:42:05 2004 +0000 *** empty log message *** Tools/F_scripts/coco/coco.pl commit 628bfa177914e36883cd27ff29ae8e0d8b7ba745 Author: car Date: Tue Jun 22 15:11:43 2004 +0000 initial Tools/F_scripts/coco/coco.pl commit c53adb7c0a46e77c401f003adc5d0e24bd3de5f5 Author: 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 Date: Tue Jun 15 19:24:16 2004 +0000 Added -mp flag Tools/C_mk/Make.defs commit 7929dbe96aa16ee9e25e765430eb5fbec688dc19 Author: car Date: Fri Jun 11 21:42:21 2004 +0000 *** empty log message *** Src/F_BaseLib/bl_timer.f90 commit 7ae0215084b7607aabbaf69510516d02bd95abda Author: car Date: Fri Jun 11 03:50:41 2004 +0000 timer Src/F_BaseLib/bl_timer.f90 Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_main.f90 Src/F_BaseLib/timer_c.c Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_main.f90 commit 65d9574f6f012c4351ef51898225ed7172163616 Author: car Date: Tue Jun 8 18:14:34 2004 +0000 *** empty log message *** Tools/F_mk/GMakerules.mak commit f59d86e7c3c51f36450a16c733c771add521f5bf Author: car Date: Tue Jun 8 01:01:16 2004 +0000 *** empty log message *** Src/F_BaseLib/list_box.f90 Src/F_BaseLib/test/makefile Tests/F_BaseLib/makefile commit 1c9ae8a21ce967aa40058d08c09c4ab75169eeb6 Author: car Date: Mon Jun 7 16:05:55 2004 +0000 *** empty log message *** Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/test/.cvsignore Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/def_knapsack.out Src/F_BaseLib/test/t_knapsack.f90 Tests/F_BaseLib/.cvsignore Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/def_knapsack.out Tests/F_BaseLib/t_knapsack.f90 commit 363cae8822785d89f3248568bf3b3078352b561d Author: car Date: Mon Jun 7 15:56:59 2004 +0000 formatted output Src/F_BaseLib/test/knapsack.out Tests/F_BaseLib/knapsack.out commit 6501fe356392b4b9c5230d4572487d5c7ed84f9c Author: car Date: Sat Jun 5 16:23:08 2004 +0000 *** empty log message *** Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/test/knapsack.out Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/knapsack.out Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_main.f90 Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak Tools/F_scripts/f90doc/stmts.pl commit 37a7bddfcf3ae9f34b7abf1f4331f9bca0f1cf4c Author: car Date: Sat Jun 5 15:29:01 2004 +0000 conn_defs no longer uses processor defs Src/F_BaseLib/test/conn_defs Tests/F_BaseLib/conn_defs commit 14fd6638f790424d31790a16d61877261908d21d Author: car Date: Sat Jun 5 15:07:18 2004 +0000 *** empty log message *** Src/F_BaseLib/GPackage.mak Tools/F_mk/GMakedefs.mak commit a553dc438b106269fb89df6c088a282ba8a4cc0c Author: car Date: Sat Jun 5 00:16:42 2004 +0000 Fixes for Intel8 Src/F_BaseLib/cluster.f90 Src/F_BaseLib/test/inputs.domain Src/F_BaseLib/test/main.f90 Tests/F_BaseLib/inputs.domain Tests/F_BaseLib/main.f90 Tools/F_mk/GMakedefs.mak commit 040b644d2917423108971883f11649e72f786c16 Author: car Date: Fri Jun 4 17:03:19 2004 +0000 OMP typos Src/F_BaseLib/multifab.f90 Src/LinearSolvers/F_MG/mg_smoother.f90 commit 172a734048cd6a21c6b58e73608e455d0f39bdf3 Author: car Date: Fri Jun 4 16:48:42 2004 +0000 OMP typos Src/F_BaseLib/multifab.f90 Src/F_BaseLib/test/GNUmakefile Tests/F_BaseLib/GNUmakefile commit e1a9316f5d8575f59208c51fb344dba8aa4e81de Author: car Date: Thu Jun 3 21:10:20 2004 +0000 86 ieee Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_ieee.f90 Src/F_BaseLib/bl_ieee_c.c Src/F_BaseLib/bl_ieee_c.h Src/F_BaseLib/knapsack.f90 Src/F_BaseLib/layout.f90 Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/t_ieee.f90 Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/stencil.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/t_ieee.f90 Tools/F_mk/GMakedefs.mak commit bbcbdafcff3365d2aa2be028a4821de07778b779 Author: car Date: Tue Jun 1 04:46:59 2004 +0000 more refinements on windows makefiles Src/F_BaseLib/NPackage.mak Src/F_BaseLib/test/makefile Tests/F_BaseLib/makefile Tools/F_mk/NMakedefs.mak Tools/F_mk/NMakerules.mak Tools/F_scripts/mkdep.pl commit aa7128751bdc66db2756c2474d632656b70f74e0 Author: car Date: Mon May 31 19:29:17 2004 +0000 *** empty log message *** Src/F_BaseLib/NPackage.mak Src/F_BaseLib/f2kgetcl.c Src/F_BaseLib/test/makefile Tests/F_BaseLib/makefile Tools/F_mk/NMakedefs.mak Tools/F_mk/NMakerules.mak commit 443aeceb41b4691c6250b1cda85af7cd1e89b396 Author: car Date: Sun May 30 04:09:53 2004 +0000 *** empty log message *** Src/F_BaseLib/bl_ieee_c.c Src/F_BaseLib/bl_ieee_c.h Tools/F_mk/GMakedefs.mak Tools/F_scripts/mkdep.pl commit c7ebd079b02a683f0584aec5672c119ecf144ddb Author: car Date: Sat May 29 22:07:59 2004 +0000 *** empty log message *** Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak Tools/F_scripts/mkdep.pl commit 89329559317c76be46eeb1086800988bb08afbd0 Author: car Date: Sat May 29 19:02:46 2004 +0000 *** empty log message *** Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_ieee.f90 Src/F_BaseLib/bl_ieee_c.c Src/F_BaseLib/bl_ieee_c.h Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_ieee.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_ieee.f90 Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak Tools/F_scripts/mkdep.pl commit 8dbbb0e9279b940a35b2880df43370858eeadbb4 Author: car Date: Sat May 29 16:05:34 2004 +0000 *** empty log message *** Src/F_BaseLib/fabio_c.c Src/F_BaseLib/test/inputs.domain Src/F_BaseLib/test/main.f90 Tests/F_BaseLib/inputs.domain Tests/F_BaseLib/main.f90 commit 704ff60a87090371e438e77f3bdd9066fd714419 Author: car Date: Fri May 28 22:48:01 2004 +0000 john wants comments Src/F_BaseLib/bl_IO.f90 Src/F_BaseLib/bl_constants.f90 Src/F_BaseLib/bl_error.f90 Src/F_BaseLib/bl_kiss.f90 Src/F_BaseLib/bl_mem_stat.f90 Src/F_BaseLib/bl_parmparse.f90 Src/F_BaseLib/bl_types.f90 Src/F_BaseLib/fab.f90 Src/F_BaseLib/fabio.f90 Src/F_BaseLib/test/GNUmakefile Tests/F_BaseLib/GNUmakefile commit 49ca32d8c587c7fee72546097bb219c80ad10be7 Author: car Date: Thu May 27 22:32:25 2004 +0000 more makefile fixes Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c Src/F_BaseLib/plotfile.f90 Src/F_BaseLib/test/GNUmakefile Tests/F_BaseLib/GNUmakefile Tools/F_mk/GMakedefs.mak Tools/F_mk/GMakerules.mak commit ac7d7fb6419ace3a862cc5518aadcfa06f921393 Author: car Date: Wed May 26 21:48:51 2004 +0000 *** empty log message *** Src/F_BaseLib/fabio.f90 Src/F_BaseLib/fabio_c.c Src/F_BaseLib/test/GNUmakefile Src/F_BaseLib/test/main.f90 Src/F_BaseLib/test/t_main.f90 Tests/F_BaseLib/GNUmakefile Tests/F_BaseLib/main.f90 Tests/F_BaseLib/t_main.f90 commit 25803efb44659888162eb5c82470b70c5c3d9d42 Author: car Date: Wed May 26 13:05:51 2004 +0000 *** empty log message *** Src/F_BaseLib/test/.cvsignore commit 846c4a6c05a1b37562a86086b5892c4e7fd16ced Author: 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 Date: Wed May 26 13:01:39 2004 +0000 *** empty log message *** Tests/F_BaseLib/.cvsignore commit e7e34a1713e1fb922ac8ceb35248f50b1abafa47 Author: 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 Date: Tue May 25 04:27:55 2004 +0000 module name mismatch Src/F_BaseLib/bl_parmparse.f90 commit ba98df7da8e59a7650a48ed9ce79dad861035866 Author: 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 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 Date: Tue May 25 02:00:45 2004 +0000 aux-->extern Src/LinearSolvers/F_MG/GPackage.mak commit 7d77ea17736f29e19cc8ce5334c7edb13f453941 Author: car Date: Mon May 24 22:58:04 2004 +0000 f90doc; mostly ignore for 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Src/F_BaseLib/filler.f90 Src/F_BaseLib/plotfile.f90 Src/F_BaseLib/test/t_main.f90 Src/LinearSolvers/F_MG/GPackage.mak Src/LinearSolvers/F_MG/stencil.f90 Tests/F_BaseLib/t_main.f90 commit 0031d6c45fae24aef51d743870d85ecec81321ff Author: car Date: Mon May 24 22:10:10 2004 +0000 split files Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_IO.f90 Src/F_BaseLib/bl_kiss.f90 Src/F_BaseLib/bl_mem_stat.f90 Src/F_BaseLib/bl_parmparse.f90 Src/F_BaseLib/bl_stream.f90 Src/F_BaseLib/bl_string.f90 Src/F_BaseLib/bl_timer.f90 Src/F_BaseLib/bl_utility.f90 commit a86f9ca50f60b35942beb7d742c633c61fa8d590 Author: car Date: Mon May 24 21:59:14 2004 +0000 *** empty log message *** Tools/F_scripts/ibm_sp_batch.poe commit b3d55561dfd2d51a821f8fb56c0a4d6230ed386e Author: car Date: Mon May 24 21:50:06 2004 +0000 Initial revision Src/F_BaseLib/BoxLib.f90 Src/F_BaseLib/GPackage.mak Src/F_BaseLib/bl_constants.f90 Src/F_BaseLib/bl_error.f90 Src/F_BaseLib/bl_space.f90 Src/F_BaseLib/bl_types.f90 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type fix. Src/C_BaseLib/BoxList.cpp commit c2a1202df53ab577d766f8db2aa71ac4438d128c Author: car Date: Tue Apr 27 17:04:05 2004 +0000 no longer builds by default Src/C_BaseLib/GNUmakefile commit 90cbcc3b44b5cac1bae0d5ced9dd7a19c313ee17 Author: car Date: Tue Apr 27 17:00:44 2004 +0000 cout -->> std::cout needed by gcc 3.4.0 Src/C_BaseLib/FabArray.H Src/C_BaseLib/test/GNUmakefile Tests/C_BaseLib/GNUmakefile commit 5f71ba225886f5e9a9eddfb3672eda7010895de2 Author: 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 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 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 Date: Tue Mar 9 18:35:37 2004 +0000 PathScale support Tools/C_mk/Make.Linux commit 1045ed89e9d43b8ad46d768c89f10bdede7d3a34 Author: car Date: Tue Mar 9 18:28:51 2004 +0000 cpp seems to the right way to invoke pre-processor Tools/C_mk/Make.Linux commit ffa6f543158bf0709d571781bbb6cd7c905e0384 Author: 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 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 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 Date: Thu Mar 4 18:09:40 2004 +0000 PathScale Src/C_BaseLib/FPC.cpp commit fb1ad123abea9559bcd0dfca7b003afdb1c39cde Author: car Date: Thu Mar 4 18:09:01 2004 +0000 *** empty log message *** Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/tFB.cpp Src/C_BaseLib/test/tMF.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tMF.cpp commit e4a715a0c9a616cf3bff33cf582ccd5559a77922 Author: car Date: Fri Feb 27 21:20:32 2004 +0000 We should care if the bottom solve fails, print a warning and break; what really should matter is that the composite solve itself converge. Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit f13c8185f03d341f0e66a28a399cb863762799a5 Author: 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 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 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 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 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 Date: Tue Jan 20 21:54:10 2004 +0000 Added tParmParse Src/C_BaseLib/test/GNUmakefile Tests/C_BaseLib/GNUmakefile commit c8721639f57de7c22ace34592325d8ecf10117b4 Author: lijewski Date: Tue Jan 20 21:53:31 2004 +0000 fixed bug Src/C_BaseLib/ParmParse.cpp commit 3c0a35e70679cfa3842ed52450028f466691b2da Author: car Date: Wed Jan 7 21:45:03 2004 +0000 tweak for std::size_t Src/C_BaseLib/winstd.H commit 5d62ad51712f6c8c8f3fe25f93370b8086274c74 Author: car Date: Wed Jan 7 21:44:20 2004 +0000 windows tweaks for std::size_t Src/C_BaseLib/Arena.H Src/C_BaseLib/winstd.H commit f207e31aaea2e9cf74471161c1eb82bda85af545 Author: car Date: Wed Jan 7 21:18:19 2004 +0000 for some compilers size_t, pow, sqrt, etc, need to be in the std namespace Src/C_AMRLib/Interpolater.cpp Src/C_BaseLib/Arena.H Src/C_BaseLib/Arena.cpp Src/C_BaseLib/BArena.H Src/C_BaseLib/BArena.cpp Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/Tuple.H Src/C_BaseLib/Utility.cpp Src/C_BoundaryLib/InterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit d262d75544068ba4aa663fe2a8622769ead9ff99 Author: car Date: Wed Dec 10 18:09:43 2003 +0000 support for BGL and Intel 8.0 Tools/C_mk/Make.bgl Tools/C_mk/Make.defs commit 9e280b84180e490274baf6576b0b2725a0c2f12f Author: car Date: Mon Dec 8 23:13:46 2003 +0000 powerpc for BGL Src/C_BaseLib/FPC.cpp commit 659bbddd63acd9cc6ee51135b94dc81eb9a34b4a Author: marc Date: Wed Oct 15 18:01:33 2003 +0000 Add quarter time levels into which_time Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 9b13c5691837d8676c6ac8023de32762b75ff9e6 Author: lijewski Date: Thu Sep 18 19:21:00 2003 +0000 Got rid of cdir$ ivdep stuff Src/LinearSolvers/C_CellMG/MG_2D.F Src/LinearSolvers/C_CellMG/MG_3D.F Src/LinearSolvers/C_NodalMG/amr_real2d.f Src/LinearSolvers/C_NodalMG/amr_real3d.f Src/LinearSolvers/C_NodalMG/hg_multi2d.f Src/LinearSolvers/C_NodalMG/hg_multi2d_full.f Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.f Src/LinearSolvers/C_NodalMG/hg_multi3d.f Src/LinearSolvers/C_NodalMG/hg_multi3d_full.f Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.f commit 72bda6b604d5ca106b815cdc75e549b63d18c02a Author: almgren Date: Tue Sep 16 18:39:45 2003 +0000 Changes in FORT_LINCCINTERP so that in the case of being next to a HOEXTRAP or EXT_DIR boundary, but with xok or yok (or zok) not true, we now use a correct stencil to incorporate a wall-based value instead of defaulting to the centered stencil as before. Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F commit 1df444b492c3aa79f3cfe40e6a79f6b000c7fb1a Author: lijewski Date: Mon Sep 15 21:17:03 2003 +0000 removed CellConservative Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp commit 864d92fc3c726cdd973e7c93ba56c692ae2f0abb Author: lijewski Date: Mon Sep 8 22:22:38 2003 +0000 some bringing up-to-date Tools/C_util/TV_TempWrite.H Tools/C_util/ViewMF/GNUmakefile Tools/C_util/ViewMF/MFNorm.cpp Tools/C_util/ViewMF/viewMF.cpp Tools/C_util/ViewMF/viewMFdiff.cpp commit 624f352c2a4adf085c77b42e118234ea149c3439 Author: 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 Date: Thu Aug 28 17:17:27 2003 +0000 __amd64__ Src/C_BaseLib/FPC.cpp commit 9fabc6e22a40bd508462d628e19c53b9b31367f6 Author: car Date: Tue Aug 19 15:19:42 2003 +0000 strip72 doesn't work with f90 Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 4c7102f2f4c9186a3468ff98ed24db0effdaa3a5 Author: lijewski Date: Thu Aug 14 22:26:57 2003 +0000 some cleanup Src/C_AMRLib/TagBox.cpp commit 7873006852ec9aa9187bd6b5ed0cb1a22b9902e5 Author: lijewski Date: Thu Aug 14 19:18:14 2003 +0000 minimized comm costs in collate() Src/C_AMRLib/TagBox.cpp commit 791ed94cd5028904482a203d62df92841a5ffea2 Author: lijewski Date: Wed Aug 6 21:04:01 2003 +0000 added -cm to Intel Fortran Tools/C_mk/Make.defs commit 48ce640fcdebf6342958665df5f77978d7af6d3f Author: car Date: Wed Jul 30 15:07:34 2003 +0000 debugging changes Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/main.cpp commit 780821817df97be36693006043ab4eb7b1209d8b Author: 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 Date: Fri Jul 18 04:57:11 2003 +0000 Gather -> Alltoall Src/C_AMRLib/FluxRegister.cpp commit cbbf9a8608e9d261418692e105ad4d603879f3b3 Author: lijewski Date: Fri Jul 18 04:51:46 2003 +0000 Gather -> Alltoall Src/C_BaseLib/FabArray.H commit 849a1cfc73520c7f6271bf761a67b3aaa4e5543a Author: car Date: Tue Jul 8 20:48:23 2003 +0000 cleanup Src/LinearSolvers/C_TensorMG/visc2d.m commit 961dbf10bbc06cf974cd5f73a769a69d0c3bd207 Author: car Date: Tue Jul 8 20:19:30 2003 +0000 *** empty log message *** Src/LinearSolvers/C_TensorMG/visc2d.m Src/LinearSolvers/C_TensorMG/visc3d.m commit 4c74c18df0471b4158bae9acb8e8b75ed5343508 Author: car Date: Tue Jul 8 20:04:02 2003 +0000 *** empty log message *** Src/LinearSolvers/C_TensorMG/visc3d.m commit f1ca27135358d4760fa650826d0114a23ca34c84 Author: car Date: Tue Jul 8 19:42:33 2003 +0000 *** empty log message *** Src/LinearSolvers/C_TensorMG/visc3d.m commit dd8fe0f0d13400261a1f44060849b966c19c410e Author: car Date: Tue Jul 8 19:10:52 2003 +0000 stripped out mathematica code for tensor solve generation Src/LinearSolvers/C_TensorMG/visc2d.m Src/LinearSolvers/C_TensorMG/visc3d.m commit 51838d94594079c4ad6e2b4ffa884cc31553d21d Author: car Date: Sat Jul 5 15:22:30 2003 +0000 *** empty log message *** Src/LinearSolvers/C_TensorMG/Format.m commit 751872b8c14a09307b6259ae4f4a71a8ea9235f8 Author: car Date: Fri Jul 4 21:58:36 2003 +0000 Mathematica 5.0 fixes Src/LinearSolvers/C_TensorMG/Format.m commit 2797519e34993f7635ba8eb5b3a6fde42b6316cb Author: car Date: Fri Jul 4 17:24:27 2003 +0000 Mathematica packages need by the notebooks Src/LinearSolvers/C_TensorMG/Format.m Src/LinearSolvers/C_TensorMG/Optimize.m commit 978e2e0ccd2d1d3c1744139b955560c52c45e31a Author: lijewski Date: Tue Jun 24 17:18:21 2003 +0000 merged in d_numPts() Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Cluster.cpp Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 9cdbf85b45ac7e253763172cb796e39b92456720 Author: car Date: Fri Jun 20 19:37:11 2003 +0000 *** empty log message *** Tools/C_mk/Make.IRIX64 commit 894dda803579c9f9d707faaa0282c2f1c1f3d7d4 Author: car Date: Fri Jun 13 22:03:23 2003 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.H commit 87c256510cac08738a0705ef7d131127d34e78bd Author: car Date: Fri Jun 13 19:50:47 2003 +0000 inline out of order Src/LinearSolvers/C_NodalMG/interface.H commit 2b5f729ed3d38979c3948d6cd8cfef3b15ca765d Author: car Date: Wed Jun 4 21:41:56 2003 +0000 redhat 7.1 fortran Tools/C_mk/Make.defs commit 75fae46b373d039b59e1737b80e2ccc0498808cd Author: vince Date: Wed May 21 22:47:52 2003 +0000 fix for escher Tools/C_mk/Make.defs commit 9a913c10cdf86a576e9c2221a180d5ca4874c99c Author: vince Date: Wed May 21 22:47:13 2003 +0000 fix for escher. Tools/C_mk/Make.IRIX64 commit be3e3f2ae39862cff5033264db8ee893254761ea Author: lijewski Date: Thu May 15 22:01:01 2003 +0000 Removed the BL_PROFILE() line. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp commit 37ec404c770ddccb43ba0eb198478ed8666c4266 Author: car Date: Fri Apr 11 17:16:06 2003 +0000 redhat 7.1 Tools/C_mk/Make.defs commit f5c066460fb717acf68599635c3eb9adae4cb4bd Author: marc Date: Wed Apr 9 22:35:24 2003 +0000 change constant to a long Src/C_BaseLib/DistributionMapping.cpp commit b02f7e8c8aa94edb459b611978f1b17d95d79de5 Author: 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 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 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 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 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 Date: Fri Mar 7 16:59:25 2003 +0000 ParmParse'd in max_efficiency Src/C_BaseLib/DistributionMapping.cpp commit 552146a99f23e69989854b73c4db8c86d3e7640f Author: lijewski Date: Thu Mar 6 23:57:38 2003 +0000 wrapped knapsack times in verbose Src/C_BaseLib/DistributionMapping.cpp commit 214d8c775da2c484e736bfa2c6881bbed9bddedc Author: lijewski Date: Thu Mar 6 22:34:56 2003 +0000 print out some knapsack() timings Src/C_BaseLib/DistributionMapping.cpp commit 9dd333dd4709669a48315e5dbf228c7905db4665 Author: lijewski Date: Fri Feb 28 22:42:15 2003 +0000 removed the static collate space in TagBox Src/C_AMRLib/Amr.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit db9705b152febf75915c8a2ef137703121f36d84 Author: lijewski Date: Wed Feb 26 18:07:08 2003 +0000 added verbose option Src/C_BaseLib/DistributionMapping.cpp commit 778f752b6b6d5443fa185097411cdf32616346a3 Author: 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 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 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 Date: Tue Feb 18 20:55:00 2003 +0000 strstream -> sstream Src/C_AMRLib/AmrLevel.cpp commit cc1684ef0c093ee002ce759583a0dcd89dd38c4a Author: car Date: Tue Feb 18 20:54:40 2003 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/ABec_UTIL.F commit fc0b74a760e477f21b7299bffc562a78de0d6e1b Author: car Date: Wed Feb 12 22:31:53 2003 +0000 *** empty log message *** Tools/C_mk/Make.defs commit 04b205ee4cf423c05e4975ce0504616c4ebbd24e Author: car Date: Wed Feb 12 22:31:12 2003 +0000 *** empty log message *** Tools/C_mk/Make.defs commit b16410aaba28bd9f7409ba6c0f769f5c57bde927 Author: car Date: Fri Feb 7 17:42:26 2003 +0000 minor problem, periodic fillpatch Src/C_AMRLib/AmrLevel.cpp commit b1244a917f23e2ae605ff6659d552b785ab747b2 Author: car Date: Fri Feb 7 16:34:12 2003 +0000 some additional diagnostics; now don't solve the CGSolve if norm is initially zero. Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit b972d0560963871df814e2a346e2bf72aa3f3087 Author: lijewski Date: Thu Feb 6 18:14:29 2003 +0000 more work on bunching fill operations Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp commit 75b24134e7d7f556b9070b610700b3c49754c7b2 Author: car Date: Wed Feb 5 16:33:24 2003 +0000 fixes, I think, for Intel compilers Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit 8b69b749ab9f3351a3ab636e133425e4893a3b91 Author: marc Date: Tue Jan 28 20:55:35 2003 +0000 Modernize lib builder Tools/C_scripts/dsp.lib.mak commit a6fd45d7208593fc14a69b4535dc19ba384bfdc4 Author: car Date: Mon Jan 27 17:10:36 2003 +0000 bl_pd_is_ioproc Src/C_BaseLib/ParallelDescriptor.cpp commit e20040e185d6c526c4c2f12fe3daabe3cea4ced9 Author: car Date: Thu Jan 23 20:10:01 2003 +0000 win32 hates templates Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp commit 2840e4494233aebbfde098778dc1f0ff922e5d0b Author: lijewski Date: Wed Jan 22 22:39:44 2003 +0000 Mods to Fill_Boundary() multiple comps at once Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp commit 9f34392395196807be6388ea2cb7557c45401567 Author: car Date: Wed Jan 22 19:19:27 2003 +0000 optimization for Intel compilers Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit f53ef7678ab59f93f9c5016912b46a3e7b13d8cb Author: car Date: Fri Jan 3 19:25:11 2003 +0000 foolish mistakes Src/C_BaseLib/BLParmParse_F.f Src/C_BaseLib/ParmParse.cpp commit e794af81264b3e7382fb7dd4ba3bba6b820eaf57 Author: car Date: Thu Jan 2 22:30:26 2003 +0000 libpthread Tools/C_mk/Make.Linux commit 3fb32b456a1bf26773498b24f7149cee32b08732 Author: car Date: Thu Jan 2 14:59:30 2003 +0000 *** empty log message *** Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit 5e83e8d74b427ef8d5ab948fece11e31bcdda2fd Author: almgren Date: Mon Dec 30 22:09:45 2002 +0000 Making area(i,j) = abs(a) instead of area(i,j) = a in FORT_SETAREA for the r-z case. NOte that FORT_SETVOL and all other cases of FORT_SETAREA already return guaranteed-positive values. Src/C_BaseLib/COORDSYS_2D.F commit b64082d2275e9504c433a5b405c08a833f90931a Author: car Date: Fri Dec 20 23:05:39 2002 +0000 fix for FluxRegister::ADD Src/C_AMRLib/FluxRegister.cpp commit 7a86d45ec62e0b70ea7f95f5c1a59d4fbf8f3698 Author: lijewski Date: Wed Dec 18 18:44:23 2002 +0000 fixed comment Src/C_BaseLib/FabArray.H commit 60b4a0589ac33ddd7ba7c45ab32754a82812cbb8 Author: almgren Date: Tue Dec 17 22:19:56 2002 +0000 Fix for inflow on hi-side boundaries...was screwing up before, all better now. Src/LinearSolvers/C_NodalMG/boundary.cpp commit b9997d434614be6fecd1ecbe6a9b84b90bfa8442 Author: almgren Date: Wed Dec 11 20:43:22 2002 +0000 In the case where the fine cells didn't cover all of the coarse cell being interpolated from, there was an index bust. It has been fixed so that the fine correction is only modified on cells where it actually exists. Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F commit 824afb82c6ba1026397fc6eff3d9c3e1e162db0b Author: almgren Date: Wed Dec 11 18:33:45 2002 +0000 Should have used cvol instead of ratiox*ratioy for denominator in icase=1. Src/C_AMRLib/INTERP_2D.F commit f6e5c3a495b1b8b495b2f576493e155655dcddfe Author: lijewski Date: Wed Dec 11 17:02:16 2002 +0000 removed an assertion that isn't correct in serial Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.cpp commit b7fedf0598fcf4e80ee1586da8b4247ca4bfb7c4 Author: 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 Date: Sat Dec 7 16:25:26 2002 +0000 fixed syntax error Src/C_AMRLib/INTERP_3D.F commit 44a39427269360a2fb8e6d575ae0fcb6c7707ec9 Author: lijewski Date: Sat Dec 7 16:09:16 2002 +0000 increased the cache hit rate Src/C_BoundaryLib/FabSet.cpp commit 75b430922240f134c7e9b543d057ef1c2379ff20 Author: almgren Date: Sat Dec 7 05:59:35 2002 +0000 Do the right thing for icase=1 when fine_state is zero to start with. Same as the recent fixes in 3d. Src/C_AMRLib/INTERP_2D.F commit a744aa1a34c9040599833037285d25c83e5d6795 Author: almgren Date: Sat Dec 7 05:57:09 2002 +0000 Same problem as before for icase=1; the correction wasn't being zeroed out first for states which were 0 at first. Src/C_AMRLib/INTERP_3D.F commit 2fce9df1eadb5f904621e8ab09474aecc69df3a8 Author: lijewski Date: Wed Dec 4 23:06:53 2002 +0000 same error in plus() as in copy() in CrseInit Src/C_AMRLib/FluxRegister.cpp commit 39dcc0a59d929b80056e7b31934241c6de224e7d Author: lijewski Date: Tue Dec 3 18:35:38 2002 +0000 improved FillPeriodic cache hit ratio Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 8e57f0e75bc1d92bad5ad434e7010833fc3aba9a Author: lijewski Date: Tue Dec 3 18:03:27 2002 +0000 improved FillBoundary cache hit ratio Src/C_BaseLib/MultiFab.cpp commit e4de0f67f29d7ce7df938359e79fb568586dc7e3 Author: lijewski Date: Tue Dec 3 00:02:42 2002 +0000 added new accessor functions Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/ParallelDescriptor.H commit 008d49a5d4ddd8f88b12242433570725b4cc3ac8 Author: jbb Date: Mon Dec 2 20:45:01 2002 +0000 Need to restrict the copy in FluxRegister::CrseInit to be only on the region that was just filled from the coarse grid, NOT from the whole fab, some of which is still unfilled. This was causing errors and core dumps. Src/C_AMRLib/FluxRegister.cpp commit 579fe9bbd1c4c96367b5566f01551e6c11dd7270 Author: car Date: Fri Nov 29 22:12:18 2002 +0000 no trailing semicolons Src/C_BaseLib/SPECIALIZE_F.H commit 066515e99d39ad930b40fe06abb3daf6ef97fcc9 Author: car Date: Wed Nov 27 21:54:19 2002 +0000 replace a stop Src/C_AMRLib/SLABSTAT_2D.F Src/C_AMRLib/SLABSTAT_3D.F Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/LO_2D.F Src/LinearSolvers/C_CellMG/LO_3D.F commit 358de07df1e9bd23fe7afe65cbe3a0b244344116 Author: lijewski Date: Tue Nov 26 22:47:22 2002 +0000 modest performance improvement Src/C_BoundaryLib/BndryData.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp commit 6704ac5bd8e29a3168c860b5d261ad3ab178af2b Author: lijewski Date: Tue Nov 26 22:37:40 2002 +0000 modest performance improvement Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BoundaryLib/FabSet.cpp commit 897b54c6dcb4b5e2ae68cc6b69d80e8e66ced5fe Author: lijewski Date: Wed Nov 20 16:55:55 2002 +0000 additional arg to compFlux() Src/LinearSolvers/C_CellMG/ABecLaplacian.H commit 4a25a28f3499c50c0d4ea219af747d2cfbb2f46f Author: lijewski Date: Wed Nov 20 16:52:07 2002 +0000 Added addition signature for compFlux() that avoids applyBC() call. Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp commit 55969ce784ca55e01aec8f0dafeb74e79740125c Author: lijewski Date: Thu Nov 14 23:04:56 2002 +0000 using bl_abort() in place of stop Src/C_AMRLib/FLUXREG_1D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_BaseLib/COORDSYS_1D.F Src/C_BaseLib/COORDSYS_2D.F Src/C_BaseLib/COORDSYS_3D.F commit 00be8fe22bcc571d1c57b48e71086b3b59523bb2 Author: lijewski Date: Thu Nov 14 21:13:08 2002 +0000 removed statics from template functions Src/C_BaseLib/FabArray.H commit 52c3cd0f97c04b48f55e9188fc2c35c8a476decb Author: car Date: Thu Nov 14 18:43:29 2002 +0000 *** empty log message *** Src/C_BaseLib/BLBoxLib_F.f Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/ParallelDescriptor.cpp commit e3729d0a2c222d292de922cd727b02361fa6e220 Author: marc Date: Thu Nov 14 07:08:32 2002 +0000 Add option to add instead of copy on CrseInit operations Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 944dd6e27f96ec5e8ec6db5cab2f33d73c68e935 Author: marc Date: Thu Nov 14 00:13:23 2002 +0000 fix Mikes extra arg fix Src/C_AMRLib/AmrLevel.cpp commit 8c1d3054516982bf53570db1eb06d96137b00241 Author: lijewski Date: Wed Nov 13 17:15:20 2002 +0000 quiet valgrind Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp commit 0e6e765cf2025d0ff5d9d54933c3945f8f86e59f Author: lijewski Date: Wed Nov 13 05:04:58 2002 +0000 tad rearrangment Src/C_AMRLib/AmrLevel.cpp commit 43c724d14aba7845a1af1c9a48971505168c36bf Author: lijewski Date: Tue Nov 12 20:49:35 2002 +0000 to shut up valgrind Src/C_BaseLib/PArray.H commit a330d19e00eaae217b6faf8c983e00f57f0e3f3c Author: lijewski Date: Tue Nov 12 17:08:48 2002 +0000 fixed mismatched deltes Src/C_BoundaryLib/InterpBndryData.cpp commit 2d155f78b6e2786de6d3e2aa95d59a64f323be42 Author: 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 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 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 Date: Fri Nov 8 22:00:51 2002 +0000 added some BL_PROFILE()s Src/C_AMRLib/Interpolater.cpp commit 0660a6fb33edbd784fc51f11337bab2c5710a10a Author: car Date: Fri Nov 8 18:34:42 2002 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/lo_bctypes.fi commit dd76c9ff44fd4ee97b946c6a563bda77d60ad74d Author: lijewski Date: Thu Nov 7 19:04:01 2002 +0000 specialized performCopy() for Reals Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H commit 29740f5716a65d8ec46082d6cb0005900aad09ae Author: lijewski Date: Wed Nov 6 20:51:41 2002 +0000 tad bit o cleanup Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp commit 051df1e02cdbfe0126797f71064b1ecc969c0d4d Author: almgren Date: Tue Nov 5 21:21:58 2002 +0000 Restored cmax and cmin seeing the corner data (we believe it should be there). Put a test for alpha > 1. Protected against divide by zero in computation of alpha. Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F commit 0a6368d0066e23bac7eb8d9692f61d3586d7cbe1 Author: lijewski Date: Tue Nov 5 21:06:17 2002 +0000 +K2 -> +K1 Tools/C_mk/Make.AIX commit b0498c697354ed04e8627461335bbec506c0cd97 Author: lijewski Date: Tue Nov 5 05:34:21 2002 +0000 removed extraneous end do Src/C_AMRLib/INTERP_3D.F commit 9a4ea298a0cb1b7c485989f594421473c40c23c3 Author: almgren Date: Mon Nov 4 18:43:06 2002 +0000 Modified calculation of cmax/cmin in CCINTERP so that it doesn't see corner values, which may not be filled since they aren't used in the actual slope calculation. Src/C_AMRLib/INTERP_2D.F commit 696eb878682bcbadaf707559045548ba4eb27cca Author: almgren Date: Mon Nov 4 18:39:50 2002 +0000 Modified the calculation of cmax/cmin in CCINTERP so that it doesn't see corner values (since they may not be filled, they aren't used in the slope calculations.) Src/C_AMRLib/INTERP_3D.F commit 15bd466933453dbc08f5fd104a1a7acca579a099 Author: lijewski Date: Thu Oct 31 21:59:21 2002 +0000 Added -qrtti=all when debugging. Tools/C_mk/Make.AIX commit 570d074f89552d9c351ac326cf540c6f4b71433b Author: lijewski Date: Thu Oct 31 21:56:33 2002 +0000 removed excess profiling gunk Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/StateData.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 0b2e08c3e78ddb591e7328bc6785e19d87eaa224 Author: lijewski Date: Thu Oct 31 21:01:30 2002 +0000 removed excess profiling gunk Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 204689191bcbea32cd97cff4692ccb362ab058ae Author: car Date: Thu Oct 31 18:44:00 2002 +0000 fixes for microsoft Src/C_BaseLib/ParallelDescriptor.H commit 7d9981e4eaf04618e237096ddce425436b680318 Author: car Date: Thu Oct 31 18:09:00 2002 +0000 some inlineing Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit ee3920ae5c05727b2e548550cac08faba0b30cc7 Author: lijewski Date: Thu Oct 31 17:01:50 2002 +0000 more profiling stuff Src/C_BaseLib/BaseFab.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 4118f6ed547d7d7a5217fdd8be69e285b627486b Author: lijewski Date: Wed Oct 30 21:33:13 2002 +0000 added some profiling calls Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 6513a8713e176428a29ba9a505b5b9d8cae452da Author: lijewski Date: Fri Oct 25 22:21:44 2002 +0000 speed improvements Src/C_BaseLib/Utility.cpp commit 36133143305506193bd7629ea1ae1835cd2ff2dd Author: lijewski Date: Thu Oct 24 21:56:00 2002 +0000 added InvNormDist stuff Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit d46b86c2a8729643c3fcde8ed93318d341112d1d Author: car Date: Sat Oct 19 18:33:28 2002 +0000 silence warnings Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_BoundaryLib/INTERPBNDRYDATA_2D.F Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F Src/C_BoundaryLib/LO_UTIL.F commit 0c218e12d0e07dc4588d2de4b1da86e94849f7bc Author: almgren Date: Fri Oct 11 18:23:00 2002 +0000 Missed a subcase in the first logic case. Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F commit 5fbcd19215eac08f651e59bc69cae310e7d556cc Author: car Date: Fri Oct 11 18:20:44 2002 +0000 improved error message Src/C_BaseLib/BLProfiler.cpp commit 75131d9d2b22e2211d1fc94b8b1df2d0fec52eeb Author: car Date: Fri Oct 11 18:20:29 2002 +0000 profiling fix Src/C_AMRLib/TagBox.cpp commit da6e0aeb92c1a06750482642d2b4f9955bcd8b26 Author: 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 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 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 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 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 Date: Mon Oct 7 20:28:10 2002 +0000 remove MISMATCH stuff ... Src/C_AMRLib/INTERP_2D.F commit b7908824111efc7162e974fe7a9b1b7170f3fbec Author: car Date: Sun Oct 6 18:02:43 2002 +0000 more profiling Src/C_BaseLib/DistributionMapping.cpp commit c6899428eff72a736d516bbcc22e7e35ec4bf22b Author: 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 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 Date: Tue Oct 1 22:38:42 2002 +0000 ensure sprintf() buffer big enough Src/C_BaseLib/Utility.cpp commit 775d87c9115b151d3c09d46fc288790a60b4e602 Author: lijewski Date: Sat Sep 28 19:03:35 2002 +0000 silenced compiler warnings Src/C_AMRLib/Interpolater.cpp commit e34c2c2cf5e8f13a85147150e96e25894c3de450 Author: lijewski Date: Sat Sep 28 19:03:07 2002 +0000 bug fix for AIX Src/C_AMRLib/INTERP_F.H commit 79831cdf82191f3425b30839f7789cb4bac775fb Author: almgren Date: Fri Sep 27 19:20:00 2002 +0000 New interpolation code which allows one to modify the interpolated corrections to a field in order to keep that field non-negative as much as possible. Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp commit 08ed79196b188b0804d9a993a542055ada631c33 Author: lijewski Date: Mon Sep 23 19:06:21 2002 +0000 *** empty log message *** Tools/C_scripts/compressor commit 0a456eb72b474179ebee79759de5abb2e0d2a9fd Author: car Date: Mon Sep 23 17:02:45 2002 +0000 compressor has a lock file Tools/C_scripts/compressor commit 5447a6f1e4b9cf53ac51598ac9fe4db9bd52fd32 Author: car Date: Mon Sep 23 16:57:36 2002 +0000 testing new compressor Tools/C_scripts/compressor commit d4bc55bdc1e5c2e63d2dafad84ea4a2d0a727976 Author: car Date: Thu Sep 19 21:02:14 2002 +0000 do'h Src/C_BaseLib/Utility.cpp commit b3e6473b590dcd7439c428d358f66a85d80128a9 Author: car Date: Thu Sep 19 19:26:22 2002 +0000 fort call to initrand Src/C_BaseLib/Utility.cpp commit 5f282fb4f987f61dfde1528afb54242e5210fc38 Author: lijewski Date: Fri Sep 13 19:19:41 2002 +0000 Added MinimizeCommCosts() Src/C_BaseLib/DistributionMapping.cpp commit 5034bb0138f087d92b96901b98a4915dd3a7549b Author: car Date: Fri Sep 13 14:00:47 2002 +0000 say GPROF=TRUE to got F/C/C++ -pg Tools/C_mk/Make.defs commit 7322f3b27672b1e1dd9c4095070696788022de56 Author: car Date: Tue Sep 10 19:41:59 2002 +0000 3d corrected Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/inputs commit 1819256d67f00e195e992d240b8f9726f1119997 Author: car Date: Tue Sep 10 18:25:27 2002 +0000 oops Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit f8044c77b4caa12970e04217e96d029cb0fa05ff Author: car Date: Tue Sep 10 18:19:57 2002 +0000 more debugging output Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 847c4f1505a8a2100719a7f933e41529753bb570 Author: car Date: Tue Sep 10 16:03:05 2002 +0000 3d re-rolled, un-rolled Src/LinearSolvers/C_NodalMG/hg_multi3d.f Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.f commit 19da89cb6efee2ad7a61abbaa3e7348d0dd3e2a0 Author: car Date: Tue Sep 10 14:07:14 2002 +0000 re-rolled, unrolled routines Src/LinearSolvers/C_NodalMG/hg_multi2d.f Src/LinearSolvers/C_NodalMG/hg_multi3d.f commit 208b9aca634040c9e82a5d610593b8e3ebf39f48 Author: marc Date: Mon Sep 9 22:30:33 2002 +0000 remove __kcc... define-it breaks compiles on brainerd Tools/C_mk/Make.defs commit 3581d402e37a971303f7dc4a02348701a1c376cf Author: car Date: Mon Sep 9 22:00:57 2002 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2d.f Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 38e1e3f54051608ab55c82c7f699310770fc6d77 Author: car Date: Mon Sep 9 20:52:24 2002 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2d.f Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit c6ea945bb58d0727fa2a5d6f1a7eed102ed4b567 Author: car Date: Thu Sep 5 20:59:10 2002 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2d.f commit 6fb4cd6848bd27570a6580a07ae35478e5c1abc7 Author: car Date: Thu Sep 5 16:34:41 2002 +0000 e200 might have been to fierce, changed 'infinity' to e50 (should still be ok for sne Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 23797562c934cee3d5ee1c8c1080e4acde9b6890 Author: car Date: Wed Sep 4 15:29:53 2002 +0000 use .f not .F Src/LinearSolvers/C_NodalMG/GNUmakefile commit 14bffb1f8811f3bf03d58670ab6c1113e00a6419 Author: 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 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 Date: Tue Sep 3 16:42:40 2002 +0000 let fortran be fortran Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/amr_real2d.f Src/LinearSolvers/C_NodalMG/amr_real3d.f Src/LinearSolvers/C_NodalMG/hg_avg2d.f Src/LinearSolvers/C_NodalMG/hg_avg3d.f Src/LinearSolvers/C_NodalMG/hg_multi2d.f Src/LinearSolvers/C_NodalMG/hg_multi2d_full.f Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.f Src/LinearSolvers/C_NodalMG/hg_multi3d.f Src/LinearSolvers/C_NodalMG/hg_multi3d_full.f Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.f Src/LinearSolvers/C_NodalMG/hg_proj2d.f Src/LinearSolvers/C_NodalMG/hg_proj3d.f commit 42a522787627f88f64e4e14bfc6541d7787ed3f1 Author: car Date: Tue Sep 3 16:34:54 2002 +0000 useless Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hgdebug.F Src/LinearSolvers/C_NodalMG/hgdebug_F.H Src/LinearSolvers/C_NodalMG/proj.cpp commit a8c3f02ff1d95e595e1362a92c673c22727d3aa7 Author: lijewski Date: Fri Aug 30 22:10:34 2002 +0000 *** empty log message *** Tools/C_mk/Make.AIX commit 2c8b4056b4659d898c70c7ee3d27c939b8e10609 Author: 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 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 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 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 Date: Tue Aug 20 21:00:55 2002 +0000 Increased data size ... Tools/C_mk/Make.AIX commit d7c16d60054c0be5a05e8b14710cb9c8f758be48 Author: car Date: Fri Aug 16 23:15:27 2002 +0000 change infinity from e20 to e200 Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 6a92d11f7d6e899fd8b1b535691d7b20a560ab03 Author: car Date: Fri Aug 16 22:07:07 2002 +0000 Intel 7.0 support Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit 567805711c7d63fc624cc899ae90d000ec1ace9f Author: car Date: Wed Aug 7 17:23:56 2002 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit d2c3c81096e73a6291ebf8a14b546dcb946d4657 Author: car Date: Tue Aug 6 18:09:06 2002 +0000 *** empty log message *** Src/C_AMRLib/AmrLevel.cpp commit b9619730801951d5484a4af9abce51241fcfb2e8 Author: car Date: Mon Aug 5 15:41:22 2002 +0000 remove intel temp files Tools/C_mk/Make.rules commit c0c667d7c9110d495d3f5ca819f72271058b023e Author: lijewski Date: Wed Jul 31 22:32:02 2002 +0000 got formulas consistent Src/C_AMRLib/FILCC_2D.F Src/C_AMRLib/FILCC_3D.F commit dc8e9304dd720584c470e9a04b99f3d6f385e348 Author: car Date: Wed Jul 24 23:42:57 2002 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/CGSolver.cpp commit db36f4b41128ff04305bed44765e94455e8b1475 Author: car Date: Wed Jul 24 21:18:16 2002 +0000 changed bicg so that if the solution criteria is met before the iteration begins, we return Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 83f988ef506e23729275a92cc02e69fdd60c7f07 Author: lijewski Date: Thu Jul 18 21:28:15 2002 +0000 *** empty log message *** Src/C_AMRLib/FILCC_2D.F Src/C_AMRLib/FILCC_3D.F commit a7458394c0ec91590ed85ca934e7481461d2f4e5 Author: lijewski Date: Fri Jul 12 23:07:38 2002 +0000 was NOT right Src/C_BaseLib/DistributionMapping.cpp commit 4a621026afd2c62c59399f864177130b5c1cc4ee Author: marc Date: Wed Jun 26 18:06:44 2002 +0000 Add lf to result file Tools/C_scripts/dsp.mak commit 4dcf62268b2f9a5d963c36d8ce8885c7dc31765e Author: marc Date: Wed Jun 26 00:02:01 2002 +0000 Fix up dsp generation to allow config changes, ie independent/concurrent Release and Debug builds Tools/C_scripts/dsp.mak commit fbad2e60697d24e3c1bc5d6d4ecf94669941a2a8 Author: car Date: Thu Jun 20 18:28:00 2002 +0000 another fortran header file Src/C_AMRLib/bc_types.fi commit 5bb5ad58fd1c2b06f61c8401b6c33fc54fedd867 Author: 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 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 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 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 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 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 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 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 Date: Mon Jun 17 19:36:46 2002 +0000 *** empty log message *** Src/C_BaseLib/BLParmParse_F.f commit b9f6ee68d53b6877b47dc065711d8c68718ff143 Author: car Date: Mon Jun 17 19:34:49 2002 +0000 *** empty log message *** Src/C_BaseLib/BLParmParse_F.f Src/C_BaseLib/Make.package commit 3b0ab7d351140defa39d277f958497f87ce3ab37 Author: car Date: Mon Jun 17 17:01:27 2002 +0000 isStateVariable, is a bool Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 1104c57200cc834c4b5681371ca0785690a8ca3f Author: car Date: Mon Jun 17 17:00:40 2002 +0000 *** empty log message *** Src/C_BaseLib/BLParmParse_F.f Src/C_BaseLib/BLutil_F.f Src/C_BaseLib/Make.package Src/C_BaseLib/ParmParse.cpp commit fc8382a216c638645962c2d79b1a5b670f117b65 Author: 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 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 Date: Wed May 29 22:37:47 2002 +0000 gcc 3.1 needs to include Src/C_BaseLib/BLProfiler.cpp commit eecb5589aa4c511e087018914526469522d81087 Author: marc Date: Tue May 28 23:21:12 2002 +0000 Add a routine to hoextrap to cc Src/C_AMRLib/FILCC_2D.F commit 1592396dfb0fac7f68eb3d413b21ba27aa249c09 Author: car Date: Thu May 23 22:22:49 2002 +0000 set BL_FORT_STRICT_REAL_T if you want REAL_T to be DOUBLE PRECISION or REAL depending on BL_USE_FLOAT setting Src/C_BaseLib/REAL.H commit 5ed76116050a26e1c1c8049bd0b6773bc1b993c4 Author: car Date: Thu May 23 19:10:38 2002 +0000 BoxLib\BLFort.H Src/C_BaseLib/BLFort.H commit f9e44ec3453df77a9a85e786d86e90200eb7fd39 Author: car Date: Thu May 23 18:22:13 2002 +0000 *** empty log message *** Src/C_BaseLib/Make.package commit 352307f7267e3f2651e4e857bf9009aaebbfecc5 Author: 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 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 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 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 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 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 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 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 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 Date: Wed Apr 24 22:25:20 2002 +0000 another fix for ICC Src/C_BaseLib/winstd.H commit 42b8c0416bb581ddc21b8a9d09ffa8e6dee2ce93 Author: car Date: Wed Apr 24 17:55:30 2002 +0000 support for 6.0 Intel compilers Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit de124467543d8111597891d8c3f536b5b801df7d Author: vince Date: Wed Apr 17 22:22:19 2002 +0000 added flag for null KCC version parse. Src/C_BaseLib/VisMF.cpp Tools/C_mk/Make.defs commit d99ba5fe07e2b46cdcbe1f22e0d0902278415c32 Author: vince Date: Tue Apr 16 18:06:28 2002 +0000 added synchronization of random tables in parallel. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/PROB_AMR_F.H commit d37872e6799389542932628aa21f1c4d0478ae71 Author: lijewski Date: Tue Apr 16 15:20:28 2002 +0000 forgot to update LDFLAGS earlier Tools/C_mk/Make.AIX commit d17095b45ec6e699248bcadd008e24b7f8611f5b Author: car Date: Mon Apr 15 20:12:26 2002 +0000 oops Src/C_BaseLib/BLThread.cpp commit ba5c805cbbaefc385a630a1a35c8801cbfb0fa0d Author: car Date: Fri Apr 12 17:24:52 2002 +0000 tweak for f77/g77; if you compile COMP=Intel then FCOMP=Intel seems necessary for now. This is not enforced Tools/C_mk/Make.Linux commit 6f84245fbbc3a41dc2e6b217d72940944562b128 Author: car Date: Fri Apr 12 17:09:17 2002 +0000 better support for icc Tools/C_mk/Make.Linux Tools/C_mk/Make.defs commit 6bf64c777ca95fe0793fc9527bd3970ab7e9bd7c Author: car Date: Thu Apr 11 19:40:29 2002 +0000 icc support Src/C_BaseLib/Thread.H Src/C_BaseLib/winstd.H Tools/C_mk/Make.Linux commit 17f02da2362d7077d8d269defe3d5fcb8642121c Author: car Date: Mon Apr 8 20:51:36 2002 +0000 *** empty log message *** Src/C_BaseLib/Thread.H commit 7a89f86cc48e7fecf7b5a92b720eaaf1de3817e5 Author: car Date: Mon Apr 8 20:46:46 2002 +0000 max_threads is now unsigned long Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/Thread.H commit 08d032bb83349780ac1faab95f4d807427346c0a Author: car Date: Mon Apr 8 17:25:05 2002 +0000 f90 and f no longer preprocess, F90 and F do Tools/C_mk/Make.rules commit 4e77108fa360566a6d618f0c567fc6f24eb415fd Author: car Date: Sun Apr 7 17:00:44 2002 +0000 *** empty log message *** Src/C_BaseLib/BLThread.cpp Tools/C_mk/Make.FreeBSD commit 6e76d0c03f1d46cf110eb6edb1540d7070d56252 Author: lijewski Date: Thu Mar 28 21:00:12 2002 +0000 *** empty log message *** Tools/C_mk/Make.OSF1 commit 67431e34769f1cb0bf183db49ec3e5752dba92d7 Author: car Date: Wed Mar 27 23:58:50 2002 +0000 std::abs on BL_OSF1 Src/C_BaseLib/winstd.H commit e53fb043a04f24dac3553dace264519dc38048fd Author: lijewski Date: Wed Mar 27 23:49:07 2002 +0000 *** empty log message *** Tools/C_mk/Make.OSF1 commit e8b74b9591a24e385f16048d27a451aa25e404e1 Author: car Date: Wed Mar 27 21:35:59 2002 +0000 *** empty log message *** Tools/C_mk/Make.OSF1 Tools/C_mk/Make.mpi commit 80054ef9b2738152ef362011311cb9772cf9d88d Author: lijewski Date: Wed Mar 27 19:21:54 2002 +0000 *** empty log message *** Tools/C_mk/Make.AIX commit 6f68d692ab542621acdaab4253ca9fa87128cad9 Author: lijewski Date: Wed Mar 27 17:54:34 2002 +0000 mods to quiet xlC Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 9aec6659d59ea92930cc0f27e32de52c52a2f77b Author: lijewski Date: Wed Mar 27 17:10:20 2002 +0000 *** empty log message *** Src/C_AMRLib/AmrLevel.H commit c8fa1c422ae811daa0614a0b385cc99c23a1178d Author: lijewski Date: Tue Mar 26 23:59:29 2002 +0000 *** empty log message *** Tools/C_mk/Make.AIX commit f361ea8361ba6f88a6a6858fdc60b41c8f588a7c Author: lijewski Date: Tue Mar 26 22:23:58 2002 +0000 *** empty log message *** Src/C_BaseLib/Utility.cpp commit 420c332ab5552cae6a1e45e17e0b63916e6e06c1 Author: car Date: Tue Mar 26 22:15:43 2002 +0000 different support for f90/f/F/F90 Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 7c4c5a0c763b437bde265271ab9a7ed8f5aad3e5 Author: car Date: Tue Mar 26 22:14:33 2002 +0000 only sleep Src/C_BaseLib/BLThread.cpp commit 5a845b9c0b1e89d9f0499e170034e721f1f86277 Author: lijewski Date: Tue Mar 26 21:50:49 2002 +0000 *** empty log message *** Tools/C_mk/Make.AIX Tools/C_mk/Make.defs commit 8e860ab2c2f086ee61e241fd2249a64efe75780a Author: lijewski Date: Tue Mar 26 20:47:02 2002 +0000 changes to work with xlC Src/C_BaseLib/ParmParse.cpp commit 41db2c66b7785026c28ffa0042eec720f37d69db Author: lijewski Date: Tue Mar 26 20:04:06 2002 +0000 changes to work with xlC Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/ParallelDescriptor.cpp commit 50d05247953df82ac63bb423da142cde578f2f01 Author: car Date: Fri Mar 22 23:29:24 2002 +0000 Small change: Only print unused ParmParse variables if there are any unused ParmParse variables. Src/C_BaseLib/ParmParse.cpp commit d64b94aa06f19b6d8048df2c7d7587f92d010bbf Author: vince Date: Thu Mar 21 00:41:08 2002 +0000 added -ieee flag for opal. Tools/C_mk/Make.OSF1 commit 16a16c70b8ce2dedeaab9854a6513255139b37fc Author: almgren Date: Mon Mar 18 22:31:54 2002 +0000 Modifications needed to correct for the fact that the scalings of Du, S and DGphi are different between the v5 and v9 versions. Src/LinearSolvers/C_NodalMG/hg_avg2d.F commit fda4fed36ab65026252e2dd2cfc759b33a7e1058 Author: almgren Date: Fri Mar 15 20:47:52 2002 +0000 Modified the weighting of the source term in hgavg, hgfavg, hgcavg for use with the 9-pt instead of 5-pt stencil. Src/LinearSolvers/C_NodalMG/hg_avg2d.F commit e6be28de6ef81c5012d12876e94041fe61a982a8 Author: marc Date: Fri Mar 15 20:20:32 2002 +0000 Rework frac calc to avoid using domain.numPts Src/C_AMRLib/Amr.cpp commit f4d29a5b96f3172c7160f9eb1abd5e1e6300b79c Author: marc Date: Fri Mar 15 19:01:47 2002 +0000 dsp maker for libs Tools/C_scripts/dsp.lib.mak commit 1a2aae2a35292283ee7aea3073b24d3ecf6e66d7 Author: car Date: Thu Mar 14 23:56:07 2002 +0000 fix for gcc3 and KCC Tools/C_mk/Make.defs commit 67a8b7f7a26f5016eab0df32a1d40d6f637dba7e Author: car Date: Thu Mar 14 23:05:16 2002 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.dsp commit 7280f362b17135f87d0f1e67000324743caccb77 Author: vince Date: Thu Mar 14 01:48:58 2002 +0000 changes for kcc 3.9 Tools/C_mk/Make.defs commit 2f6b56e5e456c7309633886e2902802a0950b34d Author: vince Date: Thu Mar 14 00:27:03 2002 +0000 changes for brainerd. Src/C_BaseLib/VisMF.cpp commit 5706a47b53290026041fef7dcd8dc40c97928008 Author: almgren Date: Wed Mar 13 22:07:49 2002 +0000 Updated version of test results with 2-d test cases. Src/LinearSolvers/C_NodalMG/files.2d commit 9aeb3926cbf49d3f38339f54d859d6cf30b22438 Author: almgren Date: Wed Mar 13 21:54:59 2002 +0000 Improved version of the test code. Fixed some bugs even. Src/LinearSolvers/C_NodalMG/proj.cpp commit a2bd9985be187b7ef51d1f7940b0795a90d2ec33 Author: almgren Date: Wed Mar 13 21:54:24 2002 +0000 We dont do factor of 8 refinement. Src/LinearSolvers/C_NodalMG/tests/gr.19s8 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s8 commit a12077709dc3cd9768693e427e1f6b0222f1b703 Author: almgren Date: Wed Mar 13 21:52:54 2002 +0000 This test case fails because it needs an absolute tolerance in the CG solver. Not worth worrying about here. Src/LinearSolvers/C_NodalMG/tests/gr1rick Tests/LinearSolvers/C_NodalMG/test_grids/gr1rick commit e3da6dcb90d0f749c752aa74e81c3718490fbcb0 Author: almgren Date: Wed Mar 13 21:49:16 2002 +0000 A grid 201 long does not coarsen! Try making this 0-199 instead of 0-200... Src/LinearSolvers/C_NodalMG/tests/gr1rick2 Tests/LinearSolvers/C_NodalMG/test_grids/gr1rick2 commit 35414c34a785792fc401ffb3fa5aeaeb7abbcea7 Author: 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 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 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 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 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 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 Date: Wed Mar 13 19:07:00 2002 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/files.2d commit 7ac1323ad3bc679a9eea15c479c9bacb47f4f3ad Author: lijewski Date: Wed Mar 13 18:31:42 2002 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/files.2d commit 557072c9b51a5fd38f0a66159585a12f031ed2e6 Author: almgren Date: Wed Mar 13 18:29:38 2002 +0000 Fixes for 2d only: length --> size, etc... Src/LinearSolvers/C_NodalMG/proj.cpp commit 00c3ae75b9ef914f869f85ff40f06ea6fe418b2b Author: almgren Date: Wed Mar 13 00:57:35 2002 +0000 New test problem which failed with previous code but now works. A smaller version of the critical grids of this problem are in gtclearsmall. Src/LinearSolvers/C_NodalMG/tests/gtclearlarge Tests/LinearSolvers/C_NodalMG/test_grids/gtclearlarge commit 32fb46a9fa29f66f14abb0d3702409ceaa09d942 Author: almgren Date: Wed Mar 13 00:56:56 2002 +0000 New test problem which failed with the previous version of the code. This is extracted from gtclearlarge. Src/LinearSolvers/C_NodalMG/tests/gtclearsmall Tests/LinearSolvers/C_NodalMG/test_grids/gtclearsmall commit 0be87707101752df7288f054d735d8b705ee2523 Author: almgren Date: Wed Mar 13 00:56:02 2002 +0000 Updated list of which of the tests/gt* files are 3-d problems, and whether they work with the current version of the code. Src/LinearSolvers/C_NodalMG/files.3d commit b3d1c40d6b2053d77e5bfdb851d43556ce580c17 Author: almgren Date: Wed Mar 13 00:55:33 2002 +0000 Fixed a bug in the construction of the level interface objects - code used to fail on test code gtclearsmall and now works. Replaced "contains" by a box by "contains" by a BoxArray. Src/LinearSolvers/C_NodalMG/interface.cpp commit fa0f4828fbda8b82198b4fab280e0ef83bef27a7 Author: lijewski Date: Mon Mar 11 23:05:53 2002 +0000 added Src/LinearSolvers/C_NodalMG/proj.cpp commit 1db1cf8f21bc862763e1e0aab5b1e2c304830e9b Author: car Date: Mon Mar 11 21:53:57 2002 +0000 Now an empty BoxList is constructed from an empty BoxArray. Src/C_BaseLib/BoxArray.cpp commit d19d40fe0409287d42896eadd5e8d68f25f2b800 Author: lijewski Date: Mon Mar 11 19:24:08 2002 +0000 got rid of unsigned on aux() -- it's an int Src/LinearSolvers/C_NodalMG/interface.H commit c645c423c43c0edbc4c0afd991470473677dbd01 Author: car Date: Tue Feb 26 23:41:45 2002 +0000 gcc 3 Tools/C_mk/Make.defs commit ac773995f938aa74a7f277f82f4d38ce7266b436 Author: 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 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 Date: Fri Feb 22 20:53:54 2002 +0000 Fixed FixUpPyhsCorners() bug Src/C_AMRLib/AmrLevel.cpp commit 37c5c93cf3eea0d55cbf8513c70d6db7120116dd Author: car Date: Tue Feb 19 23:36:06 2002 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.dsp commit 65708e227dd6c8bb938aa11958d997cd5122412b Author: car Date: Wed Feb 6 18:14:46 2002 +0000 Fixed random number seeding. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 40f18af7f515a218909d95552fb162b41d7f9bc3 Author: car Date: Tue Jan 8 16:30:24 2002 +0000 no message Src/C_BaseLib/BLProfiler.cpp commit 84ae1dc576e16216b9a0d4f091415a87d7f896e1 Author: car Date: Fri Jan 4 00:17:23 2002 +0000 no message Src/C_BaseLib/BoxLib.dsp commit 340126013477222f685556d51bdef3e19ab3ed74 Author: car Date: Thu Dec 13 23:46:08 2001 +0000 properly initialize m_used Src/C_BaseLib/CArena.cpp commit 0153c0121760b213e82d64987c997b7bd00b4b83 Author: car Date: Thu Dec 13 18:24:59 2001 +0000 makefile system knows fortran Tools/C_mk/Make.defs commit 943c3078102e14915169b8cd77532d1ac4b6c361 Author: car Date: Tue Dec 4 21:28:17 2001 +0000 OSF1 now discriminates between V3 and all others Tools/C_mk/Make.OSF1 Tools/C_mk/Make.defs commit 7338c3102b9e9e68de937b5512c797459422f0a0 Author: lijewski Date: Mon Dec 3 22:35:54 2001 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp commit b8fffd2d095a50aa7765df1a0cc1faf7dc781a5c Author: lijewski Date: Mon Dec 3 22:24:54 2001 +0000 removed mpi_data_type() stuff Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/ccse-mpi.H Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp commit f67ebf1d87578a29aa579c39bda572c39d28d316 Author: car Date: Mon Nov 26 18:17:58 2001 +0000 fix for max_threads Src/C_BaseLib/BLThread.cpp commit 72b1b8d357a72efdd80fd2b93f98bc3cce866557 Author: car Date: Mon Nov 26 18:14:26 2001 +0000 refinement of BLThread.cpp for WINNT Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/Utility.cpp commit ebfe4014d13e0bbcec95aacabd448559863d2794 Author: car Date: Wed Nov 21 19:50:44 2001 +0000 CriticalSections seem to work better for mutex's Src/C_BaseLib/BLThread.cpp commit bc1964c02aed918d0cad48518a69298c924e2ca3 Author: car Date: Mon Nov 19 19:10:49 2001 +0000 *** empty log message *** Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BoxLib.dsp commit 95489da9ba2256959f4ee197711f7ca5019f4ae0 Author: car Date: Fri Nov 16 18:19:33 2001 +0000 cv needs to be mutable Src/C_BaseLib/WorkQueue.H commit 87a79af96c58dd4833f0a614ed9341bc9d6005bf Author: car Date: Fri Nov 16 18:05:16 2001 +0000 numthreads needs a lock Src/C_BaseLib/BLWorkQueue.cpp commit 1512164f13f9816fb51ddf730d9145f7b557ea77 Author: car Date: Tue Nov 13 00:08:29 2001 +0000 KCC doesn't always like PTHREAD_STACK_MIN? Src/C_BaseLib/BLThread.cpp commit 593758b9158c12f7ee1e39cfc41a1bfdc4459fee Author: 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 Date: Mon Nov 12 21:38:21 2001 +0000 *** empty log message *** Tools/C_mk/Make.AIX commit 0c2923f84cd4bfa17bafa3b79046dc34a5969beb Author: car Date: Fri Nov 9 14:33:10 2001 +0000 fix for unix threads Src/C_BaseLib/BLThread.cpp commit 4fbf018518c7e3e45d0c89b9c83342141cd1d297 Author: car Date: Wed Nov 7 22:00:57 2001 +0000 More WIN32 support Src/C_BaseLib/BLThread.cpp commit 59ef849076489e3c12244f45809e14b4a78cf011 Author: lijewski Date: Wed Nov 7 19:05:01 2001 +0000 *** empty log message *** Tools/C_mk/Make.AIX commit 21c9b91122d3ca0d517904565273e7e847a5e579 Author: car Date: Thu Nov 1 23:52:50 2001 +0000 restored a user-specified TSD destructor Src/C_BaseLib/Thread.H Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/tWorkQueue.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tWorkQueue.cpp commit 6ad4de3a6c65a0a15808dc7660d4247024ad5d61 Author: lijewski Date: Thu Nov 1 23:21:34 2001 +0000 *** empty log message *** Src/C_BaseLib/BLThread.cpp commit 561b9d1587b491bef887ba1db57d66ba4abecc36 Author: car Date: Thu Nov 1 18:53:15 2001 +0000 baseThread Src/C_BaseLib/BLThread.cpp commit c232f425afcd75f8d08d1a167fed5200ccbfad7c Author: car Date: Thu Nov 1 18:46:37 2001 +0000 *** empty log message *** Src/C_BaseLib/BLThread.cpp commit 66bd00cdca768fe158edea725612dc65455a83e9 Author: lijewski Date: Thu Nov 1 17:57:30 2001 +0000 re-added BLMpi.cpp Src/C_BaseLib/FabArray.H commit b071e97be32c80a07c4968c95649614f7f970184 Author: car Date: Thu Nov 1 17:08:41 2001 +0000 *** empty log message *** Src/C_BaseLib/BLThread.cpp commit 3f6fd83617547211452bf2da1436c8dab7b69ec4 Author: lijewski Date: Thu Nov 1 16:50:38 2001 +0000 *** empty log message *** Src/C_BaseLib/BLMpi.cpp commit 00bee9bc74ee65d750c9ef2b2c36d4889432a2ac Author: lijewski Date: Wed Oct 31 22:42:01 2001 +0000 re-added BLMpi.cpp Src/C_BaseLib/Make.package commit e627e541b531dc34fa913bdd7a11f048914d11b5 Author: lijewski Date: Tue Oct 30 22:03:42 2001 +0000 more threading work Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit ed45f4779f07b8c1e3ab170b8e04d3f0d050cfe6 Author: lijewski Date: Tue Oct 30 20:26:29 2001 +0000 removed no-threadsafe constructs Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp commit 73776b926285e5ad8ad53d47eff3a2643dad0ed7 Author: 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 Date: Tue Oct 23 17:31:02 2001 +0000 *** empty log message *** Src/C_AMRLib/FluxRegister.cpp commit cd6a59b480c2872fecf1caa29708cf7c68fe4487 Author: lijewski Date: Tue Oct 23 17:01:02 2001 +0000 added BoxLib::ResetArena() Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/Arena.H Src/C_BaseLib/BaseFab.cpp commit a4831f7b56e3a8422955c758e3255399c69a7d3a Author: car Date: Mon Oct 22 22:49:53 2001 +0000 Fix for windows Src/C_BaseLib/BLThread.cpp commit 809eada7024f1a18ff23f9cba0302964326a2a93 Author: lijewski Date: Mon Oct 22 21:12:45 2001 +0000 thread stacksize stuff Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BLWorkQueue.cpp Src/C_BaseLib/Thread.H Tools/C_mk/Make.OSF1 commit f5889c9f31afe0c954987954f85507c228dc1d72 Author: car Date: Sat Oct 20 22:45:32 2001 +0000 *** empty log message *** Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BLWorkQueue.cpp Src/C_BaseLib/Thread.H commit c9909b4dd2a8063f7f8177ecf0da9454c31a4589 Author: car Date: Thu Oct 18 21:54:13 2001 +0000 Added BaseFab.cpp Src/C_BaseLib/BoxLib.dsp commit 5fccc81c64ee73f248f17fd4947af122596e4422 Author: lijewski Date: Thu Oct 18 17:55:31 2001 +0000 some thread fixes Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BaseFab.cpp Src/C_BaseLib/CArena.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/Thread.H commit fefc4f87d6ef604efee3e8229b5ffa6a2e3c0d5c Author: lijewski Date: Wed Oct 17 17:53:33 2001 +0000 removed unneeded BL_USE_SETBUF and BL_USE_NEW_HFILES Src/C_BaseLib/test/tCArena.cpp Src/C_BaseLib/test/tFB.cpp Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Tests/C_BaseLib/tCArena.cpp Tests/C_BaseLib/tFB.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp Tools/C_mk/Make.CRAY Tools/C_mk/Make.CYGWIN_NT Tools/C_mk/Make.IRIX64 Tools/C_mk/Make.Linux Tools/C_mk/Make.T3E Tools/C_util/Convergence/Add.cpp Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffPlot.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileNormB.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/ViewMF/MFNorm.cpp Tools/C_util/ViewMF/checkMFghostcells.cpp Tools/C_util/ViewMF/main.cpp Tools/C_util/ViewMF/viewMF.cpp Tools/C_util/ViewMF/viewMFdiff.cpp Tools/C_util/ViewMF/viewMFdiffHardWire.cpp Tools/C_util/WritePlotFile.cpp Tools/C_util/dbgTools/crsGrids.cpp Tools/C_util/dbgTools/intersectGrids.cpp commit e54230af302a6f45e042432a77ee54f2739dbbf4 Author: 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 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 Date: Tue Oct 16 22:45:34 2001 +0000 got rid of libmiranda.a Tools/C_mk/Make.AIX commit e649e1df22dda44fa7f63ba342bcac5dd8dd0dc4 Author: lijewski Date: Tue Oct 16 19:59:51 2001 +0000 Integrated in BoxLib::The_Arena() Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/Arena.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/FabArray.H Src/LinearSolvers/C_NodalMG/proj.cpp commit 6ccd715d7d452b1067575222282b97aa5df438f8 Author: car Date: Mon Oct 15 23:01:27 2001 +0000 debugging flags for PGI Tools/C_mk/Make.Linux commit e404bf1f7116996057c874d0e1f640de99781256 Author: 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 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 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 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 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 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 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 Date: Wed Oct 10 15:44:41 2001 +0000 *** empty log message *** Src/C_BaseLib/BLProfiler.cpp commit 54edbd0d50c809df8174036e6bb7a4fcc1632258 Author: 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 Date: Fri Oct 5 19:47:55 2001 +0000 Up'd -bmaxdata size ... Tools/C_mk/Make.AIX commit d01fe1b5a1f083acaeb6afa7c6cfa8e4487ec93b Author: marc Date: Fri Oct 5 07:19:55 2001 +0000 iAdd check for instability (due typically to case where initial residual is very small). this code was basically copied from the scalar solver stuff, except that the expert setting to turn it on was put into the cg parm parse stuff. Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp commit 656bc02b52f7b929775c4f67a4b4d1731116f6b4 Author: lijewski Date: Wed Oct 3 19:53:51 2001 +0000 output maxthreads only if verbose Src/C_BaseLib/BLWorkQueue.cpp commit 1537db3322396d3e8b4772420f03f71050206491 Author: 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 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 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 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 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 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 Date: Thu Sep 27 16:11:49 2001 +0000 -DBL_KCC_VERSION added Tools/C_mk/Make.defs commit c1d92c0d97a1f89f4b0db61fd8ca9fb67912c144 Author: lijewski Date: Wed Sep 26 16:59:53 2001 +0000 removed unused variable Src/C_AMRLib/FluxRegister.cpp commit 94fa6304ba411508807038059c0e3581d702cfe7 Author: lijewski Date: Wed Sep 26 15:47:54 2001 +0000 for clarity ... Src/C_BaseLib/FabArray.cpp commit a2ac2dbf22024f43d9499e0d4f2019cd08f9c641 Author: car Date: Wed Sep 26 15:43:31 2001 +0000 debugging of MFIters taken from HG removed 2 static array decls in Collect Data that broke MSVC. Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 010f082397c359aa34b5e21d8458332c77faf825 Author: car Date: Wed Sep 26 02:16:58 2001 +0000 HG_is_debugging is only defined in IAMR CollectData not in macros triggers a bug in VC++ Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp commit 615a7e37f25fa5611280bf440deb8f6d13d2d04a Author: lijewski Date: Tue Sep 25 22:45:40 2001 +0000 more hiding of MPI-specifics Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ccse-mpi.H commit bc45a27eedb79b48cf1020fc42bf363f415417f7 Author: car Date: Tue Sep 25 21:02:54 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.dsp commit d14ad5bb55ba306d060ffc7e4b86ff1ab5d6f9aa Author: 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 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 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 Date: Wed Sep 19 17:04:43 2001 +0000 no dependencies in real fortran Tools/C_mk/Make.rules commit 563494a2e228cfc5cf12bcb14b0c418156315b50 Author: car Date: Wed Sep 19 17:03:58 2001 +0000 in serial ParallelDescriptor::second now returns wall clock time Src/C_BaseLib/ParallelDescriptor.cpp commit 952c4815d20dbb1d8ed588dd25c0ec1119b256be Author: 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 Date: Wed Sep 19 02:39:53 2001 +0000 -CB loses mostly Tools/C_mk/Make.Linux commit 41b498cefb973fa40e6122d5657362cb4cc5ff89 Author: car Date: Wed Sep 19 02:37:20 2001 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile commit 56f758554522df3a46fc6bddf2c73689dec87c95 Author: car Date: Wed Sep 19 02:36:47 2001 +0000 need header Src/C_BaseLib/BLWorkQueue.cpp commit 96738b65d66cee03e76e6b6f529398beab719dd6 Author: 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 Date: Tue Sep 18 18:15:03 2001 +0000 Split out tests for defined junk. Src/C_BaseLib/std/limits commit b6123d3def1832d49bafa18a0d1db887750cbf7f Author: car Date: Tue Sep 18 03:34:49 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.dsp commit 1af15535aed4c51625435aed2405108f0fb01c45 Author: lijewski Date: Mon Sep 17 22:03:03 2001 +0000 add thread_safe for mpKCC Tools/C_mk/Make.defs commit 9f672695eb89ff0b03cc9a339ff8d92598f9f59f Author: car Date: Sun Sep 16 16:44:24 2001 +0000 more support for Intel, must upgrade set gigan:/var/tmp/RPMS/extra Tools/C_mk/Make.Linux commit c0ec7a91985fce6cae6666710a76c2490c4d1b73 Author: marc Date: Sat Sep 15 05:29:29 2001 +0000 Fix for little-f files Tools/C_mk/Make.Linux commit e11c4c3e107ec45f41a8e43344ee17eaf9955215 Author: lijewski Date: Fri Sep 14 21:03:06 2001 +0000 Now always print out workqueue.maxthreads at startup ... Src/C_BaseLib/BLWorkQueue.cpp commit ad51eeaf15f9a17eab346f35aaa4c0f4f6608c77 Author: car Date: Fri Sep 14 04:03:39 2001 +0000 fixes for KCC Src/C_BaseLib/Thread.H commit 4ed862dda8fb12d8b5335357bd2629efbaa7dfb2 Author: lijewski Date: Thu Sep 13 23:09:16 2001 +0000 Now print out # of cells advanced at each level as we go ... Src/C_AMRLib/Amr.cpp commit f9e972c082fc9e209dc823890cc0a8f9d847ba55 Author: lijewski Date: Fri Sep 7 23:06:44 2001 +0000 *** empty log message *** Src/C_AMRLib/FluxRegister.cpp commit 7ee4ea07b513769d4162ea38c473206bae7ce20e Author: car Date: Fri Sep 7 22:03:21 2001 +0000 *** empty log message *** Src/C_BaseLib/BLThread.cpp commit 1571ac2fe7d8f61f5e950fb63fcaeab602c9c2a6 Author: car Date: Fri Sep 7 00:35:02 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.dsp commit 7ffd979694028bb5cee2a5014d5e0451f4ec9236 Author: lijewski Date: Thu Sep 6 22:49:19 2001 +0000 added a default getID() for USE_THREADS=TRUE. Src/C_BaseLib/BLThread.cpp commit bff607f2c7410026c398a34d92d4480f57a4b452 Author: car Date: Wed Sep 5 19:29:59 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.dsp commit 7bf8fbdeb8ec8be84f216ea6c089e2463181735a Author: car Date: Tue Sep 4 16:59:41 2001 +0000 Threading Fixes Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BLWorkQueue.cpp Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Thread.H commit cb249f2d02b38887bd56a58d0349cc0714bd082c Author: 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 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 Date: Thu Aug 23 20:07:43 2001 +0000 *** empty log message *** Src/C_AMRLib/FluxRegister.cpp commit 74f59b971996583ef9f4de210d6a25224903fb39 Author: lijewski Date: Wed Aug 22 21:35:25 2001 +0000 removed an assert() Src/C_AMRLib/AmrLevel.cpp commit 6e907020406359bf8d19a1685358bee189082d32 Author: 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 Date: Wed Aug 22 19:21:00 2001 +0000 reverted to older style copy constructor Src/C_BaseLib/Geometry.cpp commit 294a49a60fe976b3b65eac227d64991b8882e9ff Author: car Date: Tue Aug 21 22:15:37 2001 +0000 revitalized threads Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BLWorkQueue.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/WorkQueue.H Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/tWorkQueue.cpp Src/C_BoundaryLib/InterpBndryData.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/macprojTest.cpp Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tWorkQueue.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/macprojTest.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit d1464e70248a4cd6e37253ebd2c5cdea368c5e26 Author: car Date: Tue Aug 21 20:30:02 2001 +0000 *** empty log message *** Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/Thread.H commit 9d26ecb067c76786ed77c84309fa2116741d1eb7 Author: 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 Date: Tue Aug 21 18:08:46 2001 +0000 simplification Src/C_BaseLib/FArrayBox.cpp commit 2cbb6355ba144bb86384f0d09ee8f7464a0fac68 Author: car Date: Tue Aug 21 17:10:31 2001 +0000 minor leak Src/C_BaseLib/BoxLib.cpp commit db02b5832f404c7ba96390c719a8a44378d84498 Author: car Date: Mon Aug 20 02:48:50 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.dsp commit c9859153f8a77b678e659352afd0cb30d48b1d39 Author: car Date: Sat Aug 18 23:39:10 2001 +0000 added souce numega filters. Src/C_BaseLib/.cvsignore commit ae2120d7fa4996b5d70a9c643d4edd4687a90bfa Author: lijewski Date: Fri Aug 17 15:41:33 2001 +0000 Reverted out the greeno stuff; shouldn't have been checked in :-( Src/C_AMRLib/Amr.cpp commit 090cf8eca641b690acc31e6ec8c3f94ee254118b Author: lijewski Date: Thu Aug 16 23:06:47 2001 +0000 Modifications as per greeno. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/FILCC_1D.F Src/C_AMRLib/FLUXREG_1D.F Src/C_AMRLib/INTERP_1D.F Src/C_AMRLib/Interpolater.cpp commit 6231b257f417a2d9a4cd61beda4fe9d9082b3549 Author: 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 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 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 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 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 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 Date: Tue Aug 14 22:14:00 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.dsp commit 91219641f2fbe46d4e8bbe1887d08e34e376b978 Author: car Date: Tue Aug 14 16:07:31 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.dsp commit 4b818a9c8be2dda01064db24595a4de795b91e27 Author: car Date: Mon Aug 13 22:34:45 2001 +0000 MSVC fixes Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxLib.dsp Src/C_BaseLib/FArrayBox.cpp commit d924a7884add39a21663040dc725534262ef1978 Author: car Date: Mon Aug 13 01:54:26 2001 +0000 *** empty log message *** Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit 13f80b3c8c1dd6551a33dad7ac7d491aca831200 Author: 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 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 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 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 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 Date: Fri Aug 10 19:52:21 2001 +0000 Changed the way we input periodic. Src/C_BaseLib/Geometry.cpp commit 3f31888d2bb5b9b2a02db3939ef3f7e90c46f200 Author: 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 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 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 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 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 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 Date: Mon Aug 6 19:39:25 2001 +0000 windows Src/C_BaseLib/VisMF.cpp commit 4f5eb76456f5ffafb99dfd61df6d4af43ea7a653 Author: car Date: Thu Aug 2 16:37:49 2001 +0000 Typo Src/C_BaseLib/CONSTANTS.H commit 179787a5fcb97aee0a66f197b80b819b2f0422bc Author: car Date: Thu Aug 2 16:18:15 2001 +0000 CONSTANTS change, use BL_REAL Src/C_BaseLib/CONSTANTS.H commit 13e54b2d1c1f686e482c8074db62fa16cf7da65c Author: car Date: Thu Aug 2 16:04:11 2001 +0000 append->push_back Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/SlabStat.cpp Src/C_BaseLib/RealBox.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp commit 4861cf84a28a810339a8c2be7a7c4434332627ee Author: car Date: Thu Aug 2 16:01:43 2001 +0000 append->push_back, prepend->push_front, Fab[] stubs, Fab=, MultiFab= Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 0c2aef455851de50e4f28bd5d4da20c2544d2ce2 Author: 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 Date: Thu Aug 2 01:22:48 2001 +0000 removed fwd decl of ConstFabArrayIterator Src/C_BaseLib/FabArray.H commit 50b636e221288017b1f4f1379d4a21e5ce6e8e80 Author: 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 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 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 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 Date: Wed Aug 1 18:14:13 2001 +0000 now include where needed for std::abs() Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/CArena.cpp Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Utility.H commit e5a20cd0b01f1dc15fdc9ec74fb827e4fe67d3d7 Author: lijewski Date: Tue Jul 31 22:43:16 2001 +0000 Inlined trivial functions. Without inlining I was 20% slower than old code on my example. Src/C_BaseLib/Array.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/IndexType.H Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/Orientation.H Src/C_BaseLib/Orientation.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Pointers.H Src/C_BaseLib/Tuple.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/UseCount.cpp commit 6307a984e3a5f386a66ead7c89b38d01b1fa0e59 Author: lijewski Date: Tue Jul 31 19:24:10 2001 +0000 No more RunStats. Src/C_BaseLib/Make.package Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp commit c070e2981e4189999c5442833935e8510d94d01d Author: lijewski Date: Tue Jul 31 17:56:24 2001 +0000 Some cleanup Src/C_BaseLib/Arena.H Src/C_BaseLib/Array.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BLMpi.cpp Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit b978fe82474e143ca4ce1ec7a641436c47b2bbdc Author: lijewski Date: Tue Jul 31 15:03:42 2001 +0000 Got rid or old Iterator stuff Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.H commit d541d3f7b9cac1eb84cd20c85213ad7482767877 Author: car Date: Thu Jul 26 20:50:05 2001 +0000 more winstd.H uses Src/C_BaseLib/CArena.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/ccse-mpi.H Src/C_BaseLib/winstd.H commit 02bbcf0a2b49553e63fc3b8050bc00ac07e299e5 Author: car Date: Thu Jul 26 20:31:38 2001 +0000 include file tweaks; Utility.H need iostream defns Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/Utility.H commit 66888f56bb1435e81e20f78b47094a6f8a95f8da Author: car Date: Thu Jul 26 20:27:27 2001 +0000 *** empty log message *** Src/C_BaseLib/BLWorkQueue.cpp commit 610ec6d59f5d089366c4542245db84cd7f5192b0 Author: lijewski Date: Thu Jul 26 20:08:43 2001 +0000 More forward declaration including Src/C_BaseLib/Array.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabConv.H Src/C_BaseLib/IndexType.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/Orientation.H Src/C_BaseLib/Orientation.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Pointers.H Src/C_BaseLib/Profiler.H Src/C_BaseLib/RunStats.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.H commit fe0ade6dac7c302227c0f8dca448ced9c609996a Author: lijewski Date: Thu Jul 26 14:55:25 2001 +0000 *** empty log message *** Src/C_BaseLib/FabArray.cpp commit de3b98c192c6a519f0dd9dda0d1f0956727a3097 Author: car Date: Thu Jul 26 13:51:54 2001 +0000 Removed redundant member Src/C_BaseLib/FabArray.H commit 28db7d5e9b348f876b3119dbd3fda41e4a5e3b35 Author: lijewski Date: Wed Jul 25 23:42:02 2001 +0000 *** empty log message *** Src/C_BaseLib/FabArray.H commit a9f26ce1933ba28ed14b55b8bd5801441b22700e Author: lijewski Date: Wed Jul 25 23:39:18 2001 +0000 oops Src/C_BaseLib/FabArray.H commit cb1d70a6bb1881d4c58dd20ef8fbed4ce1a3726b Author: lijewski Date: Wed Jul 25 23:36:15 2001 +0000 *** empty log message *** Src/C_BaseLib/Array.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 45acd51c22e4d75490c23853287efccf40a07a96 Author: car Date: Wed Jul 25 05:22:56 2001 +0000 BL_NO_LEGACY_ITERATORS Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/VisMF.cpp commit e55d22dfe61e499614e94a95d4b4ffeed3631c81 Author: 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 Date: Wed Jul 25 01:15:13 2001 +0000 *** empty log message *** Src/C_BaseLib/ParmParse.cpp commit dd982e93bc711e72fc0d8f054948c8bbe3ec9222 Author: car Date: Tue Jul 24 22:42:12 2001 +0000 MFIter... Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabArray.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 46f2c7ff7f39bea759610ba00225f720453fec32 Author: lijewski Date: Tue Jul 24 22:04:47 2001 +0000 *** empty log message *** Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit 4aafeaf6107718f38b66bdc7a4f7505e7f4c85e1 Author: lijewski Date: Tue Jul 24 20:15:38 2001 +0000 *** empty log message *** Src/C_BaseLib/ParmParse.cpp commit 5be9e729ec5e8ce47dd7bc7656fa013fdd79e12c Author: car Date: Tue Jul 24 19:47:17 2001 +0000 *** empty log message *** Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit dd5db6e07b5e70ed390dd991bf5db2e5392dcb1c Author: lijewski Date: Tue Jul 24 18:16:51 2001 +0000 Now use size() instead of length() Src/C_BaseLib/Array.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/List.H Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit f89eef51f99818d02eee1f4edd3a6606021779c6 Author: car Date: Tue Jul 24 18:16:26 2001 +0000 *** empty log message *** Src/C_BaseLib/BaseFab.H commit 5bf0c158e55a5649574012b9f07ca0175acbd74a Author: car Date: Tue Jul 24 18:12:34 2001 +0000 Fab Copy constructor Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit c59fef3681f7ad957123ca0e6af1d80e81ec032f Author: 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 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 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 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 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 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 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 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 Date: Mon Jul 23 19:34:23 2001 +0000 *** empty log message *** Src/C_BaseLib/WorkQueue.H commit 0651a14b63b76d0d06be3aea87a0adbd40414eb0 Author: car Date: Mon Jul 23 19:33:36 2001 +0000 *** empty log message *** Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit ddfa7c339a96f74bd0163562fc11fc80b9ece313 Author: lijewski Date: Mon Jul 23 18:15:21 2001 +0000 aString is gone for good Src/C_BaseLib/ParmParse.cpp commit b7578effe6d5ebb9c15951a6e64fc16f3e6f78c1 Author: lijewski Date: Mon Jul 23 17:55:32 2001 +0000 *** empty log message *** Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/Make.package Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp commit 1fd3e638cf5535f69ed85184557dfba1235adb59 Author: lijewski Date: Mon Jul 23 17:39:00 2001 +0000 asdfdfasdfkasdf asdf Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Utility.H commit 76d21a521fb315769e65a08a07b53e0537396865 Author: car Date: Mon Jul 23 04:31:03 2001 +0000 *** empty log message *** Src/C_BaseLib/.cvsignore Src/C_BaseLib/BoxLib.dsp Src/C_BaseLib/GNUmakefile Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/GNUmakefile.tCArena Src/C_BaseLib/test/tCArena.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/GNUmakefile.tCArena Tests/C_BaseLib/tCArena.cpp commit 93d8e018a7dc489f25f23b36f81f422c44f14365 Author: 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 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 Date: Sun Jul 22 23:46:40 2001 +0000 *** empty log message *** Src/C_BaseLib/ParmParse.cpp commit db0180ceaa5ab6f6233e6264c0500c2b506fed86 Author: car Date: Sun Jul 22 23:41:27 2001 +0000 *** empty log message *** Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit 1a57891e2be31cae33c200263e17aea08d147bb2 Author: car Date: Sun Jul 22 23:25:24 2001 +0000 *** empty log message *** Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Profiler.H commit 1b4363143dff469f4e0d03721eb526949c4cdf32 Author: car Date: Sun Jul 22 22:12:22 2001 +0000 WIN32 Fixes Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/test/tProfiler.cpp Tests/C_BaseLib/tProfiler.cpp commit da1cf99634256e3c24142c8a8a48ef53661dc73c Author: car Date: Sun Jul 22 22:12:10 2001 +0000 Hides Profiling stuff in Initialize Src/C_BaseLib/BoxLib.cpp commit f786c7ec9fb5c9cda2f47cf69994a1818659a55f Author: car Date: Sun Jul 22 22:11:43 2001 +0000 parm parses into std::string instead of aStrings Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit ab969a191c953ba0459d83b1962f4a02b9b870b0 Author: car Date: Sun Jul 22 20:44:30 2001 +0000 *** empty log message *** Src/C_BaseLib/FabArray.H Src/C_BaseLib/Utility.cpp commit df18db60a52d2fecf8dd2806fd0d412111b73cd4 Author: car Date: Sun Jul 22 20:21:16 2001 +0000 *** empty log message *** Src/C_BaseLib/test/tRan.cpp Tests/C_BaseLib/tRan.cpp commit 3a1cbcd2165138cd136dfde1eb40784eb65785f9 Author: car Date: Sun Jul 22 19:38:15 2001 +0000 *** empty log message *** Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/Thread.H commit c0e639ebc0bf85295111e10ea0eb4c7225593eec Author: car Date: Sun Jul 22 18:52:16 2001 +0000 *** empty log message *** Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/CArena.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/ParallelDescriptor.H commit b4cf407b840b46a0160274912dd5b65463e07cfe Author: car Date: Sun Jul 22 18:25:48 2001 +0000 upto BoxLib spec Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/tDir.cpp Src/C_BaseLib/test/tFAC.cpp Src/C_BaseLib/test/tFB.cpp Src/C_BaseLib/test/tProfiler.cpp Src/C_BaseLib/test/tThread.cpp Src/C_BaseLib/test/tVisMF.cpp Src/C_BaseLib/test/tWorkQueue.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tDir.cpp Tests/C_BaseLib/tFAC.cpp Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tProfiler.cpp Tests/C_BaseLib/tThread.cpp Tests/C_BaseLib/tVisMF.cpp Tests/C_BaseLib/tWorkQueue.cpp commit 8a0a69325b2062fd9c510a748edd5234b3fa4b27 Author: car Date: Sun Jul 22 18:11:02 2001 +0000 *** empty log message *** Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/test/GNUmakefile Tests/C_BaseLib/GNUmakefile commit ceded93d6adac91197a69582f4fdf5be72b7b6d6 Author: car Date: Sun Jul 22 18:10:45 2001 +0000 Random number validation file Src/C_BaseLib/test/mt19937int.out Tests/C_BaseLib/mt19937int.out commit 263fd452085b6dda3cd605f54125d8b9060ecbdb Author: car Date: Sat Jul 21 17:37:09 2001 +0000 *** empty log message *** Src/C_BaseLib/Array.H Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/aString.cpp Src/C_BaseLib/winstd.H commit 2a9592e912a3c19c1d7bb0c9d77c1dfd83f53217 Author: car Date: Sat Jul 21 17:37:09 2001 +0000 *** empty log message *** Src/C_BaseLib/BLProfiler.cpp commit 3a22eedb143798978d9cce343267c73439e486f2 Author: car Date: Sat Jul 21 01:17:25 2001 +0000 *** empty log message *** Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 6072d84b6ee1aa1d564552408c4cdec34cefa3d9 Author: car Date: Sat Jul 21 00:53:50 2001 +0000 *** empty log message *** Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/Thread.H Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/tProfiler.cpp Src/C_BaseLib/test/tThread.cpp Src/C_BaseLib/test/tWorkQueue.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tProfiler.cpp Tests/C_BaseLib/tThread.cpp Tests/C_BaseLib/tWorkQueue.cpp commit e747b131a2c6e9760f2b9b34b3fdf006e4271c60 Author: car Date: Sat Jul 21 00:33:15 2001 +0000 *** empty log message *** Src/C_BaseLib/BLWorkQueue.cpp commit 17cc3e4c642e156d30c8928f8e5e725d0ecad6b2 Author: car Date: Sat Jul 21 00:32:37 2001 +0000 *** empty log message *** Src/C_BaseLib/BLWorkQueue.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/WorkQueue.H commit 9eb9fe061d135736d5a027b0988f4f618922ad1a Author: car Date: Sat Jul 21 00:32:37 2001 +0000 *** empty log message *** Src/C_BaseLib/WorkQueue.H commit 4da74c2fc81d0a15f730210a9f005ee80eef4bc3 Author: lijewski Date: Fri Jul 20 23:06:17 2001 +0000 *** empty log message *** Src/C_BaseLib/Array.H Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/PArray.H Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/Thread.H Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp commit 3e0fc393251268c16c2bfa81cff9fcf7b33b9cfe Author: car Date: Fri Jul 20 19:52:54 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp commit 119805bbd493a4855f33193ec6566b7fbfd3d0f0 Author: car Date: Fri Jul 20 19:44:24 2001 +0000 *** empty log message *** Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Thread.H Src/C_BaseLib/Utility.H Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/tProfiler.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tProfiler.cpp commit ee185be69acb0a96e0d5c95cf34c3163653a871c Author: car Date: Fri Jul 20 19:37:36 2001 +0000 *** empty log message *** Src/C_BaseLib/test/GNUmakefile Src/C_BaseLib/test/tProfiler.cpp Src/C_BaseLib/test/tThread.cpp Src/C_BaseLib/test/tWorkQueue.cpp Tests/C_BaseLib/GNUmakefile Tests/C_BaseLib/tProfiler.cpp Tests/C_BaseLib/tThread.cpp Tests/C_BaseLib/tWorkQueue.cpp commit bf5ac26094ad942aed1aff5c6d5e3f053c2ac4b9 Author: car Date: Fri Jul 20 19:31:06 2001 +0000 Parallel Fixes Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp commit 4cb4eb940846c55f088b9b0b029250f18a13d18d Author: car Date: Fri Jul 20 18:18:42 2001 +0000 *** empty log message *** Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp commit d0c4d1e7f611409b2130ba6069b36676b048f7e5 Author: car Date: Fri Jul 20 17:57:27 2001 +0000 Fixes for Parallel Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.cpp commit 00ec88d8a6d469dd2248bfed4c421b66eeff7d09 Author: lijewski Date: Fri Jul 20 17:28:16 2001 +0000 Removed index>=0 checks ... Src/C_BaseLib/aString.cpp commit 458d2b7758915ecfe31f4e0c1c049207bcff8ed7 Author: car Date: Fri Jul 20 17:24:30 2001 +0000 windows normalization Src/C_BaseLib/winstd.H commit 8708f598def753a4c4c47750c25a430f3274fea8 Author: car Date: Fri Jul 20 17:20:48 2001 +0000 FabArray takes only one template arg Src/C_BaseLib/BaseFab.H Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 895fe410de54820a8113decdc08f0d167cd4be84 Author: car Date: Fri Jul 20 17:01:44 2001 +0000 *** empty log message *** Src/C_BaseLib/Array.H Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BLTimer.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/Make.package Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/SPACE.H Src/C_BaseLib/Thread.H Src/C_BaseLib/Timer.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp Src/C_BaseLib/ccse-mpi.H commit d3dd6c8883c9d7f081db2aa5c63288f5d2b04065 Author: lijewski Date: Fri Jul 20 16:54:07 2001 +0000 Merged BaseFab among other tweaks. Src/C_BaseLib/ArithFab.H Src/C_BaseLib/Array.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/NormedFab.H Src/C_BaseLib/OrderedFab.H commit 492b2dd33dbc132cf2e580ed3ee08e8e4d115f4a Author: car Date: Fri Jul 20 04:46:21 2001 +0000 profiling works in serial Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/BLTimer.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Thread.H Src/C_BaseLib/Timer.H Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp commit 541ab33dc1f2c68c40741c5cb1120ef296077723 Author: car Date: Fri Jul 20 01:45:48 2001 +0000 *** empty log message *** Src/C_BaseLib/Array.H Src/C_BaseLib/PArray.H commit db544835aae20e557145739964c8fd4b065b5b03 Author: 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 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 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 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 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 Date: Thu Jul 19 17:19:33 2001 +0000 *** empty log message *** Src/C_BaseLib/BoxList.cpp commit fe6d382d47a6b657ed2d7089d5111da4359de195 Author: car Date: Thu Jul 19 17:19:32 2001 +0000 *** empty log message *** Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/Profiler.H Src/C_BaseLib/Thread.H commit a09146b8a8d5240ebfb5f7721e6b504178136702 Author: lijewski Date: Thu Jul 19 16:57:30 2001 +0000 Got rid of namespace. Src/C_BaseLib/Arena.H Src/C_BaseLib/Arena.cpp Src/C_BaseLib/ArithFab.H Src/C_BaseLib/Array.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FPC.H Src/C_BaseLib/FPC.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/IndexType.H Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/List.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/NormedFab.H Src/C_BaseLib/OrderedFab.H Src/C_BaseLib/Orientation.H Src/C_BaseLib/Orientation.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Pointers.H Src/C_BaseLib/REAL.H Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/SPACE.H Src/C_BaseLib/Tuple.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp Src/C_BaseLib/ccse-mpi.H commit 04dc038efd1583da3cc53d6c6f499ec5eb20404f Author: car Date: Thu Jul 19 16:51:22 2001 +0000 *** empty log message *** Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp commit c25819a54c677da47d0c12ac295bbd196d393596 Author: lijewski Date: Thu Jul 19 15:26:47 2001 +0000 We've now got an Arena.cpp. Src/C_BaseLib/Arena.H Src/C_BaseLib/Arena.cpp Src/C_BaseLib/Make.package commit 7b07ed5fd5bbb0ec00d96b207beb080b36da31f8 Author: lijewski Date: Wed Jul 18 23:07:06 2001 +0000 More work toward the one true BoxLib ... Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.cpp commit a5ae665e58d0066e544d7108630538e88e49b8df Author: car Date: Wed Jul 18 22:21:15 2001 +0000 Profiling stuff Src/C_BaseLib/BLMpi.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/GNUmakefile Src/C_BaseLib/Make.package Src/C_BaseLib/MultiFab.cpp commit c08d75c01dd3c9619320fa19301c67fe72c70707 Author: car Date: Wed Jul 18 22:20:29 2001 +0000 Initial loads, don't work Src/C_BaseLib/BLMpi.cpp Src/C_BaseLib/BLMpi.w Src/C_BaseLib/BLProfiler.cpp Src/C_BaseLib/BLThread.cpp Src/C_BaseLib/Profiler.H Src/C_BaseLib/Thread.H commit 07096d004bd7634eae125585c7130e9e080e9cd2 Author: car Date: Wed Jul 18 20:41:04 2001 +0000 Max->std::max Src/C_BaseLib/MultiFab.cpp commit 0fdbdc32420aeb09ba4a5763480fa055393b704c Author: car Date: Wed Jul 18 20:40:29 2001 +0000 Abs->std::abs Src/C_BaseLib/NormedFab.H commit ece515b8b90c8b6d88b87338b0ca906fcc591f8c Author: lijewski Date: Wed Jul 18 19:37:19 2001 +0000 A few more tweaks ... Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.cpp commit 960998ddc9854bb8808455e236877e348c59e268 Author: car Date: Wed Jul 18 17:33:04 2001 +0000 another Max Src/C_BaseLib/RunStats.cpp commit 3dda2c5f913b99365660b22883af83dd2bfb16b7 Author: lijewski Date: Wed Jul 18 17:31:06 2001 +0000 2-D bug Src/C_BaseLib/FArrayBox.H commit 9ac5650570454de8b4c6ff84714dbfb2030cff65 Author: car Date: Wed Jul 18 16:46:09 2001 +0000 fix for KCC 4.0f Tools/C_mk/Make.defs commit 4b9dcba225837ec76148a5f35ae0bc093ff7fb66 Author: car Date: Tue Jul 17 23:40:08 2001 +0000 Fortran process // comments Src/C_BaseLib/CONSTANTS.H commit 49dabc84220dae228faa94be94e23a55fb1d214a Author: car Date: Tue Jul 17 23:14:38 2001 +0000 Fortran can't process // comments Src/C_BaseLib/REAL.H commit d2b02bb9fd9a4e68cdc11e39ecd7749d775c0e15 Author: car Date: Tue Jul 17 23:14:13 2001 +0000 inline changes Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp commit ebc4348b0ea25c18de05280b3b5c8f46264085e4 Author: lijewski Date: Tue Jul 17 23:02:17 2001 +0000 numerous changes Src/C_BaseLib/Arena.H Src/C_BaseLib/ArithFab.H Src/C_BaseLib/Array.H Src/C_BaseLib/ArrayLim.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BLVERSION.H Src/C_BaseLib/BLassert.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/CONSTANTS.H Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FPC.H Src/C_BaseLib/FPC.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/IndexType.H Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/List.H Src/C_BaseLib/Looping.H Src/C_BaseLib/Make.package Src/C_BaseLib/Misc.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/NormedFab.H Src/C_BaseLib/OrderedFab.H Src/C_BaseLib/Orientation.H Src/C_BaseLib/Orientation.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Pointers.H Src/C_BaseLib/REAL.H Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/SPACE.H Src/C_BaseLib/SPACE_F.H Src/C_BaseLib/Tuple.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp Src/C_BaseLib/ccse-mpi.H commit 20ea450d5bacb94a138f4e68d4f2f994eb3e7a22 Author: marc Date: Tue Jul 17 21:21:12 2001 +0000 Remove Wimplicit for little-f files, as they are generally written by 'someone else', and we don't want to rewrite everything... Tools/C_mk/Make.Linux commit d26c95901637953609e9658acf3fee0b4a05a8f4 Author: lijewski Date: Tue Jul 17 16:58:05 2001 +0000 Added for GNU Src/C_BaseLib/std/limits commit 9cf1b03da1783de2f245ce6765cf646cb90e0364 Author: lijewski Date: Tue Jul 17 16:47:35 2001 +0000 Getting rid of some stuff. Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H Src/C_BaseLib/Specialize.cpp Src/C_BaseLib/Tracer.H Src/C_BaseLib/Tracer.cpp commit 8c57c289f5f0a571e29b688b274ba8a37c887db4 Author: car Date: Fri May 18 16:49:24 2001 +0000 ampersand is a better continuation character, RE: Fortran standard Tools/C_scripts/strip72 commit 45bf7856a1b4e60f65a06cba1bacfeec09545941 Author: car Date: Thu May 17 21:52:13 2001 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit 2f33619f91dbbb8edd38dbcae15165cc9b4bc49e Author: car Date: Tue May 15 16:31:23 2001 +0000 changes in flags Tools/C_mk/Make.Linux commit 474211cbed5e054dcc83dbdd3443e6e66b9ceecf Author: lijewski Date: Mon May 14 17:48:12 2001 +0000 Removed tar_and_rm_files stuff. The compressor utility seems to work fine. Src/C_AMRLib/Amr.cpp commit accac0edbdde7da47aee66bffcfc435c7c720bf8 Author: 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 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 Date: Wed May 9 22:42:22 2001 +0000 Simplified report(). Src/C_BaseLib/RunStats.cpp commit f752ef017bc6bcd6eab57be6cd0280934da94d7b Author: lijewski Date: Wed May 9 22:41:45 2001 +0000 Removed more RunStats stuff. Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 9f82b3a331ea3dd3276717c7bd9cf159190a5bdd Author: lijewski Date: Wed May 9 22:30:59 2001 +0000 Simplified how RunStats is used in code. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/SlabStat.cpp Src/C_AMRLib/StateData.cpp Src/C_AMRLib/TagBox.cpp commit d25966fbbb681b52756b28963a254b756b65366c Author: 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 Date: Fri Apr 27 20:07:11 2001 +0000 Added support for Intel compiler Tools/C_mk/Make.Linux commit d095581fc3a671b6e671dd984526c7dcfd57c3f8 Author: 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 Date: Wed Apr 25 04:16:20 2001 +0000 isDouble should return bool Src/C_BaseLib/ParmParse.H commit 4320997c40c7a076bfa26ad151f982f439c21add Author: car Date: Tue Apr 24 19:42:19 2001 +0000 quiet warnings Src/C_BaseLib/CArena.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/aString.cpp commit 05a794911c8fa1895116458712f4ad2110a9f0e1 Author: car Date: Mon Apr 23 20:08:20 2001 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/Test/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile commit 54915ae813efe0e899252b662a7cba8317cfb610 Author: car Date: Mon Apr 23 19:33:30 2001 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/main.cpp commit 5c56faf642d0ecf9f1c0edb53a3859a7bf714a7f Author: car Date: Fri Apr 20 14:25:30 2001 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile commit 9a76ca7865c972547e473676673f7fdcd98960e0 Author: lijewski Date: Thu Apr 19 22:24:19 2001 +0000 Removed some RunStats. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/VisMF.cpp Src/C_BoundaryLib/FabSet.cpp commit 69c03f399e9669a8b531e586b595f3c254d949fb Author: car Date: Mon Apr 16 22:38:17 2001 +0000 *** empty log message *** Tools/C_util/wrappergen/Makefile Tools/C_util/wrappergen/wrappergen.c commit 442b07a5ef7ad2834ab366f5d055a6b12aa5a7ee Author: car Date: Mon Apr 16 22:20:49 2001 +0000 *** empty log message *** Tools/C_util/wrappergen/Makefile Tools/C_util/wrappergen/args.c Tools/C_util/wrappergen/readproto.c Tools/C_util/wrappergen/wrappergen.c Tools/C_util/wrappergen/wrappergen.h commit 4e814f50a627ee16f5a785f3c048568fceab53a8 Author: car Date: Mon Apr 16 21:32:55 2001 +0000 *** empty log message *** Tools/C_util/wrappergen/wrappergen.c commit 7726a96ae89ed840e28abffae41bbe190b8a1d9f Author: car Date: Fri Apr 13 17:18:54 2001 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit 2c3a61dc1989b2dcb8b9ed74559fcdb38f3b8f38 Author: lijewski Date: Wed Apr 11 18:11:04 2001 +0000 Further simplification to copy(). Src/C_BaseLib/FabArray.H commit cc6a1f5887637dbe83a1c9a0daf679ca9249293a Author: car Date: Fri Apr 6 20:27:52 2001 +0000 *** empty log message *** Tools/C_util/wrappergen/Makefile Tools/C_util/wrappergen/PROTO Tools/C_util/wrappergen/README commit 9e44d7658f6a6e6098828077bb0f26e00e8800d3 Author: car Date: Fri Apr 6 20:17:03 2001 +0000 minor changes Tools/C_util/wrappergen/.cvsignore Tools/C_util/wrappergen/Makefile Tools/C_util/wrappergen/PROTO commit 7788fa29ae4a64a331133d5092781237f27a3911 Author: car Date: Fri Apr 6 20:12:14 2001 +0000 Initial revision Tools/C_util/wrappergen/Makefile Tools/C_util/wrappergen/PROTO Tools/C_util/wrappergen/README Tools/C_util/wrappergen/args.c Tools/C_util/wrappergen/args.h Tools/C_util/wrappergen/doc.c Tools/C_util/wrappergen/doc.h Tools/C_util/wrappergen/driver.c Tools/C_util/wrappergen/expandingList.h Tools/C_util/wrappergen/mpifn Tools/C_util/wrappergen/petsccfg.h Tools/C_util/wrappergen/prof.c Tools/C_util/wrappergen/prof_wrapper.c Tools/C_util/wrappergen/readproto.c Tools/C_util/wrappergen/sample.c Tools/C_util/wrappergen/sample.w Tools/C_util/wrappergen/system.c Tools/C_util/wrappergen/system.h Tools/C_util/wrappergen/tools.h Tools/C_util/wrappergen/wrappergen.c Tools/C_util/wrappergen/wrappergen.h Tools/C_util/wrappergen/write_proto.c commit b80511fe127a3c79c71da7e7d12686e058de3366 Author: car Date: Fri Apr 6 20:04:52 2001 +0000 MPI off fix Src/C_BaseLib/VisMF.cpp commit b889ecda54866c6f6062cce4e7060225c44f0773 Author: lijewski Date: Mon Apr 2 17:58:59 2001 +0000 Now use MPI_Waitsome() instead of MPI_Wait() ... Src/C_AMRLib/FluxRegister.cpp commit c523a2c3c5fcfded4ac2212dccfed152f83e6c0d Author: 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 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 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 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 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 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 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 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 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 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 Date: Tue Mar 20 19:42:02 2001 +0000 maxorder flag Src/LinearSolvers/C_CellMG/LinOp.cpp commit 9e7d560f5940144e8ce863e335ec40ff932600a8 Author: car Date: Tue Mar 20 19:41:42 2001 +0000 verbose flags Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit f7ec482f6e979fb2ad975af96bac4e51ec14d6b8 Author: car Date: Tue Mar 20 19:40:43 2001 +0000 namespace correction Src/C_BaseLib/ParallelDescriptor.cpp commit f98dd1d369a6d4b9c4e5771f346fe736da268400 Author: lijewski Date: Wed Mar 14 22:02:29 2001 +0000 Removed some virtual calls and other simplifications. Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 9ce53ef9b3f9dbd8acec52ec7bdeb6f154b832ac Author: wyc Date: Thu Mar 1 21:17:34 2001 +0000 added preprocessor foobah to protect squirrelly namespace stuff Src/C_BaseLib/ParallelDescriptor.cpp commit fe4623ab58a814823b7a0502a68608cc0d8abc74 Author: lijewski Date: Wed Feb 28 18:07:31 2001 +0000 Removed FORT_FLUSH stuff ... Src/LinearSolvers/C_NodalMG/hgdebug.F commit 26590854a8d32d17ab97f8c4f315be2ea071ef29 Author: lijewski Date: Tue Feb 27 18:49:14 2001 +0000 Rearranged some HG_DEBUG stuff. Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 9c2fecb29d3bfc25899f0b6114e93d929f498d98 Author: marc Date: Sat Feb 17 01:17:36 2001 +0000 A little more fixup for Athlon compile of stuff. Tools/C_scripts/dsp.mak commit e87c37ea4d565279be53c6909d4e83cae7af2694 Author: 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 Date: Wed Feb 14 19:05:44 2001 +0000 Deprecated BL_USE_ARLIM junk Src/C_BaseLib/ArrayLim.H commit 608b37605fcf53f34c94f2a0514e9179f91faf22 Author: lijewski Date: Wed Feb 14 17:57:57 2001 +0000 Deprecated BL_USE_ARLIM ... Src/C_BaseLib/ArrayLim.H commit 4cbe6b88621882c0e5d46b933a4686557c36c4f3 Author: lijewski Date: Thu Feb 1 23:39:35 2001 +0000 Removed AlternateApplyBC junk. Src/LinearSolvers/C_CellMG/LinOp.cpp commit 9497fe6569d65936ff8791b0c839626f5cc9cb43 Author: lijewski Date: Thu Feb 1 23:17:57 2001 +0000 BiCG is now default CG solver. Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 2f9df0984b5181857887781cfe7736bf45040643 Author: 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 Date: Thu Feb 1 00:49:02 2001 +0000 Added support for cygwin. Tools/C_mk/Make.defs commit 915c11625d2e44d074a9e873d3ec35e933f86635 Author: lijewski Date: Fri Jan 26 18:08:14 2001 +0000 Forgot the non-MPI section Src/C_BaseLib/ParallelDescriptor.cpp commit 615cc7c8ea2317260c103d425341bb51cd762c11 Author: lijewski Date: Thu Jan 25 23:53:23 2001 +0000 Removed a BL_ASSERT() ... Src/C_BoundaryLib/FabSet.cpp commit 554df82eef286c07119bb52721e389e982ca7a90 Author: lijewski Date: Thu Jan 25 23:52:36 2001 +0000 Added NProcsCFD() to ParallelDescriptor. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 2319790954670e34791848da20227528bf935bb3 Author: lijewski Date: Wed Jan 24 22:50:47 2001 +0000 Now compiles. Src/C_BaseLib/test/tCArena.cpp Tests/C_BaseLib/tCArena.cpp commit 8f4ee998bc991029d3650a27e71ff07cfc884893 Author: marc Date: Fri Jan 19 22:57:48 2001 +0000 Incorporate larger stencil in tang interp at c-f Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/INTERPBNDRYDATA_2D.F Src/C_BoundaryLib/InterpBndryData.cpp commit cd402d553859c9b47281a06d5124d1ab0b4405c0 Merge: 6af1b9924 f4b1e81cf Author: Matthew Emmett 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 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 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 Date: Thu Jan 4 00:49:52 2001 +0000 Fix up script a little more... Tools/C_scripts/dsp.mak commit 7bf13ad9d41cd15de8f4db03761d88edf4f08c07 Author: car Date: Mon Dec 11 18:45:53 2000 +0000 main.cpp Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/main.cpp commit cd05d23c7e5844d1658a741eb1c564a4d3d973c9 Author: 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 Date: Wed Dec 6 23:44:28 2000 +0000 Set maxmem stuff to be unlimited Tools/C_mk/Make.AIX commit 0c16ad5499e6279f098aa67279be67604664dd3d Author: almgren Date: Wed Dec 6 23:13:58 2000 +0000 Modified AddFPB to allow the Geometry::FillPeriodicBoundary call to handle edge-centered as well as cell- and node-centered data. Src/C_BaseLib/Geometry.cpp commit 654f0af7157028ab18bf91f31c250874903f7b3a Author: marc Date: Tue Dec 5 01:05:29 2000 +0000 Fix up to build on Athlon with W2K + MSVC 6 Tools/C_scripts/dsp.mak commit 717d426583d34f9fa468fb7415a6b97d31aec4d3 Author: marc Date: Fri Dec 1 23:35:19 2000 +0000 Move stop tests to avoid relax/print if incoming problem already solved. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit d5055592ae171fad801b9cd6c168aab11f3db290 Author: lijewski Date: Fri Nov 17 18:01:09 2000 +0000 Consolidated some duplicated code. Src/C_AMRLib/StateData.cpp commit 2ce475ab450077b2f7bf27113d4ca2668d0f4c13 Author: lijewski Date: Fri Nov 17 18:00:55 2000 +0000 Little simplification ... Src/C_AMRLib/Interpolater.cpp commit 4a23d6ba0d3f64303e446eb1dfbf7e8fbce2b680 Author: car Date: Wed Nov 15 20:12:02 2000 +0000 D_PICK expands to 1st, 2nd, or 3rd argument dependinging on BL_SPACEDIM; Happy Compiling Src/C_BaseLib/SPACE.H commit a177b8a4b8df9c42b57ec49ec148db337edc4e91 Author: car Date: Sun Nov 12 17:26:12 2000 +0000 added a NumPts to BoxArray Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit ad65d4ca7dc1e208eadecc5c6a314c4c30920312 Author: car Date: Wed Nov 8 22:01:50 2000 +0000 book != bool Src/C_BaseLib/BaseFab.H commit 372e4f3d2953477cc8fa7823d854bf73be7e7161 Author: lijewski Date: Wed Nov 8 21:48:21 2000 +0000 Added bool isAllocated () ... Src/C_BaseLib/BaseFab.H commit 5d258cebfdcfcfd5c09ebfe376340cdd7f3ff1bc Author: lijewski Date: Thu Nov 2 23:07:27 2000 +0000 A tad simplification ... Src/LinearSolvers/C_TensorMG/DivVis.cpp commit 19ef426a2df4d45548331254f71a807606b32b74 Author: lijewski Date: Wed Nov 1 18:29:37 2000 +0000 A little simplification ... Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/RealBox.cpp commit 777012a28e662cc6369c56b682d8fa9f67de6f53 Author: lijewski Date: Wed Nov 1 18:06:14 2000 +0000 A little simplification ... Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp commit 95bde516e944c08ea75648116dde5cd64244c6cf Author: 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 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 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 Date: Tue Oct 3 20:26:49 2000 +0000 Small change for BL_AIX Src/C_BaseLib/Utility.cpp commit 39eb97cda4f5388271cb3e2e6d1ca890ae30bdb9 Author: 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 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 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 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 Date: Tue Sep 26 18:19:25 2000 +0000 helper macro for FORTRAN calls Src/C_BaseLib/ArrayLim.H commit a4f4bb39e485eba0d0b395e771627bcce55d7725 Author: car Date: Tue Sep 26 18:18:57 2000 +0000 fix for min max Src/C_BaseLib/MultiFab.cpp commit 4871a2a2a7650117374f1ccdee11a8ba51c732ac Author: almgren Date: Thu Sep 14 19:44:06 2000 +0000 Changes to allow for multiple datalog files if more than one file name is specified in the inputs file. It's up to the user to not try to access more files than names are given. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit cfc4838f0feef303f9784ff0f0f5a79fa4d03ab1 Author: lijewski Date: Thu Sep 14 15:25:26 2000 +0000 Cut down on sleep time. Tools/C_scripts/compressor commit f90bf5d33476ce0b7ad156a8053bb7f973c8eca3 Author: lijewski Date: Wed Sep 13 20:09:12 2000 +0000 BiCG is now the default ... Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 74def7afe2743f35c1f9e04b45ca5755a5509794 Author: almgren Date: Mon Sep 11 22:03:57 2000 +0000 Fix to propp's re-write of build_sigma...we need to copy the zeros in ghost cells when for_sync_reg != 0. Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit c3e40459c4fea2aab32bd6fd7ea2f43c7413c646 Author: car Date: Tue Sep 5 17:40:54 2000 +0000 filter profiling files Src/LinearSolvers/C_CellMG/Test/.cvsignore Tests/LinearSolvers/C_CellMG/.cvsignore commit b3c233c679d93ff3de07fd7114de63e8aa2c6050 Author: car Date: Wed Aug 30 19:19:13 2000 +0000 New convergence criteria: relative tolerances may need to be reduced by a factor of 5 or 10. Absolute tolerances may not be needed at all. Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit bbfe3a7fe6b93ca4ed297ace0ea583a6e67a6748 Author: car Date: Mon Aug 28 15:54:01 2000 +0000 Use new convergence criteria by default; must still select BiCGStab in ParmParse Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp commit e18930dd8980331b3db00b8da636f31d39646f73 Author: car Date: Sat Aug 26 19:41:00 2000 +0000 3D Norm Src/LinearSolvers/C_CellMG/ABec_3D.F commit 1005091f9b69669c6118bc91b239c146710c6c30 Author: car Date: Fri Aug 25 19:23:28 2000 +0000 fix for bicg with initial zero residual Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 8027c545e31dca56d82c4cb7b783d53568e1be81 Author: car Date: Fri Aug 25 17:50:25 2000 +0000 annotation tweak Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 48f5dd911040a2300a34e25aa432ed4ffb233e18 Author: car Date: Thu Aug 24 22:45:46 2000 +0000 profiling fix Src/LinearSolvers/C_CellMG/LinOp.cpp commit b1396521f4c307c983ef96f9137ab09a0aaa7af1 Author: car Date: Thu Aug 24 22:39:02 2000 +0000 solver selection, timing Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit e9cc8cc18dc55469731909f6a21c863603c6051c Author: car Date: Thu Aug 24 20:28:28 2000 +0000 fix initialize, add norm Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_F.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/LP_2D.F Src/LinearSolvers/C_CellMG/LP_F.H Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit dda17304a1fd7d40ab3120d1875fa011a857cf45 Author: car Date: Thu Aug 24 16:02:46 2000 +0000 Added BiCGStab Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/CG_2D.F Src/LinearSolvers/C_CellMG/CG_3D.F Src/LinearSolvers/C_CellMG/CG_F.H Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 8250cc7d59aef20787e938ce45dc2ad914b0bec2 Author: lijewski Date: Wed Aug 23 20:16:29 2000 +0000 Fixed some PlotVar stuff ... Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp commit ef2f6f0408b5ce50fe1b440ee4ec430205c27464 Author: marc Date: Thu Aug 17 17:31:00 2000 +0000 Enable array of blocking factors. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit a19ba918b0818a1b0a60bc2c06a6be6fe8a83b8b Author: 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 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 Date: Wed Aug 9 20:23:04 2000 +0000 Removed an unnecessary parallel reduction. Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit 3eb3ab21e37f06866e6bf48d1e3738e446547239 Author: lijewski Date: Wed Aug 9 15:38:50 2000 +0000 Removed unnecessary paralllel reduction. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 3021b995053a410a82f28944c1b6622450002d25 Author: car Date: Fri Aug 4 18:06:22 2000 +0000 another Profile Src/C_BaseLib/FabArray.H commit 87f0536024bc437703a24c8d8861204209130a69 Author: 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 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 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 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 Date: Wed Aug 2 16:09:45 2000 +0000 MPICH 1.2.0 Support Tools/C_mk/Make.mpi commit 20cfbc5f4114692f0b3504f53281d5fa4f07f0dd Author: car Date: Wed Aug 2 16:08:35 2000 +0000 Thread Safety Support Tools/C_mk/Make.defs commit 25a81c68d12d649896e8704c2913d5854c02a1e9 Author: car Date: Wed Aug 2 16:08:10 2000 +0000 profiling support Tools/C_mk/Make.Linux commit 121e11bcb567a312a97cf6fe4b54baea89db40d4 Author: car Date: Wed Aug 2 16:06:32 2000 +0000 BoxLib3 Profiling code; commented out Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 297b4da4482ff10708962eb582ed69bc49da1eef Author: car Date: Wed Aug 2 16:00:53 2000 +0000 Added Profiling Code; ParallelDescriptor::StartParallel fixed to allow multiple calls with no error Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.cpp commit f80d6376d625c79fc0a8c1c5080dd4d471bcf9de Author: lijewski Date: Tue Jul 25 19:10:38 2000 +0000 which_time() now asserts that time is in (oldtime,newtime) interval Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit a6e43c29167e907b36fa2ac9c9655981e2840a33 Author: almgren Date: Fri Jul 21 22:45:04 2000 +0000 Added code to take a velocity field and return the stream function. This is done by computing the vorticity and solving Laplacian(phi ) = vort. Called from Projection::getStreamFunction in iamrlib. The computation of vorticity and inversion of the Laplacian are full multilevel operations. Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit ea8150399aa431d51be7c59d41c0ce4615e09441 Author: lijewski Date: Fri Jul 21 20:45:21 2000 +0000 Added AmrHalfTime to support rho_half in NS. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit e956870b64038e4b18bf763a8029198316756d05 Author: 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 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 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 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 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 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 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 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 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 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 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 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 Date: Mon Jul 3 23:40:02 2000 +0000 Tad more simplification ... Tools/C_scripts/compressor commit 971f20a69172962eb6f62eaad21e827fd7ed9f83 Author: 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 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 Date: Tue Jun 27 20:54:50 2000 +0000 Removed "inline" from isBoolean() definition. Src/C_BaseLib/ParmParse.cpp commit e8e18cc1d0d6fb24896df0f3aa3aee160319d420 Author: 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 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 Date: Thu Jun 22 20:56:22 2000 +0000 ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp commit 42cdda2aae628627a99cce611624c34eb7a693f1 Author: 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 Date: Thu Jun 22 18:34:50 2000 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/LinOp.cpp commit 11204ec79c2f39258ba1664fcbb9524409b6f0a8 Author: car Date: Thu Jun 22 18:33:45 2000 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/main.cpp commit a9553f052da123848f68617f923424e488e25cab Author: 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 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 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 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 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 Date: Tue Jun 20 21:44:11 2000 +0000 A little more finagling with sleeps. Tools/C_scripts/compressor commit f53524a86239e12f1e8cb769b51d4d9b2da44800 Author: lijewski Date: Tue Jun 20 20:45:51 2000 +0000 Changed sleep interval. Tools/C_scripts/compressor commit 3a347c6156dd367e7d64f4d879a4ed64b3ecd7d6 Author: lijewski Date: Fri Jun 16 17:39:49 2000 +0000 Fixed bug in grid_places(). Probably needs more testing, but ... Src/C_AMRLib/Amr.cpp commit 8574964f67dc368e8e99341dcd70184c06ed2f17 Author: lijewski Date: Thu Jun 15 17:29:01 2000 +0000 Got rid of CXXFLAGS; moved stuff to CXXOPTS & CXXDBG. Tools/C_mk/Make.AIX commit eed44d5efc8638f4eab151bbfe5cb93c44bfbf4c Author: lijewski Date: Thu Jun 15 16:57:41 2000 +0000 Now print grid info to cout as well as gridlogout. Src/C_AMRLib/Amr.cpp commit 17046cc985d854838fb1583f56b77d7c2b736c42 Author: lijewski Date: Tue Jun 13 16:52:28 2000 +0000 Don't tar up last plotfile. Wait till next one is written. Tools/C_scripts/compressor commit 317f2e0f37dcb96ab6dc717a1469673f1a99e169 Author: almgren Date: Mon Jun 12 23:43:03 2000 +0000 Now pass iteration into post_timestep so it will eventually get passed into the sync project in IAMR. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H commit 26725162ae72c0a69b58a4ad9edaf70be78825dc Author: sstanley Date: Fri Jun 9 21:25:51 2000 +0000 Changed errorEstimate to work properly on all levels, not just level 0. Midfied the logic slightly when dumping residuals in the bottom smoother. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit de276e2b8688d319a9038624f3b36058b0f4afa2 Author: lijewski Date: Fri Jun 9 21:10:31 2000 +0000 Use CXXFLAGS instead of XTRADEFS in one case. Tools/C_mk/Make.AIX commit 4b31e60de2c5f613f19d2ff19e945ce20bfa6ccb Author: 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 Date: Thu Jun 8 17:38:02 2000 +0000 Increased maxmem a tad more. Tools/C_mk/Make.AIX commit 8bf76dd598f730dc086606d3a2e2f5ac21640a80 Author: 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 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 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 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 Date: Mon Jun 5 19:11:16 2000 +0000 namespace fix Src/C_BaseLib/ParallelDescriptor.cpp commit 3331e600a69c44a664d861da3d12222ad2e99b49 Author: car Date: Mon Jun 5 18:56:08 2000 +0000 another bc buster Src/LinearSolvers/C_NodalMG/tests/gt.sstanley_3 Tests/LinearSolvers/C_NodalMG/test_grids/gt.sstanley_3 commit a07c853a550b3f5f0c16c965b749fe956444ad77 Author: car Date: Mon Jun 5 18:39:31 2000 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 3dbbacf2b3469a3af4c83a12837a00f3f4fa3adf Author: marc Date: Fri Jun 2 22:58:53 2000 +0000 extern c chuck you moron Src/C_BaseLib/ParallelDescriptor.cpp commit 74f77cf3177e042b851323800882206b7268b234 Author: lijewski Date: Fri Jun 2 22:37:40 2000 +0000 Added new intersect() functions. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit 7d91c82c62913cd4a8d4863a4b7309bce47dc75b Author: almgren Date: Fri Jun 2 17:59:53 2000 +0000 Chnage the time interpolation so it allows t >= t1-teps instead of just t > t1-teps. This matters in the case where t1=t2 so teps = 0. Src/C_BaseLib/MultiFab.cpp commit a7dec4a8b5ab2a2f2118dd0b655a3106bb1fae84 Author: lijewski Date: Fri Jun 2 17:09:16 2000 +0000 Cleaned up a bit. Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F commit 20ec429a523487e42e602a968f0a569b3ea2d248 Author: car Date: Fri Jun 2 01:04:12 2000 +0000 Bad BL_PD_ABORT defn Src/C_BaseLib/ParallelDescriptor.cpp commit 1cb8722dbb90f3d20629386caf82300e6fa1af3c Author: car Date: Thu Jun 1 23:10:36 2000 +0000 Support for KCC 3.4, Thread, and Strict compilation Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit f77e6c9871ec9ac4afdc8644707a865d4a5af587 Author: car Date: Thu Jun 1 23:09:28 2000 +0000 use ksh in Make Tools/C_mk/Make.OSF1 commit b26efc2f2c26507d4ebfa610d59b250ba9a439fa Author: car Date: Thu Jun 1 22:59:47 2000 +0000 g++ fixes Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/inputs commit 9f5057babfbfa106058b6b6e46fdcaa0eac0bd64 Author: car Date: Thu Jun 1 21:39:54 2000 +0000 using ParallelDescriptor::Communicator() Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit e8d07b45053e7c02eefcd98244ab3fcba947f75d Author: lijewski Date: Thu Jun 1 21:28:57 2000 +0000 Added extrap() member to StateDescriptor & integrated into code. Really only used in FillPatch(). Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp commit 308defdbb9389e44df2aaa3ab513202b40072530 Author: car Date: Thu Jun 1 21:22:31 2000 +0000 using ParallelDescriptor::Communicator() Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/PltFileNormB.cpp commit a8cce260432ec0be7f7010bd381a447da481657a Author: car Date: Thu Jun 1 21:07:51 2000 +0000 Two Parallel Changes: 1) ParallelDescriptor::Communicator() should be used instead of MPI_COMM_WORLD. This will allow us to mix other libraries that use MPI without message passing tag collisions. 2) Added a few FORTRAN bindings to ParallelDescriptor calls: BL_PD_ABORT BL_PD_COMMUNICATOR BL_PD_NPROCS BL_PD_IOPROC BL_PD_MYPROC BL_PD_BARRIER Its probably not worthwhile to add any others. Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/ccse-mpi.H commit 1a575fb977ad1a16c7278d8d0273246fa438a4b7 Author: car Date: Thu Jun 1 20:59:38 2000 +0000 not needed here: --one_instantiation_per_object Src/LinearSolvers/C_CellMG/GNUmakefile Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/main.cpp commit 1c3924a702b48b8b0f28328c42334f2aadc29e13 Author: sstanley Date: Thu Jun 1 16:41:14 2000 +0000 Fixed a problem with how quoted strings were broken up. This caused file name problems on the SP machines. Tools/C_scripts/strip72 commit b4e8061a3aadbdbcc43706537463e8a966e420a2 Author: car Date: Thu Jun 1 15:39:16 2000 +0000 boolean values are now parsed 'true', non-zero numerics ---> true 'false', zero numerics ---> false Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit f34d641c4ca95250da82927596f67a8b9f283bd3 Author: car Date: Wed May 31 20:35:25 2000 +0000 const-ness issue Src/C_BaseLib/Geometry.H commit f5fd13c1a4b0d7154045083dc30f4f8d1eaec8cd Author: car Date: Wed May 31 20:33:40 2000 +0000 Silence a warning Tools/C_util/WritePlotFile.cpp commit f4573b187ad5a7ec137453bec3c16cbebb6fba98 Author: car Date: Wed May 31 20:33:14 2000 +0000 KCC 4.0 support Src/C_BaseLib/Utility.H Src/C_BaseLib/VisMF.H commit 8a04fd129a260aeebe380628a6624c5e9cc4148a Author: lijewski Date: Wed May 31 17:44:24 2000 +0000 Removed FillCoarsePress() -- figured out how to reuse FillCoarsePatch(). Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 239bd369f22b4b1a9bd595ef767a14c1cbfeda93 Author: almgren Date: Tue May 30 21:10:47 2000 +0000 Added SetNewTimeLevel and SetOldTimeLevel calls in StateData. Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit dc30bac210f78b61d6f82a74847796000bb8e3a1 Author: almgren Date: Tue May 30 20:24:54 2000 +0000 Added AmrLevel::FillCoarsePress routine which is willing and able to fill ghost cells as well as valid region of NODAL data only. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit c39122c9947fd2e4095f05a82bab3ca61c0877ec Author: 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 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 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 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 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 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 Date: Mon May 22 20:14:25 2000 +0000 Added gt.sas. Src/LinearSolvers/C_NodalMG/files.3d commit b04f4e490151fc6bf22e8dd778698d323dbe6561 Author: lijewski Date: Mon May 22 20:13:45 2000 +0000 Tests some doubly-periodic stuff. Src/LinearSolvers/C_NodalMG/tests/gt.sas Tests/LinearSolvers/C_NodalMG/test_grids/gt.sas commit 031bd92f81e1cac71df7c3d3570d71ec7946c952 Author: sstanley Date: Mon May 22 19:54:00 2000 +0000 Minor changes to the slabstat files. Added $Id: $ fields to the fortran and changed the #define variable to force only single inclusion of the header file. Src/C_AMRLib/SLABSTAT_2D.F Src/C_AMRLib/SLABSTAT_3D.F Src/C_AMRLib/SLABSTAT_F.H commit d3fd564b846e3a11c8f86fea178eb00641388e62 Author: lijewski Date: Thu May 18 20:13:42 2000 +0000 More periodic fixes. Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit b6624f5e5aaec8fbd6d7aebed5122e9cc42e6f04 Author: lijewski Date: Thu May 18 20:02:16 2000 +0000 Added some comments on how to set boundary conditions. Src/LinearSolvers/C_NodalMG/inputs commit b6d074d4446223f7e778195973e06f0674ce386e Author: 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 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 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 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 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 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 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 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 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 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 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 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 Date: Wed May 3 17:12:11 2000 +0000 changed default for NAMESPACE to be FALSE Src/C_BaseLib/GNUmakefile commit b05468c094c5dacb42a2955a2967f0103d078b2c Author: propp Date: Wed May 3 03:36:40 2000 +0000 fixed bug so libraries would be built correctly Src/C_AMRLib/Make.package commit ddcbd3c91bd0ab652c25d895426c665e913c0be5 Author: sstanley Date: Tue May 2 22:13:59 2000 +0000 Further fix to how the values in the cen array are calculated and dealt with. Added logic in thew hgcen_full and hgcen_terrain to set cen=0 when the sigmas sum to zero. Changed logic in hgres_terrain and hgres_full to deal properly with the zero values in the cen array. Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi2d_full.F Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_full.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F commit 0216b6bc6ccd510a84edc9a7b9d77dfac3904c3a Author: car Date: Tue May 2 17:17:41 2000 +0000 add fp exceptions for Linux Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Tools/C_mk/Make.Linux commit e8162fe988f77c114335859ea22c9fc75bb89111 Author: car Date: Tue May 2 15:55:33 2000 +0000 modified hgcen to give cen=0 when sigma's are zero Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F commit 8d9b198173a3b3f9a60c7c8acba9d54dbcb5a6dd Author: sstanley Date: Mon May 1 22:06:38 2000 +0000 Fixed a problem in build_sigma when for_fill_sync_reg==1. Turns out you don;t need to calculate cen for this case since it never gets used. Also, it can not be calculated since the sigma_node is set up so it is zero on all covered cells and we divide by sigma_node when calculating cen. Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit bea13d73c116399cefb5f8499b65836094a9b8bc Author: 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 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 Date: Tue Apr 25 16:29:56 2000 +0000 more namespace fluff Src/C_BaseLib/FabArray.H commit 9984efe981b0b4f9746734f4134e8cb84dc94c24 Author: car Date: Mon Apr 24 18:00:52 2000 +0000 missed one Src/C_BaseLib/SPACE.H commit a4f8a4dc4072af4e35e388fc08f6b2645a805559 Author: car Date: Mon Apr 24 17:52:32 2000 +0000 Minimal namespace support. The changes here should have no impact on user code. Two c-preprocesor symbols are used to control the changes: 1) BL_NAMESPACE: if defined, BoxLib code is wrapped within a namespace whose name is given by the BL_NAMESPACE macro. 2) BL_NO_USING_DIRECTIVE: if defined, no 'using namespace BL_NAMESPACE;' is implicitly given in for each module. The Makefile system was made namespace aware about a month ago. If you say 'NAMESPACE = TRUE' you will get the effect of saying: BL_NAMESPACE=BoxLib2. The default is 'NAMESPACE=FALSE' The intent is that two versions of BoxLib can be used within the same program. I don't expect that apart from a forced recompile that there will be any changes required to user code. Src/C_BaseLib/.cvsignore Src/C_BaseLib/Arena.H Src/C_BaseLib/ArithFab.H Src/C_BaseLib/Array.H Src/C_BaseLib/Assert.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FPC.H Src/C_BaseLib/FPC.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/GNUmakefile Src/C_BaseLib/IndexType.H Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/List.H Src/C_BaseLib/Looping.H Src/C_BaseLib/Misc.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/NormedFab.H Src/C_BaseLib/OrderedFab.H Src/C_BaseLib/Orientation.H Src/C_BaseLib/Orientation.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Pointers.H Src/C_BaseLib/REAL.H Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/SPECIALIZE_F.H Src/C_BaseLib/Specialize.cpp Src/C_BaseLib/Tracer.H Src/C_BaseLib/Tracer.cpp Src/C_BaseLib/Tuple.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp Src/C_BaseLib/ccse-mpi.H commit bf1b07db7b269afee8014cea11d86ecbb29ea04a Author: sstanley Date: Sat Apr 22 00:34:14 2000 +0000 Moved the storage of the statistics data from being in the checkpoint files to being in their own directory, 'slabstats'. The data for each level 0 timestep where it is saved is stored under subdirectories, 'slabstats/stats0000', etc. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/SlabStat.H Src/C_AMRLib/SlabStat.cpp commit 5096152affdbb76912a4b38d46f6848fddb13342 Author: sstanley Date: Sat Apr 22 00:16:26 2000 +0000 Modified the constructors for SlabStatList and SlabStatRec so that if the boxes are read form the file, then the level is read from the file as well. If the boxes are included in the constructor, then the level is included in the constructor. Makes sense since the boxes are defined on a specific level and are generally not valid except on this level. Src/C_AMRLib/SlabStat.H Src/C_AMRLib/SlabStat.cpp commit 31d67be32f3e1a796c0177691faf2b9d41cfb3dd Author: sstanley Date: Fri Apr 21 22:31:04 2000 +0000 Corrected a couple of problems with the derive function which takes a multifab to be filled. There were a few things still in place which assumed you were working with the level multifabs. Src/C_AMRLib/AmrLevel.cpp commit 56c07943d98d47e81f1bcc1471cdfd6ce9c2d7dd Author: sstanley Date: Fri Apr 21 22:29:39 2000 +0000 Corrected a problem with the ordering of the variables passed into the running statistics fortan routines. Src/C_AMRLib/SLABSTAT_2D.F Src/C_AMRLib/SLABSTAT_3D.F commit fa8772fac5754a89926dcea4ac48f933c38f6a6b Author: 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 Date: Fri Apr 21 18:46:06 2000 +0000 fix for g++ Src/LinearSolvers/C_NodalMG/hg_multi2.cpp commit 8ae5f622ae837d66bf67e4a7aeb7b598837839a7 Author: sstanley Date: Fri Apr 21 16:26:15 2000 +0000 Added a couple of general SlabStat statistics routines that save the values required to calculate the first four moments of whatever state components are passed in. Routines were added to do this using Reynolds averages and Favre averages. These are likely to be used in NS, HT as well as HCAll, so they were added here. Src/C_AMRLib/Make.package Src/C_AMRLib/SLABSTAT_2D.F Src/C_AMRLib/SLABSTAT_3D.F Src/C_AMRLib/SLABSTAT_F.H commit fbcdca2331ab99004058a52ba730ec54ac698116 Author: sstanley Date: Fri Apr 21 16:24:02 2000 +0000 Corrected a typo in an error message about the format if the ParmParse inputs. Src/C_AMRLib/SlabStat.cpp commit 45e21172c6f8bbe1012bef85eea51e4d7777f8f7 Author: car Date: Fri Apr 21 16:23:32 2000 +0000 *** empty log message *** Src/C_BaseLib/CoordSys.H commit 3e927f22569018c2067cc93d2dfe998c650c398e Author: sstanley Date: Fri Apr 21 16:20:21 2000 +0000 Added ARRAYLIM_2D.F and ARRAYLIM_3D.F to amrlib. These contain a couple of helper fortran routines that convert back and forth from the DIMDEC type cpp defined array dimensions to dimensions stored in arrays, lo(SDIM) and hi(SDIM). Src/C_AMRLib/ARRAYLIM_2D.F Src/C_AMRLib/ARRAYLIM_3D.F commit f1891ab2813d2f172d53506c152d1b76726c541d Author: car Date: Fri Apr 21 14:22:24 2000 +0000 fixes for fill_sync_reg memory allocation problems Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/RegType.H Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi2d_full.F Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_full.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgdebug.F Src/LinearSolvers/C_NodalMG/hgdebug_F.H Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.H Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 78d0c11815866e83ac6f224672787eea8b1bd3a7 Author: car Date: Thu Apr 20 17:46:47 2000 +0000 noquotes in fortran Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F commit 48343ad8bb3dd3a5c0cc8165b057a2b8bd864cba Author: car Date: Mon Apr 17 21:16:10 2000 +0000 partial backout fix for fill_sync_reg Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit a69bffa413ed30002881489a30911b184a6417d0 Author: car Date: Mon Apr 17 20:53:29 2000 +0000 partial backout fix for fill_sync_reg Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 7c707ab930ac1bb7cc2ffa8077342797d9e14f35 Author: car Date: Mon Apr 17 17:58:37 2000 +0000 I think a fix for fill_sync_reg allocation Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/inputs commit 6e388474f9521a84ff4d0c134c0041049d5fbe4e Author: propp Date: Fri Apr 14 20:56:12 2000 +0000 deleted extra arguments Src/LinearSolvers/C_NodalMG/hg_multi2d_full.F Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.F Src/LinearSolvers/C_NodalMG/hg_multi3d_full.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F commit 4ccdb9f8d7620c118d509cec3cec22cd78c884c2 Author: lijewski Date: Fri Apr 14 20:45:48 2000 +0000 Fixed some bugs. Src/LinearSolvers/C_NodalMG/proj.cpp commit e5e3970b4ff125735ca2240bf3e997de973fd071 Author: sstanley Date: Wed Apr 12 16:14:23 2000 +0000 Added a newline at the end to eliminate a warning message on mothra. Src/C_BaseLib/Utility.cpp commit 1fbd50443b55845db851d345f4e27528f5a3bf29 Author: sstanley Date: Thu Apr 6 17:05:39 2000 +0000 Changed some comments from // to /* */ since cpp on cobalt isn't stripping the // comments. Src/C_BaseLib/SPACE.H commit 075e18f56eb448f0de23d82d8a09398324a12bb4 Author: sstanley Date: Wed Apr 5 18:22:02 2000 +0000 Rewrote the nodal interpolation routines in 2-d and 3-d. This was done in order to make them give the same results for nodes which are periodically duplicated. The new interpolation does not give identical results to the old however the changes are extremely small (<1.0e-14). Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.cpp commit f282bc9a96fc5580d9b04f79c856732fe5c9f1e1 Author: sstanley Date: Tue Apr 4 18:28:59 2000 +0000 Changed the box definitions. Tools/C_util/ViewMF/viewMFdiffHardWire.cpp commit ef3b5b43de8f27727cacb4201103fd0ebad46fb5 Author: vince Date: Tue Apr 4 00:20:13 2000 +0000 Added a denormal fix option. Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp commit 185a90916847c0bf1622ab06b51e0b1b8ad54b9b Author: marc Date: Mon Apr 3 23:13:03 2000 +0000 ifdef out os stuff...see Utility.[H,cpp] Src/C_AMRLib/Amr.cpp commit 3bc827d18ad13b949228c68ca3dfd7cc190b118a Author: marc Date: Mon Apr 3 23:11:40 2000 +0000 ifdef out pid stuff for WIN32...there's probably a way to implement this, but it's low priority. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit ab992492c3e1503dd893f52eda2da9e275b5a904 Author: 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 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 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 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 Date: Mon Mar 27 20:06:07 2000 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgdebug.F commit fff5422e32ad009632a0f22b8137f0d65c970274 Author: lijewski Date: Mon Mar 27 16:26:13 2000 +0000 Added some copy constructors and copy assignment operators. Src/C_BoundaryLib/BoundCond.H Src/C_BoundaryLib/InterpBndryData.H commit 0ca56248cc2e76335d40be7ec8fe06fbf95e7388 Author: lijewski Date: Fri Mar 24 22:10:01 2000 +0000 Some mods for AuxBoundayrData ... Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit cfc544e0ab50402d21189081cbb20391d8407b53 Author: 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 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 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 Date: Thu Mar 23 21:39:06 2000 +0000 Turned off a couple things. Src/LinearSolvers/C_NodalMG/GNUmakefile commit ed4f5b615e985364d7ca0ccef78b26b17d955672 Author: lijewski Date: Thu Mar 23 21:38:27 2000 +0000 These are 3d test cases that are known to work with periodic bcs. Src/LinearSolvers/C_NodalMG/files.3d commit ef83e4f5fb2f6a9550c893c0e3d7033a58071ba4 Author: car Date: Thu Mar 23 21:16:59 2000 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/RegType.H Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 5c950afd4f8d5ca1d8d4fa19f35b94bfccbca7d2 Author: car Date: Wed Mar 22 21:10:11 2000 +0000 inflow bug fix: grow the srcbox Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 74d1d8cdced2e6e778d74084a41f3feb5554736b Author: lijewski Date: Wed Mar 22 15:51:45 2000 +0000 Some mods for g++ and cxx. Don't use -lm_sqrt with V4 OSF1 Tools/C_mk/Make.OSF1 commit db900b3622a1cfe3818fdb4246e9f45a009d8150 Author: 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 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 Date: Fri Mar 17 21:58:59 2000 +0000 k Src/LinearSolvers/C_NodalMG/hgdebug.F commit c105d321e7a567f455b8e27d7ccddc92952fbbe0 Author: car Date: Thu Mar 16 23:15:07 2000 +0000 Added BL_NAMESPACE support Tools/C_mk/Make.defs commit e9064ad02a1bcb7c99f22c4cc885520670db46c2 Author: 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 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 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 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 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 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 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 Date: Wed Mar 1 21:58:51 2000 +0000 Upped the precision in checkPoint(). Src/C_AMRLib/SlabStat.cpp commit 342fcf82cf3d27395f32718cff6d8def2661f091 Author: lijewski Date: Wed Mar 1 20:19:02 2000 +0000 More work getting SlabStats going. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/SlabStat.cpp commit 09f3631fc25c4e75e4b93de62fcc3ba9cd43f703 Author: lijewski Date: Wed Mar 1 15:43:34 2000 +0000 Stuff for checkPoint()ing SlabStat stuff Src/C_AMRLib/Amr.cpp Src/C_AMRLib/SlabStat.H Src/C_AMRLib/SlabStat.cpp commit 05e9477560a1ae935431c6d689acd477dc2a944d Author: lijewski Date: Wed Mar 1 15:43:03 2000 +0000 Defaulted another argument. Src/C_BaseLib/VisMF.H commit ed54762ea1f5d1c0e2c233a91b486707798831c3 Author: lijewski Date: Mon Feb 28 23:27:00 2000 +0000 Some mods for the statistics stuff ... Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 82cd39b725038910aa2053c79ccfb71b13b6634a Author: lijewski Date: Mon Feb 28 23:26:36 2000 +0000 Mods for some statistics stuff ... Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Make.package Src/C_AMRLib/SlabStat.H Src/C_AMRLib/SlabStat.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit db90940911dd2d04793b114578e03a37af333675 Author: sstanley Date: Fri Jan 28 01:14:05 2000 +0000 Modification to the doc++ stuff to make it work properly. Src/C_AMRLib/StateDescriptor.H commit 99c69312d60706098610b4abceb7dc6a5d708695 Author: vince Date: Mon Jan 10 23:55:15 2000 +0000 Added support for yukon (ARSC). Tools/C_mk/Make.defs commit c5d2fa7261f922124c2264b1bc280467d15bc6c1 Author: 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 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 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 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 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 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 Date: Wed Dec 1 16:37:24 1999 +0000 Shut up a warning on SGI ... Src/C_BoundaryLib/BoundCond.H commit 8e31696d339ce3c929576ad0ca3a57a03aa29829 Author: lijewski Date: Wed Dec 1 16:17:10 1999 +0000 Shut up a warning ... Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.H commit 079dbca7c1182cf7b0805d0d0fc2609009bacc8a Author: lijewski Date: Wed Dec 1 16:16:45 1999 +0000 Shut up warnings ... Src/C_BaseLib/BoxList.H Src/C_BaseLib/MultiFab.cpp commit 1b4ffb7fcec75008698513831d70378eb932c061 Author: lijewski Date: Sun Nov 28 19:48:51 1999 +0000 Don't try to read .profile Tools/C_scripts/compressor commit 896cd1e1f83cfcbd6afb028d7eaccd94e74fd047 Author: lijewski Date: Sun Nov 28 19:48:22 1999 +0000 Mod to fix bug on T3E Tools/C_scripts/compressor commit b9442eceb14157c1746e91d016b7d9fe25e1d843 Author: lijewski Date: Fri Nov 26 20:02:41 1999 +0000 Strip out any possible tar files. Tools/C_scripts/compressor commit bb4bfa388a42c423f3e00ff8951b5f3f663a3763 Author: lijewski Date: Sat Nov 20 19:41:38 1999 +0000 Direct error output of `ls' commands to /dev/null. Tools/C_scripts/compressor commit bd12e5e077580de9a2bf4e6d9882547830a64741 Author: lijewski Date: Sat Nov 20 00:09:12 1999 +0000 Beefed it up a bit so job chaining will work. Tools/C_scripts/compressor commit 802aadaa4eec261a2989edafa482647d83ca86ad Author: car Date: Thu Nov 18 22:19:43 1999 +0000 We think we fixed inflow on the high side of an idim. Src/LinearSolvers/C_NodalMG/boundary.cpp commit b8a7f653625276809d59433c77e51156bd53912d Author: 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 Date: Thu Nov 18 00:27:51 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit aa804eb4c739d97239bb6cb237d7fb46954a52c3 Author: car Date: Thu Nov 18 00:09:07 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/tests/gr.ann.1 Src/LinearSolvers/C_NodalMG/tests/gr.sstanley.1 Tests/LinearSolvers/C_NodalMG/test_grids/gr.ann.1 Tests/LinearSolvers/C_NodalMG/test_grids/gr.sstanley.1 commit 5abd2e6612fedd66d8535ca5bd04aff13c16dcc2 Author: lijewski Date: Fri Nov 12 21:37:54 1999 +0000 A ksh script to tar up and rm chk and plt directories. Mostly useful in batch scripts :-) Tools/C_scripts/compressor commit 8152fb10af5b5fe642c2b1cf98c7f612c35630fb Author: lijewski Date: Thu Nov 11 21:26:08 1999 +0000 Make the default for tar_and_rm_files to false, even on T3E ... Src/C_AMRLib/Amr.cpp commit 2187698c5953534ab99adcac5c4d0c94b31922d5 Author: propp Date: Wed Nov 3 16:33:25 1999 +0000 eliminated inlined function to make totalview happy Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 2dde6cf4d4a2fa4e1155c84e715992732522a6c4 Author: propp Date: Sat Oct 30 00:01:36 1999 +0000 moved static function to appease totalview Src/C_AMRLib/Amr.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 5fee1f8bbca752c4022f0f1f12ad898ac179181c Author: sstanley Date: Fri Oct 29 17:31:48 1999 +0000 Fixed a problem with the level used from the exact data. The old code is still intact. Tools/C_util/Convergence/DiffUniform.cpp commit 3339ee0e4fca84dfb439a6a620a66ff878fc1e02 Author: sstanley Date: Fri Oct 29 16:36:03 1999 +0000 Small modifications to DiffSameGrid.cpp (all documentation) and added the routine DiffSameGridRefined.cpp which does the same thing as DiffSameGrid.cpp but allows the two plotfiles to have different levels of refinement, as long as they have the same physical region refined. Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffSameGridRefined.cpp Tools/C_util/Convergence/GNUmakefile commit d0782c216b9ed3ef52f2b239e881940bbdb5813a Author: lijewski Date: Thu Oct 28 21:49:52 1999 +0000 When amr.tar_and_rm_files is true ... We now stagger deleting the ckfiles to support restart() and job chaining. Src/C_AMRLib/Amr.cpp commit 35a430931fb16e61d00ccaa9526e6372a3d6744d Author: vince Date: Wed Oct 27 21:24:40 1999 +0000 Moved a flag. Tools/C_mk/Make.T3E commit f8175b0a85867e5c14cba1b5053e8ccab5e77b5e Author: marc Date: Mon Oct 25 18:31:33 1999 +0000 Do explicit C-style caststo shut gcc up on my Linux box Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit 63d43bd126d580dea29e56c0689d66c0f6a2892d Author: 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 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 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 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 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 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 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 Date: Fri Oct 8 20:54:50 1999 +0000 added plotfile_on_restart option Src/C_AMRLib/Amr.cpp commit 0c1118de8b708494220111d1fd7442d946cc94d8 Author: sstanley Date: Thu Sep 30 15:55:12 1999 +0000 Minor change to doc++ stuff, but it seemed like a good time... Src/C_BaseLib/BoxArray.H commit 9d6dc43ca6d80bf07d960543d1988244fbf3c0b6 Author: lijewski Date: Thu Sep 30 14:56:19 1999 +0000 Removed cached MultiFabCopyDescriptor stuff ... Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit b02bf9e5c3c335c53a8112f7c00cc7647c5ce4b9 Author: 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 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 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 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 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 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 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 Date: Fri Sep 17 17:22:47 1999 +0000 tweak Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 2ef76af06a6eda4ef7c2f64227b2ec7c422ac852 Author: lijewski Date: Thu Sep 16 23:12:41 1999 +0000 Some mods to allow regridding at level 0 if max_grid_size changes. Src/C_AMRLib/Amr.cpp commit 4fe867dd39d882dc1d0202d56b0448f3a8bef39a Author: car Date: Wed Sep 15 16:58:32 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit 1b6529088ee98e29dec423a935befc7ebbae9aa2 Author: car Date: Tue Sep 14 18:26:56 1999 +0000 support for dense stencils is added Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi2d_full.F Src/LinearSolvers/C_NodalMG/hg_multi2d_terrain.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_full.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.H Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 352c1dc7e986a3c1ee627c6206e3fdd3747bf395 Author: lijewski Date: Fri Sep 10 21:07:30 1999 +0000 Added -qdpc to promote FP constants to double precision ... Tools/C_mk/Make.AIX commit a58c280f46a173ea246dd5ee5874517f8fcf9fa2 Author: 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 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 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 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 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 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 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 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 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 Date: Tue Aug 24 21:02:22 1999 +0000 Use new hfiles with KCC ... Tools/C_mk/Make.AIX commit 8d94aa25cc0a76a5be4e77a1c97e79c16bae61a1 Author: lijewski Date: Tue Aug 24 20:08:46 1999 +0000 Simplified some settings. Tools/C_mk/Make.AIX commit 6572319b9288c8489773948dad885b68cbd7d7ad Author: lijewski Date: Tue Aug 24 16:28:29 1999 +0000 Cleaned up the FillPatch stuff a tad more. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit c7bf6a9576a62e5bb2b9719a0326f7a49d71d4a8 Author: 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 Date: Mon Aug 23 21:16:49 1999 +0000 support for Geometry Src/LinearSolvers/C_NodalMG/inputs commit ae6c9ca046532e51eee3966977b0697af4ea3d97 Author: lijewski Date: Fri Aug 20 21:54:22 1999 +0000 Oops -- needed to define FillPatch::operator++() ... Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 90f6047d28de926b311f0980d31ac12255c082c8 Author: lijewski Date: Fri Aug 20 17:52:55 1999 +0000 Removed --no_restrict; Crays header files use it :-( Tools/C_mk/Make.T3E commit 7268f829d58f541f4818e89dbf6c107566d8805f Author: lijewski Date: Fri Aug 20 17:38:02 1999 +0000 Added --no_restrict Tools/C_mk/Make.T3E commit 05ae30bc0ac3d53c6486da44650ed977af1d314d Author: 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 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 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 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 Date: Wed Aug 11 19:52:05 1999 +0000 Added FOPTF+=-O for default case Tools/C_mk/Make.Linux commit 287493048f303bef45dc3b2cd800d47f89e07bc0 Author: marc Date: Tue Aug 10 00:12:42 1999 +0000 Generalize for prversion/parallel junk Tools/C_scripts/dsp.mak commit af60930bbbca3c51d36e5224b0030134fdca8cb0 Author: car Date: Mon Aug 9 16:44:41 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit 17a6b3dede33c235b64f9e31dddc76075af403ff Author: car Date: Fri Aug 6 23:10:05 1999 +0000 bndrylib is now needed Src/LinearSolvers/C_NodalMG/GNUmakefile commit dd8c4d29a6897f79e44a32e744fba45b53567438 Author: sstanley Date: Fri Aug 6 22:45:28 1999 +0000 Fix to BoxArray::contains(BoxArray ). Src/C_BaseLib/BoxArray.cpp commit 7379d6123cead861f671e0e1de6c42d1fdda149c Author: propp Date: Fri Aug 6 21:48:35 1999 +0000 deleted parmparse variable verbose, now must use parmparse variable v Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit 84dbffaae444602f2fc81f30a6b581c11d81c6c2 Author: propp Date: Fri Aug 6 18:20:16 1999 +0000 eliminated verbose ParmParse argument; it was being overwritten by v ParmParse argument Src/LinearSolvers/C_CellMG/CGSolver.cpp commit 0e22c47508422d5adaf8116806e92a6c68f9bbbd Author: almgren Date: Tue Aug 3 07:03:37 1999 +0000 Need to include bndrylib now because we're using a Geometry object. Src/LinearSolvers/C_NodalMG/GNUmakefile commit c25c2949730b5fd4b6b51929488923958961ff62 Author: almgren Date: Tue Aug 3 07:02:35 1999 +0000 A different paradigm for doing Sync_resid_fine - the previous way just wouldnt work for periodic in 3d. Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 39345ec178dc8788a03886f9049aed3005ec9c33 Author: propp Date: Tue Aug 3 00:37:24 1999 +0000 Fixed bug in FORT_APPLYBC where 1st component of bc array was used to determine bc type instead of the dir-th component of bc array. This change has already been made in the 2D version of the code. Src/LinearSolvers/C_TensorMG/DV_3D4.F Src/LinearSolvers/C_TensorMG/DV_3D4.mF commit c4f9a9b48ecdadf0ae17fa8b47f7b1c11f6f2c21 Author: almgren Date: Mon Aug 2 20:24:16 1999 +0000 Need to fill rhs_local periodically as well in fill_sync_reg. Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 1b73999462c5aeddcdea538abd3d2ebb4f9c9923 Author: sstanley Date: Mon Aug 2 19:22:16 1999 +0000 Minor changes in the location of the doc++ information. Put it after the forward declarations instead of before. Src/C_BaseLib/Box.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/MultiFab.H commit 8d7c1542cfbe87f1004e97971c80773f5a0080a6 Author: almgren Date: Sun Aug 1 15:11:44 1999 +0000 Changes in order to get periodic right. Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 085c7d251738bf147db320858a911009a0abc4d8 Author: 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 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 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 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 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 Date: Tue Jul 27 17:34:06 1999 +0000 Make physicalBndryTrpes available to Fortran Src/C_AMRLib/BC_TYPES.H commit 0385bbc21d4edf51415323a01ffaa76d1fca1e07 Author: lijewski Date: Mon Jul 26 16:59:42 1999 +0000 Updated a comment :-( Src/C_BaseLib/ParallelDescriptor.H commit d7ced55b981c9875bfab74adfa80b04e1d88eb78 Author: almgren Date: Fri Jul 23 23:56:13 1999 +0000 Made a bunch of changes having to do with how the sync register stuff is computed. In this new version, the contributions to the sync registers are computed in hgproj, not in SyncRegister... Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 99a523be56448807a55a62f76744350225832fc1 Author: car Date: Fri Jul 23 21:29:13 1999 +0000 test case for inflow bust Src/LinearSolvers/C_NodalMG/tests/gr2.inf Tests/LinearSolvers/C_NodalMG/test_grids/gr2.inf commit 37ab5cd15d9b977fd70b868c53191a3ce6fb1a10 Author: 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 Date: Fri Jul 23 21:28:00 1999 +0000 fix for array bounds bust Src/LinearSolvers/C_NodalMG/boundary.cpp commit 1175c5dde1bd9a208a328e6c2d3a78b3a8620dff Author: car Date: Fri Jul 23 17:56:40 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit b9d5aa0f3178c105f8b751e272d09472f29848c9 Author: sstanley Date: Wed Jul 21 21:09:20 1999 +0000 Modified the location of the call to manual_tags_placement(). Src/C_AMRLib/Amr.cpp commit 940436807b005c4a6b62f40dc0d0029ef2712ccf Author: lijewski Date: Wed Jul 21 21:07:38 1999 +0000 Output CArena stats ... Src/LinearSolvers/C_NodalMG/proj.cpp commit 7b7995f45f15e1a2a26ab5bb2c3d5de363935899 Author: lijewski Date: Wed Jul 21 21:06:08 1999 +0000 Oops -- forgot to remove a commented out #if Src/C_BaseLib/CArena.cpp commit 427dd1774924ee043a5a258b1d0621465d59c6ce Author: lijewski Date: Wed Jul 21 21:02:49 1999 +0000 Added heap_space_used(). Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp commit a123cce9e549467fb7003813e0b3e8eb225e3873 Author: lijewski Date: Wed Jul 21 21:02:40 1999 +0000 Added extra newline to an output message for additional separation ... Src/C_BaseLib/RunStats.cpp commit cbdb16f824aa372a663cb64b90b9d7000642da32 Author: lijewski Date: Wed Jul 21 17:26:08 1999 +0000 Removed commented out line ... Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 6175dd27fa7f655896b3232e64de1a6a7c193c18 Author: lijewski Date: Wed Jul 21 17:20:34 1999 +0000 Got memory mods working with periodic. Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 6624dfe32d317b0348e25317813c058b28615777 Author: lijewski Date: Wed Jul 21 15:28:00 1999 +0000 Some mods to minimize communication when in parallel. Src/LinearSolvers/C_NodalMG/restrictor.cpp commit e8573b9fb11b5dbea4adea3edd09f808c50165c8 Author: lijewski Date: Tue Jul 20 23:45:02 1999 +0000 The restrict_level stuff wan't quite right ... Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 8bb5238628b51e60b4cc30fa9016603a30e0566c Author: almgren Date: Tue Jul 20 20:42:13 1999 +0000 Added manual_tags_placement which will replace manual_grid_placement. It is only virtual here, to be defined in applications. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H commit 7a3313c6a3b74b66f1eb79e056474797bfc5cd7f Author: lijewski Date: Tue Jul 20 17:13:59 1999 +0000 Slight mod of what I checked in yesterday. Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 5f9df0de7d34a4a9fb1ce96dce917585ed898ca7 Author: lijewski Date: Tue Jul 20 15:45:04 1999 +0000 Made restrict_level() more memory efficient in parallel. Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 5a71b010bf48cccadb84971acc30d3183d63f88d Author: lijewski Date: Mon Jul 19 23:05:06 1999 +0000 Added some statistics to track parallel data transfer. FillPatch routines now transfer less data in parallel. Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 58dc566e89193d5b3099c8577224ae481e23a06a Author: almgren Date: Mon Jul 19 19:54:24 1999 +0000 Fixed code for r-z with 5-point stencil, also removed some routines which weren't being used. Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit e6e4cd1fe4e58d569a6285b92f5f87e7602357c2 Author: propp Date: Mon Jul 19 17:40:48 1999 +0000 added 3d fortran routines... Tools/C_util/Convergence/AVGDOWN_3D.F Tools/C_util/Convergence/Make.package commit 67482dd53b9f8b3847f28d6ccca6d73d15bcfe92 Author: sstanley Date: Fri Jul 16 18:23:49 1999 +0000 Increased the precision at which the Header in plotfiles and checkpoint files gets written. We were losing precision in the timestep. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/StationData.cpp Tools/C_util/WritePlotFile.cpp commit cbad680fb7b5a8fe0aa422bb55a9837bc0cb4591 Author: almgren Date: Fri Jul 16 17:14:46 1999 +0000 Fix in hgcdiv to correctly do 5-point stencil at r=0 (for r-z only!). Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 1aeb22504c752b1ff8a9718f1a0c549d1bffaab2 Author: lijewski Date: Thu Jul 15 17:07:04 1999 +0000 Got rid of all those computeBoxLen() calls. Now only call it when length() is called. Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit b0f2dab58130a1e27467df446432fa1034740b4b Author: 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 Date: Wed Jul 14 23:06:15 1999 +0000 Did copy constructor correctly. Src/C_BaseLib/Geometry.cpp commit 2848911cdfca739d7e9d7db5552f44309a364c41 Author: lijewski Date: Wed Jul 14 19:20:44 1999 +0000 Added malloc_stats(0) call for BL_T3E in OutOfMemory(). Src/C_BaseLib/Utility.cpp commit 5715ddd56a2cb141c28ad272aa3a7cedff4c6cbb Author: marc Date: Tue Jul 13 01:30:48 1999 +0000 Fix a few little problems...still work-in-progress Tools/C_scripts/dsp.mak commit 00a77cd7c3a034d068c1e50212d4438f4d9ce258 Author: lijewski Date: Mon Jul 12 16:42:11 1999 +0000 Fix for periodic-nonperiodic boundary cells. Also moved more heap-based stuff into FillPatchIterator data member area. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 1d714d8fde0e59f91917197daa138750fa306fdd Author: car Date: Wed Jul 7 22:48:33 1999 +0000 MPI type safety Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/ccse-mpi.H commit 4af45f42abd2696dc704c0a336df3ef6d78c92ce Author: almgren Date: Wed Jul 7 21:45:12 1999 +0000 IsRZ() only exists if BL_SPACEDIM == 2. Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit f42d05541b369b027e5faeaf80d784a516527de7 Author: almgren Date: Wed Jul 7 18:30:43 1999 +0000 IsRZ() is only defined in 2-d Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit e6583456a216291beb56d44444565fbfc481298a Author: almgren Date: Thu Jul 1 23:18:31 1999 +0000 Modifications to correct the 5-point stencil in r-z at r=0. Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_proj2d.F commit 0b5afd0c298ea89568e7661252fdcb0de39f1f60 Author: lijewski Date: Thu Jul 1 20:12:24 1999 +0000 Changed how RunStats stuff was done ... Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit af7a48d174f6b9a2b0702debcec1adfe9e5d2b88 Author: lijewski Date: Thu Jul 1 19:44:49 1999 +0000 Added ReduceIt() to fix bug with how the List is reduce()d. Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp commit d244437c2521900c7ee2849375fd3b0fa16716f4 Author: 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 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 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 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 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 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 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 Date: Thu Jun 24 22:09:47 1999 +0000 Bone headed IntVect usage Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 2b4aa326408155a0800ece339b36090cdc1db99d Author: marc Date: Thu Jun 24 21:21:55 1999 +0000 Oops! src was written as rc... Src/LinearSolvers/C_NodalMG/hg_avg2d.F commit 1e81f608e8fed61141354b1d902604cca7c73dfc Author: car Date: Wed Jun 23 17:59:40 1999 +0000 changes to support KCC 3.4 Src/C_BaseLib/VisMF.H Tools/C_mk/Make.defs commit 94aa9fea94d25fa296153b4a74335c894a966502 Author: lijewski Date: Tue Jun 22 20:06:43 1999 +0000 Redid how HG RunStats are setup to work around RunStats bug. Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 9bf486f75d3af50efe414648b8805a7ae2bf08f0 Author: 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 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 Date: Fri Jun 18 16:01:57 1999 +0000 Some cleanup. Src/C_BaseLib/Geometry.cpp commit 6d3d2bc4664ae760862f74de138de73cbdbb4e84 Author: almgren Date: Wed Jun 16 22:51:16 1999 +0000 The extra terms for r-z should only be used with the 9-point stencil. Src/LinearSolvers/C_NodalMG/hg_avg2d.F commit f6153de4923242cc3a4aae4458315ba549b75b9d Author: lijewski Date: Wed Jun 16 22:13:03 1999 +0000 Removed some dead code. Src/C_BaseLib/RunStats.cpp commit ddcd7450218dd7021bc8ba09a4e0e98b8f528a72 Author: car Date: Mon Jun 14 17:07:26 1999 +0000 defused loop Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 4fb6699fa567c11d96812c69a107a15b4e117555 Author: marc Date: Sat Jun 12 00:10:14 1999 +0000 First cut at a script to make MSVC project input file. Tools/C_scripts/dsp.mak commit 54b1a15785f6a07bdd0deb40ce8c0ef790690424 Author: almgren Date: Wed Jun 9 18:25:35 1999 +0000 We don't want to use the additional rz terms for the five-point stencil. These terms *should* be included for the nine-point stencil only. Src/LinearSolvers/C_NodalMG/hg_proj2d.F commit 749ace3c9a45f23f6d16c382b45f1ee9f0b12159 Author: car Date: Tue Jun 8 14:39:54 1999 +0000 *** empty log message *** Tools/C_mk/Make.mpi commit 190c9d8a05d5eea029a6bf606f0d69b20c4f7c17 Author: marc Date: Tue Jun 8 00:57:37 1999 +0000 Hack a little more on the derive_plot_vars junk. Src/C_AMRLib/Amr.cpp commit 87b2282ad53ac294d6011e4184a9b34a17a6fb3a Author: marc Date: Mon Jun 7 20:57:38 1999 +0000 Remove rz assertion Src/LinearSolvers/C_NodalMG/amr_multi.H commit 4b520cb87e7e7a9886fde687c2314538d99ec126 Author: car Date: Sun Jun 6 19:07:42 1999 +0000 *** empty log message *** Tools/C_mk/Make.Linux commit ac3f683be06453a96cd6a7386fc71f595fbed368 Author: sstanley Date: Fri Jun 4 17:03:52 1999 +0000 Changes to make it work properly in parallel. Tools/C_util/Convergence/DiffSameGrid.cpp commit 1e70bc2ecad3499bd5551aca7b4272d6f6410df8 Author: sstanley Date: Fri Jun 4 01:03:25 1999 +0000 Modification to make it work on the T3E. Tools/C_util/Convergence/GNUmakefile commit bbaa614cf87692046362f8d898f8c34eb9a78d5b Author: sstanley Date: Thu Jun 3 23:38:43 1999 +0000 Converted to allow building in place. Also removed nProc from ParallelDescriptor::StartParallel() call. Tools/C_util/Convergence/GNUmakefile Tools/C_util/Convergence/PltFileNorm.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp commit ca85091137aeadd821e1029db7537c91c02fece1 Author: lijewski Date: Thu Jun 3 22:57:14 1999 +0000 Changed way MPI message tags are calculated. Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit c91bd3dc783b4dc62d4439e4fa7bb2fcd3e5c486 Author: lijewski Date: Wed Jun 2 20:09:00 1999 +0000 Don't add MPI_HOME/include to INCLUDE_LOCATIONS if MPI_HOME is null Tools/C_mk/Make.mpi commit b549c7163e84148f33e622429e9ae6f1fa406736 Author: 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 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 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 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 Date: Tue May 25 23:09:02 1999 +0000 Fix include for WIN32 Src/C_BaseLib/CoordSys.cpp commit d02b9a2f5793573a88c05460ce520d34b4688dc3 Author: lijewski Date: Tue May 25 22:02:20 1999 +0000 small bug fix ... Src/C_BaseLib/FArrayBox.cpp commit 93f07f042b4a599cae4c370a660f423a04b63a80 Author: car Date: Mon May 24 18:11:44 1999 +0000 Makefile system now MPI aware Src/C_AMRLib/GNUmakefile Src/C_BaseLib/GNUmakefile Src/C_BoundaryLib/GNUmakefile Src/LinearSolvers/C_CellMG/GNUmakefile Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_TensorMG/GNUmakefile Tools/C_mk/Make.defs Tools/C_util/Convergence/GNUmakefile Tools/C_util/ViewMF/GNUmakefile commit 680293170af6837d9f6c60290771642101577544 Author: car Date: Mon May 24 17:51:57 1999 +0000 mpi support Tools/C_mk/Make.Linux Tools/C_mk/Make.OSF1 Tools/C_mk/Make.defs Tools/C_mk/Make.mpi commit ec6c3a95d7f3489c56c314b718756e7130510e1a Author: lijewski Date: Tue May 11 17:42:59 1999 +0000 Got rid of remove(int) and clear(int) -- they're weren't parallel safe. Src/C_BaseLib/FabArray.H commit 865cc988f6b6695b92f4dd437e07d0dbc41a0dc2 Author: car Date: Mon May 10 21:32:52 1999 +0000 tune for absoft, g77 Tools/C_mk/Make.Linux commit 3e81b537891d329618bd0b2787b3c163aba8c6b3 Author: car Date: Mon May 10 21:26:31 1999 +0000 tune for absoft, g77 Tools/C_mk/Make.Linux commit 48267356f3e0676ee1a0c4c622e5d3d8dd254c79 Author: car Date: Mon May 10 21:25:32 1999 +0000 Added LOWERCASE Fortran Types Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 375320a8cca7c1c271a415afc5213f8b21097323 Author: lijewski Date: Mon May 10 20:44:50 1999 +0000 DBL_MIN -> -DBL_MAX and likewise for FLT_??? Src/C_BaseLib/MultiFab.cpp commit cecf9555c742079a438dbc347512f5a45e6ecb68 Author: marc Date: Mon May 10 20:31:14 1999 +0000 Move logical reset inside loop to behave correctly. Src/C_AMRLib/Amr.cpp commit 183cca625a6e1c59eb0575c33e1a82055b6bcb4a Author: car Date: Mon May 10 18:54:07 1999 +0000 BLassert -->> BL_ASSERT. Good luck typing it. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/BCRec.cpp Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/DatasetClient.cpp Src/C_AMRLib/Derive.cpp Src/C_AMRLib/ErrorList.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp Src/C_AMRLib/StationData.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/Array.H Src/C_BaseLib/BLassert.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/List.H Src/C_BaseLib/Looping.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/NormedFab.H Src/C_BaseLib/Orientation.H Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Pointers.H Src/C_BaseLib/RealBox.H Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/Specialize.cpp Src/C_BaseLib/Tuple.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp Src/C_BaseLib/test/tCArena.cpp Src/C_BaseLib/test/tFAC.cpp Src/C_BaseLib/test/tFB.cpp Src/C_BaseLib/test/tVisMF.cpp Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/BoundCond.H Src/C_BoundaryLib/FabSet.cpp Src/C_BoundaryLib/InterpBndryData.cpp Src/C_BoundaryLib/Mask.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.cpp Tests/C_BaseLib/tCArena.cpp Tests/C_BaseLib/tFAC.cpp Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tVisMF.cpp Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffPlot.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/ViewMF/MFNorm.cpp Tools/C_util/ViewMF/viewMFdiff.cpp commit 91d741305621d8aa66980578b66b326c18f0d8b3 Author: car Date: Mon May 10 17:18:27 1999 +0000 Replace all asserts with BLassert. Replace all #include Assert.H with #include BLassert.H This avoids incompatiblities on systems which insist on using the system assert in their library header files. Assert.H will be removed soon. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/BCRec.cpp Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/DatasetClient.cpp Src/C_AMRLib/Derive.cpp Src/C_AMRLib/ErrorList.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp Src/C_AMRLib/StationData.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/Array.H Src/C_BaseLib/Assert.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/List.H Src/C_BaseLib/Looping.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/NormedFab.H Src/C_BaseLib/Orientation.H Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Pointers.H Src/C_BaseLib/RealBox.H Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/Specialize.cpp Src/C_BaseLib/Tuple.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp Src/C_BaseLib/test/tCArena.cpp Src/C_BaseLib/test/tFAC.cpp Src/C_BaseLib/test/tFB.cpp Src/C_BaseLib/test/tVisMF.cpp Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/BoundCond.H Src/C_BoundaryLib/FabSet.cpp Src/C_BoundaryLib/InterpBndryData.cpp Src/C_BoundaryLib/Mask.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.cpp Tests/C_BaseLib/tCArena.cpp Tests/C_BaseLib/tFAC.cpp Tests/C_BaseLib/tFB.cpp Tests/C_BaseLib/tVisMF.cpp Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp Tools/C_mk/Make.Linux Tools/C_util/Convergence/DiffFab.cpp Tools/C_util/Convergence/DiffPlot.cpp Tools/C_util/Convergence/DiffSameGrid.cpp Tools/C_util/Convergence/DiffUniform.cpp Tools/C_util/Convergence/PltFileScalConvRate.cpp Tools/C_util/ViewMF/MFNorm.cpp Tools/C_util/ViewMF/viewMFdiff.cpp commit d2593cabeb7e1e6aca63c8a61cc7e867d87c2d85 Author: marc Date: Fri May 7 20:39:40 1999 +0000 Add manual grid placement function in grid_places routine for hacking with grid distributions during regrid operation. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H commit 9332cb1d75799da5b2255c383c7aaf8c9272a4b1 Author: lijewski Date: Fri May 7 15:36:56 1999 +0000 We now output list of unused variables on final destructor call. Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp commit b144514c4e4c42cc4cd6f9fc8842c8f4c1e57fb9 Author: car Date: Thu May 6 16:57:28 1999 +0000 Allows quiet_nans even when running ndebug Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp commit e0bfa7e6c661509f626279637f1bffc4d33c2bb4 Author: lijewski Date: Thu May 6 16:31:41 1999 +0000 Hack to work around array bounds error ... Src/LinearSolvers/C_NodalMG/boundary.cpp commit 85b36e25f94dd6db6b654b27b59d2d03089a8fde Author: car Date: Tue May 4 17:59:06 1999 +0000 assertion for intersection of src,dest boxes Src/LinearSolvers/C_NodalMG/boundary.cpp commit 672aa4affe33a69e8d6fae2b2dfcf84a2c5e0fc4 Author: car Date: Tue May 4 17:58:59 1999 +0000 ofstream truncate??? Src/LinearSolvers/C_NodalMG/proj.cpp commit 4918d2a0689b941ddfc63e83e4a3285f329ae28d Author: lijewski Date: Tue May 4 17:54:22 1999 +0000 periodic in x & z and refWall in y Src/LinearSolvers/C_NodalMG/proj.cpp commit dff88d99716d60e60e5c7af4cea270c3385b6636 Author: car Date: Mon May 3 21:32:00 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/tests/gt.jbb.1 Tests/LinearSolvers/C_NodalMG/test_grids/gt.jbb.1 commit a48ce8bab13d7269619327a42da0ce9da495a8fb Author: lijewski Date: Thu Apr 29 20:41:45 1999 +0000 Now properly call constructor and destructor of T. Src/C_BaseLib/BaseFab.H commit 7f2a6ff234b5d2447e70e97ffbaeb27d93246c11 Author: car Date: Wed Apr 28 15:41:52 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit e35ff1504500d3811d4485feb13424bf0f6e5e63 Author: car Date: Wed Apr 28 00:01:26 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/tests/gt.scott.1 Tests/LinearSolvers/C_NodalMG/test_grids/gt.scott.1 commit fee187bb51b0042558e6570b6a3598f65d3c5fe9 Author: lijewski Date: Tue Apr 27 21:38:04 1999 +0000 Removed BoxAssoc ... Src/C_BaseLib/BoxAssoc.H Src/C_BaseLib/BoxAssoc.cpp Src/C_BaseLib/Make.package commit b95331a3184a073b2e09276851d62208f19e1474 Author: lijewski Date: Tue Apr 27 18:24:45 1999 +0000 Made proj_project() a static member function. Added hack to add back in level 0 procmap after regrid at level 0. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit f2f0e7600713fe69a614c1a0c23ea506d1f7102f Author: lijewski Date: Mon Apr 26 20:09:56 1999 +0000 Removed MaxSizeBox() -- it's now BoxList::maxSize(const IntVect&). Src/C_AMRLib/Amr.cpp commit e76527e0fcc4ba7097a129676f639403cf3f3e5e Author: lijewski Date: Mon Apr 26 20:09:22 1999 +0000 SpaceDim -> BL_SPACEDIM. Src/C_BaseLib/IndexType.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/Looping.H Src/C_BaseLib/Orientation.H commit d2226550ad8e636961cad6186795c99703e8c205 Author: lijewski Date: Mon Apr 26 20:09:11 1999 +0000 Added maxSize(const IntVect&); maxSize(int) calls it. Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit 2d1994db58454ac7eab9fc43892b1b8c56383f4c Author: lijewski Date: Fri Apr 23 18:42:26 1999 +0000 Removed the BoxList data member from FillBoxId -- wasn't used. Src/C_BaseLib/FabArray.H commit 956e6dc7c9f781ab7e925779aa248bd1a2751659 Author: 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 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 Date: Thu Apr 22 17:13:19 1999 +0000 YAAF: yet another access function. Src/C_AMRLib/Amr.H commit 008eba6bb349a379d4676c3c16a1116ffed7c0ae Author: sstanley Date: Tue Apr 20 23:54:55 1999 +0000 Fixed a 3-d bug in compFlux. yflux was passed into the fortran instead of zflux. Src/LinearSolvers/C_TensorMG/DivVis.cpp commit 9af4860e40088f7e8048b5d45113e122e4567207 Author: car Date: Tue Apr 20 01:26:16 1999 +0000 added BLassert.H, will remove Assert.H later Src/C_BaseLib/BLassert.H Src/C_BaseLib/Make.package commit 16c62036d421cd18cf32a8b8b5d64c8a4c8bb994 Author: lijewski Date: Mon Apr 19 23:17:03 1999 +0000 Some mods to CollectData() ... Src/C_BaseLib/FabArray.H commit e02f36f4ee84405e825eb5f957819eeefc18b783 Author: 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 Date: Fri Apr 16 19:19:48 1999 +0000 tune ev5 -> tune host Tools/C_mk/Make.OSF1 commit 17d7e8093a65a4757a71e61954fc741ac5f40f18 Author: propp Date: Fri Apr 16 18:17:55 1999 +0000 added -C and -u flags for debugging on mothra. Note that -u only produces a warning for undeclared variables Tools/C_mk/Make.OSF1 commit 891aa7763e0070d7627e0f75f935e06379d89c40 Author: lijewski Date: Fri Apr 16 17:38:06 1999 +0000 Reverting out random_shuffle() stuff -- not a big win. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/DistributionMapping.cpp commit da8e89ac15866d5531b7e672210a30f345462798 Author: lijewski Date: Fri Apr 16 00:19:05 1999 +0000 Didn't get the optimization options quite right. Tools/C_mk/Make.T3E commit f11d44fe599e60edbec14d663fd074ca3c6ecc07 Author: lijewski Date: Fri Apr 16 00:09:23 1999 +0000 More CXXOPTF options for backend C compiler with KCC. Tools/C_mk/Make.T3E commit 3be33f442829a0928eb91a41e25b960daf9b9d97 Author: lijewski Date: Thu Apr 15 23:29:12 1999 +0000 Updated to make random_shuffle() stuff in knapsack work. Src/C_AMRLib/Amr.cpp commit 0b32824a7c523abce3962d8ae529fa344957c5c9 Author: 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 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 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 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 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 Date: Tue Apr 13 00:09:14 1999 +0000 Modest simplification of FabArray -> FabArray copy(). Src/C_BaseLib/FabArray.H commit 97d34c4f5fddc3fde698acdc3d1a96894ae2b7ea Author: marc Date: Tue Apr 13 00:09:11 1999 +0000 Remove ProxyGeometry class, in favor of "explicit" modifier to Geometry ctr preventing auto-type-conversion Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp commit f7b906b717b067b76404d86306294ebc153ee2a8 Author: marc Date: Tue Apr 13 00:08:05 1999 +0000 Prohibit auto-type-conversion from box to Geometry, enable removal of ProxyGeometry class. Src/C_BaseLib/Geometry.H commit e40ca7b62c2adc648725205ac62f4513197525f8 Author: lijewski Date: Mon Apr 12 20:31:47 1999 +0000 Added additional assert() in ::Copy(). Src/C_BaseLib/MultiFab.cpp commit 3cb3de4157354bc366aea8b181236046f4776263 Author: lijewski Date: Sun Apr 11 23:31:22 1999 +0000 Added truesize data member to make resize() really work as expected. Also inlined some more stuff. Src/C_BaseLib/BaseFab.H commit 80ec22b162692f01a05c343cc8d91698dedc17ec Author: lijewski Date: Sun Apr 11 23:30:47 1999 +0000 Simplified FabArray -> FArrayBox copy(). Src/C_BaseLib/FabArray.H commit a3d96dade2ede2b0aa240e0f6cf9e256c411d768 Author: lijewski Date: Sun Apr 11 23:30:26 1999 +0000 Inlined some more stuff. Removed unnecessary new of length 1 in default constructor. Src/C_BaseLib/Array.H commit 4d3c2612d4260d7585c2a305bcdcc6f42092e466 Author: lijewski Date: Sun Apr 11 23:29:58 1999 +0000 Inlined some more stuff. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BoundaryLib/FabSet.cpp commit 2889ea36e38fed4cd9fbfa93f2db6f384bd94ada Author: car Date: Thu Apr 8 21:00:56 1999 +0000 rename hgparallel.h --> hgparallel.H Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/hgparallel.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit b36a235cce7994660b4ccd6c7f407d4b42d2d99f Author: lijewski Date: Thu Apr 8 20:52:11 1999 +0000 Fixed problem with INFINITY macro being redefined on Suns. Src/C_BaseLib/MultiFab.cpp commit d891e2051ec60eb1e7a96bf2c39ce7e5ea8ad5f5 Author: lijewski Date: Thu Apr 8 20:22:43 1999 +0000 Also now cache FasSet/MultiFab BoxArray intersection junk. Src/C_BoundaryLib/FabSet.cpp commit 58c695d4bb3e726e4d17cc0473b355bcc51989c9 Author: marc Date: Thu Apr 8 17:49:12 1999 +0000 Remove unnecessary copy-on-intersect when loading boundary data objects Src/C_BoundaryLib/InterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp commit 26d7d4c6a32aef5c9766e617c5f1d9da22f53f3a Author: lijewski Date: Thu Apr 8 17:01:45 1999 +0000 Fixed latent bug in plusFrom() Src/C_BoundaryLib/FabSet.cpp commit e140fe84ec172156b124f8e1bcdf95d3f15ba993 Author: lijewski Date: Wed Apr 7 17:11:45 1999 +0000 Devirtualized task_fab::fab() and inlined it as well. Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 9cc4f5c84a0415e28bca04746bafe6a1d3e5afe2 Author: lijewski Date: Tue Apr 6 18:15:59 1999 +0000 Some cleanup. Src/C_BaseLib/Array.H commit 9320d63c06e74dd08d992b2c375a2716447fcda5 Author: lijewski Date: Tue Apr 6 16:53:37 1999 +0000 Added -M 1110 to FC Tools/C_mk/Make.T3E commit 669e03b1cae6a569ed4a53358dc81ea96bc696a0 Author: lijewski Date: Tue Apr 6 16:41:18 1999 +0000 Ignore additional warning 7212 Tools/C_mk/Make.T3E commit 67a9f87b07f096ac46ee125bbe05002b72712f72 Author: car Date: Mon Apr 5 17:39:20 1999 +0000 BL_AIX --> BL_FORT_USE_LOWERCASE, where appropriate. Makefile tweaks in pAmrvis and DataServices. Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/MAKESLICE_F.H Src/C_AMRLib/PROB_AMR_F.H Src/C_BaseLib/COORDSYS_F.H Src/LinearSolvers/C_NodalMG/GNUmakefile Tools/C_mk/Make.AIX commit 9b9a3c5bbecb23fd86e59fba2ea12602372e94ae Author: car Date: Mon Apr 5 16:49:25 1999 +0000 fix non-inplace compile Src/LinearSolvers/C_TensorMG/Make.package commit 445852ec513aa6cb8436fdb568555b325f7878dd Author: sstanley Date: Fri Apr 2 20:47:23 1999 +0000 Added a -r in one of the $(RM) lines under clean: to allow removing a directory. Thsi didn't work properly on the T3E. Tools/C_mk/Make.rules commit 14eea6d1d47f9ca47e9b592fa986674cb8b7bb78 Author: lijewski Date: Thu Apr 1 23:52:55 1999 +0000 A special FORTPREP for T3E ... Tools/C_mk/Make.T3E commit 0104d8c5cb0499d098429666de5b1ca6baf024a9 Author: lijewski Date: Thu Apr 1 22:31:01 1999 +0000 Fixed bug in FabArray::copy(FabArray). I had a improperly nested parallel loop :-( Src/C_BaseLib/FabArray.H commit e3c2cd07861c61b9ba120064d6b6fc9281629660 Author: car Date: Thu Apr 1 21:43:10 1999 +0000 harmless, I think, makefile thrashing Src/C_AMRLib/Make.package Src/LinearSolvers/C_CellMG/Make.package Src/LinearSolvers/C_TensorMG/Make.package commit 63114453f953f3395161c6fd70336bb610cc54d7 Author: car Date: Thu Apr 1 21:42:49 1999 +0000 FORT_FLUX added Src/LinearSolvers/C_CellMG/LP_F.H commit 744636e36353492cf112e0ac17bcf514e107cc7a Author: car Date: Thu Apr 1 16:57:48 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile commit 513648693bdd9e1e32afde892a2f29966a4c70d1 Author: car Date: Wed Mar 31 22:52:27 1999 +0000 Linux updates Src/C_AMRLib/GNUmakefile Src/C_BaseLib/GNUmakefile Src/C_BoundaryLib/GNUmakefile Src/LinearSolvers/C_CellMG/GNUmakefile Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_TensorMG/GNUmakefile commit 732981adce80ec23f7154206b930b31bbdc34be2 Author: car Date: Wed Mar 31 18:19:37 1999 +0000 linux changes Src/C_AMRLib/GNUmakefile Src/C_BaseLib/GNUmakefile Src/C_BoundaryLib/GNUmakefile Src/LinearSolvers/C_CellMG/GNUmakefile Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_TensorMG/GNUmakefile Tools/C_mk/Make.Linux commit 3197e5acd7a1c78758d4648992ae812d7828dd01 Author: lijewski Date: Wed Mar 31 18:19:03 1999 +0000 Turn off message warning 1135 Tools/C_mk/Make.T3E commit fea4352137e74279a70fd1b517eeb5fcb59662ae Author: lijewski Date: Wed Mar 31 17:04:48 1999 +0000 Now also call FabSet::FlushCache() to clear some cached CollectData() stuff. Src/C_AMRLib/Amr.cpp commit 966059b05e50352680296285480715be7185c975 Author: lijewski Date: Wed Mar 31 17:04:17 1999 +0000 FabSets now cache some CollectData() stuff. Now use CommDataCache for the cache in question. Src/C_BaseLib/Geometry.H Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 9f410ead16efe66dd402c734a4ba8030568bbdfc Author: lijewski Date: Wed Mar 31 17:03:47 1999 +0000 Fixed deadlock I introduced in CollectData(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp commit 41ee92f803015a26b1ed2687a3e19cce133e4ea4 Author: car Date: Tue Mar 30 00:54:06 1999 +0000 New defines for linux Src/C_BaseLib/FPC.cpp commit 03396ad20ff9f08cf599c80f2375b4cfc8ce1909 Author: 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 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 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 Date: Mon Mar 29 19:27:52 1999 +0000 Yet another bug fix to CollectNumPts(). Src/C_BaseLib/RunStats.cpp commit 218078d3758d9801c8be72bf52769a995c2dcd68 Author: lijewski Date: Sat Mar 27 01:00:58 1999 +0000 Mods to cache some CommData stuff in CollectData(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.cpp commit 4fa7dc71f662ab3b390079d01e5d0149c8c28dc2 Author: lijewski Date: Sat Mar 27 01:00:23 1999 +0000 Added operator<<() for CommData. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 2e7be105cbcbcce66f9665b0546f965e51f3dc1d Author: lijewski Date: Fri Mar 26 19:19:34 1999 +0000 Added operator==() and operator!=() for CommData. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit d7226d499140cad4ad062bac659a17058f8a52ac Author: 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Fri Mar 12 02:55:26 1999 +0000 Some cleanup and simplification. Src/C_BaseLib/MultiFab.cpp commit 887023bc158e574e2fc7421e150976d35c45f7c0 Author: lijewski Date: Fri Mar 12 01:09:24 1999 +0000 Mod for T3E. Src/C_BaseLib/Utility.cpp commit 01967220f81a4a98df3caa440f8bcc3ba4060b5a Author: 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 Date: Wed Feb 17 21:44:17 1999 +0000 Added Lp.alternateApplyBC flag. Src/LinearSolvers/C_CellMG/LinOp.cpp commit 0cbaed4792b8ef146f53e27823747ea0af1a532e Author: lijewski Date: Wed Feb 17 00:10:35 1999 +0000 Explicitly turn off exceptions. Tools/C_mk/Make.T3E commit 8a3b6950cf3a7c8dbfc5b6e25330d9816a9f0745 Author: lijewski Date: Fri Feb 12 00:07:05 1999 +0000 +K2 -> +K3 when COMP=KCC Tools/C_mk/Make.T3E commit 6a159f8af4b128c851ec486188a5cd225648a21d Author: marc Date: Thu Feb 11 18:07:23 1999 +0000 Modernize driver Src/LinearSolvers/C_TensorMG/Test/GNUmakefile Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/C_TensorMG/testVI.cpp commit b90606a24dd6590856431a1c85b1e81000f5be69 Author: marc Date: Thu Feb 11 18:06:59 1999 +0000 Remove area multiplies in compFlux fortran. Extensive fluxes obtained by setting transport coefficient to include local areas. Fix up Mma and fortran manually. Src/LinearSolvers/C_TensorMG/DV_2D.F Src/LinearSolvers/C_TensorMG/DV_2D.mF Src/LinearSolvers/C_TensorMG/DV_3D2.F Src/LinearSolvers/C_TensorMG/DV_3D2.mF commit ea1bc03c8cb1574b7153cea5459159460d644a00 Author: car Date: Thu Feb 11 17:07:01 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile commit 734711a54d390191d801b67a3ab1c1897aa30d69 Author: lijewski Date: Wed Feb 10 21:09:44 1999 +0000 Boolean.H has been removed from Parallel BoxLib. Src/C_BaseLib/Array.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Boolean.H Src/C_BaseLib/Box.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxAssoc.H Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/CArena.H Src/C_BaseLib/FabArray.H Src/C_BaseLib/IndexType.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/List.H Src/C_BaseLib/Make.package Src/C_BaseLib/Orientation.H Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParmParse.H Src/C_BaseLib/Pointers.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.H Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_TensorMG/DivVis.H Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.H commit 47a76350d86eda74980eab7a0948868b4b59f51c Author: lijewski Date: Tue Feb 9 21:21:45 1999 +0000 Little cleanup suggested by Bill. Src/C_BaseLib/Boolean.H commit c5038da249d2a34a4c90c74cb58f1a5e6c6e96ec Author: lijewski Date: Mon Feb 8 17:49:37 1999 +0000 From Matt Bettencourt. Tools/C_mk/Make.IRIX64 commit 94cc16b39f161ed9ae07b9c2630eb48aea8a0bd0 Author: lijewski Date: Fri Feb 5 18:56:06 1999 +0000 Some cleanup. Elided some do-while loops in Iterators when !BL_USE_MPI. Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H commit 79f6b7fb4964962e1462a35c0f1c2d564106a635 Author: 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 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 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 Date: Wed Feb 3 21:56:58 1999 +0000 Fixed typo. Src/C_BaseLib/RunStats.cpp commit 3fa2d1ab600d899a1e41f4509cf9ea57e48eda49 Author: lijewski Date: Wed Feb 3 21:55:32 1999 +0000 Made some RunStats objects static. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp commit 2dd2cc06b9d1b359c3db082d362acc4d741273d8 Author: lijewski Date: Wed Feb 3 21:55:15 1999 +0000 *** empty log message *** Src/C_BaseLib/RunStats.cpp commit f456111737b66d6a7bc1c14f7d271676f7cadd6c Author: lijewski Date: Wed Feb 3 21:48:51 1999 +0000 Removed RunStats junk. Src/C_BaseLib/CArena.cpp commit 86f7180ec2e4b75d1d4127d3b0c155639fa027ed Author: lijewski Date: Wed Feb 3 19:29:57 1999 +0000 Fixed bug in CollectNumPts(). Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp commit e8e66866184262ba9b16a638bf0694edf60e5765 Author: lijewski Date: Wed Feb 3 19:29:26 1999 +0000 Cleaned up checkPoint() a bit. Src/C_AMRLib/Amr.cpp commit 03757b3e35d0bc78757054a0e67e7b1db6464389 Author: lijewski Date: Wed Feb 3 00:39:25 1999 +0000 Needed to include Src/LinearSolvers/C_CellMG/LO_2D.F Src/LinearSolvers/C_CellMG/MG_2D.F commit e9e385effad4f864681488a799439062455018fb Author: lijewski Date: Wed Feb 3 00:16:31 1999 +0000 Replaced some fp constants with macros. Src/C_BaseLib/COORDSYS_2D.F Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/LO_2D.F Src/LinearSolvers/C_CellMG/MG_2D.F commit 02fb3d481c18d2873d4c96012871614d8f0ffac0 Author: lijewski Date: Tue Feb 2 23:36:05 1999 +0000 Removed FORT_SCALADDTO Src/C_AMRLib/FLUXREG_2D.F commit 40b07b91037a221a460050d211478902ef381dc0 Author: car Date: Tue Feb 2 23:24:41 1999 +0000 d comment line! Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit 13a0118c2453659e63e1d41cf15a7812ab82a5b6 Author: car Date: Tue Feb 2 17:14:57 1999 +0000 no 2d rz Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/interface.H commit 68a3a4c9acad9717ae71484a5a90edb00807ab12 Author: lijewski Date: Tue Feb 2 00:24:03 1999 +0000 Substituted BL_SPACEDIM for some numbers. Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit ff984f2c0434cf61f4f02b699644ba7c376403df Author: car Date: Mon Feb 1 18:17:35 1999 +0000 Make task_proxy a friend of task so that it can access protected members. Is this a bug in MSVC5? Src/LinearSolvers/C_NodalMG/hgparallel.h commit ba3fe48d16c2bc42eaa892cf28045007440e64ed Author: lijewski Date: Sat Jan 30 17:57:00 1999 +0000 Simplified task_proxy. Cuts way down on heap allocations. Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 667aeefb5afc52c3e1377c0040120be91f124c15 Author: lijewski Date: Fri Jan 29 23:20:25 1999 +0000 Removed CVS ID string. Src/LinearSolvers/C_NodalMG/hgparallel.h commit 51238c16f44db1fcc40c49bec00bf7569a26348a Author: lijewski Date: Fri Jan 29 23:19:50 1999 +0000 Yet more performance enhancements. Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 3539ef7b109b1279a05679206078338c3e7575cb Author: car Date: Fri Jan 29 20:13:52 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 7cd5842e691bc3193304d92fefeb570328996574 Author: lijewski Date: Fri Jan 29 19:23:57 1999 +0000 Some cleanup and copyright macro insertion. Src/LinearSolvers/C_NodalMG/RegType.H Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.H Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit f235e554cf4d784972f8159d737303606f8b4546 Author: 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 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 Date: Fri Jan 29 17:50:10 1999 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_proj2d.F commit 5a4ebf39ce5f8c00d2e7a959187649757a0259f0 Author: car Date: Fri Jan 29 00:20:27 1999 +0000 more 2d Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 25aaeee6ed89131a1b01281c09e4ca0649d42e32 Author: car Date: Thu Jan 28 23:36:13 1999 +0000 changes for 2D Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 5c1ab54091665fbefb399c0f0bcc6bf39345c370 Author: lijewski Date: Thu Jan 28 21:00:49 1999 +0000 More performance enhancements. Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit b44dfaeb85819105ae93f7aae548cd4239f06e7b Author: lijewski Date: Thu Jan 28 18:50:38 1999 +0000 More performance enhancements. Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit d7f4937dc68529d99d7fa3d481537cf1a777bd21 Author: lijewski Date: Thu Jan 28 16:58:28 1999 +0000 More performance enhancements. Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 63ceffee61a43cd905218d36464e9252ce2d6627 Author: lijewski Date: Wed Jan 27 17:35:51 1999 +0000 Some performance enhancements. Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 387bd56bda65ca05e4f88fe75a89ed86a9c28173 Author: marc Date: Fri Jan 22 21:34:16 1999 +0000 Prettier still... Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit c457656985690b796ab5e02e02d56696e822ee72 Author: marc Date: Fri Jan 22 21:24:41 1999 +0000 Make verbose out a little prettier...nothing significant here... Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit c85010584877c0f7cfc04131aefcb4e67e741589 Author: vince Date: Fri Jan 22 21:05:07 1999 +0000 Deleted an assertion in copy(...). It was causing problems in parallel. The assertion is checked later, so it was also redundant. Src/C_BaseLib/FabArray.H commit 0f76f304e123ee409bcd026abadafc1244f56206 Author: lijewski Date: Thu Jan 21 22:03:14 1999 +0000 FillCoarsePatch() was still doing some ghost cells when didn't need to. Src/C_AMRLib/AmrLevel.cpp commit 35fb8644cc6aa10f206f980514fbfa84f50fd7ad Author: lijewski Date: Thu Jan 21 20:27:05 1999 +0000 Fixed bug in and added argument to FillCoarsePatch(). Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit a3c7c1903a05aa41345436dd99c6d9522aaad531 Author: lijewski Date: Wed Jan 20 19:24:00 1999 +0000 Must do physical bndry conditions after periodic junk in isValid(). Src/C_AMRLib/AmrLevel.cpp commit 54b18d0967f2553047ef9946ab83f813e49ed90d Author: lijewski Date: Wed Jan 20 04:41:36 1999 +0000 Fixed bug in FillPeriodicBoundary(). Src/C_BaseLib/Geometry.cpp commit f03b11de5a7057590fc440923c1905e4d3acad33 Author: lijewski Date: Fri Jan 15 21:44:22 1999 +0000 Dealt with periodic nodal quantities in FillPatchIterator::Initialize(). Src/C_AMRLib/AmrLevel.cpp commit c8f80ae98375f8adc3a94076217fddb00734c897 Author: car Date: Thu Jan 14 22:48:47 1999 +0000 Really old comments Src/LinearSolvers/C_NodalMG/README Src/LinearSolvers/C_NodalMG/Rewrite commit 04f52ff17e52b1dce7faba673ce75ea9b53ec1aa Author: lijewski Date: Wed Jan 13 04:14:19 1999 +0000 Removed the hash junk. Simplified things a bit. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 33da55ebacde774237048c4b9e0dc63b874e3e18 Author: lijewski Date: Tue Jan 12 19:00:18 1999 +0000 Added carena RunStats for CArena::alloc() and CArena::free() Src/C_BaseLib/CArena.cpp commit a97b92beea6a8eb1fa66ac4915bb7ab58df32945 Author: lijewski Date: Tue Jan 12 17:56:46 1999 +0000 Added RunStats for regrid. Src/C_AMRLib/Amr.cpp commit 4ae03dea172561c5b214531b16a5eee6be34f391 Author: lijewski Date: Wed Jan 6 21:27:58 1999 +0000 Changing how the DatasetClient stuff is wired into the code. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/DatasetClient.H Src/C_AMRLib/GNUmakefile Src/C_AMRLib/Make.package commit 8022608150ae38264505048597c5a9a5ef9e26c9 Author: 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 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 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 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 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 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 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 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 Date: Mon Jan 4 18:27:14 1999 +0000 Add target Src/C_AMRLib/GNUmakefile commit a26311bd5cfc0eb4458820ef1191c7ddde7470a3 Author: marc Date: Mon Jan 4 18:26:32 1999 +0000 Add arg for lib make Src/LinearSolvers/C_TensorMG/GNUmakefile commit db67136d13911ade825c1920662a1c8c7729544b Author: marc Date: Mon Jan 4 18:12:08 1999 +0000 Make it better Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 3d5365c98e7a3a4b70739723b697d9e7c0f3975a Author: marc Date: Mon Jan 4 18:11:45 1999 +0000 Add code for flux compute member, similar to that in tensor stuff. Src/LinearSolvers/C_CellMG/LP_2D.F Src/LinearSolvers/C_CellMG/LP_3D.F Src/LinearSolvers/C_CellMG/LP_F.H Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H commit 7921275e20a66001e2d36adbe19257aed39db36d Author: marc Date: Mon Jan 4 18:11:14 1999 +0000 Add multicomponent stuff. Make first stab at output function for ||. Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp commit ba20383a0a7bfd30955d21c12f4d81c3df0f7b96 Author: marc Date: Mon Jan 4 18:10:22 1999 +0000 Increase verbose output, for mg add code for mg.v>2 to dump mg levels Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit ac3edde3b3d950b5c70321b96efcc576eee66cdf Author: marc Date: Mon Jan 4 18:09:36 1999 +0000 Add multi-component stuff. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp commit 18ec3315ee07dab34a892b108293eb2d447f90e2 Author: marc Date: Mon Jan 4 18:09:00 1999 +0000 Add flux compute member function, similar to that in the tensor stuff. Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/ABec_F.H commit 0d81b18eada9a15d309d2a3b48c0681106c065b0 Author: lijewski Date: Fri Dec 25 18:58:09 1998 +0000 Minimized more heap allocations in FillPatchIterator. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 0ac2f5e8f03ea3e373fab87ea006b89d65084779 Author: lijewski Date: Wed Dec 23 23:14:07 1998 +0000 FillPatch now does periodic correctly. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 661adf8f068b5898eb0c0e7a1dc949c4b5cb6fbf Author: almgren Date: Tue Dec 22 22:42:56 1998 +0000 OOPS - pc_domain was a coarsened domain, what I really wanted was geom[levf].Domain() Src/C_AMRLib/Amr.cpp commit e933a6aaaca64bcc7b4b861ad59de37ab29a0705 Author: lijewski Date: Fri Dec 18 16:47:52 1998 +0000 Added catenate(). Src/C_BaseLib/BoxList.H commit 81a2198d1f0d86b4ffbd8946f09dc5f0a4d366ee Author: wyc Date: Fri Dec 18 00:40:41 1998 +0000 Its miraculous that this bug never was noticed before. ncx and ncy were declared as logicals, despinte being used as integers...... Src/C_AMRLib/INTERP_2D.F commit 64f2231a267fe04b96b5196389db4baff825045a Author: lijewski Date: Wed Dec 16 22:27:39 1998 +0000 Fixed memory leak. Src/LinearSolvers/C_NodalMG/hgparallel.h commit 7096ccee2008ef3d0ebcbcb530b2ecf56182f517 Author: car Date: Wed Dec 16 20:51:00 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/machinefile.mpi commit 752b122df527af7208af84ac5c4639550d953c9f Author: car Date: Wed Dec 16 18:54:14 1998 +0000 a new bad grid set Src/LinearSolvers/C_NodalMG/tests/gt.inputs.3d.spin.grids Tests/LinearSolvers/C_NodalMG/test_grids/gt.inputs.3d.spin.grids commit ee0c9beaa576fe469d683b3622fcb5c02e14ef3b Author: car Date: Wed Dec 16 18:42:53 1998 +0000 test infrastructure Src/LinearSolvers/C_NodalMG/inputs Src/LinearSolvers/C_NodalMG/proj.cpp commit be6d5d1a0fc4a5fd66b9a6338ffba9338120aefa Author: car Date: Wed Dec 16 17:51:17 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit f92e68da5345f17ad442958e22dacb3f783b522a Author: car Date: Wed Dec 16 17:33:42 1998 +0000 fix for task_copy::depends_on_q Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit b408b79a1f762a10a9bf56586eee91d30a0365a2 Author: car Date: Tue Dec 15 23:34:56 1998 +0000 more checking options Src/LinearSolvers/C_NodalMG/proj.cpp commit 33fab28dc32f79b1b9255bca4007286da63caedd Author: lijewski Date: Tue Dec 15 18:51:27 1998 +0000 Attempt to speed up processing of local tasks. Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit a93bca36bcd6a4173468177089fd12cabfac02fc Author: lijewski Date: Tue Dec 15 18:13:24 1998 +0000 Had a bug in task_list::execute(). Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 55f79ce7f039fbb5aa43377bdfdcd8315b166ba2 Author: lijewski Date: Tue Dec 15 17:32:32 1998 +0000 Prepended cout's with "HG:" Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit e89b39ab210640da51a120bb8362e119255248a5 Author: lijewski Date: Tue Dec 15 17:22:47 1998 +0000 An improvement to task_list::execute() loop. Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit b98e9caf68b013743f947e16b75739f7c98a0797 Author: car Date: Tue Dec 15 17:01:30 1998 +0000 better execute loop Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 28421c74cc83dabbae74a80ad1723a456446e13b Author: car Date: Tue Dec 15 04:01:33 1998 +0000 Fix for explosion in number of tasks. The ParmParse parameter HG.max_live_tasks, limits the number of tasks that can be pending in a task loop. The default limit is 50. Since tasks always are issued in pairs, and the tasks are asynchronous sends/recvs this should not deadlock. The fortran change is to get the line length of a few lines back down to 72 or smaller. Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 81d772f6311a06bca814a02510a13a678a1bb5af Author: lijewski Date: Mon Dec 14 22:43:11 1998 +0000 Integrated in and . Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit 75a348803a50352bf77f29930d4092e4750c0895 Author: lijewski Date: Mon Dec 14 20:23:47 1998 +0000 Got rid of hard-wired double-precision constants to snuff T3E warnings. Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LP_3D.F Src/LinearSolvers/C_CellMG/MG_3D.F commit 01f9c2795efb946bb636af81b17208671aabb340 Author: car Date: Sun Dec 13 01:21:38 1998 +0000 sleep flag Src/LinearSolvers/C_NodalMG/proj.cpp commit cedeb6981f552afca3ea8ac5ab182c0c2dac45f3 Author: car Date: Fri Dec 11 21:55:40 1998 +0000 T3E KCC change Src/C_BaseLib/Utility.cpp Tools/C_mk/Make.T3E commit cdfaaa1ba1c6c59c004d4084601338776386c57a Author: 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 Date: Fri Dec 11 19:21:26 1998 +0000 fix for rwtime == 0 Src/C_BaseLib/RunStats.cpp commit 343c629dec8627b3e996768014547794039cf7ca Author: car Date: Fri Dec 11 18:55:32 1998 +0000 added inputs file Src/LinearSolvers/C_NodalMG/inputs commit bd3a90c0be4d1eca8be2c5244bd97ba7e7329d07 Author: car Date: Fri Dec 11 18:54:57 1998 +0000 Additional ParmParse support Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 452f7c05c7865c9c2651eecd9345d6734d0f753f Author: car Date: Fri Dec 11 18:37:46 1998 +0000 ParmParse and RunStats support Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit d623e0b55d6d1f00f57f349c32b0025245f6415f Author: lijewski Date: Fri Dec 11 02:47:14 1998 +0000 Removed IncrementPeriodicBoundary(). Shouldn't have been checked in. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 476926dfa78561842541463d7351b4edde958e03 Author: lijewski Date: Fri Dec 11 02:46:18 1998 +0000 Removed the FillFabPlus() stuff. Shouldn't have been checked in. Src/C_BaseLib/FabArray.H commit c92be1e9df16ae88c1d0786fe324f357f25a6f33 Author: car Date: Fri Dec 11 00:26:57 1998 +0000 *** empty log message *** Src/C_BaseLib/pBoxLib_2.dsp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 3bc6f5fdf06f3368768ca435cea389c6ad24bd5b Author: car Date: Fri Dec 11 00:01:22 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit a4364e6b2daf5aa07edd87d9034cad5025cbb948 Author: lijewski Date: Thu Dec 10 23:34:58 1998 +0000 Added FillFabPlus(). Src/C_BaseLib/FabArray.H commit 7134b731d184ef98b880f47e0fde111d9c793fa1 Author: lijewski Date: Thu Dec 10 23:31:58 1998 +0000 The node centered stuff in buildPIRMMap() wasn't quite right. Src/C_BaseLib/Geometry.cpp commit d943a9da8c8856a09d83f39767324e8bdf0cfd68 Author: lijewski Date: Thu Dec 10 23:24:14 1998 +0000 Fixed a bad assert(). Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 426ec31f940efa3d63b0355e05f7b0821e4cb867 Author: car Date: Thu Dec 10 23:16:01 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 059600064f10d8b819308879c37a184a17e74794 Author: car Date: Thu Dec 10 23:10:41 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 14923aafea7b18da8f307f0b0b71d1fafc7d0d1f Author: car Date: Thu Dec 10 22:54:32 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/.cvsignore Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit 55125e31ed5be1b7a69335439633d59e002fc8c0 Author: 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 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 Date: Thu Dec 10 18:41:21 1998 +0000 remove extraneous dependency check Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 4d29e1de51d21248209a347394855e8664105218 Author: car Date: Thu Dec 10 01:02:38 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 961c8d80d3864d63361fb6126d123017fa9113b8 Author: car Date: Thu Dec 10 01:00:32 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 99f8a0997759824ffe4f6164031e101b804cadf8 Author: car Date: Wed Dec 9 23:13:31 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/tests/gt.bill1 Tests/LinearSolvers/C_NodalMG/test_grids/gt.bill1 commit f6d04474e01c8d1a2f8356603672c28587989ba1 Author: wyc Date: Wed Dec 9 21:56:28 1998 +0000 Mike put some T3E defines where he meant BL_T3E. Src/C_BaseLib/Utility.cpp commit 740ab6953b5858070cf1c3b3c2f3da9e326e3819 Author: lijewski Date: Wed Dec 9 20:21:30 1998 +0000 In buildPIRMap(), restrict src box to be in Domain(). Src/C_BaseLib/Geometry.cpp commit 73f6df42166b2b1539d99dce2b7f49666daf3629 Author: wyc Date: Tue Dec 8 18:25:44 1998 +0000 These changes allow CGSolver to recognise a loss-of-accuracy event and deal with it gracefully. By default, CGSolver will act in the old-die- horribly mode. However, you can activate expert mode which will allow CGSolver::solve() to return an integer indicating status. MultiGrid.cpp has been modified to use expert mode. Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 72612ac1e291535d7336cbc271e8eb7985ba8e7f Author: lijewski Date: Tue Dec 8 18:13:20 1998 +0000 A fix to task_copy::depends_on_q(). Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit f3d3064190aac34955af49fa27b912624e46e0d5 Author: 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 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 Date: Fri Dec 4 21:32:48 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 9cd6eaeca22dcc6dc51dbd1d973ebe5cacab39b6 Author: car Date: Fri Dec 4 21:19:31 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit fa8ee8d315029adfb85e87d1e8a084e84f68a8e3 Author: lijewski Date: Fri Dec 4 17:33:24 1998 +0000 time -> time+dt_level[level] in station.report() call. Src/C_AMRLib/Amr.cpp commit dcda95e59a6cda0c841b654d13fcb45c777d1198 Author: lijewski Date: Wed Dec 2 18:36:45 1998 +0000 Removed bad assert(). Src/C_AMRLib/AmrLevel.cpp commit 6b3ba309e1847503b5ee5cee986131a6e994a7ce Author: 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 Date: Wed Dec 2 05:58:57 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile commit 2ff5274c6c8ee320f66568ad3c22b2c27ef4f18c Author: lijewski Date: Wed Dec 2 00:04:37 1998 +0000 Added poe junk ... Src/C_AMRLib/GNUmakefile Src/C_BoundaryLib/GNUmakefile Src/LinearSolvers/C_CellMG/GNUmakefile Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_TensorMG/GNUmakefile commit ccca50c5406553eea50df2607e6b2706addee1dd Author: lijewski Date: Wed Dec 2 00:04:06 1998 +0000 A tad cleanup. Src/C_BaseLib/GNUmakefile commit 4fc12c17bd04416c63d32d3d55a916a3fb8a27a0 Author: lijewski Date: Tue Dec 1 21:56:39 1998 +0000 Reverted out the cache stuff. Not a significant win. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit f56bee7d41171cbb980ac12e2b8330bae471b256 Author: lijewski Date: Tue Dec 1 21:56:23 1998 +0000 Reverted out the cache junk. Not a significant win. Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp commit 31cfa49f6f9edaed451ce263639c4359d2422dd5 Author: lijewski Date: Mon Nov 30 21:30:09 1998 +0000 Added more assert()s in operator() per Dan Graves. Src/C_BaseLib/BaseFab.H commit ce24534953f4b6bb7d23953f9011c0805c004c46 Author: 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 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 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 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 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 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 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 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 Date: Thu Nov 26 20:30:13 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 1fec37eac74c676c84414960ce5be1b4f9cf05ec Author: lijewski Date: Wed Nov 25 23:58:22 1998 +0000 Progress moving from AmrSS to current amrlib ... Still a work in progress though. Src/C_AMRLib/StationData.H Src/C_AMRLib/StationData.cpp commit 16b902920f8a239c15aafe8aa5b45a97a0461ea1 Author: car Date: Wed Nov 25 23:52:34 1998 +0000 Fixes for HGPROJ MultiLevel Src/LinearSolvers/C_NodalMG/.cvsignore Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 1fa5d5196f335092c8a06b1bf8cde2d4a0f6a592 Author: lijewski Date: Wed Nov 25 19:14:16 1998 +0000 From very old amrSS code ... Src/C_AMRLib/StationData.H Src/C_AMRLib/StationData.cpp commit 4eb687baa573803736f65fd21c9e2f1d82f13c13 Author: wyc Date: Tue Nov 24 23:17:52 1998 +0000 added chuck's patch for a problem which was causeing hg not to converge Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit fcf009fe889ec30a85694e1de43970949e945409 Author: lijewski Date: Tue Nov 24 19:22:57 1998 +0000 Now caching Snds stuff for CollectData(). Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 0ef188efe02c12f4516bb888e1d298eefb467135 Author: lijewski Date: Tue Nov 24 19:22:38 1998 +0000 Now cacheing Snds stuff in CollectData(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp commit 034b6f01dd9fae10396d7dac9b3f8ecc89c0e74c Author: lijewski Date: Tue Nov 24 01:01:14 1998 +0000 Merged in new Reduce() functions. Src/C_AMRLib/Amr.cpp commit 070ac872c42ad2a0bced22bab810ae20dbce654e Author: lijewski Date: Tue Nov 24 01:00:54 1998 +0000 Merged in new Reduce() functions taking cpu to reduce to. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/RunStats.cpp commit 817b9bd43156533113830742231c41c63c1b8a09 Author: 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 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 Date: Mon Nov 23 17:56:42 1998 +0000 Fix for busted gmake on T3E. Tools/C_mk/Make.rules commit 73c74592599f7b6fbc47d04225e4c9c2d6cf7e3e Author: car Date: Mon Nov 23 17:31:36 1998 +0000 *** empty log message *** Src/C_BaseLib/pBoxLib_2.dsp commit 4ed2b516d2b9f666704b75f9c4bff3e8ccd9eb8b Author: car Date: Mon Nov 23 00:50:23 1998 +0000 *** empty log message *** Src/C_BaseLib/pBoxLib_2.dsp commit cb1e08598a66a755d58238b104115e953f8e9673 Author: lijewski Date: Sun Nov 22 17:42:54 1998 +0000 Wrapped the closelib junk into a canned procedure. Tools/C_mk/Make.rules commit 7e616ec0198a19ecb0fed2aa044a65680e196eae Author: 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 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 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 Date: Sat Nov 21 02:49:39 1998 +0000 Simplified the library closure junk. Tools/C_mk/Make.rules commit 48452fc953f89c267b8f9c3b0fa8bd1de2c37e1e Author: lijewski Date: Sat Nov 21 00:27:43 1998 +0000 Yet more OUTPUT_OPTION mods. Tools/C_mk/Make.defs commit 8dd7468e4493a0f4fb43cbf6d81d15f18ae95e59 Author: lijewski Date: Sat Nov 21 00:24:14 1998 +0000 Bug fix to form of *LIB_OUTPUT_OPTION. Tools/C_mk/Make.defs commit f77afe0060da3e89d642997d266c7b95f5040b8f Author: lijewski Date: Sat Nov 21 00:15:40 1998 +0000 Now have four *_OUTPUT_OPTION variables. Tools/C_mk/Make.AIX Tools/C_mk/Make.CRAY Tools/C_mk/Make.T3E Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 5974512f34a2f81f92c6719f3544c1efe6c87239 Author: lijewski Date: Fri Nov 20 23:18:02 1998 +0000 Some fixes relating to OUTPUT_OPTION & FORT_OUTPUT_OPTION Tools/C_mk/Make.OSF1 Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 3c32b18940e630726e8df21ea6ef774068a37b1c Author: lijewski Date: Fri Nov 20 21:58:24 1998 +0000 Added real time clock routines for second() & wsecond() on T3E. Src/C_BaseLib/Utility.cpp commit 7d4aa028c32bb9d71bc8c0c1808deaa3958efdca Author: car Date: Fri Nov 20 21:42:41 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit ce8d5081f10fcba310cc10909e371e4baeeb1455 Author: 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 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 Date: Fri Nov 20 20:29:45 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 8ec28562b53e6460f70ec3183825547b01495620 Author: car Date: Fri Nov 20 19:09:48 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit f577d3f16febad5c1787df31b7c99579920e2e7b Author: car Date: Fri Nov 20 05:01:10 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 9975e0df32088945b7ef5dcd18d0c7acf2685209 Author: car Date: Fri Nov 20 00:01:03 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 49db930eb54de4a8b84c531ce5bd7e9d6682a559 Author: car Date: Thu Nov 19 22:32:45 1998 +0000 fixed task_fecdiv_2 Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 302677eb22eb4fb47e3795d36aaf3d1672fa817e Author: car Date: Thu Nov 19 22:10:17 1998 +0000 parallel hgproj changes Src/C_BaseLib/FabArray.H Src/C_BaseLib/pBoxLib_2.dsp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 447f168cdc7a593a0d373a79ae08e947db747e77 Author: car Date: Thu Nov 19 18:09:53 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/bl_abort.cpp Src/LinearSolvers/C_NodalMG/matherr.f90 commit 88a27b71bd3941d4fd7cf419198325db33d600ff Author: car Date: Thu Nov 19 16:48:23 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/bl_abort.cpp Src/LinearSolvers/C_NodalMG/matherr.f90 commit 6db0e8287b333ea32d8df747049582c9818487c8 Author: car Date: Thu Nov 19 02:20:46 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 551df3472d3e69f0a0a3c7302d3f7a0ab41cfded Author: car Date: Wed Nov 18 23:01:23 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp commit 939ad0b8848b5b971d0fec8d46935e87548729c0 Author: car Date: Wed Nov 18 21:46:44 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 1dd96aedde70d36b4d1161fa40c98b41c751af04 Author: car Date: Wed Nov 18 21:08:15 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit ea3b10dbb4389f401497d48357cb1af1fee2d9d9 Author: 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 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 Date: Wed Nov 18 20:34:50 1998 +0000 Updated to reflect MPI in machineSuffix. Src/LinearSolvers/C_TensorMG/GNUmakefile commit f3894c0aea05057e29998c1ca821e1038fa8c7da Author: lijewski Date: Wed Nov 18 20:33:02 1998 +0000 Updated to reflect MPI in library names. Src/C_AMRLib/GNUmakefile Src/C_BaseLib/GNUmakefile Src/C_BaseLib/test/GNUmakefile.test Src/C_BoundaryLib/GNUmakefile Src/LinearSolvers/C_CellMG/GNUmakefile Tests/C_BaseLib/GNUmakefile.test commit 886736fb8cbd2d00c91abccb3022f2e5f18a7c61 Author: lijewski Date: Wed Nov 18 20:32:40 1998 +0000 Now distinguish between libraries built w/ or w/o MPI. Tools/C_mk/Make.defs commit 403fa1ce963b268db579b5845e9f8c2dcb818451 Author: lijewski Date: Wed Nov 18 20:31:56 1998 +0000 Removed the unneeded first argument to StartParallel(). Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit f9e647742040d5f611e6330023c0084b42f64973 Author: car Date: Wed Nov 18 19:19:30 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 5e5304efb17d7b7149ee55da6fa2242930b7dccf Author: car Date: Wed Nov 18 17:59:07 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 55e2d77d851f186f79eebdedce9890b5b3b6aaa9 Author: car Date: Wed Nov 18 17:57:45 1998 +0000 fixed up for LIB AND EXE support in same directories and Makefiles. Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit aa61f39ebe8767f9af24acd7bcceb8401dd0ae14 Author: car Date: Wed Nov 18 01:30:51 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp commit c715b4a404c5594bf37ee75e2ed8db634ce9f401 Author: car Date: Wed Nov 18 01:00:24 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 201970be052024a0c639e99e8c08488e57793eb6 Author: car Date: Tue Nov 17 20:07:53 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interpolator.H Src/LinearSolvers/C_NodalMG/restrictor.H commit 35e209c9ccb2b20dac9e1df5020c69ebee4363d2 Author: lijewski Date: Tue Nov 17 19:15:39 1998 +0000 Small touchup. Src/LinearSolvers/C_TensorMG/MCLinOp.cpp commit ed22fe92ffb33576101f74d7a881246cf293ac18 Author: lijewski Date: Tue Nov 17 19:11:09 1998 +0000 Brought up-to-date with latest Parallel stuff. Src/LinearSolvers/C_TensorMG/GNUmakefile Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCLO_2D.F Src/LinearSolvers/C_TensorMG/MCLO_F.H Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/Make.package commit 8a4e999d9684460fb61b99ea6bb2a21701f218d7 Author: car Date: Tue Nov 17 18:00:49 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 3d156a47245d44ab5154705a7efabbdc9b411e04 Author: car Date: Tue Nov 17 17:48:36 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.h commit 146faefe9823616eeb99ba430418491b2cc8a53e Author: car Date: Tue Nov 17 00:51:16 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit dbce7d325c1ca0eec06011678f2fce72688e7f2b Author: car Date: Tue Nov 17 00:48:50 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 2820cb5a3fa81b20c3d04154c08afc68a130bd4b Author: car Date: Tue Nov 17 00:38:05 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 5a52bf2ea58f5894908c09bf3a8bb34228f5310f Author: car Date: Tue Nov 17 00:18:14 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 7e4f5bd1f2e44ca1343a9b96ebe8f1d05c163ebd Author: car Date: Mon Nov 16 23:52:36 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit c219930a6d8ad2b1f644d95c987cc923ff603200 Author: car Date: Mon Nov 16 22:54:15 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 855ba6e164ece01b106cecdb60fc70f6c62f6798 Author: car Date: Mon Nov 16 21:57:23 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit d614cd22c4da61d595d6aadbf2abfdec43ae7f23 Author: car Date: Mon Nov 16 21:44:10 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit d4daf18e8c0392679a203541011344adc9cfdd26 Author: car Date: Mon Nov 16 18:11:49 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit fab3cce418eb22ff022fbd95104b363f897d5bbf Author: car Date: Mon Nov 16 17:47:58 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 75bcd00d45cf2134e76ef494cc7a92d63afcd935 Author: car Date: Mon Nov 16 17:31:01 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 200f3394c1b0570dae3f41037503c51a308d0863 Author: car Date: Mon Nov 16 15:53:17 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp commit 2f30e89dc2d772c6db4d9ed3429cfd5d5d912b94 Author: car Date: Mon Nov 16 03:52:11 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit e4cc952417abcfc1985c3ad907bdc071482e55d7 Author: car Date: Mon Nov 16 00:47:47 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit e488e7ffbfb0aa28cf44cc70598c9df4fa131ff8 Author: car Date: Sun Nov 15 23:40:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit b3c3d6dfa05754297f8e14564a23086ddb47bc98 Author: car Date: Sun Nov 15 00:01:27 1998 +0000 win32 support Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 26bf1132774b740f936cd035b2a6f834ba64514d Author: car Date: Sat Nov 14 19:38:21 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 121fc22589b71cc0b68607026a34c612107f99bd Author: car Date: Sat Nov 14 00:34:13 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgproj.dsp commit cdaa86c34d295bbcf736f74b80a326c40fa12971 Author: car Date: Sat Nov 14 00:34:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp commit 2c13a0bfc7ac08f70bc4b885fa4d7ce39aee7116 Author: car Date: Fri Nov 13 22:14:39 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 7c3b71fc168e23527ee70309c885facaae8a12a1 Author: car Date: Fri Nov 13 20:09:28 1998 +0000 Temp file name. Src/LinearSolvers/C_NodalMG/.cvsignore commit ef9948b061f008c9e9e865f6507aafb872462fa4 Author: car Date: Fri Nov 13 20:08:45 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 9ddae75afabf11a9b2ad495a86400632fc1c1b24 Author: car Date: Fri Nov 13 17:25:52 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 922cf0a2d9af33988cc6542c0c53808bb5482a22 Author: car Date: Fri Nov 13 16:03:51 1998 +0000 EBASE should be null Src/LinearSolvers/C_NodalMG/GNUmakefile commit 5b7e7bd2e95a2769a4ad696bb3e9eddb638bfcc9 Author: car Date: Fri Nov 13 16:03:07 1998 +0000 quiet some warnings Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit f44f6033e44f9aceaa195869c25c0539ce40c1af Author: car Date: Fri Nov 13 00:25:01 1998 +0000 fixes for parallel, throws find bugs Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit ed4b454cf58c8e3a3d2c86087a5145b3cefc74a2 Author: marc Date: Fri Nov 13 00:16:14 1998 +0000 Fix up a couple of 1D-specific bugs. Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/Looping.H commit bf18f8ae1d80dc1ca5e4b546f4ccff5968437cad Author: car Date: Tue Nov 10 02:21:59 1998 +0000 libs target Src/LinearSolvers/C_NodalMG/GNUmakefile commit 19086d0b786f91aa58f38cb54122af23e99bac89 Author: car Date: Mon Nov 9 23:13:14 1998 +0000 Makefile tweaks: no type make COMP=... EBASE=proj to buildlocally Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/Make.package commit 0b3d5ac6ef8a6eba182dc62dedc9efccd0bef466 Author: car Date: Sat Nov 7 21:42:14 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit dcf254c4acc8074c36be7cab1ddaaf0766ea24c8 Author: car Date: Sat Nov 7 21:34:16 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.h commit 1906d0a7c8492c12a792dd5a7e69a4768c4f7b76 Author: car Date: Sat Nov 7 21:19:56 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit df4207780b774f99bc8c2fedac57b43ff7acdd3c Author: 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 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 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 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 Date: Sat Nov 7 00:30:43 1998 +0000 Mods for FillPeriodicBoundary(). Src/C_BaseLib/MultiFab.H commit 00423c5a794702277e7fddc5ee7e3872c404b1cb Author: car Date: Fri Nov 6 21:35:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/RegType.H commit 88137956ff1f2c2d6e1491163929ee5bcfd9943c Author: car Date: Fri Nov 6 21:31:53 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/RegType.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit e0943b3adeca0fb1466e1d265d91767a99fa2b46 Author: car Date: Fri Nov 6 04:22:35 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit af91c0be23d01e95250d0df9898b1c7aa75ebcb9 Author: car Date: Fri Nov 6 04:03:28 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 18b5c57cdc2d7de6bbf32fa7a273eb606b657a0a Author: almgren Date: Thu Nov 5 06:42:59 1998 +0000 Fixed a bug in the recent fix to not buffer the buffer cells - we can't assume that grid cells next to a domain boundary were buffer, not tagged, cells... Src/C_AMRLib/Amr.cpp commit 946f44e2d868a4f8fdde3a13c4735212e06718e8 Author: almgren Date: Wed Nov 4 20:30:22 1998 +0000 Removed the following snippet of code: if (!sub_cycle) { // must adjust regridding trigger int factor = 1; for (k = max_level-1; k >= 0; k--) { factor *= MaxRefRatio(k); regrid_int[k] = ri*factor; } } which for no subcycling did funny things to regrid_int. Now regrid_int at each level is just what is set in the inputs file, which means effectively you will now regrid every regrid_int time steps with lbase = 0. Src/C_AMRLib/Amr.cpp commit 67e5f5134cfad193953cb09432f9bf240184e8b7 Author: lijewski Date: Wed Nov 4 00:45:16 1998 +0000 Added DataLog() ... Src/C_AMRLib/Amr.H commit 0302d3f164260b7e07f011459cde6f81e4ba8505 Author: marc Date: Tue Nov 3 21:56:08 1998 +0000 Add write for AmrData object as well. Tools/C_util/WritePlotFile.H Tools/C_util/WritePlotFile.cpp commit da8bfdf9524001f7eee861e79ade076886e2114f Author: almgren Date: Tue Nov 3 21:53:05 1998 +0000 Two changes are made in regridding: first, an "intersect with domain" is added to a loop which tests whether fine grids are properly nested within coarser grids. Second, the way that fine grids affect coarse grids is modified in that only the boxes around fine *tagged* cells are coarsened to re-tag at the coarser levels, not the boxes around tagged *and* buffered fine cells. Src/C_AMRLib/Amr.cpp commit a2e16ae83686c7cf618b726a8bc77b6c9bd5f163 Author: lijewski Date: Tue Nov 3 18:16:36 1998 +0000 Sync'd with serial _amr. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/MAKESLICE_3D.F Src/C_AMRLib/MAKESLICE_F.H Src/C_AMRLib/PROB_AMR_F.H Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp commit a4bb32c2898c792f75df11afbc22b64b1e182307 Author: lijewski Date: Mon Nov 2 18:35:55 1998 +0000 HG_DEBUG is defined only when building executable. Src/LinearSolvers/C_NodalMG/GNUmakefile commit 77815d491376c8f311e06385fe083d4ddb89ae7f Author: lijewski Date: Mon Nov 2 18:19:48 1998 +0000 Added PROB_AMR_F.H Src/C_AMRLib/Make.package commit 985caaf4125d68508fe6701e05b533d2283ed57d Author: 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 Date: Mon Nov 2 17:13:25 1998 +0000 Added LevelBld.H. Src/C_AMRLib/Make.package commit 1c011c778cbcd97a6f81e0aa610e431104ead0c2 Author: lijewski Date: Fri Oct 30 19:02:44 1998 +0000 Mods to get doc++ to build proper TeX. Src/C_AMRLib/Amr.H Src/C_AMRLib/TagBox.H commit 52278f5cf706e59f410b95371e124dd7b11ab232 Author: lijewski Date: Thu Oct 29 21:56:56 1998 +0000 Fixup for doc++ DVI generation. Src/C_BaseLib/VisMF.H commit 9a827884baac6f0775e404075918ea00b18449a8 Author: car Date: Thu Oct 29 21:56:26 1998 +0000 *** empty log message *** Tools/C_mk/Make.defs commit 30c073d37302988cc85f9f3bd10f9453b312ed52 Author: lijewski Date: Thu Oct 29 17:33:53 1998 +0000 More work on Parallel GNUmakefile consistency. Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/Make.package commit 273fc3b441d7e94b3075e21a35a072aa36298b79 Author: lijewski Date: Thu Oct 29 16:54:03 1998 +0000 More work on Parallel GNUmakefile consistency. Src/C_AMRLib/GNUmakefile Src/C_BaseLib/GNUmakefile Src/C_BoundaryLib/GNUmakefile Src/LinearSolvers/C_CellMG/GNUmakefile commit 99c494d38907ca3b3b614f7c2470d9d9e25c1afc Author: 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 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 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 Date: Wed Oct 28 22:01:15 1998 +0000 Forgot BC_TYPES.H Src/C_AMRLib/Make.package commit 5f143673aa3370829e96de6b87d2128df0917cbc Author: car Date: Wed Oct 28 18:43:04 1998 +0000 __GNUC__ Src/C_BaseLib/FArrayBox.cpp commit 52b0460e5803173a36caaedc2af8ea892a98ff3f Author: lijewski Date: Wed Oct 28 18:15:13 1998 +0000 More work on getting standalone library to build. Src/C_AMRLib/GNUmakefile Src/C_AMRLib/Make.package commit 2287f5a6d1c3406d7f9d85f907c4f4afa7cbf45a Author: lijewski Date: Wed Oct 28 17:49:32 1998 +0000 More work on building standalone libraries. Src/C_BoundaryLib/GNUmakefile Src/C_BoundaryLib/Make.package commit abb47a3f1bc4659b2022c42d93603ae29f7857f6 Author: 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 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 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 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 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 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 Date: Mon Oct 26 23:58:50 1998 +0000 __GNUC -> __GNUC__ Src/C_BaseLib/FArrayBox.cpp commit 4366b688a14db282fac170e61a79254bc1124104 Author: 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 Date: Mon Oct 26 20:51:15 1998 +0000 Optimized MPI communication in copy(). Src/C_BaseLib/FabArray.H commit 39ebb17ec26519512149e89e77b81ce72050e570 Author: lijewski Date: Mon Oct 26 20:50:53 1998 +0000 Added tFAC.cpp Src/C_BaseLib/test/GNUmakefile.test Src/C_BaseLib/test/tFAC.cpp Tests/C_BaseLib/GNUmakefile.test Tests/C_BaseLib/tFAC.cpp commit 9717a6dbf4a04326a581e8eb91f1f9dabcaba6f2 Author: lijewski Date: Sat Oct 24 22:26:42 1998 +0000 Figured out the bug in 1.49 -- Yes! Src/C_AMRLib/FluxRegister.cpp commit 7953ce0a46b483118c6d2692bee21e48b22b65d5 Author: lijewski Date: Sat Oct 24 20:24:49 1998 +0000 Reverting to previous version; something's not quite right :-( Src/C_AMRLib/FluxRegister.cpp commit 22feb3137276d6b665c68aefa407df9ec057899b Author: lijewski Date: Sat Oct 24 16:49:25 1998 +0000 Optimized communication in CrseInitFinish(). Src/C_AMRLib/FluxRegister.cpp commit 7674180b05ae882ec555890cec7cdb4faf42fdce Author: car Date: Fri Oct 23 23:46:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit f08bcca8aa92e71005192c0c2d59f2bcd4c2417d Author: lijewski Date: Fri Oct 23 16:54:00 1998 +0000 A little cleanup. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/VisMF.cpp commit 75e636653172ebaf9826b84135f04bc2488906fd Author: lijewski Date: Fri Oct 23 01:59:35 1998 +0000 Added immediate return in CollectData() if NProcs() == 1. Src/C_BaseLib/FabArray.H commit 4a0659761fdee5a021fc8723460b7cb8dc148390 Author: lijewski Date: Thu Oct 22 17:27:56 1998 +0000 Added a few strategically placed ios::binary in open() calls. Src/C_BaseLib/VisMF.cpp commit cee51ace7cd1b3c3d9161ac4d41158d82b42f3b8 Author: lijewski Date: Sun Oct 18 03:48:16 1998 +0000 Now use coalescing FAB heap for FAB data in CollectData(). Src/C_BaseLib/FabArray.H commit 650e23337104bc82cdd1e846ac9eef8c707211de Author: lijewski Date: Sun Oct 18 01:44:17 1998 +0000 Added new cut at CollectData() minimizing # of communications. Src/C_BaseLib/FabArray.H commit ecf60026bf8029db9b2ab5250027895fefbd13a5 Author: lijewski Date: Sun Oct 18 01:43:50 1998 +0000 Added copy constructor and assignment operator for CommData. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 1d158ca48899b6fc2176a31754e61f7684ccb8bd Author: lijewski Date: Thu Oct 15 21:53:02 1998 +0000 Now cache the AddBox() info in the CopyDescriptor. Src/C_BaseLib/Geometry.cpp commit 80989c21a2c9997223bdf0dd7746e90676d43ffa Author: lijewski Date: Thu Oct 15 21:52:40 1998 +0000 Now cache the AddBox() gunk in the CopyDescriptor. Src/C_BaseLib/MultiFab.cpp commit 0211f4f7640923e1d42fd0d43f8e0505a4775d68 Author: lijewski Date: Thu Oct 15 21:52:15 1998 +0000 No longer clear fabComTagList() in CollectData(). This allows caching of CopyDescriptors between calls to CollectData(). Src/C_BaseLib/FabArray.H commit 25e70fb0cad58a31effe9d9a5e1f123e747d9d14 Author: lijewski Date: Thu Oct 15 17:14:32 1998 +0000 Added instrumentation code. Src/C_BaseLib/FabArray.H commit 7902f0d1fdd3ba604e195c8a44bb7812dc3fd302 Author: car Date: Tue Oct 13 18:20:32 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit f2c6765639833f2c61f405e037f26e00b947e442 Author: car Date: Tue Oct 13 18:19:34 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 1a3b44f5340774d6a9448bed899c9f8f6d041640 Author: sstanley Date: Mon Oct 12 23:22:54 1998 +0000 Replacement of EXTRAP with FOEXTRAP to be consistent with change in amrlib/BC_TYPES.H from v.1.3 to v.1.4. Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.cpp Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp commit d3cc009312f42acfbea0fa8d2522286e5a8338c5 Author: car Date: Thu Oct 8 20:23:57 1998 +0000 minor refinement of message Src/C_BaseLib/BoxLib.cpp commit bf2a48a9bf1a0bd0e4d8bfe6232d050bc3f2cf9a Author: car Date: Thu Oct 8 18:19:42 1998 +0000 oops Src/C_BaseLib/BoxLib.cpp commit de8ca3e63e9ae8c31d27ffee235c1660c411d09b Author: car Date: Thu Oct 8 18:05:45 1998 +0000 id string for abort/error Src/C_BaseLib/BoxLib.cpp commit fbe24966640f4fef23ebf4e5ede7e7b434910499 Author: vince Date: Wed Oct 7 21:18:18 1998 +0000 Added modifications for Multifluid and a few changes for the pc. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/BC_TYPES.H Src/C_AMRLib/FILCC_2D.F Src/C_AMRLib/FILCC_3D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/MAKESLICE_F.H Src/C_AMRLib/PROB_AMR_F.H Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_BaseLib/COORDSYS_2D.F Src/C_BaseLib/COORDSYS_F.H Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/SPECIALIZE_F.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/test/tDir.cpp Tests/C_BaseLib/tDir.cpp commit 0f855d3507e9e08726ce1e8ac6162ffef979995f Author: vince Date: Wed Oct 7 20:51:59 1998 +0000 Added Make.AIX for blue. Tools/C_mk/Make.AIX commit 16b6440841387b7187583b20c136dbd5fbc19822 Author: lijewski Date: Tue Oct 6 23:00:10 1998 +0000 Don't need -DBL_SETBUF_SIGNED_CHAR with KCC Tools/C_mk/Make.T3E commit 751906b9cd5d5408df8a1473c081b2c1c79434f1 Author: lijewski Date: Tue Oct 6 22:56:47 1998 +0000 Removed -e I option to FC. hgproj needs more cleanup before it'll pass this. Tools/C_mk/Make.T3E commit a7b9886bd51fc1631b1260b1d5855802fc3ad1ca Author: lijewski Date: Tue Oct 6 22:54:08 1998 +0000 Removed a unary plus that killed T3E compiler. Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F commit 9273d7d44c38e118010f48611145c5be01cff434 Author: car Date: Tue Oct 6 20:11:01 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 41f8e3383f33447905d95a324f13aa1c71c35017 Author: 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 Date: Fri Oct 2 18:42:13 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.h commit 608f2614a6001eb331a0c8f3bb7d872180a3a590 Author: car Date: Thu Oct 1 17:17:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 706195614ed9d963f7c8a1d95e5898449b266cb4 Author: lijewski Date: Wed Sep 30 20:07:18 1998 +0000 Added tad more useful error output for bldTable(). Src/C_BaseLib/ParmParse.cpp commit 89643e1933e7a87a259c64ed22a78a1b2453b509 Author: lijewski Date: Wed Sep 30 19:28:56 1998 +0000 Fixed bug in & simplified FillPeriodicBoundary(). Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.H commit 157241cb30e13e1e23efed18fde719217659608c Author: lijewski Date: Wed Sep 30 17:07:39 1998 +0000 Added tFB.cpp. Src/C_BaseLib/test/GNUmakefile.test Src/C_BaseLib/test/tFB.cpp Tests/C_BaseLib/GNUmakefile.test Tests/C_BaseLib/tFB.cpp commit 527b7ae09575d76b767808334221ed915309d6cc Author: lijewski Date: Wed Sep 30 17:05:55 1998 +0000 Fixed bug in FillBoundary() in parallel. Simplified it as well. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 568a0d5cf5befbd5d68ac3c196c74d780105958f Author: lijewski Date: Tue Sep 29 20:08:27 1998 +0000 Added copyright macro. Src/C_AMRLib/DatasetClient.cpp commit d6999623cc1ebed83a5ec1eab40567cbe5afadd2 Author: car Date: Tue Sep 29 18:05:20 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.h commit 385bc52345be13819da1c849295c91dadad12f0a Author: car Date: Fri Sep 25 23:00:22 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit f4ed19d4460349ac24f67146f282e336e790235f Author: lijewski Date: Fri Sep 25 17:57:13 1998 +0000 Added t8BIT.cpp Src/C_BaseLib/test/GNUmakefile.test Src/C_BaseLib/test/t8BIT.cpp Tests/C_BaseLib/GNUmakefile.test Tests/C_BaseLib/t8BIT.cpp commit b52c7d3befe04273b88897afd1cd8d16030e49ec Author: car Date: Wed Sep 23 22:46:17 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 2c6e0d158d9256bfbd66731d97589c66dea0248a Author: lijewski Date: Wed Sep 23 22:00:10 1998 +0000 Needed to use finest_level instead of max_level in bldFinestLevels(). Src/C_AMRLib/Amr.cpp commit ec195f309cc92eecce4cc52412310a7a4db83863 Author: lijewski Date: Wed Sep 23 20:19:38 1998 +0000 bldFineLevels() now iterates through regrid() till grids don't change. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit bd3839d5c8232b2e792a72c271ef4d9e9bdc32ef Author: lijewski Date: Tue Sep 22 23:42:59 1998 +0000 Removed Amr_Auxil.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Amr_auxil.H commit 734a2318e50a581578596eaa436cd3c8e68afa1d Author: car Date: Tue Sep 22 20:29:00 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit 710021567886544cc673812d4b99f52ae13cff71 Author: car Date: Tue Sep 22 18:06:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit be35caf639e93ec17646bc70e0ecc8916dc60496 Author: car Date: Fri Sep 18 20:26:12 1998 +0000 proj.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 9e7e421614024e3afc00485723e095bd513e64cc Author: car Date: Fri Sep 18 18:03:46 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit db6788cc56eb184e6702e8e66ded4af9b11d95cc Author: car Date: Fri Sep 18 00:09:28 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit db7d37acb2a5e983cfa7512d36d8da59ea7d7dab Author: car Date: Thu Sep 17 17:05:35 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 2d94c7ecf8ee39531847b0f553caadf4103b20e5 Author: car Date: Thu Sep 17 16:46:06 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 4418bb1175f9d2bd2e0b552350e0e21f8c4939f4 Author: car Date: Wed Sep 16 18:18:37 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 47c0da5e9155b149fdd28f6c376530d92a38b0c3 Author: car Date: Wed Sep 16 03:36:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit 2329a2e804320ca3b13ca306a60c235f9fd7a730 Author: lijewski Date: Tue Sep 15 22:31:40 1998 +0000 Added amr.plot_vars ParmParse variable and a couple supporting functions. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit da893f7ec4c65231499debfd1c1bde9c0bbf4ac9 Author: lijewski Date: Tue Sep 15 00:11:06 1998 +0000 Undid 1.20. Src/C_AMRLib/StateData.cpp commit 639ed6b3264abf7849b00c5e5cf89d97e9362278 Author: lijewski Date: Mon Sep 14 23:28:56 1998 +0000 Ability to set ghost cells to average of min/max in Write() Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 40e1430ca7e72c4da435a3b8bbeda375f8550b56 Author: lijewski Date: Mon Sep 14 23:28:13 1998 +0000 Set ghost cells to average of min/max on VisMF::Write() in checkPoint(). Src/C_AMRLib/StateData.cpp commit 5c996ae3cfafab438523901f4d292cd9022ddcec Author: lijewski Date: Mon Sep 14 21:50:34 1998 +0000 format and fabio weren't in sync after an init() or setFormat(). Src/C_BaseLib/FArrayBox.cpp commit 24e8f374c12bbca71d98a7c77807c146abcb6efb Author: 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 Date: Fri Sep 11 21:15:42 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit bb60f21f571e36cc9a7d52b7dd1bc914379e6146 Author: lijewski Date: Fri Sep 11 20:04:17 1998 +0000 Added some stat output stuff in #if 0 ... #endif block. Src/C_BaseLib/DistributionMapping.cpp commit d9c2a723e7b3e3788c8c742a33495c92d69f7daf Author: lijewski Date: Fri Sep 11 19:58:15 1998 +0000 Minor cleanup to linInterp stuff. Src/C_AMRLib/StateData.cpp commit 923cfd6a71957e6068ef1b84ee530a62a1959076 Author: lijewski Date: Thu Sep 10 17:59:13 1998 +0000 StartParallel() now does a MPI_Barrier() as a last step. Src/C_BaseLib/ParallelDescriptor.cpp commit f012b4f26632a6eea623d6ac84f3465287756a77 Author: car Date: Wed Sep 9 23:49:28 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 9aacfb93dd2687dd9695c108cb69bbe3c0db3662 Author: car Date: Wed Sep 9 19:57:26 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 3ed433555c6e3fdcaf1b2365f1eb906f7a00a2fe Author: car Date: Wed Sep 9 17:17:45 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 45cf93d29364c41f5c55df12b0f7e3e3c0c0d950 Author: car Date: Tue Sep 8 23:12:15 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hglib.dsp commit 2b5620225cef07a946c57b847ba64b416f8113ab Author: car Date: Tue Sep 8 23:06:26 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 90eb70b66b3de157095e03734f4543a4423e8663 Author: car Date: Tue Sep 8 23:00:04 1998 +0000 *** empty log message *** Src/C_BaseLib/pBoxLib_2.dsp commit 57cdd7b13035302d505ed24cad4f7c06443b6e4b Author: car Date: Tue Sep 8 22:59:40 1998 +0000 cleanup Src/LinearSolvers/C_NodalMG/GNUmakefile commit d6331628bc751ea0cafab9f8b235038123b4545a Author: car Date: Tue Sep 8 22:35:55 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit ce05e0a9949fdf04b2a3e679b73eec41dc79cad4 Author: car Date: Tue Sep 8 21:07:32 1998 +0000 counted pointer Src/LinearSolvers/C_NodalMG/hgparallel.h commit 4d254df0da070078dcad99ce1053944eb887c79c Author: car Date: Fri Sep 4 22:31:12 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/interface.H commit 4aef54aa70c7acb1b9bf8b3c5433911eb1b16686 Author: car Date: Fri Sep 4 19:30:28 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 8e6bff33f49f788ea4dec30c87c6727be4d753d0 Author: car Date: Thu Sep 3 18:30:15 1998 +0000 Really No changes. Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit a2c4039db8020fe224960dc83e4fab1ed57f24f8 Author: car Date: Wed Aug 26 17:48:15 1998 +0000 added back graph stuff Src/LinearSolvers/C_NodalMG/interface.cpp commit 3aeba57bb0280faf4bc23fc4898d4dc309ec0e04 Author: 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 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 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 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 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 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 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 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 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 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 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 Date: Wed Aug 19 17:22:00 1998 +0000 Minor changes. Src/LinearSolvers/C_NodalMG/amr_defs.H commit ee526c123e5427ca7c24792e137000008f0314ea Author: car Date: Fri Aug 14 22:51:08 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 023511f96d7603fa699be254cc6bef5e347d36fe Author: car Date: Fri Aug 14 17:26:39 1998 +0000 Fix for g++, no limits header file Src/C_BaseLib/FArrayBox.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit df7a663a1f3e7b2e55627f4c0a43c20867469d23 Author: car Date: Fri Aug 14 16:37:34 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.h commit 174066e21cd0f617b0d18ffe31cb881452a58b82 Author: car Date: Fri Aug 14 16:36:19 1998 +0000 Fixes for WIN32 Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp commit 251295b9ce2a2337d5dcb7f5753225f80ef382d2 Author: 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 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 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 Date: Thu Aug 13 22:54:40 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 78d09767d022606b4a60e2124c1be14736aba265 Author: car Date: Thu Aug 13 22:48:56 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 06a6729f1cbf94655818eee0adca6b7baab576e0 Author: lijewski Date: Wed Aug 12 18:00:53 1998 +0000 Added more MPI RunStats. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp commit f15f4d21f8e5de4610a84deeca6e0e04d7d8ce66 Author: lijewski Date: Tue Aug 11 20:33:38 1998 +0000 Added mpi RunStats Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp commit 794c4ec7b68a14699302138e4e369f5f24c300c6 Author: lijewski Date: Tue Aug 11 20:33:20 1998 +0000 Added mpi RunStats. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit 8e605cebccf49ba1a0c4c3cde3e362684bd187ae Author: lijewski Date: Mon Aug 10 17:03:57 1998 +0000 Didn't get BL_T3E & BL_CRAY stuff quite right. Src/C_BaseLib/CONSTANTS.H commit 787b7b6560c790c475e77b51bcdd2491e2e1cba4 Author: lijewski Date: Sat Aug 8 17:25:23 1998 +0000 Merged in BL_OLD_STL Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/CArena.cpp Src/C_BaseLib/CONSTANTS.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp Tools/C_mk/Make.CRAY Tools/C_mk/Make.OSF1 Tools/C_mk/Make.T3E Tools/C_mk/Make.defs commit 9fe2a51522b53693d387edcfb62fff45d8df42aa Author: car Date: Fri Aug 7 17:46:59 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit e45483ef193af3d0c5f14de7525236f0964ddeaa Author: car Date: Thu Aug 6 23:12:04 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 10208691aa2058cb1ce050e5704f762177552677 Author: car Date: Thu Aug 6 20:56:37 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H commit 5abff0168516d716a637cd24c40c141723a5457e Author: car Date: Thu Aug 6 20:31:09 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H commit d3388ac98b339c73ceb568f07412a5db1d0e86ca Author: car Date: Thu Aug 6 20:30:04 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 7d4253e6c6eb258e4ffb46bb5ea1fd32d28cae81 Author: car Date: Thu Aug 6 03:46:58 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 08bc7c2665412566fc185ad36c5ac783ac50927d Author: car Date: Wed Aug 5 21:42:15 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit fbb95001f0b6191b17ae8e4b78567b98d6e5dd89 Author: car Date: Wed Aug 5 21:24:42 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp commit 5fa7d7b60bbb7c88c6191ba2b1c50715922a783d Author: car Date: Wed Aug 5 20:57:59 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 007cfb6e9849c5e05da601f500aaea84edfe7373 Author: car Date: Wed Aug 5 19:21:34 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/.cvsignore Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/proj.cpp commit f8d3229288dbc5dce9daaefb33d10876e896e76d Author: car Date: Wed Aug 5 17:49:25 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit e115dda27f62ee113bb17fbbe5a0d85cefd10160 Author: car Date: Wed Aug 5 17:38:20 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit c125fa3ab24760bc37c51ed60b1d56c0fa288d44 Author: car Date: Tue Aug 4 22:57:33 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/hgproj.pg commit 79dd7a9adc41dbbba69612d75040c24edecb50d9 Author: car Date: Tue Aug 4 21:48:58 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit d1c3a2bc4a6b9ffd48ab63d441a0c054c76111f2 Author: car Date: Tue Aug 4 18:25:22 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit e13e57670382dbca52f93356f6f2e33a0c83b4cb Author: lijewski Date: Tue Aug 4 16:41:55 1998 +0000 Removed verbose output referring to flushing various caches. Open gridlog, datalog and runlog in append mode. Src/C_AMRLib/Amr.cpp commit bb3ec38dfd561cc40ae83cd7f07856b2333e1f16 Author: car Date: Mon Aug 3 20:35:00 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit b7a7ff9995f8b7701dcbb45d18901aebe2a88645 Author: car Date: Mon Aug 3 20:02:39 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 9b327ebfd51915b6b698fe569c1f8b2aa6c1d5ab Author: car Date: Mon Aug 3 19:26:26 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit ebbcc980f3b957c7724b1e1d77951b76caffd80d Author: car Date: Mon Aug 3 18:01:56 1998 +0000 Some parallel fixes for single level. Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit 679f6914e0ac47151744c6bd3761cb999ffb8184 Author: car Date: Fri Jul 31 17:23:04 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit b0815ad94beb95de0cf13e4729629bfca08b840d Author: car Date: Thu Jul 30 23:14:14 1998 +0000 Removing BSP Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/Make.package Src/LinearSolvers/C_CellMG/Test/main.cpp Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/Make.package Tests/LinearSolvers/C_CellMG/main.cpp commit 6d94a74e21b57539482876ebf434e50658bb5c39 Author: car Date: Thu Jul 30 23:13:45 1998 +0000 more preload removal mods Tools/C_util/README commit b2098def6a6026dc2590862aafc00c1e87a44b24 Author: car Date: Thu Jul 30 23:06:43 1998 +0000 Rid ourselves of BSP files... Tools/C_util/preload.cpp commit 15db0bbaa5f0448f68038e7e30a1c1715f92e0bf Author: car Date: Thu Jul 30 21:01:06 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 89e694a20d0ed460e009d8321602232905b87ed1 Author: lijewski Date: Wed Jul 29 20:44:12 1998 +0000 Use Barrier() instead of Synchronize() to sync across processors. Tools/C_util/WritePlotFile.cpp commit 15dd75d476de16e43c36ff87b254834e45016bf7 Author: lijewski Date: Wed Jul 29 20:25:55 1998 +0000 Brought up-to-date with latest ParallelDescriptor mods. Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp commit b7e2bbc06e0526d6a36897213c8e46a5920765ce Author: lijewski Date: Wed Jul 29 20:04:35 1998 +0000 Added back in Broadcast() -- needed by some vis code. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 485500429a2cd95e69a7f53778fe5cc97ac81605 Author: lijewski Date: Wed Jul 29 19:26:39 1998 +0000 Only use cache if BL_USE_MPI && !BL_NO_PROCMAP_CACHE Src/C_BaseLib/DistributionMapping.cpp commit 9030d8571f83858bd1adfe7c5f7b7eef642c11ee Author: lijewski Date: Wed Jul 29 19:09:30 1998 +0000 Brought up-to-date with new ParallelDescriptor and FabArray.H. Src/C_BoundaryLib/FabSet.cpp commit 3b1547bdaf4c8869499a7369c74d312a95b519fd Author: lijewski Date: Wed Jul 29 19:09:05 1998 +0000 Brought up-to-date with new ParallelDescriptor and FabArray.H Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/InterpBndryData.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit 96b9b8da958f5a3afb204b48d3e7b43f0987a4bb Author: car Date: Wed Jul 29 17:21:30 1998 +0000 Added comment for Windows. Src/C_BaseLib/Utility.H commit d5b0688f85d231c49f7493d735a18590c24f4149 Author: car Date: Wed Jul 29 00:06:04 1998 +0000 Dosify. Src/C_BaseLib/Utility.cpp commit 03ab66c88ff98fc63527503489dc985c980e7990 Author: lijewski Date: Tue Jul 28 17:47:49 1998 +0000 Undid the static RunStat -- T3E had a bug. Src/C_BaseLib/DistributionMapping.cpp commit 983a7ea49f2ebc9dcac7d88b0245c3ab46f852b9 Author: car Date: Tue Jul 28 17:16:06 1998 +0000 Added ccse-mpi.H as a T_source. Src/C_BaseLib/Make.package commit b9b41c38318f0c73abae5183e3d248488ecfb078 Author: car Date: Tue Jul 28 03:21:17 1998 +0000 windows fixes Src/C_BaseLib/ccse-mpi.H Src/C_BaseLib/pBoxLib_2.dsp commit f7d6ecedae89a0c4c65d3d5891a9628a6293cddd Author: lijewski Date: Mon Jul 27 21:33:36 1998 +0000 Now using instead of Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit 1c6ee150c88ce41e7c6ea8aab39122d84e60f1fa Author: lijewski Date: Mon Jul 27 21:33:06 1998 +0000 Now using Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/VisMF.cpp commit 9035c2abfdaf9d10ffe56145d59e0be31c6dd161 Author: lijewski Date: Mon Jul 27 21:32:46 1998 +0000 Encapsulates making it slightly easier to change from using BL_USE_MPI or not. Src/C_BaseLib/ccse-mpi.H commit 4fcd9ade357920b0ab2c60c2e1c0e2bc92de7d91 Author: 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 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 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 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 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 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 Date: Thu Jul 23 16:34:00 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 794045ce5858735a3fbcf44d0b55aa9279af8332 Author: car Date: Thu Jul 23 02:49:27 1998 +0000 Not needed Src/LinearSolvers/C_NodalMG/Notes.doc commit 6f9863c1118b358861a5e5097ee2ed5e5ccd7dc1 Author: car Date: Wed Jul 22 21:23:33 1998 +0000 *** empty log message *** Src/C_AMRLib/amrlib.dsp Src/C_BoundaryLib/bndrylib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 57c624c594de17c6b4c328ca8afacc21f1a37d57 Author: car Date: Wed Jul 22 19:45:25 1998 +0000 *** empty log message *** Src/C_AMRLib/amrlib.dsp Src/C_BaseLib/pBoxLib_2.dsp Src/C_BoundaryLib/bndrylib.dsp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 3605dd2ebe46f3838819e30f56b0008981b67c64 Author: car Date: Tue Jul 21 17:44:45 1998 +0000 MSVC change Src/C_AMRLib/TagBox.cpp commit ce3c2836480db709d06c3f3fff6987a9511aedbe Author: lijewski Date: Tue Jul 21 15:23:40 1998 +0000 Now can use this stuff in serial w/o calling Start & Stop routines. Src/C_BaseLib/ParallelDescriptor.cpp commit 2f470ac120279c0a8e363bc8e84d7db1d9b854c9 Author: car Date: Fri Jul 17 17:59:07 1998 +0000 Testing. Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 2cb093275c08d8a72a3d7f4960a96edd12fb0c85 Author: car Date: Fri Jul 17 17:32:59 1998 +0000 Minor changes. Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 82d3ee109d905d79cff863a1d8ed2663ada40dba Author: lijewski Date: Thu Jul 16 18:19:18 1998 +0000 Make sure CoarseBox() for NodeBilinear doesn't produce degenerate boxes. Src/C_AMRLib/Interpolater.cpp commit 3b9549d8754c04a0360b0ea095a5f20dd076ed03 Author: car Date: Thu Jul 16 17:34:59 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/Notes.doc Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 2172b1188966f260a12c63a54afbaa11739507cb Author: lijewski Date: Wed Jul 15 22:42:09 1998 +0000 Removed TagBoxArray::mergeUnique(). TagBoxArray::collate() now removes the duplicate IntVects. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 03da4ee53fb957d688eba4aaa60ac9ae28d241f7 Author: car Date: Tue Jul 14 20:47:26 1998 +0000 test Src/LinearSolvers/C_NodalMG/Notes.doc commit e838de8b51745f07687efe71c75688822b8e6bc0 Author: car Date: Tue Jul 14 20:23:41 1998 +0000 Anal changes Src/LinearSolvers/C_CellMG/ABec_UTIL.F Src/LinearSolvers/C_CellMG/CG_2D.F Src/LinearSolvers/C_CellMG/CG_3D.F commit 6a90849e2c05c1296c1ee84a63b4c187a312b197 Author: car Date: Mon Jul 13 21:40:42 1998 +0000 First CHeckin Src/LinearSolvers/C_NodalMG/Notes.doc commit b33116cde52aaa784a503928a6ccfd11da642534 Author: car Date: Mon Jul 13 18:17:39 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit e6b61468f222a9752446318d558e2e0dc0b00c94 Author: car Date: Fri Jul 10 22:32:05 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.h commit e935e1d652ba1fe6e8e734001abe988b0ffe227f Author: car Date: Fri Jul 10 21:56:16 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h commit bd91e2f71567ccad5ddf2304b3e09ea73361643e Author: car Date: Fri Jul 10 20:13:51 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit f5abc83f76dff2d19ba47f1141ba4c04008de3a6 Author: lijewski Date: Thu Jul 9 18:27:33 1998 +0000 Added back in dest_comp argument to FillCoarsePatch(). Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit e569238abbbf0bc0c8a1de470c967be49e650b4f Author: lijewski Date: Thu Jul 9 17:59:24 1998 +0000 Assume dest_comp==0 in FillPatchIterator and FillCoarsePatch Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit b07338ec1e04f88955fe54c1779d09789fd3f5de Author: car Date: Thu Jul 9 00:53:37 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 955335d8250861659872020751f63d31f02f5da3 Author: car Date: Thu Jul 9 00:50:19 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 8fbd155950a8880e9e6f871dc05b744f6ac61d8d Author: lijewski Date: Wed Jul 8 22:26:37 1998 +0000 Modest speedup in how we build PIRMMap. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 02f7e3f533cbd09857f0208ed6f069c08ec902be Author: lijewski Date: Wed Jul 8 21:56:21 1998 +0000 Fixed very subtle bug in FillBoundary() caching mechanism. Src/C_BaseLib/MultiFab.cpp commit 3f3fa8d46f29085d2df28140a417ebb9889c602b Author: car Date: Wed Jul 8 20:19:57 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit a8ee404a15d2cf41b3798314a1d6b50af5f54810 Author: car Date: Wed Jul 8 19:59:19 1998 +0000 *** empty log message *** Src/C_BaseLib/pBoxLib_2.dsp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/hgproj.dsp commit af1c9464de0f3298074d39e107e50270f975ac0d Author: lijewski Date: Wed Jul 8 19:17:51 1998 +0000 Added updated version of self-intersection caching for FillBoundary(). Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 7a71136316a8c1b4b5c0023d5ca1aea36756cad3 Author: 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 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 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 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 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 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 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 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 Date: Tue Jul 7 15:41:52 1998 +0000 Support for g++ 2.8.1 Tools/C_mk/Make.defs commit 754652b595de30289816fa70b1dab04634fe64fa Author: lijewski Date: Mon Jul 6 21:17:24 1998 +0000 Got the sense of a #ifdef wrong. Src/C_AMRLib/Amr.cpp Src/C_BaseLib/VisMF.cpp commit c57eddb2f93289fc1b871db3769f1e410ae6fd0b Author: lijewski Date: Mon Jul 6 20:44:47 1998 +0000 Now use pubsetbuf() by default instead of setbuf(). BL_USE_SETBUF now means to use setbuf() instead of pubsetbuf(). Tools/C_mk/Make.OSF1 Tools/C_mk/Make.T3E commit 4840c7b81fa724b9a64486c1fa4285c9d22d9f0d Author: lijewski Date: Mon Jul 6 20:44:18 1998 +0000 Now use pubsetbuf() instead of setbuf() by default. Src/C_BaseLib/VisMF.cpp commit e2be62ecc3b37c7b479ccd8d934da5df66ec49c6 Author: lijewski Date: Mon Jul 6 20:44:00 1998 +0000 Now use pubsetbuf() by default. Src/C_AMRLib/Amr.cpp commit f3993df69ae507281ca8aec608d096107b2d0a57 Author: lijewski Date: Mon Jul 6 18:05:03 1998 +0000 Removed a setVal(0). Inverted a swith statement and a for loop. Src/LinearSolvers/C_CellMG/LinOp.cpp commit ac7f3aa07d83fe87c1ed6cb81f2b945487ac1243 Author: lijewski Date: Sat Jul 4 03:35:14 1998 +0000 Fixed bug in FillCoarsePatch(). Src/C_AMRLib/AmrLevel.cpp commit e1e04edb5c2bb679643903978bdd6c23d82a7ffc Author: car Date: Thu Jul 2 20:17:06 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/interface.H commit ab5273f2bbaff483b3b64429a13ecc1d1c55b4c8 Author: vince Date: Wed Jul 1 20:43:52 1998 +0000 Added distinction between OSF1 versions 3 and 4. Tools/C_mk/Make.OSF1 Tools/C_mk/Make.defs commit c69cc6b6dd724f1657d7d70a32e72346e7e85603 Author: lijewski Date: Wed Jul 1 19:20:39 1998 +0000 Removed FPMINBOX stuff as well as SerialFillPatch() gunk. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit cdb659e5c140792f73744b4ae1990db9dacf15d5 Author: lijewski Date: Tue Jun 30 23:43:45 1998 +0000 More simplification to FillPatchIterator. Src/C_AMRLib/AmrLevel.cpp commit 23dd6aa740dfc451b5d19333038519b2f336cc70 Author: lijewski Date: Tue Jun 30 15:11:21 1998 +0000 Make sure not to call SerialFillPatch if NProcs != 1. Src/C_AMRLib/AmrLevel.cpp commit 8f0a2bac6616a64b011d9d90531798374eb91f6d Author: lijewski Date: Tue Jun 30 04:33:56 1998 +0000 Fixed bug in FillPatchIterator. Left in some fill patch debugging code. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 81865f1e5014e662a20cf3c448645d5e31b9087e Author: 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 Date: Mon Jun 29 17:03:29 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit 172595fffcd810bb189767bf332239a698e28943 Author: car Date: Mon Jun 29 17:01:54 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit ccefddec778b88dd61d1af52d264f6aa0d9b62cb Author: car Date: Mon Jun 29 16:44:27 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit 22c89a74fa2ccc99704fc6c46a4814edf8c9a85d Author: car Date: Mon Jun 29 16:34:21 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit 8588295485449eb7fe8e827898d4aa0a653d3cd4 Author: lijewski Date: Sat Jun 27 21:34:42 1998 +0000 Some cleanup in FillPatch() FillCoarsePatch() is now more memory efficient. FillPatch() now sets course ghost cells outside of physical boundary. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit bfaf56a3b1d62a9171f517cc097353634e18548e Author: car Date: Fri Jun 26 20:09:31 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit dbc844c5e13d8fae00c60f77f63f76ee96787434 Author: car Date: Fri Jun 26 19:54:02 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 415e30d1ae8587e56353de1b47bd688acc14f357 Author: car Date: Thu Jun 25 21:54:33 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp commit 16e41cb8936a255f94ba5548a3d567d38207a98e Author: car Date: Thu Jun 25 21:26:58 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit f1981df61c70fd9715c4581a97db6732fbb6dc80 Author: car Date: Thu Jun 25 16:34:37 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit 9e458484ce54f6860827013ef1c559a746b4a439 Author: car Date: Thu Jun 25 15:54:12 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit d35510814f7ae67d619701650a0965dfb9e9db8e Author: car Date: Thu Jun 25 00:15:55 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 411c96aca5dc622df51bca351ebedd9504e8e9aa Author: car Date: Wed Jun 24 23:46:21 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 9a5083fa8874e1599531449374bb20d31f2b678c Author: car Date: Wed Jun 24 20:49:06 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 10cf77a7e7d8e79b5047ce059ce9523a749fdf84 Author: car Date: Wed Jun 24 17:34:36 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 13e8f84cf9b6fd53e0261af7f7085d80cc4c8037 Author: car Date: Wed Jun 24 17:26:13 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F commit 7f064dbc747e63f66ff03ea74a43111484704b2c Author: car Date: Tue Jun 23 23:57:52 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit d08288b885ba317206f2431eda6b4a507d396076 Author: car Date: Tue Jun 23 21:52:08 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 6eeb04d508fc40d9684dff415fc6fc790ce9852b Author: car Date: Sun Jun 21 22:10:35 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp commit 69be6883dd8c39175842910aa39c5867bdb18084 Author: car Date: Sun Jun 21 21:53:28 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit c66ece1948676785108625dea0b752360321d157 Author: lijewski Date: Sun Jun 21 18:02:39 1998 +0000 Added additional assert()s re: AddBox() return values. Src/C_BaseLib/Geometry.cpp Src/C_BoundaryLib/FabSet.cpp commit c229d9c30402b7a0df164d271610dd6027430fab Author: lijewski Date: Sun Jun 21 17:56:23 1998 +0000 Added additional assert()s re: AddBox() return values. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit 33e89c8fe55c2f3904e519674396879bfa3c2e73 Author: lijewski Date: Sat Jun 20 16:16:09 1998 +0000 Added copyright notice macro. Src/C_AMRLib/Interpolater.H commit 633a460d95812c6a74818a52b0194d46a8ac7f6b Author: lijewski Date: Sat Jun 20 03:20:02 1998 +0000 Fixed bug in mapPeriodic(). Src/C_AMRLib/TagBox.cpp commit efed1cc469397715266be52febaaa47d10e28298 Author: car Date: Fri Jun 19 22:47:15 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit f3955f2b7a210de23fa6ca5501e5182b98f94c01 Author: car Date: Fri Jun 19 19:06:45 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit bdc7f5dae242534a53fb50a724ba2a6c92b25e6f Author: car Date: Fri Jun 19 18:18:21 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 4bf971d51746922cc2be0ad92ea186e076aba81e Author: car Date: Fri Jun 19 18:18:20 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit f889f5d7e31c53fe044ef330867fedf608a7a9a2 Author: lijewski Date: Thu Jun 18 23:45:52 1998 +0000 Added another assert(). Src/C_BoundaryLib/FabSet.cpp commit 8005805006ecbcd15a8ae7fec0fb682f8e46fc1f Author: car Date: Thu Jun 18 19:44:50 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 71eeaa3e0a792707ffc9c123164d36f96c82b010 Author: car Date: Thu Jun 18 18:09:22 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 1cf82a23ecaccb03b5df29f617932ea97682251f Author: car Date: Thu Jun 18 17:54:29 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit c144a79a6279c685e4d4ba1401259113560d9e1d Author: car Date: Thu Jun 18 15:36:57 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit bd14e91d873b2927586cbec69cb29d353ee6add9 Author: lijewski Date: Thu Jun 18 04:12:41 1998 +0000 Fixed a bug in the caching of FPBs. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 4b859a41aacfa2e453ad8f272381c4f329295300 Author: car Date: Wed Jun 17 23:20:31 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 67e915b53391f7f10c0209f32f3fc91d21814ea1 Author: car Date: Wed Jun 17 19:15:52 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit c2cf6e594a54b930313777e9e2e3a846a960f9e6 Author: car Date: Wed Jun 17 18:16:57 1998 +0000 2D Changes.2D Changes. Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 463a91959d376534fce6a6ff37161f7739034c91 Author: car Date: Wed Jun 17 18:15:55 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 7a62ed5399b7fc51b377e2eed2390047f72865e7 Author: car Date: Wed Jun 17 17:23:25 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit e75c09420c3d8d1773053a02414cfef9a61a5454 Author: car Date: Wed Jun 17 17:00:43 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 8d47ca3625fc533cb62d03a1c04df7d06bef89d3 Author: car Date: Tue Jun 16 23:30:05 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F commit cdf50693ac914da1496404b3245b7d22d3c76950 Author: car Date: Tue Jun 16 20:53:48 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/pBoxLib_2.dsp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 9d9f353d2f211dc0e74d8717b42886dd5db6580c Author: lijewski Date: Tue Jun 16 18:02:04 1998 +0000 Slight change regarding how we get MFCD from MultiFab. Src/C_BaseLib/Geometry.cpp commit 0b8283371464b3b023e12cd9a3bc636940583e71 Author: lijewski Date: Tue Jun 16 18:01:37 1998 +0000 Removed call to FlushSICache(). Src/C_AMRLib/Amr.cpp commit eee472c2de77c73d72eaf47c15bcefec80909a0f Author: lijewski Date: Tue Jun 16 18:01:13 1998 +0000 Removed the self-intersection cache. Doesn't look to have been really useful. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit fcf7e67b8a08e6227c968711d68789aa365992d7 Author: lijewski Date: Tue Jun 16 18:00:46 1998 +0000 Made FabArrayCopyDescriptor::clear() really work. Src/C_BaseLib/FabArray.H commit 34490600ebd8622fb2dd61a33b9f65b89c37b34f Author: car Date: Tue Jun 16 16:02:03 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit c05d5ba365e6efa6ae3657db501620fbdef7d9c2 Author: car Date: Tue Jun 16 16:01:06 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit ea6e6271240198016287e99933aea1a8e96364d9 Author: car Date: Tue Jun 16 15:59:43 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 7742841d0d357066184e5cd40054c7e802af863b Author: car Date: Tue Jun 16 15:41:38 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit a908a29917e1d4d7f490f4d6e7cc696333b9853d Author: car Date: Tue Jun 16 03:39:03 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 01b01a3aa32a01b5c5dafeb41d21f5b775e858ea Author: car Date: Tue Jun 16 00:04:49 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 4a84e4d6cc701e737441be9fb383012137b62d4d Author: lijewski Date: Mon Jun 15 23:55:36 1998 +0000 Added MultiGrid::FlushSICache(). Src/C_AMRLib/Amr.cpp commit 6fb6ea6a2c96af797ccd30ec7595bee5ecf07a50 Author: lijewski Date: Mon Jun 15 23:55:13 1998 +0000 Decreased size of cache. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit c6a0ed164acd968030eb14db750fd18b94e7165a Author: lijewski Date: Mon Jun 15 23:54:24 1998 +0000 Added grid self-intersection cache for FillBoundary(). Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit e45ca94d4f9e68a25da6a47b0445c1d994f11c45 Author: lijewski Date: Mon Jun 15 23:53:44 1998 +0000 Inlined operator==()s. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 163788f5968a2952684dedd7debd4cdce2f8811d Author: lijewski Date: Mon Jun 15 23:52:57 1998 +0000 Simplified operator==() a tad. Src/C_BaseLib/Array.H commit 65d766483954b56d98fd9579a4893cd233db1a49 Author: car Date: Mon Jun 15 21:18:17 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 3d4ec5cb5927a196d925c4356e44be8579364707 Author: lijewski Date: Mon Jun 15 20:06:16 1998 +0000 Rearranged how FPB stuff is done. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 57ce3103b2b9580058aa91b73b2385b928b5645b Author: car Date: Mon Jun 15 16:07:17 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 3e5773e32432cdf123390035ba7841c26028aec8 Author: lijewski Date: Mon Jun 15 15:13:25 1998 +0000 Added fabarray_copy RunStat. Src/C_BaseLib/FabArray.H commit 8b3b3bf6af182eb9c92a54cde938d342305c5fcc Author: 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 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 Date: Sat Jun 13 21:12:28 1998 +0000 Added more RunStats. Src/C_BoundaryLib/FabSet.cpp commit 060c83eda88e567d5f8231ee42c1692b08c3a162 Author: lijewski Date: Sat Jun 13 21:07:34 1998 +0000 Added reflux RunStat. Src/C_AMRLib/FluxRegister.cpp commit 96f54fc316fa9a64727c486b84b230e3b0b11970 Author: lijewski Date: Sat Jun 13 21:00:35 1998 +0000 Use vector instead of List for cache. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 45cfc77319d7eb4b31fe8c132364332de90ae0c5 Author: lijewski Date: Sat Jun 13 21:00:09 1998 +0000 Some performance mods and additional RunStats. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BoundaryLib/FabSet.cpp commit 268aa7d4068988d171587a1edf6c88fa37248ade Author: lijewski Date: Sat Jun 13 17:28:58 1998 +0000 Added theFPBmfcd() for cacheing FillPeriodicBoundary info. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 5ceb440691ee08060545f3d222d29341cd0cd5e8 Author: lijewski Date: Sat Jun 13 17:28:30 1998 +0000 Now use MultiFab::theFPBmfcd() Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 6a929bf1a8cd8517ff78f31d5538fad088b36dc3 Author: lijewski Date: Sat Jun 13 15:50:01 1998 +0000 Geometry now caches PIRM stuff. Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit 31f369285847bd84741c0f3f44a60823c5806a85 Author: lijewski Date: Sat Jun 13 15:49:43 1998 +0000 Added a CacheSize() member. Src/C_BaseLib/DistributionMapping.H commit 5a54165d5efff962532b19bf540df9509eb435c6 Author: lijewski Date: Sat Jun 13 15:49:08 1998 +0000 Now cache PIRM stuff. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 08f292a438ee7e35c23ab06f901d4ec29aec054c Author: 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 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 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 Date: Fri Jun 12 16:47:08 1998 +0000 Added BL_COALESCE_FABS. Tools/C_mk/Make.T3E commit 8d1ad158a7b0e28ec80ab37cc6d0e7f9b79b7a2c Author: 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 Date: Fri Jun 12 16:25:18 1998 +0000 Performance mods for second Reflux(). Src/C_AMRLib/FluxRegister.cpp commit e66d5561e4e0f540ae18216ae97a122e27c167e0 Author: lijewski Date: Fri Jun 12 00:11:14 1998 +0000 Performance enhancement to first Reflux(). Src/C_AMRLib/FluxRegister.cpp commit 10f17f08af0962957bf203de7276618fef694137 Author: lijewski Date: Thu Jun 11 22:37:45 1998 +0000 Performance mods for mapPeriodic(). Src/C_AMRLib/TagBox.cpp commit 27001f90d0d60bdae05c8b201d0514e8ff5386e5 Author: lijewski Date: Thu Jun 11 21:24:25 1998 +0000 Performance enhancement to CrseInit(). Src/C_AMRLib/FluxRegister.cpp commit 1bb988c51bfe279695802d24303804fdbe2923a7 Author: lijewski Date: Thu Jun 11 18:21:29 1998 +0000 Some FillBoundary() optimizations (hacks?). Src/C_BaseLib/FabArray.H commit 117a1ecfecb1b93a175454b80265ddc38f893e84 Author: 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 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 Date: Wed Jun 10 23:30:13 1998 +0000 windows fix Src/C_BaseLib/FabArray.H commit 64e926f1f4db4e2d2b4f86e32c8a987cbd92374c Author: lijewski Date: Wed Jun 10 22:24:32 1998 +0000 Added RunStats to FillBoundary. Src/C_BaseLib/FabArray.H commit c7f2bcb85d50e5e1bb4d09caaf8a7d681ec33c38 Author: lijewski Date: Wed Jun 10 22:19:49 1998 +0000 Use std::vector instead of Array. They're much more efficient when resize()d often. Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp commit a50e7e4e9722df5e6930d81e25040ed9b2779cae Author: lijewski Date: Wed Jun 10 22:18:58 1998 +0000 Reverted out latest FillPeriodicFabArray mods. Got to be a better way ... Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit dfc91906f8ae0fae9ae47b9409a8458cda3c7ffd Author: lijewski Date: Wed Jun 10 19:40:49 1998 +0000 Added second version of FillPeriodicFabArray(). Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 2dca999ec4eebd18a4b60827d35a8511381321d7 Author: lijewski Date: Wed Jun 10 19:20:00 1998 +0000 Now use std::vector instead of Array<> in FabArrayCopyDescriptor. Src/C_BaseLib/FabArray.H commit a134bff23972343a0cf81b149cc6350fb6e6ff0f Author: 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 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 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 Date: Tue Jun 9 23:04:48 1998 +0000 Added fill_patch RunStats variable. Src/C_AMRLib/AmrLevel.cpp commit e7051171a985c9f35700da66111e2144d523b517 Author: lijewski Date: Tue Jun 9 21:41:39 1998 +0000 Put ifdef USE_BSP around the sync in isValid(). Src/C_BaseLib/FabArray.H commit cd3a323fbe7a060eb6c5e5ec4600db9f81937bcc Author: 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 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 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 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 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 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 Date: Fri May 29 19:46:52 1998 +0000 Removed a couple unnecessary lines. Src/C_AMRLib/TagBox.cpp commit 82bb64a255d90863ffa63814b5c9aa8941e3b357 Author: lijewski Date: Fri May 29 18:01:37 1998 +0000 Added toDouble(), toInteger() and toLong(). Src/C_BaseLib/aString.H commit 8621f57ed33a13d1f1784e7eff7c5da925f3839c Author: lijewski Date: Thu May 28 21:34:29 1998 +0000 Parallel copy() now generalized to accept num_comp, src_comp & dest_comp. Src/C_BaseLib/FabArray.H commit 3e43b6cc7ad43d4dbddfe9ba28595df9636ba8f7 Author: lijewski Date: Thu May 28 21:34:01 1998 +0000 A little cleanup. Src/C_BaseLib/MultiFab.cpp commit 0e37e973b4464691d4c30c95edbc5ce6200670e9 Author: lijewski Date: Thu May 28 21:33:45 1998 +0000 copyTo(MultiFab) & copyFrom(MultiFab) implemented in terms of FabArray copy Src/C_BoundaryLib/FabSet.cpp commit 1eb0857e05dd72d99c6b196f03de23de7308e65d Author: lijewski Date: Thu May 28 21:32:03 1998 +0000 Some more cleanup. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit f0508c21ccab87492f454c80c3a32fdc39768cea Author: lijewski Date: Thu May 28 18:19:29 1998 +0000 boxarray is now mutable so FabSet can change it in const member functions. Src/C_BaseLib/FabArray.H commit e34584cd349f6831a972a514f8cf7331221fe469 Author: lijewski Date: Thu May 28 18:18:55 1998 +0000 copyTo(MultiFab) is now implemented with FabArray::copy(FabArray). Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 4d4893bfc79a6ba01b1665c534538fb30506dec4 Author: 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 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 Date: Wed May 27 22:46:11 1998 +0000 Added Broadcast for MPI. Src/C_BaseLib/ParallelDescriptor.cpp commit 22bb2ce03152b7e75db8d6e1673770d44c6c60f9 Author: lijewski Date: Tue May 26 22:58:40 1998 +0000 Merged in new FillFab() routine. Not so fast-n-loose with FillBoxId copying. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit 1a896efc7b5cb406aef5f1468fa70b66565b1651 Author: lijewski Date: Tue May 26 22:58:17 1998 +0000 Merged in second FillFab() routine. Not so fast-n-loose with FillBoxId copying. Src/C_BaseLib/Geometry.cpp Src/C_BoundaryLib/FabSet.cpp commit 367acbaee06e3c8567eaf0348e41fc5d86505a5f Author: lijewski Date: Tue May 26 22:57:43 1998 +0000 Added second FillFab() taking a destination Box. Merged common code in two AddBox()s into AddBoxDoIt(). Src/C_BaseLib/FabArray.H commit 539345f912154875620e8c0692fca0c54d124142 Author: lijewski Date: Tue May 26 17:08:54 1998 +0000 Integrated in vector::iterator. Src/C_AMRLib/FluxRegister.cpp commit 3bb35c72513baaf54e1436dedcd41f6bf566d4cc Author: lijewski Date: Tue May 26 16:17:16 1998 +0000 Oops. Didn't check BSP. Src/C_BaseLib/FabArray.H commit aa21e359e0d43b46db42069e05041eedb82eb591 Author: lijewski Date: Tue May 26 00:27:07 1998 +0000 Now use the form of AddBox() in Reflux() taking FabArray grid index. Src/C_AMRLib/FluxRegister.cpp commit 463c99a3a6cdbc921b8d041e48a38e8961b6b8ba Author: lijewski Date: Tue May 26 00:01:48 1998 +0000 Optimized size of temp FAB used in CrseInit(). Src/C_AMRLib/FluxRegister.cpp commit 4775cdb3ade185292ab9e5b4c88f6825dfca177c Author: lijewski Date: Mon May 25 22:55:24 1998 +0000 Optimized away the temp FAB in copyFrom() and plusFrom(). Src/C_BoundaryLib/FabSet.cpp commit d3299d7c2703e2ccad62726ded19c5ab8eaf3940 Author: lijewski Date: Mon May 25 06:01:24 1998 +0000 Fixed bug in FillBoundary(). Src/C_BaseLib/FabArray.H commit 868f65d7e04b8cc5e1db5826c94420d055fcd232 Author: lijewski Date: Mon May 25 05:06:25 1998 +0000 Fixed some latent bugs in AddBox() calls. Did some simplification. Src/C_AMRLib/FluxRegister.cpp commit ba558424cab579716bb9366485f9475761de1146 Author: lijewski Date: Mon May 25 05:01:10 1998 +0000 Minor fixup. Src/C_AMRLib/TagBox.cpp commit e8eb1ff7952a70522565a2e6864a3ac48afbf3e2 Author: lijewski Date: Mon May 25 05:00:19 1998 +0000 Fixed some bugs in srccomp/destcomp in AddBox() calls. Src/C_BoundaryLib/FabSet.cpp commit d13fc15f84bcd3ec66aa5f32b034bad7f7c0d711 Author: lijewski Date: Fri May 22 23:52:27 1998 +0000 Moved more FABs out of inner loops. Using resize() instead. Src/C_BaseLib/FabArray.H commit 5f7c2e4659bf80ddd6ecb282fd3cf88b53d77213 Author: 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 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 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 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 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 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 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 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 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 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 Date: Thu May 21 22:44:51 1998 +0000 CXXOPTF=+K2 Tools/C_mk/Make.T3E commit eb3dad0708a4a4c04c5bc134b472b4adcf9fe0cc Author: car Date: Thu May 21 21:28:43 1998 +0000 assert foolishness Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit a28d2bc7c5eda3dfa47905e7c11cea30efa0209a Author: lijewski Date: Thu May 21 18:16:52 1998 +0000 Added final newline in file to quiet KCC Src/LinearSolvers/C_NodalMG/hgparallel.cpp commit 892f18b47b39782f7c3a388aa4b56133f230b125 Author: lijewski Date: Thu May 21 16:48:39 1998 +0000 DependentFabArrayIterators now check for equality of processor maps. Src/C_BaseLib/FabArray.H commit ab7ffc5cc06a3d8d463f1a367ac5a07b1f189866 Author: lijewski Date: Thu May 21 15:04:29 1998 +0000 Removed DependentMultiFabIterator stuff from FillBoundary(). Src/C_AMRLib/StateData.cpp commit d42f519ad18667b6809aacaaf500ac461f79e93f Author: car Date: Wed May 20 18:10:05 1998 +0000 *** empty log message *** Src/C_BaseLib/pBoxLib_2.dsp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/proj.cpp commit 1fdab4261eda62fd3971ec2dfad2ee05280b89f6 Author: marc Date: Wed May 20 00:10:45 1998 +0000 Make contains() const Src/C_BaseLib/RealBox.H Src/C_BaseLib/RealBox.cpp commit 6d4f14a3e5695db7225091fe36790cf46d79d9b2 Author: 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 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 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 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 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 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 Date: Fri May 15 22:31:29 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F commit feb564285830642f75497aa77ca536ae809b4801 Author: car Date: Fri May 15 22:28:48 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/restrictor.cpp commit a488695861c248581cbbaa0f4a654bbf5d8fed8f Author: lijewski Date: Fri May 15 18:13:12 1998 +0000 Fixed bugs in TagBoxArray::mapPeriodic() and TagBoxArray::coarsen(). Src/C_AMRLib/TagBox.cpp commit 2752cdb382deb3c1c06fce9e7fdd0dad0a33ede8 Author: car Date: Fri May 15 16:36:06 1998 +0000 some 2D fixes Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 2f17a886cd9b761563ebc0cda5f669858cfa51ef Author: car Date: Fri May 15 16:16:22 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F commit a10bce6b33a83bf105edef470034e8d502bb8edb Author: car Date: Fri May 15 16:05:36 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F commit 8ac19652c9550ad8f80e002f2173497a6d298e89 Author: car Date: Fri May 15 00:32:20 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgproj.dsp commit b1d3ad8c402f324b4443165eff3eddcbe3e5dd14 Author: car Date: Fri May 15 00:31:48 1998 +0000 3D only, sorry Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hgparallel.cpp Src/LinearSolvers/C_NodalMG/hgparallel.h Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 196f33518fa19219cb852828f86df2ef60fbb982 Author: 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 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 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 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 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 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 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 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 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 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 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 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 Date: Fri May 8 15:58:50 1998 +0000 Added more Doc++ comments. Src/C_AMRLib/FluxRegister.H commit 9b1f50a42174838fe6733881ea567864c817d0f1 Author: lijewski Date: Fri May 8 15:57:12 1998 +0000 Updated Doc++ comments. Src/C_BaseLib/Box.H commit 50116d837fba3e7caa7641e606ad19f55c3a21c2 Author: marc Date: Fri May 8 00:23:56 1998 +0000 Fix up stuff in Reflux that was wrong for certain combinations of src_comp/dest_comp/etc. Src/C_AMRLib/FluxRegister.cpp commit 74f6da13dfb38a3d8926038a1cde95d465c63564 Author: 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 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 Date: Thu May 7 18:28:59 1998 +0000 Microsoft VC++ bug with nested classes Src/C_BaseLib/Geometry.H commit 7c299d637344479a114d6762e0e18f568c936478 Author: lijewski Date: Wed May 6 22:36:14 1998 +0000 Added doc++ comments. Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/RealBox.H Src/C_BaseLib/RealBox.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/FabSet.H commit 04f6e3a2f05e6deda8f6cbb5e86aa286813d25b8 Author: car Date: Wed May 6 22:21:07 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 29a476612c11eb7d4b25b7ab9c88cfe90f09e9a2 Author: car Date: Wed May 6 20:11:54 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit a76fe3014c9100bac09f27eadd48ab5c95ed14a4 Author: 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 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 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 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 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 Date: Mon May 4 23:13:13 1998 +0000 Implemented ReduceBoolAnd() and ReduceBoolOr() for MPI. Src/C_BaseLib/ParallelDescriptor.cpp commit 501687e6c569be69267e0c1147ee507526ef4b2f Author: lijewski Date: Mon May 4 21:24:53 1998 +0000 Added doc++ comments. Src/C_BaseLib/Array.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/CArena.H Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/NormedFab.H Src/C_BaseLib/OrderedFab.H Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/Pointers.H Src/C_BaseLib/RunStats.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.H Src/C_BaseLib/VisMF.H commit 3d75d1791fc253af1ce8335418c4b236459f2d07 Author: car Date: Mon May 4 17:36:56 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 725ebfb1c1db546741aacba43b93ba5f375b7c91 Author: car Date: Fri May 1 19:18:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit d6af5171f4fc2700f4bda59bd14a5948e1de9768 Author: car Date: Fri May 1 18:23:58 1998 +0000 *** empty log message *** Src/C_BaseLib/GNUmakefile Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 82cfbb3faf9026d05f31dd4cd42417fc3cefdf4c Author: lijewski Date: Fri May 1 17:12:32 1998 +0000 Mods to FillFab() so g++ 2.8.1 will compile. Src/C_BaseLib/FabArray.H commit 6f593dc5666a88e24c0783aa6e4ad71544bb8860 Author: lijewski Date: Thu Apr 30 18:04:33 1998 +0000 Removed member template OpMin(). Src/C_BaseLib/Utility.H commit 47d83a41751b99cbb214fc7551af82bc2f95b9f6 Author: lijewski Date: Thu Apr 30 16:35:03 1998 +0000 Mods to quiet g++ 2.8.1 Src/C_AMRLib/Amr.cpp Src/C_BaseLib/ArithFab.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/Utility.cpp commit 6cfe0d492fa84f34438274f3aebe564fd2ceb85f Author: lijewski Date: Thu Apr 30 15:51:19 1998 +0000 Removed BL_AUTO_INSTANTIATE Tools/C_mk/Make.OSF1 Tools/C_mk/Make.defs commit 994f11573bdcf568e0880f35303f2fcbea8eaed9 Author: lijewski Date: Wed Apr 29 23:12:37 1998 +0000 fixed typo for GNUG workaround Src/C_BaseLib/Geometry.H commit 10c49047a59f44ddf4b2b4003cd0a821d5f87ab8 Author: car Date: Wed Apr 29 22:39:44 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 4f2c5e7e8244fe9aa07bfade539d3bc41637bc5f Author: lijewski Date: Wed Apr 29 20:06:10 1998 +0000 Changed way GNUG workaround was coded. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 1e5580caa9084f08f3ee3c643c47a2b6bd25368d Author: car Date: Tue Apr 28 15:43:09 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/proj.cpp commit 18becd91ca618f6fdf0fa530b05118f6fb746fd2 Author: car Date: Mon Apr 27 21:27:26 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 6facb8f3ad66e230b1db90d97b567923bc023d38 Author: car Date: Mon Apr 27 20:27:18 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 85457a0015bcd8874831f4b1b98320ec84d8763e Author: lijewski Date: Mon Apr 27 19:43:46 1998 +0000 The BoxList argument to AddBox is now passed as a BoxList*. Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 5c36262f7fce8561002659217a7232903c037425 Author: lijewski Date: Mon Apr 27 19:43:19 1998 +0000 The BoxList argument to AddBox is now passed as a BoxList* Src/C_BaseLib/Geometry.cpp Src/C_BoundaryLib/FabSet.cpp commit c1b87b90e593c2544768e6a84f2a340479e22a72 Author: lijewski Date: Mon Apr 27 19:42:54 1998 +0000 The BoxList argument to AddBox is now passed as a pointer to make it easier to deal with the case where we aren't interested in the BoxList. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_AMRLib/TagBox.cpp commit 5f0f443c491388c86caa476b0967694ce76c7d52 Author: car Date: Mon Apr 27 17:37:40 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/restrictor.cpp commit feb36aedcfce10c9c217e0e1581183d00902b1c4 Author: car Date: Mon Apr 27 17:30:25 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 3117be3c7078a956d406790498ef73d8b1ae9713 Author: lijewski Date: Mon Apr 27 16:31:42 1998 +0000 Mods to work on non-standard conformant compilers. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit 74c9a98670185ed2f8f56c46f1bae16b61b59367 Author: car Date: Fri Apr 24 21:23:00 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/interface.cpp commit 63316837b5f93d26e2db98edf4dd01185286c3d9 Author: car Date: Fri Apr 24 21:19:47 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/interface.cpp commit 27a90a275414f655f6ded544b7dc29ea990063fc Author: lijewski Date: Fri Apr 24 17:52:19 1998 +0000 Now maintain NProcs() and MyProc() in static data members. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit d6c79da717ed38c092f58fba68f3ef33d272d3c3 Author: lijewski Date: Fri Apr 24 17:10:18 1998 +0000 Collapsed a number of data members of FabComTag. Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H commit 54253935b5c4ee778db372d394e471f2be806e39 Author: lijewski Date: Fri Apr 24 16:28:57 1998 +0000 Fixed typo. Src/C_AMRLib/FluxRegister.cpp commit 079352692c511336842938d7fe2a73f1c9d48ee3 Author: lijewski Date: Fri Apr 24 16:23:58 1998 +0000 Use query() instead of contains() to set amr.v Src/C_AMRLib/Amr.cpp commit 36bb7bd43d760cb0e52c6ce5490b5b13a82b7e5b Author: car Date: Fri Apr 24 01:03:30 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/interface.cpp commit 45011638c793f40ba1a1611093b3d4e9633e7c38 Author: 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 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 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 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 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 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 Date: Thu Apr 23 04:48:44 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F commit d505119d824ea4e5e82630f06474e4d3e3827c17 Author: car Date: Thu Apr 23 04:46:04 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F commit 396fa27a89de8e666edf4a37e915c54f4e0671a9 Author: car Date: Thu Apr 23 04:31:27 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F commit ee7d29c456c06d82ea2a7824c8646ac0b0fba3f6 Author: car Date: Thu Apr 23 04:13:12 1998 +0000 *** empty log message *** Src/C_AMRLib/Amr.cpp Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit 85f761238cad71087dfc1735a0d05c6a6ee40800 Author: almgren Date: Wed Apr 22 23:56:20 1998 +0000 Removed the trace, debug and silent flags, and replaced them with the verbose flag. Also made verbose be defined by pp.contains("v") rather than pp.contains("verbose"). This is in keeping with how verbose is defined in the IAMR files. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit b59392da518ec3f471d8d4af94cd8e07643440b9 Author: car Date: Wed Apr 22 23:48:13 1998 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/LinOp.H commit fac082321f94478e10ed08880bd00331296ddf0d Author: marc Date: Wed Apr 22 23:39:31 1998 +0000 Added info for periodic boundaries. Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp commit d7d03e61321535750297ed90e0c0cd27cdc608aa Author: car Date: Wed Apr 22 23:39:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 1e67c7076bf42af7b61af4105c6a16468de508d0 Author: car Date: Wed Apr 22 22:51:24 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit b184bd934885569564f65f040d5a6768bf49b7af Author: lijewski Date: Wed Apr 22 22:40:37 1998 +0000 Bug in TagBoxArray::collate(); used sizeof(IntVect) instead of BL_SPACEDIM. Src/C_AMRLib/TagBox.cpp commit 59448e32c7730938bd22d8483c490204c597a497 Author: lijewski Date: Wed Apr 22 21:02:48 1998 +0000 Wasn't erase()ing fabComTagList in MPI case. Src/C_BaseLib/FabArray.H commit 109dfddae71856ea891512c278e5906487301568 Author: car Date: Wed Apr 22 19:58:20 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 45169e70271d7c38f7e02784881c95f78654e862 Author: lijewski Date: Wed Apr 22 19:39:06 1998 +0000 Add setVal() to bad value when debugging on OSF1. Src/C_BaseLib/FArrayBox.cpp commit d475c6b66dc146fae3d5397c6059cbf15698ce7e Author: lijewski Date: Tue Apr 21 23:09:42 1998 +0000 Added TRACER objects to all code making direct MPI calls. Src/C_BaseLib/VisMF.cpp commit ee8a107cc852629b3a1260f17969d1860ae15097 Author: car Date: Tue Apr 21 22:24:25 1998 +0000 *** empty log message *** Src/C_BaseLib/pBoxLib_2.dsp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/proj.cpp commit 3c409a7c87275b0b3ace53558555635be2adf358 Author: almgren Date: Tue Apr 21 22:22:41 1998 +0000 Slight cleanup. Src/LinearSolvers/C_NodalMG/proj.cpp commit edc01757682052d39c38320033e671463d50e66e Author: almgren Date: Tue Apr 21 22:16:50 1998 +0000 Modified proj.cpp to add init calls for m.length() = 3 before each test of the projection so that each test would have the right initial conditions. Also modified the timing routines so they would time the projections and not the initializations. Src/LinearSolvers/C_NodalMG/proj.cpp commit 6c26d5dd8ecce000f1c9d3ac882af45fb581de23 Author: car Date: Tue Apr 21 21:04:03 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/restrictor.H commit 75b5b6073112c848756156c1785eff858bf6db4e Author: marc Date: Tue Apr 21 19:32:43 1998 +0000 Limit optimization reduction to terrain file. Possibly to remove this if we split up the terrain code further Src/LinearSolvers/C_NodalMG/GNUmakefile commit d520452f814de9c3034a7385976354b4e75160a4 Author: car Date: Tue Apr 21 16:40:04 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp commit c735ed463ce53fe9be5a081b5f8adc2ac6b42317 Author: lijewski Date: Tue Apr 21 05:21:08 1998 +0000 Made parallel-aware. Src/C_BaseLib/Tracer.cpp commit d57e0c1e60bffbc47eebf8513ff2535f2b9f6c55 Author: lijewski Date: Tue Apr 21 05:20:27 1998 +0000 Commented out TRACER in StartParallel(). Src/C_BaseLib/ParallelDescriptor.cpp commit e0625861331c0ee5efd1cbb2c9a53a8782a83cd7 Author: car Date: Tue Apr 21 02:01:36 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 3c462c581ce1f9fdfbc13f03dda39e3dcbab6dd6 Author: marc Date: Tue Apr 21 01:44:55 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 7bd9340f4e9f8d6c063b0b14bedb2ed5d30b3b18 Author: car Date: Mon Apr 20 23:44:01 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp commit 845495a0be5b93eafc274574e698f479bbf5dcb3 Author: car Date: Mon Apr 20 22:57:07 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/interface.H commit ea7c26ad081e872fbe127eb7a063048f3ca1a303 Author: lijewski Date: Mon Apr 20 22:43:03 1998 +0000 Added a few TRACER objects in functions making MPI calls. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit 6370aca561925253107e6487bbff3c9570967513 Author: lijewski Date: Mon Apr 20 22:34:09 1998 +0000 Added a few TRACER objects for functions that make MPI calls. Src/C_BaseLib/FabArray.H commit d6e9549ee1d97dabc77a5c6da0f3868b84fe7ca6 Author: 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 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 Date: Mon Apr 20 22:16:38 1998 +0000 Added fflush(stdout) after printf(). Src/C_BaseLib/Tracer.cpp commit 98465ca1c0ab9328a7d9b2cbc2a792c10fbe3b63 Author: car Date: Mon Apr 20 20:24:56 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit d67593938194375bde67bbac520dbb888c510c8a Author: car Date: Mon Apr 20 19:14:08 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.cpp commit fe17ebe460f04f1c49c3004e9485812b2f1db6c5 Author: car Date: Mon Apr 20 19:14:07 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp commit c94d744109f8d8cddc4a9281242b45ce38d1a1d7 Author: 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 Date: Mon Apr 20 04:18:14 1998 +0000 Fixed some MPI-specific bugs. Src/C_BaseLib/VisMF.cpp commit b21629ffdd60d5b4c084ca12f1b1f93ba67c7ece Author: lijewski Date: Sun Apr 19 03:46:41 1998 +0000 Added SetMessageHeaderSize(), ShareVar() and UnshareVar() in MPI as no-ops. Src/C_BaseLib/ParallelDescriptor.cpp commit c384ae692b80b26970506e695293d4e0684fe1a5 Author: 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 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 Date: Fri Apr 17 23:25:08 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit b4301d3c7f381b43df39f2d3b6c4687a0c39c0db Author: car Date: Fri Apr 17 23:25:07 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 8da2bf87fa56c08a4ef775b81b0e062a35cdf89a Author: lijewski Date: Fri Apr 17 22:22:06 1998 +0000 Added three more integers to CommData. Wrote MPI-specific code for CollectData(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 7fe0771fe1c9a71836e5a1cd4edac9efafdbcfd4 Author: lijewski Date: Fri Apr 17 22:21:31 1998 +0000 Added three more integers to CommData. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit 605051d8e388aeac8803d6cf098f7e2194f2137c Author: car Date: Fri Apr 17 20:57:04 1998 +0000 *** empty log message *** Src/C_BaseLib/pBoxLib_2.dsp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 98b6ea565333a32e32f83e9cf51bae36abc72973 Author: car Date: Fri Apr 17 19:22:41 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 23db9b19cd634a9bdcffa28a6377956c291f9220 Author: lijewski Date: Fri Apr 17 18:14:12 1998 +0000 Added fromproc() and id() to CommData. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp commit 5cb1ad0b09f01fb47959384789d4fa61db708396 Author: lijewski Date: Fri Apr 17 18:13:51 1998 +0000 Added fromproc() and id() to CommData. Now use the combination of these two values to match up fab boxes and the data on those fab boxes that are sent separately. Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit c8413243d4a265b6079812215bc155f04b9310fa Author: 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 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 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 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 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 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 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 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 Date: Thu Apr 16 20:31:47 1998 +0000 Fixed minor nit found by dbs. Src/C_BaseLib/IntVect.cpp commit 410c0c78db86ddfe8d589ebbc5dda54ad1f33131 Author: 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 Date: Thu Apr 16 18:00:41 1998 +0000 List<> -> vector<> ... Src/C_BaseLib/FabArray.H commit 44118e52e5a266d3a3543ba2bdae4d95436235a9 Author: car Date: Thu Apr 16 16:15:48 1998 +0000 *** empty log message *** Src/C_BaseLib/pBoxLib_2.dsp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 0cc33d8c42736b2242b36682694f06ae3be672e5 Author: lijewski Date: Thu Apr 16 00:12:29 1998 +0000 List -> vector. Src/C_BoundaryLib/FabSet.cpp commit 3e2db34f65fc7c4db12456707e4f3957882c60da Author: marc Date: Wed Apr 15 23:47:53 1998 +0000 reinstate files Tools/C_util/DatasetClient.H Tools/C_util/DatasetClient.cpp Tools/C_util/README commit 3a437bfd8b1c981c3dc6c7a3b013000f0096ab6a Author: car Date: Wed Apr 15 23:42:26 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 66e4dbf342615b7c135eeb894f68816154fbd8db Author: lijewski Date: Wed Apr 15 23:31:28 1998 +0000 List<> -> vector<> ... Src/C_AMRLib/TagBox.cpp commit e90d0210d6a545be9a1085389c0800b5d6c21fa1 Author: marc Date: Wed Apr 15 23:29:14 1998 +0000 Oops! these were already in DataServices Tools/C_util/README commit 6d7a67405236448059d8e68b89f2b7e98dae52a4 Author: marc Date: Wed Apr 15 23:25:30 1998 +0000 Clean up file Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/Make.package Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/Make.package commit cfecb97b2a206af7f93f2ba3f8bca7bcb59c3dca Author: marc Date: Wed Apr 15 23:19:05 1998 +0000 Clean up the file a little Src/LinearSolvers/C_TensorMG/Test/GNUmakefile Src/LinearSolvers/C_TensorMG/Test/Make.package Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/C_TensorMG/Make.package commit a6e58bc1d9037574fe43cd52830956a969804762 Author: marc Date: Wed Apr 15 23:17:40 1998 +0000 Initial revision Tools/C_util/ArrayView.H Tools/C_util/README Tools/C_util/TV_TempWrite.H Tools/C_util/ViewMF/GNUmakefile Tools/C_util/ViewMF/Make.package Tools/C_util/ViewMF/main.cpp Tools/C_util/WritePlotFile.H Tools/C_util/WritePlotFile.cpp Tools/C_util/preload.cpp commit 8bed072465d592f19e49dacb0a0ceabc65459323 Author: lijewski Date: Wed Apr 15 22:49:54 1998 +0000 List -> vector List -> vector. Src/C_AMRLib/FluxRegister.cpp commit e0ba06555178afb70df28208b280649956908751 Author: marc Date: Wed Apr 15 22:36:20 1998 +0000 Move to util directory Src/LinearSolvers/C_CellMG/Test/WritePlotFile.H Src/LinearSolvers/C_CellMG/Test/WritePlotFile.cpp Src/LinearSolvers/C_CellMG/Test/preload.cpp Src/LinearSolvers/C_TensorMG/Test/WritePlotFile.H Src/LinearSolvers/C_TensorMG/Test/WritePlotFile.cpp Src/LinearSolvers/C_TensorMG/Test/preload.cpp Tests/LinearSolvers/C_CellMG/WritePlotFile.H Tests/LinearSolvers/C_CellMG/WritePlotFile.cpp Tests/LinearSolvers/C_CellMG/preload.cpp Tests/LinearSolvers/C_TensorMG/WritePlotFile.H Tests/LinearSolvers/C_TensorMG/WritePlotFile.cpp Tests/LinearSolvers/C_TensorMG/preload.cpp commit c2c612f07b659317bb8f90cb912d65b798eda1f1 Author: marc Date: Wed Apr 15 22:14:58 1998 +0000 Update to properly extend to multiple components Src/LinearSolvers/C_CellMG/Test/WritePlotFile.cpp Tests/LinearSolvers/C_CellMG/WritePlotFile.cpp commit fe261f8f85593ad868cfcb82d217a114971170ac Author: marc Date: Wed Apr 15 21:48:09 1998 +0000 Enter changes necessary for multiprocessor solves. Src/LinearSolvers/C_TensorMG/DivVis.H Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/MCBndryData.H Src/LinearSolvers/C_TensorMG/MCBndryData.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp commit cdea52552748b2672f813314d4e03c9c6c3158ac Author: marc Date: Wed Apr 15 21:34:44 1998 +0000 Add test files for multiprocessor version of tensor solve Src/LinearSolvers/C_TensorMG/Test/GNUmakefile Src/LinearSolvers/C_TensorMG/Test/Make.package Src/LinearSolvers/C_TensorMG/Test/WritePlotFile.H Src/LinearSolvers/C_TensorMG/Test/WritePlotFile.cpp Src/LinearSolvers/C_TensorMG/Test/amrvis.defaults Src/LinearSolvers/C_TensorMG/Test/inputs2D Src/LinearSolvers/C_TensorMG/Test/inputs3D Src/LinearSolvers/C_TensorMG/Test/inputs8 Src/LinearSolvers/C_TensorMG/Test/main_2D.F Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Src/LinearSolvers/C_TensorMG/Test/vpramps.dat Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/C_TensorMG/Make.package Tests/LinearSolvers/C_TensorMG/WritePlotFile.H Tests/LinearSolvers/C_TensorMG/WritePlotFile.cpp Tests/LinearSolvers/C_TensorMG/amrvis.defaults Tests/LinearSolvers/C_TensorMG/inputs2D Tests/LinearSolvers/C_TensorMG/inputs3D Tests/LinearSolvers/C_TensorMG/inputs8 Tests/LinearSolvers/C_TensorMG/main_2D.F Tests/LinearSolvers/C_TensorMG/testVI.cpp Tests/LinearSolvers/C_TensorMG/vpramps.dat commit 470c9d1936a2f5b1f9c821c77c7b2bff3fc9c6cc Author: marc Date: Wed Apr 15 21:28:32 1998 +0000 Add a couple of test grids. Src/LinearSolvers/C_TensorMG/Test/grids/gr.3_2x3x4 Src/LinearSolvers/C_TensorMG/Test/grids/gr2D Tests/LinearSolvers/C_TensorMG/grids/gr.3_2x3x4 Tests/LinearSolvers/C_TensorMG/grids/gr2D commit 5bd08df7dda6bc1ae1bcf38e322fd26169231f6e Author: marc Date: Wed Apr 15 21:25:55 1998 +0000 Commit cosmetic and other changes to (nearly) complete the port to parallel. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BoundCond.H Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp Src/C_BoundaryLib/Mask.H Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/MultiGrid.cpp Src/LinearSolvers/C_CellMG/WriteMultiFab.H Src/LinearSolvers/C_CellMG/WriteMultiFab.cpp commit 9d97b3659269fc0b29c4b079fee676c79f8dfec2 Author: 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 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 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 Date: Wed Apr 15 18:04:11 1998 +0000 More MPI-specific code. Src/C_AMRLib/FluxRegister.cpp commit 73af34280fa44f348ead07585326ef683eade25c Author: lijewski Date: Wed Apr 15 16:50:45 1998 +0000 Some MPIification .... More to come. Src/C_AMRLib/FluxRegister.cpp commit 3e236e2080a28ecaab01a9c2fb58736ab52d19fa Author: 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 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 Date: Tue Apr 14 23:01:50 1998 +0000 Rearranged CrseInit() to facilitate MPI implementation. Src/C_AMRLib/FluxRegister.cpp commit 22b54ab9f8fd29e590d1418a583149f2140fb62e Author: lijewski Date: Tue Apr 14 21:01:45 1998 +0000 Some more simplification and cleanup before doing MPI work. Src/C_AMRLib/FluxRegister.cpp commit e21fc3c2a428e8c5ba2895892556573c64861f6f Author: lijewski Date: Tue Apr 14 20:24:03 1998 +0000 Now pass integer and Box in MPI as int[1+3*BL_SPACEDIM]. Src/C_AMRLib/TagBox.cpp commit 23fb2a6854a46ed10df7a0158ded29fa5bafe4db Author: lijewski Date: Tue Apr 14 19:38:49 1998 +0000 Optimized a few setVal() calls. Src/C_BaseLib/FabArray.H commit 64f0ccbcd3365da399009c5e5eb0c7dd9427ebfa Author: car Date: Tue Apr 14 17:30:53 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi.cpp commit a8122b0b5f21d5eba1503614f85899c4b208c61d Author: car Date: Tue Apr 14 17:07:24 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi.cpp commit 2930465c7de5d633e88c2e81dab7654a3ce89012 Author: lijewski Date: Tue Apr 14 16:51:39 1998 +0000 Added some (as yet untested) MPI-specific code. Src/C_AMRLib/TagBox.cpp commit f6b1c0a077d4e542841dcb6319df9ef8c953414b Author: lijewski Date: Tue Apr 14 16:50:53 1998 +0000 Fixed some syntax errors in MPI-specific code. Src/C_BaseLib/VisMF.cpp commit 4987f80397ca23815d4e432fc0d5ca04cfccd790 Author: lijewski Date: Mon Apr 13 21:50:13 1998 +0000 Some more (as yet untested) MPI-specific code. Src/C_BaseLib/VisMF.cpp commit 517d20716c7230f29f3b8f0607b8d2c0bd1f10d9 Author: lijewski Date: Mon Apr 13 19:44:42 1998 +0000 Added some (as yet) untested MPI-specific code. Src/C_BaseLib/VisMF.cpp commit 3c153e4425c6a0fb9192154e2349fae7ebfbe832 Author: lijewski Date: Mon Apr 13 19:44:26 1998 +0000 Added Abort(int) for MPI. Now check the return code of MPI calls. Src/C_BaseLib/ParallelDescriptor.cpp commit d1e7119e1b682c019e2314ebe6ff229ffbf885b2 Author: 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 Date: Thu Apr 9 22:37:27 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp commit 85c6f3514cadf0198fa0e28c0e2b553b88ded72b Author: car Date: Thu Apr 9 19:27:54 1998 +0000 fixed makefiles Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/GNUmakefile.main Src/LinearSolvers/C_NodalMG/Make.package commit 49aba79f5804c9f040204d1bfa7f26109fd2da7a Author: car Date: Thu Apr 9 16:18:10 1998 +0000 added serial Gather Src/C_BaseLib/ParallelDescriptor.cpp commit bb74878615df02f0bef789096896ea4b4143d2eb Author: lijewski Date: Wed Apr 8 23:42:52 1998 +0000 Some more simplification. Src/C_AMRLib/TagBox.cpp commit 90034b2762c3f6721fb14b1995095170c847108e Author: lijewski Date: Wed Apr 8 23:29:16 1998 +0000 Some simplification. Src/C_BaseLib/VisMF.cpp commit c0cce08129441844e4899cbd62fc2bec46659492 Author: lijewski Date: Wed Apr 8 21:04:28 1998 +0000 Added ParallelDescriptor::Gather(). Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/RunStats.cpp commit d8efd9235a3fa469a26317eb41ff3952f6ed9fe2 Author: car Date: Wed Apr 8 19:45:20 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp commit 03c24fcab890792b4ffa375d892106b0863e3cff Author: car Date: Wed Apr 8 17:51:11 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit a1cb2b93af61d55733668b0b348ce9f174e2f0f1 Author: lijewski Date: Tue Apr 7 23:10:18 1998 +0000 Only compile in core of knapsack if BSP or MPI is being used. Src/C_BaseLib/DistributionMapping.cpp commit b1fe498fa99587db9f2d35f8628b9509896f7a1a Author: lijewski Date: Tue Apr 7 22:24:44 1998 +0000 More simplification. Src/C_BaseLib/FabArray.H commit af5b86effc4e36eb4e45cebede54a35fc1142727 Author: lijewski Date: Tue Apr 7 20:13:48 1998 +0000 Simplified mergeUnique() a tad. Src/C_AMRLib/TagBox.cpp commit bf784f91509d66634b24344608e5fe46cc3aa3ae Author: car Date: Tue Apr 7 20:03:17 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit b8c55136a41fe773c3b2b6701806ac243cf8206c Author: car Date: Tue Apr 7 19:43:54 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile.main Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 3a82fbb293b21aff8c70291c295887a14d29ce10 Author: car Date: Tue Apr 7 17:36:02 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 7b6666c3b48b6587e937cfd0e06e8f0a5f31fc35 Author: car Date: Tue Apr 7 17:24:21 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 604d85e7fdec50236ae7a1c51b3c8bfdf5764c34 Author: lijewski Date: Tue Apr 7 15:52:23 1998 +0000 Some minor things found by KCC --strict_warnings. Src/C_AMRLib/Derive.H Src/C_AMRLib/ErrorList.H Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/PROB_AMR_F.H Src/C_AMRLib/StateDescriptor.H Src/C_BaseLib/COORDSYS_F.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H commit eb3945456a8c11f1aafac650f60165020eb042a0 Author: car Date: Mon Apr 6 22:43:19 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F commit 4e8a4c256ebd8799b684d8b6dc3788bb735c0e3f Author: lijewski Date: Thu Apr 2 00:14:07 1998 +0000 Removed cacheRemoteData data member; it was always true. Removed faName data member and the two access functions. Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H commit 423664a90559e42a39bcf21afe127db8b965e872 Author: lijewski Date: Thu Apr 2 00:13:02 1998 +0000 Updated to reflect mods to FabArray. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit da85cac2695c143bca21304b5ae5e8d888066070 Author: lijewski Date: Wed Apr 1 18:22:27 1998 +0000 Removed commented out Synchronize() calls. Src/C_BaseLib/FabArray.H commit f3bb677a5c1cf9d506ce3a8445b5f61c041c9aec Author: lijewski Date: Wed Apr 1 18:21:50 1998 +0000 Merged in Barrier(). Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp commit 683d22edce837a47230f1e8c4d57be941bab4fde Author: lijewski Date: Wed Apr 1 17:52:37 1998 +0000 Added Barrier() to the interface. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit e550b5945589dac5ec2370871fe8e2bf5e2c2417 Author: car Date: Wed Apr 1 17:38:35 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F commit 9e402f58ab6949ea45c0d8d9058275845b9c93ba Author: 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 Date: Wed Apr 1 17:01:55 1998 +0000 *** empty log message *** Src/C_BaseLib/test/tVisMF.cpp Src/LinearSolvers/C_CellMG/Test/main.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Tests/C_BaseLib/tVisMF.cpp Tests/LinearSolvers/C_CellMG/main.cpp commit 09f6fbb6b238095dc66b235ad74eaf7b888be8e0 Author: lijewski Date: Wed Apr 1 16:55:04 1998 +0000 Cleaned up code. Implemented Synchronize() for MPI using MPI_Barrier(). Src/C_BaseLib/ParallelDescriptor.cpp commit fd9d4b8767526bdd70aafe429dc6a2ecf415f85e Author: car Date: Wed Apr 1 00:34:07 1998 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/main.cpp Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp commit dbf7eef80773688866ef21c5409fc25b46814338 Author: car Date: Wed Apr 1 00:32:27 1998 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/main.cpp Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/C_TensorMG/testVI.cpp commit effe4482e8d2c52baa8c7daa1d59f94cdb4c559d Author: car Date: Wed Apr 1 00:29:43 1998 +0000 Made Start/EndParallel static Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/test/tVisMF.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Tests/C_BaseLib/tVisMF.cpp commit 501126c3081c37821739ed8c34a697aa147ccf09 Author: marc Date: Wed Apr 1 00:27:32 1998 +0000 Move forward declarations to fix Doc++ doc generation. Src/C_BaseLib/MultiFab.H commit db32bc53c3f404ae8f38161401f6455b6d596f33 Author: car Date: Tue Mar 31 22:58:08 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 6f6868db0b09e2f644cb75bef18eed4f133a46d5 Author: car Date: Tue Mar 31 20:43:12 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 8802d6ce0152cc6234e9c5373d86d3c46a0199fe Author: car Date: Tue Mar 31 18:43:52 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit 9251f066547a179b1d14c69c2382bb7510857a20 Author: car Date: Tue Mar 31 18:25:31 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F commit 679baf2c91d5c6dae1097e4df72b0360f56eb5f7 Author: lijewski Date: Tue Mar 31 00:23:59 1998 +0000 Some reformatting ... Src/C_AMRLib/FILCC_3D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/MAKESLICE_3D.F Src/C_BaseLib/COORDSYS_2D.F Src/C_BaseLib/COORDSYS_3D.F commit 423bef95a2313b969916a4ba11d84a40bc9fe25b Author: lijewski Date: Mon Mar 30 21:57:32 1998 +0000 Cleaned up the code for release. Src/C_AMRLib/BCRec.H Src/C_AMRLib/BCRec.cpp Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H commit e6faecbcc1723d43513c5b52f7ef5f9abf0e0336 Author: lijewski Date: Mon Mar 30 20:45:51 1998 +0000 Removed print() and two unimplemented CrseInit()s. Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp commit 2e5ccce351605e8b01e8bd4a83d58d44deaeabcb Author: lijewski Date: Mon Mar 30 20:23:45 1998 +0000 Removed copyTo(MultiFab). Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 75ae0db1a89fcf0669c232266a0fe3088ecfc74d Author: lijewski Date: Mon Mar 30 20:05:34 1998 +0000 Removed I/O functions. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 67a14231d13b0d4a1a889d59d6b94c6910fe29f9 Author: lijewski Date: Mon Mar 30 20:04:18 1998 +0000 Removed linInterp(). Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 6d0bcaafd93d7ecb19c8cf39393bf5706798f09f Author: lijewski Date: Mon Mar 30 18:59:27 1998 +0000 Removed linInterp(). Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit cdfec93638f4f6efb5f8f9f12769f4cfd4a1f7da Author: car Date: Mon Mar 30 18:35:57 1998 +0000 *** empty log message *** Src/C_AMRLib/amrlib.dsp Src/C_BaseLib/pBoxLib_2.dsp Src/C_BoundaryLib/bndrylib.dsp Src/LinearSolvers/C_CellMG/mglib.dsp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 3474716fcda8d2bc90f17c8e40caef8612fbffd4 Author: lijewski Date: Mon Mar 30 18:14:49 1998 +0000 Removed operator<<(). Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit cbfd49040eaee2c3ea913104f358530c91cd2dfa Author: lijewski Date: Mon Mar 30 18:03:00 1998 +0000 Removed MultiFab(istream). Removed readFrom() and writeOn(). Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 80ce96576533c95076feb9918307323312b4b8aa Author: lijewski Date: Mon Mar 30 17:28:57 1998 +0000 Removed FillPatch(). Removed FillCoarsePatch(FAB). Removed USEUNRAVELEDFILLPATCH define. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit afd277debb8c5a73a028e1d625292024e46ef7be Author: car Date: Sun Mar 29 16:46:11 1998 +0000 *** empty log message *** Src/C_AMRLib/amrlib.dsp Src/C_BaseLib/pBoxLib_2.dsp Src/C_BoundaryLib/bndrylib.dsp Src/LinearSolvers/C_CellMG/mglib.dsp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 8f6861223b52ea34179fa3cd6ded89b2eb82b176 Author: car Date: Sun Mar 29 16:25:55 1998 +0000 *** empty log message *** Src/C_AMRLib/amrlib.dsp Src/C_BaseLib/pBoxLib_2.dsp Src/C_BoundaryLib/bndrylib.dsp Src/LinearSolvers/C_CellMG/mglib.dsp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 5b28850c79690d9b3ae704bb2e132243c89d1b18 Author: lijewski Date: Sat Mar 28 00:45:04 1998 +0000 NEWFPMINBOX -> BL_NEWFPMINBOX Src/C_AMRLib/AmrLevel.cpp commit 72302898b276f59704c360a816981d364651b4f7 Author: lijewski Date: Fri Mar 27 23:53:20 1998 +0000 Removed BL_PARALLEL_IO define. Removed USEOLDFILLPATCH define. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit c1119048349a6656814bc5229911966298e0ebbc Author: vince Date: Fri Mar 27 18:34:00 1998 +0000 Minor additions. Tools/C_mk/Make.T3E commit 8d2ee8f94a3e9b66b87f7e1f73c5f345107b19e7 Author: marc Date: Fri Mar 27 00:41:26 1998 +0000 Remove extra copy of tridiag routine Src/LinearSolvers/C_CellMG/ABec_2D.F commit e989933a8fc150cc8344bc58d07306bce83b1f56 Author: lijewski Date: Fri Mar 27 00:06:39 1998 +0000 Removed unused rangeType() and corresponding member data. Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp commit 09043219e1bcdceac254114ab7c1a8b9f6ac1b2d Author: lijewski Date: Thu Mar 26 22:40:26 1998 +0000 A useless commit ... Src/LinearSolvers/C_CellMG/Test/GNUmakefile Tests/LinearSolvers/C_CellMG/GNUmakefile commit 54927ebd36f6d65358717f9c32b6fe95c0e4bc90 Author: marc Date: Thu Mar 26 22:24:04 1998 +0000 Add PBOXLIB def Src/C_BaseLib/GNUmakefile Src/C_BaseLib/test/GNUmakefile.tCArena Src/C_BaseLib/test/GNUmakefile.test Src/LinearSolvers/C_NodalMG/GNUmakefile.main Src/LinearSolvers/C_TensorMG/MCBndryData.H Src/LinearSolvers/C_TensorMG/MCBndryData.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp Tests/C_BaseLib/GNUmakefile.tCArena Tests/C_BaseLib/GNUmakefile.test Tools/C_mk/Make.T3E Tools/C_mk/Make.defs commit efb5d9a489d249fdcbdcb4fbe7c85d53a3d4471d Author: marc Date: Thu Mar 26 19:31:39 1998 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/Test/grids/gr.2_19boxes Src/LinearSolvers/C_CellMG/Test/grids/gr.2_2x2_a Src/LinearSolvers/C_CellMG/Test/grids/gr.2_2x2_b Src/LinearSolvers/C_CellMG/Test/grids/gr.2_2x2_c Src/LinearSolvers/C_CellMG/Test/grids/gr.2_3boxes_a Src/LinearSolvers/C_CellMG/Test/grids/gr.2_3boxes_b Src/LinearSolvers/C_CellMG/Test/grids/gr.2_3boxes_c Src/LinearSolvers/C_CellMG/Test/grids/gr.2_3x2 Src/LinearSolvers/C_CellMG/Test/grids/gr.2_big Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_a Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_b Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_c Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_d Src/LinearSolvers/C_CellMG/Test/grids/gr.2_disjoint_e Src/LinearSolvers/C_CellMG/Test/grids/gr.2_small_a Src/LinearSolvers/C_CellMG/Test/grids/gr.2_small_b Src/LinearSolvers/C_CellMG/Test/grids/gr.2_stack_a Src/LinearSolvers/C_CellMG/Test/grids/gr.2_stack_b Src/LinearSolvers/C_CellMG/Test/grids/gr.2_stack_c Src/LinearSolvers/C_CellMG/Test/grids/gr.2_stack_d Src/LinearSolvers/C_CellMG/Test/grids/gr.3_2boxes_a Src/LinearSolvers/C_CellMG/Test/grids/gr.3_2x3x4 Src/LinearSolvers/C_CellMG/Test/grids/gr.3_big Src/LinearSolvers/C_CellMG/Test/grids/gr.3_disjoint_a Src/LinearSolvers/C_CellMG/Test/grids/gr.3_disjoint_b Src/LinearSolvers/C_CellMG/Test/grids/gr.3_disjoint_c Src/LinearSolvers/C_CellMG/Test/grids/gr.3_shiftedUp Src/LinearSolvers/C_CellMG/Test/grids/gr.3_small_a Src/LinearSolvers/C_CellMG/Test/grids/gr.3_stack_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_19boxes Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_2x2_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_3boxes_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_3x2 Src/LinearSolvers/C_CellMG/Test/grids/in.2_big Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_d Src/LinearSolvers/C_CellMG/Test/grids/in.2_disjoint_e Src/LinearSolvers/C_CellMG/Test/grids/in.2_small_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_small_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_a Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_b Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_c Src/LinearSolvers/C_CellMG/Test/grids/in.2_stack_d Src/LinearSolvers/C_CellMG/Test/grids/in.3_2boxes_a Src/LinearSolvers/C_CellMG/Test/grids/in.3_2x3x4 Src/LinearSolvers/C_CellMG/Test/grids/in.3_big Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_a Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_b Src/LinearSolvers/C_CellMG/Test/grids/in.3_disjoint_c Src/LinearSolvers/C_CellMG/Test/grids/in.3_shiftedUp Src/LinearSolvers/C_CellMG/Test/grids/in.3_small_a Src/LinearSolvers/C_CellMG/Test/grids/in.3_stack_a Tests/LinearSolvers/C_CellMG/grids/gr.2_19boxes Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_a Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_b Tests/LinearSolvers/C_CellMG/grids/gr.2_2x2_c Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_a Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_b Tests/LinearSolvers/C_CellMG/grids/gr.2_3boxes_c Tests/LinearSolvers/C_CellMG/grids/gr.2_3x2 Tests/LinearSolvers/C_CellMG/grids/gr.2_big Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_a Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_b Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_c Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_d Tests/LinearSolvers/C_CellMG/grids/gr.2_disjoint_e Tests/LinearSolvers/C_CellMG/grids/gr.2_small_a Tests/LinearSolvers/C_CellMG/grids/gr.2_small_b Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_a Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_b Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_c Tests/LinearSolvers/C_CellMG/grids/gr.2_stack_d Tests/LinearSolvers/C_CellMG/grids/gr.3_2boxes_a Tests/LinearSolvers/C_CellMG/grids/gr.3_2x3x4 Tests/LinearSolvers/C_CellMG/grids/gr.3_big Tests/LinearSolvers/C_CellMG/grids/gr.3_disjoint_a Tests/LinearSolvers/C_CellMG/grids/gr.3_disjoint_b Tests/LinearSolvers/C_CellMG/grids/gr.3_disjoint_c Tests/LinearSolvers/C_CellMG/grids/gr.3_shiftedUp Tests/LinearSolvers/C_CellMG/grids/gr.3_small_a Tests/LinearSolvers/C_CellMG/grids/gr.3_stack_a Tests/LinearSolvers/C_CellMG/grids/in.2_19boxes Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_a Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_b Tests/LinearSolvers/C_CellMG/grids/in.2_2x2_c Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_a Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_b Tests/LinearSolvers/C_CellMG/grids/in.2_3boxes_c Tests/LinearSolvers/C_CellMG/grids/in.2_3x2 Tests/LinearSolvers/C_CellMG/grids/in.2_big Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_a Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_b Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_c Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_d Tests/LinearSolvers/C_CellMG/grids/in.2_disjoint_e Tests/LinearSolvers/C_CellMG/grids/in.2_small_a Tests/LinearSolvers/C_CellMG/grids/in.2_small_b Tests/LinearSolvers/C_CellMG/grids/in.2_stack_a Tests/LinearSolvers/C_CellMG/grids/in.2_stack_b Tests/LinearSolvers/C_CellMG/grids/in.2_stack_c Tests/LinearSolvers/C_CellMG/grids/in.2_stack_d Tests/LinearSolvers/C_CellMG/grids/in.3_2boxes_a Tests/LinearSolvers/C_CellMG/grids/in.3_2x3x4 Tests/LinearSolvers/C_CellMG/grids/in.3_big Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_a Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_b Tests/LinearSolvers/C_CellMG/grids/in.3_disjoint_c Tests/LinearSolvers/C_CellMG/grids/in.3_shiftedUp Tests/LinearSolvers/C_CellMG/grids/in.3_small_a Tests/LinearSolvers/C_CellMG/grids/in.3_stack_a commit 54906dbca6fda685521cc67f1ea1a1fb92185c2d Author: marc Date: Thu Mar 26 19:15:27 1998 +0000 Add tensorMG to Parallel repo Src/LinearSolvers/C_TensorMG/DV_2D.F Src/LinearSolvers/C_TensorMG/DV_2D.mF Src/LinearSolvers/C_TensorMG/DV_3D1.F Src/LinearSolvers/C_TensorMG/DV_3D1.mF Src/LinearSolvers/C_TensorMG/DV_3D2.F Src/LinearSolvers/C_TensorMG/DV_3D2.mF Src/LinearSolvers/C_TensorMG/DV_3D3.F Src/LinearSolvers/C_TensorMG/DV_3D3.mF Src/LinearSolvers/C_TensorMG/DV_3D4.F Src/LinearSolvers/C_TensorMG/DV_3D4.mF Src/LinearSolvers/C_TensorMG/DivVis.H Src/LinearSolvers/C_TensorMG/DivVis.cpp Src/LinearSolvers/C_TensorMG/DivVis_F.H Src/LinearSolvers/C_TensorMG/MCBndryData.H Src/LinearSolvers/C_TensorMG/MCBndryData.cpp Src/LinearSolvers/C_TensorMG/MCCGSolver.H Src/LinearSolvers/C_TensorMG/MCCGSolver.cpp Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_2D.F Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_3D.F Src/LinearSolvers/C_TensorMG/MCINTERPBNDRYDATA_F.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.H Src/LinearSolvers/C_TensorMG/MCInterpBndryData.cpp Src/LinearSolvers/C_TensorMG/MCLO_2D.F Src/LinearSolvers/C_TensorMG/MCLO_3D.F Src/LinearSolvers/C_TensorMG/MCLO_F.H Src/LinearSolvers/C_TensorMG/MCLinOp.H Src/LinearSolvers/C_TensorMG/MCLinOp.cpp Src/LinearSolvers/C_TensorMG/MCMultiGrid.H Src/LinearSolvers/C_TensorMG/MCMultiGrid.cpp Src/LinearSolvers/C_TensorMG/Test/GNUmakefile Src/LinearSolvers/C_TensorMG/Test/Make.package Src/LinearSolvers/C_TensorMG/Test/Palette Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.H Src/LinearSolvers/C_TensorMG/Test/TestMCViscBndry.cpp Src/LinearSolvers/C_TensorMG/Test/amrvis.defaults Src/LinearSolvers/C_TensorMG/Test/doit Src/LinearSolvers/C_TensorMG/Test/dotest Src/LinearSolvers/C_TensorMG/Test/grids/gr16.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr16x8.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr32.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr32x8.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr64.dog Src/LinearSolvers/C_TensorMG/Test/grids/gr8.dog Src/LinearSolvers/C_TensorMG/Test/inputs Src/LinearSolvers/C_TensorMG/Test/main_2D.F Src/LinearSolvers/C_TensorMG/Test/main_3D.F Src/LinearSolvers/C_TensorMG/Test/main_F.H Src/LinearSolvers/C_TensorMG/Test/preload.cpp Src/LinearSolvers/C_TensorMG/Test/probin Src/LinearSolvers/C_TensorMG/Test/testVI.cpp Src/LinearSolvers/C_TensorMG/Test/vpramps.dat Src/LinearSolvers/C_TensorMG/visc2d.ma Src/LinearSolvers/C_TensorMG/visc3d.ma Tests/LinearSolvers/C_TensorMG/GNUmakefile Tests/LinearSolvers/C_TensorMG/Make.package Tests/LinearSolvers/C_TensorMG/Palette Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.H Tests/LinearSolvers/C_TensorMG/TestMCViscBndry.cpp Tests/LinearSolvers/C_TensorMG/amrvis.defaults Tests/LinearSolvers/C_TensorMG/doit Tests/LinearSolvers/C_TensorMG/dotest Tests/LinearSolvers/C_TensorMG/grids/gr16.dog Tests/LinearSolvers/C_TensorMG/grids/gr16x8.dog Tests/LinearSolvers/C_TensorMG/grids/gr32.dog Tests/LinearSolvers/C_TensorMG/grids/gr32x8.dog Tests/LinearSolvers/C_TensorMG/grids/gr64.dog Tests/LinearSolvers/C_TensorMG/grids/gr8.dog Tests/LinearSolvers/C_TensorMG/inputs Tests/LinearSolvers/C_TensorMG/main_2D.F Tests/LinearSolvers/C_TensorMG/main_3D.F Tests/LinearSolvers/C_TensorMG/main_F.H Tests/LinearSolvers/C_TensorMG/preload.cpp Tests/LinearSolvers/C_TensorMG/probin Tests/LinearSolvers/C_TensorMG/testVI.cpp Tests/LinearSolvers/C_TensorMG/vpramps.dat commit 51466191c70b6e0f1e4be55945cf84afd2ae2def Author: marc Date: Thu Mar 26 18:58:17 1998 +0000 Added test directory files Src/LinearSolvers/C_CellMG/Test/GNUmakefile Src/LinearSolvers/C_CellMG/Test/Make.package Src/LinearSolvers/C_CellMG/Test/Palette Src/LinearSolvers/C_CellMG/Test/amrvis.defaults Src/LinearSolvers/C_CellMG/Test/main.cpp Src/LinearSolvers/C_CellMG/Test/preload.cpp Src/LinearSolvers/C_CellMG/Test/vpramps.dat Tests/LinearSolvers/C_CellMG/GNUmakefile Tests/LinearSolvers/C_CellMG/Make.package Tests/LinearSolvers/C_CellMG/Palette Tests/LinearSolvers/C_CellMG/amrvis.defaults Tests/LinearSolvers/C_CellMG/main.cpp Tests/LinearSolvers/C_CellMG/preload.cpp Tests/LinearSolvers/C_CellMG/vpramps.dat commit d2012999fb58b439a60f6e8dbbfaec0767d0ce25 Author: marc Date: Thu Mar 26 18:55:51 1998 +0000 Incorporate changes from Bill's tensor solve directory Src/LinearSolvers/C_CellMG/CG_2D.F Src/LinearSolvers/C_CellMG/CG_3D.F commit 9ea73fed1be32867a0a71a635db7fca0c84d7312 Author: almgren Date: Thu Mar 26 17:51:58 1998 +0000 Remove geom from setBndryConds call. Src/C_BoundaryLib/InterpBndryData.cpp commit 27aceb303de91d1d15f7416e9279ffc5a570dcc8 Author: almgren Date: Thu Mar 26 17:51:33 1998 +0000 Remove geom from the setBndryConds call. Src/C_BoundaryLib/InterpBndryData.H commit 494156ce680b792910a36b9b6c6b9a5fc9b2412b Author: lijewski Date: Thu Mar 26 17:32:16 1998 +0000 Added new convert() function. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 6dfbcb7295ad7412d9a11ca6531f377da1b24aca Author: lijewski Date: Thu Mar 26 17:31:50 1998 +0000 Uses new BoxArray::convert() function. Src/C_AMRLib/AmrLevel.cpp commit d60730e7b8a18b0a97f707f5e32862c1b36c044f Author: lijewski Date: Wed Mar 25 21:32:18 1998 +0000 First cut at parallelized AmrLevel::derive(). Needs to be checked out better. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 42f7b8c782cf8b9e12184a405a2afe72f34dff67 Author: car Date: Wed Mar 25 20:59:54 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp commit fa287ca43aab056bfcdd5f8344a9a6438a603e1a Author: car Date: Wed Mar 25 20:54:31 1998 +0000 *** empty log message *** Src/C_BaseLib/GNUmakefile Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/LinearSolvers/C_CellMG/WriteMultiFab.cpp commit cbb89488c4064c612ec55c1df0af76ced40ee085 Author: car Date: Wed Mar 25 19:20:50 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp commit 69287608d46a6b3d28e275e048f17f5f4f060809 Author: car Date: Wed Mar 25 19:17:47 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.cpp commit b80eb3e3c7460bd9523c66a7c247744c5a41645f Author: car Date: Wed Mar 25 19:03:06 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit c552012402c2bd395db846b09a428c16598d49b5 Author: car Date: Wed Mar 25 18:23:08 1998 +0000 *** empty log message *** Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/pBoxLib_2.dsp commit ed078c269f69e382ed28feab5f9132398aa67532 Author: car Date: Tue Mar 24 23:45:14 1998 +0000 *** empty log message *** Src/LinearSolvers/C_CellMG/.cvsignore Src/LinearSolvers/C_CellMG/mglib.dsp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit d8c225f640708d95fc60f8f8289da557c6587851 Author: car Date: Tue Mar 24 20:18:49 1998 +0000 *** empty log message *** Src/C_AMRLib/amrlib.dsp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BoundaryLib/bndrylib.dsp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hglib.dsp commit 9971aec3582f9b51fde496bcf79d2209e384dc1b Author: lijewski Date: Tue Mar 24 19:08:41 1998 +0000 Commented out bunch of cout's in old FillPatch routines. Src/C_AMRLib/AmrLevel.cpp commit e1942293c0be7a47ae80aaa2e1af721d5db7a11d Author: lijewski Date: Tue Mar 24 18:28:29 1998 +0000 Some work in preparation for parallelizing FillDerive(). Src/C_AMRLib/AmrLevel.cpp commit 993f07b149f3f4673b8928614528dcb5790e1109 Author: almgren Date: Tue Mar 24 07:05:10 1998 +0000 Moved this file from ../IAMRAll. Src/C_BoundaryLib/BndryData.H Src/C_BoundaryLib/BndryData.cpp Src/C_BoundaryLib/BoundCond.H Src/C_BoundaryLib/INTERPBNDRYDATA_2D.F Src/C_BoundaryLib/INTERPBNDRYDATA_3D.F Src/C_BoundaryLib/INTERPBNDRYDATA_F.H Src/C_BoundaryLib/InterpBndryData.H Src/C_BoundaryLib/InterpBndryData.cpp Src/C_BoundaryLib/LO_BCTYPES.H Src/C_BoundaryLib/LO_UTIL.F Src/C_BoundaryLib/Mask.H Src/C_BoundaryLib/Mask.cpp Src/LinearSolvers/C_CellMG/ABecLaplacian.H Src/LinearSolvers/C_CellMG/ABecLaplacian.cpp Src/LinearSolvers/C_CellMG/ABec_2D.F Src/LinearSolvers/C_CellMG/ABec_3D.F Src/LinearSolvers/C_CellMG/ABec_F.H Src/LinearSolvers/C_CellMG/ABec_UTIL.F Src/LinearSolvers/C_CellMG/CGSolver.H Src/LinearSolvers/C_CellMG/CGSolver.cpp Src/LinearSolvers/C_CellMG/CG_2D.F Src/LinearSolvers/C_CellMG/CG_3D.F Src/LinearSolvers/C_CellMG/CG_F.H Src/LinearSolvers/C_CellMG/LO_2D.F Src/LinearSolvers/C_CellMG/LO_3D.F Src/LinearSolvers/C_CellMG/LO_F.H Src/LinearSolvers/C_CellMG/LP_2D.F Src/LinearSolvers/C_CellMG/LP_3D.F Src/LinearSolvers/C_CellMG/LP_F.H Src/LinearSolvers/C_CellMG/Laplacian.H Src/LinearSolvers/C_CellMG/Laplacian.cpp Src/LinearSolvers/C_CellMG/LinOp.H Src/LinearSolvers/C_CellMG/LinOp.cpp Src/LinearSolvers/C_CellMG/MG_2D.F Src/LinearSolvers/C_CellMG/MG_3D.F Src/LinearSolvers/C_CellMG/MG_F.H Src/LinearSolvers/C_CellMG/MultiGrid.H Src/LinearSolvers/C_CellMG/WriteMultiFab.H Src/LinearSolvers/C_CellMG/WriteMultiFab.cpp commit 18dd515c42ab7847eb2f640c2b187ae27d403a89 Author: almgren Date: Mon Mar 23 23:36:17 1998 +0000 Moving this file from ../IAMRAll. Src/LinearSolvers/C_CellMG/MultiGrid.cpp commit d06c8e8ec64b18fb1909079f100118c6a57d8fe1 Author: lijewski Date: Mon Mar 23 21:03:17 1998 +0000 Now maintain DeriveRec in List instead of List Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp commit 9de50888e7e7ea480229214ec169ac4393f3402f Author: lijewski Date: Mon Mar 23 21:02:56 1998 +0000 Now maintain ErrorRec in List not List Src/C_AMRLib/ErrorList.H Src/C_AMRLib/ErrorList.cpp commit b823cc551e8037d7eaf09d78517ced580412f9aa Author: lijewski Date: Mon Mar 23 20:20:14 1998 +0000 Removed default constructor and DeriveFuncSrc stuff. Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp commit e06890b6773064c664a03153c8ece3a885e47b75 Author: lijewski Date: Mon Mar 23 17:23:58 1998 +0000 Cleaned up the code ... Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp commit 500f80b5d940ee5b35f34b9a2081e101ff33edcf Author: car Date: Thu Mar 19 19:02:47 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/GNUmakefile.main Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit ed2f3d02c3db7603aa902e140671ccccadc18548 Author: car Date: Mon Mar 16 18:26:33 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/proj.cpp commit 78cad0cf04d5dadc1576576f9c0359691b7640d8 Author: car Date: Sun Mar 15 23:44:53 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F commit 061a52241c3255ff6eb4f32993b8c31afd4822f5 Author: car Date: Sun Mar 15 20:41:04 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit d1c3ee873995175bf0d1d5a81a5c9f1a77f397fb Author: car Date: Fri Mar 13 23:10:31 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit cadf06710b601e167485c418c76d51922b8a4eb6 Author: car Date: Fri Mar 13 22:18:43 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 3db41b0e97acff5837d93fd5f4e3ca97a9bca63e Author: car Date: Fri Mar 13 20:50:30 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit c85294e902d5f40f0f0bc8ebf8870c0fd998bc45 Author: car Date: Thu Mar 12 23:21:13 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 6970820bc9a7f6d71d7c56dfdfea039162ab0307 Author: car Date: Thu Mar 12 21:07:13 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 8be5b29236e3468e034411c1ba575a046ae7555d Author: car Date: Wed Mar 11 21:31:05 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 8a60655758cf1c23673f083b6857ab613a18b0d5 Author: car Date: Tue Mar 10 23:31:12 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 58ef77c733899e23ca2cf6133395e9bcace0fb83 Author: car Date: Fri Mar 6 00:28:22 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp commit ebb64b1d69c3142654d3890b90e2d785105a666b Author: car Date: Thu Mar 5 00:40:33 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 352d330720256f90bf32558458243afc0006b221 Author: car Date: Wed Mar 4 22:44:31 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 75b92dedf7566b09530d4f82e00257cb09744f88 Author: car Date: Wed Mar 4 21:16:37 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit 21878921bdbbe06dd8304b87fe4a4d3883c955ba Author: car Date: Wed Mar 4 03:05:19 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 3cf9a5e9667aa56135deb03a46e35eb975f8cf2d Author: car Date: Wed Mar 4 02:31:23 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit d3204a9d42cc08a726f6e0c8bcec78cc44299e7d Author: car Date: Wed Mar 4 00:55:42 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hgproj.dsp commit ad21d479ebd8e34dfbe4aed8578993deb248d6c2 Author: car Date: Tue Mar 3 23:19:47 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 84032fab90e533e6068e24bdb975500a16ec03b9 Author: car Date: Mon Mar 2 17:57:04 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/cache.cpp commit 30a32794f0af360ed93f9e5b9840e8fabd692019 Author: car Date: Sun Mar 1 22:17:46 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 53a1e97f0def542902a922f992aaf076e1dadfee Author: car Date: Sun Mar 1 21:58:36 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d_terrain.F commit 9fba3e2fb35260266b531312956e15edeb8ad08e Author: car Date: Sun Mar 1 21:51:51 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F commit 6a52dfb6666a010b61c2873c79f5341c1a7e02d1 Author: car Date: Sat Feb 28 17:56:51 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit 18ff5814921f13fa454e553ef4a5090b756925de Author: car Date: Fri Feb 27 22:49:06 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 040c4955055a835aa1e2edb9b42f0cd4471383f4 Author: car Date: Fri Feb 27 21:03:44 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F commit 0398cf30094464180464c32a7b1dcbf5f43af0ef Author: car Date: Fri Feb 27 21:01:17 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F commit a0565f3f87cbee8af57f78825fb2a549aac6d0f8 Author: car Date: Fri Feb 27 20:59:27 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F commit d7ab03739737010b94d4fb22d180406feef80901 Author: lijewski Date: Thu Feb 26 22:07:57 1998 +0000 Made isStateVariable() static. Src/C_AMRLib/AmrLevel.H commit c38372b5d6f5474df5301bf23164cb6b000c7483 Author: car Date: Wed Feb 25 23:24:16 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F commit 72ed30f6a11b06e4439257dc08e70818243a49cd Author: car Date: Wed Feb 25 22:27:33 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 04e17e6fff4a524e8873937a4145f5c2f3cfd77e Author: car Date: Wed Feb 25 21:05:04 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 6a16fca94e170e366f74dca7c9b32af05fe885b2 Author: car Date: Tue Feb 24 19:25:37 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit e9b1951bda3b8fa68fa781f360c6ad0dda440175 Author: car Date: Tue Feb 24 00:27:08 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 62a1db5165620770bf04945b538a6076dcdffe9d Author: car Date: Mon Feb 23 22:55:47 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/proj.cpp commit 20359df7d47d23fe26c73c10ab801c797161e8b6 Author: car Date: Sun Feb 22 20:50:10 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 199545865962fd9e9b72326db5b4f1ad22e363d6 Author: car Date: Sun Feb 22 19:24:25 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_proj2d.F commit 0e2eebe0744aabdf9613bf9b89865de8d4b7fc1b Author: car Date: Sun Feb 22 19:06:57 1998 +0000 anal changes to fortran Src/C_AMRLib/FILCC_2D.F Src/C_AMRLib/FILCC_3D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/MAKESLICE_3D.F Src/C_BaseLib/COORDSYS_2D.F Src/C_BaseLib/COORDSYS_3D.F Src/C_BaseLib/GNUmakefile Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F commit 21a6a7678fee732eedec6b76472cf94fa408b81f Author: car Date: Sun Feb 22 17:29:22 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit 4126cbd50d6a9e0af61cb7433c30b5a87116f78d Author: car Date: Sun Feb 22 04:16:19 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hgproj.dsp commit e6bc0ed5fa4185457a26beb2ad6162c37bfc725a Author: car Date: Sun Feb 22 01:36:39 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit c7c57052a1d62e6ced9fe59c09b0a73930b28f4e Author: car Date: Sun Feb 22 01:35:39 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit eb32a57e2feb407515678c1b7cf1a3fc18ebb53b Author: car Date: Sun Feb 22 01:32:20 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit 0a51bb21226c81586d647f8b8ad9e3b952575c20 Author: car Date: Sun Feb 22 01:30:02 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit 7c77304daba83b6ca60b4f868570c08232e6b1c5 Author: car Date: Fri Feb 20 23:00:55 1998 +0000 *** empty log message *** Src/C_BaseLib/FabArray.H Src/LinearSolvers/C_NodalMG/hgproj.dsp commit e3d53f27fcf21cec025d32de3d6c352d4b0ba05d Author: car Date: Fri Feb 20 22:53:09 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit 21c149ea3be4767d1b99e4c02afe32125e342f71 Author: car Date: Fri Feb 20 21:49:27 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit d3bcb9cab2afcdf74b7dd8ee98b52b5f8cf0161d Author: car Date: Fri Feb 20 21:46:52 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit c769567ce01d62880f0dfd8d32514802c5a9f0b6 Author: car Date: Fri Feb 20 21:42:58 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit e40ee2c7831c132431b95f1aa3205ed59b89407b Author: car Date: Fri Feb 20 21:37:14 1998 +0000 *** empty log message *** Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F commit 4c40f6be906b881eff9c35bff5f79e6e66db39e8 Author: car Date: Fri Feb 20 21:07:11 1998 +0000 changes Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit 16f8272630399bdb20ae851d25bec0bf7ebf47e8 Author: vince Date: Fri Feb 20 18:30:47 1998 +0000 Optimized FillFab and fabCopyDescList. Src/C_BaseLib/FabArray.H commit 25c020128bd956dcf07eb6c1f0e78b9b162357ad Author: car Date: Thu Feb 19 23:26:40 1998 +0000 fiddle: Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 914588858e15f1dcdc746f2ef14306535d8628cd Author: lijewski Date: Thu Feb 19 18:10:46 1998 +0000 Added default constructor to TagBoxMergeDesc. Src/C_AMRLib/TagBox.cpp commit 64833abe26920c9f796f1660f983b28f285b216f Author: lijewski Date: Thu Feb 19 17:15:52 1998 +0000 Added default constructor to FabComTag so that all values get set to some valid value; i.e. I wanted to shut up 3rd about reading unset values when BSP does a memcpy() of a FabComTag. Src/C_BaseLib/ParallelDescriptor.H commit 332e670a47e3e88973cf4a5dfa94e88e866b66ca Author: car Date: Thu Feb 19 01:51:35 1998 +0000 fixes 2 d Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 64f3d2d2b8f0e83de0fa0e45bd06dd003bb7ece5 Author: car Date: Wed Feb 18 23:09:55 1998 +0000 fiddle Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 60a41e742bc4a3ab78617a8aa94877ace0417e84 Author: vince Date: Wed Feb 18 21:38:11 1998 +0000 Removed fortran apprentice flag. Tools/C_mk/Make.T3E commit 03bbc3c5d1060720fcdd181c664a1f88d0ae8ef0 Author: vince Date: Wed Feb 18 21:35:32 1998 +0000 Removed unnecessary syncs. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/StateData.cpp Src/C_AMRLib/TagBox.cpp Src/C_BoundaryLib/FabSet.cpp commit a6b3b7adbb1238c1b88cb85c2a92885bb3132a99 Author: lijewski Date: Wed Feb 18 21:34:37 1998 +0000 Only FlushCache when at lbase==0 Src/C_AMRLib/Amr.cpp commit a9fa8447e30df9f7cc15d70f2840c2a18c483ffe Author: vince Date: Wed Feb 18 21:31:12 1998 +0000 Removed unnecessary syncs and added functionality to support amrvis. Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/NormedFab.H Src/C_BaseLib/Utility.cpp commit b970099acba6d2b86dd3019b86fc2d6ab1c38284 Author: lijewski Date: Wed Feb 18 16:14:42 1998 +0000 Had to remove parallel_sync RunStats stuff. Can't do that since RunStats::report() uses ParallelDescriptor::Synchronize() which leads to inconsistencies and weird numbers. Src/C_BaseLib/ParallelDescriptor.cpp commit d94013ece9266715ff2842b09e1b8a2a935b65fd Author: car Date: Tue Feb 17 23:02:16 1998 +0000 nothing Src/C_BaseLib/CoordSys.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit e2237736f5375680a911b371330f7c9b82863ba4 Author: lijewski Date: Tue Feb 17 22:42:04 1998 +0000 Added a RunStats variable for parallel sync time. No longer need to include in . Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 6255667f18e56878cc262b6f42e82a773605afd4 Author: car Date: Tue Feb 17 17:29:13 1998 +0000 small changes Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 42df6f40c9b3b2579cbadc82eeeb1f02a74f8910 Author: lijewski Date: Fri Feb 13 21:13:07 1998 +0000 Added rules for .f90 that exectly mirror those for .F files. Eventually we'd like to remove the need for FORTPREP (split77) for .f90 files. Tools/C_mk/Make.rules commit c65613de80f4e54028e7103f59e0ec2ac13ace26 Author: car Date: Thu Feb 12 22:47:46 1998 +0000 tweaks Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp commit c6deab694c84b0c67d250ef5cccc2df889c3f3ce Author: wyc Date: Thu Feb 12 22:37:13 1998 +0000 fixed a bug in VisMF.H where there was ambiguity about which index was what in the clear(int,int) function. Src/C_BaseLib/VisMF.H commit 24c29e0d25d67d56ca3de3297198b2d64e79dea5 Author: vince Date: Thu Feb 12 22:16:24 1998 +0000 Initialized m_pa. Src/C_BaseLib/VisMF.cpp commit 00571d09626ce3a98a5fe324d94dc3d521851f47 Author: lijewski Date: Thu Feb 12 18:13:27 1998 +0000 Added calloc() and realloc() so can emulate malloc(3) functionality. Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp commit 133ad8afe411a42541a311819a77425275858d6b Author: car Date: Thu Feb 12 17:32:10 1998 +0000 win32 changes Src/C_BaseLib/Utility.cpp commit c36759a831238ee7427d7d62b1b0c7a9a4d0db9c Author: lijewski Date: Thu Feb 12 16:56:08 1998 +0000 Fixed bug in getline(). Src/C_BaseLib/aString.cpp commit e304a4e09dbd0a086ffcf5f1f8d967f6b62ec1d3 Author: car Date: Wed Feb 11 21:41:12 1998 +0000 Small changes. Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 277ec8c4dfd06731c7fd6faec309ff05ff6d5c4f Author: car Date: Tue Feb 10 15:15:33 1998 +0000 win32 change Src/C_BaseLib/CArena.H Src/LinearSolvers/C_NodalMG/proj.cpp commit 7ee2df6eeaeb73a9d6009673c9db7e27ee0db33b Author: lijewski Date: Mon Feb 9 22:45:58 1998 +0000 Mods for T3E and g++. Src/C_BaseLib/CArena.cpp commit 15611985d70f567879568b465b10497ee49fdfd2 Author: lijewski Date: Mon Feb 9 22:02:14 1998 +0000 Added a couple more insert() hints. Src/C_BaseLib/CArena.cpp commit 1e1fbf25e56da12fd1a1bd3fdc598784c74836ce Author: lijewski Date: Mon Feb 9 22:01:27 1998 +0000 Fixed using declaration: using std::list -> using std::set Src/C_BaseLib/CArena.H commit 31515f5379a847561769b1104fdfd5b34b7cca18 Author: lijewski Date: Mon Feb 9 20:46:52 1998 +0000 We're now using the CArena stuff. Src/C_BaseLib/Arena.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/test/tCArena.cpp Tests/C_BaseLib/tCArena.cpp commit 71869768d73f85d47725d086fb58a64c1bb58ca2 Author: car Date: Mon Feb 9 20:33:29 1998 +0000 doodle Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/proj.cpp commit 92090db6522a5207d7b2dbeac6e0a97c3555e313 Author: lijewski Date: Sun Feb 8 21:13:31 1998 +0000 Increased the count on a few for loops to up test strength. Src/C_BaseLib/test/tCArena.cpp Tests/C_BaseLib/tCArena.cpp commit 4c545e4a876ea148f8ad8b66b8b4a6a0167c0e84 Author: lijewski Date: Sun Feb 8 20:03:59 1998 +0000 Free()d blocks are now coalesed with lo and hi neighbors. Src/C_BaseLib/CArena.cpp commit fa8220ec6b22c99f7cf11d8ae9985b3bd5a97033 Author: lijewski Date: Sun Feb 8 18:19:48 1998 +0000 Test code for CArena Src/C_BaseLib/test/GNUmakefile.tCArena Src/C_BaseLib/test/tCArena.cpp Tests/C_BaseLib/GNUmakefile.tCArena Tests/C_BaseLib/tCArena.cpp commit a6e042e77145dd8e45d6ad7fed1155df58bda17d Author: lijewski Date: Sun Feb 8 18:19:28 1998 +0000 A start at a rewrite using STL. Doesn't do compact()ing yet. Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp commit 7bc488840836e6651bb01828067c2710e3892bc1 Author: lijewski Date: Sun Feb 8 17:52:07 1998 +0000 Added a function pointer to Word union. Src/C_BaseLib/Arena.H commit b7b6a26435c2ce7ce6211b6c1ea7c1fdddaf0375 Author: lijewski Date: Sat Feb 7 23:41:55 1998 +0000 Still doesn't work. Looks like I need to rewrite this. Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp commit 914719adf92a079b89ea7a0cf02a1688f35c394e Author: lijewski Date: Fri Feb 6 23:44:09 1998 +0000 Closer to working code. Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp commit 4e37176e7af7724850337bebd9e4dd9f264fbd00 Author: car Date: Fri Feb 6 22:26:26 1998 +0000 some fixes for win32 Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp Src/C_BaseLib/pBoxLib_2.dsp commit 466d7f721dd6c8eaf3993c699d81da49d0f7f184 Author: car Date: Fri Feb 6 22:19:19 1998 +0000 CleanUp Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 80d5bfbaed2b0599d96240f62afa723b084dd9cf Author: vince Date: Fri Feb 6 22:09:13 1998 +0000 Deleted warning for deprecated FArrayBox::setOrdering() and FArrayBox::getOrdering(). (amrvis needs these). Src/C_BaseLib/FArrayBox.cpp commit 08031b6e6aef590e6cd0011db5ecfce8a1848dc2 Author: lijewski Date: Fri Feb 6 18:22:03 1998 +0000 Uses ::operator new and ::operator delete instead of new and delete. Src/C_BaseLib/BArena.cpp commit d2b47d8cc9473abe4036f7d838e8b9d4a1c84a75 Author: lijewski Date: Fri Feb 6 18:21:34 1998 +0000 The initial cut. Hasn't even been compiled. Src/C_BaseLib/CArena.H Src/C_BaseLib/CArena.cpp commit 289c256767ed83fe616f671fb02349f958551f01 Author: car Date: Fri Feb 6 16:53:10 1998 +0000 Array bust Src/LinearSolvers/C_NodalMG/amr_real3d.F commit ea263bbdb882b15f46b627d76dd003cf75db315e Author: vince Date: Thu Feb 5 23:01:34 1998 +0000 Changed VisMF to use an I/O granularity of a single component of a fab in a multifab and to not store data. Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit 12a8a67226460c56cacf386ce8d01afba274e4fd Author: car Date: Thu Feb 5 22:18:10 1998 +0000 Frob Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 48d4276946b5b321bf419c1a3b6b64188afc82b0 Author: vince Date: Thu Feb 5 22:15:55 1998 +0000 Fixed a typo. Src/C_BaseLib/COORDSYS_3D.F commit ce8e8875aaa54119fc5223e0300bc22a452e5295 Author: lijewski Date: Thu Feb 5 17:02:28 1998 +0000 Removed cout call when bumping collate space size. Src/C_AMRLib/TagBox.cpp commit 14ec52da85a4a0208ecc61d206cce6283dbf03a8 Author: car Date: Thu Feb 5 00:38:19 1998 +0000 Fiddling. Src/C_AMRLib/amrlib.dsp Src/C_BaseLib/pBoxLib_2.dsp Src/C_BoundaryLib/bndrylib.dsp Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/restrictor.H commit 45fb895cbbb28355927dcccd82b6c60086de6bee Author: car Date: Thu Feb 5 00:37:59 1998 +0000 Fiddling Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 80293e5f80e68a315f1f8b4a5897f5b590b5c73a Author: lijewski Date: Wed Feb 4 16:25:50 1998 +0000 Fixes for Visual C++. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit bf9998d4c4db7f00c3a8a9de265ef8172d224ae2 Author: lijewski Date: Wed Feb 4 01:03:20 1998 +0000 We're now reference-counted. Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp commit 5e109466e0da9ec7cd720e6eaab0d7b7ca29a40d Author: lijewski Date: Tue Feb 3 19:33:53 1998 +0000 In copy, check that the processor maps are equal, not the boxarrays. Src/C_BaseLib/FabArray.H commit 7553bebf1777d585d63cac104778816447d8e64e Author: lijewski Date: Tue Feb 3 19:33:12 1998 +0000 We now only flush the processor map cache in regrid if we're at the coarsest level. Otherwise we can run into problems in LevelAdvance. Src/C_AMRLib/Amr.cpp commit a741ddf34570d42ea25dea51027cc931c8982fbc Author: car Date: Sat Jan 31 00:12:26 1998 +0000 Minor Changes. Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit db51f51aeea00f50ae54dcd46e33e442c7bb6a53 Author: lijewski Date: Thu Jan 29 18:59:36 1998 +0000 Lowered the size of ChunkSize. Src/C_AMRLib/TagBox.H commit 9ea937d02230e09230daea9ecc46f9a8f94fd56d Author: car Date: Wed Jan 28 22:54:23 1998 +0000 Minor changes Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 5f4de625b3196fc2dc35761db626339befabea2f Author: car Date: Wed Jan 28 22:29:15 1998 +0000 A little more general, another stupid fill_patch fix. Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 196bba89948a18ed325201eda957028d26a0b552 Author: car Date: Wed Jan 28 22:11:15 1998 +0000 Stupid fix in fill_patch. Src/LinearSolvers/C_NodalMG/fill_patch.cpp commit 199d81602aa1069825f86af64bbf3e58da4f2196 Author: car Date: Wed Jan 28 21:58:32 1998 +0000 Thrashing. Src/LinearSolvers/C_NodalMG/RegType.H Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/hglib.dsp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.H Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit f2d1de6e75c0de276c0815f124737b7e6608e00f Author: lijewski Date: Wed Jan 28 18:35:07 1998 +0000 Latest mods to Cluster have now been ported to T3E. Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 822e3a00d9e271118d6f584f2e9921aed4adef1f Author: lijewski Date: Wed Jan 28 04:55:10 1998 +0000 First cut at having the Cluster code work exclusively with a hardwired IntVect array built and maintained by the TagBox::collate() code. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 06eafb51535cb9abdc4f440fb6036431e157c79e Author: car Date: Tue Jan 27 00:15:05 1998 +0000 Fixes cleanups. Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 43a7536450459ff4e1bae7b2caae11014a527cd1 Author: car Date: Tue Jan 27 00:14:50 1998 +0000 Fixes, cleanups. Src/LinearSolvers/C_NodalMG/RegType.H Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit 36374282171f75c1e5b4a28a6adeb8e70b78fe53 Author: car Date: Mon Jan 26 23:27:00 1998 +0000 No longer need cbasics.H, and updated .cvsignore to ignore louis's lib directory. Src/LinearSolvers/C_NodalMG/.cvsignore Src/LinearSolvers/C_NodalMG/cbasics.H commit 8935fa74e5deccc5b00787fa45e2ff9e8d705fa6 Author: lijewski Date: Mon Jan 26 23:16:20 1998 +0000 Removed unused function. Src/C_AMRLib/Cluster.H commit 1283da021cd32ef3581fcd626b6c4f0eff7b6832 Author: lijewski Date: Mon Jan 26 22:00:00 1998 +0000 Cleaned up the code a bit. Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp commit d621d1ec8511a6451c3e0a710be1a052f8891a40 Author: lijewski Date: Mon Jan 26 21:57:18 1998 +0000 We're now derived from BaseFab Added tags() and tags(Array) to support Fortran. Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 92cfb5d77a6ce97826b8a16ccba328c747852823 Author: car Date: Mon Jan 26 20:56:19 1998 +0000 Fixes. Src/LinearSolvers/C_NodalMG/GNUmakefile.main commit 0c8d38d2efd648d98d406865f649ac5809efeb09 Author: car Date: Mon Jan 26 20:20:55 1998 +0000 for loop index Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 3f9d86f2c7ef25aa91fb662bed03e15ee7c05105 Author: car Date: Mon Jan 26 19:18:19 1998 +0000 Changes for 2 D. Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 2807adec0d82d3286093e0af6835e14cd92533e1 Author: lijewski Date: Sat Jan 24 01:35:58 1998 +0000 Forgot a 'endif' in the previous merge. Src/C_AMRLib/INTERP_2D.F commit 4755b9df6a7f81ae1ea2f51c8f8174d3c8cc194e Author: lijewski Date: Fri Jan 23 22:48:38 1998 +0000 bsp_put() -> bsp_hpput() bsp_get() -> bsp_hpget() Src/C_BaseLib/ParallelDescriptor.H commit 00ded7dab63a03132f215a5f995ed6f88043bbc5 Author: car Date: Fri Jan 23 18:34:00 1998 +0000 Changes. Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 0f95128dc20326fbe55cbfeb48097973fce4d1de Author: lijewski Date: Fri Jan 23 17:51:31 1998 +0000 Reduced memory usage in colate(). Src/C_AMRLib/TagBox.cpp commit f2e77a3fe0028db1bb5e80d8395894e7bdaa1c8f Author: car Date: Thu Jan 22 23:25:31 1998 +0000 Const correctness... Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/interpolator.H Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit bcfe5b1079d12c7364d5fa5a454d059aa4e57c8e Author: lijewski Date: Thu Jan 22 16:39:53 1998 +0000 Added [] to delete in a few places. Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/Derive.cpp Src/C_AMRLib/Interpolater.cpp commit ea8a9a5689e9ae1a0e4b8c6a52f59aba5fa1ca52 Author: car Date: Wed Jan 21 22:57:52 1998 +0000 Caching removed. Src/LinearSolvers/C_NodalMG/hgproj.dsp commit 3a6802b773dc2e15ed9e50def231b79dc077d623 Author: car Date: Wed Jan 21 22:57:38 1998 +0000 Removed caching. Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 1515006855aba48d472f5bf09e7a74010edcdb91 Author: car Date: Wed Jan 21 22:57:21 1998 +0000 Removed caching Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/cache.H Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/restrictor.H commit 4a6da3ee9b07976eca40502ea2d257af84afa368 Author: car Date: Wed Jan 21 22:56:52 1998 +0000 Removed include Files Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit 9ab04286ebba7f75ac30eba243160d3478ee1af5 Author: car Date: Wed Jan 21 21:39:20 1998 +0000 Removed more useless stuff. Src/LinearSolvers/C_NodalMG/mall_info.cpp commit 61d280f3f0c3429dbb20d0086dc702a443011e85 Author: car Date: Wed Jan 21 21:35:50 1998 +0000 Removed graphics. Src/LinearSolvers/C_NodalMG/GNUmakefile.main Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_graph.H Src/LinearSolvers/C_NodalMG/amr_graph.cpp Src/LinearSolvers/C_NodalMG/cont2d.F Src/LinearSolvers/C_NodalMG/cont3d.F Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/proj.cpp commit e66b4a82793437cd2db8599549a8cc2c7a3c1603 Author: car Date: Wed Jan 21 20:57:54 1998 +0000 Changes for Parallel. Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_graph.H Src/LinearSolvers/C_NodalMG/amr_graph.cpp Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp Src/LinearSolvers/C_NodalMG/interpolator.H Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 04d5f5a28de9f57f9e6e051742c934797547395d Author: vince Date: Wed Jan 21 19:32:12 1998 +0000 Minor change for the cray. Src/C_AMRLib/DatasetClient.cpp commit cb75afca46ce7b18430e6d9f2813854612a297e8 Author: lijewski Date: Fri Jan 16 23:14:23 1998 +0000 Merged in some fixes Ann added to _amr. Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/Interpolater.cpp commit 33eeb22fea7df2ad8dbe82cca743be21e64a084d Author: lijewski Date: Fri Jan 16 22:53:01 1998 +0000 Mods to compile with g++ 2.8.0 Src/C_BaseLib/DistributionMapping.cpp commit 2d87fde7c686efb60dc38d11fb888b1553a2da45 Author: car Date: Thu Jan 15 20:37:18 1998 +0000 Changes for WIN32 Src/LinearSolvers/C_NodalMG/.cvsignore Src/LinearSolvers/C_NodalMG/hglib.dsp commit 6760927a889f6827ea3646e97574403e9c5d9032 Author: car Date: Thu Jan 15 19:15:59 1998 +0000 New files for WIN32 and cvs bookkeeping. Bug Fixes for WIN32. Src/LinearSolvers/C_NodalMG/.cvsignore Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hgproj.dsp Src/LinearSolvers/C_NodalMG/proj.cpp commit 0ab68793ee5ccf234611183c3db02a9d68569eba Author: lijewski Date: Thu Jan 15 18:52:35 1998 +0000 Removed references to Arena stuff ... The Arena junk still exists, it just isn't used or referenced anywhere. Src/C_BaseLib/Make.package commit f4b1741d6f30bd056dc5ac0fae090a137dde4956 Author: car Date: Wed Jan 14 21:56:49 1998 +0000 Don't need Src/LinearSolvers/C_NodalMG/amr_grav2d.F Src/LinearSolvers/C_NodalMG/amr_grav3d.F Src/LinearSolvers/C_NodalMG/amr_gravity.H Src/LinearSolvers/C_NodalMG/amr_gravity.cpp Src/LinearSolvers/C_NodalMG/hg_elliptic.H Src/LinearSolvers/C_NodalMG/hg_elliptic.cpp commit f554eb86590e351feaaf108c5f95570a17fd66e9 Author: car Date: Wed Jan 14 21:51:02 1998 +0000 Parallel BoxLib_2 compatible first cut. Remove elliptic and other. Src/LinearSolvers/C_NodalMG/GNUmakefile Src/LinearSolvers/C_NodalMG/GNUmakefile.main Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/driver.cpp Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/poisson.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit a2662247c9141341c55a73a2ca83132f74e45c80 Author: car Date: Mon Jan 12 21:21:46 1998 +0000 Turned on browser. Src/C_AMRLib/amrlib.dsp Src/C_BaseLib/pBoxLib_2.dsp Src/C_BoundaryLib/bndrylib.dsp commit b9f7ca673b5f8efe52d003e64a4349a6cd8eb3d0 Author: vince Date: Thu Jan 8 23:06:04 1998 +0000 Added ReduceBoolOr. Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Utility.H commit 00f672699c71006d5c77769a34285363ad1e9c82 Author: lijewski Date: Thu Jan 8 18:59:59 1998 +0000 Now up-to-date with _amr. Had to add in Steven's new stuff. Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp commit 603443b53d94e8518f8e0101e9cea7b6347aba57 Author: lijewski Date: Tue Jan 6 23:43:56 1998 +0000 Brought into line with stuff in _amr. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp commit 391c896479aac886fb2f0b53458e0971595acf1e Author: car Date: Tue Dec 23 19:22:34 1997 +0000 VC++ changes. Src/C_AMRLib/amrlib.dsp Src/C_BoundaryLib/bndrylib.dsp commit a1a0ac5a53aa194d881420f2854d2245f3d924e8 Author: car Date: Tue Dec 23 05:15:52 1997 +0000 Fix for win32. Src/C_BoundaryLib/bndrylib.dsp commit 9473074d92c11a725ce89060e0726e3cfc07441d Author: car Date: Tue Dec 23 05:15:15 1997 +0000 Change for Win32. Src/C_AMRLib/amrlib.dsp commit 1249c6591b446e9c0902092644a64d75d90ee257 Author: car Date: Mon Dec 22 23:12:04 1997 +0000 Updates for Win32 Src/C_AMRLib/amrlib.dsp Src/C_BaseLib/pBoxLib_2.dsp Src/C_BoundaryLib/bndrylib.dsp commit 61e8f6ffd62167301124c561045c3afdf3105f9b Author: lijewski Date: Fri Dec 19 22:21:39 1997 +0000 operator&() is now implemented in terms of operator&=(). Likewise for the friend versions of surroundingNodes() and enclosedNodes(). Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp commit 5bdc6dfdaadf33eb1544ca2bb94ff62595c12d4f Author: lijewski Date: Fri Dec 19 21:54:45 1997 +0000 Removed List::copy(). Just a memory leak waiting to happen. Src/C_BaseLib/List.H commit 681924cacad520171cc2d8f8f88d0808a19ebb7f Author: lijewski Date: Fri Dec 19 19:08:55 1997 +0000 Got rid of the ugly and dangerour (int*) cast. Src/C_AMRLib/Interpolater.cpp commit b1edb225eff063539eb70f4bc8b776944691064a Author: lijewski Date: Fri Dec 19 18:43:51 1997 +0000 getBCArray() now returns Array not int*. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit fcf695131501679e53d72e44cb0fde25017848c1 Author: lijewski Date: Thu Dec 18 18:44:38 1997 +0000 These are specialized versions of performCopy() and setVal(). They're being checked in only for informational purposes at the moment. That is, they're aren't integrated into the code. Turns out, they don't buy you anything on the DEC Alpha. They do though on a vector machine such as the Cray. Src/C_BaseLib/SPECIALIZE_2D.F Src/C_BaseLib/SPECIALIZE_3D.F Src/C_BaseLib/SPECIALIZE_F.H Src/C_BaseLib/Specialize.cpp commit f13ea356e3e9f1a8151468253dbfbf76aadf4814 Author: lijewski Date: Wed Dec 17 23:04:53 1997 +0000 Now need Src/C_AMRLib/AmrLevel.cpp commit f352fec4d8eb703e3e1b3afbd6a043a3dc931ccd Author: lijewski Date: Wed Dec 17 23:04:32 1997 +0000 Removed need for Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/Orientation.cpp Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/RealBox.cpp Src/C_BaseLib/VisMF.cpp commit 021cb575ad5915e0057c73aa06830e6b74f0b4e3 Author: lijewski Date: Wed Dec 17 18:09:33 1997 +0000 Don't allow Mersenne prime as seed. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit a1c009ce34a57cebf12483cc121368bfd712d568 Author: vince Date: Tue Dec 16 23:34:14 1997 +0000 Added pierre.nersc.gov (the T3E-600). Tools/C_mk/Make.defs commit 95f6693518a56f14211ab81a9825feee3fcc2228 Author: vince Date: Tue Dec 16 19:05:51 1997 +0000 Changed the profile tool from apprentice (which is broken) to pat. Tools/C_mk/Make.T3E commit 1ed7f8b7e0c9f5d2c6fa62f8510a3a5a44648c6f Author: lijewski Date: Tue Dec 16 16:44:54 1997 +0000 I've made it clearer in the code that only processor #0 writes to or does anything useful with the plotfile or checkpoint file header. Src/C_AMRLib/Amr.cpp commit 7c9896f0ac62d8fbe932547f6ac1e4f34de79375 Author: car Date: Tue Dec 16 15:27:47 1997 +0000 Make a warning go away. Src/C_BaseLib/RunStats.cpp commit fa0ef937808dc73214eb9a10f457dd217bdb8358 Author: lijewski Date: Tue Dec 16 00:41:28 1997 +0000 DIMV -> DIMENSION DIMV macro conflicted with the one in ArrayLim.H. Src/C_AMRLib/MAKESLICE_3D.F commit 17b3dbbf54051e26084d7f54aad368e3400aafc1 Author: lijewski Date: Mon Dec 15 17:00:52 1997 +0000 utilrand() -> blutilrand(). Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit e62ad3c067a13ec0a61485aad0bf0e2f19d5cb9b Author: lijewski Date: Sun Dec 14 23:34:59 1997 +0000 Added Random(), InitRandom() and Fortran entry points for Random(). Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 302e9a2796342c636dca4b9499073f79fc15ce9a Author: lijewski Date: Sun Dec 14 23:34:14 1997 +0000 Added CVS ID in C comment. Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/MAKESLICE_F.H Src/C_AMRLib/PROB_AMR_F.H Src/C_BaseLib/COORDSYS_F.H commit 647d2727d72d7bbfbf855e0b12ecd5e392f3c3fa Author: lijewski Date: Sun Dec 14 01:05:52 1997 +0000 Reverted out the merged of FAB stuff in BaseFab. It tickles a bug with the Cray CC compiler on the T3E. Quite pernicious. Src/C_BaseLib/ArithFab.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/Make.package Src/C_BaseLib/NormedFab.H Src/C_BaseLib/OrderedFab.H commit a37fa9cae782a4c4f8d753928ad0d7fe1120d1e7 Author: car Date: Sat Dec 13 21:09:28 1997 +0000 Compile rule changes. Src/C_AMRLib/amrlib.dsp commit 0a499e0803a493c0ca5adddc4eb347505878e82d Author: lijewski Date: Sat Dec 13 19:53:07 1997 +0000 Fixed some inconsistencies between declarations in the _F.H file and the definition/usage. Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/Interpolater.cpp commit 2ac9a7c7226b48c009e3e1c0917a40bf2c943fa6 Author: lijewski Date: Sat Dec 13 19:48:03 1997 +0000 Mod to keep T3E quite re: usage of real*8 Src/C_AMRLib/FLUXREG_3D.F commit 605213228d415d6bab0a44fb00eeb5948e564a6a Author: lijewski Date: Fri Dec 12 23:23:40 1997 +0000 Only the I/O processor tries to build the required directory tree. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp commit 18788d705427dafc3064380d1b9ca1091168703b Author: lijewski Date: Fri Dec 12 22:44:54 1997 +0000 DIMS.H has been merged in. Src/C_BaseLib/ArrayLim.H commit c1c2ce6a09b6bca8ec3e5db780f4e0e70702fd0f Author: lijewski Date: Fri Dec 12 22:42:42 1997 +0000 DIMS.H has been merged into ArrayLim.H All .F files now have leading comment containing CVS ID. Src/C_AMRLib/DIMS.H Src/C_AMRLib/FILCC_2D.F Src/C_AMRLib/FILCC_3D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/MAKESLICE_3D.F Src/C_BaseLib/COORDSYS_2D.F Src/C_BaseLib/COORDSYS_3D.F commit e85bc2df3102bda72a4bd16ba4a1b0adffb28aae Author: lijewski Date: Fri Dec 12 16:10:14 1997 +0000 Now use f90 instead of f77. Tools/C_mk/Make.OSF1 commit 935d811fa8891e5ccaec9fb350052eb3ff75a742 Author: car Date: Fri Dec 12 00:17:15 1997 +0000 Changes for VC++ Src/C_AMRLib/.cvsignore Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/MAKESLICE_3D.F Src/C_AMRLib/amrlib.dsp commit 96a8a983fc82bb0a21f3975d37a45b3a2d326138 Author: car Date: Fri Dec 12 00:15:57 1997 +0000 VC++ fixes. Src/C_BaseLib/COORDSYS_3D.F Src/C_BoundaryLib/.cvsignore Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/bndrylib.dsp commit c6e44f8fa73ce93a38fe6c78e152bb53a7015be2 Author: car Date: Fri Dec 12 00:14:57 1997 +0000 Changles for VC++ Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/pBoxLib_2.dsp commit 16aa03f3b1f8b7235f5037208f44d468fbba0d35 Author: lijewski Date: Thu Dec 11 23:26:58 1997 +0000 Removed all checks on the return value of new. We now rely on a set_new_handler() being installed. See Parallel/HCAll/main.cpp for details. Brought up-to-date with the serial version of BndryLib. Src/C_BaseLib/COORDSYS_F.H Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/RealBox.H Src/C_BaseLib/RealBox.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 174ae4a6f67c5648d78bde2487850264fc3ee234 Author: lijewski Date: Thu Dec 11 23:25:38 1997 +0000 Removed all checks on the return value of new. We now rely on a set_new_handler() being installed. See Parallel/HCAll/main.cpp for details. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/BCRec.H Src/C_AMRLib/BCRec.cpp Src/C_AMRLib/BC_TYPES.H Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/DatasetClient.cpp Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp Src/C_AMRLib/ErrorList.cpp Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/LevelBld.H Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/Array.H Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/BoxAssoc.H Src/C_BaseLib/BoxAssoc.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/List.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Pointers.H Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp Src/C_BaseLib/Tracer.cpp Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp commit 073b10ae7e3d6767e5b5cf7bc1a013461ce496d7 Author: lijewski Date: Thu Dec 11 06:14:02 1997 +0000 A few more endls added. Src/C_AMRLib/Amr.cpp commit 611e3a3d57d80e13fc2f0708c1514d790d26b911 Author: lijewski Date: Thu Dec 11 06:07:47 1997 +0000 Added some strategically placed endl's. The T3E iostream library doesn't flush on newline :-( Src/C_AMRLib/Amr.cpp commit 5df40bb4168d53c00db762cf974cc80d0d25b328 Author: lijewski Date: Thu Dec 11 05:01:08 1997 +0000 Brought up-to-date with servial version of BndryLib stuff. Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/RealBox.H Src/C_BaseLib/RealBox.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp commit 2ff8299f66f1621d39f03fab4f4fbafb8fca7945 Author: lijewski Date: Wed Dec 10 22:04:42 1997 +0000 Added DIMS==1 stuff. Src/C_AMRLib/DIMS.H commit 941c34764fdce5a833861ed1591a436c1ec63709 Author: lijewski Date: Wed Dec 10 21:56:01 1997 +0000 Merged in mods from IAMRAll. Inlined all FabSetIterator gunk. Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/RealBox.H Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit d622c9c131c70a12ccad7e91fdc09f1e0f34e321 Author: lijewski Date: Wed Dec 10 19:07:38 1997 +0000 Moved from HCAll. Src/C_BaseLib/COORDSYS_2D.F Src/C_BaseLib/COORDSYS_3D.F Src/C_BaseLib/COORDSYS_F.H Src/C_BaseLib/CoordSys.H Src/C_BaseLib/CoordSys.cpp Src/C_BaseLib/Geometry.H Src/C_BaseLib/Geometry.cpp Src/C_BaseLib/RealBox.H Src/C_BaseLib/RealBox.cpp Src/C_BoundaryLib/BndryRegister.H Src/C_BoundaryLib/BndryRegister.cpp Src/C_BoundaryLib/FabSet.H Src/C_BoundaryLib/FabSet.cpp commit 5f003658c365112a12258ac3825e4f401e06213f Author: lijewski Date: Tue Dec 9 23:29:59 1997 +0000 ArithFab, NormedFab and OrderedFab have been merged into BaseFab. BaseFab is no longer a virtual baseclass of FArrayBox. Removed the maskLT-type operations. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/Make.package commit bc51b60088e7011f61acc22c8f9d8b471bdca318 Author: lijewski Date: Tue Dec 9 21:54:52 1997 +0000 TagBoxArray::numTags() now returns long. Merged in TagType typedef everywhere. TagBox::numTags(Box&) now calls TagBox::numTags(). Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit b2f43254817e87dcd6021a324ef594ff706ba105 Author: lijewski Date: Tue Dec 9 17:46:20 1997 +0000 Delayed some of the new's until after sync()s as much as possible. Src/C_AMRLib/TagBox.cpp commit d15fb5d669354198bdde126ea7d54d9413709509 Author: lijewski Date: Mon Dec 8 23:12:59 1997 +0000 The define() functions now have a guard that checks to see if we're running in parallel or not. Also, the one that returns PArray* now returns MultiFab* Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit ec10bf416228adf4d62f11e3f7a0b93ad46ad0f3 Author: lijewski Date: Sat Dec 6 01:04:47 1997 +0000 Added in Marc's fix for non-nested grids. Src/C_AMRLib/Amr.cpp commit 5b31a6c2e087b856a33b7f7a520e424bcc7b8974 Author: lijewski Date: Fri Dec 5 22:07:31 1997 +0000 Some consolidation. Tools/C_mk/Make.T3E commit 73822ae6714999728658448baccaf85b36fb90b4 Author: car Date: Fri Dec 5 19:07:30 1997 +0000 Give an argument to ::time() Src/C_BaseLib/Utility.cpp commit 041888b9739ec659c8e5a6cf0a69146730f0a9bb Author: lijewski Date: Fri Dec 5 17:59:25 1997 +0000 Merged couple more mods from IAMR. One was a setVal() in isValid() that had been removed -- it's needed in IAMR. Src/C_AMRLib/AmrLevel.cpp commit 06abebbad7523ba283fee6222e867f2be63123d6 Author: lijewski Date: Fri Dec 5 16:18:22 1997 +0000 Added clear() and clear(int). Src/C_BaseLib/VisMF.H commit d814232dc3a7f7da34ce84fb069cfb1e9e990f94 Author: lijewski Date: Fri Dec 5 00:07:31 1997 +0000 If not BL_USE_SETBUF setbuf -> pubsetbuf Src/C_AMRLib/Amr.cpp Src/C_BaseLib/VisMF.cpp commit cbed681d37f6aa4355b2220152120eed9a520068 Author: lijewski Date: Thu Dec 4 22:57:08 1997 +0000 Using .isNull() instead of == "". Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.cpp commit a7482eb8f13bb825f8bb4185dcbca80adc30160c Author: lijewski Date: Thu Dec 4 22:33:20 1997 +0000 Fixed weird requirement that ParmParse must be init'd from command line. Src/C_BaseLib/ParmParse.cpp commit 40ee356ed8994303486ca644e4bec0be668a64e9 Author: lijewski Date: Thu Dec 4 21:32:06 1997 +0000 Moved from amrlib. Src/C_BaseLib/Make.package Src/C_BaseLib/RunStats.H Src/C_BaseLib/RunStats.cpp commit 609c3231920fd66265b515ccd27aa3e819df4e9a Author: lijewski Date: Thu Dec 4 21:31:52 1997 +0000 Moved to pBoxLib_2 Src/C_AMRLib/RunStats.H Src/C_AMRLib/RunStats.cpp commit e91598b114acb9e481c054faa791e7a1a316b739 Author: lijewski Date: Thu Dec 4 20:58:48 1997 +0000 Changed plotfile and checkpoint file formats slightly to facilitate reading and writing them to directories different from the one in which you're running. Merged more gunk from IAMRAll. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit d43432b60b1b500f976ff3c000471133691eb70f Author: lijewski Date: Thu Dec 4 20:11:01 1997 +0000 Mods to allow writing of plotfiles and checkpoint files in directories other than the one in which you're running. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 062fc873b23ccf26d68bea215849aca5319ae743 Author: lijewski Date: Wed Dec 3 23:26:11 1997 +0000 chkfile -> chfile when not using BL_PARALLEL_IO. Src/C_AMRLib/Amr.cpp commit 6522fc97765ebc19f0e15e3713d1afd03f794145 Author: lijewski Date: Wed Dec 3 21:09:54 1997 +0000 Cleaned up a tad. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit d5d40ca423116d44fabde4856d67ca109410580b Author: vince Date: Wed Dec 3 19:24:54 1997 +0000 Added a variable to distinguish between the NERSC T3E and the NAVO T3E. Tools/C_mk/Make.defs commit d9eec7e93e4b6e5256fa3e904614b04858e533f2 Author: lijewski Date: Wed Dec 3 03:26:57 1997 +0000 Performance modification to performSetVal(). Src/C_BaseLib/BaseFab.H commit b9d9755a1441e78a36b7d7252e284ac3d7fcaede Author: lijewski Date: Tue Dec 2 23:59:29 1997 +0000 Merged in from IAMRAll. Src/C_AMRLib/FILCC_2D.F Src/C_AMRLib/FILCC_3D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F commit aca53b646f5b030c636c16c9248c287b5383eda7 Author: lijewski Date: Tue Dec 2 23:40:32 1997 +0000 Merged with one from IAMRAll. Src/C_AMRLib/FluxRegister.cpp commit dcaba019a2fd0d31427420f46d3336a3a1e3d933 Author: lijewski Date: Tue Dec 2 23:05:28 1997 +0000 Merged with IAMRAll. Src/C_AMRLib/TagBox.cpp commit 3cc8b18f0d6eb3ed26891ea45ec2f832e6fcbf28 Author: lijewski Date: Tue Dec 2 21:30:56 1997 +0000 Updated from IAMRAll. Src/C_AMRLib/StateData.cpp commit a211f6340f445ba6a77b020c09761aaa8717764a Author: lijewski Date: Tue Dec 2 21:15:47 1997 +0000 Updated from IAMRAll. Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp commit b3e9cce89a07963e0ed3e3bcaf25f6ccc047480f Author: lijewski Date: Tue Dec 2 19:12:17 1997 +0000 ErrorType and ErrorFunc are now member of ErrorRec. Src/C_AMRLib/ErrorList.H Src/C_AMRLib/ErrorList.cpp commit bdc75be87999dab12a261d04ccc2d71a1518ea21 Author: lijewski Date: Tue Dec 2 00:08:55 1997 +0000 Added virtual aString thePlotFileType() const. Removed an extraneous include directive. Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp commit 9a49fb840866a5c3dcb4888ab7cfcc763a04ba2d Author: vince Date: Mon Dec 1 21:01:29 1997 +0000 Moved BSP defines to the appropriate Make.machine file. Tools/C_mk/Make.OSF1 Tools/C_mk/Make.T3E commit b8498d60b70124f9e5da6a89a37d13cd5f59c4b2 Author: vince Date: Mon Dec 1 20:49:58 1997 +0000 Added ifdefs for the T3E. Src/C_BaseLib/CONSTANTS.H commit bdbd2a0966e7027277119d5c831377780c7add9a Author: lijewski Date: Mon Dec 1 18:23:11 1997 +0000 Mods to compile with Cray compiler on T3E. Src/C_BaseLib/DistributionMapping.cpp commit bcf073c9c4f7686dcdb40526adc585921c249c04 Author: lijewski Date: Fri Nov 28 18:30:25 1997 +0000 Removed maximum cache size mumbo-jumbo. The cache must now be flushed manually. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 6d2120e6876df2a34915fb4a49c942180001f7e2 Author: lijewski Date: Fri Nov 28 18:14:42 1997 +0000 Call DistributionMapping::FlushCache() in regrid() after grid_places(). Src/C_AMRLib/Amr.cpp commit 0a1c87390b127de07f8023f0159f87f4dc461a39 Author: lijewski Date: Fri Nov 28 17:27:37 1997 +0000 Bypass the processor cache when using ROUNDROBIN. Src/C_BaseLib/DistributionMapping.cpp commit f93718ec08ebe1f09cd17646961f86b6e23b720c Author: lijewski Date: Fri Nov 28 16:45:13 1997 +0000 Added assert(rwtime > 0). Now that we're using wsecond() this shouldn't happen, but ... Src/C_AMRLib/RunStats.cpp commit a0c694a9f73c331d3e354c343f56aafe3a64f27d Author: lijewski Date: Fri Nov 28 00:00:45 1997 +0000 Am now caching processor maps. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 710697e5ad818b19abb8170f622298aaa0c04719 Author: lijewski Date: Wed Nov 26 20:51:36 1997 +0000 CLUSTER -> Cluster Src/C_AMRLib/Amr.cpp Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp commit dc7efde597f5e2f7be1d2b06a0f9b4b186843236 Author: nazgul Date: Wed Nov 26 20:46:17 1997 +0000 Testing errors in divergence of a linear velocity field Src/LinearSolvers/C_NodalMG/amr_graph.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit c5d04257975f57cda908e22201800e12cc88d6ec Author: nazgul Date: Wed Nov 26 20:44:08 1997 +0000 Grids for convergence test with single refined patch Src/LinearSolvers/C_NodalMG/tests/gr2r1 Src/LinearSolvers/C_NodalMG/tests/gr2r2 Src/LinearSolvers/C_NodalMG/tests/gr2r3 Tests/LinearSolvers/C_NodalMG/test_grids/gr2r1 Tests/LinearSolvers/C_NodalMG/test_grids/gr2r2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2r3 commit 875e4cf3add35beaed7a90cf0eb42230e3fb831e Author: lijewski Date: Wed Nov 26 20:41:41 1997 +0000 The return value of all "new"s is now checked. Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/Derive.cpp Src/C_AMRLib/ErrorList.cpp Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.cpp Src/C_AMRLib/TagBox.cpp commit 43c49db0947ea7a55dc0c8a1232fba1a2093192c Author: lijewski Date: Wed Nov 26 19:18:46 1997 +0000 BOX -> Box REAL -> Real TAGBOX -> TagBox INTVECT -> IntVect FARRAYBOX -> FArrayBox Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/BCRec.H Src/C_AMRLib/BCRec.cpp Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/Derive.H Src/C_AMRLib/ErrorList.H Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/LevelBld.H Src/C_AMRLib/MAKESLICE_F.H Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit d35e1c6a9cc6b6db290b737a0bbb5c2d4c88242b Author: lijewski Date: Wed Nov 26 18:27:45 1997 +0000 setTimeLevel() now takes three arguments. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp commit 909029aaab141527b8d9c59575ac5134efc8f654 Author: lijewski Date: Wed Nov 26 17:46:22 1997 +0000 enum TimeCenter is now nested in StateDescriptor. Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp commit 10e5b26984d8391b48badf150356992e293db849 Author: lijewski Date: Wed Nov 26 06:26:45 1997 +0000 Made wsecond() initializers explicitly extern. Don't want anyone to think they should be static :-) Src/C_BaseLib/Utility.cpp commit e173ec034764e9e29755b5e909030a1e2417b10d Author: lijewski Date: Wed Nov 26 05:07:25 1997 +0000 init() is now protected. The constructors call it if it hasn't already been called. Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp commit ff669c441728a23f4ab81774d965e633679b9833 Author: lijewski Date: Wed Nov 26 04:22:34 1997 +0000 Don't call knapsack code if on 1 cpu -- use roundrobin. Guarantee that all versions of wsecond() get initialized at program startup. Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 741d07df888ffa7adfa3dc0db507d3ec9f48221f Author: lijewski Date: Wed Nov 26 04:21:46 1997 +0000 init() is now protected. It's called by the constructor if it hasn't already been called. Src/C_AMRLib/RunStats.H Src/C_AMRLib/RunStats.cpp commit 090da2f19dc49617370b4ecfb56fc80254bc071b Author: lijewski Date: Tue Nov 25 22:17:51 1997 +0000 Added four types of create functions. Call them through a static pointer to member function. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 966bcb45cc7c113576d08c8bfbd3989aa843d9f9 Author: car Date: Tue Nov 25 19:55:15 1997 +0000 Assertion for nprocessors > 1 Src/C_BaseLib/DistributionMapping.cpp commit e343caa0f06827f5ad07b57e1aed6a9c06be2f14 Author: lijewski Date: Tue Nov 25 19:23:31 1997 +0000 Regularized os.precision() mumbo-jumbo a tad. Src/C_AMRLib/RunStats.cpp commit 9e1091c89357c16a7905d2dce40c01aacab92524 Author: lijewski Date: Tue Nov 25 19:09:42 1997 +0000 Different way to guarantee wall clock time gets initialized. Src/C_BaseLib/Utility.cpp commit 65fd1ea0ff17a71e0339ece4c461dfe68a17ea7a Author: car Date: Tue Nov 25 19:00:36 1997 +0000 Improvements in DistributionMapping for Knapsack Src/C_BaseLib/DistributionMapping.cpp commit dbaffef3482714b2aa5279b0eccfb7fc6c22d7fa Author: lijewski Date: Tue Nov 25 18:47:05 1997 +0000 Added init() and strategy(). Turned on knapsack(). Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 2a4d5a0869b1b90cf48d31e4f4ce23a02e7c3e06 Author: lijewski Date: Tue Nov 25 17:08:25 1997 +0000 Small changes ... Src/C_BaseLib/DistributionMapping.cpp commit 68fa915dfbc2338a1e6c57fa9a09c358d55e8db2 Author: car Date: Tue Nov 25 14:49:30 1997 +0000 Removed use of member template. Src/C_BaseLib/DistributionMapping.cpp commit 07c667a8064c45af21efc3b105b3c94482d8cb13 Author: lijewski Date: Mon Nov 24 23:45:51 1997 +0000 Added initializer for wsecond(). Src/C_BaseLib/Utility.cpp commit d713dc76066ff10d8180db70214104cb995a8a03 Author: car Date: Mon Nov 24 22:05:10 1997 +0000 Commiting some knapsack code, to see if it compiles on T3E. Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/GNUmakefile commit 47c36e3f35abcc63b00f57b54cbfd534b088cf16 Author: lijewski Date: Mon Nov 24 21:04:37 1997 +0000 Am now using Utility::wsecond() in place of ParallelDescriptor::second(). Src/C_AMRLib/RunStats.H Src/C_AMRLib/RunStats.cpp commit 30b300234dddd73ff35d87c877869e537e629290 Author: lijewski Date: Mon Nov 24 18:52:26 1997 +0000 Merged in BL_COPYRIGHT_NOTICE macro. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Amr_auxil.H Src/C_AMRLib/BCRec.H Src/C_AMRLib/BCRec.cpp Src/C_AMRLib/BC_TYPES.H Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp Src/C_AMRLib/ErrorList.H Src/C_AMRLib/ErrorList.cpp Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/LevelBld.H Src/C_AMRLib/RunStats.H Src/C_AMRLib/RunStats.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 03a1edc77cfe304eb20a15dbb6c1f4403dab42eb Author: lijewski Date: Mon Nov 24 18:40:53 1997 +0000 Minor mod to output formatting. Src/C_AMRLib/RunStats.cpp commit 2d82e5ad5a4d6db9004cf9cff738e996bba85906 Author: lijewski Date: Sun Nov 23 21:42:50 1997 +0000 Removed m_numpts stuff. It's now in RunStats. Src/C_BaseLib/FabArray.H commit 927df7ff08765882c95dd7c3118e2e383683ef68 Author: lijewski Date: Sun Nov 23 21:42:31 1997 +0000 NumPts() stuff from FabArray::AllocFabs() is now in here. Src/C_AMRLib/RunStats.H Src/C_AMRLib/RunStats.cpp commit 4acbf7cb9f02a0106d17b0bd0b22b7d82c09e1e5 Author: lijewski Date: Sun Nov 23 18:19:59 1997 +0000 We now return # of bytes written to disk. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 1ac4be59b81ef4dbef44a7adf63376379fa4a13d Author: lijewski Date: Sun Nov 23 18:18:49 1997 +0000 RunStats now accumulates bytes written to disk. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/RunStats.H Src/C_AMRLib/RunStats.cpp Src/C_AMRLib/StateData.cpp commit 1223356c10c46af6ea34b84421af5108b5f7ad56 Author: lijewski Date: Sun Nov 23 00:12:08 1997 +0000 Don't print out stats if the particular stat is 0. Src/C_BaseLib/FabArray.H commit 972bf74ed43f8cf8d61a0ed0cd0a2c13df086c14 Author: lijewski Date: Sun Nov 23 00:10:55 1997 +0000 Merged in a saner RunStats. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/RunStats.H Src/C_AMRLib/RunStats.cpp commit d287254ecf1008f08a69bcf26ee8b8bc8b553854 Author: lijewski Date: Sat Nov 22 17:52:06 1997 +0000 Moved FileOpenFailed() to Utility. Added CreateDirectoryFailed() to Utility. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 35f09d2306022d65900f0bc0f7f109fe2747bccd Author: lijewski Date: Sat Nov 22 17:51:31 1997 +0000 Moved FileOpenFailed() and CreateDirectoryFailed() to Utility. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.cpp commit 254c7f4c0205435dec780b6cac6e305655f3d874 Author: lijewski Date: Sat Nov 22 01:10:41 1997 +0000 Merged in VisMF::FileOpenFailed(). Src/C_AMRLib/Amr.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit d61c5cbf2174d79225ef99fa57f15535b1f0071d Author: lijewski Date: Sat Nov 22 00:44:44 1997 +0000 Merged in I/O statistics stuff. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 80b42b44834d0175d518a45e2e14b3478eaebe75 Author: lijewski Date: Sat Nov 22 00:44:22 1997 +0000 Merged in I/O statistics. Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp commit 3a29dc686b6c227c96d1b1114799e0940f9e4c80 Author: lijewski Date: Fri Nov 21 20:33:25 1997 +0000 Added typedef to describe first argument of bsp_fold(). Src/C_BaseLib/ParallelDescriptor.cpp commit d7c140a2b36bf60ea5f45ed33ee9d407a5a4c3a3 Author: lijewski Date: Fri Nov 21 03:50:35 1997 +0000 Now accumlate numPts() in m_numpts. Src/C_BaseLib/FabArray.H commit 273e77e9682043b051ce8fa8ab14ea43f32ec972 Author: lijewski Date: Fri Nov 21 03:50:10 1997 +0000 Fixed a bug in RunStats. Still needs work. The name of WritePlotFile RunStats variable didn't match that in inputs. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/RunStats.H Src/C_AMRLib/RunStats.cpp commit b6259f73d32732e0f2187202b66f00d0f892ecc8 Author: lijewski Date: Thu Nov 20 18:26:59 1997 +0000 Small changes Tools/C_mk/Make.OSF1 Tools/C_mk/Make.T3E commit 14ea1a3b9bfee6907b4d30e11a5ddf1bf975db69 Author: lijewski Date: Thu Nov 20 18:14:32 1997 +0000 Removed a `return' following a `stop' that compiler warned was unreachable. Src/C_AMRLib/INTERP_3D.F commit ebde3cbef4316373d3f53360e10de25a88312d56 Author: lijewski Date: Thu Nov 20 17:05:10 1997 +0000 Small mod to compile on T3E. Src/C_BaseLib/VisMF.cpp commit d1144ac0f339e530ca652fa427ad8a7d75f740cd Author: lijewski Date: Thu Nov 20 17:04:57 1997 +0000 Small mod to get to compile on T3E. Src/C_AMRLib/Amr.cpp commit f93dce4316880b343263c358a1c8490f204d2931 Author: lijewski Date: Thu Nov 20 16:13:38 1997 +0000 A small simplification. Src/C_BaseLib/ParallelDescriptor.H commit 3b1715cd2d8567bb8161758b1dcf21e051413a2a Author: lijewski Date: Thu Nov 20 00:49:42 1997 +0000 ParallelDescriptor::SetMessageHeaderSize() now takes int not int&. Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/TagBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/VisMF.cpp commit 26f5efae06b0e670322d2d2ef0c8e55b222c93b7 Author: lijewski Date: Thu Nov 20 00:19:50 1997 +0000 Added PrintStats() to FabArray. Src/C_BaseLib/FabArray.H commit 69d07d5b9af87d1a4313555ae1b6f5d918958d4d Author: lijewski Date: Thu Nov 20 00:19:30 1997 +0000 Prettified report() a tad. Src/C_AMRLib/RunStats.cpp commit 235c008475187c04dd7ae36eb8f520deded123b9 Author: lijewski Date: Wed Nov 19 17:31:19 1997 +0000 Removed some unused arrays in FabArrayCopyDescriptor and general cleanup. Src/C_BaseLib/FabArray.H commit fc1aebf5a3a40ccded9a994bdc6f5c376c631b1d Author: lijewski Date: Wed Nov 19 16:25:54 1997 +0000 Added write_pltfile and write_chkfile RunStats. Moved some RunStats functions inline. Src/C_AMRLib/Amr.cpp Src/C_AMRLib/RunStats.H Src/C_AMRLib/RunStats.cpp commit e93560b695d6d4509d99f56e101b34eb4955e7d0 Author: lijewski Date: Wed Nov 19 04:42:27 1997 +0000 Simplified a tad bit of code. Src/C_AMRLib/RunStats.cpp commit 706190ebc65e593fd47687703c81e3752f7a4cf4 Author: lijewski Date: Wed Nov 19 00:01:26 1997 +0000 Modified to deal with bsp_time() possible returning zero. Src/C_AMRLib/RunStats.cpp commit 411ed2fc60c77998ad4c5970761e3040f3a8296b Author: car Date: Tue Nov 18 21:45:28 1997 +0000 Start some changes. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp commit 88a4eaf6e05cdf6172364fe40dfb55d13e884cac Author: lijewski Date: Tue Nov 18 19:30:19 1997 +0000 Copied from Parallel/HCAll Src/C_AMRLib/Amr.H Src/C_AMRLib/Amr.cpp Src/C_AMRLib/AmrLevel.H Src/C_AMRLib/AmrLevel.cpp Src/C_AMRLib/Amr_auxil.H Src/C_AMRLib/BCRec.H Src/C_AMRLib/BCRec.cpp Src/C_AMRLib/BC_TYPES.H Src/C_AMRLib/Cluster.H Src/C_AMRLib/Cluster.cpp Src/C_AMRLib/DIMS.H Src/C_AMRLib/Derive.H Src/C_AMRLib/Derive.cpp Src/C_AMRLib/ErrorList.H Src/C_AMRLib/ErrorList.cpp Src/C_AMRLib/FILCC_2D.F Src/C_AMRLib/FILCC_3D.F Src/C_AMRLib/FLUXREG_2D.F Src/C_AMRLib/FLUXREG_3D.F Src/C_AMRLib/FLUXREG_F.H Src/C_AMRLib/FluxRegister.H Src/C_AMRLib/FluxRegister.cpp Src/C_AMRLib/INTERP_2D.F Src/C_AMRLib/INTERP_3D.F Src/C_AMRLib/INTERP_F.H Src/C_AMRLib/Interpolater.H Src/C_AMRLib/Interpolater.cpp Src/C_AMRLib/LevelBld.H Src/C_AMRLib/MAKESLICE_3D.F Src/C_AMRLib/MAKESLICE_F.H Src/C_AMRLib/PROB_AMR_F.H Src/C_AMRLib/RunStats.H Src/C_AMRLib/RunStats.cpp Src/C_AMRLib/StateData.H Src/C_AMRLib/StateData.cpp Src/C_AMRLib/StateDescriptor.H Src/C_AMRLib/StateDescriptor.cpp Src/C_AMRLib/TagBox.H Src/C_AMRLib/TagBox.cpp commit 7580dbc50250fc98c65d6287899469a168b556df Author: lijewski Date: Tue Nov 18 18:51:53 1997 +0000 PerFile -> PerFab Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit b1b43805e1d22020c38aa4e7f205657818871126 Author: lijewski Date: Tue Nov 18 18:48:13 1997 +0000 Fixed a bug. Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit 2bed7fd7983f1060808bd0b38f3607313e42e485 Author: lijewski Date: Tue Nov 18 18:22:24 1997 +0000 Mods to compile on NAVO T3E. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit b4c40aa369442e197db0fd969f3636726bedd8c8 Author: lijewski Date: Tue Nov 18 00:04:45 1997 +0000 Added explicit to all single-argument constructors. Removed IntVect::operator const int * Wrote BoxList::contains(BoxArray). Src/C_BaseLib/Array.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxAssoc.H Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/IndexType.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/List.H Src/C_BaseLib/Looping.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/PArray.H Src/C_BaseLib/ParmParse.H Src/C_BaseLib/Pointers.H Src/C_BaseLib/Tracer.H Src/C_BaseLib/Tuple.H Src/C_BaseLib/aString.H commit da5f8ca65647b43377ab0c0250333b5fdc16b9a4 Author: lijewski Date: Mon Nov 17 21:09:30 1997 +0000 Removed ToString(). Got rid of GetTheChar(). Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit be34251f063aae0ba8373b5b0065b3d93c923b47 Author: car Date: Mon Nov 17 19:05:31 1997 +0000 A little better way: just pass in a dummy mode variable in WIN32. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit 02be1b6435f232df319cc65b3cfcc03b56bfcbba Author: car Date: Mon Nov 17 19:02:03 1997 +0000 Fix for WIN32 not supporting mkdir. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp commit da2dca39383022b04afc87f7c728283a761f0b5a Author: lijewski Date: Sat Nov 15 00:52:38 1997 +0000 Added VisMF::Read(). Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit a55ffec0d73f28c2ad91559bf836b35f719cb9ba Author: vince Date: Fri Nov 14 21:43:35 1997 +0000 Added better optimization flags. Tools/C_mk/Make.T3E commit 42f1aeaee1b13f53c6dba9329afa8d4224b6b43e Author: lijewski Date: Fri Nov 14 20:22:40 1997 +0000 The IO_Bufffer object needs to be created before the [io]fstream one! Src/C_BaseLib/VisMF.cpp commit 171470f55904913285ebfadbb1ee003299edbea4 Author: lijewski Date: Fri Nov 14 00:59:55 1997 +0000 Removed Large_IO_Buffer() and replaced with Array usage. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 93d90f6eb05e1fd98ebda7e80c851c0348d47b54 Author: lijewski Date: Thu Nov 13 23:55:44 1997 +0000 Made IO Buffer stuff public so Amr could use it as well. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 627d0ed0a2a41ba363d9626167273d917bc8ec81 Author: lijewski Date: Thu Nov 13 21:47:46 1997 +0000 Removed ios::binary junk. Integrated in BL_USE_SETBUF and BL_SETBUF_CHAR_SIGNED. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit dcbcb4aa1f46879a8733fdff360e506e3e77866f Author: lijewski Date: Thu Nov 13 21:41:23 1997 +0000 Added BL_USE_SETBUF. Tools/C_mk/Make.T3E commit 8bf2453b733cc05f0dc021a7de03d5e2c32e9813 Author: lijewski Date: Thu Nov 13 21:28:01 1997 +0000 Added -DBL_SETBUF_SIGNED_CHAR when using CC. Tools/C_mk/Make.T3E commit 36023a9e0532dc4dbb50e1375ea48066b3c583cf Author: lijewski Date: Thu Nov 13 18:45:14 1997 +0000 Now uniformly use BoxLib::Error() for error reporting. It now uses ParallelDescriptor::Abort() internally, when needed. Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/VisMF.cpp commit 8fe14ed9529726e90c08c6bfd1bf68fa6c0bcab1 Author: lijewski Date: Thu Nov 13 16:38:54 1997 +0000 Replaced abort() with BoxLib::Abort(). Src/C_BaseLib/ParallelDescriptor.H commit 6f6535f7e59c6cb39deb231ee6499dfeec634d69 Author: lijewski Date: Thu Nov 13 16:34:00 1997 +0000 Maxed out the precision when outputting the Header. Replaced BoxLib::Error() with ParallelDescriptor::Abort(). Src/C_BaseLib/VisMF.cpp commit 3e4f7350c5ebdc3cacf3fc4433c1a2b7aff00419 Author: lijewski Date: Thu Nov 13 15:47:34 1997 +0000 Bug in the relative path portion of CreateDirectory() Src/C_BaseLib/Utility.cpp commit 0e7688ec40ee9c57120f60205799349f4bc2e004 Author: vince Date: Thu Nov 13 01:14:43 1997 +0000 Make definitions for the T3E. Tools/C_mk/Make.T3E commit 34c3ce53861205acf3f172113da3aed1cd192bcf Author: lijewski Date: Thu Nov 13 01:05:12 1997 +0000 Signatures of Abort() were not consistent in sequential/parallel code. Src/C_BaseLib/ParallelDescriptor.H commit 9deac822f6de4d5afa4c1ce513f5fe0989d37f6e Author: nazgul Date: Wed Nov 12 22:10:30 1997 +0000 fiddling with test problems Src/LinearSolvers/C_NodalMG/proj.cpp commit ea17c0a6c99aacaa2f5f90d2ac06e4c7ddbd54bd Author: lijewski Date: Wed Nov 12 21:57:26 1997 +0000 Added Utility:CreateDirectory() and a test case. Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/test/GNUmakefile.test Src/C_BaseLib/test/tDir.cpp Tests/C_BaseLib/GNUmakefile.test Tests/C_BaseLib/tDir.cpp commit 974ebd6a6402d98bd84879e9d24a1cc2cb1143ea Author: nazgul Date: Wed Nov 12 21:42:33 1997 +0000 New tests for 3d terrain stencils Src/LinearSolvers/C_NodalMG/tests/gt2t1 Src/LinearSolvers/C_NodalMG/tests/gt2t2 Src/LinearSolvers/C_NodalMG/tests/gt2t3 Tests/LinearSolvers/C_NodalMG/test_grids/gt2t1 Tests/LinearSolvers/C_NodalMG/test_grids/gt2t2 Tests/LinearSolvers/C_NodalMG/test_grids/gt2t3 commit d5405f554e8fa7292d1344340eb07c40e7707898 Author: nazgul Date: Wed Nov 12 21:39:29 1997 +0000 Fix to problems with sigmas in terrain stencils? Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 6eafa3faf7a3a63e0442c7aac32bb7ef9df9fdce Author: lijewski Date: Wed Nov 12 17:40:33 1997 +0000 VisMF.cpp currently compiles on T3E. Added -nboxs flag to test case. Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit c3b2b9decf9bed0c9cebc7a2a1f17827651a4e70 Author: lijewski Date: Wed Nov 12 04:12:24 1997 +0000 Made the open modes I expect explicit. Now longer clean up previous output files in test case. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit 8477ccb607366879f486ff382f8e6a724229d993 Author: lijewski Date: Wed Nov 12 00:22:57 1997 +0000 Added .cvsignore Src/C_BaseLib/.cvsignore commit 7b0886b7799558836552352318143a04261bea94 Author: lijewski Date: Wed Nov 12 00:16:56 1997 +0000 Added some code to use large I/O buffers on T3E. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit b2a4849bd98ec80bc920200f1c98c648dafabfef Author: lijewski Date: Tue Nov 11 22:18:59 1997 +0000 Needed a ParallelDescriptor::Synchronize() between writing and reading. Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit 1d2d9c7f876b9ae83a21881650a8f0e4119cb4c1 Author: lijewski Date: Tue Nov 11 21:38:37 1997 +0000 Added a call to MultiFab::setBndry(0). Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit 6efd06bd71aacccf2e7fe7e0ab8ab68daed64c99 Author: lijewski Date: Tue Nov 11 21:22:50 1997 +0000 Consolidated some of the code into larger routine. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 05dd332fe75a4cb053c9de15d88b0de4b521c900 Author: vince Date: Tue Nov 11 21:04:52 1997 +0000 Added sync argument: FabArrayIterator::isValid(bool bDoSync = true); Src/C_BaseLib/Box.H Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Utility.cpp commit 1cec386f02ec5642acf31469fe3f77a9d5b140dd Author: lijewski Date: Tue Nov 11 21:02:19 1997 +0000 Now the OneFilePerFab is working in Parallel. Src/C_BaseLib/VisMF.cpp commit ce90c46d9f36c971a0c99753ffe77e6765d5ba8d Author: nazgul Date: Tue Nov 11 20:51:05 1997 +0000 Added compiler options necessary to get optimization to work with KCC 3.1a and 3d terrain level solves. (Cannot use higher than +K2). Src/LinearSolvers/C_NodalMG/GNUmakefile.main commit 7ea8288dc1d5e51f9d5caf8af9702155e569d23c Author: lijewski Date: Tue Nov 11 20:29:56 1997 +0000 Added -how flag. Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit e1e01db38ee3abd6a9cf5f6d27d910d90dacb444 Author: lijewski Date: Tue Nov 11 19:20:05 1997 +0000 Got the VisMF::OneFilePerCPU working in Parallel. Had to Change the signature of ParallelDescriptor::SendData(). Src/C_BaseLib/FabArray.H Src/C_BaseLib/GNUmakefile Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/test/GNUmakefile.test Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/GNUmakefile.test Tests/C_BaseLib/tVisMF.cpp commit 69ba94f24fa738ddcdcbfe61b9885fc21d29f5fc Author: lijewski Date: Tue Nov 11 01:18:13 1997 +0000 Added some more parallel code. Yet more to come. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit 4a85cfa5eb28722d7b729beb300a73fb11769a06 Author: lijewski Date: Mon Nov 10 22:41:21 1997 +0000 Did the MultiFab loops using proper Parallel construct. All that remains is to do the reduction of the VisMF::Header. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 28b1d733eece835af8947f32f9deef7af6fb994e Author: almgren Date: Mon Nov 10 22:22:33 1997 +0000 These files now have the correct subroutines for the 3-d multilevel terrain stencils (faces / edges / corners) for residual and divergence. They are ifdef'ed for TERRAIN. Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit 917a5935e1339560e318e7762442f5bf340fb02d Author: lijewski Date: Mon Nov 10 22:14:47 1997 +0000 Added length() member to VisMF.H Now test reading and writing both ways at once. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit e0511943b7c79a843f58a3bdf20a68794e3586aa Author: car Date: Mon Nov 10 21:36:17 1997 +0000 Some changes for parallel file I/O. Src/C_BaseLib/Box.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/pBoxLib_2.dsp commit 42fc8aca600e7d443e836e807c733361a6a34f81 Author: lijewski Date: Mon Nov 10 21:29:48 1997 +0000 Got working for -DUSE_NEW_HFILES macro. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit e9fda6fc2ba520eeef6937b9d5fa0fe55862609e Author: lijewski Date: Mon Nov 10 21:17:10 1997 +0000 Got OneFilePerFab working. Parallel to come .... Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/tVisMF.cpp commit 1f3f0335cc9c42666dcc88444a4ef099483238cd Author: lijewski Date: Mon Nov 10 19:30:12 1997 +0000 The OneFilePerCPU stuff seems to work. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp Src/C_BaseLib/test/GNUmakefile.test Src/C_BaseLib/test/tVisMF.cpp Tests/C_BaseLib/GNUmakefile.test Tests/C_BaseLib/tVisMF.cpp commit 319f3a350a8b72b3e98e939024107c93036638f7 Author: lijewski Date: Mon Nov 10 17:54:40 1997 +0000 BoxArray(istream&) wasn't implemented. Now can read the VisMF::Header that has been written to disk. Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit d90e806f32a69eacb746ce65e5aa5a5bd0002ce6 Author: lijewski Date: Mon Nov 10 03:55:46 1997 +0000 Forgot about the ghost cells :-( Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 1cba5e03c9ab1744917afd85365f1713d946a920 Author: lijewski Date: Mon Nov 10 03:37:29 1997 +0000 Wrote the stream extraction operators. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit c915e63bbd7e6df69b00621ca657334e050b0b1c Author: lijewski Date: Sun Nov 9 20:31:40 1997 +0000 OneFilePerCPU output is more or less done. Now for the testing. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit d2639f853837afbfac5d509a4e247b69c6fd8ef9 Author: lijewski Date: Sun Nov 9 20:11:25 1997 +0000 Just cosmetic guff. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 5c2d5d466f4e3b8e5ef92adc066d15897ec27c7d Author: lijewski Date: Sun Nov 9 19:45:29 1997 +0000 Slight cosmetic changes -- no more static stuff in .cpp file. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 0168fa96dd8c6b533f83b746594dfd07a59ab040 Author: lijewski Date: Sun Nov 9 00:58:56 1997 +0000 Added some more code. Lots more to follow. Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit 7450ac6ba2d45882ffd2d2e2cb0371873b53af3f Author: lijewski Date: Sat Nov 8 23:24:16 1997 +0000 Added VisMF stuff -- just getting started with it. Src/C_BaseLib/Make.package Src/C_BaseLib/VisMF.H Src/C_BaseLib/VisMF.cpp commit b6a549645833f8e7a91bd753baa11ebad0d6ab96 Author: jbb Date: Sat Nov 8 01:42:02 1997 +0000 Fixed nested comments Src/C_BaseLib/Utility.H commit 9e289e25a32fda9c0bf218d99f2b66a2320861ae Author: almgren Date: Thu Oct 30 22:44:32 1997 +0000 Added subroutines hgfdiv, hgediv and hgcdiv for TERRAIN defined. Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit 61c404f39f962c7079aa6908f789cb7385de8a89 Author: almgren Date: Thu Oct 30 22:44:13 1997 +0000 Cosmetic changes only. Src/LinearSolvers/C_NodalMG/hg_proj2d.F commit 6cd1d16687afdf6e5465cc44323f4c35c4d37cde Author: vince Date: Tue Oct 21 22:00:52 1997 +0000 Bug fixes for parallel multilevel IAMR (minus the nodal projection). Also other fixes and code cleanup. Src/C_AMRLib/DatasetClient.cpp commit 70e92eff9aac7b20539be29a390d0a5b616cf076 Author: vince Date: Tue Oct 21 21:55:53 1997 +0000 Minor changes to AddBox interface. Src/C_BaseLib/Box.H Src/C_BaseLib/FabArray.H commit 15b8ce2bab58de1b394fb1c2634e6aba90ecb577 Author: car Date: Thu Oct 9 18:23:10 1997 +0000 Added more access functions to the iterators: more STL like. Src/C_BaseLib/FabArray.H commit 7bff2a1aa5af7fbef7a9848b58034a1bf02c9c0b Author: car Date: Thu Sep 25 21:57:17 1997 +0000 Small changes. Src/C_BaseLib/pBoxLib_2.dsp commit 949841b53c75d1a257cc5db73618a1155deb50c9 Author: lijewski Date: Wed Sep 24 22:06:41 1997 +0000 Replaced most endl's with '\n'. Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxAssoc.cpp Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/ParmParse.cpp commit fea6a8fd2fd994433230de2174cdc937f9e4d4da Author: lijewski Date: Wed Sep 24 04:24:50 1997 +0000 Removed the BoxList intersect with BoxList function. It wasn't implemented properly. Will add a correct one if the need arises. Removed ostrstream usage from BoxLib.cpp. Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp commit 328fb178b241ca4a5ef2e36272078cbcada758d9 Author: car Date: Wed Sep 24 03:01:20 1997 +0000 Removed a strstream.h file inclusion, not needed. Src/C_BaseLib/ParmParse.cpp commit 2688be7c705eb08803aea6d09ef471eff637cceb Author: lijewski Date: Tue Sep 23 19:25:39 1997 +0000 Merged in BL_USE_NEW_HFILES. Removed many unnecessary #include directives. Removed a couple more instances of RASTER and CONTOUR usage. Src/C_AMRLib/DatasetClient.cpp commit 5e700a0626be21d946af44dde9b1b618535c7c9a Author: nazgul Date: Tue Sep 23 18:13:44 1997 +0000 Minor modifications occasioned by the 4 level test problem, and letting the convergence test see the norm of the coarse_source. Src/LinearSolvers/C_NodalMG/amr_graph.cpp Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 41ba3fc0532f526083919b4f456c54fdf9a6efb6 Author: nazgul Date: Tue Sep 23 18:11:24 1997 +0000 4 level test problem Src/LinearSolvers/C_NodalMG/tests/gr4level Tests/LinearSolvers/C_NodalMG/test_grids/gr4level commit 0a58d792af5203d76118b7de867caf3ed626c901 Author: car Date: Fri Sep 19 18:20:02 1997 +0000 Quiet down a warning about conversion of long to bool. Update the Project file. Src/C_BaseLib/FabArray.H Src/C_BaseLib/pBoxLib_2.dsp commit 29bcd0f20dd53cfb57133ed6472464de7189838c Author: vince Date: Fri Sep 19 18:04:34 1997 +0000 Bug fix for T3E (ReduceBoolAnd problems). Src/C_BaseLib/FabArray.H Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp Src/C_BaseLib/Utility.H commit c5fa29a9b4d3e3d87cb797108451e28b3e9956c4 Author: car Date: Fri Sep 19 16:17:30 1997 +0000 Change Comment. Src/C_BaseLib/ArrayLim.H commit 111550f24a68ea03c41d1098dd55de0b050e3340 Author: lijewski Date: Thu Sep 18 23:34:18 1997 +0000 Only output continuation line count if > 19 of them. Tools/C_scripts/strip72 commit e90fb1730737fa0b457463be6b821356ce3808a9 Author: lijewski Date: Thu Sep 18 22:09:24 1997 +0000 Changed a few functions that took `const int' to take simply a `int'. Src/C_BaseLib/FabArray.H Src/C_BaseLib/MultiFab.H commit c8450b894ea404e3bf808210f0ee49a2c324cdff Author: lijewski Date: Thu Sep 18 21:22:19 1997 +0000 Removed some lines that had been commented out. Src/C_BaseLib/PArray.H commit f225a6529dfa29d22f9c0b740debbf04f0dabed2 Author: lijewski Date: Thu Sep 18 20:12:42 1997 +0000 Added BL_USE_NEW_HFILES macro. Src/C_BaseLib/Arena.H Src/C_BaseLib/Array.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/IndexType.H Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/Orientation.H Src/C_BaseLib/PArray.H Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/SPACE_F.H Src/C_BaseLib/Tracer.cpp Src/C_BaseLib/Tuple.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp commit 86435a01bb3b77326b190f9d6e9e1da616314109 Author: car Date: Thu Sep 18 18:25:19 1997 +0000 Added some stuff. Src/C_BaseLib/pBoxLib_2.dsp commit 2dd0ee07696f36f5b6bf3400857e317ebfcefd6a Author: car Date: Thu Sep 18 18:18:01 1997 +0000 Broke a comment. Src/C_BaseLib/Utility.H commit cb25311b3520630c59588f83a55157e4913dd78e Author: car Date: Thu Sep 18 18:03:33 1997 +0000 C++ style comments can't be in fortran include files. Src/C_BaseLib/CONSTANTS.H Src/C_BaseLib/REAL.H Src/C_BaseLib/SPACE_F.H Src/C_BaseLib/Utility.H commit 1f40f94399e7412e75333277525647f9bed65bdc Author: lijewski Date: Wed Sep 17 22:51:11 1997 +0000 Enforced all files having a copyright macro. Prepended all file inclusion macros with BL_ Src/C_BaseLib/Arena.H Src/C_BaseLib/Array.H Src/C_BaseLib/ArrayLim.H Src/C_BaseLib/Assert.H Src/C_BaseLib/BArena.H Src/C_BaseLib/Boolean.H Src/C_BaseLib/Box.H Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxAssoc.H Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxList.H Src/C_BaseLib/CONSTANTS.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FPC.H Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/IndexType.H Src/C_BaseLib/IntVect.H Src/C_BaseLib/List.H Src/C_BaseLib/Looping.H Src/C_BaseLib/Misc.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/Orientation.H Src/C_BaseLib/PArray.H Src/C_BaseLib/ParmParse.H Src/C_BaseLib/Pointers.H Src/C_BaseLib/REAL.H Src/C_BaseLib/SPACE.H Src/C_BaseLib/SPACE_F.H Src/C_BaseLib/Tracer.H Src/C_BaseLib/Tuple.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.H Src/C_BaseLib/aString.H commit 99622cae738f6bbc75e357a7a772f552eba5f178 Author: lijewski Date: Wed Sep 17 22:22:49 1997 +0000 Inlined the constructors. Prepended BL_ to file inclusion macros. Src/C_BaseLib/BaseFab.H commit 66551db6f06b7bfc85866db12c71673cd5e30304 Author: lijewski Date: Wed Sep 17 17:46:31 1997 +0000 Inlined the constructors. Regularized the indentation. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit 066bb95aeba8b0191008de0b02df29ed36dae9d2 Author: lijewski Date: Wed Sep 17 17:15:59 1997 +0000 Inlined all the MultiFabIterator stuff. Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp commit bac52e53c8d6289c982089535d698a2b0d43166e Author: lijewski Date: Wed Sep 17 00:03:49 1997 +0000 Now check assignments of Box::numPts() to integers. Src/C_AMRLib/DatasetClient.cpp commit 35b9afb0a67b852b8a53164aba70e5ffb155081d Author: lijewski Date: Wed Sep 17 00:03:26 1997 +0000 Check assignments of Box::numPts() to integers. Src/C_BaseLib/FabArray.H commit 847fc06b03eec118f13783e69ad0eeaa654fa99e Author: lijewski Date: Tue Sep 16 22:28:14 1997 +0000 Removed `inline' from class definitions. Src/C_BaseLib/Array.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/List.H Src/C_BaseLib/PArray.H Src/C_BaseLib/Pointers.H Src/C_BaseLib/Tuple.H commit e03036067d3b0f437fa6dc36e9770ad34cb25f4f Author: lijewski Date: Tue Sep 16 22:12:43 1997 +0000 The previous virtual stuff that was removed consisted only of the stuff in FabArrayIterator. This mod removes all the virtual stuff from the three remaining Iterators in this module, as well as the virtual stuff from FabArrayCopyDescriptor. Src/C_BaseLib/FabArray.H commit ccc3769a13049b3460aaa750596c0c517633a30d Author: lijewski Date: Tue Sep 16 21:11:34 1997 +0000 Removed all virtual stuff. Src/C_BaseLib/FabArray.H commit 980dde8029d140ae76d2d05700648d63159e2d93 Author: lijewski Date: Tue Sep 16 19:18:11 1997 +0000 Some cleanup and code simplification. Inlined more stuff. Src/C_BaseLib/Array.H Src/C_BaseLib/BLVERSION.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/FabArray.H commit 673ec7d486b8830c16b6ef68674375adafd104ab Author: lijewski Date: Tue Sep 16 16:04:59 1997 +0000 Removed all DPtr stuff. Src/C_BaseLib/AliasedDPtr.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/DPtr.H Src/C_BaseLib/Make.package Src/C_BaseLib/SimpleDPtr.H commit 3e687e8125c007bc433b3516f46555ebf67927ff Author: lijewski Date: Tue Sep 16 03:30:36 1997 +0000 Removed all aliasing stuff from BaseFab. Src/C_BaseLib/BaseFab.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/Looping.H commit 536217df33fa117181fd3a1d19481209c7e841e8 Author: lijewski Date: Mon Sep 15 23:33:19 1997 +0000 Removed aliasing stuff. Removed LPARX stuff. Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BaseFab.H Src/C_BaseLib/DPtr.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FabArray.H commit 18db379740d74a888d2946a9160a5cb99ae2c099 Author: lijewski Date: Mon Sep 15 22:24:10 1997 +0000 From Guthamr release. Tools/C_scripts/install-sh Tools/C_scripts/mkdep Tools/C_scripts/strip72 commit a8e7104301a3df86d54708c4964a4934017e3b8d Author: lijewski Date: Mon Sep 15 21:53:51 1997 +0000 Now assumes there is ../scripts directory. Tools/C_mk/Make.defs commit dcaa46f8a809e222b61ad27a01b4b511779f36ee Author: lijewski Date: Mon Sep 15 20:46:01 1997 +0000 Now assume things at ../mk Tools/C_mk/Make.defs commit 296a7d000fe41bc59e4b42fa1f3ba2b2a5ec2196 Author: lijewski Date: Mon Sep 15 20:45:43 1997 +0000 Now assume ../mk existance. Src/C_BaseLib/GNUmakefile commit 1c282a382a7493b9332146ca3a08220cb1374021 Author: lijewski Date: Mon Sep 15 20:37:04 1997 +0000 Moved from IARMAll directory. Tools/C_mk/Make.OSF1 Tools/C_mk/Make.defs Tools/C_mk/Make.rules commit 4b417c9677f32d29e5c8813d176d1f3085186baa Author: lijewski Date: Mon Sep 15 19:45:24 1997 +0000 Removed Tuple.cpp and rearranged some things. Src/C_BaseLib/Make.package commit 12c046f524fc5d203748dc36a37d2da7b206750a Author: lijewski Date: Mon Sep 15 19:40:05 1997 +0000 Brought some stuff up to the indentation style of previous boxlib. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/GNUmakefile Src/C_BaseLib/Make.package Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit ad1c15eb80c200afabbd3559f95935d870fa1e63 Author: vince Date: Mon Sep 15 16:39:38 1997 +0000 Added files. Src/C_BaseLib/DistributionMapping.H Src/C_BaseLib/DistributionMapping.cpp Src/C_BaseLib/ParallelDescriptor.H Src/C_BaseLib/ParallelDescriptor.cpp commit 75deac98e0431fa3322aa21ab9f75e3513659f58 Author: lijewski Date: Fri Sep 12 17:59:59 1997 +0000 Moved from IAMRAll directory. Src/C_BaseLib/AliasedDPtr.H Src/C_BaseLib/Arena.H Src/C_BaseLib/Array.H Src/C_BaseLib/ArrayLim.H Src/C_BaseLib/Assert.H Src/C_BaseLib/BArena.H Src/C_BaseLib/BArena.cpp Src/C_BaseLib/BLVERSION.H Src/C_BaseLib/BaseFab.H Src/C_BaseLib/Boolean.H Src/C_BaseLib/Box.H Src/C_BaseLib/Box.cpp Src/C_BaseLib/BoxArray.H Src/C_BaseLib/BoxArray.cpp Src/C_BaseLib/BoxAssoc.H Src/C_BaseLib/BoxAssoc.cpp Src/C_BaseLib/BoxDomain.H Src/C_BaseLib/BoxDomain.cpp Src/C_BaseLib/BoxLib.H Src/C_BaseLib/BoxLib.cpp Src/C_BaseLib/BoxList.H Src/C_BaseLib/BoxList.cpp Src/C_BaseLib/CONSTANTS.H Src/C_BaseLib/DPtr.H Src/C_BaseLib/FArrayBox.H Src/C_BaseLib/FArrayBox.cpp Src/C_BaseLib/FPC.H Src/C_BaseLib/FPC.cpp Src/C_BaseLib/FabArray.H Src/C_BaseLib/FabConv.H Src/C_BaseLib/FabConv.cpp Src/C_BaseLib/IndexType.H Src/C_BaseLib/IndexType.cpp Src/C_BaseLib/IntVect.H Src/C_BaseLib/IntVect.cpp Src/C_BaseLib/List.H Src/C_BaseLib/Looping.H Src/C_BaseLib/Make.package Src/C_BaseLib/Misc.H Src/C_BaseLib/MultiFab.H Src/C_BaseLib/MultiFab.cpp Src/C_BaseLib/Orientation.H Src/C_BaseLib/Orientation.cpp Src/C_BaseLib/PArray.H Src/C_BaseLib/ParmParse.H Src/C_BaseLib/ParmParse.cpp Src/C_BaseLib/Pointers.H Src/C_BaseLib/REAL.H Src/C_BaseLib/SPACE.H Src/C_BaseLib/SPACE_F.H Src/C_BaseLib/SimpleDPtr.H Src/C_BaseLib/Tracer.H Src/C_BaseLib/Tracer.cpp Src/C_BaseLib/Tuple.H Src/C_BaseLib/UseCount.H Src/C_BaseLib/Utility.H Src/C_BaseLib/Utility.cpp Src/C_BaseLib/aString.H Src/C_BaseLib/aString.cpp commit afb9a89932bb568e849656b2aca95cb63feb8549 Author: car Date: Mon Aug 11 23:45:38 1997 +0000 Fortran tweaks. Src/C_AMRLib/DatasetClient.cpp commit dd6443e646e9f29410d9c7ff897a43bbbc280159 Author: nazgul Date: Tue Aug 5 03:26:59 1997 +0000 Yet more test grids. Src/LinearSolvers/C_NodalMG/tests/gr2.0 Src/LinearSolvers/C_NodalMG/tests/gr2.1 Src/LinearSolvers/C_NodalMG/tests/gt010 Src/LinearSolvers/C_NodalMG/tests/gt012 Tests/LinearSolvers/C_NodalMG/test_grids/gr2.0 Tests/LinearSolvers/C_NodalMG/test_grids/gr2.1 Tests/LinearSolvers/C_NodalMG/test_grids/gt010 Tests/LinearSolvers/C_NodalMG/test_grids/gt012 commit 67e0489383acac4ceeea54af5758ff197f3da3d4 Author: nazgul Date: Tue Aug 5 03:24:54 1997 +0000 Level project now works in the t27 stencil (no line solves yet). Line solves work in any direction in the v7 stencil. Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit bbb2dd4d390208db69facd61f2fa460ea3cb7571 Author: car Date: Mon Jul 28 23:16:02 1997 +0000 Make _OSF_... complient for KCC-3.2b Src/C_AMRLib/DatasetClient.cpp commit f157f5d78378df1e8cf0cfdc0dc8431dd9cc9e45 Author: nazgul Date: Sun Jul 27 06:11:46 1997 +0000 A simple 16 cube Src/LinearSolvers/C_NodalMG/tests/gt016 Tests/LinearSolvers/C_NodalMG/test_grids/gt016 commit 1f57183141ec47999aec76e91ea7c9bbcfcef59a Author: vince Date: Thu Jul 24 20:31:14 1997 +0000 Added more FillPatchIterators. Src/C_AMRLib/DatasetClient.cpp commit 3976a1d77302700e9b5717fe6712f60c2578f5ea Author: nazgul Date: Sat Jul 12 06:10:39 1997 +0000 2d 9-point terrain stencils now working fully. line solves implemented, fixed bug in sync project. Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit c75230faf043996fcee66a2e1aa2cc265dd188b8 Author: nazgul Date: Fri Jul 11 22:02:56 1997 +0000 2d 9-point terrain stencils appear to work for level and sync project, except that line solves are not yet implemented. Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.H Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit bbabf6d5f39a13d17f4ef25ec2f0d62be585c126 Author: nazgul Date: Thu Jul 3 21:44:21 1997 +0000 test file for 2 small level 0 grids Src/LinearSolvers/C_NodalMG/tests/gr0b Tests/LinearSolvers/C_NodalMG/test_grids/gr0b commit 197f0fa7276b0152fc83f02191a036cfcaaabf0d Author: nazgul Date: Thu Jul 3 21:43:56 1997 +0000 terrain now implemented for level project Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp commit 8722964b1385f26566d2c489c227c1c6d6fb9681 Author: nazgul Date: Fri Jun 27 21:54:00 1997 +0000 integration form of restriction for terrain stencils declarations added Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/cont3d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit ebbaf3120c60bc03aef836660a8c09146b7b7c59 Author: nazgul Date: Thu Jun 26 23:19:35 1997 +0000 Beginnings of terrain additions. Src/LinearSolvers/C_NodalMG/amr_multi.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 5b809cac28f31826f5a42f235aba46640dda8596 Author: nazgul Date: Thu Jun 26 23:17:46 1997 +0000 Declarations added to fortran. Beginnings of terrain additions. Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/cont2d.F Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit 5829c65425db170a84df9b2ad5390f2e3a773f53 Author: nazgul Date: Thu Jun 26 23:05:43 1997 +0000 Test grids which exceed the size the cg bottom solver can easily handle Src/LinearSolvers/C_NodalMG/tests/gr1rick Src/LinearSolvers/C_NodalMG/tests/gr1rick2 Tests/LinearSolvers/C_NodalMG/test_grids/gr1rick Tests/LinearSolvers/C_NodalMG/test_grids/gr1rick2 commit 73897d51f8a7c0a69bac0a2b6c7372b6338e26bc Author: nazgul Date: Tue Jun 10 21:50:31 1997 +0000 Extend line solves to rz and dimension 0 in 2d. Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit 7bae9431fcf243eecf446eedb0675699386ec75b Author: nazgul Date: Tue Jun 10 00:50:17 1997 +0000 Minor fixes: forward line solve made vectorizable, conjugate gradient failure made non-fatal, just prints an error message (if pcode >= 2) and goes on. Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit 7acc39a95d9f35073c84419212b1d9285274b36e Author: nazgul Date: Fri Jun 6 16:59:08 1997 +0000 Full-level line solves, in dimension BL_SPACEDIM - 1, for stencils v5, v9 and v7, in Cartesian coordinates only. Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/proj.cpp commit 2cb536d60338abae0b1fbf19629c168fc29b8fef Author: nazgul Date: Fri Jun 6 16:49:29 1997 +0000 Yet another test grid Src/LinearSolvers/C_NodalMG/tests/gt05 Tests/LinearSolvers/C_NodalMG/test_grids/gt05 commit e7c2f6c4c99cd7c38f01326be4a9b208d3128c76 Author: nazgul Date: Mon Jun 2 20:56:14 1997 +0000 Test for case where domain can't be coarsened but a grid (apparently) can. Src/LinearSolvers/C_NodalMG/tests/gr2dave Tests/LinearSolvers/C_NodalMG/test_grids/gr2dave commit 588e910984fa921a0891b02b645817b0111e6f73 Author: nazgul Date: Mon Jun 2 20:55:51 1997 +0000 Bug fix for case where domain can't be coarsened but a grid (apparently) can. Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit 0221b7d7797f7fcccc64081bfa6664c66b0f5a18 Author: nazgul Date: Fri May 30 20:55:08 1997 +0000 Fixed a routine that isn't used yet so that the file will compile. Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit 180f1301d3af355a06bc8cee7813505b5ac5d487 Author: nazgul Date: Fri May 30 20:32:54 1997 +0000 Corrections to handle (4,1) refinement correctly. Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/interface.H Src/LinearSolvers/C_NodalMG/interface.cpp commit 4842b6e5470bf7b21457af87a793e7d6e36e1ee3 Author: nazgul Date: Fri May 30 20:32:11 1997 +0000 Adding (4,1) test grids. Src/LinearSolvers/C_NodalMG/tests/gr.19s4.1 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s4.1 commit 8206143d920174ac0ab88e14dc1e357510246696 Author: nazgul Date: Wed May 28 19:16:03 1997 +0000 Adds changes to support IntVect refinement ratios. Minor: fixes bug where cell-based source average trashes some interface divergence values that were already calculated. Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_graph.H Src/LinearSolvers/C_NodalMG/amr_graph.cpp Src/LinearSolvers/C_NodalMG/amr_gravity.cpp Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.cpp Src/LinearSolvers/C_NodalMG/cont3d.F Src/LinearSolvers/C_NodalMG/fill_patch.H Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_avg2d.F Src/LinearSolvers/C_NodalMG/hg_avg3d.F Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F Src/LinearSolvers/C_NodalMG/hg_proj2d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/interpolator.H Src/LinearSolvers/C_NodalMG/interpolator.cpp Src/LinearSolvers/C_NodalMG/proj.cpp Src/LinearSolvers/C_NodalMG/restrictor.H Src/LinearSolvers/C_NodalMG/restrictor.cpp commit bb56e75a5fff449325f871ed0c70285fd8f0f831 Author: nazgul Date: Wed May 28 19:12:32 1997 +0000 Tests for variable refinement ratios. Src/LinearSolvers/C_NodalMG/tests/gr.19s2.4 Src/LinearSolvers/C_NodalMG/tests/gt4s2.4.4 Src/LinearSolvers/C_NodalMG/tests/gt4s4 Src/LinearSolvers/C_NodalMG/tests/gt4s4.2.4 Src/LinearSolvers/C_NodalMG/tests/gt4s4.4.2 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s2.4 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s2.4.4 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s4 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s4.2.4 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s4.4.2 commit c3ca852054668ca71425ea5c4950cac13b3a11e6 Author: nazgul Date: Wed May 14 20:33:27 1997 +0000 line solve bug fix for degenerate case of 1-point line solves Src/LinearSolvers/C_NodalMG/hg_multi2d.F Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit ccf827a86e46802ea327329177ff0cb1ab824a02 Author: nazgul Date: Thu May 8 15:18:17 1997 +0000 Removed the function type(const PArray& a). It was too prone to errors caused by partially-filled arrays. Use type(const FabArray& r) instead. Src/LinearSolvers/C_NodalMG/amr_defs.H Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit d54a21c35d4f3cb5f27d0371773cdc75f00afef6 Author: nazgul Date: Wed May 7 22:24:26 1997 +0000 fix type index bug Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 44bc484391ff0051173bbfcc8674a5f20ef5363b Author: nazgul Date: Wed May 7 21:35:06 1997 +0000 fix to sync source correction Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 8e8bc933eeba15314d227303c8e9b30cca05e59c Author: nazgul Date: Wed May 7 21:29:19 1997 +0000 sync source solvability correction Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_projector.H Src/LinearSolvers/C_NodalMG/hg_projector.cpp commit 93c2d649c1627732aedae0ffa64483674110b569 Author: nazgul Date: Wed May 7 01:37:55 1997 +0000 adding line solve Src/LinearSolvers/C_NodalMG/hg_multi3d.F commit 5bca72009eeb1c3d2f869563ae4261a411f18a97 Author: nazgul Date: Wed May 7 00:35:43 1997 +0000 adding line solve Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/hg_multi.H Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit c0c90778cefc358ca49b6132afc6e7ffde36d79c Author: nazgul Date: Tue May 6 03:11:18 1997 +0000 fix index bug Src/LinearSolvers/C_NodalMG/amr_multi.cpp commit bad568c5614578c49cbee45558f823110a6ab6e9 Author: nazgul Date: Mon May 5 22:18:35 1997 +0000 Bug fix to build_index Src/LinearSolvers/C_NodalMG/amr_multi.cpp commit 37257f0bd58dd5c3099205e98974e1daa0fb6877 Author: nazgul Date: Fri May 2 22:06:26 1997 +0000 Fixed memory leak in test program Src/LinearSolvers/C_NodalMG/Make.package Src/LinearSolvers/C_NodalMG/proj.cpp commit c0b6bc499b3f85c4a7821027396d181cc57f7e6c Author: nazgul Date: Fri May 2 17:35:14 1997 +0000 Fixes for variable density now work. Src/LinearSolvers/C_NodalMG/GNUmakefile.main Src/LinearSolvers/C_NodalMG/Rewrite Src/LinearSolvers/C_NodalMG/hg_multi1.cpp Src/LinearSolvers/C_NodalMG/hg_multi2.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit 97e6e31d7d751d014563aabcec43b390fa0b0d1f Author: nazgul Date: Wed Apr 30 22:04:33 1997 +0000 Corrections for 3D. Src/LinearSolvers/C_NodalMG/Rewrite Src/LinearSolvers/C_NodalMG/amr_graph.H Src/LinearSolvers/C_NodalMG/amr_graph.cpp Src/LinearSolvers/C_NodalMG/amr_multi.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit e4f0a563c5d1dd000ec4903229699b9a1c2525f1 Author: nazgul Date: Wed Apr 30 20:28:51 1997 +0000 adding GNUmakefile manually since import ignores it. 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20:41:56 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/fill_patch.cpp Src/LinearSolvers/C_NodalMG/hg_multi3.cpp Src/LinearSolvers/C_NodalMG/hg_projector.cpp Src/LinearSolvers/C_NodalMG/proj.cpp commit c686e8eb909d6bc9e1470687eba613f8979febe1 Author: nazgul Date: Tue Apr 29 20:38:16 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/fill_patch.H commit 5e43618b9ba22ff0405611be875aed141fb2971a Author: nazgul Date: Tue Apr 29 20:15:56 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/hg_multi1.cpp commit ba18f4dd9f6dfa86e00df173cf66154acc1ead2e Author: nazgul Date: Tue Apr 29 18:29:40 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/hg_multi2d.F commit 94ffd818a9bf1ab6c86ec18e6e4565395f40ff4e Author: nazgul Date: Mon Apr 28 21:51:56 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/amr_multi.H commit a498100b0a43479409605ec9eaa464600fe1621b Author: nazgul Date: Fri Apr 25 23:30:33 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/Make.package commit 0f2561a87bce705882fc6124212c47013f79abea Author: nazgul Date: Wed Apr 23 22:34:37 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/GNUmakefile.main commit f686b4bc929214d97a8b0588608fe3b6731e46dc Author: nazgul Date: Thu Mar 27 22:05:28 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/hg_multi.H commit 52d19b7261ae7399004472ae95a884a86413590c Author: nazgul Date: Thu Mar 27 21:24:11 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/hg_projector.H commit 6b3d4c19412bdbce7f963ddded8121c512d600c1 Author: nazgul Date: Wed Mar 26 17:38:08 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/tests/gr2ann.p5 Src/LinearSolvers/C_NodalMG/tests/gr2ann.p6 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p5 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p6 commit 8ff71095cc689bc66f398bc1ee37ae130abe0c75 Author: nazgul Date: Tue Mar 25 18:58:20 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/amr_real2d.F Src/LinearSolvers/C_NodalMG/amr_real3d.F Src/LinearSolvers/C_NodalMG/boundary.H commit 1d73e974b0ad30060d63baa15439940bbbfff0a3 Author: nazgul Date: Fri Mar 21 20:13:36 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/amr_gravity.cpp Src/LinearSolvers/C_NodalMG/restrictor.cpp commit a3cf04d3be4853c18b48d3189cb7d77c1e01860d Author: nazgul Date: Fri Mar 21 20:09:06 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/cache.cpp Src/LinearSolvers/C_NodalMG/interface.H commit 92deacad1bee7c78f20a98ca485ca87363e4a677 Author: nazgul Date: Thu Mar 20 21:13:29 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/Rewrite commit 2e93f82c5955ee9919b5c73c2a318745843ac9f0 Author: nazgul Date: Tue Mar 18 23:51:41 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/cache.H commit 003ce6b53e5b81ecd219bc5a44af8d244e71f26a Author: nazgul Date: Tue Mar 18 20:16:26 1997 +0000 Initial revision Src/LinearSolvers/C_NodalMG/tests/gt3ann2 Tests/LinearSolvers/C_NodalMG/test_grids/gt3ann2 commit 007298ac68b21503d37eaf44a9cae210ad49c333 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Tests/LinearSolvers/C_NodalMG/test_grids/gr3rick Tests/LinearSolvers/C_NodalMG/test_grids/gr3rick2 Tests/LinearSolvers/C_NodalMG/test_grids/gt3ann Tests/LinearSolvers/C_NodalMG/test_grids/gtjbb commit 6830436830288f40cd9ae3c8829073031ee040db Author: nazgul Date: Thu Apr 25 16:46:17 1996 +0000 Initial revision Src/LinearSolvers/C_NodalMG/hg_proj2d.F commit 1f04efac2dc02158cf22a7c3d2f3f87082487dc6 Author: nazgul Date: Wed Mar 13 22:28:35 1996 +0000 Initial revision Src/LinearSolvers/C_NodalMG/cbasics.H Src/LinearSolvers/C_NodalMG/tests/gr0a Tests/LinearSolvers/C_NodalMG/test_grids/gr0a commit f87f1b2d83b7fe9c512ddc0ca43ae9bcd434670f Author: nazgul Date: Tue Nov 7 22:26:32 1995 +0000 Initial revision Src/LinearSolvers/C_NodalMG/amr_grav2d.F Src/LinearSolvers/C_NodalMG/amr_grav3d.F Src/LinearSolvers/C_NodalMG/cont2d.F Src/LinearSolvers/C_NodalMG/cont3d.F Src/LinearSolvers/C_NodalMG/hg_proj3d.F commit c139797864292915ccc5ebea761e68615309b970 Author: nazgul Date: Mon Oct 30 22:35:09 1995 +0000 Initial revision Src/LinearSolvers/C_NodalMG/README commit cfefdf25849ecf2ab5a5b2b6573a4f2bc43a21dd Author: nazgul Date: Mon Sep 18 20:37:46 1995 +0000 Initial revision Src/LinearSolvers/C_NodalMG/poisson.cpp commit d3a6d7bfeffcf89aa95b004c4aabb44f9243f13c Author: nazgul Date: Mon Sep 18 18:20:14 1995 +0000 Initial revision Src/LinearSolvers/C_NodalMG/hg_elliptic.cpp commit e7ab65e98df0bd6814dab6ea6bb540296b1b4677 Author: nazgul Date: Thu Aug 24 21:25:02 1995 +0000 Initial revision Src/LinearSolvers/C_NodalMG/tests/gr2ann.l2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.l2 commit ef57898a17aac4dd83b5457c8f70d6b4c4e42a2e Author: nazgul Date: Thu Aug 24 21:12:20 1995 +0000 Initial revision Src/LinearSolvers/C_NodalMG/tests/gr2ann.l1 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.l1 commit 642554a3d74ed89dfdb89c9049612fbcfb061494 Author: nazgul Date: Thu Aug 24 21:02:50 1995 +0000 Initial revision Src/LinearSolvers/C_NodalMG/tests/gr2ann.l0 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.l0 commit 6603ce60473f65e14e871c323ac0c2fb4fda9df8 Author: nazgul Date: Fri Nov 4 23:35:41 1994 +0000 Initial revision Src/LinearSolvers/C_NodalMG/tests/gr.11 Src/LinearSolvers/C_NodalMG/tests/gr.15 Src/LinearSolvers/C_NodalMG/tests/gr.16 Src/LinearSolvers/C_NodalMG/tests/gr.19 Src/LinearSolvers/C_NodalMG/tests/gr.19s2 Src/LinearSolvers/C_NodalMG/tests/gr.19s4 Src/LinearSolvers/C_NodalMG/tests/gr.292.11 Src/LinearSolvers/C_NodalMG/tests/gr.292.25 Src/LinearSolvers/C_NodalMG/tests/gr.7 Src/LinearSolvers/C_NodalMG/tests/gr.8 Src/LinearSolvers/C_NodalMG/tests/gr.8a Src/LinearSolvers/C_NodalMG/tests/gr0 Src/LinearSolvers/C_NodalMG/tests/gr1 Src/LinearSolvers/C_NodalMG/tests/gr1mike.thin Src/LinearSolvers/C_NodalMG/tests/gr2 Src/LinearSolvers/C_NodalMG/tests/gr2a2 Src/LinearSolvers/C_NodalMG/tests/gr2a4 Src/LinearSolvers/C_NodalMG/tests/gr2ann Src/LinearSolvers/C_NodalMG/tests/gr2ann.p1 Src/LinearSolvers/C_NodalMG/tests/gr2ann.p2 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Src/LinearSolvers/C_NodalMG/tests/gt0 Src/LinearSolvers/C_NodalMG/tests/gt1 Src/LinearSolvers/C_NodalMG/tests/gt12 Src/LinearSolvers/C_NodalMG/tests/gt12.2 Src/LinearSolvers/C_NodalMG/tests/gt12.3 Src/LinearSolvers/C_NodalMG/tests/gt2 Src/LinearSolvers/C_NodalMG/tests/gt3 Src/LinearSolvers/C_NodalMG/tests/gt4 Src/LinearSolvers/C_NodalMG/tests/gt4s2 Src/LinearSolvers/C_NodalMG/tests/gt4s2a Src/LinearSolvers/C_NodalMG/tests/gt5 Src/LinearSolvers/C_NodalMG/tests/gt5s2 Src/LinearSolvers/C_NodalMG/tests/gt5s4 Src/LinearSolvers/C_NodalMG/tests/gt6 Src/LinearSolvers/C_NodalMG/tests/gt6s Src/LinearSolvers/C_NodalMG/tests/gt6s2 Src/LinearSolvers/C_NodalMG/tests/gt6s4 Src/LinearSolvers/C_NodalMG/tests/gt7a Src/LinearSolvers/C_NodalMG/tests/gt7aa Src/LinearSolvers/C_NodalMG/tests/gt8 Src/LinearSolvers/C_NodalMG/tests/gt8a Src/LinearSolvers/C_NodalMG/tests/gt8b Src/LinearSolvers/C_NodalMG/tests/gt8c Src/LinearSolvers/C_NodalMG/tests/gt8ms2 Src/LinearSolvers/C_NodalMG/tests/gtbig Src/LinearSolvers/C_NodalMG/tests/gtbig2 Src/LinearSolvers/C_NodalMG/tests/gtbig3 Src/LinearSolvers/C_NodalMG/tests/gtbig4 Src/LinearSolvers/C_NodalMG/tests/gtbig5 Src/LinearSolvers/C_NodalMG/tests/gtgrav2 Src/LinearSolvers/C_NodalMG/tests/gtgrav4 Src/LinearSolvers/C_NodalMG/tests/gtpfail Tests/LinearSolvers/C_NodalMG/test_grids/gr.11 Tests/LinearSolvers/C_NodalMG/test_grids/gr.15 Tests/LinearSolvers/C_NodalMG/test_grids/gr.16 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s2 Tests/LinearSolvers/C_NodalMG/test_grids/gr.19s4 Tests/LinearSolvers/C_NodalMG/test_grids/gr.292.11 Tests/LinearSolvers/C_NodalMG/test_grids/gr.292.25 Tests/LinearSolvers/C_NodalMG/test_grids/gr.7 Tests/LinearSolvers/C_NodalMG/test_grids/gr.8 Tests/LinearSolvers/C_NodalMG/test_grids/gr.8a Tests/LinearSolvers/C_NodalMG/test_grids/gr0 Tests/LinearSolvers/C_NodalMG/test_grids/gr1 Tests/LinearSolvers/C_NodalMG/test_grids/gr1mike.thin Tests/LinearSolvers/C_NodalMG/test_grids/gr2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2a2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2a4 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p1 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p3 Tests/LinearSolvers/C_NodalMG/test_grids/gr2ann.p4 Tests/LinearSolvers/C_NodalMG/test_grids/gr2b Tests/LinearSolvers/C_NodalMG/test_grids/gr2c Tests/LinearSolvers/C_NodalMG/test_grids/gr2cross Tests/LinearSolvers/C_NodalMG/test_grids/gr2d Tests/LinearSolvers/C_NodalMG/test_grids/gr2d2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2d4 Tests/LinearSolvers/C_NodalMG/test_grids/gr2e Tests/LinearSolvers/C_NodalMG/test_grids/gr2f Tests/LinearSolvers/C_NodalMG/test_grids/gr2g Tests/LinearSolvers/C_NodalMG/test_grids/gr2h Tests/LinearSolvers/C_NodalMG/test_grids/gr2mike Tests/LinearSolvers/C_NodalMG/test_grids/gr2mike1 Tests/LinearSolvers/C_NodalMG/test_grids/gr2mike2 Tests/LinearSolvers/C_NodalMG/test_grids/gr2mike3 Tests/LinearSolvers/C_NodalMG/test_grids/gr3.rz Tests/LinearSolvers/C_NodalMG/test_grids/gr3a Tests/LinearSolvers/C_NodalMG/test_grids/gr3b Tests/LinearSolvers/C_NodalMG/test_grids/gr3c Tests/LinearSolvers/C_NodalMG/test_grids/gr3mike Tests/LinearSolvers/C_NodalMG/test_grids/gr3mike.3 Tests/LinearSolvers/C_NodalMG/test_grids/gr4 Tests/LinearSolvers/C_NodalMG/test_grids/gt.32 Tests/LinearSolvers/C_NodalMG/test_grids/gt0 Tests/LinearSolvers/C_NodalMG/test_grids/gt1 Tests/LinearSolvers/C_NodalMG/test_grids/gt12 Tests/LinearSolvers/C_NodalMG/test_grids/gt12.2 Tests/LinearSolvers/C_NodalMG/test_grids/gt12.3 Tests/LinearSolvers/C_NodalMG/test_grids/gt2 Tests/LinearSolvers/C_NodalMG/test_grids/gt3 Tests/LinearSolvers/C_NodalMG/test_grids/gt4 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s2 Tests/LinearSolvers/C_NodalMG/test_grids/gt4s2a Tests/LinearSolvers/C_NodalMG/test_grids/gt5 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d9792e7e53274b898d907a0f08452bef75669031 Author: nazgul Date: Tue Oct 4 22:13:47 1994 +0000 Initial revision Src/LinearSolvers/C_NodalMG/amr_gravity.H commit b06aef4481e3612148772e1a6e0aa59c3be684e4 Author: nazgul Date: Wed Mar 23 23:31:05 1994 +0000 Initial revision Src/LinearSolvers/C_NodalMG/hg_elliptic.H commit 1fc596b76899cdd13da6cd2998ba4f362c5b3130 Author: nazgul Date: Tue Oct 5 18:46:17 1993 +0000 Initial revision Src/LinearSolvers/C_NodalMG/driver.cpp commit 93dbd8bb612ee031f19d5659b3b8aac4afb85511 Author: nazgul Date: Fri Mar 12 19:37:55 1993 +0000 Initial revision Src/LinearSolvers/C_NodalMG/RegType.H