commit 6ff87bd4388d5de573cb636ae992cf3e9890f57d Merge: b88fd776 cc4d9de7 Author: Michael Zingale Date: Fri Nov 5 21:50:41 2021 -0400 Merge branch 'microphysics_initialize' into more_fortran_hacks commit b88fd776437c8e15ff2d0714582e9458b5cca623 Author: Michael Zingale Date: Fri Nov 5 21:49:05 2021 -0400 more work on being able to disable Fortran Exec/Make.Maestro Source/Make.package Source/param/meth_params.template Source/param/set_variables.py Util/model_parser/Make.package commit cc4d9de7b94092473ff057ecb2ea7fae9030a1eb Author: Michael Zingale Date: Fri Nov 5 20:13:09 2021 -0400 use the Microphysics version of the init Source/MaestroSetup.cpp commit 132e28bdb10ae2da8cf7750b87b3c5a14a097593 Merge: ab419dcf 870d12ee Author: Michael Zingale Date: Fri Nov 5 20:09:56 2021 -0400 Merge branch 'development' into microphysics_initialize commit ab419dcf4be023a5cb96e1b32058cc2c825e4d8a Author: Michael Zingale Date: Fri Nov 5 20:08:48 2021 -0400 remove maestro_init.F90 Exec/Make.Maestro Source/MaestroSetup.cpp Source/Src_nd/Make.package Source/Src_nd/burner_loop.F90 Source/Src_nd/maestro_init.F90 commit 870d12ee3c5b6999494d4de194a3baa4ba4b11e5 Author: Michael Zingale Date: Fri Nov 5 19:54:04 2021 -0400 burner_loop.F90 is dead code (#281) Source/Src_nd/burner_loop.F90 commit f2c3b3ad27517afb2a9cd775199047bc47c85f5b Author: Michael Zingale Date: Fri Nov 5 19:08:58 2021 -0400 fix tileBox -> tilebox (#279) Exec/science/urca/MaestroTagging.cpp commit 1252cc27d07f4e434f1a78ab40d73a5b6cae048e Author: Doreen Fan Date: Mon Nov 1 15:00:45 2021 -0700 November 2021 release notes CHANGES.md commit 8e090eed958ab2e422cf8c3d78203ec8f8d98850 Author: Doreen Fan Date: Mon Nov 1 14:59:15 2021 -0700 Update AMReX and Microphysics to release 21.11 external/Microphysics external/amrex commit d40aa651e3c03b0bf4be9e7ea631b86ba9176f7f Author: Doreen Fan Date: Sat Oct 2 20:14:16 2021 -0700 October 2021 release notes CHANGES.md commit 93b6adf8ad9dbe4f1011a8cc6fd8619c6207d923 Author: Doreen Fan Date: Sat Oct 2 20:09:16 2021 -0700 Update AMReX and Microphysics to release 21.10 external/Microphysics external/amrex commit e2662372b3bba1010e2563f909470ee82aa433ec Author: Alice Harpole Date: Wed Sep 15 14:28:14 2021 +0100 add css files to conf.py (#277) sphinx_docs/source/conf.py commit ba2b7b98904531287335d66f2d1930402b1b0049 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Tue Sep 14 16:46:25 2021 -0700 Fix get release info for github action (#276) .github/workflows/get_release_txt.py commit 1bc20df097aa0fdf800414643e3c9052842c2f35 Author: Andy Nonaka Date: Thu Sep 9 11:02:42 2021 -0700 bion is now 1-based (#274) Exec/test_problems/reacting_bubble/MaestroInitData.cpp commit d364d0a799ea48083d8b76274aca04697eb8a2b2 Author: Alice Harpole Date: Thu Sep 9 18:55:21 2021 +0100 Fix compilation for NSE problems (#266) * Fix compilation for NSE problems * Clang-format has tidied up the code. * Clang-format has tidied up the code. * indentation * Clang-format has tidied up the code. Co-authored-by: GitHub Action Co-authored-by: Andy Nonaka Source/Maestro.H Source/MaestroAdvanceAvg.cpp Source/MaestroBaseState.cpp Source/MaestroEnforceHSE.cpp Source/MaestroMakew0.cpp Source/MaestroPlot.cpp commit 958c010a5bd53782a2053d2b7a0d5b5b91583183 Author: Justin Lague Date: Thu Sep 9 13:32:20 2021 -0400 Update getting_started.rst (#265) Fixed usage of "git submodule" "git submodule --init" is invalid since no command is specified sphinx_docs/source/getting_started.rst commit fff9fc0fb8e7e6babe995d04bfba91ba60a7869b Author: Doreen Fan Date: Wed Sep 1 12:07:11 2021 -0700 September 2021 release notes CHANGES.md commit 7432f437a8eabce22b55778a0234c04a8d8e254f Author: Doreen Fan Date: Wed Sep 1 11:58:16 2021 -0700 Update AMReX and Microphysics to release 21.09 external/Microphysics external/amrex commit 99914ccd8b0f2aff86dc1c8573be2a703a98cd42 Author: Doreen Fan Date: Mon Aug 2 10:51:24 2021 -0700 August 2021 release notes CHANGES.md commit 57e31ade09b1d1fa89234f50f5e0cfa979fb44a4 Author: Doreen Fan Date: Mon Aug 2 10:47:46 2021 -0700 Update AMReX and Microphysics to release 21.08 external/Microphysics external/amrex commit b753a5a880317161221d4c0315e5f65ec1feac55 Author: Doreen Fan Date: Tue Jul 6 10:40:13 2021 -0700 Zero out w0_cart at beginning of time step just to be safe Source/MaestroAdvanceAvg.cpp commit 87409b5443bdb54b23e9c99422adc641da4e698f Author: Doreen Fan Date: Thu Jul 1 23:41:05 2021 -0700 Need to zero out w0 when plotting magvel and divw0 Source/Maestro.H Source/MaestroPlot.cpp commit 9615c070c301d220dcf6cda96e670cc9f7dfadb5 Merge: ffd21859 93c9ac54 Author: doreenfan Date: Tue Jul 6 14:10:54 2021 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 93c9ac54cef93a1579ad3ca525e484eee5747ed2 Author: Doreen Fan Date: Thu Jul 1 23:45:25 2021 -0700 July 2021 release notes CHANGES.md commit 965b94c0472a054d0ffb29f58af78129ff6e3871 Author: Doreen Fan Date: Thu Jul 1 23:43:15 2021 -0700 Update AMReX and Microphysics to release 21.07 external/Microphysics external/amrex commit 6aca1f7d49538544fdd9a04f94e90db5193f1937 Author: Michael Zingale Date: Fri Jun 11 09:57:23 2021 -0400 fix compilation with new Microphysics changes (#270) Exec/Make.Maestro Exec/science/fully_convective_star/MaestroInitData.cpp Source/BaseState.H commit 3de8ef4ef80da4570c253741f9b6b3fe57bed3d9 Author: Michael Zingale Date: Wed Jun 2 14:45:38 2021 -0400 fix sphinx4 latex macro rendering (#268) sphinx_docs/source/conf.py commit 82b11fd33a99f858a0db68fa7141f7f6ea345e1e Author: Doreen Fan Date: Tue Jun 1 21:06:53 2021 -0700 June 2021 release notes CHANGES.md commit bbc7acb3be396aee54e1a3cb22bd8f35d2ae1530 Author: Doreen Fan Date: Tue Jun 1 21:04:17 2021 -0700 Update AMReX and Microphysics to release 21.06 external/Microphysics external/amrex commit ffd21859980e9d12011df3a73e2eb053a189f4ee Merge: 1a431b21 8ef9b527 Author: asnodin Date: Tue May 25 10:34:31 2021 +0100 Merge branch 'AMReX-Astro:development' into development commit 8ef9b52772287818beac424ba0e8c69cdd927c9f Author: Doreen Fan Date: Wed May 5 14:18:53 2021 -0700 Change to blocking_factor=8 because blocking_factor=4 is too small Exec/test_problems/reacting_bubble/inputs_2d_C.2levels Exec/test_problems/reacting_bubble/inputs_2d_C.3levels Exec/test_problems/reacting_bubble/inputs_2d_amr_regression Exec/test_problems/reacting_bubble/inputs_2d_regression Exec/test_problems/reacting_bubble/inputs_3d_amr_regression Exec/test_problems/reacting_bubble/inputs_3d_gpu_regression Exec/test_problems/reacting_bubble/inputs_3d_regression Exec/test_problems/reacting_bubble/inputs_omp_2d_regression Exec/test_problems/reacting_bubble/inputs_omp_3d_regression commit e46f6cf5901148af8ed706bcd07368a3fbfa346f Author: Doreen Fan Date: Mon May 3 19:33:11 2021 -0700 May 2021 release notes CHANGES.md commit 0204a8f2b8300758fec0ce1703c39757f07c1b96 Author: Doreen Fan Date: Mon May 3 19:21:32 2021 -0700 Update AMReX and Microphysics to release 21.05 external/Microphysics external/amrex commit 745fdbde5c903450f8836976316e4d64aa2e51ba Author: Michael Zingale Date: Mon May 3 12:49:26 2021 -0400 remove references to [ra]tol_temp (#267) this syncs up with Microphysics PR 665 Exec/science/plane_parallel_star/inputs_2d Exec/science/plane_parallel_star/inputs_2d_sdc Exec/science/rotating_star/inputs_files/inputs_3d Exec/science/rotating_star/inputs_files/inputs_3d_MESA Exec/science/rotating_star/inputs_files/inputs_3d_burnrange Exec/science/rotating_star/inputs_files/inputs_3d_burntocore Exec/science/rotating_star/inputs_files/inputs_3d_cutoff Exec/science/rotating_star/inputs_files/inputs_3d_drdxfac Exec/science/rotating_star/inputs_files/inputs_3d_fullstar_heating Exec/science/rotating_star/inputs_files/inputs_3d_heating Exec/science/rotating_star/inputs_files/inputs_3d_heatinner Exec/science/rotating_star/inputs_files/inputs_3d_noburn Exec/science/rotating_star/inputs_files/inputs_3d_perturb Exec/science/urca/models/rhoc-3.5e9_Tc-6.0e8_Mconv-1.0/levels-1.1024/inputs_3d_1lev.5120 Exec/science/urca/models/rhoc-3.5e9_Tc-6.0e8_Mconv-1.0/levels-2.1024/inputs_3d_2lev.5120 Exec/science/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/levels-1.1024/inputs_3d_1lev.5120 Exec/science/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/levels-2.1024/inputs_3d_2lev.5120 Exec/science/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/levels-2.256/inputs_3d_2lev.5120 Exec/science/urca/models/rhoc-5.5e9_Tc-6.0e8_Mconv-1.0/levels-1.1024/inputs_3d_1lev.5120 Exec/science/urca/models/rhoc-5.5e9_Tc-6.0e8_Mconv-1.0/levels-2.1024/inputs_3d_2lev.5120 Exec/science/urca/models/rhoc-5.5e9_Tc-6.0e8_Mconv-1.0/levels-2.64/inputs_3d_2lev.5120.64 commit 0e534348dca50d64165d576d4d1f963f7bdb75f0 Author: asnodin Date: Mon Apr 12 21:03:42 2021 +0100 fix (swap) labels for tfromp and tfromh in the output (#262) Source/MaestroPlot.cpp commit 7a0b62c5e7eed9b0272f01bcdf0f68d164bcf074 Author: Doreen Fan Date: Thu Apr 8 20:27:45 2021 -0700 Add tempbar to base state plotfile Source/MaestroPlot.cpp commit 3e14f805620fa560f331c8ba86b97950e2d730b6 Author: Doreen Fan Date: Thu Apr 1 20:58:07 2021 -0700 April 2021 release notes CHANGES.md commit bb8840bf0a59af5ce828e140cf6857793c2b6aa6 Author: Doreen Fan Date: Thu Apr 1 20:55:21 2021 -0700 Update AMReX and Microphysics to release 21.04 Exec/Make.Maestro Exec/science/fully_convective_star/MaestroInitData.cpp external/Microphysics external/amrex commit 9e9a97795c08821e03a3b6ff2d5d1b47e22d5bee Author: Michael Zingale Date: Mon Mar 29 14:15:40 2021 -0400 add a yt VR of ECSN radial velocity (#259) Exec/science/ecsn/analysis/vol-ecsn-enuc.py Exec/science/ecsn/analysis/vol-ecsn-radvel.py commit 1ac5a4353c1e787dc8d2338a9ee8a6fb459cc16f Author: Michael Zingale Date: Wed Mar 24 20:47:33 2021 -0400 remove the travis badge -- we are not using travis anymore (#261) README.md commit 1a431b21c19059314a8a02aad4e355173e3139c5 Author: Andrew Snodin Date: Tue Mar 9 18:03:22 2021 +0000 added some comments to the closed box rt input file Exec/test_problems/rt/inputs_2d_closed_top commit 57b0d61f602f038b52478336e399171f4294b302 Author: Andrew Snodin Date: Tue Mar 9 17:01:55 2021 +0000 no need to zero w0 at the end of AdvanceAvg -- it is a useful diagnostic Source/MaestroAdvanceAvg.cpp commit 6f38c2679c33b0a1dc9b66f69aeb47f919a65d69 Author: Andrew Snodin Date: Tue Mar 9 16:40:08 2021 +0000 Added pressure correction to set the radial/vertical velocity to zero at the top when impenetrable boundary conditions are used; also correct the pressure update in EnforceHSE. Exec/test_problems/rt/inputs_2d_closed_top Source/Maestro.H Source/MaestroEnforceHSE.cpp Source/MaestroMakew0.cpp Source/param/_cpp_parameters commit 3fd02483e651cb46ca468079c1224ebfe1084384 Author: Doreen Fan Date: Mon Mar 1 18:36:50 2021 -0800 March 2021 release notes CHANGES.md commit f65c587a28bc777f9e3f7c92333bda07014db523 Author: Doreen Fan Date: Mon Mar 1 18:31:53 2021 -0800 Update AMReX and Microphysics to release 21.03 external/Microphysics external/amrex commit fe148c84eb510cf37de418d8c0a4c14bfa7b5f6a Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Wed Feb 17 10:43:49 2021 -0800 Fix GPU compiling errors (#254) * Move QuadInterp outside of Maestro class * Fix gpu issues with accessing basestate class * Remove fortran base_state_geometry variables and subroutines * Clang-format has tidied up the code. Co-authored-by: GitHub Action Source/BaseState.H Source/Maestro.H Source/MaestroFill3dData.cpp Source/MaestroMakeS.cpp Source/MaestroMakew0.cpp Source/Src_nd/base_state_geometry.F90 Source/Src_nd/maestro_init.F90 Source/param/meth_params.template commit 05af30154ed797bbc32a7ae24e644ceea258b0aa Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Thu Feb 4 09:11:29 2021 -0800 Bug fixes for simplified SDC (#257) * Fixed SDC runtime errors * Change array access since ydot is 1-based * Clang-format has tidied up the code. * Update Source/MaestroPlot.cpp Co-authored-by: GitHub Action Co-authored-by: Andy Nonaka Source/MaestroBurner.cpp Source/MaestroReact.cpp commit 2022399851704dc2e39f47d6b5a97436ecfb5a53 Author: Doreen Fan Date: Mon Feb 1 11:59:30 2021 -0800 February 2021 release notes CHANGES.md commit 09786df6c1ea025ef8ea8c468e02a99daaf584ab Author: Doreen Fan Date: Mon Feb 1 11:52:24 2021 -0800 Update AMReX and Microphysics to release 21.02 external/Microphysics external/amrex commit 58dcab80eae1fa579f5332553071f5d90f00fe5c Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Tue Jan 26 13:31:13 2021 -0800 Fix runtime issue with exact base state on (#256) * ncell is now allocated correctly * Add README to show conversion of grid size to irregularly-spaced base state * Clang-format has tidied up the code. Co-authored-by: GitHub Action Exec/science/fully_convective_star/model_files/README Exec/science/rotating_star/initial_models/README Exec/science/wdconvect/model_files/README Source/MaestroAverage.cpp commit 4d98c5211a99d3f11770713e26037fe65a187cd5 Author: Andy Nonaka Date: Mon Jan 25 16:43:44 2021 -0800 replace ca_read_model_file with input_model.ReadFile(model_file); (#255) Source/MaestroInit.cpp commit bee83d91b81cc6dbcc909e3d576eaff422716c52 Author: Michael Zingale Date: Sat Jan 9 13:20:20 2021 -0500 sync up to the latest Microphysics runtime_parameters.py (#253) Source/param/meth_params.template Source/param/parse_maestro_params.py commit be11425f4d765ebd076c1b19eb3818733365f8e3 Author: Michael Zingale Date: Fri Jan 8 12:53:29 2021 -0500 use the centralized Microphysics runtime_parameters.py (#252) requires: starkiller-astro/Microphysics#523 Exec/Make.Maestro Source/param/_cpp_parameters Source/param/parse_maestro_params.py commit d0e099a718335bbddd7f43f8aea2785ecba02b24 Author: Michael Zingale Date: Thu Jan 7 15:57:46 2021 -0500 replace findparams.py with make logic (#250) also, we no longer need to define USE_SIMPLIFIED_SDC -- Make.Microphysics_extern does it for us Exec/Make.Maestro commit ce03b56e72660819a6028af83bda080fa0ffe6e8 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Thu Jan 7 10:35:40 2021 -0800 Update test problems to C++ (#248) * Update MakeHeating subroutine for test_convect * Remove constant value outside of base cutoff radius when computing exact base state * Fix compilation and runtime errors for test_react and imposed_external_heating tests. * Convert more make_heating to C++ * Convert model_parser to C++ for rotating_star * Fix compilation errors for various unit tests * Convert all subroutines to C++ for test_basestate * Clang-format has tidied up the code. * Update Exec/science/code_comp/MaestroMakeGrav.cpp * pow() -> std::pow() * Clang-format has tidied up the code. * Remove Maestro_F.H declarations * remove fortran file * Add back ncell check in average subroutine * Clang-format has tidied up the code. Co-authored-by: GitHub Action Co-authored-by: Andy Nonaka Exec/science/code_comp/MaestroHeating.cpp Exec/science/code_comp/MaestroMakeGrav.cpp Exec/science/code_comp/Make.package Exec/science/code_comp/inputs_3d Exec/science/code_comp/make_grav.F90 Exec/science/code_comp/make_heating.F90 Exec/science/code_comp/model_util.F90 Exec/science/fully_convective_star/MaestroHeating.cpp Exec/science/fully_convective_star/make_heating.F90 Exec/science/rotating_star/MaestroHeating.cpp Exec/science/rotating_star/MaestroTagging.cpp Exec/science/rotating_star/ModelParser.H Exec/science/rotating_star/ModelParser.cpp Exec/science/rotating_star/make_heating.F90 Exec/science/toy_convect/MaestroHeating.cpp Exec/science/toy_convect/make_heating.F90 Exec/science/xrb_mixed/MaestroHeating.cpp Exec/science/xrb_mixed/make_heating.F90 Exec/test_problems/imposed_external_heating/MaestroHeating.cpp Exec/test_problems/imposed_external_heating/make_heating.F90 Exec/test_problems/test_convect/MaestroHeating.cpp Exec/test_problems/test_convect/make_heating.F90 Exec/unit_tests/test_advect/MaestroEvolve.cpp Exec/unit_tests/test_advect/MaestroInit.cpp Exec/unit_tests/test_basestate/MaestroAdvance.cpp Exec/unit_tests/test_basestate/MaestroAdvectBase2.cpp Exec/unit_tests/test_basestate/MaestroDt.cpp Exec/unit_tests/test_basestate/MaestroEvolve.cpp Exec/unit_tests/test_basestate/MaestroInit.cpp Exec/unit_tests/test_basestate/Make.package Exec/unit_tests/test_basestate/spherical/inputs-spherical_heat Exec/unit_tests/test_diffusion/MaestroInit.cpp Exec/unit_tests/test_diffusion/MaestroPlot.cpp Exec/unit_tests/test_eos/MaestroInit.cpp Exec/unit_tests/test_projection/MaestroInit.cpp Exec/unit_tests/test_projection/MaestroPlot.cpp Exec/unit_tests/test_react/MaestroHeating.cpp Exec/unit_tests/test_react/MaestroInit.cpp Exec/unit_tests/test_react/MaestroPlot.cpp Exec/unit_tests/test_react/inputs_3alpha Exec/unit_tests/test_react/inputs_aprox13 Exec/unit_tests/test_react/inputs_ignition Exec/unit_tests/test_react/inputs_mesa_carbon Exec/unit_tests/test_react/inputs_reaclib_cburn Exec/unit_tests/test_react/inputs_reaclib_ctest Exec/unit_tests/test_react/inputs_reaclib_urca Exec/unit_tests/test_react/inputs_react Exec/unit_tests/test_react/inputs_rprox Exec/unit_tests/test_react/inputs_xrb_simple Exec/unit_tests/test_react/make_heating.F90 Source/Maestro.H Source/MaestroAverage.cpp Source/MaestroInitData.cpp commit 9c24b9658970459074232a283f3ae9432acba298 Author: Michael Zingale Date: Wed Jan 6 11:55:22 2021 -0500 update format to new Microphysics extern format (#251) in particular, we remove the private clause and unused Fortran GPU stuff Source/param/runtime.probin.template commit a7cbb6bafe8a71130cf8396d410b4613494d51ab Author: Doreen Fan Date: Mon Jan 4 09:27:19 2021 -0800 January 2021 release notes CHANGES.md commit 448d1f8469217bb478b9d318f671cdb3f75b4573 Author: Doreen Fan Date: Mon Jan 4 09:16:34 2021 -0800 Update AMReX and Microphysics to release 21.01 external/Microphysics external/amrex commit d67a37a7e2dd23ebfe46e2ca6c387aa883057f41 Author: Max Katz Date: Wed Dec 30 07:20:20 2020 -0800 Update to C++17 as minimum standard (#249) C++17 is now the minimum supported standard for MAESTROeX. This means that gcc >= 7 and nvcc >= 11 are now required. Among other C++17 features we want to use inline variables (starkiller-astro/Microphysics#482) and if constexpr (starkiller-astro/Microphysics#470). CHANGES.md Exec/Make.Maestro sphinx_docs/source/getting_started.rst commit e0f4e25788642f273601bf162dde4b1eaed71291 Author: Doreen Fan Date: Wed Dec 16 10:39:32 2020 -0800 Change divu input parameters to pass regression test Exec/test_problems/test_stability/inputs_2d_C_regression commit e6d5589d34a0b711a267b023efc5a087703ab514 Author: Doreen Fan Date: Tue Dec 15 18:01:29 2020 -0800 Converted make_heating to C++ for test_convect Exec/test_problems/test_convect/MaestroHeating.cpp commit e7b60fb2eb52d06c619efd6cc788c828b67bf8ee Author: Michael Zingale Date: Tue Dec 15 15:19:14 2020 -0500 don't count Jupyter or "Roff" (#244) .gitattributes commit 45d752f0dde34fb15f0b06570d74f74d6c0ef79e Author: Michael Zingale Date: Tue Dec 15 14:55:47 2020 -0500 fix the doc build with the new bibtex parser (#247) sphinx_docs/source/conf.py commit ed1cee67f1a27569d35cb7a7de043e28b626f5e4 Author: Alice Harpole Date: Tue Dec 15 13:56:29 2020 -0500 RIP Fortran (#190) This converts all remaining routines to C++ (i.e. mainly burner_loop). It also converts all kernel launches to use amrex::ParallelFor, which means it will be much easier to debug code within lambda functions. This currently only works with networks which have a fully C++ interface in Microphysics (e.g. aprox13), so should not be merged until all networks have been converted. Exec/Make.Maestro Exec/science/code_comp/MaestroInitData.cpp Exec/science/ecsn/MaestroInitData.cpp Exec/science/ecsn/MaestroTagging.cpp Exec/science/flame/MaestroBCFill.cpp Exec/science/flame/MaestroInitData.cpp Exec/science/fully_convective_star/MaestroInitData.cpp Exec/science/fully_convective_star/MaestroTagging.cpp Exec/science/plane_parallel_star/MaestroInitData.cpp Exec/science/rotating_star/MaestroInitData.cpp Exec/science/rotating_star/MaestroTagging.cpp Exec/science/sub_chandra/MaestroInitData.cpp Exec/science/toy_convect/MaestroInitData.cpp Exec/science/urca/MaestroInitData.cpp Exec/science/urca/MaestroTagging.cpp Exec/science/wdconvect/MaestroInitData.cpp Exec/science/wdconvect/MaestroTagging.cpp Exec/test_problems/double_bubble/MaestroInitData.cpp Exec/test_problems/incomp_shear_jet/MaestroInitData.cpp Exec/test_problems/mach_jet/MaestroBCFill.cpp Exec/test_problems/mach_jet/MaestroInitData.cpp Exec/test_problems/reacting_bubble/MaestroInitData.cpp Exec/test_problems/reacting_bubble/MaestroTagging.cpp Exec/test_problems/rt/MaestroInitData.cpp Exec/test_problems/test_convect/MaestroInitData.cpp Exec/test_problems/test_planar_diag/MaestroInitData.cpp Exec/test_problems/test_stability/MaestroInitData.cpp Exec/unit_tests/test_advect/MaestroInitData.cpp Exec/unit_tests/test_average/MaestroInitData.cpp Exec/unit_tests/test_basestate/MaestroAdvance.cpp Exec/unit_tests/test_basestate/MaestroInit.cpp Exec/unit_tests/test_basestate/MaestroInitData.cpp Exec/unit_tests/test_diffusion/MaestroEvolve.cpp Exec/unit_tests/test_diffusion/MaestroInit.cpp Exec/unit_tests/test_diffusion/MaestroPlot.cpp Exec/unit_tests/test_eos/MaestroEvolve.cpp Exec/unit_tests/test_projection/MaestroPlot.cpp Exec/unit_tests/test_react/MaestroInit.cpp Source/BaseState.H Source/Maestro.H Source/MaestroAdvanceSdc.cpp Source/MaestroAdvectBase.cpp Source/MaestroAdvection.cpp Source/MaestroAverage.cpp Source/MaestroBCFill.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroBurner.cpp Source/MaestroCelltoEdge.cpp Source/MaestroCheckpoint.cpp Source/MaestroDt.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroFill3dData.cpp Source/MaestroFillData.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroHeating.cpp Source/MaestroInit.cpp Source/MaestroInitData.cpp Source/MaestroIntra.cpp Source/MaestroMacProj.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEdgeScalars.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeFlux.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakePsi.cpp Source/MaestroMakeS.cpp Source/MaestroMakeUtrans.cpp Source/MaestroMakew0.cpp Source/MaestroNodalProj.cpp Source/MaestroPPM.cpp Source/MaestroPlot.cpp Source/MaestroReact.cpp Source/MaestroRegrid.cpp Source/MaestroRhoHT.cpp Source/MaestroSetup.cpp Source/MaestroSlopes.cpp Source/MaestroSponge.cpp Source/MaestroTagging.cpp Source/MaestroThermal.cpp Source/MaestroVelPred.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/Make.package Source/Src_nd/average.F90 Source/Src_nd/fill_3d_data.F90 Source/Src_nd/inlet_bc.F90 Source/Src_nd/maestro_init.F90 Source/Src_nd/make_grav.F90 Source/Src_nd/make_heating.F90 Source/param/runtime.probin.template Util/utils/MaestroUtil.H commit 99ce3b0e3eced46d811bab1b166c716940c4cd2f Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Fri Dec 11 16:53:21 2020 -0800 Fix algorithm with irregularly spaced base state (#246) * Add irregularly spaced intial model files and input file * Update split projection algorithm for base state with irregular spacing * Fix initial model mapping to irregularly spaced base states * Clang-format has tidied up the code. * no functional changes; just cleanup to sync these files up * combine MaestroAdvanceAvg.cpp and MaestroAdvanceIrreg.cpp into one routine since they use the same temporal integration algorithm * call AdvanceTimeStepAvg * Clang-format has tidied up the code. Co-authored-by: GitHub Action Co-authored-by: Andy Nonaka Exec/science/fully_convective_star/inputs_3d.512 Exec/science/fully_convective_star/inputs_3d_amr Exec/science/fully_convective_star/inputs_files/inputs_3d.192.exactbase Exec/science/fully_convective_star/model_files/convective_M_0.30.hse.13680.dr Exec/science/fully_convective_star/model_files/convective_M_0.30.hse.24384.dr Exec/science/fully_convective_star/model_files/convective_M_0.30.hse.55008.dr Exec/science/fully_convective_star/model_files/convective_M_0.30.hse.6048.dr Exec/science/fully_convective_star/model_files/convective_M_0.30.hse.97920.dr Source/Maestro.H Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroBaseState.cpp Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/MaestroMakeBeta0.cpp Source/MaestroRegrid.cpp Source/Make.package commit 33f75f42e0dd0fbc56219fe07bc54d3371590457 Author: Max Katz Date: Thu Dec 10 14:55:14 2020 -0800 Pass small_temp and small_dens into eos_init (#245) Source/MaestroSetup.cpp commit 938464d51b21f5bed38837f26b6496f55272e966 Author: Doreen Fan Date: Tue Dec 1 13:15:16 2020 -0800 December 2020 release notes CHANGES.md commit 672c9fb50e6b56c7522b5a9668a7ba7034aeed69 Author: Alice Harpole Date: Tue Dec 1 16:03:39 2020 -0500 Actually fix action (#243) * fix release python script * fix release action .github/workflows/create_release.yml .github/workflows/get_release_txt.py commit 49c84286a75ebac4ce7ba4e11bce45f256daac86 Author: Doreen Fan Date: Tue Dec 1 12:58:21 2020 -0800 Update AMReX and Microphysics to release 20.12 external/Microphysics external/amrex commit a607e8802f34eb7157f0de75c7e11eb2b28c79e9 Author: Alice Harpole Date: Tue Dec 1 10:28:46 2020 -0500 fix release python script (#242) .github/workflows/get_release_txt.py commit 1db0a2eb28b5ff9a0725d90b218fb101529f0699 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Thu Nov 19 12:53:20 2020 -0800 Fix average base state algorithm with split projection for spherical case (#240) * Compute w0 with split_projection is moved to just before projection calls for spherical case * Clang-format has tidied up the code. * passing w0mac_dummy=0 into DensityAdvance and EnthalpyAdvance * Clang-format has tidied up the code. Co-authored-by: GitHub Action Co-authored-by: Andy Nonaka Exec/test_problems/imposed_external_heating/MaestroBaseState.cpp Exec/test_problems/imposed_external_heating/MaestroInitData.cpp Source/Maestro.H Source/MaestroAdvanceAvg.cpp Source/MaestroDebug.cpp Source/MaestroForce.cpp Source/MaestroMakeEta.cpp commit 120eabc7a0592a0a69401ac75748ae9fd7555aa6 Author: Doreen Fan Date: Thu Nov 19 11:51:56 2020 -0800 Add model files and update input files for fully_convective_star Exec/science/fully_convective_star/inputs_3d Exec/science/fully_convective_star/inputs_3d.512 Exec/science/fully_convective_star/inputs_3d_amr Exec/science/fully_convective_star/model_files/convective_M_0.20.hse.1024 Exec/science/fully_convective_star/model_files/convective_M_0.20.hse.2560 Exec/science/fully_convective_star/model_files/convective_M_0.20.hse.960 Exec/science/fully_convective_star/model_files/convective_M_0.30.hse.1024 Exec/science/fully_convective_star/model_files/convective_M_0.30.hse.1536 Exec/science/fully_convective_star/model_files/convective_M_0.30.hse.2048 Exec/science/fully_convective_star/model_files/convective_M_0.30.hse.2560 Exec/science/fully_convective_star/model_files/convective_M_0.30.hse.960 Exec/science/fully_convective_star/model_files/convective_M_0.40.hse.1024 Exec/science/fully_convective_star/model_files/convective_M_0.40.hse.2560 Exec/science/fully_convective_star/model_files/convective_M_0.40.hse.960 commit 3ee4709bd70e2d4fcac81837f2e0509c7969c7bc Author: Alice Harpole Date: Thu Nov 19 09:58:23 2020 -0500 fix create_release action (#241) .github/workflows/create_release.yml commit 2285414aaf028896d8ebcbcf22d9e28673cc045a Author: Doreen Fan Date: Thu Nov 12 11:31:46 2020 -0800 Add PrintBase debug subroutine for basestate Source/Maestro.H Source/MaestroDebug.cpp commit ed090051c29c33ca7c8eb1f06bb713d12a9efa20 Author: asnodin Date: Tue Nov 10 16:25:24 2020 +0000 Make average_base_state work for planar with split projection (#239) * Merge split projection fix * * switch to dp/dt constraint for now * minor tidy * remove unsplit projection * remove parameters relating to unsplit projection * minor comments * added imposed heating test case * use the correct files for initialization of the imposed heating test * update test details * Update Source/MaestroAdvanceAvg.cpp * Update check_imposed_heating.ipynb Exec/test_problems/imposed_external_heating/GNUmakefile Exec/test_problems/imposed_external_heating/MaestroBaseState.cpp Exec/test_problems/imposed_external_heating/MaestroInitData.cpp Exec/test_problems/imposed_external_heating/MaestroMakeS.cpp Exec/test_problems/imposed_external_heating/Make.package Exec/test_problems/imposed_external_heating/README.md Exec/test_problems/imposed_external_heating/check_imposed_heating.ipynb Exec/test_problems/imposed_external_heating/inputs_2d_C Exec/test_problems/imposed_external_heating/make_heating.F90 Exec/test_problems/imposed_external_heating/simple.net Source/Maestro.H Source/MaestroAdvanceAvg.cpp Source/MaestroMakeEta.cpp commit 9d9d36e8fac5397151f3263d6709517401b5566f Author: Doreen Fan Date: Mon Nov 2 13:22:41 2020 -0800 November 2020 release notes CHANGES.md commit 5765ad4d19f6e755b4eafa42b131cc2343f1f621 Author: Doreen Fan Date: Mon Nov 2 13:16:55 2020 -0800 Update AMReX and Microphysics to release 20.11 external/Microphysics external/amrex commit d7aafb6c7b01af7eb708959d9a0b1a0adc8ef31e Author: Alice Harpole Date: Tue Oct 6 11:20:26 2020 -0400 Update cpp linter action so it uses main (#235) * 19 species initial model * master->main in action .github/workflows/c-linter.yml Exec/science/rotating_star/initial_models/15m_aprox19.6400 commit 289304f5a8a2155002a05fc18e8dd7ba20cd7f84 Author: Doreen Fan Date: Thu Oct 1 10:36:22 2020 -0700 October 2020 release notes CHANGES.md commit f6d70b2d1a354d6f7ed270609decb5a6defa0189 Author: Doreen Fan Date: Thu Oct 1 10:22:34 2020 -0700 Update AMReX and Microphysics to release 20.10 external/Microphysics external/amrex commit 83e6e0d470fd7623fa580b170ad0213e531b15fd Author: Doreen Fan Date: Tue Sep 29 17:20:39 2020 -0700 parameter 'spherical': int -> bool Exec/science/rotating_star/make_heating.F90 commit 7b08c0c0e50df89728dea4d6d920578f033bece9 Author: Doreen Fan Date: Fri Sep 25 11:00:42 2020 -0700 Match changes to AMReX: setCGVerbose -> setBottomVerbose Source/MaestroMacProj.cpp Source/MaestroNodalProj.cpp Source/MaestroThermal.cpp commit 0745325fcc503c621f6002ed3a10d1b7a4eaf68e Author: Doreen Fan Date: Wed Sep 16 13:20:34 2020 -0700 gpu fix: make local copy of omega Source/MaestroForce.cpp commit f05a44f9510d6ba4d35c59c96288bdd864288eb0 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Wed Sep 16 09:16:19 2020 -0700 Add a compile flag for centrifugal force (#233) * Add flag to turn on/off centrifugal force * Clang-format has tidied up the code. * Revert "Add flag to turn on/off centrifugal force" This reverts commit 3ec49b7d9e491d986028de060a59e830f41e487d. * Change use_centrifugal to an input parameter instead * Clang-format has tidied up the code. Co-authored-by: GitHub Action Exec/science/fully_convective_star/inputs_files/inputs_3d Exec/science/fully_convective_star/inputs_files/inputs_3d.512 Exec/science/fully_convective_star/inputs_files/inputs_3d.768 Exec/science/fully_convective_star/inputs_files/inputs_3d_M0.30_highfreq.384 Exec/science/fully_convective_star/inputs_files/inputs_3d_M0.30_lowfreq.384 Exec/science/fully_convective_star/inputs_files/inputs_3d_M0.30_medfreq.384 Exec/science/fully_convective_star/inputs_files/inputs_3d_amr Source/MaestroForce.cpp Source/param/_cpp_parameters commit 53003eb14e87ef6a39a866c97a31ff00ef750e5e Author: Andy Nonaka Date: Tue Sep 15 10:43:11 2020 -0700 Fancy Bottom Solver Control (#232) * enable control for toggling fancy bottom solver via maestro.mg_bottom_solver and maestro.hg_bottom_solver default is on (4) for both mg and hg set it to any other value to use the default MLMG settings * Clang-format has tidied up the code. Co-authored-by: GitHub Action Source/MaestroMacProj.cpp Source/MaestroNodalProj.cpp Source/param/_cpp_parameters commit ef9db869a8e336c4ec19c515ee6413c058980ffc Author: Doreen Fan Date: Thu Sep 10 13:50:39 2020 -0700 added input files for fully_convective_star runs on cori Exec/science/fully_convective_star/inputs_files/inputs_3d Exec/science/fully_convective_star/inputs_files/inputs_3d.512 Exec/science/fully_convective_star/inputs_files/inputs_3d.768 Exec/science/fully_convective_star/inputs_files/inputs_3d_M0.30_highfreq.384 Exec/science/fully_convective_star/inputs_files/inputs_3d_M0.30_lowfreq.384 Exec/science/fully_convective_star/inputs_files/inputs_3d_M0.30_medfreq.384 Exec/science/fully_convective_star/inputs_files/inputs_3d_amr commit d85bdf45ed19d6890c4fa1f6026365d83a2b1cdd Author: Doreen Fan Date: Thu Sep 3 14:38:32 2020 -0700 revert changes to input files Exec/science/flame/inputs_2d_smallscale_sdc Exec/science/fully_convective_star/inputs_3d Exec/test_problems/mach_jet/inputs_2d commit 9735f3d7caec87a053c74f7fc5d384d99e803045 Author: Doreen Fan Date: Thu Sep 3 14:11:43 2020 -0700 September 2020 release notes CHANGES.md commit 8ed72a957a36be3073d59b552559e6812d6d35f5 Author: Doreen Fan Date: Thu Sep 3 13:59:59 2020 -0700 Update AMReX and Microphysics to release 20.09 Exec/science/flame/inputs_2d_smallscale_sdc Exec/science/fully_convective_star/inputs_3d Exec/test_problems/mach_jet/inputs_2d external/Microphysics external/amrex commit f3b03f87c9a3124714a2b662ebff8a22d9e8f5a1 Merge: 52bb3102 9a1a4eda Author: Doreen Fan Date: Thu Sep 3 13:58:10 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 9a1a4edad9ef38739f242d9016f744589ce63fac Author: Alice Harpole Date: Thu Sep 3 15:16:24 2020 -0400 minor formatting fix to release action .github/workflows/create_release.yml .github/workflows/get_release_txt.py commit e9df7fe066a3da61260438fce7c71c2ecc7d3d26 Author: Alice Harpole Date: Tue Sep 1 11:39:41 2020 -0400 Small workflow fix (#231) This combines the tab_exterminator and clang-format workflow actions so they don't conflict, and only attempts to push changes back if the PR is not a fork (Github doesn't allow this, so this currently causes the action to fail). .github/workflows/clang-format.yml .github/workflows/tab-exterminator.yml commit 52bb31023377bd26ab126c1f6738d70eb50f4846 Author: Alice Harpole Date: Tue Sep 1 11:39:41 2020 -0400 Small workflow fix (#231) This combines the tab_exterminator and clang-format workflow actions so they don't conflict, and only attempts to push changes back if the PR is not a fork (Github doesn't allow this, so this currently causes the action to fail). .github/workflows/clang-format.yml .github/workflows/tab-exterminator.yml commit 24f18d5df3b14163e228194f517778ece815e4c8 Author: Alice Harpole Date: Fri Aug 21 08:46:40 2020 -0400 Make GPU test runs deterministic (#229) This adds in a few changes to make GPU test runs (i.e. GPU runs with the flag maestro.deterministic_nodal_solve=true set) deterministic (or at least agree to within a small enough error that the test suite will consider their plotfiles to agree). The main changes are switching min and max to always use the amrex:: versions, adding a few Gpu::synchronize(); statements (which should have been there in the first place) and switching off the kernel launch region in a couple of places so that those regions always run on the CPU for tests. I've tested this for RT (2d and 3d) and wdconvect. Exec/test_problems/rt/MaestroBaseState.cpp Source/BaseStateGeometry.cpp Source/MaestroAverage.cpp Source/MaestroBaseState.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroCelltoEdge.cpp Source/MaestroDiag.cpp Source/MaestroEnforceHSE.cpp Source/MaestroFill3dData.cpp Source/MaestroFillData.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEdgeScalars.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeEta.cpp Source/MaestroMakew0.cpp Source/MaestroPPM.cpp Source/MaestroRhoHT.cpp Source/MaestroSlopes.cpp Source/MaestroVelPred.cpp Util/model_parser/ModelParser.cpp commit 515422f6504a65578ed9df6e27f4b5ac67014715 Author: Michael Zingale Date: Thu Aug 20 16:58:41 2020 -0400 bump up the required make version (#225) * bump up the required make version we don't build with 3.81 * update README README.md sphinx_docs/source/faq.rst sphinx_docs/source/getting_started.rst sphinx_docs/source/makefiles.rst commit e924d7c9f612eedd833e83e4194ce8a75fec781a Author: Andy Nonaka Date: Wed Aug 19 11:23:18 2020 -0700 Fillpatch intra on regrid (#227) addi FillPatch on intra during RemakeLevel This PR Closes #220 Source/MaestroRegrid.cpp commit 171ac0916f3421e02e0d71a0afe11144e30a03fe Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Mon Aug 17 13:34:19 2020 -0700 SDC AMR fix in debug mode for Flame (#226) * fill coarse grids that are masked by finer grids, and average down omegadot and Hnuc * Tabs have been converted to spaces by tab_exterminator.sh * Clang-format has tidied up the code. * revert adding ghost cells to stemp (they're not needed) make the PR cleaner * revert number of ghost cells in stemp to 0 (they aren't used) * clean up pr. remove ghost cells from cp and xi used for intra (not needed) * Clang-format has tidied up the code. Co-authored-by: GitHub Action Co-authored-by: Andy Nonaka Source/MaestroAdvanceSdc.cpp Source/MaestroIntra.cpp Source/MaestroReact.cpp commit 82381e52d273f2c497ae335bf3a7686aa09ea11e Author: Max Katz Date: Mon Aug 10 06:34:10 2020 -0700 Remove dependence on AMReX C_CellMG which is now removed (#224) This was removed in AMReX-Codes/amrex#1238. Exec/Make.Maestro commit da8b4716307a848b35306f3bbfd41ef2f6397745 Author: dwillcox Date: Fri Aug 7 13:17:31 2020 -0700 add inputs for 2 levels w/ 256**3 on finest level Exec/science/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/levels-2.256/inputs_3d_2lev.5120 commit 9eeffb60ea4eb4e6461b389cf2e44895d9bdd006 Author: dwillcox Date: Thu Aug 6 16:51:45 2020 -0700 turn on MPI Exec/science/urca/GNUmakefile commit a1e1fb9895f868656fbb75f82b381ef20c3bc4a0 Author: Donald E. Willcox Date: Thu Aug 6 16:47:20 2020 -0700 update initdata from wdconvect Exec/science/urca/MaestroInitData.cpp commit 9dfb5eb62d206a13e9f845ebef996357a5c81445 Author: dwillcox Date: Thu Aug 6 16:32:36 2020 -0700 turn on TINY_PROFILE Exec/science/urca/GNUmakefile commit a3cec30d9c714f1132d984727555da87f4ec01b1 Author: Donald E. Willcox Date: Fri Jul 3 19:21:52 2020 -0700 Fix formatting in Urca input models so they work with C++ model reader. Exec/science/urca/models/rhoc-3.5e9_Tc-6.0e8_Mconv-1.0/WD_urca_nuc_M-1.0_rc3.5e9_Tc6.0e8_speceq.hse.5120 Exec/science/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/WD_urca_nuc_M-1.0_rc4.5e9_Tc6.0e8_speceq.hse.5120 Exec/science/urca/models/rhoc-5.5e9_Tc-6.0e8_Mconv-1.0/WD_urca_nuc_M-1.0_rc5.5e9_Tc6.0e8_speceq.hse.5120 commit 2a61f0d6a24a060ef37621a7924c12ce352016e5 Author: Michael Zingale Date: Thu Aug 6 19:55:03 2020 -0400 explicitly ask for python 3 (#223) Source/param/parse_maestro_params.py commit 1dbe4e33c5775607b95c381477600ed934fb08bd Author: Alice Harpole Date: Wed Aug 5 09:03:12 2020 -0400 Update requirements (#222) This updates the requirements in the 'Getting Started' section of the docs to specify/update the versions of Python and GNU Make and add a section on running in parallel. sphinx_docs/source/getting_started.rst commit 41f6b142790f650a2961e69ae7c8b0014a69cb5e Author: Alice Harpole Date: Wed Aug 5 08:43:04 2020 -0400 Create parameters header files at build time & improve job_info (#221) This copies over two changes from Castro: * Header files that were previously in the param_includes directory and regenerated by running the mk_params.sh script are now created at build time and stored in tmp_build_dir/..../maestroex_sources. This should make builds less error prone. * The parameter list in the job_info file is now generated by the maestro_job_info_tests.H header file. This has the benefit of showing which parameters have been modified and which are using their default value. Exec/Make.Maestro Source/MaestroAverage.cpp Source/MaestroEvolve.cpp Source/MaestroPlot.cpp Source/Make.package Source/param/parse_maestro_params.py Source/param/set_variables.py Source/param_includes/Make.package Source/param_includes/maestro_declares.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 Source/param_includes/state_indices.H Source/param_includes/state_indices_nd.F90 Source/runparams_defaults.cpp commit 70836962efc444aae377d82d637b8b2e2b7c40ed Author: Chris DeGrendele <35853499+ChrisDeGrendele@users.noreply.github.com> Date: Mon Aug 3 17:32:56 2020 -0500 By default, run until stop_time, rather than for 1 time step (#219) * Run until stop_time or max_step, without having to provide both * Update MaestroEvolve.cpp Source/MaestroEvolve.cpp Source/param/_cpp_parameters Source/param/meth_params.template Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 Source/param_includes/state_indices.H commit 8ba524b5b0e17a9a61f832e783dc3bcbcecd183b Author: Andy Nonaka Date: Mon Aug 3 13:17:21 2020 -0700 Amrex math (#216) * round -> amrex::Math::round * copysign -> amrex::Math::copysign * std::max -> amrex::max std::min -> amrex::min * fabs -> amrex::Math::abs * Clang-format has tidied up the code. * revert std::max/min -> amrex::max/min * Clang-format has tidied up the code. * amrex::min cannot use vector as input * Tabs have been converted to spaces by tab_exterminator.sh Co-authored-by: GitHub Action Co-authored-by: Doreen Fan Exec/science/flame/MaestroBCFill.cpp Exec/science/flame/MaestroTagging.cpp Exec/test_problems/double_bubble/MaestroBaseState.cpp Exec/test_problems/mach_jet/MaestroBCFill.cpp Exec/test_problems/mach_jet/MaestroBaseState.cpp Exec/test_problems/reacting_bubble/MaestroTagging.cpp Exec/test_problems/rt/MaestroBaseState.cpp Exec/test_problems/test_planar_diag/MaestroBaseState.cpp Exec/test_problems/test_planar_diag/MaestroInitData.cpp Exec/unit_tests/test_advect/MaestroInit.cpp Exec/unit_tests/test_basestate/MaestroDt.cpp Exec/unit_tests/test_basestate/MaestroEvolve.cpp Exec/unit_tests/test_basestate/MaestroInit.cpp Exec/unit_tests/test_diffusion/MaestroDt.cpp Exec/unit_tests/test_diffusion/MaestroInit.cpp Exec/unit_tests/test_react/MaestroInit.cpp Source/BaseStateGeometry.cpp Source/Maestro.H Source/MaestroAverage.cpp Source/MaestroBaseState.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroDebug.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroEnforceHSE.cpp Source/MaestroEvolve.cpp Source/MaestroFill3dData.cpp Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEdgeScalars.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakePsi.cpp Source/MaestroMakeUtrans.cpp Source/MaestroMakew0.cpp Source/MaestroNodalProj.cpp Source/MaestroPPM.cpp Source/MaestroRegrid.cpp Source/MaestroSlopes.cpp Source/MaestroThermal.cpp Source/MaestroVelPred.cpp Util/diagnostics/main.cpp Util/model_parser/ModelParser.cpp commit 378e6ac93c908566179ec931a0b0a1a5afccc67b Author: Doreen Fan Date: Mon Aug 3 11:14:54 2020 -0700 August 2020 release notes CHANGES.md commit a0da7bec0a8510bc96135265f998ae1bbb63933b Author: Michael Zingale Date: Mon Aug 3 09:47:37 2020 -0400 fix some formatting + add submodules (#217) README.md commit 00536398ca71095824ba65fb0a90b2d3bf0b0326 Author: Michael Zingale Date: Mon Aug 3 09:38:11 2020 -0400 switch to the write_probin.py script from Microphysics (#218) this puts us in sync with Castro Exec/Make.Maestro Source/param/runtime.probin.template commit 5b232cc19c1a835c4dcd4357ffabebdb59c03e26 Author: Andy Nonaka Date: Thu Jul 30 11:42:13 2020 -0700 fix index on hi domain walls where the ghost cells begin (#215) * fix index on hi domain walls where the ghost cells begin * Tabs have been converted to spaces by tab_exterminator.sh Co-authored-by: GitHub Action Exec/science/flame/MaestroBCFill.cpp Exec/test_problems/mach_jet/MaestroBCFill.cpp Source/Maestro.H Source/MaestroBCFill.cpp Source/MaestroDebug.cpp commit 2a1ee544fef75d247565cb80575f1efbb85abefd Author: Chris DeGrendele <35853499+ChrisDeGrendele@users.noreply.github.com> Date: Thu Jul 30 11:13:36 2020 -0500 Flame with AMR (#214) * Flame with AMR * Fix bug not refining to edge * Update BaseStateGeometry.cpp * Update BaseStateGeometry.cpp * Update BaseStateGeometry.cpp Exec/science/flame/MaestroTagging.cpp Exec/science/flame/inputs_2d_smallscale.2levels Source/BaseStateGeometry.cpp commit 08077cd6adfa33a0619c0a0fb703a7099210f776 Merge: 692b1a84 5733163a Author: Andy Nonaka Date: Tue Jul 28 14:09:22 2020 -0700 Merge pull request #212 from ChrisDeGrendele/development Fix bug when finest_level was less then max_radial_level. commit 5733163a804dba12cb9b03026ebd24e2bb8851c5 Author: Chris DeGrendele <35853499+ChrisDeGrendele@users.noreply.github.com> Date: Tue Jul 28 15:21:01 2020 -0500 Update MaestroRegrid.cpp Source/MaestroRegrid.cpp commit 692b1a84e6959c23670f7941116b63f358f69926 Author: Alice Harpole Date: Tue Jul 28 13:18:14 2020 -0400 Add Aux data quantities (#211) This adds the auxiliary data (addressing #202). In this PR, the quantities are initialized in the initial data for the reacting bubble test problem, however in a subsequent PR this shall be moved to a separate post-initial data step. I also found a bug in the RhoXFlux routine that didn't look thread safe, so moved the density reset outside of the loops over the components. Exec/science/fully_convective_star/make_heating.F90 Exec/test_problems/reacting_bubble/MaestroInitData.cpp Exec/test_problems/rt/inputs_2d_C Source/MaestroAdvection.cpp Source/MaestroBaseState.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroInitData.cpp Source/MaestroIntra.cpp Source/MaestroMakeEdgeScalars.cpp Source/MaestroMakeFlux.cpp Source/MaestroMakeS.cpp Source/MaestroPlot.cpp Source/MaestroRhoHT.cpp Source/MaestroSetup.cpp Source/MaestroThermal.cpp Source/Src_nd/burner_loop.F90 Source/param/_cpp_parameters Source/param/_variables Source/param_includes/maestro_declares.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/state_indices.H Source/param_includes/state_indices_nd.F90 commit 0e928d6ff3eb4d3a39897e71452004ce397989f8 Author: Chris DeGrendele Date: Mon Jul 27 16:43:22 2020 -0400 PrintBA, with Print() Source/MaestroDebug.cpp commit 8b79038bfe7d80f21bd72e41198657393fc3c55e Author: Chris DeGrendele Date: Mon Jul 27 16:17:34 2020 -0400 Cleanup / remove small objects Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/MaestroThermal.cpp commit ce60efe02d809ea3b0095af32357f5a00aee81c6 Merge: d7f2d623 39bbd39b Author: Chris DeGrendele Date: Sun Jul 26 23:08:06 2020 -0400 Merge branch 'development' of https://github.com/ChrisDeGrendele/MAESTROeX into development commit d7f2d623a2f95269f9d5792a0532ee53efb668b5 Author: Chris DeGrendele Date: Sun Jul 26 23:04:44 2020 -0400 Assume finest level is 0 in fortran as well Source/Src_nd/base_state_geometry.F90 commit 39bbd39b276a62553a94b2ba4cfc88853d77a1c6 Author: Chris DeGrendele Date: Fri Jul 24 17:30:08 2020 -0400 Cleanup and dr->dx in InletBCs Exec/science/flame/MaestroBCFill.cpp Exec/test_problems/mach_jet/MaestroBCFill.cpp Exec/test_problems/mach_jet/MaestroInletBCs.H Exec/test_problems/mach_jet/MaestroInletBCs.cpp Exec/test_problems/mach_jet/inlet_bc.F90 Source/Maestro.H Source/MaestroBCFill.cpp Source/MaestroDebug.cpp Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/MaestroNodalProj.cpp commit 4f00d9945eaa66ce3a1b474af96e27a8a83bad79 Author: Alice Harpole Date: Fri Jul 24 15:49:00 2020 -0400 Checkout submodule development branches in GitHub action (#213) This checks out the development branches of the Microphysics and AMReX submodules in the cpp-linter GitHub action .github/workflows/c-linter.yml commit 7dc891b105d04af5c34f76c7238c9d9df0d82739 Merge: 28b82f86 fa6790e9 Author: Chris DeGrendele Date: Fri Jul 24 12:43:31 2020 -0400 Merge remote-tracking branch 'upstream/development' into development commit 28b82f8624d0fb79b5a01ee62e8c2666dd2f7c3d Author: Chris DeGrendele Date: Fri Jul 24 12:40:05 2020 -0400 Assume finest_level starts at 0 Exec/test_problems/mach_jet/MaestroInletBCs.cpp Source/BaseStateGeometry.cpp commit 5f4f4b42d2fdb53df8c33aebfafdb86fe26c50f6 Author: Doreen Fan Date: Thu Jul 23 14:37:53 2020 -0700 fix inlet bc for when finest_level < max_level Exec/test_problems/mach_jet/MaestroInletBCs.cpp commit fa6790e984f91c5c16d0b140ace1383156e2a0e5 Merge: c3d67082 b397610a Author: Andy Nonaka Date: Thu Jul 23 07:45:42 2020 -0700 Merge pull request #206 from AMReX-Astro/smallscale_sdc_dpdt_fix Smallscale sdc dpdt fix commit b397610aff1e262b3d8b2f45ab327149657f57df Author: GitHub Action Date: Thu Jul 23 01:55:52 2020 +0000 Clang-format has tidied up the code. Source/MaestroAdvanceSdc.cpp Source/MaestroEnthalpyAdvance.cpp commit ef1370e3eac7299b8d461ba1f4303791a0b55bb6 Author: Andy Nonaka Date: Wed Jul 22 18:54:53 2020 -0700 fix the SDC implementation across all 4 advance routines the delta_p increment is now peos-p0, rather than peos-peosbar Exec/science/flame/inputs_2d_smallscale_sdc Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp commit f07ecb3039c2968d55539a59894cc560904c5156 Author: Andy Nonaka Date: Wed Jul 22 17:32:28 2020 -0700 fix bug in dpdt implementation. was using delta_p_term like delta_chi. delta_p should be set to peos-p0, NOT incremented by peos-p0 Source/MaestroAdvanceSdc.cpp commit ed42b9ba3f435e39e6bd96495d8663293584c106 Author: GitHub Action Date: Tue Jul 21 22:26:25 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroAdvanceSdc.cpp Source/MaestroEnthalpyAdvance.cpp commit 4b0587c31f7e04057dfe7403d701d360d9d44415 Author: Doreen Fan Date: Tue Jul 21 15:27:51 2020 -0700 Fix bug when constructing sdc_source, and some clean up Source/MaestroAdvanceSdc.cpp Source/MaestroEnthalpyAdvance.cpp commit c3d670820f4403e6ec598663d8b0780a0cdc0dc2 Author: Alice Harpole Date: Tue Jul 21 18:24:02 2020 -0400 Fix CPUTime read routine (#210) The CPUTime string was not being parsed properly when read in, meaning that the CPU time read in from the checkpoint was not included in the total CPU time for subsequent steps. Source/MaestroCheckpoint.cpp commit 330d775ddf9d66906734a54a41aa76aad6de54e5 Author: Alice Harpole Date: Mon Jul 20 17:12:40 2020 -0400 Divide rhoX by rho instead of temperature (#208) Source/MaestroForce.cpp commit 5582da8f85db60e71b7359550705fade4cfdd463 Author: Chris DeGrendele Date: Mon Jul 20 13:29:57 2020 -0400 Define init multifabs with small_geom Source/MaestroInit.cpp commit d2ded9ebf506d5c8429cb1f148b7f1945932251d Author: Chris DeGrendele Date: Mon Jul 20 12:58:50 2020 -0400 Dont pass full geoms to amrex, same problem as before. This works?! Source/MaestroThermal.cpp commit af8daf329cb071ac35a0d373575333400006225c Author: Andy Nonaka Date: Fri Jul 17 16:30:13 2020 -0700 maestro.enthalpy_pred_type = 0 maestro.species_pred_type = 2 seem to be required for SDC with dpdt factor to be stable still under investigation Exec/science/flame/inputs_2d_smallscale_sdc commit 755da0755e25d445a2eb46f946a2697c1dacb157 Author: Chris DeGrendele Date: Fri Jul 17 18:02:20 2020 -0400 Valid data is only <= finest_level Source/MaestroRegrid.cpp commit 72fe9c3af574d781a103732baafa2c6dcdf7d904 Author: Chris DeGrendele Date: Fri Jul 17 17:47:54 2020 -0400 Don't pass undefined grids to amrex solver Source/MaestroMacProj.cpp Source/MaestroNodalProj.cpp commit 6cfc9e577bc170fc6250383f5f52cad062beb6d1 Author: Chris DeGrendele Date: Fri Jul 17 17:47:03 2020 -0400 In this loop divide by ncell(lev) for undefined levs is divide by 0 Source/MaestroAverage.cpp commit 9397af2dd757b039e97266c9e800b0ab41bc9cbd Author: Chris DeGrendele Date: Fri Jul 17 10:13:24 2020 -0400 Added debugging for Grids Source/Maestro.H Source/MaestroDebug.cpp commit 97530c869a9dec59fbee1b79c20b1c394f31826d Author: Chris DeGrendele Date: Fri Jul 17 08:57:12 2020 -0400 Make debugging multifabs readable Source/MaestroDebug.cpp commit 98abdd779d653f9dfe4e3bf4e429d2574ab3a0dc Author: Chris DeGrendele Date: Thu Jul 16 14:12:53 2020 -0400 Slice grids to prevent passing undefined boxes to amrex Source/MaestroNodalProj.cpp commit c59735cab07f31153147993efa86f1d95c57a8a7 Author: Chris DeGrendele Date: Thu Jul 16 13:42:25 2020 -0400 Prevent Tagarray from looping over undefined grids Source/MaestroRegrid.cpp commit 99f3738436c89dcf54d5704c3ac622e7e981449a Author: GitHub Action Date: Wed Jul 15 20:25:24 2020 +0000 Clang-format has tidied up the code. Source/MaestroAdvanceSdc.cpp Source/MaestroMakeS.cpp commit 40beffe6a1d7250ecf87e4bd69173da6cb7d2304 Merge: 522a8ed7 9d0c78af Author: Andy Nonaka Date: Wed Jul 15 13:24:44 2020 -0700 Merge branch 'development' into smallscale_sdc_dpdt_fix commit 522a8ed77a4358e9db90a8fb8302aec89e945d20 Author: Andy Nonaka Date: Wed Jul 15 12:46:11 2020 -0700 dpdt_factor=1 for sdc Exec/science/flame/inputs_2d_smallscale_sdc commit 24c82682e5fd7585f1d062e01ad5a0bb0f4b237b Author: Andy Nonaka Date: Wed Jul 15 12:41:32 2020 -0700 fixed the smallscale SDC implementation for both SDC and Strang, the logic for including the dpdt terms was wrong; it was looking at rho0 instead of the cutoff coordinates (rho0 is zero for smallscale) updated the iterative logic in MaestroAdvanceSdc.cpp to use the latest dpdt algorithmic methodology, where delta_p_term is incremented by (p0_new - peos_new) instead of reset to this value after each iteration Exec/science/flame/inputs_2d_smallscale Exec/science/flame/inputs_2d_smallscale_sdc Source/MaestroAdvanceSdc.cpp Source/MaestroMakeS.cpp commit 9d0c78afd8e0f54d214bfcf9c07748171438c266 Merge: 4883f178 7899c38e Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Wed Jul 15 11:37:57 2020 -0700 Merge pull request #196 from AMReX-Astro/clang-format Add action for clang-format commit 7899c38e6f754ee735859d5fad5292140acd74d1 Author: GitHub Action Date: Wed Jul 15 02:55:25 2020 +0000 Clang-format has tidied up the code. Exec/test_problems/reacting_bubble/MaestroInitData.cpp Exec/unit_tests/test_basestate/MaestroAdvance.cpp Exec/unit_tests/test_basestate/MaestroDt.cpp Exec/unit_tests/test_diffusion/MaestroPlot.cpp Exec/unit_tests/test_projection/MaestroPlot.cpp Exec/unit_tests/test_react/MaestroPlot.cpp Source/BaseState.H Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroAdvection.cpp Source/MaestroAverage.cpp Source/MaestroBCFill.cpp Source/MaestroBaseState.cpp Source/MaestroCheckpoint.cpp Source/MaestroDensityAdvance.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroEnforceHSE.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroFill3dData.cpp Source/MaestroInit.cpp Source/MaestroMakeEdgeScalars.cpp Source/MaestroMakeS.cpp Source/MaestroMakew0.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp Source/MaestroReact.cpp Source/MaestroRegrid.cpp Source/MaestroRhoHT.cpp Source/MaestroSetup.cpp Source/MaestroVelPred.cpp Source/MaestroVelocityAdvance.cpp commit 3018ecc700a199f3d266d392727b7b31e57da24f Merge: 6d6a6c2b 4883f178 Author: Doreen Fan Date: Tue Jul 14 18:22:47 2020 -0700 Merge branch 'development' into clang-format Fixed merge conflicts commit 6d6a6c2b0c9d70f5e9fe0e5e0273b8395931855e Merge: 6c97dfe6 88f2109f Author: Doreen Fan Date: Tue Jul 14 11:56:41 2020 -0700 Merge branch 'clang-format' of https://github.com/AMReX-Astro/MAESTROeX into clang-format commit 88f2109f30e5742bc9c8a7a10f01c790e44ae00f Author: GitHub Action Date: Tue Jul 14 16:49:04 2020 +0000 Clang-format has tidied up the code. Exec/science/code_comp/MaestroBaseState.cpp Exec/science/code_comp/MaestroInitData.cpp Exec/science/code_comp/Problem.cpp Exec/science/ecsn/MaestroInitData.cpp Exec/science/ecsn/MaestroTagging.cpp Exec/science/flame/MaestroBCFill.cpp Exec/science/flame/MaestroBaseState.cpp Exec/science/flame/MaestroInitData.cpp Exec/science/flame/MaestroInletBCs.H Exec/science/flame/MaestroInletBCs.cpp Exec/science/fully_convective_star/MaestroHeating.cpp Exec/science/fully_convective_star/MaestroInitData.cpp Exec/science/fully_convective_star/MaestroTagging.cpp Exec/science/fully_convective_star/Problem.cpp Exec/science/plane_parallel_star/MaestroInitData.cpp Exec/science/rotating_star/MaestroInitData.cpp Exec/science/rotating_star/MaestroTagging.cpp Exec/science/rotating_star/Problem.cpp Exec/science/sub_chandra/MaestroInitData.cpp Exec/science/toy_convect/MaestroInitData.cpp Exec/science/urca/MaestroInitData.cpp Exec/science/urca/MaestroTagging.cpp Exec/science/wdconvect/MaestroInitData.cpp Exec/science/wdconvect/MaestroTagging.cpp Exec/science/xrb_mixed/MaestroInitData.cpp Exec/science/xrb_mixed/MaestroSponge.cpp Exec/test_problems/double_bubble/MaestroBaseState.cpp Exec/test_problems/double_bubble/MaestroInitData.cpp Exec/test_problems/incomp_shear_jet/MaestroBaseState.cpp Exec/test_problems/incomp_shear_jet/MaestroInitData.cpp Exec/test_problems/mach_jet/MaestroBCFill.cpp Exec/test_problems/mach_jet/MaestroBaseState.cpp Exec/test_problems/mach_jet/MaestroInitData.cpp Exec/test_problems/mach_jet/MaestroInletBCs.H Exec/test_problems/mach_jet/MaestroInletBCs.cpp Exec/test_problems/reacting_bubble/MaestroInitData.cpp Exec/test_problems/reacting_bubble/MaestroTagging.cpp Exec/test_problems/rt/MaestroBaseState.cpp Exec/test_problems/rt/MaestroInitData.cpp Exec/test_problems/test_convect/MaestroInitData.cpp Exec/test_problems/test_planar_diag/MaestroBaseState.cpp Exec/test_problems/test_planar_diag/MaestroInitData.cpp Exec/test_problems/test_stability/MaestroInitData.cpp Exec/unit_tests/test_advect/MaestroBaseState.cpp Exec/unit_tests/test_advect/MaestroEvolve.cpp Exec/unit_tests/test_advect/MaestroInit.cpp Exec/unit_tests/test_advect/MaestroInitData.cpp Exec/unit_tests/test_average/MaestroBaseState.cpp Exec/unit_tests/test_average/MaestroEvolve.cpp Exec/unit_tests/test_average/MaestroInitData.cpp Exec/unit_tests/test_average/main.cpp Exec/unit_tests/test_basestate/MaestroAdvance.cpp Exec/unit_tests/test_basestate/MaestroDt.cpp Exec/unit_tests/test_basestate/MaestroEvolve.cpp Exec/unit_tests/test_basestate/MaestroInit.cpp Exec/unit_tests/test_basestate/MaestroInitData.cpp Exec/unit_tests/test_basestate/Problem_F.H Exec/unit_tests/test_diffusion/MaestroBaseState.cpp Exec/unit_tests/test_diffusion/MaestroDt.cpp Exec/unit_tests/test_diffusion/MaestroEvolve.cpp Exec/unit_tests/test_diffusion/MaestroInit.cpp Exec/unit_tests/test_diffusion/MaestroPlot.cpp Exec/unit_tests/test_eos/MaestroEvolve.cpp Exec/unit_tests/test_eos/MaestroInit.cpp Exec/unit_tests/test_eos/Problem_F.H Exec/unit_tests/test_new_basestate/main.cpp Exec/unit_tests/test_projection/MaestroEvolve.cpp Exec/unit_tests/test_projection/MaestroInit.cpp Exec/unit_tests/test_projection/MaestroPlot.cpp Exec/unit_tests/test_projection/Problem_F.H Exec/unit_tests/test_react/MaestroBaseState.cpp Exec/unit_tests/test_react/MaestroEvolve.cpp Exec/unit_tests/test_react/MaestroInit.cpp Exec/unit_tests/test_react/MaestroPlot.cpp Exec/unit_tests/test_react/Problem_F.H Source/BaseState.H Source/BaseStateGeometry.H Source/BaseStateGeometry.cpp Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroAdvectBase.cpp Source/MaestroAdvection.cpp Source/MaestroAverage.cpp Source/MaestroBCFill.cpp Source/MaestroBCThreads.H Source/MaestroBaseState.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroCelltoEdge.cpp Source/MaestroCheckpoint.cpp Source/MaestroConvert.cpp Source/MaestroDebug.cpp Source/MaestroDensityAdvance.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroEnforceHSE.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroEvolve.cpp Source/MaestroFill3dData.cpp Source/MaestroFillData.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroHeating.cpp Source/MaestroInit.cpp Source/MaestroInitData.cpp Source/MaestroInletBCs.H Source/MaestroInletBCs.cpp Source/MaestroIntra.cpp Source/MaestroMacProj.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEdgeScalars.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeFlux.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakePsi.cpp Source/MaestroMakeS.cpp Source/MaestroMakeUtrans.cpp Source/MaestroMakew0.cpp Source/MaestroNodalProj.cpp Source/MaestroPPM.cpp Source/MaestroPlot.cpp Source/MaestroReact.cpp Source/MaestroRegrid.cpp Source/MaestroRhoHT.cpp Source/MaestroRotation.cpp Source/MaestroSetup.cpp Source/MaestroSlopes.cpp Source/MaestroSponge.cpp Source/MaestroTagging.cpp Source/MaestroThermal.cpp Source/MaestroVelPred.cpp Source/MaestroVelocityAdvance.cpp Source/Maestro_F.H Source/PhysBCFunctMaestro.H Source/main.cpp Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/state_indices.H Util/diagnostics/Radial_F.H Util/diagnostics/main.cpp Util/model_parser/ModelParser.H Util/model_parser/ModelParser.cpp Util/model_parser/model_parser_F.H Util/simple_log/SimpleLog.H Util/simple_log/SimpleLog.cpp Util/utils/MaestroUtil.H Util/utils/MaestroUtil.cpp commit 4883f1781348e82556acb2995911531ebcd671ee Merge: b8c25a54 936e44e5 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Mon Jul 13 18:29:53 2020 -0700 Merge pull request #189 from AMReX-Astro/clang_tidied Fix warnings raised by clang-tidy commit 936e44e5f191fcd60d3edec3bd08d135e764af6c Merge: 642f4890 9724da47 Author: Doreen Fan Date: Mon Jul 13 15:20:33 2020 -0700 Merge branch 'development' into clang_tidied Fixed conficts commit b8c25a543f2eb6c7a7628795d7a86f9e7fdc7ba5 Author: Alice Harpole Date: Thu Jul 2 08:35:42 2020 -0400 Release action (#201) This adds an action which automatically creates a release whenever a tag of the form xx.xx is created. It scrapes the release text from CHANGES.md. .github/workflows/create_release.yml .github/workflows/get_release_txt.py commit 9724da472d74210f966a6f8d3b21d6768aafacab Author: Doreen Fan Date: Wed Jul 1 11:51:30 2020 -0700 July 2020 release notes CHANGES.md commit fa4de7ea240eb4309715a99f79c7ca9bc9de2af7 Author: Doreen Fan Date: Wed Jul 1 11:36:36 2020 -0700 Update AMReX and Microphysics to release 20.07 Exec/science/fully_convective_star/inputs_3d external/Microphysics external/amrex commit 3d68bf8e116b9a92f984c85813b37de813098d4b Author: Max Katz Date: Mon Jun 29 17:50:11 2020 -0700 Update CHANGES for master -> main renaming (#200) * Update CHANGES for master -> main renaming * Fix code name CHANGES.md commit aae120c2551ea87797cd79f8a9dfd776889fccdc Author: Alice Harpole Date: Mon Jun 29 13:56:45 2020 -0400 convert docs actions to use main branch instead of master and convert all mentions of master (and links to master) in the docs to main (#199) This converts the docs action to use the main branch instead of master, changes all mentions of the master branch in the docs to main and changes links which point to the master branch to point to the main branch. This will break some links in the development docs until the master branch has been converted to main. .github/workflows/gh-pages.yml README.md deploy_docs_action.sh sphinx_docs/source/_templates/dev_layout.html sphinx_docs/source/_templates/layout.html sphinx_docs/source/addproblem.rst sphinx_docs/source/architecture.rst.old sphinx_docs/source/conf.py sphinx_docs/source/faq.rst sphinx_docs/source/getting_started.rst sphinx_docs/source/index.rst commit be5df0563160c038130ff2fcbbf50e646d0acad8 Merge: 4e90d3da 002a89f5 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Mon Jun 8 14:13:35 2020 -0700 Merge pull request #194 from AMReX-Astro/remove_rhoX0 Remove rhoX0 commit 002a89f5cd7cfd4bca836deabe43027f9c59f06a Author: GitHub Action Date: Sat Jun 6 04:52:06 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/Maestro.H Source/MaestroAdvanceSdc.cpp Source/MaestroEnthalpyAdvance.cpp commit 4435462718d820d9990a08a76d8b12b8d4391667 Author: Doreen Fan Date: Fri Jun 5 21:53:56 2020 -0700 added initialization of w0_cart; works for planar and wdconvect now Exec/unit_tests/test_basestate/MaestroAdvance.cpp Exec/unit_tests/test_basestate/MaestroDt.cpp Exec/unit_tests/test_basestate/MaestroInit.cpp Exec/unit_tests/test_basestate/wdconvect_paper/inputs.rho_cutoff_1.e5 commit 4e90d3dab611dbdf1bbd5333158ffa0f6da48318 Merge: 2b4787e2 0ca87002 Author: Max Katz Date: Fri Jun 5 20:28:31 2020 -0700 Merge pull request #198 from maxpkatz/sc20_readme Add README for SC20 setup commit 0ca87002ac1c140bb031256b0e7666f3b62e78b3 Author: Max Katz Date: Fri Jun 5 23:02:12 2020 -0400 Add README for SC20 setup Exec/test_problems/reacting_bubble/scaling/sc20/README.md commit dead4b5f6285db680cbf7d97ce788a6c57209af1 Merge: 7b66134f 2b4787e2 Author: Doreen Fan Date: Fri Jun 5 15:22:11 2020 -0700 Merge branch 'development' into remove_rhoX0 commit 2b4787e270b58c01c8fa1f916fb44f354a9a930f Author: Doreen Fan Date: Fri Jun 5 14:34:12 2020 -0700 add input files for fully convective star Exec/science/fully_convective_star/inputs_3d.512 Exec/science/fully_convective_star/inputs_3d_amr commit 8a8515ed730cd1bf4c8977d1cb3c78a950022c29 Author: Andy Nonaka Date: Tue Jun 2 08:36:37 2020 -0700 add #include for getcwd() so regression tests compile on battra Exec/unit_tests/test_diffusion/MaestroPlot.cpp Exec/unit_tests/test_projection/MaestroPlot.cpp Exec/unit_tests/test_react/MaestroPlot.cpp Source/MaestroPlot.cpp commit a9a1b58d9865486cc64bb87534e20a1cf765719f Author: Doreen Fan Date: Mon Jun 1 12:52:36 2020 -0700 June 2020 release notes CHANGES.md commit c81740c4c3dfb5a291c74300605d9ca3f66bfd05 Author: Doreen Fan Date: Mon Jun 1 12:36:43 2020 -0700 Update AMReX and Microphysics to release 20.06 Exec/science/fully_convective_star/inputs_3d Exec/science/wdconvect/inputs_files/inputs_3d_C.128.sdc Exec/test_problems/reacting_bubble/inputs_3d_sdc Source/Maestro.H Source/MaestroAdvanceSdc.cpp Source/MaestroEnthalpyAdvance.cpp external/Microphysics external/amrex commit 651019c8117a522c6668ab59923b818f3481c0af Author: Max Katz Date: Sun May 31 09:01:56 2020 -0700 Add markers to SC20 scaling plot (#197) Exec/test_problems/reacting_bubble/scaling/sc20/plot.py commit 8bf7ef3e6a0fffa85c4eb382486283e5d4e313a3 Merge: 6b8192c3 45d4cd41 Author: Andy Nonaka Date: Thu May 28 15:51:23 2020 -0400 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 6b8192c37b5397ff3b6fdc88d18de75fc7349fea Author: Andy Nonaka Date: Thu May 28 15:51:02 2020 -0400 fully convective star setup Exec/science/fully_convective_star/GNUmakefile Exec/science/fully_convective_star/inputs_3d commit 6c97dfe6b512a9aafeedfbec96b14cf96bcb681e Author: GitHub Action Date: Tue May 26 16:50:57 2020 +0000 Clang-format has tidied up the code. Exec/science/code_comp/MaestroBaseState.cpp Exec/science/code_comp/MaestroInitData.cpp Exec/science/code_comp/Problem.cpp Exec/science/ecsn/MaestroInitData.cpp Exec/science/ecsn/MaestroTagging.cpp Exec/science/flame/MaestroBCFill.cpp Exec/science/flame/MaestroBaseState.cpp Exec/science/flame/MaestroInitData.cpp Exec/science/flame/MaestroInletBCs.H Exec/science/flame/MaestroInletBCs.cpp Exec/science/fully_convective_star/MaestroHeating.cpp Exec/science/fully_convective_star/MaestroInitData.cpp Exec/science/fully_convective_star/MaestroTagging.cpp Exec/science/fully_convective_star/Problem.cpp Exec/science/plane_parallel_star/MaestroInitData.cpp Exec/science/rotating_star/MaestroInitData.cpp Exec/science/rotating_star/MaestroTagging.cpp Exec/science/rotating_star/Problem.cpp Exec/science/sub_chandra/MaestroInitData.cpp Exec/science/toy_convect/MaestroInitData.cpp Exec/science/urca/MaestroInitData.cpp Exec/science/urca/MaestroTagging.cpp Exec/science/wdconvect/MaestroInitData.cpp Exec/science/wdconvect/MaestroTagging.cpp Exec/science/xrb_mixed/MaestroInitData.cpp Exec/science/xrb_mixed/MaestroSponge.cpp Exec/test_problems/double_bubble/MaestroBaseState.cpp Exec/test_problems/double_bubble/MaestroInitData.cpp Exec/test_problems/incomp_shear_jet/MaestroBaseState.cpp Exec/test_problems/incomp_shear_jet/MaestroInitData.cpp Exec/test_problems/mach_jet/MaestroBCFill.cpp Exec/test_problems/mach_jet/MaestroBaseState.cpp Exec/test_problems/mach_jet/MaestroInitData.cpp Exec/test_problems/mach_jet/MaestroInletBCs.H Exec/test_problems/mach_jet/MaestroInletBCs.cpp Exec/test_problems/reacting_bubble/MaestroInitData.cpp Exec/test_problems/reacting_bubble/MaestroTagging.cpp Exec/test_problems/rt/MaestroBaseState.cpp Exec/test_problems/rt/MaestroInitData.cpp Exec/test_problems/test_convect/MaestroInitData.cpp Exec/test_problems/test_planar_diag/MaestroBaseState.cpp Exec/test_problems/test_planar_diag/MaestroInitData.cpp Exec/test_problems/test_stability/MaestroInitData.cpp Exec/unit_tests/test_advect/MaestroBaseState.cpp Exec/unit_tests/test_advect/MaestroEvolve.cpp Exec/unit_tests/test_advect/MaestroInit.cpp Exec/unit_tests/test_advect/MaestroInitData.cpp Exec/unit_tests/test_average/MaestroBaseState.cpp Exec/unit_tests/test_average/MaestroEvolve.cpp Exec/unit_tests/test_average/MaestroInitData.cpp Exec/unit_tests/test_average/main.cpp Exec/unit_tests/test_basestate/MaestroAdvance.cpp Exec/unit_tests/test_basestate/MaestroDt.cpp Exec/unit_tests/test_basestate/MaestroEvolve.cpp Exec/unit_tests/test_basestate/MaestroInit.cpp Exec/unit_tests/test_basestate/MaestroInitData.cpp Exec/unit_tests/test_basestate/Problem_F.H Exec/unit_tests/test_diffusion/MaestroBaseState.cpp Exec/unit_tests/test_diffusion/MaestroDt.cpp Exec/unit_tests/test_diffusion/MaestroEvolve.cpp Exec/unit_tests/test_diffusion/MaestroInit.cpp Exec/unit_tests/test_diffusion/MaestroPlot.cpp Exec/unit_tests/test_eos/MaestroEvolve.cpp Exec/unit_tests/test_eos/MaestroInit.cpp Exec/unit_tests/test_eos/Problem_F.H Exec/unit_tests/test_new_basestate/main.cpp Exec/unit_tests/test_projection/MaestroEvolve.cpp Exec/unit_tests/test_projection/MaestroInit.cpp Exec/unit_tests/test_projection/MaestroPlot.cpp Exec/unit_tests/test_projection/Problem_F.H Exec/unit_tests/test_react/MaestroBaseState.cpp Exec/unit_tests/test_react/MaestroEvolve.cpp Exec/unit_tests/test_react/MaestroInit.cpp Exec/unit_tests/test_react/MaestroPlot.cpp Exec/unit_tests/test_react/Problem_F.H Source/BaseState.H Source/BaseStateGeometry.H Source/BaseStateGeometry.cpp Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroAdvectBase.cpp Source/MaestroAdvection.cpp Source/MaestroAverage.cpp Source/MaestroBCFill.cpp Source/MaestroBCThreads.H Source/MaestroBaseState.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroCelltoEdge.cpp Source/MaestroCheckpoint.cpp Source/MaestroConvert.cpp Source/MaestroDebug.cpp Source/MaestroDensityAdvance.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroEnforceHSE.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroEvolve.cpp Source/MaestroFill3dData.cpp Source/MaestroFillData.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroHeating.cpp Source/MaestroInit.cpp Source/MaestroInitData.cpp Source/MaestroInletBCs.H Source/MaestroInletBCs.cpp Source/MaestroIntra.cpp Source/MaestroMacProj.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEdgeScalars.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeFlux.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakePsi.cpp Source/MaestroMakeS.cpp Source/MaestroMakeUtrans.cpp Source/MaestroMakew0.cpp Source/MaestroNodalProj.cpp Source/MaestroPPM.cpp Source/MaestroPlot.cpp Source/MaestroReact.cpp Source/MaestroRegrid.cpp Source/MaestroRhoHT.cpp Source/MaestroRotation.cpp Source/MaestroSetup.cpp Source/MaestroSlopes.cpp Source/MaestroSponge.cpp Source/MaestroTagging.cpp Source/MaestroThermal.cpp Source/MaestroVelPred.cpp Source/MaestroVelocityAdvance.cpp Source/Maestro_F.H Source/PhysBCFunctMaestro.H Source/main.cpp Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/state_indices.H Util/diagnostics/Radial_F.H Util/diagnostics/main.cpp Util/model_parser/ModelParser.H Util/model_parser/ModelParser.cpp Util/model_parser/model_parser_F.H Util/simple_log/SimpleLog.H Util/simple_log/SimpleLog.cpp Util/utils/MaestroUtil.H Util/utils/MaestroUtil.cpp commit 2ce452daaf6ea8960249afbb7ae0d2ab76963856 Author: Alice Harpole Date: Tue May 26 12:50:14 2020 -0400 turn off ReflowComments flag so commented-out code is not broken .clang-format commit 642f489011f2f85d66183adaf71d3ee671604a8f Merge: 959326cc 45d4cd41 Author: Alice Harpole Date: Tue May 26 12:36:02 2020 -0400 merge conflicts commit ea75d20dc37bbc1151d9a501ca1a9141eb8e5ec0 Author: Alice Harpole Date: Fri May 22 16:04:15 2020 -0400 remove Delimiter line from .clang-format file .clang-format commit 67418d0ac803bd89884664cd9148b0c756cc833f Author: Alice Harpole Date: Fri May 22 15:54:03 2020 -0400 add clang-format action .clang-format .github/workflows/clang-format.yml commit 45d4cd41a1f9c47b51e4a83d987ee925d3433d2c Merge: 1ba5f4b4 012fff99 Author: Andy Nonaka Date: Thu May 21 13:50:04 2020 -0700 Merge pull request #195 from AMReX-Astro/sdc_p0_fix SDC use_tfromp=true fix commit 012fff9947912a2af6cf3954e5778009193c56f6 Author: GitHub Action Date: Thu May 21 18:57:11 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroDiag.cpp commit 2ccfbf40dc745fe727331de98b7ed36aec4a40d0 Author: Alice Harpole Date: Thu May 21 14:55:20 2020 -0400 got rid of if statement that stopped use_tfromp=true working with SDC Source/MaestroReact.cpp commit 1ba5f4b48fdc711a7f697862b229c390c49dd789 Author: Doreen Fan Date: Wed May 20 17:23:46 2020 -0700 update/add SDC input files Exec/science/wdconvect/inputs_files/inputs_3d_C.128.sdc Exec/test_problems/reacting_bubble/inputs_2d_sdc Exec/test_problems/reacting_bubble/inputs_3d_sdc commit 18375fd989bb7595aa5502368265bf32db754067 Author: Doreen Fan Date: Wed May 20 14:42:14 2020 -0700 add ReactSDC when writing diagnosis files for spherical problems Source/MaestroDiag.cpp commit 7b66134fe4b3953af589fdc1b0610ea26c5896f4 Author: Alice Harpole Date: Wed May 20 09:22:57 2020 -0400 remove rhoX0 as it's only used in one unit test Exec/unit_tests/test_basestate/MaestroAdvance.cpp Exec/unit_tests/test_basestate/MaestroInit.cpp Source/Maestro.H commit 6599511dfd9065548ddad9d9680d38a642c32f36 Author: Andy Nonaka Date: Tue May 19 07:56:30 2020 -0700 undo changes from probin_fix (#193) Undo #192 The reverted code now works with AMReX #902 fixing the PGI/IBM ParmParse bug * undo changes from branch probin_fix * Tabs have been converted to spaces by tab_exterminator.sh Co-authored-by: GitHub Action Exec/Make.Maestro Source/MaestroReact.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/param/runtime.probin.template commit fcdc8d7f604cfd8bb3f0d896e1e43f27366926b9 Author: Doreen Fan Date: Mon May 18 19:38:20 2020 -0700 add SDC flags to makefile Exec/Make.Maestro Source/MaestroReact.cpp commit 3f79dc7bc19a54e8ee6671dc128d80bfd2459084 Merge: 2116e124 2aaf624f Author: Andy Nonaka Date: Mon May 18 12:56:27 2020 -0700 Merge pull request #192 from AMReX-Astro/probin_fix Probin fix/hack commit 2116e124c3db80d86a84def609bfc128a6b70f3d Merge: 7cfdbe59 b40f2c83 Author: Andy Nonaka Date: Mon May 18 12:56:04 2020 -0700 Merge pull request #191 from AMReX-Astro/cpp_rotation C++ rotation terms commit 2aaf624f8077d64ad65d0849878c170b5555a552 Author: Alice Harpole Date: Mon May 18 14:39:08 2020 -0400 doesn't break on MPI Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/maestro_init.F90 Source/param/runtime.probin.template commit e63edad07cb828e2e2ac4e90dec00d8c076ba918 Author: Alice Harpole Date: Mon May 18 14:00:35 2020 -0400 add in ioprocess check for MPI Exec/Make.Maestro Source/param/runtime.probin.template commit 023082ee3ad158e8f0c11a28bcec393d96a06e59 Author: Alice Harpole Date: Mon May 18 13:18:30 2020 -0400 write probin to file and read back in again Source/param/runtime.probin.template commit b40f2c833935c08ffd7fda99edb30d3b80e718ec Author: Doreen Fan Date: Fri May 15 20:05:57 2020 -0700 remove duplicate of w0_cart and fix indices Source/MaestroForce.cpp commit 65523821fe268a306118103ec3a9d6ba878c8e5e Author: Andrew Nonaka Date: Fri May 15 19:24:54 2020 -0400 abort with error message if running with rotation for planar  Source/MaestroForce.cpp commit 2629fcf2547f6c5b164c0e21bb5fada9f89122aa Author: GitHub Action Date: Fri May 15 21:58:45 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroForce.cpp commit 3d7cfa5fe2a7947fac8a464c76fd377c96333c38 Author: Alice Harpole Date: Fri May 15 17:47:30 2020 -0400 added coriolis and centrifugal terms Source/Maestro.H Source/MaestroAdvection.cpp Source/MaestroDt.cpp Source/MaestroForce.cpp Source/MaestroVelocityAdvance.cpp commit 959326cc7ac192b6420d6564fd885d452c1b7543 Author: Alice Harpole Date: Fri May 15 16:21:06 2020 -0400 minor modernisations Source/BaseState.H Source/BaseStateGeometry.H Source/Maestro.cpp commit 7cfdbe59b15d80911c9ae38b9806dae09b8f88f3 Author: Doreen Fan Date: Thu May 14 18:14:28 2020 -0700 move read_model_file outside of mfi loop in MakeHeating Exec/science/fully_convective_star/MaestroHeating.cpp Exec/science/fully_convective_star/inputs_3d Exec/science/fully_convective_star/make_heating.F90 Source/Maestro_F.H Source/Src_nd/maestro_init.F90 commit 9c3490e2e4af8d156ebdc25103288811e33bab59 Merge: fbf8d1a7 fab4d613 Author: Alice Harpole Date: Wed May 13 17:26:38 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into clang_tidied commit fbf8d1a76a997bb46405900078c7850c77e70062 Author: Alice Harpole Date: Wed May 13 16:19:39 2020 -0400 commit plotfile changes Source/MaestroPlot.cpp commit 8129a083766eb77de88f115662c5c945be3d6766 Author: Alice Harpole Date: Wed May 13 16:18:18 2020 -0400 switch to using aliases Source/BaseState.H Source/Maestro.H Source/MaestroPlot.cpp commit d720f7a0d631a4449510998e40ac4550a2a06db2 Author: Alice Harpole Date: Wed May 13 09:08:04 2020 -0400 fixed some more clang-tidy complaints .github/workflows/c-linter.yml Source/BaseState.H Source/MaestroCheckpoint.cpp Source/MaestroInit.cpp Source/MaestroPlot.cpp Source/MaestroRegrid.cpp Source/main.cpp commit fab4d6133df7936788743d538211be4332cbeb42 Merge: 3a1bed29 091a061c Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Tue May 12 10:37:28 2020 -0700 Merge pull request #183 from AMReX-Astro/base_state_class6 BaseState-ification 5/n commit 091a061c2871c9d6e19cea55e8c7f8d43ded9b84 Merge: a5b4803e 3a1bed29 Author: Doreen Fan Date: Tue May 12 10:35:24 2020 -0700 Merge branch 'development' into base_state_class6 commit 3a1bed2952462dd581bc76b693da57f4178569c2 Merge: f95e055e 8c712305 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Tue May 12 10:31:50 2020 -0700 Merge pull request #181 from AMReX-Astro/base_state_class5 BaseState-ification 4/n commit 4a8bedb4e719a09159af3e7f24180743767ef9eb Author: Alice Harpole Date: Tue May 12 11:34:51 2020 -0400 fixed most of clang-tidy's complaints Exec/test_problems/reacting_bubble/MaestroInitData.cpp Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroAdvection.cpp Source/MaestroAverage.cpp Source/MaestroBCFill.cpp Source/MaestroBaseState.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroConvert.cpp Source/MaestroDensityAdvance.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroEnforceHSE.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEdgeScalars.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeS.cpp Source/MaestroMakew0.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp Source/MaestroReact.cpp Source/MaestroRegrid.cpp Source/MaestroRhoHT.cpp Source/MaestroSetup.cpp Source/MaestroThermal.cpp Source/MaestroVelPred.cpp Source/MaestroVelocityAdvance.cpp Source/Src_nd/base_state_geometry.F90 Source/Src_nd/make_grav.F90 Source/main.cpp Source/param/_cpp_parameters Source/param_includes/maestro_declares.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit a5b4803e295ed6705956f7f2d24b5aaf4e7c4e2d Author: Doreen Fan Date: Mon May 11 15:59:38 2020 -0700 make basestate explicit Source/BaseState.H Source/MaestroInit.cpp commit 8d2c90e6f505d275ccf9ed051ee86be79933229a Author: Alice Harpole Date: Fri May 8 17:38:55 2020 -0400 initialize basestate in constructor and resize Source/BaseState.H commit 0e5873391c214c43d33d5bd39b31889e8eed5ff6 Author: Andy Nonaka Date: Fri May 8 14:07:30 2020 -0700 setval psi to zero if EBS=F Source/MaestroInit.cpp commit 2bdb6c1fe655eed6c9c744d06b1991d6c84f3680 Author: Andy Nonaka Date: Fri May 8 12:28:21 2020 -0700 set w0 and gamma1bar_old to zero in Init to quiet valgrind warnings when writing an initial plotfile Source/MaestroInit.cpp commit 33359ed84566d74cb9e1794f10e53e8fd3cdb0a3 Author: GitHub Action Date: Fri May 8 18:06:10 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroAdvance.cpp Source/MaestroInit.cpp commit 399b77f2b4845002a55dbb4917eac67d4fb797dd Merge: fcda3aea 92558cc2 Author: Doreen Fan Date: Fri May 8 11:05:33 2020 -0700 Merge branch 'base_state_class6' of https://github.com/AMReX-Astro/MAESTROeX into base_state_class6 commit fcda3aeaa0a21720aaf366c189124ce4d83cfb5a Author: Doreen Fan Date: Fri May 8 11:05:13 2020 -0700 initialize w0 to zero when evolve_base_state=F Source/MaestroAdvance.cpp Source/MaestroInit.cpp commit 92558cc2d967a73eca8f882d3b60413b041d9ccc Merge: a578ddd9 b3b55365 Author: Alice Harpole Date: Thu May 7 11:10:28 2020 -0400 Merge branch 'base_state_class6' of github.com:AMReX-Astro/MAESTROeX into base_state_class6 commit a578ddd9e1ea1d7f24a71089b0294d74bb95971b Author: Alice Harpole Date: Thu May 7 11:10:09 2020 -0400 more clang-tidy fixes Source/BaseStateGeometry.H Source/BaseStateGeometry.cpp Source/MaestroAverage.cpp Source/MaestroFill3dData.cpp Source/MaestroInit.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroRhoHT.cpp Util/model_parser/ModelParser.H Util/model_parser/ModelParser.cpp Util/simple_log/SimpleLog.H Util/simple_log/SimpleLog.cpp commit 0a25921dd89da53b36421bd3c875916724ec7232 Merge: 97cc7eda f95e055e Author: Alice Harpole Date: Thu May 7 09:26:28 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into base_state_class6 commit f95e055ea15980f71076f2cc731e0f2f3044967c Author: Alice Harpole Date: Thu May 7 08:42:47 2020 -0400 fix link formatting sphinx_docs/source/faq.rst commit 3aabb60d245ed5b7d4552d45b4074eb525703713 Author: Alice Harpole Date: Thu May 7 08:36:14 2020 -0400 fix link formatting sphinx_docs/source/faq.rst commit 754abf1d00974a5d82b101874c0c8eafbbf87d39 Author: Alice Harpole Date: Thu May 7 08:26:42 2020 -0400 add documentation describing how to run clang-tidy locally sphinx_docs/source/faq.rst commit b3b55365c0509eca2215d2c77c22d6a73ec63185 Author: Doreen Fan Date: Wed May 6 20:07:07 2020 -0700 update problem specs Exec/science/code_comp/MaestroBaseState.cpp Exec/unit_tests/test_basestate/MaestroAdvance.cpp Exec/unit_tests/test_basestate/MaestroInit.cpp Source/Maestro.H commit 97cc7edad80f3f3f869b5c0a0a6208d6ac26cd61 Merge: 61817353 09f3db5c Author: Alice Harpole Date: Wed May 6 16:53:05 2020 -0400 Merge branch 'base_state_class6' of github.com:AMReX-Astro/MAESTROeX into base_state_class6 commit 618173537a78ec66f1441364fab1b4e3af2ecc10 Author: Alice Harpole Date: Wed May 6 16:52:46 2020 -0400 clang-tidy fixes Exec/science/ecsn/MaestroTagging.cpp Exec/science/fully_convective_star/MaestroTagging.cpp Exec/science/rotating_star/MaestroTagging.cpp Exec/science/urca/MaestroTagging.cpp Exec/science/wdconvect/MaestroTagging.cpp Exec/test_problems/reacting_bubble/MaestroTagging.cpp Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroDebug.cpp Source/MaestroDensityAdvance.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroEnforceHSE.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroInitData.cpp Source/MaestroMacProj.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakeS.cpp Source/MaestroMakeUtrans.cpp Source/MaestroMakew0.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp Source/MaestroRegrid.cpp Source/MaestroSetup.cpp Source/MaestroTagging.cpp commit 09f3db5c08257b24cdfb40b2b8864683c77305b2 Merge: 4a30d611 5127f040 Author: Doreen Fan Date: Wed May 6 13:31:30 2020 -0700 Merge branch 'development' into base_state_class6 commit 8c7123056c7d3986c793065da2bb5b4acd957e97 Merge: 9785cf05 5127f040 Author: Doreen Fan Date: Wed May 6 13:29:19 2020 -0700 Merge branch 'development' into base_state_class5 commit 5127f040c685114240ca3c22b72342cef5d465c8 Merge: 7ef07cdc 59dcdf41 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Wed May 6 13:18:44 2020 -0700 Merge pull request #180 from AMReX-Astro/base_state_class4 BaseState-ification 3/n commit 4a30d611356ba629d825b0bd6e57071796778c49 Merge: 11a81884 7ef07cdc Author: Alice Harpole Date: Wed May 6 08:27:39 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into base_state_class6 commit 9785cf05573ded917d35a7c528d291c8f0e40827 Merge: 228f304c 7ef07cdc Author: Alice Harpole Date: Wed May 6 08:13:29 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into base_state_class5 commit 7ef07cdc87bf8b4576a4961410436279dafa3035 Author: Alice Harpole Date: Tue May 5 14:29:52 2020 -0400 Add github pages badge README.md commit d0fb7f72768ba968699ca037618375c23accd6ad Author: Alice Harpole Date: Tue May 5 14:27:00 2020 -0400 Github action for docs build (#187) This switches to using a github action for the docs build (rather than having the docs built on travis). The setup for the github action is much simpler as the action does all of the work of dealing with tokens and pushing to the gh-pages branch. It also converts the tab exterminator script into a github action, and adds an action for the clang static analysis. * add github action for docs build * delete deploy_docs.sh * add tab exterminator action * only commit if there are changes so that the action doesn't fail * fix branch to push to * fix branch to push to * add cpp linter and turn off travis * add amrex as a submodule * add amrex as a submodule .github/workflows/c-linter.yml .github/workflows/gh-pages.yml .github/workflows/tab-exterminator.yml .gitmodules .travis.yml deploy_docs.sh deploy_docs_action.sh external/amrex commit 91c0827c384750dc93fca2150ef9cae2c483fa7d Author: Alice Harpole Date: Tue May 5 10:51:11 2020 -0400 fix AMREX_HOME in Make.Maestro so it works with submodules Exec/Make.Maestro commit 11a81884cc8f2da08dddd02de121aad9d966cd96 Merge: bb06ec33 228f304c Author: Doreen Fan Date: Mon May 4 20:55:16 2020 -0700 Merge branch 'base_state_class5' into base_state_class6 Fixed merge conflicts commit 228f304cfb19ad1b448a37a66bbc56823b3caff7 Author: Doreen Fan Date: Mon May 4 20:29:57 2020 -0700 update problem specs Exec/science/code_comp/MaestroBaseState.cpp Exec/science/code_comp/MaestroInitData.cpp Exec/science/flame/MaestroBaseState.cpp Exec/science/plane_parallel_star/MaestroInitData.cpp Exec/science/xrb_mixed/MaestroInitData.cpp Exec/science/xrb_mixed/MaestroSponge.cpp Exec/test_problems/rt/MaestroInitData.cpp Exec/test_problems/test_planar_diag/MaestroInitData.cpp Exec/unit_tests/test_advect/MaestroEvolve.cpp Exec/unit_tests/test_advect/MaestroInit.cpp Exec/unit_tests/test_basestate/MaestroAdvance.cpp Exec/unit_tests/test_basestate/MaestroInit.cpp Exec/unit_tests/test_diffusion/MaestroEvolve.cpp Exec/unit_tests/test_diffusion/MaestroInit.cpp Exec/unit_tests/test_diffusion/MaestroPlot.cpp Exec/unit_tests/test_projection/MaestroEvolve.cpp Exec/unit_tests/test_projection/MaestroPlot.cpp Exec/unit_tests/test_react/MaestroEvolve.cpp Exec/unit_tests/test_react/MaestroInit.cpp Exec/unit_tests/test_react/MaestroPlot.cpp commit 89c78d2c84f8878eab93d6b5adaf263971c11306 Merge: 425e24e8 6f62a507 Author: Doreen Fan Date: Fri May 1 20:03:34 2020 -0700 Merge branch 'base_state_class4' into base_state_class5 Fixed merge conflicts commit 6f62a507195e2f38b0707c43fe56c5168fc99da3 Merge: ad86ccf0 9b532404 Author: Doreen Fan Date: Fri May 1 19:57:48 2020 -0700 Merge branch 'development' into base_state_class4 commit 59dcdf41ed2ea96f0b1ece2066372dcda33d06c7 Author: Travis CI <> Date: Sat May 2 02:56:48 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh external/Microphysics commit ad86ccf05f83c7ee44b7e810da17c1050e27339b Author: Doreen Fan Date: Fri May 1 19:33:58 2020 -0700 more updates to problem specs Exec/unit_tests/test_advect/MaestroEvolve.cpp Exec/unit_tests/test_average/MaestroEvolve.cpp Exec/unit_tests/test_basestate/MaestroAdvance.cpp Exec/unit_tests/test_basestate/MaestroEvolve.cpp Exec/unit_tests/test_basestate/MaestroInit.cpp Exec/unit_tests/test_diffusion/MaestroBaseState.cpp Exec/unit_tests/test_diffusion/MaestroEvolve.cpp Exec/unit_tests/test_diffusion/MaestroPlot.cpp Exec/unit_tests/test_projection/MaestroEvolve.cpp Exec/unit_tests/test_projection/MaestroPlot.cpp Exec/unit_tests/test_react/MaestroEvolve.cpp Exec/unit_tests/test_react/MaestroPlot.cpp Source/Maestro.H commit 9b53240490b8c6a56b6dfd787f0bf63982a33197 Author: Doreen Fan Date: Fri May 1 11:01:24 2020 -0700 May 2020 release notes CHANGES.md commit 42ba5b713b9753fc402e9861cf1a9c3e4be16927 Author: Doreen Fan Date: Fri May 1 10:47:47 2020 -0700 Update Microphysics to release 20.05 external/Microphysics commit 2de2eaa09ee0d3ca1b3fdf95adb9143b9e78e060 Author: Doreen Fan Date: Thu Apr 30 23:13:03 2020 -0700 minor code cleanup Source/MaestroCheckpoint.cpp Source/MaestroEnforceHSE.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeS.cpp Source/MaestroMakew0.cpp commit e3ee95c0f369b7d86d1259a21a52316ead6ceb5b Merge: c4daee31 0499c845 Author: Doreen Fan Date: Thu Apr 30 14:54:59 2020 -0700 Merge branch 'development' into base_state_class4 commit 0499c845e60d2572641479aecb30a21a3b4f5540 Author: Doreen Fan Date: Thu Apr 30 14:44:17 2020 -0700 bug fix for single level planar Source/MaestroMakeEta.cpp commit bb06ec3347e51602e1b5663182d6b9eecd613352 Author: Alice Harpole Date: Thu Apr 30 16:10:07 2020 -0400 updated problem files Exec/science/flame/MaestroBaseState.cpp Exec/science/fully_convective_star/MaestroInitData.cpp Exec/science/rotating_star/MaestroInitData.cpp Exec/science/sub_chandra/MaestroInitData.cpp Exec/science/urca/MaestroInitData.cpp Exec/science/xrb_mixed/MaestroInitData.cpp Exec/science/xrb_mixed/MaestroSponge.cpp Exec/test_problems/double_bubble/MaestroBaseState.cpp Exec/test_problems/incomp_shear_jet/MaestroBaseState.cpp Exec/test_problems/rt/MaestroBaseState.cpp Exec/test_problems/rt/MaestroInitData.cpp Exec/test_problems/test_planar_diag/MaestroBaseState.cpp Exec/test_problems/test_planar_diag/MaestroInitData.cpp Exec/unit_tests/test_advect/MaestroEvolve.cpp Exec/unit_tests/test_advect/MaestroInit.cpp Exec/unit_tests/test_average/MaestroEvolve.cpp Exec/unit_tests/test_average/MaestroInitData.cpp Exec/unit_tests/test_basestate/MaestroAdvance.cpp Exec/unit_tests/test_diffusion/MaestroBaseState.cpp Exec/unit_tests/test_diffusion/MaestroEvolve.cpp Exec/unit_tests/test_diffusion/MaestroInit.cpp Exec/unit_tests/test_diffusion/MaestroPlot.cpp Exec/unit_tests/test_eos/MaestroInit.cpp Exec/unit_tests/test_projection/MaestroEvolve.cpp Exec/unit_tests/test_projection/MaestroInit.cpp Exec/unit_tests/test_projection/MaestroPlot.cpp Exec/unit_tests/test_react/MaestroEvolve.cpp Exec/unit_tests/test_react/MaestroInit.cpp Exec/unit_tests/test_react/MaestroPlot.cpp Source/BaseState.cpp Source/MaestroInitData.cpp Source/MaestroPlot.cpp Source/MaestroSponge.cpp Source/Make.package commit 981d741fcb6f088c3bde1ad8784655b3a31e71e0 Merge: 8a3c57d0 425e24e8 Author: Alice Harpole Date: Thu Apr 30 10:49:35 2020 -0400 merge with previous PR commit 425e24e8a5e43a5281e4fc55114c734f613c37f6 Author: Alice Harpole Date: Thu Apr 30 10:47:38 2020 -0400 merge with previous PR Exec/test_problems/double_bubble/MaestroBaseState.cpp Exec/test_problems/incomp_shear_jet/MaestroBaseState.cpp Exec/test_problems/mach_jet/MaestroBaseState.cpp Exec/test_problems/test_planar_diag/MaestroBaseState.cpp commit b09fdf9fcdafef995c1f941df8c8b6fe183c2ba0 Merge: df1a4053 c4daee31 Author: Alice Harpole Date: Thu Apr 30 10:33:27 2020 -0400 merge with previous PR commit c4daee315d09975f876f87ce3e40307bee8c9428 Author: Alice Harpole Date: Thu Apr 30 10:02:02 2020 -0400 fixed some more problem files Exec/science/code_comp/MaestroBaseState.cpp Exec/science/flame/MaestroBaseState.cpp Exec/test_problems/double_bubble/MaestroBaseState.cpp Exec/test_problems/incomp_shear_jet/MaestroBaseState.cpp Exec/test_problems/mach_jet/MaestroBaseState.cpp Exec/test_problems/test_planar_diag/MaestroBaseState.cpp Exec/unit_tests/test_advect/MaestroBaseState.cpp Exec/unit_tests/test_diffusion/MaestroBaseState.cpp Exec/unit_tests/test_react/MaestroBaseState.cpp commit 917c5e1625b7304cdc11676b6abf90e3bbe660da Author: Alice Harpole Date: Thu Apr 30 09:44:55 2020 -0400 fix 2d rt Exec/test_problems/rt/MaestroBaseState.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeEta.cpp commit 3e7710cd5cfe49efca2501717c5a72639eb96a2c Merge: 98e4ea35 15043f94 Author: Alice Harpole Date: Thu Apr 30 09:21:13 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into base_state_class4 commit 15043f94a40b06e2e188edb03d581226f2adf650 Author: Alice Harpole Date: Thu Apr 30 08:47:54 2020 -0400 fixed code examples sphinx_docs/source/base_state.rst commit 08910810c88ddb08d7fefba19a1aa6a93fdb7303 Author: Alice Harpole Date: Thu Apr 30 08:45:52 2020 -0400 added documentation for BaseStateGeometry sphinx_docs/source/base_state.rst commit dc391a62a3695ae6cb9fbccb59a50517d4a7aa1a Author: Alice Harpole Date: Thu Apr 30 08:08:05 2020 -0400 fix 2d compilation Source/Maestro.H Source/MaestroFill3dData.cpp Source/MaestroInit.cpp commit 8a3c57d0063451cd6615ef05f98e36e166574ca8 Author: Travis CI <> Date: Thu Apr 30 05:17:48 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroFill3dData.cpp commit b8ece4d7c775ac0f1b29fd726b37555969cda1fa Merge: 1d9d0fba 0241fce9 Author: Doreen Fan Date: Wed Apr 29 22:07:54 2020 -0700 Merge branch 'development' into base_state_class6 Fixed merge conflict commit df1a4053c1e46e40512e96e7480b49d97e22b6b7 Author: Travis CI <> Date: Thu Apr 30 05:07:19 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroFill3dData.cpp commit 66037fa02ff47fdc5a9f54a3ddbe3af20d522d4c Merge: 314937a4 0241fce9 Author: Doreen Fan Date: Wed Apr 29 22:05:47 2020 -0700 Merge branch 'development' into base_state_class5 commit 98e4ea3549b378ba0813e45be83b96d4451d58f1 Author: Travis CI <> Date: Thu Apr 30 05:04:27 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroFill3dData.cpp commit d5f40abacf308d5f043529a822d403d9125a513f Merge: 8931e73c 0241fce9 Author: Doreen Fan Date: Wed Apr 29 22:04:22 2020 -0700 Merge branch 'development' into base_state_class4 commit 0241fce93a5d52f70e502090f04b29b4aff8ba25 Merge: 4be011ec 3c563089 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Wed Apr 29 22:00:37 2020 -0700 Merge pull request #177 from AMReX-Astro/base_state_class2 BaseState-ifying base state 1/n commit 3c563089f0ddac6a920cc9ac61d20622627b7f6e Author: Doreen Fan Date: Wed Apr 29 22:00:28 2020 -0700 update problem specs Exec/unit_tests/test_basestate/MaestroAdvance.cpp Exec/unit_tests/test_basestate/MaestroInit.cpp Exec/unit_tests/test_projection/MaestroEvolve.cpp commit ae250c50cb313cf32d36999d4d150121638a24b9 Merge: c0c62909 fff4bc17 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Wed Apr 29 21:35:20 2020 -0700 Merge pull request #179 from AMReX-Astro/base_state_class3 BaseState-ification 2/n commit 4be011ec7169da89e874b0cb0843f218bc288ec9 Author: Doreen Fan Date: Wed Apr 29 16:36:21 2020 -0700 add C++ init function to subroutine Source/MaestroFill3dData.cpp commit 1d9d0fba9d0bf80ec5c946b569126029113e8445 Author: Alice Harpole Date: Wed Apr 29 16:30:40 2020 -0400 static analysis warnings Source/MaestroAdvectBase.cpp Source/MaestroAdvection.cpp Source/MaestroAverage.cpp Source/MaestroBaseState.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroConvert.cpp Source/MaestroDensityAdvance.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroEvolve.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakeS.cpp Source/MaestroSponge.cpp commit 72e64bd7a893eae528f60ff4d831dcff4d9c1b49 Merge: 2e9cbaf9 314937a4 Author: Alice Harpole Date: Wed Apr 29 14:41:04 2020 -0400 Merge branch 'base_state_class5' of github.com:AMReX-Astro/MAESTROeX into base_state_class6 commit 314937a43af67f519ca86227c55f2e48445178a9 Merge: 2a69452f 8931e73c Author: Alice Harpole Date: Wed Apr 29 14:40:44 2020 -0400 Merge branch 'base_state_class4' of github.com:AMReX-Astro/MAESTROeX into base_state_class5 commit 8931e73ca173c0337e61760343707ddedd4b78b9 Merge: 847051d6 fff4bc17 Author: Alice Harpole Date: Wed Apr 29 14:40:26 2020 -0400 Merge branch 'base_state_class3' of github.com:AMReX-Astro/MAESTROeX into base_state_class4 commit fff4bc175d031e68e32900fe80568598707e5f27 Merge: c73d84c7 c0c62909 Author: Doreen Fan Date: Tue Apr 28 15:12:47 2020 -0700 Merge branch 'base_state_class2' into base_state_class3 commit c0c62909fd4a846d45c6e1402e83d96758269814 Merge: e45c3786 7ed5e17e Author: Alice Harpole Date: Tue Apr 28 16:43:10 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into base_state_class2 commit 7ed5e17ec7db06649e4bf161710690ad91fb58c9 Author: Alice Harpole Date: Tue Apr 28 13:10:20 2020 -0400 Convert make_explicit_thermal.F90 to C++ (#175) The converted code looks good and the output diffs are reasonable given the differences in conductivity values between Fortran and C++. Co-authored-by: Doreen Fan Source/Maestro.H Source/MaestroSetup.cpp Source/MaestroThermal.cpp Source/Src_nd/Make.package Source/Src_nd/make_explicit_thermal.F90 commit 2e9cbaf976478209776b6f1fe5e71549a9b48088 Author: Alice Harpole Date: Tue Apr 28 09:22:24 2020 -0400 converted some problem files Exec/science/code_comp/MaestroBaseState.cpp Exec/science/code_comp/MaestroInitData.cpp Exec/science/ecsn/MaestroInitData.cpp Exec/science/flame/MaestroBCFill.cpp Exec/science/flame/MaestroBaseState.cpp Exec/science/flame/MaestroInitData.cpp Exec/science/fully_convective_star/MaestroInitData.cpp Exec/science/plane_parallel_star/MaestroInitData.cpp Exec/science/rotating_star/MaestroInitData.cpp Exec/science/sub_chandra/MaestroInitData.cpp Exec/science/toy_convect/MaestroInitData.cpp Exec/science/urca/MaestroInitData.cpp Exec/science/xrb_mixed/MaestroInitData.cpp Exec/test_problems/double_bubble/MaestroBaseState.cpp Exec/test_problems/double_bubble/MaestroInitData.cpp Exec/test_problems/incomp_shear_jet/MaestroBaseState.cpp Exec/test_problems/incomp_shear_jet/MaestroInitData.cpp Exec/test_problems/mach_jet/MaestroBaseState.cpp Exec/test_problems/mach_jet/MaestroInitData.cpp Exec/test_problems/reacting_bubble/MaestroInitData.cpp Exec/test_problems/rt/MaestroBaseState.cpp Exec/test_problems/rt/MaestroInitData.cpp Exec/test_problems/test_convect/MaestroInitData.cpp Exec/test_problems/test_planar_diag/MaestroBaseState.cpp Exec/test_problems/test_planar_diag/MaestroInitData.cpp Exec/unit_tests/test_advect/MaestroInitData.cpp commit 00f7222a5f84fe11f3212f2fa4dccff5337c4386 Author: Alice Harpole Date: Tue Apr 28 08:36:47 2020 -0400 compiles and runs on CPU Exec/science/wdconvect/MaestroInitData.cpp Exec/test_problems/reacting_bubble/MaestroInitData.cpp Source/MaestroAdvectBase.cpp Source/MaestroAverage.cpp Source/MaestroBaseState.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroCelltoEdge.cpp Source/MaestroCheckpoint.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakew0.cpp Source/MaestroSetup.cpp Source/MaestroSponge.cpp commit 00c86eb983a614950aa2dd80d8b733df94b6f7e2 Merge: 27ed82e3 2a69452f Author: Alice Harpole Date: Mon Apr 27 17:25:58 2020 -0400 merge with previous PR commit 2a69452f30d5845e2e2e3d76b5742f3f9ccb8f59 Author: Alice Harpole Date: Mon Apr 27 14:56:31 2020 -0400 compiles and runs on GPU Exec/test_problems/double_bubble/MaestroInitData.cpp Exec/test_problems/incomp_shear_jet/MaestroBaseState.cpp Exec/test_problems/mach_jet/MaestroBaseState.cpp Exec/test_problems/reacting_bubble/MaestroInitData.cpp Exec/test_problems/rt/MaestroBaseState.cpp Exec/test_problems/test_planar_diag/MaestroBaseState.cpp Exec/unit_tests/test_advect/MaestroBaseState.cpp Exec/unit_tests/test_average/MaestroBaseState.cpp Exec/unit_tests/test_diffusion/MaestroBaseState.cpp Exec/unit_tests/test_react/MaestroBaseState.cpp Source/BaseState.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroAdvectBase.cpp Source/MaestroBaseState.cpp Source/MaestroCheckpoint.cpp Source/MaestroDiag.cpp Source/MaestroFill3dData.cpp Source/MaestroInit.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeFlux.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakew0.cpp Source/MaestroReact.cpp Source/MaestroRegrid.cpp commit b9562eff618e9559a56cddfb085c5951643a5618 Merge: c28f914c 847051d6 Author: Alice Harpole Date: Mon Apr 27 12:58:49 2020 -0400 merge with previous PR commit 847051d6fbf2b3b33a501aec910ebc1ba6fc3ff4 Author: Alice Harpole Date: Mon Apr 27 11:59:53 2020 -0400 runs on GPU Source/BaseState.H Source/MaestroAverage.cpp Source/MaestroCelltoEdge.cpp Source/MaestroDt.cpp Source/MaestroEnforceHSE.cpp Source/MaestroForce.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeEta.cpp Source/MaestroRegrid.cpp commit 0bd8e13c38e6cc1706b05e5f17117e17a3de5b70 Merge: 39b723ae c73d84c7 Author: Alice Harpole Date: Fri Apr 24 16:43:04 2020 -0400 merge with previous PR commit c73d84c7f73134681b9032ff7a4f40016e1f38e3 Merge: 3bebd06e ed241e1a Author: Alice Harpole Date: Fri Apr 24 07:35:51 2020 -0400 merge conflicts commit 3bebd06ea27f204511b876bb3620aad782c82663 Merge: ba98de5d e45c3786 Author: Alice Harpole Date: Fri Apr 24 07:26:51 2020 -0400 merge conflicts commit ed241e1ae776a68eef2f7bc8bdd3a1d186e34eb9 Author: Doreen Fan Date: Thu Apr 23 20:53:01 2020 -0700 GPU fixes Source/Maestro.H Source/MaestroAdvectBase.cpp Source/MaestroMakeGrav.cpp commit 9b32701243c4ebd773a96a3dab21230a3a4fd14e Merge: ba98de5d e45c3786 Author: Doreen Fan Date: Thu Apr 23 19:44:43 2020 -0700 Merge branch 'base_state_class2' into base_state_class3 Fixed merge conflicts commit e45c3786a8ac7b24ba4960f51d29a350993f9b1e Author: Doreen Fan Date: Thu Apr 23 19:30:22 2020 -0700 more updates to problem specs Exec/science/code_comp/MaestroBaseState.cpp Exec/science/flame/MaestroBaseState.cpp Exec/science/sub_chandra/MaestroInitData.cpp Exec/test_problems/double_bubble/MaestroBaseState.cpp Exec/test_problems/incomp_shear_jet/MaestroBaseState.cpp Exec/test_problems/incomp_shear_jet/MaestroInitData.cpp Exec/test_problems/mach_jet/MaestroBaseState.cpp Exec/test_problems/mach_jet/MaestroInletBCs.cpp Exec/test_problems/rt/MaestroBaseState.cpp Exec/test_problems/rt/MaestroInitData.cpp Exec/test_problems/test_planar_diag/MaestroBaseState.cpp Exec/unit_tests/test_advect/MaestroEvolve.cpp Exec/unit_tests/test_average/MaestroEvolve.cpp Exec/unit_tests/test_basestate/MaestroAdvance.cpp Exec/unit_tests/test_basestate/MaestroInit.cpp Exec/unit_tests/test_diffusion/MaestroBaseState.cpp Exec/unit_tests/test_diffusion/MaestroInit.cpp Source/MaestroDiag.cpp Source/MaestroEnforceHSE.cpp Source/MaestroMakeBeta0.cpp commit 73d7fbeb7f36507df27effaee0902f205add3c32 Merge: b5da2aa7 5fd329a5 Author: Alice Harpole Date: Thu Apr 23 17:44:55 2020 -0400 merge conflicts commit b5da2aa7cd57293e1d6e2f3d27c7cebddd311dea Author: Alice Harpole Date: Thu Apr 23 17:42:05 2020 -0400 update problem specs Exec/science/code_comp/MaestroBaseState.cpp Exec/science/code_comp/MaestroInitData.cpp Exec/science/ecsn/MaestroInitData.cpp Exec/science/flame/MaestroBaseState.cpp Exec/science/flame/MaestroInitData.cpp Exec/science/fully_convective_star/MaestroInitData.cpp Exec/science/plane_parallel_star/MaestroInitData.cpp Exec/science/rotating_star/MaestroInitData.cpp Exec/science/sub_chandra/MaestroInitData.cpp Exec/science/toy_convect/MaestroInitData.cpp Exec/science/urca/MaestroInitData.cpp Exec/science/xrb_mixed/MaestroInitData.cpp Exec/science/xrb_mixed/MaestroSponge.cpp Exec/test_problems/double_bubble/MaestroBaseState.cpp Exec/test_problems/double_bubble/MaestroInitData.cpp Exec/test_problems/incomp_shear_jet/MaestroBaseState.cpp Exec/test_problems/mach_jet/MaestroBaseState.cpp Exec/test_problems/mach_jet/MaestroInitData.cpp Exec/test_problems/rt/MaestroBaseState.cpp Exec/test_problems/test_convect/MaestroInitData.cpp Exec/test_problems/test_planar_diag/MaestroInitData.cpp Exec/test_problems/test_stability/MaestroInitData.cpp Exec/unit_tests/test_advect/MaestroBaseState.cpp Exec/unit_tests/test_advect/MaestroEvolve.cpp Exec/unit_tests/test_advect/MaestroInit.cpp Exec/unit_tests/test_advect/MaestroInitData.cpp Exec/unit_tests/test_average/MaestroBaseState.cpp Exec/unit_tests/test_average/MaestroEvolve.cpp Exec/unit_tests/test_average/MaestroInitData.cpp Exec/unit_tests/test_average/main.cpp Exec/unit_tests/test_basestate/MaestroAdvance.cpp Exec/unit_tests/test_basestate/MaestroDt.cpp Exec/unit_tests/test_basestate/MaestroInit.cpp Exec/unit_tests/test_basestate/MaestroInitData.cpp Exec/unit_tests/test_diffusion/MaestroBaseState.cpp Exec/unit_tests/test_diffusion/MaestroDt.cpp Exec/unit_tests/test_diffusion/MaestroInit.cpp Exec/unit_tests/test_projection/MaestroPlot.cpp Exec/unit_tests/test_react/MaestroBaseState.cpp Exec/unit_tests/test_react/MaestroInit.cpp commit 5fd329a5f0e6b0975afb581bfe2ada710cad983d Author: Doreen Fan Date: Thu Apr 23 14:24:20 2020 -0700 fix merge bugs Source/MaestroAdvectBase.cpp Source/MaestroBaseState.cpp Source/MaestroEnforceHSE.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeFlux.cpp commit ba98de5da3fe8a172949d5f8f999300df9f133ff Author: Alice Harpole Date: Thu Apr 23 16:53:35 2020 -0400 it compiles for reacting_bubble Source/BaseState.H Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroAdvectBase.cpp Source/MaestroCheckpoint.cpp Source/MaestroEnforceHSE.cpp Source/MaestroForce.cpp Source/MaestroMacProj.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakePsi.cpp Source/MaestroMakeS.cpp Source/MaestroMakew0.cpp Source/MaestroRegrid.cpp commit 292abe3a50b37198365a49e5336f43e0a654f87e Merge: a7d1d449 acb0a469 Author: Doreen Fan Date: Thu Apr 23 13:51:34 2020 -0700 Merge branch 'development' into base_state_class2 commit acb0a4697e2b8a31f1aede7be06a0c6e858888bc Merge: a6cb6c53 86e4a01b Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Thu Apr 23 13:36:30 2020 -0700 Merge pull request #186 from AMReX-Astro/base_state_geometry Base state geometry class commit 8af6480245e309068c847864b4117aa08b7f94f1 Merge: 0a848841 d861ad25 Author: Alice Harpole Date: Thu Apr 23 15:35:04 2020 -0400 merge with previous PR commit a7d1d449a0b623a41e7d95abb1e98bad25c6a8ea Merge: 38309aae d861ad25 Author: Doreen Fan Date: Thu Apr 23 11:45:01 2020 -0700 Merge branch 'base_state_class2' of https://github.com/AMReX-Astro/MAESTROeX into base_state_class2 Fixed merge conflicts commit a6cb6c53d54927f1b028ef9c138fa27ba4cd76bc Merge: 24a156ef cb5418fd Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Thu Apr 23 11:39:51 2020 -0700 Merge pull request #185 from AMReX-Astro/runtime_params Make runtime parameters be global variables commit 86e4a01b828978225667a38ce46234e9ec989d56 Merge: 0f429eec cb5418fd Author: Alice Harpole Date: Thu Apr 23 14:20:43 2020 -0400 merge with runtime_params commit d861ad25416bf606df049d3027bc95847f60032f Author: Alice Harpole Date: Thu Apr 23 14:15:57 2020 -0400 compiles and runs on GPU Source/MaestroMakeEdgeScalars.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeUtrans.cpp Source/MaestroPPM.cpp Source/MaestroVelPred.cpp commit 4157c7519de0f22103605ba5c3990480fbfa02b0 Author: Alice Harpole Date: Thu Apr 23 11:33:12 2020 -0400 wdconvect compiles and runs on the CPU Source/BaseState.H Source/BaseStateGeometry.H Source/BaseStateGeometry.cpp Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroCheckpoint.cpp Source/MaestroDt.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEdgeScalars.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakeUtrans.cpp Source/MaestroMakew0.cpp Source/MaestroPPM.cpp Source/MaestroRegrid.cpp Source/MaestroSetup.cpp Source/MaestroVelPred.cpp commit 08e467d14f9bafe53f0c09e0cb75f481811a1465 Merge: b765b468 cb5418fd Author: Alice Harpole Date: Thu Apr 23 07:55:43 2020 -0400 merging runtime parameters commit cb5418fd6cf2f77d52070d70f1b436b503d84067 Author: Alice Harpole Date: Thu Apr 23 07:46:57 2020 -0400 add maestro_declares.H and runparams_defaults.cpp Source/param_includes/maestro_declares.H Source/param_includes/runparams_defaults.cpp commit 24a156efb535c6b15991d4505668d8b8201e4213 Author: Max Katz Date: Thu Apr 23 03:05:52 2020 -0400 Add scaling plot script Exec/test_problems/reacting_bubble/scaling/sc20/plot.py commit 38309aae387c194001a33c4da1a76707e8c3f76b Merge: c4e49241 b765b468 Author: Doreen Fan Date: Wed Apr 22 17:14:22 2020 -0700 Merge branch 'base_state_class2' of https://github.com/AMReX-Astro/MAESTROeX into base_state_class2 Fixed merge conflicts commit b3f442135355689bf62bd6f5f66d3c047aca0b10 Author: Alice Harpole Date: Wed Apr 22 17:19:42 2020 -0400 make runtime parameters be global variables Source/Maestro.H Source/Maestro.cpp Source/MaestroEvolve.cpp Source/MaestroSetup.cpp Source/Make.package Source/param/_cpp_parameters Source/param/parse_maestro_params.py Source/param_includes/Make.package Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H commit b765b468dada5445f9d40624b606924869c202ff Author: Alice Harpole Date: Wed Apr 22 16:35:22 2020 -0400 need to fix runtime parameters before this works Exec/science/wdconvect/MaestroInitData.cpp Source/BaseStateGeometry.cpp Source/MaestroSetup.cpp commit afed66ee5a1e6e6d22aaac414501f97a172929d4 Author: Travis CI <> Date: Wed Apr 22 18:02:47 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh external/Microphysics commit 13a489e397d9d51b5d49f8435534a3ef3e6dc6c3 Author: Alice Harpole Date: Wed Apr 22 13:52:41 2020 -0400 reacting bubble compiles and runs Exec/test_problems/reacting_bubble/MaestroInitData.cpp Exec/test_problems/reacting_bubble/MaestroTagging.cpp Source/BaseState.H Source/BaseStateGeometry.cpp Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroAdvectBase.cpp Source/MaestroAverage.cpp Source/MaestroBaseState.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroCelltoEdge.cpp Source/MaestroCheckpoint.cpp Source/MaestroDebug.cpp Source/MaestroDensityAdvance.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroEnforceHSE.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroInitData.cpp Source/MaestroMacProj.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeFlux.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakePsi.cpp Source/MaestroMakeS.cpp Source/MaestroMakew0.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp Source/MaestroRegrid.cpp Source/MaestroRhoHT.cpp Source/MaestroSetup.cpp Source/MaestroSponge.cpp Source/MaestroTagging.cpp commit cc6449b3a7137ec65d357aa6da97da3f36f691bf Author: Alice Harpole Date: Wed Apr 22 11:37:01 2020 -0400 compiles for CPU Exec/science/sub_chandra/MaestroInitData.cpp Exec/science/wdconvect/MaestroInitData.cpp Exec/test_problems/reacting_bubble/MaestroTagging.cpp Source/BaseState.H Source/BaseStateGeometry.H Source/BaseStateGeometry.cpp Source/Maestro.H Source/MaestroAdvectBase.cpp Source/MaestroAverage.cpp Source/MaestroBaseState.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroCelltoEdge.cpp Source/MaestroDebug.cpp Source/MaestroDiag.cpp Source/MaestroEnforceHSE.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeFlux.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakePsi.cpp Source/MaestroMakeS.cpp Source/MaestroMakew0.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp Source/MaestroRegrid.cpp Source/MaestroSetup.cpp Source/MaestroSponge.cpp commit 25e93e86dac18cb0492a18473ab221f192b043c8 Author: Max Katz Date: Wed Apr 22 02:54:11 2020 -0400 Increase max_step Exec/test_problems/reacting_bubble/scaling/sc20/inputs_3d_x3 Exec/test_problems/reacting_bubble/scaling/sc20/inputs_3d_x4 Exec/test_problems/reacting_bubble/scaling/sc20/inputs_3d_x5 commit 58b75fbb03d3a51a83d1022d57b4153270bf17b9 Author: Max Katz Date: Tue Apr 21 21:45:31 2020 -0400 Update Microphysics submodule external/Microphysics commit 830f1bb9bfd44154c4a7af92d2f2807712e85cf8 Author: Max Katz Date: Tue Apr 21 21:44:17 2020 -0400 Update SC20 tests Exec/test_problems/reacting_bubble/scaling/sc20/cpu_submit.sh Exec/test_problems/reacting_bubble/scaling/sc20/cpu_submit2.sh Exec/test_problems/reacting_bubble/scaling/sc20/cpu_submit3.sh Exec/test_problems/reacting_bubble/scaling/sc20/cpu_submit4.sh Exec/test_problems/reacting_bubble/scaling/sc20/cpu_submit5.sh Exec/test_problems/reacting_bubble/scaling/sc20/gpu_submit.sh Exec/test_problems/reacting_bubble/scaling/sc20/gpu_submit2.sh Exec/test_problems/reacting_bubble/scaling/sc20/gpu_submit3.sh Exec/test_problems/reacting_bubble/scaling/sc20/gpu_submit4.sh Exec/test_problems/reacting_bubble/scaling/sc20/gpu_submit5.sh Exec/test_problems/reacting_bubble/scaling/sc20/inputs_3d Exec/test_problems/reacting_bubble/scaling/sc20/inputs_3d_x2 Exec/test_problems/reacting_bubble/scaling/sc20/run_script.sh Exec/test_problems/reacting_bubble/scaling/sc20/run_script2.sh Exec/test_problems/reacting_bubble/scaling/sc20/run_script3.sh Exec/test_problems/reacting_bubble/scaling/sc20/run_script4.sh Exec/test_problems/reacting_bubble/scaling/sc20/run_script5.sh commit c4e49241eda28aa2fec6e99d697156425ac486b1 Author: Doreen Fan Date: Tue Apr 21 11:39:38 2020 -0700 convert tests to use BaseStateArray Exec/science/code_comp/MaestroBaseState.cpp Exec/science/flame/MaestroBaseState.cpp Exec/science/xrb_mixed/MaestroSponge.cpp Exec/test_problems/double_bubble/MaestroBaseState.cpp Exec/test_problems/incomp_shear_jet/MaestroBaseState.cpp Exec/test_problems/mach_jet/MaestroBaseState.cpp Exec/test_problems/reacting_bubble/MaestroTagging.cpp Exec/test_problems/rt/MaestroBaseState.cpp Exec/test_problems/test_planar_diag/MaestroBaseState.cpp Exec/unit_tests/test_advect/MaestroEvolve.cpp Exec/unit_tests/test_average/MaestroBaseState.cpp Exec/unit_tests/test_diffusion/MaestroBaseState.cpp commit f6b5f64433eb1e31499c20971ab57f1f32862a13 Merge: d6aedcaa 0f429eec Author: Alice Harpole Date: Tue Apr 21 17:22:50 2020 -0400 started converting to use new basestatearray and basestategeometry classes commit 0f429eec0d028643fecd0ed3047938769162bed7 Author: Alice Harpole Date: Tue Apr 21 16:39:40 2020 -0400 added BaseStateGeometry routines to simulation code Source/BaseStateGeometry.H Source/BaseStateGeometry.cpp Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroInit.cpp Source/MaestroRegrid.cpp Source/MaestroSetup.cpp commit 823b2e1273fa5879303accff588495b1dfc53183 Author: Alice Harpole Date: Tue Apr 21 15:50:05 2020 -0400 move function implementation out of header file so it links properly Source/BaseState.H Source/BaseStateGeometry.H Source/BaseStateGeometry.cpp Source/Make.package commit 895fe60980c57c3134ac924bf75db78f35329875 Author: Alice Harpole Date: Tue Apr 21 14:13:32 2020 -0400 created a base state geometry class to store base state geometry data Source/BaseState.H Source/BaseStateGeometry.H Source/Maestro.H Source/MaestroBaseStateGeometry.cpp Source/Make.package commit d6aedcaa077f5f430bf3befcba54b17474782455 Merge: af6e5be8 a3236579 Author: Alice Harpole Date: Tue Apr 21 08:06:49 2020 -0400 merge with development commit 11473e81208fcf1dff2eb53938dd6bda0c788392 Author: Travis CI <> Date: Tue Apr 21 05:48:39 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroAdvectBase.cpp Source/MaestroDiag.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroMakeFlux.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakew0.cpp commit e782818bc12e1fde9308414b865ff0eb57b8acfa Author: Doreen Fan Date: Mon Apr 20 22:44:38 2020 -0700 convert to new BaseStateArray class Source/Maestro.H Source/MaestroAdvectBase.cpp Source/MaestroAverage.cpp Source/MaestroBaseState.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroCelltoEdge.cpp Source/MaestroDebug.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroEnforceHSE.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeFlux.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakePsi.cpp Source/MaestroMakeS.cpp Source/MaestroMakew0.cpp Source/MaestroPlot.cpp Source/MaestroRegrid.cpp Source/MaestroSponge.cpp commit d7b440143fdbb753552e79fd192628944bac0d00 Merge: 31ed3f79 a3236579 Author: Doreen Fan Date: Mon Apr 20 16:04:44 2020 -0700 Merge branch 'development' into base_state_class2 Fix merge conflicts commit a32365791956b5f7482e6533f4663a049414cb86 Merge: 77506741 68324a8b Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Mon Apr 20 15:53:33 2020 -0700 Merge pull request #184 from AMReX-Astro/base_state_array BaseStateArray struct commit 68324a8b2b9190466fb89aabb8b02d89a7b6f2d2 Author: Alice Harpole Date: Mon Apr 20 17:45:26 2020 -0400 add docstrings to BaseState class Source/BaseState.H sphinx_docs/source/base_state.rst commit 1fbbeb2f1a0ac2d61799c4cee44a6c0e39e89c64 Author: Alice Harpole Date: Mon Apr 20 17:39:01 2020 -0400 add base_state.rst docs sphinx_docs/source/base_state.rst sphinx_docs/source/index.rst commit 28f46de2d759c2f29c70c1931da60fa5cec4a8f5 Author: Alice Harpole Date: Mon Apr 20 16:56:23 2020 -0400 added BaseStateArray struct so that underlying data structure is accessed properly within lambdas Exec/unit_tests/test_new_basestate/main.cpp Source/BaseState.H commit 31ed3f796c1ed09661df9449ded03c5477dbd3ce Author: Travis CI <> Date: Thu Apr 16 19:27:31 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroMakew0.cpp commit 5421838fab66841abb42ab1050bdfb37e8d08145 Author: Doreen Fan Date: Thu Apr 16 12:27:46 2020 -0700 GPU fixes Source/Maestro.H Source/MaestroMakeGrav.cpp Source/MaestroMakew0.cpp commit 0a848841db7199a11d73ac2be6bc15f2df431b85 Merge: 1c5d780a af6e5be8 Author: Alice Harpole Date: Thu Apr 16 08:03:53 2020 -0400 merging with previous PR commit af6e5be85d5ae143f4cd2fee9776a975a5d66f6a Merge: 8491eba4 f1578751 Author: Alice Harpole Date: Wed Apr 15 17:30:30 2020 -0400 Merge branch 'base_state_class2' of github.com:AMReX-Astro/MAESTROeX into base_state_class2 commit 8491eba4b7a5d1f12da533c528007f2fc04f801b Author: Alice Harpole Date: Wed Apr 15 17:30:12 2020 -0400 (finally) fixed GPU bug by initializing the predicted edge state in AdvectBaseDens/Enthalpy Source/MaestroAdvectBase.cpp Source/MaestroMakeEdgeState.cpp commit f1578751b3f58cdfa7d10bc391d3ab2b5831d748 Author: Alice Harpole Date: Tue Apr 14 17:35:03 2020 -0400 fix MakeEdgeStateSphr Source/MaestroMakeEdgeState.cpp commit 520c1b796dc6e3de94ae49b7223eb9ca160e6ca1 Author: Travis CI <> Date: Tue Apr 14 21:24:20 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroDiag.cpp Source/MaestroInit.cpp commit 5aabcf3d76efaf1d422dfad8b3e617caab5cc152 Author: Doreen Fan Date: Tue Apr 14 14:23:30 2020 -0700 fix array access from IntVector to BaseState Source/MaestroAverage.cpp Source/MaestroDebug.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroEnforceHSE.cpp Source/MaestroRegrid.cpp Source/MaestroSponge.cpp commit 7f73dc5a2b37651d0ac13cd67d187cba61334f9a Merge: 70794546 14099bb9 Author: Doreen Fan Date: Tue Apr 14 13:06:11 2020 -0700 Merge branch 'base_state_class2' of https://github.com/AMReX-Astro/MAESTROeX into base_state_class2 commit 14099bb9eb3d598c7dcd3b38e986b8fc8b12e1f7 Merge: 6941e28d 77506741 Author: Alice Harpole Date: Tue Apr 14 11:46:05 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into base_state_class2 commit 1c5d780a687f374f903ca8e8342d394d092a2046 Merge: 2e6af097 77506741 Author: Alice Harpole Date: Tue Apr 14 08:59:42 2020 -0400 merge with development commit 2e6af0977407a881098457ccb789c9f0eed8f6bb Author: Alice Harpole Date: Tue Apr 14 08:55:31 2020 -0400 fix compilation Source/MaestroMakeEta.cpp Util/model_parser/ModelParser.cpp Util/simple_log/SimpleLog.cpp Util/utils/MaestroUtil.H Util/utils/MaestroUtil.cpp commit f301f085ab1d3bf5fced693a438c7c7d58aad2cc Author: Alice Harpole Date: Tue Apr 14 08:47:21 2020 -0400 fix compilation Source/MaestroMakeS.cpp commit 7750674199c9b4fb41fa69212f25c2e2d495c355 Author: Alice Harpole Date: Tue Apr 14 08:09:58 2020 -0400 add sc20 inputs and submit files Exec/test_problems/reacting_bubble/scaling/sc20/cpu_submit.sh Exec/test_problems/reacting_bubble/scaling/sc20/cpu_submit2.sh Exec/test_problems/reacting_bubble/scaling/sc20/cpu_submit3.sh Exec/test_problems/reacting_bubble/scaling/sc20/cpu_submit4.sh Exec/test_problems/reacting_bubble/scaling/sc20/cpu_submit5.sh Exec/test_problems/reacting_bubble/scaling/sc20/gpu_submit.sh Exec/test_problems/reacting_bubble/scaling/sc20/gpu_submit2.sh Exec/test_problems/reacting_bubble/scaling/sc20/gpu_submit3.sh Exec/test_problems/reacting_bubble/scaling/sc20/gpu_submit4.sh Exec/test_problems/reacting_bubble/scaling/sc20/gpu_submit5.sh Exec/test_problems/reacting_bubble/scaling/sc20/inputs_3d Exec/test_problems/reacting_bubble/scaling/sc20/inputs_3d_x2 Exec/test_problems/reacting_bubble/scaling/sc20/inputs_3d_x3 Exec/test_problems/reacting_bubble/scaling/sc20/inputs_3d_x4 Exec/test_problems/reacting_bubble/scaling/sc20/inputs_3d_x5 commit 70794546039f66f51022cee3428dc2a82503dc4d Author: Doreen Fan Date: Mon Apr 13 15:24:06 2020 -0700 code cleanup Source/MaestroBaseState.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroInit.cpp commit 27ed82e335e1bc471743b1397be3fd16fe224318 Author: Alice Harpole Date: Mon Apr 13 15:59:11 2020 -0400 static analysis warnings Exec/test_problems/reacting_bubble/MaestroInitData.cpp Source/BaseState.H Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvectBase.cpp Source/MaestroAverage.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroDiag.cpp Source/MaestroEnforceHSE.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeFlux.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakew0.cpp Source/MaestroRegrid.cpp Source/MaestroSetup.cpp Source/MaestroSponge.cpp Source/Maestro_F.H Source/Src_nd/average.F90 Source/Src_nd/base_state_geometry.F90 commit bcc9f2be926c41bb2437740e2cc2555c145cb473 Merge: b9bd366d c28f914c Author: Alice Harpole Date: Mon Apr 13 12:55:22 2020 -0400 Merge branch 'base_state_class5' of github.com:AMReX-Astro/MAESTROeX into base_state_class6 commit c28f914c31436c1fb4856267221e1c3f0bb477f6 Merge: a6adfa49 39b723ae Author: Alice Harpole Date: Mon Apr 13 12:55:00 2020 -0400 Merge branch 'base_state_class4' of github.com:AMReX-Astro/MAESTROeX into base_state_class5 commit 39b723ae7b5603df386929dfd0b159f7592f0188 Author: Alice Harpole Date: Mon Apr 13 12:54:43 2020 -0400 fixed bug in dr0 Source/MaestroAverage.cpp commit b9bd366daec7534d6dd886861a7f8627da4989cc Author: Alice Harpole Date: Fri Apr 10 17:20:59 2020 -0400 small diffs from reductions changing order Source/MaestroMakeEdgeState.cpp Source/MaestroMakeEta.cpp commit a7efb21f2493df2a489a6a4bedca732fe51073d1 Author: Alice Harpole Date: Fri Apr 10 17:10:35 2020 -0400 get rid of RealVectors and tidy up Source/Maestro.H Source/MaestroAverage.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroCelltoEdge.cpp Source/MaestroConvert.cpp Source/MaestroDt.cpp Source/MaestroFill3dData.cpp Source/MaestroMakeEdgeState.cpp commit 70aee862e76ee34b5f957c2fae07ba10badac2d8 Author: Alice Harpole Date: Fri Apr 10 16:52:58 2020 -0400 some cleaning up. Small diff because switched an Average from a RealVector to a BaseState Source/Maestro.H Source/MaestroAdvectBase.cpp Source/MaestroAdvection.cpp Source/MaestroAverage.cpp Source/MaestroBaseState.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroDensityAdvance.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroEnforceHSE.cpp Source/MaestroEvolve.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeFlux.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakePsi.cpp Source/MaestroMakeS.cpp Source/MaestroMakew0.cpp Source/MaestroPlot.cpp Source/MaestroReact.cpp Source/MaestroRegrid.cpp Source/MaestroSetup.cpp Source/MaestroSponge.cpp Source/Src_nd/Make.package Source/Src_nd/enforce_HSE.F90 Source/Src_nd/initdata.F90 commit 0a38537a7c0b237dac89a23478c88cb3c7dba0f9 Author: Alice Harpole Date: Fri Apr 10 16:14:13 2020 -0400 fixed spherical initdata bug Exec/science/ecsn/MaestroInitData.cpp Exec/science/fully_convective_star/MaestroInitData.cpp Exec/science/rotating_star/MaestroInitData.cpp Exec/science/sub_chandra/MaestroInitData.cpp Exec/science/urca/MaestroInitData.cpp Exec/science/wdconvect/MaestroInitData.cpp Exec/test_problems/reacting_bubble/MaestroInitData.cpp Source/BaseState.H Source/MaestroBaseState.cpp Source/MaestroFill3dData.cpp Source/MaestroInit.cpp Source/MaestroInitData.cpp Source/MaestroMakeEdgeState.cpp Util/model_parser/ModelParser.H commit cd7f369a7c11bae5be0ae9371a066dd70bf3ed7a Merge: eee126ce a6adfa49 Author: Alice Harpole Date: Fri Apr 10 09:04:04 2020 -0400 fixed MaestroBaseState.cpp problem files commit a6adfa49f7f70fe536660e6dc473cf2705b0935f Merge: 91410524 36fe5d9c Author: Alice Harpole Date: Fri Apr 10 08:47:47 2020 -0400 fixed MaestroBaseState.cpp problem files commit 36fe5d9c519ca446cc4f64b0a1d10872f61c83fe Author: Alice Harpole Date: Fri Apr 10 08:35:11 2020 -0400 fixed MaestroBaseState.cpp problem files Exec/science/code_comp/MaestroBaseState.cpp Exec/science/flame/MaestroBaseState.cpp Exec/test_problems/double_bubble/MaestroBaseState.cpp Exec/test_problems/incomp_shear_jet/MaestroBaseState.cpp Exec/test_problems/mach_jet/MaestroBaseState.cpp Exec/test_problems/rt/MaestroBaseState.cpp Exec/test_problems/test_planar_diag/MaestroBaseState.cpp Exec/unit_tests/test_advect/MaestroBaseState.cpp Exec/unit_tests/test_average/MaestroBaseState.cpp Exec/unit_tests/test_diffusion/MaestroBaseState.cpp Exec/unit_tests/test_react/MaestroBaseState.cpp commit eee126ce2149aff68affb9acee451c4c89dc8a00 Author: Alice Harpole Date: Fri Apr 10 08:28:04 2020 -0400 converted some problem files Exec/science/code_comp/MaestroBaseState.cpp Exec/science/code_comp/MaestroInitData.cpp Exec/science/ecsn/MaestroInitData.cpp Exec/science/flame/MaestroBaseState.cpp Exec/science/flame/MaestroInitData.cpp Exec/science/fully_convective_star/MaestroInitData.cpp Exec/science/plane_parallel_star/MaestroInitData.cpp Exec/science/rotating_star/MaestroInitData.cpp Exec/science/sub_chandra/MaestroInitData.cpp Exec/science/toy_convect/MaestroInitData.cpp Exec/science/urca/MaestroInitData.cpp Exec/science/wdconvect/MaestroInitData.cpp Exec/science/xrb_mixed/MaestroInitData.cpp Exec/test_problems/double_bubble/MaestroInitData.cpp Exec/test_problems/incomp_shear_jet/MaestroInitData.cpp Exec/test_problems/mach_jet/MaestroInitData.cpp Exec/test_problems/reacting_bubble/MaestroInitData.cpp Exec/test_problems/rt/MaestroInitData.cpp Exec/test_problems/test_convect/MaestroInitData.cpp Exec/test_problems/test_planar_diag/MaestroInitData.cpp Exec/test_problems/test_stability/MaestroInitData.cpp Source/Maestro.H Source/MaestroBaseState.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroInitData.cpp Source/MaestroSetup.cpp commit 6941e28dd36d92f787ac4818924c067139f259b8 Author: Doreen Fan Date: Thu Apr 9 17:02:07 2020 -0700 code cleanup Source/MaestroBaseStateGeometry.cpp commit d6f623b6ba367f5950d3aa2120634ac130aa3b8e Author: Doreen Fan Date: Thu Apr 9 16:24:01 2020 -0700 remove Fortran calls to numdisjointchunks Source/MaestroDebug.cpp Source/MaestroRegrid.cpp commit 25e4633529d122b62227942112d2f67a992fe97a Author: Alice Harpole Date: Thu Apr 9 17:20:11 2020 -0400 converted w0 Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroAdvectBase.cpp Source/MaestroCheckpoint.cpp Source/MaestroDiag.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeFlux.cpp Source/MaestroMakePsi.cpp Source/MaestroMakew0.cpp Source/MaestroPlot.cpp Source/MaestroSetup.cpp commit b9bb2e268cad4e60dca2f658169c292a110a6e65 Author: Doreen Fan Date: Thu Apr 9 12:20:19 2020 -0700 fix calls to BaseState data pointer Source/MaestroDebug.cpp Source/MaestroRegrid.cpp commit bfecc617f9f0ea50287a4a2488550f221de42826 Merge: e0a3f701 b3b19087 Author: Doreen Fan Date: Thu Apr 9 12:13:38 2020 -0700 Merge branch 'development' into base_state_class2 commit dfe604d4e52d5f643a8d14234cb3a566e6d88e1a Merge: 801679f5 b3b19087 Author: Alice Harpole Date: Thu Apr 9 14:45:40 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into base_state_class6 commit b3b19087ed89ac4b58da717e70dc19a5af14ad34 Author: Alice Harpole Date: Thu Apr 9 14:40:10 2020 -0400 fix GPU compilation Source/MaestroSponge.cpp commit 20813473bd602f196096b8bab0de3f430e4cad08 Merge: 67fcd8fa 5ab78b2d Author: Alice Harpole Date: Thu Apr 9 14:27:54 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 67fcd8fad9074b28ab45d01266ff5a9ef4fbafc7 Author: Alice Harpole Date: Thu Apr 9 14:27:34 2020 -0400 fix GPU compilation Util/model_parser/ModelParser.cpp Util/simple_log/SimpleLog.cpp Util/utils/MaestroUtil.H Util/utils/MaestroUtil.cpp commit 801679f503c21cc77748e95e5f0f1e9dcd56369f Author: Alice Harpole Date: Thu Apr 9 10:21:52 2020 -0400 converted w0_old Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroMakew0.cpp commit 3c9f6e5fa78e07d96bb150c262e7f356a5da8f69 Author: Alice Harpole Date: Thu Apr 9 09:49:40 2020 -0400 converted delta_gamma1_termbar Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroInit.cpp Source/MaestroMakeS.cpp commit caac582a2bdd0d2c139a45a172cc87a8e2e171b8 Author: Alice Harpole Date: Thu Apr 9 09:32:53 2020 -0400 removed delta_chi_w0 RealVector Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroInit.cpp Source/MaestroMakew0.cpp commit 3b66bea7fa34021b2e83ea64008f5c2ffe8f0c7d Author: Alice Harpole Date: Thu Apr 9 08:53:38 2020 -0400 convert w0_force Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroAdvection.cpp Source/MaestroDt.cpp Source/MaestroInit.cpp Source/MaestroMakew0.cpp Source/MaestroSetup.cpp Source/MaestroVelocityAdvance.cpp commit 1140fa783880b7d532feeef3f40c06eb94a6bd75 Author: Alice Harpole Date: Thu Apr 9 08:24:24 2020 -0400 fix merge Source/MaestroFill3dData.cpp commit 8729f059612ea112ddbd5b1b25673b17622e1cec Author: Alice Harpole Date: Thu Apr 9 08:23:40 2020 -0400 fix merge Source/MaestroFill3dData.cpp commit 91410524614a20e322b607c71b54b1d82b60e46a Merge: 5ced1227 75ef8563 Author: Alice Harpole Date: Thu Apr 9 08:23:06 2020 -0400 merge with development commit 75ef85631ced4f5d34b57f78fd1a6ad290a71a14 Merge: 6c89fe48 f7ea1390 Author: Alice Harpole Date: Thu Apr 9 08:21:44 2020 -0400 merge with development commit f7ea1390126153403ae000a971f30a4ee1f64f61 Merge: 9eae8234 5ab78b2d Author: Alice Harpole Date: Thu Apr 9 08:19:53 2020 -0400 merge with development commit 5ced122726059082536c61db91f0f31a898b60d5 Merge: 241ad0a2 5ab78b2d Author: Alice Harpole Date: Thu Apr 9 08:17:02 2020 -0400 merge with development commit e0a3f7012d5438de19cac7289c5f32586820559f Merge: 5d98c4c5 5ab78b2d Author: Doreen Fan Date: Wed Apr 8 15:20:55 2020 -0700 Merge branch 'development' into base_state_class2 Fixed merge conflicts commit 5ab78b2d32ba4b470aed51d006c0fca4d8331cc3 Merge: fe57a8d5 dd600aaf Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Wed Apr 8 15:11:03 2020 -0700 Merge pull request #176 from AMReX-Astro/base_state_class New base state class commit 241ad0a2c32d810b19735aa25f7602fa46c14d38 Author: Alice Harpole Date: Wed Apr 8 17:32:46 2020 -0400 made initdata problem files compatible with new BaseState Exec/science/code_comp/MaestroInitData.cpp Exec/science/ecsn/MaestroInitData.cpp Exec/science/flame/MaestroInitData.cpp Exec/science/fully_convective_star/MaestroInitData.cpp Exec/science/plane_parallel_star/MaestroInitData.cpp Exec/science/rotating_star/MaestroInitData.cpp Exec/science/sub_chandra/MaestroInitData.cpp Exec/science/toy_convect/MaestroInitData.cpp Exec/science/urca/MaestroInitData.cpp Exec/science/wdconvect/MaestroInitData.cpp Exec/science/xrb_mixed/MaestroInitData.cpp Exec/test_problems/double_bubble/MaestroInitData.cpp Exec/test_problems/incomp_shear_jet/MaestroInitData.cpp Exec/test_problems/mach_jet/MaestroInitData.cpp Exec/test_problems/reacting_bubble/MaestroInitData.cpp Exec/test_problems/rt/MaestroInitData.cpp Exec/test_problems/test_convect/MaestroInitData.cpp Exec/test_problems/test_planar_diag/MaestroInitData.cpp Exec/test_problems/test_stability/MaestroInitData.cpp Exec/unit_tests/test_advect/MaestroInit.cpp Exec/unit_tests/test_advect/MaestroInitData.cpp Exec/unit_tests/test_average/MaestroInitData.cpp Exec/unit_tests/test_basestate/MaestroInit.cpp Exec/unit_tests/test_basestate/MaestroInitData.cpp Exec/unit_tests/test_diffusion/MaestroInit.cpp Source/Maestro.H Source/MaestroInit.cpp Source/MaestroInitData.cpp commit 6aac2a4fc4e7cddb33ce604fb3c67710aea1a296 Author: Alice Harpole Date: Wed Apr 8 16:55:28 2020 -0400 fixed wdconvect Source/Maestro.H Source/MaestroFill3dData.cpp commit e9af06385b47fa7c73f07526b7baffe834bcda3e Merge: 82fbb400 fe57a8d5 Author: Alice Harpole Date: Wed Apr 8 16:45:22 2020 -0400 merge with development commit 82fbb400b80801d676a4d99864da9047a7908938 Author: Alice Harpole Date: Wed Apr 8 16:33:47 2020 -0400 diffs are entirely due to averaging of rho0_new and rho0_old Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroInit.cpp Source/MaestroRegrid.cpp commit 6c89fe48eeffe2ba902a4c823438797c9c047025 Merge: 3b36278c 9eae8234 Author: Alice Harpole Date: Wed Apr 8 08:32:57 2020 -0400 Merge branch 'base_state_class3' of github.com:AMReX-Astro/MAESTROeX into base_state_class4 commit 9eae8234835828d2af80f6904da8b2960296b695 Author: Alice Harpole Date: Wed Apr 8 08:30:40 2020 -0400 fix indexing in MaestroRegrid Source/MaestroRegrid.cpp commit f5921cd02c3733162cee76f2c1bdc02821cdc49c Merge: 1badc8ec 3b36278c Author: Alice Harpole Date: Wed Apr 8 08:27:55 2020 -0400 merging with development commit dd600aaf7d7b4527fb6b9744bcd383d5dfe335bc Merge: 35ebc7a1 fe57a8d5 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Tue Apr 7 20:27:27 2020 -0700 Merge branch 'development' into base_state_class commit fe57a8d599cccb5da6e9f85bfcd87366b8f2b23a Merge: fbf32696 4051c5b6 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Tue Apr 7 20:25:23 2020 -0700 Merge pull request #174 from AMReX-Astro/cpp_init Convert initdata to C++ commit 4051c5b6f0b977dc8980cc0f13aa96aef10a1dff Author: Travis CI <> Date: Wed Apr 8 01:22:46 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroMakeEdgeState.cpp commit cfd90d795746569c4d1711dc8a9da41c2438f9fb Merge: ce1bdc67 791359ad Author: Doreen Fan Date: Tue Apr 7 18:22:22 2020 -0700 Merge branch 'cpp_init' of https://github.com/AMReX-Astro/MAESTROeX into cpp_init commit ce1bdc67b1bd8db0f4f6528f5b2ebce9724ce716 Author: Doreen Fan Date: Tue Apr 7 17:34:46 2020 -0700 more travis clang static fixes Source/MaestroAverage.cpp Source/MaestroEnforceHSE.cpp Source/MaestroFill3dData.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakew0.cpp commit 791359adef11604f616b416b4737fd6ee348344b Author: Travis CI <> Date: Wed Apr 8 00:34:23 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroMakeEdgeState.cpp commit b1e212ed4e5330db20d244b118a948895cce8e6b Author: Doreen Fan Date: Tue Apr 7 17:34:46 2020 -0700 more travis clang static fixes Source/MaestroAverage.cpp Source/MaestroEnforceHSE.cpp Source/MaestroFill3dData.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEdgeState.cpp commit 36f1f5a29c8428d98d7f542a133368e1394621d8 Author: Travis CI <> Date: Tue Apr 7 23:44:49 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroDt.cpp Source/MaestroMakeEdgeState.cpp commit b66dc180f461845d26545a704e12efb900a21c29 Author: Doreen Fan Date: Tue Apr 7 16:45:07 2020 -0700 fix some travis clang static errors Source/MaestroAverage.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroFill3dData.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroSponge.cpp commit ae01f7bc70980a2ffa8c2e60c0fa4d08e6187771 Merge: d4d8b8b5 fbf32696 Author: Doreen Fan Date: Tue Apr 7 15:34:01 2020 -0700 Merge branch 'development' into cpp_init commit 3b36278c02da544bc260fb761b1871de139ca6cb Author: Alice Harpole Date: Tue Apr 7 17:49:26 2020 -0400 fix rhoh0_halftime Source/MaestroRhoHT.cpp commit 1badc8ecc997014f6d7a8d01d5759c09a40057c1 Author: Alice Harpole Date: Tue Apr 7 17:43:39 2020 -0400 converted rho0_old and rho0_new Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroAdvectBase.cpp Source/MaestroBaseState.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroCheckpoint.cpp Source/MaestroDensityAdvance.cpp Source/MaestroDiag.cpp Source/MaestroEnforceHSE.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroEvolve.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeFlux.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakeS.cpp Source/MaestroMakew0.cpp Source/MaestroPlot.cpp Source/MaestroRegrid.cpp Source/MaestroRhoHT.cpp Source/MaestroSetup.cpp Source/MaestroSponge.cpp Source/MaestroVelocityAdvance.cpp commit e331ae5bdaf50e358cfa4bfb2876380bada6b557 Author: Alice Harpole Date: Tue Apr 7 16:06:58 2020 -0400 converted p0_init Source/Maestro.H Source/MaestroBaseState.cpp Source/MaestroInit.cpp Source/MaestroSetup.cpp commit 5036cd845596151e09b5d06de7fb69007772272a Author: Alice Harpole Date: Tue Apr 7 15:56:04 2020 -0400 converted tempbar Source/Maestro.H Source/MaestroBaseState.cpp Source/MaestroInit.cpp Source/MaestroReact.cpp Source/MaestroSetup.cpp commit c4871e863f8ab91aea78ca853c1c7444f972090a Author: Alice Harpole Date: Tue Apr 7 13:54:22 2020 -0400 converted Sbar Source/BaseState.H Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroInit.cpp Source/MaestroMakePsi.cpp Source/MaestroMakeS.cpp Source/MaestroMakew0.cpp commit 35ebc7a1e086ecc0924e4611788fd69a7f2e4e3c Merge: 52f7accb fbf32696 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Mon Apr 6 20:07:37 2020 -0700 Merge branch 'development' into base_state_class commit b42c768b77d59ca9c956c5ebbb27ec0efb2a5da9 Author: Alice Harpole Date: Mon Apr 6 17:18:49 2020 -0400 ditto for planar Source/MaestroAverage.cpp commit 1fac9659036d9e52dff1f4723918bf14203c1b81 Author: Alice Harpole Date: Mon Apr 6 17:13:53 2020 -0400 switched RealVectors in Average to BaseStates - output is changed as reduction now done in a different order Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroAverage.cpp Source/MaestroGamma.cpp Source/MaestroInit.cpp Source/MaestroRegrid.cpp commit e5ce512d648e1b8a446b1db0134705aec19b3ea1 Merge: 77ac9f8c fbf32696 Author: Alice Harpole Date: Mon Apr 6 15:18:35 2020 -0400 convert gradp0 commit fbf326967375c49573db07c07df5b630bf5669fc Author: Alice Harpole Date: Mon Apr 6 15:13:41 2020 -0400 fix indexing in gradp0 for spherical Source/MaestroMakeS.cpp commit 77ac9f8cdd815bfec4cd4047769e394d8acd2b8f Author: Alice Harpole Date: Mon Apr 6 15:06:28 2020 -0400 converted p0_old and p0_new Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroBaseState.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroEnforceHSE.cpp Source/MaestroEvolve.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroInit.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakePsi.cpp Source/MaestroMakeS.cpp Source/MaestroMakew0.cpp Source/MaestroPlot.cpp Source/MaestroReact.cpp Source/MaestroRhoHT.cpp Source/MaestroSetup.cpp Source/MaestroThermal.cpp commit 285d87da1380145b4fb0594daba0203f55e8bd3d Merge: 7a7bc72b 26a4d5b9 Author: Alice Harpole Date: Mon Apr 6 11:56:18 2020 -0400 merging with development commit 26a4d5b94a60ac744e5b1b972cb984f28cd7b00d Merge: bb56a241 507afa6b Author: Alice Harpole Date: Mon Apr 6 11:55:24 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit bb56a241c2eb05e2ef457c2fb8729e0c89090ac4 Author: Alice Harpole Date: Mon Apr 6 11:55:13 2020 -0400 fix indexing for bottom and top edge cases for planar gradp0 Source/MaestroMakeS.cpp commit d4d8b8b58a46a8d2547342f3d40dc0d253eb0a80 Merge: 76ec42d7 507afa6b Author: Doreen Fan Date: Fri Apr 3 13:28:41 2020 -0700 Merge branch 'development' into cpp_init Fixed merge conflicts commit 76ec42d7fa80c73b9b4d7aac3a18078480f11a75 Author: Doreen Fan Date: Fri Apr 3 13:27:23 2020 -0700 convert initdata to C++ for sub_chandra Exec/science/sub_chandra/MaestroInitData.cpp Exec/science/sub_chandra/initdata.F90 commit 354098351613b29f175dd2de39c33e95dde2a70c Author: Doreen Fan Date: Fri Apr 3 13:20:44 2020 -0700 uncomment normk Exec/science/ecsn/MaestroInitData.cpp Exec/science/rotating_star/MaestroInitData.cpp Exec/science/urca/MaestroInitData.cpp commit 7a7bc72b2e29be49da53089273d822baa31b7a47 Author: Alice Harpole Date: Fri Apr 3 15:45:52 2020 -0400 converted rhoh0_old and rhoh0_new Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroAdvectBase.cpp Source/MaestroBaseState.cpp Source/MaestroConvert.cpp Source/MaestroDensityAdvance.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroEvolve.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeFlux.cpp Source/MaestroPlot.cpp Source/MaestroRegrid.cpp Source/MaestroRhoHT.cpp Source/MaestroSetup.cpp commit 507afa6b385400c262aa29d0d6fac086688a8d9c Author: Andy Nonaka Date: Fri Apr 3 10:10:59 2020 -0700 submodule documentation in Getting Started sphinx_docs/source/getting_started.rst commit 2b930f51191bfbd303c6087728e5f6e63e298471 Author: Andy Nonaka Date: Fri Apr 3 09:32:56 2020 -0700 change the default behavior to use the Microphysics submodule, unless you have a global environment variable for MICROPHYSICS_HOME pointing elsewhere if the submodule hasn't been initialized, throw an error message with instructions on how to Exec/science/code_comp/GNUmakefile Exec/science/ecsn/GNUmakefile Exec/science/flame/GNUmakefile Exec/science/fully_convective_star/GNUmakefile Exec/science/plane_parallel_star/GNUmakefile Exec/science/rotating_star/GNUmakefile Exec/science/sub_chandra/GNUmakefile Exec/science/toy_convect/GNUmakefile Exec/science/urca/GNUmakefile Exec/science/wdconvect/GNUmakefile Exec/science/xrb_mixed/GNUmakefile Exec/test_problems/double_bubble/GNUmakefile Exec/test_problems/incomp_shear_jet/GNUmakefile Exec/test_problems/mach_jet/GNUmakefile Exec/test_problems/reacting_bubble/GNUmakefile Exec/test_problems/rt/GNUmakefile Exec/test_problems/test_convect/GNUmakefile Exec/test_problems/test_planar_diag/GNUmakefile Exec/test_problems/test_stability/GNUmakefile Exec/unit_tests/test_advect/GNUmakefile Exec/unit_tests/test_average/GNUmakefile Exec/unit_tests/test_basestate/GNUmakefile Exec/unit_tests/test_diffusion/GNUmakefile Exec/unit_tests/test_eos/GNUmakefile Exec/unit_tests/test_projection/GNUmakefile Exec/unit_tests/test_react/GNUmakefile Util/diagnostics/GNUmakefile commit ffbd1a9d7f542f319905632ff7aff3e6c516be70 Author: Alice Harpole Date: Fri Apr 3 09:08:30 2020 -0400 converted grav_cell_old and grav_cell_new Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroEnforceHSE.cpp Source/MaestroEvolve.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakePsi.cpp Source/MaestroPlot.cpp Source/MaestroSetup.cpp Source/MaestroVelocityAdvance.cpp commit a8ede76b7d39d006313c3233eb695af2204af2f0 Author: Doreen Fan Date: Thu Apr 2 16:18:42 2020 -0700 April 2020 second release notes CHANGES.md commit 50cf68b5019bb79bace341fd134d2d2c1b67485a Author: Doreen Fan Date: Thu Apr 2 16:11:45 2020 -0700 Update Microphysics to release 20.04 external/Microphysics commit 1647f048572e8b4a3c0bc35a31d3a26a495e95af Author: Alice Harpole Date: Thu Apr 2 17:42:25 2020 -0400 converted gamma1bar_old and gamma1bar_new Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroDt.cpp Source/MaestroEvolve.cpp Source/MaestroGamma.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakePsi.cpp Source/MaestroMakeS.cpp Source/MaestroMakew0.cpp Source/MaestroPlot.cpp Source/MaestroSetup.cpp commit 880c203bc4da6b048918809bfe222faed38d1c98 Author: Alice Harpole Date: Thu Apr 2 16:39:40 2020 -0400 delete redundant RealVector functions Source/Maestro.H Source/MaestroMacProj.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeS.cpp commit c6123d84beef414a1a819cf776976c3623e28e2d Author: Alice Harpole Date: Thu Apr 2 16:23:26 2020 -0400 Finally got beta0 working Source/BaseState.H Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroCelltoEdge.cpp Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp Source/MaestroSetup.cpp commit 32380b6d8a0329102a365ee1e0bb69d69632eaae Author: Doreen Fan Date: Mon Mar 30 20:30:53 2020 -0700 changes to some initdata subroutines to more closely match previous values Exec/science/code_comp/MaestroInitData.cpp Exec/science/fully_convective_star/MaestroInitData.cpp Exec/science/plane_parallel_star/MaestroInitData.cpp Exec/science/toy_convect/MaestroInitData.cpp Exec/science/xrb_mixed/MaestroInitData.cpp Exec/test_problems/test_convect/MaestroInitData.cpp Exec/test_problems/test_planar_diag/MaestroInitData.cpp Exec/unit_tests/test_projection/initdata.F90 commit 106d3d6ce5c1900c8516bd06dc6de2854a90a6ea Merge: bda189af 1438cc2a Author: Doreen Fan Date: Wed Apr 1 13:09:02 2020 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit bda189af39390fc09bb0ebb8321971b9d7688fd7 Author: Doreen Fan Date: Wed Apr 1 13:07:17 2020 -0700 April 2020 release notes CHANGES.md commit 581fe892179b1986751b9747667ab935747ad330 Merge: ec5c6bc4 1438cc2a Author: Alice Harpole Date: Wed Apr 1 14:33:13 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into base_state_class3 commit 1438cc2a1054443c50b84569b1beb6a2584004b8 Merge: 384009ac c12489ad Author: Alice Harpole Date: Wed Apr 1 14:32:43 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 384009ace4df823d513c54a5f3bd61af06c73f68 Author: Alice Harpole Date: Wed Apr 1 14:32:39 2020 -0400 remove MaestroMacProj_level.cpp Source/MaestroMacProj_level.cpp commit ec5c6bc4c5ace6aafe94d8424acecb292db36d72 Author: Alice Harpole Date: Wed Apr 1 11:39:11 2020 -0400 converted etarho_cc and etarho_ec Source/BaseState.H Source/Maestro.H Source/MaestroInit.cpp Source/MaestroMakeEta.cpp Source/MaestroMakePsi.cpp Source/MaestroMakew0.cpp Source/MaestroSetup.cpp commit 73885dfb345337b752b868dc207712e7c1c8a722 Author: Alice Harpole Date: Wed Apr 1 10:00:08 2020 -0400 actually converted psi Source/Maestro.H Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroAdvectBase.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroMakePsi.cpp Source/MaestroMakeS.cpp Source/MaestroRegrid.cpp Source/MaestroSetup.cpp commit 743a77d14bd1c21e54d6a6fbdca4bae8b6b47dc0 Author: Alice Harpole Date: Wed Apr 1 09:54:15 2020 -0400 & signs are important Source/BaseState.H Source/Maestro.H Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroAdvectBase.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroMakePsi.cpp Source/MaestroMakeS.cpp Source/MaestroRegrid.cpp Source/MaestroSetup.cpp commit af4f3a8b53f2b144ad5712d357cf706a11871b3e Author: Alice Harpole Date: Wed Apr 1 08:06:18 2020 -0400 make eta Source/MaestroMakeEta.cpp commit 288b51bde8b78a96196e4ca976c20ad50aac006e Author: Alice Harpole Date: Wed Apr 1 07:49:12 2020 -0400 Revert "converted psi" This reverts commit 9bc56bd7b45d1f0bd07e5d836e4919a832cf91c5. Source/BaseState.H Source/Maestro.H Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroAdvectBase.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroMakeEta.cpp Source/MaestroMakePsi.cpp Source/MaestroMakew0.cpp Source/MaestroSetup.cpp commit c12489adb9a79f47eaf2a99f23b7f16765bd1d7b Author: Doreen Fan Date: Tue Mar 31 23:05:58 2020 -0700 some compile fixes for unit_test Exec/unit_tests/test_advect/MaestroInit.cpp Exec/unit_tests/test_average/MaestroEvolve.cpp Exec/unit_tests/test_basestate/MaestroAdvance.cpp Exec/unit_tests/test_basestate/MaestroInit.cpp Exec/unit_tests/test_diffusion/MaestroInit.cpp Exec/unit_tests/test_react/MaestroInit.cpp commit 9bc56bd7b45d1f0bd07e5d836e4919a832cf91c5 Author: Alice Harpole Date: Tue Mar 31 10:40:02 2020 -0400 converted psi Source/BaseState.H Source/Maestro.H Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroAdvectBase.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroMakeEta.cpp Source/MaestroMakePsi.cpp Source/MaestroMakew0.cpp Source/MaestroSetup.cpp commit 15722162248b7b5ddb02ca6c437f9bff8d9668ab Author: Alice Harpole Date: Mon Mar 30 17:54:06 2020 -0400 BaseState-ified Makew0 Source/Maestro.H Source/MaestroAdvectBase.cpp Source/MaestroForce.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakew0.cpp commit 8a1ad2fca93f81810170ff15325f1a97c5558bdf Author: Alice Harpole Date: Mon Mar 30 17:07:26 2020 -0400 BaseState-ified EnforceHSE Source/BaseState.H Source/Maestro.H Source/MaestroDebug.cpp Source/MaestroDiag.cpp Source/MaestroEnforceHSE.cpp Source/MaestroMakeGrav.cpp Source/MaestroRegrid.cpp commit 33d284174801220f6321adf0d4082986357acd12 Merge: f95bee21 673a650d Author: Doreen Fan Date: Mon Mar 30 13:48:40 2020 -0700 Merge branch 'development' into cpp_init commit 9058bc1bc1bce958b73e3a7558680b07c04b7bcf Merge: 5d98c4c5 673a650d Author: Alice Harpole Date: Mon Mar 30 15:32:20 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into base_state_class2 commit 673a650d5e3d9cc7ff367ce564c5eebe2d841a85 Author: Alice Harpole Date: Mon Mar 30 15:31:35 2020 -0400 Convert debug. diag and tagging routines to C++ (#173) This converts the debug, diagnostics and tagging routines to C++. It does not depend on any previous PRs and should not change the output. Note that by default all routines will now use the tagging routines defined in MaestroTagging.cpp, and they do not need to create a local copy for tagging to work. A local copy is now only needed if problem-specific customizations are required. Exec/science/ecsn/MaestroTagging.cpp Exec/science/ecsn/tagging.F90 Exec/science/fully_convective_star/MaestroTagging.cpp Exec/science/fully_convective_star/tagging.F90 Exec/science/plane_parallel_star/tagging.F90 Exec/science/rotating_star/MaestroTagging.cpp Exec/science/rotating_star/tagging.F90 Exec/science/urca/MaestroTagging.cpp Exec/science/urca/tagging.F90 Exec/science/wdconvect/MaestroTagging.cpp Exec/science/wdconvect/tagging.F90 Exec/test_problems/double_bubble/tagging.F90 Exec/test_problems/incomp_shear_jet/tagging.F90 Exec/test_problems/reacting_bubble/MaestroTagging.cpp Exec/test_problems/reacting_bubble/tagging.F90 Exec/test_problems/rt/tagging.F90 Exec/test_problems/test_convect/tagging.F90 Source/Maestro.H Source/MaestroDebug.cpp Source/MaestroDiag.cpp Source/MaestroEvolve.cpp Source/MaestroRegrid.cpp Source/MaestroTagging.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/Make.package Source/Src_nd/debug.F90 Source/Src_nd/diag.F90 Source/Src_nd/regrid.F90 Source/Src_nd/tagging.F90 commit 5d98c4c530e8e88247c266fbc49c37b7bfa428a0 Author: Alice Harpole Date: Mon Mar 30 15:04:58 2020 -0400 GPU fix Source/Maestro.H Source/MaestroMakew0.cpp commit 359a775c0d94d72d2b31e505fff157afce4bb0ff Author: Alice Harpole Date: Mon Mar 30 14:47:44 2020 -0400 BaseState-ified DensityAdvance Source/BaseState.H Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroAdvectBase.cpp Source/MaestroDensityAdvance.cpp Source/MaestroForce.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeFlux.cpp commit a874cc7ce22a48426905f72b6364e7d2b602c0ca Author: Alice Harpole Date: Mon Mar 30 12:55:18 2020 -0400 added basestate versions of put1darrayoncart and makes0mac Source/Maestro.H Source/MaestroCelltoEdge.cpp Source/MaestroFill3dData.cpp Source/MaestroMakeBeta0.cpp commit 6d94e6607f262a60909c7c4fb9918902ada9fe5b Author: Alice Harpole Date: Mon Mar 30 09:11:14 2020 -0400 cleaning up Source/Maestro.H Source/MaestroAdvectBase.cpp Source/MaestroAverage.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroCelltoEdge.cpp Source/MaestroDt.cpp Source/MaestroEnforceHSE.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakePsi.cpp Source/MaestroMakew0.cpp Source/MaestroSetup.cpp Source/MaestroSponge.cpp commit 2321ee1b82eb683015e709bcf4c5d6d5cc84e905 Merge: 4e0aa927 63d6ad45 Author: Alice Harpole Date: Mon Mar 30 08:32:24 2020 -0400 merging with development commit 4e0aa927ea3dd28440c808c958305d4fc2dbe29e Author: Alice Harpole Date: Mon Mar 30 08:21:52 2020 -0400 fix center Source/MaestroBaseStateGeometry.cpp commit f95bee215081b7676e814858c055ed4eda3e274a Merge: d4cca200 63d6ad45 Author: Doreen Fan Date: Fri Mar 27 15:32:52 2020 -0700 Merge branch 'development' into cpp_init Fixed merge conflicts commit 63d6ad45f55c1914dfa6b9b23e909b8aa13e95e7 Merge: 8fb4005e 57cd48e7 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Fri Mar 27 14:47:51 2020 -0700 Merge pull request #161 from AMReX-Astro/cpp_average Convert average routines to C++ commit bd0ccdc142611e4478265271f4f125f04ce8adc3 Author: Alice Harpole Date: Fri Mar 27 17:09:33 2020 -0400 BaseState-ified some more RealVectors in Makew0.cpp Source/Maestro.H Source/MaestroBaseStateGeometry.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakew0.cpp commit 57cd48e7f41da30dc1885371a7ef4ba64065a4b2 Author: Doreen Fan Date: Fri Mar 27 14:09:11 2020 -0700 fix center variable assignment Source/MaestroAverage.cpp Source/MaestroFill3dData.cpp commit 13f8057f456293b2f9d4f07386556c368769e5e4 Author: Travis CI <> Date: Fri Mar 27 20:48:25 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroVelPred.cpp commit 3a1fd6dc8e3ac10d1d2f3f53b169076b712ea047 Merge: 4fd7974f 8426a5ce Author: Doreen Fan Date: Fri Mar 27 13:48:05 2020 -0700 Merge branch 'development' into cpp_average Fixed merge conflicts commit 34e40785f5575d72efa41367452fe1a0977b3a9d Merge: 905e9723 8fb4005e Author: Alice Harpole Date: Fri Mar 27 16:36:08 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into base_state_class2 commit 8fb4005e4f721ad25d3ada814d5fda48db71a51b Author: Alice Harpole Date: Fri Mar 27 16:34:58 2020 -0400 fix center in MaestroSponge.cpp Source/MaestroSponge.cpp commit 905e9723356422c5b4e11955631bcac0156cbdb6 Merge: cf622ca4 c496d1b4 Author: Alice Harpole Date: Fri Mar 27 16:32:30 2020 -0400 merging with development commit 4fd7974fc6622d4c721b83e27b97733a73e1c48c Merge: 340a864f aaf1e4aa Author: Doreen Fan Date: Fri Mar 27 13:30:38 2020 -0700 Merge branch 'cpp_average' of https://github.com/AMReX-Astro/MAESTROeX into cpp_average commit cf622ca4069b776378b42f8fa34aab38f9f6ecf7 Author: Alice Harpole Date: Fri Mar 27 16:28:17 2020 -0400 BaseState-ified some RealVectors in Makew0.cpp Source/BaseState.H Source/Maestro.H Source/MaestroMakeEdgeState.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakew0.cpp commit c496d1b49c207c50efc90f8d7345e13909b4ebbf Merge: 8426a5ce 39d9f38d Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Fri Mar 27 13:26:40 2020 -0700 Merge pull request #172 from AMReX-Astro/cpp_dt_force Convert timestep, mktempforce and sponge to C++ commit 39d9f38daa81aa0ae6e175fc55dbffb644900e83 Merge: 13e8a6b0 8426a5ce Author: Doreen Fan Date: Fri Mar 27 13:27:39 2020 -0700 Merge branch 'development' into cpp_dt_force Fixed merge conflicts commit d4cca2003a0e57413ea1d6d1e48f36c90c922c0b Author: Doreen Fan Date: Fri Mar 27 13:24:16 2020 -0700 ecsn and urca compile with ignition_simple network. Both still can't compile with their appropriate networks. Exec/science/ecsn/MaestroInitData.cpp Exec/science/urca/MaestroInitData.cpp commit 752a2963affbfab0f5ad8b9c36a6fb73d72e7035 Author: Alice Harpole Date: Fri Mar 27 14:20:10 2020 -0400 BaseState-ified nr, dr Source/Maestro.H Source/MaestroAdvectBase.cpp Source/MaestroBaseState.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroCelltoEdge.cpp Source/MaestroEnforceHSE.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakePsi.cpp Source/MaestroMakew0.cpp Source/MaestroPlot.cpp commit a35631dcf9dae3c0f6406c188eba92f9dda18b6a Merge: 3547cb40 8426a5ce Author: Doreen Fan Date: Fri Mar 27 10:50:15 2020 -0700 Merge branch 'development' into cpp_init commit 3547cb40497f287e45641335866a540768b8ab6c Author: Doreen Fan Date: Fri Mar 27 10:49:35 2020 -0700 small changes to initdata for wdconvect Exec/science/wdconvect/MaestroInitData.cpp commit 374fbf44749eaa2d544b4f128307a21fa3668641 Author: Alice Harpole Date: Fri Mar 27 13:41:15 2020 -0400 BaseState-ified cutoff_density_coords Source/Maestro.H Source/MaestroBaseStateGeometry.cpp Source/MaestroEnforceHSE.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakePsi.cpp Source/MaestroMakeS.cpp commit fea607654c27ccaa9085d31f8b3e19d61cd8a658 Author: Alice Harpole Date: Fri Mar 27 13:23:28 2020 -0400 BaseState-ified r_start_coord, r_end_coord and numdisjointchunks Source/BaseState.H Source/Maestro.H Source/MaestroAdvectBase.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroCelltoEdge.cpp Source/MaestroEnforceHSE.cpp Source/MaestroInit.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakePsi.cpp Source/MaestroMakew0.cpp Source/MaestroRegrid.cpp Source/MaestroSetup.cpp commit 0b9e5134606060882f827b3e0aa97844d8453457 Merge: c706e678 8426a5ce Author: Alice Harpole Date: Fri Mar 27 11:38:02 2020 -0400 merging with development commit 8426a5ced9054972fd1336eca5d9e5c05ea4e806 Author: Alice Harpole Date: Fri Mar 27 11:37:08 2020 -0400 GPU fix Source/MaestroFill3dData.cpp commit c706e6789ab58e3bd9aa7c42ffb59403bc09041b Author: Alice Harpole Date: Fri Mar 27 09:37:52 2020 -0400 BaseState'ified r_cc_loc and r_edge_loc Source/MaestroAdvectBase.cpp Source/MaestroBaseState.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroEnforceHSE.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakePsi.cpp Source/MaestroMakeS.cpp Source/MaestroMakew0.cpp Source/MaestroPlot.cpp commit 1a30f398339b16a9989c4df37c45a03f9ab57ec8 Merge: eba1787a 38413f06 Author: Doreen Fan Date: Thu Mar 26 14:44:24 2020 -0700 Merge branch 'development' into cpp_init commit 22fa3498ebf954c4b020b575e7051092e039064c Merge: dbdd1efd 38413f06 Author: Alice Harpole Date: Thu Mar 26 17:31:10 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into base_state_class2 commit 38413f06cfee5797fe25d54aecbb912285f5680e Author: Alice Harpole Date: Thu Mar 26 17:26:33 2020 -0400 growntilebox -> grow(tilebox) Source/MaestroMakeUtrans.cpp commit dbdd1efd0d6f3cb0ca43ff38c148ac4d1e3a5166 Author: Alice Harpole Date: Thu Mar 26 16:42:45 2020 -0400 started testing out new base state in code Source/BaseState.H Source/Maestro.H Source/MaestroAdvectBase.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroMakeGrav.cpp Source/MaestroSetup.cpp commit 58a1f6bf28af9596811b4601a3c75dc759f6087b Merge: 52f7accb 8feb4e05 Author: Alice Harpole Date: Thu Mar 26 16:11:16 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into base_state_class commit 52f7accb70d8287638bfa30de0acde7ffe6ef779 Author: Alice Harpole Date: Thu Mar 26 15:47:25 2020 -0400 added a constructor that converts existing Fortran-ordered base state Vectors into C++-ordered BaseState objects Exec/unit_tests/test_new_basestate/main.cpp Source/BaseState.H commit e238475c93d68cfb14a00c0d577cda4bd3c4c376 Author: Alice Harpole Date: Thu Mar 26 15:08:21 2020 -0400 now works on the GPU Exec/unit_tests/test_new_basestate/main.cpp Source/BaseState.H commit 4834f175c5bcaba83224e8ace10a98d730609f9d Author: Alice Harpole Date: Thu Mar 26 12:47:28 2020 -0400 trying to debug memory access issues Exec/unit_tests/test_new_basestate/main.cpp Source/BaseState.H commit eba1787ab2af3425dff92a4f59ed39801bd7f79b Author: Travis CI <> Date: Wed Mar 25 23:45:33 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/Maestro.H commit b4a396d3e1eed88002200a2683418e57666237af Merge: 4b5cfe89 f44f2355 Author: Doreen Fan Date: Wed Mar 25 16:44:58 2020 -0700 Merge branch 'cpp_init' of https://github.com/AMReX-Astro/MAESTROeX into cpp_init commit 4b5cfe89f516f520f26d6598d96aa69c80bc84c1 Author: Doreen Fan Date: Wed Mar 25 16:44:33 2020 -0700 fixes to get all tests to compile Exec/science/code_comp/MaestroInitData.cpp Exec/science/flame/MaestroInitData.cpp Exec/science/fully_convective_star/MaestroInitData.cpp Exec/science/plane_parallel_star/MaestroInitData.cpp Exec/science/rotating_star/MaestroInitData.cpp Exec/science/wdconvect/MaestroInitData.cpp Exec/test_problems/double_bubble/MaestroInitData.cpp Exec/test_problems/incomp_shear_jet/MaestroInitData.cpp Exec/test_problems/mach_jet/MaestroInitData.cpp Exec/test_problems/reacting_bubble/MaestroInitData.cpp Exec/test_problems/rt/MaestroInitData.cpp Exec/test_problems/test_convect/MaestroInitData.cpp Exec/test_problems/test_planar_diag/MaestroInitData.cpp Exec/test_problems/test_stability/MaestroInitData.cpp Exec/unit_tests/test_advect/MaestroInit.cpp Exec/unit_tests/test_advect/MaestroInitData.cpp Exec/unit_tests/test_average/MaestroEvolve.cpp Exec/unit_tests/test_average/MaestroInitData.cpp Exec/unit_tests/test_basestate/MaestroAdvance.cpp Exec/unit_tests/test_basestate/MaestroInit.cpp Exec/unit_tests/test_basestate/MaestroInitData.cpp Exec/unit_tests/test_diffusion/MaestroEvolve.cpp Exec/unit_tests/test_diffusion/MaestroInit.cpp Exec/unit_tests/test_projection/MaestroPlot.cpp Exec/unit_tests/test_react/MaestroInit.cpp Source/Maestro.H commit f44f2355fcf67091a869d59086afbeae6c6270be Author: Travis CI <> Date: Wed Mar 25 00:53:53 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroVelPred.cpp commit c0d5e9b8a283f022ba2cdfa7c1de59162a6c94ef Merge: 28e97550 8feb4e05 Author: Doreen Fan Date: Tue Mar 24 17:48:17 2020 -0700 Merge branch 'development' into cpp_init Fixed conflicts commit a997c1733dc604fb7926033d2400a26189ffd539 Author: Alice Harpole Date: Tue Mar 24 14:17:46 2020 -0400 fixed overloaded operators Exec/unit_tests/test_new_basestate/main.cpp Source/BaseState.H commit 8feb4e05a5689870aa7e8f7d05c787beb4690859 Author: Doreen Fan Date: Mon Mar 23 18:38:44 2020 -0700 some growntilebox() -> grow() to prevent illegal memory access Source/MaestroVelPred.cpp commit eef0405e3a3466d1c49cf523aac5dd387545a302 Author: Alice Harpole Date: Fri Mar 20 17:45:59 2020 -0400 started testing with unit test Exec/unit_tests/test_new_basestate/GNUmakefile Exec/unit_tests/test_new_basestate/Make.package Exec/unit_tests/test_new_basestate/README Exec/unit_tests/test_new_basestate/main.cpp Source/BaseState.H Source/BaseState.cpp Source/Maestro.H Source/Make.package Source/Src_nd/initdata.F90 commit 85308858188fca9d028d9c36c61ad8d851c15356 Author: Alice Harpole Date: Fri Mar 20 15:04:58 2020 -0400 overloaded some operators Source/BaseState.H Source/BaseState.cpp commit 8cf8989fe9d0946dab1064c20e5655ee3adfff93 Author: Alice Harpole Date: Fri Mar 20 11:56:10 2020 -0400 Started working on new base state class Source/BaseState.H Source/BaseState.cpp Source/Maestro.H commit a4976836e3e378f545a1ffb0f26bdf84a3a90bce Author: Alice Harpole Date: Fri Mar 20 10:22:58 2020 -0400 some more tidying up Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroAdvection.cpp Source/MaestroBaseState.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroCheckpoint.cpp Source/MaestroConvert.cpp Source/MaestroDensityAdvance.cpp Source/MaestroDiag.cpp Source/MaestroEnforceHSE.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroFill3dData.cpp Source/MaestroFillData.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp Source/MaestroMakeEdgeScalars.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeFlux.cpp Source/MaestroMakePsi.cpp Source/MaestroMakeS.cpp Source/MaestroMakeUtrans.cpp Source/MaestroMakew0.cpp Source/MaestroPPM.cpp Source/MaestroRhoHT.cpp Source/MaestroVelPred.cpp Source/MaestroVelocityAdvance.cpp commit 13e8a6b004153dc67579261375843cebeb6d669e Author: Doreen Fan Date: Thu Mar 19 22:50:53 2020 -0700 convert sponge to C++ for xrb_mixed Exec/science/xrb_mixed/MaestroSponge.cpp commit e1b24be70dfeddd053b9bed423c0a7cb7ff2e60a Author: Doreen Fan Date: Thu Mar 19 16:28:15 2020 -0700 match parameters in local InitBaseState subroutines to those declared in Maestro.H Exec/science/code_comp/MaestroBaseState.cpp Exec/science/flame/MaestroBaseState.cpp Exec/test_problems/double_bubble/MaestroBaseState.cpp Exec/test_problems/incomp_shear_jet/MaestroBaseState.cpp Exec/test_problems/mach_jet/MaestroBaseState.cpp Exec/test_problems/rt/MaestroBaseState.cpp Exec/test_problems/test_planar_diag/MaestroBaseState.cpp Exec/unit_tests/test_advect/MaestroBaseState.cpp Exec/unit_tests/test_average/MaestroBaseState.cpp Exec/unit_tests/test_diffusion/MaestroBaseState.cpp Exec/unit_tests/test_react/MaestroBaseState.cpp Source/MaestroBaseStateGeometry.cpp commit d7e55f77f64d9049fea584e4a53e97bece9e6b15 Merge: 22dc4a24 a30302b8 Author: Alice Harpole Date: Thu Mar 19 16:43:33 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 22dc4a242d868be9e74a1f081b1055ff2a842860 Author: Alice Harpole Date: Thu Mar 19 16:43:24 2020 -0400 fixed some static analysis warnings Source/Maestro.H Source/MaestroAdvectBase.cpp Source/MaestroAdvection.cpp Source/MaestroBaseState.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroFill3dData.cpp Source/MaestroFillData.cpp Source/MaestroInit.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeEta.cpp Source/MaestroMakePsi.cpp Source/MaestroMakew0.cpp Source/MaestroRhoHT.cpp commit bbed5d7b9680754203c7bd6e4bfa03e2480e9491 Merge: a50d8109 a30302b8 Author: Doreen Fan Date: Thu Mar 19 11:26:26 2020 -0700 Merge branch 'development' into cpp_dt_force commit a30302b87bc30dd383fb1f08a58c13fc44c5289c Author: Doreen Fan Date: Thu Mar 19 11:23:57 2020 -0700 GPU fix Source/MaestroPlot.cpp commit d491c1eea75500aed72a3e78e612116d8cb1e77a Author: Michael Zingale Date: Thu Mar 19 13:10:17 2020 -0400 update Microphysics external/Microphysics commit 28e97550763d688170ef649dae22e01ae7cfef5e Author: Alice Harpole Date: Thu Mar 19 12:53:26 2020 -0400 converted initial data for unit_tests Exec/unit_tests/test_advect/MaestroInitData.cpp Exec/unit_tests/test_advect/initdata.F90 Exec/unit_tests/test_average/MaestroInitData.cpp Exec/unit_tests/test_basestate/MaestroInitData.cpp Exec/unit_tests/test_diffusion/MaestroEvolve.cpp Exec/unit_tests/test_diffusion/MaestroInit.cpp Exec/unit_tests/test_diffusion/Make.package Exec/unit_tests/test_diffusion/Problem_F.H Exec/unit_tests/test_diffusion/initdata.F90 Exec/unit_tests/test_diffusion/make_analytic_solution.F90 Exec/unit_tests/test_eos/MaestroEvolve.cpp Exec/unit_tests/test_eos/initdata.F90 Exec/unit_tests/test_react/MaestroInit.cpp Source/Src_nd/Make.package Source/Src_nd/initdata.F90 commit a50d8109594794c97f5e27cfbeea80666bae56a0 Author: Doreen Fan Date: Wed Mar 18 19:51:47 2020 -0700 Added lots of to fix GPU compilation Exec/unit_tests/test_basestate/MaestroDt.cpp Source/MaestroDt.cpp commit 0924ad8c233ed5c3ac4ffe08fdc9f705dfec6aff Merge: e467c0ec 912f4487 Author: Doreen Fan Date: Wed Mar 18 19:10:09 2020 -0700 Merge branch 'development' into cpp_dt_force commit e467c0eca601687a17f3193bff4f3068610637d5 Author: Doreen Fan Date: Wed Mar 18 19:09:38 2020 -0700 convert compute_dt to C++ for test_basestate Exec/unit_tests/test_basestate/MaestroDt.cpp Exec/unit_tests/test_basestate/compute_dt.F90 commit ef3efb7540b6e24636711754d5c730a158e1110f Author: Doreen Fan Date: Wed Mar 18 17:17:18 2020 -0700 convert compute_dt to C++ for test_diffusion Exec/unit_tests/test_diffusion/MaestroDt.cpp Exec/unit_tests/test_diffusion/compute_dt.F90 commit 8cf77d7dfaf6be7901ddd07a2f3daaac76f14087 Author: Alice Harpole Date: Wed Mar 18 17:51:35 2020 -0400 converted initial data for urca and xrb_mixed Exec/science/urca/MaestroInitData.cpp Exec/science/xrb_mixed/MaestroInitData.cpp commit 96cefe8f2ffece22c5b6a923629cb9489a4657a6 Merge: 39294eef 912f4487 Author: Alice Harpole Date: Wed Mar 18 15:39:23 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_init commit 912f448708daaa7bc3c890fa8eda08a59b1fa80b Author: Alice Harpole Date: Wed Mar 18 15:12:39 2020 -0400 add to Fab functions to fix GPU compilation Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp commit 39294eef7f0b43fa6d40cd4e4fc06ae50c0c1fb2 Author: Alice Harpole Date: Wed Mar 18 14:37:12 2020 -0400 converted toy convect Exec/science/toy_convect/MaestroInitData.cpp commit afd808948f8ed98cd4dc820a6b44dde6f33dec49 Author: Alice Harpole Date: Wed Mar 18 13:57:42 2020 -0400 converted subch but the errors are very large and not sure why Exec/science/rotating_star/MaestroInitData.cpp Exec/science/sub_chandra/initdata.F90 Source/MaestroInitData.cpp commit a4395fe647c47b03c82090f1e6fd51d2b57e12c2 Author: Alice Harpole Date: Wed Mar 18 09:48:35 2020 -0400 fixed ecsn and fully_convective_star, but cannot get existing problems to run so cannot test Exec/science/ecsn/MaestroInitData.cpp Exec/science/fully_convective_star/MaestroInitData.cpp Exec/science/wdconvect/MaestroInitData.cpp Exec/science/wdconvect/initdata.F90 Source/MaestroInitData.cpp commit 4094f131bef04f84cc973424973d7dd514418534 Author: Alice Harpole Date: Wed Mar 18 08:53:15 2020 -0400 convert initial data for wdconvect Exec/science/ecsn/MaestroInitData.cpp Exec/science/ecsn/initdata.F90 Exec/science/flame/MaestroInitData.cpp Exec/science/flame/initdata.F90 Exec/science/fully_convective_star/MaestroInitData.cpp Exec/science/plane_parallel_star/MaestroInitData.cpp Exec/science/wdconvect/MaestroInitData.cpp Exec/science/wdconvect/initdata.F90 Source/Maestro.H Source/MaestroFill3dData.cpp Source/MaestroInit.cpp Source/MaestroInitData.cpp Source/Src_nd/Make.package commit 281a0d38d1cea93a08082a807cd204342e9dc522 Author: Travis CI <> Date: Tue Mar 17 22:08:41 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroDt.cpp commit 393c57e1013fcd6b61f93ec44312528d5e84e8d0 Author: Doreen Fan Date: Tue Mar 17 14:08:58 2020 -0700 need 4th index for w0_arr Source/MaestroDt.cpp commit 28e51b3f5ee9d342df5e7a3097d4d6884cb6e974 Merge: 52dd4455 5ba2e282 Author: Alice Harpole Date: Tue Mar 17 14:57:34 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_init commit 5ba2e2822a25bdfea1a3c4224e5f2cdb239af444 Author: Alice Harpole Date: Tue Mar 17 14:57:09 2020 -0400 GPU fixes for flame Exec/science/flame/MaestroBCFill.cpp commit 52dd4455424fdb288abd7e7a80d62a0ba711b471 Author: Alice Harpole Date: Tue Mar 17 14:10:18 2020 -0400 converted initial data for code_comp and ecsn Exec/science/code_comp/MaestroInitData.cpp Exec/science/code_comp/initdata.F90 Exec/science/ecsn/MaestroInitData.cpp Exec/test_problems/test_stability/initdata.F90 commit 3a2db8730dacf72ae4b9a62ebe8893a44c1827eb Author: Alice Harpole Date: Tue Mar 17 11:48:30 2020 -0400 converted initial data for other test_problems Exec/test_problems/double_bubble/MaestroInitData.cpp Exec/test_problems/double_bubble/initdata.F90 Exec/test_problems/double_bubble/inputs_2d_C Exec/test_problems/incomp_shear_jet/MaestroInitData.cpp Exec/test_problems/incomp_shear_jet/initdata.F90 Exec/test_problems/mach_jet/MaestroInitData.cpp Exec/test_problems/mach_jet/initdata.F90 Exec/test_problems/reacting_bubble/initdata.F90 Exec/test_problems/rt/MaestroInitData.cpp Exec/test_problems/rt/initdata.F90 Exec/test_problems/test_convect/MaestroInitData.cpp Exec/test_problems/test_convect/initdata.F90 Exec/test_problems/test_planar_diag/MaestroInitData.cpp Exec/test_problems/test_planar_diag/initdata.F90 Exec/test_problems/test_stability/MaestroInitData.cpp Source/MaestroInitData.cpp commit aaf1e4aaae4848b3902547b54134297a378b5c33 Merge: f4a1b4bb 32ea0a85 Author: Alice Harpole Date: Tue Mar 17 07:44:53 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_average commit dd9ef9fbebd9daeba0c15cf6bcfb6fa032287aa3 Merge: 370ad960 32ea0a85 Author: Alice Harpole Date: Tue Mar 17 07:43:55 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_init commit 370ad960ada720fa319569153edba17318c10fee Author: Alice Harpole Date: Tue Mar 17 07:43:36 2020 -0400 converted initial data for double_bubble Exec/test_problems/double_bubble/MaestroInitData.cpp Exec/test_problems/reacting_bubble/MaestroInitData.cpp Source/MaestroInitData.cpp commit e6b7c19ff87af25ea3703797eb74195280054a19 Author: Doreen Fan Date: Mon Mar 16 20:33:16 2020 -0700 remove old Fortran file Source/Src_nd/Make.package commit 2ac8f2f2c06132e54b926be4cc8f9ce31965aabc Merge: 39171176 32ea0a85 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Mon Mar 16 18:43:29 2020 -0700 Merge branch 'development' into cpp_dt_force commit 39171176e8cdb1e873e9d8305065a86575c57d26 Merge: b4e912d5 c0035d1f Author: Doreen Fan Date: Mon Mar 16 18:45:06 2020 -0700 Merge branch 'development' into cpp_dt_force commit 32ea0a85de9088324329b67196e9c09133c84af7 Merge: c0035d1f a40d2c79 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Mon Mar 16 18:21:57 2020 -0700 Merge pull request #170 from AMReX-Astro/cpp_more_eos Convert plot variables routines to C++ commit a40d2c79ed93ed54c5c3673eda6b18c5a2048971 Author: Travis CI <> Date: Tue Mar 17 00:30:36 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroPlot.cpp commit 298978d306e20d2506f02f64f1c3245931428303 Author: Doreen Fan Date: Mon Mar 16 17:32:12 2020 -0700 fix spherical magvel and circ_vel Source/MaestroPlot.cpp commit c0035d1f66c86935fb39834a8ecb2bfa3c39b359 Author: Alice Harpole Date: Mon Mar 16 20:07:32 2020 -0400 Convert base_state.F90 to C++ (#167) This converts the init_base_state routine to C++, both in the Src_nd directory and for all the custom base state initialization functions in the problem directories. It also converts some of the functions in the Util directory (model_parser and simple_log, and adds another util directory, the purpose of which is to contain general small utility functions (e.g. so far it contains a function for trimming C++ strings of whitespace). This PR depends on #165, and is untested except for rt. .travis.yml Exec/Make.Maestro Exec/science/code_comp/MaestroBaseState.cpp Exec/science/code_comp/base_state.F90 Exec/science/flame/MaestroBCFill.cpp Exec/science/flame/MaestroBaseState.cpp Exec/science/flame/MaestroInletBCs.H Exec/science/flame/MaestroInletBCs.cpp Exec/science/flame/base_state.F90 Exec/science/flame/inlet_bc.F90 Exec/test_problems/double_bubble/MaestroBaseState.cpp Exec/test_problems/double_bubble/base_state.F90 Exec/test_problems/incomp_shear_jet/MaestroBaseState.cpp Exec/test_problems/incomp_shear_jet/base_state.F90 Exec/test_problems/mach_jet/MaestroBCFill.cpp Exec/test_problems/mach_jet/MaestroBaseState.cpp Exec/test_problems/mach_jet/MaestroInletBCs.H Exec/test_problems/mach_jet/MaestroInletBCs.cpp Exec/test_problems/mach_jet/base_state.F90 Exec/test_problems/mach_jet/inlet_bc.F90 Exec/test_problems/rt/MaestroBaseState.cpp Exec/test_problems/rt/base_state.F90 Exec/test_problems/test_planar_diag/MaestroBaseState.cpp Exec/test_problems/test_planar_diag/base_state.F90 Exec/unit_tests/test_advect/MaestroBaseState.cpp Exec/unit_tests/test_advect/MaestroInit.cpp Exec/unit_tests/test_advect/base_state.F90 Exec/unit_tests/test_average/MaestroBaseState.cpp Exec/unit_tests/test_average/MaestroEvolve.cpp Exec/unit_tests/test_average/base_state.F90 Exec/unit_tests/test_basestate/MaestroAdvance.cpp Exec/unit_tests/test_basestate/MaestroDt.cpp Exec/unit_tests/test_basestate/MaestroInit.cpp Exec/unit_tests/test_basestate/Make.package Exec/unit_tests/test_basestate/compute_dt.F90 Exec/unit_tests/test_basestate/make_edge_state.F90 Exec/unit_tests/test_diffusion/MaestroBaseState.cpp Exec/unit_tests/test_diffusion/MaestroInit.cpp Exec/unit_tests/test_diffusion/base_state.F90 Exec/unit_tests/test_react/MaestroBaseState.cpp Exec/unit_tests/test_react/MaestroInit.cpp Exec/unit_tests/test_react/base_state.F90 Source/Maestro.H Source/MaestroBCFill.cpp Source/MaestroBaseState.cpp Source/MaestroInit.cpp Source/MaestroInletBCs.H Source/MaestroInletBCs.cpp Source/Make.package Source/PhysBCFunctMaestro.H Source/Src_nd/Make.package Source/Src_nd/base_state.F90 Source/Src_nd/inlet_bc.F90 Util/model_parser/Make.package Util/model_parser/ModelParser.H Util/model_parser/ModelParser.cpp Util/simple_log/Make.package Util/simple_log/SimpleLog.H Util/simple_log/SimpleLog.cpp Util/utils/MaestroUtil.H Util/utils/MaestroUtil.cpp Util/utils/Make.package deploy_docs.sh sphinx_docs/source/conf.py commit 9a207be12132dc20caf03343f323aa711fd16906 Merge: 19c3378f e0055e04 Author: Doreen Fan Date: Mon Mar 16 16:11:44 2020 -0700 Merge branch 'cpp_base_state' into cpp_more_eos commit 7d2eb0b8ca7a1a8a29f4683258f4f1ae80504797 Author: Alice Harpole Date: Mon Mar 16 18:05:32 2020 -0400 converted initial data for reacting_bubble Exec/test_problems/reacting_bubble/MaestroInitData.cpp Source/Maestro.H Source/MaestroInit.cpp Source/MaestroInitData.cpp commit e0055e04f85e5dc8dc91f3b6240d33cad05a144d Author: Doreen Fan Date: Mon Mar 16 12:08:56 2020 -0700 bug fixes for unit tests Exec/unit_tests/test_advect/MaestroBaseState.cpp Exec/unit_tests/test_advect/MaestroInit.cpp Exec/unit_tests/test_average/MaestroEvolve.cpp Exec/unit_tests/test_basestate/MaestroAdvance.cpp Exec/unit_tests/test_basestate/MaestroDt.cpp Exec/unit_tests/test_basestate/MaestroInit.cpp Exec/unit_tests/test_basestate/Make.package Exec/unit_tests/test_basestate/compute_dt.F90 Exec/unit_tests/test_basestate/make_edge_state.F90 Exec/unit_tests/test_diffusion/MaestroBaseState.cpp Exec/unit_tests/test_diffusion/MaestroInit.cpp Exec/unit_tests/test_react/MaestroBaseState.cpp Exec/unit_tests/test_react/MaestroInit.cpp commit c4fb81e2de7811f3b4e089135ac524288508ce36 Author: Alice Harpole Date: Mon Mar 16 15:05:02 2020 -0400 Started converting initial data Source/Maestro.H Source/MaestroFill3dData.cpp Source/MaestroInitData.cpp Source/Make.package commit 491bc60e757dc35675538f6c5491008a38df68c6 Author: Doreen Fan Date: Sun Mar 15 23:24:03 2020 -0700 remove Fortran file Exec/test_problems/test_planar_diag/base_state.F90 commit 8dc83570822d2467e1928b0e7a383a8addccccaa Author: Doreen Fan Date: Sun Mar 15 21:39:23 2020 -0700 bug fixes for mach_jet and test_planar_diag Exec/test_problems/mach_jet/MaestroBaseState.cpp Exec/test_problems/test_planar_diag/MaestroBaseState.cpp commit e965ef6ad27eb843fa24ee1d7d09322ad2cdd5c7 Author: Doreen Fan Date: Fri Mar 13 16:18:10 2020 -0700 bug fixes for double_bubble Exec/test_problems/double_bubble/MaestroBaseState.cpp commit adedf2f7d2e604be9bb3194c9c1dff53e5c0ebca Author: Alice Harpole Date: Fri Mar 13 17:31:53 2020 -0400 fixed inlet_bcs for mach_jet Exec/science/flame/MaestroBCFill.cpp Exec/test_problems/mach_jet/MaestroBCFill.cpp Exec/test_problems/mach_jet/MaestroInletBCs.H Exec/test_problems/mach_jet/MaestroInletBCs.cpp Source/MaestroBCFill.cpp Source/MaestroInletBCs.H Source/MaestroInletBCs.cpp commit 9031c0fc63a67d7f5efd3130e80f230859d7538d Author: Alice Harpole Date: Fri Mar 13 17:21:43 2020 -0400 fixed inlet_bcs so it actually runs Exec/science/flame/MaestroBCFill.cpp Exec/science/flame/MaestroBaseState.cpp Exec/science/flame/MaestroInletBCs.H Exec/science/flame/MaestroInletBCs.cpp Exec/test_problems/mach_jet/MaestroBaseState.cpp Exec/test_problems/mach_jet/MaestroInletBCs.H Exec/test_problems/mach_jet/MaestroInletBCs.cpp Source/Maestro.H Source/MaestroBaseState.cpp Source/Maestro_F.H Source/PhysBCFunctMaestro.H commit 9d9c3faac85fb8dd5fa0a65af97ce2658ee261bf Author: Alice Harpole Date: Fri Mar 13 16:25:42 2020 -0400 Inlet bcs for flame Exec/science/flame/MaestroInletBCs.H Exec/science/flame/MaestroInletBCs.cpp Source/Maestro.H Source/MaestroInletBCs.H Source/MaestroInletBCs.cpp Source/Make.package commit 07d61a7b2cbbd087940240c91b2a23300a9a52a9 Merge: 037c180d b3eedafb Author: Alice Harpole Date: Fri Mar 13 15:58:46 2020 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_base_state commit b3eedafbd5f0803b131c43de079614b00755e871 Author: Doreen Fan Date: Thu Mar 12 14:06:28 2020 -0700 bug fixes: all unit tests now compile Exec/unit_tests/test_advect/MaestroInit.cpp Exec/unit_tests/test_average/MaestroEvolve.cpp Exec/unit_tests/test_diffusion/MaestroDt.cpp Exec/unit_tests/test_diffusion/MaestroInit.cpp Exec/unit_tests/test_diffusion/MaestroPlot.cpp Exec/unit_tests/test_eos/MaestroInit.cpp Exec/unit_tests/test_projection/MaestroInit.cpp Exec/unit_tests/test_projection/MaestroPlot.cpp Exec/unit_tests/test_projection/test_projection.F90 Exec/unit_tests/test_react/MaestroEvolve.cpp Exec/unit_tests/test_react/MaestroInit.cpp Exec/unit_tests/test_react/MaestroPlot.cpp commit 037c180db6a2a5663f3ee05822a9ddbd50435da0 Author: Doreen Fan Date: Thu Mar 12 11:47:46 2020 -0700 Use fortran version of set_inlet_bc for now. Will convert to C++ later Exec/science/flame/MaestroBaseState.cpp Exec/science/flame/inlet_bc.F90 Exec/test_problems/mach_jet/MaestroBaseState.cpp Exec/test_problems/mach_jet/inlet_bc.F90 Source/MaestroBaseState.cpp Source/Maestro_F.H Source/Src_nd/inlet_bc.F90 commit e1650254869b53f4a8399ce24fd8b56e0f915a2e Author: Doreen Fan Date: Thu Mar 12 11:39:34 2020 -0700 small bug fix Exec/science/flame/MaestroBaseState.cpp commit dc0738c886aaffa97134fe71a50a43a86d8d4976 Author: Alice Harpole Date: Wed Mar 11 15:54:01 2020 -0400 fixed bug for multilevel spherical Source/Src_nd/base_state_geometry.F90 commit 5a93583671c69676b553d706bad20f405e76593a Author: Alice Harpole Date: Wed Mar 11 14:43:48 2020 -0400 make sure reductions are done over threads for diag files Source/MaestroDiag.cpp commit b4e912d54a954588438c8a572c2cb1f0dab6deb4 Author: Alice Harpole Date: Wed Mar 11 10:36:58 2020 -0400 2d fixes Source/MaestroDt.cpp Source/MaestroForce.cpp Source/MaestroSponge.cpp commit ba518dda90ee8b64915153881f880eda2bece45f Merge: 0f945295 f028f96e Author: Doreen Fan Date: Tue Mar 10 16:44:17 2020 -0700 Merge branch 'cpp_base_state' of https://github.com/AMReX-Astro/MAESTROeX into cpp_base_state commit 0f94529549b17434b8f21238c4380cd184e71fdf Author: Doreen Fan Date: Tue Mar 10 16:43:24 2020 -0700 reordered lambda functions and capture lambdas within lambdas Exec/science/code_comp/MaestroBaseState.cpp commit b483bd98e116011c10c1840061c0359af3892f6c Author: Alice Harpole Date: Tue Mar 10 16:28:42 2020 -0400 tidy up Source/MaestroDt.cpp commit a957f308347c068a73f643ecc6efe542b125f233 Author: Alice Harpole Date: Tue Mar 10 16:15:38 2020 -0400 wdconvect runs with OMP and MPI again Source/MaestroDt.cpp commit 797711f274fb164f4bcacef16449a806ef9da1d5 Author: Alice Harpole Date: Tue Mar 10 12:30:06 2020 -0400 MaestroDt seems to run on the GPU Source/MaestroDt.cpp commit f028f96e6698f9c0f1b574c2802cdc0d35cbcedf Author: Travis CI <> Date: Mon Mar 9 23:45:41 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroInit.cpp commit 9cdb2d28e1bc3314284894e12ea3c34fa9948002 Author: Doreen Fan Date: Mon Mar 9 16:45:41 2020 -0700 bug fix: rho and p are switched Exec/test_problems/test_planar_diag/MaestroBaseState.cpp commit 5d94a09f3e6b76577f3a73dd2eb19dc71d9043e0 Author: Doreen Fan Date: Mon Mar 9 16:44:47 2020 -0700 set psi to zero during initialization Source/MaestroInit.cpp commit eb78ea0cc93fbbeddf65dd1d885218994f95ddc9 Author: Doreen Fan Date: Mon Mar 9 16:32:27 2020 -0700 fix inequality signs -> initial max HSE error now makes more sense Source/MaestroBaseState.cpp commit 299cf43b0f02b86c80915916da265d2bad6494e6 Author: Alice Harpole Date: Mon Mar 9 17:51:02 2020 -0400 attempting to fix MaestroDt on GPU Source/Maestro.H Source/MaestroAdvection.cpp Source/MaestroDt.cpp Source/MaestroSponge.cpp commit 37c2e449c5ee07378e2795b5257bd3ef1735e600 Author: Doreen Fan Date: Mon Mar 9 14:18:01 2020 -0700 indices bug fix Source/MaestroBaseState.cpp commit 7fc8bccd4b16d005d30cb83db8c1231798196813 Merge: 1d6081dd 05b85037 Author: Doreen Fan Date: Mon Mar 9 13:19:56 2020 -0700 Merge branch 'development' into cpp_base_state commit c7511d3d0176215a2e3861e79b82d4ce99113e00 Author: Alice Harpole Date: Fri Mar 6 17:40:03 2020 -0500 goodbye Fortran sponge Exec/Make.Maestro Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroDt.cpp Source/MaestroInit.cpp Source/MaestroPlot.cpp Source/MaestroRotation.cpp Source/MaestroSetup.cpp Source/MaestroSponge.cpp Source/Make.package Source/Src_nd/Make.package Source/Src_nd/rotation.F90 Source/Src_nd/sponge.F90 commit b77aa9d934b037c67b1b10531ed6045cba748d03 Author: Alice Harpole Date: Fri Mar 6 13:18:27 2020 -0500 goodbye compute_dt.F90 Source/Maestro.H Source/MaestroDt.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/compute_dt.F90 commit 6e12616bc89abb5944a425480f7b70cd3dc1270e Author: Alice Harpole Date: Fri Mar 6 11:57:09 2020 -0500 converted firstdt Source/MaestroDt.cpp commit 90be189c6ff8effe40d85c936094b46db67b622a Author: Alice Harpole Date: Fri Mar 6 11:36:08 2020 -0500 converted estdt_sphr. It is deterministic but gives some differences which are likely because now comparing plotfiles at (sightly?) different simulation times Source/MaestroDt.cpp commit a3ec8bc213d2c7894ba5fd1d1b412ffadc6024b5 Author: Alice Harpole Date: Fri Mar 6 10:27:49 2020 -0500 converte estdt Source/MaestroDt.cpp Source/MaestroForce.cpp Source/Src_nd/Make.package commit 7c2157fde8fb353551b63d009c76bd334be76543 Author: Alice Harpole Date: Fri Mar 6 09:21:10 2020 -0500 converted mktempforce Source/MaestroForce.cpp Source/Src_nd/make_scal_force.F90 commit 340a864f4f9651f391d6679af1ca1d8399e96ac3 Merge: f4a1b4bb 05b85037 Author: Doreen Fan Date: Thu Mar 5 15:15:50 2020 -0800 Merge branch 'development' into cpp_average commit 19c3378f2157fdcf9c11b8ca9d422fff5dfc0e18 Author: Alice Harpole Date: Thu Mar 5 16:46:11 2020 -0500 GPU fixes Source/MaestroPlot.cpp commit 68502a9eafe0fea0f8e64250aa1452fa6c3d7dee Merge: ec194f49 05b85037 Author: Alice Harpole Date: Thu Mar 5 16:06:20 2020 -0500 merging with development commit 05b85037bc118409e774d100b846da75b37a56d2 Author: Doreen Fan Date: Thu Mar 5 12:10:19 2020 -0800 bug fix for double_bubble problem to compile Source/MaestroFillData.cpp commit f4a1b4bb34f184ef856c12ae6ca9079789960236 Merge: aea262f6 a933188e Author: Doreen Fan Date: Thu Mar 5 09:52:56 2020 -0800 Merge branch 'development' into cpp_average Fixed merge conflicts commit a933188e81837ffbaf95a87cb2328bcfdd4c23f6 Author: Michael Zingale Date: Thu Mar 5 12:25:40 2020 -0500 Convert bc_fill_nd.F90 to C++ (#162) This converts the bc fill routines to C++. I've tested for wdconvect and reacting bubble, and it should not change the outputs. Co-authored-by: doreenfan <35239173+doreenfan@users.noreply.github.com> Exec/science/flame/MaestroBCFill.cpp Exec/science/flame/bc_fill_nd.F90 Exec/science/flame/inlet_bc.F90 Exec/test_problems/mach_jet/MaestroBCFill.cpp Exec/test_problems/mach_jet/bc_fill_nd.F90 Exec/test_problems/mach_jet/inlet_bc.F90 Source/Maestro.H Source/MaestroBCFill.cpp Source/MaestroFillData.cpp Source/Maestro_F.H Source/Make.package Source/PhysBCFunctMaestro.H Source/Src_nd/Make.package Source/Src_nd/bc_fill_nd.F90 Source/Src_nd/inlet_bc.F90 commit 0d2ebaae1053063d904edb2dec52c2945b9f8e4b Author: Michael Zingale Date: Thu Mar 5 11:22:55 2020 -0500 Converted fill_umac_ghosts.F90 to C++ (#164) This converts the routines in fill_umac_ghosts.F90 to C++. It does not depend on any previous PRs and should produce no changes in the outputs. Co-authored-by: doreenfan <35239173+doreenfan@users.noreply.github.com> Source/MaestroFillData.cpp Source/Src_nd/Make.package Source/Src_nd/fill_umac_ghost.F90 commit 76b3265e2d5b4d27d9b2677dd2659d79cf785aa0 Author: Michael Zingale Date: Thu Mar 5 10:57:10 2020 -0500 Convert cell_to_edge to C++ (#159) This converts the routine cell_to_edge to C++. It should not change the output. Co-authored-by: doreenfan <35239173+doreenfan@users.noreply.github.com> Source/Maestro.H Source/MaestroCelltoEdge.cpp Source/MaestroDensityAdvance.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp Source/MaestroRhoHT.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/Make.package Source/Src_nd/cell_to_edge.F90 Source/Src_nd/compute_grad_phi.F90 Source/Src_nd/make_eta.F90 Source/Src_nd/make_psi.F90 commit e91c6f8d467b3aae18eaa8c95764ac1478eba67b Author: Michael Zingale Date: Thu Mar 5 10:40:07 2020 -0500 Convert MakePsi and MakeEtarho routines to C++ (#158) This converts the routines in make_psi.F90 and make_eta.F90 to C++. Compared to PR #154, there should be no change in the output. If this produces any errors in the test suite, it's probably due to MakeEtarho and some error in the reduction over threads. Co-authored-by: doreenfan <35239173+doreenfan@users.noreply.github.com> Exec/science/wdconvect/inputs_files/inputs_3d_amr_regression Exec/science/wdconvect/inputs_files/inputs_3d_regression Exec/science/wdconvect/inputs_files/inputs_3d_regression.2levels Exec/science/wdconvect/inputs_files/inputs_omp_3d_regression Exec/test_problems/double_bubble/inputs_2d_regression Exec/test_problems/incomp_shear_jet/inputs_2d_regression Exec/test_problems/mach_jet/inputs_2d Exec/test_problems/mach_jet/inputs_2d_stratified Exec/test_problems/reacting_bubble/inputs_2d_C Exec/test_problems/reacting_bubble/inputs_2d_C.2levels Exec/test_problems/reacting_bubble/inputs_2d_C.3levels Exec/test_problems/reacting_bubble/inputs_2d_C.avgbase Exec/test_problems/reacting_bubble/inputs_2d_amr_regression Exec/test_problems/reacting_bubble/inputs_2d_regression Exec/test_problems/reacting_bubble/inputs_2d_regression.2levels Exec/test_problems/reacting_bubble/inputs_3d_amr_regression Exec/test_problems/reacting_bubble/inputs_3d_gpu_regression Exec/test_problems/reacting_bubble/inputs_3d_regression Exec/test_problems/reacting_bubble/inputs_omp_2d_regression Exec/test_problems/reacting_bubble/inputs_omp_3d_regression Exec/test_problems/rt/inputs_2d_C Exec/test_problems/rt/inputs_2d_regression Exec/test_problems/test_convect/inputs_2d_regression Exec/test_problems/test_planar_diag/inputs_2d_C Exec/test_problems/test_stability/inputs_2d_C_regression Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeEta.cpp Source/MaestroMakePsi.cpp Source/MaestroNodalProj.cpp Source/Make.package commit 1351cecf935281181752f1095cf9c0e14071815e Author: Alice Harpole Date: Thu Mar 5 09:38:11 2020 -0500 fix bug in MakeS.cpp so wdconvect_amr test no longer crashes Source/MaestroMakeS.cpp commit aea262f6be4afb211f6ca20af119f5c21ece97c7 Author: Doreen Fan Date: Wed Mar 4 16:03:08 2020 -0800 validbox -> tilebox Source/MaestroAverage.cpp commit a6479e798d183dfb3db337917ad4dfb5315163b8 Author: Doreen Fan Date: Wed Mar 4 15:26:15 2020 -0800 replaced Gpu::Atomic::Add with HostDevice::Atomic::Add Source/MaestroAverage.cpp commit df272463be7b4fcbcd954bd9d68510059ade8484 Merge: 6503b9e0 0f71222c Author: Doreen Fan Date: Wed Mar 4 14:50:03 2020 -0800 Merge branch 'cpp_average' of https://github.com/AMReX-Astro/MAESTROeX into cpp_average Fix conflicts commit ec194f49640ff251a752a28ec1733846b69c7252 Merge: ddcf7a83 1d6081dd Author: Alice Harpole Date: Wed Mar 4 17:33:29 2020 -0500 Merge branch 'cpp_base_state' of github.com:AMReX-Astro/MAESTROeX into cpp_more_eos commit 1d6081ddc3ecb4f581d12fa3c4c65e4bdf151477 Merge: cd49f2d0 58689607 Author: Alice Harpole Date: Wed Mar 4 17:27:41 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_base_state commit 586896075f7d5576c135c47f0a5664ed05b1bf03 Author: Alice Harpole Date: Wed Mar 4 17:27:07 2020 -0500 GPU fixes Source/MaestroGamma.cpp Source/MaestroMakeS.cpp Source/MaestroRhoHT.cpp commit 0f71222c427037b7ed20da1b11f2baaa4175853c Author: Alice Harpole Date: Wed Mar 4 16:49:44 2020 -0500 made the reductions deterministic Source/MaestroAverage.cpp commit 3d45cb9011981bdc937636ddf3327f9d380565ff Merge: 58c140bb 80ed04b1 Author: Alice Harpole Date: Wed Mar 4 16:47:09 2020 -0500 Merge branch 'cpp_celltoedge' of github.com:AMReX-Astro/MAESTROeX into cpp_average commit 80ed04b144eac1ae4ca8da6de92c278e6aaabe76 Merge: 6998d1a7 d713a147 Author: Alice Harpole Date: Wed Mar 4 16:45:53 2020 -0500 merge conflicts commit d713a1474faa0501af577c9f562657339bb0ae48 Author: Alice Harpole Date: Wed Mar 4 16:42:59 2020 -0500 tidy up Source/MaestroMakeEta.cpp commit 58eeb23282420dc4ff2ce3f52f03861703f983b5 Author: Alice Harpole Date: Wed Mar 4 16:37:23 2020 -0500 fixed inputs files so they set amrex.regtest_reduction instead of system.regtest_reduction, made the omp parallel in MakeEta conditional on this flag so reduction is deterministic for testing Exec/science/wdconvect/inputs_files/inputs_3d_amr_regression Exec/science/wdconvect/inputs_files/inputs_3d_regression Exec/science/wdconvect/inputs_files/inputs_3d_regression.2levels Exec/science/wdconvect/inputs_files/inputs_omp_3d_regression Exec/test_problems/double_bubble/inputs_2d_regression Exec/test_problems/incomp_shear_jet/inputs_2d_regression Exec/test_problems/mach_jet/inputs_2d Exec/test_problems/mach_jet/inputs_2d_stratified Exec/test_problems/reacting_bubble/inputs_2d_C Exec/test_problems/reacting_bubble/inputs_2d_C.2levels Exec/test_problems/reacting_bubble/inputs_2d_C.3levels Exec/test_problems/reacting_bubble/inputs_2d_C.avgbase Exec/test_problems/reacting_bubble/inputs_2d_amr_regression Exec/test_problems/reacting_bubble/inputs_2d_regression Exec/test_problems/reacting_bubble/inputs_2d_regression.2levels Exec/test_problems/reacting_bubble/inputs_3d_amr_regression Exec/test_problems/reacting_bubble/inputs_3d_gpu_regression Exec/test_problems/reacting_bubble/inputs_3d_regression Exec/test_problems/reacting_bubble/inputs_omp_2d_regression Exec/test_problems/reacting_bubble/inputs_omp_3d_regression Exec/test_problems/rt/inputs_2d_C Exec/test_problems/rt/inputs_2d_regression Exec/test_problems/test_convect/inputs_2d_regression Exec/test_problems/test_planar_diag/inputs_2d_C Exec/test_problems/test_stability/inputs_2d_C_regression Source/MaestroMakeEta.cpp commit ddcf7a8360f343ae38a0c4a81ca9e33ddd9beb6c Author: Alice Harpole Date: Wed Mar 4 14:33:10 2020 -0500 converted all plot variable functions Source/MaestroPlot.cpp Source/Src_nd/Make.package Source/Src_nd/make_plot_variables.F90 commit 2136da27c00411dd7142cb3e9bd763cb8d40ea0e Author: Alice Harpole Date: Wed Mar 4 13:42:42 2020 -0500 converted plot functions. Moved division by rho outside of loop in abar and it introduced a small roundoff error Source/MaestroPlot.cpp commit 50e022833ae459425409146feaea39dba8965607 Author: Alice Harpole Date: Wed Mar 4 12:35:40 2020 -0500 converted more EoS-using functions Source/MaestroIntra.cpp Source/MaestroPlot.cpp Source/Src_nd/Make.package Source/Src_nd/make_intra_coeffs.F90 commit cd49f2d04f2c12b987e0ab8dc37d16e447ccd1fd Author: Alice Harpole Date: Wed Mar 4 08:38:34 2020 -0500 fix trim function so model parser works Source/MaestroBaseState.cpp Util/utils/MaestroUtil.cpp commit 692a5af95bbd99a1e20856fba9482a2d5866dc42 Merge: d31e9ba5 dc249dee Author: Doreen Fan Date: Tue Mar 3 17:40:16 2020 -0800 Merge branch 'development' into cpp_psi_eta commit d31e9ba5cfd1998dcf90a74f986493e13a7e1bd2 Author: Doreen Fan Date: Tue Mar 3 17:40:09 2020 -0800 Change loVect -> loVect3d and hiVect -> hiVect3d Source/MaestroMakeEta.cpp commit 7cd606671eb53dd8e926d0fa66162a70ec54c270 Author: Alice Harpole Date: Tue Mar 3 16:28:30 2020 -0500 converted base_state.F90 for more problems Exec/test_problems/incomp_shear_jet/MaestroBaseState.cpp Exec/test_problems/incomp_shear_jet/base_state.F90 Exec/test_problems/mach_jet/MaestroBaseState.cpp Exec/test_problems/mach_jet/base_state.F90 Exec/test_problems/test_planar_diag/MaestroBaseState.cpp deploy_docs.sh sphinx_docs/source/conf.py commit f299af50925baf90cfed816a8ff9338e62fbf8ee Merge: 3efb11d7 dc249dee Author: Alice Harpole Date: Tue Mar 3 15:21:53 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_base_state commit dc249dee1ba95915a3d56285489a617ea39667a7 Author: Alice Harpole Date: Tue Mar 3 13:05:03 2020 -0500 Convert EoS calls to C++ (#165) This beings the conversion of routines calling the EoS to C++. Exec/Make.Maestro Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvection.cpp Source/MaestroGamma.cpp Source/MaestroMakeS.cpp Source/MaestroRhoHT.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/maestro_init.F90 Source/Src_nd/make_S.F90 Source/Src_nd/make_gamma.F90 Source/Src_nd/make_scal_force.F90 Source/Src_nd/rhoh_vs_t.F90 Source/Src_nd/update_scal.F90 Source/param/_variables Source/param/meth_params.template Source/param/runtime.probin.template Source/param/set_variables.py Source/param_includes/Make.package Source/param_includes/meth_params.F90 Source/param_includes/state_indices.H Source/param_includes/state_indices_nd.F90 Source/param_includes/state_sizes.F90 commit 3efb11d7a3c2c8cde5f215af07f4f57d8c67835a Merge: 4c4e51c8 44b6d6d5 Author: Alice Harpole Date: Tue Mar 3 09:53:43 2020 -0500 Merge branch 'cpp_eos' of github.com:AMReX-Astro/MAESTROeX into cpp_base_state commit 44b6d6d57937ff1a955e46f7f7e27b1a73a8df52 Merge: ee7aacc2 7a2eeb93 Author: Alice Harpole Date: Tue Mar 3 09:49:18 2020 -0500 fix merge conflicts with development commit 7a2eeb939fbd6486ff48884867480851b98ac595 Author: Alice Harpole Date: Tue Mar 3 09:02:41 2020 -0500 use a separate layout template file for master and dev branches to get the links correct deploy_docs.sh sphinx_docs/source/_templates/dev_layout.html sphinx_docs/source/_templates/layout.html sphinx_docs/source/regtest.rst commit adf0fdf3b3ada2912ba4467120011d90eeb551ae Author: Alice Harpole Date: Tue Mar 3 08:28:00 2020 -0500 add spaces to force docs build sphinx_docs/source/regtest.rst commit c1bf59a8b2e290773a1597c52e1f6e480980f716 Merge: e56a0d2f 07aad87d Author: Alice Harpole Date: Tue Mar 3 08:27:35 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit e56a0d2fb94877c0ffb198fa8c3d0b1470401324 Author: Alice Harpole Date: Tue Mar 3 08:27:24 2020 -0500 another attempt to fix master/development branch links sphinx_docs/source/_templates/layout.html commit 07aad87dc47d630c5528bee267b25c1ba0486c3c Author: Michael Zingale Date: Mon Mar 2 21:01:16 2020 -0500 remove the C++ extern parameter files on make clean Exec/Make.Maestro commit df61f758fc3b28cfdd8428381146cb52ea34b691 Author: Michael Zingale Date: Mon Mar 2 20:59:54 2020 -0500 Convert MAESTROeX over to use Microphysics directly (#166) This removes the local copy of Microphysics and switches us over to directly use the main Microphysics repo. As part of this change, the only eos interface that took pt_index was dropped. We will also make Microphysics a git submodule to MAESTROeX to make it easier to use. .gitmodules Exec/Make.Maestro Exec/science/code_comp/GNUmakefile Exec/science/ecsn/GNUmakefile Exec/science/ecsn/initdata.F90 Exec/science/flame/GNUmakefile Exec/science/flame/initdata.F90 Exec/science/fully_convective_star/GNUmakefile Exec/science/fully_convective_star/initdata.F90 Exec/science/fully_convective_star/inputs_3d Exec/science/plane_parallel_star/GNUmakefile Exec/science/plane_parallel_star/initdata.F90 Exec/science/rotating_star/GNUmakefile Exec/science/rotating_star/initdata.F90 Exec/science/sub_chandra/GNUmakefile Exec/science/sub_chandra/initdata.F90 Exec/science/toy_convect/GNUmakefile Exec/science/urca/GNUmakefile Exec/science/urca/initdata.F90 Exec/science/wdconvect/GNUmakefile Exec/science/wdconvect/initdata.F90 Exec/science/xrb_mixed/GNUmakefile Exec/test_problems/double_bubble/GNUmakefile Exec/test_problems/incomp_shear_jet/GNUmakefile Exec/test_problems/mach_jet/GNUmakefile Exec/test_problems/mach_jet/initdata.F90 Exec/test_problems/reacting_bubble/GNUmakefile Exec/test_problems/reacting_bubble/initdata.F90 Exec/test_problems/rt/GNUmakefile Exec/test_problems/rt/initdata.F90 Exec/test_problems/test_convect/GNUmakefile Exec/test_problems/test_planar_diag/GNUmakefile Exec/test_problems/test_stability/GNUmakefile Exec/unit_tests/test_advect/GNUmakefile Exec/unit_tests/test_average/GNUmakefile Exec/unit_tests/test_basestate/GNUmakefile Exec/unit_tests/test_diffusion/GNUmakefile Exec/unit_tests/test_eos/GNUmakefile Exec/unit_tests/test_projection/GNUmakefile Microphysics/EOS/Make.package Microphysics/EOS/README Microphysics/EOS/_parameters Microphysics/EOS/eos.F90 Microphysics/EOS/eos_override.F90 Microphysics/EOS/eos_type.F90 Microphysics/EOS/gamma_law/Make.package Microphysics/EOS/gamma_law/_parameters Microphysics/EOS/gamma_law/gamma_law.F90 Microphysics/conductivity/Make.package Microphysics/conductivity/conductivity.F90 Microphysics/conductivity/constant/Make.package Microphysics/conductivity/constant/_parameters Microphysics/conductivity/constant/constant_conductivity.F90 Microphysics/networks/Make.package Microphysics/networks/_parameters Microphysics/networks/burn_type.F90 Microphysics/networks/burner.F90 Microphysics/networks/general_null/H_He.net Microphysics/networks/general_null/H_core.net Microphysics/networks/general_null/Make.package Microphysics/networks/general_null/README Microphysics/networks/general_null/actual_burner.F90 Microphysics/networks/general_null/actual_rhs.F90 Microphysics/networks/general_null/aprox13.net Microphysics/networks/general_null/gammalaw.net Microphysics/networks/general_null/hotcno.net Microphysics/networks/general_null/ignition.net Microphysics/networks/general_null/ignition_wdconvect.net Microphysics/networks/general_null/network.template Microphysics/networks/general_null/network_header.template Microphysics/networks/general_null/pphotcno.net Microphysics/networks/general_null/simple.net Microphysics/networks/general_null/simple3.net Microphysics/networks/general_null/triple_alpha_plus_o.net Microphysics/networks/general_null/write_network.py Microphysics/networks/network.F90 Microphysics/networks/sdc_type.F90 Source/Src_nd/burner_loop.F90 Source/Src_nd/compute_dt.F90 Source/Src_nd/initdata.F90 Source/Src_nd/make_S.F90 Source/Src_nd/make_gamma.F90 Source/Src_nd/make_plot_variables.F90 Source/Src_nd/make_scal_force.F90 Source/Src_nd/rhoh_vs_t.F90 Source/Src_nd/update_scal.F90 external/Microphysics commit e17f134722e9880af7e654e75b0ac250cc2d59e1 Author: Alice Harpole Date: Mon Mar 2 17:52:55 2020 -0500 build doesn't know whether it's a dev or master version so pagename doesnt' contain dev string sphinx_docs/source/_templates/layout.html commit 8d8f9037fd90d8f30bd1072e7348f546ff1576c5 Author: Alice Harpole Date: Mon Mar 2 17:38:51 2020 -0500 fix jinja sphinx_docs/source/_templates/layout.html sphinx_docs/source/regtest.rst commit 9d49b0b4245e29d306d1be4720031016751dbcba Author: Alice Harpole Date: Mon Mar 2 17:08:39 2020 -0500 bash doesn't like -eq for strings deploy_docs.sh commit ff15b8de3b06c36cbfe89b610faf2530c640fba6 Author: Alice Harpole Date: Mon Mar 2 17:04:05 2020 -0500 bash doesn't like == deploy_docs.sh commit 93d64096b5be8f34662b3e42ebfc09f0f6c76cd0 Author: Alice Harpole Date: Mon Mar 2 16:57:37 2020 -0500 actually fix logic in deploy_docs.sh deploy_docs.sh commit 43774927b24085f791d3dde28b8e45b6891fa4e2 Author: Alice Harpole Date: Mon Mar 2 16:44:46 2020 -0500 fix logic in deploy_docs.sh deploy_docs.sh sphinx_docs/source/conf.py commit 7c7417a56c9e33ccb8dcdb22653cf3c4351b17a3 Author: Alice Harpole Date: Mon Mar 2 16:35:41 2020 -0500 add links to master and development branch to sidebar sphinx_docs/source/_static/theme_overrides.css sphinx_docs/source/_templates/layout.html sphinx_docs/source/conf.py commit 658ce6bb5c12e3d46fb816fb11807ec5fa54cf66 Author: Alice Harpole Date: Mon Mar 2 11:04:57 2020 -0500 modify deploy_docs.sh and travis build to generate dev version .travis.yml deploy_docs.sh commit d174093adaa297259f884603fe73fd948bdc01d7 Author: Doreen Fan Date: Mon Mar 2 12:09:59 2020 -0800 March 2020 release notes CHANGES.md commit a4e471c9edfdc9dbfc6c5d4418fd6af5e97e5cd3 Author: Doreen Fan Date: Mon Mar 2 11:25:28 2020 -0800 Set deterministic_nodal_solve=true in regression test inputs Exec/science/wdconvect/inputs_files/inputs_3d_amr_regression Exec/science/wdconvect/inputs_files/inputs_3d_regression Exec/science/wdconvect/inputs_files/inputs_omp_3d_regression Exec/test_problems/double_bubble/inputs_2d_regression Exec/test_problems/incomp_shear_jet/inputs_2d_regression Exec/test_problems/reacting_bubble/inputs_2d_amr_regression Exec/test_problems/reacting_bubble/inputs_2d_regression Exec/test_problems/reacting_bubble/inputs_2d_regression.2levels Exec/test_problems/reacting_bubble/inputs_3d_amr_regression Exec/test_problems/reacting_bubble/inputs_omp_2d_regression Exec/test_problems/reacting_bubble/inputs_omp_3d_regression Exec/test_problems/rt/inputs_2d_regression Exec/test_problems/test_convect/inputs_2d_regression Exec/test_problems/test_stability/inputs_2d_C_regression commit 3e5cb8de68d058a60e8025a4e5b1ea3365c69439 Merge: 464a20d4 77f1870f Author: Doreen Fan Date: Mon Mar 2 09:51:10 2020 -0800 merge conflicts commit 58c140bbe8e0c55ae87f235a5bb8ec92c4dc2a4d Merge: 88373ad6 6998d1a7 Author: Alice Harpole Date: Mon Mar 2 10:12:35 2020 -0500 Merge branch 'cpp_celltoedge' of github.com:AMReX-Astro/MAESTROeX into cpp_average commit 6998d1a72acb0f941cddb7dd6b00295dd04512c3 Merge: ea39bd2a 461ffd5c Author: Alice Harpole Date: Mon Mar 2 10:11:26 2020 -0500 merge conflicts commit ea39bd2a7335625a4f05228a8f0ee58ba3a31a48 Merge: 61712ed2 77f1870f Author: Alice Harpole Date: Mon Mar 2 10:10:19 2020 -0500 Merge branch 'cpp_psi_eta' of github.com:AMReX-Astro/MAESTROeX into cpp_celltoedge commit 77f1870f3d4ab0b311deaf50308b61372b395a3e Author: Alice Harpole Date: Mon Mar 2 10:08:45 2020 -0500 fix indexing Source/MaestroMakeEta.cpp commit 6e70a72f39c9b4486661ef167035705197bae295 Author: Alice Harpole Date: Mon Mar 2 09:58:49 2020 -0500 replaced Gpu::Atomic::Add with HostDevice::Atomic::Add and 2d reacting bubble now agrees with development to round off levels Source/MaestroMakeEta.cpp commit 219a501549080c30dfd240da23a68d1a2677f9d5 Merge: 3272ffa1 3605092a Author: Alice Harpole Date: Mon Mar 2 09:04:36 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_psi_eta commit 6503b9e047c7e9c1c909f478a72c4656e0993d69 Author: Travis CI <> Date: Fri Feb 28 22:43:20 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroAverage.cpp commit 4c4e51c8822f8e6d1a356d454cd7fbde389250ec Author: Alice Harpole Date: Fri Feb 28 17:16:44 2020 -0500 deleted base_state.F90 files Exec/science/code_comp/base_state.F90 Exec/science/flame/base_state.F90 Exec/test_problems/double_bubble/base_state.F90 Exec/test_problems/rt/base_state.F90 Exec/unit_tests/test_advect/base_state.F90 Exec/unit_tests/test_average/base_state.F90 Exec/unit_tests/test_diffusion/base_state.F90 Exec/unit_tests/test_react/base_state.F90 Source/MaestroInit.cpp Source/Src_nd/Make.package Source/Src_nd/base_state.F90 commit c7096e147fcd6b0a18ca99a9b6f3662831c50368 Author: Alice Harpole Date: Fri Feb 28 17:07:07 2020 -0500 converted base_state.F90 for code_comp Exec/science/code_comp/MaestroBaseState.cpp commit 028f653d772f2093d245fb21762a9fa83f38ce72 Author: Alice Harpole Date: Fri Feb 28 16:41:38 2020 -0500 converted base_state.F90 for test_react Exec/unit_tests/test_react/MaestroBaseState.cpp commit 93edbafcfa6f3ea67d340458e7a186dc3227db57 Author: Alice Harpole Date: Fri Feb 28 16:39:59 2020 -0500 converted base_state.F90 for test_diffusion Exec/unit_tests/test_diffusion/MaestroBaseState.cpp commit beb989e3b8febe016f723dbb4192186cd31b89df Author: Alice Harpole Date: Fri Feb 28 16:34:06 2020 -0500 converted base_state.F90 for test_average Exec/unit_tests/test_average/MaestroBaseState.cpp commit da530ef12da178ead94a056a453ead6a90c1f808 Author: Doreen Fan Date: Thu Feb 27 16:01:49 2020 -0800 remove tiling when computing phisum Source/MaestroAverage.cpp commit 3bb1ddda04dd8b5c19dcef7555300953372fe100 Author: Alice Harpole Date: Fri Feb 28 16:30:58 2020 -0500 converted base_state.F90 for test_advect Exec/unit_tests/test_advect/MaestroBaseState.cpp commit 52af525bf6fa77175e2ae03a382bc22f844162c1 Author: Alice Harpole Date: Fri Feb 28 16:18:32 2020 -0500 converted base_state.F90 for flame Exec/science/flame/MaestroBaseState.cpp commit c67c1c95a57ef382b7d14e5c8892e18d293f5886 Author: Alice Harpole Date: Fri Feb 28 15:46:34 2020 -0500 converted base_state.F90 for reacting_bubble Exec/test_problems/double_bubble/MaestroBaseState.cpp Exec/test_problems/rt/MaestroBaseState.cpp Source/MaestroBaseState.cpp commit adea3adb45627a261e84b0780d3ea01ae3b38c92 Author: Alice Harpole Date: Fri Feb 28 15:12:15 2020 -0500 converted base_state.F90 for rt Exec/test_problems/rt/MaestroBaseState.cpp Source/MaestroBaseState.cpp Source/MaestroInit.cpp Util/model_parser/ModelParser.H Util/model_parser/ModelParser.cpp commit aa921cf57f75aa27d145d6e159cca0c436c01e4d Author: Alice Harpole Date: Fri Feb 28 13:05:19 2020 -0500 InitBaseState compiles and links Exec/Make.Maestro Source/Maestro.H Source/MaestroBaseState.cpp Source/MaestroInletBC.cpp Source/Make.package Util/model_parser/ModelParser.H Util/model_parser/ModelParser.cpp Util/simple_log/SimpleLog.H Util/simple_log/SimpleLog.cpp Util/utils/MaestroUtil.H Util/utils/MaestroUtil.cpp Util/utils/Make.package commit 3605092a9c728f45a6544f74f6dbe81804ea47b3 Merge: c60f72aa f1f452b6 Author: Michael Zingale Date: Fri Feb 28 12:10:03 2020 -0500 Merge branch 'development' of github.com:amrex-astro/MAESTROeX into development commit c60f72aae366e0c9b58bf82ae625257446b6a7de Author: Michael Zingale Date: Fri Feb 28 12:09:51 2020 -0500 fix cuda compilation Microphysics/networks/network.F90 commit 900d3c2b64d5b470ee58550598f4cab280cac4e6 Author: Alice Harpole Date: Fri Feb 28 09:49:08 2020 -0500 added a simplelog class Source/MaestroBCFill.cpp Util/model_parser/ModelParser.H Util/model_parser/ModelParser.cpp Util/simple_log/Make.package Util/simple_log/SimpleLog.H Util/simple_log/SimpleLog.cpp commit 5c5251b990be1319a783d5317e73ae21340cbabe Merge: edd998ce f1f452b6 Author: Alice Harpole Date: Fri Feb 28 08:57:50 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_base_state commit edd998cec2f0d2f6ac7607f465de0d050ee2e22a Author: Alice Harpole Date: Fri Feb 28 08:57:48 2020 -0500 merge conflicts Source/MaestroBCFill.cpp commit 60588079628adae8d89a711227c10c6f16f6a36a Author: Alice Harpole Date: Thu Feb 27 16:37:07 2020 -0500 model parser class .travis.yml Source/Maestro.H Source/MaestroBaseState.cpp Source/Make.package Util/model_parser/Make.package Util/model_parser/ModelParser.H Util/model_parser/ModelParser.cpp commit cd205595fab791733e8d7a8d6e26cacf0e752fd0 Author: Doreen Fan Date: Thu Feb 27 11:36:56 2020 -0800 Remove omp threading when computing phisum Source/MaestroAverage.cpp commit ee7aacc20b449fafb20aacba8c84b685ec1fb035 Author: Alice Harpole Date: Wed Feb 26 17:44:46 2020 -0500 converted update_scal.F90 Source/MaestroAdvection.cpp Source/Src_nd/Make.package Source/Src_nd/update_scal.F90 commit 3320e2fc3169e3cc9973b2864bf9a32b3a825a4f Author: Alice Harpole Date: Wed Feb 26 17:35:22 2020 -0500 converted make_S.F90 Source/MaestroMakeS.cpp Source/Src_nd/Make.package Source/Src_nd/make_S.F90 commit a86f6b791aaaf7585138e8dcb0401ca911b017d5 Author: Doreen Fan Date: Wed Feb 26 13:44:35 2020 -0800 fix merge conflicts Source/MaestroMakeEta.cpp commit 9ac0e8d559e5d0c0de1753f74e63d6632236d9ff Merge: 88373ad6 461ffd5c Author: Doreen Fan Date: Wed Feb 26 12:45:13 2020 -0800 Merge branch 'cpp_celltoedge' into cpp_average commit ac67157831dedfca80146197144f06311ebcbbfb Author: Alice Harpole Date: Wed Feb 26 15:41:15 2020 -0500 converted make_gamma.F90 Source/MaestroGamma.cpp Source/MaestroRhoHT.cpp Source/Src_nd/Make.package Source/Src_nd/make_gamma.F90 Source/Src_nd/rhoh_vs_t.F90 commit 7ac4371e1690b3aaf29d85d9d26b33eeb71f477c Author: Alice Harpole Date: Wed Feb 26 15:13:58 2020 -0500 converted rhoh_vs_t.F90 Source/Maestro.H Source/MaestroRhoHT.cpp commit f0fbe0fb54da40b91557091fba26ad9e3377d12b Author: Alice Harpole Date: Wed Feb 26 10:00:43 2020 -0500 it compiles and runs! Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/maestro_init.F90 Source/param/meth_params.template Source/param/set_variables.py Source/param_includes/meth_params.F90 commit b47f3b82c59b51412a201eaa831d95e769528963 Author: Alice Harpole Date: Wed Feb 26 09:12:35 2020 -0500 it compiles and links Exec/Make.Maestro Source/param/runtime.probin.template commit 461ffd5c2d882c4667ec446d4279875623429488 Merge: 61712ed2 464a20d4 Author: Doreen Fan Date: Tue Feb 25 16:17:57 2020 -0800 Merge branch 'cpp_psi_eta' into cpp_celltoedge commit 464a20d49d58eabedd99d23d42d5d03ff0dca447 Author: Doreen Fan Date: Tue Feb 25 15:56:52 2020 -0800 remove omp threading from MakeEtarho planar Source/MaestroMakeEta.cpp commit f1f452b6cc3d79c4b1d07d924698e3cce37c0a61 Author: Donald E. Willcox Date: Tue Feb 25 15:42:32 2020 -0800 generalize print-extrema to use AMReXDataset so it works with other codes. Exec/science/urca/analysis/scripts/print-extrema commit 42388ddfcebf8b28266bef8972885636ff8022bb Author: Donald E. Willcox Date: Wed Jan 8 12:15:44 2020 -0800 cleanup comments, specify maestro.sum_interval=1 Exec/science/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/levels-1.1024/inputs_3d_1lev.5120 Exec/science/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/levels-2.1024/inputs_3d_2lev.5120 commit ef612749b31b036cc7e44bdeaa6e040a11a7454d Author: Donald E. Willcox Date: Wed Jan 8 12:13:25 2020 -0800 add yt script just for printing field extrema Exec/science/urca/analysis/scripts/print-extrema commit 22143f2f7afcb2a52ef46aac19bef4a9f0715723 Author: Donald E. Willcox Date: Wed Jan 8 12:05:49 2020 -0800 fix indentation Exec/science/urca/tagging.F90 commit 6a7f6df3816069047a53079aae0cf5f10c613e38 Author: Donald E. Willcox Date: Wed Jan 8 12:05:25 2020 -0800 remove duplicates Exec/science/urca/_parameters commit 300f77ba0c88f706dc929f2b17cdd84d210d2e81 Author: Alice Harpole Date: Tue Feb 25 16:52:31 2020 -0500 almost compiles to fails to link as cannot find eos_gamma Source/Maestro.H Source/MaestroRhoHT.cpp Source/MaestroSetup.cpp commit b6f10d2a25f384eab0b5ee8820b65fd3b6d60f37 Author: Alice Harpole Date: Tue Feb 25 16:41:45 2020 -0500 refigured the variables set up so that the indices can be defined as constexpr's Source/Maestro.H Source/Maestro.cpp Source/MaestroSetup.cpp Source/param/_variables Source/param/meth_params.template Source/param/set_variables.py Source/param_includes/Make.package Source/param_includes/meth_params.F90 Source/param_includes/state_indices.H Source/param_includes/state_indices_nd.F90 Source/param_includes/state_sizes.F90 commit 53ba1a9762a019deee2ce8f33333417757303286 Author: Alice Harpole Date: Tue Feb 25 15:42:16 2020 -0500 RT compiles Exec/Make.Maestro Exec/test_problems/rt/initdata.F90 Microphysics/EOS/Make.package Microphysics/interfaces/Make.package Microphysics/interfaces/README.md Microphysics/interfaces/burn_type.F90 Microphysics/interfaces/burner.F90 Microphysics/interfaces/conductivity.F90 Microphysics/interfaces/eos.F90 Microphysics/interfaces/eos.H Microphysics/interfaces/eos_F.H Microphysics/interfaces/eos_data.H Microphysics/interfaces/eos_data.cpp Microphysics/interfaces/eos_override.F90 Microphysics/interfaces/eos_override.H Microphysics/interfaces/eos_type.F90 Microphysics/interfaces/eos_type.H Microphysics/interfaces/extern_probin.template Microphysics/interfaces/fundamental_constants.H Microphysics/interfaces/microphysics.F90 Microphysics/interfaces/network.F90 Microphysics/interfaces/network.H Microphysics/interfaces/sdc_type.F90 Microphysics/networks/burner.F90 Source/Maestro.H Source/Src_nd/compute_dt.F90 Source/Src_nd/initdata.F90 Source/Src_nd/make_S.F90 Source/Src_nd/make_gamma.F90 Source/Src_nd/make_plot_variables.F90 Source/Src_nd/make_scal_force.F90 Source/Src_nd/rhoh_vs_t.F90 Source/Src_nd/update_scal.F90 commit 88373ad61009c08d712a22221c5d2ea6f0fbd923 Merge: 734defb4 61712ed2 Author: Alice Harpole Date: Tue Feb 25 14:54:51 2020 -0500 merge conflicts commit 61712ed27a7eaf40b50f2908f3297aabee09d3b8 Merge: 6bc7c8ac 3272ffa1 Author: Alice Harpole Date: Tue Feb 25 14:53:26 2020 -0500 merge conflicts commit 3272ffa1d743ac20a4b198953077d0fd1e1154d7 Merge: f54e5c9e 1192dae1 Author: Alice Harpole Date: Tue Feb 25 14:47:32 2020 -0500 merge conflicts commit f54e5c9ee2b4eb503da64e4ff069cca0c4c097a0 Author: Alice Harpole Date: Tue Feb 25 14:46:46 2020 -0500 fix 2d and 3d tests Source/MaestroAdvance.cpp Source/MaestroMakeEta.cpp Source/Src_nd/make_eta.F90 commit 1192dae18d0511719ff241877b2b25ac0148690c Author: Travis CI <> Date: Tue Feb 25 19:43:15 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroMakeEta.cpp commit 82bf2cbaebbde48af77977724217c644ffaf9b6e Merge: e88b6e39 7a8c4e3e Author: Doreen Fan Date: Tue Feb 25 11:44:08 2020 -0800 Merge branch 'cpp_psi_eta' of https://github.com/AMReX-Astro/MAESTROeX into cpp_psi_eta commit e88b6e3955eb732e1e79241ff4972828aa10d96e Author: Doreen Fan Date: Tue Feb 25 11:43:56 2020 -0800 more index fixes Source/MaestroMakeEta.cpp commit 4b3cef34b3d272806b9d0c75d6408f6f6a211ce2 Merge: 7a8c4e3e d0a3ea03 Author: Alice Harpole Date: Tue Feb 25 14:34:02 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_psi_eta commit d0a3ea030de9919e40c878c5367132b7e7b0770d Author: Alice Harpole Date: Tue Feb 25 12:31:14 2020 -0500 fix loop step size for EDGE_INTERP Source/Src_nd/fill_umac_ghost.F90 commit 734defb4246d606c1c4a1d66712c5745e24c411d Merge: 45ba8aee 6bc7c8ac Author: Alice Harpole Date: Tue Feb 25 09:25:05 2020 -0500 merge conflicts commit 6bc7c8ac405418653515260801dcf1f46206ab0d Merge: cd5fc0c8 7a8c4e3e Author: Alice Harpole Date: Tue Feb 25 09:23:23 2020 -0500 Merge branch 'cpp_psi_eta' of github.com:AMReX-Astro/MAESTROeX into cpp_celltoedge commit 7a8c4e3e3aa692f14a7dee981f529223368cb5b5 Merge: 63690ff5 99800e5d Author: Alice Harpole Date: Tue Feb 25 09:22:58 2020 -0500 merge conflicts commit 99800e5d5a61738174f20e7f52e8eba4a60d5453 Merge: 8d4d2c68 c4b3fbbc Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Mon Feb 24 19:17:27 2020 -0800 Merge pull request #156 from AMReX-Astro/cpp_enforce_HSE Convert enforce_HSE to C++ commit 63690ff5466e71ad54a8c1769997cb1c57aa8aff Merge: 9e0fda36 8d4d2c68 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Mon Feb 24 18:40:36 2020 -0800 Merge branch 'development' into cpp_psi_eta commit c4b3fbbc67e0417ecff28f8b54a91e05bb4fc0b9 Merge: 4c82b698 598edb7c Author: Michael Zingale Date: Mon Feb 24 21:16:15 2020 -0500 Merge branch 'cpp_makebeta0' into cpp_enforce_HSE commit 598edb7c0362861f5128fdc95b75571b7fa4bd8f Merge: deea5404 8d4d2c68 Author: Michael Zingale Date: Mon Feb 24 21:16:02 2020 -0500 Merge branch 'development' into cpp_makebeta0 commit 9e0fda36fd79fb4599a4d71c7461c10ee3d8fc1b Merge: 257612d3 4c82b698 Author: Doreen Fan Date: Mon Feb 24 18:15:58 2020 -0800 Merge branch 'cpp_enforce_HSE' into cpp_psi_eta commit 4c82b698145d48b77642e2422022a8e2ec64b700 Merge: c15d8a38 deea5404 Author: Doreen Fan Date: Mon Feb 24 18:15:28 2020 -0800 Merge branch 'cpp_makebeta0' into cpp_enforce_HSE commit 8d4d2c686b9b3f76794c951dbf7301608d249b6f Author: Alice Harpole Date: Mon Feb 24 21:14:02 2020 -0500 Convert make_beta0 to C++ (#155) This converts the routines in make_beta0.F90 to C++. It combines the standard and irregular base state versions, therefore significantly reducing the amount of code duplication. Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakew0.cpp Source/MaestroPlot.cpp Source/MaestroRegrid.cpp Source/Make.package Source/Src_nd/Make.package Source/Src_nd/make_beta0.F90 Source/Src_nd/make_w0.F90 commit deea5404ff26d2305e5d95f97c5c0bdae8b4685c Merge: 50260b85 b4dc5bec Author: Michael Zingale Date: Mon Feb 24 21:00:18 2020 -0500 Merge branch 'development' into cpp_makebeta0 commit 257612d39628af58be694a7fc203c7ee6da3c0da Author: Doreen Fan Date: Mon Feb 24 16:23:52 2020 -0800 GPU index fix Source/MaestroMakeEta.cpp commit b4dc5bec393e546cce50fdebf10fff620bcfdbb1 Author: Michael Zingale Date: Mon Feb 24 19:17:25 2020 -0500 update general_null to sync with the main Microphysics Exec/test_problems/rt/GNUmakefile Microphysics/networks/general_null/Make.package Microphysics/networks/general_null/network.template Microphysics/networks/general_null/network_header.template Microphysics/networks/general_null/write_network.py commit 3d823f485f72c60b21d8073e12e4856a52bec80b Author: Alice Harpole Date: Mon Feb 24 15:40:32 2020 -0500 get rid of aion_inv from network.F90 Microphysics/networks/network.F90 commit 6f723db10c255d1b72e029f76654a62cc09bece6 Author: Alice Harpole Date: Mon Feb 24 11:55:51 2020 -0500 fix static analysis complaints Source/MaestroMakew0.cpp commit 45ba8aeee3f9be3bf7aa76b551201ebc9ce5f7d5 Author: Alice Harpole Date: Mon Feb 24 10:05:48 2020 -0500 fix static analysis complaints Source/MaestroAdvance.cpp Source/MaestroAdvectBase.cpp Source/MaestroAverage.cpp Source/MaestroFill3dData.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeEta.cpp Source/MaestroMakePsi.cpp Source/MaestroMakew0.cpp commit e425f376effd36be1901cb1d035b4b55c77ac481 Author: Alice Harpole Date: Mon Feb 24 09:23:36 2020 -0500 GPU fixes Source/MaestroAverage.cpp commit 0ad642d2b5d9e7e2b2abd98c6112a37c9188bffd Author: Alice Harpole Date: Fri Feb 21 17:46:20 2020 -0500 hardcode a max level and abort if exceeded (#160) This hardcodes a maximum level and will cause the code to abort before it tries to do set up any grids if that level is exceeded. This is needed to define some C arrays within C++ lambda regions (as they require the size to be known at compile time). Source/Maestro.H Source/MaestroSetup.cpp Source/main.cpp commit ce904852297a79a86a6af5939c2c98713aaf41c5 Merge: 80181468 8ab5eb20 Author: Alice Harpole Date: Fri Feb 21 17:21:22 2020 -0500 Merge branch 'max_level_limit' of github.com:AMReX-Astro/MAESTROeX into cpp_average commit 8ab5eb2021923093899917ff76e66dd0abeeb292 Author: Alice Harpole Date: Fri Feb 21 17:14:29 2020 -0500 hardcode a max level and abort if exceeded Source/Maestro.H Source/MaestroSetup.cpp Source/main.cpp commit 80181468d836132a0d2b9f405d9567fc4e6a04c3 Author: Alice Harpole Date: Fri Feb 21 16:19:23 2020 -0500 fix multilevel wdconvect so it agrees with development Source/MaestroAverage.cpp Source/Src_nd/average.F90 commit 34617edc35fd9725e0c0b65155b116e8a1942735 Merge: 8d5fbb5b cd5fc0c8 Author: Alice Harpole Date: Fri Feb 21 09:58:43 2020 -0500 Merge branch 'cpp_celltoedge' of github.com:AMReX-Astro/MAESTROeX into cpp_average commit cd5fc0c84e23f82bc36939d4e7e4735e3d3991fc Merge: 55b06d59 f6e7508a Author: Alice Harpole Date: Fri Feb 21 09:58:19 2020 -0500 Merge branch 'cpp_psi_eta' of github.com:AMReX-Astro/MAESTROeX into cpp_celltoedge commit f6e7508a0888a1b4fba23bd15852d2f4ed543a1f Merge: 46b8def3 c15d8a38 Author: Alice Harpole Date: Fri Feb 21 09:57:23 2020 -0500 Merge branch 'cpp_enforce_HSE' of github.com:AMReX-Astro/MAESTROeX into cpp_psi_eta commit c15d8a380a30af1e6bd4e686c29a7671ebb9d24d Merge: a18d8257 50260b85 Author: Alice Harpole Date: Fri Feb 21 09:56:29 2020 -0500 Merge branch 'cpp_makebeta0' of github.com:AMReX-Astro/MAESTROeX into cpp_enforce_HSE commit 50260b852daf17e373aa51b01accfd7dbabfc128 Merge: 95d74f96 c7b8a90d Author: Alice Harpole Date: Fri Feb 21 09:55:55 2020 -0500 merge conflicts commit c7b8a90d8a9d5164b3592c98c92b0bd7a6b76041 Author: Alice Harpole Date: Fri Feb 21 09:52:57 2020 -0500 yet more indexing fixes Source/MaestroMakew0.cpp commit 95d74f966033bd9939bb6917178ac5bde668b41e Merge: 134af510 ec2b9c0d Author: Alice Harpole Date: Fri Feb 21 09:39:53 2020 -0500 merge conflicts commit 134af51070eccf658db68c24cfc1545a1f329bc6 Author: Alice Harpole Date: Fri Feb 21 09:38:51 2020 -0500 some more indexing fixes Source/MaestroMakew0.cpp commit ec2b9c0d1341389087c27884d28d1beb6c4a4bb1 Author: Doreen Fan Date: Thu Feb 20 16:07:53 2020 -0800 GPU fixes for Makew0 PlanarVarg and SphrIrreg Source/MaestroMakew0.cpp commit d7e9726255404e0d5d40b050776ffc655c6f8110 Merge: 57cc9307 3b3ce892 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Thu Feb 20 14:03:24 2020 -0800 Merge pull request #154 from AMReX-Astro/cpp_makew0 Convert routines in make_w0.F90 to C++ commit 8d5fbb5b700ad97808a517d5da3fecbeaf531327 Merge: d1fe7bff 55b06d59 Author: Alice Harpole Date: Thu Feb 20 16:08:50 2020 -0500 merge conflicts commit 55b06d593c87428707422b5d6f1577be58b65f8e Merge: e04df68c 46b8def3 Author: Alice Harpole Date: Thu Feb 20 16:07:25 2020 -0500 Merge branch 'cpp_psi_eta' of github.com:AMReX-Astro/MAESTROeX into cpp_celltoedge commit 46b8def3c8a7d7a507f9718ac22071d89296f458 Merge: 3db24185 a18d8257 Author: Alice Harpole Date: Thu Feb 20 16:06:57 2020 -0500 Merge branch 'cpp_enforce_HSE' of github.com:AMReX-Astro/MAESTROeX into cpp_psi_eta commit a18d82574219a3ae41469d632a7777165f3cbdcd Merge: 3de0377e c280baa4 Author: Alice Harpole Date: Thu Feb 20 16:06:34 2020 -0500 Merge branch 'cpp_makebeta0' of github.com:AMReX-Astro/MAESTROeX into cpp_enforce_HSE commit c280baa4fa9ff71ec4fb8f41cf30313a071ad066 Merge: 2d686d03 3b3ce892 Author: Alice Harpole Date: Thu Feb 20 16:06:05 2020 -0500 Merge branch 'cpp_makew0' of github.com:AMReX-Astro/MAESTROeX into cpp_makebeta0 commit 3b3ce8929dcdcb2e70a812789432f74eb4a67bcf Author: Alice Harpole Date: Thu Feb 20 16:02:03 2020 -0500 fixed more array accesses Source/MaestroMakew0.cpp commit 257147b6a7a68f6aecb591e0ad62f0600578b1b3 Author: Doreen Fan Date: Thu Feb 20 12:23:52 2020 -0800 need to sync host and gpu values before calling tridiag Source/MaestroMakew0.cpp commit 57cc9307a364cddd46636f1825adf3c03e93adaa Author: Michael Zingale Date: Thu Feb 20 14:56:12 2020 -0500 better parameters Exec/science/fully_convective_star/inputs_3d commit 3711f2e890430279e2eb997344b184e21249b1a6 Author: Alice Harpole Date: Thu Feb 20 14:48:09 2020 -0500 fix some array accesses Source/MaestroMakew0.cpp commit 9bc7ac4eb69a4b84a1066274b74c2d9b535838e0 Author: Michael Zingale Date: Thu Feb 20 13:19:18 2020 -0500 add a perturbation to make the projections easier Exec/science/fully_convective_star/initdata.F90 Exec/science/fully_convective_star/inputs_3d commit 17f09d8a39bc28464fa7098352e0f2ec591a8e81 Merge: d21dc55b 8e8157c4 Author: Alice Harpole Date: Thu Feb 20 13:04:25 2020 -0500 Merge branch 'cpp_makew0' of github.com:AMReX-Astro/MAESTROeX into cpp_makew0 commit d21dc55bdac946e8fe174fbf298e91e29f35eb0a Author: Alice Harpole Date: Thu Feb 20 13:03:50 2020 -0500 fix illegal memory access Source/MaestroMakew0.cpp commit 31d92edc5893d0ef8c8fa11230918d938d636cd1 Merge: 7cb04840 f37eb3c0 Author: Alice Harpole Date: Thu Feb 20 12:51:27 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_makew0 commit d1fe7bfff6891e35a804d6541d09098d8a7e061f Author: Alice Harpole Date: Thu Feb 20 11:42:01 2020 -0500 GPU fixes Source/MaestroAdvance.cpp Source/MaestroAverage.cpp Source/MaestroMakeBeta0.cpp Source/MaestroMakew0.cpp commit f37eb3c0d69f0c14b4af353420c0b13daf5ed960 Author: Michael Zingale Date: Thu Feb 20 11:25:15 2020 -0500 turn off rotation fix anelastic_cutoff Exec/science/fully_convective_star/GNUmakefile Exec/science/fully_convective_star/inputs_3d commit 8e8157c499b376487df6f66c9b55606651f20255 Merge: 7cb04840 6f22b22b Author: Doreen Fan Date: Wed Feb 19 13:41:54 2020 -0800 Merge branch 'development' into cpp_makew0 commit 0d7f06ed22f8581fb1a296a4ab8adbb42b0ebd72 Merge: f080692c 6f22b22b Author: Alice Harpole Date: Wed Feb 19 14:36:11 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_average commit 6f22b22b8044a18633ed6cc7669fa43602955598 Author: Alice Harpole Date: Wed Feb 19 14:34:31 2020 -0500 GPU fixes Source/MaestroForce.cpp Source/MaestroMakeEdgeState.cpp commit f080692cb55e697e3e64254d1351921c796cc6ab Author: Alice Harpole Date: Wed Feb 19 11:15:08 2020 -0500 converted average_sphr Source/Maestro.H Source/MaestroAverage.cpp Source/MaestroFill3dData.cpp Source/MaestroMakeEta.cpp Source/Src_nd/average.F90 commit a0f2146c891d56a0beaf4e4709339e0a76930a83 Author: Alice Harpole Date: Tue Feb 18 16:08:59 2020 -0500 converted divide_phisum_by_cell Source/MaestroAverage.cpp Source/MaestroMakeEta.cpp commit e04df68ce6c5d8750e69dd673b066530b9aa3dd6 Author: Alice Harpole Date: Tue Feb 18 15:23:11 2020 -0500 deleted file Source/Src_nd/cell_to_edge.F90 commit ab2aea4cb08ca472955dcc6794ef16d286c2b7b3 Author: Alice Harpole Date: Tue Feb 18 15:11:07 2020 -0500 converted cell_to_edge Source/Maestro.H Source/MaestroCelltoEdge.cpp Source/MaestroDensityAdvance.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp Source/MaestroRhoHT.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/Make.package Source/Src_nd/compute_grad_phi.F90 Source/Src_nd/make_eta.F90 Source/Src_nd/make_psi.F90 commit 3db24185b3d04baee102486ce3063b76595e98cc Author: Alice Harpole Date: Tue Feb 18 14:42:07 2020 -0500 fix gpu bug Source/MaestroAdvance.cpp Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroMakeEta.cpp Source/MaestroMakePsi.cpp Source/MaestroNodalProj.cpp commit b6bbf34732598cbf9ccd9a8fdcb0709cec376111 Author: Alice Harpole Date: Tue Feb 18 10:19:43 2020 -0500 convert MakeEtarho Source/MaestroMakeEta.cpp commit 25d0a887d44b0a53358140a8ba8d35743fc42aad Merge: a441c541 e18e6861 Author: Alice Harpole Date: Tue Feb 18 09:14:36 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_psi_eta commit a441c541b2017ea9a0dffa996f5ca37a494882be Author: Alice Harpole Date: Mon Feb 17 17:22:48 2020 -0500 converted sum_etarho Source/MaestroMakeEta.cpp Source/MaestroMakePsi.cpp Source/Src_nd/make_eta.F90 commit 7cb0484030066fbc1a2a6080fbbb450dda001ee6 Merge: 2fc9ba38 e18e6861 Author: Alice Harpole Date: Mon Feb 17 16:00:18 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_makew0 commit e18e686152688d87dca66740c6250660f29bcc93 Merge: 8f9e9c19 0e7d4688 Author: Alice Harpole Date: Mon Feb 17 15:59:56 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 8f9e9c19d0399280e19aa45cbda15a12d0e9e395 Author: Alice Harpole Date: Mon Feb 17 15:59:45 2020 -0500 restrict base and fill ghost base on the cell centered quantity Source/Src_nd/make_eta.F90 commit 0e7d468851788b651965df92d684cfbe2c7f205c Author: Michael Zingale Date: Mon Feb 17 15:45:50 2020 -0500 put autogenerated source files in their own subdirectory (#157) Exec/Make.Maestro commit 3f630bb11707bcd82d5048cae857e2d061143c7c Merge: 0e30e959 3de0377e Author: Alice Harpole Date: Mon Feb 17 15:22:32 2020 -0500 Merge branch 'cpp_enforce_HSE' of github.com:AMReX-Astro/MAESTROeX into cpp_psi_eta commit 3de0377e249fb2752a3df48349b10c785b49a6b9 Merge: cc892aa7 2d686d03 Author: Alice Harpole Date: Mon Feb 17 14:55:20 2020 -0500 Merge branch 'cpp_makebeta0' of github.com:AMReX-Astro/MAESTROeX into cpp_enforce_HSE commit 2d686d034dda315383f7caf8d85d24266c8aaaa3 Merge: c7071214 2fc9ba38 Author: Alice Harpole Date: Mon Feb 17 14:54:53 2020 -0500 merge conflicts commit 2fc9ba381f58f347018b487fc1f893d210417f2e Author: Alice Harpole Date: Mon Feb 17 14:42:57 2020 -0500 git merge broke things Source/MaestroBaseStateGeometry.cpp commit 603f2a86538615be1da3c17f21cfe701af1b59d2 Merge: 0c8db411 f1d73f7e Author: Alice Harpole Date: Mon Feb 17 13:26:41 2020 -0500 merge conflicts commit f1d73f7e428f698f2d05b28ea886fa523fb47d6b Author: Alice Harpole Date: Mon Feb 17 13:07:32 2020 -0500 added inputs file for GPU regression test with relaxed nodal solver tolerance Exec/test_problems/reacting_bubble/inputs_3d_gpu_regression Source/MaestroBaseStateGeometry.cpp commit 334a2d9e4f5169fb1c5c916da6a317ff0be3b127 Author: Alice Harpole Date: Mon Feb 17 12:42:14 2020 -0500 define local copy of dt for GPU runs Source/MaestroMakeEdgeScalars.cpp commit 14a178ca478608e85a29375d79d6199751618cf0 Author: Alice Harpole Date: Mon Feb 17 10:25:33 2020 -0500 actually fix image formatting sphinx_docs/source/regtest.rst commit e2b8c1c3c2c1bdf3e3f7d59fa9b911721b27b686 Author: Alice Harpole Date: Mon Feb 17 10:12:50 2020 -0500 fix image formatting sphinx_docs/source/regtest.rst commit 32fa8ffde442e76d86113418995b2b3c492a7a5e Author: Alice Harpole Date: Mon Feb 17 10:05:01 2020 -0500 added some documentation on travis sphinx_docs/source/regtest.rst commit 0c8db411331d7c6d9870e117c321e41ddff9ca0e Author: Alice Harpole Date: Mon Feb 17 09:16:17 2020 -0500 fixed base state routines so multilevel planar problems now agree with development branch Source/MaestroBaseStateGeometry.cpp Source/MaestroMakew0.cpp Source/Src_nd/make_w0.F90 commit 0e30e9592448459d29406fea8d5f4751e40367d7 Author: Alice Harpole Date: Fri Feb 14 16:12:33 2020 -0500 MakePsi works for reacting bubble 3d Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroMakePsi.cpp commit 426c39e7646b32427300035dea6b5165e0950e18 Merge: a2309c4c cc892aa7 Author: Alice Harpole Date: Fri Feb 14 15:44:42 2020 -0500 Merge branch 'cpp_enforce_HSE' of github.com:AMReX-Astro/MAESTROeX into cpp_psi_eta commit cc892aa7ef4577ec34ade5b424010ce22a7b6796 Merge: 3dc81ae8 c7071214 Author: Alice Harpole Date: Fri Feb 14 15:44:13 2020 -0500 Merge branch 'cpp_makebeta0' of github.com:AMReX-Astro/MAESTROeX into cpp_enforce_HSE commit c70712142299493f597cbc50e11606188e930895 Merge: 6367cb53 728f2742 Author: Alice Harpole Date: Fri Feb 14 15:43:39 2020 -0500 Merge branch 'cpp_makew0' of github.com:AMReX-Astro/MAESTROeX into cpp_makebeta0 commit 728f27428b4c067e3f0d9c687f221baca9ecdae4 Merge: 06fdffc6 7097d2eb Author: Alice Harpole Date: Fri Feb 14 15:43:07 2020 -0500 merge conflicts commit a2309c4cba0ed9ca3d1efa162a94a21bdd15f5e8 Author: Alice Harpole Date: Fri Feb 14 15:36:08 2020 -0500 started converting make_psi Source/MaestroMakePsi.cpp Source/Make.package commit 7097d2ebbd387ff318d6416489c253a77378658a Author: Alice Harpole Date: Fri Feb 14 15:35:44 2020 -0500 Convert advect_base.F90 routines to C++ (#148) This converts the routines in advect_base.F90 and make_edge_scal.F90 to C++. It also converts a couple of the routines in base_state_geometry.F90 in order to do base state restriction and ghost filling. The indexing of the 1d base states is quite messy at the moment, but should become clearer when we switch to storing the base state as a Vector of RealVectors. This should not change the results of single level problems. Testing 3d reacting_bubble with 3 levels gives no changes for ppm_type=0, and small round-off level changes for types 1 and 2. It compiles and runs on the GPU. * converting make_edge_state * fixed compilation * started converting make_edge_state_1d_planar * (mostly) converted advect_base * it compiles * it works for spherical=1, ppm_type=0 * it works for spherical=1, ppm_type=0 * it works for spherical=1, ppm_type=1 * it works for spherical=1, ppm_type=2 * it works for spherical=0, ppm_type=0 * it works for spherical=0, ppm_type=1 * it works for spherical=0, ppm_type=2 * RestructBase and FillGhostBase seem to work with amr * gives no diffs for AMR for ppm_type=0, and round-off diffs for ppm_type=1 or 2 * removed fortran files * GPU fixes * fixed some loops to reduce errors in multilevel wdconvect * max_radial_level -> finest_radial_level Co-authored-by: Adam Jacobs Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvectBase.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroMakeEdgeState.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/Make.package Source/Src_nd/advect_base.F90 Source/Src_nd/base_state_geometry.F90 Source/Src_nd/make_edge_state.F90 commit 3dc81ae8176058710435441c1281d9055155fcec Merge: a47412ee 6e233d2c Author: Alice Harpole Date: Fri Feb 14 15:27:49 2020 -0500 merge conflicts commit 6367cb53997762ef81007f6c3f2ca65f4165492b Merge: 38eb992e 6e233d2c Author: Alice Harpole Date: Fri Feb 14 15:26:56 2020 -0500 merge conflicts commit 06fdffc618c30bec5a30588f77b39278d3ca4972 Merge: a0a564c1 6e233d2c Author: Alice Harpole Date: Fri Feb 14 15:25:44 2020 -0500 merge conflicts commit 6e233d2cd87582c60f994ef2e53ab80ea9cf1fe7 Merge: 2dcd7118 919727cc Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Fri Feb 14 12:23:07 2020 -0800 Merge pull request #153 from AMReX-Astro/cpp_fill_3d_data Convert routines in fill_3d_data to C++ commit 2dcd71181b51db8efae361e3414fb8b39ca48f3f Author: Alice Harpole Date: Fri Feb 14 15:17:48 2020 -0500 add cron to job type .travis.yml commit 919727cc93ce85effe39ba12c54f9b3249ae8f75 Author: Travis CI <> Date: Fri Feb 14 20:12:29 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/MaestroCheckpoint.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroMakeEdgeScalars.cpp commit b7f5c10c49435b81986da69ff4adb00c6c3b9906 Merge: 40e56fbf d52443ea Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Fri Feb 14 12:08:09 2020 -0800 Merge branch 'development' into cpp_fill_3d_data commit a47412eeaf1591465291eca1301616794cfea0d4 Author: Alice Harpole Date: Fri Feb 14 15:07:51 2020 -0500 fix static analysis complaints Source/MaestroEnforceHSE.cpp commit 2ae8db487f5d8e8a3b6ce9b85f09b7b76b80519e Author: Alice Harpole Date: Fri Feb 14 13:22:09 2020 -0500 converted enforce_HSE to C++ Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroEnforceHSE.cpp Source/MaestroInit.cpp Source/MaestroRegrid.cpp Source/Make.package commit 38eb992e3520e4636687d142be8cefbe6c7a55ae Author: Alice Harpole Date: Fri Feb 14 12:43:29 2020 -0500 got rid of more make_grav_cell's Source/MaestroAdvance.cpp Source/MaestroForce.cpp Source/MaestroPlot.cpp Source/MaestroRegrid.cpp commit 2dca4a9c4abdaeb196a34d388231ad202c9bfc43 Author: Alice Harpole Date: Fri Feb 14 11:53:38 2020 -0500 fix compilation Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/Src_nd/Make.package Source/Src_nd/make_w0.F90 commit 3aa5e62f0ac04e6b09981c6c8f6de562fd12fccd Author: Alice Harpole Date: Fri Feb 14 10:28:42 2020 -0500 GPU fixes Source/MaestroMakeBeta0.cpp commit 47621f21b9d4537a65a2399d1354848a138d7ddc Author: Alice Harpole Date: Fri Feb 14 10:26:13 2020 -0500 switched out a load of make_grav_cell's for MakeGravCell Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroInit.cpp Source/MaestroMakeBeta0.cpp Source/Src_nd/Make.package Source/Src_nd/make_beta0.F90 commit 824770a3be5f1ce5d3c411c068295b317ec4e8d7 Author: Alice Harpole Date: Fri Feb 14 09:58:52 2020 -0500 MakeBeta0 works for reacting bubble 2d and 3d with OMP and MPI Source/MaestroAdvance.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroInit.cpp Source/MaestroMakeBeta0.cpp Source/MaestroRegrid.cpp Source/Src_nd/make_beta0.F90 commit 5104f8dc7dfb0a80d9d14e565f3519d343f46212 Author: Alice Harpole Date: Fri Feb 14 08:57:34 2020 -0500 added flag for make_beta0_irreg so can reduce code duplication Source/Maestro.H Source/MaestroMakeBeta0.cpp commit d52443ea608f603c393ec1f4c2c2c1fe8e56a1f0 Author: Doreen Fan Date: Thu Feb 13 17:49:11 2020 -0800 bugfix: need to reset tagging array for planar plroblems after reading in checkpoint file Source/MaestroInit.cpp commit cfa5ed7bf8c24ef48aea9c3d9c12249855fc3b38 Author: Doreen Fan Date: Thu Feb 13 17:38:40 2020 -0800 Initialize variables after reading in checkpoint files Source/MaestroInit.cpp commit 6d9bfec24a8bd3076513cdbe9ae090fd04c88660 Author: Doreen Fan Date: Thu Feb 13 16:21:03 2020 -0800 bugfix: cannot have repeating variable names when writing plotfile Source/MaestroDebug.cpp commit a4fb56909f6e78ed888134c1c7fb055668c1cbbc Author: Alice Harpole Date: Thu Feb 13 16:39:57 2020 -0500 converted make_beta0 Source/MaestroMakeBeta0.cpp Source/Make.package commit a0a564c1af5e7f8a5a914dd878d62df67a05c5b2 Merge: ae3728fc 5e10ed0f Author: Alice Harpole Date: Thu Feb 13 15:48:28 2020 -0500 Merge branch 'cpp_makew0' of github.com:AMReX-Astro/MAESTROeX into cpp_makew0 commit ae3728fc082a913241c422f7623ac3069f4a16b3 Merge: a38f237d 96e5f373 Author: Alice Harpole Date: Thu Feb 13 15:48:07 2020 -0500 fixed merge conflicts commit 96e5f373b58888edf83a8626e892b7ab4569ddad Merge: fd644118 d5d5ef1f Author: Alice Harpole Date: Thu Feb 13 15:43:34 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit fd6441189d7b8562bf8a823e6b019299b15603d0 Author: Alice Harpole Date: Thu Feb 13 15:43:25 2020 -0500 fixed travis pr script Util/scripts/pr_tab_remover.sh commit 5e10ed0f3d9032e861a3eaf801840d5f19e66d1b Author: Travis CI <> Date: Thu Feb 13 20:41:57 2020 +0000 Tabs have been converted to spaces by tab_exterminator.sh Source/Maestro.H Source/MaestroCheckpoint.cpp Source/MaestroForce.cpp Source/MaestroMakeEdgeScalars.cpp commit a38f237d9e3f5d5ba131d25cf02069e977afc0c6 Author: Alice Harpole Date: Thu Feb 13 15:40:18 2020 -0500 set git config to get all remote branche Util/scripts/pr_tab_remover.sh commit 682f2be593e70061ddc9a9ad61edd34a001118fb Author: Alice Harpole Date: Thu Feb 13 15:33:00 2020 -0500 make sure are in the build directory Util/scripts/pr_tab_remover.sh commit ab870c3c65c390e3290a500c4293bdb48801256d Author: Alice Harpole Date: Thu Feb 13 15:26:56 2020 -0500 git checkout --track Util/scripts/pr_tab_remover.sh commit 5e2d98ac98e5a8667d137cdf251a5ed147137f76 Author: Alice Harpole Date: Thu Feb 13 15:19:13 2020 -0500 set remote url Util/scripts/pr_tab_remover.sh commit 867fc7684d9807d7535acb677f74074421d50fc3 Author: Alice Harpole Date: Thu Feb 13 15:07:02 2020 -0500 create new branch when checkout remote Util/scripts/pr_tab_remover.sh commit 9072183cfc360df1af3fa9e3236ea8a04a7deb51 Author: Alice Harpole Date: Thu Feb 13 15:03:49 2020 -0500 create new branch when checkout remote Util/scripts/pr_tab_remover.sh commit 96aa112adbb4bb3b895a9842ee7208c5bdcc6071 Author: Alice Harpole Date: Thu Feb 13 14:59:10 2020 -0500 need to checkout PR branch Util/scripts/pr_tab_remover.sh commit 918d95f6b38655a7b7bb0bbb015f82724b1b4244 Author: Alice Harpole Date: Thu Feb 13 14:57:28 2020 -0500 need to checkout PR branch Util/scripts/pr_tab_remover.sh commit 49c0db22b8fe0e69577abd70d82042a75addd96d Author: Alice Harpole Date: Thu Feb 13 14:49:21 2020 -0500 push to ssh_repo Util/scripts/pr_tab_remover.sh commit 7c567faebd100e970858009e98704c34e1be53c2 Author: Alice Harpole Date: Thu Feb 13 14:39:10 2020 -0500 fixed static analysis warnings Source/Maestro.H Source/MaestroBaseStateGeometry.cpp Source/MaestroDiag.cpp Source/MaestroForce.cpp Source/MaestroMakeS.cpp Source/MaestroMakew0.cpp Source/MaestroPlot.cpp Util/scripts/pr_tab_remover.sh commit 93e0da48baf1d1a44663d8f7ea54a7c14e2449f7 Merge: 230f9c2b 20847c9f Author: Alice Harpole Date: Thu Feb 13 14:01:25 2020 -0500 Merge branch 'cpp_makew0' of github.com:AMReX-Astro/MAESTROeX into cpp_makew0 commit 230f9c2b380a8cfb95db1e0ef1107a3cdefa7cc8 Author: Alice Harpole Date: Thu Feb 13 12:52:09 2020 -0500 GPU fixes Source/MaestroAdvance.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakew0.cpp commit 6eeb5c5879378f25397c00d3f63122495999897b Author: Alice Harpole Date: Thu Feb 13 10:14:49 2020 -0500 converted loops in MakeGrav.cpp to AMREX_PARALLEL_FOR's Source/MaestroBaseStateGeometry.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakew0.cpp commit 33398663dc974e4f163f37012c186d1f6244c2b1 Author: Alice Harpole Date: Thu Feb 13 09:16:17 2020 -0500 converted loops in Makew0.cpp to AMREX_PARALLEL_FOR's Source/MaestroAdvance.cpp Source/MaestroMakew0.cpp commit 9cf5ca87e148a4f1ff8ad092efea5e3f977f5655 Author: Alice Harpole Date: Wed Feb 12 16:43:14 2020 -0500 tidying up Source/MaestroMakew0.cpp commit 4417fe4b030b944ff9280d518b26a9796d92f1a2 Author: Alice Harpole Date: Wed Feb 12 16:40:20 2020 -0500 convert makew0sphericalirreg Source/Maestro.H Source/MaestroMakew0.cpp commit 1bb32afcf4d26a1dd67792ad81402c5d9c7398c6 Author: Alice Harpole Date: Wed Feb 12 16:31:45 2020 -0500 converted makew0planarvarg Source/Maestro.H Source/MaestroMakew0.cpp commit f209fb6fcc90295021e1508a8072ebca4499b9fa Author: Alice Harpole Date: Wed Feb 12 15:05:19 2020 -0500 all changes in wdconvect seem to come from tridiag solver Source/MaestroAdvance.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroForce.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakew0.cpp Source/Maestro_F.H Source/Src_nd/base_state_geometry.F90 Source/Src_nd/make_w0.F90 commit 6ddb7e6047340c1f64718c4a3941b781b0dae16d Author: Alice Harpole Date: Tue Feb 11 16:43:27 2020 -0500 Makew0 works for single level 3d reacting bubble Source/MaestroAdvance.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroMakew0.cpp Source/Src_nd/base_state_geometry.F90 Source/Src_nd/make_w0.F90 commit 3a565ee62e479777e51e64be0e2223a29df32d27 Author: Alice Harpole Date: Tue Feb 11 14:47:21 2020 -0500 fixed invalid pointers Source/Maestro.H Source/MaestroBaseStateGeometry.cpp Source/MaestroFill3dData.cpp Source/MaestroInit.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakew0.cpp Source/MaestroSetup.cpp Source/Src_nd/base_state_geometry.F90 commit 32de1b12261163717086a28dd39bb636c85f9074 Author: Alice Harpole Date: Fri Feb 7 08:32:28 2020 -0500 converting make_grav Source/MaestroMakeGrav.cpp commit 3140a08be840f1a994c0a18a25cb3ebdb58d550e Author: Alice Harpole Date: Thu Feb 6 11:18:07 2020 -0500 converting make_grav_edge and make_grav_cell Source/Maestro.H Source/MaestroInit.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakew0.cpp Source/Make.package commit 9c1168405e34dba94602a914c4264badbd99010e Author: Alice Harpole Date: Wed Feb 5 17:06:17 2020 -0500 converted makew0spherical Source/Maestro.H Source/MaestroMakew0.cpp commit 1fd8c1bd0a2e3b02480a9d32cd67453f025fb626 Author: Alice Harpole Date: Wed Feb 5 16:25:23 2020 -0500 converted makew0planar Source/Maestro.H Source/MaestroBaseStateGeometry.cpp Source/MaestroMakew0.cpp Source/Make.package commit 194c4194657028e803ced7d1e5118b3cec444b9b Author: Alice Harpole Date: Wed Feb 5 14:55:45 2020 -0500 started converting base_state_geometry routines in preparation for switching to Vectors Source/Maestro.H Source/MaestroBaseStateGeometry.cpp commit 960b7de1d8f8a75a395db6b50878b088a9ce4c12 Author: Alice Harpole Date: Wed Feb 5 13:26:01 2020 -0500 added MaestroBaseStateGeometry.cpp Source/Maestro.H Source/MaestroAverage.cpp Source/MaestroBaseStateGeometry.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/average.F90 Source/Src_nd/make_w0.F90 commit 51839a00132935fd9aec16f30b90a200e6844fe4 Author: Alice Harpole Date: Tue Feb 4 16:51:17 2020 -0500 started moving loops over levels outside of the Fortran Source/MaestroAdvance.cpp Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/advect_base.F90 Source/Src_nd/base_state.F90 Source/Src_nd/debug.F90 Source/Src_nd/make_w0.F90 commit 20847c9f72aad7c5ce7c585e9ad1b3917500c872 Author: Alice Harpole Date: Thu Feb 13 12:52:09 2020 -0500 GPU fixes Source/MaestroAdvance.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakew0.cpp commit fc4617ac2fc692ba9b184ad3276d1a2d94ff2884 Author: Alice Harpole Date: Thu Feb 13 10:14:49 2020 -0500 converted loops in MakeGrav.cpp to AMREX_PARALLEL_FOR's Source/MaestroBaseStateGeometry.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakew0.cpp commit 819bccdb0584d75c781e266b665f001eccf9fdf0 Author: Alice Harpole Date: Thu Feb 13 09:16:17 2020 -0500 converted loops in Makew0.cpp to AMREX_PARALLEL_FOR's Source/MaestroAdvance.cpp Source/MaestroMakew0.cpp commit d5d5ef1fa1f9562b9ec4b4f306468e07c5c8b61a Author: Doreen Fan Date: Wed Feb 12 13:44:54 2020 -0800 bugfix: fix time output in checkpoint file Source/MaestroCheckpoint.cpp commit c337b37d5d18c1166f233197ea922e60830c4331 Author: Alice Harpole Date: Wed Feb 12 16:43:14 2020 -0500 tidying up Source/MaestroMakew0.cpp commit cad1b1e2e838d62b8126b98e651f1750a3694ad1 Author: Alice Harpole Date: Wed Feb 12 16:40:20 2020 -0500 convert makew0sphericalirreg Source/Maestro.H Source/MaestroMakew0.cpp commit b4b293ac77a27bc6c90d13d6acc7e22d76cd15c8 Author: Alice Harpole Date: Wed Feb 12 16:31:45 2020 -0500 converted makew0planarvarg Source/Maestro.H Source/MaestroMakew0.cpp commit 4613c8d0787d0296ef3d874f15c8c050379a8281 Author: Alice Harpole Date: Wed Feb 12 15:05:19 2020 -0500 all changes in wdconvect seem to come from tridiag solver Source/MaestroAdvance.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroForce.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakew0.cpp Source/Maestro_F.H Source/Src_nd/base_state_geometry.F90 Source/Src_nd/make_w0.F90 commit 491d12cfabc181bffb66952c89fd6aa36e8d3005 Merge: 7e6b5359 5a6a5da8 Author: Alice Harpole Date: Wed Feb 12 09:50:21 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_makew0 commit 5a6a5da81e53c77b69220d231d1c3ae78a1804d5 Author: Alice Harpole Date: Wed Feb 12 09:47:35 2020 -0500 tell travis to only run deplot_docs for development branch .travis.yml Util/scripts/pr_tab_remover.sh commit 40e56fbf585ecd9cb784f81926d1a517626faecd Author: Alice Harpole Date: Wed Feb 12 09:43:23 2020 -0500 fix static analysis complaints Source/MaestroFill3dData.cpp Util/scripts/pr_tab_remover.sh commit ce740c5d10e50da52b9bc5a68c97f3bceec94856 Merge: 2d4aa624 ce419e77 Author: Alice Harpole Date: Wed Feb 12 09:25:27 2020 -0500 merge with development commit 2d4aa6244aa62ad661d2a6445dbedcc080a8a9c8 Author: Alice Harpole Date: Wed Feb 12 09:18:06 2020 -0500 get rid of extraneous code Source/Src_nd/fill_3d_data.F90 Source/Src_nd/make_eta.F90 commit 4cfe0d37a659db781ac1574c5a904fcc14f6e8a6 Author: Alice Harpole Date: Wed Feb 12 08:45:39 2020 -0500 fix bug in put_data_on_faces Source/MaestroFill3dData.cpp Source/Src_nd/fill_3d_data.F90 commit ce419e772b5b664e687fcb8cde65c11ac4511b81 Author: Alice Harpole Date: Wed Feb 12 08:36:16 2020 -0500 fix bug in put_data_on_faces Source/Src_nd/fill_3d_data.F90 commit e1206208bc19048675832cb57430318d997e2d7e Author: Alice Harpole Date: Wed Feb 12 08:35:35 2020 -0500 revert fill_3d_data Source/Src_nd/fill_3d_data.F90 commit c7753c6a88cc679b77910ff1c0840c60e0028323 Author: Alice Harpole Date: Wed Feb 12 08:35:06 2020 -0500 convert max_lev+1 -> max_lev for readability Source/MaestroFill3dData.cpp commit 7327d077b5ab5927274575bea7e59c015764f352 Author: Alice Harpole Date: Wed Feb 12 08:09:45 2020 -0500 Revert "Convert fill data 3d routines to C++" (#152) Source/Maestro.H Source/MaestroFill3dData.cpp Source/Maestro_F.H Source/Src_nd/fill_3d_data.F90 commit e84b703ffdc7b29c1c3816f9d56f75a5761da918 Author: Alice Harpole Date: Wed Feb 12 08:01:38 2020 -0500 fixed 2d flame wave test so it runs Source/MaestroFill3dData.cpp commit 8b042c5f9eec70223e5b269387a2d0fcc2511938 Merge: c00863c1 6cfc4a95 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Tue Feb 11 14:08:49 2020 -0800 Merge pull request #141 from AMReX-Astro/cpp_fill_3d_data Convert fill data 3d routines to C++ commit 6cfc4a95972831bb767b819972e78c2de95f74aa Author: Doreen Fan Date: Tue Feb 11 13:48:41 2020 -0800 small typo Source/MaestroFill3dData.cpp commit 7e6b535966b772450b2fd5e0278ea7e4fe85a448 Author: Alice Harpole Date: Tue Feb 11 16:43:27 2020 -0500 Makew0 works for single level 3d reacting bubble Source/MaestroAdvance.cpp Source/MaestroBaseStateGeometry.cpp Source/MaestroMakew0.cpp Source/Src_nd/base_state_geometry.F90 Source/Src_nd/make_w0.F90 commit c00863c1d34bdc3266c610b7fe0490976b70f3e7 Author: Alice Harpole Date: Tue Feb 11 15:59:26 2020 -0500 added a flag (which is now set in all the tests in the GPU regression test suite) which will prevent non-deterministic functions in the nodal solver from being offloaded to GPUs Exec/science/wdconvect/inputs_files/inputs_3d_regression.2levels Exec/test_problems/reacting_bubble/inputs_2d_regression.2levels Exec/test_problems/reacting_bubble/inputs_3d_regression Exec/test_problems/rt/inputs_2d_regression Source/MaestroNodalProj.cpp Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H commit 374846907a4706a48779aa684d4063ea9b66a42b Author: Alice Harpole Date: Tue Feb 11 14:47:21 2020 -0500 fixed invalid pointers Source/Maestro.H Source/MaestroBaseStateGeometry.cpp Source/MaestroFill3dData.cpp Source/MaestroInit.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakew0.cpp Source/MaestroSetup.cpp Source/Src_nd/base_state_geometry.F90 commit 473cab9b9da0bc7c2b9af9779cb54f19d4a6895f Merge: 2d2c99ba a13a0e33 Author: Alice Harpole Date: Tue Feb 11 14:38:18 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_makew0 commit a13a0e33f1cf9b433a00d43c64cb7fa01a0ee345 Merge: c73c783d 207ab51a Author: Alice Harpole Date: Tue Feb 11 14:37:52 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit c73c783dcc5a9b81c43ed6c5906f735f86947859 Author: Alice Harpole Date: Tue Feb 11 14:37:42 2020 -0500 fixed rsa keys Util/scripts/pr_tab_remover.sh commit 2d2c99baa21412c5c5845eda49a5c3d0a37fb634 Author: Alice Harpole Date: Tue Feb 11 14:26:25 2020 -0500 fixed rsa keys Util/scripts/pr_tab_remover.sh commit bcaf25e212384cfa570acf500878018719652655 Merge: ea42d9ee 207ab51a Author: Doreen Fan Date: Tue Feb 11 11:19:30 2020 -0800 Merge branch 'development' into cpp_fill_3d_data Fixed conflicts commit 207ab51a4b3ceb52d2f8e5f04b76349487f0809d Merge: 182e5d0d 7af5ebe5 Author: Doreen Fan Date: Tue Feb 11 11:11:12 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit e9cdf47f9851fe43966d3c1b1e7a1e132292a160 Merge: e91b6517 7af5ebe5 Author: Alice Harpole Date: Tue Feb 11 13:03:05 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_makew0 commit 7af5ebe542d0e484542fdacbe173ae396e8af543 Author: Alice Harpole Date: Tue Feb 11 12:10:31 2020 -0500 uncommented git push Util/scripts/pr_tab_remover.sh commit b50010376f60166416082e10d6be09e205dcc6ac Author: Alice Harpole Date: Tue Feb 11 12:06:54 2020 -0500 do git stuff in build directory Util/scripts/pr_tab_remover.sh commit 6aa63128e7b667c80edde6bf7b0d3283673a0fa2 Author: Alice Harpole Date: Tue Feb 11 12:02:01 2020 -0500 added .sh Util/scripts/pr_tab_remover.sh commit 7631286cf24e0295999cdfbac3d9300d31c3520e Author: Alice Harpole Date: Tue Feb 11 11:59:15 2020 -0500 added script to travis build to run tab exterminator script on PRs and push changes .travis.yml Util/scripts/pr_tab_remover.sh Util/scripts/tab_exterminator.sh commit b864f5abce379d38013c25e5708e98f7f0d7e481 Author: Alice Harpole Date: Tue Feb 11 10:54:00 2020 -0500 fixed some more things found by static analysis, including a bug in MakeEdgeScalars.cpp that could potentially change the output of 2d tests Source/Maestro.H Source/MaestroAdvanceSdc.cpp Source/MaestroEvolve.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroMakeEdgeScalars.cpp Source/MaestroMakeFlux.cpp Source/MaestroMakeS.cpp Source/MaestroMakeUtrans.cpp Source/MaestroPPM.cpp Source/MaestroPlot.cpp Source/MaestroSlopes.cpp Source/MaestroVelPred.cpp commit e91b6517c542b43c9d9ba8222b1a60910d33e3b2 Merge: 0488c300 cd3794d6 Author: Alice Harpole Date: Tue Feb 11 10:03:51 2020 -0500 merging with development commit cd3794d6cd9fdb60872d45ac6bf588023dee41d4 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Tue Feb 11 05:37:17 2020 -0800 Convert force subroutines to C++ (#151) This converts the subroutines in make_vel_force.F90 and make_scal_force.F90. I've tested both reacting_bubble and wdconvect, and the changes give zero output errors. Note also that mktempforce had not been converted due eos calls. This will be converted later when eos subroutines are put on GPUs. * change compute_grad_phi_rad to C++ for loop * Put compute_grad_phi_rad on GPU using amrex_parallel_for_1d * changed dx to gpu managed vector * converted make_vel_force * convert mkrhohforce * add get_base_cutoff_density_coord(); now compiles * code cleanup * code cleanup * converted modify_scal_force and fixed bug in make_vel_force * converted modify_scal_force_sphr * Move spherical-only terms into spherical loops and some code cleanup * bugfix: need to add 'comp' parameter when accessing scal and force. * remove converted Fortran subroutines * fix clang static analysis error * initialize buoyancy_cutoff_factor * converted tabs to spaces * shrunk array4 sizes Co-authored-by: Alice Harpole Source/Maestro.H Source/MaestroForce.cpp Source/MaestroVelPred.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/base_state_geometry.F90 Source/Src_nd/make_scal_force.F90 Source/Src_nd/make_vel_force.F90 commit 182e5d0dd7b46868ad9ddc690d8e68062f8e7d9f Author: Doreen Fan Date: Mon Feb 10 23:07:55 2020 -0800 create a C++ rel_eps since it is now being used mainly in C++ lambdas Source/Maestro.H Source/MaestroCheckpoint.cpp Source/MaestroDt.cpp Source/MaestroMakeEdgeScalars.cpp Source/MaestroMakeUtrans.cpp Source/MaestroPPM.cpp Source/MaestroVelPred.cpp commit b5a6f8eb55ca6a0d89293fee7cb5c53fafb9f8cb Author: Michael Zingale Date: Mon Feb 10 15:43:16 2020 -0500 turn off pert Exec/science/fully_convective_star/inputs_3d commit 8aaaac54aaa26d28413d9bf227146d86294f41ba Author: Michael Zingale Date: Mon Feb 10 15:41:37 2020 -0500 add a heating term Exec/science/fully_convective_star/inputs_3d Exec/science/fully_convective_star/make_heating.F90 commit b28a62b735abf70257552ee1a39146f38730edc1 Author: Michael Zingale Date: Mon Feb 10 15:12:25 2020 -0500 some tweaks Exec/science/fully_convective_star/inputs_3d commit ea42d9eeed155b0a4e9dc776fabf36eccec8d220 Merge: ef34db6b 380e72d9 Author: Alice Harpole Date: Mon Feb 10 14:22:24 2020 -0500 Merge branch 'cpp_fill_3d_data' of github.com:AMReX-Astro/MAESTROeX into cpp_fill_3d_data commit ef34db6bb45b17577e592be4e070383cd570a863 Merge: 221b2432 49f85fc0 Author: Alice Harpole Date: Mon Feb 10 14:22:05 2020 -0500 merging with development commit 49f85fc09b17660c98c0fe21d601201fc3b08a6c Merge: 918d9636 9449b73e Author: Andy Nonaka Date: Mon Feb 10 11:02:28 2020 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 918d9636ce34b2a9aa651305596a2506eb6fa192 Author: Andy Nonaka Date: Mon Feb 10 11:01:49 2020 -0800 add back inputs files wdconvect/inputs_files/inputs_3d_regression.2levels reacting_bubble/inputs_regression.2levels Exec/science/wdconvect/inputs_files/inputs_3d_regression.2levels Exec/test_problems/reacting_bubble/inputs_2d_regression.2levels commit 9449b73eb2700552c62114c1a8ad445d3023d8e7 Author: Alice Harpole Date: Mon Feb 10 12:31:53 2020 -0500 convert tabs to spaces Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvection.cpp Source/MaestroCheckpoint.cpp Source/MaestroConvert.cpp Source/MaestroDensityAdvance.cpp Source/MaestroDt.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroEvolve.cpp Source/MaestroFill3dData.cpp Source/MaestroFillData.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroIntra.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeFlux.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp Source/MaestroReact.cpp Source/MaestroRegrid.cpp Source/MaestroRhoHT.cpp Source/MaestroSetup.cpp Source/MaestroThermal.cpp Source/MaestroVelPred.cpp Source/MaestroVelocityAdvance.cpp Source/Maestro_F.H Source/PhysBCFunctMaestro.H Source/main.cpp Source/param/_cpp_parameters commit 80915aee8378a74f1b96e9fd8f41d91ed678f1b5 Author: Alice Harpole Date: Mon Feb 10 12:07:34 2020 -0500 script to convert tabs to spaces Util/scripts/tab_exterminator.sh commit 6748d3a2d0a4f806e97dbe3aa114c155979894f1 Author: Alice Harpole Date: Mon Feb 10 10:06:37 2020 -0500 fix 2d GPU compilation Source/MaestroVelPred.cpp commit b5f0b0c3bcc2cdd193268b2a2a446c4a1ef1e4e0 Author: Michael Zingale Date: Sat Feb 8 20:04:25 2020 -0500 this merges the _parameters into a single module (#146) This merges the _parameters into a single module previously we had two sets of parameters, some lived in probin_module and some in extern_probin_module, but they were initialized with the same namelist. This made the script more complicated to maintain. Now all the parameters live in probin_module and a stub extern_probin_module is created that just `uses` probin_module to ensure the Microphysics works. Exec/Make.Maestro Source/param/runtime.probin.template commit 73a27780d0e0622af2c478a37dcd99cc1501fb9e Merge: 819eb8ac 11739c4e Author: Doreen Fan Date: Fri Feb 7 10:54:03 2020 -0800 add slope_order=2 to regression test commit 819eb8ac9fd58d66355f95c43e0d002da5c1df53 Author: Doreen Fan Date: Fri Feb 7 10:45:06 2020 -0800 update wdconvect regression tests Exec/science/wdconvect/inputs_files/inputs_3d_amr_regression Exec/science/wdconvect/inputs_files/inputs_3d_regression Exec/science/wdconvect/inputs_files/inputs_3d_regression.2levels Exec/science/wdconvect/inputs_files/inputs_omp_3d_regression commit 11739c4e1c8238dda2db00dc44ca194f7a4f31bb Author: Doreen Fan Date: Fri Feb 7 10:45:06 2020 -0800 update wdconvect regression tests Exec/science/wdconvect/inputs_files/inputs_3d_amr_regression Exec/science/wdconvect/inputs_files/inputs_3d_regression Exec/science/wdconvect/inputs_files/inputs_3d_regression.2levels Exec/science/wdconvect/inputs_files/inputs_omp_3d_regression commit 038995480e776c84c2af2a7cb8c68fa9a1bf3819 Author: Andy Nonaka Date: Fri Feb 7 09:52:30 2020 -0800 update reacting bubble regression tests covering all 3 ppm_types OMP tests are now AMR Exec/test_problems/reacting_bubble/inputs_2d_amr_regression Exec/test_problems/reacting_bubble/inputs_2d_regression Exec/test_problems/reacting_bubble/inputs_3d_amr_regression Exec/test_problems/reacting_bubble/inputs_3d_regression Exec/test_problems/reacting_bubble/inputs_omp_2d_regression Exec/test_problems/reacting_bubble/inputs_omp_3d_regression commit df2b9c54647555881df12a2003d4fd67151d5918 Author: Andy Nonaka Date: Fri Feb 7 09:21:22 2020 -0800 remove unused inputs file Exec/test_problems/reacting_bubble/inputs_2d_regression.2levels commit af9512e8d75af273dcb785eede8efa1c0cb336f5 Author: Alice Harpole Date: Fri Feb 7 09:35:30 2020 -0500 fix 2d compilation Source/MaestroMakeFlux.cpp commit 0488c3003e06f5e9291a7da49a00b16da711182e Author: Alice Harpole Date: Fri Feb 7 08:32:28 2020 -0500 converting make_grav Source/MaestroMakeGrav.cpp commit 99479701e8f5f4b7149331ed5b0de8b5eb2f7d1f Merge: a655c5f6 9ec71e68 Author: Alice Harpole Date: Thu Feb 6 12:36:25 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit a655c5f6df3d6b389dbe1d051d820b7d357436f5 Author: Alice Harpole Date: Thu Feb 6 12:35:58 2020 -0500 return error code if scan-build finds bugs Util/scripts/clang_static_analysis.py commit 9ec71e68e063ed4fc3180ab0398048129b5074e4 Author: Andy Nonaka Date: Thu Feb 6 09:27:01 2020 -0800 Fix non-deterministic OMP+MPI behavior (#150) * put the PPM/Slope calculation and the usage of Ip/Im in separate MFIters - avoiding possibilities of race conditions * clean up this file so the splitting is only done by dimension (so in spirit it's the same as branch utrans_omp_fix). I suggest merging this branch with development (rather than utrans_omp_fix2) since it uses less memory * omp bugfix in MakeRhoXFlux - need to use nodaltileboxes rather than nodally growing the cell-centered tilebox * disable tiling and GPU for computation of rho0 = rhoh0 / rho0; it was causing sub-machine level differences for some reason fixing this can be opened up as a separate issue once we close #149. not tiling/GPUing this routine for now will enable regression to work again * removed some redundant code from MaestroMakeFlux.cpp Co-authored-by: Alice Harpole This fixes #149. I had to: Split up the dimensionality of MaestroMakeUtrans so avoid race conditions in writing to temporaries Fix a nodal tile box issue in MakeRhoXFlux Disable tiling/GPU of computation of rho0 in MaestroPlot.cpp Test this with reacting_bubble/inputs_3d_amr_regression and inputs_2d_amr_regression with multiple MPIs and multiple OMPs before merging Source/MaestroMakeFlux.cpp Source/MaestroMakeUtrans.cpp Source/MaestroPlot.cpp commit 59a626984f6d8fb31563efa5a73e9b54a62a166e Author: Alice Harpole Date: Thu Feb 6 11:18:07 2020 -0500 converting make_grav_edge and make_grav_cell Source/Maestro.H Source/MaestroInit.cpp Source/MaestroMakeGrav.cpp Source/MaestroMakew0.cpp Source/Make.package commit 8b922269b4f3f9df7982255ab58d42ae30710863 Author: Alice Harpole Date: Wed Feb 5 17:06:17 2020 -0500 converted makew0spherical Source/Maestro.H Source/MaestroMakew0.cpp commit 4ac045583a98dad70bb29a233fcdf5f0dc5cc80d Author: Alice Harpole Date: Wed Feb 5 16:25:23 2020 -0500 converted makew0planar Source/Maestro.H Source/MaestroBaseStateGeometry.cpp Source/MaestroMakew0.cpp Source/Make.package commit 03a70c5aa189bfd0b6f1bd73d80a8ecced2ea755 Author: Michael Zingale Date: Wed Feb 5 15:23:53 2020 -0500 change tagging Exec/science/fully_convective_star/_parameters commit 6eebd7c3c75a25612f042f7cdd96dd70ce94833d Author: Michael Zingale Date: Wed Feb 5 15:17:52 2020 -0500 set a better rotation frequency Exec/science/fully_convective_star/inputs_3d commit 96a8f9c6bc8d78c1cde482ccb8aa7377a5859152 Merge: 6e16b4e7 f23e76f8 Author: Michael Zingale Date: Wed Feb 5 15:14:54 2020 -0500 Merge branch 'development' of github.com:amrex-astro/MAESTROeX into development commit 6e16b4e7a5af8377cbffb4c30c90e452de884d72 Author: Michael Zingale Date: Wed Feb 5 15:14:25 2020 -0500 add some initial models generated by initial_models/low_mass_convective_star Exec/science/fully_convective_star/convective_M_0.20.hse.1024 Exec/science/fully_convective_star/convective_M_0.30.hse.1024 Exec/science/fully_convective_star/convective_M_0.40.hse.1024 commit 6364ba35023868a151cb8b4c6154d2a62516a81c Author: Michael Zingale Date: Wed Feb 5 15:14:10 2020 -0500 first cut at an inputs Exec/science/fully_convective_star/inputs_3d commit bf7a24660215abe96f8db254b0095d6d5953caeb Author: Alice Harpole Date: Wed Feb 5 14:55:45 2020 -0500 started converting base_state_geometry routines in preparation for switching to Vectors Source/Maestro.H Source/MaestroBaseStateGeometry.cpp commit d1ed5308e5d8de707b4660b02f18bd1b445861c4 Merge: 80db17d5 f23e76f8 Author: Alice Harpole Date: Wed Feb 5 13:32:11 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into base_vectors commit f23e76f82b3775886a753f898ef7d1f4391e61f2 Author: Alice Harpole Date: Wed Feb 5 13:31:57 2020 -0500 added getter routines for numdisjointchunks, r_start_coord and r_end_coord Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/base_state_geometry.F90 commit 80db17d5362eb11259ff119f159f26eb3027f188 Author: Alice Harpole Date: Wed Feb 5 13:26:01 2020 -0500 added MaestroBaseStateGeometry.cpp Source/Maestro.H Source/MaestroAverage.cpp Source/MaestroBaseStateGeometry.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/average.F90 Source/Src_nd/make_w0.F90 commit d805134d58474d3602725aab143f76ee05a88081 Merge: e8412938 920f76ee Author: Alice Harpole Date: Wed Feb 5 13:11:27 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into base_vectors commit 920f76ee09dc05377595e75a553696a5c66431db Author: Michael Zingale Date: Wed Feb 5 11:45:03 2020 -0500 problem stub for fully convective rotating stars Exec/science/fully_convective_star/GNUmakefile Exec/science/fully_convective_star/Make.package Exec/science/fully_convective_star/Problem.cpp Exec/science/fully_convective_star/_parameters Exec/science/fully_convective_star/initdata.F90 Exec/science/fully_convective_star/make_heating.F90 Exec/science/fully_convective_star/tagging.F90 commit d7caf36e91984c8caa87bace03442766e2f08f20 Merge: 1688d00d 6c476ca0 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Tue Feb 4 18:22:35 2020 -0800 Merge pull request #144 from AMReX-Astro/cpp_advection Convert MaestroAdvection.cpp routines to C++ commit 380e72d9a2bacf345f959ac5d6dd28f4102189c9 Author: Doreen Fan Date: Tue Feb 4 16:52:17 2020 -0800 missing sqrt in make_normal Source/MaestroFill3dData.cpp commit 1688d00d80d3feaea73bc7af2ca79681de93289a Merge: 03b93b45 b1362bc3 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Tue Feb 4 15:16:21 2020 -0800 Merge pull request #143 from AMReX-Astro/cpp_nodal_proj Convert MaestroNodalProj.cpp functions to C++ commit e8412938a79f9fbc008ae82244bb1a7893d79f52 Author: Alice Harpole Date: Tue Feb 4 16:51:17 2020 -0500 started moving loops over levels outside of the Fortran Source/MaestroAdvance.cpp Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/advect_base.F90 Source/Src_nd/base_state.F90 Source/Src_nd/debug.F90 Source/Src_nd/make_w0.F90 commit 05760499534d4733c23a45f57203996eb289c7cf Merge: 9ceeaae4 4e124188 Author: Doreen Fan Date: Tue Feb 4 12:49:54 2020 -0800 Merge branch 'development' into cpp_fill_3d_data commit 03b93b458fa37eac2dc38c3b54786944eaa3f655 Merge: 4e124188 fc05ee27 Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Tue Feb 4 11:46:31 2020 -0800 Merge pull request #140 from AMReX-Astro/cpp_mac_solver Convert routines in mac_solver.F90 to C++ commit 4e1241886ccbd07738ec73e8f1656bfb7997ad8c Merge: 344bc6ce 1a041f5d Author: Alice Harpole Date: Tue Feb 4 09:44:24 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 344bc6ce8eb4de60a11813f079bbd51642c929ab Author: Alice Harpole Date: Tue Feb 4 09:44:14 2020 -0500 fix bug in restrict_base Source/Src_nd/base_state_geometry.F90 commit 9ceeaae4233f13aedcc4bd943c0852933294ff98 Merge: 221b2432 1a041f5d Author: Doreen Fan Date: Mon Feb 3 17:38:00 2020 -0800 Merge branch 'development' into cpp_fill_3d_data commit 1a041f5dcc8a2d843ae20e3b7079597d29c7d1cc Author: Alice Harpole Date: Mon Feb 3 19:08:17 2020 -0500 Convert vorticity routines to C++ (#139) This converts to vorticity routines to C++. These routines are called to calculate the vorticity when generating plotfiles, and were not offloaded to GPU because they included Fortran functions defined within a subroutine. Converting them to C++ lambda functions therefore significantly speeds up the generation of plotfile data for GPU runs. Source/MaestroPlot.cpp commit fc05ee27f438f087d9c36e8fed977556910ab455 Author: Doreen Fan Date: Mon Feb 3 15:02:33 2020 -0800 remove ppm.F90 and mkutrans.F90 from Make.package Source/Src_nd/Make.package commit b3e4384e545ce3a43ab4a1b13dc93c5cd79ce58d Merge: 6af37cfa b5721cd7 Author: Michael Zingale Date: Mon Feb 3 17:23:25 2020 -0500 Merge branch 'development' into cpp_mac_solver commit b5721cd7d485d802098d4aec76c147ab7a046250 Author: Alice Harpole Date: Mon Feb 3 17:19:28 2020 -0500 Convert MakeUtrans routines to C++ (#137) This converts the MakeUtrans.cpp routines to C++ and does some cleaning up to delete some Fortran files that are no longer needed. I've tested against the development branch for flame_2d and flame_3d (with burning turned off) and there are no diffs between plotfiles. It also runs on the GPU without giving errors. Source/Maestro.H Source/MaestroHydro.cpp Source/MaestroHydro_F.H Source/MaestroMakeEdgeScalars.cpp Source/MaestroMakeUtrans.cpp Source/MaestroPPM.cpp Source/MaestroVelPred.cpp Source/Make.package Source/Src_nd/Make.package Source/Src_nd/mkutrans.F90 Source/Src_nd/ppm.F90 Source/Src_nd/slope.F90 commit 02d05e1fca0b51b0968c9ac6f65e40eb7f8e9674 Merge: c986d728 b30f30ca Author: doreenfan <35239173+doreenfan@users.noreply.github.com> Date: Mon Feb 3 11:09:31 2020 -0800 Merge pull request #142 from AMReX-Astro/fix_exact_base_state Bug fix for use_exact_base_state commit c986d7289bfd161c8f50c8391fdb85c62eb4b604 Author: Doreen Fan Date: Mon Feb 3 09:56:46 2020 -0800 Feb 2020 release notes CHANGES.md commit 175f9c86e378b2b1638f5a11486e6129e0473a1b Author: Michael Zingale Date: Mon Feb 3 08:42:09 2020 -0500 a script to clean builds Exec/clean_probs.sh commit 3a199d08951c79f8f19062229902a4f951b3b63e Author: Alice Harpole Date: Thu Jan 30 15:39:59 2020 -0500 fixed static analysis warnings for 2d Source/Maestro.H Source/MaestroPPM.cpp Source/MaestroSetup.cpp Source/MaestroSlopes.cpp commit 6c476ca0665fa050e370f93f63bab383ddbb1b2c Merge: 292b4c3a 38f18ee2 Author: Alice Harpole Date: Thu Jan 30 14:45:03 2020 -0500 Merge branch 'development' into cpp_advection commit b1362bc3fe41c699e356b91638a381b32dadc25a Merge: 6725f6aa 38f18ee2 Author: Alice Harpole Date: Thu Jan 30 14:44:35 2020 -0500 Merge branch 'development' into cpp_nodal_proj commit 221b2432235f9d1900e8d6df96bf78a27eb721de Merge: 6a2fe27f 38f18ee2 Author: Alice Harpole Date: Thu Jan 30 14:44:06 2020 -0500 Merge branch 'development' into cpp_fill_3d_data commit 6af37cfa11dc23c46bdbe4ac7038ce5c2bc8b9f6 Merge: 04b749fc 38f18ee2 Author: Alice Harpole Date: Thu Jan 30 14:43:48 2020 -0500 Merge branch 'development' into cpp_mac_solver commit 38f18ee2ae39f2f6c26055f3a8a2d1112b0e779b Author: Alice Harpole Date: Thu Jan 30 14:30:27 2020 -0500 combined PPM_2D and PPM_3D. Also fixed a couple of bugs in PPM_3D, so tests may fail for 3D Source/Maestro.H Source/MaestroHydro.cpp Source/MaestroPPM.cpp commit 292b4c3a986e8851027666f33ed6714f839da87c Merge: 96318963 ba5d2844 Author: Alice Harpole Date: Thu Jan 30 09:39:29 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_advection commit 6725f6aa7a3801bf775879d2c8376fff18b0e402 Author: Alice Harpole Date: Thu Jan 30 09:38:30 2020 -0500 merge with development Source/MaestroNodalProj.cpp commit 5416e1d053320402f1b596dea8981f8e68af740e Merge: f959c3ab ba5d2844 Author: Alice Harpole Date: Thu Jan 30 09:33:50 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_nodal_proj commit b30f30cae994db85cae028ba01a396c941d9c898 Merge: a0ce2bcd ba5d2844 Author: Alice Harpole Date: Thu Jan 30 09:33:26 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into fix_exact_base_state commit 6a2fe27f474ad0d775c0f6777d70481eebc5929e Author: Alice Harpole Date: Thu Jan 30 09:32:55 2020 -0500 merge with development Source/MaestroFill3dData.cpp commit 979a3c5898139b365aa4c5ce1dbaa2a86899e0f4 Merge: 14b40225 ba5d2844 Author: Alice Harpole Date: Thu Jan 30 09:27:34 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_fill_3d_data commit 04b749fcd87e2e5ddbb05eb9796b9e512ea4b63e Author: Alice Harpole Date: Thu Jan 30 09:26:40 2020 -0500 merge with development Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp commit bae9e1ed3c522afe5b11c56d9c8b0f07d27dbcc9 Merge: 0646491d ba5d2844 Author: Alice Harpole Date: Thu Jan 30 09:19:24 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into cpp_mac_solver commit ba5d28449c7b31f53d4add750fbd8d51b6327ea0 Author: Alice Harpole Date: Wed Jan 29 17:40:45 2020 -0500 Add travis clang static analysis (#145) This tells travis to run the clang static analyzer on PRs. * added clang static analyzer to travis build * fixed path? * fixed path? * fixed path? * actually fixed path * only compile one test as it's very slow * ignore AMReX files and only trigger on PRs * don't ignore header files * turn AMReX and Microphysics back on, save output to file * added python script to travis build * added python script to travis build * only print out unique warnings, ignore pragma gpu warnings .travis.yml Util/scripts/clang_static_analysis.py commit 96318963e91ccc8d6b4460fb27eed0f0044e6e6a Author: Alice Harpole Date: Wed Jan 29 17:36:35 2020 -0500 fix merge conflicts with development Source/MaestroAdvection.cpp commit 75388bb6a4372410e9ba45c20e2f2066666d9eaf Merge: 933b5438 e481e312 Author: Alice Harpole Date: Wed Jan 29 17:32:29 2020 -0500 fix merge conflicts with development commit 933b5438a7d22063c559dca6bd4f4ccb6382beac Author: Alice Harpole Date: Wed Jan 29 17:28:54 2020 -0500 GPU fixes Source/MaestroAdvection.cpp Source/MaestroMakeFlux.cpp Source/Maestro_F.H commit 52e4932ad7b1e8dc4bb3e2dff6d3d806aba59383 Author: Alice Harpole Date: Wed Jan 29 17:00:38 2020 -0500 converted update_velocity_sphr Source/MaestroAdvection.cpp Source/Src_nd/Make.package Source/Src_nd/update_vel.F90 commit 43d105bba779fd0d7708f03e1b2bac3b5b916e6f Author: Alice Harpole Date: Wed Jan 29 15:26:41 2020 -0500 converted update_velocity Source/MaestroAdvection.cpp Source/Maestro_F.H Source/Src_nd/update_vel.F90 commit bc1535f5b297447795390f95979f8c0265154b79 Author: Alice Harpole Date: Wed Jan 29 14:34:11 2020 -0500 converted update_rhoX and update_rhoh (apart from EoS calls in update_rhoh) Source/MaestroAdvection.cpp Source/MaestroMakeFlux.cpp Source/Maestro_F.H Source/Src_nd/update_scal.F90 commit 6407d7ba1b0ba4c2764399ffe7c6cf015aba45a9 Author: Alice Harpole Date: Wed Jan 29 13:37:02 2020 -0500 moved make flux routines into a separate file Source/MaestroAdvection.cpp Source/MaestroMakeFlux.cpp Source/Make.package commit 2abebbc2df809e1fe1433c4f4bd52979382af8cb Author: Alice Harpole Date: Wed Jan 29 13:32:19 2020 -0500 converted all make_flux routines Source/MaestroAdvection.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/make_flux.F90 commit e481e312cf36150ca0d303e2629ccc82938f1729 Author: Alice Harpole Date: Wed Jan 29 13:25:16 2020 -0500 make_rhoh_flux_3d_sphr_irreg should take rhoh0mac_edge, not rho0mac_edge Source/MaestroAdvection.cpp commit 8f9de5b637ddc76d08ef389e78e75afba3277dbf Author: Alice Harpole Date: Wed Jan 29 12:03:38 2020 -0500 converted make_rhoh_flux_sphr Source/MaestroAdvection.cpp commit cb94d69ba63482f74cb3fa1118248b29b4ce563f Author: Alice Harpole Date: Wed Jan 29 10:26:26 2020 -0500 converted make_rhoh_flux Source/MaestroAdvection.cpp Source/Maestro_F.H Source/Src_nd/make_flux.F90 commit 97fcf06e09bfaff5c0d337cdf086f3a30c5bfdd3 Author: Alice Harpole Date: Wed Jan 29 09:30:29 2020 -0500 clean up and fix spherical Source/MaestroAdvection.cpp commit a8c1400810a0c4ba7f383a8ac70329ebe0ae4215 Author: Alice Harpole Date: Tue Jan 28 16:55:45 2020 -0500 converted make_rhoX_flux Source/MaestroAdvection.cpp Source/Src_nd/make_flux.F90 commit 709551ba019f03f26c26cf7bdb6f021d360506c9 Author: Alice Harpole Date: Tue Jan 28 13:32:08 2020 -0500 fix warnings flagged by static analysis Source/MaestroCheckpoint.cpp Source/MaestroDiag.cpp Source/MaestroHydro.cpp Source/MaestroIntra.cpp Source/MaestroMakeEdgeScalars.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp Source/MaestroPPM.cpp Source/MaestroPlot.cpp Source/MaestroRhoHT.cpp Source/MaestroVelPred.cpp commit f959c3ab1a62d2ce7165f92166c4cc8f74b0eb10 Author: Alice Harpole Date: Mon Jan 27 16:29:16 2020 -0500 converted make_pi_cc Source/MaestroNodalProj.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/make_pi_cc.F90 commit ecda15a2f383c51e1e56fb315ad2c65243516ada Author: Alice Harpole Date: Mon Jan 27 16:15:10 2020 -0500 converted compute_grad_phi Source/MaestroNodalProj.cpp Source/Maestro_F.H Source/Src_nd/compute_grad_phi.F90 commit 14b402257c0f73932a6c71f0c88712514bef3b88 Author: Alice Harpole Date: Mon Jan 27 15:53:51 2020 -0500 fix indexing for r_cc_loc Source/MaestroFill3dData.cpp commit 5b3a45ec272a0710a301333f4c115dabeb19cc1c Merge: 8219092b a0ce2bcd Author: Alice Harpole Date: Mon Jan 27 15:51:02 2020 -0500 Merge branch 'fix_exact_base_state' into cpp_fill_3d_data commit a0ce2bcd7c157d2bea4a2a6555056299990fd477 Author: Alice Harpole Date: Mon Jan 27 15:37:12 2020 -0500 make sure that Sbar gets initialized Source/MaestroInit.cpp commit 3620f608c4f02b68bfae31a383f26613dc528c7e Author: Alice Harpole Date: Mon Jan 27 15:09:34 2020 -0500 don't read off the edges of r_cc_loc and r_edge_loc Source/MaestroInit.cpp Source/Src_nd/base_state_geometry.F90 Source/Src_nd/fill_3d_data.F90 Source/Src_nd/make_beta0.F90 commit f5c137881c54a1e0a73ed0144a450519aa7c844e Author: Alice Harpole Date: Mon Jan 27 14:09:51 2020 -0500 allocate sponge quantities for init_sponge_irreg Source/MaestroInit.cpp Source/Src_nd/sponge.F90 commit 8219092bb94b4d753c74f94a2efeaca958ba4839 Author: Alice Harpole Date: Mon Jan 27 13:27:16 2020 -0500 GPU fixes Source/MaestroFill3dData.cpp commit 3b3653a134d3a3b18ade892d43e6808c313076fb Author: Alice Harpole Date: Mon Jan 27 12:59:55 2020 -0500 converted make_s0mac_sphr_irreg Source/Maestro.H Source/MaestroFill3dData.cpp Source/Maestro_F.H Source/Src_nd/fill_3d_data.F90 commit 59d9b8732e4cfbd311b71ee0f03b0ea6f4c15c19 Author: Alice Harpole Date: Mon Jan 27 12:29:05 2020 -0500 moved if statements within for loops to reduce repeated code Source/MaestroFill3dData.cpp commit 96a61d82a46fc4bb447a98fe634bc8cd1e29e6c7 Author: Alice Harpole Date: Mon Jan 27 11:32:23 2020 -0500 converted make_s0mac and make_normal. The C++ version of make_normal seems to produce large diffs (I'm guessing because normal is used a lot by other functions so small differences become magnified) Source/MaestroFill3dData.cpp Source/Maestro_F.H Source/Src_nd/fill_3d_data.F90 commit baf331fafba69316d286655e7cde68315a192dc3 Author: Alice Harpole Date: Mon Jan 27 09:57:02 2020 -0500 converted make_w0mac Source/MaestroFill3dData.cpp Source/Maestro_F.H Source/Src_nd/fill_3d_data.F90 commit 57894d3a113205fbef97621e81febaad6505a89e Author: Alice Harpole Date: Mon Jan 27 09:09:34 2020 -0500 converted addw0_sphr Source/MaestroFill3dData.cpp Source/Maestro_F.H Source/Src_nd/fill_3d_data.F90 commit 8c3a668eb574d567fe85c6c7a423abc020aed6fa Author: Alice Harpole Date: Mon Jan 27 09:00:17 2020 -0500 converted addw0 Source/MaestroFill3dData.cpp commit 275c3fbb5a00f7d4cfa003a9c01c7c15ddbf8e09 Author: Alice Harpole Date: Fri Jan 24 17:01:58 2020 -0500 converted put_1d_array_on_cart Source/Maestro.H Source/MaestroFill3dData.cpp Source/Maestro_F.H Source/Src_nd/fill_3d_data.F90 commit 0646491db1a0aed93a9d298883a6e30e1a31964b Author: Alice Harpole Date: Fri Jan 24 14:09:41 2020 -0500 dx is a Real array not a ManagedVector so need to convert to a GpuArray Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp commit 49c3b78fae2e91f8ee28253aa44f7ee59bb9fd4f Author: Alice Harpole Date: Fri Jan 24 13:42:47 2020 -0500 use pointer to dx rather than copying to new array Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp commit 7eac36afa540b995ea209df9680cc81fec9ae36a Author: Alice Harpole Date: Fri Jan 24 13:37:56 2020 -0500 converted mac_bcoef Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/mac_solver.F90 commit c7552635a8ef6d1d649f10b5d64042ac1c9e72d9 Author: Alice Harpole Date: Fri Jan 24 13:06:20 2020 -0500 converted mult_beta0 Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp commit 99aed41b5cc349d2e96914294b5e40d67ae0246f Author: Alice Harpole Date: Fri Jan 24 09:58:49 2020 -0500 converted mac_solver_rhs Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp Source/Maestro_F.H Source/Src_nd/mac_solver.F90 commit 1777bfa43387a675c6a6502fec8a0500809a5d9e Author: Alice Harpole Date: Thu Jan 23 16:08:41 2020 -0500 test_advect runs again with MPI Exec/unit_tests/test_advect/MaestroEvolve.cpp commit 7e8c7c3b5c29ff60755235a7bb3594540d63d17f Author: Alice Harpole Date: Thu Jan 23 11:40:56 2020 -0500 test_advect compiles again Exec/unit_tests/test_advect/MaestroInit.cpp commit c3205870520a65d2b26b929c7abf95a17a0fb106 Author: Alice Harpole Date: Wed Jan 22 11:18:14 2020 -0500 Convert VelPred routines to C++ (#136) This converts the velocity prediction routines to C++ lambda functions. Testing this for reacting_bubble with the burning switched off, there are some reasonably large differences for all routines apart from VelPredInterface. I can't see any obvious errors so this is hopefully just due to roundoff error, but it could be that there are one or more bugs lurking that I haven't spotted. It compiles and runs on the GPU without dying. Source/Maestro.H Source/MaestroHydro.cpp Source/MaestroMakeEdgeScalars.cpp Source/MaestroPPM.cpp Source/MaestroSlopes.cpp Source/MaestroVelPred.cpp Source/Make.package Source/Src_nd/Make.package Source/Src_nd/velpred.F90 commit 36050d1dfaa6f471fb93891dde98c04d5acb2d2d Author: Michael Zingale Date: Sat Jan 18 08:38:00 2020 -0500 fix headers Exec/unit_tests/test_advect/MaestroEvolve.cpp Exec/unit_tests/test_advect/MaestroInit.cpp commit 507f9533c3e1b21ee2c03271df8417d0b91ef868 Author: Alice Harpole Date: Fri Jan 17 15:38:34 2020 -0500 move boundaries to inside if statements in vorticity Source/Src_nd/make_plot_variables.F90 commit 54ea8d6d326cdc23f7ffd2ebce2a67db81dd7585 Author: Alice Harpole Date: Fri Jan 17 15:16:03 2020 -0500 fixed vorticity routines so that they use the domain boundaries rather than the grid boundaries Source/MaestroPlot.cpp Source/Maestro_F.H Source/Src_nd/make_plot_variables.F90 commit c2dbdbb2ea1f119736a147c142f863c6daed91f0 Author: Alice Harpole Date: Fri Jan 17 09:45:02 2020 -0500 fig bug ul -> ur Source/Src_nd/velpred.F90 commit 84cc53f0e870a60af57bf2f6e9e5e408cb52bd55 Author: Alice Harpole Date: Wed Jan 15 20:01:13 2020 -0500 Convert slope routines to C++ (#135) This converts the Fortran slope routines to C++ lambda functions. Comparing against the development branch, diffs appear to be negligible. Source/Maestro.H Source/MaestroHydro.cpp Source/MaestroPPM.cpp Source/MaestroSlopes.cpp Source/Make.package commit a1a0aa799072ff1609fbb738db7845d58c5f06f7 Author: Alice Harpole Date: Wed Jan 15 10:28:44 2020 -0500 fix merge conflicts Source/Maestro.H commit f0900e1bf7f089f62fa9abadf4f867e989ec1cf0 Author: Alice Harpole Date: Wed Jan 15 10:20:26 2020 -0500 Convert 2d MakeEdgeScal routines to C++ lambda functions (#134) This follows #133, converting the 2d routines in MakeEdgeScal to C++ lambda functions. I've tested this for 2d reacting_bubble and RT (with OMP this time) and they seem to give zero/negligible diffs. Source/Maestro.H Source/MaestroHydro.cpp Source/MaestroMakeEdgeScalars.cpp Source/MaestroPPM.cpp Source/Src_nd/Make.package Source/Src_nd/make_edge_scal.F90 commit 109e909ecb232aaaef5e574ae17a9b782fd9a701 Author: Alice Harpole Date: Tue Jan 14 15:54:43 2020 -0500 Convert MakeEdgeScal Fortran kernels to C++ lambdas (#133) This converts the Fortran kernel launches in the MakeEdgeScal routine to C++ lambda functions. The performance on CPU is essentially unchanged, but on GPU I see a speed up of 20-30x for this function, leading to an speed up overall of ~30% for Maestro::Evolve. The actual code itself is essentially unchanged - I've just added punctuation and fixed the array indexing to match C++ counting from 0. I've tested this for 3d reacting_bubble and wdconvect and the answers seem to match development. Conversion of the 2d routines and slope routines (for ppm type 0) will come in later PRs. Source/Maestro.H Source/MaestroHydro.cpp Source/MaestroHydro_F.H Source/MaestroMakeEdgeScalars.cpp Source/MaestroPPM.cpp Source/Make.package Source/Src_nd/make_edge_scal.F90 Source/Src_nd/ppm.F90 commit 126b3305fb9745172d48a8cc977468f420961344 Merge: ebbe794c 0fa5af44 Author: dwillcox Date: Fri Jan 10 16:53:18 2020 -0500 Merge branch 'development' of github.com:amrex-astro/MaestroEx into development commit ebbe794c0d83cddf54d48d6c94469fbfc7471d94 Author: dwillcox Date: Fri Jan 10 16:16:52 2020 -0500 Update scripts to import UrcaShellFields the new way. Exec/science/urca/analysis/scripts/lineout-field Exec/science/urca/analysis/scripts/slice-field Exec/science/urca/analysis/scripts/sum-field Exec/science/urca/analysis/scripts/volume-plot-field commit eb3509432572b9b91bf9841cc823d0841beb8f91 Author: dwillcox Date: Fri Jan 10 16:16:19 2020 -0500 more fixes to packaging. Exec/science/urca/analysis/UrcaAnalysis/tools/__init__.py Exec/science/urca/analysis/UrcaAnalysis/yt/__init__.py Exec/science/urca/analysis/UrcaAnalysis/yt_extensions/__init__.py Exec/science/urca/analysis/UrcaAnalysis/yt_extensions/yt_extensions.py Exec/science/urca/analysis/setup.py commit 4c7bc6178d4f0017b37d3d55e42e9d2a8b5b52ed Author: dwillcox Date: Fri Jan 10 16:02:54 2020 -0500 For yt slicing scripts, use yt.enable_parallelism() Exec/science/urca/analysis/scripts/slice-enucdot Exec/science/urca/analysis/scripts/slice-field Exec/science/urca/analysis/scripts/slice-vel commit 17d9462330f1f81b02ffcebfeed5699a6989a134 Author: dwillcox Date: Fri Jan 10 16:02:01 2020 -0500 Fixed some python packaging for analysis scripts. Exec/science/urca/analysis/UrcaAnalysis/__init__.py Exec/science/urca/analysis/UrcaAnalysis/tools/FileToolkit.py Exec/science/urca/analysis/UrcaAnalysis/tools/__init__.py Exec/science/urca/analysis/UrcaAnalysis/yt/__init__.py Exec/science/urca/analysis/UrcaAnalysis/yt/yt_urca_fields.py Exec/science/urca/analysis/setup.py commit 0fa5af44605f535ad24c795a3ab14b1d7fe928e4 Author: Alice Harpole Date: Thu Jan 9 11:45:32 2020 -0500 Ipf -> Imf Source/Src_nd/make_edge_scal.F90 commit 3bd1273b5ee5b20f4e26d2db2470335ce91b2694 Merge: 5c1ea923 4f92628c Author: Alice Harpole Date: Wed Jan 8 09:23:28 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 5c1ea923db35154d045f32ab7c3d617b395e37b9 Author: Alice Harpole Date: Wed Jan 8 09:23:20 2020 -0500 fix indices in bcs Source/Src_nd/make_edge_scal.F90 commit 4f92628c9bf9d34ace4044c9ee6a75e319acb18c Author: Alice Harpole Date: Tue Jan 7 13:00:37 2020 -0500 Offload more GPU routines (#131) This offloads the remaining routines that I think are possible to offload to GPU. I've tested it for a number of problems with MPI and/or OMP and it doesn't seem to cause any issues. This Exec/science/rotating_star/_parameters Exec/science/rotating_star/make_heating.F90 Exec/science/rotating_star/model_parser.F90 Exec/science/rotating_star/probin Exec/science/rotating_star/probin_regression Source/MaestroAdvanceSdc.cpp Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp Source/MaestroMakeEta.cpp Source/MaestroReact.cpp Source/Maestro_F.H Source/Src_nd/burner_loop.F90 Source/Src_nd/mac_solver.F90 Source/Src_nd/make_eta.F90 Util/model_parser/Make.package Util/model_parser/model_parser.F90 Util/model_parser/model_parser_F.H commit 70ba451566064873501b815a1b337f1547041c70 Author: Alice Harpole Date: Tue Jan 7 10:18:36 2020 -0500 switch multiple if statements to else if Source/Src_nd/make_edge_scal.F90 Source/Src_nd/mkutrans.F90 Source/Src_nd/ppm.F90 Source/Src_nd/velpred.F90 commit f94e57abc73e226d329975d57e21201f67f1b83a Author: Alice Harpole Date: Mon Jan 6 10:59:17 2020 -0500 Offload MaestroFill3dData routines to GPU (#129) This offloads a number of the routines in MaestroFill3dData.cpp to GPU. I've tested it with wdconvect for OMP, MPI and CUDA with various different flags and it seems to give the same results as the dev branch. Exec/science/wdconvect/initdata.F90 Source/MaestroAdvection.cpp Source/MaestroFill3dData.cpp Source/MaestroHydro.cpp Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/base_state_geometry.F90 Source/Src_nd/fill_3d_data.F90 commit 966e36808c0944f55f37ed118c867ba04e156729 Author: Michael Zingale Date: Fri Jan 3 15:40:13 2020 -0500 update refs CITATION commit e3f5c6ef0c655d56f2121ede2f850842b1e5f092 Author: Andy Nonaka Date: Fri Jan 3 12:34:28 2020 -0800 move RELEASE_NOTES into CHANGES.md CHANGES.md RELEASE_NOTES commit 2d2f67017c4a8b6f48043e39cd522fad710a0077 Author: Andy Nonaka Date: Fri Jan 3 10:24:52 2020 -0800 Jan 2020 release notes RELEASE_NOTES commit e94f791c1c0ec9ffa85b107e92d87c3223b334d7 Merge: 6c0a681b b9652b4b Author: Alice Harpole Date: Fri Jan 3 10:49:37 2020 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 6c0a681bbad6b9d49384bf9ee89bfb84f927dd50 Author: Alice Harpole Date: Fri Jan 3 10:49:22 2020 -0500 convert tabs to spaces in MaestroAdvanceSdc Source/MaestroAdvanceSdc.cpp commit b9652b4b598225ff73e25fc94752abf27a4670ef Merge: 2e4edf50 a30a1005 Author: Michael Zingale Date: Tue Dec 31 20:49:15 2019 -0500 Merge branch 'master' into development commit 2e4edf5064d0a47c7d561f4618e3463509fd4d5f Author: Alice Harpole Date: Tue Dec 31 13:02:05 2019 -0500 fix intra initialization Source/MaestroCheckpoint.cpp Source/MaestroInit.cpp commit 1853787016e204bead84116a955f2b8e5ca4c2a5 Author: Alice Harpole Date: Mon Dec 30 11:23:41 2019 -0500 make sure heating is properly initialized in rotating_star if restarting from a checkpoint file Exec/science/rotating_star/make_heating.F90 commit 8e47654a94d383601edfbde7bd9f103856991632 Merge: ce506764 90e2d9d9 Author: Alice Harpole Date: Fri Dec 27 09:02:19 2019 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit ce50676460615268de742d785c69c307662465bf Author: Alice Harpole Date: Fri Dec 27 09:02:09 2019 -0500 fix reacting_bubble_3d test Source/MaestroAdvection.cpp Source/MaestroHydro.cpp commit 90e2d9d9015b4e76dd0cd5c2e6a1c53319c7b273 Author: Doreen Fan Date: Mon Dec 23 11:40:49 2019 -0800 drdxfac does not match with spacing in model file; but produces convection in Si shell Exec/science/rotating_star/inputs_files/inputs_3d_drdxfac commit 846368498a2646c2d9588c25258164510fc0c39f Author: Alice Harpole Date: Mon Dec 23 11:02:06 2019 -0500 switched some boxes to nodal boxes, initialized some MultiFabs so that use_exact_base_state=true works for wdconvect Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroHydro.cpp commit cb871bc357e8d1a6e7d00fe1111e899f457d18df Author: Alice Harpole Date: Fri Dec 20 13:59:32 2019 -0500 switch to using TilingIfNotGPU() flag in MFIter loops Source/MaestroAdvection.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroHeating.cpp Source/MaestroHydro.cpp Source/MaestroInit.cpp Source/MaestroIntra.cpp Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp Source/MaestroReact.cpp Source/MaestroRegrid.cpp Source/MaestroRhoHT.cpp Source/MaestroSponge.cpp Source/MaestroThermal.cpp commit 8cb73785756b566e48c880c2b84f4ee862afd045 Author: Alice Harpole Date: Fri Dec 20 09:55:09 2019 -0500 .f90 -> .F90 Exec/science/code_comp/base_state.F90 Exec/science/code_comp/initdata.F90 Exec/science/code_comp/make_grav.F90 Exec/science/ecsn/initdata.F90 Exec/science/flame/base_state.F90 Exec/science/flame/initdata.F90 Exec/science/flame/inlet_bc.F90 Exec/science/plane_parallel_star/initdata.F90 Exec/science/rotating_star/initdata.F90 Exec/science/rotating_star/model_parser.F90 Exec/science/sub_chandra/initdata.F90 Exec/science/toy_convect/initdata.F90 Exec/science/urca/initdata.F90 Exec/science/wdconvect/initdata.F90 Exec/science/xrb_mixed/initdata.F90 Exec/test_problems/double_bubble/base_state.F90 Exec/test_problems/double_bubble/initdata.F90 Exec/test_problems/incomp_shear_jet/base_state.F90 Exec/test_problems/incomp_shear_jet/initdata.F90 Exec/test_problems/mach_jet/base_state.F90 Exec/test_problems/mach_jet/initdata.F90 Exec/test_problems/mach_jet/inlet_bc.F90 Exec/test_problems/reacting_bubble/initdata.F90 Exec/test_problems/rt/base_state.F90 Exec/test_problems/rt/initdata.F90 Exec/test_problems/test_convect/initdata.F90 Exec/test_problems/test_planar_diag/base_state.F90 Exec/test_problems/test_planar_diag/initdata.F90 Exec/test_problems/test_stability/initdata.F90 Exec/unit_tests/test_advect/base_state.F90 Exec/unit_tests/test_advect/initdata.F90 Exec/unit_tests/test_average/base_state.F90 Exec/unit_tests/test_average/initdata.F90 Exec/unit_tests/test_basestate/Make.package Exec/unit_tests/test_basestate/initdata.F90 Exec/unit_tests/test_basestate/test_basestate.F90 Exec/unit_tests/test_diffusion/Make.package 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Util/diagnostics/radial_util.F90 Util/model_parser/Make.package Util/model_parser/model_parser.F90 Util/simple_log/Make.package Util/simple_log/simple_log.F90 constants/Make.package constants/constants_cgs.F90 commit 9252399b6ebaccde1f591c3e8d2329ad75ee118c Author: Alice Harpole Date: Thu Dec 19 13:53:51 2019 -0500 stripped out all launch region switches Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroAdvection.cpp Source/MaestroConvert.cpp Source/MaestroDt.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroHydro.cpp Source/MaestroInit.cpp Source/MaestroIntra.cpp Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp Source/MaestroReact.cpp Source/MaestroRhoHT.cpp Source/MaestroSponge.cpp Source/MaestroThermal.cpp Source/main.cpp commit a30a10054e4ac489e3f15ddbc2bdbe048ecb96fc Author: Arfon Smith Date: Thu Dec 19 13:20:00 2019 -0500 Adding AAS DOI (#128) paper/paper.md commit 030bfb6ba2185b431af6d6643ffb55ae61f91136 Author: Alice Harpole Date: Wed Dec 18 11:23:39 2019 -0500 remove extra launch region ifdefs from MaestroAdvance Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp commit 4b6b978d5fcbf79cb184d33769aa94689a6e7126 Merge: a08c7835 8ebc8efe Author: Alice Harpole Date: Mon Dec 16 17:12:33 2019 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit a08c7835ec94ff0162be6505013b2f9b72de7c8d Author: Alice Harpole Date: Mon Dec 16 17:12:26 2019 -0500 offload cell-centered mac solver Source/MaestroMacProj.cpp commit 8ebc8efe85e0abf7bcc4587007e895582486ba59 Author: Michael Zingale Date: Mon Dec 16 16:43:23 2019 -0500 fix compilation Microphysics/networks/general_null/actual_rhs.F90 commit 9c7ed173d4887f6684f4e97d006b9edb2ffa25eb Author: Alice Harpole Date: Mon Dec 16 14:18:32 2019 -0500 put nodal solver within launch regions so it runs on GPU Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroInit.cpp commit f494b32a4f476f36cad6f4f573518b646af31c81 Author: Michael Zingale Date: Sat Dec 14 16:17:24 2019 -0500 update to new actual_rhs interface Microphysics/networks/burn_type.F90 Source/Src_nd/burner_loop.F90 commit a22c2f646c8090935cb6af962cd48f531d696a99 Author: Andy Nonaka Date: Fri Dec 13 07:48:07 2019 -0800 setting up full star... needs testing Exec/science/rotating_star/inputs_files/inputs_3d_fullstar_heating commit 74c40da96f6699dee7fd8a126aca495f63eb31f3 Author: Andy Nonaka Date: Thu Dec 12 12:38:11 2019 -0800 new run Exec/science/rotating_star/inputs_files/README Exec/science/rotating_star/inputs_files/inputs_3d_burntocore commit ce992f84cc3c78fe54195ff4eb56aa4f919f4754 Author: Michael Zingale Date: Thu Dec 12 14:57:36 2019 -0500 add use_omegadot_terms_in_S to spherical too Source/Src_nd/make_S.F90 commit 646e1d84182328df1f83093daa4ccf1ff02de047 Author: Michael Zingale Date: Thu Dec 12 14:48:29 2019 -0500 add new option -- use_omegadot_terms_in_S Source/Src_nd/make_S.F90 Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit 696cb44220872b49e4eb20fdec372b851036abec Author: Andy Nonaka Date: Thu Dec 12 08:21:57 2019 -0800 apply heating_cutoff_density_lo/hi to rotating star problem provide inputs file to apply heating fro Si shell inward to the core Exec/science/rotating_star/inputs_files/README Exec/science/rotating_star/inputs_files/inputs_3d_heatinner Exec/science/rotating_star/make_heating.F90 commit 3053b81bb0a0bb436a90e1ac8bd79d33e86854b8 Author: Andy Nonaka Date: Thu Dec 12 08:21:25 2019 -0800 add heating_cutoff_density_lo and _hi Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit 30bfae6b7d5dcf6f1f589fd47750765e19ceb271 Author: Andy Nonaka Date: Wed Dec 11 12:44:45 2019 -0800 revert a make_heating change. accidentally committed a version that restricts the radius based on the burning_cutoff_densities Exec/science/rotating_star/make_heating.F90 commit d565f5717d238a7a94d44345a48af0b203631686 Merge: 5dbf3aab 3ff7310c Author: Doreen Fan Date: Wed Dec 11 12:37:14 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 5dbf3aabc8842d642de85c8a5f95badf029d2ce9 Author: Doreen Fan Date: Wed Dec 11 12:36:22 2019 -0800 Revert "need to multiply pi by beta0 if using alt_energy_fix" This is already done in make_pi_cc subroutine. This reverts commit 77a366bcbc194a44a1125dc859d2730154b67e37. Source/MaestroNodalProj.cpp commit 3ff7310cba4264a59a70145fe9c0a698ae4f2539 Author: Andy Nonaka Date: Wed Dec 11 12:30:02 2019 -0800 increase initial velocity perturbation strength Exec/science/rotating_star/inputs_files/inputs_3d Exec/science/rotating_star/inputs_files/inputs_3d_MESA Exec/science/rotating_star/inputs_files/inputs_3d_burnrange Exec/science/rotating_star/inputs_files/inputs_3d_cutoff Exec/science/rotating_star/inputs_files/inputs_3d_heating Exec/science/rotating_star/inputs_files/inputs_3d_noburn Exec/science/rotating_star/inputs_files/inputs_3d_perturb Exec/science/rotating_star/make_heating.F90 commit 77a366bcbc194a44a1125dc859d2730154b67e37 Author: Doreen Fan Date: Wed Dec 11 12:14:30 2019 -0800 need to multiply pi by beta0 if using alt_energy_fix Source/MaestroNodalProj.cpp commit 0321b4138005384dd8036894bad77da1ea5f3cbb Author: Andy Nonaka Date: Wed Dec 11 11:44:45 2019 -0800 new inputs Exec/science/rotating_star/inputs_files/README Exec/science/rotating_star/inputs_files/inputs_3d_burnrange commit 9b058299ba6ac721b95923ec6aa5cecbbb969e84 Author: Andy Nonaka Date: Wed Dec 11 11:22:04 2019 -0800 remove burning_cutoff_density completely since it was replaced by burning_cutoff_density_lo Source/param/_cpp_parameters Source/param/meth_params.template Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit a4ece5700d907772e3ac3ab6a3ce3f1917a95abc Author: Andy Nonaka Date: Wed Dec 11 11:21:14 2019 -0800 fix README to indicate actual burning cutoff Exec/science/rotating_star/inputs_files/README commit 00656d103c1ce80d0718344e281c88e41352a7c3 Merge: 827cace5 d8889ec2 Author: Andy Nonaka Date: Wed Dec 11 09:18:10 2019 -0800 Merge pull request #126 from AMReX-Astro/cutoff_limits low and high limits for burning_cutoff_density commit 827cace59efaa5e3f6e5419a9319d7104e7b8bf5 Author: Donald E. Willcox Date: Wed Dec 11 09:05:38 2019 -0800 Add spherical geometry for rotating star artificial heating (#127) * If we are in spherical 3D geometry, find our radial index in the 1D profile. * Simplify by finding rloc for 2D/3D/3D spherical and interpolating to that instead of finding the radial index. In addition to 2D/3D cartesian, this adds 3D spherical interpolation for the artificial heating in the rotating star setup. Slicing the S field in the plotfiles shows this is spherical interpolation with the spherical octant geometry. Exec/science/rotating_star/make_heating.F90 commit d8889ec20b51bc859c2cf76216fe244b724cce06 Author: Alice Harpole Date: Wed Dec 11 10:52:49 2019 -0500 added burning_cutoff_density_lo/hi Exec/science/rotating_star/inputs_files/inputs_3d Exec/science/rotating_star/inputs_files/inputs_3d_MESA Exec/science/rotating_star/inputs_files/inputs_3d_cutoff Exec/science/rotating_star/inputs_files/inputs_3d_heating Exec/science/rotating_star/inputs_files/inputs_3d_noburn Exec/science/rotating_star/inputs_files/inputs_3d_perturb Source/Src_nd/base_state_geometry.F90 Source/Src_nd/burner_loop.F90 Source/param/_cpp_parameters Source/param/meth_params.template Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit 5762b7da34afee0482eb49c6c1fe77d465ea3b1f Merge: 86129b20 696d9991 Author: Alice Harpole Date: Wed Dec 11 09:23:13 2019 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 86129b20e6fa3f2b649a132bb8443431def3da04 Author: Alice Harpole Date: Wed Dec 11 09:23:08 2019 -0500 add new line to parameters file Exec/science/rotating_star/_parameters commit 696d99915534cec1be5fc05b335fb515a7c0589b Author: Andy Nonaka Date: Tue Dec 10 14:17:06 2019 -0800 add initial velocity perturbation turn on burning in Si shell Exec/science/rotating_star/initdata.f90 Exec/science/rotating_star/inputs_files/README Exec/science/rotating_star/inputs_files/inputs_3d Exec/science/rotating_star/inputs_files/inputs_3d_MESA Exec/science/rotating_star/inputs_files/inputs_3d_cutoff Exec/science/rotating_star/inputs_files/inputs_3d_heating Exec/science/rotating_star/inputs_files/inputs_3d_noburn Exec/science/rotating_star/inputs_files/inputs_3d_perturb commit 39b9c394b23ae4d6a02741b321654046e49ce3be Author: Andy Nonaka Date: Tue Dec 10 13:24:52 2019 -0800 fixed a tiling but in the velocity initialization... was overwriting the entire grid velocity to be zero, not just the tile Exec/science/sub_chandra/initdata.f90 Exec/science/toy_convect/initdata.f90 Exec/science/xrb_mixed/initdata.f90 Exec/test_problems/mach_jet/initdata.f90 Exec/test_problems/test_planar_diag/initdata.f90 commit c813ca5aac5372bcfcbf82beae6a6b7b5ea3f853 Author: Michael Zingale Date: Tue Dec 10 15:09:30 2019 -0500 Revert "rename directories to be lower case :)" This reverts commit d8f5dacb171d6924b7e15357dd6f51335457b54d. 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758e8024 Author: Michael Zingale Date: Tue Dec 10 15:08:07 2019 -0500 Merge branch 'development' of github.com:amrex-astro/MAESTROeX into development commit 3737e637c9a86bb4409a93e266062f16068e574f Author: Michael Zingale Date: Tue Dec 10 15:07:52 2019 -0500 rename to lowercase Exec/science/README Exec/science/code_comp/GNUmakefile Exec/science/code_comp/Make.package Exec/science/code_comp/Problem.cpp Exec/science/code_comp/_parameters Exec/science/code_comp/analysis/image_animator.py Exec/science/code_comp/analysis/plot_generator.py Exec/science/code_comp/base_state.f90 Exec/science/code_comp/initdata.f90 Exec/science/code_comp/inputs_3d Exec/science/code_comp/make_grav.f90 Exec/science/code_comp/make_heating.F90 Exec/science/code_comp/model_util.F90 Exec/science/code_comp/simple.net Exec/science/ecsn/ECSN-ONe6040-final.hse.40960 Exec/science/ecsn/GNUmakefile Exec/science/ecsn/Make.package Exec/science/ecsn/_parameters Exec/science/ecsn/ecsn.hse.25600 Exec/science/ecsn/initdata.f90 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Exec/unit_tests/test_react/xin.mesa_carbon Exec/unit_tests/test_react/xin.reaclib_cburn Exec/unit_tests/test_react/xin.reaclib_ctest Exec/unit_tests/test_react/xin.reaclib_ctest_null Exec/unit_tests/test_react/xin.reaclib_urca Exec/unit_tests/test_react/xin.reaclib_urca_trans Exec/unit_tests/test_react/xin.rprox Exec/unit_tests/test_react/xin.xrb_simple commit 758e80241a379921b617c7c5c37f3720049583f2 Merge: 1603fd5d 7d37d24b Author: Donald E. Willcox Date: Tue Dec 10 12:05:21 2019 -0800 Merge branch 'development' of github.com:AMReX-Astro/MAESTROex into development commit 1603fd5dae8e73e95d06a500183923dfcfa4eae7 Author: Donald E. Willcox Date: Tue Dec 10 12:05:13 2019 -0800 enucdot->Hnuc for yt script. Exec/SCIENCE/urca/analysis/scripts/slice-vel commit d8f5dacb171d6924b7e15357dd6f51335457b54d Author: Michael Zingale Date: Tue Dec 10 15:03:14 2019 -0500 rename directories to be lower case :) syncs with Castro Exec/science/README Exec/science/code_comp/GNUmakefile Exec/science/code_comp/Make.package Exec/science/code_comp/Problem.cpp Exec/science/code_comp/_parameters Exec/science/code_comp/analysis/image_animator.py Exec/science/code_comp/analysis/plot_generator.py Exec/science/code_comp/base_state.f90 Exec/science/code_comp/initdata.f90 Exec/science/code_comp/inputs_3d Exec/science/code_comp/make_grav.f90 Exec/science/code_comp/make_heating.F90 Exec/science/code_comp/model_util.F90 Exec/science/code_comp/simple.net Exec/science/ecsn/ECSN-ONe6040-final.hse.40960 Exec/science/ecsn/GNUmakefile Exec/science/ecsn/Make.package Exec/science/ecsn/_parameters Exec/science/ecsn/initdata.f90 Exec/science/ecsn/input_ecsn Exec/science/ecsn/model.orig Exec/science/ecsn/model.uniform 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Exec/unit_tests/test_react/xin.reaclib_urca_trans Exec/unit_tests/test_react/xin.rprox Exec/unit_tests/test_react/xin.xrb_simple commit 7d37d24b165f0e706f1ada52984ae51ae4c1ca8f Author: Andy Nonaka Date: Tue Dec 10 11:49:54 2019 -0800 more tests Exec/SCIENCE/rotating_star/inputs_files/README Exec/SCIENCE/rotating_star/inputs_files/inputs_3d_cutoff Exec/SCIENCE/rotating_star/inputs_files/inputs_3d_heating Exec/SCIENCE/rotating_star/inputs_files/inputs_3d_noburn commit 850429079806d9ad3788d226cc021b4ef1eec954 Author: Donald E. Willcox Date: Tue Dec 10 11:44:23 2019 -0800 Fix module imports. Exec/SCIENCE/urca/analysis/UrcaAnalysis/__init__.py commit 844749fa15f018a4aeaaf1e5b890247450429ccf Author: Donald E. Willcox Date: Tue Dec 10 11:43:55 2019 -0800 Updates for MaestroEx. Exec/SCIENCE/urca/analysis/scripts/slice-vel commit 922a6111da975f2401d510936403f2c5b7a10c8b Author: Donald E. Willcox Date: Tue Dec 10 11:42:00 2019 -0800 Fix some issues with slicing for cylindrical geometry. Exec/SCIENCE/urca/analysis/scripts/slice-field commit 341fe33400a783ac7f4dcc263f9d77f9557e46b1 Author: Donald E. Willcox Date: Tue Dec 10 11:40:53 2019 -0800 Fix module imports. Exec/SCIENCE/urca/analysis/scripts/lineout-field commit 1823b1e533dfb85d4b91dbe0bb2ffd754bb4f6ed Author: Andy Nonaka Date: Tue Dec 10 11:27:30 2019 -0800 remove 17-variable initdata.256 and replace it with the 25-variable one Exec/SCIENCE/rotating_star/initial_models/initdat.256 Exec/SCIENCE/rotating_star/inputs_files/initdat.256 commit 5346e71e56b0a9d05393d442bac0a929bafa9360 Author: Andy Nonaka Date: Tue Dec 10 11:10:52 2019 -0800 plot int = 1 Exec/SCIENCE/rotating_star/inputs_files/inputs_3d Exec/SCIENCE/rotating_star/inputs_files/inputs_3d_MESA commit 502368d4203b6456a622de7fa5dfbd84c7764205 Author: Andy Nonaka Date: Tue Dec 10 11:08:58 2019 -0800 more cleanup Exec/SCIENCE/rotating_star/inputs_2d Exec/SCIENCE/rotating_star/inputs_3d_C Exec/SCIENCE/rotating_star/inputs_test commit 598e75dd5d8754ca2223020725257fc74b3463ab Author: Andy Nonaka Date: Tue Dec 10 11:06:08 2019 -0800 re-org inputs files Exec/SCIENCE/rotating_star/initial_models/15m_500_sec.hse.6400 Exec/SCIENCE/rotating_star/initial_models/initdat.320 Exec/SCIENCE/rotating_star/inputs_files/README Exec/SCIENCE/rotating_star/inputs_files/initdat.256 Exec/SCIENCE/rotating_star/inputs_files/inputs_3d Exec/SCIENCE/rotating_star/inputs_files/inputs_3d_MESA commit d808972d617fe084a1a5978134ad589f74beac34 Merge: bcc48332 7bf0afb1 Author: Donald E. Willcox Date: Tue Dec 10 09:31:28 2019 -0800 Merge branch 'development' of github.com:AMReX-Astro/MAESTROex into development commit bcc483327f43691e5817f004c6d20eb83f4f1970 Author: Donald E. Willcox Date: Tue Dec 10 09:17:51 2019 -0800 Add newline so extern module builds correctly on linux. Exec/SCIENCE/rotating_star/_parameters commit 7bf0afb195145aa559fa885092b37943341f4269 Author: Alice Harpole Date: Tue Dec 10 12:01:59 2019 -0500 made folders to organise initial data Exec/SCIENCE/rotating_star/inputs_3d_C Exec/SCIENCE/rotating_star/inputs_files/inputs_3d_C commit e6b762a437cdbd23588acf5918690606c1464ac9 Author: Alice Harpole Date: Tue Dec 10 11:33:07 2019 -0500 added analytic heating Exec/SCIENCE/rotating_star/_parameters Exec/SCIENCE/rotating_star/initial_models/initdat.256 Exec/SCIENCE/rotating_star/inputs_3d_C Exec/SCIENCE/rotating_star/make_heating.F90 sphinx_docs/source/faq.rst commit c4a72e94c451c5b638be55a413e616650269221b Author: Michael Zingale Date: Thu Dec 5 15:41:34 2019 -0500 another overflow Source/Src_nd/compute_dt.F90 commit 8d53f70c3ed2858f0ad094746996f8c323a0f377 Merge: a76284fb db68490b Author: Michael Zingale Date: Thu Dec 5 15:39:20 2019 -0500 Merge branch 'development' of github.com:amrex-astro/MAESTROeX into development commit a76284fb9ead3361998a2398e648978eb7c99301 Author: Michael Zingale Date: Thu Dec 5 15:39:07 2019 -0500 fix floating point overflow Source/Src_nd/compute_dt.F90 commit db68490b67fb9fb6d8818e8d0df61159c30da7dc Author: XinlongSBU <42697364+XinlongSBU@users.noreply.github.com> Date: Thu Dec 5 11:40:52 2019 -0500 updates to the ECSN problem Exec/SCIENCE/ecsn/ecsn.hse.25600 Exec/SCIENCE/ecsn/input_ecsn Exec/SCIENCE/ecsn/tagging.F90 commit 27869f53c5ea19ae5414d24c2e54f1a03e376031 Author: Alice Harpole Date: Thu Dec 5 10:38:45 2019 -0500 fix macros so SDC code will compile for GPU Source/MaestroReact.cpp commit fbf369e9a455e9ff80d62fa6e9abbe309e4a4d10 Merge: 305a1ec3 9e498f63 Author: Donald E. Willcox Date: Wed Dec 4 21:47:18 2019 -0800 Merge branch 'development' of github.com:AMReX-Astro/MAESTROex into development commit 305a1ec3d9c4a9e8dc555e7229b2acee6df42897 Author: Donald E. Willcox Date: Wed Dec 4 21:47:04 2019 -0800 Initialize burn_t % self_heat before calling actual_rhs where it is checked. Makes Valgrind happy. Source/Src_nd/burner_loop.F90 commit 9e498f63df1c152f436ce5e6ba74a727f430f393 Author: Michael Zingale Date: Wed Dec 4 17:53:33 2019 -0500 set success Source/Src_nd/burner_loop.F90 commit 5f26089bc91db063131ee7382a943ea5033e36a7 Author: Alice Harpole Date: Wed Dec 4 13:33:07 2019 -0500 offload put_data_on_faces Source/MaestroFill3dData.cpp Source/MaestroMacProj_level.cpp Source/Maestro_F.H Source/Src_nd/fill_3d_data.F90 commit 01acf4c8ecea48eec3a27b1192300ceb76195693 Author: Alice Harpole Date: Wed Dec 4 12:09:31 2019 -0500 offload mac_bcoef_face Source/MaestroMacProj.cpp Source/Maestro_F.H Source/Src_nd/mac_solver.F90 commit 46655b97f11a295dfd89ac5dd3720d8d8d728774 Author: Alice Harpole Date: Wed Dec 4 11:19:50 2019 -0500 added in some missing launch regions Source/MaestroHydro.cpp Source/MaestroNodalProj.cpp commit 0d338f213e95cc4c50a6e19935e1c871cc6eb32c Author: Alice Harpole Date: Tue Dec 3 16:52:18 2019 -0500 added a couple more launch regions Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/Maestro_F.H Source/Src_nd/fill_3d_data.F90 commit 7cc2be25109c36f36b1e62238c8d11e8b7e7e866 Author: Alice Harpole Date: Tue Dec 3 11:40:33 2019 -0500 turn off launch region for mac_mlmg.solve Source/MaestroMacProj.cpp commit 9373d919c4fb3a895d7e05270c5c546d5ac136e2 Merge: 191129f8 afdc97b0 Author: Alice Harpole Date: Mon Dec 2 19:08:40 2019 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 191129f8ee7bd3e3af46cc471b0cc1647b7b69aa Author: Alice Harpole Date: Mon Dec 2 19:08:20 2019 -0500 fixed GPU non-determinism Exec/SCIENCE/code_comp/analysis/plot_generator.py Exec/SCIENCE/rotating_star/initdat.256 Exec/SCIENCE/rotating_star/initdat.320 Exec/SCIENCE/rotating_star/initdata.f90 Exec/SCIENCE/rotating_star/inputs_3d_C Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroMacProj_level.cpp sphinx_docs/source/conf.py commit afdc97b0e8b2d5d429e65e988d8673101f0cd43f Author: Doreen Fan Date: Mon Dec 2 14:21:25 2019 -0800 Dec 2019 Release Notes RELEASE_NOTES commit 8b536e40d6bfa99063383cf7f936e0533504287b Merge: 576ba079 7f4c42f2 Author: Doreen Fan Date: Mon Dec 2 14:02:44 2019 -0800 Merge branch 'development' commit 7f4c42f29805dfd59b56238b396ac708d2349c63 Author: Doreen Fan Date: Mon Dec 2 14:02:16 2019 -0800 add release notes to development branch RELEASE_NOTES commit c31659652fb4dca1249ad30a67e9eb9e83362a60 Merge: b8945331 011d3fd1 Author: Michael Zingale Date: Sat Nov 30 20:19:58 2019 -0500 Merge branch 'development' of github.com:amrex-astro/MAESTROeX into development commit b894533167a3fef9be51bd5bc17d66a3ddcb8fa5 Author: Michael Zingale Date: Sat Nov 30 20:19:41 2019 -0500 add success to sync with Microphysics changes Microphysics/networks/sdc_type.F90 commit 011d3fd1b05a7beff0a217c377c568bb9f5ee864 Author: Doreen Fan Date: Tue Nov 26 21:10:40 2019 -0800 remove assumption that base_density_cutoff_coord < nr_fine Source/Src_nd/make_w0.f90 commit 6b3cb09a0315b9493b89ae778384010af0f049ce Author: Doreen Fan Date: Tue Nov 26 21:09:44 2019 -0800 use w0mac instead of w0mac_dummy for density and enthalpy advance subroutines Source/MaestroAdvanceSdc.cpp commit 2e9880d2720f966398d89139b65ba734ffb5318b Merge: 458d072b 4ab7490d Author: Michael Zingale Date: Sun Nov 24 14:01:38 2019 -0500 Merge branch 'development' of github.com:amrex-astro/MAESTROeX into development commit 458d072b9de6de411e4baffbc10e88fceaa5ea83 Author: Michael Zingale Date: Sun Nov 24 13:23:03 2019 -0500 switch to markdown and match style of Castro and Microphysics CHANGES.md RELEASE_NOTES commit 4ab7490df9c8f7210c725ef2140e232bf01a970d Author: Doreen Fan Date: Fri Nov 22 15:43:00 2019 -0800 add back w0 before calling EnthalpyAdvance in advance subroutine Source/MaestroAdvance.cpp commit 969d1cdbe6a57d8c0129b627da995b9220606612 Author: Doreen Fan Date: Fri Nov 22 15:21:32 2019 -0800 remove extra w0 terms from flux calculations that were added due to SDC merge Source/Src_nd/make_flux.F90 commit 3cfd3694a4b5a47fe8a871145d90cc33517672c4 Author: Doreen Fan Date: Fri Nov 22 13:11:23 2019 -0800 zero omegadot and Hnuc if do_burning=false Source/MaestroReact.cpp commit 944ca615bf646da6b1397eb2fb42627628cc9195 Author: Alice Harpole Date: Fri Nov 22 14:18:53 2019 -0500 add burner invert cutoff density flag to SDC burner loop Source/Src_nd/burner_loop.F90 commit d76859c65e8efbbd625c7cc5dff8a1a4d412ef15 Author: Michael Zingale Date: Thu Nov 21 20:13:32 2019 -0500 set the default integrator to VODE90 Exec/Make.Maestro commit 8f6f714f716f391be5d3e9be7ebd2940245536c2 Merge: d7a8df5f 5ea7c2f2 Author: Michael Zingale Date: Thu Nov 21 18:52:17 2019 -0500 Merge branch 'development' of github.com:amrex-astro/MAESTROeX into development commit d7a8df5f817461652add2810b0540e9419f75384 Author: Michael Zingale Date: Thu Nov 21 18:51:03 2019 -0500 add JOSS badge README.md commit 5ea7c2f2729aa4721d79641b69758ef6ea661ecf Merge: 9c39eda1 5779950f Author: Doreen Fan Date: Thu Nov 21 15:30:46 2019 -0800 Merge branch 'sdc' into development Resolved conflicts with latest GPU hydro PR commit 5779950f49902fa57dd06d5764345dce7ff22f55 Author: Doreen Fan Date: Thu Nov 21 15:15:35 2019 -0800 change integrator to VODE90 for most test problems Exec/SCIENCE/code_comp/GNUmakefile Exec/SCIENCE/ecsn/GNUmakefile Exec/SCIENCE/flame/GNUmakefile Exec/SCIENCE/plane_parallel_star/GNUmakefile Exec/SCIENCE/rotating_star/GNUmakefile Exec/SCIENCE/sub_chandra/GNUmakefile Exec/SCIENCE/toy_convect/GNUmakefile Exec/SCIENCE/urca/GNUmakefile Exec/SCIENCE/wdconvect/GNUmakefile Exec/SCIENCE/xrb_mixed/GNUmakefile Exec/TEST_PROBLEMS/double_bubble/GNUmakefile Exec/TEST_PROBLEMS/incomp_shear_jet/GNUmakefile Exec/TEST_PROBLEMS/mach_jet/GNUmakefile Exec/TEST_PROBLEMS/reacting_bubble/GNUmakefile Exec/TEST_PROBLEMS/rt/GNUmakefile Exec/TEST_PROBLEMS/test_convect/GNUmakefile Exec/TEST_PROBLEMS/test_planar_diag/GNUmakefile Exec/TEST_PROBLEMS/test_stability/GNUmakefile commit 64d01a620cca5cf299c8a1b80f10fc98d3267c43 Author: Doreen Fan Date: Thu Nov 21 14:43:15 2019 -0800 change SIMPLIFIED_SDC to SDC Microphysics/networks/burner.F90 commit 9c39eda1cc6cb4a7e53ae35f587eeeaafff8ea45 Author: Michael Zingale Date: Wed Nov 20 19:22:49 2019 -0500 add Zenodo badge README.md commit 2d9978a0013c7acad200ff158f2215243c00c39e Author: Michael Zingale Date: Wed Nov 20 19:20:46 2019 -0500 fix some .zenodo errors .zenodo.json commit cf0f9014d71cb77abcb112997bcefb31961a834b Author: Michael Zingale Date: Wed Nov 20 19:18:02 2019 -0500 fix tags .zenodo.json commit 54aa62e712c1560ab47ca6537df3aa0bf8e3f8e9 Author: Michael Zingale Date: Wed Nov 20 19:15:25 2019 -0500 update the zenodo to be in the same sequence as the JOSS paper .zenodo.json commit 8853581b00a2e9bfec025f66bfcb619c002bc2a2 Author: Alice Harpole Date: Wed Nov 20 18:48:41 2019 -0500 added initial data for 128 cubed rotating star run Exec/SCIENCE/rotating_star/initdat.256 Exec/SCIENCE/rotating_star/inputs_3d_C commit b11fe7383c5d61befbbbe7b536980a53575e6044 Author: Donald E. Willcox Date: Tue Nov 19 17:14:21 2019 -0800 Use new EOS composition module in Src_nd/make_intra_coeffs.F90. Source/Src_nd/make_intra_coeffs.F90 commit 912e946a75172b1382778b7d14738995bb0c07b7 Author: Donald E. Willcox Date: Tue Nov 19 17:13:49 2019 -0800 If we are using Simplified SDC then in the burner, use the integrator interface directly instead of actual_burner. Microphysics/networks/burner.F90 commit bae6d4b8fd21c5fa7c83c6db39ec59da0ba0d29e Author: Donald E. Willcox Date: Tue Nov 19 17:13:07 2019 -0800 Update conductivity interface to be current with StarKiller Microphysics. Microphysics/conductivity/conductivity.F90 commit e367433f884d11496f9354e6f99919ccb1a98b9b Author: Donald E. Willcox Date: Tue Nov 19 17:12:37 2019 -0800 Re-add include statements for Maestro_F.H. Source/MaestroAdvanceSdc.cpp Source/MaestroIntra.cpp commit 07ec1c5fd1ed7a0849464f1043de50c5aef845cf Author: Donald E. Willcox Date: Tue Nov 19 16:21:25 2019 -0800 Revert "re-add X derivatives to eos_t to compile with Microphysics sdc-maestroex branch" This reverts commit 65c30c584b9afd6870354cfa3deb448b0f355f84. Source/MaestroAdvanceSdc.cpp Source/MaestroIntra.cpp Source/Src_nd/make_S.F90 Source/Src_nd/make_explicit_thermal.F90 commit 472f5dad5a905dcbfa54f078c880143b811d93e0 Author: Donald E. Willcox Date: Tue Nov 19 16:21:13 2019 -0800 Revert "revert to Microphysics subroutines that do not use composition module so that code compiles with microphysics sdc-maestroex branch" This reverts commit df4ae79ae247765e16ad4bc91e2627ef27bb2e1b. Microphysics/EOS/eos.F90 Microphysics/EOS/eos_type.F90 commit 3b0a41a38b8c699063fca133cd58ef3ae9c17ce1 Author: Donald E. Willcox Date: Tue Nov 19 16:02:51 2019 -0800 Switch from using SDC_METHOD to defining SDC_EVOLVE_ENTHALPY now supported in Microphysics. Revert changes to the burner for SDC since we now call the integrator directly. Exec/Make.Maestro Exec/TEST_PROBLEMS/reacting_bubble/GNUmakefile Microphysics/networks/burn_type.F90 Microphysics/networks/burner.F90 Microphysics/networks/sdc_type.F90 commit 252a1da4d191489805fa76c9e4cce614ea42b0ce Author: Donald E. Willcox Date: Tue Nov 19 16:00:52 2019 -0800 For simplified SDC, switch to Castro approach to call the integrator subroutine directly instead of burner, since that will not require changes to the individual networks. Source/Src_nd/burner_loop.F90 commit 66f18bb4584081e225b6be03a7e3a9d8ec967394 Author: Alice Harpole Date: Tue Nov 19 13:41:30 2019 -0500 GPU make rho flux (GPU hydro PR 8/n) (#83) This offloads themake_rhox_flux_* and make_rhoh_flux_* routines to the GPU. It has been tested for the 2d & 3d reacting bubble and wdconvect problems compiled for MPI and GPU. Note: It is likely that this version will not work if compiled with OpenMP (this will come in a future PR) Source/MaestroAdvection.cpp Source/MaestroRhoHT.cpp Source/Maestro_F.H Source/Src_nd/make_flux.F90 Source/Src_nd/ppm.F90 Source/Src_nd/rhoh_vs_t.F90 commit 1c62bed0437d3d227bbf55c095cf413fb4ad9256 Merge: 2072e9bc 9a46794c Author: Alice Harpole Date: Mon Nov 18 10:29:26 2019 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 2072e9bca4a1b543c21c146fc003858afd2981d8 Author: Alice Harpole Date: Mon Nov 18 10:29:11 2019 -0500 turned burning off in core and added VODE90 to rotating star Exec/SCIENCE/rotating_star/GNUmakefile Exec/SCIENCE/rotating_star/inputs_3d_C commit 9a46794caea545bbb9a5ee59127d961617010665 Author: Michael Zingale Date: Sun Nov 17 09:23:52 2019 -0500 fix renders Util/logo/maestroex_100px.png Util/logo/maestroex_1600px.png Util/logo/maestroex_200px.png Util/logo/maestroex_400px.png Util/logo/maestroex_800px.png commit 42a930aff5d6f47fda8683d221b32235f1d6460e Merge: 7fabe37f f148c182 Author: Michael Zingale Date: Fri Nov 15 18:09:46 2019 -0500 Merge branch 'development' of github.com:amrex-astro/MAESTROeX into development commit 7fabe37f8dc0252ca87f9cf2bdd44da83cc15e46 Author: Michael Zingale Date: Fri Nov 15 18:09:42 2019 -0500 fix name Source/MaestroPlot.cpp commit 145da65dbc6929e855a72c5315b34480d962d68d Author: Alice Harpole Date: Fri Nov 15 15:23:03 2019 -0500 get model parser to read in enuc and omegadot for rotating star Exec/SCIENCE/rotating_star/18m_500_s_rot_b_eq_1.hse.51200 Exec/SCIENCE/rotating_star/18m_500_s_rot_b_eq_1.hse.6400 Exec/SCIENCE/rotating_star/initdat.320 Exec/SCIENCE/rotating_star/initdata.F90 Exec/SCIENCE/rotating_star/initdata.f90 Exec/SCIENCE/rotating_star/model_parser.f90 commit 576ba0790d0ba09d6a120a66afd7922286e951f4 Author: Arfon Smith Date: Fri Nov 15 10:18:45 2019 -0500 Update paper.md (#123) paper/paper.md commit a8aa9cc159dbda8bd1ec5907fe89706b62e2c57d Author: Alice Harpole Date: Thu Nov 14 15:25:28 2019 -0500 updated inputs file Exec/SCIENCE/rotating_star/inputs_3d_C commit 32899595c58eacd8b54f7b7c23c7e4a5048e9009 Author: Doreen Fan Date: Thu Nov 14 14:04:22 2019 -0800 add use_tfromp options if evolve_base_state=T Source/MaestroAdvanceSdc.cpp commit df4ae79ae247765e16ad4bc91e2627ef27bb2e1b Author: Doreen Fan Date: Thu Nov 14 14:03:26 2019 -0800 revert to Microphysics subroutines that do not use composition module so that code compiles with microphysics sdc-maestroex branch Microphysics/EOS/eos.F90 Microphysics/EOS/eos_type.F90 commit 55489862073e40cc2e249dccc481c81cb7b25cc5 Author: Doreen Fan Date: Thu Nov 14 14:02:21 2019 -0800 also compute cell-centered pi for sdc algorithm Source/MaestroNodalProj.cpp commit f148c182bf01a4607d443fcbe20a7179d084c1fb Author: Alice Harpole Date: Thu Nov 14 15:25:28 2019 -0500 updated inputs file Exec/SCIENCE/rotating_star/inputs_3d_C commit 7a70694985b7819cbcae3d509bd9439b9f2ee25b Merge: 4f217b61 43c058d0 Author: Alice Harpole Date: Thu Nov 14 15:24:16 2019 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 4f217b61dd1a2d97b5f7635696aa9d208b654a19 Author: Alice Harpole Date: Thu Nov 14 15:23:59 2019 -0500 latest version of initdat.320 Exec/SCIENCE/rotating_star/initdat.320 commit 43c058d019fa09e7a08f0d3b816a9aebffc4c9c0 Author: Michael Zingale Date: Thu Nov 14 11:26:47 2019 -0500 fix some formatting sphinx_docs/source/makefiles.rst commit da3a10fe6887cbedb25550672ba8ffec731e1208 Author: Michael Zingale Date: Thu Nov 14 08:34:20 2019 -0500 a bunch of cleaning sphinx_docs/source/makefiles.rst commit 5c68d334a60830d9e24d865649b4c61fe46c380f Author: Michael Zingale Date: Wed Nov 13 15:14:05 2019 -0500 output the GPU info to the job_info (#121) Source/MaestroPlot.cpp commit 6d7d0485b20e4de40df036fd21005a59f2e22753 Author: Alice Harpole Date: Wed Nov 13 15:01:02 2019 -0500 specified that the deviceQuery script must be compiled first sphinx_docs/source/gpu.rst commit 293a5c0047a21968ede0b18a6e3f6618060866e4 Author: Alice Harpole Date: Wed Nov 13 14:55:44 2019 -0500 added information about setting the CUDA compute capability to the GPU docs sphinx_docs/source/gpu.rst commit 68ee1ca65bb430eec10aa32ad25a82861a98f8a0 Author: Alice Harpole Date: Wed Nov 13 13:13:54 2019 -0500 Fix GPU compilation Source/Maestro.H commit 65c30c584b9afd6870354cfa3deb448b0f355f84 Author: Doreen Fan Date: Thu Nov 7 15:34:59 2019 -0800 re-add X derivatives to eos_t to compile with Microphysics sdc-maestroex branch Source/MaestroAdvanceSdc.cpp Source/MaestroIntra.cpp Source/Src_nd/make_S.F90 Source/Src_nd/make_explicit_thermal.F90 commit 2c69e04f9d4c0d5fcf069a930c95adf564afdea8 Merge: 0105ab5f b7a0b0e8 Author: Doreen Fan Date: Thu Nov 7 12:54:17 2019 -0800 Merge branch 'development' into sdc commit b7a0b0e89b3a580f5c161726c097c39b1c335668 Author: Alice Harpole Date: Wed Nov 6 14:42:33 2019 -0500 update initdat file Exec/SCIENCE/rotating_star/initdat.320 Exec/SCIENCE/rotating_star/inputs_3d_C commit 7fe1d12c811ca68fcdb5e19b04488049783775c7 Author: Alice Harpole Date: Wed Nov 6 12:12:35 2019 -0500 update initdat file Exec/SCIENCE/rotating_star/initdat.320 Exec/SCIENCE/rotating_star/inputs_3d_C commit dfc9b5af45448e98b556e5d3e8d7f24babeeb910 Author: Alice Harpole Date: Wed Nov 6 11:29:41 2019 -0500 initial data Exec/SCIENCE/rotating_star/initdat.320 Exec/SCIENCE/rotating_star/inputs_3d_C Exec/SCIENCE/rotating_star/inputs_3d_C.128 Exec/SCIENCE/rotating_star/inputs_3d_C.128.2levels Exec/SCIENCE/rotating_star/inputs_3d_C.128.exactbase Exec/SCIENCE/rotating_star/inputs_3d_C.64 Exec/SCIENCE/rotating_star/inputs_3d_C.64.exactbase Exec/SCIENCE/rotating_star/inputs_3d_regression commit 0105ab5ff461fd19bd041bd40d583643589cad32 Author: Doreen Fan Date: Tue Nov 5 10:46:42 2019 -0800 Add evolve_base_state=T option for sdc solver. Currently tested on reacting_bubble_2d. Source/MaestroAdvanceSdc.cpp Source/MaestroInit.cpp commit f5a021d6e1277fc88563d0973e9f4bf059d4ca0a Author: Michael Zingale Date: Mon Nov 4 16:35:22 2019 -0500 remove X derivatives from eos_t (#119) This removes the species derivatives from the eos_t to save memory and boost GPU performance. This coordinates with starkiller-astro/Microphysics#207 Microphysics/EOS/eos.F90 Microphysics/EOS/eos_type.F90 Source/MaestroRhoHT.cpp Source/Src_nd/make_S.F90 Source/Src_nd/make_explicit_thermal.F90 commit 4a69946821ebfe32d8652a9b370e7572cea1390c Author: Alice Harpole Date: Mon Nov 4 15:50:45 2019 -0500 fix GPU compilation for 3d Source/MaestroRhoHT.cpp commit f9256880cc2bf50e54fbb7346c371fb00839859b Merge: 809c64aa 1d7e8936 Author: Alice Harpole Date: Sun Nov 3 07:59:12 2019 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 809c64aa0f237ce4937034ae0a2ac57689da0a14 Author: Alice Harpole Date: Sun Nov 3 07:59:00 2019 -0500 fix gpu compilation Source/MaestroRhoHT.cpp commit 1d7e89365379eea57680f738f271c93d7f28e513 Author: Doreen Fan Date: Fri Nov 1 14:31:27 2019 -0700 Nov 2019 Release Notes RELEASE_NOTES commit 53b6da91821be9e0d69c43abde6a1b7d6ea9ca46 Author: Doreen Fan Date: Thu Oct 31 11:40:31 2019 -0700 only call estdt_divu when spherical==1 Source/MaestroDt.cpp commit 9ab5232c548c58333abd6c711efd856577d1bc32 Author: Alice Harpole Date: Wed Oct 30 12:34:52 2019 -0400 GPU make edge scal 3d (GPU hydro PR 7/n) (#82) This offloads make_edge_scal_3d to the GPU. It has been tested for the 3d reacting bubble & wdconvect problems compiled for MPI and GPU. This also adds in the CUDA launch statements (and does some restructuring of the ppm-dependent routines to enable register capping) so all of the hydro routines offloaded so far now actually run on the GPU. Exec/Make.Maestro Exec/Make.cuda_rules Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvection.cpp Source/MaestroAverage.cpp Source/MaestroCheckpoint.cpp Source/MaestroConvert.cpp Source/MaestroDebug.cpp Source/MaestroDensityAdvance.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroEvolve.cpp Source/MaestroFill3dData.cpp Source/MaestroFillData.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroHeating.cpp Source/MaestroHydro.cpp Source/MaestroHydro_F.H Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp Source/MaestroReact.cpp Source/MaestroRegrid.cpp Source/MaestroRhoHT.cpp Source/MaestroSetup.cpp Source/MaestroSponge.cpp Source/MaestroThermal.cpp Source/MaestroVelocityAdvance.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/make_edge_scal.F90 Source/Src_nd/ppm.F90 Source/main.cpp commit c3d1cf41ac8da05d528210ff66cb427ff3f922a5 Author: Michael Zingale Date: Wed Oct 30 10:49:58 2019 -0400 add log oto navbar sphinx_docs/source/conf.py sphinx_docs/source/maestroex_logo.png commit d24e4a9a893a2db1104a27554fd2eebd3c4e2e34 Author: Michael Zingale Date: Wed Oct 30 08:32:21 2019 -0400 add regtest sphinx_docs/source/index.rst sphinx_docs/source/regtest.rst commit 17c3dd293ad6f9ec908853f22794d251dcb98cb1 Author: Andy Nonaka Date: Tue Oct 29 12:49:14 2019 -0700 disable openMP from tagging routines for the moment; planar version causes segfaults Source/MaestroRegrid.cpp commit eb162a49f27caed803e604ef1cd67ab6e8cd1071 Author: Michael Zingale Date: Tue Oct 29 10:38:17 2019 -0400 2 level test problem Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_regression.2levels commit 0ce0156d097dac995263e2c8fdba903189a244ca Author: Michael Zingale Date: Tue Oct 29 10:37:10 2019 -0400 2 level test suite Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_regression.2levels commit b07beb439498594a6cfc3ba32e7bf5aad1ee3aaf Merge: bbd0eae6 7f7b6dde Author: Doreen Fan Date: Mon Oct 28 13:21:26 2019 -0700 Merge branch 'development' into sdc commit 7f7b6ddee8beb518feba827a5f1e27b384a65852 Author: Doreen Fan Date: Fri Oct 25 17:35:34 2019 -0700 add multilevel planar regression tests Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_amr_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_amr_regression commit 908ba2475edac735078460629419eaa853d5af73 Author: Andy Nonaka Date: Fri Oct 25 17:13:33 2019 -0700 w0_cart needs 2 ghost cells since w0mac has 1 ghost cell Source/MaestroInit.cpp Source/MaestroRegrid.cpp commit 2f80d68c0d401ea567aa0dd85aa9522d7ddc3fae Author: Andy Nonaka Date: Fri Oct 25 16:47:06 2019 -0700 bugfix: fill w0_cart after regrid Source/MaestroRegrid.cpp commit 03ef599f9fdfa3eaa9542ed79329abf332d46759 Author: Andy Nonaka Date: Fri Oct 25 16:29:23 2019 -0700 fixed one restart bug (still may be others). Need to fill in w0_cart after reading in w0 from checkpoint. This problem was introduced once we decided to make w0_cart persistent for GPU purposes Source/MaestroCheckpoint.cpp Source/MaestroInit.cpp commit bbd0eae6e9bb34566f554dcc936925c64f0406fa Author: Doreen Fan Date: Fri Oct 25 15:37:54 2019 -0700 fix for dpdt_factor>0 to work properly Source/MaestroAdvanceSdc.cpp commit df7f2724d3236cefc3d81fa2dbf1da51c9515d46 Author: Michael Zingale Date: Fri Oct 25 15:26:03 2019 -0400 remove old header README.md commit 818018213d62951b8e2eecd457cfb18dee3fd881 Author: Michael Zingale Date: Fri Oct 25 15:24:50 2019 -0400 add logo README.md commit 34bed0a16a18b04ea4257a94c503453650c3fbc5 Author: Doreen Fan Date: Thu Oct 24 17:31:20 2019 -0700 fixed sign of div(hcoeff grad h) term Source/MaestroThermal.cpp commit 0152621fbe24c119ab80cae42f9188debf820810 Author: Doreen Fan Date: Thu Oct 24 16:46:50 2019 -0700 update inflow boundary conditions and enthalpy_pred_types in sdc subroutines Source/MaestroEnthalpyAdvance.cpp Source/MaestroThermal.cpp commit c4a5e41edfff28e516612e0e08c2489e825154fe Merge: 7abfb010 3522513a Author: Doreen Fan Date: Thu Oct 24 16:01:07 2019 -0700 Merge branch 'development' into sdc commit 3522513a2bb2760c95c8540c7ca5c0e86b2940b9 Author: Doreen Fan Date: Thu Oct 24 15:57:03 2019 -0700 add 3d flame test Exec/SCIENCE/flame/bc_fill_nd.F90 Exec/SCIENCE/flame/inputs_3d_smallscale commit d927b85c4bd495a2fe294885fcf64451e3499059 Merge: 638c50f8 c43374c6 Author: Andy Nonaka Date: Thu Oct 24 14:50:48 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 638c50f89cdad74182a32a8a083ec369602c1323 Author: Andy Nonaka Date: Thu Oct 24 14:50:25 2019 -0700 outflow should be neumann for thermal operator and solver Source/MaestroThermal.cpp commit c43374c60703b75386c6cdd062ac21825aaf067d Author: Doreen Fan Date: Thu Oct 24 14:03:41 2019 -0700 update subroutines to compile test properly Exec/UNIT_TESTS/test_diffusion/MaestroDt.cpp Exec/UNIT_TESTS/test_diffusion/MaestroPlot.cpp commit 13129d7b20f3a3f497a7be86a7f6ddef5a30e3a1 Author: Alice Harpole Date: Thu Oct 24 12:56:20 2019 -0400 add base_state.f90 Exec/SCIENCE/code_comp/base_state.f90 Exec/SCIENCE/code_comp/inputs_3d commit 3b125bbba8add95ddb105fa1f137bfaa026d4140 Author: Alice Harpole Date: Thu Oct 24 11:52:53 2019 -0400 unadded rst files Exec/SCIENCE/code_comp/analysis/plot_generator.py Exec/SCIENCE/code_comp/inputs_3d sphinx_docs/source/Src_nd_files.rst sphinx_docs/source/classlist.rst sphinx_docs/source/filelist.rst sphinx_docs/source/param_includes_files.rst commit fe87a66dd6a467d24f058662755041c8fa58239f Author: Alice Harpole Date: Thu Oct 24 11:51:58 2019 -0400 update Amrvis installation instructions sphinx_docs/source/Src_nd_files.rst sphinx_docs/source/classlist.rst sphinx_docs/source/filelist.rst sphinx_docs/source/gpu.rst sphinx_docs/source/param_includes_files.rst sphinx_docs/source/visualization.rst commit e61359d7f05e67f93d2760d645e73c72345bf3d2 Author: Alice Harpole Date: Wed Oct 23 11:11:35 2019 -0400 some minor edits to gpu docs Util/yt/plotsinglevar.py sphinx_docs/source/gpu.rst commit fc3fdd8333e3fcb9c9da0e340f627891c749bd8a Merge: 27b6a665 bbda996e Author: Michael Zingale Date: Wed Oct 23 04:42:12 2019 -0400 Merge branch 'development' of github.com:amrex-astro/MAESTROeX into development commit 27b6a6650e6a90a068377627df04fbc098ca9c61 Author: Michael Zingale Date: Wed Oct 23 04:41:52 2019 -0400 the script used to create the logo bitmap that was then traced Util/logo/slice_multi.py commit bbda996eb512b0b7ef74ce465c9fc492dfa3047d Author: Doreen Fan Date: Tue Oct 22 17:39:19 2019 -0700 added gpu section in user's guide sphinx_docs/source/faq.rst sphinx_docs/source/gpu.rst sphinx_docs/source/index.rst commit 649338d74c4bfd17778a6324cff8b25a0d5d2630 Author: Doreen Fan Date: Tue Oct 22 17:36:00 2019 -0700 changed subroutine to be used as gpu example in user's guide Source/Src_nd/compute_dt.F90 commit d9a5b83563956a93ba5746679e1a211956cfaa06 Author: Andy Nonaka Date: Tue Oct 22 17:06:47 2019 -0700 JOSS paper updates paper/paper.bib paper/paper.md commit fbf9db7b0b5ccbf085d7b9d7a47783b16c67f484 Author: Alice Harpole Date: Tue Oct 22 15:53:20 2019 -0400 updated docs to reflect new scripts Exec/TEST_PROBLEMS/reacting_bubble/GNUmakefile Util/yt/contourcompare.py Util/yt/plotsinglevar.py Util/yt/runtimevis.py sphinx_docs/source/plt00000_tfromp.png sphinx_docs/source/plt00000_tfromp_Hnuc.png sphinx_docs/source/plt00000_tfromp_enucdot.png sphinx_docs/source/visualization.rst commit e753f152212a2989e6ec80be909f3d953479cc02 Author: Alice Harpole Date: Tue Oct 22 14:38:05 2019 -0400 runtimevis script Util/scripts/contourcompare.py Util/scripts/plotsinglevar.py Util/scripts/runtimevis.py commit 6067da80ada1f3a7ef1d7e2f3febf9dc581345ee Merge: c5b69605 b8b31a6e Author: Alice Harpole Date: Tue Oct 22 13:44:09 2019 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit c5b6960545ba1fe41a73d3bdafa15a1e091398df Author: Alice Harpole Date: Tue Oct 22 13:44:05 2019 -0400 contour compare script Util/scripts/contourcompare.py Util/scripts/plotsinglevar.py commit 74b8b15bf66400ac4edf4881b3616d717276604e Merge: 4c1a1e4d b8b31a6e Author: Michael Zingale Date: Tue Oct 22 13:21:27 2019 -0400 Merge branch 'development' of github.com:amrex-astro/MAESTROeX into development commit 4c1a1e4dd1b78e77ff578a9cc1cca9a0151588c0 Author: Michael Zingale Date: Tue Oct 22 13:21:13 2019 -0400 some renders Util/logo/maestroex_100px.png Util/logo/maestroex_1600px.png Util/logo/maestroex_200px.png Util/logo/maestroex_400px.png Util/logo/maestroex_800px.png Util/logo/maestroex_logo.svg commit b8b31a6e483377fcb92a318b50b2541177f2911e Author: Andy Nonaka Date: Tue Oct 22 09:25:26 2019 -0700 acknowledge original MAESTRO authors paper/paper.md commit b32bffe6daf261f63788b96823769c85ccd878c9 Author: Alice Harpole Date: Tue Oct 22 12:18:12 2019 -0400 added more functionality to plotsinglevar.py Util/scripts/plotsinglevar.py commit 77885ee8d6eea8aaf778d2019344da459fa9f888 Merge: 3e63ed65 86cceb7b Author: Alice Harpole Date: Tue Oct 22 11:32:09 2019 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 3e63ed6599493dcc18daab053cc9a379bd85804c Author: Alice Harpole Date: Tue Oct 22 11:31:59 2019 -0400 added script for producing sliceplots Util/scripts/plotsinglevar.py commit 86cceb7b5bdc0c5ee0912e927dbea99dc16b16d8 Author: Michael Zingale Date: Tue Oct 22 11:02:05 2019 -0400 remove the hidden bitmap Util/logo/maestroex_logo.svg commit 986a4afb23d93f1c1f351551ba799185f89508cd Author: Michael Zingale Date: Tue Oct 22 10:57:46 2019 -0400 add logo proposal Util/logo/maestroex_logo.svg commit b05960c5a0b433a76cf3fc1504d9c7d9dc22ecc8 Author: Alice Harpole Date: Tue Oct 22 09:35:59 2019 -0400 add requirements to README and update reacting_bubble inputs file Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C README.md commit 115f582f27e3b14eede2b586a9263e3f24324f69 Author: Alice Harpole Date: Tue Oct 22 09:25:00 2019 -0400 instruct users to submit a PR from their fork sphinx_docs/source/getting_started.rst commit 8b0cfde4a813a4d64bc8351f25a647c6be9ea494 Author: Doreen Fan Date: Thu Oct 17 19:26:14 2019 -0700 bugfix: edge value arrays should be edge-centered when put on cartesian grid Source/MaestroEnthalpyAdvance.cpp Source/MaestroRhoHT.cpp commit 3bef6e930338ed9ec66d510afe9c2a5c60c4043a Author: Doreen Fan Date: Thu Oct 17 16:38:56 2019 -0700 SDC input file based on same MAESTRO test problem Exec/SCIENCE/flame/inputs_2d_smallscale_sdc commit 0d829c69ace77d377af4a9dbf19471dddf922f19 Author: Doreen Fan Date: Thu Oct 17 16:17:16 2019 -0700 added missing if statement for enthalpy_pred_type = predict_T_then_rhohprime in make_flux subroutines Source/Src_nd/make_flux.F90 commit 7abfb010d8448f060855c2c84f067b91ee502b7e Merge: 92721596 e23fca24 Author: Doreen Fan Date: Thu Oct 17 09:34:22 2019 -0700 Merge branch 'development' into sdc commit e23fca246fedc1842298d24b2a343e9375f7a313 Author: Andy Nonaka Date: Thu Oct 17 08:13:14 2019 -0700 typo s -> scal. 3d compiles again Source/Src_nd/make_scal_force.F90 commit 927215960e605d55118f950f73cb218a434908e9 Merge: 13cbc7fe b76d17aa Author: Doreen Fan Date: Wed Oct 16 18:42:41 2019 -0700 Merge branch 'development' into sdc commit b76d17aa6247a9e53215d6a69b4d9a676d6444f6 Author: Doreen Fan Date: Wed Oct 16 18:40:02 2019 -0700 add subroutines to enable enthalpy_pred_type = predict_T_then_rhohprime, predict_T_then_h, predict_Tprime_then_h during enthalpy advance Source/Maestro.H Source/MaestroEnthalpyAdvance.cpp Source/MaestroForce.cpp Source/MaestroRhoHT.cpp Source/Maestro_F.H Source/Src_nd/make_scal_force.F90 Source/Src_nd/rhoh_vs_t.F90 commit d7e2fffc0368388722f9875d303a78de1ac6563e Author: Alice Harpole Date: Tue Oct 15 11:11:54 2019 -0400 added mailing list back in README.md commit d483be020af546047a05372834960f192cf5a375 Merge: 0eb8340d f6645448 Author: Alice Harpole Date: Tue Oct 15 10:58:50 2019 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 0eb8340d9b6ffeb10427a8be35d6adcb8f00441c Author: Alice Harpole Date: Tue Oct 15 10:58:43 2019 -0400 changed getting help section of the README to ask users to submit github issues, addressing #106 Exec/SCIENCE/rotating_star/inputs_3d_C README.md commit 13cbc7fe48007e39226bdd51e73aa4142d00bec5 Author: Michael Zingale Date: Sun Oct 13 17:05:36 2019 -0400 Microphysics is in the process of renaming the original SDC "simplified SDC" this defines the new preprocessor stuff needed. Exec/Make.Maestro commit f664544823e1bc4a9dc8e34e07c71ac6ffb87224 Merge: 7795091f b2253352 Author: Andy Nonaka Date: Fri Oct 11 14:58:40 2019 -0700 Merge pull request #105 from tukss/doc_fix fix rendering of formula in the docs commit 57e3f93031097683abf6e7740f77ea3eb02da48f Merge: df9f4b23 7795091f Author: Doreen Fan Date: Fri Oct 11 14:56:27 2019 -0700 Merge branch 'development' into sdc commit b2253352ee9e0dd7820c309484161200d87a211c Author: Philipp Edelmann Date: Fri Oct 11 15:48:09 2019 +0100 fix rendering of formula in the docs sphinx_docs/source/thermo_notes.rst commit df9f4b23a6f7490074a944d57943e9aa8a096f64 Author: Doreen Fan Date: Tue Oct 8 15:16:39 2019 -0700 Inputs for strang/sdc algorithm comparison. Note that init_shrink must be decreased significantly in order for the problem to run properly using sdc. Exec/SCIENCE/plane_parallel_star/inputs_2d_sdc commit 7897af629aaccd6ee945d5a6f29e1d700ded5056 Author: Doreen Fan Date: Tue Oct 8 15:14:15 2019 -0700 code can now be compiled with USE_SDC=FALSE on Microphysics sdc-maestroex branch Microphysics/conductivity/conductivity.F90 Source/MaestroPlot.cpp commit 7795091f79d566b15b035c9769f834a966967fac Author: Alice Harpole Date: Tue Oct 8 14:55:15 2019 -0400 changed resolution and fixed header Exec/SCIENCE/rotating_star/15m_500_sec.hse.6400 Exec/SCIENCE/rotating_star/15m_500_sec.hse.8960 Exec/SCIENCE/rotating_star/inputs_3d_C commit 2417773857ccffb8076d377269afba55dd053a52 Author: Alice Harpole Date: Tue Oct 8 14:40:18 2019 -0400 15 solar mass intial model Exec/SCIENCE/rotating_star/15m_500_sec.hse.8960 commit 743ae1b5bfe4ab57a8c0fb412c03036d43f78ad8 Author: Alice Harpole Date: Tue Oct 8 11:26:48 2019 -0400 fixed a typo sphinx_docs/source/getting_started.rst commit 0ac47ae2ab1b763eab726513ce0985b63dc88d56 Author: Alice Harpole Date: Tue Oct 8 11:21:53 2019 -0400 added a section describing software requirements in docs sphinx_docs/source/getting_started.rst commit 153996835f6aedccaba6bcdaf2a687d282749938 Merge: 243bd9aa 9b51a286 Author: Alice Harpole Date: Thu Oct 3 15:35:51 2019 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 243bd9aa272c8740f2e1fcfe48e2c74048a4204b Author: Alice Harpole Date: Thu Oct 3 15:35:31 2019 -0400 inputs file for rotating star Exec/SCIENCE/rotating_star/inputs_3d_C commit edeeb35c96d28ec289a39c1bb34689d39f36f562 Author: Doreen Fan Date: Wed Oct 2 11:36:01 2019 -0700 move instantaneous_reaction_rates subroutine to burner_loop_module and limit computations to region within burning_cutoff_density Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/burner_loop.F90 Source/Src_nd/make_reaction_rates.F90 commit 9b51a286e5e9e2f0dd4ef6f41599c6c409275c37 Author: Andy Nonaka Date: Wed Oct 2 07:58:14 2019 -0700 bugfix: p0_cart needs a ghost cell Source/MaestroMakeS.cpp commit 5c87ed46e64478c0cd8df9e82e0c06c10fdfffed Author: Doreen Fan Date: Tue Oct 1 13:07:09 2019 -0700 Oct 2019 Release Notes RELEASE_NOTES commit a385ebbf921ea55f1e5c9861ebce0132224ef4c5 Author: Jonathan Thurgood <42877905+JOThurgood@users.noreply.github.com> Date: Tue Oct 1 17:53:43 2019 +0100 Add diagnostics for planar geometries (#90) Diagnostics currently are spherical only, this PR extends the same measurements to a planar geometry. In 2D, things like z-components are just recorded as zero, and spherical-specific things such as measurements at the star centre are not recorded. The fortran now has separate diag and diag_sphr subroutines (where diag_sphr is what was previously diag). They basically do the same thing in this PR. Gravitational potential energy is defined differently so it too has separate planar and spherical subroutines. * add diagnostics for planar mode * tidy comments * remove 1d support * rename variables from coordenuc2 -> coord_enuc_y etc * remove remenants of a bad copy paste * T_max -> temp_max, coord_Tmax -> coord_temp_max, etc, in the fortran * bug fix - coord_enuc was being set to coord_tmax * remove the rest of the unnecessary AMREX_SPACEDIM < 2 conditionals (remove 1d support) * move module to 1st line to make work with sphinx (I think this is all thats required? * guard star center calculations with preprocessor directive * clarify comments that will end up in docs * add a rudimentary test problem for planar diagnostics * fix a typo in the python notebook * remove hard-coded dimensional factor * delete print statement / unnecessary print statement Exec/TEST_PROBLEMS/test_planar_diag/GNUmakefile Exec/TEST_PROBLEMS/test_planar_diag/Make.package Exec/TEST_PROBLEMS/test_planar_diag/README.md Exec/TEST_PROBLEMS/test_planar_diag/_parameters Exec/TEST_PROBLEMS/test_planar_diag/base_state.f90 Exec/TEST_PROBLEMS/test_planar_diag/check_diagnostics.ipynb Exec/TEST_PROBLEMS/test_planar_diag/initdata.f90 Exec/TEST_PROBLEMS/test_planar_diag/inputs_2d_C Exec/TEST_PROBLEMS/test_planar_diag/simple.net Source/MaestroDiag.cpp Source/Maestro_F.H Source/Src_nd/diag.F90 commit a5b3da559c1094f40016909cce352ae5e1f52a65 Author: Alice Harpole Date: Tue Oct 1 11:27:04 2019 -0400 forgot to add these files back after f90 -> F90 Source/Src_nd/enforce_HSE.F90 Source/Src_nd/make_grav.F90 commit bfb233911604d1c04903039b55718634d10104cc Author: Alice Harpole Date: Tue Oct 1 09:13:15 2019 -0400 added invert threshold density flag so can turn off burning *above* a certain density threshold Exec/SCIENCE/plane_parallel_star/inputs_2d Source/Src_nd/burner_loop.F90 Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit 0fca6f12f37461d8ffd4d6ccc431394cfbcb32e4 Author: Alice Harpole Date: Tue Oct 1 08:40:57 2019 -0400 merging with development Source/MaestroAdvance.cpp Source/MaestroMacProj.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/base_state_geometry.F90 Source/Src_nd/enforce_HSE.f90 Source/Src_nd/fill_3d_data.F90 Source/Src_nd/make_grav.f90 commit 112ea7e3ce63f3a61ec0d507b763ca70afd7caf7 Merge: 8126e3c9 e2574c6e Author: Doreen Fan Date: Mon Sep 30 15:58:22 2019 -0700 Merge branch 'sdc' of https://github.com/AMReX-Astro/MAESTROeX into sdc commit 8126e3c9430b1950db7ee6ff56c2edfea7abbb27 Author: Doreen Fan Date: Mon Sep 30 15:28:53 2019 -0700 turn off use_delta_gamma1_term Exec/SCIENCE/plane_parallel_star/inputs_2d commit 375ebd310cc1634d0e1699fe08c405e9c83ed450 Author: Doreen Fan Date: Mon Sep 30 15:28:53 2019 -0700 turn off use_delta_gamma1_term Exec/SCIENCE/plane_parallel_star/inputs_2d commit e2574c6e3936106bda80c4741ac62bc3fdc32216 Author: Doreen Fan Date: Mon Sep 30 13:06:44 2019 -0700 compute gradp0 outside of fortran subroutine so that we don't need to access ghost cells for p0 Source/MaestroMakeS.cpp Source/Maestro_F.H Source/Src_nd/make_S.F90 commit c32d092cab22a9189cac18dc71829a5fb80e3a5d Author: Michael Zingale Date: Fri Sep 27 21:50:14 2019 -0400 update to python3 + argparse Microphysics/networks/general_null/write_network.py commit cdf18dc8d896d1955d22a6da1e7d2b00da39a896 Author: Doreen Fan Date: Fri Sep 27 15:27:31 2019 -0700 Changed make_flux to use full umac velocities instead of split umac and w0mac. This is done so that the split mac velocities are only used during projection steps Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroAdvection.cpp Source/MaestroDensityAdvance.cpp Source/MaestroEnthalpyAdvance.cpp Source/Maestro_F.H Source/Src_nd/make_flux.F90 commit df8ef622887e9183fa93e4f095a63ad3111129c2 Author: Doreen Fan Date: Thu Sep 26 18:57:47 2019 -0700 bug fix: set sdc_off parameter to false Source/MaestroInit.cpp commit d2bdbe93c94edd720bc0f65445336305a16663bc Author: Doreen Fan Date: Thu Sep 26 12:35:10 2019 -0700 add inputs for nonaka plot Exec/SCIENCE/plane_parallel_star/GNUmakefile Exec/SCIENCE/plane_parallel_star/inputs_2d commit 4ef9080aad6f4b7e136ee32f56d29e075a0656b4 Author: Doreen Fan Date: Thu Sep 26 12:35:10 2019 -0700 add inputs for nonaka plot Exec/SCIENCE/plane_parallel_star/GNUmakefile Exec/SCIENCE/plane_parallel_star/inputs_2d commit 5171fad6f2b501ecfd52bd5ae596347e6d4c847d Author: Doreen Fan Date: Wed Sep 25 18:06:08 2019 -0700 enthalpy_pred_type=predict_rhohprime and species_pred_type=predict_rhoprime_and_X now works with sdc when evolve_base_state=F Source/MaestroAdvanceSdc.cpp Source/MaestroDensityAdvance.cpp commit c23e0fe541d28d569fb2a55b76813fbeb5b0547f Merge: 38ea7d43 cac09729 Author: Michael Zingale Date: Mon Sep 23 21:49:39 2019 -0400 Merge branch 'development' of github.com:amrex-astro/MAESTROeX into development commit 38ea7d436eb6cbd1484822b3e3eb782a60b2c985 Author: Michael Zingale Date: Mon Sep 23 21:48:46 2019 -0400 some doc fixes sphinx_docs/source/beta0.rst sphinx_docs/source/mg.rst sphinx_docs/source/networks.rst sphinx_docs/source/pert.rst commit cac0972922d617101ead7f2e62b773bde64d6213 Author: Doreen Fan Date: Mon Sep 23 11:01:29 2019 -0700 bcs_u -> bcs Source/MaestroAdvection.cpp commit ba059073cb1ae9bd93fe5deb687e776837fbeb59 Author: Alice Harpole Date: Mon Sep 23 12:16:19 2019 -0400 RealVector is now an alias for amrex::GPU:ManagedVector Source/Maestro.H commit 6fbdda37c093364cd5d9491f1fcfcd10f88aac9e Author: Alice Harpole Date: Mon Sep 23 11:23:28 2019 -0400 fixed GPU compilation Source/Maestro.cpp Source/MaestroBCThreads.H Source/MaestroSetup.cpp commit 977c35fa7f4fec02a92c84cf35c1597165462060 Author: Michael Zingale Date: Sun Sep 22 22:55:25 2019 -0400 fix typo sphinx_docs/source/pert.rst commit 89a5401a52aebaf474d21b86068117e769a48745 Author: Michael Zingale Date: Sun Sep 22 22:53:33 2019 -0400 change fixed font format sphinx_docs/source/_static/theme_overrides.css commit 3114ec00b994184353067db23b29deba594f0105 Author: Michael Zingale Date: Sun Sep 22 22:53:01 2019 -0400 fix some formatting sphinx_docs/source/Godunov.rst sphinx_docs/source/pert.rst sphinx_docs/source/thermo_notes.rst commit 4e0658b2d1c1c8580dabf5d2b40ca55afa09ee08 Author: Michael Zingale Date: Sun Sep 22 20:19:35 2019 -0400 some more fixes sphinx_docs/source/Godunov.rst sphinx_docs/source/rotation.rst sphinx_docs/source/volume_discrepancy.rst commit 390711b602a97f7642999838974ddf1d87c6beb7 Author: Michael Zingale Date: Sun Sep 22 20:05:31 2019 -0400 port over some figures sphinx_docs/source/compare_castro.png sphinx_docs/source/compare_tF_d0_h1_s123.png sphinx_docs/source/compare_tfromp.png sphinx_docs/source/mom_filaments.png sphinx_docs/source/pert.rst sphinx_docs/source/spec1_cfl_1vs7.png sphinx_docs/source/spec1_vs_23.png sphinx_docs/source/tfromh_unphysical.png sphinx_docs/source/tfrompF_cfl_1vs7.png sphinx_docs/source/tfrompF_unphys.png commit a5430ef3f7be72eeab74b11a30e1beb5de1a7b50 Author: Michael Zingale Date: Sun Sep 22 18:28:54 2019 -0400 a bunch more reference fixes sphinx_docs/source/beta0.rst sphinx_docs/source/enthalpy.rst sphinx_docs/source/eta.rst sphinx_docs/source/pert.rst commit 15aabd00bc4f433b749c41ade3364756b9a32b14 Author: Michael Zingale Date: Sun Sep 22 18:17:39 2019 -0400 fix lots of references sphinx_docs/source/HG_mg2.png sphinx_docs/source/MAC_mg2.png sphinx_docs/source/beta0.rst sphinx_docs/source/conf.py sphinx_docs/source/eta.rst sphinx_docs/source/mg.rst sphinx_docs/source/pert.rst sphinx_docs/source/planar_invsq_basestate.rst sphinx_docs/source/thermo_notes.rst sphinx_docs/source/visualization.rst commit bdc6376e3412cf008c538e43b6cd9f477de00763 Merge: a6871374 0f0db8da Author: Michael Zingale Date: Sat Sep 21 16:03:01 2019 -0400 Merge branch 'master' into development commit a6871374e052d84e4eadac2263b3a829614f4eb5 Author: Alice Harpole Date: Sat Sep 21 15:56:47 2019 -0400 GPU make edge scal 2d (GPU hydro PR 6/n) (#81) This offloads make_edge_scal_2d to the GPU. It has been tested for the 2d reacting bubble problem compiled for MPI and GPU. Note: It is likely that this version will not work if compiled with OpenMP (this will come in a future PR) Source/MaestroAdvection.cpp Source/Maestro_F.H Source/Src_nd/make_edge_scal.F90 commit febd7458fdc7d2c1f567001cb3d7e67b40fdc704 Author: Andy Nonaka Date: Fri Sep 20 09:53:34 2019 -0700 corner ghost cell issue fixed Source/MaestroAdvection.cpp commit 0f0db8dad724290348507af328adc4bea7d4fea5 Author: Andy Nonaka Date: Fri Sep 20 09:33:48 2019 -0700 Update README.md README.md commit 5330d0ed942b3498b694ea366cd5700bd30b43d6 Author: Doreen Fan Date: Thu Sep 19 20:09:10 2019 -0700 declare w0_force_cart in non-spherical cases as well Source/MaestroAdvanceAvg.cpp Source/MaestroForce.cpp commit 82759912aaedea0607897991059b87fd98969afb Author: Doreen Fan Date: Thu Sep 19 19:56:26 2019 -0700 must declare w0_force_cart at all times Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroForce.cpp Source/MaestroReact.cpp commit 50a688a584167a7188d547bc30e608452578ddd0 Merge: 00624285 032feac4 Author: Doreen Fan Date: Thu Sep 19 18:02:28 2019 -0700 Merge branch 'development' into sdc commit 00624285f2f9b3fec902c8337c95e199aab8526f Author: Doreen Fan Date: Thu Sep 19 18:02:20 2019 -0700 resolved conflicts with latest merge Source/MaestroDensityAdvance.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroPlot.cpp commit 032feac482df11337bbaad53eb35fb92e5aba891 Author: Andy Nonaka Date: Thu Sep 19 15:09:10 2019 -0700 only copy w0 onto w0_cart immediately after make_w0 Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvection.cpp Source/MaestroDt.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroPlot.cpp commit 15cbaa54ff5318e790b6065237137f61e64fdbde Merge: 6a62a897 3d3a6419 Author: Doreen Fan Date: Thu Sep 19 14:24:32 2019 -0700 Merge branch 'development' into sdc commit 6a62a89718d77c2b5d58c66ef07e83949b9b4b7b Merge: 8e7631dc fac19708 Author: Doreen Fan Date: Thu Sep 19 14:21:53 2019 -0700 compute intra only for species and enthalpy (no density) Merge branch 'development' into sdc commit 3d3a6419b8afc61c97d29e276d0f8a265cbaf5e7 Author: Andy Nonaka Date: Thu Sep 19 12:53:07 2019 -0700 bugfixes in several calls to filling w0_cart from w0. many of the routines were assuming w0 was cell-centered regression results will change for many problems Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvection.cpp Source/MaestroDt.cpp Source/MaestroForce.cpp Source/MaestroPlot.cpp commit fac19708689413ab35a8646f9a0c71e5039ac842 Author: Andy Nonaka Date: Thu Sep 19 12:29:49 2019 -0700 w0_cart is now part of the MAESTRO class there are no more temporary w0_carts created this does not address the fact that filling in w0_cart from w0 may be happening more times than it should Source/Maestro.H Source/MaestroAdvection.cpp Source/MaestroCheckpoint.cpp Source/MaestroDt.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroPlot.cpp Source/MaestroRegrid.cpp Source/MaestroSetup.cpp commit 7bb658e0e651b408aeaf95b7562cd318c8fd9d09 Author: Andy Nonaka Date: Thu Sep 19 10:30:20 2019 -0700 indentation only Source/Maestro_F.H commit d2bfea6b1b1e3a3074ef4b068a071bfc7d97dea1 Author: Andy Nonaka Date: Thu Sep 19 09:45:23 2019 -0700 now all instances of the temporary w0_cart have only 1 ghost cell cleaned up indentation in MaestroPlot.cpp Source/MaestroFill3dData.cpp Source/MaestroPlot.cpp commit 5767728fce1cb130a0e7577c81c5eae3af274282 Author: Alice Harpole Date: Wed Sep 18 15:43:30 2019 -0400 added some analysis scripts for the code comp problem (taken from the Castro flame_wave directory) Exec/SCIENCE/code_comp/analysis/image_animator.py Exec/SCIENCE/code_comp/analysis/plot_generator.py commit dfc1a3a593bbd9730577225265a8eea16576ea38 Author: Doreen Fan Date: Tue Sep 17 19:09:24 2019 -0700 pass reaction start time to the burner Microphysics/networks/burner.F90 Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroDiag.cpp Source/MaestroInit.cpp Source/MaestroPlot.cpp Source/MaestroReact.cpp Source/Maestro_F.H Source/Src_nd/burner_loop.F90 commit 8fbbfc82bf1cc0318fa30abea7a4942ae3ca9c4a Author: Doreen Fan Date: Mon Sep 16 19:33:23 2019 -0700 Always set i,j,k for burn states regardless of USE_NONAKA_PLOT Source/Src_nd/burner_loop.F90 commit 878ce90eb039e65e97391272d5023ed91b107ee3 Author: Alice Harpole Date: Sat Sep 14 11:30:25 2019 -0400 GPU velpred 3d (GPU hydro PR 5/n) (#80) This offloads velpred_3d to the GPU. It has been tested for the 3d reacting bubble & wdconvect problems compiled for MPI and GPU. Note: It is likely that this version will not work if compiled with OpenMP (this will come in a future PR) Source/MaestroAdvection.cpp Source/Maestro_F.H Source/Src_nd/velpred.F90 commit 0bf75b05c2f1ea92b212a6a0667fc93b0d7f498d Author: Doreen Fan Date: Fri Sep 13 18:22:24 2019 -0700 rho0_old_cart was not initialized to zero, which caused failure in debug mode Source/MaestroDensityAdvance.cpp Source/MaestroForce.cpp commit df6fcd547739f13369ee63f41142a92fdf74e48c Author: Doreen Fan Date: Fri Sep 13 14:17:05 2019 -0700 make_flux subroutines use split velocities instead of full velocities, so we need to delay adding w0 until after advection routines have been called Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp commit 0477ee2e873bf830cb6638c6a2bf075d9f251645 Author: Alice Harpole Date: Fri Sep 13 16:11:41 2019 -0400 fixed test_stability Source/MaestroDensityAdvance.cpp Source/MaestroForce.cpp Source/MaestroPlot.cpp commit fd6f14c3b742c0efa53ba759a50776d18125f710 Author: Alice Harpole Date: Thu Sep 12 12:09:05 2019 -0400 this fixed #98 so that ppm_2d no longer assumes the bcs have AMREX_SPACEDIM components Exec/SCIENCE/code_comp/initdata.f90 Exec/SCIENCE/code_comp/inputs_3d Source/MaestroAdvection.cpp Source/Maestro_F.H Source/Src_nd/make_edge_scal.F90 Source/Src_nd/ppm.F90 commit bea500ed1842353351e9ab62db3e4923ebfe2da2 Merge: 06490434 e02884ce Author: Andy Nonaka Date: Thu Sep 12 08:52:19 2019 -0700 Merge pull request #97 from AMReX-Astro/gpu_moved_base_state Move base state out of Fortran routines commit 064904343565001e7519b840a14fcfed36fa875a Author: Andy Nonaka Date: Wed Sep 11 17:35:03 2019 -0700 make MultiFab inputs to the MaestroDebug routine 'const' Source/Maestro.H Source/MaestroDebug.cpp commit e02884ce8a83b82a660726712ce6bb7cf54953f0 Author: Alice Harpole Date: Wed Sep 11 17:24:33 2019 -0400 fixed wdconvect Source/Src_nd/make_gamma.F90 Source/Src_nd/make_vel_force.F90 Source/Src_nd/rhoh_vs_t.F90 commit dce622333682b37cea6ea8429018f9ee4bb146bd Author: Alice Harpole Date: Wed Sep 11 16:18:34 2019 -0400 fixed some boundary conditions Source/MaestroAdvance.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroMakeS.cpp Source/Src_nd/make_gamma.F90 commit 46cccaa76f8f7484a66f80c58d16da9289eaf1bf Merge: 039772ef 1c667355 Author: Alice Harpole Date: Wed Sep 11 15:15:29 2019 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into gpu_moved_base_state commit 039772efffbbd8a294c41b78d9759b1f072acc9f Author: Alice Harpole Date: Wed Sep 11 14:50:09 2019 -0400 fixed test_stability Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroDt.cpp Source/MaestroForce.cpp Source/MaestroPlot.cpp Source/Maestro_F.H Source/Src_nd/compute_dt.F90 Source/Src_nd/make_plot_variables.F90 Source/Src_nd/make_scal_force.F90 Source/Src_nd/make_vel_force.F90 Source/Src_nd/mkutrans.F90 Source/Src_nd/update_vel.F90 commit 1c6673550bea06055e98881a5bb278c48faa1ead Author: Alice Harpole Date: Wed Sep 11 12:14:38 2019 -0400 fixed k slope index in slopey_2d Source/Src_nd/slope.F90 commit 8621f80dfb1785bc6e25a292c960cc8d7c0578be Author: Alice Harpole Date: Wed Sep 11 11:57:13 2019 -0400 fixed spherical issue and missing k = in slopey_2d Source/MaestroAdvection.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/Maestro_F.H Source/Src_nd/make_edge_scal.F90 Source/Src_nd/make_gamma.F90 Source/Src_nd/ppm.F90 Source/Src_nd/slope.F90 Source/Src_nd/velpred.F90 commit 47701e6d9a7d77e1fcf1d967d2d597babe731b7e Author: Alice Harpole Date: Wed Sep 11 11:24:04 2019 -0400 GPU velpred 2d (GPU hydro PR 4/n) (#79) This offloads velpred_2d to the GPU. It has been tested for the 2d reacting bubble problem compiled for MPI and GPU. Note: It is likely that this version will not work if compiled with OpenMP (this will come in a future PR) Source/MaestroAdvection.cpp Source/Maestro_F.H Source/Src_nd/velpred.F90 commit 1bc5af9bf1e77cc13071c73be797700f0fda82ac Author: Alice Harpole Date: Tue Sep 10 15:56:18 2019 -0400 actually fixed heating rate Exec/SCIENCE/code_comp/make_heating.F90 commit 96f4854159d9b2267f84a6495bb93722c43ad4ed Author: Alice Harpole Date: Tue Sep 10 14:25:41 2019 -0400 fixed heating rate Exec/SCIENCE/code_comp/inputs_3d Exec/SCIENCE/code_comp/make_heating.F90 commit 09f07baa6d79bb27883eebe9d4bafb7b30681c18 Author: Alice Harpole Date: Tue Sep 10 13:47:30 2019 -0400 fixed setup and inputs file for code comp problem Exec/SCIENCE/code_comp/initdata.f90 Exec/SCIENCE/code_comp/inputs_3d Exec/SCIENCE/code_comp/make_heating.F90 commit 789642687d8d831729bab9f181f699f82bbe34b6 Author: Alice Harpole Date: Tue Sep 10 11:53:34 2019 -0400 new code comparison problem compiles Exec/SCIENCE/code_comp/Make.package Exec/SCIENCE/code_comp/_parameters Exec/SCIENCE/code_comp/hcore.dat Exec/SCIENCE/code_comp/initdata.f90 Exec/SCIENCE/code_comp/inputs_3d Exec/SCIENCE/code_comp/make_grav.f90 Exec/SCIENCE/code_comp/make_heating.F90 Exec/SCIENCE/code_comp/model_util.F90 Exec/SCIENCE/code_comp/simple.net Exec/SCIENCE/code_comp/sponge.F90 Exec/SCIENCE/code_comp/tagging.F90 commit c7b922acc69eb5021a2c4a1019e1e6466084b79b Author: Alice Harpole Date: Tue Sep 10 10:13:56 2019 -0400 fixed 3d Source/Maestro.H Source/MaestroAdvection.cpp Source/MaestroDt.cpp Source/MaestroForce.cpp Source/MaestroVelocityAdvance.cpp Source/Maestro_F.H Source/Src_nd/compute_dt.F90 Source/Src_nd/make_vel_force.F90 commit 46da875342d71460c30057b4f32f777be4375d50 Author: Alice Harpole Date: Mon Sep 9 16:55:13 2019 -0400 moved base state from some more routines Source/Maestro.H Source/MaestroAdvection.cpp Source/MaestroDensityAdvance.cpp Source/MaestroDt.cpp Source/MaestroForce.cpp Source/MaestroMakeS.cpp Source/MaestroPlot.cpp Source/MaestroRhoHT.cpp Source/Maestro_F.H Source/Src_nd/compute_dt.F90 Source/Src_nd/make_S.F90 Source/Src_nd/make_plot_variables.F90 Source/Src_nd/make_scal_force.F90 Source/Src_nd/mkutrans.F90 Source/Src_nd/rhoh_vs_t.F90 Source/Src_nd/update_vel.F90 commit 5fca2fbb8ba0e7044d250ac0e2993562f9b66bab Author: Alice Harpole Date: Thu Sep 5 17:54:40 2019 -0400 moved base state from some more routines Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvection.cpp Source/MaestroDensityAdvance.cpp Source/MaestroDt.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroForce.cpp Source/MaestroMakeS.cpp Source/MaestroRhoHT.cpp Source/Maestro_F.H Source/Src_nd/make_S.F90 Source/Src_nd/make_scal_force.F90 Source/Src_nd/make_vel_force.F90 Source/Src_nd/rhoh_vs_t.F90 Source/Src_nd/update_scal.F90 commit 64f2f53a544eb6693ddbdde13e0bac69b4bbeb28 Merge: df731d9a da065113 Author: Alice Harpole Date: Thu Sep 5 09:33:55 2019 -0400 Merge branch 'development' into gpu_moved_base_state commit df731d9a4ff38d568fe04651bf40ce23080a6310 Author: Alice Harpole Date: Thu Sep 5 09:23:12 2019 -0400 moved base state from makeTfromRhoH Source/MaestroPlot.cpp Source/MaestroRhoHT.cpp Source/Maestro_F.H Source/Src_nd/make_plot_variables.F90 Source/Src_nd/rhoh_vs_t.F90 commit da0651134e744d88f88757ee76442c5774e65b4d Author: Alice Harpole Date: Thu Sep 5 06:17:56 2019 -0400 GPU ppm type 0 (GPU hydro PR 3/n) (#78) This offloads slope.F90 to the GPU (used by ppm type 0). It has been tested for the 2d and 3d reacting bubble problems compiled for MPI and GPU. Note: It is likely that this version will not work if compiled with OpenMP (this will come in a future PR) Source/Maestro.H Source/MaestroAdvection.cpp Source/Maestro_F.H Source/Src_nd/make_edge_scal.F90 Source/Src_nd/mkutrans.F90 Source/Src_nd/ppm.F90 Source/Src_nd/slope.F90 Source/Src_nd/velpred.F90 commit 97da3c05416e519a473631bf516a4954f0aa68be Author: Alice Harpole Date: Wed Sep 4 17:36:09 2019 -0400 moved base state from make_gamma Source/MaestroGamma.cpp Source/Maestro_F.H Source/Src_nd/make_gamma.F90 commit 7ee9b6d241551ba02eea836a6a3cf83b95b3cbea Merge: 8ad0b0d7 cdcf5896 Author: Andy Nonaka Date: Tue Sep 3 18:14:34 2019 -0700 Merge pull request #96 from arfon/patch-1 JOSS paper fixes commit cdcf58960da8c05b920b519f3585fb2f3b84ae7a Author: Arfon Smith Date: Tue Sep 3 20:24:57 2019 -0400 Update paper.bib paper/paper.bib commit b14f5131360963c1f924607bdfffeb291224d7f8 Author: Arfon Smith Date: Tue Sep 3 20:24:25 2019 -0400 Matching quote fix in title paper/paper.md commit c1cb719f933d9cb73ef96e44291c50441acee4f5 Author: Andy Nonaka Date: Tue Sep 3 14:43:48 2019 -0700 update citation to include MAESTROeX paper. Didn't include JOSS citation yet CITATION commit fa8ebd7a2720c23cf5518967c7012c63de5d04ce Author: Alice Harpole Date: Tue Sep 3 15:48:04 2019 -0400 GPU ppm 3d (GPU hydro PR 2/n) (#77) This offloads ppm_2d and mkutrans_2d to the GPU for ppm types 1 and 2. It has been tested for the 2d reacting bubble problem compiled for MPI and GPU. Note: this version will not work for ppm type 0, as this is not yet implemented (see #78). It is also likely that it shall not work if compiled with OpenMP (this will come in a future PR) This offloads mkutrans_3d and ppm_3d to the GPU for ppm types 1 and 2.It has been tested for the 3d reacting bubble & wdconvect problems compiled for MPI and GPU. Note: this version will not work for ppm type 0, as this is not yet implemented (see #78). It is also likely that it shall not work if compiled with OpenMP (this will come in a future PR) Exec/Make.Maestro Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroBCThreads.H Source/MaestroFill3dData.cpp Source/MaestroMacProj.cpp Source/MaestroPlot.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/make_edge_scal.F90 Source/Src_nd/mkutrans.F90 Source/Src_nd/ppm.F90 Source/Src_nd/velpred.F90 commit 8ad0b0d71a6cb11e4e7d71f4590c4a9151525578 Author: Andy Nonaka Date: Tue Sep 3 12:03:53 2019 -0700 Sept. 2019 Release Notes RELEASE_NOTES commit 8e7631dc2717d385cb104bc29f19d48fc653bec8 Author: Doreen Fan Date: Fri Aug 30 18:31:06 2019 -0700 added t_old parameter to reaction subroutines Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroDiag.cpp Source/MaestroInit.cpp Source/MaestroPlot.cpp commit 1cd69e70a3dbb559820f1d55398b0f408b234754 Author: Donald E. Willcox Date: Fri Aug 30 18:21:38 2019 -0700 Pass reaction start time to the burner. Microphysics/networks/burner.F90 Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceSdc.cpp Source/MaestroReact.cpp Source/Maestro_F.H Source/Src_nd/burner_loop.F90 commit 5652a1456c63f8dbdd72dc2d5bf4acb1aeb3900a Author: Donald E. Willcox Date: Fri Aug 30 17:22:27 2019 -0700 Always set i,j,k for burn and sdc states regardless USE_NONAKA_PLOT. Source/Src_nd/burner_loop.F90 commit 9599f8e18e9069da9665aaed436034f8334d7ba8 Author: Donald E. Willcox Date: Fri Aug 30 17:13:45 2019 -0700 If we want to make a Nonaka plot, set i, j, k for input state to burner. Source/Src_nd/burner_loop.F90 commit bc057c65270dcbd05113850f79856c5eca78a6e5 Author: Michael Zingale Date: Fri Aug 30 19:00:32 2019 -0400 fix formatting sphinx_docs/source/flowchart.rst commit e68d0b5a17deb37d882df629a26c58444015b040 Author: Andy Nonaka Date: Fri Aug 30 15:35:44 2019 -0700 add doi paper/paper.bib commit a2321ebfae054fcbe266393a62c2c9f317143ab0 Author: Andy Nonaka Date: Fri Aug 30 15:18:11 2019 -0700 minor updates to JOSS paper. added Don to JOSS paper paper/paper.md commit 9770fe4be2efdf9b5a21d5a20ec0767e94dafee3 Author: Andy Nonaka Date: Fri Aug 30 14:31:05 2019 -0700 some re-org of introductory material sphinx_docs/source/flowchart.rst sphinx_docs/source/introduction.rst commit 7bf624ee8c2708b44399d45c5ec6cbb1bb861ae9 Author: Doreen Fan Date: Fri Aug 30 14:07:11 2019 -0700 bug fix of indices when make force for h; and some comments Source/MaestroEnthalpyAdvance.cpp Source/MaestroReact.cpp Source/MaestroThermal.cpp commit 7f2065ff865155c4f8a698e3afcfc87945c63603 Author: Doreen Fan Date: Thu Aug 29 17:30:40 2019 -0700 add intra to regrid subroutines Source/MaestroRegrid.cpp commit e4bf19baf4de56cdd49845de325ab2bd302c7fda Author: Doreen Fan Date: Thu Aug 29 17:29:20 2019 -0700 change bc of scal_force: bc_s->bc_f Source/MaestroDensityAdvance.cpp Source/MaestroEnthalpyAdvance.cpp commit 99c803aedb4ef8bc081cabd02f573b60d9368d57 Author: Doreen Fan Date: Thu Aug 29 12:14:06 2019 -0700 match eps_divu_cart with maestro Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_sdc commit 9900b5d9f4f54caf85920e00065d748a274d0a43 Author: Doreen Fan Date: Thu Aug 29 11:00:23 2019 -0700 bug fix: indices were flipped when computing rho component of sedge for species_pred_type = predict_rhoX Source/MaestroDensityAdvance.cpp commit 2f4598517a9d3cc8b598bea679476bfa6439aace Author: Doreen Fan Date: Wed Aug 28 18:47:35 2019 -0700 bug fix for sedge when species_pred_type = predict_rhoX Source/MaestroDensityAdvance.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroInit.cpp commit b1986d2ddc1d19a8461865850ef6d26558a5e0da Author: Andy Nonaka Date: Tue Aug 27 17:08:39 2019 -0700 notes on w0 sphinx_docs/source/introduction.rst commit d5accf23a9eed54656cb55c9dd2c473c0da8a207 Author: Andy Nonaka Date: Tue Aug 27 15:47:15 2019 -0700 work on intro/governing equations/methodology - very much WIP trying to give a better sense of the differences between old and new temporal integrator sphinx_docs/source/flowchart.rst sphinx_docs/source/index.rst sphinx_docs/source/introduction.rst sphinx_docs/source/planar_invsq_basestate.rst commit 999b2d1f3e9791970ebe2c330007f9764f7daf32 Author: Doreen Fan Date: Mon Aug 26 15:31:19 2019 -0700 code cleanup Source/MaestroAdvanceSdc.cpp Source/MaestroReact.cpp commit c720a389fbe042b77441ded349fc804c64317ca6 Author: Doreen Fan Date: Mon Aug 26 15:10:21 2019 -0700 second pass at joss paper paper/paper.md commit c754b44c7e5fd11caa94b2f1ac7fc2f0a515c4d1 Author: Alice Harpole Date: Mon Aug 26 17:16:22 2019 -0400 add --describe command line option Source/Maestro.H Source/MaestroPlot.cpp Source/main.cpp sphinx_docs/source/faq.rst commit 5536e89c973db0efcdf564aca6ab99ad885361a2 Author: Alice Harpole Date: Mon Aug 26 08:54:29 2019 -0400 changed inputs of plane_parallel_star Exec/SCIENCE/plane_parallel_star/inputs_2d commit b82ebc012d3bb74a14b59f934e7e611eda8bc856 Author: Michael Zingale Date: Sun Aug 25 12:28:06 2019 -0400 new test suite versions Exec/SCIENCE/flame/inputs_2d_smallscale.testsuite Exec/SCIENCE/flame/inputs_3d_smallscale.testsuite commit 67ebf0469e4b1d64e2aa2402a5e43889557a725b Author: Doreen Fan Date: Thu Aug 22 15:45:44 2019 -0700 add intra to checkpoint file Source/MaestroCheckpoint.cpp Source/MaestroInit.cpp commit 1e3872137b57c51b5c2523b72019b19b6b5ffdf6 Author: Doreen Fan Date: Thu Aug 22 15:32:51 2019 -0700 bug fix: initialization of intra Source/MaestroInit.cpp commit 716dae56c967b178744ba626a81a4ba2e7a7c7d3 Author: Doreen Fan Date: Thu Aug 22 12:28:21 2019 -0700 bug fix: use ReactSDC when plotting Source/MaestroPlot.cpp commit eeb5655b0147d3b01668af26f164d57c37637435 Author: Doreen Fan Date: Thu Aug 22 11:18:00 2019 -0700 add same sdc reacting bubble test as original maestro Exec/TEST_PROBLEMS/reacting_bubble/GNUmakefile Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_sdc commit c70705cfeb1b52d783e2d0a832d83b1950a788db Author: XinlongSBU <42697364+XinlongSBU@users.noreply.github.com> Date: Thu Aug 22 13:51:43 2019 -0400 ECSN (#94) Exec/SCIENCE/ecsn/ECSN-ONe6040-final.hse.40960 Exec/SCIENCE/ecsn/input_ecsn Exec/SCIENCE/ecsn/inputs_3d_kepler Exec/SCIENCE/ecsn/kepler_xinlong_ONe6040-final.hse.1280 Exec/SCIENCE/ecsn/kepler_xinlong_ONe6040-final.hse.5120 commit 78f47b1ab1613f885850fdc2d7a68047257f51a1 Author: Doreen Fan Date: Wed Aug 21 17:39:39 2019 -0700 add thermal diffusion subroutine for sdc Source/MaestroThermal.cpp Source/Src_nd/burner_loop.F90 commit 43fb7079f821ecb4edc8c0544bfabb0672dd1330 Author: Doreen Fan Date: Wed Aug 21 14:21:10 2019 -0700 add instantaneous_reaction_rates subroutine for sdc Source/Maestro.H Source/MaestroHeating.cpp Source/MaestroReact.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/make_reaction_rates.F90 commit c12db6025b11b34a57c435a9781be079c19953cb Author: Doreen Fan Date: Wed Aug 21 13:51:22 2019 -0700 fixes to get burner compiling with microphysics sdc-maestroex branch Exec/Make.Maestro Microphysics/conductivity/conductivity.F90 Microphysics/networks/burn_type.F90 Microphysics/networks/burner.F90 Microphysics/networks/general_null/Make.package Microphysics/networks/sdc_type.F90 Source/Maestro.H Source/MaestroReact.cpp Source/Maestro_F.H Source/Src_nd/burner_loop.F90 Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/meth_params.F90 commit 74f585c191faeab8eb2b93c059aa4ebfce5e9591 Author: Alice Harpole Date: Wed Aug 21 16:32:44 2019 -0400 added plane_parallel_star problem to study burning in the massive star Exec/SCIENCE/plane_parallel_star/18m_500_s_rot_b_eq_1.hse.6400 Exec/SCIENCE/plane_parallel_star/GNUmakefile Exec/SCIENCE/plane_parallel_star/Make.package Exec/SCIENCE/plane_parallel_star/_parameters Exec/SCIENCE/plane_parallel_star/convert_backtrace.py Exec/SCIENCE/plane_parallel_star/initdata.f90 Exec/SCIENCE/plane_parallel_star/inputs_2d Exec/SCIENCE/plane_parallel_star/tagging.F90 commit dd5d540be5d89e9a1c9c4988a5eec798607170ff Author: Doreen Fan Date: Wed Aug 21 11:14:25 2019 -0700 some fixes for burner to work with sdc Exec/Make.Maestro Microphysics/networks/Make.package Microphysics/networks/burner.F90 Microphysics/networks/sdc_type.F90 Source/Src_nd/burner_loop.F90 commit 2ff3eee2f06735c7034f3632bd9752c4b633bee4 Author: Michael Zingale Date: Wed Aug 21 08:11:27 2019 -0400 add missing figs sphinx_docs/source/cutoff.png sphinx_docs/source/cutoff_multi.png sphinx_docs/source/lo_density.rst commit 36db67c93db8f4d797af02fa19aa2629d73dd263 Author: Michael Zingale Date: Wed Aug 21 08:08:35 2019 -0400 rename so it is not built sphinx_docs/source/architecture.rst.old commit 2735a49d756dcd6abcc5f57ad64d02655fd9c559 Author: Michael Zingale Date: Wed Aug 21 08:08:07 2019 -0400 fix title lengths sphinx_docs/source/architecture.rst commit ca1be4a47259c1fee0f19aa21ec7389fa74a0116 Author: Michael Zingale Date: Wed Aug 21 08:06:37 2019 -0400 add figure sphinx_docs/source/rotation.rst sphinx_docs/source/rotation_spherical.png commit 93b3ac06cf55f7a2ac3fce86b9cfad61c57dd392 Author: Michael Zingale Date: Wed Aug 21 07:59:09 2019 -0400 rename so it is not built sphinx_docs/source/sdc.rst.old commit 75489e6ac41363a148aecfd707a8bbf8268786f7 Merge: ef08fc5f 89103063 Author: Michael Zingale Date: Wed Aug 21 07:58:17 2019 -0400 Merge branch 'development' of github.com:amrex-astro/MAESTROeX into development commit ef08fc5fde7f0bee0df2b88fbe9559192cd26576 Author: Michael Zingale Date: Wed Aug 21 07:56:31 2019 -0400 quite some warnings sphinx_docs/source/Godunov.rst commit 8910306341c58bd79b1a679ea3e806cc7f828ca1 Author: Andy Nonaka Date: Tue Aug 20 18:06:58 2019 -0700 when physical boundaries are present in two spatial directions, the FillPatch routine requires ghost cells to begin with an initialize value so the corner ghost cell doesn't use uninitialized data. In every case where this was an issue, the multifab is now initialized to zero in valid+ghost Source/MaestroAdvance.cpp Source/MaestroDt.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroMacProj.cpp Source/MaestroNodalProj.cpp Source/MaestroVelocityAdvance.cpp commit 1cf3aec15789f580c83979a4dc0a96859f2306ec Author: Andy Nonaka Date: Tue Aug 20 17:24:40 2019 -0700 first cut at the JOSS paper. a lot of the text is ripped from the MAESTROeX intro. feel free to modify paper/paper.md commit 672c04da4a4e54063ed6b53f4a9aa7e93410b4c7 Author: Andy Nonaka Date: Tue Aug 20 17:04:47 2019 -0700 smoothing out model section sphinx_docs/source/flowchart.rst commit ef8398e96c180cd5d5db78e4c35573d74df39f5a Merge: 01a588c3 2bf03156 Author: Andy Nonaka Date: Tue Aug 20 15:54:59 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 01a588c36dbe40726226a3e960fe4273f3f511d9 Author: Andy Nonaka Date: Tue Aug 20 15:54:42 2019 -0700 minor changes to intro sphinx_docs/source/introduction.rst commit 2bf0315691f0917cb751fb2bd58ba8ad3114181a Author: Andy Nonaka Date: Tue Aug 20 13:27:56 2019 -0700 shell of the JOSS paper paper/paper.bib paper/paper.md commit 9f25055bb54b8fdb751ebd6e034e957050173952 Author: Andy Nonaka Date: Tue Aug 20 09:48:43 2019 -0700 test commit sphinx_docs/source/flowchart.rst commit de0637f3f0ba06ddd9f6c33bc26ec3dfe124d04b Author: Michael Zingale Date: Tue Aug 20 11:47:19 2019 -0400 more figs sphinx_docs/source/my_cool_images_Slice_x_tfromp_trim.png sphinx_docs/source/plt00000_tfromp.png sphinx_docs/source/plt00000_tfromp_enucdot.png sphinx_docs/source/visualization.rst commit 07c78559b4e47ec46162806ce0c76ad04426b647 Author: Michael Zingale Date: Tue Aug 20 11:24:32 2019 -0400 pass through the flowchart sphinx_docs/Makefile sphinx_docs/source/flowchart.png sphinx_docs/source/flowchart.rst sphinx_docs/source/flowchart_4_8.png sphinx_docs/source/introduction.rst sphinx_docs/source/maestro_doc.bib sphinx_docs/source/mg.rst sphinx_docs/source/preface.rst commit 7357be2c3c858551cd68550fb9e9d5373d0d9516 Author: Michael Zingale Date: Tue Aug 20 10:15:00 2019 -0400 update testing README.md commit 7beab29cf9a9e04b2c53a6b216822ee037250bb7 Author: Michael Zingale Date: Tue Aug 20 10:03:51 2019 -0400 add header Exec/SCIENCE/xrb_mixed/README.md commit 1dcddaef0e979801aa8f337dd013d141049749ad Merge: 25aa9527 4f8b58fc Author: Michael Zingale Date: Tue Aug 20 10:00:02 2019 -0400 Merge branch 'development' of github.com:amrex-astro/MAESTROeX into development commit 25aa95273d41ce0041437899c1c6acd5b2b79248 Author: Michael Zingale Date: Tue Aug 20 09:59:53 2019 -0400 add some readmes Exec/SCIENCE/sub_chandra/README.md Exec/SCIENCE/wdconvect/README.md Exec/SCIENCE/xrb_mixed/README.md commit a82b373e1d881ece5f3c6826e09f96b3f129b9e2 Author: Doreen Fan Date: Mon Aug 19 17:55:00 2019 -0700 added burner_loop subroutines for sdc. still need to fix burner subroutine Source/Maestro.H Source/MaestroReact.cpp Source/Maestro_F.H Source/Src_nd/burner_loop.F90 commit fd1185875b21c75c2b214d204d91fc9c59a29aba Author: Doreen Fan Date: Mon Aug 19 11:54:42 2019 -0700 added MakeIntraCoeffs subroutine with gpu Source/Maestro.H Source/MaestroIntra.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/make_intra_coeffs.F90 commit 4f8b58fc399d3f05edab93beab3d9f8162149181 Author: Michael Zingale Date: Sun Aug 18 11:05:21 2019 -0400 add regression inputs Exec/TEST_PROBLEMS/test_stability/inputs_2d_C_regression commit cebdbe6c7261d432d29dc46a3a9db5e6baec577b Author: Doreen Fan Date: Thu Aug 15 19:26:19 2019 -0700 added divu_iter subroutine for sdc Source/MaestroInit.cpp commit df1a7250360799341096b672bddc6c9b422ca589 Author: Doreen Fan Date: Thu Aug 15 19:04:54 2019 -0700 added USE_SDC compile option in makefile Exec/Make.Maestro Source/Maestro.H Source/MaestroEvolve.cpp Source/MaestroInit.cpp commit a91a87f2746971fb55f4f5589036a4ffaf4cd0cb Author: Doreen Fan Date: Thu Aug 15 17:43:36 2019 -0700 added density and enthalpy advance sdc subroutines Source/MaestroAdvanceSdc.cpp Source/MaestroDensityAdvance.cpp Source/MaestroEnthalpyAdvance.cpp commit e1348975b1f693e9f29e328230677c7cc82181ca Author: Doreen Fan Date: Thu Aug 15 12:25:50 2019 -0700 nodal proj step complete. Still need to add other sdc subroutines Source/Maestro.H Source/MaestroAdvanceSdc.cpp Source/MaestroNodalProj.cpp commit 9d91cd7b5c62d0f6768ba176bb767ac1e9bec0ff Author: Doreen Fan Date: Wed Aug 14 18:44:28 2019 -0700 corrector loop complete. nodal project WIP. Source/Maestro.H Source/MaestroAdvanceSdc.cpp Source/MaestroHeating.cpp Source/MaestroIntra.cpp Source/MaestroReact.cpp Source/MaestroThermal.cpp commit 0c66a1ba731a97a25ff1ae275836a4f4fdef5cbd Author: Doreen Fan Date: Wed Aug 14 14:10:12 2019 -0700 Predictor step complete. Still need to fix/add sdc subroutines Source/Maestro.H Source/MaestroAdvanceSdc.cpp Source/MaestroDensityAdvance.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroInit.cpp Source/MaestroIntra.cpp Source/MaestroReact.cpp Source/MaestroSetup.cpp Source/MaestroThermal.cpp Source/Make.package commit f394a1df978b5d063317c88102e77690d55a365b Author: Doreen Fan Date: Mon Aug 12 12:43:42 2019 -0700 started outline of sdc advance routine Source/MaestroAdvanceSdc.cpp commit 11ce6e07336ec7dada24aa29aa91659af1b00d51 Author: Alice Harpole Date: Fri Aug 9 17:27:35 2019 -0400 expanded docstrings in Maestro.H to improve docs Source/Maestro.H Source/Src_nd/average.f90 sphinx_docs/Doxyfile sphinx_docs/postprocess_files.py commit 3a73215cd1996a03e7c41d6eb5b8d6def460802f Author: Doreen Fan Date: Thu Aug 8 15:42:15 2019 -0700 update answers to debugging sphinx_docs/source/addproblem.rst sphinx_docs/source/faq.rst commit e1fa32b48783d5beef609779be5c0f436bb872f6 Author: Doreen Fan Date: Thu Aug 8 14:56:14 2019 -0700 fix a syntax error sphinx_docs/source/addproblem.rst commit 61e824180ea9a4c962a1f4c96f65cda39ad9471a Author: Doreen Fan Date: Thu Aug 8 14:50:25 2019 -0700 include Add a new problem section sphinx_docs/source/addproblem.rst sphinx_docs/source/architecture.rst sphinx_docs/source/index.rst sphinx_docs/source/initial_models.rst commit 30845806d313d03e86c40752584c395764f2014f Author: Alice Harpole Date: Thu Aug 8 16:27:43 2019 -0400 Sphinx-fortran (#89) * moves module and subroutine comments so they can be processed by sphinx-fortran * made header file doxygen friendly Source/Maestro.H Source/PhysBCFunctMaestro.H Source/Src_nd/advect_base.F90 Source/Src_nd/base_state.f90 Source/Src_nd/base_state_geometry.F90 Source/Src_nd/bc_fill_nd.F90 Source/Src_nd/diag.F90 Source/Src_nd/inlet_bc.f90 Source/Src_nd/maestro_init.f90 Source/Src_nd/make_edge_scal.F90 Source/Src_nd/make_edge_state.f90 Source/Src_nd/make_eta.F90 Source/Src_nd/make_explicit_thermal.F90 Source/Src_nd/make_flux.F90 Source/Src_nd/make_gamma.F90 Source/Src_nd/make_grav.f90 Source/Src_nd/make_psi.F90 Source/Src_nd/make_scal_force.F90 Source/Src_nd/make_w0.f90 Source/Src_nd/ppm.F90 Source/Src_nd/regrid.f90 Source/Src_nd/rotation.f90 Source/Src_nd/sponge.F90 Source/Src_nd/tagging.F90 Source/Src_nd/velpred.F90 sphinx_docs/Doxyfile sphinx_docs/Makefile sphinx_docs/postprocess_files.py sphinx_docs/preprocess_files.py commit 6c98ac62933d8646a8b8c58e7e455dd4219b0b4f Author: Alice Harpole Date: Thu Aug 8 16:17:40 2019 -0400 MAESTRO -> MAESTROeX in docs sphinx_docs/source/Godunov.rst sphinx_docs/source/beta0.rst sphinx_docs/source/enthalpy.rst sphinx_docs/source/initial_models.rst sphinx_docs/source/lo_density.rst sphinx_docs/source/mg.rst sphinx_docs/source/networks.rst sphinx_docs/source/pert.rst sphinx_docs/source/rotation.rst sphinx_docs/source/unit_tests.rst sphinx_docs/source/visualization.rst sphinx_docs/source/volume_discrepancy.rst commit 9e0c413a3faba337ec7150795432c5c0b5c29ff8 Author: Alice Harpole Date: Thu Aug 8 15:55:16 2019 -0400 updated runtime parameters sphinx_docs/source/analysis.rst sphinx_docs/source/common_parameters.rst sphinx_docs/source/index.rst sphinx_docs/source/param_intro.rst sphinx_docs/source/unit_tests.rst commit 1c91b9ff483fa47e7431b4bd0195b1a1391b6158 Author: Alice Harpole Date: Thu Aug 8 15:25:52 2019 -0400 updated requirements.txt to include breathe minimum version and numpy requirements.txt commit 5ae8eb9ec685250db68abe72fdda95356bf21a3e Author: Alice Harpole Date: Thu Aug 8 15:10:16 2019 -0400 updated the analysis section sphinx_docs/source/analysis.rst sphinx_docs/source/faq.rst commit 62fe828fcf7374bda0717964c4aa6f332a1b8309 Merge: 15a2b1ca 449cf016 Author: Alice Harpole Date: Thu Aug 8 14:42:56 2019 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 15a2b1ca1b23c96a213f4b9a25d47fc90b895023 Author: Alice Harpole Date: Thu Aug 8 14:42:44 2019 -0400 updated the FAQ sphinx_docs/rp.py sphinx_docs/source/faq.rst sphinx_docs/source/flowchart.rst commit 449cf01613dfac91407bb31c0633b9e799315993 Author: Michael Zingale Date: Thu Aug 8 14:30:10 2019 -0400 fix some math rendering sphinx_docs/source/introduction.rst commit aaca7869d68247b1805a1bdc000191227467e100 Author: Michael Zingale Date: Thu Aug 8 14:24:00 2019 -0400 center figs sphinx_docs/source/initial_models.rst commit 14ed8149fb1e03b2327a068cddbc7f680aae50ae Author: Michael Zingale Date: Thu Aug 8 14:21:27 2019 -0400 replace managing jobs with link to workflow docs sphinx_docs/source/managingjobs.rst commit 6b6cbe460cd7673c8bbc83a4012d170866f2d52c Merge: 166fc0df 8e7632fd Author: Michael Zingale Date: Thu Aug 8 14:10:39 2019 -0400 Merge branch 'development' of github.com:amrex-astro/MAESTROeX into development commit 166fc0dfe2be15740d9bbb354aea3069a9002cc8 Author: Michael Zingale Date: Thu Aug 8 14:10:29 2019 -0400 clean up the initial models sphinx_docs/source/ctof.png sphinx_docs/source/ftoc.png sphinx_docs/source/initial_models.rst sphinx_docs/source/multilevel_init.png commit 8e7632fddff483ebdb7f05abf37cc6f5a0ded998 Merge: 76cdf312 11f95054 Author: Alice Harpole Date: Thu Aug 8 13:44:16 2019 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 76cdf31201de9125321209397214b058437dfca8 Author: Alice Harpole Date: Thu Aug 8 13:43:58 2019 -0400 updated the runtime parameters docs sphinx_docs/source/param_intro.rst commit 11f95054f99c2a2657965c3570e0f4b9505c2976 Author: Michael Zingale Date: Thu Aug 8 13:42:14 2019 -0400 fix some math symbols sphinx_docs/Makefile sphinx_docs/source/mathsymbols.tex commit 6ce3f161e890402533b3f528acfd8975dd2ec28e Merge: 96618852 33eb0645 Author: Andy Nonaka Date: Thu Aug 8 10:15:46 2019 -0700 Merge pull request #88 from AMReX-Astro/contributors add contributing statement commit 33eb064572c3f7084db4fd8fcf7748f9466f9062 Author: Michael Zingale Date: Thu Aug 8 10:31:53 2019 -0400 add contributing statement README.md commit 966188525f603204c08c02ba14f464d4df229ac6 Author: Alice Harpole Date: Thu Aug 8 09:28:38 2019 -0400 add doxyfile and python scripts needed for docs build sphinx_docs/Doxyfile sphinx_docs/make_api.py sphinx_docs/preprocess_files.py commit 8d4a9309626efc58f2c192d237f1747743365105 Author: Alice Harpole Date: Thu Aug 8 09:26:44 2019 -0400 add doxygen, breathe and sphinx-fortran to docs build to create API requirements.txt sphinx_docs/Makefile sphinx_docs/source/_static/theme_overrides.css sphinx_docs/source/_templates/layout.html sphinx_docs/source/conf.py sphinx_docs/source/index.rst commit c84a881ac71bd6f518c84fa2300ce15b0e9acc06 Author: Michael Zingale Date: Wed Aug 7 19:18:01 2019 -0400 disable sdc sphinx_docs/source/index.rst commit 45a150af6116f358cf80f08dd66e97d1cbf39266 Author: Michael Zingale Date: Wed Aug 7 19:01:23 2019 -0400 remove architecture -- it is for old Maestro sphinx_docs/source/index.rst commit 245c97d6636353a40676840655cb89ac2b68333d Author: Michael Zingale Date: Wed Aug 7 18:56:55 2019 -0400 lots of flowchart cleaning sphinx_docs/source/flowchart.rst sphinx_docs/source/pert.rst commit b791511f727ad9e09337c49b58e7bdc53aabe496 Author: Doreen Fan Date: Wed Aug 7 14:50:27 2019 -0700 doc updates sphinx_docs/source/getting_started.rst commit 23d1317df60a31a8fc71019944ec26ac5472a090 Author: Michael Zingale Date: Wed Aug 7 17:33:20 2019 -0400 some more docs fixing sphinx_docs/source/flowchart.rst sphinx_docs/source/introduction.rst sphinx_docs/source/planar_invsq_basestate.rst sphinx_docs/source/preface.rst commit 6d5e87abef4d2656738b2f803596c8ec938a5e4b Author: Michael Zingale Date: Wed Aug 7 16:09:56 2019 -0400 fix missing figures and some sphinx reference errors sphinx_docs/source/getting_started.rst sphinx_docs/source/index.rst sphinx_docs/source/particle_paths.png sphinx_docs/source/test_project_3d.png sphinx_docs/source/unit_tests.rst sphinx_docs/source/wall_u_init_x-velocity.png sphinx_docs/source/wall_u_new_x-velocity.png sphinx_docs/source/wall_u_plus_grad_phi_x-velocity.png sphinx_docs/source/zreferences.rst commit a8b0d4a801d52a43ce0db6fc44ebac7970818cdd Author: Michael Zingale Date: Wed Aug 7 09:41:06 2019 -0400 fix some figures sphinx_docs/source/dens_2d_orig_density.png sphinx_docs/source/dens_2d_ppm1_xp_final_abserror.png sphinx_docs/source/dens_2d_ppm1_xp_final_density.png sphinx_docs/source/unit_tests.rst commit bbff66eb6520c0c6b379765937cc546811b7ab53 Author: Michael Zingale Date: Wed Aug 7 09:28:35 2019 -0400 fix a lot of section cross links sphinx_docs/source/analysis.rst sphinx_docs/source/flowchart.rst sphinx_docs/source/getting_started.rst sphinx_docs/source/makefiles.rst sphinx_docs/source/param_intro.rst sphinx_docs/source/visualization.rst commit 8f80dd69146599c86932d7352978514fe1509179 Author: Michael Zingale Date: Tue Aug 6 22:07:03 2019 -0400 enable equation numbering and referencing also fix a bug in sphinx_rtd for equation alignment sphinx_docs/source/_templates/layout.html sphinx_docs/source/conf.py sphinx_docs/source/introduction.rst commit e9e4692a994efb26f63ace28a208686e652c022c Author: Michael Zingale Date: Tue Aug 6 21:20:05 2019 -0400 switch color to inherit sphinx_docs/source/_templates/layout.html commit 6c34eea431af36ab3d649f7a4a08b7a7be3dab2b Author: Michael Zingale Date: Tue Aug 6 21:12:51 2019 -0400 fix mathjax color in toc sidebar sphinx_docs/source/_templates/layout.html commit 53b2f5a855a54f84a02bdd099d945f8d9ddd0c03 Author: Doreen Fan Date: Tue Aug 6 17:26:20 2019 -0700 updated README to include more info README.md commit 8f789e03eaa445ca5e33c45b7f47675e27d3f855 Author: Alice Harpole Date: Tue Aug 6 19:31:03 2019 -0400 Remove 1d support (#87) * removed all 1d routines and all #if AMREX_SPACEDIM >= 2 statements * added line to Make.Maestro to raise an error if compilation is attempted with DIM=1 Exec/Make.Maestro Exec/SCIENCE/flame/initdata.f90 Source/Maestro.cpp Source/MaestroAdvection.cpp Source/MaestroAverage.cpp Source/MaestroDt.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp Source/MaestroMakeEta.cpp Source/Maestro_F.H Source/Src_nd/average.f90 Source/Src_nd/bc_fill_nd.F90 Source/Src_nd/burner_loop.F90 Source/Src_nd/compute_dt.F90 Source/Src_nd/compute_grad_phi.F90 Source/Src_nd/debug.F90 Source/Src_nd/diag.F90 Source/Src_nd/fill_3d_data.F90 Source/Src_nd/initdata.f90 Source/Src_nd/mac_solver.F90 Source/Src_nd/make_S.F90 Source/Src_nd/make_edge_scal.F90 Source/Src_nd/make_eta.F90 Source/Src_nd/make_flux.F90 Source/Src_nd/make_gamma.F90 Source/Src_nd/make_pi_cc.F90 Source/Src_nd/make_plot_variables.F90 Source/Src_nd/make_scal_force.F90 Source/Src_nd/make_vel_force.F90 Source/Src_nd/mkutrans.F90 Source/Src_nd/ppm.F90 Source/Src_nd/rhoh_vs_t.F90 Source/Src_nd/slope.F90 Source/Src_nd/sponge.F90 Source/Src_nd/tagging.F90 Source/Src_nd/update_scal.F90 Source/Src_nd/update_vel.F90 Source/Src_nd/velpred.F90 commit 77cb0cfbfb348478c1c9907f8bf4de77c4d6a290 Merge: b06fe588 526cddde Author: Alice Harpole Date: Tue Aug 6 11:24:32 2019 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit b06fe5882300cedcaa3751cf898f368064848d8c Author: Alice Harpole Date: Tue Aug 6 11:23:43 2019 -0400 fixed index of prob_lo in base_state_geometry.F90 Source/Src_nd/base_state_geometry.F90 commit 526cdddefaaf66182df24ed918e544612a658167 Author: Michael Zingale Date: Thu Aug 1 20:51:26 2019 -0400 fix formatting of the species table in job_info Source/MaestroPlot.cpp commit 44a96188a6c4d393516a4e4eafd5689a5fa79e89 Author: Doreen Fan Date: Thu Aug 1 16:49:07 2019 -0700 Turn on delta gamma correction by default. Keep regression tests as they were Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_amr_regression Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_regression Exec/SCIENCE/wdconvect/inputs_files/inputs_omp_3d_regression Exec/TEST_PROBLEMS/double_bubble/inputs_2d_regression Exec/TEST_PROBLEMS/incomp_shear_jet/inputs_2d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_omp_2d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_omp_3d_regression Exec/TEST_PROBLEMS/rt/inputs_2d_regression Exec/TEST_PROBLEMS/test_convect/inputs_2d_regression Source/MaestroMakeS.cpp Source/param/_cpp_parameters commit 0e60594ca6ca9dd435a0dd8e0d164614b472b442 Author: Doreen Fan Date: Thu Aug 1 14:49:07 2019 -0700 add do_smallscale when reading from a checkpoint file Source/MaestroCheckpoint.cpp commit 7ce99f46155ef7559bcfd3c8dd76c30b2b505a85 Merge: 9c40275e 9e49277b Author: Doreen Fan Date: Thu Aug 1 12:24:55 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 9c40275e3a30921526f83ad961ecfbd68be28830 Author: Doreen Fan Date: Thu Aug 1 12:24:30 2019 -0700 changed thermal diffusion inflow bc to match solution with original maestro Source/MaestroThermal.cpp commit 9e49277b7fa5749d9149eb036488f682328a339c Author: Andy Nonaka Date: Thu Aug 1 09:15:36 2019 -0700 August 2019 Release Notes RELEASE_NOTES commit 3b8c78348917cc9f5de7668a5297f2c35b634736 Author: Doreen Fan Date: Tue Jul 30 18:45:48 2019 -0700 same input file as smallscale flame in MAESTRO Exec/SCIENCE/flame/inputs_2d_smallscale commit 42aa837a1f0be22e949a7e3eb33e438d7176ab37 Merge: ad05050b b3e7ce65 Author: Doreen Fan Date: Tue Jul 30 16:30:08 2019 -0700 computing timestep subroutines ported to GPUs complete Merge branch 'gpu_dt' into development commit b3e7ce65fc55076926a9cd30eca835595782e8b4 Author: Doreen Fan Date: Tue Jul 30 13:46:42 2019 -0700 port estdt_sphr to gpu Source/MaestroDt.cpp Source/Maestro_F.H Source/Src_nd/compute_dt.F90 commit 94afc01901eb9f8acdc140bc87d1154622af6bab Author: Doreen Fan Date: Tue Jul 30 11:32:32 2019 -0700 split firstdt_sphr() to offload to gpu and remove prefetch calls Source/MaestroDt.cpp Source/Maestro_F.H Source/Src_nd/compute_dt.F90 commit f1fe744d2d61b4e3dd8e153558642c373f6e2e87 Author: Doreen Fan Date: Mon Jul 29 18:04:42 2019 -0700 trying cuda prefetch to see if there is a speedup with routine Source/MaestroDt.cpp commit ad05050b4a90753d4ce012a23b96681fdcecf82a Author: Alice Harpole Date: Mon Jul 29 15:31:35 2019 -0400 fixed some boundary conditions in make_edge_scal_2d Source/Src_nd/make_edge_scal.F90 commit 5c51ad0b87f5f868b33d9073d057efdfa0da13ac Author: Doreen Fan Date: Thu Jul 25 17:46:04 2019 -0700 port estdt planar to gpu Source/MaestroDt.cpp Source/Maestro_F.H Source/Src_nd/compute_dt.F90 commit 4463a9344e266962c4d28ea565c76b85a22ebbcb Author: Doreen Fan Date: Thu Jul 25 13:24:06 2019 -0700 fix bug causing 2d compilation to fail Source/MaestroDt.cpp Source/Src_nd/compute_dt.F90 commit 86214a56d97635dee0b3926cc190aa29dbf035cd Author: Doreen Fan Date: Wed Jul 24 15:51:40 2019 -0700 fixed allocation bug in firstdt_sphr when using gpus Source/MaestroDt.cpp Source/Maestro_F.H Source/Src_nd/compute_dt.F90 commit 14cad28d5525d5f9a811000d88141ae55161b5f1 Author: Doreen Fan Date: Wed Jul 24 15:01:36 2019 -0700 port firstdt_sphr on gpu Source/MaestroDt.cpp Source/Src_nd/compute_dt.F90 commit e654e55adfe77f4ccd390061c7f993ea3f1bfcfd Author: Doreen Fan Date: Fri Jul 19 11:15:11 2019 -0700 port FirstDt() to gpus Source/MaestroDt.cpp Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/compute_dt.F90 commit b0ad77e9c7cc6bfdf81beb12bd1594bd6bcfc498 Author: Alice Harpole Date: Wed Jul 17 12:45:14 2019 -0400 fixed a bug in an index in ppm 2 Source/Src_nd/ppm.F90 commit 549d30ccd5117e3652afd89af05ac7f7f1af5b78 Author: Alice Harpole Date: Wed Jul 10 11:11:09 2019 -0400 expanded CUDA launch regions to reduce page faults Source/MaestroAdvection.cpp Source/MaestroConvert.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp Source/MaestroReact.cpp Source/MaestroRhoHT.cpp Source/MaestroSponge.cpp Source/MaestroThermal.cpp commit 15c7bed38bd8d0ee23e0dcbaff864015f6316ca6 Author: Alice Harpole Date: Mon Jul 8 09:54:53 2019 -0400 Added option to output checkpoints at simulation time intervals Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H commit 98939c4cdbe7c901712ebc8924dea3cfeacc297c Author: Alice Harpole Date: Mon Jul 8 09:42:36 2019 -0400 Added option to plot gravitational acceleration Exec/SCIENCE/code_comp/initdata.f90 Source/Maestro.H Source/MaestroPlot.cpp Source/Src_nd/make_grav.f90 Source/Src_nd/make_plot_variables.F90 Source/param/_cpp_parameters Source/param/_variables Source/param/set_variables.py Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H commit ce2c05d9a6c4455cb337cc2f30170e05470f5f9d Author: Doreen Fan Date: Tue Jul 2 13:07:46 2019 -0700 July 2019 release notes RELEASE_NOTES commit 2bd1c2d4774684cdddabda29279802122e65bbe5 Author: Alice Harpole Date: Tue Jul 2 17:24:10 2019 +0200 5.0/3.0 -> 1.666666667d0 in inputs files for rt problem Exec/TEST_PROBLEMS/rt/inputs_2d_C Exec/TEST_PROBLEMS/rt/inputs_2d_regression commit 6016d421ee95a022fa17a70a824c82c70970aff9 Author: Alice Harpole Date: Tue Jul 2 17:06:17 2019 +0200 moved diagnostics file printing outside of chk_int > 0 if statement in MaestroInit.cpp Source/MaestroInit.cpp commit 4d3f69543cf3aca9bf80c735fe021c28dd82e4ad Author: Alice Harpole Date: Tue Jun 25 17:30:01 2019 +0100 add diagnostics for producing radially averaged profiles Util/diagnostics/GNUmakefile Util/diagnostics/Make.package Util/diagnostics/README.md Util/diagnostics/Radial_F.H Util/diagnostics/initdata.f90 Util/diagnostics/main.cpp Util/diagnostics/radial_util.f90 commit fef28d568b2461b5052922a4a0ff1e2c1520c1c3 Merge: 8ca119b9 cb2df83a Author: Donald E. Willcox Date: Mon Jun 24 16:32:03 2019 -0700 Merge branch 'development' of github.com:AMReX-Astro/MAESTROex into development commit 8ca119b910d6b3c007342a1c64ddfe237efdd528 Author: Donald E. Willcox Date: Mon Jun 24 16:31:05 2019 -0700 Fix Python typo for multiple input files case. Exec/SCIENCE/urca/analysis/scripts/profile-field commit cb2df83a1bf94dac2827ac9802a4051a0bcb5012 Author: Andy Nonaka Date: Mon Jun 24 14:13:14 2019 -0700 bugfix; was using max_radial_level, finest_radial_level, nr_fine, dr_fine, and nr_irreg before initializing them :( Source/Src_nd/base_state_geometry.F90 commit ddc37c3242816698faa5c41db5885812d46c07f0 Author: Andy Nonaka Date: Mon Jun 24 13:22:35 2019 -0700 new broken test Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.512.2levels commit e91c2007b6a6dc2b061c70d00dd6ded7218bf3e3 Author: Alice Harpole Date: Wed Jun 19 16:55:26 2019 -0400 fixed heating rate Exec/SCIENCE/code_comp/GNUmakefile Exec/SCIENCE/code_comp/Problem.cpp Exec/SCIENCE/code_comp/make_heating.F90 Exec/SCIENCE/rotating_star/Problem.cpp commit dc91e8cdf7f8307650ec4fe729471ec926ad4677 Merge: 28ee5407 2a188ae5 Author: Alice Harpole Date: Wed Jun 19 10:24:40 2019 -0400 Merge branch 'code_comp' into development commit 2a188ae512e60ae2e89368437340dd8a8d31d6e1 Author: Alice Harpole Date: Wed Jun 19 07:21:49 2019 -0400 add parameters and sponge files Exec/SCIENCE/code_comp/sponge.F90 commit ef36a1d9ff28c3c67efeccbc89b20c294e283eab Author: Alice Harpole Date: Wed Jun 19 06:13:55 2019 -0400 saving changes Exec/SCIENCE/code_comp/inputs_3d Exec/SCIENCE/code_comp/simple.net commit 28ee540717d941c5e5e7513cc3931db93513093d Author: Alice Harpole Date: Wed Jun 12 17:39:56 2019 -0400 Added BSD-3 license LICENSE commit 89b9f9ee25f3f262e0ea86dcf682a10636db7f07 Author: Alice Harpole Date: Wed Jun 12 17:37:26 2019 -0400 changed settings so that it runs and looks reasonable Exec/SCIENCE/code_comp/GNUmakefile Exec/SCIENCE/code_comp/_parameters Exec/SCIENCE/code_comp/hcore.dat Exec/SCIENCE/code_comp/inputs_3d commit ab445ecef101fbe0bebf1e3cb8f8a97813ba042d Author: Alice Harpole Date: Wed Jun 12 10:44:55 2019 -0400 started code comparison problem Exec/SCIENCE/code_comp/GNUmakefile Exec/SCIENCE/code_comp/Make.package Exec/SCIENCE/code_comp/_parameters Exec/SCIENCE/code_comp/hcore.dat Exec/SCIENCE/code_comp/initdata.f90 Exec/SCIENCE/code_comp/inputs_3d Exec/SCIENCE/code_comp/make_heating.F90 Exec/SCIENCE/code_comp/simple.net Exec/SCIENCE/code_comp/tagging.F90 Exec/SCIENCE/rotating_star/initdata.F90 commit 6cabebcdaf5eccd35d07e6923c3057b3add942c3 Author: Alice Harpole Date: Tue Jun 11 17:23:35 2019 -0400 Fixed test_stability so that it runs Exec/TEST_PROBLEMS/test_stability/5peaks_const_grav.dat Exec/TEST_PROBLEMS/test_stability/initdata.f90 Exec/TEST_PROBLEMS/test_stability/inputs_2d_C Exec/TEST_PROBLEMS/test_stability/make_heating.F90 Exec/TEST_PROBLEMS/test_stability/model.hse commit 4fe742b4eac71b7057cfdae10b29233153a73aee Merge: 8b214db3 eb26c271 Author: Andy Nonaka Date: Mon Jun 10 13:11:32 2019 -0700 Merge pull request #72 from AMReX-Astro/weiqun/cudanamespace Cuda::setLaunchRegion -> Gpu::setLaunchRegion commit eb26c271de64054a4ce9fc43dbd3a3783b8483e9 Author: Weiqun Zhang Date: Thu Jun 6 09:50:02 2019 -0700 Cuda::setLaunchRegion -> Gpu::setLaunchRegion Source/MaestroAdvection.cpp Source/MaestroDt.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp Source/MaestroReact.cpp Source/MaestroRhoHT.cpp Source/MaestroSponge.cpp Source/MaestroThermal.cpp Source/main.cpp commit 8b214db3b9e13afa592888fbad69a46d5fed9d46 Author: Doreen Fan Date: Mon Jun 3 14:53:48 2019 -0700 June 2019 release notes RELEASE_NOTES commit e4d10115bcf5680d7a0793dd22988c83b4c0950a Author: Alice Harpole Date: Thu May 30 16:52:02 2019 -0400 Offload plotting routines (#71) This offloads make_pi_cc and almost all the routines from make_plot_variables.F90, significantly reducing the time taken to write plotfiles for GPU runs. * offloaded put_1d_array_on_cart and make_pi_cc * offloaded plotting routines * minor changes Source/MaestroAdvection.cpp Source/MaestroFill3dData.cpp Source/MaestroMacProj_level.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp Source/Maestro_F.H Source/Src_nd/make_pi_cc.F90 Source/Src_nd/make_plot_variables.F90 Source/Src_nd/update_scal.F90 commit 3f31d866ae565228b2baeaf5c43c202b5db45b2d Author: Alice Harpole Date: Thu May 30 11:03:22 2019 -0400 fixed lev,k -> lev,r in make_S.F90 and burner_loop.F90 Source/Src_nd/burner_loop.F90 Source/Src_nd/make_S.F90 commit 9640fb7fd64a68f0724c757a771e1af131f29daf Author: Alice Harpole Date: Thu May 30 10:50:44 2019 -0400 fixed a couple of bugs in Maestro_F.H for update_rhoh_3d_spherical Source/MaestroAdvection.cpp Source/MaestroFill3dData.cpp Source/Maestro_F.H Source/Src_nd/fill_3d_data.F90 commit 60e0ee2d2f2bbe0378098f14163c3bfcb0ce6b5d Author: Alice Harpole Date: Thu May 30 10:09:55 2019 -0400 nc_f -> nscal Source/Src_nd/update_scal.F90 commit dc2b39fc73a82598ddfdfd75de85daa25919f1f1 Author: Alice Harpole Date: Thu May 30 10:08:41 2019 -0400 fixed update_rhoh to reverse slowdown caused by new_nugpu merge Source/MaestroAdvection.cpp Source/Maestro_F.H Source/Src_nd/update_scal.F90 commit 8a3c08e34e1f4d8205dffa163520340c6b7f976c Author: Alice Harpole Date: Wed May 29 15:35:18 2019 -0400 tilebox -> growntilebox Source/MaestroThermal.cpp commit 8f97f79a47e63b47fe663e5a1cf24e4e0c181ca8 Author: Alice Harpole Date: Wed May 29 15:21:46 2019 -0400 growntilebox -> tilebox Source/MaestroThermal.cpp commit c0f0b1dcb4ce7380c63dde8671be69573d6017d9 Author: Alice Harpole Date: Tue May 28 17:26:26 2019 -0400 removed factor of 1/2 Source/MaestroMakeS.cpp commit 5525495e2a5a146590cd1fa24a55024a706b55c9 Author: Alice Harpole Date: Tue May 28 17:24:50 2019 -0400 added missing factor of 1/2 Source/MaestroMakeS.cpp commit 65bb726613ec673610ccdee1aa2a50e13b1d3fff Author: Alice Harpole Date: Tue May 28 17:23:49 2019 -0400 added missing dr Source/MaestroMakeS.cpp commit 4a012f6f6428e6274965788b9bb3c756de881269 Author: Alice Harpole Date: Tue May 28 17:22:56 2019 -0400 removed loop over level in calculation of gradp0 in MaestroMakeS.cpp Source/MaestroMakeS.cpp commit 83fa6aa1e3b117cc77753f5ea958ebe2fa57a367 Author: Andy Nonaka Date: Tue May 28 14:17:21 2019 -0700 fixed 2 bugs: when computing 1d divu for spherical problems in ModifyScalForce, do not loop over levels (base state only has 1 level), and loop from r=0 to nr_fine-1 (instead of 1 to nr_fine) Source/MaestroForce.cpp commit 1621155502198bc7b3f76f8ff00fa0cb9019dd09 Author: Alice Harpole Date: Tue May 28 16:10:13 2019 -0400 Offloads routines to the GPU (#69) This offloads a number of thermodynamics and source term routines to the GPU. I've moved all of the put_1d_array_on_cart_sphr calls out of the Fortran GPU code to the C++ CPU code in order to eliminate the allocate statements on the GPU. * offloaded burner_loop * If USE_CUDA=TRUE, then set USE_GPU_PRAGMA=TRUE and add CUDA to defines. * Markup eos subroutines with !$gpu * Preprocess network module, make aion_inv managed if CUDA enabled. * Add macros for spherical burner loop, add macros to header entries for global Fortran subroutines. * Add !$gpu for spherical burner loop and preprocess the Fortran. * Make some of the module variables in base state geometry managed if CUDA is enabled. Preprocess some Fortran sources. * Update runtime probin template to use managed memory if CUDA is enabled. * add cuda managed attributes to meth_params.F90 via parse_maestro_params.py * fixed up some routines in Microphysics so they work with the gpu, fixed meth_params * uncommented burner_loop * fixed burner_loop so it compiles and runs * offloaded make_thermal_coeffs * offloaded mk_sponge * offloading rhoh_vs_t * Fix function interfaces * offloaded all routines in MaestroRhoHT.cpp, however have commented out setLaunchRegion commands around those that produce illegal memory access errors * offloaded make_gamma (however also see illegal memory access errors it it's run on the gpu) * offloaded mhrhohforce * saving changes * FAB -> ANYD for burner_loop * FAB -> ANYD for make_thermal_coeffs * FAB -> ANYD for rhoh_vs_t subroutines * FAB -> ANYD for make_gamma * set nscal as a parameter using script adapted from Castro * offloaded make_S routines * offloaded compute_dt routines * Add RealVector typedef so that Real Vectors can be CUDA managed * Compiles and runs again * More stuff running on the GPU * Replace Vectors by RealVectors * offloaded update_scal and update_vel * remove numThreadsMin * turn off launch region for estdt because AMREX_REDUCE_MIN/MAX will not work if called together at the same time * revert estdt and firstdt * moving put_1d_array_on_sphr calls to C++ in order to avoid allocate calls on the GPU * moved the rest of the 1d base state to cart calls to C++ * fixed bugs in spherical routines * fixed some boundary conditions Exec/Make.Maestro Microphysics/EOS/eos.F90 Microphysics/EOS/eos_override.F90 Microphysics/conductivity/conductivity.F90 Microphysics/conductivity/constant/Make.package Microphysics/conductivity/constant/constant_conductivity.F90 Microphysics/networks/Make.package Microphysics/networks/burner.F90 Microphysics/networks/general_null/Make.package Microphysics/networks/general_null/actual_burner.F90 Microphysics/networks/general_null/actual_rhs.F90 Microphysics/networks/general_null/network.template Microphysics/networks/network.F90 Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvection.cpp Source/MaestroAverage.cpp Source/MaestroConvert.cpp Source/MaestroDensityAdvance.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroEvolve.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp Source/MaestroReact.cpp Source/MaestroRhoHT.cpp Source/MaestroSponge.cpp Source/MaestroThermal.cpp Source/MaestroVelocityAdvance.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/advect_base.F90 Source/Src_nd/base_state_geometry.F90 Source/Src_nd/burner_loop.F90 Source/Src_nd/compute_grad_phi.F90 Source/Src_nd/fill_3d_data.F90 Source/Src_nd/mac_solver.F90 Source/Src_nd/maestro_init.f90 Source/Src_nd/make_S.F90 Source/Src_nd/make_explicit_thermal.F90 Source/Src_nd/make_gamma.F90 Source/Src_nd/make_scal_force.F90 Source/Src_nd/make_vel_force.F90 Source/Src_nd/rhoh_vs_t.F90 Source/Src_nd/sponge.F90 Source/Src_nd/update_scal.F90 Source/Src_nd/update_vel.F90 Source/main.cpp Source/param/_variables Source/param/meth_params.template Source/param/mk_params.sh Source/param/parse_maestro_params.py Source/param/runtime.probin.template Source/param/set_variables.py Source/param_includes/Make.package Source/param_includes/meth_params.F90 Source/param_includes/state_sizes.f90 commit 0c07a44fc7acdc06dde4ef12f626bfe22f643553 Author: Weiqun Zhang Date: Tue May 21 09:29:36 2019 -0700 Call Geometry static functions through an object. This prepares MAESTROeX for upcoming AMReX changes Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp Source/MaestroNodalProj.cpp Source/MaestroSetup.cpp Source/MaestroThermal.cpp commit 6d09d0324c7e9f607c9ce991877c2abcd3ac5627 Merge: 1a66c8a5 3b0b8b52 Author: Andy Nonaka Date: Tue May 14 14:28:00 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 1a66c8a5ecebe766f9c6132b590be2e0eaaf56ed Author: Andy Nonaka Date: Tue May 14 14:27:26 2019 -0700 bugfix - pass in 0 velocity (w0mac_dummy) into MakeEtarhoSphr since in this algorithm, umac contains the full velocity Source/MaestroAdvanceAvg.cpp commit 3b0b8b528ff6ca36a3ecda1ba1ce49b3c47a35ad Author: Andy Nonaka Date: Mon May 13 19:06:41 2019 -0700 code cleanup - don't pass beta0 or is_predictor into AdvancePremac Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvection.cpp commit 37f96127708b54f1f3219cf6bc02415160b564f6 Author: Andy Nonaka Date: Mon May 13 19:02:41 2019 -0700 code cleanup - no need to pass beta0 or is_predictor into MakeVelForce Exec/UNIT_TESTS/test_basestate/MaestroDt.cpp Source/Maestro.H Source/MaestroAdvection.cpp Source/MaestroDt.cpp Source/MaestroForce.cpp Source/MaestroVelocityAdvance.cpp commit 54dbbd37e18b4e0ea367da60eb449ef65efe7bc8 Author: Andy Nonaka Date: Mon May 13 12:17:53 2019 -0700 add sum_interval = 1 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.1024 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.128 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.128.2levels Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.128.2levels_onegrid Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.128.avgbase Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.128.exactbase Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.1280 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.1536 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.256 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.256.2levels Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.256.3levels Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.256.avgbase Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.256.exactbase Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.384 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.512 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.512.3levels Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.512.avgbase.3levels Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.512.exactbase Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.64 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.64.avgbase Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.64.exactbase Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.768 commit 1cce95f4b486d284efb7ae310dc830d0b7e5cb83 Author: dwillcox Date: Thu May 9 21:39:12 2019 -0400 Add 3 density tags for urca problem. Exec/SCIENCE/urca/tagging.F90 commit 3cd2d31b32bdbb49cab1a397b3cbc97e1ef1a9ab Author: dwillcox Date: Thu May 9 21:38:09 2019 -0400 Fix bug in process.titan where ftime was not run properly. Exec/SCIENCE/urca/run/titan/process.titan commit a24f57a72903c1373bfe24d113ffd1c5f7fa2c6b Author: Andy Nonaka Date: Tue May 7 12:28:20 2019 -0700 bugfix in writing out base state for spherical AMR - need to loop over max_radial_level, not finest_level Source/MaestroPlot.cpp commit 0d2b2f89bec7e0c44f93b753a2209fc3fcf0c427 Author: Andy Nonaka Date: Mon May 6 18:23:17 2019 -0700 writing out base state to different files now (1 per level). Note that ghost data (4 ghost cells) is also written out Source/MaestroPlot.cpp commit b069323df7e3ee35b632a6cabc3d49922b01ba8b Merge: 9d2102ef fc9990bf Author: Andy Nonaka Date: Mon May 6 15:50:37 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 9d2102ef6af78b039556b0b8d1674278c0518e02 Author: Andy Nonaka Date: Mon May 6 15:49:38 2019 -0700 write out base state to plotfile. only works properly for spherical and single-level planar (where base state has 1 level of refinement). For multilevel planar it dumps out the entire base state arrays for now, much of which does not correspond to valid region. Source/MaestroPlot.cpp commit fc9990bfcd0b32d9419f4b047a230b547ba20d63 Author: dwillcox Date: Mon May 6 16:45:31 2019 -0400 Update titan file processing script for 7-digit chk and plt files. Exec/SCIENCE/urca/run/titan/process.titan commit a35e497f511bf5703d987c191fe1df782f6435db Author: Donald E. Willcox Date: Fri May 3 19:37:28 2019 -0700 Enable fpe trapping Exec/SCIENCE/urca/models/rhoc-5.5e9_Tc-6.0e8_Mconv-1.0/levels-2.64/inputs_3d_2lev.5120.64 commit 393a98c9f6a395363e00be4b3b21365bcecb1e73 Author: Donald E. Willcox Date: Fri May 3 19:36:51 2019 -0700 Add a 64^3 inputs file for debugging. Exec/SCIENCE/urca/models/rhoc-5.5e9_Tc-6.0e8_Mconv-1.0/levels-2.64/inputs_3d_2lev.5120.64 commit 2ccd6dab8c33c274240933a00c31548ad974d930 Author: Alice Harpole Date: Thu May 2 14:29:40 2019 -0400 implement sum_interval and sum_per so that diagnostics are only calculated if one/both of these are > 0 Source/MaestroEvolve.cpp commit 1e56ac8a878dce1fb6ffbec2465b5f540df16ffa Author: Doreen Fan Date: Wed May 1 18:13:43 2019 -0700 Can tag multiple levels of AMR using different values (ex. tag_density_1, tag_density_2, etc.) Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.512.3levels Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.512.avgbase.3levels Exec/SCIENCE/wdconvect/tagging.F90 commit 5dfcb5ccca28a957ba7ad47a6f3aa1769b71cd5c Author: Andy Nonaka Date: Wed May 1 11:14:40 2019 -0700 May 2019 release notes RELEASE_NOTES commit d217929227fdc72f257995c550324ee0519bfb69 Merge: 47f14c15 383146a2 Author: Andy Nonaka Date: Tue Apr 30 12:47:36 2019 -0700 Merge pull request #65 from AMReX-Astro/cutoff_cleanup Cutoff Density Cleanup commit 383146a28bceba5536a29b12caeb39b0f618df60 Author: Andy Nonaka Date: Tue Apr 30 12:45:25 2019 -0700 require anelastic and base_cutoff_density to be supplied in the inputs file - code aborts if not supplied burning_cutoff_density takes on the value of base_cutoff_density if not supplied in the inputs file all inputs files updated to retain the old defaults (3.e6) if nothing was supplied Exec/SCIENCE/flame/inputs_2d Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C.avgbase Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_omp_2d_regression Exec/TEST_PROBLEMS/test_convect/inputs_2d_C Exec/TEST_PROBLEMS/test_convect/inputs_2d_regression Exec/TEST_PROBLEMS/test_stability/inputs_2d_C Exec/UNIT_TESTS/test_advect/inputs_2d Exec/UNIT_TESTS/test_advect/inputs_3d Exec/UNIT_TESTS/test_average/inputs_2d_planar Exec/UNIT_TESTS/test_average/inputs_3d.128.5dr.eq.dx Exec/UNIT_TESTS/test_diffusion/inputs_2d Exec/UNIT_TESTS/test_diffusion/inputs_2d-32 Exec/UNIT_TESTS/test_diffusion/inputs_2d-64 Exec/UNIT_TESTS/test_eos/inputs_eos.gammalaw Exec/UNIT_TESTS/test_eos/inputs_eos.helmeos Exec/UNIT_TESTS/test_projection/inputs_2d_per Exec/UNIT_TESTS/test_projection/inputs_2d_per.cross Exec/UNIT_TESTS/test_projection/inputs_2d_per_mac Exec/UNIT_TESTS/test_projection/inputs_2d_wall Exec/UNIT_TESTS/test_projection/inputs_2d_wall.cross Exec/UNIT_TESTS/test_projection/inputs_2d_wall_mac Exec/UNIT_TESTS/test_projection/inputs_3d_per Exec/UNIT_TESTS/test_projection/inputs_3d_per_mac Exec/UNIT_TESTS/test_projection/inputs_3d_wall Exec/UNIT_TESTS/test_projection/inputs_3d_wall_mac Exec/UNIT_TESTS/test_react/inputs_3alpha Exec/UNIT_TESTS/test_react/inputs_aprox13 Exec/UNIT_TESTS/test_react/inputs_ignition Exec/UNIT_TESTS/test_react/inputs_mesa_carbon Exec/UNIT_TESTS/test_react/inputs_reaclib_cburn Exec/UNIT_TESTS/test_react/inputs_reaclib_ctest Exec/UNIT_TESTS/test_react/inputs_reaclib_urca Exec/UNIT_TESTS/test_react/inputs_react Exec/UNIT_TESTS/test_react/inputs_rprox Exec/UNIT_TESTS/test_react/inputs_xrb_simple Source/param/_cpp_parameters Source/param/meth_params.template Source/param_includes/maestro_defaults.H Source/param_includes/meth_params.F90 sphinx_docs/source/lo_density.rst commit f430814d6764e5f07af07cc21d6b7f506ab78a1c Author: Andy Nonaka Date: Tue Apr 30 12:10:20 2019 -0700 renname anelastic_cutoff -> anelastic_cutoff_density Exec/SCIENCE/ecsn/inputs_3d_C.128 Exec/SCIENCE/ecsn/inputs_3d_kepler Exec/SCIENCE/flame/base_state.f90 Exec/SCIENCE/rotating_star/inputs_2d Exec/SCIENCE/rotating_star/inputs_3d_C Exec/SCIENCE/rotating_star/inputs_3d_C.128 Exec/SCIENCE/rotating_star/inputs_3d_C.128.2levels Exec/SCIENCE/rotating_star/inputs_3d_C.128.exactbase Exec/SCIENCE/rotating_star/inputs_3d_C.64 Exec/SCIENCE/rotating_star/inputs_3d_C.64.exactbase Exec/SCIENCE/rotating_star/inputs_3d_regression Exec/SCIENCE/rotating_star/inputs_test Exec/SCIENCE/sub_chandra/inputs_3d Exec/SCIENCE/toy_convect/inputs_2d Exec/SCIENCE/urca/models/rhoc-3.5e9_Tc-6.0e8_Mconv-1.0/levels-1.1024/inputs_3d_1lev.5120 Exec/SCIENCE/urca/models/rhoc-3.5e9_Tc-6.0e8_Mconv-1.0/levels-2.1024/inputs_3d_2lev.5120 Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/levels-1.1024/inputs_3d_1lev.5120 Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/levels-2.1024/inputs_3d_2lev.5120 Exec/SCIENCE/urca/models/rhoc-5.5e9_Tc-6.0e8_Mconv-1.0/levels-1.1024/inputs_3d_1lev.5120 Exec/SCIENCE/urca/models/rhoc-5.5e9_Tc-6.0e8_Mconv-1.0/levels-2.1024/inputs_3d_2lev.5120 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.1024 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.128 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.128.2levels Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.128.2levels_onegrid Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.128.avgbase Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.128.exactbase Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.1280 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.1536 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.256 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.256.2levels Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.256.3levels Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.256.avgbase Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.256.exactbase Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.384 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.512 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.512.3levels Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.512.avgbase.3levels Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.512.exactbase Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.64 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.64.avgbase Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.64.exactbase Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.768 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_amr_regression Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_regression Exec/SCIENCE/wdconvect/inputs_files/inputs_omp_3d_regression Exec/SCIENCE/xrb_mixed/inputs_2d Exec/SCIENCE/xrb_mixed/sponge.F90 Exec/TEST_PROBLEMS/double_bubble/base_state.f90 Exec/TEST_PROBLEMS/double_bubble/inputs_2d_C Exec/TEST_PROBLEMS/double_bubble/inputs_2d_regression Exec/TEST_PROBLEMS/incomp_shear_jet/base_state.f90 Exec/TEST_PROBLEMS/incomp_shear_jet/inputs_2d_C Exec/TEST_PROBLEMS/incomp_shear_jet/inputs_2d_regression Exec/TEST_PROBLEMS/mach_jet/base_state.f90 Exec/TEST_PROBLEMS/mach_jet/inputs_2d Exec/TEST_PROBLEMS/mach_jet/inputs_2d_stratified Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C.2levels Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C.3levels Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_dpdt Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C.2levels Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C.3levels Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C.avgbase Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_omp_3d_regression Exec/TEST_PROBLEMS/rt/base_state.f90 Exec/TEST_PROBLEMS/rt/inputs_2d_C Exec/TEST_PROBLEMS/rt/inputs_2d_regression Exec/UNIT_TESTS/test_basestate/planar-invsq/inputs-planar-invsq Exec/UNIT_TESTS/test_basestate/planar/inputs-planar Exec/UNIT_TESTS/test_basestate/spherical/inputs-spherical_heat Exec/UNIT_TESTS/test_basestate/sub_chandra/inputs-subchandra Exec/UNIT_TESTS/test_basestate/urca/inputs-urca_cold Exec/UNIT_TESTS/test_basestate/urca/inputs-urca_hot Exec/UNIT_TESTS/test_basestate/urca/inputs-uref Exec/UNIT_TESTS/test_basestate/wdconvect_paper/inputs.rho_cutoff_1.e-4 Exec/UNIT_TESTS/test_basestate/wdconvect_paper/inputs.rho_cutoff_1.e5 Exec/UNIT_TESTS/test_basestate/wdconvect_paper/inputs.rho_cutoff_1.e6 Source/Src_nd/base_state_geometry.f90 Source/Src_nd/make_S.F90 Source/Src_nd/make_beta0.f90 Source/Src_nd/make_psi.F90 Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 sphinx_docs/source/lo_density.rst commit 47f14c1526c4ebe499710d1867fd7d12251294ee Author: Andy Nonaka Date: Mon Apr 29 12:24:50 2019 -0700 replace "do_reflux" with "reflux_type". Default 1. So no changes to any runs. removed do_reflux from all inputs files. Exec/SCIENCE/flame/inputs_2d Exec/SCIENCE/rotating_star/inputs_2d Exec/SCIENCE/rotating_star/inputs_3d_C Exec/SCIENCE/rotating_star/inputs_3d_C.128.2levels Exec/SCIENCE/rotating_star/inputs_3d_C.128.exactbase Exec/SCIENCE/rotating_star/inputs_3d_C.64.exactbase Exec/SCIENCE/rotating_star/inputs_3d_regression Exec/SCIENCE/rotating_star/inputs_test Exec/SCIENCE/urca/models/rhoc-3.5e9_Tc-6.0e8_Mconv-1.0/levels-1.1024/inputs_3d_1lev.5120 Exec/SCIENCE/urca/models/rhoc-3.5e9_Tc-6.0e8_Mconv-1.0/levels-2.1024/inputs_3d_2lev.5120 Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/levels-1.1024/inputs_3d_1lev.5120 Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/levels-2.1024/inputs_3d_2lev.5120 Exec/SCIENCE/urca/models/rhoc-5.5e9_Tc-6.0e8_Mconv-1.0/levels-1.1024/inputs_3d_1lev.5120 Exec/SCIENCE/urca/models/rhoc-5.5e9_Tc-6.0e8_Mconv-1.0/levels-2.1024/inputs_3d_2lev.5120 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.128.2levels Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.128.2levels_onegrid Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.256.2levels Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.256.3levels Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.512.3levels Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.512.avgbase.3levels Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_amr_regression Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_regression Exec/SCIENCE/wdconvect/inputs_files/inputs_omp_3d_regression Exec/TEST_PROBLEMS/double_bubble/inputs_2d_C Exec/TEST_PROBLEMS/double_bubble/inputs_2d_regression Exec/TEST_PROBLEMS/incomp_shear_jet/inputs_2d_C Exec/TEST_PROBLEMS/incomp_shear_jet/inputs_2d_regression Exec/TEST_PROBLEMS/mach_jet/inputs_2d Exec/TEST_PROBLEMS/mach_jet/inputs_2d_stratified Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C.2levels Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C.3levels Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C.avgbase Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_dpdt Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C.2levels Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C.3levels Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C.avgbase Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_omp_2d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_omp_3d_regression Exec/TEST_PROBLEMS/rt/inputs_2d_C Exec/TEST_PROBLEMS/rt/inputs_2d_regression Source/MaestroAdvection.cpp Source/MaestroCheckpoint.cpp Source/MaestroInit.cpp Source/MaestroRegrid.cpp Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H commit 066c77aac83d692307d507ad0ecaf18adf439612 Author: Michael Zingale Date: Mon Apr 29 14:29:16 2019 -0400 a simple script to plot the initial model Exec/SCIENCE/rotating_star/analysis/initial_model.py commit 3c223b65436a39dfda11e4b7eb4cf4c5c559c9b6 Author: Andy Nonaka Date: Fri Apr 26 14:08:37 2019 -0700 compute total density fluxes by summing the rhoX fluxes. This fixes the refluxing bug Source/Src_nd/make_flux.F90 commit 7c9a970f53ba1d758d9ea9c7d8424e6cf2b07b11 Author: Andy Nonaka Date: Fri Apr 26 14:08:15 2019 -0700 always average down edge velocities (since we do convective update, not conservative, so we don't use flux registers here) Source/MaestroAdvection.cpp commit fc297254d18a77480f818f27ecc8e6491ac645b8 Merge: e194829b a6d4b16f Author: Alice Harpole Date: Thu Apr 25 14:48:12 2019 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit e194829bbf9ae7fc28358dd75fe6df00756103f0 Author: Alice Harpole Date: Thu Apr 25 14:48:06 2019 -0400 add slack scripts Util/slack_scripts/make_plot.py Util/slack_scripts/post_to_slack.sh Util/slack_scripts/slack_vars commit a6d4b16ff7583ce38d2a671cd622fba9f45d7ea9 Author: Michael Zingale Date: Thu Apr 25 13:19:31 2019 -0400 use Urca tagging Exec/SCIENCE/ecsn/tagging.F90 commit fa5596788bcfee69fc3c2ec735f97dc53c122598 Author: dwillcox Date: Wed Apr 24 20:16:36 2019 -0400 Use maestro.restart_file instead of amr.restart Exec/SCIENCE/urca/run/titan/titan.run commit 7ed89daf16aa2f4ccca81b00064c8c4b0452f11b Merge: fa054342 7245fff5 Author: Alice Harpole Date: Wed Apr 24 10:20:46 2019 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit fa0543423c1cadbb2a43396ba32fb440909b7fce Author: Alice Harpole Date: Wed Apr 24 10:20:26 2019 -0400 copy rho0_old to rho0_temp in MaestroRegrid.cpp for spherical=1 so it doesn't be set to zero later on Source/MaestroRegrid.cpp commit 7245fff542851fa588c3e96788ebbfff7bf5b276 Author: Andy Nonaka Date: Tue Apr 23 13:41:45 2019 -0700 amr regression test Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_amr_regression commit d297134475f0c362c514b20a0a8c4c8c06eed8db Author: Andy Nonaka Date: Tue Apr 23 13:39:52 2019 -0700 implemented "plot_base" (and rennamed it "plot_base_state"). Default is true so nothing should be affected. Source/MaestroPlot.cpp Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H commit 0801cc9b6ab66340e37b282f1aba579fa338f101 Author: Donald E. Willcox Date: Mon Apr 22 23:16:21 2019 -0700 Update Urca inputs to enable ppm_trace_forces, use species_pred_type=3, and use average down instead of refluxing. Exec/SCIENCE/urca/models/rhoc-3.5e9_Tc-6.0e8_Mconv-1.0/levels-1.1024/inputs_3d_1lev.5120 Exec/SCIENCE/urca/models/rhoc-3.5e9_Tc-6.0e8_Mconv-1.0/levels-2.1024/inputs_3d_2lev.5120 Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/levels-1.1024/inputs_3d_1lev.5120 Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/levels-2.1024/inputs_3d_2lev.5120 Exec/SCIENCE/urca/models/rhoc-5.5e9_Tc-6.0e8_Mconv-1.0/levels-1.1024/inputs_3d_1lev.5120 Exec/SCIENCE/urca/models/rhoc-5.5e9_Tc-6.0e8_Mconv-1.0/levels-2.1024/inputs_3d_2lev.5120 commit 4863f518f448e95ecd1c9ed50602cea614400d11 Merge: 6d1d40a3 f3bfc138 Author: Andy Nonaka Date: Mon Apr 22 12:44:04 2019 -0700 Merge pull request #54 from AMReX-Astro/actual_plot_variables Add momentum, entropy, entropypert and processor_number to plotfiles commit f3bfc138331edcd4b7d56a8b4d5ce45fea3c6606 Merge: e4fe675f 6d1d40a3 Author: Andy Nonaka Date: Mon Apr 22 12:41:31 2019 -0700 Merge branch 'development' into actual_plot_variables commit 6d1d40a32abc1c2da9743f2024ab898f89a30ce8 Author: Andy Nonaka Date: Mon Apr 22 12:07:17 2019 -0700 add momentum to plotfile Source/MaestroPlot.cpp commit 9d211ee318cf0526cbf209eab054fcf489c4715d Merge: 6c8289ae d781b9e2 Author: Alice Harpole Date: Fri Apr 19 14:33:27 2019 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 6c8289ae859bd0c71d3568bc51db3a4c49880969 Author: Alice Harpole Date: Fri Apr 19 14:33:01 2019 -0400 add sub_chandra problem from MAESTRO Exec/SCIENCE/README Exec/SCIENCE/sub_chandra/GNUmakefile Exec/SCIENCE/sub_chandra/Make.package Exec/SCIENCE/sub_chandra/_parameters Exec/SCIENCE/sub_chandra/initdata.f90 Exec/SCIENCE/sub_chandra/inputs_3d Exec/SCIENCE/sub_chandra/sub_chandra.M_WD-1.00.M_He-0.05.hse.C.1280.hotcutoff Exec/SCIENCE/xrb_mixed/inputs_2d commit d781b9e27b4449bc9b6b7036c79cfb355a65bff2 Author: Doreen Fan Date: Fri Apr 19 11:22:19 2019 -0700 Remove ambiguity of psi Source/Maestro.H Source/MaestroMakeS.cpp commit a57fc46e321ff769f6f40a33ca5fd5748e955894 Author: Alice Harpole Date: Thu Apr 18 17:18:57 2019 -0400 xrb_mixed problem Exec/SCIENCE/xrb_mixed/GNUmakefile Exec/SCIENCE/xrb_mixed/Make.package Exec/SCIENCE/xrb_mixed/_parameters Exec/SCIENCE/xrb_mixed/initdata.f90 Exec/SCIENCE/xrb_mixed/inputs_2d Exec/SCIENCE/xrb_mixed/make_heating.F90 Exec/SCIENCE/xrb_mixed/sponge.F90 Exec/SCIENCE/xrb_mixed/xrb_new.hse.dx_6.000cm commit 9a546863b45a5c8603ebbeb1c8b88ae2fc0f132c Author: Alice Harpole Date: Thu Apr 18 15:11:34 2019 -0400 add initdata.f90 Exec/SCIENCE/toy_convect/initdata.f90 commit 5a32c0c55a46ad51b4dd653cceb9a7df659e7a77 Merge: 94734caf 0c25b24b Author: Alice Harpole Date: Thu Apr 18 15:10:27 2019 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 94734caf12492d5c3299aeb24506904ad17364b9 Author: Alice Harpole Date: Thu Apr 18 15:10:19 2019 -0400 fixed toy_convect initdata file and inputs file Exec/SCIENCE/toy_convect/initdata.F90 Exec/SCIENCE/toy_convect/inputs_2d commit 0c25b24bbea276e25cb24d8b05329b2942ffa9fb Merge: f7699536 e6300d93 Author: Doreen Fan Date: Thu Apr 18 11:48:37 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit f7699536c0ca6b353a2eb0b0dc1fe2a66bfc1acf Author: Doreen Fan Date: Thu Apr 18 11:46:00 2019 -0700 bug fix: Only subtract/add w0mac before/after projection steps if spherical == 1 Also added 2d/3d reacting bubble input files for testing new temporal algorithm. Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C.avgbase Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C.avgbase Source/MaestroAdvanceAvg.cpp Source/Src_nd/make_w0.f90 commit e6300d936df666b1c0f9cf0dcf3f31e9f3df0a41 Merge: 0f747702 6e674edc Author: Alice Harpole Date: Thu Apr 18 14:45:08 2019 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 0f74770264316d9db3dea31ed2f0e3f7cc0ebb57 Author: Alice Harpole Date: Thu Apr 18 14:38:02 2019 -0400 merge conflicts Exec/SCIENCE/flame/inputs_2d Exec/SCIENCE/toy_convect/GNUmakefile Exec/SCIENCE/toy_convect/Make.package Exec/SCIENCE/toy_convect/_parameters Exec/SCIENCE/toy_convect/initdata.F90 Exec/SCIENCE/toy_convect/inputs_2d Exec/SCIENCE/toy_convect/make_heating.F90 Exec/SCIENCE/toy_convect/toy_nova_constg_tanh2.hse.smooth_3.00.1024 Exec/TEST_PROBLEMS/test_convect/initdata.f90 Source/MaestroEvolve.cpp Source/MaestroInit.cpp commit 6e674edc32d1b3c8eec869282d7bb0dfe0ced282 Author: Donald E. Willcox Date: Thu Apr 18 10:57:26 2019 -0700 Add 2 levels input file for rc5.5/tc6.0 Urca model. Exec/SCIENCE/urca/models/rhoc-5.5e9_Tc-6.0e8_Mconv-1.0/levels-1.1024/inputs_3d_1lev.5120 Exec/SCIENCE/urca/models/rhoc-5.5e9_Tc-6.0e8_Mconv-1.0/levels-2.1024/inputs_3d_2lev.5120 commit 688c79f37a7d3057ebd345d74faeb269162e87cc Author: Donald E. Willcox Date: Thu Apr 18 10:55:58 2019 -0700 Enable amr.refine_grid_layout Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/levels-2.1024/inputs_3d_2lev.5120 commit e59ab34afaf50729a4a8c8ad4b9c573b28d2a044 Author: Donald E. Willcox Date: Thu Apr 18 10:55:22 2019 -0700 Add 2 level inputs file for rc3.5/tc6.0 Urca model. Exec/SCIENCE/urca/models/rhoc-3.5e9_Tc-6.0e8_Mconv-1.0/levels-1.1024/inputs_3d_1lev.5120 Exec/SCIENCE/urca/models/rhoc-3.5e9_Tc-6.0e8_Mconv-1.0/levels-2.1024/inputs_3d_2lev.5120 commit b4ed6ac09b9132545d498082c1968b0aa488e078 Author: Donald E. Willcox Date: Thu Apr 18 10:52:19 2019 -0700 Add inputs file for 2 levels for rc4.5/Tc6.0 Urca model. Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/levels-1.1024/inputs_3d_1lev.5120 Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/levels-2.1024/inputs_3d_2lev.5120 commit a50973d139ae77969c940574e409cd3cf28cf765 Author: Donald E. Willcox Date: Thu Apr 18 10:46:40 2019 -0700 Add rhoc=3.5e9, Tc=6.0e8 Urca model. Exec/SCIENCE/urca/models/rhoc-3.5e9_Tc-6.0e8_Mconv-1.0/WD_urca_nuc_M-1.0_rc3.5e9_Tc6.0e8_speceq.hse.5120 Exec/SCIENCE/urca/models/rhoc-3.5e9_Tc-6.0e8_Mconv-1.0/WD_urca_nuc_M-1.0_rc3.5e9_Tc6.0e8_speceq.hse.5120.report Exec/SCIENCE/urca/models/rhoc-3.5e9_Tc-6.0e8_Mconv-1.0/inputs_3d_1lev.5120 Exec/SCIENCE/urca/models/rhoc-3.5e9_Tc-6.0e8_Mconv-1.0/inputs_urca_model_equilibrium.5120 commit 04bf09e6150c126c237628421a3118ab823d4ff0 Author: Donald E. Willcox Date: Thu Apr 18 10:42:38 2019 -0700 Add rhoc=5.5e9, Tc=6.0e8 Urca model. Exec/SCIENCE/urca/models/rhoc-5.5e9_Tc-6.0e8_Mconv-1.0/WD_urca_nuc_M-1.0_rc5.5e9_Tc6.0e8_speceq.hse.5120 Exec/SCIENCE/urca/models/rhoc-5.5e9_Tc-6.0e8_Mconv-1.0/WD_urca_nuc_M-1.0_rc5.5e9_Tc6.0e8_speceq.hse.5120.report Exec/SCIENCE/urca/models/rhoc-5.5e9_Tc-6.0e8_Mconv-1.0/inputs_3d_1lev.5120 Exec/SCIENCE/urca/models/rhoc-5.5e9_Tc-6.0e8_Mconv-1.0/inputs_urca_model_equilibrium.5120 commit 113e4eef7c798ccd313a345bea778122f37af401 Author: Alice Harpole Date: Thu Apr 18 10:17:35 2019 -0400 updated inputs file for flame problem Exec/SCIENCE/flame/inputs_2d commit 1da41f73d0436ee9fd4b0d5bdb839a8ff72e802e Author: Alice Harpole Date: Thu Apr 18 09:25:59 2019 -0400 updated print statements in initialization to reflect user defined plot_base_name Exec/SCIENCE/flame/inputs_2d Source/MaestroInit.cpp commit df0e4b192dd95aa8d3bc444d2ab01bd247b7130d Merge: d458d169 086515cc Author: Alice Harpole Date: Thu Apr 18 09:02:59 2019 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit d458d1693ad90235ce6493b149ba1ed1a0cd43a9 Author: Alice Harpole Date: Thu Apr 18 09:00:49 2019 -0400 started porting flame problem, fixed MaestroPlot.cpp so default small_plot_vars are used correctly Exec/SCIENCE/flame/GNUmakefile Exec/SCIENCE/flame/Make.package Exec/SCIENCE/flame/_parameters Exec/SCIENCE/flame/base_state.f90 Exec/SCIENCE/flame/bc_fill_nd.F90 Exec/SCIENCE/flame/initdata.f90 Exec/SCIENCE/flame/inlet_bc.f90 Exec/SCIENCE/rotating_star/GNUmakefile Exec/SCIENCE/rotating_star/inputs_test Exec/TEST_PROBLEMS/mach_jet/inputs_2d_stratified Source/MaestroPlot.cpp Source/MaestroSetup.cpp commit 086515cc70809438e4dd9e1c6e3889c45200e907 Merge: b11618e0 85e375a9 Author: Doreen Fan Date: Wed Apr 17 15:54:31 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit b11618e0e265c7efe185bff460830ab9397fcc6a Author: Doreen Fan Date: Wed Apr 17 15:48:09 2019 -0700 Remove psi from input parameter when calling make_w0. Psi in make_w0 subroutine is now computed directly from etarho_cc. This is done so that we can distinguish the psi term from dp/dt term in the new temporal algorithm. Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/make_scal_force.F90 Source/Src_nd/make_w0.f90 commit 85e375a9494f29306403d0ad0d1b206661fa1cce Author: Alice Harpole Date: Wed Apr 17 18:04:36 2019 -0400 update inputs_2d_stratified so it's MAESTROeX-friendly Exec/TEST_PROBLEMS/mach_jet/inputs_2d_stratified commit 1c638dfcd46e47629b5702fb7feec6292e87205b Author: Alice Harpole Date: Wed Apr 17 13:48:37 2019 -0400 initial data for 512^3 run Exec/SCIENCE/rotating_star/18m_500_s_rot_b_eq_1.hse.51200 Exec/SCIENCE/rotating_star/18m_500_s_rot_b_eq_1.hse.6144 commit 315bb75131651381f67425330641bdee37e2a6ec Author: Alice Harpole Date: Wed Apr 17 12:55:06 2019 -0400 remove fstring Util/scripts/convert_backtrace.py commit c4a1bdb984f7cafdac6a701a80e74c9ebe40937a Author: Alice Harpole Date: Wed Apr 17 12:54:01 2019 -0400 add convert_backtrace.py script Util/scripts/convert_backtrace.py commit 93034f0ae366e3347dc68cf9aa7d0ba591d925da Author: Donald E. Willcox Date: Wed Apr 17 09:43:52 2019 -0700 Update plotfile & checkpoint writing logic (#58) Previously we had all the plotfile writing conditions dependent on plot_int, including the conditions set for plot_deltat, plotting on the maximum timestep, and plotting on the maximum simulation time. This PR makes plot_deltat, max timestep, and max time plotfile conditions independent of the plot_int > 0 condition for plotfiles and small plotfiles. This PR does the same for checkpoint writing conditions. There is no deltat condition for writing checkpoint files, but previously checkpoints would not be written at the maximum step or maximum simulation time if chk_int > 0 were not satisfied. This PR makes it so the maximum step and maximum simulation time checkpoints are always written. * Make plot_deltat, max timestep, and max time plotfile conditions independent of plot_int > 0 condition for plotfiles and small plotfiles. * Make checkpoint writing similarly independent of chk_int for non-interval conditions. Source/MaestroEvolve.cpp commit 6a43959e7db39217711f4ef37dc8e935783f2f4a Author: Doreen Fan Date: Tue Apr 16 19:44:00 2019 -0700 bug fix: remove assumption that the new temporal algorithm is only for spherical problems Source/MaestroAdvanceAvg.cpp commit 71c03e7ce2a4a7ca668e6901804e73dafafc35e4 Merge: 43bcadfe a0e1a625 Author: dwillcox Date: Tue Apr 16 21:52:12 2019 -0400 Merge branch 'development' of github.com:amrex-astro/MaestroEx into development commit 43bcadfeb9749f78639c8f608c3a4381c29391e1 Author: dwillcox Date: Tue Apr 16 21:51:57 2019 -0400 Update inputs file for this model with the working MG tolerances, use single precision plotfiles, settings for running on Titan. Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/inputs_3d_1lev.5120 commit 8ec60e3a59e44ce68a5014ee1eeb5e1d3f2ef4dd Author: dwillcox Date: Tue Apr 16 21:50:50 2019 -0400 Fixed Titan PBS script so MaestroEx runs. Exec/SCIENCE/urca/run/titan/titan.run commit a0e1a62587e85bd5b66dda1c5548659a8e9b6aef Merge: 6b292f8d ba327a78 Author: Doreen Fan Date: Mon Apr 15 13:47:55 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 6b292f8d4087eff6dd98dfd68d395f838272a54b Author: Doreen Fan Date: Mon Apr 15 13:47:45 2019 -0700 Remove aborts from external Dirichlet bcs for velocity. Only abort if scalar external Dirichlet bc is declared but not defined. Note that only Pi component does not need to satisfy this condition. Exec/TEST_PROBLEMS/reacting_bubble/bc_fill_nd.F90 Source/Src_nd/bc_fill_nd.F90 commit c82dcecc66dfadd3b0cdda5a9491a3464b733d9e Author: Doreen Fan Date: Mon Apr 15 13:42:20 2019 -0700 Should still do split_projection for non-spherical problems Source/MaestroAdvanceAvg.cpp commit ba327a78e01d770bfb8040da76358736da23b4e4 Merge: 2045f36e 0d2514fb Author: Alice Harpole Date: Mon Apr 15 16:35:36 2019 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 2045f36ea42dd48703dc782e6633a306b1dad889 Author: Alice Harpole Date: Mon Apr 15 16:35:23 2019 -0400 only apply rho=INLET_RHO when the y-velocity is non-zero Exec/TEST_PROBLEMS/mach_jet/GNUmakefile Exec/TEST_PROBLEMS/mach_jet/bc_fill_nd.F90 Exec/TEST_PROBLEMS/mach_jet/inputs_2d commit 0d2514fbcba9bdee1d1053115d7168e9548d945f Merge: e5654779 954e64d0 Author: Michael Zingale Date: Mon Apr 15 15:46:11 2019 -0400 Merge branch 'development' of github.com:amrex-astro/MAESTROeX into development commit e5654779e46c7673ae744ab37a7f23265f8248fe Author: Michael Zingale Date: Mon Apr 15 15:45:54 2019 -0400 remove old debugging code Source/param/runtime.probin.template commit 954e64d0d6dea213c1bc2d1a9109a19e6ee6f4aa Author: Doreen Fan Date: Fri Apr 12 17:35:27 2019 -0700 add some OMP calls Source/Src_nd/make_w0.f90 commit 962691efc2d81f36f5d549e362a796f0a8a4098c Author: Andy Nonaka Date: Fri Apr 12 15:23:30 2019 -0700 fix the fact that fortran component indices are 1 larger than c++ Exec/TEST_PROBLEMS/mach_jet/bc_fill_nd.F90 Source/PhysBCFunctMaestro.H commit 85956fa120da5d3cf6f6f453724169adc3879851 Author: Andy Nonaka Date: Fri Apr 12 14:06:28 2019 -0700 properly set zero normal velocity at the bottom walls using the new dirichlet bc code. Exec/TEST_PROBLEMS/reacting_bubble/bc_fill_nd.F90 commit 0407620ad2e0dbc3bb3da2cc863ccfc301410779 Merge: 2ef9b1ee 5e0b9aef Author: Andy Nonaka Date: Fri Apr 12 14:00:55 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 2ef9b1ee6b5d3d226f4bfa31e7d8854c598becb9 Author: Andy Nonaka Date: Fri Apr 12 13:59:51 2019 -0700 git rid of the aborts if you encounter a dirichlet condition for scalars... pressure for outflow is homogeneous Dirichelt. So all the codes were crashing. There's still a problem in the code in that the fortran rho_comp, rhoh_comp, etc., are offset by +1 from the C++ versions Density, etc. So I'm not sure how mach_jet is actually working at the moment. Exec/TEST_PROBLEMS/mach_jet/bc_fill_nd.F90 Source/Src_nd/bc_fill_nd.F90 commit 5e0b9aef1bedab112cef9ebd41fcdab45bbd987a Author: Doreen Fan Date: Thu Apr 11 16:11:31 2019 -0700 Remove fill_ext_bc for reacting bubble problem Exec/TEST_PROBLEMS/reacting_bubble/bc_fill_nd.F90 commit ba21946ad704773da7954dc42c6b6d6feac2a3fb Author: Andy Nonaka Date: Thu Apr 11 12:42:57 2019 -0700 clean up boundary condition codes so these match except for the version in mach_jet illustrates how to add Dirichlet conditions Exec/TEST_PROBLEMS/mach_jet/bc_fill_nd.F90 Source/Src_nd/bc_fill_nd.F90 commit ec13df6f10389caa9acdd80ecc93e0ec2239441a Merge: d12bda96 4bdaa1b9 Author: Andy Nonaka Date: Thu Apr 11 07:55:58 2019 -0700 Merge pull request #57 from AMReX-Astro/mach_jet Mach jet commit 4bdaa1b9c8640837444ad8b8501410f1917bf564 Author: Andy Nonaka Date: Thu Apr 11 07:50:37 2019 -0700 fix input gamma to be 1.66666666 instead of 5.0/3.0. fix some other parameters so they match the MAESTRO version of this test. Exec/TEST_PROBLEMS/mach_jet/inputs_2d commit d12bda966f66dcd084de4fbf819d925dd932a489 Author: dwillcox Date: Thu Apr 11 03:20:36 2019 -0400 Add run directory with run scripts for Titan. Exec/SCIENCE/urca/run/titan/process.titan Exec/SCIENCE/urca/run/titan/titan.run commit 014b2b06edd76c0914e32f9856bb7768228dbe32 Author: dwillcox Date: Thu Apr 11 03:18:45 2019 -0400 Add inputs for the 1024**3 problem on Titan. Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/inputs_3d_1lev.5120 commit 967f8bf293193bdfc79ab1d3738d3d3075cb0cef Author: Donald E. Willcox Date: Wed Apr 10 17:21:10 2019 -0700 Rearrange urca analysis scripts into a python package UrcaAnalysis. Exec/SCIENCE/urca/analysis/UrcaAnalysis/FileToolkit.py Exec/SCIENCE/urca/analysis/UrcaAnalysis/__init__.py Exec/SCIENCE/urca/analysis/UrcaAnalysis/yt_urca_fields.py Exec/SCIENCE/urca/analysis/scripts/ffmpeg_make_mp4 Exec/SCIENCE/urca/analysis/scripts/lineout-field Exec/SCIENCE/urca/analysis/scripts/lineout-field-testing Exec/SCIENCE/urca/analysis/scripts/mk_gradpi_slices Exec/SCIENCE/urca/analysis/scripts/plot-diags Exec/SCIENCE/urca/analysis/scripts/plot-edot Exec/SCIENCE/urca/analysis/scripts/plot-neutrino-spectrum Exec/SCIENCE/urca/analysis/scripts/plot_fconv_slopes Exec/SCIENCE/urca/analysis/scripts/power-spectrum Exec/SCIENCE/urca/analysis/scripts/profile-field Exec/SCIENCE/urca/analysis/scripts/slice-convgrad Exec/SCIENCE/urca/analysis/scripts/slice-enucdot Exec/SCIENCE/urca/analysis/scripts/slice-field Exec/SCIENCE/urca/analysis/scripts/slice-vel Exec/SCIENCE/urca/analysis/scripts/sort-strings Exec/SCIENCE/urca/analysis/scripts/streamlines Exec/SCIENCE/urca/analysis/scripts/sum-field Exec/SCIENCE/urca/analysis/scripts/track-enucdot-profile Exec/SCIENCE/urca/analysis/scripts/urca-quick-post Exec/SCIENCE/urca/analysis/scripts/urca23-quick-post Exec/SCIENCE/urca/analysis/scripts/volume-plot-circum_vel Exec/SCIENCE/urca/analysis/scripts/volume-plot-enucdot Exec/SCIENCE/urca/analysis/scripts/volume-plot-field Exec/SCIENCE/urca/analysis/scripts/volume-plot-rad_vel Exec/SCIENCE/urca/analysis/scripts/volume-plot-testing Exec/SCIENCE/urca/analysis/scripts/volume-plot-ye Exec/SCIENCE/urca/analysis/setup.py commit 9d8899def926465f771d7fe6e3f4acae532011a3 Author: Donald E. Willcox Date: Wed Apr 10 17:19:10 2019 -0700 Use 5120 points instead of 10240 in this initial model so drdxfac=5. Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/WD_urca_nuc_M-1.0_rc4.5e9_Tc6.0e8_speceq.hse.10240 Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/WD_urca_nuc_M-1.0_rc4.5e9_Tc6.0e8_speceq.hse.10240.report Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/WD_urca_nuc_M-1.0_rc4.5e9_Tc6.0e8_speceq.hse.5120 Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/WD_urca_nuc_M-1.0_rc4.5e9_Tc6.0e8_speceq.hse.5120.report Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/inputs_3d_1lev.5120 Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/inputs_urca_model_equilibrium.5120 commit f1749c5daf4704e0df699ee054165387beae2334 Author: Andy Nonaka Date: Wed Apr 10 17:07:56 2019 -0700 fix MLMG boundary condition types. For phi in the projection linear solves, outflow is Dirichlet, everything else physical is Neumann Source/MaestroMacProj.cpp Source/MaestroNodalProj.cpp commit 6da0a458c2634930550bb0f449e0d7393503eb9d Author: Andy Nonaka Date: Wed Apr 10 17:07:34 2019 -0700 fix boundary conditions - inflow on bottom, outflow on top Exec/TEST_PROBLEMS/mach_jet/inputs_2d commit 6b0337353c4fe64ae1da8a47e259ba5faaa0948a Author: Donald E. Willcox Date: Wed Apr 10 12:36:34 2019 -0700 Add urca analysis tools, formerly in MAESTRO/Util/postprocessing/urca-tools. Some of the f90 may require FBoxLib so WIP. Exec/SCIENCE/urca/analysis/.ipynb_checkpoints/Plot-Thermo-Slopes-checkpoint.ipynb Exec/SCIENCE/urca/analysis/FileToolkit.py Exec/SCIENCE/urca/analysis/GNUmakefile Exec/SCIENCE/urca/analysis/_parameters Exec/SCIENCE/urca/analysis/fad_excess.f90 Exec/SCIENCE/urca/analysis/fconv_radial.f90 Exec/SCIENCE/urca/analysis/fconv_slopes.f90 Exec/SCIENCE/urca/analysis/ffmpeg_make_mp4.py Exec/SCIENCE/urca/analysis/fneutrinos.f90 Exec/SCIENCE/urca/analysis/frates.f90 Exec/SCIENCE/urca/analysis/furcashell.f90 Exec/SCIENCE/urca/analysis/lineout-field-testing.py Exec/SCIENCE/urca/analysis/lineout-field.py Exec/SCIENCE/urca/analysis/mk_gradpi_slices.sh Exec/SCIENCE/urca/analysis/plot-diags.py Exec/SCIENCE/urca/analysis/plot-edot.py Exec/SCIENCE/urca/analysis/plot-neutrino-spectrum.py Exec/SCIENCE/urca/analysis/plot_fconv_slopes.py Exec/SCIENCE/urca/analysis/power_spectrum.py Exec/SCIENCE/urca/analysis/probin.f90 Exec/SCIENCE/urca/analysis/profile-field.py Exec/SCIENCE/urca/analysis/slice-convgrad.py Exec/SCIENCE/urca/analysis/slice-enucdot.py Exec/SCIENCE/urca/analysis/slice-field.py Exec/SCIENCE/urca/analysis/slice-vel.py Exec/SCIENCE/urca/analysis/sort-strings.py Exec/SCIENCE/urca/analysis/streamlines.py Exec/SCIENCE/urca/analysis/sum-field.py Exec/SCIENCE/urca/analysis/track-enucdot-profile.py Exec/SCIENCE/urca/analysis/urca-quick-post.sh Exec/SCIENCE/urca/analysis/urca23-quick-post.sh Exec/SCIENCE/urca/analysis/volume-plot-circum_vel.py Exec/SCIENCE/urca/analysis/volume-plot-enucdot.py Exec/SCIENCE/urca/analysis/volume-plot-field.py Exec/SCIENCE/urca/analysis/volume-plot-rad_vel.py Exec/SCIENCE/urca/analysis/volume-plot-testing.py Exec/SCIENCE/urca/analysis/volume-plot-ye.py Exec/SCIENCE/urca/analysis/yt_urca_fields.py commit ef242234cf8112aef9d9c0545684915aefe6ae4f Author: Andy Nonaka Date: Wed Apr 10 12:36:15 2019 -0700 forgot to copy base state from s0_init and p0_init to s0 and p0 Exec/TEST_PROBLEMS/mach_jet/base_state.f90 commit babf64a9ec27647f1729820d0f87ae47bab747cf Author: Alice Harpole Date: Wed Apr 10 11:38:31 2019 -0400 missing icomp's in bc_fill_nd.F90 Source/Src_nd/bc_fill_nd.F90 commit 2c9dc49a067579093a59ffd000beb5ea632fe9d8 Author: Alice Harpole Date: Wed Apr 10 11:33:18 2019 -0400 Added BndryFuncArrayMaestro, a class which inherits from AMReX's BndryFuncArray but passes the MultiFab's component to the Fortran boundary function Exec/TEST_PROBLEMS/mach_jet/AMReX_PhysBCFunct.H Exec/TEST_PROBLEMS/mach_jet/AMReX_PhysBCFunct.cpp Exec/TEST_PROBLEMS/mach_jet/bc_fill_nd.F90 Source/MaestroFillData.cpp Source/PhysBCFunctMaestro.H commit b337acfa9d393d783b9df372a8d22632989c45b9 Author: Alice Harpole Date: Wed Apr 10 10:50:57 2019 -0400 phifill -> scalarfill, bool is_vel -> int variable_type Exec/TEST_PROBLEMS/mach_jet/bc_fill_nd.F90 Source/Maestro.H Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvection.cpp Source/MaestroDiag.cpp Source/MaestroFill3dData.cpp Source/MaestroFillData.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp Source/MaestroRegrid.cpp Source/Maestro_F.H Source/PhysBCFunctMaestro.H Source/Src_nd/bc_fill_nd.F90 commit 13da06e729ea45fe8523bfd25531a8c306bd0e33 Author: Alice Harpole Date: Tue Apr 9 17:13:32 2019 -0400 adds fill_scalar_ext_bc and fill_vel_ext_bc routines which fill the scalar and velocity exterior boundaries Exec/TEST_PROBLEMS/mach_jet/bc_fill_nd.F90 Source/Src_nd/bc_fill_nd.F90 commit 921324abb403faa837b4330651e48fd61c5c1616 Author: Alice Harpole Date: Tue Apr 9 16:09:08 2019 -0400 added fill_ext_bc routine to bc_fill_nd.F90 for filling the exterior boundaries Source/Src_nd/AMReX_filcc_mod.F90 Source/Src_nd/bc_fill_nd.F90 commit 9a7dbbaa3c849796849b3a81fdb08fc79fa0c093 Author: Alice Harpole Date: Tue Apr 9 14:09:37 2019 -0400 add is_vel flag to functions that apply physical boundaries Exec/TEST_PROBLEMS/mach_jet/bc_fill_nd.F90 Source/Maestro.H Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvection.cpp Source/MaestroDiag.cpp Source/MaestroFill3dData.cpp Source/MaestroFillData.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp Source/MaestroRegrid.cpp commit 5bdefbef5adaa36ccd974cbe8365a1b73f62de38 Author: Alice Harpole Date: Tue Apr 9 13:11:12 2019 -0400 added other mach_jet files Exec/TEST_PROBLEMS/mach_jet/bc_fill_nd.F90 Exec/TEST_PROBLEMS/mach_jet/initdata.f90 Exec/TEST_PROBLEMS/mach_jet/inputs_2d Exec/TEST_PROBLEMS/mach_jet/inputs_2d_stratified commit f189300bb781164cc8cc58ec3a6b57e86fcf23ef Author: Alice Harpole Date: Tue Apr 9 13:10:22 2019 -0400 added custom AMReX functions Exec/TEST_PROBLEMS/mach_jet/AMReX_PhysBCFunct.H Exec/TEST_PROBLEMS/mach_jet/AMReX_PhysBCFunct.cpp commit a6ad38c74ffd412e4486bbdf853ca0c5b233ee43 Author: Alice Harpole Date: Tue Apr 9 13:09:29 2019 -0400 add velfill function Source/Maestro.H Source/MaestroFillData.cpp Source/Maestro_F.H Source/Src_nd/bc_fill_nd.F90 commit 9e71eda28302daa9157fafeb5018e54a7182a091 Author: Alice Harpole Date: Tue Apr 9 11:59:54 2019 -0400 synced up AMReX version of fillcc_mod.F90 Source/MaestroFillData.cpp Source/Src_nd/AMReX_filcc_mod.F90 commit d944153cc03a3086feb50ecc8d4270a1b0594087 Author: Donald E. Willcox Date: Mon Apr 8 23:41:22 2019 -0700 Add preliminary urca setup with model. Exec/SCIENCE/urca/GNUmakefile Exec/SCIENCE/urca/Make.package Exec/SCIENCE/urca/_parameters Exec/SCIENCE/urca/initdata.f90 Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/WD_urca_nuc_M-1.0_rc4.5e9_Tc6.0e8_speceq.hse.10240 Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/WD_urca_nuc_M-1.0_rc4.5e9_Tc6.0e8_speceq.hse.10240.report Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/inputs_3d_1lev.10240 Exec/SCIENCE/urca/models/rhoc-4.5e9_Tc-6.0e8_Mconv-1.0/inputs_urca-hot_equilibrium.10240 Exec/SCIENCE/urca/tagging.F90 commit 19280f102000a1a31def9d45290a799436798d89 Author: Alice Harpole Date: Mon Apr 8 19:18:11 2019 -0400 need to find some way to differentiate between velocity and scalar components when passing component index to phifill Exec/TEST_PROBLEMS/mach_jet/base_state.f90 Exec/TEST_PROBLEMS/mach_jet/inlet_bc.f90 commit 526b83a9da157d99fe35af2009c49c16ca178e94 Author: Alice Harpole Date: Mon Apr 8 13:42:32 2019 -0400 adding mach_jet problem Exec/TEST_PROBLEMS/mach_jet/GNUmakefile Exec/TEST_PROBLEMS/mach_jet/Make.package Exec/TEST_PROBLEMS/mach_jet/_parameters Exec/TEST_PROBLEMS/mach_jet/base_state.f90 Exec/TEST_PROBLEMS/mach_jet/inlet_bc.f90 Source/Maestro_F.H commit 4dee98c3414d0611b8644f2f5733b70d860ba667 Author: Doreen Fan Date: Fri Apr 5 13:02:40 2019 -0700 bug fix: need to check if do_smallscale=T Source/MaestroSetup.cpp commit 96d926ffffb1396c014705ff7314abe37c082367 Author: Alice Harpole Date: Thu Apr 4 13:29:51 2019 -0400 fix parse_maestro_params.py so it can deal with default arguments which are strings containing spaces Source/param/parse_maestro_params.py commit 880ec10f4da52343d7f0b793f56d753d9643ed84 Author: Jonathan Thurgood <42877905+JOThurgood@users.noreply.github.com> Date: Thu Apr 4 18:20:31 2019 +0100 add check for do_smallscale and make available to fortran (#53) Adds a check in `MaestroSetup.cpp` to make sure that if `do_smallscale` is set, other flags that may conflict are also set to valid values. Also makes `do_smallscale` available to Fortran routines. * make do_smallscale available to fortran * remove misleading comment * if do_smallscale, check beta0_type =3 and evolve_base_state=F also or abort * move from MaestroInit to MaestroSetup * manually fix header files Source/MaestroAdvance.cpp Source/MaestroSetup.cpp Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit e4fe675f19f93fdef9bc85cd9330eb22b45cb8c8 Author: Alice Harpole Date: Thu Apr 4 12:19:36 2019 -0400 set processor num at MultiFab level rather than iterate over Fabs Source/MaestroPlot.cpp commit 08f6d834cb60bbb3064f0fc9e72f427683f93d7d Author: Alice Harpole Date: Thu Apr 4 11:59:34 2019 -0400 added momentum, entropy, entropypert and processor_number to plotfile Source/Maestro.H Source/MaestroEvolve.cpp Source/MaestroPlot.cpp Source/Maestro_F.H Source/Src_nd/make_plot_variables.F90 commit ac72354afdfb3fb8039d9996a9bd2efdf0b1f1b2 Author: Alice Harpole Date: Wed Apr 3 14:31:55 2019 -0400 remove filelists sphinx_docs/source/Src_nd_files.rst sphinx_docs/source/param_includes_files.rst commit 5baebfc27664e399e978b2a200041c99463cbde5 Author: Alice Harpole Date: Wed Apr 3 14:28:49 2019 -0400 fixed some of the formatting in the docs sphinx_docs/source/Src_nd_files.rst sphinx_docs/source/beta0.rst sphinx_docs/source/common_parameters.rst sphinx_docs/source/enthalpy.rst sphinx_docs/source/eos_notes.rst sphinx_docs/source/eta.rst sphinx_docs/source/flowchart.rst sphinx_docs/source/initial_models.rst sphinx_docs/source/lo_density.rst sphinx_docs/source/param_includes_files.rst sphinx_docs/source/pert.rst sphinx_docs/source/planar_invsq_basestate.rst sphinx_docs/source/sdc.rst sphinx_docs/source/spherical_basestate.rst sphinx_docs/source/volume_discrepancy.rst commit f727d4d565342a055d6e763acdd233e9a1fa6ee0 Author: Alice Harpole Date: Wed Apr 3 11:20:30 2019 -0400 stop plotfiles from being printed at the end if plot_int or small_plot_int <= 0 Source/MaestroEvolve.cpp commit 86d268a3892c288777139d8751df9e4e8712f30d Author: Alice Harpole Date: Tue Apr 2 10:15:20 2019 -0400 updated travis badge Badge was showing that tests were failing as it needed updating from travis-ci.org -> travis-ci.com README.md commit 5d4566a416f140f4abb20265cda0ff943942d932 Merge: 668117b2 537a31f6 Author: Doreen Fan Date: Mon Apr 1 18:54:38 2019 -0700 Merge branch 'master' into development commit 537a31f617b35be81508099d2bcc63d7b2f2a946 Author: Doreen Fan Date: Mon Apr 1 18:53:01 2019 -0700 April 2019 release notes RELEASE_NOTES commit 668117b2ddc61634b5eb6e179080d64fbcd10973 Merge: 9780ac67 6718e26f Author: Andy Nonaka Date: Tue Mar 26 16:55:08 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 9780ac67e6292682ef36bfdb3d50032ad6188c52 Author: Andy Nonaka Date: Tue Mar 26 16:54:47 2019 -0700 new 2 level test Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.256.2levels commit 6718e26fc94473058fcc8343100ce1349b1fb965 Author: Duoming Fan Date: Tue Mar 26 12:44:29 2019 -0700 same w0 bugfix for uneven base state spacing Source/MaestroAdvanceIrreg.cpp commit e5525a93028aee95a31f9afa11a16287dc2dd5a3 Author: Andy Nonaka Date: Tue Mar 26 09:45:01 2019 -0700 bugfix... only add/subtract w0 to velocites after/before projections if evolve_base_state=T Source/MaestroAdvanceAvg.cpp commit d117a779d37579ca04933ea5083d521a2fb25401 Author: Donald E. Willcox Date: Mon Mar 25 17:34:39 2019 -0700 Enable burn retries. Exec/SCIENCE/rotating_star/inputs_3d_C commit 74afad0dc0496129137862926b937a307df0ab12 Author: Doreen Fan Date: Mon Mar 25 16:57:56 2019 -0700 more input files for longer science runs Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.256.avgbase Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.256.exactbase commit a788a29a93737d53c36764e98bbb8fcef4546fb7 Author: Donald E. Willcox Date: Mon Mar 25 14:59:17 2019 -0700 Allocate and initialize eos type module variables in eos_init. Microphysics/EOS/eos.F90 commit c686592865a2c819f3de1d2ec7a4347663b178a9 Author: Donald E. Willcox Date: Mon Mar 25 14:02:44 2019 -0700 Update eos type to match the interface in Microphysics. Microphysics/EOS/Make.package Microphysics/EOS/eos_type.F90 commit c3cff4a57676656f1948d544b99b2d8e282241b6 Author: Andy Nonaka Date: Fri Mar 22 09:55:54 2019 -0700 bugfix - for any MFIter routines that operate on face, edge, or nodal data, you cannot tile these routines if the routine is *updating* (as opposed to computing and setting a value) the values, since the tileboxes are defined with respect to cell-centers. You get double counting on faces. For *writing* to data (instead of *updating*), this is ok since both threads are writing the same value. so addw0 and mult_faces_by_beta fall into the routine of updating variables (add stuff to, or multiply existing values by a number), so these operations were being done twice at some edges For these routines I removed tiling and put OpenMP statements directly into the F90 Source/MaestroFill3dData.cpp Source/MaestroMacProj.cpp Source/Src_nd/fill_3d_data.F90 Source/Src_nd/mac_solver.F90 commit 336c39d857e27a36fcee562966c5521b8bd4655d Author: Andy Nonaka Date: Fri Mar 22 09:53:59 2019 -0700 tileBox -> validBox since not using tiling in this routine Source/MaestroMakeEta.cpp commit be49fd562ff8181e016424529eed073f60dcc2d7 Author: Alice Harpole Date: Thu Mar 21 14:22:05 2019 -0400 update rotating_star files Exec/SCIENCE/rotating_star/GNUmakefile Exec/SCIENCE/rotating_star/initdata.F90 Exec/SCIENCE/rotating_star/initdata.f90 Exec/SCIENCE/rotating_star/inputs_3d_C commit 285e692219a90fc637c0e843af5d01ba08fec0b6 Merge: ddd9f9bc 0a621a36 Author: Alice Harpole Date: Thu Mar 21 13:35:44 2019 -0400 merge conflicts commit ddd9f9bccb16ad701bfaaa2b5bbbeaa8454ef4fd Author: Alice Harpole Date: Thu Mar 21 13:35:22 2019 -0400 added 6400 initial model Exec/SCIENCE/rotating_star/18m_500_s_rot_b_eq_1.hse.6400 commit 0a621a36d1868003c692fe0c3b3bba281b763e02 Author: Michael Zingale Date: Thu Mar 21 13:12:40 2019 -0400 new model at different resolution Exec/SCIENCE/rotating_star/18m_500_s_rot_b_eq_1.hse.6400 commit b0a39da37c854d9bd47a5a9beadde4b96d714a5b Author: Andy Nonaka Date: Wed Mar 20 19:13:41 2019 -0700 added a local variable "split_projection" (default true) to the new temporal algorithm with even dr to allow for a comparison between splitting out the w0 computation Source/MaestroAdvanceAvg.cpp commit e402b61c4883b9cf15412edda4609fb1082a7ceb Author: Andy Nonaka Date: Wed Mar 20 18:21:54 2019 -0700 1d base state routine cumulative timer Source/MaestroAdvance.cpp commit 23a4b3dca3eb2da03ef01aacad68e65c7dcfbbd8 Author: Doreen Fan Date: Wed Mar 20 17:54:16 2019 -0700 more openmp Source/MaestroAdvection.cpp Source/MaestroDt.cpp Source/MaestroFill3dData.cpp Source/MaestroMacProj.cpp Source/MaestroMakeEta.cpp Source/Src_nd/make_edge_scal.F90 Source/Src_nd/mkutrans.F90 Source/Src_nd/ppm.F90 Source/Src_nd/velpred.F90 commit b906b8aab7f1e7f703742e2df03e09952290f123 Author: Andy Nonaka Date: Wed Mar 20 15:15:13 2019 -0700 added timers for full profiling Source/Src_nd/advect_base.F90 Source/Src_nd/base_state_geometry.f90 Source/Src_nd/cell_to_edge.f90 Source/Src_nd/enforce_HSE.f90 Source/Src_nd/make_beta0.f90 Source/Src_nd/make_edge_state.f90 Source/Src_nd/make_grav.f90 Source/Src_nd/make_psi.F90 Source/Src_nd/make_w0.f90 commit ad84b79fb591719f7317c92ec8c8b4170529e8bf Merge: e41686e4 3f9a4082 Author: Andy Nonaka Date: Wed Mar 20 12:22:56 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit e41686e4951d23a92a71eb364715de73b6b0cf4b Author: Andy Nonaka Date: Wed Mar 20 12:22:33 2019 -0700 fix timers so the sum of each timer time is broadcast after performing the max Source/MaestroAdvance.cpp commit 3f9a4082d2743d1abcfd0f243b4efd00fa4692f1 Author: Alice Harpole Date: Wed Mar 20 09:46:26 2019 -0400 added external parameters to jobinfo file Source/MaestroPlot.cpp Source/Maestro_F.H Source/param/runtime.probin.template commit 1108b26e78255a30a45fdaf49636c7414e00f9af Merge: c88ff41f e52566cc Author: Alice Harpole Date: Wed Mar 20 09:39:01 2019 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit e52566cc3be62d3f4d1f61e214044dba7bbbf336 Author: Doreen Fan Date: Mon Mar 18 17:16:49 2019 -0700 Use max block size of 32 for multilevel testing on 512^3 grids or else multigrid solve does not converge. Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.512.3levels Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.512.avgbase.3levels commit d5e3e5f5a04c409ae971551653385c214eef9ed4 Author: Andy Nonaka Date: Mon Mar 18 12:33:21 2019 -0700 added Diag timing info Source/MaestroEvolve.cpp commit 264687241d8dac052374f649bb3c55126f888c07 Merge: 040d4378 492ed0f6 Author: Andy Nonaka Date: Mon Mar 18 11:18:49 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 040d43784fd0123648d05d59973729ba42f1049f Author: Andy Nonaka Date: Mon Mar 18 11:18:04 2019 -0700 fix timers for the original algorithm to look like the classic MAESTRO timers (for direct comparison). Only problem is the diagnostic stuff right now, which is no included in "misc_time" in MAESTROeX report Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroEvolve.cpp Source/MaestroInit.cpp commit 492ed0f61244b9483a0783176ba54afc3f453ff1 Author: Donald E. Willcox Date: Fri Mar 15 21:43:40 2019 -0700 Re-enable tiling in initdata after fixing race condition. Exec/UNIT_TESTS/test_react/MaestroInit.cpp Exec/UNIT_TESTS/test_react/initdata.f90 commit e7553cd0a1aff7c7efce0ceeb0101073241938c6 Author: Donald E. Willcox Date: Fri Mar 15 21:23:51 2019 -0700 Disable tiling when initializing test_react to avoid NaNs. Exec/UNIT_TESTS/test_react/MaestroInit.cpp commit 70b9c31042a69096941b077813a8bbf76e89fc87 Author: Andy Nonaka Date: Fri Mar 15 17:03:31 2019 -0700 omp Source/Src_nd/make_eta.F90 commit 613c7a8818184d619dd10d2ad5646a32ee13a53c Author: Andy Nonaka Date: Fri Mar 15 16:55:01 2019 -0700 fix omp statement Source/Src_nd/average.f90 commit 9ada785fa0dbc54d3389ae239db77cf9204f2f04 Merge: 63badf42 1f7320a7 Author: Andy Nonaka Date: Fri Mar 15 16:53:22 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 63badf422bb7dee53b437632980b34de50b80314 Author: Andy Nonaka Date: Fri Mar 15 16:53:12 2019 -0700 openMP Source/Src_nd/average.f90 Source/Src_nd/make_w0.f90 commit 1f7320a78846c7fdef2260a7832e8863870c16c3 Author: Donald E. Willcox Date: Fri Mar 15 11:23:17 2019 -0700 cleanup makefile Exec/UNIT_TESTS/test_react/GNUmakefile commit f16ee012b3b8adebb478423cc29471d6173f8566 Author: Donald E. Willcox Date: Fri Mar 15 11:23:04 2019 -0700 Fix compilation for test_react unit test. Exec/UNIT_TESTS/test_react/MaestroPlot.cpp Exec/UNIT_TESTS/test_react/make_heating.F90 Exec/UNIT_TESTS/test_react/problem_functions.f90 commit c88ff41f690a28e3b142ab5afef07cec848da84e Author: Alice Harpole Date: Fri Mar 15 12:48:32 2019 -0400 saving changes Exec/SCIENCE/rotating_star/initdata.f90 commit 93662097768d6950e0333855182e1e6042c7bdde Author: Donald E. Willcox Date: Thu Mar 14 17:36:51 2019 -0700 fix compilation for ECSN problem. Exec/SCIENCE/ecsn/GNUmakefile Exec/SCIENCE/ecsn/initdata.f90 commit af31a9abf07d7a137155ae3d4aa218862c0c9086 Author: Andy Nonaka Date: Thu Mar 14 17:13:56 2019 -0700 more scaling...now up to 13,824 grids Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.1536 Exec/SCIENCE/wdconvect/model_files/kepler_new_6.25e8.hybrid.hse.7680 commit 0ac743c50fead8b64903c50823fd164c85321313 Author: Andy Nonaka Date: Thu Mar 14 15:15:42 2019 -0700 larger test. scaling up!! Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.1280 Exec/SCIENCE/wdconvect/model_files/kepler_new_6.25e8.hybrid.hse.6400 commit 178ff7284177b8a6073347eb8accc81a7b43376b Merge: 4f7d8574 228a052b Author: Donald E. Willcox Date: Thu Mar 14 13:46:20 2019 -0700 Merge branch 'development' of github.com:AMReX-Astro/MAESTROex into development commit 4f7d85740982b4f8d357614bd23add623714e2f0 Author: Donald E. Willcox Date: Thu Mar 14 13:46:12 2019 -0700 Revert "Delete runtime.probin.template" This reverts commit a9288ce2703541f9556ff372b48dd02d4cdebeb8. Source/param/runtime.probin.template commit 228a052b08177c96fde79875bb70bbe6151081ef Merge: 21d5a72c 307781ff Author: Andy Nonaka Date: Thu Mar 14 13:42:37 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 21d5a72ccc8026964358cb8020a3187993447084 Author: Andy Nonaka Date: Thu Mar 14 13:42:27 2019 -0700 timing info Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp commit 307781ff82352749e91bbd79240e29116b29080f Author: Donald E. Willcox Date: Thu Mar 14 13:39:40 2019 -0700 Deleted broken symlinks and rearranged files. Exec/SCIENCE/ecsn/20f-20ne_betadecay.dat Exec/SCIENCE/ecsn/20f-20o_electroncapture.dat Exec/SCIENCE/ecsn/20ne-20f_electroncapture.dat Exec/SCIENCE/ecsn/20o-20f_betadecay.dat Exec/SCIENCE/ecsn/inputs_3d_kepler Exec/SCIENCE/ecsn/kepler_xinlong_ONe6040-final.hse.5120 Exec/SCIENCE/ecsn/reaclib_rate_metadata.dat Exec/SCIENCE/wd/diag_temp.out commit 25e39af1188a43621d67ea45a5a91193be3ed3c2 Merge: 84353e3b a9288ce2 Author: Donald E. Willcox Date: Thu Mar 14 13:36:54 2019 -0700 Merge pull request #47 from sailoridy/development rename wd into ecsn commit a9288ce2703541f9556ff372b48dd02d4cdebeb8 Author: Xinlong <42697364+sailoridy@users.noreply.github.com> Date: Thu Mar 14 15:54:56 2019 -0400 Delete runtime.probin.template Source/param/runtime.probin.template commit adf6b09686ae0db4facb2520040d13432202fe82 Merge: a0832128 ad0aa8b8 Author: Xinlong Li Date: Thu Mar 14 12:51:48 2019 -0700 rename wd to ecsn commit a0832128413282b67e5e0e2f6ad55d4b6beca45f Author: Xinlong Li Date: Thu Mar 14 12:50:58 2019 -0700 rename wd to ecsn Exec/SCIENCE/ecsn/20f-20ne_betadecay.dat Exec/SCIENCE/ecsn/20f-20o_electroncapture.dat Exec/SCIENCE/ecsn/20ne-20f_electroncapture.dat Exec/SCIENCE/ecsn/20o-20f_betadecay.dat Exec/SCIENCE/ecsn/GNUmakefile Exec/SCIENCE/ecsn/Make.package Exec/SCIENCE/ecsn/_parameters Exec/SCIENCE/ecsn/initdata.f90 Exec/SCIENCE/ecsn/inputs_3d_C.128 Exec/SCIENCE/ecsn/kepler_xinlong_ONe6040-final.hse.1280 Exec/SCIENCE/ecsn/model.orig Exec/SCIENCE/ecsn/model.uniform Exec/SCIENCE/ecsn/probin_regression Exec/SCIENCE/ecsn/reaclib_rate_metadata.dat Exec/SCIENCE/ecsn/tagging.F90 Exec/SCIENCE/wd/20f-20o.dat Exec/SCIENCE/wd/20ne-20f.dat Exec/SCIENCE/wd/diag_temp.out Exec/SCIENCE/wd/inputs_3d_C Exec/SCIENCE/wd/inputs_3d_C.128.2levels Exec/SCIENCE/wd/inputs_3d_C.128.avgbase.dr Exec/SCIENCE/wd/inputs_3d_C.128.avgbase.dx Exec/SCIENCE/wd/inputs_3d_C.128.exactbase Exec/SCIENCE/wd/inputs_3d_C.64 Exec/SCIENCE/wd/inputs_3d_C.64.exactbase Exec/SCIENCE/wd/inputs_3d_regression Exec/SCIENCE/wd/inputs_omp_3d_regression Source/param/runtime.probin.template commit 84353e3bab9f0600f7eee78bc700d24a865764f8 Author: Doreen Fan Date: Thu Mar 14 11:28:24 2019 -0700 Multilevel setup with 3 levels of AMR Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.256.3levels Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.512.3levels commit 108c533a3e95be9ef939caca16b7f1cd8de3c8f5 Author: Andy Nonaka Date: Thu Mar 14 11:04:38 2019 -0700 timing output of mac/nodal/reactions in standard output Source/MaestroAdvance.cpp commit 9a2b112a693ea840a9a3457df2bba05f03c04c4f Author: Doreen Fan Date: Wed Mar 13 16:30:50 2019 -0700 Added diagnostics for future science runs. Now outputs nuclear generation data in diag_enuc.out, and velocity data in diag_vel.out Source/Maestro.H Source/MaestroDiag.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/diag.F90 commit 3c06cc077869b530c52dacef2d2eecf60da908c4 Merge: 63e55d42 ca7349eb Author: Andy Nonaka Date: Wed Mar 13 14:51:25 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 63e55d423bb7ff1605620addaccf7beb2b966688 Author: Andy Nonaka Date: Wed Mar 13 14:50:35 2019 -0700 3d setup with 1, 2 3 levels. time per timestep: 72, 14, and 8 seconds moved the bubble and changed the bubble with; will update 3d regression tests Exec/TEST_PROBLEMS/reacting_bubble/initdata.f90 Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C.2levels Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C.3levels commit ca7349eb24253de05777c518c26b0c81149d50e9 Author: Andy Nonaka Date: Wed Mar 13 11:55:20 2019 -0700 change enthalpy forcing dp0/dt term to be (p0^{n+1,*} - p0^n) / dt in the predictor Source/MaestroAdvanceIrreg.cpp commit b7ac6ebf148a21971f9abfad9fef978b55732a68 Author: Andy Nonaka Date: Wed Mar 13 11:48:42 2019 -0700 change enthalpy forcing dp0/dt term to be (p0^{n+1,*} - p0^n) / dt in the predictor Source/MaestroAdvanceAvg.cpp commit 2b6b75a3ea4b5f66912ce1aab06b7facc58320ec Author: Doreen Fan Date: Tue Mar 12 14:13:10 2019 -0700 Store dp/dt term in psi for enthalpy advance. Original psi is not used anywhere in the new temporal scheme for spherical problems. Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp commit af53b736a5448100f96e64e7823fc45caef70ba4 Merge: ffb9b42b 48389d22 Author: Doreen Fan Date: Mon Mar 11 17:44:31 2019 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit ffb9b42b3b2e1553302c23779810666477ad52cd Author: Doreen Fan Date: Mon Mar 11 17:29:46 2019 -0700 Correct discretization of derivative terms in make_w0 for uneven base state spacing. Also fixed edge etarho interpolation. Source/MaestroMakeEta.cpp Source/Src_nd/make_w0.f90 commit bb248756d4970f887bc2954e5b286580ff0631b5 Author: Doreen Fan Date: Mon Mar 11 17:27:51 2019 -0700 Same bug fix as for AdvanceAvg subroutine: need to subtract w0mac from umac before mac projection Source/MaestroAdvanceIrreg.cpp commit 30c8b1a7523d0961655f2928633fd07382bf3b2a Author: Doreen Fan Date: Mon Mar 11 17:09:04 2019 -0700 Bug fix: need to subtract w0mac from umac before mac projection Source/MaestroAdvanceAvg.cpp commit 48389d22428d9ef81a9604ccb1a548a0e3e6d452 Author: Andy Nonaka Date: Mon Mar 11 17:08:25 2019 -0700 turn off make_w0_spherical_simple for now (and revert to the original make_w0_spherical) Source/MaestroAdvanceAvg.cpp Source/Src_nd/make_w0.f90 commit a1055cad8d1de04e9c66403a9bd4df9efc135f7d Author: Andy Nonaka Date: Mon Mar 11 14:17:47 2019 -0700 forgot dr factor Source/Src_nd/make_w0.f90 commit 8144958e400ecc88e61ee536255bb432cc28a426 Author: Andy Nonaka Date: Mon Mar 11 12:53:13 2019 -0700 sign error Source/Src_nd/make_w0.f90 commit 79c7284cb7d1e7569137eec592e46dd6f1e83159 Merge: fbb12db9 7857708f Author: Andy Nonaka Date: Mon Mar 11 12:31:48 2019 -0700 Merge branch 'ebs_test' into development commit 7857708faf9649c38bb20bf84b821ff78f79a4f9 Author: Andy Nonaka Date: Mon Mar 11 12:25:57 2019 -0700 first attempt at simplified make_w0_spherical for new temporal integrator Source/MaestroAdvanceAvg.cpp Source/Src_nd/make_w0.f90 Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit f5ac1bc14fd0bf1971136597b94eeace8594c1bd Author: Andy Nonaka Date: Mon Mar 11 12:21:59 2019 -0700 index fix; now computing grav_edge to the nr_fine face Source/Src_nd/make_grav.f90 commit fbb12db9b1335fe60464e1762a4eb4cd4f148653 Author: Alice Harpole Date: Mon Mar 11 12:45:22 2019 -0400 Small plotfiles (#44) Adds the ability to produce small plotfiles consisting of a subset of the available plot variables Exec/SCIENCE/rotating_star/initdata.F90 Exec/SCIENCE/rotating_star/inputs_3d_C Exec/SCIENCE/rotating_star/tagging.F90 Source/Maestro.H Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/MaestroPlot.cpp Source/MaestroRegrid.cpp Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H sphinx_docs/source/visualization.rst commit e65930b65e83508905962c0bb6d3255e1d66ed27 Author: Alice Harpole Date: Mon Mar 11 12:02:50 2019 -0400 use enum type with -ve values to flag setup plots (#45) This uses an enum type with -ve values to tell WritePlotFile to generate plots during setup. Source/Maestro.H Source/MaestroInit.cpp Source/MaestroPlot.cpp commit b204657445a4aaf2b5391e383f337d3ee0a1d721 Author: Alice Harpole Date: Mon Mar 11 12:01:35 2019 -0400 plot abar (#46) Adds a routine to plot abar - this will be helpful for the small plotfiles where we don't want to output the mass fractions of all the species. Source/Maestro.H Source/MaestroPlot.cpp Source/Maestro_F.H Source/Src_nd/make_plot_variables.F90 commit 8cb7aa2431fd6b035d3c3f77523cc92cbd03bf2a Author: Doreen Fan Date: Fri Mar 8 22:45:16 2019 -0800 Fixed if statement for computing spherical w0. Also added w0 output and w0_interp_type options for uneven base state spacing. Source/MaestroPlot.cpp Source/Src_nd/fill_3d_data.F90 Source/Src_nd/make_w0.f90 commit 7a498b00a734d116234373e838898510cb0448d7 Author: Doreen Fan Date: Fri Mar 8 18:26:23 2019 -0800 Apply new temporal algorithm with velocity splitting to uneven base state spacing Source/MaestroAdvanceIrreg.cpp Source/MaestroMakeEta.cpp Source/Src_nd/make_w0.f90 commit ed06471b6d16c77bf36c6ddf10d5b3f6d031295d Author: Doreen Fan Date: Fri Mar 8 14:29:52 2019 -0800 should also subtract w0 from unew before nodalproj Source/MaestroAdvanceAvg.cpp commit db7533ad288c5bf198d12664bc3daac278d37b82 Author: Doreen Fan Date: Fri Mar 8 13:03:16 2019 -0800 Change new temporal scheme by solving each projection solve with perturbational velocity instead of full velocity Source/MaestroAdvanceAvg.cpp commit c921812109dc2a1063fac20cc9c428f819413c52 Author: Doreen Fan Date: Fri Mar 8 12:59:43 2019 -0800 Code cleanup: removed alt_energy_fix specific subroutine Source/MaestroForce.cpp Source/MaestroMacProj.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/make_vel_force.F90 commit 41567967d0a5f4ae87ee8847106d123abd6aabe7 Author: Andy Nonaka Date: Tue Mar 5 11:12:57 2019 -0800 get more examples compiling again Exec/UNIT_TESTS/test_basestate/test_basestate.f90 Microphysics/EOS/gamma_law/gamma_law.F90 Microphysics/networks/general_null/actual_burner.f90 Microphysics/networks/general_null/network.template Source/Src_nd/tagging.F90 commit 91d5ca33706e6a721217a4b5a9cda7cf47d763b8 Author: Andy Nonaka Date: Mon Mar 4 13:19:18 2019 -0800 many changes to get wdconvect compiling again with the removal of F_BaseLib. mainly, all the "bl_" stuff should now be "amrex_" stuff, with the appropriate modules changed more builds will break for the short term, but the compiler errors will guide the way, along with regression tests Exec/Make.Maestro Exec/SCIENCE/rotating_star/initdata.f90 Exec/SCIENCE/wdconvect/initdata.f90 Exec/SCIENCE/wdconvect/tagging.F90 Exec/TEST_PROBLEMS/double_bubble/base_state.f90 Exec/TEST_PROBLEMS/double_bubble/initdata.f90 Exec/TEST_PROBLEMS/incomp_shear_jet/base_state.f90 Exec/TEST_PROBLEMS/incomp_shear_jet/initdata.f90 Exec/TEST_PROBLEMS/rt/base_state.f90 Exec/TEST_PROBLEMS/rt/initdata.f90 Exec/TEST_PROBLEMS/test_convect/initdata.f90 Exec/TEST_PROBLEMS/test_convect/make_heating.F90 Exec/TEST_PROBLEMS/test_stability/initdata.f90 Exec/TEST_PROBLEMS/test_stability/make_heating.F90 Exec/UNIT_TESTS/test_advect/base_state.f90 Exec/UNIT_TESTS/test_advect/initdata.f90 Exec/UNIT_TESTS/test_average/initdata.f90 Exec/UNIT_TESTS/test_basestate/initdata.f90 Exec/UNIT_TESTS/test_basestate/test_basestate.f90 Exec/UNIT_TESTS/test_diffusion/base_state.f90 Exec/UNIT_TESTS/test_diffusion/initdata.f90 Exec/UNIT_TESTS/test_diffusion/make_analytic_solution.f90 Exec/UNIT_TESTS/test_projection/test_projection.F90 Exec/UNIT_TESTS/test_react/initdata.f90 Exec/UNIT_TESTS/test_react/make_heating.f90 Exec/UNIT_TESTS/test_react/problem_functions.f90 Exec/UNIT_TESTS/test_react/scripts/fsnapshot.f90 Microphysics/EOS/eos.F90 Microphysics/EOS/eos_type.f90 Microphysics/EOS/gamma_law/gamma_law.F90 Microphysics/networks/burner.F90 Microphysics/networks/general_null/actual_burner.f90 Microphysics/networks/general_null/actual_rhs.f90 Microphysics/networks/general_null/network.template Microphysics/networks/sdc_type.F90 Source/Src_nd/advect_base.F90 Source/Src_nd/base_state.f90 Source/Src_nd/base_state_geometry.f90 Source/Src_nd/burner_loop.f90 Source/Src_nd/debug.F90 Source/Src_nd/enforce_HSE.f90 Source/Src_nd/fill_3d_data.F90 Source/Src_nd/initdata.f90 Source/Src_nd/maestro_init.f90 Source/Src_nd/make_edge_scal.F90 Source/Src_nd/make_edge_state.f90 Source/Src_nd/make_eta.F90 Source/Src_nd/make_explicit_thermal.F90 Source/Src_nd/make_flux.F90 Source/Src_nd/make_grav.f90 Source/Src_nd/make_heating.F90 Source/Src_nd/make_psi.F90 Source/Src_nd/make_vel_force.F90 Source/Src_nd/make_w0.f90 Source/Src_nd/mkutrans.F90 Source/Src_nd/ppm.F90 Source/Src_nd/regrid.f90 Source/Src_nd/sponge.F90 Source/Src_nd/tagging.F90 Source/Src_nd/velpred.F90 Util/model_parser/model_parser.f90 sphinx_docs/source/architecture.rst commit 8c8cceb432bc8b468347d4ca2bdc8cb8dfa0814b Author: Doreen Fan Date: Fri Mar 1 12:59:25 2019 -0800 March 2019 release notes RELEASE_NOTES commit e0e420b7d07b4700a82eb06cce21ae0122eb8182 Merge: 876bed41 2c365524 Author: Alice Harpole Date: Fri Feb 22 11:58:49 2019 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 876bed4131929b2b15c58c5d3a574adcf4212e3f Author: Alice Harpole Date: Fri Feb 22 11:58:40 2019 -0500 added section to FAQ on extern namelist error sphinx_docs/source/faq.rst commit 2c365524c2aacb91c07c9d7d257dddd9d6f30f4d Author: Andy Nonaka Date: Thu Feb 21 10:20:54 2019 -0800 move inputs files to sub directory Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.1024 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.128 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.128.2levels Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.128.2levels_onegrid Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.128.avgbase Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.128.exactbase Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.256 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.384 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.512 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.512.exactbase Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.64 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.64.avgbase Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.64.exactbase Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_C.768 Exec/SCIENCE/wdconvect/inputs_files/inputs_3d_regression Exec/SCIENCE/wdconvect/inputs_files/inputs_omp_3d_regression commit 13e1377e463286fa397700f5035a05e0839fa812 Author: Andy Nonaka Date: Thu Feb 21 10:18:28 2019 -0800 weak scaling inputs files Exec/SCIENCE/wdconvect/inputs_3d_C.1024 Exec/SCIENCE/wdconvect/inputs_3d_C.256 Exec/SCIENCE/wdconvect/inputs_3d_C.384 Exec/SCIENCE/wdconvect/inputs_3d_C.768 commit 17257bef61750d2bb6384486eb0e00ac16f75815 Author: Andy Nonaka Date: Thu Feb 21 10:13:57 2019 -0800 change max_grid_size for all problems with base resolution >= 128 to 64 Exec/SCIENCE/wdconvect/inputs_3d_C.128 Exec/SCIENCE/wdconvect/inputs_3d_C.128.avgbase Exec/SCIENCE/wdconvect/inputs_3d_C.128.exactbase commit a1ab70f0337a84d9e0a0259e5eff06b13555dfeb Author: Andy Nonaka Date: Fri Feb 15 16:43:10 2019 -0800 cleanup only Source/MaestroAdvanceAvg.cpp commit 522439b91c69bc2c1c7fdf727e575c8fc8baaba8 Author: Andy Nonaka Date: Fri Feb 15 09:34:11 2019 -0800 typo in inputs file... didn't have average_base_state enabled correctly Exec/SCIENCE/wdconvect/inputs_3d_C.128.avgbase Exec/SCIENCE/wdconvect/inputs_3d_C.64.avgbase commit fb39dde5693911e689b9be058ff0dc8d08480d08 Author: Andy Nonaka Date: Thu Feb 14 14:24:03 2019 -0800 64^3 new temporal integrator, fixed dr Exec/SCIENCE/wdconvect/inputs_3d_C.64.avgbase commit fcc6e826915db79a954be5ab7147f8e4f4460ba6 Author: Andy Nonaka Date: Thu Feb 14 07:55:07 2019 -0800 C++ reads in "e" format from inputs file, not "d" format (that only works in the fortran namelist part) this should fix the broken regression tests Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_dpdt Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C.2levels Exec/TEST_PROBLEMS/reacting_bubble/inputs_omp_2d_regression commit b80835ce14a3f34e91009081e03f88234484718e Author: Andy Nonaka Date: Tue Feb 12 14:40:33 2019 -0800 moved model files to ./model_files. Included all constant dr for 64, 128, 256, 384, 512, 768, and 1024^3 cases. Included all variable dr for 64, 128, 256, 384, and 512^3 Exec/SCIENCE/wdconvect/model_files/kepler_new_6.25e8.hybrid.hse.1280 Exec/SCIENCE/wdconvect/model_files/kepler_new_6.25e8.hybrid.hse.1488.dr Exec/SCIENCE/wdconvect/model_files/kepler_new_6.25e8.hybrid.hse.1920 Exec/SCIENCE/wdconvect/model_files/kepler_new_6.25e8.hybrid.hse.24384.dr Exec/SCIENCE/wdconvect/model_files/kepler_new_6.25e8.hybrid.hse.2560 Exec/SCIENCE/wdconvect/model_files/kepler_new_6.25e8.hybrid.hse.320 Exec/SCIENCE/wdconvect/model_files/kepler_new_6.25e8.hybrid.hse.3840 Exec/SCIENCE/wdconvect/model_files/kepler_new_6.25e8.hybrid.hse.5120 Exec/SCIENCE/wdconvect/model_files/kepler_new_6.25e8.hybrid.hse.55008.dr Exec/SCIENCE/wdconvect/model_files/kepler_new_6.25e8.hybrid.hse.6048.dr Exec/SCIENCE/wdconvect/model_files/kepler_new_6.25e8.hybrid.hse.640 Exec/SCIENCE/wdconvect/model_files/kepler_new_6.25e8.hybrid.hse.97920.dr commit 1601e56c13373cf9849a460fe236fd02180a8eea Author: Andy Nonaka Date: Tue Feb 12 14:28:51 2019 -0800 cleanup Exec/SCIENCE/wdconvect/inputs_3d_C.128.2levels Exec/SCIENCE/wdconvect/inputs_3d_C.128.2levels_onegrid commit 767076cb7e9df82c506b5809328ce52c3e25c1a4 Author: Andy Nonaka Date: Tue Feb 12 14:25:46 2019 -0800 the .avgbase suffix refers to constant dr with the new temporal integrator Exec/SCIENCE/wdconvect/inputs_3d_C.128.avgbase commit 9ea9fee8a6f901a7d823dae4084246fbd5291b7e Author: Andy Nonaka Date: Tue Feb 12 14:24:10 2019 -0800 remove this - it's redundant with inputs_3d_C.128.exactbase Exec/SCIENCE/wdconvect/inputs_3d_C.128.avgbase.dr commit 285e88598929617e4dcc74954c24f02a4fee285a Author: Andy Nonaka Date: Tue Feb 12 14:21:18 2019 -0800 more inputs file syncing Exec/SCIENCE/wdconvect/inputs_3d_C.128 Exec/SCIENCE/wdconvect/inputs_3d_C.128.exactbase Exec/SCIENCE/wdconvect/inputs_3d_C.512 Exec/SCIENCE/wdconvect/inputs_3d_C.512.exactbase Exec/SCIENCE/wdconvect/kepler_new_6.25e8.hybrid.hse.2560 commit 666ef357ccaae24694e5185408ee13366922fb71 Author: Andy Nonaka Date: Tue Feb 12 14:18:00 2019 -0800 remove this Exec/SCIENCE/wdconvect/inputs_3d_C commit a49bcfb3889fc52b28795ecb898279b16c98c578 Author: Andy Nonaka Date: Tue Feb 12 14:02:37 2019 -0800 sync up inputs_3d_C.64 and inputs_3d_C.64.exactbase so they are the exact same run, except for the use of use_exact_base_state next: going to fix up the rest of the inputs files as well so they are consistent with these runs Exec/SCIENCE/wdconvect/inputs_3d_C.64 Exec/SCIENCE/wdconvect/inputs_3d_C.64.exactbase commit d816d607bf0306ad958a190120b0b4d4d1e88ba2 Author: Andy Nonaka Date: Tue Feb 12 13:51:35 2019 -0800 tag based on tag_density_1, not _3 Exec/SCIENCE/wdconvect/tagging.F90 commit 7df194e10ae090653c3b3942ca59a17cc15a54e5 Author: Andy Nonaka Date: Mon Feb 11 17:32:38 2019 -0800 new test problem Exec/SCIENCE/wdconvect/inputs_3d_C.512.exactbase commit 95a4c4f1ebfdc165b64a57918be1b976eac63f4f Author: Andy Nonaka Date: Mon Feb 11 17:31:00 2019 -0800 initial model cleanup Exec/SCIENCE/wdconvect/README_MODELS Exec/SCIENCE/wdconvect/inputs_3d_C.128.avgbase.dx Exec/SCIENCE/wdconvect/kepler_new_6.25e8.hybrid.hse.320.dx Exec/SCIENCE/wdconvect/kepler_new_6.25e8.hybrid.hse.640.dx commit 48d69793324e18fc66b8a6fe3ba8249c9f86472a Merge: 92deb6fa c39ed696 Author: Andy Nonaka Date: Mon Feb 11 17:26:06 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 92deb6fa8402d3ebcb258ad0c8182d1fcae38538 Author: Andy Nonaka Date: Mon Feb 11 17:25:45 2019 -0800 variable base state initial models for 256^3, 384^3, and 512^3 Exec/SCIENCE/wdconvect/kepler_new_6.25e8.hybrid.hse.24384.dr Exec/SCIENCE/wdconvect/kepler_new_6.25e8.hybrid.hse.55008.dr Exec/SCIENCE/wdconvect/kepler_new_6.25e8.hybrid.hse.97920.dr commit c39ed6968fff0b2ee9d24930e0d945c47bc97004 Author: Doreen Fan Date: Mon Feb 11 11:31:22 2019 -0800 Compute_cutoff_coords should be called after init_multilevel when restarting from multilevel checkpoint file Source/MaestroInit.cpp commit 10b39e01b89698b0fcb562beb49b0f038a9b4047 Merge: a67fabf5 2e5bff20 Author: Alice Harpole Date: Mon Feb 11 09:15:46 2019 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 2e5bff207c3ba0dd94c2e9ab81c691fd7ce7aff0 Author: Andy Nonaka Date: Fri Feb 8 16:49:39 2019 -0800 get rid of flux_reg_u. velocity doesn't need it since it's discretized convectively, not conservatively. So what is done is an average-down of the edge states Source/Maestro.H Source/MaestroAdvection.cpp Source/MaestroCheckpoint.cpp Source/MaestroInit.cpp Source/MaestroRegrid.cpp Source/MaestroSetup.cpp commit 2bc021da8bd59adb62d33021f03217ddbfd33cc7 Author: Andy Nonaka Date: Fri Feb 8 15:01:04 2019 -0800 modified multilevel inputs. inputs_3d_C.128.2levels now has lots of level 1 grids Exec/SCIENCE/wdconvect/inputs_3d_C.128.2levels Exec/SCIENCE/wdconvect/inputs_3d_C.128.2levels_onegrid commit 5abd5cd796e61d4cbec4f80fda5ce832f3789096 Author: Andy Nonaka Date: Fri Feb 8 14:44:50 2019 -0800 fix indentation Source/MaestroRhoHT.cpp commit 1f90bddbbbd3f561e3fc6ef5f58d577d55d6c35f Author: Andy Nonaka Date: Fri Feb 8 14:00:43 2019 -0800 move the call to PutInPertForm for temperature in the tpret tagging to outside of the OMP region. Seems to fix segfaults for 3-level planar bubble rise Source/MaestroRegrid.cpp commit b223ab8466b20507dceb7d354161c9e37b3130a8 Author: Andy Nonaka Date: Fri Feb 8 12:39:44 2019 -0800 remove openmp from TagArray. It wasn't thread safe because we need a reduction over the vector tag_array Source/MaestroRegrid.cpp commit a67fabf51a82b7e822c3ea3a05731292125d8d29 Author: Alice Harpole Date: Wed Feb 6 15:55:05 2019 -0500 fixed varnames for gphi Exec/UNIT_TESTS/test_projection/MaestroPlot.cpp commit 12aedfe00b339c04bf59e9499a19d8f6a449438e Merge: bb6464d2 5c4d578f Author: Alice Harpole Date: Wed Feb 6 15:42:57 2019 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit bb6464d2fffb58dada6d2118899726b54add655d Author: Alice Harpole Date: Wed Feb 6 15:42:47 2019 -0500 added plotting to test_projection Exec/UNIT_TESTS/test_diffusion/MaestroPlot.cpp Exec/UNIT_TESTS/test_projection/MaestroEvolve.cpp Exec/UNIT_TESTS/test_projection/MaestroPlot.cpp Exec/UNIT_TESTS/test_projection/inputs_2d_per Exec/UNIT_TESTS/test_projection/inputs_2d_per.cross Exec/UNIT_TESTS/test_projection/inputs_2d_per_mac Exec/UNIT_TESTS/test_projection/inputs_2d_wall Exec/UNIT_TESTS/test_projection/inputs_2d_wall.cross Exec/UNIT_TESTS/test_projection/inputs_2d_wall_mac commit 5c4d578f781f37a9d3d90bc97349e1d60c71cd53 Merge: a5c65167 6abc008e Author: Andy Nonaka Date: Wed Feb 6 12:27:11 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit a5c65167f259a83e65f1a1d7813382b3a53e1fe1 Author: Andy Nonaka Date: Wed Feb 6 12:26:56 2019 -0800 comments and cleanup of tagging routines Exec/SCIENCE/wdconvect/tagging.F90 Exec/TEST_PROBLEMS/reacting_bubble/tagging.F90 Source/MaestroRegrid.cpp commit 6abc008e3bcd56eb803eca373ce10e5d4cbfe1da Author: Alice Harpole Date: Wed Feb 6 14:57:03 2019 -0500 test_diffusion now outputs to file Exec/UNIT_TESTS/test_diffusion/MaestroEvolve.cpp Exec/UNIT_TESTS/test_diffusion/MaestroPlot.cpp Exec/UNIT_TESTS/test_diffusion/inputs_2d commit 7dc30a1ac97d83b4e9640de9a8e25ffa7c70fe22 Author: Doreen Fan Date: Wed Feb 6 10:34:55 2019 -0800 TagArray() is used only for planar problems Source/MaestroRegrid.cpp commit a5db1270a69f6e962afd3f3b06ab4b10e7b09423 Merge: 6b6b420f 76a566e7 Author: Doreen Fan Date: Wed Feb 6 10:04:59 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 76a566e743f0207c0945e092046a42e0a66e90db Author: Andy Nonaka Date: Wed Feb 6 09:48:32 2019 -0800 apparently maestro_extern_init does not require arguments anymore. this quiets a make typecheck warning Source/Src_nd/maestro_init.f90 commit 7791718affc399682254ae9152e0f13c7891c73b Author: Andy Nonaka Date: Wed Feb 6 09:41:35 2019 -0800 major change how the tagging is done. There is no more temperr or denserr in the inputs files There is no more tag_err construct in the code What you do, for each problem, is add something in the local _parameters file, e.g., "tag_density_lev1". Then in your local copy of tagging.F90 you can include this from the probin module Exec/SCIENCE/rotating_star/inputs_2d Exec/SCIENCE/rotating_star/inputs_3d_C Exec/SCIENCE/rotating_star/inputs_3d_C.128.2levels Exec/SCIENCE/rotating_star/inputs_3d_C.128.exactbase Exec/SCIENCE/rotating_star/inputs_3d_C.64.exactbase Exec/SCIENCE/rotating_star/inputs_3d_regression Exec/SCIENCE/rotating_star/inputs_test Exec/SCIENCE/rotating_star/tagging.f90 Exec/SCIENCE/wdconvect/inputs_3d_C Exec/SCIENCE/wdconvect/inputs_3d_C.128.2levels Exec/SCIENCE/wdconvect/inputs_3d_C.128.avgbase.dr Exec/SCIENCE/wdconvect/inputs_3d_C.128.avgbase.dx Exec/SCIENCE/wdconvect/inputs_3d_C.128.exactbase Exec/SCIENCE/wdconvect/inputs_3d_C.64.exactbase Exec/SCIENCE/wdconvect/inputs_3d_regression Exec/SCIENCE/wdconvect/inputs_omp_3d_regression Exec/SCIENCE/wdconvect/tagging.F90 Exec/TEST_PROBLEMS/double_bubble/inputs_2d_C Exec/TEST_PROBLEMS/double_bubble/inputs_2d_regression Exec/TEST_PROBLEMS/double_bubble/tagging.F90 Exec/TEST_PROBLEMS/incomp_shear_jet/inputs_2d_C Exec/TEST_PROBLEMS/incomp_shear_jet/inputs_2d_regression Exec/TEST_PROBLEMS/incomp_shear_jet/tagging.F90 Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C.2levels Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C.3levels Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_dpdt Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C.2levels Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_omp_2d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_omp_3d_regression Exec/TEST_PROBLEMS/reacting_bubble/tagging.F90 Exec/TEST_PROBLEMS/rt/inputs_2d_C Exec/TEST_PROBLEMS/rt/inputs_2d_regression Exec/TEST_PROBLEMS/rt/tagging.F90 Exec/TEST_PROBLEMS/test_convect/tagging.F90 Source/Maestro.H Source/MaestroRegrid.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/tagging.F90 commit 2e5459cda239a59b4eb2e0a21dfb9e8b50dc0fcb Author: Andy Nonaka Date: Wed Feb 6 09:40:48 2019 -0800 delete probin_regression note the probin files don't need to exist anymore; they are appended at the end of the inputs files Exec/SCIENCE/wdconvect/probin_regression commit bd275bb157bed89969e3cbbb77d92b16e2f49840 Author: Michael Zingale Date: Wed Feb 6 12:07:22 2019 -0500 the F_MG solver is no longer part of AMReX. Also some prep for the impending removal of F_BaseLib Exec/Make.Maestro Microphysics/networks/network.f90 Source/Maestro.H Source/Src_nd/base_state_geometry.f90 Util/simple_log/simple_log.f90 constants/constants_cgs.f90 commit 3a4be90686be6440a3a3b63f72c083b2adf3682a Author: Alice Harpole Date: Wed Feb 6 09:14:25 2019 -0500 added conductivity_init Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/maestro_init.f90 commit 64470c498416252b7d667933393f718a1af1abfc Merge: c724eb76 0e263eb9 Author: Alice Harpole Date: Tue Feb 5 17:22:08 2019 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit c724eb76dac75afae7736988ffb5141f6541ca7f Author: Alice Harpole Date: Tue Feb 5 17:21:57 2019 -0500 test_diffusion error reduced by factor of a fifth, but still larger than expected Exec/UNIT_TESTS/test_diffusion/MaestroInit.cpp Exec/UNIT_TESTS/test_diffusion/make_analytic_solution.f90 commit 6b6b420f1a00cd7a7f7beb31a9178071229209f9 Merge: 3578d113 0e263eb9 Author: Doreen Fan Date: Tue Feb 5 13:46:59 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 0e263eb9921468e66cbb9d1f8e4d60d81bd64a1d Merge: 168cb34b d4beb4aa Author: Andy Nonaka Date: Tue Feb 5 13:43:07 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 168cb34b4d4e7ba3d211c9d03b02a1cf1f2c759a Author: Andy Nonaka Date: Tue Feb 5 13:42:30 2019 -0800 TagArray needed a call to ParallelDescriptor::ReduceIntMax(tag_array.dataPtr() the 3-level, 2d reacting bubble rise problem looks good right now (no known issues) Source/MaestroRegrid.cpp commit d4beb4aa48b8349e68c6733df38a02c2b29b6d4e Author: Alice Harpole Date: Tue Feb 5 16:15:44 2019 -0500 alternative relative error calculation for test_advect gives much more reasonable answers Exec/UNIT_TESTS/test_advect/MaestroEvolve.cpp commit 462931c56ecc88060bc4c48be3baf5f8ca306187 Author: Michael Zingale Date: Tue Feb 5 10:04:20 2019 -0500 need to call actual_rhs_init() to allocate screening stuff Source/Src_nd/maestro_init.f90 commit 3578d113c5adb752a331449ccee1c3c3fce74499 Merge: a34d9c79 9f4f9ab8 Author: Doreen Fan Date: Mon Feb 4 12:53:48 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 9f4f9ab850783d7851748fad2afd1a65627d9708 Author: Andy Nonaka Date: Mon Feb 4 12:26:54 2019 -0800 Feb 2019 release notes RELEASE_NOTES commit ad0aa8b8218f6aee33e8793186d3c8a19808ba65 Author: sailoridy Date: Fri Feb 1 01:20:11 2019 -0500 modify ECSN Exec/SCIENCE/wd/diag_temp.out Exec/SCIENCE/wd/inputs_3d_C Exec/SCIENCE/wd/inputs_3d_C.128 Exec/SCIENCE/wd/inputs_3d_C.128.2levels Exec/SCIENCE/wd/inputs_3d_C.128.avgbase.dr Exec/SCIENCE/wd/inputs_3d_C.128.avgbase.dx Exec/SCIENCE/wd/inputs_3d_C.128.exactbase Exec/SCIENCE/wd/inputs_3d_C.64.exactbase Exec/SCIENCE/wd/inputs_3d_kepler Exec/SCIENCE/wd/inputs_3d_regression Exec/SCIENCE/wd/inputs_omp_3d_regression Exec/SCIENCE/wd/kepler_xinlong_ONe6040-final.hse.1280 Exec/SCIENCE/wd/kepler_xinlong_ONe6040-final.hse.5120 Source/param/runtime.probin.template commit a34d9c790cf43ffe1d89bd95d197a475dae7a2fb Author: Doreen Fan Date: Wed Jan 30 15:39:44 2019 -0800 Rewrite average subroutine to look more like MAESTRO average subroutine Source/Src_nd/average.f90 commit e07bc8d857b4b135abf3b221c8ee26ed11586aac Author: Doreen Fan Date: Wed Jan 30 15:37:11 2019 -0800 Fixed initialization problem with >1 processors Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C.3levels Source/Src_nd/base_state_geometry.f90 commit 0bc9ed260353375d2e135b4d27391d194c79d589 Author: Doreen Fan Date: Wed Jan 30 15:35:14 2019 -0800 Fixed bug to loop over correct number of fine grids Source/Src_nd/make_w0.f90 commit 333b676d0ed2ccd589b98945e453a7e751462a93 Merge: a1545244 5e04b44b Author: Doreen Fan Date: Mon Jan 28 18:10:10 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit a15452448d9b5db62b2695e75668bd581867c0cc Author: Doreen Fan Date: Mon Jan 28 18:09:55 2019 -0800 Added subroutines to fill data for each level of AMR separately. Needed for tagging using tpert. Source/Maestro.H Source/MaestroAdvection.cpp Source/MaestroConvert.cpp Source/MaestroDensityAdvance.cpp Source/MaestroFill3dData.cpp Source/MaestroRegrid.cpp commit 5e04b44b0140b472ba09a855db75cae304c270f0 Author: Alice Harpole Date: Mon Jan 28 16:33:45 2019 -0500 forgot to add fsnapshot.f90 Exec/UNIT_TESTS/test_react/scripts/fsnapshot.f90 commit 46fec4a051f114cc268cd16881fbc9f2e3a07e4a Author: Alice Harpole Date: Mon Jan 28 16:32:51 2019 -0500 recon.py seems to work Exec/UNIT_TESTS/test_react/scripts/GNUmakefile Exec/UNIT_TESTS/test_react/scripts/README.recon Exec/UNIT_TESTS/test_react/scripts/recon.py commit b06303debb6cbbc4bee29de0327c5771ff757184 Author: Alice Harpole Date: Mon Jan 28 15:41:05 2019 -0500 xinGen.py script works Exec/UNIT_TESTS/test_react/GNUmakefile Exec/UNIT_TESTS/test_react/MaestroEvolve.cpp Exec/UNIT_TESTS/test_react/inputs_aprox13 Exec/UNIT_TESTS/test_react/scripts/README.xinGen Exec/UNIT_TESTS/test_react/scripts/xinGen.py commit c24341c9c5d215746df74d905a717b3a40ddf24c Author: Alice Harpole Date: Mon Jan 28 13:28:52 2019 -0500 some minor bug fixes Exec/UNIT_TESTS/test_advect/MaestroEvolve.cpp Exec/UNIT_TESTS/test_advect/base_state.f90 Exec/UNIT_TESTS/test_advect/inputs_2d Exec/UNIT_TESTS/test_average/initdata.f90 Exec/UNIT_TESTS/test_basestate/initdata.f90 Exec/UNIT_TESTS/test_diffusion/MaestroEvolve.cpp Exec/UNIT_TESTS/test_diffusion/base_state.f90 Exec/UNIT_TESTS/test_diffusion/compute_dt.F90 Exec/UNIT_TESTS/test_diffusion/initdata.f90 Exec/UNIT_TESTS/test_diffusion/make_analytic_solution.f90 Exec/UNIT_TESTS/test_eos/GNUmakefile Exec/UNIT_TESTS/test_react/GNUmakefile Exec/UNIT_TESTS/test_react/MaestroEvolve.cpp Exec/UNIT_TESTS/test_react/MaestroInit.cpp Exec/UNIT_TESTS/test_react/base_state.f90 Exec/UNIT_TESTS/test_react/initdata.f90 Exec/UNIT_TESTS/test_react/problem_functions.f90 commit 5ce1c5fa6b5f98a479c4480a1b5d66c7cb0cc248 Author: Alice Harpole Date: Mon Jan 28 09:33:53 2019 -0500 uncomment abort statement Source/MaestroForce.cpp commit 83a1dbc4d8a9fbace511b22b0136fb31aa01ad86 Merge: 27983dff b9fc35ad Author: Alice Harpole Date: Mon Jan 28 09:12:09 2019 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into unit_tests commit b9fc35adfa306b851f1711f174148229755c0eb2 Author: Andy Nonaka Date: Fri Jan 25 15:12:56 2019 -0800 new 3-level planar test file... problem BREAKS out the gate (look at plt_InitData and it's gibberish) Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C.3levels commit a64642f8b8a29c96f5468c8afbfcf6190caca217 Author: Andy Nonaka Date: Fri Jan 25 15:02:00 2019 -0800 change the 3d AMR test to make it run faster (shrink domain; change location of hotspot) I will update the single-level 3d regression test Exec/TEST_PROBLEMS/reacting_bubble/initdata.f90 Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C.2levels commit e52e95e82bddf373c33849f81ec42ee991153d2a Author: Andy Nonaka Date: Fri Jan 25 14:29:59 2019 -0800 turn off hyperbolic refluxing (and use averageDownFaces of edge fluxes) for now... it works, but does more work than it has to because it averages down all faces, not just the C-F interface faces Exec/SCIENCE/rotating_star/inputs_2d Exec/SCIENCE/rotating_star/inputs_3d_C Exec/SCIENCE/rotating_star/inputs_3d_C.128.2levels Exec/SCIENCE/rotating_star/inputs_test Exec/SCIENCE/wdconvect/inputs_3d_C Exec/SCIENCE/wdconvect/inputs_3d_C.128.2levels Exec/TEST_PROBLEMS/double_bubble/inputs_2d_C Exec/TEST_PROBLEMS/double_bubble/inputs_2d_regression Exec/TEST_PROBLEMS/incomp_shear_jet/inputs_2d_C Exec/TEST_PROBLEMS/incomp_shear_jet/inputs_2d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C.2levels Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_dpdt Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C.2levels Exec/TEST_PROBLEMS/rt/inputs_2d_C Exec/TEST_PROBLEMS/rt/inputs_2d_regression Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H commit 90fc29005c9445a8c5ef316f58a414bcf358c13b Author: Andy Nonaka Date: Fri Jan 25 11:44:19 2019 -0800 setting do_reflux=F now turns on averageDownFaces on species and enthalpy fluxes (to match the original maestro). do_reflux=F seems to work for planar, but averageDownFaces is much less efficient than using flux registers Source/MaestroAdvection.cpp commit 837ad20e1cdea2d08bd6a5c10622f26193503874 Author: Andy Nonaka Date: Fri Jan 25 11:02:45 2019 -0800 fix 2D/3D area weighting for rhoh advection Source/MaestroAdvection.cpp commit 4c540441c8a7d668b809955b14fb4061013bb6f4 Author: Doreen Fan Date: Fri Jan 25 09:27:54 2019 -0800 Fixed area value for grid coarsening and refinement for 2D problems Source/MaestroAdvection.cpp commit ac1dc045813362482575640b0c39b54312a30f61 Merge: 8206c2bb 16d04344 Author: Andy Nonaka Date: Thu Jan 24 15:42:49 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 8206c2bb7a60af407b6220be2fe8a4f1f7f76ff3 Author: Andy Nonaka Date: Thu Jan 24 15:42:17 2019 -0800 fix endcomp for species advection. doesn't change results at all *phew* so it wasn't a functional bug Source/MaestroAdvection.cpp commit 16d0434471fb36327bd11b2dee87fcd0c8f88da6 Author: Alice Harpole Date: Thu Jan 24 13:56:35 2019 -0800 Added rotating_star problem Exec/SCIENCE/rotating_star/18m_500_s_rot_b_eq_1.hse.6144 Exec/SCIENCE/rotating_star/GNUmakefile Exec/SCIENCE/rotating_star/Make.package Exec/SCIENCE/rotating_star/_parameters Exec/SCIENCE/rotating_star/initdata.f90 Exec/SCIENCE/rotating_star/inputs_2d Exec/SCIENCE/rotating_star/inputs_3d_C Exec/SCIENCE/rotating_star/inputs_3d_C.128 Exec/SCIENCE/rotating_star/inputs_3d_C.128.2levels Exec/SCIENCE/rotating_star/inputs_3d_C.128.exactbase Exec/SCIENCE/rotating_star/inputs_3d_C.64 Exec/SCIENCE/rotating_star/inputs_3d_C.64.exactbase Exec/SCIENCE/rotating_star/inputs_3d_regression Exec/SCIENCE/rotating_star/inputs_test Exec/SCIENCE/rotating_star/probin Exec/SCIENCE/rotating_star/probin_regression Exec/SCIENCE/rotating_star/tagging.f90 commit f9365c0ec601783743705ae095509cb3864dcd42 Author: Doreen Fan Date: Wed Jan 23 17:42:07 2019 -0800 Need to tag boxes right after calling state_error() in ErrorEst Source/MaestroRegrid.cpp commit 77aa32e98350a6a35c7e25b458177bd6d45392b7 Author: Doreen Fan Date: Fri Jan 18 17:44:58 2019 -0800 Include a 3D planar multilevel problem to test Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C.2levels commit f28900d0dc44e28704d024a3d26d8347ad55f018 Author: Doreen Fan Date: Fri Jan 18 15:01:47 2019 -0800 Input file now uses tpert for tagging Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C.2levels Exec/TEST_PROBLEMS/reacting_bubble/tagging.F90 Source/MaestroRegrid.cpp Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit 27983dffa798c030d1edd1a83f8eb10c73d32b8f Merge: 67752cb7 cdecb85a Author: Alice Harpole Date: Fri Jan 18 14:31:42 2019 -0500 resolved merge conflicts commit 67752cb76f6f671c8fab323cae23b7d9fe9453d4 Author: Alice Harpole Date: Fri Jan 18 14:30:02 2019 -0500 More tidying up Exec/UNIT_TESTS/test_advect/initdata.f90 Exec/UNIT_TESTS/test_average/initdata.f90 Exec/UNIT_TESTS/test_basestate/initdata.f90 Exec/UNIT_TESTS/test_eos/initdata.f90 Exec/UNIT_TESTS/test_projection/MaestroEvolve.cpp Exec/UNIT_TESTS/test_projection/initdata.f90 Exec/UNIT_TESTS/test_projection/test_projection.F90 commit 7cd991545fe8c99af8e32d94537caa7c07569191 Author: Alice Harpole Date: Fri Jan 18 13:53:29 2019 -0500 better plotfilenames for test_react Exec/UNIT_TESTS/test_basestate/MaestroDt.cpp Exec/UNIT_TESTS/test_diffusion/MaestroDt.cpp Exec/UNIT_TESTS/test_diffusion/MaestroEvolve.cpp Exec/UNIT_TESTS/test_diffusion/MaestroInit.cpp Exec/UNIT_TESTS/test_diffusion/Problem_F.H Exec/UNIT_TESTS/test_diffusion/base_state.f90 Exec/UNIT_TESTS/test_diffusion/compute_dt.F90 Exec/UNIT_TESTS/test_diffusion/initdata.f90 Exec/UNIT_TESTS/test_diffusion/make_analytic_solution.f90 Exec/UNIT_TESTS/test_react/GNUmakefile Exec/UNIT_TESTS/test_react/MaestroEvolve.cpp Exec/UNIT_TESTS/test_react/MaestroPlot.cpp Exec/UNIT_TESTS/test_react/Problem_F.H Exec/UNIT_TESTS/test_react/problem_functions.f90 commit cdecb85aaa4fd4432546e829553efc6c0da23412 Author: Doreen Fan Date: Fri Jan 18 10:38:01 2019 -0800 Need to regrid w0 as well Source/MaestroRegrid.cpp commit 8c68ee312fd9279a68a91a9ec923594b1deb92dd Author: Andy Nonaka Date: Fri Jan 18 10:23:32 2019 -0800 at the beginning of ErrorEst, need to reset tag_array to zero Source/MaestroRegrid.cpp commit 8db74794504edbacc4a2aae9774b15b6e839fedb Author: Andy Nonaka Date: Fri Jan 18 10:02:02 2019 -0800 parallel safe IO Source/MaestroDiag.cpp commit a16e2a46c4948bbad8465d1317b44fa38bbc623c Author: Andy Nonaka Date: Fri Jan 18 09:58:16 2019 -0800 bugfix... don't wrap the base state std::swap with a loop over levels! Source/MaestroEvolve.cpp commit 4aa36b292d4ec4eecc8520e00194c7215e437f09 Author: Andy Nonaka Date: Fri Jan 18 09:47:37 2019 -0800 parallel safe output of base state Source/Src_nd/debug.F90 commit 810022bdd9426ec192701478d1403a4ab6cb8d86 Author: Andy Nonaka Date: Fri Jan 18 09:24:25 2019 -0800 wrote fortran utilities to write out the base state; including the multilevel chunk stuff (to help with debugging) Source/Maestro_F.H Source/Src_nd/debug.F90 commit 655e3ff0453ee4f1f1212f72cecbc7cd06e2f3f5 Author: Alice Harpole Date: Thu Jan 17 17:40:51 2019 -0500 Cleaned up version of MaestroInit for test_advect Exec/UNIT_TESTS/test_advect/MaestroEvolve.cpp Exec/UNIT_TESTS/test_advect/MaestroInit.cpp Exec/UNIT_TESTS/test_advect/base_state.f90 Exec/UNIT_TESTS/test_advect/inputs_2d commit 6e1b2682a590cee3e2ea5b5d964555426bdf6085 Author: Alice Harpole Date: Thu Jan 17 15:00:52 2019 -0500 3d test_advect runs but has large errorr Exec/UNIT_TESTS/test_advect/MaestroEvolve.cpp Exec/UNIT_TESTS/test_advect/inputs_2d Exec/UNIT_TESTS/test_advect/inputs_3d Exec/UNIT_TESTS/test_eos/MaestroEvolve.cpp Exec/UNIT_TESTS/test_eos/README commit e093e48aed0523c6256e461adde30638442421c9 Author: Alice Harpole Date: Thu Jan 17 14:20:56 2019 -0500 test_eos works Exec/UNIT_TESTS/test_eos/GNUmakefile Exec/UNIT_TESTS/test_eos/MaestroEvolve.cpp Exec/UNIT_TESTS/test_eos/MaestroInit.cpp Exec/UNIT_TESTS/test_eos/Make.package Exec/UNIT_TESTS/test_eos/Problem_F.H Exec/UNIT_TESTS/test_eos/README Exec/UNIT_TESTS/test_eos/_parameters Exec/UNIT_TESTS/test_eos/initdata.f90 Exec/UNIT_TESTS/test_eos/inputs_eos.gammalaw Exec/UNIT_TESTS/test_eos/inputs_eos.helmeos Exec/UNIT_TESTS/test_eos/test_eos.f90 Exec/UNIT_TESTS/test_projection/test_projection.F90 commit 7972e394f160dd2e8f87d5b70d1de6fdc2231465 Author: Alice Harpole Date: Thu Jan 17 11:49:59 2019 -0500 works for periodic boundary conditions, not for slipwall Exec/UNIT_TESTS/test_projection/MaestroEvolve.cpp Exec/UNIT_TESTS/test_projection/inputs_2d_per Exec/UNIT_TESTS/test_projection/inputs_2d_per.cross Exec/UNIT_TESTS/test_projection/inputs_2d_per_mac Exec/UNIT_TESTS/test_projection/inputs_2d_wall Exec/UNIT_TESTS/test_projection/inputs_2d_wall.cross Exec/UNIT_TESTS/test_projection/inputs_2d_wall_mac Exec/UNIT_TESTS/test_projection/inputs_3d_per Exec/UNIT_TESTS/test_projection/inputs_3d_per_mac Exec/UNIT_TESTS/test_projection/inputs_3d_wall Exec/UNIT_TESTS/test_projection/inputs_3d_wall_mac Exec/UNIT_TESTS/test_projection/test_projection.F90 commit 15737bcb40506bcf69c073a3125be5f43cea3f4d Author: Alice Harpole Date: Thu Jan 17 10:27:35 2019 -0500 2d periodic seems to work, wall does not Exec/UNIT_TESTS/test_projection/MaestroEvolve.cpp Exec/UNIT_TESTS/test_projection/MaestroInit.cpp Exec/UNIT_TESTS/test_projection/inputs_2d_per Exec/UNIT_TESTS/test_projection/inputs_2d_per.cross Exec/UNIT_TESTS/test_projection/inputs_2d_wall Exec/UNIT_TESTS/test_projection/test_projection.F90 commit 0fec50bac4776e8fabbb5e9e4f13f5c1e58f689b Author: Alice Harpole Date: Wed Jan 16 17:16:19 2019 -0500 update n_cell for 3d inputs files Exec/UNIT_TESTS/test_projection/MaestroEvolve.cpp Exec/UNIT_TESTS/test_projection/inputs_3d_per Exec/UNIT_TESTS/test_projection/inputs_3d_per_mac Exec/UNIT_TESTS/test_projection/inputs_3d_wall Exec/UNIT_TESTS/test_projection/inputs_3d_wall_mac commit ec07c93ca2a43773360d44af24ae4448334f6358 Author: Alice Harpole Date: Wed Jan 16 17:06:53 2019 -0500 mac projection seems to work, but suspect am not setting up correct rhs for nodal projection Exec/UNIT_TESTS/test_projection/MaestroEvolve.cpp commit ee08d51ec3251903cb53c0cfcea11aea5e3da706 Merge: abf2546f c70400c8 Author: Alice Harpole Date: Wed Jan 16 16:17:06 2019 -0500 mac projectin also compiles and runs commit abf2546f32d90f2106bb75b392e9b48a5802acbf Author: Alice Harpole Date: Wed Jan 16 15:10:39 2019 -0500 compiles and runs without segfaulting Exec/UNIT_TESTS/test_projection/MaestroEvolve.cpp Exec/UNIT_TESTS/test_projection/MaestroInit.cpp Exec/UNIT_TESTS/test_projection/Problem_F.H Exec/UNIT_TESTS/test_projection/initdata.f90 Exec/UNIT_TESTS/test_projection/test_projection.F90 commit 27ccfa22f310cdd2b2f61973b2c5614aa4527468 Author: Alice Harpole Date: Wed Jan 16 12:01:51 2019 -0500 fixed mac multifab indexing so test_projection compiles Exec/UNIT_TESTS/test_projection/MaestroEvolve.cpp Exec/UNIT_TESTS/test_projection/MaestroInit.cpp Exec/UNIT_TESTS/test_projection/Make.package Exec/UNIT_TESTS/test_projection/Problem_F.H Exec/UNIT_TESTS/test_projection/initdata.f90 Exec/UNIT_TESTS/test_projection/test_projection.F90 Exec/UNIT_TESTS/test_projection/test_projection.f90 commit 4dc69e52efdcf87b76564d782892f91b3878c1e0 Author: Alice Harpole Date: Wed Jan 16 10:24:32 2019 -0500 converted more of the varden_aux functions in test_projection Exec/UNIT_TESTS/test_projection/MaestroEvolve.cpp Exec/UNIT_TESTS/test_projection/MaestroInit.cpp Exec/UNIT_TESTS/test_projection/Problem_F.H Exec/UNIT_TESTS/test_projection/initdata.f90 Exec/UNIT_TESTS/test_projection/inputs_2d_per Exec/UNIT_TESTS/test_projection/inputs_2d_per.cross Exec/UNIT_TESTS/test_projection/inputs_2d_per_mac Exec/UNIT_TESTS/test_projection/inputs_2d_wall Exec/UNIT_TESTS/test_projection/inputs_2d_wall.cross Exec/UNIT_TESTS/test_projection/inputs_2d_wall_mac Exec/UNIT_TESTS/test_projection/inputs_3d_per Exec/UNIT_TESTS/test_projection/inputs_3d_per_mac Exec/UNIT_TESTS/test_projection/inputs_3d_wall Exec/UNIT_TESTS/test_projection/inputs_3d_wall_mac Exec/UNIT_TESTS/test_projection/test_projection.f90 commit c70400c8bf1d050995bf95d7ac28e74769b264a3 Author: Doreen Fan Date: Tue Jan 15 16:25:08 2019 -0800 Remove alt_energy_fix in predictor step of velocity projection for new time evolution scheme Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvection.cpp Source/MaestroCheckpoint.cpp Source/MaestroDt.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/MaestroSetup.cpp Source/MaestroVelocityAdvance.cpp Source/Maestro_F.H Source/Src_nd/make_vel_force.F90 commit e44c4890182dfa650914e285c7deb8811e324d63 Author: Alice Harpole Date: Tue Jan 15 15:33:23 2019 -0500 test_project Exec/UNIT_TESTS/test_projection/GNUmakefile Exec/UNIT_TESTS/test_projection/MaestroEvolve.cpp Exec/UNIT_TESTS/test_projection/Make.package Exec/UNIT_TESTS/test_projection/Problem_F.H Exec/UNIT_TESTS/test_projection/_parameters Exec/UNIT_TESTS/test_projection/initdata.f90 Exec/UNIT_TESTS/test_projection/test_projection.f90 commit 796eb47cdd177cd59139e5f9571943cd09394b75 Author: Alice Harpole Date: Tue Jan 15 15:29:10 2019 -0500 runs for heating but segfaults for burning Exec/UNIT_TESTS/test_react/GNUmakefile Exec/UNIT_TESTS/test_react/MaestroEvolve.cpp Exec/UNIT_TESTS/test_react/MaestroInit.cpp Exec/UNIT_TESTS/test_react/initdata.f90 Exec/UNIT_TESTS/test_react/inputs_3alpha Exec/UNIT_TESTS/test_react/inputs_aprox13 Exec/UNIT_TESTS/test_react/inputs_ignition Exec/UNIT_TESTS/test_react/inputs_mesa_carbon Exec/UNIT_TESTS/test_react/inputs_reaclib_cburn Exec/UNIT_TESTS/test_react/inputs_reaclib_ctest Exec/UNIT_TESTS/test_react/inputs_reaclib_urca Exec/UNIT_TESTS/test_react/inputs_react Exec/UNIT_TESTS/test_react/inputs_rprox Exec/UNIT_TESTS/test_react/inputs_xrb_simple commit 969dcf9ddba07d6b96b33c98a1d28cb3f7899a84 Author: Alice Harpole Date: Tue Jan 15 11:55:59 2019 -0500 xin files Exec/UNIT_TESTS/test_react/xin Exec/UNIT_TESTS/test_react/xin.3alpha_plus_o Exec/UNIT_TESTS/test_react/xin.aprox13 Exec/UNIT_TESTS/test_react/xin.ignition Exec/UNIT_TESTS/test_react/xin.ignition.64 Exec/UNIT_TESTS/test_react/xin.mesa_carbon Exec/UNIT_TESTS/test_react/xin.reaclib_cburn Exec/UNIT_TESTS/test_react/xin.reaclib_ctest Exec/UNIT_TESTS/test_react/xin.reaclib_ctest_null Exec/UNIT_TESTS/test_react/xin.reaclib_urca Exec/UNIT_TESTS/test_react/xin.reaclib_urca_trans Exec/UNIT_TESTS/test_react/xin.rprox Exec/UNIT_TESTS/test_react/xin.xrb_simple commit f57fd622053ad859db63ebc06654b45301ab217e Author: Alice Harpole Date: Tue Jan 15 11:55:27 2019 -0500 inputs files Exec/UNIT_TESTS/test_react/GNUmakefile Exec/UNIT_TESTS/test_react/inputs_3alpha Exec/UNIT_TESTS/test_react/inputs_aprox13 Exec/UNIT_TESTS/test_react/inputs_ignition Exec/UNIT_TESTS/test_react/inputs_mesa_carbon Exec/UNIT_TESTS/test_react/inputs_reaclib_cburn Exec/UNIT_TESTS/test_react/inputs_reaclib_ctest Exec/UNIT_TESTS/test_react/inputs_reaclib_urca Exec/UNIT_TESTS/test_react/inputs_react Exec/UNIT_TESTS/test_react/inputs_rprox Exec/UNIT_TESTS/test_react/inputs_xrb_simple commit 33d3e66e092fbd215464c0633c80b818f94ca31a Author: Alice Harpole Date: Tue Jan 15 11:43:50 2019 -0500 test_react compiles Exec/UNIT_TESTS/test_react/MaestroEvolve.cpp Exec/UNIT_TESTS/test_react/MaestroInit.cpp Exec/UNIT_TESTS/test_react/MaestroPlot.cpp Exec/UNIT_TESTS/test_react/Problem_F.H Exec/UNIT_TESTS/test_react/base_state.f90 Exec/UNIT_TESTS/test_react/initdata.f90 Exec/UNIT_TESTS/test_react/make_heating.f90 Exec/UNIT_TESTS/test_react/problem_functions.f90 commit 0d9e4c569c7ec039ac5fbadc300f27cf1bb13183 Author: Alice Harpole Date: Tue Jan 15 10:27:38 2019 -0500 test_react unit test Exec/UNIT_TESTS/test_react/GNUmakefile Exec/UNIT_TESTS/test_react/MaestroEvolve.cpp Exec/UNIT_TESTS/test_react/MaestroInit.cpp Exec/UNIT_TESTS/test_react/Make.package Exec/UNIT_TESTS/test_react/Problem_F.H Exec/UNIT_TESTS/test_react/README Exec/UNIT_TESTS/test_react/README.tutorial Exec/UNIT_TESTS/test_react/_parameters Exec/UNIT_TESTS/test_react/problem_functions.f90 commit 948fc0404f875e728976790925315460a60c6a54 Author: Alice Harpole Date: Tue Jan 15 09:58:48 2019 -0500 more inputs files Exec/UNIT_TESTS/test_advect/Make.package Exec/UNIT_TESTS/test_diffusion/MaestroEvolve.cpp Exec/UNIT_TESTS/test_diffusion/inputs_2d Exec/UNIT_TESTS/test_diffusion/inputs_2d-32 Exec/UNIT_TESTS/test_diffusion/inputs_2d-64 Exec/UNIT_TESTS/test_diffusion/make_analytic_solution.f90 commit 7420bc4946ca99e4cc22bf5f1814922745d32b0c Author: Alice Harpole Date: Tue Jan 15 09:44:30 2019 -0500 it runs but the error is too large Exec/UNIT_TESTS/test_diffusion/MaestroAdvance.cpp Exec/UNIT_TESTS/test_diffusion/MaestroEvolve.cpp Exec/UNIT_TESTS/test_diffusion/MaestroInit.cpp Exec/UNIT_TESTS/test_diffusion/inputs_2d commit 4bac2451b74f7cc0a772d0e52e1b6076c5be192c Author: Alice Harpole Date: Mon Jan 14 17:36:02 2019 -0500 no longer seg faults but there are nans in the norms Exec/UNIT_TESTS/test_diffusion/MaestroAdvance.cpp Exec/UNIT_TESTS/test_diffusion/MaestroDt.cpp Exec/UNIT_TESTS/test_diffusion/MaestroEvolve.cpp Exec/UNIT_TESTS/test_diffusion/MaestroInit.cpp Exec/UNIT_TESTS/test_diffusion/Problem_F.H Exec/UNIT_TESTS/test_diffusion/inputs_2d Exec/UNIT_TESTS/test_diffusion/make_analytic_solution.f90 commit 7a4b936b48ae0f0168f3edf1d67a06bee5f09717 Author: Alice Harpole Date: Mon Jan 14 17:03:36 2019 -0500 weird error for test_diffusion Exec/UNIT_TESTS/test_diffusion/MaestroAdvance.cpp Exec/UNIT_TESTS/test_diffusion/MaestroDt.cpp Exec/UNIT_TESTS/test_diffusion/MaestroEvolve.cpp Exec/UNIT_TESTS/test_diffusion/MaestroInit.cpp Exec/UNIT_TESTS/test_diffusion/Make.package Exec/UNIT_TESTS/test_diffusion/_parameters Exec/UNIT_TESTS/test_diffusion/base_state.f90 Exec/UNIT_TESTS/test_diffusion/compute_dt.F90 Exec/UNIT_TESTS/test_diffusion/initdata.f90 Exec/UNIT_TESTS/test_diffusion/inputs_2d Microphysics/EOS/eos.F90 Source/Src_nd/fill_3d_data.F90 commit b6a2d389afd3790f834077194b4fb7618434334d Author: Alice Harpole Date: Mon Jan 14 11:36:48 2019 -0500 test_diffusion unit test Exec/UNIT_TESTS/test_basestate/urca/inputs-urca_cold Exec/UNIT_TESTS/test_basestate/urca/inputs-urca_hot Exec/UNIT_TESTS/test_basestate/urca/inputs-uref Exec/UNIT_TESTS/test_basestate/wdconvect_paper/inputs.rho_cutoff_1.e-4 Exec/UNIT_TESTS/test_basestate/wdconvect_paper/inputs.rho_cutoff_1.e5 Exec/UNIT_TESTS/test_basestate/wdconvect_paper/inputs.rho_cutoff_1.e6 Exec/UNIT_TESTS/test_diffusion/GNUmakefile Exec/UNIT_TESTS/test_diffusion/MaestroAdvance.cpp Exec/UNIT_TESTS/test_diffusion/MaestroInit.cpp Exec/UNIT_TESTS/test_diffusion/Make.package Exec/UNIT_TESTS/test_diffusion/README Exec/UNIT_TESTS/test_diffusion/_parameters Exec/UNIT_TESTS/test_diffusion/base_state.f90 Exec/UNIT_TESTS/test_diffusion/compute_dt.F90 Exec/UNIT_TESTS/test_diffusion/initdata.f90 Exec/UNIT_TESTS/test_diffusion/inputs_2d commit af53704dc1fec5ab1de595804363b24c961900fa Author: Alice Harpole Date: Mon Jan 14 09:33:26 2019 -0500 inverse planar requires pphotcno network which is not in Microphysics Exec/UNIT_TESTS/test_basestate/CNO/inputs-CNO Exec/UNIT_TESTS/test_basestate/planar-invsq/inputs-planar-invsq Exec/UNIT_TESTS/test_basestate/planar/inputs-planar commit a4b11de77379921281cae29d740dd1e1dbc57fca Merge: ec75977e a7759e15 Author: Alice Harpole Date: Mon Jan 14 09:19:43 2019 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into unit_tests commit f874ba5ba33e1b46d029ed4c79122006ede2354c Merge: bbbc1579 1f46f04b Author: Xinlong Li Date: Mon Jan 7 14:08:45 2019 -0800 Merge branch 'development' of https://github.com/sailoridy/MAESTROeX into development commit 1f46f04b85dabaea43dc80d834539986c5beaab8 Author: sailoridy Date: Mon Jan 7 17:04:24 2019 -0500 add wd Exec/SCIENCE/wd/20f-20o.dat Exec/SCIENCE/wd/20ne-20f.dat Exec/SCIENCE/wd/GNUmakefile Exec/SCIENCE/wd/Make.package Exec/SCIENCE/wd/_parameters Exec/SCIENCE/wd/diag_temp.out Exec/SCIENCE/wd/initdata.f90 Exec/SCIENCE/wd/inputs_3d_C Exec/SCIENCE/wd/inputs_3d_C.128 Exec/SCIENCE/wd/inputs_3d_C.128.2levels Exec/SCIENCE/wd/inputs_3d_C.128.avgbase.dr Exec/SCIENCE/wd/inputs_3d_C.128.avgbase.dx Exec/SCIENCE/wd/inputs_3d_C.128.exactbase Exec/SCIENCE/wd/inputs_3d_C.64 Exec/SCIENCE/wd/inputs_3d_C.64.exactbase Exec/SCIENCE/wd/inputs_3d_regression Exec/SCIENCE/wd/inputs_omp_3d_regression Exec/SCIENCE/wd/kepler_xinlong_ONe6040-final.hse.1280 Exec/SCIENCE/wd/model.orig Exec/SCIENCE/wd/model.uniform Exec/SCIENCE/wd/probin_regression Exec/SCIENCE/wd/reaclib_rate_metadata.dat Exec/SCIENCE/wd/tagging.F90 commit bbbc157984b9c26254cb54b1e9f100d4fabc3bdf Merge: 54477984 a7759e15 Author: Xinlong <42697364+sailoridy@users.noreply.github.com> Date: Sun Jan 6 12:51:10 2019 -0500 Merge pull request #2 from AMReX-Astro/development Development commit a7759e15e1f5ee45e0f5b126a811486eda7dab20 Author: Andy Nonaka Date: Fri Jan 4 13:29:50 2019 -0800 correction - don't regrid at istep=1 (the first real time step) Source/MaestroEvolve.cpp commit c4721ff780ed5836289b56bd565c459b8b27c61e Author: Andy Nonaka Date: Fri Jan 4 13:22:06 2019 -0800 regrid code cleanup Source/MaestroRegrid.cpp commit ff4ea85dbaea8a4f7681f19cf2c0634bb36c98b4 Author: Andy Nonaka Date: Fri Jan 4 13:21:53 2019 -0800 don't regrid at step 0 Source/MaestroEvolve.cpp commit 789ee6ba388957584882cb3a0736ce9c5c0fdfbb Merge: ea04e76f db4b7e8a Author: Andy Nonaka Date: Fri Jan 4 12:47:40 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit ea04e76f72600b4ed24faec985f629494e60a336 Author: Andy Nonaka Date: Fri Jan 4 12:47:28 2019 -0800 more regridding progress Source/MaestroRegrid.cpp commit db4b7e8a7f18877ff3c96cf976052ddfb756a3a3 Author: Michael Zingale Date: Fri Jan 4 13:18:45 2019 -0500 some nets have rate tables (with .dat files) that we need to link in Exec/Make.Maestro commit e8c5b0ee41c978c584d98ee97da3d26f7aa500aa Author: Andy Nonaka Date: Thu Jan 3 18:13:00 2019 -0800 more regridding progress - still buggy. some multifabs in the Maestro class need to be rebuilt upon regridding.. I have added FIXME's in MaestroRegrid.cpp Source/MaestroRegrid.cpp commit 6da7aee67eb0c2f93a0a0dcbdb46c215d998fe40 Author: Andy Nonaka Date: Thu Jan 3 17:40:21 2019 -0800 regrid fix - I think after regrid we want the output state to live in sold, uold, etc., (not snew, unew, etc.). Now advances through most of time step 1 Source/MaestroRegrid.cpp commit 1e78a809e6ac637ba08a0be1a42404d7281cf715 Author: Andy Nonaka Date: Thu Jan 3 14:50:09 2019 -0800 change an error message to a warning message (since it doesn't abort) Source/MaestroDiag.cpp commit db5f4b7fe1c8552f79967cce5f6026ce375bb3bf Author: Andy Nonaka Date: Thu Jan 3 14:40:20 2019 -0800 fix parallel regridding bug. need to exit the MFIter loop before collecting the lateral height indicies that are tagged Source/MaestroRegrid.cpp commit ec75977ebbcab9dcaa1b6195e98fac74f3f9234a Author: Alice Harpole Date: Thu Jan 3 17:08:04 2019 -0500 test_basestate appears to work but could be improved - this isn't very robust to changes in the main code as I've customised lots of existing functions Exec/UNIT_TESTS/test_basestate/CNO/inputs-CNO Exec/UNIT_TESTS/test_basestate/GNUmakefile Exec/UNIT_TESTS/test_basestate/MaestroAdvance.cpp Exec/UNIT_TESTS/test_basestate/MaestroDt.cpp Exec/UNIT_TESTS/test_basestate/MaestroEvolve.cpp Exec/UNIT_TESTS/test_basestate/MaestroInit.cpp Exec/UNIT_TESTS/test_basestate/Problem_F.H Exec/UNIT_TESTS/test_basestate/compute_dt.F90 Exec/UNIT_TESTS/test_basestate/planar-invsq/inputs-planar-invsq Exec/UNIT_TESTS/test_basestate/planar/inputs-planar Exec/UNIT_TESTS/test_basestate/spherical/inputs-spherical_heat Exec/UNIT_TESTS/test_basestate/sub_chandra/inputs-subchandra Exec/UNIT_TESTS/test_basestate/test_basestate.f90 Exec/UNIT_TESTS/test_basestate/urca/inputs-urca_cold Exec/UNIT_TESTS/test_basestate/urca/inputs-urca_hot Exec/UNIT_TESTS/test_basestate/urca/inputs-uref Exec/UNIT_TESTS/test_basestate/wdconvect_paper/inputs.rho_cutoff_1.e-4 Exec/UNIT_TESTS/test_basestate/wdconvect_paper/inputs.rho_cutoff_1.e5 Exec/UNIT_TESTS/test_basestate/wdconvect_paper/inputs.rho_cutoff_1.e6 Source/Maestro.H Source/MaestroForce.cpp Source/Src_nd/base_state.f90 Source/Src_nd/diag.F90 Source/Src_nd/enforce_HSE.f90 Source/main.cpp commit 39597e13d78606692da76d27c9c9ec25ab96f165 Merge: 9641d2ca de133cef Author: Alice Harpole Date: Thu Jan 3 10:00:46 2019 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into unit_tests commit 9641d2ca08198051fd1026eb4e577681a8efb5e3 Author: Alice Harpole Date: Thu Jan 3 09:17:32 2019 -0500 inputs files for test_basestate Exec/UNIT_TESTS/test_basestate/CNO/inputs-CNO Exec/UNIT_TESTS/test_basestate/planar-invsq/inputs-planar-invsq Exec/UNIT_TESTS/test_basestate/planar-invsq/toy_nova_invsq.hse.1280 Exec/UNIT_TESTS/test_basestate/planar/inputs-planar Exec/UNIT_TESTS/test_basestate/planar/model.planar.768 Exec/UNIT_TESTS/test_basestate/spherical/inputs-spherical_heat Exec/UNIT_TESTS/test_basestate/spherical/spherical.hse.640 Exec/UNIT_TESTS/test_basestate/sub_chandra/README Exec/UNIT_TESTS/test_basestate/sub_chandra/inputs-subchandra Exec/UNIT_TESTS/test_basestate/sub_chandra/sub_chandra.M_WD-1.00.M_He-0.05.hse.C.768 Exec/UNIT_TESTS/test_basestate/urca/README Exec/UNIT_TESTS/test_basestate/urca/WD_M-0.5_hot.hse.5120 Exec/UNIT_TESTS/test_basestate/urca/WD_urca_nuc_M-0.5_cold_002.hse.5120 Exec/UNIT_TESTS/test_basestate/urca/WD_urca_nuc_M-0.5_hot_002.hse.5120 Exec/UNIT_TESTS/test_basestate/urca/inputs-urca_cold Exec/UNIT_TESTS/test_basestate/urca/inputs-urca_hot Exec/UNIT_TESTS/test_basestate/urca/inputs-uref Exec/UNIT_TESTS/test_basestate/wdconvect_paper/README Exec/UNIT_TESTS/test_basestate/wdconvect_paper/inputs.rho_cutoff_1.e-4 Exec/UNIT_TESTS/test_basestate/wdconvect_paper/inputs.rho_cutoff_1.e5 Exec/UNIT_TESTS/test_basestate/wdconvect_paper/inputs.rho_cutoff_1.e6 Exec/UNIT_TESTS/test_basestate/wdconvect_paper/kepler_new_6.25e8.hybrid.hse.1280 commit d2741b9d1a1674ff7cf7ac1d7307e6941f1ada6d Author: Alice Harpole Date: Wed Jan 2 17:07:29 2019 -0500 test_basestate Exec/UNIT_TESTS/test_basestate/MaestroAdvance.cpp Exec/UNIT_TESTS/test_basestate/Make.package Exec/UNIT_TESTS/test_basestate/Problem_F.H Exec/UNIT_TESTS/test_basestate/initdata.f90 Exec/UNIT_TESTS/test_basestate/test_basestate.f90 commit de133ceffb953ee3fbea7bef21bc144e094aeb8a Merge: ae71c8e4 497a8f65 Author: Andy Nonaka Date: Wed Jan 2 12:21:55 2019 -0800 Merge branch 'master' into development commit 497a8f653e6be95aceef781e4d702da8406f4275 Author: Andy Nonaka Date: Wed Jan 2 12:18:27 2019 -0800 Jan 2019 release notes RELEASE_NOTES commit 73071c7112f97a2e374267a6a805cc27f0c0231f Author: Alice Harpole Date: Wed Jan 2 14:24:36 2019 -0500 fixes so that it compiles in 1d Source/Maestro.cpp Source/MaestroAdvection.cpp Source/MaestroDt.cpp Source/Src_nd/diag.F90 Source/Src_nd/fill_3d_data.F90 Source/Src_nd/initdata.f90 Source/Src_nd/make_S.F90 Source/Src_nd/make_edge_scal.F90 Source/Src_nd/make_flux.F90 Source/Src_nd/make_scal_force.F90 Source/Src_nd/make_vel_force.F90 Source/Src_nd/mkutrans.F90 Source/Src_nd/rhoh_vs_t.F90 Source/Src_nd/update_vel.F90 Source/Src_nd/velpred.F90 commit ae71c8e4a9de8ae0e5ab779ee069f067dbbebefe Merge: eb065e0b ad46fd50 Author: Andy Nonaka Date: Wed Jan 2 11:16:57 2019 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit eb065e0b933ec876104b7c183d31295e80c222c9 Author: Andy Nonaka Date: Wed Jan 2 11:16:34 2019 -0800 index bug fix in computation of tpert for plotfile Source/MaestroPlot.cpp commit ad46fd50938c5d109f898bbe79f4988c4529f227 Author: Alice Harpole Date: Wed Jan 2 13:58:53 2019 -0500 fixed bug in 1d compilation Source/MaestroAdvection.cpp commit cace7854835eddc1a633e63ddbbeaec860d11522 Author: Alice Harpole Date: Wed Jan 2 13:58:16 2019 -0500 test_basestate Exec/UNIT_TESTS/test_basestate/GNUmakefile Exec/UNIT_TESTS/test_basestate/README Exec/UNIT_TESTS/test_basestate/_parameters Source/MaestroAdvection.cpp commit 1beae583f564ab019925c342bee3bbf67948b396 Author: Alice Harpole Date: Wed Jan 2 13:50:52 2019 -0500 test_average seems to work Exec/UNIT_TESTS/test_advect/MaestroEvolve.cpp Exec/UNIT_TESTS/test_advect/inputs_2d Exec/UNIT_TESTS/test_average/GNUmakefile Exec/UNIT_TESTS/test_average/MaestroEvolve.cpp Exec/UNIT_TESTS/test_average/Make.package Exec/UNIT_TESTS/test_average/README Exec/UNIT_TESTS/test_average/_parameters Exec/UNIT_TESTS/test_average/base_state.f90 Exec/UNIT_TESTS/test_average/initdata.f90 Exec/UNIT_TESTS/test_average/inputs_2d_planar Exec/UNIT_TESTS/test_average/inputs_3d.128.5dr.eq.dx Exec/UNIT_TESTS/test_average/main.cpp Exec/UNIT_TESTS/test_average/model.hse commit 09be81f31d06eaf39599df421148543bd2ca0ae6 Author: Alice Harpole Date: Mon Dec 31 16:36:47 2018 -0500 fixed a bug Exec/UNIT_TESTS/test_advect/MaestroEvolve.cpp Exec/UNIT_TESTS/test_advect/initdata.f90 Exec/UNIT_TESTS/test_advect/inputs_2d commit ca2a25e32b83f5e298e80d1ab0eeaa2a3d217b03 Author: Alice Harpole Date: Mon Dec 31 16:04:51 2018 -0500 It sort of works Exec/UNIT_TESTS/test_advect/MaestroEvolve.cpp Exec/UNIT_TESTS/test_advect/inputs_2d Source/Maestro.H Source/MaestroEvolve.cpp commit 3b86b57d24fbce01d80aca297e7a8a612dd29180 Author: Alice Harpole Date: Mon Dec 31 13:56:05 2018 -0500 porting test_advect Exec/UNIT_TESTS/README Exec/UNIT_TESTS/test_advect/GNUmakefile Exec/UNIT_TESTS/test_advect/MaestroEvolve.cpp Exec/UNIT_TESTS/test_advect/README Exec/UNIT_TESTS/test_advect/_parameters Exec/UNIT_TESTS/test_advect/base_state.f90 Exec/UNIT_TESTS/test_advect/initdata.f90 Exec/UNIT_TESTS/test_advect/inputs_2d commit ff79bceead577c2b00a6fd65507cc8024198067e Author: Andy Nonaka Date: Fri Dec 21 10:31:03 2018 -0800 fix array shaping bug Source/Src_nd/make_plot_variables.F90 commit c030eacadfa7c8042a2e8d6bde4c88c91dfe20dc Author: Doreen Fan Date: Wed Dec 19 15:01:32 2018 -0800 Fixed a typo. Regrid still not working for multilevel Source/Src_nd/regrid.f90 commit 676618dfa14c08de466c528558b525833b3f115e Author: Doreen Fan Date: Wed Dec 19 14:49:14 2018 -0800 Multilevel test problem in 2D Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C.2levels commit 31729dacccd0679ac85825aefccae1b10c46770e Author: Doreen Fan Date: Tue Dec 18 16:50:55 2018 -0800 Add subroutines to include buffer zone in tagging array after regrid. Planar multilevel still WIP Exec/SCIENCE/wdconvect/tagging.F90 Exec/TEST_PROBLEMS/double_bubble/tagging.F90 Exec/TEST_PROBLEMS/incomp_shear_jet/tagging.F90 Exec/TEST_PROBLEMS/reacting_bubble/tagging.F90 Exec/TEST_PROBLEMS/rt/tagging.F90 Exec/TEST_PROBLEMS/test_convect/tagging.F90 Source/Maestro.H Source/MaestroInit.cpp Source/MaestroRegrid.cpp Source/Maestro_F.H Source/Src_nd/base_state_geometry.f90 Source/Src_nd/tagging.F90 commit 634928c915de4bceb0094169cabd554afc6521ee Merge: 8176401f 81173e17 Author: Doreen Fan Date: Tue Dec 18 12:09:28 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 8176401fbb908cfa46ad15075e0186d48443ff58 Author: Doreen Fan Date: Tue Dec 18 12:09:17 2018 -0800 Initialize normal variable before writing plt_InitData for regression testing Source/MaestroInit.cpp commit 81173e17260eb4b8413d5519ead869d624832462 Author: Michael Zingale Date: Tue Dec 18 09:48:19 2018 -0500 add travis badge README.md commit bdf3df604e8b7c3891da11d77065569b37dbcfab Merge: a218ff7f 3d70a26f Author: Doreen Fan Date: Mon Dec 17 19:23:11 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit a218ff7fe0ced2ee7fd9a24b4c6dee59bf7f3531 Author: Doreen Fan Date: Mon Dec 17 19:22:58 2018 -0800 Add subroutines for planar multilevel functionality Source/MaestroAverage.cpp Source/MaestroRegrid.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/base_state_geometry.f90 Source/Src_nd/regrid.f90 commit 7340e18eb7d6bc1316eeb4613bb9c1bcb133a31e Author: Doreen Fan Date: Mon Dec 17 19:21:45 2018 -0800 Change shape of tagging array input in Fortran Exec/SCIENCE/wdconvect/tagging.F90 Exec/TEST_PROBLEMS/double_bubble/tagging.F90 Exec/TEST_PROBLEMS/incomp_shear_jet/tagging.F90 Exec/TEST_PROBLEMS/reacting_bubble/tagging.F90 Exec/TEST_PROBLEMS/rt/tagging.F90 Exec/TEST_PROBLEMS/test_convect/tagging.F90 Source/Maestro_F.H Source/Src_nd/tagging.F90 commit 3d70a26fcdae61f7e8f27ee838c9803773492af9 Author: Michael Zingale Date: Mon Dec 17 19:34:43 2018 -0500 no longer needed _config.yml commit 8a2e69ca58094cfd8b28072908dc7b7650a02ba0 Author: Michael Zingale Date: Mon Dec 17 19:20:44 2018 -0500 more doc fixes deploy_docs.sh sphinx_docs/source/getting_started.rst commit ca030d687f703ea0288db64089fd4377853c8612 Author: Michael Zingale Date: Mon Dec 17 19:13:57 2018 -0500 fix table deploy_docs.sh sphinx_docs/source/introduction.rst commit e0d9d5b76361be0e32d4f0959b23db57747a9540 Author: Michael Zingale Date: Mon Dec 17 18:35:17 2018 -0500 comment out the bit about no changes deploy_docs.sh commit 7911dec06958eb5b4e9293aa43f5d5b7c23747ab Author: Michael Zingale Date: Mon Dec 17 18:29:40 2018 -0500 add a first pass at a zenodo JSON for DOI minting .zenodo.json commit 4adaf7c87d1abe5f47de63a996a0a196b86b97d0 Merge: 8e6189dd 64b0922d Author: Doreen Fan Date: Mon Dec 17 15:29:11 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 64b0922d9342f67f7d93a1da479a1e07f79d2f0c Author: Michael Zingale Date: Mon Dec 17 18:27:18 2018 -0500 convert docs to sphinx (#34) This creates a new webpage, converts the User's Guide to sphinx, and sets up travis. .gitignore .travis.yml Docs/FAQ/GNUmakefile Docs/FAQ/faq.tex Docs/FAQ/paper.tex Docs/GNUmakefile Docs/Godunov_notes/GNUmakefile Docs/Godunov_notes/Godunov.tex Docs/Godunov_notes/paper.tex Docs/MAESTROeXUsersGuide.tex Docs/MESA/GNUmakefile Docs/MESA/README Docs/MESA/hopper_compile.tex Docs/MESA/instructions.tex Docs/MESA/paper.tex Docs/SDC/GNUmakefile Docs/SDC/README Docs/SDC/flowchart_SDC.eps Docs/SDC/flowchart_SDC.odg Docs/SDC/paper.tex Docs/SDC/sdc.tex Docs/analysis/GNUmakefile Docs/analysis/analysis.tex Docs/analysis/paper.tex Docs/architecture/GNUmakefile Docs/architecture/amrex_directory.odg Docs/architecture/amrex_directory2.eps Docs/architecture/architecture.tex Docs/architecture/base_grid.eps 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sphinx_docs/source/Godunov.rst sphinx_docs/source/_static/theme_overrides.css sphinx_docs/source/analysis.rst sphinx_docs/source/architecture.rst sphinx_docs/source/beta0.rst sphinx_docs/source/common_parameters.rst sphinx_docs/source/conf.py sphinx_docs/source/ctof.rst sphinx_docs/source/enthalpy.rst sphinx_docs/source/eos_notes.rst sphinx_docs/source/eta.rst sphinx_docs/source/faq.rst sphinx_docs/source/flowchart.rst sphinx_docs/source/getting_started.rst sphinx_docs/source/index.rst sphinx_docs/source/initial_models.rst sphinx_docs/source/introduction.rst sphinx_docs/source/lo_density.rst sphinx_docs/source/maestro_doc.bib sphinx_docs/source/makefiles.rst sphinx_docs/source/managingjobs.rst sphinx_docs/source/mathsymbols.tex sphinx_docs/source/mg.rst sphinx_docs/source/networks.rst sphinx_docs/source/param_intro.rst sphinx_docs/source/pert.rst sphinx_docs/source/planar_invsq_basestate.rst sphinx_docs/source/plt00133_tfromp.png sphinx_docs/source/preface.rst sphinx_docs/source/problems.rst sphinx_docs/source/references.rst sphinx_docs/source/rotation.rst sphinx_docs/source/sdc.rst sphinx_docs/source/spherical_basestate.rst sphinx_docs/source/thermo_notes.rst sphinx_docs/source/unit_tests.rst sphinx_docs/source/visualization.rst sphinx_docs/source/volume_discrepancy.rst commit 8e6189dddf01a7a6c1aa7e8083a6c9e2adac52ed Author: Doreen Fan Date: Mon Dec 17 14:30:35 2018 -0800 Cleanup advance routine Source/MaestroAdvanceIrreg.cpp commit 6ff3a5e1e9c753865e7da74efae2a6550fa9aa68 Author: Doreen Fan Date: Thu Dec 13 17:32:09 2018 -0800 Updated init_multilevel subroutine for planar multilevel problems. Source/Maestro.H Source/MaestroInit.cpp Source/MaestroRegrid.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/base_state_geometry.f90 commit 13b2c4bfca2aa4692eb823f9f97c0cb21cb14285 Author: Doreen Fan Date: Thu Dec 13 17:30:49 2018 -0800 Fix bug in MakeMagvel for DIM=2. Source/MaestroPlot.cpp commit 3425ebc6abc7d2b36be7e7a7098eaa7e243f3072 Author: Doreen Fan Date: Thu Dec 13 10:53:39 2018 -0800 Some groundwork for >1 chunks of data in init_multilevel subroutine. Source/MaestroInit.cpp Source/MaestroRegrid.cpp Source/Maestro_F.H Source/Src_nd/base_state_geometry.f90 commit 8a57ad955f66e4b31baa625fe31f4b647387f33a Author: Michael Zingale Date: Thu Dec 13 10:04:16 2018 -0500 add a CITATION file CITATION commit 2defa92189a88314e82e629bf2959cb5713bfb4c Merge: 4d94c00d e9554919 Author: Andy Nonaka Date: Wed Dec 12 09:46:52 2018 -0800 Merge pull request #32 from AMReX-Astro/plot_variables Plot variables commit e9554919f7d899f8f63f66d34c6f09cc8eb25258 Author: Andy Nonaka Date: Wed Dec 12 09:45:48 2018 -0800 resolving conflict Exec/TEST_PROBLEMS/test_stability/probin commit 0402ef5a9fa4a3980f0a6c7a1d7c68e72f0b1f4e Author: Andy Nonaka Date: Wed Dec 12 09:30:29 2018 -0800 fix a bug in spherical magvel for plotfile Source/Maestro.H Source/MaestroPlot.cpp Source/Maestro_F.H Source/Src_nd/make_plot_variables.F90 commit 4d94c00d0f14e50a5c983e45289b1176b0b74b28 Author: Doreen Fan Date: Tue Dec 11 17:50:47 2018 -0800 Modify and add tagging subroutines for multilevel planar solver. Exec/SCIENCE/wdconvect/tagging.F90 Exec/TEST_PROBLEMS/double_bubble/tagging.F90 Exec/TEST_PROBLEMS/incomp_shear_jet/tagging.F90 Exec/TEST_PROBLEMS/reacting_bubble/tagging.F90 Exec/TEST_PROBLEMS/rt/tagging.F90 Exec/TEST_PROBLEMS/test_convect/tagging.F90 Exec/TEST_PROBLEMS/test_convect/tagging.f90 Source/Maestro.H Source/MaestroAdvanceIrreg.cpp Source/MaestroRegrid.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/tagging.F90 Source/Src_nd/tagging.f90 commit 6e4f189c6bdbac40b7aa7cb1348ae1608b6ef4d0 Author: Doreen Fan Date: Tue Dec 11 15:50:38 2018 -0800 Update new temporal scheme for even base state spacing Source/MaestroAdvanceAvg.cpp commit 2dfd848b4fa912bd04f0f4f6b7a4b0c7a0e3930f Author: Andy Nonaka Date: Mon Dec 10 19:17:58 2018 -0800 get rid of probin files; embed at bottom of inputs files. regression test underway Exec/SCIENCE/wdconvect/inputs_3d_C Exec/SCIENCE/wdconvect/inputs_3d_C.128 Exec/SCIENCE/wdconvect/inputs_3d_C.128.2levels Exec/SCIENCE/wdconvect/inputs_3d_C.128.avgbase.dr Exec/SCIENCE/wdconvect/inputs_3d_C.128.avgbase.dx Exec/SCIENCE/wdconvect/inputs_3d_C.128.exactbase Exec/SCIENCE/wdconvect/inputs_3d_C.64 Exec/SCIENCE/wdconvect/inputs_3d_C.64.exactbase Exec/SCIENCE/wdconvect/inputs_3d_regression Exec/SCIENCE/wdconvect/inputs_omp_3d_regression Exec/SCIENCE/wdconvect/probin Exec/TEST_PROBLEMS/double_bubble/inputs_2d_C Exec/TEST_PROBLEMS/double_bubble/inputs_2d_regression Exec/TEST_PROBLEMS/double_bubble/probin Exec/TEST_PROBLEMS/incomp_shear_jet/inputs_2d_C Exec/TEST_PROBLEMS/incomp_shear_jet/inputs_2d_regression Exec/TEST_PROBLEMS/incomp_shear_jet/probin Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_dpdt Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_omp_2d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_omp_3d_regression Exec/TEST_PROBLEMS/reacting_bubble/probin Exec/TEST_PROBLEMS/rt/inputs_2d_C Exec/TEST_PROBLEMS/rt/inputs_2d_regression Exec/TEST_PROBLEMS/rt/probin Exec/TEST_PROBLEMS/test_convect/inputs_2d_C Exec/TEST_PROBLEMS/test_convect/inputs_2d_regression Exec/TEST_PROBLEMS/test_convect/probin Exec/TEST_PROBLEMS/test_stability/inputs_2d_C Exec/TEST_PROBLEMS/test_stability/probin Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/maestro_init.f90 Source/param/_cpp_parameters Source/param/runtime.probin.template Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H commit cc4f031197654fe3db535975c1766e01dbe8756b Author: Andy Nonaka Date: Mon Dec 10 18:55:08 2018 -0800 unneeded file Source/param/extern_probin.template commit ea1bfad6cc0c900a98459d4e60ce205bc60ba7be Author: Alice Harpole Date: Mon Dec 10 16:23:34 2018 -0500 only calculate nPlot once Source/Maestro.H Source/MaestroPlot.cpp commit 1849113311aee61e524751eb16eed7d1a9948a2d Merge: 9fb1f94a 3051c96a Author: Alice Harpole Date: Mon Dec 10 12:44:37 2018 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into plot_variables commit 3051c96a743cc040080be2b289a5f135e0d9a35b Author: Weiqun Zhang Date: Wed Dec 5 14:26:50 2018 -0800 amrex changed Source/Src_nd/AMReX_filcc_mod.F90 commit 9fd0b91572b5f6f36d5112dcc21acaf55d8aeb8a Merge: a613883d 47affde7 Author: Doreen Fan Date: Wed Dec 5 14:15:49 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit a613883d9faf2b23ef165dd67a769fbc9878b921 Author: Doreen Fan Date: Wed Dec 5 14:15:33 2018 -0800 Compute dp/dt term in 1) Predictor step: using psi, and 2) Corrector step: using p0 and dt. This makes sure that enforce_HSE is applied correctly at the end of each time step. Source/MaestroAdvanceIrreg.cpp Source/Src_nd/enforce_HSE.f90 Source/Src_nd/make_psi.F90 commit 9fb1f94a70eeca68f865cdab222f0dcb955965fe Author: Alice Harpole Date: Wed Dec 5 15:33:23 2018 -0500 reverse changes to inputs files Exec/TEST_PROBLEMS/incomp_shear_jet/inputs_2d_C Exec/TEST_PROBLEMS/rt/inputs_2d_C Exec/TEST_PROBLEMS/test_convect/inputs_2d_C commit c6ceb58072952e59c0bf9592b043af488e926d26 Author: Alice Harpole Date: Wed Dec 5 15:30:11 2018 -0500 checked plotting works for all example problems Exec/TEST_PROBLEMS/incomp_shear_jet/inputs_2d_C Exec/TEST_PROBLEMS/reacting_bubble/GNUmakefile Exec/TEST_PROBLEMS/rt/inputs_2d_C Exec/TEST_PROBLEMS/test_convect/inputs_2d_C Exec/TEST_PROBLEMS/test_stability/make_heating.F90 Exec/TEST_PROBLEMS/test_stability/probin Source/Maestro.H Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/MaestroPlot.cpp Source/Src_nd/burner_loop.f90 commit 5b44f4415134efc8dcd7026f390cc4b7f42919ee Author: Alice Harpole Date: Wed Dec 5 11:32:24 2018 -0500 tpert, S, sponge Source/Maestro.H Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/MaestroPlot.cpp commit b53d278805f4361dbee2f7ea8540b346495a900c Author: Alice Harpole Date: Wed Dec 5 10:17:41 2018 -0500 h, deltap Source/MaestroPlot.cpp commit 98766be5e7d6af288f17c0fb79a281781e25dda7 Author: Alice Harpole Date: Tue Dec 4 17:29:24 2018 -0500 pi_divu Source/Maestro.H Source/MaestroPlot.cpp Source/Maestro_F.H Source/Src_nd/make_plot_variables.F90 commit 0efbbcde6cf0b17ae185d8bf31a620b068b60395 Author: Alice Harpole Date: Tue Dec 4 15:09:11 2018 -0500 conductivity and thermal Source/MaestroPlot.cpp commit a402be7866bc90fd2f666b8d2697e80cf4a6ed7d Author: Alice Harpole Date: Tue Dec 4 14:51:18 2018 -0500 h0 Source/MaestroPlot.cpp commit 7d5f30963514e0b6e26f6410cc4932f607af5374 Author: Alice Harpole Date: Tue Dec 4 14:44:35 2018 -0500 divw0 Source/Maestro.H Source/MaestroPlot.cpp Source/Maestro_F.H Source/Src_nd/make_plot_variables.F90 commit 55eee8fb2d8648c666f13fc94ccc733c2e3a37ab Author: Alice Harpole Date: Tue Dec 4 13:48:59 2018 -0500 soundspeed, fixed indexing Exec/TEST_PROBLEMS/rt/inputs_2d_C Source/Maestro.H Source/MaestroPlot.cpp Source/MaestroRhoHT.cpp Source/Maestro_F.H Source/Src_nd/rhoh_vs_t.F90 commit 8d794087728b2573f0a6c24c4948ca510de112f1 Author: Alice Harpole Date: Tue Dec 4 11:49:19 2018 -0500 gpi, added if statements Source/MaestroPlot.cpp commit fbf0671e68bc7755b1ec6260c09e5ecc8dda29f1 Author: Alice Harpole Date: Tue Dec 4 11:17:28 2018 -0500 Hext, enucdot Source/MaestroPlot.cpp commit a1027dad091ce6cb5a14f88de8acdb131e2f2b32 Author: Alice Harpole Date: Tue Dec 4 11:09:41 2018 -0500 p0pluspi and pioverp0 Source/MaestroPlot.cpp commit fba87cdde0877eb2d9ed9d7d3ead1700ccdb6a97 Author: Alice Harpole Date: Tue Dec 4 10:54:11 2018 -0500 omegadot Source/MaestroPlot.cpp commit 6933328549a43d27775fe7b64d32298e9bb03560 Author: Alice Harpole Date: Tue Dec 4 10:21:02 2018 -0500 deltgamma_sphr Source/MaestroPlot.cpp Source/Maestro_F.H Source/Src_nd/make_plot_variables.F90 commit 019ae480596a7ab4164b2f85987c8afcc905d41d Merge: 8663b83a 47affde7 Author: Alice Harpole Date: Tue Dec 4 10:12:58 2018 -0500 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into plot_variables commit 8663b83a7ffb2e165a135d9d8a7a51d65c0061c4 Author: Alice Harpole Date: Tue Dec 4 10:12:43 2018 -0500 deltagamma Source/Maestro.H Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/MaestroPlot.cpp Source/Maestro_F.H Source/Src_nd/make_plot_variables.F90 commit 3db7ebd25c570c86ae02396099856449754d902b Merge: 044fe1ef 2307b9f8 Author: Alice Harpole Date: Mon Dec 3 17:27:19 2018 -0500 vorticity commit 47affde7229978452a180ef3ab77bab63b0b40c6 Author: Andy Nonaka Date: Mon Dec 3 12:18:03 2018 -0800 December 2018 release notes RELEASE_NOTES commit 044fe1efbfa41cd2f30c9adfdd03f41dcf6cb427 Author: Alice Harpole Date: Mon Dec 3 14:56:29 2018 -0500 adiabatic excess Source/Maestro.H Source/MaestroPlot.cpp Source/Maestro_F.H Source/Src_nd/make_plot_variables.F90 commit d17f1ee265f51ce91877797b2ca0ee7c3a6e6a31 Author: Alice Harpole Date: Mon Dec 3 14:37:40 2018 -0500 Added radial and circular velocities Exec/TEST_PROBLEMS/rt/inputs_2d_C Source/Maestro.H Source/MaestroPlot.cpp Source/Maestro_F.H Source/Src_nd/make_plot_variables.F90 commit 2307b9f8e65f1441cdb9447e051e9bb9e896eb80 Author: Andy Nonaka Date: Mon Dec 3 11:24:45 2018 -0800 fix comment Source/MaestroPlot.cpp commit 43d8aa0ac148f3bd2d15d1543592295841a8b1ac Author: Andy Nonaka Date: Mon Dec 3 11:23:51 2018 -0800 fixed bug in writing mach number to plotfile Source/MaestroPlot.cpp commit e24b76f10506fc7844b0f236515fcea5225058be Author: Andy Nonaka Date: Mon Dec 3 11:05:00 2018 -0800 fix 2d compilation issue Source/Src_nd/rhoh_vs_t.F90 commit a4d8eeee096cc8481fdd6fdc63cccb133363fdc9 Author: Alice Harpole Date: Mon Dec 3 13:53:39 2018 -0500 Added magvel Source/Maestro.H Source/MaestroPlot.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/make_plot_variables.F90 Source/Src_nd/rhoh_vs_t.F90 commit 53710c71b63598ca42f4466776d24a9523e1ab55 Author: Doreen Fan Date: Fri Nov 30 13:17:40 2018 -0800 Use non-constant gravity to compute dp/dt term on irregularly spaced grid Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrreg.cpp Source/Maestro_F.H Source/Src_nd/make_psi.F90 commit 790189f874bc95fd8452a5bdbff7fe888e7c24d0 Author: Doreen Fan Date: Thu Nov 29 15:40:51 2018 -0800 Compute dp/dt term using etarho instead of p0 and dt. Test in progress. Source/MaestroAdvanceIrreg.cpp Source/MaestroInit.cpp Source/Src_nd/average.f90 commit 946d88d6380799699217a821a1b4ca99f1746747 Merge: 7aebe72d 55c53944 Author: Andy Nonaka Date: Thu Nov 29 11:52:21 2018 -0800 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 7aebe72d8365527b55cf1966625179a956242f70 Author: Andy Nonaka Date: Thu Nov 29 11:51:49 2018 -0800 remove unused code (Weiqun simplified the boundary condition class by making the AMReX classes be more flexible) Source/MaestroAdvance.cpp Source/Make.package Source/PhysBCFunctMaestro.H Source/PhysBCFunctMaestro.cpp commit 55c539441857c2b4035f1e7643c958e73823ebef Author: Alice Harpole Date: Wed Nov 28 12:39:01 2018 -0500 Output Mach number to plotfile Source/Maestro.H Source/MaestroPlot.cpp Source/MaestroRhoHT.cpp Source/Maestro_F.H Source/Src_nd/rhoh_vs_t.F90 commit b7531092e571f5875c65f3cdd6d87efcc73d8105 Author: Doreen Fan Date: Mon Nov 26 18:55:58 2018 -0800 Fix bugs in make_beta0_irreg and clean up AdvanceIrreg. evolve_base_state still WIP. Source/MaestroAdvanceIrreg.cpp Source/Src_nd/make_beta0.f90 commit e7848df301fdb8da04fd43fae41ee004a0f1cd81 Author: Doreen Fan Date: Mon Nov 26 18:29:54 2018 -0800 Reformulate make_beta0 for irregular base state spacing Source/MaestroAdvanceIrreg.cpp Source/Src_nd/average.f90 Source/Src_nd/make_beta0.f90 Source/Src_nd/make_psi.F90 commit 5b7b2e06c28d162092124e9331a691a124105a58 Author: Andy Nonaka Date: Mon Nov 26 12:45:53 2018 -0800 remove extra (unnneeded) OMP pragmas in ErrorEst (tagging) routine Source/MaestroRegrid.cpp commit a7248567b33666c4924d57133789548fbcaddab9 Author: Andy Nonaka Date: Fri Nov 16 14:27:33 2018 -0800 add tile size to job_info file for OMP runs Source/MaestroPlot.cpp commit 231041dc08b44f55678c7f13fe51c37e1087a420 Author: Andy Nonaka Date: Fri Nov 16 13:27:25 2018 -0800 OMP regression tests Exec/TEST_PROBLEMS/reacting_bubble/inputs_omp_2d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_omp_3d_regression commit f6ba1d30e05d9d677253ab8c72567142b8d51fa4 Author: Andy Nonaka Date: Fri Nov 16 13:24:06 2018 -0800 setting up threaded regression Exec/SCIENCE/wdconvect/inputs_omp_3d_regression commit 150368513365e7af331cb56c5e077f85269fd204 Author: Andy Nonaka Date: Fri Nov 16 12:54:08 2018 -0800 change these test problems so they have multiple grids Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_regression commit 97c1bbd5ba1ad919b77a03daa028fe66571f7319 Author: Alice Harpole Date: Thu Nov 15 16:13:36 2018 -0500 check temperr and denserr have enough elements before assigning them to tag_err Source/MaestroSetup.cpp commit 105627d4d6c57841102a6189e2475366d60dd16e Author: Alice Harpole Date: Thu Nov 15 14:04:09 2018 -0500 deallocated some arrays to fix another leak Source/Src_nd/velpred.F90 commit 9dd14eb54de630f8f4bdbb68a66e8c45e02c2ea3 Author: Alice Harpole Date: Thu Nov 15 13:01:21 2018 -0500 Fixed a memory leak Source/MaestroPlot.cpp commit 05ed377e6a5d12a0bfe3da6edac35d8f5546de1c Author: Alice Harpole Date: Thu Nov 15 12:25:03 2018 -0500 Initialised some Multifabs flagged by valgrind Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp commit a4dcbdcc4ccb5d773dab04e2b00116926f819afd Author: Alice Harpole Date: Wed Nov 14 18:01:08 2018 -0500 Fixed a couple of (small) memory leaks Source/MaestroPlot.cpp commit 36fe42de380a25e66d136742ee138e7af701fdfa Author: Andy Nonaka Date: Tue Nov 13 11:35:49 2018 -0800 fix OMP bug Source/Src_nd/make_psi.F90 commit 9e13343beca84219e08a0818ce01942af1b0124a Merge: 364aa0c1 29dff1ac Author: Andy Nonaka Date: Tue Nov 13 11:22:30 2018 -0800 Merge pull request #28 from AMReX-Astro/physbc changes due to AMReX changes commit 29dff1ac8c00784c7629e18f2f02daf7f629c74a Author: Weiqun Zhang Date: Tue Nov 13 11:03:59 2018 -0800 changes due to AMReX changes Source/MaestroFillData.cpp Source/PhysBCFunctMaestro.H Source/PhysBCFunctMaestro.cpp commit 364aa0c1722e936f988b6f7978c1510bfc5ce10a Author: Donald E. Willcox Date: Wed Nov 7 16:28:28 2018 -0800 Update interface to StarKiller Microphysics conductivity routine. (#23) * Put conductivity in eos_type. Revise interface to conductivity routine. * Update actual_conductivity interface in constant conductivity. Microphysics/EOS/eos_type.f90 Microphysics/conductivity/conductivity.F90 Microphysics/conductivity/constant/constant_conductivity.f90 RELEASE_NOTES Source/Src_nd/make_explicit_thermal.F90 commit be778ec7e2bd13298ae1f6255c8b0b037db641d6 Author: Andy Nonaka Date: Wed Nov 7 16:24:30 2018 -0800 for the new temporal integrator, there is no need to at dt*dp0/dt to rhoh0_new in the corrector step. This was already taken care of in the enthalpy forcing for the cell update Source/MaestroEnthalpyAdvance.cpp commit 5b444d6080e5a541ee2f9e35c1b87617a527ad71 Author: Doreen Fan Date: Tue Nov 6 13:55:42 2018 -0800 Test runs with new time-stepping scheme: *.dx = even spacing, *.dr = uneven spacing of base states Exec/SCIENCE/wdconvect/inputs_3d_C.128.avgbase.dr Exec/SCIENCE/wdconvect/inputs_3d_C.128.avgbase.dx commit 624393d4ee79b92110db8aa69e8845ddc1664f6f Author: Doreen Fan Date: Tue Nov 6 13:53:19 2018 -0800 Add option (average_base_state) to use new time stepping scheme with even base state spacing. Source/Maestro.H Source/MaestroAdvanceAvg.cpp Source/MaestroAdvanceIrregTest.cpp Source/MaestroDt.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/Make.package Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H commit d2fa3f227fd0d3197eb32232c81b716fc4bdc902 Author: Doreen Fan Date: Tue Nov 6 11:02:40 2018 -0800 fixed bug in make_edge_scal_3d with ppm_trace_forces option on Source/Src_nd/make_edge_scal.F90 Source/Src_nd/velpred.F90 commit 8df6ff9c452c2437ba0eebf7b07700fa1505413a Author: Doreen Fan Date: Mon Nov 5 15:13:19 2018 -0800 Port ppm_trace_forces functionality from MAESTRO. Did not change default value. Source/MaestroAdvance.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvection.cpp Source/MaestroVelocityAdvance.cpp Source/Maestro_F.H Source/Src_nd/make_edge_scal.F90 Source/Src_nd/velpred.F90 Source/param/_cpp_parameters Source/param_includes/maestro_params.H Source/param_includes/meth_params.F90 commit a564eb64fa0b22f8a36f2aa4f7ebc5b767c47507 Author: Doreen Fan Date: Mon Nov 5 10:13:44 2018 -0800 Remove dpdt terms, and instead compute psi as dpdt term for irregular base state Source/MaestroAdvanceIrreg.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/make_psi.F90 commit e761f6a4aa9a7c76ddbc6dd2a3f3ffc35c24db7a Author: Michael Zingale Date: Fri Nov 2 14:20:13 2018 -0400 port of Johann's gravity wave problem Exec/TEST_PROBLEMS/test_stability/GNUmakefile Exec/TEST_PROBLEMS/test_stability/Make.package Exec/TEST_PROBLEMS/test_stability/README.md Exec/TEST_PROBLEMS/test_stability/_parameters Exec/TEST_PROBLEMS/test_stability/initdata.f90 Exec/TEST_PROBLEMS/test_stability/inputs_2d_C Exec/TEST_PROBLEMS/test_stability/model.hse Exec/TEST_PROBLEMS/test_stability/probin commit fe4c2b00abf489f26a04154e3fe1d80c6af88a88 Author: Doreen Fan Date: Thu Nov 1 14:31:25 2018 -0700 Add make_rhoh_flux subroutine for irregular base state that uses rhoh0 values instead of rho0 and h0 Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvection.cpp Source/Maestro_F.H Source/Src_nd/make_flux.F90 Source/Src_nd/make_scal_force.F90 commit bead35fe85e5469196990c3cff59a61eeab8a043 Author: Andy Nonaka Date: Thu Nov 1 08:33:51 2018 -0700 November 2018 release notes RELEASE_NOTES commit 54477984cc72b9e3e07cd2ea863161de15fa1fcf Author: Andy Nonaka Date: Fri Oct 19 14:24:25 2018 -0700 indexing bug Source/MaestroPlot.cpp commit e9008a32ae9628a25c29dd19a342e405f574e9ee Author: Andy Nonaka Date: Fri Oct 19 13:49:35 2018 -0700 fix error in plotfile writing... still something wrong Source/MaestroPlot.cpp commit e1dd077348ec21fb1ef8be383759242ee1f085b4 Author: Andy Nonaka Date: Fri Oct 19 11:47:50 2018 -0700 write out rhoh0, rhopert, and rhohpert to plotfile. will update benchmarks Source/Maestro.H Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/MaestroPlot.cpp commit 3bd5082ca4e8b32b94cba0026fc4c8b0b1d823dd Author: Andy Nonaka Date: Wed Oct 17 17:12:17 2018 -0700 print out what level you are at on each line Source/Src_nd/debug.F90 commit 7487f1d5df98f09e353712813353197140ce3bcc Merge: 3e5af6f9 9ad31b25 Author: Andy Nonaka Date: Wed Oct 17 16:23:43 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 3e5af6f9c01e6cf44ee60641dce576d61c7b720c Author: Andy Nonaka Date: Wed Oct 17 16:23:31 2018 -0700 sync up with single level case Exec/SCIENCE/wdconvect/inputs_3d_C.128.2levels commit 9ad31b25d17199096a5aa55ee5a3141a099bc771 Author: Doreen Fan Date: Tue Oct 16 18:36:38 2018 -0700 gamma1bar_old should be set to gamma1bar_new at end of each time step Source/MaestroEvolve.cpp commit f28c60e42094cc7af82f374fbfc96e5d388b572b Author: Andy Nonaka Date: Tue Oct 16 17:10:48 2018 -0700 sync with MAESTRO Exec/SCIENCE/wdconvect/inputs_3d_C.64 commit 72f8b656d29e0c3b930c88946e3721aa42969679 Author: Andy Nonaka Date: Tue Oct 16 17:08:21 2018 -0700 sync up with MAESTRO Exec/SCIENCE/wdconvect/inputs_3d_C.128 commit c42e3cfb4683a7d3024026fd6c26f11b6a0b39b0 Merge: 24060a3b de9d0f6d Author: Doreen Fan Date: Mon Oct 15 16:27:45 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 24060a3be22c45c9e7060e51b8df1abd8f080385 Author: Doreen Fan Date: Mon Oct 15 15:22:15 2018 -0700 need to extend diagfile buffer to include max Mach Source/MaestroDiag.cpp Source/MaestroSetup.cpp commit de9d0f6d02c70124603fa41e4b21cb4dd457ff6e Author: Andy Nonaka Date: Mon Oct 15 13:32:38 2018 -0700 revert files I accidentally commited with the last commit Exec/SCIENCE/wdconvect/GNUmakefile Exec/SCIENCE/wdconvect/inputs_3d_C.128.2levels Source/MaestroForce.cpp commit 05b758e3dbdf3559fd4337e298693be8df6f02d0 Author: Andy Nonaka Date: Mon Oct 15 13:29:28 2018 -0700 wrote a utility Maestro::WriteMF, that can write the contents of a multilevel cell-centered multifab to an actual plotfile (as opposed to VisMF::Write, which can only write out 1 level at a time) Exec/SCIENCE/wdconvect/GNUmakefile Exec/SCIENCE/wdconvect/inputs_3d_C.128.2levels Source/Maestro.H Source/MaestroDebug.cpp Source/MaestroForce.cpp commit 5a6ff77f8c3d5fcb950a6ca352be5221377c7969 Merge: fbe283aa 710f8d4b Author: Doreen Fan Date: Mon Oct 15 10:17:41 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit fbe283aae8b68d2948e72b84fcdb4da5947cc4f1 Author: Doreen Fan Date: Mon Oct 15 10:17:29 2018 -0700 output max Mach number for diagnosis Source/MaestroDiag.cpp commit f2a855616ab77e754c4fff710808f113b264a4a9 Author: Doreen Fan Date: Mon Oct 15 10:16:54 2018 -0700 must include dpdt term in forcing term with irregularly spaced base state Source/Src_nd/make_scal_force.F90 commit 710f8d4b135fc989a7fb9127b61465c84f14807b Author: Donald E. Willcox Date: Sat Oct 13 22:05:28 2018 -0400 Updated burn type and DEFINES for sparse jacobian interface in Microphysics. Exec/Make.Maestro Microphysics/networks/burn_type.F90 commit e0b700aad0556bacde7c0ffdbacbf104e08788a7 Author: Doreen Fan Date: Thu Oct 11 15:09:43 2018 -0700 create make_s0mac subroutine for irregularly spaced base state Source/MaestroFill3dData.cpp Source/Maestro_F.H Source/Src_nd/fill_3d_data.F90 commit 0a0b08466c0ed2b0f7ae45ad247c5058a8b51bec Author: Doreen Fan Date: Thu Oct 11 15:08:08 2018 -0700 added irregular base state considerations Microphysics/networks/burn_type.F90 Source/Src_nd/compute_dt.F90 Source/Src_nd/make_edge_state.f90 commit b8f0a957857ccf257aa533ef2d4a8c367a735f06 Author: Doreen Fan Date: Thu Oct 11 14:14:04 2018 -0700 Update burn_type to be compatible with latest Microphysics update Microphysics/networks/burn_type.F90 commit 1c173759041756bb60c10b6dd9a76ef790024899 Author: Doreen Fan Date: Wed Oct 10 16:06:07 2018 -0700 Need new subroutine for computing sponge on irregular base state array Source/MaestroAdvanceIrreg.cpp Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/sponge.F90 commit 1c3107b26e9ab3cb8d16d77766e7eff81cedaaec Merge: 84c76fea 3b4e10ba Author: Doreen Fan Date: Wed Oct 10 14:17:44 2018 -0700 change HALF to 0.5d0 commit 84c76fea52fc13a0a9ad8aaf465e05451bb871b6 Author: Doreen Fan Date: Wed Oct 10 14:11:59 2018 -0700 change HALF to 0.5d0 Source/Src_nd/diag.F90 commit 3b4e10ba3675b00a84445929afdd75545d6a38cb Author: Alice Harpole Date: Tue Oct 9 17:12:25 2018 -0700 elseif -> elif Source/Src_nd/diag.F90 commit fdec08d3b84b704c7ab26535d0056b6eac30e16a Merge: bbec23e9 4643ef76 Author: Alice Harpole Date: Tue Oct 9 17:17:21 2018 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit bbec23e9d950b8e8188922bf68ddca113eb4e27f Author: Alice Harpole Date: Tue Oct 9 17:16:57 2018 -0400 elsif -> elseif Source/Src_nd/diag.F90 commit 4643ef76d349ee3f7c3a094f08ebc54152428d60 Author: Doreen Fan Date: Mon Oct 8 16:05:00 2018 -0700 allow computation of edge states when use_exact_base is turned on Source/MaestroAdvanceIrreg.cpp Source/MaestroAdvection.cpp commit fede234930211c4e7e1b62ba2a752fa5f9a016c7 Author: Andy Nonaka Date: Fri Oct 5 16:50:08 2018 -0700 fixed fill_umac_ghost to fill the corner ghost cells correctly. Note I had to disable tiling in this routine only to do this easily. Source/MaestroFillData.cpp Source/Src_nd/fill_umac_ghost.F90 commit 025eba1b71ebe53574c30a0b494d0b546406ebcb Author: Andy Nonaka Date: Fri Oct 5 15:37:38 2018 -0700 predict (rhoh)' predict rho' and X Exec/SCIENCE/wdconvect/inputs_3d_C.128.exactbase Exec/SCIENCE/wdconvect/inputs_3d_C.64.exactbase commit 5e419c4678802f77a77ff5874d5957787f122793 Author: Andy Nonaka Date: Wed Oct 3 18:22:51 2018 -0700 fix typecheck issue Source/Src_nd/initdata.f90 commit 1dc484314d02f3c258e62bd196f8142ffbad74f7 Author: Andy Nonaka Date: Wed Oct 3 18:22:14 2018 -0700 fix a typecheck problem Exec/SCIENCE/wdconvect/initdata.f90 commit 8b04128dba9bf5faa8c18f9e902181bdb42b99cd Author: Andy Nonaka Date: Wed Oct 3 18:20:36 2018 -0700 make mask non-optional Source/MaestroAverage.cpp Source/MaestroDiag.cpp Source/Maestro_F.H Source/Src_nd/average.f90 Source/Src_nd/diag.F90 commit b19a3f73a6d55d38589ecbd01e94b74b54f6df91 Author: Andy Nonaka Date: Wed Oct 3 17:55:35 2018 -0700 fix the mask issue (which was also an AMR bug) in the Reactions Source/MaestroReact.cpp Source/Maestro_F.H Source/Src_nd/burner_loop.f90 commit 28c9c86a6f5c8a8135091c5e5aac52be78917261 Author: Andy Nonaka Date: Tue Oct 2 16:44:48 2018 -0700 turn burning back on Exec/SCIENCE/wdconvect/inputs_3d_regression commit 6b1422f6aa7e871cf06828fb53d8d8372f20a052 Author: Andy Nonaka Date: Tue Oct 2 16:06:02 2018 -0700 revert regression tests to 3 time steps Exec/SCIENCE/wdconvect/inputs_3d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_regression commit 89f4264a1cd0edb6c11be98387bfaa0f145f02bb Author: Alice Harpole Date: Tue Oct 2 16:34:37 2018 -0400 remove merge conflicts accidentally commited to make_flux Source/Src_nd/make_flux.F90 commit 8d1a64632c84f4435f8f67eaf925f3631301ca1b Author: Alice Harpole Date: Tue Oct 2 16:20:27 2018 -0400 initialize umac Source/MaestroAdvance.cpp commit ea05efe24ffa76b353a5c1e5c8aa2152a850e444 Author: Alice Harpole Date: Tue Oct 2 16:06:25 2018 -0400 initialize utrans MultiFab Source/MaestroAdvection.cpp commit 1e550c6ca53cd37e14b7cb3bda13f90928ad94cc Merge: 825bfa42 497a1059 Author: Alice Harpole Date: Tue Oct 2 14:36:37 2018 -0400 merge conflicts commit 497a1059642933cc97cb603291990984e09b7dce Author: Andy Nonaka Date: Mon Oct 1 17:18:04 2018 -0700 remove 'lev' from argument list to create_correction_cc_sphr Source/Src_nd/make_S.F90 commit 404577239e68a475e4de46ee259213e90b8a70bf Merge: 68550305 a4880d99 Author: Andy Nonaka Date: Mon Oct 1 16:03:12 2018 -0700 Merge pull request #10 from AMReX-Astro/tiling Tiling commit a4880d99573a93e08868f01d172b2cc32a4a7617 Merge: e68d0cd4 68550305 Author: Andy Nonaka Date: Mon Oct 1 16:02:53 2018 -0700 Merge branch 'development' into tiling commit 68550305d7f8234e72ad4b2eba0c181ba6ab7094 Author: Andy Nonaka Date: Mon Oct 1 12:45:27 2018 -0700 the probin files need to use the namelist "probin", not "probdata". Thus, they weren't being read in to change the default values. Exec/SCIENCE/wdconvect/probin Exec/SCIENCE/wdconvect/probin_regression Exec/TEST_PROBLEMS/double_bubble/probin Exec/TEST_PROBLEMS/incomp_shear_jet/probin Exec/TEST_PROBLEMS/reacting_bubble/probin Exec/TEST_PROBLEMS/rt/probin Exec/TEST_PROBLEMS/test_convect/probin commit 927cab89a83b30646973a9a20224d2cd90748fba Merge: 2aceb682 2df13384 Author: Michael Zingale Date: Mon Oct 1 14:16:47 2018 -0400 Merge branch 'development' of github.com:amrex-astro/MAESTROeX into development commit 2aceb682b050bb33b4914daaf8cc792bcf809a0b Author: Michael Zingale Date: Mon Oct 1 14:16:40 2018 -0400 don't need EXTERN_TEMPALTE Exec/Make.Maestro commit 2df13384eac374c9c8d17c52598a9f8b251f9cb6 Author: Andy Nonaka Date: Mon Oct 1 11:12:38 2018 -0700 add ltest to Source/param/runtime.probin.template clean up Make.Maestro to avoid duplicate lines Exec/Make.Maestro Source/param/runtime.probin.template commit 825bfa42d2bff4125f4952394eabd839aba41e9b Merge: 2ed4d7ba 1f01d51a Author: Alice Harpole Date: Mon Oct 1 13:20:49 2018 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 1f01d51a0fd30573e544afd06c1265240f528581 Author: Andy Nonaka Date: Mon Oct 1 09:58:29 2018 -0700 FBOXLIB_HOME -> AMREX_HOME MAESTROeX shouldn't require FBOXLIB Exec/Make.Maestro commit a1bd315a8575f9c03a781ef7d1c7d9cdfeae99d4 Merge: 164af6cb 27947b22 Author: Andy Nonaka Date: Mon Oct 1 09:50:11 2018 -0700 Merge pull request #16 from AMReX-Astro/parameters problem-specific runtime parameters commit 27947b22cec6c3b0907c301b1d2b94f72b5a3711 Merge: 1e8d606e 164af6cb Author: Andy Nonaka Date: Mon Oct 1 09:49:49 2018 -0700 Merge branch 'development' into parameters commit e68d0cd49e5a9cfd867900da15411f697ca29511 Author: Doreen Fan Date: Fri Sep 28 16:05:34 2018 -0700 code cleanup Source/MaestroThermal.cpp commit fc6fe49e0c2d4f7f66be16cc719f5ba85e569c31 Author: Alice Harpole Date: Fri Sep 28 15:14:24 2018 -0400 tiling tested for reacting bubble and wdconvert (with randomness turned off in initdata) 3d problems and appears to work Exec/SCIENCE/wdconvect/initdata.f90 Exec/SCIENCE/wdconvect/inputs_3d_regression Source/Src_nd/base_state_geometry.f90 commit f38120e99521c033121fbacef31310ca089c131e Author: Alice Harpole Date: Thu Sep 27 17:34:17 2018 -0400 now at same level of error as between serial and omp on development branch Source/MaestroAdvection.cpp commit 9914f248c722e42006807b3bfc630bd4cf0b766d Author: Alice Harpole Date: Thu Sep 27 14:47:13 2018 -0400 3d serial agrees but still some errors in omp Source/MaestroAdvection.cpp Source/PhysBCFunctMaestro.cpp Source/Src_nd/make_edge_scal.F90 commit 4b593a8f6a288a8a26d2b4f1c06614ed8ab0528c Author: Alice Harpole Date: Wed Sep 26 17:48:29 2018 -0400 fixed some more issues so errors reduced further Source/MaestroAdvection.cpp Source/MaestroAverage.cpp Source/MaestroEvolve.cpp Source/MaestroFill3dData.cpp Source/MaestroInit.cpp Source/MaestroMakeEta.cpp commit b7b4009b3aae707cd450b0077776d059916ca2bb Author: Alice Harpole Date: Wed Sep 26 15:24:15 2018 -0400 fix make_edge_scal to reduce errors Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_regression Source/MaestroAdvection.cpp Source/Src_nd/initdata.f90 Source/Src_nd/make_edge_scal.F90 Source/Src_nd/mkutrans.F90 Source/Src_nd/ppm.F90 Source/Src_nd/sponge.F90 Source/Src_nd/update_vel.F90 commit 2ed4d7ba1ce9f3c544d33caa28f1b9f739173705 Merge: 57c9f263 164af6cb Author: Alice Harpole Date: Wed Sep 26 12:12:57 2018 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into development commit 191301af1db5b1a8d3320ab8101c7caaa3a290f0 Author: Alice Harpole Date: Wed Sep 26 12:05:53 2018 -0400 optimised bl_deallocates in velpred Source/MaestroInit.cpp Source/Src_nd/make_flux.F90 Source/Src_nd/update_scal.F90 Source/Src_nd/velpred.F90 commit c43be1662fa0fbbe0fcdc78244ec4284e9a21140 Merge: e6f0e583 164af6cb Author: Alice Harpole Date: Wed Sep 26 10:31:15 2018 -0400 fixed merge conflicts commit e6f0e583c44263e6ce925be609b8e66e9c4686ba Author: Alice Harpole Date: Wed Sep 26 10:03:47 2018 -0400 fixed make_edge_scal_3d Exec/SCIENCE/wdconvect/GNUmakefile Exec/SCIENCE/wdconvect/inputs_3d_regression Exec/TEST_PROBLEMS/reacting_bubble/GNUmakefile Exec/TEST_PROBLEMS/reacting_bubble/initdata.f90 Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_regression Source/MaestroAdvance.cpp Source/MaestroDensityAdvance.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroFill3dData.cpp Source/MaestroFillData.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp Source/MaestroReact.cpp Source/MaestroRegrid.cpp Source/MaestroSetup.cpp Source/MaestroThermal.cpp Source/Src_nd/Make.package Source/Src_nd/fill_3d_data.F90 Source/Src_nd/make_edge_scal.F90 Source/Src_nd/make_flux.F90 Source/Src_nd/update_vel.F90 commit 57c9f2639d067ded6683ed9d4683f6f4c0b84ebf Author: Alice Harpole Date: Tue Sep 25 16:07:54 2018 -0400 fix OMP DO PRIVATE variables Source/Src_nd/make_flux.F90 commit d6af629319769a62a407c2ff90175fd2c5f4396c Author: Alice Harpole Date: Tue Sep 25 16:04:03 2018 -0400 fix OMP DO PRIVATE variables Source/Src_nd/make_flux.F90 commit 164af6cb9ab8d26b5ad1bfc050f590b245071e74 Author: Michael Zingale Date: Tue Sep 25 15:15:42 2018 -0400 add ltest to work with updated write_probin.py Source/param/extern_probin.template commit d87136ec4208ec3fe183204154c8350e774620a1 Author: Doreen Fan Date: Tue Sep 18 10:39:29 2018 -0700 Add use_delta_gamma1_term to meth_params in Fortran Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit fbc9410cf32a8559b2818afb278be1f97610e8a1 Author: Max Katz Date: Mon Sep 17 18:15:21 2018 -0400 extern.f90 -> extern.F90 Exec/Make.Maestro commit 30f3f887ec1903ddbbac23eac4af3f791e6cd058 Author: Max Katz Date: Mon Sep 17 16:40:48 2018 -0400 Maestro_F.H should be in FEXE_headers Source/Make.package commit a19122b02f501c9bd1b762552d1a1c87544b0b4a Author: Doreen Fan Date: Fri Sep 14 17:38:20 2018 -0700 Need to compute cell-centered to radial mapping after reading from checkpoint file Source/Maestro.H Source/MaestroAdvanceIrregTest.cpp Source/MaestroCheckpoint.cpp Source/MaestroFill3dData.cpp Source/MaestroInit.cpp commit b6419dff9323a6fcab77235cf7ca16dfbcb29f44 Author: Alice Harpole Date: Fri Sep 14 15:19:26 2018 -0400 Added reduction clauses to omp in MaestroDt - all tests now agree for serial runs vs 4 omp threads Exec/SCIENCE/wdconvect/GNUmakefile Exec/SCIENCE/wdconvect/initdata.f90 Exec/TEST_PROBLEMS/double_bubble/initdata.f90 Exec/TEST_PROBLEMS/incomp_shear_jet/initdata.f90 Exec/TEST_PROBLEMS/reacting_bubble/GNUmakefile Exec/TEST_PROBLEMS/reacting_bubble/initdata.f90 Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Exec/TEST_PROBLEMS/rt/initdata.f90 Exec/TEST_PROBLEMS/rt/inputs_2d_C Exec/TEST_PROBLEMS/test_convect/GNUmakefile Exec/TEST_PROBLEMS/test_convect/initdata.f90 Exec/TEST_PROBLEMS/test_convect/make_heating.F90 Source/MaestroDt.cpp Source/MaestroEvolve.cpp Source/MaestroReact.cpp Source/MaestroThermal.cpp Source/Src_nd/velpred.F90 commit 5448f3fb38c936aa661b501439877f8faabf52fd Merge: dda8cfd0 b637417d Author: Alice Harpole Date: Fri Sep 14 09:50:59 2018 -0400 fixed tiling in MaestroThermal commit b637417d99fbba3c0af4b1d42758c5fb4ef8ba96 Author: Doreen Fan Date: Thu Sep 13 15:01:48 2018 -0700 Initialize delta_gamma1_term to zero Source/MaestroAdvanceIrreg.cpp commit dda8cfd0f58ec90ca00bfaf94ff10099d74ebad7 Author: Alice Harpole Date: Thu Sep 13 17:43:10 2018 -0400 Found MFIters which should not be tiled Exec/TEST_PROBLEMS/double_bubble/GNUmakefile Exec/TEST_PROBLEMS/double_bubble/inputs_2d_C Exec/TEST_PROBLEMS/incomp_shear_jet/GNUmakefile Exec/TEST_PROBLEMS/incomp_shear_jet/inputs_2d_C Exec/TEST_PROBLEMS/rt/GNUmakefile Exec/TEST_PROBLEMS/rt/inputs_2d_C Source/MaestroAdvection.cpp Source/MaestroAverage.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroEvolve.cpp Source/MaestroFill3dData.cpp Source/MaestroFillData.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroHeating.cpp Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp Source/MaestroReact.cpp Source/MaestroRegrid.cpp Source/MaestroRhoHT.cpp Source/MaestroSponge.cpp Source/MaestroThermal.cpp commit 1e8d606ebaab6536bb7cbe4be3a98ac1b37d8af4 Author: Alice Harpole Date: Thu Sep 13 16:01:18 2018 -0400 Got rid of redundant maestro_probdata_init Source/Maestro.H Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/maestro_init.f90 commit 412a3edc41cd94ada438544cce3c4a1e791f9d48 Merge: e6eac020 271ed673 Author: Alice Harpole Date: Thu Sep 13 15:56:47 2018 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into parameters commit e6eac020b5ff44c6597265454dbb524344493c4f Author: Alice Harpole Date: Thu Sep 13 15:56:41 2018 -0400 restored probin files Exec/Make.Maestro Exec/SCIENCE/wdconvect/_parameters_regression Exec/SCIENCE/wdconvect/inputs_3d_C Exec/SCIENCE/wdconvect/inputs_3d_C.128 Exec/SCIENCE/wdconvect/inputs_3d_C.128.2levels Exec/SCIENCE/wdconvect/inputs_3d_C.128.exactbase Exec/SCIENCE/wdconvect/inputs_3d_C.64.exactbase Exec/SCIENCE/wdconvect/inputs_3d_regression Exec/SCIENCE/wdconvect/probin Exec/SCIENCE/wdconvect/probin_regression Exec/TEST_PROBLEMS/double_bubble/inputs_2d_C Exec/TEST_PROBLEMS/double_bubble/inputs_2d_regression Exec/TEST_PROBLEMS/double_bubble/probin Exec/TEST_PROBLEMS/incomp_shear_jet/inputs_2d_C Exec/TEST_PROBLEMS/incomp_shear_jet/inputs_2d_regression Exec/TEST_PROBLEMS/incomp_shear_jet/probin Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_dpdt Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_regression Exec/TEST_PROBLEMS/reacting_bubble/probin Exec/TEST_PROBLEMS/rt/inputs_2d_C Exec/TEST_PROBLEMS/rt/inputs_2d_regression Exec/TEST_PROBLEMS/rt/probin Exec/TEST_PROBLEMS/test_convect/inputs_2d_C Exec/TEST_PROBLEMS/test_convect/inputs_2d_regression Exec/TEST_PROBLEMS/test_convect/probin Source/Src_nd/Make.package Source/Src_nd/probdata.f90 commit 271ed673ba16724b2c6365789e75ccc98aface07 Author: Alice Harpole Date: Thu Sep 13 14:46:49 2018 -0400 Fixed OMP statements so compiles with OpenMP Source/Src_nd/fill_3d_data.F90 Source/Src_nd/make_S.F90 Source/Src_nd/make_explicit_thermal.F90 Source/Src_nd/make_scal_force.F90 Source/Src_nd/make_vel_force.F90 commit a9126521848bab5d5979cd7c7a41a5a8cd60d769 Merge: e846f059 322dc1c2 Author: Alice Harpole Date: Thu Sep 13 10:12:05 2018 -0400 merged with dev branch, but double_bubble doesn't work commit 212afee9302d76da5d7cc06e233d760042208d32 Merge: f194f977 322dc1c2 Author: Alice Harpole Date: Thu Sep 13 09:20:18 2018 -0400 fixed merge conflict commit 322dc1c2d4e6e9c3021e51abb730244f93fbec2f Merge: f9a1d971 6ef0497a Author: Andy Nonaka Date: Wed Sep 12 17:37:13 2018 -0700 Merge pull request #15 from AMReX-Astro/deltagamma Ported deltagamma from MAESTRO commit 6ef0497afc4ecf0d288f4258225db47b23fc1158 Author: Alice Harpole Date: Wed Sep 12 14:37:16 2018 -0400 reset settings for inputs files back to their dev branch values Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Exec/TEST_PROBLEMS/rt/GNUmakefile Exec/TEST_PROBLEMS/rt/inputs_2d_C commit 94a9990304e023a90b808f4a8ccf210e0a505d0a Author: Alice Harpole Date: Wed Sep 12 14:30:22 2018 -0400 Added use_delta_gamma1_term flags Source/MaestroAdvance.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroInit.cpp Source/MaestroMakeS.cpp Source/Src_nd/make_S.F90 Source/param_includes/meth_params.F90 commit dca9445d6bd1b4a80d8ebba86f5a3314ed8a56dc Author: Alice Harpole Date: Wed Sep 12 14:02:29 2018 -0400 checked *_sphr routines with wdconvect - compiles and runs Source/MaestroInit.cpp Source/Src_nd/make_S.F90 commit 052e16cb2c96451a0a1eba1e474435878c76b653 Author: Alice Harpole Date: Wed Sep 12 13:05:13 2018 -0400 Added make_S_cc_sphr Source/MaestroMakeS.cpp Source/Maestro_F.H Source/Src_nd/make_S.F90 commit f9a1d9716b6b9dc0481e0b210c6d6870cd30f5e1 Author: Andy Nonaka Date: Wed Sep 12 09:57:41 2018 -0700 change velpert_amplitude back to 1.e5 for all problems Exec/SCIENCE/wdconvect/inputs_3d_C.64 Exec/SCIENCE/wdconvect/probin Exec/SCIENCE/wdconvect/probin_C.64 commit 8cbcc5b4afd2b021c1b4cddf5c614ce234fae3cb Author: Alice Harpole Date: Wed Sep 12 11:15:18 2018 -0400 Added in horizontal averaging and Sbar correction Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroInit.cpp Source/MaestroMakeS.cpp Source/Maestro_F.H Source/Src_nd/make_S.F90 commit 7a8b9c561e97a3e63f52b3312581a6dcd292ca9d Author: Alice Harpole Date: Wed Sep 12 09:38:45 2018 -0400 Compiles and runs without crashing Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroInit.cpp Source/MaestroMakeS.cpp Source/Maestro_F.H Source/Src_nd/make_S.F90 commit 5c0b38171bac3bcb70be57ccaf313e80b3142548 Author: Alice Harpole Date: Tue Sep 11 17:32:31 2018 -0400 almost compiles Source/Maestro.H Source/MaestroInit.cpp Source/MaestroMakeS.cpp Source/Maestro_F.H Source/Src_nd/make_S.F90 commit f7d75f194a6658e74badacb82cf739e58edc9363 Author: Alice Harpole Date: Tue Sep 11 17:13:38 2018 -0400 added all the delta_gamma terms to functions in make_S, fixed those called by MaestroAdvance Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroInit.cpp Source/MaestroMakeS.cpp Source/Maestro_F.H Source/Src_nd/make_S.F90 commit 4773bd81ffca8924700a398d3ee03196fe32a213 Author: Alice Harpole Date: Tue Sep 11 15:45:12 2018 -0400 started porting over deltagamma Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Exec/TEST_PROBLEMS/rt/GNUmakefile Exec/TEST_PROBLEMS/rt/inputs_2d_C Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/Src_nd/mac_solver.F90 Source/Src_nd/make_S.F90 commit 65a0ea638d48581de8000f474291114cf2d899ac Author: Andy Nonaka Date: Mon Sep 10 18:44:17 2018 -0700 change velpert_amplitude Exec/SCIENCE/wdconvect/inputs_3d_C.64 Exec/SCIENCE/wdconvect/probin_C.64 commit 46a3a68df4d8243600ff4a4d9453c96aac443194 Author: Andy Nonaka Date: Mon Sep 10 18:20:34 2018 -0700 revert files I accidentally committed Exec/SCIENCE/wdconvect/initdata.f90 Source/MaestroInit.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp commit f092a05898abce4acb0806c408e7bf23fce72529 Author: Andy Nonaka Date: Mon Sep 10 16:38:12 2018 -0700 move to AMReX-Astro/paper Exec/SCIENCE/wdconvect/initdata.f90 Papers/VariableBase/GNUmakefile Papers/VariableBase/aasjournal.bst Papers/VariableBase/aastex62.cls Papers/VariableBase/paper.tex Papers/VariableBase/references.bib Source/MaestroInit.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp commit 976bad302773dbe834708dd34d3365f088cfbf97 Author: Andy Nonaka Date: Mon Sep 10 15:41:18 2018 -0700 variable base state paper Papers/VariableBase/GNUmakefile Papers/VariableBase/aasjournal.bst Papers/VariableBase/aastex62.cls Papers/VariableBase/paper.tex Papers/VariableBase/references.bib commit f194f97703e8c46f1449ea84e681e558cb67319a Author: Alice Harpole Date: Mon Sep 10 17:55:03 2018 -0400 minor change to extern Exec/SCIENCE/wdconvect/extern Exec/SCIENCE/wdconvect/extern_regression commit 070bd7ff02c0878ad60851dc8d2f420eff0fb6b3 Author: Alice Harpole Date: Mon Sep 10 17:44:17 2018 -0400 Changed all problems so they work with the _parameters file - is there a way to get rid of the extern file too? Exec/Make.Maestro Exec/SCIENCE/wdconvect/GNUmakefile Exec/SCIENCE/wdconvect/Make.package Exec/SCIENCE/wdconvect/_parameters Exec/SCIENCE/wdconvect/_parameters_regression Exec/SCIENCE/wdconvect/extern Exec/SCIENCE/wdconvect/extern_regression Exec/SCIENCE/wdconvect/initdata.f90 Exec/SCIENCE/wdconvect/inputs_3d_C Exec/SCIENCE/wdconvect/inputs_3d_C.128 Exec/SCIENCE/wdconvect/inputs_3d_C.128.2levels Exec/SCIENCE/wdconvect/inputs_3d_C.128.exactbase Exec/SCIENCE/wdconvect/inputs_3d_C.64.exactbase Exec/SCIENCE/wdconvect/inputs_3d_regression Exec/SCIENCE/wdconvect/probdata.f90 Exec/SCIENCE/wdconvect/tagging.f90 Exec/TEST_PROBLEMS/double_bubble/GNUmakefile Exec/TEST_PROBLEMS/double_bubble/Make.package Exec/TEST_PROBLEMS/double_bubble/_parameters Exec/TEST_PROBLEMS/double_bubble/base_state.f90 Exec/TEST_PROBLEMS/double_bubble/extern Exec/TEST_PROBLEMS/double_bubble/initdata.f90 Exec/TEST_PROBLEMS/double_bubble/inputs_2d_C Exec/TEST_PROBLEMS/double_bubble/inputs_2d_regression Exec/TEST_PROBLEMS/double_bubble/probdata.f90 Exec/TEST_PROBLEMS/incomp_shear_jet/GNUmakefile Exec/TEST_PROBLEMS/incomp_shear_jet/Make.package Exec/TEST_PROBLEMS/incomp_shear_jet/_parameters Exec/TEST_PROBLEMS/incomp_shear_jet/base_state.f90 Exec/TEST_PROBLEMS/incomp_shear_jet/extern Exec/TEST_PROBLEMS/incomp_shear_jet/initdata.f90 Exec/TEST_PROBLEMS/incomp_shear_jet/inputs_2d_C Exec/TEST_PROBLEMS/incomp_shear_jet/inputs_2d_regression Exec/TEST_PROBLEMS/incomp_shear_jet/probdata.f90 Exec/TEST_PROBLEMS/reacting_bubble/GNUmakefile Exec/TEST_PROBLEMS/reacting_bubble/Make.package Exec/TEST_PROBLEMS/reacting_bubble/_parameters Exec/TEST_PROBLEMS/reacting_bubble/extern Exec/TEST_PROBLEMS/reacting_bubble/initdata.f90 Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_dpdt Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_regression Exec/TEST_PROBLEMS/reacting_bubble/probdata.f90 Exec/TEST_PROBLEMS/rt/GNUmakefile Exec/TEST_PROBLEMS/rt/Make.package Exec/TEST_PROBLEMS/rt/inputs_2d_regression Exec/TEST_PROBLEMS/test_convect/GNUmakefile Exec/TEST_PROBLEMS/test_convect/Make.package Exec/TEST_PROBLEMS/test_convect/_parameters Exec/TEST_PROBLEMS/test_convect/extern Exec/TEST_PROBLEMS/test_convect/initdata.f90 Exec/TEST_PROBLEMS/test_convect/inputs_2d_C Exec/TEST_PROBLEMS/test_convect/inputs_2d_regression Exec/TEST_PROBLEMS/test_convect/probdata.f90 Exec/TEST_PROBLEMS/test_convect/probin Source/param/runtime.probin.template commit e3f3065317b6b1206aad3cdf79c751c3d9e5ebda Merge: 861d5cce bbb30666 Author: Michael Zingale Date: Sat Sep 8 08:42:26 2018 -0400 Merge branch 'development' of github.com:amrex-astro/MAESTROeX into development commit 861d5ccea78875caecb809f0245b741ed5732016 Author: Michael Zingale Date: Sat Sep 8 08:42:17 2018 -0400 add a .gitignore .gitignore commit bbb30666610f64341ccc57e81c7b33d307430ca3 Author: Andy Nonaka Date: Fri Sep 7 17:23:08 2018 -0700 comparison using this file, compared to MAESTROeX fails after first divu_iter. note you must edi initdata.f90 for the deterministic seed for the velocity Fourier modes Exec/SCIENCE/wdconvect/inputs_3d_C.64 commit d176f236dcfcb730ca88a4c25aad762577f0016b Author: Andy Nonaka Date: Fri Sep 7 15:56:06 2018 -0700 64^3 test file Exec/SCIENCE/wdconvect/inputs_3d_C.64 commit 18130382ca5ed00fa5d816412c8a2238a3530aa3 Author: Andy Nonaka Date: Fri Sep 7 14:41:09 2018 -0700 update interface to average_cellcenter_to_face so this code compiles with the latest development version of amrex Source/MaestroMacProj.cpp commit 6ffcd1feebcd1b9439d70de58421f56c1639b31d Merge: 7c15214a daf7b1be Author: Alice Harpole Date: Fri Sep 7 16:43:44 2018 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into parameters commit 7c15214a96a8140666cbb125ace07bf1752b94be Author: Alice Harpole Date: Fri Sep 7 16:41:04 2018 -0400 cleaned up (and added) parameters file for rt problem Exec/TEST_PROBLEMS/rt/_parameters commit f92018afe3c4fdc04ffb12ecbb34a4c7716e57d2 Author: Alice Harpole Date: Fri Sep 7 16:35:47 2018 -0400 It appears to work Exec/Make.Maestro Exec/TEST_PROBLEMS/rt/extern Exec/TEST_PROBLEMS/rt/inputs_2d_C Source/Src_nd/maestro_init.f90 commit e846f0595e9f02e520052741acabe3214a1079f6 Merge: c92626de daf7b1be Author: Alice Harpole Date: Fri Sep 7 11:36:11 2018 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into tiling commit 87e822b524239540d89a021c7b45bab69d3332e1 Author: Alice Harpole Date: Fri Sep 7 09:11:38 2018 -0400 may have made things worse Exec/Make.Maestro Exec/TEST_PROBLEMS/rt/GNUmakefile Exec/TEST_PROBLEMS/rt/Make.package Exec/TEST_PROBLEMS/rt/base_state.f90 Exec/TEST_PROBLEMS/rt/initdata.f90 Exec/TEST_PROBLEMS/rt/inputs_2d_C Exec/TEST_PROBLEMS/rt/probdata.f90 Exec/TEST_PROBLEMS/rt/probin Source/MaestroPlot.cpp Source/Maestro_F.H Source/Src_nd/maestro_init.f90 Source/Src_nd/probdata.f90 commit daf7b1be90894734b35826961d8dbed08530b00c Author: Andy Nonaka Date: Thu Sep 6 16:15:12 2018 -0700 don't compute 1/gamma1bar dp0/dt term if evolve_base_state=F. This term should have been 0 only since p0 is fixed for evolve_base_state=F Source/MaestroAdvanceIrreg.cpp commit 06f9e7fc7b03203cff10ed691a46af9e075489fd Author: Andy Nonaka Date: Thu Sep 6 15:42:18 2018 -0700 switch this to use the variable-base state model file Exec/SCIENCE/wdconvect/inputs_3d_C.64.exactbase commit 7ec16d2c7cbb6ea49e6963b3e95d77070dadaea7 Merge: c0814fd1 29720e77 Author: Andy Nonaka Date: Thu Sep 6 15:40:54 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 29720e77314a3c764de9aeae0b777408c1a2676b Author: Doreen Fan Date: Thu Sep 6 12:23:00 2018 -0700 Added initial model files for fixed and variable base states on 64^3 grid Exec/SCIENCE/wdconvect/kepler_new_6.25e8.hybrid.hse.1488.dr Exec/SCIENCE/wdconvect/kepler_new_6.25e8.hybrid.hse.320.dx commit c0814fd1f2e0d8c7f80e13bfe1810df5f21102b4 Author: Andy Nonaka Date: Thu Sep 6 10:44:41 2018 -0700 smaller test problem Exec/SCIENCE/wdconvect/inputs_3d_C.64.exactbase commit c92626defeaa209d05bc23ae142e7c22644ca949 Author: Alice Harpole Date: Thu Sep 6 13:26:27 2018 -0400 removed todo list Source/Tiling_TODO.txt commit 6865f219a0ed8cbc20fba3bd6b0454b318a50d9b Author: Alice Harpole Date: Thu Sep 6 10:12:25 2018 -0400 checked pragma omps Source/MaestroNodalProj.cpp Source/PhysBCFunctMaestro.cpp Source/Tiling_TODO.txt commit 3e33389fa05fa058d139e56ec545144a1c7f62be Merge: 40bc2bde f20344f5 Author: Alice Harpole Date: Thu Sep 6 10:02:45 2018 -0400 Merge branch 'development' of github.com:AMReX-Astro/MAESTROeX into tiling commit f20344f5337403c649c7806d5d9ba0d1e22574b9 Author: Andy Nonaka Date: Wed Sep 5 16:42:19 2018 -0700 index bugfix caught in debug mode - don't define drc unless you are sure r is not equal to 0 or nr(n)-1 Source/Src_nd/make_beta0.f90 commit a802de032ef19ddb9381521f15ccf1997129efd0 Merge: d7379a77 02f26309 Author: Michael Zingale Date: Wed Sep 5 15:57:05 2018 -0600 Merge pull request #9 from AMReX-Astro/job_info Copied extra job_info from Castro commit 02f263093198b0a6d3f025040851a54c44b640ec Author: Alice Harpole Date: Wed Sep 5 17:55:29 2018 -0400 MaestroCheckpoint.cpp reads and writes the CPUtime to checkpoint files Source/MaestroCheckpoint.cpp commit cfa10e813eac706b64461e26ce972a43633b4e98 Author: Alice Harpole Date: Wed Sep 5 17:01:11 2018 -0400 Copied extra job_info from Castro Source/Maestro.H Source/Maestro.cpp Source/MaestroPlot.H Source/MaestroPlot.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/maestro_init.f90 Source/main.cpp Source/param/_cpp_parameters Source/param/extern_probin.template Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H commit 40bc2bde7b00dcd9e374715589d9500efe8e3c12 Author: Alice Harpole Date: Wed Sep 5 16:17:04 2018 -0400 removed some OMP calls from the fortran Source/Src_nd/compute_dt.F90 Source/Src_nd/make_edge_scal.F90 Source/Src_nd/ppm.F90 Source/Tiling_TODO.txt commit 97b66ec14f517cf519dbb6658d096abef15d196c Author: Alice Harpole Date: Wed Sep 5 15:49:09 2018 -0400 Added lots of bl_deallocates to stop memory leaks Exec/TEST_PROBLEMS/rt/GNUmakefile Exec/TEST_PROBLEMS/rt/inputs_2d_C Source/Src_nd/fill_3d_data.F90 Source/Src_nd/make_edge_scal.F90 Source/Src_nd/make_eta.F90 Source/Src_nd/mkutrans.F90 Source/Src_nd/rhoh_vs_t.F90 Source/Src_nd/velpred.F90 commit 2d78b9b4279186253f964074e0108e0d7579ed2d Author: Alice Harpole Date: Wed Sep 5 14:39:10 2018 -0400 compiles Source/Src_nd/compute_dt.F90 Source/Src_nd/fill_3d_data.F90 Source/Src_nd/make_S.F90 Source/Src_nd/make_edge_scal.F90 Source/Src_nd/make_eta.F90 Source/Src_nd/make_gamma.F90 Source/Src_nd/make_scal_force.F90 Source/Src_nd/make_vel_force.F90 Source/Src_nd/mkutrans.F90 Source/Src_nd/ppm.F90 Source/Src_nd/rhoh_vs_t.F90 Source/Src_nd/velpred.F90 commit e384b0ffef0b120803dd765559f7c2bf043b83b1 Author: Alice Harpole Date: Wed Sep 5 12:25:33 2018 -0400 Added more tiling, started fixing errors Exec/TEST_PROBLEMS/rt/GNUmakefile Source/MaestroAdvection.cpp Source/MaestroAverage.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroFill3dData.cpp Source/MaestroFillData.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp Source/MaestroRegrid.cpp Source/Src_nd/advect_base.F90 Source/Src_nd/average.f90 Source/Src_nd/compute_dt.F90 Source/Src_nd/compute_grad_phi.F90 Source/Src_nd/diag.F90 Source/Src_nd/fill_3d_data.F90 Source/Src_nd/fill_umac_ghost.F90 Source/Src_nd/mac_solver.F90 Source/Src_nd/make_S.F90 Source/Src_nd/make_edge_scal.F90 Source/Src_nd/make_eta.F90 Source/Src_nd/make_gamma.F90 Source/Src_nd/make_pi_cc.F90 Source/Src_nd/make_scal_force.F90 Source/Src_nd/make_vel_force.F90 Source/Src_nd/mkutrans.F90 Source/Src_nd/ppm.F90 Source/Src_nd/slope.F90 Source/Src_nd/tagging.f90 Source/Src_nd/update_scal.F90 Source/Src_nd/velpred.F90 Source/Tiling_TODO.txt commit d7379a777f1502144c758e9cd916cba15b5f7227 Author: Andy Nonaka Date: Tue Sep 4 10:28:44 2018 -0700 Sept 2018 release notes RELEASE_NOTES commit f684ab7941a2228a4af3c4a2302a711dad016b91 Author: Alice Harpole Date: Tue Sep 4 11:16:48 2018 -0400 more tiling Source/MaestroReact.cpp Source/MaestroRhoHT.cpp Source/MaestroThermal.cpp Source/Src_nd/make_explicit_thermal.F90 Source/Src_nd/rhoh_vs_t.F90 Source/Tiling_TODO.txt commit 6e758d2daa881a8c4fefbcb2013f52e4f0aa7657 Author: Alice Harpole Date: Fri Aug 31 17:56:49 2018 -0400 More tiling Source/MaestroAverage.cpp Source/MaestroDiag.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroHeating.cpp Source/MaestroInit.cpp Source/MaestroMakeS.cpp Source/MaestroSponge.cpp Source/Src_nd/average.f90 Source/Src_nd/initdata.f90 Source/Src_nd/make_S.F90 Source/Src_nd/make_gamma.F90 Source/Src_nd/make_scal_force.F90 Source/Src_nd/make_vel_force.F90 Source/Src_nd/sponge.F90 Source/Tiling_TODO.txt commit 006415f7e50a2c854e6a7f111611941d157a26de Author: Alice Harpole Date: Fri Aug 31 16:48:49 2018 -0400 more tiling Source/MaestroDt.cpp Source/MaestroFillData.cpp Source/MaestroMacProj.cpp Source/MaestroMacProj_level.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp Source/MaestroRegrid.cpp Source/Src_nd/compute_dt.F90 Source/Src_nd/fill_umac_ghost.F90 Source/Src_nd/make_S.F90 Source/Src_nd/make_eta.F90 Source/Tiling_TODO.txt commit 31e16c5d0935ed4bdb3d86a2b4351a5363e03a41 Author: Alice Harpole Date: Fri Aug 31 16:04:25 2018 -0400 Made a TODO list of all files with MFIters in Source/MaestroMakeEta.cpp Source/Src_nd/fill_3d_data.F90 Source/Src_nd/make_eta.F90 Source/Tiling_TODO.txt commit f59cb10b6336cf1b3784e28eaaaf76eeecb5e864 Author: Andy Nonaka Date: Fri Aug 31 09:05:15 2018 -0700 define microphysics_home Exec/TEST_PROBLEMS/test_convect/GNUmakefile commit 678a1a12d27d36e539b38f38e5da3d6c82726eb3 Author: Andy Nonaka Date: Fri Aug 31 08:51:50 2018 -0700 regression test Exec/TEST_PROBLEMS/test_convect/inputs_2d_regression commit 45a1bcbb022d191b31c7d5bdb6c88b74f3bd3cea Author: Andy Nonaka Date: Fri Aug 31 08:51:21 2018 -0700 add stub for initdata_spherical Exec/TEST_PROBLEMS/test_convect/initdata.f90 commit 1d2f3ef91b3101206a119afca041e318f4772fe6 Author: Andy Nonaka Date: Fri Aug 31 08:45:44 2018 -0700 regression test Exec/TEST_PROBLEMS/rt/inputs Exec/TEST_PROBLEMS/rt/inputs_2d_regression commit 2d8f9c535eb8345b1cefdec00f2ed2574ef49f25 Author: Andy Nonaka Date: Fri Aug 31 08:38:07 2018 -0700 regression test Exec/TEST_PROBLEMS/incomp_shear_jet/inputs_2d_regression commit a0bc0a9015d8356a16de1134aed13912aeeaa4a9 Author: Andy Nonaka Date: Fri Aug 31 08:27:05 2018 -0700 include proper plot/check file base name Exec/TEST_PROBLEMS/double_bubble/inputs_2d_regression commit 6121e5cbf07ae8aa952a67bdf9047c739ca85ab8 Author: Andy Nonaka Date: Fri Aug 31 07:59:49 2018 -0700 bugfix in sizing the flux registers. They actually need to be sized with "max_level+2" elements. flux_reg[0] is not used. flux_reg[1] is associated with the level 1/0 interface and has grid spacing associated with level 0 Source/MaestroSetup.cpp commit 5af5b89fa9b04ced4cb2675e050f91052a0e1c63 Author: Andy Nonaka Date: Thu Aug 30 15:51:10 2018 -0700 double bubble regression test README file for TEST_PROBLEMS Exec/TEST_PROBLEMS/README Exec/TEST_PROBLEMS/double_bubble/inputs_2d_regression commit cfdadd9aad50b80cad47301f105f80a054f78836 Author: Doreen Fan Date: Wed Aug 29 18:21:28 2018 -0700 Both input files now use density predict_rhoX and enthalpy predict_rhoh Exec/SCIENCE/wdconvect/inputs_3d_C.128 Exec/SCIENCE/wdconvect/inputs_3d_C.128.exactbase commit 30c9e8761498cf29a315ab69ae23913f807ea828 Merge: 9ec2c41f 8f7b3e24 Author: Doreen Fan Date: Wed Aug 29 18:17:47 2018 -0700 Merge branch 'development' of https://github.com/AMReX-Astro/MAESTROeX into development commit 9ec2c41f8b3ce443c5a4d13c486f5a3b8c24b8f6 Author: Doreen Fan Date: Wed Aug 29 18:17:29 2018 -0700 Fixed bug with species_pred_type=predict_rhoX Source/MaestroDensityAdvance.cpp Source/Src_nd/make_grav.f90 commit 8f7b3e248924209887a37c1f7fb3ad70a0735707 Author: Alice Harpole Date: Mon Aug 27 16:37:30 2018 -0400 Added shear jet problem Exec/TEST_PROBLEMS/incomp_shear_jet/GNUmakefile Exec/TEST_PROBLEMS/incomp_shear_jet/Make.package Exec/TEST_PROBLEMS/incomp_shear_jet/base_state.f90 Exec/TEST_PROBLEMS/incomp_shear_jet/initdata.f90 Exec/TEST_PROBLEMS/incomp_shear_jet/inputs_2d_C Exec/TEST_PROBLEMS/incomp_shear_jet/probdata.f90 Exec/TEST_PROBLEMS/incomp_shear_jet/probin Exec/TEST_PROBLEMS/incomp_shear_jet/tagging.f90 commit f521392f5edefbd8e971dcaff1655364cca1895f Author: Alice Harpole Date: Mon Aug 27 16:27:16 2018 -0400 Added Rayleigh-Taylor problem Exec/TEST_PROBLEMS/rt/GNUmakefile Exec/TEST_PROBLEMS/rt/Make.package Exec/TEST_PROBLEMS/rt/base_state.f90 Exec/TEST_PROBLEMS/rt/initdata.f90 Exec/TEST_PROBLEMS/rt/inputs_2d_C Exec/TEST_PROBLEMS/rt/probdata.f90 Exec/TEST_PROBLEMS/rt/probin Exec/TEST_PROBLEMS/rt/tagging.f90 commit 15eb10a65db7e5b800c6771cdcda673e7ec7b1d8 Author: Alice Harpole Date: Mon Aug 27 16:11:56 2018 -0400 Added double bubble problem Exec/TEST_PROBLEMS/double_bubble/GNUmakefile Exec/TEST_PROBLEMS/double_bubble/Make.package Exec/TEST_PROBLEMS/double_bubble/base_state.f90 Exec/TEST_PROBLEMS/double_bubble/initdata.f90 Exec/TEST_PROBLEMS/double_bubble/inputs_2d_C Exec/TEST_PROBLEMS/double_bubble/probdata.f90 Exec/TEST_PROBLEMS/double_bubble/probin Exec/TEST_PROBLEMS/double_bubble/tagging.f90 commit 7fa6743b000b28bb84ccdac3a311a6ab1651553d Author: Doreen Fan Date: Wed Aug 15 15:23:45 2018 -0700 Added chi term in projection steps Source/MaestroAdvanceIrreg.cpp commit d60eb92dfe26ece2a3434449a6c5c63df13d7339 Author: Weiqun Zhang Date: Wed Aug 8 16:14:23 2018 -0700 fix io buffer Source/MaestroCheckpoint.cpp commit 27039a4232fb4cb6e8c353363e66140262640f16 Author: Andy Nonaka Date: Wed Aug 1 11:21:05 2018 -0700 August 2018 release notes RELEASE_NOTES commit 74b31126b191a2900ddb90accbedb7eb229506bf Author: Doreen Fan Date: Fri Jul 27 15:41:06 2018 -0700 Include missing dp/dt term in RHS of MAC projection step Source/Maestro.H Source/MaestroAdvanceIrreg.cpp Source/MaestroEvolve.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroSetup.cpp Source/Src_nd/make_scal_force.F90 commit e1151608306fb031142d27ef6e4963a36d7111a0 Author: Doreen Fan Date: Tue Jul 24 18:46:09 2018 -0700 Add option for advance routine using variable base state spacing Source/MaestroEvolve.cpp commit fae7b10f88c7c66f67ddfb353e4d924a99b83be9 Author: Doreen Fan Date: Tue Jul 24 18:36:31 2018 -0700 Add back some variables that are needed to write checkpoint files Source/MaestroSetup.cpp commit d20cf2a63df4e239dd9b226920d46b2a97e4de87 Author: Doreen Fan Date: Tue Jul 24 17:56:48 2018 -0700 Remove debug outputs Source/Src_nd/make_scal_force.F90 commit b25d048236a4b597a346e1383adb989947e59d8e Author: Doreen Fan Date: Tue Jul 24 17:52:37 2018 -0700 Changes to density and enthalpy advance subroutines for variable base state spacing Source/MaestroAdvanceIrreg.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/make_scal_force.F90 commit 66ff5f45a6b1fc6b6495ebc0b9d821c9f93fcb65 Author: Doreen Fan Date: Mon Jul 23 17:02:10 2018 -0700 Compute beta0 with variable base state spacing Source/MaestroAdvanceIrreg.cpp Source/MaestroInit.cpp Source/MaestroRegrid.cpp Source/Maestro_F.H Source/Src_nd/make_beta0.f90 commit 4d3474944bb64f43f3f6e790d70d4bbc3be8239f Author: Doreen Fan Date: Mon Jul 23 17:00:31 2018 -0700 Keep base state values constant outside of cutoff coordinates for variable grid spacing Source/Src_nd/average.f90 commit 28a4901a9ce19beb2fdf53071afc207afa3e2bd0 Author: Andy Nonaka Date: Fri Jul 20 09:59:12 2018 -0700 implement proper corner coupling for conservative quantity advection. regression results for 3d will change for anything that advects rho, (rhoX), or (rhoh) Source/Src_nd/make_edge_scal.F90 commit 03299b8f4bbeab3d592cc81e49f2557b989529fd Author: Doreen Fan Date: Thu Jul 19 15:00:27 2018 -0700 Model file for variable base state spacing is now read in properly. Exec/SCIENCE/wdconvect/kepler_new_6.25e8.hybrid.hse.6048.dr Source/Src_nd/base_state.f90 commit 0a9d7e18368dc7f284d39a48d97f4412e1877027 Author: Andy Nonaka Date: Thu Jul 19 14:39:37 2018 -0700 model file needed for AMR debugging Exec/SCIENCE/wdconvect/kepler_new_6.25e8.hybrid.hse.640 commit d592b52ba3e70e20b8251ef5c85878d77476e45d Author: Doreen Fan Date: Wed Jul 11 10:19:25 2018 -0700 Compute rhog at cell edges Source/Src_nd/base_state.f90 commit f9cc9f35b02c2a054ab5ec5414d18c5ae99ecf72 Author: Doreen Fan Date: Wed Jul 11 09:49:10 2018 -0700 Use rhoh to compute enthalpy for variable base state spacing Exec/SCIENCE/wdconvect/inputs_3d_C.128.exactbase commit 899f54cc259061a54e6bdce6acc8f12fe6fe562e Author: Doreen Fan Date: Tue Jul 10 11:50:13 2018 -0700 Include constant edge interpolation needed when outputting w0 Source/MaestroSetup.cpp Source/Src_nd/fill_3d_data.F90 commit 30f287638f897d442c10c198489e65278ca85cfe Author: Doreen Fan Date: Mon Jul 9 17:58:55 2018 -0700 Added input and model files to test variable base state spacing. Also avoid dividing by zero in average subroutine. Exec/SCIENCE/wdconvect/inputs_3d_C.128 Exec/SCIENCE/wdconvect/inputs_3d_C.128.exactbase Exec/SCIENCE/wdconvect/kepler_new_6.25e8.hybrid.hse.6048.dr Exec/SCIENCE/wdconvect/kepler_new_6.25e8.hybrid.hse.640.dx Source/Src_nd/average.f90 Source/Src_nd/base_state_geometry.f90 commit 9a2d3da99e45809951f92818825c96242a6307b3 Author: Doreen Fan Date: Thu Jul 5 16:21:33 2018 -0700 Average subroutine now has option for variable spherical base state spacing Source/MaestroAverage.cpp Source/Maestro_F.H Source/Src_nd/average.f90 commit 6357ee7ae5cfecba85c38e77bc0dfcc41e5b43ab Author: Doreen Fan Date: Thu Jul 5 15:03:33 2018 -0700 Use variable spherical base state spacing for enforce_HSE(). Does not work for planar problems. Source/MaestroAdvance.cpp Source/MaestroAdvanceIrreg.cpp Source/MaestroInit.cpp Source/MaestroRegrid.cpp Source/Maestro_F.H Source/Src_nd/enforce_HSE.f90 commit 58ed51e0729baad7a45cb292107f300c5c98a6e3 Author: Doreen Fan Date: Mon Jul 2 18:26:37 2018 -0700 Added release notes RELEASE_NOTES commit 66b388da5e52d156515a8bd1a189e57d06e57bd2 Author: Doreen Fan Date: Mon Jul 2 17:33:50 2018 -0700 Include extra parameters for variable base state spacing flag Exec/TEST_PROBLEMS/reacting_bubble/initdata.f90 commit 3f04660fae6922b2be68dcc110bb6abb3b1f326b Merge: f00eeae2 e3b66012 Author: Doreen Fan Date: Mon Jul 2 15:54:49 2018 -0700 Merge branch 'master' of https://github.com/AMReX-Astro/MAESTROeX commit f00eeae24c4509cd16a238bccd197ebd2ae91ba2 Author: Doreen Fan Date: Mon Jul 2 15:54:32 2018 -0700 Modified put_1d_array_on_cart_sphr for variable spherical base state spacing Exec/SCIENCE/wdconvect/initdata.f90 Source/MaestroDt.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroMakeEta.cpp Source/MaestroMakeS.cpp Source/MaestroRhoHT.cpp Source/Maestro_F.H Source/Src_nd/base_state.f90 Source/Src_nd/compute_dt.F90 Source/Src_nd/fill_3d_data.F90 Source/Src_nd/initdata.f90 Source/Src_nd/make_S.F90 Source/Src_nd/make_eta.F90 Source/Src_nd/make_gamma.F90 Source/Src_nd/make_scal_force.F90 Source/Src_nd/make_vel_force.F90 Source/Src_nd/rhoh_vs_t.F90 commit e3b660127acd42e625402d5f4217580f00df7f47 Author: Weiqun Zhang Date: Mon Jul 2 11:52:20 2018 -0700 break boundary cells boxarray into small chunks for load balance Source/MaestroFillData.cpp commit 2ff4eb0c6dfff40e240ff6114cc535625bf5e09d Author: Doreen Fan Date: Thu Jun 28 19:10:21 2018 -0700 Initialize base states from model file with variable spherical grid spacing Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/base_state.f90 commit 5c579443307a02cdb46f50577865b4a2d668008e Author: Doreen Fan Date: Wed Jun 27 15:38:00 2018 -0700 Include a multifab that contains the mapping of cell centers to spherical base state array indices Exec/SCIENCE/wdconvect/initdata.f90 Source/Maestro.H Source/MaestroInit.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/base_state_geometry.f90 Source/Src_nd/initdata.f90 commit 47e977abd617cda6add79634676ec86016ada34a Author: Michael Zingale Date: Wed Jun 20 13:35:53 2018 -0400 add copy_burn_t Microphysics/networks/burn_type.F90 commit 56d87a1e4814fea8fee7aa3fb3f0a35f1360ed37 Author: Doreen Fan Date: Mon Jun 18 17:20:13 2018 -0700 Renamed unnecessary variables with _dummy suffix Source/MaestroAdvanceIrreg.cpp commit 952060578d1bd510b05bb782a384941777924c8b Author: Doreen Fan Date: Mon Jun 18 10:52:30 2018 -0700 Modified advance routine for running with variable base state spacing Source/Maestro.H Source/MaestroAdvanceIrreg.cpp Source/Make.package commit f51063a1c73741d9e064c4b98c851434346da491 Author: Doreen Fan Date: Fri Jun 15 14:27:04 2018 -0700 Revert back to original AdvanceTimeStep subroutine. Will write new advance subroutine for variable base state spacing Source/MaestroAdvance.cpp commit 89ff0271a21cccb179cd45bdc26021ff4f7cec61 Author: Doreen Fan Date: Thu Jun 14 18:42:43 2018 -0700 Define nr_fine=nr_irreg+1 when using irregular base states to reduce the number of subroutines that need to be rewritten Source/MaestroAdvance.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroRegrid.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/base_state_geometry.f90 commit 445f0e07bf0b8ae89a8b1e603d746656ced10e96 Author: Doreen Fan Date: Wed Jun 13 19:06:57 2018 -0700 Initialize geometry parameters with exact spherical base states Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/base_state_geometry.f90 commit dd8484d9bbc975609a2e8062e39f68414525e49a Author: Doreen Fan Date: Wed Jun 13 10:47:47 2018 -0700 Fixed compiling bug Source/Src_nd/make_flux.F90 commit 30dcbd0246de55736b357d66d9f238b2132ccd2e Author: Doreen Fan Date: Tue Jun 12 19:48:59 2018 -0700 Added flags for turning on use_exact_base_state option and placeholders for future related functions Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroDt.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroMacProj_level.cpp Source/MaestroPlot.cpp Source/MaestroRegrid.cpp Source/Src_nd/make_flux.F90 commit 296f945ea3324aba19db0d0df898c1ab3f44a8b6 Author: Michael Zingale Date: Tue Jun 12 18:19:37 2018 -0400 add success Microphysics/networks/burn_type.F90 commit 72307380849647285090e44d66c9953920f9159e Author: Doreen Fan Date: Tue Jun 12 11:39:00 2018 -0700 Revert regression test back to random numbers for velocities Exec/SCIENCE/wdconvect/initdata.f90 commit eb1966db48aa355b07e98ea2d86ff2cf8bbc38de Author: Doreen Fan Date: Mon Jun 11 18:27:19 2018 -0700 Declare new base states for when flag use_exact_base_state is on Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/base_state_geometry.f90 commit b4cb52fd133690c0b600d11407526edae81daeb1 Author: Doreen Fan Date: Mon Jun 11 17:31:19 2018 -0700 Added option for turning on irregularly-spaced exact base states in spherical problems Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit 81424e99008da711768e4eeb7daf0adbf8c06766 Author: Doreen Fan Date: Tue Jun 5 18:18:24 2018 -0700 Included options for using rho in addition to rho' when constructing species fluxes. Source/MaestroDensityAdvance.cpp Source/Src_nd/make_flux.F90 commit 2543950d92a4fc4c05e0c27402449d0b47f5ec7b Author: Andy Nonaka Date: Tue Jun 5 08:57:48 2018 -0700 get MAESTROeX compiling again due to amrex type changes Source/param/extern_probin.template commit 86348247cf8d0598146c67813fbd887f45bc0d09 Author: Doreen Fan Date: Thu May 31 18:04:55 2018 -0700 Change initial data to match MAESTRO for testing on multilevel grids Exec/SCIENCE/wdconvect/initdata.f90 commit cef5c5b25c2a472a555cb61ef9a209036c123bcb Author: Doreen Fan Date: Wed May 30 17:13:03 2018 -0700 Changed a couple more instance of edge restriction Source/MaestroAdvection.cpp Source/MaestroFill3dData.cpp commit bb1423f123d12e9979c998a7ad821e2539d05b40 Author: Doreen Fan Date: Fri May 25 15:10:49 2018 -0700 Fixed dt for multilevel grids. Call edge_restriction subroutines in mac projection where appropriate. Exec/SCIENCE/wdconvect/inputs_3d_C.128.2levels Exec/SCIENCE/wdconvect/probin Source/MaestroAdvection.cpp Source/MaestroDt.cpp Source/MaestroFill3dData.cpp Source/MaestroMacProj.cpp commit 3f8f4ffaa40fd0291d969837f55e632f006445b6 Author: Doreen Fan Date: Tue May 22 15:52:37 2018 -0700 Use AverageDownFaces to restrict edges for velocity update Source/MaestroAdvection.cpp Source/MaestroFill3dData.cpp commit b834c3ebcbc2283d0e7e1c1bccfe996b1861b736 Author: Doreen Fan Date: Tue May 22 15:51:37 2018 -0700 Update regression input files again Exec/SCIENCE/wdconvect/inputs_3d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_regression commit 2001b7201783ffb3bc027016510870df528a3899 Author: Doreen Fan Date: Tue May 22 11:12:19 2018 -0700 Set do_reflux=0 for regression tests Exec/SCIENCE/wdconvect/inputs_3d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_regression Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_regression commit 6bef79071203283ce667c14199a85f328a9777af Author: Doreen Fan Date: Mon May 21 18:07:58 2018 -0700 Added flux registers for density and enthalpy advection Source/MaestroAdvection.cpp Source/MaestroCheckpoint.cpp Source/MaestroInit.cpp commit 11cc1b833612006c4af00b28f6435cf5471e0676 Author: Doreen Fan Date: Fri May 18 10:46:30 2018 -0700 Include mask parameter in diagnosis subroutines Source/MaestroDiag.cpp Source/Maestro_F.H Source/Src_nd/diag.F90 commit 3e9769e92ad3574eb37a73e17f0239d34fa97ea9 Author: Doreen Fan Date: Thu May 17 18:28:33 2018 -0700 Use FillPatchUedge in place of u_mac_grown. Also, mlmg->getFluxes needs vector of multilevel arrays as input. Source/MaestroAdvection.cpp Source/MaestroFill3dData.cpp Source/MaestroFillData.cpp Source/MaestroMacProj.cpp Source/Src_nd/velpred.F90 commit 5be99b3c7f1f9e2b424d680f420de68248207ba3 Author: Andy Nonaka Date: Wed May 16 17:41:27 2018 -0700 add use parallel, only: parallel_IOProcessor Source/Src_nd/tagging.f90 commit b35c3ee32332cb15df1131009630d0f93eb3cfcb Author: Andy Nonaka Date: Wed May 16 11:06:31 2018 -0700 comment from Rupert Docs/architecture/architecture.tex commit 8e39aeb7b4fc53b5e76746e2c8aeb5c9c476b510 Author: Doreen Fan Date: Tue May 15 15:14:55 2018 -0700 Density can now be tagged for AMR Exec/SCIENCE/wdconvect/inputs_3d_C.128.2levels Exec/SCIENCE/wdconvect/tagging.f90 Exec/TEST_PROBLEMS/reacting_bubble/tagging.f90 Exec/TEST_PROBLEMS/test_convect/tagging.f90 Source/Maestro.H Source/MaestroRegrid.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/tagging.f90 commit 57c0dea72e04ce102e0c7b9f14f1f8b02ab425ff Author: Andy Nonaka Date: Fri May 11 13:31:12 2018 -0700 CASTRO -> MAESTROeX Microphysics/EOS/README Microphysics/EOS/eos.F90 Microphysics/networks/general_null/Make.package commit 368df882069d471c407feba50005f0325aaa1d79 Author: Doreen Fan Date: Thu May 10 15:58:28 2018 -0700 React works on multilevel grids Source/MaestroReact.cpp Source/Maestro_F.H Source/Src_nd/burner_loop.f90 commit 93de98a94eefba729ebb89d9f524a5e7e8743422 Author: Doreen Fan Date: Thu May 10 14:44:16 2018 -0700 Average now works on multilevel grids Source/MaestroAverage.cpp Source/Maestro_F.H Source/Src_nd/average.f90 commit 673d59d61231985752a6145a40b380de545e5167 Author: Doreen Fan Date: Wed May 9 16:23:07 2018 -0700 Typos fixed Source/Src_nd/make_flux.F90 commit b8906245c407df77677be5630be23b68c54e5278 Author: Doreen Fan Date: Tue May 8 18:03:38 2018 -0700 Changed state from snew to sold. Now detects the correct taggin, but plotfile still outputs 1 level. WIP Exec/SCIENCE/wdconvect/inputs_3d_C.128.2levels Exec/SCIENCE/wdconvect/probin Source/MaestroRegrid.cpp commit 67f08cfd53c9537d6f6674c9893feb7329ab1c60 Author: Doreen Fan Date: Thu May 3 18:02:40 2018 -0700 amplitude and phase parameters are now randomly generated Exec/SCIENCE/wdconvect/initdata.f90 commit d0b9afd4128bd6ec5aec44fed27e2797507ed994 Author: Doreen Fan Date: Mon Apr 23 14:24:33 2018 -0700 Added MICROPHYSICS_HOME for wdconvect regression testing Exec/SCIENCE/wdconvect/GNUmakefile commit cf2f8877916e594c83f89573ec3f7db649ef4d7f Author: Doreen Fan Date: Mon Apr 23 13:22:23 2018 -0700 Added wdconvect regression testing. Exec/SCIENCE/wdconvect/inputs_3d_regression Exec/SCIENCE/wdconvect/probin_regression commit aff625f71ddca8c4a00102ca2b5128f9466e5aa8 Author: Doreen Fan Date: Mon Apr 23 11:30:17 2018 -0700 changed plot and check file names for regression testing Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_regression commit 65debbd5876045b424cda2823dd4777834c2974b Author: Doreen Fan Date: Mon Apr 23 11:21:00 2018 -0700 Add regression test problem Exec/SCIENCE/wdconvect/probin Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_regression commit 10139980fcd24db537401a66ef9fd8f80c2d8e23 Author: Andy Nonaka Date: Fri Apr 20 17:18:55 2018 -0700 plot_file -> plot_base_name Exec/SCIENCE/wdconvect/inputs_3d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_dpdt Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C Exec/TEST_PROBLEMS/rt/inputs Exec/TEST_PROBLEMS/test_convect/inputs_2d_C commit d11c3b0c481a5b2fffaef964230f4e8efb7ddae0 Author: Andy Nonaka Date: Fri Apr 20 17:17:04 2018 -0700 regression plot base name plot 9999999, etc., are now called "plt_InitData", "plt_after_DivuIter", "plt_after_InitProj" Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_regression Source/MaestroInit.cpp Source/MaestroPlot.cpp commit 253a63d468d06f6a4f171077fc6ec350c6ebd50e Author: Andy Nonaka Date: Fri Apr 20 16:02:37 2018 -0700 sync this up with amrex source for now Source/Src_nd/AMReX_filcc_mod.F90 commit 15d4f532db90cf276e654d433eb45fcbfe266c07 Author: Andy Nonaka Date: Fri Apr 20 16:02:22 2018 -0700 temporarily disable diag file for planar Source/MaestroDiag.cpp commit a02d8b1d02cda4e49ad38790cf61ab3a35ed1749 Merge: a884d63a 631018ce Author: Andy Nonaka Date: Fri Apr 20 15:48:50 2018 -0700 Merge branch 'master' of https://github.com/AMReX-Astro/MAESTROeX commit a884d63a864230b282aaf0664e414ab7335086a1 Author: Andy Nonaka Date: Fri Apr 20 15:48:31 2018 -0700 endl -> std::endl Source/MaestroAdvance.cpp Source/MaestroDebug.cpp Source/MaestroDensityAdvance.cpp Source/MaestroDiag.cpp Source/MaestroDt.cpp Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/MaestroNodalProj.cpp Source/MaestroSetup.cpp Source/MaestroThermal.cpp commit 631018ce8c465c4a02497ddbb33eaf95ebba07da Author: Regression Tester Date: Fri Apr 20 15:42:38 2018 -0700 point to Microphysics Exec/TEST_PROBLEMS/reacting_bubble/GNUmakefile commit 097ada5bbaf4431ddf372a9a36fdc5faafa39de6 Author: Regression Tester Date: Fri Apr 20 15:29:45 2018 -0700 regression test Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_regression commit 3488c38209c639700199406aab5c5ccf5ea8e03b Author: Doreen Fan Date: Thu Apr 19 17:02:50 2018 -0700 Changed if statement from (dpdt >= 0) to (dpdt > 0) to avoid dividing by 0 Source/Src_nd/make_S.F90 commit f1f6ab8990adcdf0ae7eb7db4242e05f00928f19 Author: Doreen Fan Date: Wed Apr 18 14:29:04 2018 -0700 Make sure combustion abundances sum to 1 when not burning in spherical case. Removed previous abort call. Source/Src_nd/burner_loop.f90 commit e594869e8ea73178b29ebdc9b88cde45195b5b44 Author: Doreen Fan Date: Tue Apr 17 12:07:13 2018 -0700 Diag subroutines complete. Now includes diag_buf_size parameter, same as in MAESTRO. Source/Maestro.H Source/MaestroDiag.cpp Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/MaestroSetup.cpp Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H commit 9c5c62e7f7f7ae5985e9d5e4fea68c6a75b245f3 Author: Doreen Fan Date: Mon Apr 16 14:45:25 2018 -0700 Added additional parameter ncenter needed to compute T_center Source/Maestro.H Source/MaestroDiag.cpp Source/Maestro_F.H Source/Src_nd/diag.F90 commit 38d920758c1b06420fb941aa98a00bdefdf84624 Author: Doreen Fan Date: Fri Apr 13 17:33:35 2018 -0700 completed diagnostics subroutine for outputs related to maximum temperature Source/MaestroDiag.cpp commit 05e4aab9003b0e9e4131b6dc93c898c20280d883 Author: Doreen Fan Date: Thu Apr 12 19:12:40 2018 -0700 Added subroutines for diagnosis output of maximum temperature. Still WIP. Source/Maestro.H Source/MaestroDiag.cpp Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/Make.package Source/Src_nd/diag.F90 commit 01f8a9ff02a184d6af1fcd65aaa24410a8928026 Author: Doreen Fan Date: Wed Apr 11 18:15:12 2018 -0700 Added averaging for tempbar variable and comments for future diagnosis functions Source/MaestroAdvance.cpp Source/MaestroAverage.cpp Source/MaestroEvolve.cpp Source/MaestroInit.cpp commit 4fa0a1485416a71419da31123b64194826d43c07 Author: Weiqun Zhang Date: Wed Apr 11 15:49:10 2018 -0700 DEBUG --> AMREX_DEBUG Source/param/parse_maestro_params.py commit d7dad4320a5478d5eef96e9daebd0a22e58ced65 Author: Doreen Fan Date: Tue Apr 10 18:27:10 2018 -0700 Cleanup code: removed comments and unnecessary variables Source/MaestroDensityAdvance.cpp Source/Src_nd/advect_base.F90 Source/Src_nd/make_S.F90 Source/Src_nd/velpred.F90 commit dfab38ce2b082bb41d5d4c9c14b234f6eb6b09b8 Author: Doreen Fan Date: Mon Apr 9 13:33:57 2018 -0700 Bug fix for non-spherical option Source/MaestroAdvection.cpp commit 1dfc8fe9f95804a068b2a8cbc34b7088bcec8ff9 Author: Doreen Fan Date: Thu Apr 5 16:27:50 2018 -0700 Bugfixes: mainly allocation errors Exec/SCIENCE/wdconvect/inputs_3d_C Source/MaestroAdvection.cpp Source/MaestroDensityAdvance.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroForce.cpp Source/MaestroMacProj.cpp commit 320cc3e799fe9a1cdfcbc98e029fdfc46f995617 Author: Doreen Fan Date: Thu Apr 5 14:12:42 2018 -0700 Fixed initialization of tempbar_init and tempbar_init_cart Source/MaestroInit.cpp Source/MaestroReact.cpp Source/Maestro_F.H Source/Src_nd/base_state.f90 commit d6d183900b09d282b2e3e7d11f209dfe31ebc8e9 Author: Doreen Fan Date: Thu Apr 5 12:17:07 2018 -0700 Forgot to add init_shrink parameter Exec/SCIENCE/wdconvect/inputs_3d_C commit 0554d9c0a3e2bb99b557ebe96a0a2fe44c6bacd3 Author: Doreen Fan Date: Wed Apr 4 19:16:11 2018 -0700 Fixed index and initialization issues. Debugging in progress. Source/MaestroAverage.cpp Source/Src_nd/average.f90 Source/Src_nd/base_state_geometry.f90 commit 586ff8d347ec505c855d56d810df9703e8de5caf Author: Doreen Fan Date: Wed Apr 4 15:40:10 2018 -0700 Corrected format of parameters in input file Exec/SCIENCE/wdconvect/probin commit 2b5fa2d2d3654b254e328fedc611d6264a3e329e Author: Doreen Fan Date: Wed Apr 4 15:28:15 2018 -0700 Added wdconvect problem to test spherical implementation Exec/SCIENCE/wdconvect/GNUmakefile Exec/SCIENCE/wdconvect/Make.package Exec/SCIENCE/wdconvect/initdata.f90 Exec/SCIENCE/wdconvect/inputs_3d_C Exec/SCIENCE/wdconvect/kepler_new_6.25e8.hybrid.hse.320 Exec/SCIENCE/wdconvect/probdata.f90 Exec/SCIENCE/wdconvect/probin commit 4051a48bb2c7265fcb60aa4579620c4afe5e1c97 Author: Doreen Fan Date: Tue Apr 3 16:53:06 2018 -0700 Completed Average() subroutine for spherical option Source/Maestro.H Source/MaestroAverage.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/average.f90 Source/Src_nd/base_state_geometry.f90 commit 6a146e09d4b9c00c80360ef82f3891f81b995d07 Author: Doreen Fan Date: Mon Apr 2 18:53:18 2018 -0700 Adding Average() subroutines for spherical option. WIP Source/MaestroAverage.cpp Source/Maestro_F.H Source/Src_nd/average.f90 Source/Src_nd/fill_3d_data.F90 commit 951005531a440c33a937356e367d01c77ebe8dfd Author: Doreen Fan Date: Mon Apr 2 16:29:44 2018 -0700 Continue to add subroutines needed for enabling spherical option Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/MaestroMakeEta.cpp Source/MaestroRegrid.cpp Source/MaestroVelocityAdvance.cpp Source/Maestro_F.H Source/Src_nd/make_eta.F90 Source/Src_nd/update_vel.F90 Source/Src_nd/velpred.F90 commit 5c15a9657ca453e07f65d184c4b039b48bd1b9d2 Author: Doreen Fan Date: Thu Mar 29 19:25:53 2018 -0700 Added more subroutines to enable spherical option. Now working on UpdateVelocity(). Source/Maestro.H Source/MaestroAdvection.cpp Source/MaestroDensityAdvance.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroReact.cpp Source/MaestroRhoHT.cpp Source/Maestro_F.H Source/Src_nd/burner_loop.f90 Source/Src_nd/make_scal_force.F90 Source/Src_nd/mkutrans.F90 Source/Src_nd/rhoh_vs_t.F90 Source/Src_nd/sponge.F90 Source/Src_nd/update_scal.F90 commit 266f6b1b0cc91ac66fd6a99df3b0c7be0c0eb60e Author: Doreen Fan Date: Tue Mar 27 17:17:22 2018 -0700 Added necessary spherical-related subroutines in DensityAdvance and EnthalpyAdvance functions. Source/Maestro.H Source/MaestroAdvection.cpp Source/MaestroDensityAdvance.cpp Source/MaestroEnthalpyAdvance.cpp Source/Maestro_F.H Source/Src_nd/make_flux.F90 commit 847b1a16b19ec278b316e04d1a5cae81539c9fb0 Author: Doreen Fan Date: Mon Mar 26 19:30:51 2018 -0700 Continue to add subroutines for spherical option. Now working on DensityAdvance(). Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroDensityAdvance.cpp Source/MaestroGamma.cpp Source/MaestroMakeS.cpp Source/MaestroPlot.cpp Source/Maestro_F.H Source/Src_nd/make_S.F90 Source/Src_nd/make_flux.F90 Source/Src_nd/make_gamma.F90 commit 78362da75335ea5fab53e326540230aee2c623a1 Author: Doreen Fan Date: Fri Mar 23 18:02:39 2018 -0700 Continue to add subroutines for enabling spherical option Exec/TEST_PROBLEMS/reacting_bubble/initdata.f90 Source/MaestroDt.cpp Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/compute_dt.F90 Source/Src_nd/initdata.f90 commit ae97a47af98386a6c455bc49d8924e719e205fb9 Author: Andy Nonaka Date: Fri Mar 23 15:39:00 2018 -0700 the PrintMF debugging routines now allow you to modify the contents of the MultiFab Source/Maestro.H Source/MaestroDebug.cpp Source/Src_nd/debug.F90 commit 5aaee6d80cca2c1cdae00b282614dae4aad8610f Author: Doreen Fan Date: Thu Mar 22 18:03:53 2018 -0700 Continue to add subroutines to enable spherical option Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroDensityAdvance.cpp Source/MaestroDt.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroVelocityAdvance.cpp Source/Maestro_F.H Source/Src_nd/compute_dt.F90 Source/Src_nd/compute_grad_phi.F90 Source/Src_nd/fill_3d_data.F90 Source/Src_nd/make_vel_force.F90 commit 6299a0b937f868e9c36eb2b7956b8cdd4dc75ce9 Author: Doreen Fan Date: Tue Mar 20 18:32:43 2018 -0700 Started to add if statements and subroutines needed for using the spherical option Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroDensityAdvance.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroFill3dData.cpp Source/MaestroMacProj.cpp Source/MaestroVelocityAdvance.cpp Source/Maestro_F.H Source/Src_nd/fill_3d_data.F90 Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit 59f6f0e630884a83089adbb877b26ea15b9f50f2 Author: Doreen Fan Date: Fri Mar 16 14:54:58 2018 -0700 Removed create_correction_nodal() as it was unnecessary. Results from test problem now matches Fortran MAESTRO. Source/MaestroMakeS.cpp Source/Maestro_F.H Source/Src_nd/make_S.F90 commit cee240e1f4a41769cce8bc14ae7b57acbb1b7455 Author: FanD Date: Fri Mar 16 14:45:50 2018 -0700 Misspelled amr_levels parameter Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_dpdt commit 3476f214a4626c7a7dbcfa2e6fad77712c4dd9f3 Author: Doreen Fan Date: Thu Mar 15 15:59:24 2018 -0700 Includes test problem for dpdt_factor = 1 Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_dpdt commit c17415ab37c576a871af0fdb94967b0a059186b1 Author: Doreen Fan Date: Thu Mar 15 15:04:04 2018 -0700 Added CorrectRHCCforNodalProj() subroutine to accomodate nonzero dpdt_factor Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroMakeS.cpp Source/Maestro_F.H Source/Src_nd/make_S.F90 commit dd47909d0eced0657600a4dd74b1eedeac49c3a0 Author: Doreen Fan Date: Thu Mar 15 13:37:43 2018 -0700 Added makePfromRhoH() subroutines to accomodate nonzero dpdt_factor Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroRhoHT.cpp Source/Maestro_F.H Source/Src_nd/rhoh_vs_t.F90 commit 268195f8af46f87150eb93ee06c47b7ac93ac902 Author: Doreen Fan Date: Wed Mar 14 19:00:15 2018 -0700 Modified MakeRHCCforMacProj() to include terms relevant for when dpdt_factor is turned on Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroMakeS.cpp Source/Maestro_F.H Source/Src_nd/make_S.F90 commit aa15750d75d88274bd2ba28bb8ec9d1d2c2bab40 Author: Doreen Fan Date: Wed Mar 14 17:17:08 2018 -0700 Cleanup file Source/MaestroPlot.cpp commit 3272ac9b0c975d679064baca84fbcfdb77c92f85 Author: Doreen Fan Date: Wed Mar 14 17:15:55 2018 -0700 Plot file now outputs deltaT Source/MaestroPlot.cpp commit 8cfbe6149095bdd4fceae7164c000734fe0d447e Author: Doreen Fan Date: Wed Mar 14 15:09:12 2018 -0700 Bugfix: use s2 instead of s1 on RHS of ThermalConduct() Source/MaestroThermal.cpp commit 0cbdbdbff3d0c60b607ce49a505f5de7f73058ec Author: Doreen Fan Date: Wed Mar 14 14:47:34 2018 -0700 Thermal diffusion bugfix: scalar coefficients when solving div(B grad phi) are of the wrong sign Source/MaestroAdvance.cpp Source/MaestroThermal.cpp commit a20eb9d8f08ebd7a34382f046b6dde0e7d266e65 Author: Doreen Fan Date: Tue Mar 13 16:50:23 2018 -0700 Add remaining thermal diffusion subroutines. Now runs but solution is not quite correct. WIP. Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroInit.cpp Source/MaestroThermal.cpp commit 57ff0db168b4ec3389a4fbee8b45acef8c5750cb Author: Doreen Fan Date: Tue Mar 13 14:18:26 2018 -0700 Added subroutines required for thermal diffusion. Not yet tested. Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroThermal.cpp Source/Make.package Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit ddb4f2063141e2e90f2d58e431f0a03296fbc6ab Author: Andy Nonaka Date: Tue Mar 13 12:39:51 2018 -0700 sync up test problems with MAESTRO. now enabling ppm, alt_energy_fix, and evolve_base_state Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C commit 5c3abf9ba840ade6efcc62372bde0f3fd2baefcd Author: Andy Nonaka Date: Tue Mar 13 11:06:48 2018 -0700 add ppm to make_edge_scal Source/MaestroAdvection.cpp Source/Maestro_F.H Source/Src_nd/make_edge_scal.F90 commit 1643ace53e9e93697b1d887dd5d076912ccede01 Author: Andy Nonaka Date: Tue Mar 13 10:27:32 2018 -0700 implemented ppm for mkutrans Source/MaestroAdvection.cpp Source/Maestro_F.H Source/Src_nd/mkutrans.F90 commit 854c3544ab88efbef11877667b6656b4270b5e69 Author: Andy Nonaka Date: Tue Mar 13 10:06:21 2018 -0700 allocate arrays on the heap instead of the stack. also no need to explicitly deallocate arrays in F90 since this happens when they go out of scope Source/Src_nd/velpred.F90 commit c9f96c975eb76f33b57f9b72ea9b9ccfc834a24b Author: Andy Nonaka Date: Tue Mar 13 09:47:51 2018 -0700 implement ppm for 1d and 3d Source/Src_nd/velpred.F90 commit 294edc25a1967bf864d57232730e3bbe71930335 Author: Andy Nonaka Date: Tue Mar 13 09:47:47 2018 -0700 code cleanup Source/MaestroAdvection.cpp Source/MaestroFillData.cpp commit 4b8cd5ad20d4f81e5a014b6e5b1838f60f2748be Author: Andy Nonaka Date: Tue Mar 13 09:11:11 2018 -0700 enable alt_energy_fix Exec/TEST_PROBLEMS/test_convect/inputs_2d_C commit 35c603b58eea9f9ee1e4c598b4e1eca7a61b7de1 Author: Andy Nonaka Date: Tue Mar 13 09:09:11 2018 -0700 cleanup function Source/MaestroAverage.cpp commit 4e36859ab94b5ca85fbb8e9634969a08e77eef10 Author: Andy Nonaka Date: Tue Mar 13 09:07:52 2018 -0700 bugfix in that ncell wasn't being computed for all radii on every processor since the computation was being done within an MFIter loop - not every processor has a grid at a given radius also simplified ncell treatment so it's simply a vector over levels - we don't need to have a 2nd dimension for coordinate since it's the same over the entire level Source/MaestroMakeEta.cpp Source/Maestro_F.H Source/Src_nd/make_eta.F90 commit b2ae849e653827922edacdb128f733d19876f474 Author: Andy Nonaka Date: Mon Mar 12 19:20:29 2018 -0700 fix array error for computing etarho_ec Source/Src_nd/make_eta.F90 commit 8cb030ca8f03728d5dc67556ca4c826cb5ed4ff0 Author: Andy Nonaka Date: Mon Mar 12 18:50:26 2018 -0700 implement ppm in velpred Source/MaestroAdvection.cpp Source/Maestro_F.H Source/Src_nd/ppm.F90 Source/Src_nd/velpred.F90 commit 760e4f54c3121a9f28ca35c357e17c92862f65a8 Author: Andy Nonaka Date: Mon Mar 12 18:50:19 2018 -0700 sync up with 2d problem Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C commit a9462fda7667bb43527858d0a8d063fae0dcba91 Author: Andy Nonaka Date: Mon Mar 12 18:47:21 2018 -0700 point 3d problem to probin file Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C commit f71c8bf36ee05edd02fed728b1347241e6792643 Author: Andy Nonaka Date: Mon Mar 12 18:09:11 2018 -0700 ppm advection routines - not being called yet but 'converted' to work with MAESTROeX Exec/TEST_PROBLEMS/test_convect/inputs_2d_C Source/Src_nd/Make.package Source/Src_nd/ppm.F90 commit 013d1852b37b612013c8cc1daea50ceab55297ac Author: Andy Nonaka Date: Mon Mar 12 16:41:39 2018 -0700 the number of ghost cells for sold/new and uold/new depends on the advection type (only supporting piecewise linear the moment but ppm coming soon). We store this number now in "ng_s" in the Maestro class Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroCheckpoint.cpp Source/MaestroDensityAdvance.cpp Source/MaestroInit.cpp Source/MaestroSetup.cpp commit 85607a5a884f8d755bfcd7677366bb6550d11ea9 Merge: 69f8fa7f 7c49e23d Author: Andy Nonaka Date: Mon Mar 12 16:26:53 2018 -0700 Merge branch 'master' of https://github.com/AMReX-Astro/MAESTROeX commit 69f8fa7f5981bf74d8de989ee3351f9ca6d62a76 Author: Andy Nonaka Date: Mon Mar 12 16:26:36 2018 -0700 remove multifabs that will never be needed in Advance() Source/MaestroAdvance.cpp commit 7c49e23dad2370e4c95d7812d7f0862777ebfb55 Author: Doreen Fan Date: Mon Mar 12 15:46:25 2018 -0700 Added PutDataOnFaces() and related subroutines Source/Maestro.H Source/MaestroFill3dData.cpp Source/MaestroVelocityAdvance.cpp Source/Maestro_F.H Source/Src_nd/fill_3d_data.F90 Source/Src_nd/make_explicit_thermal.F90 commit c946e83107dffca1d480113e2051b4c5cf27fa04 Author: Andy Nonaka Date: Mon Mar 12 15:43:30 2018 -0700 implemented use_alt_energy_fix. testing on reacting bubble and it compares fine to the original MAESTRO Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroMacProj.cpp Source/MaestroNodalProj.cpp Source/Maestro_F.H Source/Src_nd/make_pi_cc.F90 Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit b4db1f1b54824822bcc070cf8c13f48ec19a0037 Author: Andy Nonaka Date: Mon Mar 12 14:39:48 2018 -0700 fix argument list for default make_heating Source/Src_nd/make_heating.F90 commit 830538e6718e763e9ae97dbe9baddfc8517d1a8b Author: Andy Nonaka Date: Fri Mar 9 17:11:27 2018 -0800 bugfix - forgot to index into the base state r correctly for part of the velocity forcing Source/Src_nd/make_vel_force.F90 commit c40d3a24d348e39cda23b051f7a90b611a36db89 Author: Andy Nonaka Date: Fri Mar 9 13:44:01 2018 -0800 write w0 to plotfile Source/MaestroPlot.cpp commit c35f90ca34a9a016927b85bca68cfe37350001ea Author: Andy Nonaka Date: Fri Mar 9 13:06:37 2018 -0800 set initial conditions in probin now, not inputs file Exec/TEST_PROBLEMS/test_convect/inputs_2d_C commit 5b9dab1cb8765d7f7ac5970bc57de51df9c8c091 Author: Andy Nonaka Date: Fri Mar 9 13:03:55 2018 -0800 match MAESTRO example Exec/TEST_PROBLEMS/test_convect/inputs_2d_C commit 17ed5acbd5552aaeba60cf1b585ea0f6d88e0cb0 Author: Andy Nonaka Date: Fri Mar 9 10:32:11 2018 -0800 bugfix - was applying init_shrink for regular dt computation Source/MaestroDt.cpp commit 878e754be2d3769bcdaad9a6eb44b6cd0315b420 Author: Doreen Fan Date: Thu Mar 8 18:38:59 2018 -0800 Added comments and subroutines to include thermal diffusion. Subroutines are still WIP. Source/MaestroAdvance.cpp Source/MaestroInit.cpp Source/MaestroNodalProj.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/make_explicit_thermal.F90 Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit d0ecf5c6aee51473cb425c2a151f59622f045ca7 Author: Andy Nonaka Date: Thu Mar 8 18:35:07 2018 -0800 updated test_convect setup. after the initial pressure iteration, pi does not look the same in the codes at all Exec/TEST_PROBLEMS/test_convect/inputs_2d_C commit e50e4001600ca8f3faee79d458056de7b8042ce9 Author: Andy Nonaka Date: Thu Mar 8 18:06:46 2018 -0800 turn off heating after t=200 Exec/TEST_PROBLEMS/test_convect/make_heating.F90 commit 50770fe6b55424f569fa0f3d7ec8db3aec90ddad Author: Andy Nonaka Date: Thu Mar 8 17:49:24 2018 -0800 progress on test_convect - pretty close to working now Exec/TEST_PROBLEMS/test_convect/inputs_2d_C Exec/TEST_PROBLEMS/test_convect/make_heating.F90 Source/MaestroHeating.cpp Source/Maestro_F.H commit 018d7246d6be56cc5296310630008f13901156c0 Author: Andy Nonaka Date: Thu Mar 8 16:51:17 2018 -0800 setting up general make_heating interface Exec/TEST_PROBLEMS/reacting_bubble/probdata.f90 Exec/TEST_PROBLEMS/test_convect/probdata.f90 Source/Maestro.H Source/MaestroHeating.cpp Source/MaestroReact.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/make_heating.F90 Source/Src_nd/probdata.f90 commit 021397d9ab040305356c89b503f4dd0c13055942 Author: Andy Nonaka Date: Thu Mar 8 15:59:01 2018 -0800 test_convect routines in place. still need problem-specific heating - WIP Exec/TEST_PROBLEMS/test_convect/GNUmakefile Exec/TEST_PROBLEMS/test_convect/Make.package Exec/TEST_PROBLEMS/test_convect/initdata.f90 Exec/TEST_PROBLEMS/test_convect/inputs_2d_C Exec/TEST_PROBLEMS/test_convect/probdata.f90 Exec/TEST_PROBLEMS/test_convect/probin Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit 0b20d392d57dbe03ec417773af3336db62c4c306 Author: Andy Nonaka Date: Thu Mar 8 15:58:44 2018 -0800 only use plot_deltat if it's a positive number Source/MaestroEvolve.cpp commit 2b34b66e00a9b331843edf776f9a82189aff7cb5 Author: Andy Nonaka Date: Thu Mar 8 14:41:43 2018 -0800 s0_init and p0_init should be declared "in", not "inout" Exec/TEST_PROBLEMS/reacting_bubble/initdata.f90 Source/Src_nd/initdata.f90 commit 787397e3e045c064878cd71f304d2d9cfd9115de Author: Andy Nonaka Date: Thu Mar 8 14:37:26 2018 -0800 giving MAESTROeX some flexibility to handle different problem setups in the same style as Castro Now, each problem needs its own copies of the following: 1. initdata.f90: initializes velocity and scalars 2. probdata.f90: contains problem-specific variables (typically used in initialization) and puts them in the "probdata" namelist module. You specify these in the probin file (not the inputs file) 3. probin: change the default values of namelist parameters (probdata and extern). extern is for the network and EOS. probdata is problem-specific Exec/TEST_PROBLEMS/reacting_bubble/GNUmakefile Exec/TEST_PROBLEMS/reacting_bubble/Make.package Exec/TEST_PROBLEMS/reacting_bubble/initdata.f90 Exec/TEST_PROBLEMS/reacting_bubble/probdata.f90 Exec/TEST_PROBLEMS/reacting_bubble/probin Source/Maestro.H Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/maestro_init.f90 Source/Src_nd/probdata.f90 Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit c88e6695e23ae987e3c058c4ff7c8413fc6ec638 Author: Doreen Fan Date: Thu Mar 8 13:46:39 2018 -0800 is_predictor variable in MakeRhoHForce() should be which_step Source/Maestro.H Source/MaestroEnthalpyAdvance.cpp Source/MaestroForce.cpp commit f4e444c83e0b953c9251688813f51c98dc98f93a Author: Andy Nonaka Date: Thu Mar 8 12:34:19 2018 -0800 each problem in maestro now requires its own initdata.f90 that will sit in the build directory. The version of initdata.f90 in Source/Src_nd/ is a sample initialization with an abort message indicating to create a local copy Exec/TEST_PROBLEMS/reacting_bubble/initdata.f90 Source/Src_nd/initdata.f90 commit 7ebe324ed94fcf3413eeaf9a09625e23d0267808 Author: Andy Nonaka Date: Wed Mar 7 14:24:40 2018 -0800 MAESTRO now requires a probin file to read in external namelist parameters. Right now the "extern" namelist is implemented (for EOS and network) starting to put together a test_convect problem Exec/TEST_PROBLEMS/reacting_bubble/GNUmakefile Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Exec/TEST_PROBLEMS/reacting_bubble/probin Exec/TEST_PROBLEMS/test_convect/GNUmakefile Exec/TEST_PROBLEMS/test_convect/inputs_2d_C Exec/TEST_PROBLEMS/test_convect/model.hse Source/Maestro.H Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/maestro_init.f90 Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit a920dbda26d73d09268cc7928afddd3b85215d9c Author: Andy Nonaka Date: Wed Mar 7 09:28:27 2018 -0800 put MakeHeating in its own .cpp file - most problems have custom external heating so the problem directory will get its own local copy Source/MaestroHeating.cpp Source/MaestroReact.cpp Source/Make.package commit 46130e62befec5bcddcb05feafb311b7dd560541 Author: Andy Nonaka Date: Tue Mar 6 17:34:38 2018 -0800 for the mac projection, don't use hard-coded values of eps_mac, eps_mac_max, or mac_level_factor, and instead use the values supplied from the inputs file (which have defaults given in _cpp_parameters) Source/MaestroMacProj.cpp commit b998d79c9f4aa6b6a705c3f6b492e973345a8b59 Author: Doreen Fan Date: Tue Mar 6 17:17:21 2018 -0800 Added MakeNormal() subroutine to start implenting spherical base state Source/MaestroFill3dData.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/fill_3d_data.F90 commit 06823cffe434e4a6a8fd371a13edbca48540b265 Author: Doreen Fan Date: Mon Mar 5 18:24:15 2018 -0800 Include subroutines that were previously commented out Source/MaestroRegrid.cpp commit f10588a150e61ce9229d832a0d62dc6c4a57d283 Author: Doreen Fan Date: Mon Mar 5 18:02:52 2018 -0800 Changed subroutines to more closely resemble the Fortran subroutines. No changes in functionality. Source/MaestroDt.cpp Source/MaestroInit.cpp Source/Src_nd/make_flux.F90 commit 2a7ef17b5c65ae869a2c4d3c413e5100de885308 Author: Andy Nonaka Date: Fri Mar 2 13:16:27 2018 -0800 comments only, simplify some code - no functional changes Source/MaestroNodalProj.cpp commit b5945977e0628803c73b2dc6d46d0ff1c0417309 Author: Doreen Fan Date: Thu Mar 1 17:48:30 2018 -0800 Needed to reduce etarhosum over all processors Source/MaestroMakeEta.cpp commit 56939a6d88bf2bee6d5185343f7a84a8fecf3f21 Author: Doreen Fan Date: Thu Mar 1 15:51:48 2018 -0800 Fixed upper array index of etarho_ec Source/Src_nd/make_eta.F90 commit 6597c3f7eeed92b6351e3e863663b97c73bca7bd Author: Doreen Fan Date: Wed Feb 28 18:37:29 2018 -0800 Fixed initialization of etarhosum to outside the outermost loop Source/MaestroMakeEta.cpp Source/Src_nd/make_eta.F90 commit b0a956c26d75f40799c941f3e96e795bd11b5fcd Author: Doreen Fan Date: Wed Feb 28 17:15:32 2018 -0800 Changed inputs file to run evolve base states and set ppm_type=0 Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C commit b9b173e83f2ac161989aeda13c381d37da29a632 Merge: 22012ede 981bc897 Author: Doreen Fan Date: Wed Feb 28 17:09:28 2018 -0800 Merge branch 'master' of https://github.com/AMReX-Astro/MAESTROeX commit 22012ede02218cfa264b05683efd121fc228fc0f Author: Doreen Fan Date: Wed Feb 28 17:08:09 2018 -0800 Fixed bugs with array indices Source/Src_nd/average.f90 Source/Src_nd/make_edge_state.f90 Source/Src_nd/make_w0.f90 commit 981bc8978d44676c6b3face8362e01a92835d173 Author: Andy Nonaka Date: Wed Feb 28 16:44:35 2018 -0800 doc updates Docs/architecture/amrex_directory.odg Docs/architecture/amrex_directory2.eps Docs/architecture/architecture.tex Docs/architecture/maestro_directory.odg Docs/architecture/maestro_directory2.eps Docs/architecture/maestro_ecosystem.odg Docs/architecture/maestro_ecosystem2.eps Docs/getting_started/getting_started.tex commit 84704647608b56a78e18525656061fe6115fe442 Author: Andy Nonaka Date: Wed Feb 28 15:58:36 2018 -0800 updates to MAESTROeX docs Docs/architecture/amrex_directory.odg Docs/architecture/amrex_directory2.eps Docs/architecture/architecture.tex Docs/architecture/boxlib_directory.odg Docs/architecture/boxlib_directory2.eps Docs/architecture/maestro_ecosystem.odg Docs/architecture/maestro_ecosystem2.eps Docs/getting_started/getting_started.tex commit 762eda91e544990707935c6cb9d853a0916e5bb8 Author: Andy Nonaka Date: Wed Feb 28 15:51:09 2018 -0800 write job_info to checkpoint as well Source/MaestroCheckpoint.cpp commit a03dc981a0e325976e02bbd9f9c39e15edeabea2 Author: Andy Nonaka Date: Wed Feb 28 15:49:29 2018 -0800 job info output Source/MaestroPlot.cpp commit 5a92bcf63ce1bca662e774fcc579663a4b3f618f Author: Andy Nonaka Date: Wed Feb 28 15:45:43 2018 -0800 7-digit format for checkpoint files to match plotfiles Source/MaestroCheckpoint.cpp commit c4bfb367fd123bfb6bcdb440a346ae02d4ee7792 Author: Andy Nonaka Date: Wed Feb 28 14:50:56 2018 -0800 more changes "MAESTRO_C" -> 'MAESTROeX" Docs/MAESTROeXUsersGuide.tex Docs/flowchart/flowchart.tex Docs/getting_started/getting_started.tex Docs/introduction/introduction.tex Exec/Make.Maestro Exec/TEST_PROBLEMS/reacting_bubble/GNUmakefile Exec/TEST_PROBLEMS/rt/GNUmakefile README.md commit 64c02992a4f53148d2d4de02dbb6295b5074525d Author: Andy Nonaka Date: Tue Feb 27 19:02:45 2018 -0800 test commit Docs/MAESTROeXUsersGuide.tex commit 90f50f6143cdd9e7cd6a124927170fe49cfbd41b Author: Andy Nonaka Date: Tue Feb 27 19:01:51 2018 -0800 editing user's guide. also rennamed repo "MAESTROeX" Docs/GNUmakefile Docs/MAESTROeXUsersGuide.tex Docs/maestrosymbols.tex Docs/preface/preface.tex commit 5362a97b92bffce3d8cf0f8e66cdd4ded2fa7fff Author: Andy Nonaka Date: Tue Feb 27 18:00:14 2018 -0800 copy MAESTRO_F Docs here - this will evolve to be AMReX-specific Docs/FAQ/GNUmakefile Docs/FAQ/faq.tex Docs/FAQ/paper.tex Docs/GNUmakefile Docs/Godunov_notes/GNUmakefile Docs/Godunov_notes/Godunov.tex Docs/Godunov_notes/paper.tex Docs/MESA/GNUmakefile 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Docs/visualization/GNUmakefile Docs/visualization/my_cool_images_Slice_x_tfromp_trim.eps Docs/visualization/my_cool_images_Slice_x_tfromp_trim.png Docs/visualization/paper.tex Docs/visualization/plt00000_tfromp.eps Docs/visualization/plt00000_tfromp.png Docs/visualization/plt00000_tfromp_enucdot.eps Docs/visualization/tfromp.eps Docs/visualization/visualization.tex Docs/volume_discrepancy/GNUmakefile Docs/volume_discrepancy/paper.tex Docs/volume_discrepancy/volume_discrepancy.tex Docs/web.txt commit ad893140ac5aae8ddd833c0d3a243663484fa364 Author: Andy Nonaka Date: Thu Feb 22 16:36:56 2018 -0800 set number of bottom solver iters back to default value of 100 instead of 1000 this works now with the latest amrex MLMG solvers Source/MaestroMacProj.cpp Source/MaestroNodalProj.cpp commit eabb1fb3f4125c4c959bb70747e59cb8125d462b Author: Andy Nonaka Date: Thu Feb 22 15:57:24 2018 -0800 index bug in 3d for mult faces by beta0 Source/Src_nd/mac_solver.F90 commit b567f4914ac8401ed030cf30389544b89b64f99a Author: Doreen Fan Date: Wed Feb 21 12:54:23 2018 -0800 Added advance_base_module to evolve base states Source/MaestroAdvance.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/advect_base.F90 Source/Src_nd/make_edge_state.f90 commit d72dd5bf899f2ed94be6841fd78b40f51907574d Author: Doreen Fan Date: Tue Feb 20 18:27:40 2018 -0800 Added make_edge_state subroutine for advect base state functions. Source/Src_nd/Make.package Source/Src_nd/make_edge_state.f90 Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit 199ce018c7a8bd9363e6bab8c51a0b361ded4cee Author: Doreen Fan Date: Tue Feb 20 15:59:31 2018 -0800 Added MakeEtarho subroutines required for advecting base states Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroMacProj.cpp Source/MaestroMakeEta.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/Make.package Source/Src_nd/make_eta.F90 commit 90782b7c86b0dcb817e8f4e171e987acd3aa3384 Author: Andy Nonaka Date: Tue Feb 20 09:52:34 2018 -0800 temporarily set the number of CG bottom solver iters to 1000 so the 3d problem runs use mg_verbose and cg_verbose from _cpp_parameters to set the multigrid verbosity in both the nodal and mac solvers Source/MaestroMacProj.cpp Source/MaestroNodalProj.cpp Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H commit 014348deb1983b547f40f80b47f75ba6a85e3e69 Author: Doreen Fan Date: Thu Feb 15 15:29:45 2018 -0800 Added make_psi_module subroutines Source/MaestroAdvance.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/make_psi.F90 commit e3c07234d25bdb6c94b6492b319d0d7dc92dc83b Author: Doreen Fan Date: Thu Feb 15 13:58:52 2018 -0800 Added some preliminary subroutines that are needed to evolve base state Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroDensityAdvance.cpp Source/MaestroDt.cpp Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/MaestroNodalProj.cpp Source/MaestroRegrid.cpp Source/Maestro_F.H Source/Src_nd/make_flux.F90 Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit 7c6a7ede4b4066eaf1b684feae9aaee9be2777ad Merge: 40c6f088 2b9572aa Author: Andy Nonaka Date: Thu Feb 15 13:15:00 2018 -0800 Merge branch 'master' of https://github.com/AMReX-Astro/MAESTRO_C commit 40c6f08800ff56a193c41e40c45f2b8bb6323789 Author: Andy Nonaka Date: Thu Feb 15 12:58:38 2018 -0800 commiting this inputs file for Ann/Weiqun Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C commit 2b9572aa641a700555f7ee08836ae758a1071eaa Author: Weiqun Zhang Date: Thu Feb 15 09:36:16 2018 -0800 fix array bound Source/Src_nd/enforce_HSE.f90 commit ec691865b4cc2ad47b5b354369a512ed845491ac Author: Weiqun Zhang Date: Thu Feb 15 09:32:54 2018 -0800 add amrex:: Source/Maestro.H Source/PhysBCFunctMaestro.H commit dc42931dd015dd26ed7bb3e11a6c1d4e82dffbb0 Author: Doreen Fan Date: Wed Feb 14 17:54:35 2018 -0800 Fixed bcs in MaestroMacProj Source/MaestroMacProj.cpp commit f81cfbdba39a34718936a25681c4d667c82b6021 Author: Doreen Fan Date: Wed Feb 14 16:46:39 2018 -0800 Now fills Dirichlet bcs with zeros instead of relying on user input. Source/Src_nd/AMReX_filcc_mod.F90 commit f004631b6db7fb177ba88249602e98038993fe8f Merge: 98746e6c 9fe46387 Author: Doreen Fan Date: Tue Feb 13 18:15:08 2018 -0800 Merge branch 'master' of https://github.com/AMReX-Astro/MAESTRO_C commit 98746e6ce959939df510762ca8480b4c2e2a8de1 Author: Doreen Fan Date: Tue Feb 13 18:15:04 2018 -0800 Added 3D reacting bubble test problem.Still WIP Exec/TEST_PROBLEMS/reacting_bubble/inputs_3d_C Source/MaestroEvolve.cpp Source/Src_nd/initdata.f90 commit 9fe463876dd24422c2efea79efa24cdf63cb937e Author: Andy Nonaka Date: Tue Feb 13 17:55:57 2018 -0800 restart bugfix - still WIP Source/MaestroEvolve.cpp commit 47b7b6fa6263995a99f3804e755cea34ee153a11 Author: Doreen Fan Date: Tue Feb 13 13:08:31 2018 -0800 Added profiling function calls to all C++ subroutines. Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroAverage.cpp Source/MaestroCheckpoint.cpp Source/MaestroConvert.cpp Source/MaestroDebug.cpp Source/MaestroDensityAdvance.cpp Source/MaestroDt.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroEvolve.cpp Source/MaestroFill3dData.cpp Source/MaestroFillData.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp Source/MaestroReact.cpp Source/MaestroRegrid.cpp Source/MaestroRhoHT.cpp Source/MaestroSetup.cpp Source/MaestroSponge.cpp Source/MaestroVelocityAdvance.cpp Source/PhysBCFunctMaestro.cpp commit cb5dba7e0eff80592e52fb682b006addc6dbce9d Author: Andy Nonaka Date: Tue Feb 13 10:49:41 2018 -0800 checkpoint/restart working for reacting bubble rise problem Source/MaestroCheckpoint.cpp Source/MaestroEvolve.cpp Source/MaestroInit.cpp commit bfdacb005a5098a1bd947f8a394f57a053426d9b Author: Andy Nonaka Date: Tue Feb 13 09:24:40 2018 -0800 progress toward getting checkpoint/restart working Source/Maestro.H Source/MaestroCheckpoint.cpp Source/MaestroEvolve.cpp Source/MaestroFill3dData.cpp Source/MaestroInit.cpp Source/MaestroRegrid.cpp commit 6e2f28c31d546e2dfbdc5ec9c68de1c11a4237dc Author: Doreen Fan Date: Mon Feb 12 18:36:21 2018 -0800 Plot and checkpoint files are now written at the end of a run. Also included plot_deltat option for plot files. Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Source/MaestroEvolve.cpp commit b6b4faa9ec67d6e44ef0f56acc85e38cde587159 Author: Doreen Fan Date: Mon Feb 12 17:32:51 2018 -0800 Fixed block grid boundary issues Source/Src_nd/make_edge_scal.F90 Source/Src_nd/update_vel.F90 commit fc2c74b1edd8c7d895a66c75b3926a25e2d3d4bc Author: Doreen Fan Date: Mon Feb 12 14:37:09 2018 -0800 Turn on sponge layer in inputs file. Output looks good. Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C commit 62396f7b41ea4a451cea61f77143cbe1ac8b569d Author: Doreen Fan Date: Fri Feb 9 18:08:12 2018 -0800 fixed one small bc bug in PutInPertForm() Source/MaestroEnthalpyAdvance.cpp commit f4e4a3c93f69f771d92a48ac3ac6d467297b8292 Author: Doreen Fan Date: Fri Feb 9 15:12:09 2018 -0800 Added nonzero ghost cells to MultiFab::Copy() subroutine calls. Also included do_sponge input parameter. Source/MaestroAdvance.cpp Source/MaestroDensityAdvance.cpp Source/MaestroInit.cpp Source/MaestroNodalProj.cpp Source/Src_nd/update_vel.F90 Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit c1a5f2a46b3d6c2354827aafc6bb98528999d6d9 Author: Doreen Fan Date: Thu Feb 8 18:18:42 2018 -0800 added AverageDown() and FillPatch() to NodalProj() subroutine Source/MaestroNodalProj.cpp commit 1858c050c46ec21635022d9ee9d283433f3c13e0 Author: Doreen Fan Date: Thu Feb 8 16:48:40 2018 -0800 added AverageDown and FillPatch for UpdateScal() and UpdateVel() Source/MaestroAdvection.cpp commit 23c593de3e2476c3dcf74874e015d6b91d79ddb2 Author: Doreen Fan Date: Thu Feb 8 13:49:03 2018 -0800 Fixed bug in update_rhoh_2d() subroutine Source/Src_nd/update_scal.F90 commit 7aa6c9fd6d0f441f696131c83c4a8ac9f1ce283c Author: Doreen Fan Date: Thu Feb 8 13:39:32 2018 -0800 added do_eos_h_above_cutoff statement in update_scal() Source/Src_nd/update_scal.F90 Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit 81bbf5818db4efabbe3bd459253e9f4993b8b6e2 Author: Andy Nonaka Date: Thu Feb 8 11:22:03 2018 -0800 bugfix - update temperature on s_out, not snew Source/MaestroReact.cpp commit 7b6964c3d2973af1bd8f5a47cf86b3182e9710d6 Author: Andy Nonaka Date: Thu Feb 8 08:25:41 2018 -0800 make sure Pi appears in plt00000 by copying Pi from snew into sold after each InitIter Source/MaestroInit.cpp commit c64fd73f1a49cb4eaa937710a9d1922d45c63bb4 Author: Doreen Fan Date: Wed Feb 7 18:40:40 2018 -0800 Finished velocity advance subroutine. Code can now complete one timestep with Pi solutions comparable to the Fortran results. Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroMacProj.cpp Source/MaestroVelocityAdvance.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/update_vel.F90 commit b4e1459832c2ff0b0efc2d1c4b86310ba9bbc5e3 Author: Andy Nonaka Date: Wed Feb 7 15:52:34 2018 -0800 write routine to hook into the amrex AverageDownFaces routine Source/Maestro.H Source/MaestroFillData.cpp commit 93bdc5576a241488da1eb802bac200010d81898e Author: Andy Nonaka Date: Wed Feb 7 14:48:51 2018 -0800 first cut at completed FillPatchUedge() function Source/MaestroFillData.cpp Source/Maestro_F.H Source/Src_nd/fill_umac_ghost.F90 commit 21fbf67020458cb0ef0ffdf79cdb253590954f14 Author: Andy Nonaka Date: Wed Feb 7 14:10:34 2018 -0800 renname CreateUmacGrown -> FillPatchUedge and iterate over all levels Source/Maestro.H Source/MaestroFillData.cpp commit a79761a9ddbc38f431b78dc9df658e10605ca40e Author: Andy Nonaka Date: Wed Feb 7 11:35:10 2018 -0800 progress on create_umac_grown... a mac-velocity version of FillPatch. Mostly lifted from IAMR Source/Maestro.H Source/MaestroFillData.cpp commit 8fe4693ff803f09c1f63b25f42b08e0d71781f40 Author: Andy Nonaka Date: Wed Feb 7 08:30:52 2018 -0800 in MacProj(), fluxes returned by getFluxes() are -B*grad(phi) not -grad(phi), so remove multiplication by B Source/MaestroMacProj.cpp commit d2768f816b29d7eb6ca5dffb314fb19ebb333512 Author: Doreen Fan Date: Tue Feb 6 16:39:37 2018 -0800 added state parameter to ModifyScalForce() Source/Maestro.H Source/MaestroDensityAdvance.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroForce.cpp commit f8592190c593cd92c1be41e04ac7b7fa45c827fe Author: Andy Nonaka Date: Tue Feb 6 16:23:32 2018 -0800 first cut at checkpoint and restart (including base state). untested but the functions are ready to try Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Source/MaestroCheckpoint.cpp Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/maestro_init.f90 commit 4c5b67a0d4e4393d5525b698cdff5489a3714efb Author: Andy Nonaka Date: Tue Feb 6 15:39:30 2018 -0800 wrote a basic checkpoint read/write routine for scalars - WIP Source/Maestro.H Source/MaestroCheckpoint.cpp Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H commit 0ff1995aa4edd21db8e957691dc5fdbdb92733c5 Author: Andy Nonaka Date: Tue Feb 6 09:58:59 2018 -0800 routine to average pi from nodes to cell-centers Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroNodalProj.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/make_pi_cc.F90 commit 78fb3dbf3e228cef6927a0d098578574fe4f6069 Author: Doreen Fan Date: Mon Feb 5 18:51:47 2018 -0800 fixed some bugs in UpdateScal() subroutines Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroEnthalpyAdvance.cpp Source/Maestro_F.H Source/Src_nd/update_scal.F90 commit ad81df43e91cb03fe9f01b0c4c6cb009b3d88cd1 Author: Andy Nonaka Date: Mon Feb 5 18:13:44 2018 -0800 add job info to plotfile Source/Maestro.H Source/MaestroCheckpoint.cpp Source/MaestroPlot.cpp Source/Make.package commit 6bfeb53d17a54cdbde0e9b341c8bf475423d7ec9 Author: Doreen Fan Date: Mon Feb 5 17:48:26 2018 -0800 Added enthalpy update subroutine to UpdateScal() Source/Maestro.H Source/MaestroAdvection.cpp Source/MaestroDensityAdvance.cpp Source/MaestroEnthalpyAdvance.cpp Source/Maestro_F.H Source/Src_nd/make_flux.F90 Source/Src_nd/update_scal.F90 commit 5a990c534cea9d7044d499134c4cd5095791b0f7 Author: Andy Nonaka Date: Mon Feb 5 17:22:56 2018 -0800 add call to shrink_to_fit to all the base state quantities to ensure C++ isn't overallocating memory Source/MaestroAdvance.cpp Source/MaestroDensityAdvance.cpp Source/MaestroDt.cpp Source/MaestroEnthalpyAdvance.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/MaestroNodalProj.cpp Source/MaestroSetup.cpp commit 144cec926fb43acbd815e2247d54ae8fc51af0e6 Merge: 98d1d613 74897b82 Author: Andy Nonaka Date: Mon Feb 5 17:05:59 2018 -0800 Merge branch 'master' of https://github.com/AMReX-Astro/MAESTRO_C commit 98d1d613961ca06116cb1f2e908664308a0a1fce Author: Andy Nonaka Date: Mon Feb 5 17:05:45 2018 -0800 remove unused variables and unused arguments Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/base_state.f90 Source/Src_nd/cell_to_edge.f90 commit 74897b823dd3c3220e580b1bfc3dfce3d5e37211 Author: Doreen Fan Date: Mon Feb 5 15:57:10 2018 -0800 Added MakeRhoHFlux() subroutine in enthalpy advection step Source/Maestro.H Source/MaestroAdvection.cpp Source/MaestroEnthalpyAdvance.cpp Source/Maestro_F.H Source/Src_nd/make_flux.F90 Source/Src_nd/update_scal.F90 commit fd74f3e6854a481371abb2a8c6fbe837368531fc Author: Andy Nonaka Date: Mon Feb 5 14:30:21 2018 -0800 fix the logic on the relative multigrid tolerance calculation to match the fortran maestro code Source/MaestroNodalProj.cpp commit cdfe30b0d7b4fca8a0fd3f992a29a1dcfa318692 Author: Andy Nonaka Date: Mon Feb 5 13:10:59 2018 -0800 put in a few timers as a test change name of Maestro::set_boundary_velocity() to Maestro::SetBoundaryVelocity() Exec/TEST_PROBLEMS/reacting_bubble/GNUmakefile Source/Maestro.H Source/MaestroNodalProj.cpp Source/main.cpp commit 6a338b0a3a35994bfde1f300dff9114bd3a84fc5 Author: Doreen Fan Date: Mon Feb 5 11:02:43 2018 -0800 Completed density advection subroutine. Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroDensityAdvance.cpp Source/Src_nd/update_scal.F90 commit 337606806c43ccc7dd754bdb8016c5037e5d564c Author: Doreen Fan Date: Fri Feb 2 19:02:42 2018 -0800 Cleaned up make_rhoX_flux subroutines and removed domlo & domhi parameters. Started update_scal subroutines in DensityAdvance. Source/Maestro.H Source/MaestroAdvection.cpp Source/MaestroDensityAdvance.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/make_flux.F90 Source/Src_nd/update_scal.F90 commit de1edf1d6e279bd013a2b6a610e53aef211a7199 Author: Doreen Fan Date: Fri Feb 2 15:08:54 2018 -0800 completed MakeRhoXFlux function in density advection Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroDensityAdvance.cpp Source/Maestro_F.H Source/Src_nd/make_flux.F90 commit e3776f964e525844412bca6b2cd86ab27aa497e0 Author: Andy Nonaka Date: Fri Feb 2 13:00:33 2018 -0800 code up nodal projection in advance() Source/MaestroAdvance.cpp Source/MaestroInit.cpp Source/MaestroNodalProj.cpp Source/MaestroSetup.cpp commit 7a0ae39a4ae91c1c29aff5e836e70eaf70ce555b Author: Andy Nonaka Date: Fri Feb 2 11:21:02 2018 -0800 comments only about nodal/mac projection RHS functions Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroInit.cpp Source/MaestroMakeS.cpp commit 9c737948f4bda7dff6c7358bafbda64fabe641fc Author: Andy Nonaka Date: Fri Feb 2 09:44:28 2018 -0800 wrote VelocityAdvance() function -- only missing fortran call to update_velocity() Source/Maestro.H Source/MaestroVelocityAdvance.cpp Source/Make.package commit 37e7b92de3a071309c0128bc0f78c07c7f6150b2 Author: Andy Nonaka Date: Fri Feb 2 09:01:53 2018 -0800 wrote EnthalpyAdvance routine - but missing mk_rhoh_flux and update_scal routines still Source/MaestroEnthalpyAdvance.cpp commit 159fa95874f810d054b0d7f77ea8cae5a799c6fd Author: Andy Nonaka Date: Fri Feb 2 08:38:24 2018 -0800 hange "is_predictor" arguments to EnthalpyAdvance and DensityAdvance to "which_step" (as in step 4 or step 8 in the algorithm) as to not confuse it with "is_prediction" (for edge state prediction vs conservative cell update) Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroDensityAdvance.cpp Source/MaestroEnthalpyAdvance.cpp commit 0b32cacc4d241886657042fe9cfaabe1833377c1 Author: Andy Nonaka Date: Thu Feb 1 17:07:02 2018 -0800 call the enthalpy advance routine (not complete yet) Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroEnthalpyAdvance.cpp commit bcce52169c770c684f34f302a729e64e2541fbb8 Merge: 50f7ed94 b831e669 Author: Andy Nonaka Date: Thu Feb 1 16:43:52 2018 -0800 Merge branch 'master' of https://github.com/AMReX-Astro/MAESTRO_C commit 50f7ed9487b502318e556e0f08ac9adc7ad3e2d3 Author: Andy Nonaka Date: Thu Feb 1 16:43:32 2018 -0800 enthalpy forcing Source/Maestro.H Source/MaestroForce.cpp Source/Maestro_F.H Source/Src_nd/make_scal_force.F90 Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit b831e66912e9c72871ec609631b2d17e65e31ad8 Author: Doreen Fan Date: Thu Feb 1 16:25:35 2018 -0800 Added preliminary files for MakeRhoXFlux subroutines. Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroDensityAdvance.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/make_edge_scal.F90 Source/Src_nd/make_flux.F90 commit cacd08eab224f9f5921a5d8f28611d51e127aa36 Author: Andy Nonaka Date: Thu Feb 1 10:42:31 2018 -0800 no need to create a temporary utilde that is fillpatched from uold, since uold has ghost cells Source/MaestroAdvection.cpp commit ee51d06fa4a64053de9c849d2e09e9e3d4b8151e Author: Andy Nonaka Date: Thu Feb 1 09:26:30 2018 -0800 starting EnthalpyAdvance() routine Source/Maestro.H Source/MaestroEnthalpyAdvance.cpp Source/Make.package commit 3051e3de7a05c69a75c7da2e1f70d4a8f5754637 Author: Andy Nonaka Date: Thu Feb 1 08:18:08 2018 -0800 added FillPatch calls where needed Generalized PutInPertForm interface to handle boundary conditions Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroConvert.cpp Source/MaestroDensityAdvance.cpp Source/MaestroFillData.cpp Source/MaestroInit.cpp Source/MaestroReact.cpp Source/MaestroRhoHT.cpp commit ad822a0cea732ab4f038e2c2e746200f5d051014 Author: Andy Nonaka Date: Thu Feb 1 07:56:16 2018 -0800 wrote an overloaded FillPatch routine that contains the loop over levels within and converted our current calls to FillPatch to use this - so we don't need an outer loop over levels anymore Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroFill3dData.cpp Source/MaestroFillData.cpp Source/MaestroForce.cpp Source/MaestroMacProj.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp commit 8f8e0e9a0c35ff699ae947cfeecbde60c1b32f38 Author: Doreen Fan Date: Wed Jan 31 17:24:44 2018 -0800 Added ghost cells to state variables. Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroDensityAdvance.cpp Source/MaestroInit.cpp Source/MaestroMacProj.cpp commit 4a2083e5d8d18afd4150c0a93187051230a3e26b Author: Andy Nonaka Date: Wed Jan 31 13:47:57 2018 -0800 bugfix - forgot to loop over components in make_edge_scal Source/Maestro.H Source/MaestroAdvection.cpp commit 9613f510835095874dc145f8c543d37f071d004f Author: Andy Nonaka Date: Tue Jan 30 16:06:53 2018 -0800 use BL_TO_FORTRAN macros to simplify code Source/MaestroAdvection.cpp commit 3c722ff8ef7c515718e0bde80a71ef96130cde2d Author: Andy Nonaka Date: Tue Jan 30 15:58:53 2018 -0800 don't pass-by-reference into fortran anymore use pointers or pass-by-value, either is fine. currently, only the advection routine input # of ghost cells is pass by value. This was only done to simplify the C++ code ever so slightly and could have been done either way as well Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroAverage.cpp Source/MaestroDebug.cpp Source/MaestroDt.cpp Source/MaestroFill3dData.cpp Source/MaestroForce.cpp Source/MaestroGamma.cpp Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/MaestroMakeS.cpp Source/MaestroReact.cpp Source/MaestroRegrid.cpp Source/MaestroRhoHT.cpp Source/MaestroSetup.cpp Source/MaestroSponge.cpp Source/Maestro_F.H Source/Src_nd/make_edge_scal.F90 Source/Src_nd/mkutrans.F90 Source/Src_nd/velpred.F90 commit a48cd87796297d2063fb52f0924e2fb7c98eeee3 Author: Andy Nonaka Date: Tue Jan 30 14:48:56 2018 -0800 wrote cpp MakeEdgeScal and interface to fortran Source/Maestro.H Source/MaestroAdvection.cpp Source/Maestro_F.H Source/Src_nd/make_edge_scal.F90 commit 877d4bb17f877458817addffb36f4d216d02e644 Author: Andy Nonaka Date: Tue Jan 30 13:57:14 2018 -0800 simplify/shorten the printMF and printEdge functions and make them parallel safe when the number of grids per processor is not the same Source/Maestro.H Source/MaestroDebug.cpp Source/Maestro_F.H Source/Src_nd/debug.F90 commit 9b655d9cc60b9e04e32bfd46f0ceeaa10faa1ab8 Author: Andy Nonaka Date: Tue Jan 30 12:58:11 2018 -0800 added 3 new .cpp routines, PrintCC(), PrintEdge(), PrintNodal() that outputs the contents of an array of MultiFabs one grid at a time (calls a flush and a parallel barrier after each grid) useful for debugging - the F90 source code sits in debug.F90 where you can isolate specific points Source/Maestro.H Source/MaestroDebug.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/Make.package Source/Src_nd/debug.F90 commit 7970edcff1f11017b25a6cf9b7e128f14c179aca Author: Andy Nonaka Date: Mon Jan 29 18:09:56 2018 -0800 pass in Vector of BCRec as const & Source/Maestro.H Source/MaestroAdvection.cpp Source/MaestroFillData.cpp Source/MaestroForce.cpp commit 3be01537a879a258a3b47d9f87b3a97740aa93c0 Author: Andy Nonaka Date: Mon Jan 29 17:24:29 2018 -0800 make_edge_scal fortran routine Source/Src_nd/Make.package Source/Src_nd/make_edge_scal.F90 commit a40b749d120ee2b795d8f6f51310ca144b27adca Merge: b32a2ea9 19d8499f Author: Andy Nonaka Date: Mon Jan 29 14:33:12 2018 -0800 Merge branch 'master' of https://github.com/AMReX-Astro/MAESTRO_C commit b32a2ea996b78719abc957dc039916496c4830a9 Author: Andy Nonaka Date: Mon Jan 29 14:32:50 2018 -0800 remmove unused variables Source/Maestro.H Source/MaestroSetup.cpp commit 19d8499fde242ab2ec6444ec429ec6e2f5cf6263 Author: Doreen Fan Date: Mon Jan 29 14:16:25 2018 -0800 mac projection now working Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Source/MaestroMacProj.cpp Source/Src_nd/mac_solver.F90 commit b0a03060b6c031dc48bf0e3299dd9a704b6ecd2e Author: Andy Nonaka Date: Mon Jan 29 13:44:40 2018 -0800 bugfix - need to set t_new = t_old + dt after calling EstDt before the InitIter loop Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/MaestroSetup.cpp commit 20a2a0b59017e31630704ef069b222d470f57be9 Author: Doreen Fan Date: Mon Jan 29 13:03:29 2018 -0800 Add hoextrap option Source/MaestroMacProj.cpp commit 17ff7c46ee1b2fa971c9d685199cb065ea32ccda Author: Doreen Fan Date: Mon Jan 29 12:48:45 2018 -0800 new fillpatch interface Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C Source/Maestro.H Source/MaestroMacProj.cpp Source/Maestro_F.H Source/Src_nd/mac_solver.F90 commit a6856c3860f427c21b6c7d0a8390ed217ddd9ba0 Author: Andy Nonaka Date: Mon Jan 29 12:41:23 2018 -0800 FillPatch now takes in a starting bc comp, "sbccomp". Put1DArrayOnCart also takes in sbccomp as an optional argument (default 0) and is only used if the input multifab has ghost cells Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroFill3dData.cpp Source/MaestroFillData.cpp Source/MaestroForce.cpp Source/MaestroMacProj.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp Source/MaestroRegrid.cpp Source/PhysBCFunctMaestro.cpp commit ceb73716c691bee2d96516ec50e0666260420085 Author: Andy Nonaka Date: Mon Jan 29 11:04:20 2018 -0800 use HOEXTRAP near walls for some variables (now matching fortran MAESTRO) Source/MaestroSetup.cpp commit ef32ac19028cd3c37d0c3f98f9aabe4212864c7a Author: Andy Nonaka Date: Mon Jan 29 10:57:13 2018 -0800 index bug fix in filling physical ghost cells with FillBoundary This will fix the MacProj bug Doreen found Source/PhysBCFunctMaestro.cpp commit 547213af947bd20b0942f447f050d2fbd1a018f3 Merge: ce2464e7 227b0552 Author: Andy Nonaka Date: Thu Jan 25 13:59:19 2018 -0800 Merge branch 'master' of https://github.com/AMReX-Astro/MAESTRO_C commit ce2464e7e401240a16f8708bfbde6169dfe17595 Author: Andy Nonaka Date: Thu Jan 25 13:59:02 2018 -0800 AverageDownTo -> AverageDown Source/MaestroAdvance.cpp Source/MaestroGamma.cpp Source/MaestroMakeS.cpp Source/MaestroRhoHT.cpp Source/MaestroSponge.cpp commit 227b0552fca77ff08cf7b9b9a8be659b77ae09fc Merge: 7194bb04 a6965ad9 Author: Doreen Fan Date: Thu Jan 25 13:49:21 2018 -0800 changes in MaestroForce file, which was not touched by me Merge branch 'master' of https://github.com/AMReX-Astro/MAESTRO_C commit 7194bb046d189d2d1e38dda93679d291741f2b8c Author: Doreen Fan Date: Thu Jan 25 13:47:52 2018 -0800 added PutInPertForm subroution Source/Maestro.H Source/MaestroConvert.cpp commit a6965ad915c2e8700d454c3761c41492d2c12fe4 Author: Andy Nonaka Date: Thu Jan 25 13:47:28 2018 -0800 forgot to fill velocity ghost cellx Source/MaestroForce.cpp commit 6a087fc87e03f100f730cde58fe2d617244e3a34 Author: Andy Nonaka Date: Thu Jan 25 13:31:14 2018 -0800 more-- boundary condition bug fix - need to test to make sure the grid is at the domain boundary before applying boundary conditions mac velocity entering the MacProj() routine still isn't quite right Source/Src_nd/mkutrans.F90 Source/Src_nd/slope.F90 Source/Src_nd/velpred.F90 commit 9bb2ff5066fc66908730fa91a379b30d3e4a011b Author: Andy Nonaka Date: Thu Jan 25 12:58:41 2018 -0800 boundary condition bug fix - need to test to make sure the grid is at the domain boundary before applying boundary conditions mac velocity entering the MacProj() routine still isn't quite right Source/MaestroAdvection.cpp Source/Maestro_F.H Source/Src_nd/mkutrans.F90 Source/Src_nd/velpred.F90 commit 4950add393d2b6e984f95f842822e30d2a94e4b3 Author: Doreen Fan Date: Thu Jan 25 11:25:54 2018 -0800 bcs input to Put1dArrayOnCart is now optional. Don't call FillPatch if there are no ghost cells. Source/Maestro.H Source/MaestroAdvection.cpp Source/MaestroFill3dData.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp commit 921287695c3035c79d33da72b0f87c47a41645ce Author: Andy Nonaka Date: Thu Jan 25 11:05:30 2018 -0800 forgot to add this Source/Src_nd/make_scal_force.F90 commit 4679448dc9a2a251f6257c7fd0fa59d8922aebad Merge: 71c4f5e6 a4280c42 Author: Doreen Fan Date: Thu Jan 25 10:33:18 2018 -0800 Merge branch 'master' of https://github.com/AMReX-Astro/MAESTRO_C commit a4280c42ab1620341091d48046f6049f22120b6c Author: Andy Nonaka Date: Thu Jan 25 08:38:34 2018 -0800 wrote ConvertRhoXToX and ConvertRhoHToH routines Source/Maestro.H Source/MaestroConvert.cpp Source/MaestroDensityAdvance.cpp Source/Make.package commit cd7aeb56f7eecdf09dc5eb6dc297f2fdba176f20 Author: Andy Nonaka Date: Thu Jan 25 08:16:43 2018 -0800 convert modify_scal_force to only take in a single component of sold and force Source/MaestroForce.cpp Source/Maestro_F.H commit bca8949e81870c845d96338da17519e9a49c2646 Author: Andy Nonaka Date: Wed Jan 24 18:56:35 2018 -0800 work on density advance, forcing routines Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroDensityAdvance.cpp Source/MaestroForce.cpp Source/MaestroNodalProj.cpp Source/MaestroReact.cpp Source/MaestroSetup.cpp Source/Maestro_F.H commit ff7b1384f0b6edb2558407268c045d484bacedb5 Author: Andy Nonaka Date: Wed Jan 24 18:06:04 2018 -0800 move average_pi_to_cc into MaestroAdvance() Source/MaestroAdvance.cpp Source/MaestroNodalProj.cpp commit 8e142f56dc5c93b5c067b3590bdeb13899227f8b Author: Andy Nonaka Date: Wed Jan 24 15:10:18 2018 -0800 ComputeGradPhi and compute_grad_phi routines for nodal projection Source/Maestro.H Source/MaestroNodalProj.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/compute_grad_phi.F90 commit 4e6a78ec10fe58f484ffb6c4577387b5ed0d93fe Merge: 669186b1 0b607d62 Author: Andy Nonaka Date: Wed Jan 24 14:15:47 2018 -0800 Merge branch 'master' of https://github.com/AMReX-Astro/MAESTRO_C commit 669186b1fccde89407e05edcafa3c98083b90c6d Author: Andy Nonaka Date: Wed Jan 24 14:15:03 2018 -0800 various small changes. initializing multifabs to zero in MaestroInit Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroInit.cpp Source/MaestroNodalProj.cpp Source/MaestroSetup.cpp Source/Src_nd/Make.package commit 71c4f5e6156245d4e6098294551e2a7958c59bd3 Author: Doreen Fan Date: Tue Jan 23 18:53:53 2018 -0800 preliminary mac solver completed Source/Maestro.H Source/MaestroMacProj.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/mac_solver.F90 commit 0b607d62b1ea222dcce390d88ea042355e55bcdb Author: Weiqun Zhang Date: Tue Jan 23 11:21:57 2018 -0800 Array --> Vector Source/MaestroPlot.cpp commit 867f222286e7bb147a07f04b19058f97913720f5 Author: Andy Nonaka Date: Mon Jan 22 15:33:27 2018 -0800 Set theme jekyll-theme-cayman _config.yml commit 4362437ae15ca35f6373fae49246a74c400c83d4 Author: Andy Nonaka Date: Mon Jan 22 15:33:06 2018 -0800 Set theme jekyll-theme-slate _config.yml commit 26892abb062f9927e5b193e0f0e013599ad38a92 Author: Andy Nonaka Date: Mon Jan 22 15:32:49 2018 -0800 Set theme jekyll-theme-cayman _config.yml commit 3fd97aa03e2b4d1b8e74d427ffddddea0f93159a Author: Andy Nonaka Date: Fri Jan 19 09:37:49 2018 -0800 setting up density advection, forcing terms Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroDensityAdvance.cpp Source/MaestroForce.cpp Source/Make.package commit 727c2cacffd1d483312e68cbc8202d553ed38fbf Author: Andy Nonaka Date: Thu Jan 18 18:58:24 2018 -0800 more work on Advance routine Source/MaestroAdvance.cpp commit 909d41a1d637a6359809cfa21a03d721fd9d95c8 Author: Andy Nonaka Date: Thu Jan 18 15:01:23 2018 -0800 notes Source/Maestro.H Source/MaestroMacProj.cpp commit 98f26fbd5335feacc158515911eb1be5db42184f Author: Andy Nonaka Date: Thu Jan 18 14:10:22 2018 -0800 some advance updates Source/MaestroAdvance.cpp commit f96f958ae27d9a3f992a8ce34a5ef2dbc7b073c4 Author: Andy Nonaka Date: Thu Jan 18 13:32:01 2018 -0800 MacProj work Source/MaestroMacProj.cpp commit df24da72860202270e30973e09b5d43b216c1649 Author: Andy Nonaka Date: Thu Jan 18 10:53:26 2018 -0800 macro simplification Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroMacProj.cpp commit 0250e15127a7883e5cba68ed8d26a39ffed16074 Author: Andy Nonaka Date: Thu Jan 18 10:12:37 2018 -0800 more mac projection progress Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroMacProj.cpp commit 2f96ff179d11e844809105df35186bc45217278f Author: Andy Nonaka Date: Thu Jan 18 09:51:01 2018 -0800 more mac projection progress Source/Maestro.H Source/MaestroMacProj.cpp commit 80d6f6a1cd8fafc70d23bad1af0a93fc4dbab939 Author: Andy Nonaka Date: Thu Jan 18 08:08:13 2018 -0800 inputs file to compare to original MAESTRO Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_C commit 3304ce4ba85613b07ee47f688c5204b4ede5b3c6 Author: Andy Nonaka Date: Thu Jan 18 08:04:40 2018 -0800 cell_to_edge routine Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroMacProj.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/base_state_geometry.f90 Source/Src_nd/cell_to_edge.f90 commit adc4b7b57544313eb651e74aaf049ffdfa59cae2 Author: Andy Nonaka Date: Wed Jan 17 17:39:23 2018 -0800 setting up macproject routines Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroMacProj.cpp commit 4715b6a347c38636a3df3d12aa2e568332022d7a Author: Andy Nonaka Date: Wed Jan 17 17:25:24 2018 -0800 routine to compute S for mac projection Source/Maestro.H Source/MaestroInit.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp commit 7ca6ccc26881054f5c6d7ee67093e0c6fe8b577f Author: Andy Nonaka Date: Wed Jan 17 17:10:31 2018 -0800 working on setting up the MAC projection Source/MaestroMakeS.cpp Source/Maestro_F.H Source/Src_nd/make_S.F90 commit 990c2ec95d6362ea5211ecd66c17d26104eb71eb Author: Andy Nonaka Date: Wed Jan 17 15:09:38 2018 -0800 remove unused directories Exec/Make.Maestro Source/Src_2d/Make.package Source/Src_3d/Make.package commit caa0f124ebd4ac0389d3360d7b2ce5185dc898b5 Author: Andy Nonaka Date: Wed Jan 17 15:04:02 2018 -0800 call VelPred to compute unprojected MAC velocities Source/Maestro.H Source/MaestroAdvection.cpp Source/Maestro_F.H Source/Src_nd/velpred.F90 commit 2cf95384f68b5184af86d2eb0f20ad1a0d7614ae Author: Andy Nonaka Date: Wed Jan 17 10:19:10 2018 -0800 add velpred routines Source/Src_nd/Make.package Source/Src_nd/velpred.F90 commit dda378e51b6081cfc420238f8c25164b80c4d118 Author: Andy Nonaka Date: Tue Jan 16 17:25:52 2018 -0800 Addw0 function Source/Maestro.H Source/MaestroAdvection.cpp Source/MaestroFill3dData.cpp Source/Maestro_F.H Source/Src_nd/fill_3d_data.F90 commit d322edfc11efcc377c743d58f01df1f786f4dad9 Author: Andy Nonaka Date: Tue Jan 16 17:00:50 2018 -0800 call MakeUtrans and MakeVelFOrce in AdvancePremac() Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp commit d7b04e59fe4ad1bd66bc668f9193f94099b342e7 Author: Andy Nonaka Date: Tue Jan 16 16:52:18 2018 -0800 bugfix dimensioning of w0 Source/Src_nd/compute_dt.F90 Source/Src_nd/mkutrans.F90 commit 0eecd34d830e248a8b01bc155d49205f0df85b1b Author: Andy Nonaka Date: Tue Jan 16 14:27:33 2018 -0800 lots of mkutrans C/F90 interface work Source/MaestroAdvection.cpp Source/Maestro_F.H Source/Src_nd/compute_dt.F90 Source/Src_nd/mkutrans.F90 commit 67fc75207bcebdf3e0b8c8b4fa510b9d71c670d2 Author: Andy Nonaka Date: Tue Jan 16 11:17:56 2018 -0800 domain boundary conditions are now represented by the integer array "phys_bc" with ordering LO_X, LO_Y, (LO_Z), HI_X, HI_Y, (HI_Z) This way when we pass in this array to fortran arrays it matches with the fortran MAESTRO style Source/Maestro.H Source/MaestroFillData.cpp Source/MaestroNodalProj.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/fill_umac_ghost.F90 commit 4a976b2f2c86d64d7cbe55fd78634f8409fa441b Author: Andy Nonaka Date: Tue Jan 16 11:04:50 2018 -0800 get rid of some boundary conditions constructs we no longer need Source/Maestro.H Source/MaestroSetup.cpp commit 674e1a75852edab84076a7d52b8dbad07e005cba Author: Andy Nonaka Date: Tue Jan 16 10:59:32 2018 -0800 unused code Source/MaestroNodalProj.cpp commit a646f15accf97ae0c2c2b442d23236e5e7ea4ca3 Author: Andy Nonaka Date: Tue Jan 16 10:54:07 2018 -0800 unneeded files Source/Projection.H Source/Projection.cpp commit 94f66f3388a952efb564a24048b454fb711e03de Author: Andy Nonaka Date: Tue Jan 16 08:50:30 2018 -0800 move in some advection routines from MAESTRO Source/MaestroAdvection.cpp Source/Src_nd/Make.package Source/Src_nd/mkutrans.F90 Source/Src_nd/slope.F90 Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit af0b488b57faf23b65aa440bb966fc11cdb6cd15 Author: Andy Nonaka Date: Fri Jan 12 18:08:06 2018 -0800 small updates, starting on advection Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroInit.cpp commit c19e31e428bb7ff5de87c4b7f5059e175e1559ce Author: Andy Nonaka Date: Fri Jan 12 16:25:41 2018 -0800 dt computation logic Source/MaestroEvolve.cpp Source/MaestroFillData.cpp Source/MaestroInit.cpp commit 8ced295b26cd6fd7b47f188581eea259f8c7dbc3 Author: Andy Nonaka Date: Fri Jan 12 15:10:29 2018 -0800 implement dt computation in divu_iter step(s) Source/MaestroInit.cpp commit 0ba961f27bc0bdd8b85bf43456e1888edf93656e Author: Andy Nonaka Date: Fri Jan 12 13:41:30 2018 -0800 wrote EstDt function Source/MaestroDt.cpp Source/Maestro_F.H Source/Src_nd/compute_dt.F90 commit e283f71b677f377ce594ba1af024e2282fe79fd7 Author: Andy Nonaka Date: Fri Jan 12 09:42:19 2018 -0800 EstDt is now a copy of FirstDt (will be updated) Source/MaestroDt.cpp Source/Maestro_F.H Source/Src_nd/compute_dt.F90 commit f5a3dc842d601362fe8690caec38a41924bf7132 Author: Andy Nonaka Date: Fri Jan 12 08:10:55 2018 -0800 move solver tolerance parameters to _cpp_parameters so we can control via inputs file Exec/TEST_PROBLEMS/reacting_bubble/inputs Source/Maestro.H Source/Maestro.cpp Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H commit dadd7a20c879d05bfcb0857ecc7e0b9cf48ae603 Author: Andy Nonaka Date: Thu Jan 11 17:17:07 2018 -0800 change time step computation to use cfl=0.9 instead of fixed_dt Exec/TEST_PROBLEMS/reacting_bubble/inputs commit c1ca81021395b7cfb7724ec74b7b8d0951a603ec Author: Andy Nonaka Date: Thu Jan 11 17:16:43 2018 -0800 only use pforcez if AMREX_SPACEDIM=3 Source/Src_nd/compute_dt.F90 commit a49b0bfd227c0dbce817baa5c01ccdd3b27ead34 Author: Andy Nonaka Date: Thu Jan 11 15:09:08 2018 -0800 for arrays of face-centered multifabs - access the multifab with [lev][dir], not [dir][lev] Source/MaestroForce.cpp commit 60cb312c95915044a877eace41542efb2765ac8e Author: Andy Nonaka Date: Thu Jan 11 14:35:27 2018 -0800 firstdt progress Source/MaestroDt.cpp Source/Maestro_F.H Source/Src_nd/compute_dt.F90 Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit 88cbbbde64001f6d3d2e1a5c5e35b1897da042c4 Author: Andy Nonaka Date: Thu Jan 11 13:29:51 2018 -0800 MakeVelForce work Source/Maestro.H Source/MaestroForce.cpp Source/Maestro_F.H Source/Src_nd/make_vel_force.F90 commit 9d87048a284d45a40fa24ecdd6249b369e8aba1d Author: Andy Nonaka Date: Wed Jan 10 18:31:26 2018 -0800 set initial guess phi for nodal solver to zero set phi to zero in sold after initial projection and divu iter Source/MaestroNodalProj.cpp commit fd5b765cf427488770d663e17a3dcd44d1073bd3 Author: Andy Nonaka Date: Wed Jan 10 17:59:27 2018 -0800 add logic for chooing nodal multigrid solver tolerances to match original MAESTRO Source/Maestro.H Source/Maestro.cpp Source/MaestroInit.cpp Source/MaestroNodalProj.cpp commit 7fc5d01d7e4d4147e4d440259216c0547ce85f6b Author: Andy Nonaka Date: Wed Jan 10 17:19:50 2018 -0800 enable EXTRA_THERMO to obtain the thermodynamic derivatives needed to compute S Exec/Make.Maestro commit 6cfa415307daf873ca8099aece91dca37c86da7a Author: Andy Nonaka Date: Mon Jan 8 09:58:48 2018 -0800 comments Source/MaestroNodalProj.cpp commit 93f999ced63549e2c9bb89b080e8e865d6d7e7b9 Author: Andy Nonaka Date: Mon Jan 8 09:20:53 2018 -0800 turn off evolve_base_state Exec/TEST_PROBLEMS/reacting_bubble/inputs commit 3f29f6cebf17e05b59794ffd0012ae7e0dfbc507 Author: Andy Nonaka Date: Fri Jan 5 16:42:00 2018 -0800 comment Source/Projection.cpp commit 4b5a3608d29af9d35e40e849871e17f0f72b27e5 Author: Andy Nonaka Date: Fri Jan 5 15:33:29 2018 -0800 more init plotfiles Source/Maestro.H Source/MaestroInit.cpp Source/MaestroMakeS.cpp Source/MaestroPlot.cpp commit a45e84807626e54989755ca48f25ae825ead3d2c Author: Andy Nonaka Date: Fri Jan 5 13:58:34 2018 -0800 initial projection runs, but not actually doing anything yet for some reason Source/MaestroInit.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp commit 258582275a7f69e245171610d82883796a271781 Author: Andy Nonaka Date: Thu Jan 4 17:41:24 2018 -0800 more nodal projection progress Source/Maestro.H Source/MaestroNodalProj.cpp commit 13e174c637cebf66ac59abdde7ff1d77ba29fcaa Author: Andy Nonaka Date: Thu Jan 4 13:56:58 2018 -0800 more nodal projection work Exec/Make.Maestro Source/Maestro.H Source/MaestroInit.cpp Source/MaestroNodalProj.cpp commit 3ff2291c62cc340aa1a6f8bc95ca2760314f2699 Author: Andy Nonaka Date: Thu Jan 4 12:49:24 2018 -0800 more nodal projection work Source/Maestro.H Source/MaestroNodalProj.cpp commit fb4fe07850a104b706b7dfa5c222559c3510b7af Author: Andy Nonaka Date: Thu Jan 4 12:23:51 2018 -0800 progress toward nodal projections Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroInit.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp Source/Maestro_F.H Source/Src_nd/make_S.F90 commit 85157e6330cbed4fc0991a6ff56d5deb1cde6b45 Author: Andy Nonaka Date: Wed Jan 3 18:26:30 2018 -0800 more Projection class cleanup Source/Projection.H Source/Projection.cpp commit 492e18f3615cf4142aa8c9e7ab6a2b35dd363a6c Author: Andy Nonaka Date: Wed Jan 3 15:44:07 2018 -0800 simplify Projection class Source/Projection.H Source/Projection.cpp commit 5e780e9fdfb103978fd82520dff8bfa099c727df Author: Andy Nonaka Date: Wed Jan 3 14:07:37 2018 -0800 copy of IAMR branch mlmg Projection.* (so I can play around with - not compiling these in right now) Source/Projection.H Source/Projection.cpp commit bad371ee7dcd1286a7f6808b5629df3de372f86d Author: Andy Nonaka Date: Thu Dec 21 15:37:45 2017 -0800 more Advance work Source/MaestroAdvance.cpp commit 85ad98ffc183ce75fc60eb1a7be81f6addd43cc9 Author: Andy Nonaka Date: Thu Dec 21 09:41:49 2017 -0800 comments Source/MaestroAdvance.cpp Source/Src_nd/make_w0.f90 commit 3592d9228421cb589705e207336171affbbf2064 Author: Andy Nonaka Date: Wed Dec 20 18:19:18 2017 -0800 more advance work Source/MaestroAdvance.cpp commit 020815d8e7e76d93ebf38c507f31cbdc531407fc Author: Andy Nonaka Date: Wed Dec 20 17:55:21 2017 -0800 verbosity Source/MaestroAdvance.cpp commit 0e58eab253a27488c2f4e354d254ecbbd93b968f Author: Andy Nonaka Date: Wed Dec 20 17:31:51 2017 -0800 more velocity force work Source/Maestro.H Source/MaestroAdvection.cpp Source/MaestroForce.cpp Source/Maestro_F.H Source/Src_nd/make_vel_force.F90 Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit 3df4ca66c058b69f167152e953b9b7728dbf00d0 Author: Andy Nonaka Date: Wed Dec 20 17:05:31 2017 -0800 setting up make_vel_force Source/Maestro.H Source/MaestroAdvection.cpp Source/MaestroForce.cpp Source/MaestroInit.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/Make.package Source/Src_nd/make_vel_force.F90 commit e68ba12fc61b0901ca7bf90d0c109cc9ff4e43b2 Author: Andy Nonaka Date: Wed Dec 20 14:03:06 2017 -0800 interface, index fixes Source/MaestroAdvance.cpp Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/base_state_geometry.f90 Source/Src_nd/make_w0.f90 commit 803fc037c583cbbbfeb2dae08cc608b6fd9a36c8 Author: Andy Nonaka Date: Wed Dec 20 11:08:13 2017 -0800 fix issues with base state indexing Source/Src_nd/base_state_geometry.f90 Source/Src_nd/make_w0.f90 commit f165bfa5a61b888092d5ff6e0f3008c837aa6e00 Author: Andy Nonaka Date: Wed Dec 20 10:39:29 2017 -0800 make_w0 routines Source/MaestroInit.cpp Source/Src_nd/Make.package Source/Src_nd/enforce_HSE.f90 Source/Src_nd/make_w0.f90 Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit bf2e31dd10144cc8000026058eb69fc9eaf34ca4 Author: Andy Nonaka Date: Fri Dec 15 14:45:43 2017 -0800 more Advance work Source/MaestroAdvance.cpp Source/MaestroInit.cpp commit 6d3d01ac988a91b7da8945dcf8ce798a11ddbd3c Author: Andy Nonaka Date: Fri Dec 15 13:55:34 2017 -0800 split gamma1bar into gamma1bar_old and _new Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroGamma.cpp Source/MaestroInit.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/make_beta0.f90 commit 1584d86571e2cceae96dd3b90a986b6af6ce2298 Author: Andy Nonaka Date: Fri Dec 15 13:21:05 2017 -0800 swap grav_cell pointers after time step Exec/TEST_PROBLEMS/reacting_bubble/inputs Source/MaestroEvolve.cpp commit 53089840ac8c1380836eb81d3fcae64c3e3c342d Author: Andy Nonaka Date: Fri Dec 15 13:20:34 2017 -0800 split grav_cell into grav_cell_old and grav_cell_new Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroInit.cpp Source/MaestroRegrid.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/make_beta0.f90 commit 9f62fa3c42dd4ffbd8fbada72ce8fc143ff60fff Author: Andy Nonaka Date: Fri Dec 15 12:59:43 2017 -0800 initialize the state using the _old data structures instead of the _new (to more closely match MAESTRO_F) Source/Maestro.H Source/MaestroEvolve.cpp Source/MaestroFillData.cpp Source/MaestroGamma.cpp Source/MaestroInit.cpp Source/MaestroPlot.cpp Source/MaestroSetup.cpp commit b46845eb3c586a4b18ed34a4b90fe063e61a9667 Author: Andy Nonaka Date: Fri Dec 15 10:25:05 2017 -0800 pass in dt/2 for divu_iter react Source/MaestroReact.cpp commit d385a7d151cdd0e05d0ef52537bb02d499b6855a Author: Andy Nonaka Date: Fri Dec 15 08:55:24 2017 -0800 finished writing fillUmacGhost and moved it to MaestroFillData.cpp Source/Maestro.H Source/MaestroFillData.cpp Source/MaestroFillUmacGhost.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/fill_umac_ghost.F90 commit 9a2f9caf24a85e07475ec498de56624a7a2746bd Author: Andy Nonaka Date: Thu Dec 14 17:36:16 2017 -0800 progress toward a routine to fill umac ghost cells Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAdvection.cpp Source/MaestroFillUmacGhost.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/Make.package Source/Src_nd/fill_umac_ghost.F90 commit bae53812913b3f31787a8e8065b1eb88765a9046 Author: Andy Nonaka Date: Thu Dec 14 15:00:25 2017 -0800 setting up advection stuff Source/Maestro.H Source/MaestroAdvection.cpp Source/MaestroInit.cpp Source/MaestroSetup.cpp Source/Make.package commit 3c4ce26accf6d7daeba7445fb18caa63f6b2e490 Author: Andy Nonaka Date: Thu Dec 14 13:33:46 2017 -0800 implement sponge Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroSponge.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/sponge.F90 commit 191bd5a66c36410259f9f5254cc89c006cb98cae Author: Andy Nonaka Date: Thu Dec 14 11:01:39 2017 -0800 fortran subroutine for sponge complete prob_lo and prob_hi are now in meth_params_module so we don't have to keep passing them around to fortran Source/MaestroInit.cpp Source/MaestroRegrid.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/base_state.f90 Source/Src_nd/base_state_geometry.f90 Source/Src_nd/initdata.f90 Source/Src_nd/maestro_init.f90 Source/Src_nd/sponge.F90 Source/Src_nd/tagging.f90 Source/param/meth_params.template Source/param_includes/meth_params.F90 commit aeeb22e160e444fe03c14fd31082df4295213b6a Author: Andy Nonaka Date: Thu Dec 14 10:22:18 2017 -0800 change verbose -> maestro_verbose start work on init_sponge Source/MaestroAdvance.cpp Source/MaestroDt.cpp Source/MaestroPlot.cpp Source/MaestroRegrid.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/compute_dt.F90 Source/Src_nd/sponge.F90 Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit cb8c02063d6e7e547eb2a59e22be7eb5dbe9b63d Author: Andy Nonaka Date: Wed Dec 13 14:26:16 2017 -0800 cleanup, more small changes to match fortran MAESTRO Source/MaestroAverage.cpp Source/MaestroDt.cpp Source/MaestroInit.cpp commit 96ec3e2cc100975ebecbdf3b5694e8793d1aa863 Author: Andy Nonaka Date: Wed Dec 13 13:48:04 2017 -0800 enforce_HSE... calling it during initialization as well Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/enforce_HSE.f90 Source/Src_nd/make_grav.f90 commit eb0db6f6d556bd086f8c8023f655dd6dd08f7b1d Author: Andy Nonaka Date: Wed Dec 13 13:08:17 2017 -0800 wrote make_grav_edge Source/Maestro_F.H Source/Src_nd/make_grav.f90 commit ad458b9cf9dd0ec7150b3ba9e553538a0bd7fd42 Author: Andy Nonaka Date: Wed Dec 13 12:31:01 2017 -0800 forgot to averagedown RhoH Source/MaestroRhoHT.cpp commit 62c1ba6a5d7e20b8e5fda18d4b99c3013ab17a76 Author: Andy Nonaka Date: Wed Dec 13 12:29:17 2017 -0800 added option for TfromRhoP to also compute h instead of having 2 routines that are essentially identical except for 1 line (like we have in MAESTRO_F90) Source/Maestro.H Source/MaestroInit.cpp Source/MaestroRhoHT.cpp Source/Maestro_F.H Source/Src_nd/rhoh_vs_t.F90 commit 823994a507659dd385a8bead860dc199d3558585 Author: Andy Nonaka Date: Wed Dec 13 10:50:11 2017 -0800 more options to inputs Exec/TEST_PROBLEMS/reacting_bubble/inputs commit 43f992c03c6b9ca8844c483ec3e8695837d0dd26 Author: Andy Nonaka Date: Wed Dec 13 10:49:24 2017 -0800 bugfix in makeTfromRhoP Source/MaestroInit.cpp Source/Src_nd/rhoh_vs_t.F90 commit f7fbf0b83fcf639bb29177bae5590d7f5ca69663 Author: Andy Nonaka Date: Wed Dec 13 10:22:24 2017 -0800 plotfile progress -- TfromRhoP not working yet Source/Maestro.H Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/MaestroPlot.cpp commit 5694212713078b2c26b38253b5e6660af53c97e8 Author: Andy Nonaka Date: Wed Dec 13 09:46:00 2017 -0800 makeTfromRhoP Source/Maestro.H Source/MaestroRhoHT.cpp Source/Maestro_F.H Source/Src_nd/rhoh_vs_t.F90 commit 3d94f3185128d9a42c83ed286c0d5a3569ad39ec Author: Andy Nonaka Date: Wed Dec 13 09:15:41 2017 -0800 plot X Source/MaestroPlot.cpp commit 93410157b92fc6e4bf6e384a524fac70b65947da Author: Andy Nonaka Date: Wed Dec 13 09:15:35 2017 -0800 add more options to inputs Exec/TEST_PROBLEMS/reacting_bubble/inputs commit d345e7fe67d94d987c0b2e4bde2390bb7b2d7d86 Author: Andy Nonaka Date: Fri Dec 1 17:47:39 2017 -0800 index bugfix in average(0 Source/MaestroInit.cpp Source/Src_nd/average.f90 commit d4f8ab155610a7c6effe29d96cb183d80efa42d4 Author: Andy Nonaka Date: Fri Dec 1 15:24:06 2017 -0800 bugfix in average Source/Src_nd/average.f90 commit 2808a19d86c3c2d1ccefca6c47e213fb658698e3 Author: Andy Nonaka Date: Fri Dec 1 14:13:23 2017 -0800 add rho0 and p0 to plotfile Source/Maestro.H Source/MaestroPlot.cpp commit 2081af27c73299705ae2544bceb83807f8d81b91 Author: Andy Nonaka Date: Fri Dec 1 13:46:26 2017 -0800 dt/2 in divu_iter for reactions Source/MaestroInit.cpp commit 15236a7e402709de9234fe07373e181ff911c919 Author: Andy Nonaka Date: Wed Nov 29 17:58:19 2017 -0800 calling React in divu_iter S calculation. fixed a few index bugs Source/MaestroInit.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/burner_loop.f90 commit 48a5dcc6f98e0a1d580429e78ef91c223f0fa2c4 Author: Andy Nonaka Date: Wed Nov 29 17:27:42 2017 -0800 simple dt calculation enabled Source/MaestroDt.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/make_S.F90 Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/meth_params.F90 commit 2137ee5fe51762db965a78b676b4c279d2e24396 Author: Andy Nonaka Date: Wed Nov 29 16:32:50 2017 -0800 some time step calculation work Source/Maestro.H Source/MaestroDt.cpp Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/maestro_init.f90 Source/param/meth_params.template Source/param_includes/meth_params.F90 commit bf46a7995a3c6f375ff9bd02c02c982a415807ba Author: Andy Nonaka Date: Wed Nov 29 10:14:55 2017 -0800 class rearrangement Source/Maestro.H Source/MaestroFillData.cpp Source/Make.package Source/PhysBCFunctMaestro.H Source/PhysBCFunctMaestro.cpp commit e8b6bdb09ef3045b03b24db7f07596dddab069dd Author: Andy Nonaka Date: Mon Nov 27 17:21:54 2017 -0800 set up nodal proj Source/MaestroFill3dData.cpp Source/MaestroNodalProj.cpp commit c88d84eeba002c54b98e704e36cc1758c7af7235 Author: Andy Nonaka Date: Mon Nov 27 16:51:22 2017 -0800 simplify code Source/Src_nd/fill_3d_data.F90 commit 27b5e19e8c31f94706ff349eb6e0afbc1b0ec442 Author: Andy Nonaka Date: Mon Nov 27 16:48:31 2017 -0800 put_1d_array_on_cart Source/Maestro.H Source/MaestroFill3dData.cpp Source/MaestroReact.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/fill_3d_data.F90 commit 4b7f2f703be71dd9bbe67bb3d95eedba679f9f83 Author: Andy Nonaka Date: Mon Nov 27 15:51:17 2017 -0800 bcrec objects for rhoh and temperature (for fillpatch when rhoh or temperature get copied into component 0) Source/MaestroSetup.cpp commit c73681b988d170054a087fb26abb782de9d50c49 Author: Andy Nonaka Date: Mon Nov 27 15:46:40 2017 -0800 generalize fillpatch more Source/Maestro.H Source/MaestroFill3dData.cpp Source/MaestroFillData.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp Source/MaestroPhysBCFunct.cpp Source/MaestroRegrid.cpp Source/Make.package commit e60ade4867333495ed72ab446fd0a2d90cd87c58 Author: Andy Nonaka Date: Mon Nov 27 14:25:43 2017 -0800 div_coeff -> beta0 Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/MaestroMakeS.cpp Source/MaestroRegrid.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/make_S.F90 Source/Src_nd/make_beta0.f90 Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit ddf81ae647cba452c6fee500796e49e913503e98 Author: Andy Nonaka Date: Mon Nov 27 13:41:11 2017 -0800 commentx Source/Maestro.H Source/MaestroInit.cpp Source/MaestroNodalProj.cpp commit bd7beb22a2602bbcef908fcbaa2bbdefbe104821 Author: Andy Nonaka Date: Mon Nov 27 11:28:17 2017 -0800 CreateUVecForProjection () Source/Maestro.H Source/Maestro.cpp Source/MaestroInit.cpp Source/MaestroNodalProj.cpp commit 05a9f03be09f456d325c0f8e857d0d5f18a883fc Author: Andy Nonaka Date: Mon Nov 27 10:05:25 2017 -0800 many small fixes Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroInit.cpp Source/MaestroRegrid.cpp Source/MaestroRhoHT.cpp Source/Src_nd/rhoh_vs_t.F90 commit 59d50bd654459a2e308744524359217ead62bd05 Author: Andy Nonaka Date: Wed Nov 22 14:14:04 2017 -0800 RhoH to T Source/Maestro.H Source/MaestroRhoHT.cpp commit 742c6b7ca875891a70c7a06c051219f1a794054d Author: Andy Nonaka Date: Wed Nov 22 13:58:57 2017 -0800 generalize AverageDown to comp and ncomp Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroFillData.cpp Source/MaestroGamma.cpp Source/MaestroInit.cpp Source/MaestroMakeS.cpp Source/MaestroReact.cpp Source/Make.package commit ca0b2c9211f83a5e34ee3881c664734e6c754a3f Author: Andy Nonaka Date: Wed Nov 22 13:19:53 2017 -0800 start of rhoh_vs_t.F90 Source/Maestro_F.H Source/Src_nd/AMReX_filcc_mod.F90 Source/Src_nd/Make.package Source/Src_nd/bc_fill_nd.F90 Source/Src_nd/initdata.f90 Source/Src_nd/make_S.F90 Source/Src_nd/make_gamma.F90 Source/Src_nd/rhoh_vs_t.F90 Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit 5030804332aec3df88a9c90ad85e8f3dcf1c4cad Author: Andy Nonaka Date: Wed Nov 22 11:41:53 2017 -0800 use ARRAYLIM macros to simplify fortran interfaces Source/MaestroAverage.cpp Source/MaestroGamma.cpp Source/MaestroMakeS.cpp Source/MaestroReact.cpp Source/Maestro_F.H commit f7795fbfc92c96106399740ea22d4a6efd45bbdb Author: Andy Nonaka Date: Wed Nov 22 11:12:34 2017 -0800 interface cleanup Source/MaestroAverage.cpp Source/MaestroGamma.cpp Source/MaestroInit.cpp Source/MaestroMakeS.cpp Source/MaestroReact.cpp Source/Maestro_F.H Source/Src_nd/bc_fill_nd.F90 Source/Src_nd/initdata.f90 commit d29dd950a2dde1dfa71c2618d59f059bd468e969 Author: Andy Nonaka Date: Wed Nov 22 10:49:52 2017 -0800 simplify syntax, preparing to put in BL_TO_FORTRAN macros Source/MaestroGamma.cpp Source/MaestroMakeS.cpp Source/MaestroReact.cpp Source/Maestro_F.H Source/Src_nd/burner_loop.f90 Source/Src_nd/make_S.F90 Source/Src_nd/make_gamma.F90 commit 2e825c3590d9349502ba7e2cd10009023a4f02ef Author: Andy Nonaka Date: Wed Nov 22 10:30:26 2017 -0800 make_S_nodal work, other interface work Source/MaestroAverage.cpp Source/MaestroGamma.cpp Source/MaestroMakeS.cpp Source/MaestroPhysBCFunct.cpp Source/MaestroReact.cpp Source/MaestroRegrid.cpp Source/Maestro_F.H Source/Src_nd/make_S.F90 commit 5f44dd9000558a960371dabd6912b63cb277633c Author: Andy Nonaka Date: Wed Nov 22 09:46:08 2017 -0800 initproj progress Source/Maestro.H Source/MaestroFillData.cpp Source/MaestroInit.cpp Source/MaestroMakeS.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/make_S.F90 commit 9cd04ece6a22ca3fec89a4907cc4c78b4090e3f2 Author: Andy Nonaka Date: Wed Nov 22 08:43:57 2017 -0800 added sanity check to GetData routines to make sure it's not being called improperly Source/MaestroFillData.cpp commit e0ebd8a705b4e950e88e04ab6631b69ac415b687 Author: Andy Nonaka Date: Wed Nov 22 08:37:08 2017 -0800 S_nodal -> nodalrhs Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroInit.cpp Source/MaestroMakeS.cpp commit 35f454fe6c599e8281855f7fe62288be6d2ca48b Author: Andy Nonaka Date: Mon Nov 20 17:31:19 2017 -0800 implemented MakeGamma1bar Source/Maestro.H Source/MaestroGamma.cpp Source/MaestroInit.cpp Source/MaestroMakeS.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/make_S.f90 Source/Src_nd/make_gamma.F90 Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit ab155c2f220c31bd8070aed5cb25df4e44bbe567 Author: Andy Nonaka Date: Mon Nov 20 16:37:49 2017 -0800 forgot to add these Source/MaestroGamma.cpp Source/Src_nd/make_div_coeff.f90 commit 0ce7249498358e3fb1896b0074ce18669e8a23bf Author: Andy Nonaka Date: Mon Nov 20 16:37:18 2017 -0800 class re-org Source/Maestro.H Source/MaestroInit.cpp Source/MaestroMacProj.cpp Source/MaestroRegrid.cpp Source/MaestroSetup.cpp Source/Make.package commit 5058eb95dba9af748f2373b3997ad30173eed84b Author: Andy Nonaka Date: Mon Nov 20 16:05:37 2017 -0800 indexing bugs, other fixes Source/MaestroBaseState.cpp Source/MaestroInit.cpp Source/Make.package Source/Src_nd/base_state.f90 Source/Src_nd/base_state_geometry.f90 commit 81c8534612c676ef160e0a2e98a938893bd1222c Author: Andy Nonaka Date: Mon Nov 20 15:37:42 2017 -0800 convert bool -> int for f90/C++ interface Source/Maestro_F.H Source/Src_nd/base_state_geometry.f90 Source/Src_nd/make_grav.f90 commit e2639f1d5c831fa678656d1b5d3d9972680a9759 Author: Andy Nonaka Date: Mon Nov 20 15:09:45 2017 -0800 module cleanup Source/MaestroRegrid.cpp Source/Maestro_F.H Source/Src_nd/AMReX_filcc_mod.F90 Source/Src_nd/base_state_geometry.f90 Source/Src_nd/bc_fill_nd.F90 Source/Src_nd/maestro_init.f90 commit e39c3a121f04bd3469cb8b0d8d0e8990107e391e Author: Andy Nonaka Date: Mon Nov 20 14:52:46 2017 -0800 more module cleanup Source/Src_nd/Make.package Source/Src_nd/average.f90 Source/Src_nd/base_state.f90 Source/Src_nd/bc_fill_nd.F90 Source/Src_nd/burner_loop.f90 Source/Src_nd/initdata.f90 Source/Src_nd/maestro.f90 Source/Src_nd/maestro_init.f90 Source/Src_nd/make_grav.f90 Source/Src_nd/rotation.f90 Source/Src_nd/tagging.f90 commit 11b4d02835089d1ee2a4ccc9a2bb03aee0684245 Author: Andy Nonaka Date: Mon Nov 20 14:40:40 2017 -0800 interface cleanup Source/Maestro_F.H Source/Src_nd/average.f90 Source/Src_nd/base_state_geometry.f90 commit 564edaaa635400ccb8856e9cda036f7ac639e09f Author: Andy Nonaka Date: Mon Nov 20 14:17:57 2017 -0800 being careful with the distinction between finest_radial_level and max_radial_level 1D arrays that get passed from C to fortran or fortran to fortran need to be dimensioned as max_radial_level, whereas the work loops are over finest_radial_level Source/Src_nd/average.f90 Source/Src_nd/base_state_geometry.f90 Source/Src_nd/initdata.f90 commit d9b274b94e9782bb790a77aeb8550a1dd4d09473 Author: Andy Nonaka Date: Mon Nov 20 12:50:34 2017 -0800 module cleanup stuff WIP Source/Src_nd/base_state_geometry.f90 Source/Src_nd/make_S.f90 Source/Src_nd/make_grav.f90 commit edd1763de69c454f05b4ab7c9de32a4a1cf7494e Author: Andy Nonaka Date: Mon Nov 20 12:25:34 2017 -0800 make_div_coeff stuff Source/Maestro.H Source/MaestroBaseState.cpp Source/MaestroGravity.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/Make.package Source/Src_nd/make_grav.f90 Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit ff6bd426f41dd7759a1d6315da91247d6d737c92 Author: Andy Nonaka Date: Mon Nov 20 11:43:59 2017 -0800 add base state ghost cell fill routines Source/Maestro_F.H Source/Src_nd/base_state_geometry.f90 Source/Src_nd/make_grav.f90 commit 8af4b9cba9ec463cbf0d12d91f20ff85b9cce245 Author: Andy Nonaka Date: Mon Nov 20 11:22:44 2017 -0800 added gravity routines Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroGravity.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/Make.package Source/Src_nd/base_state_geometry.f90 Source/Src_nd/make_grav.f90 commit 64a07f0535a3c23e2ecb0e1eec109b2936e597b2 Author: Andy Nonaka Date: Fri Nov 17 17:55:46 2017 -0800 more base state Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/average.f90 Source/Src_nd/base_state_geometry.f90 commit 91538695494aa147ca1db21b332910fa77b43858 Author: Andy Nonaka Date: Fri Nov 17 17:07:44 2017 -0800 base state work Source/Maestro.H Source/MaestroRegrid.cpp Source/Maestro_F.H Source/Src_nd/average.f90 Source/Src_nd/base_state_geometry.f90 Source/Src_nd/burner_loop.f90 commit f418f0a1e2bcca72161859f3499b9b53257f02ec Author: Andy Nonaka Date: Fri Nov 17 15:21:03 2017 -0800 (untested) planar version of average Source/Maestro.H Source/MaestroAverage.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/average.f90 commit 04b887a3ad3adfbf5cb6ca14e41e05f38e7c0323 Author: Andy Nonaka Date: Fri Nov 17 12:59:46 2017 -0800 get the burner plugged in Exec/TEST_PROBLEMS/reacting_bubble/GNUmakefile Microphysics/networks/burner.F90 Source/Maestro.H Source/MaestroMakeS.cpp Source/MaestroReact.cpp Source/Maestro_F.H Source/Src_nd/Make.package Source/Src_nd/burner_loop.f90 Source/param/_cpp_parameters Source/param_includes/meth_params.F90 commit bdf974191662e3aff4bac00b660bddd91eee796e Author: Andy Nonaka Date: Fri Nov 17 09:07:58 2017 -0800 added outline of reaction function switched the state to have 0 ghost cells so we can just call helper functions to create temporary multifabs with ghost cells when needed Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroInit.cpp Source/MaestroReact.cpp Source/MaestroRegrid.cpp Source/Make.package commit 441166dcca159cc536d57851971175998e795ffd Author: Andy Nonaka Date: Wed Nov 15 17:16:09 2017 -0800 add temperature tagging Exec/TEST_PROBLEMS/reacting_bubble/inputs Exec/TEST_PROBLEMS/rt/inputs Source/Maestro.H Source/MaestroRegrid.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/tagging.f90 commit 0513bb1b1ef04f374b4bc59804bd825f1323d15a Author: Andy Nonaka Date: Wed Nov 15 17:08:35 2017 -0800 1d arrays Source/Maestro.H Source/MaestroSetup.cpp commit 67571982b99350cad8fa803bcb86b7f2da0d2dc0 Author: Andy Nonaka Date: Wed Nov 15 14:43:11 2017 -0800 more base state and 1d array init Source/Maestro.H Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/MaestroSetup.cpp Source/Maestro_F.H Source/Src_nd/base_state.f90 commit e7214f28037b000a98d8fc6786e6f4e3d0f50876 Author: Andy Nonaka Date: Wed Nov 15 14:02:19 2017 -0800 clean out files from tutorial Exec/TEST_PROBLEMS/reacting_bubble/GNUmakefile Exec/TEST_PROBLEMS/reacting_bubble/Make.package Exec/TEST_PROBLEMS/reacting_bubble/face_velocity_2d.f90 Exec/TEST_PROBLEMS/reacting_bubble/face_velocity_3d.f90 Exec/TEST_PROBLEMS/rt/GNUmakefile Exec/TEST_PROBLEMS/rt/Make.package Exec/TEST_PROBLEMS/rt/face_velocity_2d.f90 Exec/TEST_PROBLEMS/rt/face_velocity_3d.f90 Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_2d/Adv_2d.f90 Source/Src_2d/Make.package Source/Src_2d/compute_flux_2d.f90 Source/Src_2d/slope_2d.f90 Source/Src_3d/Adv_3d.f90 Source/Src_3d/Make.package Source/Src_3d/compute_flux_3d.f90 Source/Src_3d/slope_3d.f90 commit 071f2c1e8dc7c442297d6dc9ee836ceb1357ab4a Author: Andy Nonaka Date: Wed Nov 15 13:54:20 2017 -0800 set up shell of alg Source/MaestroAdvance.cpp Source/MaestroEvolve.cpp Source/MaestroSetup.cpp commit 5d0e2dcdc8fc2ea3ee3fdfbcae2ef28a397e1012 Author: Andy Nonaka Date: Wed Nov 15 13:12:34 2017 -0800 use only the maestro.verbosity (not amr.v). work on dt computation Exec/TEST_PROBLEMS/reacting_bubble/inputs Exec/TEST_PROBLEMS/rt/inputs Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroDt.cpp Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp Source/MaestroRegrid.cpp Source/main.cpp commit 786c09760cb03e4a1173787e60414f9ff6fd5ae1 Author: Andy Nonaka Date: Wed Nov 15 12:44:24 2017 -0800 minor Source/Src_nd/Make.package Source/Src_nd/base_state.f90 Source/Src_nd/inlet_bc.f90 Source/Src_nd/make_S.f90 commit a75354d8599bf569ec88eabbed9f195647e45ed6 Author: Andy Nonaka Date: Wed Nov 15 08:22:50 2017 -0800 comments only Source/Maestro.H Source/Maestro.cpp commit a09f920bcde448282107a77908d9ce6cd21e6487 Author: Andy Nonaka Date: Wed Nov 15 08:03:16 2017 -0800 revert flux_reg_s/u to be a Vector of std::unique_ptr Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroInit.cpp Source/MaestroRegrid.cpp commit 34952a3c25122e967162b9905640d42b77c17592 Author: Andy Nonaka Date: Mon Nov 13 19:05:27 2017 -0800 make_S Source/Maestro.H Source/MaestroInit.cpp Source/MaestroMakeS.cpp Source/Src_nd/make_S.f90 commit 315b4ed49676bfd953bbee8685f2d2e1faa6cd48 Author: Andy Nonaka Date: Mon Nov 13 18:19:46 2017 -0800 new amrex feature: changing all the Vectors of std::unique_ptrs for MultiFabs and FluxRegister to simply be Vectors of Multifabs and FluxRegisters simplifies code... doesn't quite work until the swap function works for MultiFabs correctly Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroAverage.cpp Source/MaestroDt.cpp Source/MaestroFillData.cpp Source/MaestroInit.cpp Source/MaestroMakeS.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp Source/MaestroRegrid.cpp Source/Maestro_F.H Source/Src_nd/make_S.f90 commit b85296d1a7623031cca94a09f47dd742207d51a3 Author: Andy Nonaka Date: Mon Nov 13 16:06:56 2017 -0800 make_S_cc() Source/Maestro.H Source/MaestroMakeS.cpp Source/Maestro_F.H Source/Src_nd/make_S.f90 commit 51fb05121012b20920fc68ccf8b56707d09b2256 Author: Andy Nonaka Date: Mon Nov 13 14:32:26 2017 -0800 move countcells to AmrCore Source/Maestro.H Source/MaestroAdvance.cpp commit 7991f6b2349fe1f9f93d6cfc68f950b6df017101 Author: Andy Nonaka Date: Mon Nov 13 14:24:32 2017 -0800 comments, cleanup of Maestro class Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroInit.cpp Source/MaestroMakeS.cpp commit addae85224875b31d9a197dd392314a53b68f4a9 Author: Andy Nonaka Date: Mon Nov 13 12:23:29 2017 -0800 re-org Exec/TEST_PROBLEMS/reacting_bubble/inputs Source/Maestro.H Source/MaestroInit.cpp Source/MaestroSetup.cpp Source/Make.package Source/main.cpp commit a561899f50f53b4af3489979fdeb80bb85e8b1dd Author: Andy Nonaka Date: Fri Nov 10 18:23:05 2017 -0800 set pi to zero initially Source/Src_nd/initdata.f90 commit 4bf68fad14a8ec2ef5f79147579ec42063bf2a2f Author: Andy Nonaka Date: Fri Nov 10 11:58:55 2017 -0800 some indexing errors Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/initdata.f90 commit 4c5450a5df7a5d134816f89afd22e04c29e7415f Author: Andy Nonaka Date: Fri Nov 10 11:15:10 2017 -0800 fix indexing bugs Exec/TEST_PROBLEMS/reacting_bubble/GNUmakefile Exec/TEST_PROBLEMS/reacting_bubble/inputs Source/Src_nd/base_state.f90 Source/Src_nd/base_state_geometry.f90 commit 70d9210c33e97971b6bb689b871a0369f03d9506 Author: Andy Nonaka Date: Fri Nov 10 10:41:35 2017 -0800 lots of changes - the big one is making the base state have 0-based indexing, even in fortran everything will have 0-based indexing except for component indices in fortran WIP - code doesn't run right now Source/Maestro.H Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/base_state.f90 Source/Src_nd/base_state_geometry.f90 commit 1ae7142e33b07bb024692a24509c52a8e870c682 Author: Andy Nonaka Date: Fri Nov 10 08:14:17 2017 -0800 more cleanup Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroInit.cpp Source/MaestroPlot.cpp Source/MaestroRegrid.cpp Source/Src_nd/base_state_geometry.f90 commit f708e1ac1a223e548ae0bcb5883261d4a9258304 Author: Andy Nonaka Date: Wed Nov 8 17:46:10 2017 -0800 comments Source/Maestro.H Source/Maestro.cpp commit e0d9c23b0604f619ee76c9cf4d46ba8485a78fae Author: Andy Nonaka Date: Wed Nov 8 17:22:53 2017 -0800 major re-org... trying to do the dimension-agnostic stuff correctly Source/Maestro.H Source/Maestro.cpp Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/base_state.f90 Source/Src_nd/base_state_geometry.f90 Source/Src_nd/initdata.f90 Source/Src_nd/maestro.f90 Source/Src_nd/rotation.f90 Source/main.cpp Source/param/meth_params.template Source/param_includes/meth_params.F90 commit 6ee690dd08709c671c29c7512f6d5a4b6faa6a45 Author: Andy Nonaka Date: Wed Nov 8 15:01:33 2017 -0800 cleanup Source/Maestro.H Source/Maestro.cpp Source/MaestroAverage.cpp Source/MaestroInit.cpp Source/Make.package Source/Src_nd/base_state_geometry.f90 commit afc862c847738e5a55647171e0d64f7c245f90cf Author: Andy Nonaka Date: Wed Nov 8 13:35:06 2017 -0800 add initial perturbation Exec/TEST_PROBLEMS/reacting_bubble/inputs Source/Maestro_F.H Source/Src_nd/initdata.f90 Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit 65063df8938680dc8faf70769903f21d0c45bf29 Author: Andy Nonaka Date: Wed Nov 8 12:44:26 2017 -0800 reading in initial data now Source/MaestroInit.cpp Source/MaestroPlot.cpp Source/Maestro_F.H Source/Src_nd/initdata.f90 Source/Src_nd/maestro.f90 commit 43275694aed829acf2e743f1bee000f496d0196b Author: Andy Nonaka Date: Wed Nov 8 12:20:55 2017 -0800 re-org Exec/TEST_PROBLEMS/reacting_bubble/Make.package Exec/TEST_PROBLEMS/rt/Make.package Exec/TEST_PROBLEMS/rt/Prob.f90 Source/Src_nd/Make.package Source/Src_nd/initdata.f90 commit 8cc5749d00ee62ce90bbf15e61508824e4746679 Author: Andy Nonaka Date: Wed Nov 8 11:20:27 2017 -0800 add astrophysical lengths to inputs Exec/TEST_PROBLEMS/reacting_bubble/inputs commit 587fd343995bc89cecb66365678c1466b5986d6d Author: Andy Nonaka Date: Wed Nov 8 11:12:11 2017 -0800 indexing errors... f90 uses 1-based for rho Source/Src_nd/base_state_geometry.f90 Source/Src_nd/maestro.f90 commit b30639e0417835d46afa11d7b9acd20f80ca0b62 Author: Andy Nonaka Date: Wed Nov 8 09:45:21 2017 -0800 some print statements Source/Maestro.cpp Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/Src_nd/base_state_geometry.f90 Source/Src_nd/maestro.f90 commit fd3a0355bf1547a46ad9003b0888f96722c15187 Author: Andy Nonaka Date: Wed Nov 8 09:30:36 2017 -0800 fix calling sequence Source/Src_nd/maestro.f90 commit c1eb74cd912bcd945ec2f9532d3440271a748e8c Author: Andy Nonaka Date: Wed Nov 8 09:26:58 2017 -0800 fix some interfaces Source/MaestroInit.cpp Source/Maestro_F.H commit ef2254616a76af2daf24baff7c8ad0ecaad5cfb1 Author: Andy Nonaka Date: Wed Nov 8 08:50:02 2017 -0800 base_state_init compiling Exec/Make.Maestro Source/Src_nd/base_state.f90 Source/param/_cpp_parameters Source/param_includes/meth_params.F90 Util/model_parser/GPackage.mak Util/model_parser/Make.package Util/model_parser/model_parser.f90 Util/simple_log/Make.package Util/simple_log/simple_log.f90 commit 22aabb55625826332358f125678074dac235af48 Author: Andy Nonaka Date: Mon Nov 6 19:05:10 2017 -0800 geometry work Source/Maestro.cpp Source/Maestro_F.H Source/Src_nd/base_state.f90 Source/Src_nd/base_state_geometry.f90 commit c5bce0e0c5d3f9b5c53a12039182eb9c7c5086c9 Author: Andy Nonaka Date: Mon Nov 6 18:08:26 2017 -0800 base state geometry work Source/Src_nd/Make.package Source/Src_nd/base_state_geometry.f90 Source/Src_nd/rotation.f90 Source/param/parse_maestro_params.py Source/param_includes/meth_params.F90 commit d2ed2bdcbe456d3a712126442017e3fdce9270d9 Author: Andy Nonaka Date: Mon Nov 6 17:39:32 2017 -0800 base state geometry stuff Source/Src_nd/Make.package Source/Src_nd/base_state_geometry.f90 Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit 71b08319f21f2a7b79665d86f723d694f503b3a6 Author: Andy Nonaka Date: Mon Nov 6 17:14:21 2017 -0800 some error checking suggestions from Weiqun Source/Maestro_F.H Source/Make.package commit 4d918f11b2af16c07af5e58763c168c89cc1ed7e Author: Andy Nonaka Date: Mon Nov 6 17:06:00 2017 -0800 various cleanup, interface corrections Source/MaestroDt.cpp Source/Src_nd/maestro.f90 Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit 0874ef2d34c42aae1c71d3609a4f19618d662de6 Author: Andy Nonaka Date: Mon Nov 6 15:57:20 2017 -0800 simplified the boundary condition classes for gpi, S, and dSdt to use one common "first-order extrap" condition (used during regridding) Source/Maestro.H Source/MaestroInit.cpp Source/MaestroRegrid.cpp commit cf9a9670d287b78ef0c822b6498e60b892645c84 Author: Andy Nonaka Date: Mon Nov 6 15:47:40 2017 -0800 change variable names to more closely match MAESTRO Source/Maestro.cpp Source/Maestro_F.H Source/Src_nd/base_state.f90 Source/Src_nd/maestro.f90 Source/param/meth_params.template Source/param_includes/meth_params.F90 commit 8dd0d502135520a1ebc6da49cf9bee06ed3f0b41 Author: Andy Nonaka Date: Mon Nov 6 15:27:11 2017 -0800 more BL -> AMREX cleanup Exec/TEST_PROBLEMS/reacting_bubble/face_velocity_2d.f90 Exec/TEST_PROBLEMS/reacting_bubble/face_velocity_3d.f90 Exec/TEST_PROBLEMS/rt/face_velocity_2d.f90 Exec/TEST_PROBLEMS/rt/face_velocity_3d.f90 Source/MaestroFillData.cpp Source/Src_2d/Adv_2d.f90 Source/Src_2d/slope_2d.f90 Source/Src_3d/Adv_3d.f90 Source/Src_3d/slope_3d.f90 Source/param/extern_probin.template commit 4aa6b7463b175f5466abcb1269fc7b693678f2f2 Author: Andy Nonaka Date: Mon Nov 6 15:07:00 2017 -0800 "bl" -> "amrex" Source/MaestroAdvance.cpp Source/MaestroDt.cpp Source/MaestroInit.cpp Source/MaestroMakeS.cpp Source/MaestroPhysBCFunct.cpp Source/Maestro_F.H Source/Src_nd/AMReX_filcc_mod.F90 Source/Src_nd/Make.package Source/Src_nd/bc_fill_nd.F90 Source/Src_nd/maestro.f90 Source/Src_nd/make_S.f90 Source/Src_nd/tagging.f90 Source/param/_cpp_parameters Source/param/meth_params.template Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit 3b6a21057948fa80962ec605aed6bff223dd9eca Author: Andy Nonaka Date: Mon Nov 6 14:40:02 2017 -0800 more init stuff Source/Maestro.cpp Source/Maestro_F.H Source/Src_nd/Maestro_nd.f90 Source/Src_nd/base_state.f90 Source/param/_cpp_parameters Source/param/meth_params.template Source/param_includes/meth_params.F90 commit 7cba6be3e77709f7477606fd4b59d5d545678509 Author: Andy Nonaka Date: Mon Nov 6 13:46:18 2017 -0800 import the MAESTRO version of _parameters into _cpp_parameters. added bool/logical support Source/param/_cpp_parameters Source/param/parse_maestro_params.py Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit c25bdb3cb7b7f6b76fe50d8cec6fd750c76c04fd Author: Andy Nonaka Date: Mon Nov 6 12:48:40 2017 -0800 split stuff into different files Source/Src_nd/Maestro_nd.f90 Source/Src_nd/Make.package Source/Src_nd/base_state.f90 commit 6a9db3209a199c4a685f03cc716db41571f2457a Author: Andy Nonaka Date: Mon Nov 6 12:34:43 2017 -0800 progress toward reading in the model file into the base state arrays Source/Maestro.cpp Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/Maestro_nd.f90 commit 71ec7d75be86bfc905c29d548cb046b39c05e55f Author: Andy Nonaka Date: Fri Nov 3 19:04:39 2017 -0700 read in model file Source/MaestroInit.cpp Source/Maestro_F.H Source/Src_nd/Maestro_nd.f90 commit 5c4f50c6d4185622657b1d93a1fe2181b9ff3996 Author: Andy Nonaka Date: Fri Nov 3 18:59:08 2017 -0700 interface work Source/Maestro.cpp Source/Maestro_F.H Source/param/README.PARAMS Source/param/meth_params.template Source/param/parse_maestro_params.py Source/param_includes/meth_params.F90 commit 63ebedc5213d6c4846733ce0163d8c8c452d6b50 Author: Andy Nonaka Date: Fri Nov 3 18:23:20 2017 -0700 get rid of ca_ convention from castro. hooks to call model file Exec/Make.Maestro Source/Maestro.cpp Source/MaestroInit.cpp Source/MaestroPlot.cpp Source/Maestro_F.H Source/Src_nd/Maestro_nd.f90 Source/Src_nd/Make.package Source/param/README.PARAMS Source/param/meth_params.template Source/param_includes/Make.package Source/param_includes/meth_params.F90 commit d3261e1071e1c9a74138cb77c9958ed65a790498 Author: Andy Nonaka Date: Fri Nov 3 18:03:52 2017 -0700 some model reading stuff Exec/TEST_PROBLEMS/reacting_bubble/inputs Exec/TEST_PROBLEMS/reacting_bubble/model.hse.cool.coulomb Source/Maestro.H Source/Src_nd/Maestro_nd.f90 Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit dd026f2e6dc3c43405432de542d3d5085c5b3dd6 Author: Andy Nonaka Date: Fri Nov 3 08:35:46 2017 -0700 switch to using AMReX_fillcc_mod (so we use the default amrex AMReX_FILCC_XD.F90) right now the local copy of AMReX_filcc_mod.F90 is a copy of the version in AMReX. This will have to change at some point if we add external dirichlet conditions Source/Src_2d/AMReX_FILCC_2D.F90 Source/Src_3d/AMReX_FILCC_3D.F90 Source/Src_nd/AMReX_filcc_mod.F90 commit 6bb8da8906a0c0564712cb389530e2e1795bfd58 Author: Andy Nonaka Date: Mon Oct 30 18:12:09 2017 -0700 more init setup Source/Maestro.H Source/MaestroInit.cpp Source/MaestroNodalProj.cpp commit 42f3ee52dce6746bc37954111d84e7021358624f Author: Andy Nonaka Date: Mon Oct 30 17:09:44 2017 -0700 small_dens, small_temp Source/Src_nd/Maestro_nd.f90 Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit 4c8267958d806dec64baabb40fdcd48495eec871 Author: Andy Nonaka Date: Mon Oct 30 16:54:40 2017 -0700 setting up another problem that uses helmholtz eos Exec/TEST_PROBLEMS/reacting_bubble/GNUmakefile Exec/TEST_PROBLEMS/reacting_bubble/Make.package Exec/TEST_PROBLEMS/reacting_bubble/Prob.f90 Exec/TEST_PROBLEMS/reacting_bubble/face_velocity_2d.f90 Exec/TEST_PROBLEMS/reacting_bubble/face_velocity_3d.f90 Exec/TEST_PROBLEMS/reacting_bubble/inputs Exec/TEST_PROBLEMS/rt/GNUmakefile commit f4df8c5fdb4f677381591a5f19f1530e9ca075b1 Author: Andy Nonaka Date: Mon Oct 30 15:54:05 2017 -0700 more setup of linear solves, boundary condition objects Source/Maestro.H Source/MaestroInit.cpp Source/MaestroNodalProj.cpp Source/MaestroRegrid.cpp commit 0114f2d3d3ec659e793c9deeb11805cc548ceaff Author: Andy Nonaka Date: Mon Oct 30 12:49:41 2017 -0700 linear solver stuff Exec/Make.Maestro Source/Maestro.H Source/MaestroNodalProj.cpp commit 9b5260e0d5807e85de768e01774f95201fdfa156 Author: Andy Nonaka Date: Fri Oct 27 16:44:14 2017 -0700 added hooks for regridding all variables that require regridding (S_cc, gpi, dSdt) Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroInit.cpp Source/MaestroRegrid.cpp commit 9a81e9bac6975d3961a71861ffb5272523bef336 Author: Andy Nonaka Date: Fri Oct 27 15:35:31 2017 -0700 all kinds of WIP Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroEvolve.cpp Source/MaestroInit.cpp Source/MaestroRegrid.cpp commit abf11ad9fc842217e712b0c988d065f0b8fc29b2 Author: Andy Nonaka Date: Fri Oct 27 08:50:14 2017 -0700 some init stuff Source/MaestroAdvance.cpp commit c2012a2d1360371006f5e7b564d355e02092eedb Author: Andy Nonaka Date: Fri Oct 27 08:26:05 2017 -0700 switch to F90 versions of FILCC to reflect changes in AMReX Source/Src_2d/AMReX_FILCC_2D.F Source/Src_2d/AMReX_FILCC_2D.F90 Source/Src_3d/AMReX_FILCC_3D.F Source/Src_3d/AMReX_FILCC_3D.F90 commit d454a6c8bfcbc34698af7d7831a8a3e8b9cb1b46 Author: Andy Nonaka Date: Wed Oct 25 19:17:44 2017 -0700 properly regridding the velocity (which stays zero at the moment) Source/MaestroInit.cpp Source/MaestroRegrid.cpp commit eb7e4d9a949f8329b9f05ff23f9de84dce4a7a47 Author: Andy Nonaka Date: Wed Oct 25 18:53:56 2017 -0700 code cleanup Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroEvolve.cpp Source/MaestroPlot.cpp Source/MaestroRegrid.cpp commit 31edf378c9c24df5990b1daa6179564d7f1e960e Author: Andy Nonaka Date: Wed Oct 25 17:26:08 2017 -0700 eliminate redundant variables Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroEvolve.cpp commit 780fb390ce2e3a314f4b96cb85b99a60ad100d98 Author: Andy Nonaka Date: Wed Oct 25 17:23:37 2017 -0700 clean out argument list Source/MaestroAdvance.cpp Source/Maestro_F.H Source/Src_2d/Adv_2d.f90 commit dab5c88975cf715db0438bd940153239beca3770 Author: Andy Nonaka Date: Wed Oct 25 16:52:58 2017 -0700 more generalizing Fill routines to any MultiFab Source/Maestro.H Source/MaestroAdvance.cpp Source/MaestroFillData.cpp Source/MaestroRegrid.cpp commit 73670860bf930d021f53576cbba6a41cb442ec1b Author: Andy Nonaka Date: Wed Oct 25 16:45:58 2017 -0700 starting to generalize the fillpatch routines so they will work for more than just scal Source/Maestro.H Source/MaestroFillData.cpp Source/MaestroRegrid.cpp commit c3c695c99efb4fe01123a99cd14692042a335708 Author: Andy Nonaka Date: Wed Oct 25 16:11:48 2017 -0700 fix some array index issues, quiet valgrind Source/MaestroAdvance.cpp Source/Maestro_F.H Source/Src_2d/Adv_2d.f90 Source/Src_3d/Adv_3d.f90 commit 5d77093fe291283feb646067b4ec4bc7e482eb23 Author: Andy Nonaka Date: Wed Oct 25 12:17:56 2017 -0700 added hooks for more functions split Evolve into its own file updated parameter list Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroDt.cpp Source/MaestroEvolve.cpp Source/MaestroMacProj.cpp Source/MaestroNodalProj.cpp Source/MaestroPlot.cpp Source/Make.package Source/Src_nd/Maestro_nd.f90 Source/param/README.PARAMS Source/param/_cpp_parameters Source/param/meth_params.template Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit 6c2f8c4a8a9736ba0c3ef266420630b471b385bf Author: Andy Nonaka Date: Wed Oct 25 11:30:27 2017 -0700 give subroutine eos an optional pt_index make_S_cc_work now uses eos_type_module and calls the eos Microphysics/EOS/eos.F90 Source/MaestroAdvance.cpp Source/MaestroMakeS.cpp Source/Maestro_F.H Source/Src_nd/MakeS_nd.f90 commit 607539a9317fcb126f193997f7d5afa480bb5a03 Author: Andy Nonaka Date: Wed Oct 25 11:25:16 2017 -0700 rename Tagging_nd.f90 -> Regrid_nd.f90 added hooks for a MakeS_cc function renname a few variables Source/Maestro.H Source/MaestroMakeS.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/Make.package Source/Src_nd/MakeS_nd.f90 Source/Src_nd/Regrid_nd.f90 commit 83563f955efc92c92a07b6b27187745ea646905a Author: Andy Nonaka Date: Wed Oct 25 11:15:49 2017 -0700 Revert "interface work" This reverts commit bc93c2766b1cbfa57582bb3b55926d6f1df71cb2. Source/Maestro.H Source/MaestroMakeS.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/Make.package Source/Src_nd/MakeS_nd.f90 Source/Src_nd/Tagging_nd.f90 commit 13068152d6ae13939711eeb3f790b84d4fdae6e7 Author: Andy Nonaka Date: Wed Oct 25 11:15:41 2017 -0700 Revert "more interface stuff" This reverts commit 707e57a50a0b52a5bfb1f5f6372af71d2188a896. Microphysics/EOS/eos.F90 Source/MaestroAdvance.cpp Source/MaestroMakeS.cpp Source/Maestro_F.H Source/Src_nd/MakeS_nd.f90 commit 8e627048cd466e8944cea5fa87ad718b304b64fc Author: Andy Nonaka Date: Wed Oct 25 11:15:31 2017 -0700 Revert "parameter stuff" This reverts commit d032c4d8e5f9d428d1fbd6dbbd543e820cd96d7b. Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroDt.cpp Source/MaestroPlot.cpp Source/Make.package Source/Src_nd/Maestro_nd.f90 Source/param/README.PARAMS Source/param/_cpp_parameters Source/param/meth_params.template Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit d9e20c83539dc1b038d0d71d416bd0c319b48e20 Author: Andy Nonaka Date: Wed Oct 25 11:15:25 2017 -0700 Revert "updates - broken right now--- WIP" This reverts commit 07d74bc1023469e5c1866b300197b5cd8112fef4. Source/MaestroEvolve.cpp Source/MaestroMacProj.cpp Source/MaestroNodalProj.cpp Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H commit 07d74bc1023469e5c1866b300197b5cd8112fef4 Author: Andy Nonaka Date: Mon Oct 23 18:27:09 2017 -0700 updates - broken right now--- WIP Source/MaestroEvolve.cpp Source/MaestroMacProj.cpp Source/MaestroNodalProj.cpp Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H commit d032c4d8e5f9d428d1fbd6dbbd543e820cd96d7b Author: Andy Nonaka Date: Mon Oct 23 17:53:13 2017 -0700 parameter stuff Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroDt.cpp Source/MaestroPlot.cpp Source/Make.package Source/Src_nd/Maestro_nd.f90 Source/param/README.PARAMS Source/param/_cpp_parameters Source/param/meth_params.template Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/param_includes/meth_params.F90 commit 707e57a50a0b52a5bfb1f5f6372af71d2188a896 Author: Andy Nonaka Date: Mon Oct 23 16:33:46 2017 -0700 more interface stuff Microphysics/EOS/eos.F90 Source/MaestroAdvance.cpp Source/MaestroMakeS.cpp Source/Maestro_F.H Source/Src_nd/MakeS_nd.f90 commit bc93c2766b1cbfa57582bb3b55926d6f1df71cb2 Author: Andy Nonaka Date: Mon Oct 23 14:32:22 2017 -0700 interface work Source/Maestro.H Source/MaestroMakeS.cpp Source/Maestro_F.H Source/Make.package Source/Src_nd/Make.package Source/Src_nd/MakeS_nd.f90 Source/Src_nd/Regrid_nd.f90 commit 6d4e17e485d7397b62b6665c3eea9d66887c37b9 Author: Andy Nonaka Date: Mon Oct 16 18:09:36 2017 -0700 more data structures Source/Maestro.H Source/MaestroAdvance.cpp commit abd31fcf04feec13abe102d6c2fede15a42aa6de Author: Andy Nonaka Date: Fri Oct 13 17:05:41 2017 -0700 more multifabs in the class Source/Maestro.H commit 4168f3868963f564d8a5243972e803db64e2d8d9 Author: Andy Nonaka Date: Wed Oct 11 18:26:28 2017 -0700 re-org, lots of comments Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroFillData.cpp Source/MaestroInit.cpp Source/MaestroRegrid.cpp Source/Make.package commit 5079be95454e237d369562a18aab9627790585fe Author: Andy Nonaka Date: Wed Oct 11 17:19:34 2017 -0700 more initialization Source/Maestro.cpp Source/Maestro_F.H Source/Src_nd/Maestro_nd.f90 Source/param_includes/meth_params.F90 commit 17192698a4c5b1922272659581f292499e290341 Author: Andy Nonaka Date: Mon Oct 9 18:27:50 2017 -0700 add u and s to plotfiles, with names Source/MaestroPlot.cpp commit c24d9e9f57d0676d703b13eec4c3896ee9bf448d Author: Andy Nonaka Date: Mon Oct 9 17:36:43 2017 -0700 various enhancements to get the species names read in properly Exec/TEST_PROBLEMS/rt/Prob.f90 Source/Maestro.H Source/Maestro.cpp Source/MaestroInit.cpp Source/MaestroPlot.cpp Source/MaestroTagFill.cpp Source/Maestro_F.H Source/Src_nd/Maestro_nd.f90 commit 93e65dc90eb14d3d436f9b4af5a323a76c5eb79d Author: Andy Nonaka Date: Mon Oct 9 15:41:36 2017 -0700 made the C++ analog of a "bc_tower" Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroInit.cpp commit c4c36b13b2edf71baf08f5d946b66145ef3b8113 Author: Andy Nonaka Date: Mon Oct 9 14:51:53 2017 -0700 various updates Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroInit.cpp Source/MaestroTagFill.cpp commit c7f2101b12b4c3dd347d18ea637473bfb6431e47 Author: Andy Nonaka Date: Mon Oct 9 13:07:17 2017 -0700 Array -> Vector where appropriate remove "using namespace amrex;" from header files and added to all .cpp files (per Weiqun's request) Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroDt.cpp Source/MaestroInit.cpp Source/MaestroPhysBCFunct.H Source/MaestroPhysBCFunct.cpp Source/MaestroPlot.cpp Source/MaestroTagFill.cpp Source/main.cpp commit 0837fd9fcaa9971c7d604c3f607a7b7bf71d891b Author: Andy Nonaka Date: Mon Oct 9 12:49:58 2017 -0700 cleanup. replace Array with Vector where appropriate Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroDt.cpp Source/MaestroPlot.cpp Source/MaestroTagFill.cpp Source/main.cpp commit 7b4e7809f31b9375404d3cd155221e93bf8389ba Author: Andy Nonaka Date: Mon Oct 9 07:25:19 2017 -0700 CONDUCTIVITY_DIR (to match castro, and EOS_DIR and NETWORK_DIR) Exec/Make.Maestro commit 99994600dc265d6f644d7ca4c76591b3e09eb16d Author: Andy Nonaka Date: Fri Oct 6 19:27:03 2017 -0700 replacing phi_old/new with sold/new Exec/TEST_PROBLEMS/rt/Prob.f90 Source/Maestro.H Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroDt.cpp Source/MaestroInit.cpp Source/MaestroPlot.cpp Source/MaestroTagFill.cpp Source/Maestro_F.H Source/Src_2d/Adv_2d.f90 Source/Src_3d/Adv_3d.f90 Source/Src_nd/Tagging_nd.f90 Source/param/meth_params.template Source/param_includes/meth_params.F90 commit f0eb4718dbca2432a39df65f28d4081013e87952 Author: Andy Nonaka Date: Fri Oct 6 17:49:07 2017 -0700 re-org Exec/TEST_PROBLEMS/rt/inputs Source/Maestro.H Source/Maestro.cpp Source/MaestroTagFill.cpp Source/param/_cpp_parameters Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H commit a05844f16c7e84a1813efa5f42c671c6f54ac521 Author: Andy Nonaka Date: Fri Oct 6 17:28:42 2017 -0700 fix bc bug, read in bc's from inputs file Exec/TEST_PROBLEMS/rt/inputs Source/Maestro.H Source/Maestro.cpp Source/MaestroInit.cpp commit b4b071112fefb105707076b730c5b400d8204fc0 Author: Andy Nonaka Date: Fri Oct 6 16:34:14 2017 -0700 create VariableSetup() Source/Maestro.H Source/Maestro.cpp Source/MaestroInit.cpp Source/MaestroTagFill.cpp Source/Maestro_F.H Source/Src_nd/Maestro_nd.f90 Source/Src_nd/Make.package commit 49a55802513d9474015c322a585ca7f8c21361cb Author: Andy Nonaka Date: Fri Oct 6 15:32:52 2017 -0700 forgot to save Source/Maestro.cpp commit b83d9cc2c7274110e96583ca35e1a788d7f52f2b Author: Andy Nonaka Date: Fri Oct 6 15:32:06 2017 -0700 more re-org Exec/Make.Maestro Source/Maestro.cpp Source/MaestroAdvance.cpp Source/MaestroPlot.cpp Source/MaestroTagFill.cpp Source/Make.package Source/param/README.PARAMS Source/param/extern_probin.template commit a781b84bed4aec4845d063228f5224e9689f75a7 Author: Andy Nonaka Date: Fri Oct 6 14:54:17 2017 -0700 more re-org Exec/TEST_PROBLEMS/rt/inputs Source/Maestro.cpp Source/Make.package Source/param/_cpp_parameters Source/param/meth_params.template Source/param/mk_params.sh Source/param/parse_maestro_params.py Source/param_includes/Make.package Source/param_includes/meth_params.F90 commit 0165f0b63e69f2cbd87bc922afddef3ec90e1dac Author: Andy Nonaka Date: Fri Oct 6 14:18:29 2017 -0700 more re-org Source/Make.package Source/Src_2d/AMReX_FILCC_2D.F Source/Src_3d/AMReX_FILCC_3D.F Source/Src_nd/Make.package Source/Src_nd/bc_fill_nd.F90 commit b4387c3b0a6d2a6eda5911584ec0b1617d614d35 Author: Andy Nonaka Date: Fri Oct 6 14:07:17 2017 -0700 start re-org Source/Maestro.H Source/Maestro.cpp Source/MaestroDt.cpp Source/MaestroInit.cpp Source/Make.package commit ab881a157e0f8514f4171d5d85b76e93d9eeca88 Author: Andy Nonaka Date: Fri Oct 6 12:40:51 2017 -0700 add in microphysics Exec/Make.Maestro Exec/TEST_PROBLEMS/rt/GNUmakefile Microphysics/EOS/Make.package Microphysics/EOS/README Microphysics/EOS/_parameters Microphysics/EOS/eos.F90 Microphysics/EOS/eos_override.F90 Microphysics/EOS/eos_type.f90 Microphysics/EOS/gamma_law/Make.package Microphysics/EOS/gamma_law/_parameters Microphysics/EOS/gamma_law/gamma_law.F90 Microphysics/conductivity/Make.package Microphysics/conductivity/conductivity.F90 Microphysics/conductivity/constant/Make.package Microphysics/conductivity/constant/_parameters Microphysics/conductivity/constant/constant_conductivity.f90 Microphysics/networks/Make.package Microphysics/networks/_parameters Microphysics/networks/burn_type.F90 Microphysics/networks/burner.F90 Microphysics/networks/general_null/H_He.net Microphysics/networks/general_null/H_core.net Microphysics/networks/general_null/Make.package Microphysics/networks/general_null/README Microphysics/networks/general_null/actual_burner.f90 Microphysics/networks/general_null/actual_rhs.f90 Microphysics/networks/general_null/aprox13.net Microphysics/networks/general_null/gammalaw.net Microphysics/networks/general_null/hotcno.net Microphysics/networks/general_null/ignition.net Microphysics/networks/general_null/ignition_wdconvect.net Microphysics/networks/general_null/network.template Microphysics/networks/general_null/pphotcno.net Microphysics/networks/general_null/simple.net Microphysics/networks/general_null/simple3.net Microphysics/networks/general_null/triple_alpha_plus_o.net Microphysics/networks/general_null/write_network.py Microphysics/networks/network.f90 Microphysics/networks/sdc_type.F90 Source/extern_probin.template Util/model_parser/GPackage.mak Util/model_parser/Make.package Util/model_parser/model_parser.f90 constants/Make.package constants/constants_cgs.f90 commit df6f642a041f53b5a4d32435b03efc22e7cb13f5 Author: Andy Nonaka Date: Wed Oct 4 11:46:53 2017 -0700 boundary condition stuff Source/AMReX_FILCC_2D.F Source/AMReX_FILCC_3D.F Source/bc_fill_nd.F90 commit 40af2ee8769f43e8373dae56df1eb29e2bf1c119 Author: Andy Nonaka Date: Mon Oct 2 18:09:38 2017 -0700 more boundary condition progress Exec/TEST_PROBLEMS/rt/Prob.f90 Exec/TEST_PROBLEMS/rt/inputs Source/Maestro.cpp commit 53b0ac4156c1c990adb80ffe449f9ca86c12bea9 Author: Andy Nonaka Date: Mon Oct 2 17:16:05 2017 -0700 trying to debug a setup with walls Exec/TEST_PROBLEMS/rt/Prob.f90 Exec/TEST_PROBLEMS/rt/inputs Source/Maestro.H Source/Maestro.cpp Source/MaestroPhysBC.H Source/MaestroPhysBC.cpp Source/MaestroPhysBCFunct.H Source/MaestroPhysBCFunct.cpp Source/Maestro_F.H Source/Make.package commit 68283a8da03a8de2b6f16ee4e10f65b7d00b82aa Author: Andy Nonaka Date: Mon Oct 2 08:32:40 2017 -0700 tweak problem, tag on both components Exec/TEST_PROBLEMS/rt/Prob.f90 Source/Src_nd/Tagging_nd.f90 commit 269cd048cfa2cd96006624a050d027f9d77c4197 Author: Andy Nonaka Date: Mon Oct 2 08:18:46 2017 -0700 multicomponent example Exec/TEST_PROBLEMS/rt/GNUmakefile Exec/TEST_PROBLEMS/rt/Prob.f90 Source/Maestro.cpp Source/Src_2d/Adv_2d.f90 Source/Src_3d/Adv_3d.f90 commit 888979eda5075b77fcfafbac985274c453258eaf Author: Andy Nonaka Date: Fri Sep 29 19:22:33 2017 -0700 starting to set up physical boundary conditions Source/MaestroPhysBC.H Source/MaestroPhysBC.cpp Source/Make.package commit 27c778add0eb3b950d52db44ec796f76561fbcb3 Author: Andy Nonaka Date: Wed Sep 27 16:25:03 2017 -0700 more setting up runtime parameters by parsing _cpp_parameters Exec/Make.Maestro Exec/TEST_PROBLEMS/rt/inputs Source/Maestro.H Source/Maestro.cpp Source/Maestro_F.H Source/Make.package Source/_cpp_parameters Source/meth_params.F90 Source/meth_params.template Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H commit 5f2cb6c3c661068f913be04cba38e03433317d9f Author: Andy Nonaka Date: Wed Sep 27 15:37:25 2017 -0700 setting up runtime parameters by parsing _cpp_parameters Exec/Make.Maestro Exec/TEST_PROBLEMS/rt/GNUmakefile Source/Maestro.H Source/Maestro.cpp Source/MaestroPhysBC.H Source/Maestro_F.H Source/Make.package Source/_cpp_parameters Source/main.cpp Source/meth_params.F90 Source/meth_params.template Source/mk_params.sh Source/param_includes/Make.package Source/param_includes/maestro_defaults.H Source/param_includes/maestro_params.H Source/param_includes/maestro_queries.H Source/parse_maestro_params.py commit e611af3903bad7e4d82953da416d969554a825dc Author: Andy Nonaka Date: Wed Sep 20 14:10:32 2017 -0700 fix comments Source/MAESTRO.H Source/MAESTRO.cpp commit 2d802096d4c58688bb51e1bb203e3fe6d8910303 Author: Andy Nonaka Date: Wed Sep 20 13:38:26 2017 -0700 clean up verbosity Source/MAESTRO.cpp commit 322d54e030b65aceb11a3acc228a017c979c18f8 Author: Andy Nonaka Date: Wed Sep 20 13:31:29 2017 -0700 clean up print statments change logic for refluxing to test on whether we are/aren't at the coarest/finest level, instead of just checking to see if the flux registers are built Source/MAESTRO.H Source/MAESTRO.cpp commit bc9fb235fa241cba22b0125ea7e8804ab7895bf1 Author: Andy Nonaka Date: Wed Sep 20 12:19:01 2017 -0700 more code cleanup Source/MAESTRO.H Source/MAESTRO.cpp commit 4c6db1602ffe71171d13318183a4fd5a18fd9cbd Author: Andy Nonaka Date: Wed Sep 20 11:39:36 2017 -0700 rewrote the time stepping routine so the loop over levels is contained withing Advance(), and there is no recursive call using the flux registers to do the refluxing, rather than the style in MAESTRO_F where we simply synchronize the fluxes Source/MAESTRO.H Source/MAESTRO.cpp commit f0d049d5df406ca14082976c958ada2c0de431ee Author: Andy Nonaka Date: Wed Sep 20 11:13:18 2017 -0700 fun with emacs macros to standardize the indentation Source/MAESTRO.H Source/MAESTRO.cpp Source/MAESTROPhysBC.H Source/MAESTRO_F.H Source/main.cpp commit b15d5532e6f49c1fa2c694298c357d45d5ba87a1 Author: Andy Nonaka Date: Wed Sep 20 09:27:26 2017 -0700 test commit 2 README.md commit cb3cba62232418451f8a878fa77b9920bf8b14c5 Author: Andy Nonaka Date: Wed Sep 20 09:25:14 2017 -0700 test commit README.md commit eeeb2eea5b1e8528ed59111bb68376d597baadcd Author: Andy Nonaka Date: Mon Sep 18 19:00:05 2017 -0700 some comments, design ideas Source/MAESTRO.H Source/MAESTRO.cpp commit e925ca3d6d566ba64b030f968df3552f8002f22e Author: Andy Nonaka Date: Mon Sep 18 18:25:20 2017 -0700 clean up time stepping Source/MAESTRO.H Source/MAESTRO.cpp commit 14fe75ecc1a3158a3d95b8a395bda498e93a6941 Author: Andy Nonaka Date: Mon Sep 18 17:50:12 2017 -0700 Create README.md README.md commit 88fef658149d9d1426fcd712b2a0f999f80bbf60 Author: Andy Nonaka Date: Mon Sep 18 17:47:09 2017 -0700 code cleanup - getting rid of some subcycling constructs Source/MAESTRO.H Source/MAESTRO.cpp Source/MAESTROPhysBC.H Source/MAESTRO_F.H Source/main.cpp commit 351df3b57b83bc7317caa7b1e5d1a7fb72a469f4 Author: Andy Nonaka Date: Mon Sep 18 16:56:18 2017 -0700 initial commit - a copy of amrex/Tutorials/Amr/Advection_AmrCore with a little bit of rennaming files and directory re-org Exec/Make.MAESTRO Exec/TEST_PROBLEMS/rt/GNUmakefile Exec/TEST_PROBLEMS/rt/Make.package Exec/TEST_PROBLEMS/rt/Prob.f90 Exec/TEST_PROBLEMS/rt/face_velocity_2d.f90 Exec/TEST_PROBLEMS/rt/face_velocity_3d.f90 Exec/TEST_PROBLEMS/rt/inputs Source/MAESTRO.H Source/MAESTRO.cpp Source/MAESTROPhysBC.H Source/MAESTRO_F.H Source/Make.package Source/Src_2d/Adv_2d.f90 Source/Src_2d/Make.package Source/Src_2d/compute_flux_2d.f90 Source/Src_2d/slope_2d.f90 Source/Src_3d/Adv_3d.f90 Source/Src_3d/Make.package Source/Src_3d/compute_flux_3d.f90 Source/Src_3d/slope_3d.f90 Source/Src_nd/Make.package Source/Src_nd/Tagging_nd.f90 Source/main.cpp