commit 6ff87bd4388d5de573cb636ae992cf3e9890f57d
Merge: b88fd776 cc4d9de7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Nov 5 21:50:41 2021 -0400
Merge branch 'microphysics_initialize' into more_fortran_hacks
commit b88fd776437c8e15ff2d0714582e9458b5cca623
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
Date: Fri Nov 5 20:09:56 2021 -0400
Merge branch 'development' into microphysics_initialize
commit ab419dcf4be023a5cb96e1b32058cc2c825e4d8a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
Date: Fri Nov 5 19:08:58 2021 -0400
fix tileBox -> tilebox (#279)
Exec/science/urca/MaestroTagging.cpp
commit 1252cc27d07f4e434f1a78ab40d73a5b6cae048e
Author: Doreen Fan <dfan@lbl.gov>
Date: Mon Nov 1 15:00:45 2021 -0700
November 2021 release notes
CHANGES.md
commit 8e090eed958ab2e422cf8c3d78203ec8f8d98850
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Sat Oct 2 20:14:16 2021 -0700
October 2021 release notes
CHANGES.md
commit 93b6adf8ad9dbe4f1011a8cc6fd8619c6207d923
Author: Doreen Fan <dfan@lbl.gov>
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 <harpolea@users.noreply.github.com>
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 <AJNonaka@lbl.gov>
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 <harpolea@users.noreply.github.com>
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 <action@github.com>
Co-authored-by: Andy Nonaka <AJNonaka@lbl.gov>
Source/Maestro.H
Source/MaestroAdvanceAvg.cpp
Source/MaestroBaseState.cpp
Source/MaestroEnforceHSE.cpp
Source/MaestroMakew0.cpp
Source/MaestroPlot.cpp
commit 958c010a5bd53782a2053d2b7a0d5b5b91583183
Author: Justin Lague <justin.lague@hotmail.com>
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 <dfan@lbl.gov>
Date: Wed Sep 1 12:07:11 2021 -0700
September 2021 release notes
CHANGES.md
commit 7432f437a8eabce22b55778a0234c04a8d8e254f
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Mon Aug 2 10:51:24 2021 -0700
August 2021 release notes
CHANGES.md
commit 57e31ade09b1d1fa89234f50f5e0cfa979fb44a4
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Thu Jul 1 23:45:25 2021 -0700
July 2021 release notes
CHANGES.md
commit 965b94c0472a054d0ffb29f58af78129ff6e3871
Author: Doreen Fan <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
Date: Tue Jun 1 21:06:53 2021 -0700
June 2021 release notes
CHANGES.md
commit bbc7acb3be396aee54e1a3cb22bd8f35d2ae1530
Author: Doreen Fan <dfan@lbl.gov>
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 <asnodin@users.noreply.github.com>
Date: Tue May 25 10:34:31 2021 +0100
Merge branch 'AMReX-Astro:development' into development
commit 8ef9b52772287818beac424ba0e8c69cdd927c9f
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Mon May 3 19:33:11 2021 -0700
May 2021 release notes
CHANGES.md
commit 0204a8f2b8300758fec0ce1703c39757f07c1b96
Author: Doreen Fan <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
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 <asnodin@users.noreply.github.com>
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 <dfan@lbl.gov>
Date: Thu Apr 8 20:27:45 2021 -0700
Add tempbar to base state plotfile
Source/MaestroPlot.cpp
commit 3e14f805620fa560f331c8ba86b97950e2d730b6
Author: Doreen Fan <dfan@lbl.gov>
Date: Thu Apr 1 20:58:07 2021 -0700
April 2021 release notes
CHANGES.md
commit bb8840bf0a59af5ce828e140cf6857793c2b6aa6
Author: Doreen Fan <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <andrew.snodin@gmail.com>
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 <andrew.snodin@gmail.com>
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 <andrew.snodin@gmail.com>
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 <dfan@lbl.gov>
Date: Mon Mar 1 18:36:50 2021 -0800
March 2021 release notes
CHANGES.md
commit f65c587a28bc777f9e3f7c92333bda07014db523
Author: Doreen Fan <dfan@lbl.gov>
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 <action@github.com>
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 <action@github.com>
Co-authored-by: Andy Nonaka <AJNonaka@lbl.gov>
Source/MaestroBurner.cpp
Source/MaestroReact.cpp
commit 2022399851704dc2e39f47d6b5a97436ecfb5a53
Author: Doreen Fan <dfan@lbl.gov>
Date: Mon Feb 1 11:59:30 2021 -0800
February 2021 release notes
CHANGES.md
commit 09786df6c1ea025ef8ea8c468e02a99daaf584ab
Author: Doreen Fan <dfan@lbl.gov>
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 <action@github.com>
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 <AJNonaka@lbl.gov>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <action@github.com>
Co-authored-by: Andy Nonaka <AJNonaka@lbl.gov>
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 <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
Date: Mon Jan 4 09:27:19 2021 -0800
January 2021 release notes
CHANGES.md
commit 448d1f8469217bb478b9d318f671cdb3f75b4573
Author: Doreen Fan <dfan@lbl.gov>
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 <maxpkatz@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
Date: Tue Dec 15 15:19:14 2020 -0500
don't count Jupyter or "Roff" (#244)
.gitattributes
commit 45d752f0dde34fb15f0b06570d74f74d6c0ef79e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <harpolea@users.noreply.github.com>
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 <action@github.com>
Co-authored-by: Andy Nonaka <AJNonaka@lbl.gov>
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 <maxpkatz@gmail.com>
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 <dfan@lbl.gov>
Date: Tue Dec 1 13:15:16 2020 -0800
December 2020 release notes
CHANGES.md
commit 672c9fb50e6b56c7522b5a9668a7ba7034aeed69
Author: Alice Harpole <harpolea@users.noreply.github.com>
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 <dfan@lbl.gov>
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 <harpolea@users.noreply.github.com>
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 <action@github.com>
Co-authored-by: Andy Nonaka <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <harpolea@users.noreply.github.com>
Date: Thu Nov 19 09:58:23 2020 -0500
fix create_release action (#241)
.github/workflows/create_release.yml
commit 2285414aaf028896d8ebcbcf22d9e28673cc045a
Author: Doreen Fan <dfan@lbl.gov>
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 <asnodin@users.noreply.github.com>
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 <dfan@lbl.gov>
Date: Mon Nov 2 13:22:41 2020 -0800
November 2020 release notes
CHANGES.md
commit 5765ad4d19f6e755b4eafa42b131cc2343f1f621
Author: Doreen Fan <dfan@lbl.gov>
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 <harpolea@users.noreply.github.com>
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 <dfan@lbl.gov>
Date: Thu Oct 1 10:36:22 2020 -0700
October 2020 release notes
CHANGES.md
commit f6d70b2d1a354d6f7ed270609decb5a6defa0189
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <action@github.com>
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 <AJNonaka@lbl.gov>
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 <action@github.com>
Source/MaestroMacProj.cpp
Source/MaestroNodalProj.cpp
Source/param/_cpp_parameters
commit ef9db869a8e336c4ec19c515ee6413c058980ffc
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Thu Sep 3 14:11:43 2020 -0700
September 2020 release notes
CHANGES.md
commit 8ed72a957a36be3073d59b552559e6812d6d35f5
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <harpolea@users.noreply.github.com>
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 <harpolea@users.noreply.github.com>
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 <harpolea@users.noreply.github.com>
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 <michael.zingale@stonybrook.edu>
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 <AJNonaka@lbl.gov>
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 <action@github.com>
Co-authored-by: Andy Nonaka <AJNonaka@lbl.gov>
Source/MaestroAdvanceSdc.cpp
Source/MaestroIntra.cpp
Source/MaestroReact.cpp
commit 82381e52d273f2c497ae335bf3a7686aa09ea11e
Author: Max Katz <maxpkatz@gmail.com>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
Date: Thu Aug 6 16:51:45 2020 -0700
turn on MPI
Exec/science/urca/GNUmakefile
commit a1e1fb9895f868656fbb75f82b381ef20c3bc4a0
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Thu Aug 6 16:47:20 2020 -0700
update initdata from wdconvect
Exec/science/urca/MaestroInitData.cpp
commit 9dfb5eb62d206a13e9f845ebef996357a5c81445
Author: dwillcox <eugene.willcox@gmail.com>
Date: Thu Aug 6 16:32:36 2020 -0700
turn on TINY_PROFILE
Exec/science/urca/GNUmakefile
commit a3cec30d9c714f1132d984727555da87f4ec01b1
Author: Donald E. Willcox <eugene.willcox@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <harpolea@users.noreply.github.com>
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 <harpolea@users.noreply.github.com>
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 <AJNonaka@lbl.gov>
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 <action@github.com>
Co-authored-by: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Mon Aug 3 11:14:54 2020 -0700
August 2020 release notes
CHANGES.md
commit a0da7bec0a8510bc96135265f998ae1bbb63933b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Aug 3 09:47:37 2020 -0400
fix some formatting + add submodules (#217)
README.md
commit 00536398ca71095824ba65fb0a90b2d3bf0b0326
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <AJNonaka@lbl.gov>
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 <action@github.com>
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 <AJNonaka@lbl.gov>
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 <harpolea@users.noreply.github.com>
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 <cjdegrendele@gmail.com>
Date: Mon Jul 27 16:43:22 2020 -0400
PrintBA, with Print()
Source/MaestroDebug.cpp
commit 8b79038bfe7d80f21bd72e41198657393fc3c55e
Author: Chris DeGrendele <cjdegrendele@gmail.com>
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 <cjdegrendele@gmail.com>
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 <cjdegrendele@gmail.com>
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 <cjdegrendele@gmail.com>
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 <harpolea@users.noreply.github.com>
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 <cjdegrendele@gmail.com>
Date: Fri Jul 24 12:43:31 2020 -0400
Merge remote-tracking branch 'upstream/development' into development
commit 28b82f8624d0fb79b5a01ee62e8c2666dd2f7c3d
Author: Chris DeGrendele <cjdegrendele@gmail.com>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <action@github.com>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <action@github.com>
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 <dfan@lbl.gov>
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 <harpolea@users.noreply.github.com>
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 <harpolea@users.noreply.github.com>
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 <cjdegrendele@gmail.com>
Date: Mon Jul 20 13:29:57 2020 -0400
Define init multifabs with small_geom
Source/MaestroInit.cpp
commit d2ded9ebf506d5c8429cb1f148b7f1945932251d
Author: Chris DeGrendele <cjdegrendele@gmail.com>
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 <AJNonaka@lbl.gov>
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 <cjdegrendele@gmail.com>
Date: Fri Jul 17 18:02:20 2020 -0400
Valid data is only <= finest_level
Source/MaestroRegrid.cpp
commit 72fe9c3af574d781a103732baafa2c6dcdf7d904
Author: Chris DeGrendele <cjdegrendele@gmail.com>
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 <cjdegrendele@gmail.com>
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 <cjdegrendele@gmail.com>
Date: Fri Jul 17 10:13:24 2020 -0400
Added debugging for Grids
Source/Maestro.H
Source/MaestroDebug.cpp
commit 97530c869a9dec59fbee1b79c20b1c394f31826d
Author: Chris DeGrendele <cjdegrendele@gmail.com>
Date: Fri Jul 17 08:57:12 2020 -0400
Make debugging multifabs readable
Source/MaestroDebug.cpp
commit 98abdd779d653f9dfe4e3bf4e429d2574ab3a0dc
Author: Chris DeGrendele <cjdegrendele@gmail.com>
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 <cjdegrendele@gmail.com>
Date: Thu Jul 16 13:42:25 2020 -0400
Prevent Tagarray from looping over undefined grids
Source/MaestroRegrid.cpp
commit 99f3738436c89dcf54d5704c3ac622e7e981449a
Author: GitHub Action <action@github.com>
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 <AJNonaka@lbl.gov>
Date: Wed Jul 15 13:24:44 2020 -0700
Merge branch 'development' into smallscale_sdc_dpdt_fix
commit 522a8ed77a4358e9db90a8fb8302aec89e945d20
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <action@github.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <action@github.com>
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 <dfan@lbl.gov>
Date: Mon Jul 13 15:20:33 2020 -0700
Merge branch 'development' into clang_tidied
Fixed conficts
commit b8c25a543f2eb6c7a7628795d7a86f9e7fdc7ba5
Author: Alice Harpole <harpolea@users.noreply.github.com>
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 <dfan@lbl.gov>
Date: Wed Jul 1 11:51:30 2020 -0700
July 2020 release notes
CHANGES.md
commit fa4de7ea240eb4309715a99f79c7ca9bc9de2af7
Author: Doreen Fan <dfan@lbl.gov>
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 <maxpkatz@gmail.com>
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 <harpolea@users.noreply.github.com>
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 <action@github.com>
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 <dfan@lbl.gov>
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 <maxpkatz@gmail.com>
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 <maxpkatz@gmail.com>
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 <dfan@lbl.gov>
Date: Fri Jun 5 15:22:11 2020 -0700
Merge branch 'development' into remove_rhoX0
commit 2b4787e270b58c01c8fa1f916fb44f354a9a930f
Author: Doreen Fan <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Tue Jun 2 08:36:37 2020 -0700
add #include <unistd.h> 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 <dfan@lbl.gov>
Date: Mon Jun 1 12:52:36 2020 -0700
June 2020 release notes
CHANGES.md
commit c81740c4c3dfb5a291c74300605d9ca3f66bfd05
Author: Doreen Fan <dfan@lbl.gov>
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 <maxpkatz@gmail.com>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <action@github.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Tue May 26 12:36:02 2020 -0400
merge conflicts
commit ea75d20dc37bbc1151d9a501ca1a9141eb8e5ec0
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Fri May 22 16:04:15 2020 -0400
remove Delimiter line from .clang-format file
.clang-format
commit 67418d0ac803bd89884664cd9148b0c756cc833f
Author: Alice Harpole <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <action@github.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <action@github.com>
Exec/Make.Maestro
Source/MaestroReact.cpp
Source/MaestroSetup.cpp
Source/Maestro_F.H
Source/param/runtime.probin.template
commit fcdc8d7f604cfd8bb3f0d896e1e43f27366926b9
Author: Doreen Fan <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <ajnonaka@login3.summit.olcf.ornl.gov>
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 <action@github.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed May 13 16:19:39 2020 -0400
commit plotfile changes
Source/MaestroPlot.cpp
commit 8129a083766eb77de88f115662c5c945be3d6766
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Mon May 11 15:59:38 2020 -0700
make basestate explicit
Source/BaseState.H
Source/MaestroInit.cpp
commit 8d2c90e6f505d275ccf9ed051ee86be79933229a
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Fri May 8 17:38:55 2020 -0400
initialize basestate in constructor and resize
Source/BaseState.H
commit 0e5873391c214c43d33d5bd39b31889e8eed5ff6
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Fri May 8 14:07:30 2020 -0700
setval psi to zero if EBS=F
Source/MaestroInit.cpp
commit 2bdb6c1fe655eed6c9c744d06b1991d6c84f3680
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <action@github.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu May 7 08:42:47 2020 -0400
fix link formatting
sphinx_docs/source/faq.rst
commit 3aabb60d245ed5b7d4552d45b4074eb525703713
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu May 7 08:36:14 2020 -0400
fix link formatting
sphinx_docs/source/faq.rst
commit 754abf1d00974a5d82b101874c0c8eafbbf87d39
Author: Alice Harpole <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Wed May 6 13:31:30 2020 -0700
Merge branch 'development' into base_state_class6
commit 8c7123056c7d3986c793065da2bb5b4acd957e97
Merge: 9785cf05 5127f040
Author: Doreen Fan <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <harpolea@users.noreply.github.com>
Date: Tue May 5 14:29:52 2020 -0400
Add github pages badge
README.md
commit d0fb7f72768ba968699ca037618375c23accd6ad
Author: Alice Harpole <harpolea@users.noreply.github.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Fri May 1 11:01:24 2020 -0700
May 2020 release notes
CHANGES.md
commit 42ba5b713b9753fc402e9861cf1a9c3e4be16927
Author: Doreen Fan <dfan@lbl.gov>
Date: Fri May 1 10:47:47 2020 -0700
Update Microphysics to release 20.05
external/Microphysics
commit 2de2eaa09ee0d3ca1b3fdf95adb9143b9e78e060
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Thu Apr 30 14:54:59 2020 -0700
Merge branch 'development' into base_state_class4
commit 0499c845e60d2572641479aecb30a21a3b4f5540
Author: Doreen Fan <dfan@lbl.gov>
Date: Thu Apr 30 14:44:17 2020 -0700
bug fix for single level planar
Source/MaestroMakeEta.cpp
commit bb06ec3347e51602e1b5663182d6b9eecd613352
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu Apr 30 10:49:35 2020 -0400
merge with previous PR
commit 425e24e8a5e43a5281e4fc55114c734f613c37f6
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu Apr 30 10:33:27 2020 -0400
merge with previous PR
commit c4daee315d09975f876f87ce3e40307bee8c9428
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu Apr 30 08:47:54 2020 -0400
fixed code examples
sphinx_docs/source/base_state.rst
commit 08910810c88ddb08d7fefba19a1aa6a93fdb7303
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Apr 30 08:45:52 2020 -0400
added documentation for BaseStateGeometry
sphinx_docs/source/base_state.rst
commit dc391a62a3695ae6cb9fbccb59a50517d4a7aa1a
Author: Alice Harpole <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Wed Apr 29 16:36:21 2020 -0700
add C++ init function to subroutine
Source/MaestroFill3dData.cpp
commit 1d9d0fba9d0bf80ec5c946b569126029113e8445
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <harpolea@users.noreply.github.com>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Apr 27 17:25:58 2020 -0400
merge with previous PR
commit 2a69452f30d5845e2e2e3d76b5742f3f9ccb8f59
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Apr 27 12:58:49 2020 -0400
merge with previous PR
commit 847051d6fbf2b3b33a501aec910ebc1ba6fc3ff4
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Fri Apr 24 16:43:04 2020 -0400
merge with previous PR
commit c73d84c7f73134681b9032ff7a4f40016e1f38e3
Merge: 3bebd06e ed241e1a
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Fri Apr 24 07:35:51 2020 -0400
merge conflicts
commit 3bebd06ea27f204511b876bb3620aad782c82663
Merge: ba98de5d e45c3786
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Fri Apr 24 07:26:51 2020 -0400
merge conflicts
commit ed241e1ae776a68eef2f7bc8bdd3a1d186e34eb9
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
Date: Thu Apr 23 17:44:55 2020 -0400
merge conflicts
commit b5da2aa7cd57293e1d6e2f3d27c7cebddd311dea
Author: Alice Harpole <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
Date: Thu Apr 23 15:35:04 2020 -0400
merge with previous PR
commit a7d1d449a0b623a41e7d95abb1e98bad25c6a8ea
Merge: 38309aae d861ad25
Author: Doreen Fan <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
Date: Thu Apr 23 14:20:43 2020 -0400
merge with runtime_params
commit d861ad25416bf606df049d3027bc95847f60032f
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu Apr 23 07:55:43 2020 -0400
merging runtime parameters
commit cb5418fd6cf2f77d52070d70f1b436b503d84067
Author: Alice Harpole <aliceharpole@gmail.com>
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 <maxpkatz@gmail.com>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <maxpkatz@gmail.com>
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 <maxpkatz@gmail.com>
Date: Tue Apr 21 21:45:31 2020 -0400
Update Microphysics submodule
external/Microphysics
commit 830f1bb9bfd44154c4a7af92d2f2807712e85cf8
Author: Max Katz <maxpkatz@gmail.com>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
Date: Tue Apr 21 17:22:50 2020 -0400
started converting to use new basestatearray and basestategeometry classes
commit 0f429eec0d028643fecd0ed3047938769162bed7
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
Date: Thu Apr 16 08:03:53 2020 -0400
merging with previous PR
commit af6e5be85d5ae143f4cd2fee9776a975a5d66f6a
Merge: 8491eba4 f1578751
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <alice@groot.astro.sunysb.edu>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Tue Apr 14 08:59:42 2020 -0400
merge with development
commit 2e6af0977407a881098457ccb789c9f0eed8f6bb
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Tue Apr 14 08:47:21 2020 -0400
fix compilation
Source/MaestroMakeS.cpp
commit 7750674199c9b4fb41fa69212f25c2e2d495c355
Author: Alice Harpole <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Apr 13 12:54:43 2020 -0400
fixed bug in dr0
Source/MaestroAverage.cpp
commit b9bd366daec7534d6dd886861a7f8627da4989cc
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Fri Apr 10 09:04:04 2020 -0400
fixed MaestroBaseState.cpp problem files
commit a6adfa49f7f70fe536660e6dc473cf2705b0935f
Merge: 91410524 36fe5d9c
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Fri Apr 10 08:47:47 2020 -0400
fixed MaestroBaseState.cpp problem files
commit 36fe5d9c519ca446cc4f64b0a1d10872f61c83fe
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Thu Apr 9 17:02:07 2020 -0700
code cleanup
Source/MaestroBaseStateGeometry.cpp
commit d6f623b6ba367f5950d3aa2120634ac130aa3b8e
Author: Doreen Fan <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Thu Apr 9 12:13:38 2020 -0700
Merge branch 'development' into base_state_class2
commit dfe604d4e52d5f643a8d14234cb3a566e6d88e1a
Merge: 801679f5 b3b19087
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu Apr 9 14:40:10 2020 -0400
fix GPU compilation
Source/MaestroSponge.cpp
commit 20813473bd602f196096b8bab0de3f430e4cad08
Merge: 67fcd8fa 5ab78b2d
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu Apr 9 08:24:24 2020 -0400
fix merge
Source/MaestroFill3dData.cpp
commit 8729f059612ea112ddbd5b1b25673b17622e1cec
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Apr 9 08:23:40 2020 -0400
fix merge
Source/MaestroFill3dData.cpp
commit 91410524614a20e322b607c71b54b1d82b60e46a
Merge: 5ced1227 75ef8563
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Apr 9 08:23:06 2020 -0400
merge with development
commit 75ef85631ced4f5d34b57f78fd1a6ad290a71a14
Merge: 6c89fe48 f7ea1390
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Apr 9 08:21:44 2020 -0400
merge with development
commit f7ea1390126153403ae000a971f30a4ee1f64f61
Merge: 9eae8234 5ab78b2d
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Apr 9 08:19:53 2020 -0400
merge with development
commit 5ced122726059082536c61db91f0f31a898b60d5
Merge: 241ad0a2 5ab78b2d
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Apr 9 08:17:02 2020 -0400
merge with development
commit e0a3f7012d5438de19cac7289c5f32586820559f
Merge: 5d98c4c5 5ab78b2d
Author: Doreen Fan <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Apr 8 16:45:22 2020 -0400
merge with development
commit 82fbb400b80801d676a4d99864da9047a7908938
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Apr 8 08:30:40 2020 -0400
fix indexing in MaestroRegrid
Source/MaestroRegrid.cpp
commit f5921cd02c3733162cee76f2c1bdc02821cdc49c
Merge: 1badc8ec 3b36278c
Author: Alice Harpole <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Tue Apr 7 15:34:01 2020 -0700
Merge branch 'development' into cpp_init
commit 3b36278c02da544bc260fb761b1871de139ca6cb
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Apr 7 17:49:26 2020 -0400
fix rhoh0_halftime
Source/MaestroRhoHT.cpp
commit 1badc8ecc997014f6d7a8d01d5759c09a40057c1
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Apr 6 17:18:49 2020 -0400
ditto for planar
Source/MaestroAverage.cpp
commit 1fac9659036d9e52dff1f4723918bf14203c1b81
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Apr 6 15:18:35 2020 -0400
convert gradp0
commit fbf326967375c49573db07c07df5b630bf5669fc
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Apr 6 15:13:41 2020 -0400
fix indexing in gradp0 for spherical
Source/MaestroMakeS.cpp
commit 77ac9f8cdd815bfec4cd4047769e394d8acd2b8f
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Apr 6 11:56:18 2020 -0400
merging with development
commit 26a4d5b94a60ac744e5b1b972cb984f28cd7b00d
Merge: bb56a241 507afa6b
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Fri Apr 3 13:28:41 2020 -0700
Merge branch 'development' into cpp_init
Fixed merge conflicts
commit 76ec42d7fa80c73b9b4d7aac3a18078480f11a75
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Thu Apr 2 16:18:42 2020 -0700
April 2020 second release notes
CHANGES.md
commit 50cf68b5019bb79bace341fd134d2d2c1b67485a
Author: Doreen Fan <dfan@lbl.gov>
Date: Thu Apr 2 16:11:45 2020 -0700
Update Microphysics to release 20.04
external/Microphysics
commit 1647f048572e8b4a3c0bc35a31d3a26a495e95af
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Wed Apr 1 13:07:17 2020 -0700
April 2020 release notes
CHANGES.md
commit 581fe892179b1986751b9747667ab935747ad330
Merge: ec5c6bc4 1438cc2a
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Apr 1 14:32:39 2020 -0400
remove MaestroMacProj_level.cpp
Source/MaestroMacProj_level.cpp
commit ec5c6bc4c5ace6aafe94d8424acecb292db36d72
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Apr 1 08:06:18 2020 -0400
make eta
Source/MaestroMakeEta.cpp
commit 288b51bde8b78a96196e4ca976c20ad50aac006e
Author: Alice Harpole <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Mon Mar 30 13:48:40 2020 -0700
Merge branch 'development' into cpp_init
commit 9058bc1bc1bce958b73e3a7558680b07c04b7bcf
Merge: 5d98c4c5 673a650d
Author: Alice Harpole <aliceharpole@gmail.com>
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 <harpolea@users.noreply.github.com>
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 <aliceharpole@gmail.com>
Date: Mon Mar 30 15:04:58 2020 -0400
GPU fix
Source/Maestro.H
Source/MaestroMakew0.cpp
commit 359a775c0d94d72d2b31e505fff157afce4bb0ff
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Mar 30 08:32:24 2020 -0400
merging with development
commit 4e0aa927ea3dd28440c808c958305d4fc2dbe29e
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Mar 30 08:21:52 2020 -0400
fix center
Source/MaestroBaseStateGeometry.cpp
commit f95bee215081b7676e814858c055ed4eda3e274a
Merge: d4cca200 63d6ad45
Author: Doreen Fan <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Fri Mar 27 16:32:30 2020 -0400
merging with development
commit 4fd7974fc6622d4c721b83e27b97733a73e1c48c
Merge: 340a864f aaf1e4aa
Author: Doreen Fan <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Fri Mar 27 13:27:39 2020 -0700
Merge branch 'development' into cpp_dt_force
Fixed merge conflicts
commit d4cca2003a0e57413ea1d6d1e48f36c90c922c0b
Author: Doreen Fan <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Fri Mar 27 10:50:15 2020 -0700
Merge branch 'development' into cpp_init
commit 3547cb40497f287e45641335866a540768b8ab6c
Author: Doreen Fan <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Fri Mar 27 11:38:02 2020 -0400
merging with development
commit 8426a5ced9054972fd1336eca5d9e5c05ea4e806
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Fri Mar 27 11:37:08 2020 -0400
GPU fix
Source/MaestroFill3dData.cpp
commit c706e6789ab58e3bd9aa7c42ffb59403bc09041b
Author: Alice Harpole <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Thu Mar 26 14:44:24 2020 -0700
Merge branch 'development' into cpp_init
commit 22fa3498ebf954c4b020b575e7051092e039064c
Merge: dbdd1efd 38413f06
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu Mar 26 17:26:33 2020 -0400
growntilebox -> grow(tilebox)
Source/MaestroMakeUtrans.cpp
commit dbdd1efd0d6f3cb0ca43ff38c148ac4d1e3a5166
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Tue Mar 24 17:48:17 2020 -0700
Merge branch 'development' into cpp_init
Fixed conflicts
commit a997c1733dc604fb7926033d2400a26189ffd539
Author: Alice Harpole <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Fri Mar 20 15:04:58 2020 -0400
overloaded some operators
Source/BaseState.H
Source/BaseState.cpp
commit 8cf8989fe9d0946dab1064c20e5655ee3adfff93
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Thu Mar 19 11:26:26 2020 -0700
Merge branch 'development' into cpp_dt_force
commit a30302b87bc30dd383fb1f08a58c13fc44c5289c
Author: Doreen Fan <dfan@lbl.gov>
Date: Thu Mar 19 11:23:57 2020 -0700
GPU fix
Source/MaestroPlot.cpp
commit d491c1eea75500aed72a3e78e612116d8cb1e77a
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Mar 19 13:10:17 2020 -0400
update Microphysics
external/Microphysics
commit 28e97550763d688170ef649dae22e01ae7cfef5e
Author: Alice Harpole <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Wed Mar 18 19:51:47 2020 -0700
Added lots of <RunOn::Device> to fix GPU compilation
Exec/unit_tests/test_basestate/MaestroDt.cpp
Source/MaestroDt.cpp
commit 0924ad8c233ed5c3ac4ffe08fdc9f705dfec6aff
Merge: e467c0ec 912f4487
Author: Doreen Fan <dfan@lbl.gov>
Date: Wed Mar 18 19:10:09 2020 -0700
Merge branch 'development' into cpp_dt_force
commit e467c0eca601687a17f3193bff4f3068610637d5
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Mar 18 15:12:39 2020 -0400
add <RunOn::Device> to Fab functions to fix GPU compilation
Source/MaestroNodalProj.cpp
Source/MaestroPlot.cpp
commit 39294eef7f0b43fa6d40cd4e4fc06ae50c0c1fb2
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Mar 18 14:37:12 2020 -0400
converted toy convect
Exec/science/toy_convect/MaestroInitData.cpp
commit afd808948f8ed98cd4dc820a6b44dde6f33dec49
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Tue Mar 17 14:57:09 2020 -0400
GPU fixes for flame
Exec/science/flame/MaestroBCFill.cpp
commit 52dd4455424fdb288abd7e7a80d62a0ba711b471
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Mon Mar 16 17:32:12 2020 -0700
fix spherical magvel and circ_vel
Source/MaestroPlot.cpp
commit c0035d1f66c86935fb39834a8ecb2bfa3c39b359
Author: Alice Harpole <harpolea@users.noreply.github.com>
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 <dfan@lbl.gov>
Date: Mon Mar 16 16:11:44 2020 -0700
Merge branch 'cpp_base_state' into cpp_more_eos
commit 7d2eb0b8ca7a1a8a29f4683258f4f1ae80504797
Author: Alice Harpole <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Thu Mar 12 11:39:34 2020 -0700
small bug fix
Exec/science/flame/MaestroBaseState.cpp
commit dc0738c886aaffa97134fe71a50a43a86d8d4976
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
Date: Tue Mar 10 16:28:42 2020 -0400
tidy up
Source/MaestroDt.cpp
commit a957f308347c068a73f643ecc6efe542b125f233
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Mar 10 16:15:38 2020 -0400
wdconvect runs with OMP and MPI again
Source/MaestroDt.cpp
commit 797711f274fb164f4bcacef16449a806ef9da1d5
Author: Alice Harpole <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Mon Mar 9 16:44:47 2020 -0700
set psi to zero during initialization
Source/MaestroInit.cpp
commit eb78ea0cc93fbbeddf65dd1d885218994f95ddc9
Author: Doreen Fan <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Mon Mar 9 14:18:01 2020 -0700
indices bug fix
Source/MaestroBaseState.cpp
commit 7fc8bccd4b16d005d30cb83db8c1231798196813
Merge: 1d6081dd 05b85037
Author: Doreen Fan <dfan@lbl.gov>
Date: Mon Mar 9 13:19:56 2020 -0700
Merge branch 'development' into cpp_base_state
commit c7511d3d0176215a2e3861e79b82d4ce99113e00
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Fri Mar 6 11:57:09 2020 -0500
converted firstdt
Source/MaestroDt.cpp
commit 90be189c6ff8effe40d85c936094b46db67b622a
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Thu Mar 5 15:15:50 2020 -0800
Merge branch 'development' into cpp_average
commit 19c3378f2157fdcf9c11b8ca9d422fff5dfc0e18
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Mar 5 16:46:11 2020 -0500
GPU fixes
Source/MaestroPlot.cpp
commit 68502a9eafe0fea0f8e64250aa1452fa6c3d7dee
Merge: ec194f49 05b85037
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Mar 5 16:06:20 2020 -0500
merging with development
commit 05b85037bc118409e774d100b846da75b37a56d2
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Thu Mar 5 09:52:56 2020 -0800
Merge branch 'development' into cpp_average
Fixed merge conflicts
commit a933188e81837ffbaf95a87cb2328bcfdd4c23f6
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Wed Mar 4 16:03:08 2020 -0800
validbox -> tilebox
Source/MaestroAverage.cpp
commit a6479e798d183dfb3db337917ad4dfb5315163b8
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Mar 4 16:49:44 2020 -0500
made the reductions deterministic
Source/MaestroAverage.cpp
commit 3d45cb9011981bdc937636ddf3327f9d380565ff
Merge: 58c140bb 80ed04b1
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Mar 4 16:45:53 2020 -0500
merge conflicts
commit d713a1474faa0501af577c9f562657339bb0ae48
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Mar 4 16:42:59 2020 -0500
tidy up
Source/MaestroMakeEta.cpp
commit 58eeb23282420dc4ff2ce3f52f03861703f983b5
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Tue Mar 3 17:40:16 2020 -0800
Merge branch 'development' into cpp_psi_eta
commit d31e9ba5cfd1998dcf90a74f986493e13a7e1bd2
Author: Doreen Fan <dfan@lbl.gov>
Date: Tue Mar 3 17:40:09 2020 -0800
Change loVect -> loVect3d and hiVect -> hiVect3d
Source/MaestroMakeEta.cpp
commit 7cd606671eb53dd8e926d0fa66162a70ec54c270
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <harpolea@users.noreply.github.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Tue Mar 3 09:49:18 2020 -0500
fix merge conflicts with development
commit 7a2eeb939fbd6486ff48884867480851b98ac595
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Mar 2 17:08:39 2020 -0500
bash doesn't like -eq for strings
deploy_docs.sh
commit ff15b8de3b06c36cbfe89b610faf2530c640fba6
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Mar 2 17:04:05 2020 -0500
bash doesn't like ==
deploy_docs.sh
commit 93d64096b5be8f34662b3e42ebfc09f0f6c76cd0
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Mar 2 16:57:37 2020 -0500
actually fix logic in deploy_docs.sh
deploy_docs.sh
commit 43774927b24085f791d3dde28b8e45b6891fa4e2
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Mon Mar 2 12:09:59 2020 -0800
March 2020 release notes
CHANGES.md
commit a4e471c9edfdc9dbfc6c5d4418fd6af5e97e5cd3
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Mon Mar 2 09:51:10 2020 -0800
merge conflicts
commit 58c140bbe8e0c55ae87f235a5bb8ec92c4dc2a4d
Merge: 88373ad6 6998d1a7
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Mar 2 10:11:26 2020 -0500
merge conflicts
commit ea39bd2a7335625a4f05228a8f0ee58ba3a31a48
Merge: 61712ed2 77f1870f
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Mar 2 10:08:45 2020 -0500
fix indexing
Source/MaestroMakeEta.cpp
commit 6e70a72f39c9b4486661ef167035705197bae295
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Thu Feb 27 16:01:49 2020 -0800
remove tiling when computing phisum
Source/MaestroAverage.cpp
commit 3bb1ddda04dd8b5c19dcef7555300953372fe100
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
Date: Fri Feb 28 12:09:51 2020 -0500
fix cuda compilation
Microphysics/networks/network.F90
commit 900d3c2b64d5b470ee58550598f4cab280cac4e6
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Fri Feb 28 08:57:48 2020 -0500
merge conflicts
Source/MaestroBCFill.cpp
commit 60588079628adae8d89a711227c10c6f16f6a36a
Author: Alice Harpole <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Thu Feb 27 11:36:56 2020 -0800
Remove omp threading when computing phisum
Source/MaestroAverage.cpp
commit ee7aacc20b449fafb20aacba8c84b685ec1fb035
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Wed Feb 26 13:44:35 2020 -0800
fix merge conflicts
Source/MaestroMakeEta.cpp
commit 9ac0e8d559e5d0c0de1753f74e63d6632236d9ff
Merge: 88373ad6 461ffd5c
Author: Doreen Fan <dfan@lbl.gov>
Date: Wed Feb 26 12:45:13 2020 -0800
Merge branch 'cpp_celltoedge' into cpp_average
commit ac67157831dedfca80146197144f06311ebcbbfb
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Tue Feb 25 16:17:57 2020 -0800
Merge branch 'cpp_psi_eta' into cpp_celltoedge
commit 464a20d49d58eabedd99d23d42d5d03ff0dca447
Author: Doreen Fan <dfan@lbl.gov>
Date: Tue Feb 25 15:56:52 2020 -0800
remove omp threading from MakeEtarho planar
Source/MaestroMakeEta.cpp
commit f1f452b6cc3d79c4b1d07d924698e3cce37c0a61
Author: Donald E. Willcox <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
Date: Wed Jan 8 12:05:49 2020 -0800
fix indentation
Exec/science/urca/tagging.F90
commit 6a7f6df3816069047a53079aae0cf5f10c613e38
Author: Donald E. Willcox <eugene.willcox@gmail.com>
Date: Wed Jan 8 12:05:25 2020 -0800
remove duplicates
Exec/science/urca/_parameters
commit 300f77ba0c88f706dc929f2b17cdd84d210d2e81
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Tue Feb 25 14:54:51 2020 -0500
merge conflicts
commit 61712ed27a7eaf40b50f2908f3297aabee09d3b8
Merge: 6bc7c8ac 3272ffa1
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Feb 25 14:53:26 2020 -0500
merge conflicts
commit 3272ffa1d743ac20a4b198953077d0fd1e1154d7
Merge: f54e5c9e 1192dae1
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Feb 25 14:47:32 2020 -0500
merge conflicts
commit f54e5c9ee2b4eb503da64e4ff069cca0c4c097a0
Author: Alice Harpole <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Tue Feb 25 11:43:56 2020 -0800
more index fixes
Source/MaestroMakeEta.cpp
commit 4b3cef34b3d272806b9d0c75d6408f6f6a211ce2
Merge: 7a8c4e3e d0a3ea03
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Tue Feb 25 09:25:05 2020 -0500
merge conflicts
commit 6bc7c8ac405418653515260801dcf1f46206ab0d
Merge: cd5fc0c8 7a8c4e3e
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
Date: Mon Feb 24 21:16:02 2020 -0500
Merge branch 'development' into cpp_makebeta0
commit 9e0fda36fd79fb4599a4d71c7461c10ee3d8fc1b
Merge: 257612d3 4c82b698
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Mon Feb 24 18:15:28 2020 -0800
Merge branch 'cpp_makebeta0' into cpp_enforce_HSE
commit 8d4d2c686b9b3f76794c951dbf7301608d249b6f
Author: Alice Harpole <harpolea@users.noreply.github.com>
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 <michael.zingale@stonybrook.edu>
Date: Mon Feb 24 21:00:18 2020 -0500
Merge branch 'development' into cpp_makebeta0
commit 257612d39628af58be694a7fc203c7ee6da3c0da
Author: Doreen Fan <dfan@lbl.gov>
Date: Mon Feb 24 16:23:52 2020 -0800
GPU index fix
Source/MaestroMakeEta.cpp
commit b4dc5bec393e546cce50fdebf10fff620bcfdbb1
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Feb 24 11:55:51 2020 -0500
fix static analysis complaints
Source/MaestroMakew0.cpp
commit 45ba8aeee3f9be3bf7aa76b551201ebc9ce5f7d5
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Feb 24 09:23:36 2020 -0500
GPU fixes
Source/MaestroAverage.cpp
commit 0ad642d2b5d9e7e2b2abd98c6112a37c9188bffd
Author: Alice Harpole <harpolea@users.noreply.github.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Fri Feb 21 09:55:55 2020 -0500
merge conflicts
commit c7b8a90d8a9d5164b3592c98c92b0bd7a6b76041
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Fri Feb 21 09:52:57 2020 -0500
yet more indexing fixes
Source/MaestroMakew0.cpp
commit 95d74f966033bd9939bb6917178ac5bde668b41e
Merge: 134af510 ec2b9c0d
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Fri Feb 21 09:39:53 2020 -0500
merge conflicts
commit 134af51070eccf658db68c24cfc1545a1f329bc6
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Fri Feb 21 09:38:51 2020 -0500
some more indexing fixes
Source/MaestroMakew0.cpp
commit ec2b9c0d1341389087c27884d28d1beb6c4a4bb1
Author: Doreen Fan <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
Date: Thu Feb 20 16:08:50 2020 -0500
merge conflicts
commit 55b06d593c87428707422b5d6f1577be58b65f8e
Merge: e04df68c 46b8def3
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu Feb 20 16:02:03 2020 -0500
fixed more array accesses
Source/MaestroMakew0.cpp
commit 257147b6a7a68f6aecb591e0ad62f0600578b1b3
Author: Doreen Fan <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
Date: Thu Feb 20 14:56:12 2020 -0500
better parameters
Exec/science/fully_convective_star/inputs_3d
commit 3711f2e890430279e2eb997344b184e21249b1a6
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Feb 20 14:48:09 2020 -0500
fix some array accesses
Source/MaestroMakew0.cpp
commit 9bc7ac4eb69a4b84a1066274b74c2d9b535838e0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu Feb 20 13:03:50 2020 -0500
fix illegal memory access
Source/MaestroMakew0.cpp
commit 31d92edc5893d0ef8c8fa11230918d938d636cd1
Merge: 7cb04840 f37eb3c0
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
Date: Wed Feb 19 13:41:54 2020 -0800
Merge branch 'development' into cpp_makew0
commit 0d7f06ed22f8581fb1a296a4ab8adbb42b0ebd72
Merge: f080692c 6f22b22b
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Feb 19 14:34:31 2020 -0500
GPU fixes
Source/MaestroForce.cpp
Source/MaestroMakeEdgeState.cpp
commit f080692cb55e697e3e64254d1351921c796cc6ab
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Tue Feb 18 15:23:11 2020 -0500
deleted file
Source/Src_nd/cell_to_edge.F90
commit ab2aea4cb08ca472955dcc6794ef16d286c2b7b3
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Tue Feb 18 10:19:43 2020 -0500
convert MakeEtarho
Source/MaestroMakeEta.cpp
commit 25d0a887d44b0a53358140a8ba8d35743fc42aad
Merge: a441c541 e18e6861
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Feb 17 14:54:53 2020 -0500
merge conflicts
commit 2fc9ba381f58f347018b487fc1f893d210417f2e
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Feb 17 14:42:57 2020 -0500
git merge broke things
Source/MaestroBaseStateGeometry.cpp
commit 603f2a86538615be1da3c17f21cfe701af1b59d2
Merge: 0c8db411 f1d73f7e
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Feb 17 13:26:41 2020 -0500
merge conflicts
commit f1d73f7e428f698f2d05b28ea886fa523fb47d6b
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Feb 17 10:25:33 2020 -0500
actually fix image formatting
sphinx_docs/source/regtest.rst
commit e2b8c1c3c2c1bdf3e3f7d59fa9b911721b27b686
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Feb 17 10:12:50 2020 -0500
fix image formatting
sphinx_docs/source/regtest.rst
commit 32fa8ffde442e76d86113418995b2b3c492a7a5e
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Feb 17 10:05:01 2020 -0500
added some documentation on travis
sphinx_docs/source/regtest.rst
commit 0c8db411331d7c6d9870e117c321e41ddff9ca0e
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Fri Feb 14 15:43:07 2020 -0500
merge conflicts
commit a2309c4cba0ed9ca3d1efa162a94a21bdd15f5e8
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Fri Feb 14 15:36:08 2020 -0500
started converting make_psi
Source/MaestroMakePsi.cpp
Source/Make.package
commit 7097d2ebbd387ff318d6416489c253a77378658a
Author: Alice Harpole <harpolea@users.noreply.github.com>
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 <ajacobs@pa.msu.edu>
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 <aliceharpole@gmail.com>
Date: Fri Feb 14 15:27:49 2020 -0500
merge conflicts
commit 6367cb53997762ef81007f6c3f2ca65f4165492b
Merge: 38eb992e 6e233d2c
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Fri Feb 14 15:26:56 2020 -0500
merge conflicts
commit 06fdffc618c30bec5a30588f77b39278d3ca4972
Merge: a0a564c1 6e233d2c
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Fri Feb 14 15:07:51 2020 -0500
fix static analysis complaints
Source/MaestroEnforceHSE.cpp
commit 2ae8db487f5d8e8a3b6ce9b85f09b7b76b80519e
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Fri Feb 14 10:28:42 2020 -0500
GPU fixes
Source/MaestroMakeBeta0.cpp
commit 47621f21b9d4537a65a2399d1354848a138d7ddc
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Thu Feb 13 17:38:40 2020 -0800
Initialize variables after reading in checkpoint files
Source/MaestroInit.cpp
commit 6d9bfec24a8bd3076513cdbe9ae090fd04c88660
Author: Doreen Fan <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu Feb 13 15:48:07 2020 -0500
fixed merge conflicts
commit 96e5f373b58888edf83a8626e892b7ab4569ddad
Merge: fd644118 d5d5ef1f
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu Feb 13 15:26:56 2020 -0500
git checkout --track
Util/scripts/pr_tab_remover.sh
commit 5e2d98ac98e5a8667d137cdf251a5ed147137f76
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Feb 13 15:19:13 2020 -0500
set remote url
Util/scripts/pr_tab_remover.sh
commit 867fc7684d9807d7535acb677f74074421d50fc3
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu Feb 13 14:49:21 2020 -0500
push to ssh_repo
Util/scripts/pr_tab_remover.sh
commit 7c567faebd100e970858009e98704c34e1be53c2
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Feb 12 16:43:14 2020 -0500
tidying up
Source/MaestroMakew0.cpp
commit 4417fe4b030b944ff9280d518b26a9796d92f1a2
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Feb 12 16:40:20 2020 -0500
convert makew0sphericalirreg
Source/Maestro.H
Source/MaestroMakew0.cpp
commit 1bb32afcf4d26a1dd67792ad81402c5d9c7398c6
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Feb 12 16:31:45 2020 -0500
converted makew0planarvarg
Source/Maestro.H
Source/MaestroMakew0.cpp
commit f209fb6fcc90295021e1508a8072ebca4499b9fa
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Fri Feb 7 08:32:28 2020 -0500
converting make_grav
Source/MaestroMakeGrav.cpp
commit 3140a08be840f1a994c0a18a25cb3ebdb58d550e
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Feb 5 17:06:17 2020 -0500
converted makew0spherical
Source/Maestro.H
Source/MaestroMakew0.cpp
commit 1fd8c1bd0a2e3b02480a9d32cd67453f025fb626
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Wed Feb 12 13:44:54 2020 -0800
bugfix: fix time output in checkpoint file
Source/MaestroCheckpoint.cpp
commit c337b37d5d18c1166f233197ea922e60830c4331
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Feb 12 16:43:14 2020 -0500
tidying up
Source/MaestroMakew0.cpp
commit cad1b1e2e838d62b8126b98e651f1750a3694ad1
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Feb 12 16:40:20 2020 -0500
convert makew0sphericalirreg
Source/Maestro.H
Source/MaestroMakew0.cpp
commit b4b293ac77a27bc6c90d13d6acc7e22d76cd15c8
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed Feb 12 16:31:45 2020 -0500
converted makew0planarvarg
Source/Maestro.H
Source/MaestroMakew0.cpp
commit 4613c8d0787d0296ef3d874f15c8c050379a8281
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Feb 12 09:25:27 2020 -0500
merge with development
commit 2d4aa6244aa62ad661d2a6445dbedcc080a8a9c8
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <harpolea@users.noreply.github.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Tue Feb 11 13:48:41 2020 -0800
small typo
Source/MaestroFill3dData.cpp
commit 7e6b535966b772450b2fd5e0278ea7e4fe85a448
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Tue Feb 11 14:37:42 2020 -0500
fixed rsa keys
Util/scripts/pr_tab_remover.sh
commit 2d2c99baa21412c5c5845eda49a5c3d0a37fb634
Author: Alice Harpole <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Tue Feb 11 12:10:31 2020 -0500
uncommented git push
Util/scripts/pr_tab_remover.sh
commit b50010376f60166416082e10d6be09e205dcc6ac
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Tue Feb 11 12:02:01 2020 -0500
added .sh
Util/scripts/pr_tab_remover.sh
commit 7631286cf24e0295999cdfbac3d9300d31c3520e
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <harpolea@users.noreply.github.com>
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 <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
Date: Mon Feb 10 15:43:16 2020 -0500
turn off pert
Exec/science/fully_convective_star/inputs_3d
commit 8aaaac54aaa26d28413d9bf227146d86294f41ba
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Feb 10 14:22:05 2020 -0500
merging with development
commit 49f85fc09b17660c98c0fe21d601201fc3b08a6c
Merge: 918d9636 9449b73e
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Feb 10 10:06:37 2020 -0500
fix 2d GPU compilation
Source/MaestroVelPred.cpp
commit b5f0b0c3bcc2cdd193268b2a2a446c4a1ef1e4e0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
Date: Fri Feb 7 10:54:03 2020 -0800
add slope_order=2 to regression test
commit 819eb8ac9fd58d66355f95c43e0d002da5c1df53
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
Date: Fri Feb 7 09:35:30 2020 -0500
fix 2d compilation
Source/MaestroMakeFlux.cpp
commit 0488c3003e06f5e9291a7da49a00b16da711182e
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Fri Feb 7 08:32:28 2020 -0500
converting make_grav
Source/MaestroMakeGrav.cpp
commit 99479701e8f5f4b7149331ed5b0de8b5eb2f7d1f
Merge: a655c5f6 9ec71e68
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <harpolea@users.noreply.github.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Feb 5 17:06:17 2020 -0500
converted makew0spherical
Source/Maestro.H
Source/MaestroMakew0.cpp
commit 4ac045583a98dad70bb29a233fcdf5f0dc5cc80d
Author: Alice Harpole <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
Date: Wed Feb 5 15:23:53 2020 -0500
change tagging
Exec/science/fully_convective_star/_parameters
commit 6eebd7c3c75a25612f042f7cdd96dd70ce94833d
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Mon Feb 3 17:38:00 2020 -0800
Merge branch 'development' into cpp_fill_3d_data
commit 1a041f5dcc8a2d843ae20e3b7079597d29c7d1cc
Author: Alice Harpole <harpolea@users.noreply.github.com>
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 <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
Date: Mon Feb 3 17:23:25 2020 -0500
Merge branch 'development' into cpp_mac_solver
commit b5721cd7d485d802098d4aec76c147ab7a046250
Author: Alice Harpole <harpolea@users.noreply.github.com>
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 <dfan@lbl.gov>
Date: Mon Feb 3 09:56:46 2020 -0800
Feb 2020 release notes
CHANGES.md
commit 175f9c86e378b2b1638f5a11486e6129e0473a1b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Feb 3 08:42:09 2020 -0500
a script to clean builds
Exec/clean_probs.sh
commit 3a199d08951c79f8f19062229902a4f951b3b63e
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu Jan 30 14:45:03 2020 -0500
Merge branch 'development' into cpp_advection
commit b1362bc3fe41c699e356b91638a381b32dadc25a
Merge: 6725f6aa 38f18ee2
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Jan 30 14:44:35 2020 -0500
Merge branch 'development' into cpp_nodal_proj
commit 221b2432235f9d1900e8d6df96bf78a27eb721de
Merge: 6a2fe27f 38f18ee2
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu Jan 30 14:43:48 2020 -0500
Merge branch 'development' into cpp_mac_solver
commit 38f18ee2ae39f2f6c26055f3a8a2d1112b0e779b
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu Jan 30 09:38:30 2020 -0500
merge with development
Source/MaestroNodalProj.cpp
commit 5416e1d053320402f1b596dea8981f8e68af740e
Merge: f959c3ab ba5d2844
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu Jan 30 09:32:55 2020 -0500
merge with development
Source/MaestroFill3dData.cpp
commit 979a3c5898139b365aa4c5ce1dbaa2a86899e0f4
Merge: 14b40225 ba5d2844
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <harpolea@users.noreply.github.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Jan 29 17:32:29 2020 -0500
fix merge conflicts with development
commit 933b5438a7d22063c559dca6bd4f4ccb6382beac
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Jan 29 12:03:38 2020 -0500
converted make_rhoh_flux_sphr
Source/MaestroAdvection.cpp
commit cb94d69ba63482f74cb3fa1118248b29b4ce563f
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Jan 29 09:30:29 2020 -0500
clean up and fix spherical
Source/MaestroAdvection.cpp
commit a8c1400810a0c4ba7f383a8ac70329ebe0ae4215
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Jan 27 15:37:12 2020 -0500
make sure that Sbar gets initialized
Source/MaestroInit.cpp
commit 3620f608c4f02b68bfae31a383f26613dc528c7e
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Jan 27 13:27:16 2020 -0500
GPU fixes
Source/MaestroFill3dData.cpp
commit 3b3653a134d3a3b18ade892d43e6808c313076fb
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Jan 27 09:00:17 2020 -0500
converted addw0
Source/MaestroFill3dData.cpp
commit 275c3fbb5a00f7d4cfa003a9c01c7c15ddbf8e09
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Fri Jan 24 13:06:20 2020 -0500
converted mult_beta0
Source/MaestroMacProj.cpp
Source/MaestroMacProj_level.cpp
commit 99aed41b5cc349d2e96914294b5e40d67ae0246f
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <harpolea@users.noreply.github.com>
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 <michael.zingale@stonybrook.edu>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Fri Jan 17 09:45:02 2020 -0500
fig bug ul -> ur
Source/Src_nd/velpred.F90
commit 84cc53f0e870a60af57bf2f6e9e5e408cb52bd55
Author: Alice Harpole <harpolea@users.noreply.github.com>
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 <aliceharpole@gmail.com>
Date: Wed Jan 15 10:28:44 2020 -0500
fix merge conflicts
Source/Maestro.H
commit f0900e1bf7f089f62fa9abadf4f867e989ec1cf0
Author: Alice Harpole <harpolea@users.noreply.github.com>
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 <harpolea@users.noreply.github.com>
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 <eugene.willcox@gmail.com>
Date: Fri Jan 10 16:53:18 2020 -0500
Merge branch 'development' of github.com:amrex-astro/MaestroEx into development
commit ebbe794c0d83cddf54d48d6c94469fbfc7471d94
Author: dwillcox <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <harpolea@users.noreply.github.com>
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 <aliceharpole@gmail.com>
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 <harpolea@users.noreply.github.com>
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 <michael.zingale@stonybrook.edu>
Date: Fri Jan 3 15:40:13 2020 -0500
update refs
CITATION
commit e3f5c6ef0c655d56f2121ede2f850842b1e5f092
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Fri Jan 3 12:34:28 2020 -0800
move RELEASE_NOTES into CHANGES.md
CHANGES.md
RELEASE_NOTES
commit 2d2f67017c4a8b6f48043e39cd522fad710a0077
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Fri Jan 3 10:24:52 2020 -0800
Jan 2020 release notes
RELEASE_NOTES
commit e94f791c1c0ec9ffa85b107e92d87c3223b334d7
Merge: 6c0a681b b9652b4b
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
Date: Tue Dec 31 20:49:15 2019 -0500
Merge branch 'master' into development
commit 2e4edf5064d0a47c7d561f4618e3463509fd4d5f
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Dec 31 13:02:05 2019 -0500
fix intra initialization
Source/MaestroCheckpoint.cpp
Source/MaestroInit.cpp
commit 1853787016e204bead84116a955f2b8e5ca4c2a5
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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
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_eos/Make.package
Exec/unit_tests/test_eos/initdata.F90
Exec/unit_tests/test_eos/test_eos.F90
Exec/unit_tests/test_projection/initdata.F90
Exec/unit_tests/test_react/Make.package
Exec/unit_tests/test_react/base_state.F90
Exec/unit_tests/test_react/initdata.F90
Exec/unit_tests/test_react/problem_functions.F90
Source/Maestro_F.H
Source/Src_nd/Make.package
Source/Src_nd/average.F90
Source/Src_nd/base_state.F90
Source/Src_nd/cell_to_edge.F90
Source/Src_nd/fill_3d_data.F90
Source/Src_nd/initdata.F90
Source/Src_nd/inlet_bc.F90
Source/Src_nd/maestro_init.F90
Source/Src_nd/make_beta0.F90
Source/Src_nd/make_edge_state.F90
Source/Src_nd/make_w0.F90
Source/Src_nd/regrid.F90
Source/Src_nd/rotation.F90
Source/param_includes/Make.package
Source/param_includes/state_sizes.F90
Util/diagnostics/Make.package
Util/diagnostics/initdata.F90
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 <aliceharpole@gmail.com>
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 <arfon@users.noreply.github.com>
Date: Thu Dec 19 13:20:00 2019 -0500
Adding AAS DOI (#128)
paper/paper.md
commit 030bfb6ba2185b431af6d6643ffb55ae61f91136
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Dec 16 17:12:26 2019 -0500
offload cell-centered mac solver
Source/MaestroMacProj.cpp
commit 8ebc8efe85e0abf7bcc4587007e895582486ba59
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 16 16:43:23 2019 -0500
fix compilation
Microphysics/networks/general_null/actual_rhs.F90
commit 9c7ed173d4887f6684f4e97d006b9edb2ffa25eb
Author: Alice Harpole <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dwillcox@users.noreply.github.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <michael.zingale@stonybrook.edu>
Date: Tue Dec 10 15:09:30 2019 -0500
Revert "rename directories to be lower case :)"
This reverts commit d8f5dacb171d6924b7e15357dd6f51335457b54d.
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
Exec/SCIENCE/ecsn/probin_regression
Exec/SCIENCE/ecsn/tagging.F90
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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/flame/inputs_2d_smallscale
Exec/SCIENCE/flame/inputs_2d_smallscale.testsuite
Exec/SCIENCE/flame/inputs_2d_smallscale_sdc
Exec/SCIENCE/flame/inputs_3d_smallscale
Exec/SCIENCE/flame/inputs_3d_smallscale.testsuite
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
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Exec/SCIENCE/plane_parallel_star/inputs_2d
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Exec/SCIENCE/plane_parallel_star/tagging.F90
Exec/SCIENCE/rotating_star/15m_500_sec.hse.6400
Exec/SCIENCE/rotating_star/GNUmakefile
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Exec/SCIENCE/rotating_star/Problem.cpp
Exec/SCIENCE/rotating_star/_parameters
Exec/SCIENCE/rotating_star/analysis/initial_model.py
Exec/SCIENCE/rotating_star/initdat.256
Exec/SCIENCE/rotating_star/initdat.320
Exec/SCIENCE/rotating_star/initdata.f90
Exec/SCIENCE/rotating_star/inputs_2d
Exec/SCIENCE/rotating_star/inputs_3d_C
Exec/SCIENCE/rotating_star/inputs_test
Exec/SCIENCE/rotating_star/model_parser.f90
Exec/SCIENCE/rotating_star/probin
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Exec/SCIENCE/rotating_star/tagging.F90
Exec/SCIENCE/sub_chandra/GNUmakefile
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Exec/SCIENCE/sub_chandra/README.md
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/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/SCIENCE/urca/GNUmakefile
Exec/SCIENCE/urca/Make.package
Exec/SCIENCE/urca/_parameters
Exec/SCIENCE/urca/analysis/.ipynb_checkpoints/Plot-Thermo-Slopes-checkpoint.ipynb
Exec/SCIENCE/urca/analysis/GNUmakefile
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/_parameters
Exec/SCIENCE/urca/analysis/fad_excess.f90
Exec/SCIENCE/urca/analysis/fconv_radial.f90
Exec/SCIENCE/urca/analysis/fconv_slopes.f90
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Exec/SCIENCE/urca/analysis/scripts/lineout-field-testing
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Exec/SCIENCE/urca/analysis/scripts/volume-plot-ye
Exec/SCIENCE/urca/analysis/setup.py
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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_urca_model_equilibrium.5120
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/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_urca_model_equilibrium.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/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_urca_model_equilibrium.5120
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commit 92d1c08bc6ebc435df9981ea683e250b4edd8e61
Merge: 3737e637 758e8024
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
Date: Tue Dec 10 15:07:52 2019 -0500
rename to lowercase
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commit 758e80241a379921b617c7c5c37f3720049583f2
Merge: 1603fd5d 7d37d24b
Author: Donald E. Willcox <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <michael.zingale@stonybrook.edu>
Date: Tue Dec 10 15:03:14 2019 -0500
rename directories to be lower case :)
syncs with Castro
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commit 7d37d24b165f0e706f1ada52984ae51ae4c1ca8f
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
Date: Tue Dec 10 11:40:53 2019 -0800
Fix module imports.
Exec/SCIENCE/urca/analysis/scripts/lineout-field
commit 1823b1e533dfb85d4b91dbe0bb2ffd754bb4f6ed
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <aliceharpole@gmail.com>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <michael.zingale@stonybrook.edu>
Date: Wed Dec 4 17:53:33 2019 -0500
set success
Source/Src_nd/burner_loop.F90
commit 5f26089bc91db063131ee7382a943ea5033e36a7
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Mon Dec 2 14:21:25 2019 -0800
Dec 2019 Release Notes
RELEASE_NOTES
commit 8b536e40d6bfa99063383cf7f936e0533504287b
Merge: 576ba079 7f4c42f2
Author: Doreen Fan <dfan@lbl.gov>
Date: Mon Dec 2 14:02:44 2019 -0800
Merge branch 'development'
commit 7f4c42f29805dfd59b56238b396ac708d2349c63
Author: Doreen Fan <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
Date: Thu Nov 21 18:51:03 2019 -0500
add JOSS badge
README.md
commit 5ea7c2f2729aa4721d79641b69758ef6ea661ecf
Merge: 9c39eda1 5779950f
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Thu Nov 21 14:43:15 2019 -0800
change SIMPLIFIED_SDC to SDC
Microphysics/networks/burner.F90
commit 9c39eda1cc6cb4a7e53ae35f587eeeaafff8ea45
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 20 19:22:49 2019 -0500
add Zenodo badge
README.md
commit 2d9978a0013c7acad200ff158f2215243c00c39e
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 20 19:20:46 2019 -0500
fix some .zenodo errors
.zenodo.json
commit cf0f9014d71cb77abcb112997bcefb31961a834b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Wed Nov 20 19:18:02 2019 -0500
fix tags
.zenodo.json
commit 54aa62e712c1560ab47ca6537df3aa0bf8e3f8e9
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <aliceharpole@gmail.com>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <harpolea@users.noreply.github.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
Date: Fri Nov 15 18:09:42 2019 -0500
fix name
Source/MaestroPlot.cpp
commit 145da65dbc6929e855a72c5315b34480d962d68d
Author: Alice Harpole <aliceharpole@gmail.com>
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 <arfon@users.noreply.github.com>
Date: Fri Nov 15 10:18:45 2019 -0500
Update paper.md (#123)
paper/paper.md
commit a8aa9cc159dbda8bd1ec5907fe89706b62e2c57d
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Thu Nov 14 15:25:28 2019 -0500
updated inputs file
Exec/SCIENCE/rotating_star/inputs_3d_C
commit 32899595c58eacd8b54f7b7c23c7e4a5048e9009
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
Date: Thu Nov 14 11:26:47 2019 -0500
fix some formatting
sphinx_docs/source/makefiles.rst
commit da3a10fe6887cbedb25550672ba8ffec731e1208
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Nov 14 08:34:20 2019 -0500
a bunch of cleaning
sphinx_docs/source/makefiles.rst
commit 5c68d334a60830d9e24d865649b4c61fe46c380f
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Nov 13 13:13:54 2019 -0500
Fix GPU compilation
Source/Maestro.H
commit 65c30c584b9afd6870354cfa3deb448b0f355f84
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Thu Nov 7 12:54:17 2019 -0800
Merge branch 'development' into sdc
commit b7a0b0e89b3a580f5c161726c097c39b1c335668
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
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 <harpolea@users.noreply.github.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Sun Nov 3 07:59:00 2019 -0500
fix gpu compilation
Source/MaestroRhoHT.cpp
commit 1d7e89365379eea57680f738f271c93d7f28e513
Author: Doreen Fan <dfan@lbl.gov>
Date: Fri Nov 1 14:31:27 2019 -0700
Nov 2019 Release Notes
RELEASE_NOTES
commit 53b6da91821be9e0d69c43abde6a1b7d6ea9ca46
Author: Doreen Fan <dfan@lbl.gov>
Date: Thu Oct 31 11:40:31 2019 -0700
only call estdt_divu when spherical==1
Source/MaestroDt.cpp
commit 9ab5232c548c58333abd6c711efd856577d1bc32
Author: Alice Harpole <harpolea@users.noreply.github.com>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <AJNonaka@lbl.gov>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
Date: Mon Oct 28 13:21:26 2019 -0700
Merge branch 'development' into sdc
commit 7f7b6ddee8beb518feba827a5f1e27b384a65852
Author: Doreen Fan <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Fri Oct 25 16:47:06 2019 -0700
bugfix: fill w0_cart after regrid
Source/MaestroRegrid.cpp
commit 03ef599f9fdfa3eaa9542ed79329abf332d46759
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
Date: Fri Oct 25 15:26:03 2019 -0400
remove old header
README.md
commit 818018213d62951b8e2eecd457cfb18dee3fd881
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Fri Oct 25 15:24:50 2019 -0400
add logo
README.md
commit 34bed0a16a18b04ea4257a94c503453650c3fbc5
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Thu Oct 24 16:01:07 2019 -0700
Merge branch 'development' into sdc
commit 3522513a2bb2760c95c8540c7ca5c0e86b2940b9
Author: Doreen Fan <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Tue Oct 22 17:06:47 2019 -0700
JOSS paper updates
paper/paper.bib
paper/paper.md
commit fbf9db7b0b5ccbf085d7b9d7a47783b16c67f484
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <AJNonaka@lbl.gov>
Date: Tue Oct 22 09:25:26 2019 -0700
acknowledge original MAESTRO authors
paper/paper.md
commit b32bffe6daf261f63788b96823769c85ccd878c9
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Tue Oct 22 11:31:59 2019 -0400
added script for producing sliceplots
Util/scripts/plotsinglevar.py
commit 86cceb7b5bdc0c5ee0912e927dbea99dc16b16d8
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 22 11:02:05 2019 -0400
remove the hidden bitmap
Util/logo/maestroex_logo.svg
commit 986a4afb23d93f1c1f351551ba799185f89508cd
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Tue Oct 22 10:57:46 2019 -0400
add logo proposal
Util/logo/maestroex_logo.svg
commit b05960c5a0b433a76cf3fc1504d9c7d9dc22ecc8
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Thu Oct 17 09:34:22 2019 -0700
Merge branch 'development' into sdc
commit e23fca246fedc1842298d24b2a343e9375f7a313
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
Date: Wed Oct 16 18:42:41 2019 -0700
Merge branch 'development' into sdc
commit b76d17aa6247a9e53215d6a69b4d9a676d6444f6
Author: Doreen Fan <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
Date: Tue Oct 15 11:11:54 2019 -0400
added mailing list back in
README.md
commit d483be020af546047a05372834960f192cf5a375
Merge: 0eb8340d f6645448
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
Date: Fri Oct 11 14:56:27 2019 -0700
Merge branch 'development' into sdc
commit b2253352ee9e0dd7820c309484161200d87a211c
Author: Philipp Edelmann <edelmann@fs.tum.de>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Tue Oct 8 11:26:48 2019 -0400
fixed a typo
sphinx_docs/source/getting_started.rst
commit 0ac47ae2ab1b763eab726513ce0985b63dc88d56
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Wed Oct 2 07:58:14 2019 -0700
bugfix: p0_cart needs a ghost cell
Source/MaestroMakeS.cpp
commit 5c87ed46e64478c0cd8df9e82e0c06c10fdfffed
Author: Doreen Fan <dfan@lbl.gov>
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 <name> 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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
Date: Mon Sep 23 11:01:29 2019 -0700
bcs_u -> bcs
Source/MaestroAdvection.cpp
commit ba059073cb1ae9bd93fe5deb687e776837fbeb59
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Mon Sep 23 12:16:19 2019 -0400
RealVector is now an alias for amrex::GPU:ManagedVector<amrex::Real>
Source/Maestro.H
commit 6fbdda37c093364cd5d9491f1fcfcd10f88aac9e
Author: Alice Harpole <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
Date: Sun Sep 22 22:55:25 2019 -0400
fix typo
sphinx_docs/source/pert.rst
commit 89a5401a52aebaf474d21b86068117e769a48745
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
Date: Sat Sep 21 16:03:01 2019 -0400
Merge branch 'master' into development
commit a6871374e052d84e4eadac2263b3a829614f4eb5
Author: Alice Harpole <harpolea@users.noreply.github.com>
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 <AJNonaka@lbl.gov>
Date: Fri Sep 20 09:53:34 2019 -0700
corner ghost cell issue fixed
Source/MaestroAdvection.cpp
commit 0f0db8dad724290348507af328adc4bea7d4fea5
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Fri Sep 20 09:33:48 2019 -0700
Update README.md
README.md
commit 5330d0ed942b3498b694ea366cd5700bd30b43d6
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Thu Sep 19 18:02:28 2019 -0700
Merge branch 'development' into sdc
commit 00624285f2f9b3fec902c8337c95e199aab8526f
Author: Doreen Fan <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
Date: Thu Sep 19 14:24:32 2019 -0700
Merge branch 'development' into sdc
commit 6a62a89718d77c2b5d58c66ef07e83949b9b4b7b
Merge: 8e7631dc fac19708
Author: Doreen Fan <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Thu Sep 19 10:30:20 2019 -0700
indentation only
Source/Maestro_F.H
commit d2bfea6b1b1e3a3074ef4b068a071bfc7d97dea1
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <harpolea@users.noreply.github.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <harpolea@users.noreply.github.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu Sep 5 09:33:55 2019 -0400
Merge branch 'development' into gpu_moved_base_state
commit df731d9a4ff38d568fe04651bf40ce23080a6310
Author: Alice Harpole <aliceharpole@gmail.com>
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 <harpolea@users.noreply.github.com>
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 <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <arfon@users.noreply.github.com>
Date: Tue Sep 3 20:24:57 2019 -0400
Update paper.bib
paper/paper.bib
commit b14f5131360963c1f924607bdfffeb291224d7f8
Author: Arfon Smith <arfon@users.noreply.github.com>
Date: Tue Sep 3 20:24:25 2019 -0400
Matching quote fix in title
paper/paper.md
commit c1cb719f933d9cb73ef96e44291c50441acee4f5
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <harpolea@users.noreply.github.com>
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 <AJNonaka@lbl.gov>
Date: Tue Sep 3 12:03:53 2019 -0700
Sept. 2019 Release Notes
RELEASE_NOTES
commit 8e7631dc2717d385cb104bc29f19d48fc653bec8
Author: Doreen Fan <dfan@lbl.gov>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <michael.zingale@stonybrook.edu>
Date: Fri Aug 30 19:00:32 2019 -0400
fix formatting
sphinx_docs/source/flowchart.rst
commit e68d0b5a17deb37d882df629a26c58444015b040
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Fri Aug 30 15:35:44 2019 -0700
add doi
paper/paper.bib
commit a2321ebfae054fcbe266393a62c2c9f317143ab0
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Thu Aug 29 17:30:40 2019 -0700
add intra to regrid subroutines
Source/MaestroRegrid.cpp
commit e4bf19baf4de56cdd49845de325ab2bd302c7fda
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Tue Aug 27 17:08:39 2019 -0700
notes on w0
sphinx_docs/source/introduction.rst
commit d5accf23a9eed54656cb55c9dd2c473c0da8a207
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
Date: Mon Aug 26 15:31:19 2019 -0700
code cleanup
Source/MaestroAdvanceSdc.cpp
Source/MaestroReact.cpp
commit c720a389fbe042b77441ded349fc804c64317ca6
Author: Doreen Fan <dfan@lbl.gov>
Date: Mon Aug 26 15:10:21 2019 -0700
second pass at joss paper
paper/paper.md
commit c754b44c7e5fd11caa94b2f1ac7fc2f0a515c4d1
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Thu Aug 22 15:32:51 2019 -0700
bug fix: initialization of intra
Source/MaestroInit.cpp
commit 716dae56c967b178744ba626a81a4ba2e7a7c7d3
Author: Doreen Fan <dfan@lbl.gov>
Date: Thu Aug 22 12:28:21 2019 -0700
bug fix: use ReactSDC when plotting
Source/MaestroPlot.cpp
commit eeb5655b0147d3b01668af26f164d57c37637435
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
Date: Wed Aug 21 08:08:07 2019 -0400
fix title lengths
sphinx_docs/source/architecture.rst
commit ca1be4a47259c1fee0f19aa21ec7389fa74a0116
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
Date: Wed Aug 21 07:56:31 2019 -0400
quite some warnings
sphinx_docs/source/Godunov.rst
commit 8910306341c58bd79b1a679ea3e806cc7f828ca1
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Tue Aug 20 15:54:42 2019 -0700
minor changes to intro
sphinx_docs/source/introduction.rst
commit 2bf0315691f0917cb751fb2bd58ba8ad3114181a
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Tue Aug 20 09:48:43 2019 -0700
test commit
sphinx_docs/source/flowchart.rst
commit de0637f3f0ba06ddd9f6c33bc26ec3dfe124d04b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
Date: Tue Aug 20 10:15:00 2019 -0400
update testing
README.md
commit 7beab29cf9a9e04b2c53a6b216822ee037250bb7
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
Date: Thu Aug 15 19:26:19 2019 -0700
added divu_iter subroutine for sdc
Source/MaestroInit.cpp
commit df1a7250360799341096b672bddc6c9b422ca589
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Mon Aug 12 12:43:42 2019 -0700
started outline of sdc advance routine
Source/MaestroAdvanceSdc.cpp
commit 11ce6e07336ec7dada24aa29aa91659af1b00d51
Author: Alice Harpole <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Thu Aug 8 14:56:14 2019 -0700
fix a syntax error
sphinx_docs/source/addproblem.rst
commit 61e824180ea9a4c962a1f4c96f65cda39ad9471a
Author: Doreen Fan <dfan@lbl.gov>
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 <harpolea@users.noreply.github.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
Date: Thu Aug 8 14:30:10 2019 -0400
fix some math rendering
sphinx_docs/source/introduction.rst
commit aaca7869d68247b1805a1bdc000191227467e100
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Thu Aug 8 14:24:00 2019 -0400
center figs
sphinx_docs/source/initial_models.rst
commit 14ed8149fb1e03b2327a068cddbc7f680aae50ae
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <AJNonaka@lbl.gov>
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 <michael.zingale@stonybrook.edu>
Date: Thu Aug 8 10:31:53 2019 -0400
add contributing statement
README.md
commit 966188525f603204c08c02ba14f464d4df229ac6
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
Date: Wed Aug 7 19:18:01 2019 -0400
disable sdc
sphinx_docs/source/index.rst
commit 45a150af6116f358cf80f08dd66e97d1cbf39266
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
Date: Wed Aug 7 14:50:27 2019 -0700
doc updates
sphinx_docs/source/getting_started.rst
commit 23d1317df60a31a8fc71019944ec26ac5472a090
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
Date: Tue Aug 6 21:20:05 2019 -0400
switch color to inherit
sphinx_docs/source/_templates/layout.html
commit 6c34eea431af36ab3d649f7a4a08b7a7be3dab2b
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
Date: Tue Aug 6 17:26:20 2019 -0700
updated README to include more info
README.md
commit 8f789e03eaa445ca5e33c45b7f47675e27d3f855
Author: Alice Harpole <harpolea@users.noreply.github.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Thu Aug 1 09:15:36 2019 -0700
August 2019 Release Notes
RELEASE_NOTES
commit 3b8c78348917cc9f5de7668a5297f2c35b634736
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Tue Jul 2 13:07:46 2019 -0700
July 2019 release notes
RELEASE_NOTES
commit 2bd1c2d4774684cdddabda29279802122e65bbe5
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dewillcox@lbl.gov>
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 <dewillcox@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Jun 19 10:24:40 2019 -0400
Merge branch 'code_comp' into development
commit 2a188ae512e60ae2e89368437340dd8a8d31d6e1
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Jun 12 17:39:56 2019 -0400
Added BSD-3 license
LICENSE
commit 89b9f9ee25f3f262e0ea86dcf682a10636db7f07
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <weiqunzhang@lbl.gov>
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 <dfan@lbl.gov>
Date: Mon Jun 3 14:53:48 2019 -0700
June 2019 release notes
RELEASE_NOTES
commit e4d10115bcf5680d7a0793dd22988c83b4c0950a
Author: Alice Harpole <harpolea@users.noreply.github.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu May 30 10:09:55 2019 -0400
nc_f -> nscal
Source/Src_nd/update_scal.F90
commit dc2b39fc73a82598ddfdfd75de85daa25919f1f1
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed May 29 15:35:18 2019 -0400
tilebox -> growntilebox
Source/MaestroThermal.cpp
commit 8f97f79a47e63b47fe663e5a1cf24e4e0c181ca8
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Wed May 29 15:21:46 2019 -0400
growntilebox -> tilebox
Source/MaestroThermal.cpp
commit c0f0b1dcb4ce7380c63dde8671be69573d6017d9
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue May 28 17:26:26 2019 -0400
removed factor of 1/2
Source/MaestroMakeS.cpp
commit 5525495e2a5a146590cd1fa24a55024a706b55c9
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue May 28 17:24:50 2019 -0400
added missing factor of 1/2
Source/MaestroMakeS.cpp
commit 65bb726613ec673610ccdee1aa2a50e13b1d3fff
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue May 28 17:23:49 2019 -0400
added missing dr
Source/MaestroMakeS.cpp
commit 4a012f6f6428e6274965788b9bb3c756de881269
Author: Alice Harpole <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <harpolea@users.noreply.github.com>
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 Vector<Real>s 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 <weiqunzhang@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <eugene.willcox@gmail.com>
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 <dewillcox@lbl.gov>
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 <dewillcox@lbl.gov>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Wed May 1 11:14:40 2019 -0700
May 2019 release notes
RELEASE_NOTES
commit d217929227fdc72f257995c550324ee0519bfb69
Merge: 47f14c15 383146a2
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <michael.zingale@stonybrook.edu>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
Date: Thu Apr 25 13:19:31 2019 -0400
use Urca tagging
Exec/SCIENCE/ecsn/tagging.F90
commit fa5596788bcfee69fc3c2ec735f97dc53c122598
Author: dwillcox <eugene.willcox@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <eugene.willcox@gmail.com>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Mon Apr 22 12:41:31 2019 -0700
Merge branch 'development' into actual_plot_variables
commit 6d1d40a32abc1c2da9743f2024ab898f89a30ce8
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Mon Apr 22 12:07:17 2019 -0700
add momentum to plotfile
Source/MaestroPlot.cpp
commit 9d211ee318cf0526cbf209eab054fcf489c4715d
Merge: 6c8289ae d781b9e2
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Fri Apr 19 11:22:19 2019 -0700
Remove ambiguity of psi
Source/Maestro.H
Source/MaestroMakeS.cpp
commit a57fc46e321ff769f6f40a33ca5fd5748e955894
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dewillcox@lbl.gov>
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 <dewillcox@lbl.gov>
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 <dewillcox@lbl.gov>
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 <dewillcox@lbl.gov>
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 <dewillcox@lbl.gov>
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 <dewillcox@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Apr 17 12:55:06 2019 -0400
remove fstring
Util/scripts/convert_backtrace.py
commit c4a1bdb984f7cafdac6a701a80e74c9ebe40937a
Author: Alice Harpole <aliceharpole@gmail.com>
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 <dwillcox@users.noreply.github.com>
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 <dfan@lbl.gov>
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 <eugene.willcox@gmail.com>
Date: Tue Apr 16 21:52:12 2019 -0400
Merge branch 'development' of github.com:amrex-astro/MaestroEx into development
commit 43bcadfeb9749f78639c8f608c3a4381c29391e1
Author: dwillcox <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
Date: Mon Apr 15 15:45:54 2019 -0400
remove old debugging code
Source/param/runtime.probin.template
commit 954e64d0d6dea213c1bc2d1a9109a19e6ee6f4aa
Author: Doreen Fan <dfan@lbl.gov>
Date: Fri Apr 12 17:35:27 2019 -0700
add some OMP calls
Source/Src_nd/make_w0.f90
commit 962691efc2d81f36f5d549e362a796f0a8a4098c
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <eugene.willcox@gmail.com>
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 <eugene.willcox@gmail.com>
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 <dewillcox@lbl.gov>
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 <dewillcox@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dewillcox@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <eugene.willcox@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <harpolea@users.noreply.github.com>
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 <dfan@lbl.gov>
Date: Mon Apr 1 18:54:38 2019 -0700
Merge branch 'master' into development
commit 537a31f617b35be81508099d2bcc63d7b2f2a946
Author: Doreen Fan <dfan@lbl.gov>
Date: Mon Apr 1 18:53:01 2019 -0700
April 2019 release notes
RELEASE_NOTES
commit 668117b2ddc61634b5eb6e179080d64fbcd10973
Merge: 9780ac67 6718e26f
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dorefan@cori11.nersc.gov>
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 <AJNonaka@lbl.gov>
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 <dewillcox@lbl.gov>
Date: Mon Mar 25 17:34:39 2019 -0700
Enable burn retries.
Exec/SCIENCE/rotating_star/inputs_3d_C
commit 74afad0dc0496129137862926b937a307df0ab12
Author: Doreen Fan <dfan@lbl.gov>
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 <dewillcox@lbl.gov>
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 <eugene.willcox@gmail.com>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu Mar 21 13:35:44 2019 -0400
merge conflicts
commit ddd9f9bccb16ad701bfaaa2b5bbbeaa8454ef4fd
Author: Alice Harpole <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Wed Mar 20 18:21:54 2019 -0700
1d base state routine cumulative timer
Source/MaestroAdvance.cpp
commit 23a4b3dca3eb2da03ef01aacad68e65c7dcfbbd8
Author: Doreen Fan <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Mon Mar 18 12:33:21 2019 -0700
added Diag timing info
Source/MaestroEvolve.cpp
commit 264687241d8dac052374f649bb3c55126f888c07
Merge: 040d4378 492ed0f6
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dewillcox@lbl.gov>
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 <dewillcox@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Fri Mar 15 17:03:31 2019 -0700
omp
Source/Src_nd/make_eta.F90
commit 613c7a8818184d619dd10d2ad5646a32ee13a53c
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dewillcox@lbl.gov>
Date: Fri Mar 15 11:23:17 2019 -0700
cleanup makefile
Exec/UNIT_TESTS/test_react/GNUmakefile
commit f16ee012b3b8adebb478423cc29471d6173f8566
Author: Donald E. Willcox <dewillcox@lbl.gov>
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 <aliceharpole@gmail.com>
Date: Fri Mar 15 12:48:32 2019 -0400
saving changes
Exec/SCIENCE/rotating_star/initdata.f90
commit 93662097768d6950e0333855182e1e6042c7bdde
Author: Donald E. Willcox <dewillcox@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dewillcox@lbl.gov>
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 <dewillcox@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Thu Mar 14 13:42:27 2019 -0700
timing info
Source/MaestroAdvanceAvg.cpp
Source/MaestroAdvanceIrreg.cpp
commit 307781ff82352749e91bbd79240e29116b29080f
Author: Donald E. Willcox <dewillcox@lbl.gov>
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 <dwillcox@users.noreply.github.com>
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 <xinlong@edison04.nersc.gov>
Date: Thu Mar 14 12:51:48 2019 -0700
rename wd to ecsn
commit a0832128413282b67e5e0e2f6ad55d4b6beca45f
Author: Xinlong Li <xinlong@edison04.nersc.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Mon Mar 11 14:17:47 2019 -0700
forgot dr factor
Source/Src_nd/make_w0.f90
commit 8144958e400ecc88e61ee536255bb432cc28a426
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Mon Mar 11 12:31:48 2019 -0700
Merge branch 'ebs_test' into development
commit 7857708faf9649c38bb20bf84b821ff78f79a4f9
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <harpolea@users.noreply.github.com>
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 <harpolea@users.noreply.github.com>
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 <harpolea@users.noreply.github.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
Date: Fri Mar 1 12:59:25 2019 -0800
March 2019 release notes
RELEASE_NOTES
commit e0e420b7d07b4700a82eb06cce21ae0122eb8182
Merge: 876bed41 2c365524
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Fri Feb 15 16:43:10 2019 -0800
cleanup only
Source/MaestroAdvanceAvg.cpp
commit 522439b91c69bc2c1c7fdf727e575c8fc8baaba8
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Tue Feb 12 14:18:00 2019 -0800
remove this
Exec/SCIENCE/wdconvect/inputs_3d_C
commit a49bcfb3889fc52b28795ecb898279b16c98c578
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Fri Feb 8 14:44:50 2019 -0800
fix indentation
Source/MaestroRhoHT.cpp
commit 1f90bddbbbd3f561e3fc6ef5f58d577d55d6c35f
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <michael.zingale@stonybrook.edu>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Mon Feb 4 12:26:54 2019 -0800
Feb 2019 release notes
RELEASE_NOTES
commit ad0aa8b8218f6aee33e8793186d3c8a19808ba65
Author: sailoridy <richardidy@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Jan 28 09:33:53 2019 -0500
uncomment abort statement
Source/MaestroForce.cpp
commit 83a1dbc4d8a9fbace511b22b0136fb31aa01ad86
Merge: 27983dff b9fc35ad
Author: Alice Harpole <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <ah1e14@soton.ac.uk>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
Date: Fri Jan 18 14:31:42 2019 -0500
resolved merge conflicts
commit 67752cb76f6f671c8fab323cae23b7d9fe9453d4
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Fri Jan 18 10:38:01 2019 -0800
Need to regrid w0 as well
Source/MaestroRegrid.cpp
commit 8c68ee312fd9279a68a91a9ec923594b1deb92dd
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Fri Jan 18 10:02:02 2019 -0800
parallel safe IO
Source/MaestroDiag.cpp
commit a16e2a46c4948bbad8465d1317b44fa38bbc623c
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Jan 16 16:17:06 2019 -0500
mac projectin also compiles and runs
commit abf2546f32d90f2106bb75b392e9b48a5802acbf
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <xinlong@edison07.nersc.gov>
Date: Mon Jan 7 14:08:45 2019 -0800
Merge branch 'development' of https://github.com/sailoridy/MAESTROeX into development
commit 1f46f04b85dabaea43dc80d834539986c5beaab8
Author: sailoridy <richardidy@gmail.com>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Fri Jan 4 13:22:06 2019 -0800
regrid code cleanup
Source/MaestroRegrid.cpp
commit ff4ea85dbaea8a4f7681f19cf2c0634bb36c98b4
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Fri Jan 4 12:47:28 2019 -0800
more regridding progress
Source/MaestroRegrid.cpp
commit db4b7e8a7f18877ff3c96cf976052ddfb756a3a3
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
Date: Wed Jan 2 12:21:55 2019 -0800
Merge branch 'master' into development
commit 497a8f653e6be95aceef781e4d702da8406f4275
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Wed Jan 2 12:18:27 2019 -0800
Jan 2019 release notes
RELEASE_NOTES
commit 73071c7112f97a2e374267a6a805cc27f0c0231f
Author: Alice Harpole <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
Date: Wed Jan 2 13:58:53 2019 -0500
fixed bug in 1d compilation
Source/MaestroAdvection.cpp
commit cace7854835eddc1a633e63ddbbeaec860d11522
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
Date: Tue Dec 18 09:48:19 2018 -0500
add travis badge
README.md
commit bdf3df604e8b7c3891da11d77065569b37dbcfab
Merge: a218ff7f 3d70a26f
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
Date: Mon Dec 17 19:34:43 2018 -0500
no longer needed
_config.yml
commit 8a2e69ca58094cfd8b28072908dc7b7650a02ba0
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
Date: Mon Dec 17 19:13:57 2018 -0500
fix table
deploy_docs.sh
sphinx_docs/source/introduction.rst
commit e0d9d5b76361be0e32d4f0959b23db57747a9540
Author: Michael Zingale <michael.zingale@stonybrook.edu>
Date: Mon Dec 17 18:35:17 2018 -0500
comment out the bit about no changes
deploy_docs.sh
commit 7911dec06958eb5b4e9293aa43f5d5b7c23747ab
Author: Michael Zingale <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
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
Docs/architecture/base_spherical.eps
Docs/architecture/boxlib_directory_bw2.eps
Docs/architecture/data_loc.odg
Docs/architecture/data_loc2.eps
Docs/architecture/index_grid.odg
Docs/architecture/index_grid2.eps
Docs/architecture/mac.odg
Docs/architecture/mac2.eps
Docs/architecture/maestro_ecosystem.odg
Docs/architecture/maestro_ecosystem2.eps
Docs/architecture/paper.tex
Docs/beta0/GNUmakefile
Docs/beta0/beta0.tex
Docs/beta0/paper.tex
Docs/enthalpy/GNUmakefile
Docs/enthalpy/enthalpy.tex
Docs/enthalpy/paper.tex
Docs/eos_notes/GNUmakefile
Docs/eos_notes/eos_notes.tex
Docs/eos_notes/paper.tex
Docs/eta_notes/GNUmakefile
Docs/eta_notes/eta.tex
Docs/eta_notes/paper.tex
Docs/flowchart/GNUmakefile
Docs/flowchart/flowchart.eps
Docs/flowchart/flowchart.odg
Docs/flowchart/flowchart.tex
Docs/flowchart/flowchart_4_8.eps
Docs/flowchart/flowchart_4_8.odg
Docs/flowchart/paper.tex
Docs/getting_started/GNUmakefile
Docs/getting_started/getting_started.tex
Docs/getting_started/paper.tex
Docs/getting_started/plt00133_tfromp.eps
Docs/initial_models/GNUmakefile
Docs/initial_models/ctof.eps
Docs/initial_models/ctof.fig
Docs/initial_models/ctof.tex
Docs/initial_models/ftoc.eps
Docs/initial_models/ftoc.fig
Docs/initial_models/ftoc.tex
Docs/initial_models/initial_models.tex
Docs/initial_models/multilevel_init.eps
Docs/initial_models/multilevel_init.fig
Docs/initial_models/paper.tex
Docs/intrepid_notes/intrepid_notes.txt
Docs/introduction/GNUmakefile
Docs/introduction/introduction.tex
Docs/introduction/paper.tex
Docs/lo_density/GNUmakefile
Docs/lo_density/cutoff.eps
Docs/lo_density/cutoff.fig
Docs/lo_density/cutoff_multi.eps
Docs/lo_density/cutoff_multi.fig
Docs/lo_density/lo_density.tex
Docs/lo_density/paper.tex
Docs/makefiles/GNUmakefile
Docs/makefiles/makefiles.tex
Docs/makefiles/paper.tex
Docs/managing_jobs/GNUmakefile
Docs/managing_jobs/managingjobs.tex
Docs/managing_jobs/paper.tex
Docs/managing_jobs/scaling/scaling_avgs.py
Docs/managing_jobs/scaling/subCh-hopper-20121128/README
Docs/managing_jobs/scaling/subCh-hopper-20121128/scaling-1536-sfc.omp6
Docs/managing_jobs/scaling/subCh-hopper-20121128/scaling-1536.omp24
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commit 8e6189dddf01a7a6c1aa7e8083a6c9e2adac52ed
Author: Doreen Fan <dfan@lbl.gov>
Date: Mon Dec 17 14:30:35 2018 -0800
Cleanup advance routine
Source/MaestroAdvanceIrreg.cpp
commit 6ff3a5e1e9c753865e7da74efae2a6550fa9aa68
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Thu Dec 13 17:30:49 2018 -0800
Fix bug in MakeMagvel for DIM=2.
Source/MaestroPlot.cpp
commit 3425ebc6abc7d2b36be7e7a7098eaa7e243f3072
Author: Doreen Fan <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
Date: Thu Dec 13 10:04:16 2018 -0500
add a CITATION file
CITATION
commit 2defa92189a88314e82e629bf2959cb5713bfb4c
Merge: 4d94c00d e9554919
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Wed Dec 12 09:45:48 2018 -0800
resolving conflict
Exec/TEST_PROBLEMS/test_stability/probin
commit 0402ef5a9fa4a3980f0a6c7a1d7c68e72f0b1f4e
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Mon Dec 10 18:55:08 2018 -0800
unneeded file
Source/param/extern_probin.template
commit ea1bfad6cc0c900a98459d4e60ce205bc60ba7be
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <weiqunzhang@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Dec 5 10:17:41 2018 -0500
h, deltap
Source/MaestroPlot.cpp
commit 98766be5e7d6af288f17c0fb79a281781e25dda7
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Tue Dec 4 15:09:11 2018 -0500
conductivity and thermal
Source/MaestroPlot.cpp
commit a402be7866bc90fd2f666b8d2697e80cf4a6ed7d
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Dec 4 14:51:18 2018 -0500
h0
Source/MaestroPlot.cpp
commit 7d5f30963514e0b6e26f6410cc4932f607af5374
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Tue Dec 4 11:49:19 2018 -0500
gpi, added if statements
Source/MaestroPlot.cpp
commit fbf0671e68bc7755b1ec6260c09e5ecc8dda29f1
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Dec 4 11:17:28 2018 -0500
Hext, enucdot
Source/MaestroPlot.cpp
commit a1027dad091ce6cb5a14f88de8acdb131e2f2b32
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Dec 4 11:09:41 2018 -0500
p0pluspi and pioverp0
Source/MaestroPlot.cpp
commit fba87cdde0877eb2d9ed9d7d3ead1700ccdb6a97
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Dec 4 10:54:11 2018 -0500
omegadot
Source/MaestroPlot.cpp
commit 6933328549a43d27775fe7b64d32298e9bb03560
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Mon Dec 3 17:27:19 2018 -0500
vorticity
commit 47affde7229978452a180ef3ab77bab63b0b40c6
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Mon Dec 3 12:18:03 2018 -0800
December 2018 release notes
RELEASE_NOTES
commit 044fe1efbfa41cd2f30c9adfdd03f41dcf6cb427
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
Date: Mon Dec 3 11:24:45 2018 -0800
fix comment
Source/MaestroPlot.cpp
commit 43d8aa0ac148f3bd2d15d1543592295841a8b1ac
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu Nov 15 13:01:21 2018 -0500
Fixed a memory leak
Source/MaestroPlot.cpp
commit 05ed377e6a5d12a0bfe3da6edac35d8f5546de1c
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Nov 14 18:01:08 2018 -0500
Fixed a couple of (small) memory leaks
Source/MaestroPlot.cpp
commit 36fe42de380a25e66d136742ee138e7af701fdfa
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <weiqunzhang@lbl.gov>
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 <dwillcox@users.noreply.github.com>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Thu Nov 1 08:33:51 2018 -0700
November 2018 release notes
RELEASE_NOTES
commit 54477984cc72b9e3e07cd2ea863161de15fa1fcf
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Fri Oct 19 14:24:25 2018 -0700
indexing bug
Source/MaestroPlot.cpp
commit e9008a32ae9628a25c29dd19a342e405f574e9ee
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Tue Oct 16 17:10:48 2018 -0700
sync with MAESTRO
Exec/SCIENCE/wdconvect/inputs_3d_C.64
commit 72f8b656d29e0c3b930c88946e3721aa42969679
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Mon Oct 15 10:17:29 2018 -0700
output max Mach number for diagnosis
Source/MaestroDiag.cpp
commit f2a855616ab77e754c4fff710808f113b264a4a9
Author: Doreen Fan <dfan@lbl.gov>
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 <eugene.willcox@gmail.com>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Wed Oct 10 14:17:44 2018 -0700
change HALF to 0.5d0
commit 84c76fea52fc13a0a9ad8aaf465e05451bb871b6
Author: Doreen Fan <dfan@lbl.gov>
Date: Wed Oct 10 14:11:59 2018 -0700
change HALF to 0.5d0
Source/Src_nd/diag.F90
commit 3b4e10ba3675b00a84445929afdd75545d6a38cb
Author: Alice Harpole <harpolea@cori04.nersc.gov>
Date: Tue Oct 9 17:12:25 2018 -0700
elseif -> elif
Source/Src_nd/diag.F90
commit fdec08d3b84b704c7ab26535d0056b6eac30e16a
Merge: bbec23e9 4643ef76
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Tue Oct 9 17:16:57 2018 -0400
elsif -> elseif
Source/Src_nd/diag.F90
commit 4643ef76d349ee3f7c3a094f08ebc54152428d60
Author: Doreen Fan <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Wed Oct 3 18:22:51 2018 -0700
fix typecheck issue
Source/Src_nd/initdata.f90
commit 1dc484314d02f3c258e62bd196f8142ffbad74f7
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Wed Oct 3 18:22:14 2018 -0700
fix a typecheck problem
Exec/SCIENCE/wdconvect/initdata.f90
commit 8b04128dba9bf5faa8c18f9e902181bdb42b99cd
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Tue Oct 2 16:44:48 2018 -0700
turn burning back on
Exec/SCIENCE/wdconvect/inputs_3d_regression
commit 6b1422f6aa7e871cf06828fb53d8d8372f20a052
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Tue Oct 2 16:20:27 2018 -0400
initialize umac
Source/MaestroAdvance.cpp
commit ea05efe24ffa76b353a5c1e5c8aa2152a850e444
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Oct 2 16:06:25 2018 -0400
initialize utrans MultiFab
Source/MaestroAdvection.cpp
commit 1e550c6ca53cd37e14b7cb3bda13f90928ad94cc
Merge: 825bfa42 497a1059
Author: Alice Harpole <aliceharpole@gmail.com>
Date: Tue Oct 2 14:36:37 2018 -0400
merge conflicts
commit 497a1059642933cc97cb603291990984e09b7dce
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Mon Oct 1 16:02:53 2018 -0700
Merge branch 'development' into tiling
commit 68550305d7f8234e72ad4b2eba0c181ba6ab7094
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
Date: Mon Oct 1 14:16:40 2018 -0400
don't need EXTERN_TEMPALTE
Exec/Make.Maestro
commit 2df13384eac374c9c8d17c52598a9f8b251f9cb6
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Mon Oct 1 09:49:49 2018 -0700
Merge branch 'development' into parameters
commit e68d0cd49e5a9cfd867900da15411f697ca29511
Author: Doreen Fan <dfan@lbl.gov>
Date: Fri Sep 28 16:05:34 2018 -0700
code cleanup
Source/MaestroThermal.cpp
commit fc6fe49e0c2d4f7f66be16cc719f5ba85e569c31
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Wed Sep 26 10:31:15 2018 -0400
fixed merge conflicts
commit e6f0e583c44263e6ce925be609b8e66e9c4686ba
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <dfan@lbl.gov>
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 <maxpkatz@gmail.com>
Date: Mon Sep 17 18:15:21 2018 -0400
extern.f90 -> extern.F90
Exec/Make.Maestro
commit 30f3f887ec1903ddbbac23eac4af3f791e6cd058
Author: Max Katz <maxpkatz@gmail.com>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Fri Sep 14 09:50:59 2018 -0400
fixed tiling in MaestroThermal
commit b637417d99fbba3c0af4b1d42758c5fb4ef8ba96
Author: Doreen Fan <dfan@lbl.gov>
Date: Thu Sep 13 15:01:48 2018 -0700
Initialize delta_gamma1_term to zero
Source/MaestroAdvanceIrreg.cpp
commit dda8cfd0f58ec90ca00bfaf94ff10099d74ebad7
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
Date: Thu Sep 13 09:20:18 2018 -0400
fixed merge conflict
commit 322dc1c2d4e6e9c3021e51abb730244f93fbec2f
Merge: f9a1d971 6ef0497a
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <michael.zingale@stonybrook.edu>
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 <michael.zingale@stonybrook.edu>
Date: Sat Sep 8 08:42:17 2018 -0400
add a .gitignore
.gitignore
commit bbb30666610f64341ccc57e81c7b33d307430ca3
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <aliceharpole@gmail.com>
Date: Thu Sep 6 13:26:27 2018 -0400
removed todo list
Source/Tiling_TODO.txt
commit 6865f219a0ed8cbc20fba3bd6b0454b318a50d9b
Author: Alice Harpole <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
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 <michael.zingale@stonybrook.edu>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <AJNonaka@lbl.gov>
Date: Tue Sep 4 10:28:44 2018 -0700
Sept 2018 release notes
RELEASE_NOTES
commit f684ab7941a2228a4af3c4a2302a711dad016b91
Author: Alice Harpole <ah1e14@soton.ac.uk>
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 <ah1e14@soton.ac.uk>
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 <ah1e14@soton.ac.uk>
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 <ah1e14@soton.ac.uk>
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 <AJNonaka@lbl.gov>
Date: Fri Aug 31 09:05:15 2018 -0700
define microphysics_home
Exec/TEST_PROBLEMS/test_convect/GNUmakefile
commit 678a1a12d27d36e539b38f38e5da3d6c82726eb3
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Fri Aug 31 08:51:50 2018 -0700
regression test
Exec/TEST_PROBLEMS/test_convect/inputs_2d_regression
commit 45a1bcbb022d191b31c7d5bdb6c88b74f3bd3cea
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <aliceharpole@gmail.com>
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 <dfan@lbl.gov>
Date: Wed Aug 15 15:23:45 2018 -0700
Added chi term in projection steps
Source/MaestroAdvanceIrreg.cpp
commit d60eb92dfe26ece2a3434449a6c5c63df13d7339
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date: Wed Aug 8 16:14:23 2018 -0700
fix io buffer
Source/MaestroCheckpoint.cpp
commit 27039a4232fb4cb6e8c353363e66140262640f16
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Wed Aug 1 11:21:05 2018 -0700
August 2018 release notes
RELEASE_NOTES
commit 74b31126b191a2900ddb90accbedb7eb229506bf
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Tue Jul 24 17:56:48 2018 -0700
Remove debug outputs
Source/Src_nd/make_scal_force.F90
commit b25d048236a4b597a346e1383adb989947e59d8e
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Mon Jul 2 18:26:37 2018 -0700
Added release notes
RELEASE_NOTES
commit 66b388da5e52d156515a8bd1a189e57d06e57bd2
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Mon Jul 2 15:54:49 2018 -0700
Merge branch 'master' of https://github.com/AMReX-Astro/MAESTROeX
commit f00eeae24c4509cd16a238bccd197ebd2ae91ba2
Author: Doreen Fan <dfan@lbl.gov>
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 <weiqunzhang@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
Date: Wed Jun 20 13:35:53 2018 -0400
add copy_burn_t
Microphysics/networks/burn_type.F90
commit 56d87a1e4814fea8fee7aa3fb3f0a35f1360ed37
Author: Doreen Fan <dfan@lbl.gov>
Date: Mon Jun 18 17:20:13 2018 -0700
Renamed unnecessary variables with _dummy suffix
Source/MaestroAdvanceIrreg.cpp
commit 952060578d1bd510b05bb782a384941777924c8b
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Wed Jun 13 10:47:47 2018 -0700
Fixed compiling bug
Source/Src_nd/make_flux.F90
commit 30dcbd0246de55736b357d66d9f238b2132ccd2e
Author: Doreen Fan <dfan@lbl.gov>
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 <michael.zingale@stonybrook.edu>
Date: Tue Jun 12 18:19:37 2018 -0400
add success
Microphysics/networks/burn_type.F90
commit 72307380849647285090e44d66c9953920f9159e
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Wed May 16 11:06:31 2018 -0700
comment from Rupert
Docs/architecture/architecture.tex
commit 8e39aeb7b4fc53b5e76746e2c8aeb5c9c476b510
Author: Doreen Fan <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Wed May 9 16:23:07 2018 -0700
Typos fixed
Source/Src_nd/make_flux.F90
commit b8906245c407df77677be5630be23b68c54e5278
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Fri Apr 20 15:48:50 2018 -0700
Merge branch 'master' of https://github.com/AMReX-Astro/MAESTROeX
commit a884d63a864230b282aaf0664e414ab7335086a1
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <ccse.lbl@gmail.com>
Date: Fri Apr 20 15:42:38 2018 -0700
point to Microphysics
Exec/TEST_PROBLEMS/reacting_bubble/GNUmakefile
commit 097ada5bbaf4431ddf372a9a36fdc5faafa39de6
Author: Regression Tester <ccse.lbl@gmail.com>
Date: Fri Apr 20 15:29:45 2018 -0700
regression test
Exec/TEST_PROBLEMS/reacting_bubble/inputs_2d_regression
commit 3488c38209c639700199406aab5c5ccf5ea8e03b
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <weiqunzhang@lbl.gov>
Date: Wed Apr 11 15:49:10 2018 -0700
DEBUG --> AMREX_DEBUG
Source/param/parse_maestro_params.py
commit d7dad4320a5478d5eef96e9daebd0a22e58ced65
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Mon Apr 9 13:33:57 2018 -0700
Bug fix for non-spherical option
Source/MaestroAdvection.cpp
commit 1dfc8fe9f95804a068b2a8cbc34b7088bcec8ff9
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Wed Mar 14 17:17:08 2018 -0700
Cleanup file
Source/MaestroPlot.cpp
commit 3272ac9b0c975d679064baca84fbcfdb77c92f85
Author: Doreen Fan <dfan@lbl.gov>
Date: Wed Mar 14 17:15:55 2018 -0700
Plot file now outputs deltaT
Source/MaestroPlot.cpp
commit 8cfbe6149095bdd4fceae7164c000734fe0d447e
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Tue Mar 13 09:47:47 2018 -0700
code cleanup
Source/MaestroAdvection.cpp
Source/MaestroFillData.cpp
commit 4b8cd5ad20d4f81e5a014b6e5b1838f60f2748be
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Tue Mar 13 09:09:11 2018 -0700
cleanup function
Source/MaestroAverage.cpp
commit 4e36859ab94b5ca85fbb8e9634969a08e77eef10
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Mon Mar 12 16:26:53 2018 -0700
Merge branch 'master' of https://github.com/AMReX-Astro/MAESTROeX
commit 69f8fa7f5981bf74d8de989ee3351f9ca6d62a76
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Fri Mar 9 13:44:01 2018 -0800
write w0 to plotfile
Source/MaestroPlot.cpp
commit c35f90ca34a9a016927b85bca68cfe37350001ea
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Mon Mar 5 18:24:15 2018 -0800
Include subroutines that were previously commented out
Source/MaestroRegrid.cpp
commit f10588a150e61ce9229d832a0d62dc6c4a57d283
Author: Doreen Fan <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
Date: Thu Mar 1 17:48:30 2018 -0800
Needed to reduce etarhosum over all processors
Source/MaestroMakeEta.cpp
commit 56939a6d88bf2bee6d5185343f7a84a8fecf3f21
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Wed Feb 28 17:09:28 2018 -0800
Merge branch 'master' of https://github.com/AMReX-Astro/MAESTROeX
commit 22012ede02218cfa264b05683efd121fc228fc0f
Author: Doreen Fan <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Wed Feb 28 15:51:09 2018 -0800
write job_info to checkpoint as well
Source/MaestroCheckpoint.cpp
commit a03dc981a0e325976e02bbd9f9c39e15edeabea2
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Wed Feb 28 15:49:29 2018 -0800
job info output
Source/MaestroPlot.cpp
commit 5a92bcf63ce1bca662e774fcc579663a4b3f618f
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Tue Feb 27 19:02:45 2018 -0800
test commit
Docs/MAESTROeXUsersGuide.tex
commit 90f50f6143cdd9e7cd6a124927170fe49cfbd41b
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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
Docs/MESA/README
Docs/MESA/hopper_compile.tex
Docs/MESA/instructions.tex
Docs/MESA/paper.tex
Docs/MaestroUsersGuide.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/architecture.tex
Docs/architecture/base_grid.eps
Docs/architecture/base_spherical.eps
Docs/architecture/boxlib_directory.odg
Docs/architecture/boxlib_directory2.eps
Docs/architecture/boxlib_directory_bw2.eps
Docs/architecture/data_loc.odg
Docs/architecture/data_loc2.eps
Docs/architecture/index_grid.odg
Docs/architecture/index_grid2.eps
Docs/architecture/mac.odg
Docs/architecture/mac2.eps
Docs/architecture/maestro_directory.odg
Docs/architecture/maestro_directory2.eps
Docs/architecture/maestro_ecosystem.odg
Docs/architecture/maestro_ecosystem2.eps
Docs/architecture/paper.tex
Docs/beta0/GNUmakefile
Docs/beta0/beta0.tex
Docs/beta0/paper.tex
Docs/enthalpy/GNUmakefile
Docs/enthalpy/enthalpy.tex
Docs/enthalpy/paper.tex
Docs/eos_notes/GNUmakefile
Docs/eos_notes/eos_notes.tex
Docs/eos_notes/paper.tex
Docs/eta_notes/GNUmakefile
Docs/eta_notes/eta.tex
Docs/eta_notes/paper.tex
Docs/flowchart/GNUmakefile
Docs/flowchart/flowchart.eps
Docs/flowchart/flowchart.odg
Docs/flowchart/flowchart.tex
Docs/flowchart/flowchart_4_8.eps
Docs/flowchart/flowchart_4_8.odg
Docs/flowchart/paper.tex
Docs/getting_started/GNUmakefile
Docs/getting_started/getting_started.tex
Docs/getting_started/paper.tex
Docs/getting_started/plt00133_tfromp.eps
Docs/initial_models/GNUmakefile
Docs/initial_models/ctof.eps
Docs/initial_models/ctof.fig
Docs/initial_models/ctof.tex
Docs/initial_models/ftoc.eps
Docs/initial_models/ftoc.fig
Docs/initial_models/ftoc.tex
Docs/initial_models/initial_models.tex
Docs/initial_models/multilevel_init.eps
Docs/initial_models/multilevel_init.fig
Docs/initial_models/paper.tex
Docs/intrepid_notes/intrepid_notes.txt
Docs/introduction/GNUmakefile
Docs/introduction/introduction.tex
Docs/introduction/paper.tex
Docs/lo_density/GNUmakefile
Docs/lo_density/cutoff.eps
Docs/lo_density/cutoff.fig
Docs/lo_density/cutoff_multi.eps
Docs/lo_density/cutoff_multi.fig
Docs/lo_density/lo_density.tex
Docs/lo_density/paper.tex
Docs/maestro_doc.bib
Docs/maestrosymbols.tex
Docs/makefiles/GNUmakefile
Docs/makefiles/makefiles.tex
Docs/makefiles/paper.tex
Docs/managing_jobs/GNUmakefile
Docs/managing_jobs/managingjobs.tex
Docs/managing_jobs/paper.tex
Docs/managing_jobs/scaling/scaling_avgs.py
Docs/managing_jobs/scaling/subCh-hopper-20121128/README
Docs/managing_jobs/scaling/subCh-hopper-20121128/scaling-1536-sfc.omp6
Docs/managing_jobs/scaling/subCh-hopper-20121128/scaling-1536.omp24
Docs/managing_jobs/scaling/subCh-hopper-20121128/scaling-1536.omp6
Docs/managing_jobs/scaling/subCh-hopper-20121128/scaling-192-sfc.omp6
Docs/managing_jobs/scaling/subCh-hopper-20121128/scaling-192.omp6
Docs/managing_jobs/scaling/subCh-hopper-20121128/scaling-384-sfc.omp6
Docs/managing_jobs/scaling/subCh-hopper-20121128/scaling-384.omp6
Docs/managing_jobs/scaling/subCh-hopper-20121128/scaling-768-sfc.omp6
Docs/managing_jobs/scaling/subCh-hopper-20121128/scaling-768.omp24
Docs/managing_jobs/scaling/subCh-hopper-20121128/scaling-768.omp6
Docs/managing_jobs/scaling/subCh-hopper-20121128/scaling_omp6.txt
Docs/managing_jobs/scaling/subCh-hopper-20121128/scaling_omp6_sfc.txt
Docs/managing_jobs/scaling/wdconvect/intrepid_042210/intrepid_BGP_scaling.eps
Docs/managing_jobs/scaling/wdconvect/intrepid_042210/mpi.txt
Docs/managing_jobs/scaling/wdconvect/intrepid_042210/omp4.txt
Docs/managing_jobs/scaling/wdconvect/intrepid_042210/output.mpi.13824
Docs/managing_jobs/scaling/wdconvect/intrepid_042210/output.mpi.1728
Docs/managing_jobs/scaling/wdconvect/intrepid_042210/output.mpi.4096
Docs/managing_jobs/scaling/wdconvect/intrepid_042210/output.omp4.16384
Docs/managing_jobs/scaling/wdconvect/intrepid_042210/output.omp4.2048
Docs/managing_jobs/scaling/wdconvect/intrepid_042210/output.omp4.55296
Docs/managing_jobs/scaling/wdconvect/intrepid_042210/output.omp4.6912
Docs/managing_jobs/scaling/wdconvect/intrepid_042210/scaling.eps
Docs/managing_jobs/scaling/wdconvect/intrepid_042210/scaling.gp
Docs/managing_jobs/scaling/wdconvect/intrepid_042210/scaling.py
Docs/managing_jobs/scaling/wdconvect/jaguarpf_031910/jaguar_xt5_scaling.eps
Docs/managing_jobs/scaling/wdconvect/jaguarpf_031910/mpi.txt
Docs/managing_jobs/scaling/wdconvect/jaguarpf_031910/omp12.txt
Docs/managing_jobs/scaling/wdconvect/jaguarpf_031910/omp6.txt
Docs/managing_jobs/scaling/wdconvect/jaguarpf_031910/output.mpi.13824
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Docs/managing_jobs/scaling/wdconvect/jaguarpf_031910/rawdata.txt
Docs/managing_jobs/scaling/wdconvect/jaguarpf_031910/scaling.gp
Docs/managing_jobs/scaling/wdconvect/jaguarpf_031910/scaling.py
Docs/managing_jobs/scaling/wdconvect/jaguarpf_031910/scaling_log.gp
Docs/managing_jobs/scaling/wdconvect/jaguarpf_052510/scaling.gp
Docs/managing_jobs/scaling/wdconvect/jaguarpf_052510/scaling.txt
Docs/managing_jobs/scaling/xrb/blend/scaling-edison.txt
Docs/managing_jobs/scaling/xrb/blend/scaling-titan.txt
Docs/managing_jobs/scaling/xrb/blend/scaling.py
Docs/managing_jobs/scaling/xrb/xrb-3d-edison-20140424/scaling.txt
Docs/managing_jobs/scaling/xrb/xrb-3d-edison-20140425/README
Docs/managing_jobs/scaling/xrb/xrb-3d-edison-20140425/scaling.py
Docs/managing_jobs/scaling/xrb/xrb-3d-edison-20140425/scaling.txt
Docs/managing_jobs/scaling/xrb/xrb-3d-edison-20140425/xrb-6cm-3d.32cubed.OMP6
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commit ad893140ac5aae8ddd833c0d3a243663484fa364
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <weiqunzhang@lbl.gov>
Date: Thu Feb 15 09:36:16 2018 -0800
fix array bound
Source/Src_nd/enforce_HSE.f90
commit ec691865b4cc2ad47b5b354369a512ed845491ac
Author: Weiqun Zhang <weiqunzhang@lbl.gov>
Date: Thu Feb 15 09:32:54 2018 -0800
add amrex::
Source/Maestro.H
Source/PhysBCFunctMaestro.H
commit dc42931dd015dd26ed7bb3e11a6c1d4e82dffbb0
Author: Doreen Fan <dfan@lbl.gov>
Date: Wed Feb 14 17:54:35 2018 -0800
Fixed bcs in MaestroMacProj
Source/MaestroMacProj.cpp
commit f81cfbdba39a34718936a25681c4d667c82b6021
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Tue Feb 13 17:55:57 2018 -0800
restart bugfix - still WIP
Source/MaestroEvolve.cpp
commit 47b7b6fa6263995a99f3804e755cea34ee153a11
Author: Doreen Fan <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Fri Feb 9 18:08:12 2018 -0800
fixed one small bc bug in PutInPertForm()
Source/MaestroEnthalpyAdvance.cpp
commit f4e4a3c93f69f771d92a48ac3ac6d467297b8292
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Thu Feb 8 18:18:42 2018 -0800
added AverageDown() and FillPatch() to NodalProj() subroutine
Source/MaestroNodalProj.cpp
commit 1858c050c46ec21635022d9ee9d283433f3c13e0
Author: Doreen Fan <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Mon Jan 29 14:32:50 2018 -0800
remmove unused variables
Source/Maestro.H
Source/MaestroSetup.cpp
commit 19d8499fde242ab2ec6444ec429ec6e2f5cf6263
Author: Doreen Fan <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
Date: Mon Jan 29 13:03:29 2018 -0800
Add hoextrap option
Source/MaestroMacProj.cpp
commit 17ff7c46ee1b2fa971c9d685199cb065ea32ccda
Author: Doreen Fan <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <dfan@lbl.gov>
Date: Thu Jan 25 13:47:52 2018 -0800
added PutInPertForm subroution
Source/Maestro.H
Source/MaestroConvert.cpp
commit a6965ad915c2e8700d454c3761c41492d2c12fe4
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Thu Jan 25 13:47:28 2018 -0800
forgot to fill velocity ghost cellx
Source/MaestroForce.cpp
commit 6a087fc87e03f100f730cde58fe2d617244e3a34
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <dfan@lbl.gov>
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 <weiqunzhang@lbl.gov>
Date: Tue Jan 23 11:21:57 2018 -0800
Array --> Vector
Source/MaestroPlot.cpp
commit 867f222286e7bb147a07f04b19058f97913720f5
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Mon Jan 22 15:33:27 2018 -0800
Set theme jekyll-theme-cayman
_config.yml
commit 4362437ae15ca35f6373fae49246a74c400c83d4
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Mon Jan 22 15:33:06 2018 -0800
Set theme jekyll-theme-slate
_config.yml
commit 26892abb062f9927e5b193e0f0e013599ad38a92
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Mon Jan 22 15:32:49 2018 -0800
Set theme jekyll-theme-cayman
_config.yml
commit 3fd97aa03e2b4d1b8e74d427ffddddea0f93159a
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Thu Jan 18 18:58:24 2018 -0800
more work on Advance routine
Source/MaestroAdvance.cpp
commit 909d41a1d637a6359809cfa21a03d721fd9d95c8
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Thu Jan 18 15:01:23 2018 -0800
notes
Source/Maestro.H
Source/MaestroMacProj.cpp
commit 98f26fbd5335feacc158515911eb1be5db42184f
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Thu Jan 18 14:10:22 2018 -0800
some advance updates
Source/MaestroAdvance.cpp
commit f96f958ae27d9a3f992a8ce34a5ef2dbc7b073c4
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Thu Jan 18 13:32:01 2018 -0800
MacProj work
Source/MaestroMacProj.cpp
commit df24da72860202270e30973e09b5d43b216c1649
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Thu Jan 18 09:51:01 2018 -0800
more mac projection progress
Source/Maestro.H
Source/MaestroMacProj.cpp
commit 80d6f6a1cd8fafc70d23bad1af0a93fc4dbab939
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Tue Jan 16 10:59:32 2018 -0800
unused code
Source/MaestroNodalProj.cpp
commit a646f15accf97ae0c2c2b442d23236e5e7ea4ca3
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Tue Jan 16 10:54:07 2018 -0800
unneeded files
Source/Projection.H
Source/Projection.cpp
commit 94f66f3388a952efb564a24048b454fb711e03de
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Mon Jan 8 09:58:48 2018 -0800
comments
Source/MaestroNodalProj.cpp
commit 93f999ced63549e2c9bb89b080e8e865d6d7e7b9
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Fri Jan 5 16:42:00 2018 -0800
comment
Source/Projection.cpp
commit 4b5a3608d29af9d35e40e849871e17f0f72b27e5
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Thu Jan 4 17:41:24 2018 -0800
more nodal projection progress
Source/Maestro.H
Source/MaestroNodalProj.cpp
commit 13e174c637cebf66ac59abdde7ff1d77ba29fcaa
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Thu Jan 4 12:49:24 2018 -0800
more nodal projection work
Source/Maestro.H
Source/MaestroNodalProj.cpp
commit fb4fe07850a104b706b7dfa5c222559c3510b7af
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Wed Jan 3 18:26:30 2018 -0800
more Projection class cleanup
Source/Projection.H
Source/Projection.cpp
commit 492e18f3615cf4142aa8c9e7ab6a2b35dd363a6c
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Wed Jan 3 15:44:07 2018 -0800
simplify Projection class
Source/Projection.H
Source/Projection.cpp
commit 5e780e9fdfb103978fd82520dff8bfa099c727df
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Thu Dec 21 15:37:45 2017 -0800
more Advance work
Source/MaestroAdvance.cpp
commit 85ad98ffc183ce75fc60eb1a7be81f6addd43cc9
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Thu Dec 21 09:41:49 2017 -0800
comments
Source/MaestroAdvance.cpp
Source/Src_nd/make_w0.f90
commit 3592d9228421cb589705e207336171affbbf2064
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Wed Dec 20 18:19:18 2017 -0800
more advance work
Source/MaestroAdvance.cpp
commit 020815d8e7e76d93ebf38c507f31cbdc531407fc
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Wed Dec 20 17:55:21 2017 -0800
verbosity
Source/MaestroAdvance.cpp
commit 0e58eab253a27488c2f4e354d254ecbbd93b968f
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Fri Dec 15 14:45:43 2017 -0800
more Advance work
Source/MaestroAdvance.cpp
Source/MaestroInit.cpp
commit 6d3d01ac988a91b7da8945dcf8ce798a11ddbd3c
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Wed Dec 13 12:31:01 2017 -0800
forgot to averagedown RhoH
Source/MaestroRhoHT.cpp
commit 62c1ba6a5d7e20b8e5fda18d4b99c3013ab17a76
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Wed Dec 13 10:50:11 2017 -0800
more options to inputs
Exec/TEST_PROBLEMS/reacting_bubble/inputs
commit 43f992c03c6b9ca8844c483ec3e8695837d0dd26
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Wed Dec 13 09:15:41 2017 -0800
plot X
Source/MaestroPlot.cpp
commit 93410157b92fc6e4bf6e384a524fac70b65947da
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Fri Dec 1 15:24:06 2017 -0800
bugfix in average
Source/Src_nd/average.f90
commit 2808a19d86c3c2d1ccefca6c47e213fb658698e3
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Fri Dec 1 13:46:26 2017 -0800
dt/2 in divu_iter for reactions
Source/MaestroInit.cpp
commit 15236a7e402709de9234fe07373e181ff911c919
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Mon Nov 27 17:21:54 2017 -0800
set up nodal proj
Source/MaestroFill3dData.cpp
Source/MaestroNodalProj.cpp
commit c88d84eeba002c54b98e704e36cc1758c7af7235
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Mon Nov 27 16:51:22 2017 -0800
simplify code
Source/Src_nd/fill_3d_data.F90
commit 27b5e19e8c31f94706ff349eb6e0afbc1b0ec442
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Mon Nov 27 13:41:11 2017 -0800
commentx
Source/Maestro.H
Source/MaestroInit.cpp
Source/MaestroNodalProj.cpp
commit bd7beb22a2602bbcef908fcbaa2bbdefbe104821
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Wed Nov 22 14:14:04 2017 -0800
RhoH to T
Source/Maestro.H
Source/MaestroRhoHT.cpp
commit 742c6b7ca875891a70c7a06c051219f1a794054d
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Wed Nov 15 17:08:35 2017 -0800
1d arrays
Source/Maestro.H
Source/MaestroSetup.cpp
commit 67571982b99350cad8fa803bcb86b7f2da0d2dc0
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Wed Nov 15 08:22:50 2017 -0800
comments only
Source/Maestro.H
Source/Maestro.cpp
commit a09f920bcde448282107a77908d9ce6cd21e6487
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Mon Nov 13 14:32:26 2017 -0800
move countcells to AmrCore
Source/Maestro.H
Source/MaestroAdvance.cpp
commit 7991f6b2349fe1f9f93d6cfc68f950b6df017101
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Fri Nov 10 18:23:05 2017 -0800
set pi to zero initially
Source/Src_nd/initdata.f90
commit 4bf68fad14a8ec2ef5f79147579ec42063bf2a2f
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Wed Nov 8 17:46:10 2017 -0800
comments
Source/Maestro.H
Source/Maestro.cpp
commit e0d9c23b0604f619ee76c9cf4d46ba8485a78fae
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Wed Nov 8 09:30:36 2017 -0800
fix calling sequence
Source/Src_nd/maestro.f90
commit c1eb74cd912bcd945ec2f9532d3440271a748e8c
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Wed Nov 8 09:26:58 2017 -0800
fix some interfaces
Source/MaestroInit.cpp
Source/Maestro_F.H
commit ef2254616a76af2daf24baff7c8ad0ecaad5cfb1
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Fri Oct 27 08:50:14 2017 -0700
some init stuff
Source/MaestroAdvance.cpp
commit c2012a2d1360371006f5e7b564d355e02092eedb
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Mon Oct 16 18:09:36 2017 -0700
more data structures
Source/Maestro.H
Source/MaestroAdvance.cpp
commit abd31fcf04feec13abe102d6c2fede15a42aa6de
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Fri Oct 13 17:05:41 2017 -0700
more multifabs in the class
Source/Maestro.H
commit 4168f3868963f564d8a5243972e803db64e2d8d9
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Fri Oct 6 15:32:52 2017 -0700
forgot to save
Source/Maestro.cpp
commit b83d9cc2c7274110e96583ca35e1a788d7f52f2b
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Wed Sep 20 14:10:32 2017 -0700
fix comments
Source/MAESTRO.H
Source/MAESTRO.cpp
commit 2d802096d4c58688bb51e1bb203e3fe6d8910303
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Wed Sep 20 13:38:26 2017 -0700
clean up verbosity
Source/MAESTRO.cpp
commit 322d54e030b65aceb11a3acc228a017c979c18f8
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Wed Sep 20 12:19:01 2017 -0700
more code cleanup
Source/MAESTRO.H
Source/MAESTRO.cpp
commit 4c6db1602ffe71171d13318183a4fd5a18fd9cbd
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
Date: Wed Sep 20 09:27:26 2017 -0700
test commit 2
README.md
commit cb3cba62232418451f8a878fa77b9920bf8b14c5
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Wed Sep 20 09:25:14 2017 -0700
test commit
README.md
commit eeeb2eea5b1e8528ed59111bb68376d597baadcd
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Mon Sep 18 19:00:05 2017 -0700
some comments, design ideas
Source/MAESTRO.H
Source/MAESTRO.cpp
commit e925ca3d6d566ba64b030f968df3552f8002f22e
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Mon Sep 18 18:25:20 2017 -0700
clean up time stepping
Source/MAESTRO.H
Source/MAESTRO.cpp
commit 14fe75ecc1a3158a3d95b8a395bda498e93a6941
Author: Andy Nonaka <AJNonaka@lbl.gov>
Date: Mon Sep 18 17:50:12 2017 -0700
Create README.md
README.md
commit 88fef658149d9d1426fcd712b2a0f999f80bbf60
Author: Andy Nonaka <AJNonaka@lbl.gov>
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 <AJNonaka@lbl.gov>
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